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Conserved domains on  [gi|56699440|ref|NP_659080|]
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ATP-dependent RNA helicase DHX8 [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HrpA super family cl34328
HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];
580-1211 0e+00

HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];


The actual alignment was detected with superfamily member COG1643:

Pssm-ID: 441249 [Multi-domain]  Cd Length: 836  Bit Score: 574.34  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  580 MSILEQRESLPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFG 659
Cdd:COG1643    1 MSLITYPPDLPVSAVLPELLAALRAHQVVVLAAPPGAGKTTQLPLALLELGWGAGGRIGMLEPRRLAARAAAERMAEELG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  660 CCLGQEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQK-RQDMKLI 738
Cdd:COG1643   81 EPVGETVGYRVRFEDKVSAATRIEVVTEGILLRELQRDPELEGVDTVIFDEFHERSLNADLLLALLLDLQPAlRPDLKLL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  739 VTSATLDAVKFSQYFYEAPIFTIPGRTYPVEILYT--KEPETDYLDASLITVMQIhLTEPPGDILVFLTGQEEIDTACEI 816
Cdd:COG1643  161 VMSATLDAERFARLLGDAPVIESSGRTYPVEVRYRplPADERDLEDAVADAVREA-LAEEPGDILVFLPGEREIRRTAEA 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  817 LyerMKSLGPDVpelIILPVYSALPSEMQTRIFDPAPPGSRKVVIATNIAETSLTIDGIYYVVDPGFVKQKVYNSKTGID 896
Cdd:COG1643  240 L---RGRLPPDT---EILPLYGRLSAAEQDRAFAPAPHGRRRIVLATNIAETSLTVPGIRYVIDSGLARIPRYDPRSGVT 313

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  897 QLVVTPISQAQAKQRAGRAGRTGPGKCYRLYTE------RAYRDemlttnvPEIQRTNLASTVLSLKAMGINDLLSFDFM 970
Cdd:COG1643  314 RLPTERISQASANQRAGRAGRLAPGICYRLWSEedfarrPAFTD-------PEILRADLASLILELAAWGLGDPEDLPFL 386

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  971 DAPPMETLITAMEQLYTLGALDDEGLLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSMLSVQNVFYRpkdkqa 1050
Cdd:COG1643  387 DPPPARAIADARALLQELGALDADGRLTPLGRALARLPLDPRLARMLLAAAELGCLREAAILAALLSERDPRRG------ 460

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440 1051 ladqkkakfhQTEGDHLTLLAVYNSWKNNKfsnpwcyENFIQARSLRRAQDIRKQMLGIMDRHKLDVVScgkSTVRVQKA 1130
Cdd:COG1643  461 ----------AAGSDLLARLNLWRRLREQQ-------REFLSYLRLREWRDLARQLRRLLGEGANEEPA---DYEAIGLL 520

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440 1131 ICSGFFRNAAKKDPQEGYRTLIDQQVVYIHPSSALFNRqpEWVVYHELVLTTKEY-MREVTTIDPRWLVEFAPAFFK-VS 1208
Cdd:COG1643  521 LALAYPDRIARRRGEGGRYLLARGRGAALFPGSPLAKK--EWLVAAELVGGAAEArIRLAAPIDPEWLEELAAHLIKrYS 598


                 ...
gi 56699440 1209 DPT 1211
Cdd:COG1643  599 EPH 601
S1_DHX8_helicase cd05684
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ...
 289-367 1.60e-43

S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.


:

Pssm-ID: 240189 [Multi-domain]  Cd Length: 79  Bit Score: 152.39  E-value: 1.60e-43
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 56699440  289 GDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQRVKVKVLSFTGTKTSLSMKDVDQETG 367
Cdd:cd05684    1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQNGKISLSMKDVDQDTG 79
GH2-like_DHX8 cd21691
GIPC-homology 2 (GH2)-like domain found in DEAH box protein 8 (DHX8) and similar proteins; ...
 25-92 1.87e-40

GIPC-homology 2 (GH2)-like domain found in DEAH box protein 8 (DHX8) and similar proteins; DHX8 (a human homolog of yeast Prp22), also called RNA helicase HRH1, is an ATP-dependent RNA helicase involved in pre-mRNA splicing as a component of the spliceosome. It facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. This model corresponds to the GH2-like domain that shows high sequence similarity with the GH2 domain found in GIPC (GAIP C-terminus-interacting protein) family of proteins, which mediate endocytosis by tethering cargo proteins to the motor myosin VI.


:

Pssm-ID: 409668  Cd Length: 68  Bit Score: 143.07  E-value: 1.87e-40
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 56699440   25 LEYLSLVSKVCTELDNHLGINDKDLAEFVISLAEKNTTFDTFKASLVKNGAEFTDSLISNLLRLIQTM 92
Cdd:cd21691    1 LEYLSLVSKVCTELENHLGISDKDLAEFIIDLAEKSKTLDEFKKALKENGAEFPDSFVESLLRLIQRM 68
 
Name Accession Description Interval E-value
HrpA COG1643
HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];
580-1211 0e+00

HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441249 [Multi-domain]  Cd Length: 836  Bit Score: 574.34  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  580 MSILEQRESLPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFG 659
Cdd:COG1643    1 MSLITYPPDLPVSAVLPELLAALRAHQVVVLAAPPGAGKTTQLPLALLELGWGAGGRIGMLEPRRLAARAAAERMAEELG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  660 CCLGQEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQK-RQDMKLI 738
Cdd:COG1643   81 EPVGETVGYRVRFEDKVSAATRIEVVTEGILLRELQRDPELEGVDTVIFDEFHERSLNADLLLALLLDLQPAlRPDLKLL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  739 VTSATLDAVKFSQYFYEAPIFTIPGRTYPVEILYT--KEPETDYLDASLITVMQIhLTEPPGDILVFLTGQEEIDTACEI 816
Cdd:COG1643  161 VMSATLDAERFARLLGDAPVIESSGRTYPVEVRYRplPADERDLEDAVADAVREA-LAEEPGDILVFLPGEREIRRTAEA 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  817 LyerMKSLGPDVpelIILPVYSALPSEMQTRIFDPAPPGSRKVVIATNIAETSLTIDGIYYVVDPGFVKQKVYNSKTGID 896
Cdd:COG1643  240 L---RGRLPPDT---EILPLYGRLSAAEQDRAFAPAPHGRRRIVLATNIAETSLTVPGIRYVIDSGLARIPRYDPRSGVT 313

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  897 QLVVTPISQAQAKQRAGRAGRTGPGKCYRLYTE------RAYRDemlttnvPEIQRTNLASTVLSLKAMGINDLLSFDFM 970
Cdd:COG1643  314 RLPTERISQASANQRAGRAGRLAPGICYRLWSEedfarrPAFTD-------PEILRADLASLILELAAWGLGDPEDLPFL 386

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  971 DAPPMETLITAMEQLYTLGALDDEGLLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSMLSVQNVFYRpkdkqa 1050
Cdd:COG1643  387 DPPPARAIADARALLQELGALDADGRLTPLGRALARLPLDPRLARMLLAAAELGCLREAAILAALLSERDPRRG------ 460

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440 1051 ladqkkakfhQTEGDHLTLLAVYNSWKNNKfsnpwcyENFIQARSLRRAQDIRKQMLGIMDRHKLDVVScgkSTVRVQKA 1130
Cdd:COG1643  461 ----------AAGSDLLARLNLWRRLREQQ-------REFLSYLRLREWRDLARQLRRLLGEGANEEPA---DYEAIGLL 520

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440 1131 ICSGFFRNAAKKDPQEGYRTLIDQQVVYIHPSSALFNRqpEWVVYHELVLTTKEY-MREVTTIDPRWLVEFAPAFFK-VS 1208
Cdd:COG1643  521 LALAYPDRIARRRGEGGRYLLARGRGAALFPGSPLAKK--EWLVAAELVGGAAEArIRLAAPIDPEWLEELAAHLIKrYS 598


                 ...
gi 56699440 1209 DPT 1211
Cdd:COG1643  599 EPH 601
DEAH_box_HrpA TIGR01967
RNA helicase HrpA; This model represents HrpA, one of two related but uncharacterized DEAH-box ...
 587-1206 2.84e-157

RNA helicase HrpA; This model represents HrpA, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria and a few high-GC Gram-positive bacteria. HrpA is about 1300 amino acids long, while its paralog HrpB, also uncharacterized, is about 800 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing. The HrpA/B homolog from Borrelia is 500 amino acids shorter but appears to be derived from HrpA rather than HrpB. [Unknown function, Enzymes of unknown specificity]


Pssm-ID: 273900 [Multi-domain]  Cd Length: 1283  Bit Score: 505.07  E-value: 2.84e-157
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440    587 ESLPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQEV 666
Cdd:TIGR01967   64 DNLPVSAKREDIAEAIAENQVVIIAGETGSGKTTQLPKICLELGRGSHGLIGHTQPRRLAARTVAQRIAEELGTPLGEKV 143

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440    667 GYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSATLDA 746
Cdd:TIGR01967  144 GYKVRFHDQVSSNTLVKLMTDGILLAETQQDRFLSRYDTIIIDEAHERSLNIDFLLGYLKQLLPRRPDLKIIITSATIDP 223

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440    747 VKFSQYFYEAPIFTIPGRTYPVEILY------TKEPETDYLDASLITVMQIhLTEPPGDILVFLTGQEEIDTACEILYER 820
Cdd:TIGR01967  224 ERFSRHFNNAPIIEVSGRTYPVEVRYrplveeQEDDDLDQLEAILDAVDEL-FAEGPGDILIFLPGEREIRDAAEILRKR 302

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440    821 mkslgpDVPELIILPVYSALPSEMQTRIFDPAppGSRKVVIATNIAETSLTIDGIYYVVDPGFVKQKVYNSKTGIDQLVV 900
Cdd:TIGR01967  303 ------NLRHTEILPLYARLSNKEQQRVFQPH--SGRRIVLATNVAETSLTVPGIHYVIDTGTARISRYSYRTKVQRLPI 374

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440    901 TPISQAQAKQRAGRAGRTGPGKCYRLYTERAYRDEMLTTNvPEIQRTNLASTVLSLKAMGINDLLSFDFMDAPPMETLIT 980
Cdd:TIGR01967  375 EPISQASANQRKGRCGRVAPGICIRLYSEEDFNSRPEFTD-PEILRTNLASVILQMLALRLGDIAAFPFIEAPDPRAIRD 453

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440    981 AMEQLYTLGALDDE---GLLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSMLSVQNVFYRPKDKQALADQKKA 1057
Cdd:TIGR01967  454 GFRLLEELGALDDDeaePQLTPIGRQLAQLPVDPRLARMLLEAHRLGCLQEVLIIASALSIQDPRERPMEKQQAADQAHA 533

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440   1058 KFHQTEGDHLTLLAVYNSWKN-------NKFSNpWCYENFIQARSLRRAQDIRKQMLGIMDRHKLDVVSCGKSTVRVQKA 1130
Cdd:TIGR01967  534 RFKDPRSDFLSRVNLWRHIEEqrqalsaNQFRN-ACRKQYLNYLRVREWQDIYRQLTQVVKELGLKLNEEPADYDAIHKA 612

                          570       580       590       600       610       620       630
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 56699440   1131 ICSGFFRNAAKKDPQEGYrTLIDQQVVYIHPSSALFNRQPEWVVYHELVLTTKEYMREVTTIDPRWLVEFAPAFFK 1206
Cdd:TIGR01967  613 LLSGLLSQIGMKDEKHEY-DGARGRKFHIFPGSPLFKKPPKWVMAAELVETSKLYARLVAKIEPEWVEPVAGHLIK 687
PRK11131 PRK11131
ATP-dependent RNA helicase HrpA; Provisional
 587-1210 6.62e-148

ATP-dependent RNA helicase HrpA; Provisional


Pssm-ID: 182986 [Multi-domain]  Cd Length: 1294  Bit Score: 479.94  E-value: 6.62e-148
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440   587 ESLPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQEV 666
Cdd:PRK11131   71 ENLPVSQKKQDILEAIRDHQVVIVAGETGSGKTTQLPKICLELGRGVKGLIGHTQPRRLAARTVANRIAEELETELGGCV 150

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440   667 GYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSATLDA 746
Cdd:PRK11131  151 GYKVRFNDQVSDNTMVKLMTDGILLAEIQQDRLLMQYDTIIIDEAHERSLNIDFILGYLKELLPRRPDLKVIITSATIDP 230

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440   747 VKFSQYFYEAPIFTIPGRTYPVEILY------TKEPETDYLDASLITVMQIHlTEPPGDILVFLTGQEEI-DTAcEILYE 819
Cdd:PRK11131  231 ERFSRHFNNAPIIEVSGRTYPVEVRYrpiveeADDTERDQLQAIFDAVDELG-REGPGDILIFMSGEREIrDTA-DALNK 308

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440   820 RmkslgpDVPELIILPVYSALPSEMQTRIFDPAppGSRKVVIATNIAETSLTIDGIYYVVDPGFVKQKVYNSKTGIDQLV 899
Cdd:PRK11131  309 L------NLRHTEILPLYARLSNSEQNRVFQSH--SGRRIVLATNVAETSLTVPGIKYVIDPGTARISRYSYRTKVQRLP 380

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440   900 VTPISQAQAKQRAGRAGRTGPGKCYRLYTERAYRDEMLTTNvPEIQRTNLASTVLSLKAMGINDLLSFDFMDAPPMETLI 979
Cdd:PRK11131  381 IEPISQASANQRKGRCGRVSEGICIRLYSEDDFLSRPEFTD-PEILRTNLASVILQMTALGLGDIAAFPFVEAPDKRNIQ 459

