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Conserved domains on  [gi|2230809455|ref|NP_001392438|]
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ATP-dependent RNA helicase A isoform 1 [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DEXHc_DHX9 cd17972
DEXH-box helicase domain of DEAH-box helicase 9; DEAH-box helicase 9 (DHX9, also known as ...
 333-566 8.96e-153

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: 460.84  E-value: 8.96e-153
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  333 VPWSPPQSNWNPWTSSNIDEGPLAYASTEQISMDLKNELTYQMEQDHNLQSVLQERELLPVKKFEAEILEAISSNSVVII 412
Cdd:cd17972      1 VPWSPPQSNWNPWTSSNIDEGPLAFATPEQISMDLKNELMYQREQDHNLQQILQERELLPVKKFREEILEAISNNPVVII 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  413 RGATGCGKTTQVPQYILDDFIQNDRAAECNIVVTQPRRISAVAVAERVAYERGEEPGKSCGYSVRFESILPRPHASIMFC 492
Cdd:cd17972     81 RGATGCGKTTQVPQYILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAFERGEEVGKSCGYSVRFESVLPRPHASILFC 160

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2230809455  493 TVGVLLRKLEAGIRGISHVIVDEIHERDINTDFLLVVLRDVVLAYPEVRIVLMSATIDTTMFCEYFFNCPIIEV 566
Cdd:cd17972    161 TVGVLLRKLEAGIRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPDLRVILMSATIDTSMFCEYFFNCPVIEV 234
HrpA super family cl34328
HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];
391-889 7.84e-106

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: 355.93  E-value: 7.84e-106
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  391 LPVKKFEAEILEAISSNSVVIIRGATGCGKTTQVPQYILDdfiqNDRAAECNIVVTQPRRISAVAVAERVAYERGEEPGK 470
Cdd:COG1643     10 LPVSAVLPELLAALRAHQVVVLAAPPGAGKTTQLPLALLE----LGWGAGGRIGMLEPRRLAARAAAERMAEELGEPVGE 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  471 SCGYSVRFESilpR--PHASIMFCTVGVLLRKLEA--GIRGISHVIVDEIHERDINTDFLLvvlrdvvlAY--------- 537
Cdd:COG1643     86 TVGYRVRFED---KvsAATRIEVVTEGILLRELQRdpELEGVDTVIFDEFHERSLNADLLL--------ALlldlqpalr 154

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  538 PEVRIVLMSATIDTTMFCEYFFNCPIIEVYGRTFPVQeyfledciqmTQFIPPPKDKKkkdkeddggedddancnlicgd 617
Cdd:COG1643    155 PDLKLLVMSATLDAERFARLLGDAPVIESSGRTYPVE----------VRYRPLPADER---------------------- 202

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  618 eygpetklsmsqlneketpfELIEALLKYIETL--NVPGAVLVFLPGWNLIYTMQKHLENnsHFGSHrYQILPLHSQIPR 695
Cdd:COG1643    203 --------------------DLEDAVADAVREAlaEEPGDILVFLPGEREIRRTAEALRG--RLPPD-TEILPLYGRLSA 259

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  696 EEQRKVFDPVPDGVTKVILSTNIAETSITINDVVYVIDSCKQKVKLFTAHNNMTNYATVWASKTNLEQRKGRAGRVRPGF 775
Cdd:COG1643    260 AEQDRAFAPAPHGRRRIVLATNIAETSLTVPGIRYVIDSGLARIPRYDPRSGVTRLPTERISQASANQRAGRAGRLAPGI 339

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  776 CFHLCSRARFDRLETHMTPEMFRTPLHEIALSIKLLRLGGIGQFlaKAIEPPPLDAVIEAEHTLRELDALDANDELTPLG 855
Cdd:COG1643    340 CYRLWSEEDFARRPAFTDPEILRADLASLILELAAWGLGDPEDL--PFLDPPPARAIADARALLQELGALDADGRLTPLG 417

                          490       500       510
                   ....*....|....*....|....*....|....
gi 2230809455  856 RILAKLPIEPRFGKMMIMGCIFYVGDAVCTISAA 889
Cdd:COG1643    418 RALARLPLDPRLARMLLAAAELGCLREAAILAAL 451
DSRM_DHX9_rpt2 cd19855
second double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; ...
 181-255 2.02e-44

second double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; DHX9 (EC 3.6.4.13; also known as ATP-dependent RNA helicase A, DExH-box helicase 9 (DDX9), Leukophysin (LKP), nuclear DNA helicase II (NDH II), NDH2, or RNA helicase A) is a multifunctional ATP-dependent nucleic acid helicase that unwinds DNA and RNA in a 3' to 5' direction and plays important roles in many processes, such as DNA replication, transcriptional activation, post-transcriptional RNA regulation, mRNA translation and RNA-mediated gene silencing. It contains two double-stranded RNA binding motifs (DSRMs) at the N-terminal region. This model corresponds to the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


:

Pssm-ID: 380684  Cd Length: 75  Bit Score: 155.07  E-value: 2.02e-44
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2230809455  181 LENAKARLNQYFQKEKIQGEYKYTQVGPDHNRSFIAEMTIYIKQLGRRIFAREHGSNKKLAAQSCALSLVRQLYH 255
Cdd:cd19855      1 LDNAKSRLNEFLQKNKIPAEYKYTSVGPDHNRSFIAELSIFVKQLGKTIYARETGSNKKLASQSCALSLVRQLYH 75
DSRM_DHX9_rpt1 cd19854
first double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; ...
 3-71 3.39e-41

first double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; DHX9 (EC 3.6.4.13; also known as ATP-dependent RNA helicase A, DExH-box helicase 9 (DDX9), Leukophysin (LKP), nuclear DNA helicase II (NDH II), NDH2, or RNA helicase A) is a multifunctional ATP-dependent nucleic acid helicase that unwinds DNA and RNA in a 3' to 5' direction and plays important roles in many processes, such as DNA replication, transcriptional activation, post-transcriptional RNA regulation, mRNA translation, and RNA-mediated gene silencing. It contains two double-stranded RNA binding motifs (DSRMs) at the N-terminal region. This model corresponds to the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


:

Pssm-ID: 380683  Cd Length: 69  Bit Score: 145.49  E-value: 3.39e-41
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2230809455    3 DIKNFLYAWCGKRKMTPAYEIRAVGNKNRQKFMCEVRVEGFNYAGMGNSTNKKDAQSNAARDFVNYLVR 71
Cdd:cd19854      1 EIKAFLYAWCGKKKLTPEYDIKEAGNKHRQRFKCEVRVEGFDYVGTGNATNKKDAQTNAARDFLNYLVR 69
OB_NTP_bind pfam07717
Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus ...
 997-1076 2.31e-19

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: 83.84  E-value: 2.31e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  997 LLAFGVYPNVCYHKEKRKILTT--EGRNALIHKSSVNCpfssQDMKYPSPFFVFGEKIRTRAISAKGMTLVTPLQLLLFA 1074
Cdd:pfam07717    4 ALAAGLYPNVARRDPKGKGYTTlsDNQRVFIHPSSVLF----NEKTFPPEWVVYQELVETTKVYIRTVTAISPEWLLLFA 79


                   ..
gi 2230809455 1075 SK 1076
Cdd:pfam07717   80 PH 81
 
Name Accession Description Interval E-value
DEXHc_DHX9 cd17972
DEXH-box helicase domain of DEAH-box helicase 9; DEAH-box helicase 9 (DHX9, also known as ...
 333-566 8.96e-153

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: 460.84  E-value: 8.96e-153
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  333 VPWSPPQSNWNPWTSSNIDEGPLAYASTEQISMDLKNELTYQMEQDHNLQSVLQERELLPVKKFEAEILEAISSNSVVII 412
Cdd:cd17972      1 VPWSPPQSNWNPWTSSNIDEGPLAFATPEQISMDLKNELMYQREQDHNLQQILQERELLPVKKFREEILEAISNNPVVII 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  413 RGATGCGKTTQVPQYILDDFIQNDRAAECNIVVTQPRRISAVAVAERVAYERGEEPGKSCGYSVRFESILPRPHASIMFC 492
Cdd:cd17972     81 RGATGCGKTTQVPQYILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAFERGEEVGKSCGYSVRFESVLPRPHASILFC 160

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2230809455  493 TVGVLLRKLEAGIRGISHVIVDEIHERDINTDFLLVVLRDVVLAYPEVRIVLMSATIDTTMFCEYFFNCPIIEV 566
Cdd:cd17972    161 TVGVLLRKLEAGIRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPDLRVILMSATIDTSMFCEYFFNCPVIEV 234
HrpA COG1643
HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];
391-889 7.84e-106

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


Pssm-ID: 441249 [Multi-domain]  Cd Length: 836  Bit Score: 355.93  E-value: 7.84e-106
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  391 LPVKKFEAEILEAISSNSVVIIRGATGCGKTTQVPQYILDdfiqNDRAAECNIVVTQPRRISAVAVAERVAYERGEEPGK 470
Cdd:COG1643     10 LPVSAVLPELLAALRAHQVVVLAAPPGAGKTTQLPLALLE----LGWGAGGRIGMLEPRRLAARAAAERMAEELGEPVGE 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  471 SCGYSVRFESilpR--PHASIMFCTVGVLLRKLEA--GIRGISHVIVDEIHERDINTDFLLvvlrdvvlAY--------- 537
Cdd:COG1643     86 TVGYRVRFED---KvsAATRIEVVTEGILLRELQRdpELEGVDTVIFDEFHERSLNADLLL--------ALlldlqpalr 154

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  538 PEVRIVLMSATIDTTMFCEYFFNCPIIEVYGRTFPVQeyfledciqmTQFIPPPKDKKkkdkeddggedddancnlicgd 617
Cdd:COG1643    155 PDLKLLVMSATLDAERFARLLGDAPVIESSGRTYPVE----------VRYRPLPADER---------------------- 202

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  618 eygpetklsmsqlneketpfELIEALLKYIETL--NVPGAVLVFLPGWNLIYTMQKHLENnsHFGSHrYQILPLHSQIPR 695
Cdd:COG1643    203 --------------------DLEDAVADAVREAlaEEPGDILVFLPGEREIRRTAEALRG--RLPPD-TEILPLYGRLSA 259

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  696 EEQRKVFDPVPDGVTKVILSTNIAETSITINDVVYVIDSCKQKVKLFTAHNNMTNYATVWASKTNLEQRKGRAGRVRPGF 775
Cdd:COG1643    260 AEQDRAFAPAPHGRRRIVLATNIAETSLTVPGIRYVIDSGLARIPRYDPRSGVTRLPTERISQASANQRAGRAGRLAPGI 339

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  776 CFHLCSRARFDRLETHMTPEMFRTPLHEIALSIKLLRLGGIGQFlaKAIEPPPLDAVIEAEHTLRELDALDANDELTPLG 855
Cdd:COG1643    340 CYRLWSEEDFARRPAFTDPEILRADLASLILELAAWGLGDPEDL--PFLDPPPARAIADARALLQELGALDADGRLTPLG 417

                          490       500       510
                   ....*....|....*....|....*....|....
gi 2230809455  856 RILAKLPIEPRFGKMMIMGCIFYVGDAVCTISAA 889
Cdd:COG1643    418 RALARLPLDPRLARMLLAAAELGCLREAAILAAL 451
SF2_C_RHA cd18791
C-terminal helicase domain of the RNA helicase A (RHA) family helicases; The RNA helicase A ...
 571-780 4.93e-73

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: 240.51  E-value: 4.93e-73
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  571 FPVQEYFLEDCIQMTQfipppkdkkkkdkeddggedddancnlicgdeygpetklsMSQLNEKETPFELIEALLKYIETL 650
Cdd:cd18791      1 FPVEVYYLEDILELLG----------------------------------------ISSEKEDPDYVDAAVRLILQIHRT 40

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  651 NVPGAVLVFLPGWNLIYTMQKHLENNSHFGS-HRYQILPLHSQIPREEQRKVFDPVPDGVTKVILSTNIAETSITINDVV 729
Cdd:cd18791     41 EEPGDILVFLPGQEEIERLCELLREELLSPDlGKLLVLPLHSSLPPEEQQRVFEPPPPGVRKVVLATNIAETSITIPGVV 120