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440   980 TAMEQLYTLGALDDEG-----LLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSMLSVQNVFYRPKDKQALADQ 1054
Cdd:PRK11131  460 DGVRLLEELGAITTDEqasayKLTPLGRQLAQLPVDPRLARMVLEAQKHGCVREVMIITSALSIQDPRERPMDKQQASDE 539

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  1055 KKAKFHQTEGDHLTLLAVYNSWK-------NNKFSNpWCYENFIQARSLRRAQDIRKQMLGIMDRHKLDVVSCGKSTVRV 1127
Cdd:PRK11131  540 KHRRFADKESDFLAFVNLWNYLQeqqkalsSNQFRR-LCRTDYLNYLRVREWQDIYTQLRQVVKELGIPVNSEPAEYREI 618

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  1128 QKAICSGFFRNAAKKDPQEGYRTLIDQQVVYIHPSSALFNRQPEWVVYHELVLTTKEYMREVTTIDPRWLVEFAPAFFK- 1206
Cdd:PRK11131  619 HTALLTGLLSHIGMKDAEKQEYTGARNARFSIFPGSGLFKKPPKWVMVAELVETSRLWGRIAARIEPEWIEPLAQHLIKr 698


                  ....*
gi 56699440  1207 -VSDP 1210
Cdd:PRK11131  699 sYSEP 703
DEXHc_DHX8 cd17971
DEXH-box helicase domain of DEAH-box helicase 8; DEAH-box helicase 8 (DHX8 ,also known as ...
 584-762 5.56e-127

DEXH-box helicase domain of DEAH-box helicase 8; DEAH-box helicase 8 (DHX8 ,also known as pre-mRNA-splicing factor ATP-dependent RNA helicase PRP22) acts late in the splicing of pre-mRNA and mediates the release of the spliced mRNA from spliceosomes. DHX8 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350729 [Multi-domain]  Cd Length: 179  Bit Score: 387.61  E-value: 5.56e-127
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  584 EQRESLPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLG 663
Cdd:cd17971    1 EQRESLPIYKLKEQLIQAVHDNQILVVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVAEEFGCCLG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  664 QEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSAT 743
Cdd:cd17971   81 QEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLSQYSVIMLDEAHERTIHTDVLFGLLKKTVQKRPDLKLIVTSAT 160

                        170
                 ....*....|....*....
gi 56699440  744 LDAVKFSQYFYEAPIFTIP 762
Cdd:cd17971  161 LDAVKFSQYFYEAPIFTIP 179
S1_DHX8_helicase cd05684
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ...
 289-367 1.60e-43

S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.


Pssm-ID: 240189 [Multi-domain]  Cd Length: 79  Bit Score: 152.39  E-value: 1.60e-43
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 56699440  289 GDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQRVKVKVLSFTGTKTSLSMKDVDQETG 367
Cdd:cd05684    1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQNGKISLSMKDVDQDTG 79
GH2-like_DHX8 cd21691
GIPC-homology 2 (GH2)-like domain found in DEAH box protein 8 (DHX8) and similar proteins; ...
 25-92 1.87e-40

GIPC-homology 2 (GH2)-like domain found in DEAH box protein 8 (DHX8) and similar proteins; DHX8 (a human homolog of yeast Prp22), also called RNA helicase HRH1, is an ATP-dependent RNA helicase involved in pre-mRNA splicing as a component of the spliceosome. It facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. This model corresponds to the GH2-like domain that shows high sequence similarity with the GH2 domain found in GIPC (GAIP C-terminus-interacting protein) family of proteins, which mediate endocytosis by tethering cargo proteins to the motor myosin VI.


Pssm-ID: 409668  Cd Length: 68  Bit Score: 143.07  E-value: 1.87e-40
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 56699440   25 LEYLSLVSKVCTELDNHLGINDKDLAEFVISLAEKNTTFDTFKASLVKNGAEFTDSLISNLLRLIQTM 92
Cdd:cd21691    1 LEYLSLVSKVCTELENHLGISDKDLAEFIIDLAEKSKTLDEFKKALKENGAEFPDSFVESLLRLIQRM 68
HA2 smart00847
Helicase associated domain (HA2) Add an annotation; This presumed domain is about 90 amino ...
 988-1070 1.04e-33

Helicase associated domain (HA2) Add an annotation; This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding.


Pssm-ID: 214852 [Multi-domain]  Cd Length: 82  Bit Score: 124.69  E-value: 1.04e-33
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440     988 LGALDDEGLLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSMLSVQNvfYRPKDKQALADQKKAKFHQTEGDHL 1067
Cdd:smart00847    2 LGALDDDGRLTPLGRKMAELPLDPRLAKMLLAAAEFGCLDEILTIVAMLSVGD--PRPKEKREDADAARRRFADPESDHL 79


                    ...
gi 56699440    1068 TLL 1070
Cdd:smart00847   80 TLL 82
HA2 pfam04408
Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in ...
 981-1069 1.39e-31

Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding.


Pssm-ID: 461295 [Multi-domain]  Cd Length: 104  Bit Score: 119.26  E-value: 1.39e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440    981 AMEQLYTLGALDDEGLLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSMLSVQNVFYRP------KDKQALADQ 1054
Cdd:pfam04408    1 ALELLYYLGALDEDGELTPLGRKMAELPLDPRLAKMLLAAAELGCLDEVLTIVAALSVRDPFVQPnfldprSAAKAARRR 80

                           90       100
                   ....*....|....*....|....
gi 56699440   1055 KKAKFHQ---------TEGDHLTL 1069
Cdd:pfam04408   81 RRAADEKarakfarldLEGDHLTL 104
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 285-363 1.56e-21

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 100.89  E-value: 1.56e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440   285 EPAIGDIYNGKVTSIMQFGCFVQLegLRKRwEGLVHISELRREgRVANVADVVSKGQRVKVKVLSFT-GTKTSLSMKDVD 363
Cdd:PRK11824  618 EPEVGEIYEGKVVRIVDFGAFVEI--LPGK-DGLVHISEIADE-RVEKVEDVLKEGDEVKVKVLEIDkRGRIRLSRKAVL 693
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 284-377 2.53e-20

Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function prediction only];


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 87.93  E-value: 2.53e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  284 EEPAIGDIYNGKVTSIMQFGCFVQLEGlrkRWEGLVHISELrREGRVANVADVVSKGQRVKVKVLSFTGT-KTSLSMKDV 362
Cdd:COG1098    1 MSIEVGDIVEGKVTGITPFGAFVELPE---GTTGLVHISEI-ADGYVKDINDYLKVGDEVKVKVLSIDEDgKISLSIKQA 76

                         90
                 ....*....|....*
gi 56699440  363 DQETGEDLNPNRRRN 377
Cdd:COG1098   77 EEKPKRPPRPRRNSR 91
S1_dom_CvfD NF040579
CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ...
 288-376 2.55e-19

CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a family of full-length homologs of RNA-binding proteins from the Firmicutes with a single copy of the S1 domain. Several members of the family have been characterized as general stress proteins, and the most recently characterized, CvfD, was shown to act as a post-transcriptional regulator.


Pssm-ID: 468553 [Multi-domain]  Cd Length: 113  Bit Score: 84.40  E-value: 2.55e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440   288 IGDIYNGKVTSIMQFGCFVQLEglrKRWEGLVHISELrREGRVANVADVVSKGQRVKVKVLS---FTGtKTSLSMKDVDQ 364
Cdd:NF040579    3 IGDIVEGKVTGIQPYGAFVALD---EHTQGLIHISEI-KHGYVKDINDFLKVGQEVKVKVLDideYTG-KISLSLRALEE 77

                          90
                  ....*....|..
gi 56699440   365 ETGEDLNPNRRR 376
Cdd:NF040579   78 APEKHRKRRKHR 89
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
288-360 2.14e-14

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 69.17  E-value: 2.14e-14
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 56699440     288 IGDIYNGKVTSIMQFGCFVQLEGlrkRWEGLVHISELRREgRVANVADVVSKGQRVKVKVLSFTGTK--TSLSMK 360
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGN---GVEGLIPISELSDK-RVKDPEEVLKVGDEVKVKVLSVDEEKgrIILSLK 72
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 286-348 6.79e-11

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 59.22  E-value: 6.79e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 56699440    286 PAIGDIYNGKVTSIMQFGCFVQLEGLRkrwEGLVHISELRREgRVANVADVVSKGQRVKVKVL 348
Cdd:pfam00575    1 PEKGDVVEGEVTRVTKGGAFVDLGNGV---EGFIPISELSDD-HVEDPDEVIKVGDEVKVKVL 59
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 276-360 4.41e-09

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 60.52  E-value: 4.41e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440    276 KHVDRPPPEEPA----IGDIYNGKVTSIMQFGCFVQL-EGLrkrwEGLVHISELRREGRVANVADVVSKGQRVKVKVLSF 350
Cdd:TIGR00717  256 KQLGEDPWEAIEkkfpVGDKITGRVTNLTDYGVFVEIeEGI----EGLVHVSEMSWVKKNSHPSKVVKKGDEVEVMILDI 331

                           90
                   ....*....|..
gi 56699440    351 --TGTKTSLSMK 360
Cdd:TIGR00717  332 dpERRRLSLGLK 343
 
Name Accession Description Interval E-value
HrpA COG1643
HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];
580-1211 0e+00

HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441249 [Multi-domain]  Cd Length: 836  Bit Score: 574.34  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  580 MSILEQRESLPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFG 659
Cdd:COG1643    1 MSLITYPPDLPVSAVLPELLAALRAHQVVVLAAPPGAGKTTQLPLALLELGWGAGGRIGMLEPRRLAARAAAERMAEELG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  660 CCLGQEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQK-RQDMKLI 738
Cdd:COG1643   81 EPVGETVGYRVRFEDKVSAATRIEVVTEGILLRELQRDPELEGVDTVIFDEFHERSLNADLLLALLLDLQPAlRPDLKLL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  739 VTSATLDAVKFSQYFYEAPIFTIPGRTYPVEILYT--KEPETDYLDASLITVMQIhLTEPPGDILVFLTGQEEIDTACEI 816
Cdd:COG1643  161 VMSATLDAERFARLLGDAPVIESSGRTYPVEVRYRplPADERDLEDAVADAVREA-LAEEPGDILVFLPGEREIRRTAEA 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  817 LyerMKSLGPDVpelIILPVYSALPSEMQTRIFDPAPPGSRKVVIATNIAETSLTIDGIYYVVDPGFVKQKVYNSKTGID 896
Cdd:COG1643  240 L---RGRLPPDT---EILPLYGRLSAAEQDRAFAPAPHGRRRIVLATNIAETSLTVPGIRYVIDSGLARIPRYDPRSGVT 313

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  897 QLVVTPISQAQAKQRAGRAGRTGPGKCYRLYTE------RAYRDemlttnvPEIQRTNLASTVLSLKAMGINDLLSFDFM 970
Cdd:COG1643  314 RLPTERISQASANQRAGRAGRLAPGICYRLWSEedfarrPAFTD-------PEILRADLASLILELAAWGLGDPEDLPFL 386

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  971 DAPPMETLITAMEQLYTLGALDDEGLLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSMLSVQNVFYRpkdkqa 1050
Cdd:COG1643  387 DPPPARAIADARALLQELGALDADGRLTPLGRALARLPLDPRLARMLLAAAELGCLREAAILAALLSERDPRRG------ 460

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440 1051 ladqkkakfhQTEGDHLTLLAVYNSWKNNKfsnpwcyENFIQARSLRRAQDIRKQMLGIMDRHKLDVVScgkSTVRVQKA 1130
Cdd:COG1643  461 ----------AAGSDLLARLNLWRRLREQQ-------REFLSYLRLREWRDLARQLRRLLGEGANEEPA---DYEAIGLL 520

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440 1131 ICSGFFRNAAKKDPQEGYRTLIDQQVVYIHPSSALFNRqpEWVVYHELVLTTKEY-MREVTTIDPRWLVEFAPAFFK-VS 1208
Cdd:COG1643  521 LALAYPDRIARRRGEGGRYLLARGRGAALFPGSPLAKK--EWLVAAELVGGAAEArIRLAAPIDPEWLEELAAHLIKrYS 598


                 ...
gi 56699440 1209 DPT 1211
Cdd:COG1643  599 EPH 601
DEAH_box_HrpA TIGR01967
RNA helicase HrpA; This model represents HrpA, one of two related but uncharacterized DEAH-box ...
 587-1206 2.84e-157

RNA helicase HrpA; This model represents HrpA, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria and a few high-GC Gram-positive bacteria. HrpA is about 1300 amino acids long, while its paralog HrpB, also uncharacterized, is about 800 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing. The HrpA/B homolog from Borrelia is 500 amino acids shorter but appears to be derived from HrpA rather than HrpB. [Unknown function, Enzymes of unknown specificity]


Pssm-ID: 273900 [Multi-domain]  Cd Length: 1283  Bit Score: 505.07  E-value: 2.84e-157
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440    587 ESLPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQEV 666
Cdd:TIGR01967   64 DNLPVSAKREDIAEAIAENQVVIIAGETGSGKTTQLPKICLELGRGSHGLIGHTQPRRLAARTVAQRIAEELGTPLGEKV 143

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440    667 GYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSATLDA 746
Cdd:TIGR01967  144 GYKVRFHDQVSSNTLVKLMTDGILLAETQQDRFLSRYDTIIIDEAHERSLNIDFLLGYLKQLLPRRPDLKIIITSATIDP 223