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|.
gi 2230809455  730 YVIDSCKQKVKLFTAHNNMTNYATVWASKTNLEQRKGRAGRVRPGFCFHLC 780
Cdd:cd18791    121 YVIDSGLVKEKVYDPRTGLSSLVTVWISKASAEQRAGRAGRTRPGKCYRLY 171
DEAH_box_HrpB TIGR01970
ATP-dependent helicase HrpB; This model represents HrpB, one of two related but ...
 391-874 8.94e-71

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: 255.08  E-value: 8.94e-71
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  391 LPVKKFEAEILEAISSNSVVIIRGATGCGKTTQVPQYILDDFIQNDRaaecnIVVTQPRRISAVAVAERVAYERGEEPGK 470
Cdd:TIGR01970    1 LPIHAVLPALRDALAAHPQVVLEAPPGAGKSTAVPLALLDAPGIGGK-----IIMLEPRRLAARSAAQRLASQLGEAVGQ 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  471 SCGYSVRFESILPrPHASIMFCTVGVLLRKLEA--GIRGISHVIVDEIHERDINTDFLLVVLRDVVLAYPE-VRIVLMSA 547
Cdd:TIGR01970   76 TVGYRVRGENKVS-RRTRLEVVTEGILTRMIQDdpELDGVGALIFDEFHERSLDADLGLALALDVQSSLREdLKILAMSA 154

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  548 TIDTTMFCEYFFNCPIIEVYGRTFPVQeyfledciqmTQFIPPPkdkkkkdkeddggedddancnlicGDEYgpetklsm 627
Cdd:TIGR01970  155 TLDGERLSSLLPDAPVVESEGRSFPVE----------IRYLPLR------------------------GDQR-------- 192

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  628 sqlneketpfeLIEALLKYIETL--NVPGAVLVFLPGWNLIYTMQKHLenNSHFGShRYQILPLHSQIPREEQRKVFDPV 705
Cdd:TIGR01970  193 -----------LEDAVSRAVEHAlaSETGSILVFLPGQAEIRRVQEQL--AERLDS-DVLICPLYGELSLAAQDRAIKPD 258

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  706 PDGVTKVILSTNIAETSITINDVVYVIDSCKQKVKLFTAHNNMTNYATVWASKTNLEQRKGRAGRVRPGFCFHLCSRARF 785
Cdd:TIGR01970  259 PQGRRKVVLATNIAETSLTIEGIRVVIDSGLARVARFDPKTGITRLETVRISQASATQRAGRAGRLEPGVCYRLWSEEQH 338

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  786 DRLETHMTPEMFRTPLHEIALsiKLLRLGGIGQFLAKAIEPPPLDAVIEAEHTLRELDALDANDELTPLGRILAKLPIEP 865
Cdd:TIGR01970  339 QRLPAQDEPEILQADLSGLAL--ELAQWGAKDPSDLRWLDAPPSVALAAARQLLQRLGALDAQGRLTAHGKAMAALGCHP 416


                   ....*....
gi 2230809455  866 RFGKMMIMG 874
Cdd:TIGR01970  417 RLAAMLLSA 425
PRK11664 PRK11664
ATP-dependent RNA helicase HrpB; Provisional
 390-872 5.51e-63

ATP-dependent RNA helicase HrpB; Provisional


Pssm-ID: 236950 [Multi-domain]  Cd Length: 812  Bit Score: 231.35  E-value: 5.51e-63
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  390 LLPVKKFEAEILEAISSNSVVIIRGATGCGKTTQVPQYILDDFIQNDRaaecnIVVTQPRRISAVAVAERVAYERGEEPG 469
Cdd:PRK11664     3 SLPVAAVLPELLTALKTAPQVLLKAPTGAGKSTWLPLQLLQHGGINGK-----IIMLEPRRLAARNVAQRLAEQLGEKPG 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  470 KSCGYSVRFESILPrPHASIMFCTVGVLLRKLE--AGIRGISHVIVDEIHERDINTDFLLVVLRDVVLAYPE-VRIVLMS 546
Cdd:PRK11664    78 ETVGYRMRAESKVG-PNTRLEVVTEGILTRMIQrdPELSGVGLVILDEFHERSLQADLALALLLDVQQGLRDdLKLLIMS 156

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  547 ATIDTTMFCEYFFNCPIIEVYGRTFPVQeyfledciqmTQFIPppkdkkkkdkeddggedddancnlicgdeygpetkLS 626
Cdd:PRK11664   157 ATLDNDRLQQLLPDAPVIVSEGRSFPVE----------RRYQP-----------------------------------LP 191

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  627 MSQlneketPFEliEALLKYIETL--NVPGAVLVFLPGWNLIYTMQKHLENNshFGSHrYQILPLHSQIPREEQRKVFDP 704
Cdd:PRK11664   192 AHQ------RFD--EAVARATAELlrQESGSLLLFLPGVGEIQRVQEQLASR--VASD-VLLCPLYGALSLAEQQKAILP 260

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  705 VPDGVTKVILSTNIAETSITINDVVYVIDSCKQKVKLFTAHNNMTNYATVWASKTNLEQRKGRAGRVRPGFCFHLCSRAR 784
Cdd:PRK11664   261 APAGRRKVVLATNIAETSLTIEGIRLVVDSGLERVARFDPKTGLTRLVTQRISQASMTQRAGRAGRLEPGICLHLYSKEQ 340

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  785 FDRLETHMTPEMFRTPLHEIALSikLLRLG--GIGQFlaKAIEPPPLDAVIEAEHTLRELDALDANDELTPLGRILAKLP 862
Cdd:PRK11664   341 AERAAAQSEPEILHSDLSGLLLE--LLQWGchDPAQL--SWLDQPPAAALAAAKRLLQQLGALDGQGRLTARGRKMAALG 416