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440    747 VKFSQYFYEAPIFTIPGRTYPVEILY------TKEPETDYLDASLITVMQIhLTEPPGDILVFLTGQEEIDTACEILYER 820
Cdd:TIGR01967  224 ERFSRHFNNAPIIEVSGRTYPVEVRYrplveeQEDDDLDQLEAILDAVDEL-FAEGPGDILIFLPGEREIRDAAEILRKR 302

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440    821 mkslgpDVPELIILPVYSALPSEMQTRIFDPAppGSRKVVIATNIAETSLTIDGIYYVVDPGFVKQKVYNSKTGIDQLVV 900
Cdd:TIGR01967  303 ------NLRHTEILPLYARLSNKEQQRVFQPH--SGRRIVLATNVAETSLTVPGIHYVIDTGTARISRYSYRTKVQRLPI 374

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440    901 TPISQAQAKQRAGRAGRTGPGKCYRLYTERAYRDEMLTTNvPEIQRTNLASTVLSLKAMGINDLLSFDFMDAPPMETLIT 980
Cdd:TIGR01967  375 EPISQASANQRKGRCGRVAPGICIRLYSEEDFNSRPEFTD-PEILRTNLASVILQMLALRLGDIAAFPFIEAPDPRAIRD 453

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440    981 AMEQLYTLGALDDE---GLLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSMLSVQNVFYRPKDKQALADQKKA 1057
Cdd:TIGR01967  454 GFRLLEELGALDDDeaePQLTPIGRQLAQLPVDPRLARMLLEAHRLGCLQEVLIIASALSIQDPRERPMEKQQAADQAHA 533

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440   1058 KFHQTEGDHLTLLAVYNSWKN-------NKFSNpWCYENFIQARSLRRAQDIRKQMLGIMDRHKLDVVSCGKSTVRVQKA 1130
Cdd:TIGR01967  534 RFKDPRSDFLSRVNLWRHIEEqrqalsaNQFRN-ACRKQYLNYLRVREWQDIYRQLTQVVKELGLKLNEEPADYDAIHKA 612

                          570       580       590       600       610       620       630
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 56699440   1131 ICSGFFRNAAKKDPQEGYrTLIDQQVVYIHPSSALFNRQPEWVVYHELVLTTKEYMREVTTIDPRWLVEFAPAFFK 1206
Cdd:TIGR01967  613 LLSGLLSQIGMKDEKHEY-DGARGRKFHIFPGSPLFKKPPKWVMAAELVETSKLYARLVAKIEPEWVEPVAGHLIK 687
PRK11131 PRK11131
ATP-dependent RNA helicase HrpA; Provisional
 587-1210 6.62e-148

ATP-dependent RNA helicase HrpA; Provisional


Pssm-ID: 182986 [Multi-domain]  Cd Length: 1294  Bit Score: 479.94  E-value: 6.62e-148
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440   587 ESLPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQEV 666
Cdd:PRK11131   71 ENLPVSQKKQDILEAIRDHQVVIVAGETGSGKTTQLPKICLELGRGVKGLIGHTQPRRLAARTVANRIAEELETELGGCV 150

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440   667 GYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSATLDA 746
Cdd:PRK11131  151 GYKVRFNDQVSDNTMVKLMTDGILLAEIQQDRLLMQYDTIIIDEAHERSLNIDFILGYLKELLPRRPDLKVIITSATIDP 230

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440   747 VKFSQYFYEAPIFTIPGRTYPVEILY------TKEPETDYLDASLITVMQIHlTEPPGDILVFLTGQEEI-DTAcEILYE 819
Cdd:PRK11131  231 ERFSRHFNNAPIIEVSGRTYPVEVRYrpiveeADDTERDQLQAIFDAVDELG-REGPGDILIFMSGEREIrDTA-DALNK 308

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440   820 RmkslgpDVPELIILPVYSALPSEMQTRIFDPAppGSRKVVIATNIAETSLTIDGIYYVVDPGFVKQKVYNSKTGIDQLV 899
Cdd:PRK11131  309 L------NLRHTEILPLYARLSNSEQNRVFQSH--SGRRIVLATNVAETSLTVPGIKYVIDPGTARISRYSYRTKVQRLP 380

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440   900 VTPISQAQAKQRAGRAGRTGPGKCYRLYTERAYRDEMLTTNvPEIQRTNLASTVLSLKAMGINDLLSFDFMDAPPMETLI 979
Cdd:PRK11131  381 IEPISQASANQRKGRCGRVSEGICIRLYSEDDFLSRPEFTD-PEILRTNLASVILQMTALGLGDIAAFPFVEAPDKRNIQ 459

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440   980 TAMEQLYTLGALDDEG-----LLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSMLSVQNVFYRPKDKQALADQ 1054
Cdd:PRK11131  460 DGVRLLEELGAITTDEqasayKLTPLGRQLAQLPVDPRLARMVLEAQKHGCVREVMIITSALSIQDPRERPMDKQQASDE 539

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  1055 KKAKFHQTEGDHLTLLAVYNSWK-------NNKFSNpWCYENFIQARSLRRAQDIRKQMLGIMDRHKLDVVSCGKSTVRV 1127
Cdd:PRK11131  540 KHRRFADKESDFLAFVNLWNYLQeqqkalsSNQFRR-LCRTDYLNYLRVREWQDIYTQLRQVVKELGIPVNSEPAEYREI 618

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  1128 QKAICSGFFRNAAKKDPQEGYRTLIDQQVVYIHPSSALFNRQPEWVVYHELVLTTKEYMREVTTIDPRWLVEFAPAFFK- 1206
Cdd:PRK11131  619 HTALLTGLLSHIGMKDAEKQEYTGARNARFSIFPGSGLFKKPPKWVMVAELVETSRLWGRIAARIEPEWIEPLAQHLIKr 698


                  ....*
gi 56699440  1207 -VSDP 1210
Cdd:PRK11131  699 sYSEP 703
DEXHc_DHX8 cd17971
DEXH-box helicase domain of DEAH-box helicase 8; DEAH-box helicase 8 (DHX8 ,also known as ...
 584-762 5.56e-127

DEXH-box helicase domain of DEAH-box helicase 8; DEAH-box helicase 8 (DHX8 ,also known as pre-mRNA-splicing factor ATP-dependent RNA helicase PRP22) acts late in the splicing of pre-mRNA and mediates the release of the spliced mRNA from spliceosomes. DHX8 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350729 [Multi-domain]  Cd Length: 179  Bit Score: 387.61  E-value: 5.56e-127
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  584 EQRESLPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLG 663
Cdd:cd17971    1 EQRESLPIYKLKEQLIQAVHDNQILVVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVAEEFGCCLG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  664 QEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSAT 743
Cdd:cd17971   81 QEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLSQYSVIMLDEAHERTIHTDVLFGLLKKTVQKRPDLKLIVTSAT 160

                        170
                 ....*....|....*....
gi 56699440  744 LDAVKFSQYFYEAPIFTIP 762
Cdd:cd17971  161 LDAVKFSQYFYEAPIFTIP 179
DEAH_box_HrpB TIGR01970
ATP-dependent helicase HrpB; This model represents HrpB, one of two related but ...
 589-1036 3.30e-103

ATP-dependent helicase HrpB; This model represents HrpB, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria, but also in a few species of other lineages. The member from Rhizobium meliloti has been designated HelO. HrpB is typically about 800 residues in length, while its paralog HrpA (TIGR01967), also uncharacterized, is about 1300 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing. [Unknown function, Enzymes of unknown specificity]


Pssm-ID: 273901 [Multi-domain]  Cd Length: 819  Bit Score: 346.37  E-value: 3.30e-103
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440    589 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQIT-QYLAEAGYTsrGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQEVG 667
Cdd:TIGR01970    1 LPIHAVLPALRDALAAHPQVVLEAPPGAGKSTAVPlALLDAPGIG--GKIIMLEPRRLAARSAAQRLASQLGEAVGQTVG 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440    668 YTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKtVQK--RQDMKLIVTSATLD 745
Cdd:TIGR01970   79 YRVRGENKVSRRTRLEVVTEGILTRMIQDDPELDGVGALIFDEFHERSLDADLGLALALD-VQSslREDLKILAMSATLD 157

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440    746 AVKFSQYFYEAPIFTIPGRTYPVEILYTKEPETDYLDASLITVMQIHLTEPPGDILVFLTGQEEIDTACEILYERmksLG 825
Cdd:TIGR01970  158 GERLSSLLPDAPVVESEGRSFPVEIRYLPLRGDQRLEDAVSRAVEHALASETGSILVFLPGQAEIRRVQEQLAER---LD 234

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440    826 PDVpelIILPVYSALPSEMQTRIFDPAPPGSRKVVIATNIAETSLTIDGIYYVVDPGFVKQKVYNSKTGIDQLVVTPISQ 905
Cdd:TIGR01970  235 SDV---LICPLYGELSLAAQDRAIKPDPQGRRKVVLATNIAETSLTIEGIRVVIDSGLARVARFDPKTGITRLETVRISQ 311

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440    906 AQAKQRAGRAGRTGPGKCYRLYTErAYRDEMLTTNVPEIQRTNLASTVLSLKAMGINDLLSFDFMDAPPMETLITAMEQL 985
Cdd:TIGR01970  312 ASATQRAGRAGRLEPGVCYRLWSE-EQHQRLPAQDEPEILQADLSGLALELAQWGAKDPSDLRWLDAPPSVALAAARQLL 390

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|.
gi 56699440    986 YTLGALDDEGLLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSML 1036
Cdd:TIGR01970  391 QRLGALDAQGRLTAHGKAMAALGCHPRLAAMLLSAHSTGLAALACDLAALL 441
DEXHc_DHX38 cd17983
DEXH-box helicase domain of DEAH-box helicase 38; DEAH-box helicase 38 (DHX38, also known as ...
 589-761 2.77e-94

DEXH-box helicase domain of DEAH-box helicase 38; DEAH-box helicase 38 (DHX38, also known as PRP16) is involved in pre-mRNA splicing. DHX38 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350741 [Multi-domain]  Cd Length: 173  Bit Score: 299.38  E-value: 2.77e-94
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  589 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQEVGY 668
Cdd:cd17983    1 LPIFAVRQELLNVIRDNNVVIVVGETGSGKTTQLTQYLHEDGYTDYGMIGCTQPRRVAAMSVAKRVSEEMGVELGEEVGY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  669 TIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSATLDAVK 748
Cdd:cd17983   81 AIRFEDCTSENTVIKYMTDGILLRESLRDPDLDKYSAIIMDEAHERSLNTDVLFGLLREVVARRRDLKLIVTSATMDADK 160

                        170
                 ....*....|...
gi 56699440  749 FSQYFYEAPIFTI 761
Cdd:cd17983  161 FADFFGNVPIFTI 173
PRK11664 PRK11664
ATP-dependent RNA helicase HrpB; Provisional
 588-1018 3.50e-94

ATP-dependent RNA helicase HrpB; Provisional


Pssm-ID: 236950 [Multi-domain]  Cd Length: 812  Bit Score: 321.10  E-value: 3.50e-94
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440   588 SLPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQIT-QYLAEAGYTsrGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQEV 666
Cdd:PRK11664    3 SLPVAAVLPELLTALKTAPQVLLKAPTGAGKSTWLPlQLLQHGGIN--GKIIMLEPRRLAARNVAQRLAEQLGEKPGETV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440   667 GYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKtVQK--RQDMKLIVTSATL 744
Cdd:PRK11664   81 GYRMRAESKVGPNTRLEVVTEGILTRMIQRDPELSGVGLVILDEFHERSLQADLALALLLD-VQQglRDDLKLLIMSATL 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440   745 DAVKFSQYFYEAPIFTIPGRTYPVEILYTKEPETDYLDASLITVMQIHLTEPPGDILVFLTGQEEIDTACEILYERmksL 824
Cdd:PRK11664  160 DNDRLQQLLPDAPVIVSEGRSFPVERRYQPLPAHQRFDEAVARATAELLRQESGSLLLFLPGVGEIQRVQEQLASR---V 236

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440   825 GPDVpelIILPVYSALPSEMQTRIFDPAPPGSRKVVIATNIAETSLTIDGIYYVVDPGFVKQKVYNSKTGIDQLVVTPIS 904
Cdd:PRK11664  237 ASDV---LLCPLYGALSLAEQQKAILPAPAGRRKVVLATNIAETSLTIEGIRLVVDSGLERVARFDPKTGLTRLVTQRIS 313

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440   905 QAQAKQRAGRAGRTGPGKCYRLYTERAYrDEMLTTNVPEIQRTNLASTVLSLKAMGINDLLSFDFMDAPPMETLITAMEQ 984
Cdd:PRK11664  314 QASMTQRAGRAGRLEPGICLHLYSKEQA-ERAAAQSEPEILHSDLSGLLLELLQWGCHDPAQLSWLDQPPAAALAAAKRL 392

                         410       420       430
                  ....*....|....*....|....*....|....
gi 56699440   985 LYTLGALDDEGLLTRLGRRMAEFPLEPMLCKMLI 1018
Cdd:PRK11664  393 LQQLGALDGQGRLTARGRKMAALGNDPRLAAMLV 426
DEXHc_DHX16 cd17974
DEXH-box helicase domain of DEAH-box helicase 16; DEAH-box helicase 16 (DHX16) is probably ...
 589-761 5.07e-89