                          490
                   ....*....|
gi 2230809455  863 IEPRFGKMMI 872
Cdd:PRK11664   417 NDPRLAAMLV 426
DSRM_DHX9_rpt2 cd19855
second double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; ...
 181-255 2.02e-44

second double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; DHX9 (EC 3.6.4.13; also known as ATP-dependent RNA helicase A, DExH-box helicase 9 (DDX9), Leukophysin (LKP), nuclear DNA helicase II (NDH II), NDH2, or RNA helicase A) is a multifunctional ATP-dependent nucleic acid helicase that unwinds DNA and RNA in a 3' to 5' direction and plays important roles in many processes, such as DNA replication, transcriptional activation, post-transcriptional RNA regulation, mRNA translation and RNA-mediated gene silencing. It contains two double-stranded RNA binding motifs (DSRMs) at the N-terminal region. This model corresponds to the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380684  Cd Length: 75  Bit Score: 155.07  E-value: 2.02e-44
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2230809455  181 LENAKARLNQYFQKEKIQGEYKYTQVGPDHNRSFIAEMTIYIKQLGRRIFAREHGSNKKLAAQSCALSLVRQLYH 255
Cdd:cd19855      1 LDNAKSRLNEFLQKNKIPAEYKYTSVGPDHNRSFIAELSIFVKQLGKTIYARETGSNKKLASQSCALSLVRQLYH 75
DSRM_DHX9_rpt1 cd19854
first double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; ...
 3-71 3.39e-41

first double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; DHX9 (EC 3.6.4.13; also known as ATP-dependent RNA helicase A, DExH-box helicase 9 (DDX9), Leukophysin (LKP), nuclear DNA helicase II (NDH II), NDH2, or RNA helicase A) is a multifunctional ATP-dependent nucleic acid helicase that unwinds DNA and RNA in a 3' to 5' direction and plays important roles in many processes, such as DNA replication, transcriptional activation, post-transcriptional RNA regulation, mRNA translation, and RNA-mediated gene silencing. It contains two double-stranded RNA binding motifs (DSRMs) at the N-terminal region. This model corresponds to the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380683  Cd Length: 69  Bit Score: 145.49  E-value: 3.39e-41
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2230809455    3 DIKNFLYAWCGKRKMTPAYEIRAVGNKNRQKFMCEVRVEGFNYAGMGNSTNKKDAQSNAARDFVNYLVR 71
Cdd:cd19854      1 EIKAFLYAWCGKKKLTPEYDIKEAGNKHRQRFKCEVRVEGFDYVGTGNATNKKDAQTNAARDFLNYLVR 69
DEXDc smart00487
DEAD-like helicases superfamily;
400-572 1.87e-22

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 96.79  E-value: 1.87e-22
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455   400 ILEAISSNSVVIIRGATGCGKTTQVPQYILDDFIQNDRaaeCNIVVTQPRRISAVAVAERVAYERGEEPGKSCGYSVRFE 479
Cdd:smart00487   17 IEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKG---GRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGGDS 93

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455   480 SI-----LPRPHASIMFCTVGVLLRKLEAG---IRGISHVIVDEIHERDiNTDFLLVVLRDVVLAYPEVRIVLMSATI-- 549
Cdd:smart00487   94 KReqlrkLESGKTDILVTTPGRLLDLLENDklsLSNVDLVILDEAHRLL-DGGFGDQLEKLLKLLPKNVQLLLLSATPpe 172

                           170       180
                    ....*....|....*....|...
gi 2230809455   550 DTTMFCEYFFNCPIIEVYGRTFP 572
Cdd:smart00487  173 EIENLLELFLNDPVFIDVGFTPL 195
HA2 smart00847
Helicase associated domain (HA2) Add an annotation; This presumed domain is about 90 amino ...
 841-922 6.31e-21

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: 88.09  E-value: 6.31e-21
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455   841 ELDALDANDELTPLGRILAKLPIEPRFGKMMIMGCIFYVGDAVCTISAATCFPEPFISE-GKRLGYIHRNFAGNRfSDHV 919
Cdd:smart00847    1 ELGALDDDGRLTPLGRKMAELPLDPRLAKMLLAAAEFGCLDEILTIVAMLSVGDPRPKEkREDADAARRRFADPE-SDHL 79


                    ...
gi 2230809455   920 ALL 922
Cdd:smart00847   80 TLL 82
HA2 pfam04408
Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in ...
 835-921 7.05e-20

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: 86.14  E-value: 7.05e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  835 AEHTLRELDALDANDELTPLGRILAKLPIEPRFGKMMIMGCIFYVGDAVCTISAATCFPEPFISEG-------------- 900
Cdd:pfam04408    1 ALELLYYLGALDEDGELTPLGRKMAELPLDPRLAKMLLAAAELGCLDEVLTIVAALSVRDPFVQPNfldprsaakaarrr 80

                           90       100
                   ....*....|....*....|....
gi 2230809455  901 --KRLGYIHRNFAGNRF-SDHVAL 921
Cdd:pfam04408   81 rrAADEKARAKFARLDLeGDHLTL 104
OB_NTP_bind pfam07717
Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus ...
 997-1076 2.31e-19

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: 83.84  E-value: 2.31e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  997 LLAFGVYPNVCYHKEKRKILTT--EGRNALIHKSSVNCpfssQDMKYPSPFFVFGEKIRTRAISAKGMTLVTPLQLLLFA 1074
Cdd:pfam07717    4 ALAAGLYPNVARRDPKGKGYTTlsDNQRVFIHPSSVLF----NEKTFPPEWVVYQELVETTKVYIRTVTAISPEWLLLFA 79


                   ..
gi 2230809455 1075 SK 1076
Cdd:pfam07717   80 PH 81
DSRM smart00358
Double-stranded RNA binding motif;
5-69 2.13e-15

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 71.91  E-value: 2.13e-15
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2230809455     5 KNFLYAWCGKRKMTPAYE-IRAVGNKNRQKFMCEVRVEGFNYaGMGNSTNKKDAQSNAARDFVNYL 69
Cdd:smart00358    2 KSLLQELAQKRKLPPEYElVKEEGPDHAPRFTVTVKVGGKRT-GEGEGSSKKEAKQRAAEAALRSL 66
DSRM smart00358
Double-stranded RNA binding motif;
184-254 2.52e-14

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 68.83  E-value: 2.52e-14
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2230809455   184 AKARLNQYFQKEKIQGEYKYT-QVGPDHNRSFIAEMTIyikqlGRRIFAREHGSNKKLAAQSCALSLVRQLY 254
Cdd:smart00358    1 PKSLLQELAQKRKLPPEYELVkEEGPDHAPRFTVTVKV-----GGKRTGEGEGSSKKEAKQRAAEAALRSLK 67
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 184-253 5.63e-13

Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training Putative motif shared by proteins that bind to dsRNA. At least some DSRM proteins seem to bind to specific RNA targets. Exemplified by Staufen, which is involved in localization of at least five different mRNAs in the early Drosophila embryo. Also by interferon-induced protein kinase in humans, which is part of the cellular response to dsRNA.


Pssm-ID: 425434 [Multi-domain]  Cd Length: 66  Bit Score: 64.94  E-value: 5.63e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2230809455  184 AKARLNQYFQKEKIQGEYKYT-QVGPDHNRSFIAEMTIyikqlGRRIFAREHGSNKKLAAQSCALSLVRQL 253
Cdd:pfam00035    1 PKSLLQEYAQKNGKPPPYEYVsEEGPPHSPKFTVTVKV-----DGKLYGSGTGSSKKEAEQLAAEKALEKL 66
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 5-69 1.17e-12

Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training Putative motif shared by proteins that bind to dsRNA. At least some DSRM proteins seem to bind to specific RNA targets. Exemplified by Staufen, which is involved in localization of at least five different mRNAs in the early Drosophila embryo. Also by interferon-induced protein kinase in humans, which is part of the cellular response to dsRNA.


Pssm-ID: 425434 [Multi-domain]  Cd Length: 66  Bit Score: 64.17  E-value: 1.17e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2230809455    5 KNFLYAWCGKRKMTPAYEIRAV-GNKNRQKFMCEVRVEGFNYaGMGNSTNKKDAQSNAARDFVNYL 69
Cdd:pfam00035    2 KSLLQEYAQKNGKPPPYEYVSEeGPPHSPKFTVTVKVDGKLY-GSGTGSSKKEAEQLAAEKALEKL 66
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 398-552 1.19e-06

DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.


Pssm-ID: 425570 [Multi-domain]  Cd Length: 165  Bit Score: 49.93  E-value: 1.19e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  398 AEILEAISSNSVVIIRGATGCGKTT--QVPqyILDDFIQNDRAAECnIVVTqPRRISAVAVAERVayergEEPGKSCGYS 475
Cdd:pfam00270    5 AEAIPAILEGRDVLVQAPTGSGKTLafLLP--ALEALDKLDNGPQA-LVLA-PTRELAEQIYEEL-----KKLGKGLGLK 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  476 VRFE----------SILPRPHasIMFCTVGVLLR--KLEAGIRGISHVIVDEIHeRDINTDFLLVVLRDVVLAYPEVRIV 543
Cdd:pfam00270   76 VASLlggdsrkeqlEKLKGPD--ILVGTPGRLLDllQERKLLKNLKLLVLDEAH-RLLDMGFGPDLEEILRRLPKKRQIL 152


                   ....*....
gi 2230809455  544 LMSATIDTT 552
Cdd:pfam00270  153 LLSATLPRN 161
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
183-253 1.03e-03

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 42.39  E-value: 1.03e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2230809455  183 NAKARLNQYFQKEKIQG-EYKYTQV-GPDHNRSFIAEMTIyikqlGRRIFAREHGSNKKLAAQSCALSLVRQL 253
Cdd:COG0571    158 DYKTALQEWLQARGLPLpEYEVVEEeGPDHAKTFTVEVLV-----GGKVLGEGTGRSKKEAEQAAAKAALEKL 225
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
13-69 5.29e-03

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 40.08  E-value: 5.29e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2230809455   13 GKRKMTPAYEIRAV-GNKNRQKFMCEVRVEGFNYA-GMGNStnKKDAQSNAARDFVNYL 69
Cdd:COG0571    169 ARGLPLPEYEVVEEeGPDHAKTFTVEVLVGGKVLGeGTGRS--KKEAEQAAAKAALEKL 225
 
Name Accession Description Interval E-value
DEXHc_DHX9 cd17972
DEXH-box helicase domain of DEAH-box helicase 9; DEAH-box helicase 9 (DHX9, also known as ...
 333-566 8.96e-153

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: 460.84  E-value: 8.96e-153
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  333 VPWSPPQSNWNPWTSSNIDEGPLAYASTEQISMDLKNELTYQMEQDHNLQSVLQERELLPVKKFEAEILEAISSNSVVII 412
Cdd:cd17972      1 VPWSPPQSNWNPWTSSNIDEGPLAFATPEQISMDLKNELMYQREQDHNLQQILQERELLPVKKFREEILEAISNNPVVII 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  413 RGATGCGKTTQVPQYILDDFIQNDRAAECNIVVTQPRRISAVAVAERVAYERGEEPGKSCGYSVRFESILPRPHASIMFC 492
Cdd:cd17972     81 RGATGCGKTTQVPQYILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAFERGEEVGKSCGYSVRFESVLPRPHASILFC 160

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2230809455  493 TVGVLLRKLEAGIRGISHVIVDEIHERDINTDFLLVVLRDVVLAYPEVRIVLMSATIDTTMFCEYFFNCPIIEV 566
Cdd:cd17972    161 TVGVLLRKLEAGIRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPDLRVILMSATIDTSMFCEYFFNCPVIEV 234
HrpA COG1643
HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];
391-889 7.84e-106

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


Pssm-ID: 441249 [Multi-domain]  Cd Length: 836  Bit Score: 355.93  E-value: 7.84e-106
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  391 LPVKKFEAEILEAISSNSVVIIRGATGCGKTTQVPQYILDdfiqNDRAAECNIVVTQPRRISAVAVAERVAYERGEEPGK 470
Cdd:COG1643     10 LPVSAVLPELLAALRAHQVVVLAAPPGAGKTTQLPLALLE----LGWGAGGRIGMLEPRRLAARAAAERMAEELGEPVGE 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  471 SCGYSVRFESilpR--PHASIMFCTVGVLLRKLEA--GIRGISHVIVDEIHERDINTDFLLvvlrdvvlAY--------- 537
Cdd:COG1643     86 TVGYRVRFED---KvsAATRIEVVTEGILLRELQRdpELEGVDTVIFDEFHERSLNADLLL--------ALlldlqpalr 154

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  538 PEVRIVLMSATIDTTMFCEYFFNCPIIEVYGRTFPVQeyfledciqmTQFIPPPKDKKkkdkeddggedddancnlicgd 617
Cdd:COG1643    155 PDLKLLVMSATLDAERFARLLGDAPVIESSGRTYPVE----------VRYRPLPADER---------------------- 202