DEXH-box helicase domain of DEAH-box helicase 16; DEAH-box helicase 16 (DHX16) is probably involved in pre-mRNA splicing. DHX16 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350732 [Multi-domain]  Cd Length: 174  Bit Score: 284.78  E-value: 5.07e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  589 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRG-KIGCTQPRRVAAMSVAKRVSEEFGCCLGQEVG 667
Cdd:cd17974    1 LPVYPYRDDLLAAVKEHQVLIIVGETGSGKTTQIPQYLHEAGYTKGGgKIGCTQPRRVAAMSVAARVAEEMGVKLGNEVG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  668 YTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSATLDAV 747
Cdd:cd17974   81 YSIRFEDCTSEKTVLKYMTDGMLLREFLTEPDLASYSVMIIDEAHERTLHTDILFGLVKDIARFRPDLKLLISSATMDAE 160

                        170
                 ....*....|....
gi 56699440  748 KFSQYFYEAPIFTI 761
Cdd:cd17974  161 KFSAFFDDAPIFRI 174
DEXHc_RHA-like cd17917
DEXH-box helicase domain of DEAD-like helicase RHA family proteins; The RNA helicase A (RHA) ...
 605-761 1.31e-87

DEXH-box helicase domain of DEAD-like helicase RHA family proteins; The RNA helicase A (RHA) family includes RHA, also called DEAH-box helicase 9 (DHX9), DHX8, DHX15-16, DHX32-38, and many others. The RHA family belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 438707 [Multi-domain]  Cd Length: 159  Bit Score: 280.50  E-value: 1.31e-87
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  605 NQILIVIGETGSGKTTQITQYLAEAGYTS--RGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQEVGYTIRFEDCTSPETVI 682
Cdd:cd17917    1 NQVVVIVGETGSGKTTQVPQFLLEDGLAKggKGRIVCTQPRRIAAISVAERVAEERGEKLGEEVGYQIRFESKTSSKTRI 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 56699440  683 KYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSATLDAVKFSQYFYEAPIFTI 761
Cdd:cd17917   81 KFCTDGILLRELLSDPLLSGYSHVILDEAHERSLDTDFLLGLLKDLLRKRPDLKVILMSATLDAEKFSSYFGGAPVIHI 159
SF2_C_RHA cd18791
C-terminal helicase domain of the RNA helicase A (RHA) family helicases; The RNA helicase A ...
 766-927 2.32e-86

C-terminal helicase domain of the RNA helicase A (RHA) family helicases; The RNA helicase A (RHA) family includes RHA, also called DEAH-box helicase 9 (DHX9), DHX8, DHX15-16, DHX32-38, and many others. The RHA family members are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350178 [Multi-domain]  Cd Length: 171  Bit Score: 277.49  E-value: 2.32e-86
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  766 YPVEILYTKEP-----------ETDYLDASLITVMQIHLTEPPGDILVFLTGQEEIDTACEILYERMKSlgPDVPELIIL 834
Cdd:cd18791    1 FPVEVYYLEDIlellgissekeDPDYVDAAVRLILQIHRTEEPGDILVFLPGQEEIERLCELLREELLS--PDLGKLLVL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  835 PVYSALPSEMQTRIFDPAPPGSRKVVIATNIAETSLTIDGIYYVVDPGFVKQKVYNSKTGIDQLVVTPISQAQAKQRAGR 914
Cdd:cd18791   79 PLHSSLPPEEQQRVFEPPPPGVRKVVLATNIAETSITIPGVVYVIDSGLVKEKVYDPRTGLSSLVTVWISKASAEQRAGR 158

                        170
                 ....*....|...
gi 56699440  915 AGRTGPGKCYRLY 927
Cdd:cd18791  159 AGRTRPGKCYRLY 171
DEXHc_DHX33 cd17978
DEXH-box helicase domain of DEAH-box helicase 33; DEAH-box helicase 33 (DHX33) stimulates RNA ...
 589-761 5.05e-86

DEXH-box helicase domain of DEAH-box helicase 33; DEAH-box helicase 33 (DHX33) stimulates RNA polymerase I transcription of the 47S precursor rRNA. DHX33 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 438710 [Multi-domain]  Cd Length: 178  Bit Score: 276.93  E-value: 5.05e-86
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  589 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQEVGY 668
Cdd:cd17978    1 LPIYSARKRLLEELRKHDTVIIIGETGSGKTTQIPQYLYEAGFARGGMIGITQPRRVAAVSVAKRVAEEMGVELGQLVGY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  669 TIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKtVQKR------QDMKLIVTSA 742
Cdd:cd17978   81 SVRFDDVTSEETRIKYMTDGMLLREAIGDPLLSKYSVIILDEAHERTVHTDVLFGLVKS-AQRRrkeqklSPLKVIIMSA 159

                        170
                 ....*....|....*....
gi 56699440  743 TLDAVKFSQYFYEAPIFTI 761
Cdd:cd17978  160 TLDADLFSEYFNGAPVLYI 178
DEXHc_DHX15 cd17973
DEXH-box helicase domain of DEAH-box helicase 15; DEAH-box helicase 15 (DHX15) is a pre-mRNA ...
 582-761 2.87e-83

DEXH-box helicase domain of DEAH-box helicase 15; DEAH-box helicase 15 (DHX15) is a pre-mRNA processing factor involved in disassembly of spliceosomes after the release of mature mRNA. DHX15 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 438709 [Multi-domain]  Cd Length: 187  Bit Score: 269.67  E-value: 2.87e-83
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  582 ILEQRESLPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGK--IGCTQPRRVAAMSVAKRVSEEFG 659
Cdd:cd17973    6 ILEKRRELPVWEQKEDFLKLLKNNQILVLVGETGSGKTTQIPQFVLDDELPHQPKklVACTQPRRVAAMSVAQRVAEEMD 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  660 CCLGQEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIV 739
Cdd:cd17973   86 VKLGEEVGYSIRFEDCSSAKTILKYMTDGMLLREAMSDPLLSRYSVIILDEAHERTLATDILMGLLKEVVRRRPDLKLIV 165

                        170       180
                 ....*....|....*....|..
gi 56699440  740 TSATLDAVKFSQYFYEAPIFTI 761
Cdd:cd17973  166 MSATLDAGKFQKYFDNAPLLKV 187
DEXHc_DHX35 cd17980
DEXH-box helicase domain of DEAH-box helicase 35; DHX35 plays a role in colorectal cancers and ...
 589-753 8.88e-76

DEXH-box helicase domain of DEAH-box helicase 35; DHX35 plays a role in colorectal cancers and seems to be associated with risk to thyroid cancers. It also has been shown to positively regulate poxviruses, such as Myxoma virus. DEAH-box helicase 35 (DHX35) belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350738 [Multi-domain]  Cd Length: 185  Bit Score: 248.54  E-value: 8.88e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  589 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGK-IGCTQPRRVAAMSVAKRVSEEFGCCLGQEVG 667
Cdd:cd17980    1 LPVFKLRNHILYLVENYQTIVIVGETGCGKSTQIPQYLAEAGWTAGGRvVGCTQPRRVAAVTVAGRVAEEMGAVLGHEVG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  668 YTIRFEDCTSP-ETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSATLDA 746
Cdd:cd17980   81 YCIRFDDCTDPqATRIKFLTDGMLVREMMLDPLLTKYSVIMLDEAHERTLYTDILIGLLKKIQKKRGDLRLIVASATLDA 160


                 ....*..
gi 56699440  747 VKFSQYF 753
Cdd:cd17980  161 EKFRDFF 167
DEXHc_DHX40 cd17984
DEXH-box helicase domain of DEAH-box helicase 40; DEAH-box helicase 40 (DHX40) belongs to the ...
 589-761 1.61e-75

DEXH-box helicase domain of DEAH-box helicase 40; DEAH-box helicase 40 (DHX40) belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350742 [Multi-domain]  Cd Length: 178  Bit Score: 247.46  E-value: 1.61e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  589 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQEVGY 668
Cdd:cd17984    1 LPIQKQRKKLVQAVRDNSFLIVTGNTGSGKTTQLPKYLYEAGFSQHGMIGVTQPRRVAAISVAQRVAEEMKCTLGSKVGY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  669 TIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQ-----DMKLIVTSAT 743
Cdd:cd17984   81 QVRFDDCSSKETAIKYMTDGCLLRHILADPNLTKYSVIILDEAHERSLTTDILFGLLKKLFQEKSpnrkeHLKVVVMSAT 160

                        170
                 ....*....|....*...
gi 56699440  744 LDAVKFSQYFYEAPIFTI 761
Cdd:cd17984  161 LELAKLSAFFGNCPVFDI 178
DEXHc_HrpA cd17989
DEXH-box helicase domain of ATP-dependent RNA helicase HrpA; HrpA is part of the HrpB-HrpA ...
 589-758 2.64e-60

DEXH-box helicase domain of ATP-dependent RNA helicase HrpA; HrpA is part of the HrpB-HrpA two-partner secretion (TPS) system, a secretion pathway important to the secretion of large virulence-associated proteins. HrpA belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350747 [Multi-domain]  Cd Length: 173  Bit Score: 204.23  E-value: 2.64e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  589 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQEVGY 668
Cdd:cd17989    1 LPVSQKRDEIAKAIAENQVVIIAGETGSGKTTQLPKICLELGRGIRGLIGHTQPRRLAARSVAERIAEELKTELGGAVGY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  669 TIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSATLDAVK 748
Cdd:cd17989   81 KVRFTDQTSDETCVKLMTDGILLAETQTDRYLRAYDTIIIDEAHERSLNIDFLLGYLKQLLPRRPDLKVIITSATIDAER 160

                        170
                 ....*....|
gi 56699440  749 FSQYFYEAPI 758
Cdd:cd17989  161 FSRHFNNAPI 170
DEXHc_DHX37 cd17982
DEXH-box helicase domain of DEAH-box helicase 37; DHX37 plays a role in the development of the ...
 589-751 7.50e-58

DEXH-box helicase domain of DEAH-box helicase 37; DHX37 plays a role in the development of the human nervous system and has been linked to schizophrenia. It also negatively regulates poxviruses such as Myxoma virus. DEAH-box helicase 37 (DHX37) belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350740 [Multi-domain]  Cd Length: 191  Bit Score: 197.96  E-value: 7.50e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  589 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSR-----GKIGCTQPRRVAAMSVAKRVSEEFGCcLG 663
Cdd:cd17982    1 LPILAEEQEIMEAINENPVVIICGETGSGKTTQVPQFLYEAGFGSPesdnpGMIGITQPRRVAAVSMAKRVAEELNV-FG 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  664 QEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDM-------- 735
Cdd:cd17982   80 KEVSYQIRYDSTVSENTKIKFMTDGVLLKEIQTDFLLRKYSVIIIDEAHERSVNTDILIGMLSRIVPLRAKLylqdqtvk 159

                        170
                 ....*....|....*...
gi 56699440  736 --KLIVTSATLDAVKFSQ 751
Cdd:cd17982  160 plKLVIMSATLRVEDFTE 177
DEXHc_DHX34 cd17979
DEXH-box helicase domain of DEAH-box helicase 34; DEAH-box helicase 34 (DHX34) plays a role in ...
 589-758 1.87e-54

DEXH-box helicase domain of DEAH-box helicase 34; DEAH-box helicase 34 (DHX34) plays a role in the nonsense-mediated decay (NMD), a surveillance mechanism that degrades aberrant mRNAs. DHX34 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350737 [Multi-domain]  Cd Length: 170  Bit Score: 187.26  E-value: 1.87e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  589 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSrgkIGCTQPRRVAAMSVAKRVSEEFGCCLGQEVGY 668
Cdd:cd17979    1 LPIAQYREKIIELLKTHQVVIVAGDTGCGKSTQVPQYLLAAGFRH---IACTQPRRIACISLAKRVAFESLNQYGSKVAY 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  669 TIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSATLDAVK 748
Cdd:cd17979   78 QIRFERTRTLATKLLFLTEGLLLRQIQRDASLPQYNVLILDEVHERHLHGDFLLGVLRCLLRLRPDLKLILMSATINIEL 157

                        170
                 ....*....|
gi 56699440  749 FSQYFYEAPI 758
Cdd:cd17979  158 FSGYFEGAPV 167
DEXHc_DHX36 cd17981
DEXH-box helicase domain of DEAH-box helicase 36; DEAH-box helicase 36 (DHX36, also known as ...
 589-761 6.76e-48

DEXH-box helicase domain of DEAH-box helicase 36; DEAH-box helicase 36 (DHX36, also known as G4-resolvase 1 or G4R1, MLE-like protein 1 and RNA helicase associated with AU-rich element or RHAU) unwinds a G4-quadruplex in human telomerase RNA. DHX36 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350739 [Multi-domain]  Cd Length: 180  Bit Score: 168.87  E-value: 6.76e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  589 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEaGYTSRGK-----IGCTQPRRVAAMSVAKRVSEEFG--CC 661
Cdd:cd17981    1 LPSYGMKQEIINMIDNNQVTVISGETGCGKTTQVTQFILD-DAIERGKgsscrIVCTQPRRISAISVAERVAAERAesCG 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  662 LGQEVGYTIRFEDCTSPETV-IKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVT 740
Cdd:cd17981   80 LGNSTGYQIRLESRKPRKQGsILYCTTGIVLQWLQSDPHLSNVSHLVLDEIHERNLQSDVLMGIVKDLLPFRSDLKVILM 159

                        170       180
                 ....*....|....*....|.
gi 56699440  741 SATLDAVKFSQYFYEAPIFTI 761
Cdd:cd17981  160 SATLNAEKFSDYFNNCPMIHI 180
DEXHc_DHX29 cd17975
DEXH-box helicase domain of DEAH-box helicase 29; DEAH-box helicase 29 (DHX29) is a part of ...
 589-761 7.20e-47

DEXH-box helicase domain of DEAH-box helicase 29; DEAH-box helicase 29 (DHX29) is a part of the 43S pre-initiation complex involved in translation initiation of mRNAs with structured 5'-UTRs. DHX29 is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350733 [Multi-domain]  Cd Length: 183  Bit Score: 166.24  E-value: 7.20e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  589 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAE-----AGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLG 663
Cdd:cd17975    1 LPVFKHRESILETLKRHRVVVVAGETGSGKSTQVPQFLLEdlllnGGTAQKCNIVCTQPRRISAMSLATRVCEELGCESG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  664 -----QEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLI 738
Cdd:cd17975   81 pggknSLCGYQIRMESRTGEATRLLYCTTGVLLRKLQEDGLLSSISHIIVDEVHERSVQSDFLLIILKEILHKRSDLHLI 160

                        170       180
                 ....*....|....*....|...
gi 56699440  739 VTSATLDAVKFSQYFYEAPIFTI 761
Cdd:cd17975  161 LMSATVDCEKFSSYFTHCPILRI 183
DEXHc_YTHDC2 cd17987
DEXH-box helicase domain of YTH domain containing 2; YTH domain containing 2 (YTHDC2) ...
 589-761 2.97e-46

DEXH-box helicase domain of YTH domain containing 2; YTH domain containing 2 (YTHDC2) regulates mRNA translation and stability via binding to N6-methyladenosine, a modified RNA nucleotide enriched in the stop codons and 3' UTRs of eukaryotic messenger RNAs. YTHDC2 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350745 [Multi-domain]  Cd Length: 176  Bit Score: 164.23  E-value: 2.97e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  589 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRG--KIGCTQPRRVAAMSVAKRVSEEFGCCLGQEV 666
Cdd:cd17987    1 LPVFEKQEQIVRIIKENKVVLIVGETGSGKTTQIPQFLLDDCYANGIpcRIFCTQPRRLAAIAVAERVAAERGEKIGQTV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  667 GYTIRFEDCTSPETVIKYMTDGMLLRECLI-DPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSATLD 745
Cdd:cd17987   81 GYQIRLESRVSPKTLLTFCTNGVLLRTLMAgDSALSTVTHVIVDEVHERDRFSDFLLTKLRDILQKHPNLKLILSSAALD 160

                        170
                 ....*....|....*.
gi 56699440  746 AVKFSQYFYEAPIFTI 761
Cdd:cd17987  161 VNLFIRYFGSCPVIYI 176
S1_DHX8_helicase cd05684
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ...
 289-367 1.60e-43

S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.


Pssm-ID: 240189 [Multi-domain]  Cd Length: 79  Bit Score: 152.39  E-value: 1.60e-43
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 56699440  289 GDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQRVKVKVLSFTGTKTSLSMKDVDQETG 367
Cdd:cd05684    1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQNGKISLSMKDVDQDTG 79
DEXHc_DHX9 cd17972
DEXH-box helicase domain of DEAH-box helicase 9; DEAH-box helicase 9 (DHX9, also known as ...
 582-761 8.32e-43

DEXH-box helicase domain of DEAH-box helicase 9; DEAH-box helicase 9 (DHX9, also known as ATP-dependent RNA helicase A or RHA and leukophysin or LKP) plays an important role in many cellular processes, including regulation of DNA replication, transcription, translation, microRNA biogenesis, RNA processing and transport, and maintenance of genomic stability. DHX9 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350730 [Multi-domain]  Cd Length: 234  Bit Score: 156.53  E-value: 8.32e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  582 ILEQRESLPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAE----AGYTSRGKIGCTQPRRVAAMSVAKRVSEE 657
Cdd:cd17972   52 ILQERELLPVKKFREEILEAISNNPVVIIRGATGCGKTTQVPQYILDdfiqNDRAAECNIVVTQPRRISAVSVAERVAFE 131

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  658 FGCCLGQEVGYTIRFEDCT-SPETVIKYMTDGMLLREclIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMK 736
Cdd:cd17972  132 RGEEVGKSCGYSVRFESVLpRPHASILFCTVGVLLRK--LEAGIRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPDLR 209

                        170       180
                 ....*....|....*....|....*
gi 56699440  737 LIVTSATLDAVKFSQYFYEAPIFTI 761
Cdd:cd17972  210 VILMSATIDTSMFCEYFFNCPVIEV 234
DEXHc_DHX32 cd17977
DEXH-box helicase domain of DEAH-box helicase 32; DEAH-box helicase 32 (DHX32) belongs to the ...
 589-758 2.20e-42

DEXH-box helicase domain of DEAH-box helicase 32; DEAH-box helicase 32 (DHX32) belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350735 [Multi-domain]  Cd Length: 176  Bit Score: 153.06  E-value: 2.20e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  589 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAE---AGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQE 665
Cdd:cd17977    1 LPVWEAKYEFMESLAHNQIVIVSGDAKTGKSSQIPQWCAEyclSAHYQHGVVVCTQVHKQTAVWLALRVADEMDVNIGHE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  666 VGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSATLD 745
Cdd:cd17977   81 VGYVIPFENCCTNETILRYCTDDMLLREMMSDPLLESYGVIILDDAHERTVSTDVLLGLLKDVLLSRPELKLVIITCPHL 160

                        170
                 ....*....|...
gi 56699440  746 AVKFSQYFYEAPI 758
Cdd:cd17977  161 SSKLLSYYGNVPL 173
DEXHc_HrpB cd17990
DEXH-box helicase domain of ATP-dependent helicase HrpB; HrpB is part of the HrpB-HrpA ...
 589-759 1.42e-41

DEXH-box helicase domain of ATP-dependent helicase HrpB; HrpB is part of the HrpB-HrpA two-partner secretion (TPS) system, a secretion pathway important to the secretion of large virulence-associated proteins. HrpB belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 438711 [Multi-domain]  Cd Length: 174  Bit Score: 150.56  E-value: 1.42e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  589 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQEVGY 668
Cdd:cd17990    1 LPIAAVLPALRAALDAGGQVVLEAPPGAGKTTRVPLALLAELWIAGGKIIVLEPRRVAARAAARRLATLLGEAPGETVGY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  669 TIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQ-KRQDMKLIVTSATLDAV 747
Cdd:cd17990   81 RVRGESRVGRRTRVEVVTEGVLLRRLQRDPELSGVGAVILDEFHERSLDADLALALLLEVQQlLRDDLRLLAMSATLDGD 160

                        170
                 ....*....|..
gi 56699440  748 KFSQYFYEAPIF 759
Cdd:cd17990  161 GLAALLPEAPVV 172
DEXHc_DHX57 cd17985
DEXH-box helicase domain of DEAH-box helicase 57; DEAH-box helicase 57 (DHX57) belongs to the ...
 589-761 5.11e-41

DEXH-box helicase domain of DEAH-box helicase 57; DEAH-box helicase 57 (DHX57) belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350743 [Multi-domain]  Cd Length: 177  Bit Score: 149.22  E-value: 5.11e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  589 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEA----GYTSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQ 664
Cdd:cd17985    1 LPAWQERETILELLEKHQVLVISGMTGCGKTTQIPQFILDNslqgPPLPVANIICTQPRRISAISVAERVAQERAERVGQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  665 EVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSATL 744
Cdd:cd17985   81 SVGYQIRLESVKSSATRLLYCTTGVLLRRLEGDPTLQGVTHVIVDEVHERTEESDFLLLVLKDLMVQRPDLKVILMSATL 160

                        170
                 ....*....|....*..
gi 56699440  745 DAVKFSQYFYEAPIFTI 761
Cdd:cd17985  161 NAELFSDYFNSCPVIHI 177
GH2-like_DHX8 cd21691
GIPC-homology 2 (GH2)-like domain found in DEAH box protein 8 (DHX8) and similar proteins; ...
 25-92 1.87e-40

GIPC-homology 2 (GH2)-like domain found in DEAH box protein 8 (DHX8) and similar proteins; DHX8 (a human homolog of yeast Prp22), also called RNA helicase HRH1, is an ATP-dependent RNA helicase involved in pre-mRNA splicing as a component of the spliceosome. It facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. This model corresponds to the GH2-like domain that shows high sequence similarity with the GH2 domain found in GIPC (GAIP C-terminus-interacting protein) family of proteins, which mediate endocytosis by tethering cargo proteins to the motor myosin VI.


Pssm-ID: 409668  Cd Length: 68  Bit Score: 143.07  E-value: 1.87e-40
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 56699440   25 LEYLSLVSKVCTELDNHLGINDKDLAEFVISLAEKNTTFDTFKASLVKNGAEFTDSLISNLLRLIQTM 92
Cdd:cd21691    1 LEYLSLVSKVCTELENHLGISDKDLAEFIIDLAEKSKTLDEFKKALKENGAEFPDSFVESLLRLIQRM 68
DEXHc_TDRD9 cd17988
DEXH-box helicase domain of tudor domain containing 9; Tudor domain containing 9 (TDRD9, also ...
 589-761 9.83e-40

DEXH-box helicase domain of tudor domain containing 9; Tudor domain containing 9 (TDRD9, also known as HIG-1or NET54 or C14orf75) is a part of the nuclear PIWI-interacting RNA (piRNA) pathway essential for transposon silencing and male fertility TDRD9 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350746 [Multi-domain]  Cd Length: 180  Bit Score: 145.34  E-value: 9.83e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  589 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAgYTSRGK---IGCTQPRRVAAMSVAKRVSEEFGCCLGQE 665
Cdd:cd17988    1 LPIYAKREEILSLIEANSVVIIKGATGCGKTTQLPQFILDH-YYKRGKycnIVVTQPRRIAAISIARRVSQEREWTLGSL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  666 VGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQ-KRQDMKLIVTSATL 744
Cdd:cd17988   80 VGYQVGLERPASEETRLIYCTTGVLLQKLINNKTLTEYTHIILDEVHERDQELDFLLLVVRRLLRtNSRHVKIILMSATI 159

                        170       180
                 ....*....|....*....|.
gi 56699440  745 DAVKFSQYF----YEAPIFTI 761
Cdd:cd17988  160 SCKEFADYFttpnNPAYVFEV 180
DEXQc_DQX1 cd17986
DEXQ-box helicase domain of DEAQ-box RNA dependent ATPase 1; DEAQ-box RNA dependent ATPase 1 ...
 589-761 4.24e-39

DEXQ-box helicase domain of DEAQ-box RNA dependent ATPase 1; DEAQ-box RNA dependent ATPase 1 (DQX1) belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350744 [Multi-domain]  Cd Length: 177  Bit Score: 143.50  E-value: 4.24e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  589 LPIYKLKEQLVQAVHDNQ-ILIVIGETGSGKTTQITQYLAEAGYT---SRGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQ 664
Cdd:cd17986    1 LPIWAAKFTFLEQLESPSgIVLVSGEPGSGKSTQVPQWCAEFALSrgfQKGQVTVTQPHPLAARSLALRVADEMDLNLGH 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  665 EVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKL-IVTSAT 743
Cdd:cd17986   81 EVGYSIPQEDCTGPNTILRFCWDRLLLQEMTSTPLLGAWGVVVLDEAQERSVASDSLLGLLKDVRLQRPELRVvVVTSPA 160

                        170
                 ....*....|....*...
gi 56699440  744 LDAvKFSQYFYEAPIFTI 761
Cdd:cd17986  161 LEP-KLRAFWGNPPVVHV 177
DEXHc_DHX30 cd17976
DEXH-box helicase domain of DEAH-box helicase 30; DEAH-box helicase 30 (DHX30) plays an ...
 589-758 5.91e-37

DEXH-box helicase domain of DEAH-box helicase 30; DEAH-box helicase 30 (DHX30) plays an important role in the assembly of the mitochondrial large ribosomal subunit. DHX30 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350734 [Multi-domain]  Cd Length: 178  Bit Score: 137.62  E-value: 5.91e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  589 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGC----TQPRRVAAMSVAKRVSEEFGCCLGQ 664
Cdd:cd17976    1 LPVDSHKESILSAIEQNPVVVISGDTGCGKTTRIPQFILEDYVLRGRGARCnvviTQPRRISAVSVAQRVAHELGPNLRR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  665 EVGYTIRFEDCTSPET-VIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSAT 743
Cdd:cd17976   81 NVGYQVRLESRPPPRGgALLFCTVGVLLKKLQSNPRLEGVSHVIVDEVHERDVNTDFLLILLKGVLQLNPELRVVLMSAT 160

                        170
                 ....*....|....*
gi 56699440  744 LDAVKFSQYFYEAPI 758
Cdd:cd17976  161 GDNQRLSRYFGGCPV 175
HA2 smart00847
Helicase associated domain (HA2) Add an annotation; This presumed domain is about 90 amino ...
 988-1070 1.04e-33

Helicase associated domain (HA2) Add an annotation; This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding.


Pssm-ID: 214852 [Multi-domain]  Cd Length: 82  Bit Score: 124.69  E-value: 1.04e-33
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440     988 LGALDDEGLLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSMLSVQNvfYRPKDKQALADQKKAKFHQTEGDHL 1067
Cdd:smart00847    2 LGALDDDGRLTPLGRKMAELPLDPRLAKMLLAAAEFGCLDEILTIVAMLSVGD--PRPKEKREDADAARRRFADPESDHL 79


                    ...
gi 56699440    1068 TLL 1070
Cdd:smart00847   80 TLL 82
HA2 pfam04408
Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in ...
 981-1069 1.39e-31

Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding.