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  618 eygpetklsmsqlneketpfELIEALLKYIETL--NVPGAVLVFLPGWNLIYTMQKHLENnsHFGSHrYQILPLHSQIPR 695
Cdd:COG1643    203 --------------------DLEDAVADAVREAlaEEPGDILVFLPGEREIRRTAEALRG--RLPPD-TEILPLYGRLSA 259

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  696 EEQRKVFDPVPDGVTKVILSTNIAETSITINDVVYVIDSCKQKVKLFTAHNNMTNYATVWASKTNLEQRKGRAGRVRPGF 775
Cdd:COG1643    260 AEQDRAFAPAPHGRRRIVLATNIAETSLTVPGIRYVIDSGLARIPRYDPRSGVTRLPTERISQASANQRAGRAGRLAPGI 339

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  776 CFHLCSRARFDRLETHMTPEMFRTPLHEIALSIKLLRLGGIGQFlaKAIEPPPLDAVIEAEHTLRELDALDANDELTPLG 855
Cdd:COG1643    340 CYRLWSEEDFARRPAFTDPEILRADLASLILELAAWGLGDPEDL--PFLDPPPARAIADARALLQELGALDADGRLTPLG 417

                          490       500       510
                   ....*....|....*....|....*....|....
gi 2230809455  856 RILAKLPIEPRFGKMMIMGCIFYVGDAVCTISAA 889
Cdd:COG1643    418 RALARLPLDPRLARMLLAAAELGCLREAAILAAL 451
SF2_C_RHA cd18791
C-terminal helicase domain of the RNA helicase A (RHA) family helicases; The RNA helicase A ...
 571-780 4.93e-73

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: 240.51  E-value: 4.93e-73
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  571 FPVQEYFLEDCIQMTQfipppkdkkkkdkeddggedddancnlicgdeygpetklsMSQLNEKETPFELIEALLKYIETL 650
Cdd:cd18791      1 FPVEVYYLEDILELLG----------------------------------------ISSEKEDPDYVDAAVRLILQIHRT 40

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  651 NVPGAVLVFLPGWNLIYTMQKHLENNSHFGS-HRYQILPLHSQIPREEQRKVFDPVPDGVTKVILSTNIAETSITINDVV 729
Cdd:cd18791     41 EEPGDILVFLPGQEEIERLCELLREELLSPDlGKLLVLPLHSSLPPEEQQRVFEPPPPGVRKVVLATNIAETSITIPGVV 120

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|.
gi 2230809455  730 YVIDSCKQKVKLFTAHNNMTNYATVWASKTNLEQRKGRAGRVRPGFCFHLC 780
Cdd:cd18791    121 YVIDSGLVKEKVYDPRTGLSSLVTVWISKASAEQRAGRAGRTRPGKCYRLY 171
DEXHc_RHA-like cd17917
DEXH-box helicase domain of DEAD-like helicase RHA family proteins; The RNA helicase A (RHA) ...
 407-566 1.13e-72

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: 238.90  E-value: 1.13e-72
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  407 NSVVIIRGATGCGKTTQVPQYILDDFIQNDRaaECNIVVTQPRRISAVAVAERVAYERGEEPGKSCGYSVRFESILPrPH 486
Cdd:cd17917      1 NQVVVIVGETGSGKTTQVPQFLLEDGLAKGG--KGRIVCTQPRRIAAISVAERVAEERGEKLGEEVGYQIRFESKTS-SK 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  487 ASIMFCTVGVLLRKLEAG--IRGISHVIVDEIHERDINTDFLLVVLRDVVLAYPEVRIVLMSATIDTTMFCEYFFNCPII 564
Cdd:cd17917     78 TRIKFCTDGILLRELLSDplLSGYSHVILDEAHERSLDTDFLLGLLKDLLRKRPDLKVILMSATLDAEKFSSYFGGAPVI 157


                   ..
gi 2230809455  565 EV 566
Cdd:cd17917    158 HI 159
DEAH_box_HrpB TIGR01970
ATP-dependent helicase HrpB; This model represents HrpB, one of two related but ...
 391-874 8.94e-71

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: 255.08  E-value: 8.94e-71
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  391 LPVKKFEAEILEAISSNSVVIIRGATGCGKTTQVPQYILDDFIQNDRaaecnIVVTQPRRISAVAVAERVAYERGEEPGK 470
Cdd:TIGR01970    1 LPIHAVLPALRDALAAHPQVVLEAPPGAGKSTAVPLALLDAPGIGGK-----IIMLEPRRLAARSAAQRLASQLGEAVGQ 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  471 SCGYSVRFESILPrPHASIMFCTVGVLLRKLEA--GIRGISHVIVDEIHERDINTDFLLVVLRDVVLAYPE-VRIVLMSA 547
Cdd:TIGR01970   76 TVGYRVRGENKVS-RRTRLEVVTEGILTRMIQDdpELDGVGALIFDEFHERSLDADLGLALALDVQSSLREdLKILAMSA 154

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  548 TIDTTMFCEYFFNCPIIEVYGRTFPVQeyfledciqmTQFIPPPkdkkkkdkeddggedddancnlicGDEYgpetklsm 627
Cdd:TIGR01970  155 TLDGERLSSLLPDAPVVESEGRSFPVE----------IRYLPLR------------------------GDQR-------- 192

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  628 sqlneketpfeLIEALLKYIETL--NVPGAVLVFLPGWNLIYTMQKHLenNSHFGShRYQILPLHSQIPREEQRKVFDPV 705
Cdd:TIGR01970  193 -----------LEDAVSRAVEHAlaSETGSILVFLPGQAEIRRVQEQL--AERLDS-DVLICPLYGELSLAAQDRAIKPD 258

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  706 PDGVTKVILSTNIAETSITINDVVYVIDSCKQKVKLFTAHNNMTNYATVWASKTNLEQRKGRAGRVRPGFCFHLCSRARF 785
Cdd:TIGR01970  259 PQGRRKVVLATNIAETSLTIEGIRVVIDSGLARVARFDPKTGITRLETVRISQASATQRAGRAGRLEPGVCYRLWSEEQH 338