Pssm-ID: 461295 [Multi-domain]  Cd Length: 104  Bit Score: 119.26  E-value: 1.39e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440    981 AMEQLYTLGALDDEGLLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSMLSVQNVFYRP------KDKQALADQ 1054
Cdd:pfam04408    1 ALELLYYLGALDEDGELTPLGRKMAELPLDPRLAKMLLAAAELGCLDEVLTIVAALSVRDPFVQPnfldprSAAKAARRR 80

                           90       100
                   ....*....|....*....|....
gi 56699440   1055 KKAKFHQ---------TEGDHLTL 1069
Cdd:pfam04408   81 RRAADEKarakfarldLEGDHLTL 104
OB_NTP_bind pfam07717
Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus ...
 1127-1203 1.73e-29

Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus of the DEAD-box helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. There do seem to be a couple of instances where it occurs by itself -. The structure PDB:3i4u adopts an OB-fold. helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. This C-terminal domain of the yeast helicase contains an oligonucleotide/oligosaccharide-binding (OB)-fold which seems to be placed at the entrance of the putative nucleic acid cavity. It also constitutes the binding site for the G-patch-containing domain of Pfa1p. When found on DEAH/RHA helicases, this domain is central to the regulation of the helicase activity through its binding of both RNA and G-patch domain proteins.


Pssm-ID: 400182 [Multi-domain]  Cd Length: 82  Bit Score: 112.35  E-value: 1.73e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440   1127 VQKAICSGFFRNAAKKDPQE-GYRTLIDQQVVYIHPSSALFN---RQPEWVVYHELVLTTKEYMREVTTIDPRWLVEFAP 1202
Cdd:pfam07717    1 LRAALAAGLYPNVARRDPKGkGYTTLSDNQRVFIHPSSVLFNektFPPEWVVYQELVETTKVYIRTVTAISPEWLLLFAP 80


                   .
gi 56699440   1203 A 1203
Cdd:pfam07717   81 H 81
DEXDc smart00487
DEAD-like helicases superfamily;
585-770 4.54e-27

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 109.89  E-value: 4.54e-27
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440     585 QRESLPIyklkeqlvqAVHDNQILIVIGETGSGKTTQITQYLAEAGY-TSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLG 663
Cdd:smart00487   13 QKEAIEA---------LLSGLRDVILAAPTGSGKTLAALLPALEALKrGKGGRVLVLVPTRELAEQWAEELKKLGPSLGL 83

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440     664 QEVGYT------IRFEDCTSPETVIKYMTDGMLLRECLIDP-DLTQYAIIMLDEAHERT--IHTDVLFGLLKKTVQKRQd 734
Cdd:smart00487   84 KVVGLYggdskrEQLRKLESGKTDILVTTPGRLLDLLENDKlSLSNVDLVILDEAHRLLdgGFGDQLEKLLKLLPKNVQ- 162

                           170       180       190
                    ....*....|....*....|....*....|....*...
gi 56699440     735 mkLIVTSATL--DAVKFSQYFYEAPIFTIPGRTYPVEI 770
Cdd:smart00487  163 --LLLLSATPpeEIENLLELFLNDPVFIDVGFTPLEPI 198
GH2_like cd21690
GIPC homology 2 (GH2) domain-like family; The GIPC (GAIP C-terminus-interacting protein) ...
 28-89 6.82e-24

GIPC homology 2 (GH2) domain-like family; The GIPC (GAIP C-terminus-interacting protein) family of proteins mediate endocytosis by tethering cargo proteins to the motor myosin VI. This model represents the C-terminal GIPC homology 2 or GH2 domain (plus the linker to the PDZ domain located N-terminally of GH2), which mediates the interaction with myosin VI and is involved in homodimerization in the autoinhibited state. The family also includes DEAH box protein 8 (DHX8) and similar proteins. DHX8 (a human homolog of yeast Prp22), also called RNA helicase HRH1, is an ATP-dependent RNA helicase involved in pre-mRNA splicing as a component of the spliceosome. It facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 contains a GH2-like domain at the N-terminus, which shows high sequence similarity with the GH2 domain found in GIPC proteins.


Pssm-ID: 409667  Cd Length: 62  Bit Score: 96.00  E-value: 6.82e-24
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 56699440   28 LSLVSKVCTELDNHLGINDKDLAEFVISLAEKNTTFDTFKASLVKNGAEFTDSLISNLLRLI 89
Cdd:cd21690    1 LSAIEKVDDLLKNYLGIDDPELAEFVISLAKKKKNPDEFAEALDENDAAFPDEFVFDLYRAI 62
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 285-363 1.56e-21

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 100.89  E-value: 1.56e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440   285 EPAIGDIYNGKVTSIMQFGCFVQLegLRKRwEGLVHISELRREgRVANVADVVSKGQRVKVKVLSFT-GTKTSLSMKDVD 363
Cdd:PRK11824  618 EPEVGEIYEGKVVRIVDFGAFVEI--LPGK-DGLVHISEIADE-RVEKVEDVLKEGDEVKVKVLEIDkRGRIRLSRKAVL 693
S1_PNPase cd04472
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ...
 289-359 1.15e-20

S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.


Pssm-ID: 239918 [Multi-domain]  Cd Length: 68  Bit Score: 86.83  E-value: 1.15e-20
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 56699440  289 GDIYNGKVTSIMQFGCFVQLEGLRkrwEGLVHISELRREgRVANVADVVSKGQRVKVKVLSF-TGTKTSLSM 359
Cdd:cd04472    1 GKIYEGKVVKIKDFGAFVEILPGK---DGLVHISELSDE-RVEKVEDVLKVGDEVKVKVIEVdDRGRISLSR 68
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 284-377 2.53e-20

Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function prediction only];


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 87.93  E-value: 2.53e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  284 EEPAIGDIYNGKVTSIMQFGCFVQLEGlrkRWEGLVHISELrREGRVANVADVVSKGQRVKVKVLSFTGT-KTSLSMKDV 362
Cdd:COG1098    1 MSIEVGDIVEGKVTGITPFGAFVELPE---GTTGLVHISEI-ADGYVKDINDYLKVGDEVKVKVLSIDEDgKISLSIKQA 76

                         90
                 ....*....|....*
gi 56699440  363 DQETGEDLNPNRRRN 377
Cdd:COG1098   77 EEKPKRPPRPRRNSR 91
S1_dom_CvfD NF040579
CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ...
 288-376 2.55e-19

CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a family of full-length homologs of RNA-binding proteins from the Firmicutes with a single copy of the S1 domain. Several members of the family have been characterized as general stress proteins, and the most recently characterized, CvfD, was shown to act as a post-transcriptional regulator.


Pssm-ID: 468553 [Multi-domain]  Cd Length: 113  Bit Score: 84.40  E-value: 2.55e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440   288 IGDIYNGKVTSIMQFGCFVQLEglrKRWEGLVHISELrREGRVANVADVVSKGQRVKVKVLS---FTGtKTSLSMKDVDQ 364
Cdd:NF040579    3 IGDIVEGKVTGIQPYGAFVALD---EHTQGLIHISEI-KHGYVKDINDFLKVGQEVKVKVLDideYTG-KISLSLRALEE 77

                          90
                  ....*....|..
gi 56699440   365 ETGEDLNPNRRR 376
Cdd:NF040579   78 APEKHRKRRKHR 89
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 284-362 1.24e-18

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 88.95  E-value: 1.24e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  284 EEPAIGDIYNGKVTSIMQFGCFVQLE-GLrkrwEGLVHISELRREGRVANVADVVSKGQRVKVKVLSF--TGTKTSLSMK 360
Cdd:COG0539  270 EKYPVGDVVKGKVTRLTDFGAFVELEpGV----EGLVHISEMSWTKRVAHPSDVVKVGDEVEVKVLDIdpEERRISLSIK 345


                 ..
gi 56699440  361 DV 362
Cdd:COG0539  346 QL 347
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 288-361 8.29e-17

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 83.56  E-value: 8.29e-17
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 56699440  288 IGDIYNGKVTSIMQFGCFVQLEGLrkrwEGLVHISELRReGRVANVADVVSKGQRVKVKVLSF--TGTKTSLSMKD 361
Cdd:COG0539  189 EGDVVEGTVKNITDFGAFVDLGGV----DGLLHISEISW-GRVKHPSEVLKVGDEVEVKVLKIdrEKERISLSLKQ 259
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
283-368 1.43e-16

bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 85.00  E-value: 1.43e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440   283 PEEPAIGDIYNGKVTSIMQFGCFVQLE-GLrkrwEGLVHISELrREGRVANVADVVSKGQRVKVKVLSFTGT--KTSLSM 359
Cdd:PRK00087  557 EEKYPVGSIVLGKVVRIAPFGAFVELEpGV----DGLVHISQI-SWKRIDKPEDVLSEGEEVKAKILEVDPEekRIRLSI 631


                  ....*....
gi 56699440   360 KDVDQETGE 368
Cdd:PRK00087  632 KEVEEEPGD 640
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 284-388 3.36e-15

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 79.15  E-value: 3.36e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440   284 EEPAIGDIYNGKVTSIMQFGCFVQL-EGLrkrwEGLVHISELRREgRVANVADVVSKGQRVKVKVLSF--TGTKTSLSMK 360
Cdd:PRK06676  273 EKLPEGDVIEGTVKRLTDFGAFVEVlPGV----EGLVHISQISHK-HIATPSEVLEEGQEVKVKVLEVneEEKRISLSIK 347

                          90       100
                  ....*....|....*....|....*...
gi 56699440   361 DVDQETGEDLNPNRRRNLVGETNEETSM 388
Cdd:PRK06676  348 ALEEAPAEEEDRREEYRQYELPEEETGF 375
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 289-362 3.78e-15

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 78.76  E-value: 3.78e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 56699440   289 GDIYNGKVTSIMQFGCFVQLEGLrkrwEGLVHISELRREgRVANVADVVSKGQRVKVKVLSF---TGtKTSLSMKDV 362
Cdd:PRK06676  193 GDVVEGTVARLTDFGAFVDIGGV----DGLVHISELSHE-RVEKPSEVVSVGQEVEVKVLSIdweTE-RISLSLKDT 263
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 289-360 4.65e-15

S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240197 [Multi-domain]  Cd Length: 69  Bit Score: 70.78  E-value: 4.65e-15
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 56699440  289 GDIYNGKVTSIMQFGCFVQL-EGLrkrwEGLVHISELRREgRVANVADVVSKGQRVKVKVLSFTGT-KTSLSMK 360
Cdd:cd05692    1 GSVVEGTVTRLKPFGAFVELgGGI----SGLVHISQIAHK-RVKDVKDVLKEGDKVKVKVLSIDARgRISLSIK 69
HELICc smart00490
helicase superfamily c-terminal domain;
815-919 1.02e-14

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 70.32  E-value: 1.02e-14
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440     815 EILYERMKSLGpdvpeLIILPVYSALPSEMQTRIFDPAPPGSRKVVIATNIAETSLTIDGIYYVVDPGFvkqkvynsktg 894
Cdd:smart00490    1 EELAELLKELG-----IKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDL----------- 64

                            90       100
                    ....*....|....*....|....*
gi 56699440     895 idqlvvtPISQAQAKQRAGRAGRTG 919
Cdd:smart00490   65 -------PWSPASYIQRIGRAGRAG 82
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
288-360 2.14e-14

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 69.17  E-value: 2.14e-14
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 56699440     288 IGDIYNGKVTSIMQFGCFVQLEGlrkRWEGLVHISELRREgRVANVADVVSKGQRVKVKVLSFTGTK--TSLSMK 360
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGN---GVEGLIPISELSDK-RVKDPEEVLKVGDEVKVKVLSVDEEKgrIILSLK 72
PRK08059 PRK08059
general stress protein 13; Validated
 288-391 1.16e-13

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 68.92  E-value: 1.16e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440   288 IGDIYNGKVTSIMQFGCFVQLEGlrkRWEGLVHISELrREGRVANVADVVSKGQRVKVKVLSF--TGTKTSLSMKdvdqE 365
Cdd:PRK08059    7 VGSVVTGKVTGIQPYGAFVALDE---ETQGLVHISEI-THGFVKDIHDFLSVGDEVKVKVLSVdeEKGKISLSIR----A 78

                          90       100
                  ....*....|....*....|....*.
gi 56699440   366 TGEDLNPNRRRNLVGETNEETSMRNP 391
Cdd:PRK08059   79 TEEAPEAKRKKGKILIPNPSEQGFNT 104
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 288-360 1.71e-13

S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240193 [Multi-domain]  Cd Length: 68  Bit Score: 66.50  E-value: 1.71e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 56699440  288 IGDIYNGKVTSIMQFGCFVQLEGLrkrwEGLVHISELRReGRVANVADVVSKGQRVKVKVLSFTGTKTSLSMK 360
Cdd:cd05688    1 EGDVVEGTVKSITDFGAFVDLGGV----DGLLHISDMSW-GRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 785-919 1.10e-12

Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.