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  786 DRLETHMTPEMFRTPLHEIALsiKLLRLGGIGQFLAKAIEPPPLDAVIEAEHTLRELDALDANDELTPLGRILAKLPIEP 865
Cdd:TIGR01970  339 QRLPAQDEPEILQADLSGLAL--ELAQWGAKDPSDLRWLDAPPSVALAAARQLLQRLGALDAQGRLTAHGKAMAALGCHP 416


                   ....*....
gi 2230809455  866 RFGKMMIMG 874
Cdd:TIGR01970  417 RLAAMLLSA 425
DEXHc_DHX30 cd17976
DEXH-box helicase domain of DEAH-box helicase 30; DEAH-box helicase 30 (DHX30) plays an ...
 391-566 1.27e-66

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: 222.75  E-value: 1.27e-66
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  391 LPVKKFEAEILEAISSNSVVIIRGATGCGKTTQVPQYILDDFIQNDRAAECNIVVTQPRRISAVAVAERVAYERGEEPGK 470
Cdd:cd17976      1 LPVDSHKESILSAIEQNPVVVISGDTGCGKTTRIPQFILEDYVLRGRGARCNVVITQPRRISAVSVAQRVAHELGPNLRR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  471 SCGYSVRFESILPRPHASIMFCTVGVLLRKLE--AGIRGISHVIVDEIHERDINTDFLLVVLRDVVLAYPEVRIVLMSAT 548
Cdd:cd17976     81 NVGYQVRLESRPPPRGGALLFCTVGVLLKKLQsnPRLEGVSHVIVDEVHERDVNTDFLLILLKGVLQLNPELRVVLMSAT 160

                          170
                   ....*....|....*...
gi 2230809455  549 IDTTMFCEYFFNCPIIEV 566
Cdd:cd17976    161 GDNQRLSRYFGGCPVVRV 178
DEXHc_DHX36 cd17981
DEXH-box helicase domain of DEAH-box helicase 36; DEAH-box helicase 36 (DHX36, also known as ...
 391-566 1.53e-63

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: 213.94  E-value: 1.53e-63
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  391 LPVKKFEAEILEAISSNSVVIIRGATGCGKTTQVPQYILDDFIQNDRAAECNIVVTQPRRISAVAVAERVAYERGEEP-- 468
Cdd:cd17981      1 LPSYGMKQEIINMIDNNQVTVISGETGCGKTTQVTQFILDDAIERGKGSSCRIVCTQPRRISAISVAERVAAERAESCgl 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  469 GKSCGYSVRFESILPRPHASIMFCTVGVLLRKLEAG--IRGISHVIVDEIHERDINTDFLLVVLRDVVLAYPEVRIVLMS 546
Cdd:cd17981     81 GNSTGYQIRLESRKPRKQGSILYCTTGIVLQWLQSDphLSNVSHLVLDEIHERNLQSDVLMGIVKDLLPFRSDLKVILMS 160

                          170       180
                   ....*....|....*....|
gi 2230809455  547 ATIDTTMFCEYFFNCPIIEV 566
Cdd:cd17981    161 ATLNAEKFSDYFNNCPMIHI 180
PRK11664 PRK11664
ATP-dependent RNA helicase HrpB; Provisional
 390-872 5.51e-63

ATP-dependent RNA helicase HrpB; Provisional


Pssm-ID: 236950 [Multi-domain]  Cd Length: 812  Bit Score: 231.35  E-value: 5.51e-63
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  390 LLPVKKFEAEILEAISSNSVVIIRGATGCGKTTQVPQYILDDFIQNDRaaecnIVVTQPRRISAVAVAERVAYERGEEPG 469
Cdd:PRK11664     3 SLPVAAVLPELLTALKTAPQVLLKAPTGAGKSTWLPLQLLQHGGINGK-----IIMLEPRRLAARNVAQRLAEQLGEKPG 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  470 KSCGYSVRFESILPrPHASIMFCTVGVLLRKLE--AGIRGISHVIVDEIHERDINTDFLLVVLRDVVLAYPE-VRIVLMS 546
Cdd:PRK11664    78 ETVGYRMRAESKVG-PNTRLEVVTEGILTRMIQrdPELSGVGLVILDEFHERSLQADLALALLLDVQQGLRDdLKLLIMS 156

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  547 ATIDTTMFCEYFFNCPIIEVYGRTFPVQeyfledciqmTQFIPppkdkkkkdkeddggedddancnlicgdeygpetkLS 626
Cdd:PRK11664   157 ATLDNDRLQQLLPDAPVIVSEGRSFPVE----------RRYQP-----------------------------------LP 191

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  627 MSQlneketPFEliEALLKYIETL--NVPGAVLVFLPGWNLIYTMQKHLENNshFGSHrYQILPLHSQIPREEQRKVFDP 704
Cdd:PRK11664   192 AHQ------RFD--EAVARATAELlrQESGSLLLFLPGVGEIQRVQEQLASR--VASD-VLLCPLYGALSLAEQQKAILP 260

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  705 VPDGVTKVILSTNIAETSITINDVVYVIDSCKQKVKLFTAHNNMTNYATVWASKTNLEQRKGRAGRVRPGFCFHLCSRAR 784
Cdd:PRK11664   261 APAGRRKVVLATNIAETSLTIEGIRLVVDSGLERVARFDPKTGLTRLVTQRISQASMTQRAGRAGRLEPGICLHLYSKEQ 340

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  785 FDRLETHMTPEMFRTPLHEIALSikLLRLG--GIGQFlaKAIEPPPLDAVIEAEHTLRELDALDANDELTPLGRILAKLP 862
Cdd:PRK11664   341 AERAAAQSEPEILHSDLSGLLLE--LLQWGchDPAQL--SWLDQPPAAALAAAKRLLQQLGALDGQGRLTARGRKMAALG 416

                          490
                   ....*....|
gi 2230809455  863 IEPRFGKMMI 872
Cdd:PRK11664   417 NDPRLAAMLV 426
PRK11131 PRK11131
ATP-dependent RNA helicase HrpA; Provisional
 389-973 1.16e-60