Pssm-ID: 459740 [Multi-domain]  Cd Length: 109  Bit Score: 65.69  E-value: 1.10e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440    785 LITVMQIHLTEPPGDILVFLTGQEEIDtaCEILYERMKslgpdvpeLIILPVYSALPSEMQTRIFDPAPPGSRKVVIATN 864
Cdd:pfam00271    3 LEALLELLKKERGGKVLIFSQTKKTLE--AELLLEKEG--------IKVARLHGDLSQEEREEILEDFRKGKIDVLVATD 72

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 56699440    865 IAETSLTIDGIYYVVDpgfvkqkvYNSKTGIDQLVvtpisqaqakQRAGRAGRTG 919
Cdd:pfam00271   73 VAERGLDLPDVDLVIN--------YDLPWNPASYI----------QRIGRAGRAG 109
PRK08582 PRK08582
RNA-binding protein S1;
294-385 4.72e-12

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 64.67  E-value: 4.72e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440   294 GKVTSIMQFGCFVQLEGLRKrweGLVHISELrREGRVANVADVVSKGQRVKVKVLSFTGT-KTSLSM-KDVDQETGEDLN 371
Cdd:PRK08582   11 GKVTGITNFGAFVELPEGKT---GLVHISEV-ADNYVKDINDHLKVGDEVEVKVLNVEDDgKIGLSIkKAKDRPKRQHDR 86

                          90
                  ....*....|....
gi 56699440   372 PNRRRNLVGETNEE 385
Cdd:PRK08582   87 PRHEDNRGGGNDVA 100
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 288-360 5.08e-12

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 70.19  E-value: 5.08e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 56699440   288 IGDIYNGKVTSIMQFGCFVQLE-GLrkrwEGLVHISELRREGRVANVADVVSKGQRVKVKVLS--FTGTKTSLSMK 360
Cdd:PRK06299  286 VGSKVKGKVTNITDYGAFVELEeGI----EGLVHVSEMSWTKKNKHPSKVVSVGQEVEVMVLEidEEKRRISLGLK 357
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 292-359 1.66e-11

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 60.86  E-value: 1.66e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 56699440  292 YNGKVTSIMQFGCFVQLEGlrkRWEGLVHISELRREgRVANVADVVSKGQRVKVKVLSFTGTKTSLSM 359
Cdd:cd00164    1 VTGKVVSITKFGVFVELED---GVEGLVHISELSDK-FVKDPSEVFKVGDEVEVKVLEVDPEKGRISL 64
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
289-362 1.77e-11

bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 68.43  E-value: 1.77e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 56699440   289 GDIYNGKVTSIMQFGCFVQLEGLrkrwEGLVHISELRReGRVANVADVVSKGQRVKVKVLSF--TGTKTSLSMKDV 362
Cdd:PRK00087  478 GDVVEGEVKRLTDFGAFVDIGGV----DGLLHVSEISW-GRVEKPSDVLKVGDEIKVYILDIdkENKKLSLSLKKL 548
rpsA PRK13806
30S ribosomal protein S1; Provisional
 289-372 2.06e-11

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 67.83  E-value: 2.06e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440   289 GDIYNGKVTSIMQFGCFVQLE-GLrkrwEGLVHISELRReGRVANVADVVSKGQRVKVKVLSF------TGTKTSLSMKD 361
Cdd:PRK13806  203 GDVVEGTVTRLAPFGAFVELApGV----EGMVHISELSW-SRVQKADEAVSVGDTVRVKVLGIerakkgKGLRISLSIKQ 277

                          90
                  ....*....|....*
gi 56699440   362 VD----QETGEDLNP 372
Cdd:PRK13806  278 AGgdpwDTVGDRLKA 292
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 286-348 6.79e-11

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 59.22  E-value: 6.79e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 56699440    286 PAIGDIYNGKVTSIMQFGCFVQLEGLRkrwEGLVHISELRREgRVANVADVVSKGQRVKVKVL 348
Cdd:pfam00575    1 PEKGDVVEGEVTRVTKGGAFVDLGNGV---EGFIPISELSDD-HVEDPDEVIKVGDEVKVKVL 59
PRK05807 PRK05807
RNA-binding protein S1;
289-360 4.32e-10

RNA-binding protein S1;


Pssm-ID: 235614 [Multi-domain]  Cd Length: 136  Bit Score: 58.99  E-value: 4.32e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 56699440   289 GDIYNGKVTSIMQFGCFVQLEGLrkrwEGLVHISELrREGRVANVADVVSKGQRVKVKVLSF-TGTKTSLSMK 360
Cdd:PRK05807    6 GSILEGTVVNITNFGAFVEVEGK----TGLVHISEV-ADTYVKDIREHLKEQDKVKVKVISIdDNGKISLSIK 73
PRK07252 PRK07252
S1 RNA-binding domain-containing protein;
288-365 4.44e-10

S1 RNA-binding domain-containing protein;


Pssm-ID: 180908 [Multi-domain]  Cd Length: 120  Bit Score: 58.56  E-value: 4.44e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440   288 IGDIYNGKVTSIMQFGCFVQLEGLRKrweGLVHISELrREGRVANVADVVSKGQRVKVKVL---SFTGtKTSLSMKDVDQ 364
Cdd:PRK07252    3 IGDKLKGTITGIKPYGAFVALENGTT---GLIHISEI-KTGFIDNIHQLLKVGEEVLVQVVdfdEYTG-KASLSLRTLEE 77


                  .
gi 56699440   365 E 365
Cdd:PRK07252   78 E 78
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 287-372 1.08e-09

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 62.37  E-value: 1.08e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440   287 AIGDIYNGKVTSIMQFGCFVQLE-GLrkrwEGLVHISELrREGRVANVADVVSKGQRVKVKV--LSFTGTKTSLSMKDVD 363
Cdd:PRK07899  292 AIGQIVPGKVTKLVPFGAFVRVEeGI----EGLVHISEL-AERHVEVPEQVVQVGDEVFVKVidIDLERRRISLSLKQAN 366

                          90
                  ....*....|..
gi 56699440   364 Q---ETGEDLNP 372
Cdd:PRK07899  367 EgvtPESEDFDP 378
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 289-360 1.42e-09

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 62.10  E-value: 1.42e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 56699440   289 GDIYNGKVTSIMQFGCFVQLEGLrkrwEGLVHISELRReGRVANVADVVSKGQRVKVKVLSFTGTKT--SLSMK 360
Cdd:PRK06299  202 GQVVEGVVKNITDYGAFVDLGGV----DGLLHITDISW-KRVNHPSEVVNVGDEVKVKVLKFDKEKKrvSLGLK 270
rpsA PRK13806
30S ribosomal protein S1; Provisional
 289-361 2.08e-09

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 61.66  E-value: 2.08e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 56699440   289 GDIYNGKVTSIMQFGCFVQLE-GLrkrwEGLVHISELRREGRVANVADVVSKGQRVKVKVLSFTGTK--TSLSMKD 361
Cdd:PRK13806  293 GDKVTGKVVRLAPFGAFVEILpGI----EGLVHVSEMSWTRRVNKPEDVVAPGDAVAVKIKDIDPAKrrISLSLRD 364
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 289-349 2.31e-09

S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.


Pssm-ID: 240190 [Multi-domain]  Cd Length: 68  Bit Score: 54.55  E-value: 2.31e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 56699440  289 GDIYNGKVTSIMQFGCFVQLeGLRKrwEGLVHISELRrEGRVANVADVVSKGQRVKVKVLS 349
Cdd:cd05685    1 GMVLEGVVTNVTDFGAFVDI-GVKQ--DGLIHISKMA-DRFVSHPSDVVSVGDIVEVKVIS 57
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 283-365 3.25e-09

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 59.07  E-value: 3.25e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440   283 PEEpaiGDIYNGKVTSIMQFGCFVQLE---GLrkrwEGLVHISELRReGRVANVADVVSKGQRVKVKVLSFTGTKTS--L 357
Cdd:PRK03987    6 PEE---GELVVGTVKEVKDFGAFVTLDeypGK----EGFIHISEVAS-GWVKNIRDHVKEGQKVVCKVIRVDPRKGHidL 77


                  ....*....
gi 56699440   358 SMKDV-DQE 365
Cdd:PRK03987   78 SLKRVnEHQ 86
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
288-368 3.95e-09

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 60.81  E-value: 3.95e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  288 IGDIYNGKVTSIMQFGCFV-----QleglrkrwEGLVHISELRrEGRVANVADVVSKGQRVKVKVLSFTGTK--TSLSMK 360
Cdd:COG2183  641 PGMILEGTVTNVTDFGAFVdigvhQ--------DGLVHISQLS-DRFVKDPREVVKVGDIVKVKVLEVDLKRkrISLSMK 711


                 ....*...
gi 56699440  361 DVDQETGE 368
Cdd:COG2183  712 LDDEAGAA 719
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 276-360 4.41e-09

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 60.52  E-value: 4.41e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440    276 KHVDRPPPEEPA----IGDIYNGKVTSIMQFGCFVQL-EGLrkrwEGLVHISELRREGRVANVADVVSKGQRVKVKVLSF 350
Cdd:TIGR00717  256 KQLGEDPWEAIEkkfpVGDKITGRVTNLTDYGVFVEIeEGI----EGLVHVSEMSWVKKNSHPSKVVKKGDEVEVMILDI 331

                           90
                   ....*....|..
gi 56699440    351 --TGTKTSLSMK 360
Cdd:TIGR00717  332 dpERRRLSLGLK 343
S1_IF2_alpha cd04452
S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ...
 286-348 8.52e-09

S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to complete the initiation complex, which is competent to begin translation. The IF2a subunit is a major site of control of the translation initiation process, via phosphorylation of a specific serine residue. This alpha subunit is well conserved in eukaryotes and archaea but is not present in bacteria. IF2 is a cold-shock-inducible protein.


Pssm-ID: 239899 [Multi-domain]  Cd Length: 76  Bit Score: 53.36  E-value: 8.52e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 56699440  286 PAIGDIYNGKVTSIMQFGCFVQLEGLRKRwEGLVHISELRReGRVANVADVVSKGQRVKVKVL 348
Cdd:cd04452    1 PEEGELVVVTVKSIADMGAYVSLLEYGNI-EGMILLSELSR-RRIRSIRKLVKVGRKEVVKVI 61
S1_RNase_R cd04471
S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, ...
 288-368 1.04e-08

S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.


Pssm-ID: 239917 [Multi-domain]  Cd Length: 83  Bit Score: 53.17  E-value: 1.04e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  288 IGDIYNGKVTSIMQFGCFVQLEGLRKrwEGLVHISEL----------------RREGRVANVadvvskGQRVKVKVlsft 351
Cdd:cd04471    1 VGEEFDGVISGVTSFGLFVELDNLTV--EGLVHVSTLgddyyefdeenhalvgERTGKVFRL------GDKVKVRV---- 68

                         90
                 ....*....|....*..
gi 56699440  352 gtktslsmKDVDQETGE 368
Cdd:cd04471   69 --------VRVDLDRRK 77
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 288-360 2.09e-08

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 58.25  E-value: 2.09e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 56699440   288 IGDIYNGKVTSIMQFGCFVQLE-GLrkrwEGLVHISELRREGRVANVADVVSKGQRVKVKVLSF--TGTKTSLSMK 360
Cdd:PRK06299  373 VGDVVEGKVKNITDFGAFVGLEgGI----DGLVHLSDISWDKKGEEAVELYKKGDEVEAVVLKVdvEKERISLGIK 444
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 287-360 2.82e-08

S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240213 [Multi-domain]  Cd Length: 77  Bit Score: 51.95  E-value: 2.82e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 56699440  287 AIGDIYNGKVTSIMQFGCFVQLEGlrKRWEGLVHISELRrEGRVANVADVVSKGQRVKVKVLSF--TGTKTSLSMK 360
Cdd:cd05708    1 KVGQKIDGTVRRVEDYGVFIDIDG--TNVSGLCHKSEIS-DNRVADASKLFRVGDKVRAKVLKIdaEKKRISLGLK 73
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 288-370 3.20e-08

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 57.82  E-value: 3.20e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440    288 IGDIYNGKVTSIMQFGCFVQLEGLrkrwEGLVHISELRReGRVANVADVVSKGQRVKVKVLSFTGTKT--SLSMKDVDQE 365
Cdd:TIGR00717  187 EGDVVKGVVKNITDFGAFVDLGGV----DGLLHITDMSW-KRVKHPSEYVKVGQEVKVKVIKFDKEKGriSLSLKQLGED 261


                   ....*
gi 56699440    366 TGEDL 370
Cdd:TIGR00717  262 PWEAI 266
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 289-359 5.41e-08

S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240195 [Multi-domain]  Cd Length: 69  Bit Score: 50.96  E-value: 5.41e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 56699440  289 GDIYNGKVTSIMQFGCFVQLEGlrkRWEGLVHISELRREGRVANVADVVSKGQRVKVKVLSFTGTKTSLSM 359
Cdd:cd05690    1 GTVVSGKIKSITDFGIFVGLDG---GIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVERERISL 68
PLN00207 PLN00207
polyribonucleotide nucleotidyltransferase; Provisional
 286-417 6.37e-08

polyribonucleotide nucleotidyltransferase; Provisional


Pssm-ID: 215104 [Multi-domain]  Cd Length: 891  Bit Score: 57.21  E-value: 6.37e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440   286 PAIGDIY-NGKVTSIMQFGCFVQLEGLRkrwEGLVHISELrREGRVANVADVVSKGQRVKVKVLSFT-GTKTSLSMKDVD 363
Cdd:PLN00207  751 PTVGDIYrNCEIKSIAPYGAFVEIAPGR---EGLCHISEL-SSNWLAKPEDAFKVGDRIDVKLIEVNdKGQLRLSRRALL 826

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 56699440   364 QETGEDLNPNRRRNlvGETNEETSMRN----PDRPTHLSLVSAPEVEDDSLERKRLTR 417
Cdd:PLN00207  827 PEANSEKSSQKQQG--GSTKDKAPQKKyvntSSRPRRAAQAEKNSAENAAVPKKKDYK 882
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 287-365 2.81e-07

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 54.79  E-value: 2.81e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440   287 AIGDIYNGKVTSIMQFGCFVQLEGLRkrwEGLVHISELRREgRVANVADVVSKGQRVKVKVLSFtGTKT---SLSMKDVD 363
Cdd:PRK06299  459 KKGSIVTGTVTEVKDKGAFVELEDGV---EGLIRASELSRD-RVEDATEVLKVGDEVEAKVINI-DRKNrriSLSIKALD 533


                  ..
gi 56699440   364 QE 365
Cdd:PRK06299  534 EA 535
PHA02653 PHA02653
RNA helicase NPH-II; Provisional
 700-928 3.91e-07

RNA helicase NPH-II; Provisional


Pssm-ID: 177443 [Multi-domain]  Cd Length: 675  Bit Score: 54.60  E-value: 3.91e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440   700 LTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIvtSATL-DAVKFSQYFYEAPIFT-IPGRT-YPVEILYTK-- 774
Cdd:PHA02653  289 LFDYGTVIIDEVHEHDQIGDIIIAVARKHIDKIRSLFLM--TATLeDDRDRIKEFFPNPAFVhIPGGTlFPISEVYVKnk 366

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440   775 ----------EPETDYLDASLITvmqihLTEPPG-DILVFLTGQEEIDTACEILYERMkslgpdvPELIILPVYSALPS- 842
Cdd:PHA02653  367 ynpknkrayiEEEKKNIVTALKK-----YTPPKGsSGIVFVASVSQCEEYKKYLEKRL-------PIYDFYIIHGKVPNi 434

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440   843 -EMQTRIFDPAPPgsrKVVIATNIAETSLTIDGIYYVVDPGfvkqKVYNSKT-GIDQLVvtpISQAQAKQRAGRAGRTGP 920
Cdd:PHA02653  435 dEILEKVYSSKNP---SIIISTPYLESSVTIRNATHVYDTG----RVYVPEPfGGKEMF---ISKSMRTQRKGRVGRVSP 504


                  ....*...
gi 56699440   921 GKCYRLYT 928
Cdd:PHA02653  505 GTYVYFYD 512
S1_RPS1_repeat_ec4 cd05689
S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 294-359 1.07e-06

S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240194 [Multi-domain]  Cd Length: 72  Bit Score: 47.19  E-value: 1.07e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 56699440  294 GKVTSIMQFGCFVQLE-GLrkrwEGLVHISELRREGRVANVADVVSKGQRVKVKVLSFTGTKTSLSM 359
Cdd:cd05689    9 GKVTNLTDYGCFVELEeGV----EGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEERRRISL 71
VacB COG0557
Exoribonuclease R [Transcription];
288-349 2.67e-06

Exoribonuclease R [Transcription];


Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 51.65  E-value: 2.67e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 56699440  288 IGDIYNGKVTSIMQFGCFVQLEGLRKrwEGLVHISEL----------------RREGRVANVadvvskGQRVKVKVLS 349
Cdd:COG0557  622 VGEEFEGVISGVTSFGLFVELDELGV--EGLVHVSSLgddyyeyderrqalvgERTGKRYRL------GDRVEVRVVR 691
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 289-369 3.10e-06

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 51.20  E-value: 3.10e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440   289 GDIYNGKVTSIMQFGCFVQLEGLrkrwEGLVHISELRREgRVANVADVVSKGQRVKVKVLS--FTGTKTSLSMKdvdqET 366
Cdd:PRK07899  209 GQVRKGVVSSIVNFGAFVDLGGV----DGLVHVSELSWK-HIDHPSEVVEVGQEVTVEVLDvdMDRERVSLSLK----AT 279


                  ...
gi 56699440   367 GED 369
Cdd:PRK07899  280 QED 282
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 608-743 9.87e-06

N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily 2 helicases comprise a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This N-terminal domain contains the ATP-binding region.


Pssm-ID: 350668 [Multi-domain]  Cd Length: 146  Bit Score: 46.63  E-value: 9.87e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  608 LIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGccLGQEVGYTIRFedcTSPETV------ 681
Cdd:cd00046    4 VLITAPTGSGKTLAALLAALLLLLKKGKKVLVLVPTKALALQTAERLRELFG--PGIRVAVLVGG---SSAEEReknklg 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 56699440  682 ---IKYMTDGMLLRECLID--PDLTQYAIIMLDEAHERTIHTDVLFgLLKKTVQKRQ--DMKLIVTSAT 743
Cdd:cd00046   79 dadIIIATPDMLLNLLLREdrLFLKDLKLIIVDEAHALLIDSRGAL-ILDLAVRKAGlkNAQVILLSAT 146
DEXHc_viral_Ns3 cd17931
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
 614-712 2.25e-05

DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional protein found in pestiviruses that contains an N-terminal protease and a C-terminal helicase. The N-terminal domain is a chymotrypsin-like serine protease, which is responsible for most of the maturation cleavages of the polyprotein precursor in the cytosolic side of the endoplasmic reticulum membrane. The C-terminal domain, about two-thirds of NS3, is a helicase belonging to superfamily 2 (SF2) thought to be important for unwinding highly structured regions of the RNA genome during replication. NS3 plays an essential role in viral polyprotein processing and genome replication. NS3 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350689 [Multi-domain]  Cd Length: 151  Bit Score: 45.62  E-value: 2.25e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  614 TGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSeefgcclGQEVGY-TIRFEDCTSPETVIKYMTDGMLLR 692
Cdd:cd17931   10 PGAGKTTRVLPQIIREAIKKRLRTLVLAPTRVVAAEMYEALR-------GLPIRYrTGAVKEEHGGNEIVDYMCHGTFTC 82

                         90       100
                 ....*....|....*....|
gi 56699440  693 ECLIDPDLTQYAIIMLDEAH 712
Cdd:cd17931   83 RLLSPKRVPNYNLIIMDEAH 102
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 289-360 3.20e-05

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 48.19  E-value: 3.20e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 56699440    289 GDIYNGKVTSIMQFGCFVQLEGlrkRWEGLVHISELRREgRVANVADVVSKGQRVKVKVLSF--TGTKTSLSMK 360
Cdd:TIGR00717  447 GSVVKGKVTEIKDFGAFVELPG---GVEGLIRNSELSEN-RDEDKTDEIKVGDEVEAKVVDIdkKNRKVSLSVK 516
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 287-370 1.20e-04

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 46.63  E-value: 1.20e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440   287 AIGDIYNGKVTSIMQFGCFVQL-EGLrkrwEGLVHISELRREGRVANVADVVSKGQRVKVKVLSF--TGTKTSLSMKDVD 363
Cdd:PRK12269  577 GVNDVVKGRVTKIADFGAFIELaEGI----EGLAHISEFSWVKKTSKPSDMVKIGDEVECMILGYdiQAGRVSLGLKQVT 652


                  ....*..
gi 56699440   364 QETGEDL 370
Cdd:PRK12269  653 ANPWEEI 659
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
 858-927 2.25e-04

C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases include DEAD-box helicases, UvrB, RecG, Ski2, Sucrose Non-Fermenting (SNF) family helicases, and dicer proteins, among others. Similar to SF1 helicases, they do not form toroidal structures like SF3-6 helicases. SF2 helicases are a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Their helicase core is surrounded by C- and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains, or domains engaged in protein-protein interactions. The core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350172 [Multi-domain]  Cd Length: 77  Bit Score: 40.77  E-value: 2.25e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 56699440  858 KVVIATNIAETSLTIDGIYYVVDPGFvkqkvynsktgidqlvvtPISQAQAKQRAGRAGRTG--PGKCYRLY 927
Cdd:cd18785   24 EILVATNVLGEGIDVPSLDTVIFFDP------------------PSSAASYIQRVGRAGRGGkdEGEVILFV 77
S1_RNase_E cd04453
S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential ...
 284-354 3.05e-04

S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain that is highly homologous to that of RNase E. RNase G not only shares sequence similarity with RNase E, but also functionally overlaps with RNase E. In Escherichia coli, RNase G is involved in the maturation of the 5' end of the 16S rRNA. RNase G plays a secondary role in mRNA decay.


Pssm-ID: 239900 [Multi-domain]  Cd Length: 88  Bit Score: 40.66  E-value: 3.05e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 56699440  284 EEPAIGDIYNGKVTSI---MQfGCFVQLeGLRKrwEGLVHISELRR--EGRVANVADVVSKGQRVKVKVL-SFTGTK 354
Cdd:cd04453    3 REPIVGNIYLGRVKKIvpgLQ-AAFVDI-GLGK--NGFLHLSDILPayFKKHKKIAKLLKEGQEILVQVVkEPIGTK 75
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 284-365 1.55e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 42.55  E-value: 1.55e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440   284 EEPAIGDIYNGKVTSIMQFGCFVQLEGlrKRWEGLVHISELRREgRVANVADVVSKGQRVKVKVLSFTGTKTS--LSMKD 361
Cdd:PRK06676   13 KEVEVGDVVTGEVLKVEDKQVFVNIEG--YKVEGVIPISELSND-HIEDINDVVKVGDELEVYVLKVEDGEGNllLSKRR 89


                  ....
gi 56699440   362 VDQE 365
Cdd:PRK06676   90 LEAE 93
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 288-360 2.57e-03

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 42.03  E-value: 2.57e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 56699440    288 IGDIYNGKVTSIMQFGCFVQLEGlrkRWEGLVHISELR--REGRVANVadVVSKGQRVKVKVLS--FTGTKTSLSMK 360
Cdd:TIGR00717  359 VGDRVTGKIKKITDFGAFVELEG---GIDGLIHLSDISwdKDGREADH--LYKKGDEIEAVVLAvdKEKKRISLGVK 430
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 284-349 2.70e-03

S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 239908 [Multi-domain]  Cd Length: 83  Bit Score: 37.95  E-value: 2.70e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 56699440  284 EEPAIGDIYNGKVTSIMQFGCFVQLEGlrkRWEGLVHISELRREgRVANVADVVSKGQRVKVKVLS 349
Cdd:cd04461   10 SDLKPGMVVHGYVRNITPYGVFVEFLG---GLTGLAPKSYISDE-FVTDPSFGFKKGQSVTAKVTS 71
AAA_22 pfam13401
AAA domain;
606-712 2.74e-03

AAA domain;


Pssm-ID: 379165 [Multi-domain]  Cd Length: 129  Bit Score: 39.25  E-value: 2.74e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440    606 QILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGcclgqevgytIRFEDCTSPETVIKYM 685
Cdd:pfam13401    6 GILVLTGESGTGKTTLLRRLLEQLPEVRDSVVFVDLPSGTSPKDLLRALLRALG----------LPLSGRLSKEELLAAL 75

                           90       100
                   ....*....|....*....|....*..
gi 56699440    686 TDgmLLRECLIDPdltqyaIIMLDEAH 712
Cdd:pfam13401   76 QQ--LLLALAVAV------VLIIDEAQ 94
Cas3_I cd09639
CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short ...
 607-927 2.79e-03

CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; DEAD/DEAH box helicase DNA helicase cas3'; Often but not always is fused to HD nuclease domain; signature gene for Type I


Pssm-ID: 187770 [Multi-domain]  Cd Length: 353  Bit Score: 41.65  E-value: 2.79e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  607 ILIVIGETGSGKTTQITQYLAEAGYTS-RGKIGCTQPRRVAAMSVAKRVSEEFG-CCLGQEVGYTIRFEDCTSPETVIK- 683
Cdd:cd09639    1 LLVIEAPTGYGKTEAALLWALHSLKSQkADRVIIALPTRATINAMYRRAKEAFGeTGLYHSSILSSRIKEMGDSEEFEHl 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  684 ---YMTDGML-----LRECLIDP------------DLTQ----YAIIMLDEAHERTIHTDVLF-GLLKktVQKRQDMKLI 738
Cdd:cd09639   81 fplYIHSNDTlfldpITVCTIDQvlksvfgefghyEFTLasiaNSLLIFDEVHFYDEYTLALIlAVLE--VLKDNDVPIL 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  739 VTSATLDAVkFSQYF--YEAPIFTIPGRTYPVEILYT-KEPETDYLDASLITVMqIHLTEPPGDILVFLTgqeEIDTACE 815
Cdd:cd09639  159 LMSATLPKF-LKEYAekIGYVEENEPLDLKPNERAPFiKIESDKVGEISSLERL-LEFIKKGGSVAIIVN---TVDRAQE 233

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56699440  816 IlYERMKSLGPDVPELII----LPVYSALPSEMQTRIFDPAPPGsrkVVIATNIAETSLTIDGIYYVVDPgfvkqkvyns 891
Cdd:cd09639  234 F-YQQLKEKGPEEEIMLIhsrfTEKDRAKKEAELLLEFKKSEKF---VIVATQVIEASLDISVDVMITEL---------- 299

                        330       340       350
                 ....*....|....*....|....*....|....*.
gi 56699440  892 kTGIDQLVvtpisqaqakQRAGRAGRTGPGKCYRLY 927
Cdd:cd09639  300 -APIDSLI----------QRLGRLHRYGEKNGEEVY 324
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 289-350 6.52e-03

S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240203 [Multi-domain]  Cd Length: 70  Bit Score: 36.43  E-value: 6.52e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 56699440  289 GDIYNGKVTSIMQFGCFVQ-LEGLRkrweGLVHISELrREGRVANVADVVSKGQRVKVKVLSF 350
Cdd:cd05698    1 GLKTHGTIVKVKPNGCIVSfYNNVK----GFLPKSEL-SEAFIKDPEEHFRVGQVVKVKVLSC 58
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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