ATP-dependent RNA helicase HrpA; Provisional


Pssm-ID: 182986 [Multi-domain]  Cd Length: 1294  Bit Score: 228.79  E-value: 1.16e-60
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  389 ELLPVKKFEAEILEAISSNSVVIIRGATGCGKTTQVPQYILddfiQNDRAAECNIVVTQPRRISAVAVAERVAYERGEEP 468
Cdd:PRK11131    71 ENLPVSQKKQDILEAIRDHQVVIVAGETGSGKTTQLPKICL----ELGRGVKGLIGHTQPRRLAARTVANRIAEELETEL 146

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  469 GKSCGYSVRF-ESILPRPHASIMfcTVGVLLRKLEAGiRGISH---VIVDEIHERDINTDFLLVVLRDVVLAYPEVRIVL 544
Cdd:PRK11131   147 GGCVGYKVRFnDQVSDNTMVKLM--TDGILLAEIQQD-RLLMQydtIIIDEAHERSLNIDFILGYLKELLPRRPDLKVII 223

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  545 MSATIDTTMFCEYFFNCPIIEVYGRTFPVQeyfledciqmTQFIPppkdkkkkdkeddggedddancnlICGDEYGPETk 624
Cdd:PRK11131   224 TSATIDPERFSRHFNNAPIIEVSGRTYPVE----------VRYRP------------------------IVEEADDTER- 268

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  625 lsmSQLneketpfeliEALLKYIETLNV--PGAVLVFLPGWNLIYTMQKHLE--NNSHfgshrYQILPLHSQIPREEQRK 700
Cdd:PRK11131   269 ---DQL----------QAIFDAVDELGRegPGDILIFMSGEREIRDTADALNklNLRH-----TEILPLYARLSNSEQNR 330

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  701 VFDpvPDGVTKVILSTNIAETSITINDVVYVIDSCKQKVKLFTAHNNMTNYATVWASKTNLEQRKGRAGRVRPGFCFHLC 780
Cdd:PRK11131   331 VFQ--SHSGRRIVLATNVAETSLTVPGIKYVIDPGTARISRYSYRTKVQRLPIEPISQASANQRKGRCGRVSEGICIRLY 408

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  781 SRARFDRLETHMTPEMFRTPLHEIALSIKLLRLGGIGQFlaKAIEPPPLDAVIEAEHTLRELDALDAND-----ELTPLG 855
Cdd:PRK11131   409 SEDDFLSRPEFTDPEILRTNLASVILQMTALGLGDIAAF--PFVEAPDKRNIQDGVRLLEELGAITTDEqasayKLTPLG 486

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  856 RILAKLPIEPRFGKMMI----MGCIfyvgDAVCTISAATCFPEPF--------ISEGKrlgyiHRNFAgNRFSDHVALLS 923
Cdd:PRK11131   487 RQLAQLPVDPRLARMVLeaqkHGCV----REVMIITSALSIQDPRerpmdkqqASDEK-----HRRFA-DKESDFLAFVN 556

                          570       580       590       600       610
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2230809455  924 VfqaWDDAR-----MSGEEAEiRFCEQKRLNMATLRMTWEAKVQLKEILINSGFP 973
Cdd:PRK11131   557 L---WNYLQeqqkaLSSNQFR-RLCRTDYLNYLRVREWQDIYTQLRQVVKELGIP 607
DEXHc_DHX57 cd17985
DEXH-box helicase domain of DEAH-box helicase 57; DEAH-box helicase 57 (DHX57) belongs to the ...
 391-566 1.65e-54

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: 187.74  E-value: 1.65e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  391 LPVKKFEAEILEAISSNSVVIIRGATGCGKTTQVPQYILDDFIQNDRAAECNIVVTQPRRISAVAVAERVAYERGEEPGK 470
Cdd:cd17985      1 LPAWQERETILELLEKHQVLVISGMTGCGKTTQIPQFILDNSLQGPPLPVANIICTQPRRISAISVAERVAQERAERVGQ 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  471 SCGYSVRFESILPRPhASIMFCTVGVLLRKLEAG--IRGISHVIVDEIHERDINTDFLLVVLRDVVLAYPEVRIVLMSAT 548
Cdd:cd17985     81 SVGYQIRLESVKSSA-TRLLYCTTGVLLRRLEGDptLQGVTHVIVDEVHERTEESDFLLLVLKDLMVQRPDLKVILMSAT 159

                          170
                   ....*....|....*...
gi 2230809455  549 IDTTMFCEYFFNCPIIEV 566
Cdd:cd17985    160 LNAELFSDYFNSCPVIHI 177
DEXHc_YTHDC2 cd17987
DEXH-box helicase domain of YTH domain containing 2; YTH domain containing 2 (YTHDC2) ...
 391-566 1.51e-52

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: 182.34  E-value: 1.51e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  391 LPVKKFEAEILEAISSNSVVIIRGATGCGKTTQVPQYILDDFIQNdrAAECNIVVTQPRRISAVAVAERVAYERGEEPGK 470
Cdd:cd17987      1 LPVFEKQEQIVRIIKENKVVLIVGETGSGKTTQIPQFLLDDCYAN--GIPCRIFCTQPRRLAAIAVAERVAAERGEKIGQ 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  471 SCGYSVRFESILpRPHASIMFCTVGVLLRKLEAG---IRGISHVIVDEIHERDINTDFLLVVLRDVVLAYPEVRIVLMSA 547
Cdd:cd17987     79 TVGYQIRLESRV-SPKTLLTFCTNGVLLRTLMAGdsaLSTVTHVIVDEVHERDRFSDFLLTKLRDILQKHPNLKLILSSA 157

                          170
                   ....*....|....*....
gi 2230809455  548 TIDTTMFCEYFFNCPIIEV 566
Cdd:cd17987    158 ALDVNLFIRYFGSCPVIYI 176
DEXHc_DHX29 cd17975
DEXH-box helicase domain of DEAH-box helicase 29; DEAH-box helicase 29 (DHX29) is a part of ...
 391-566 1.07e-48

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: 171.64  E-value: 1.07e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  391 LPVKKFEAEILEAISSNSVVIIRGATGCGKTTQVPQYILDDFIQN-DRAAECNIVVTQPRRISAVAVAERVAYERGEEPG 469
Cdd:cd17975      1 LPVFKHRESILETLKRHRVVVVAGETGSGKSTQVPQFLLEDLLLNgGTAQKCNIVCTQPRRISAMSLATRVCEELGCESG 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  470 KS-----CGYSVRFESilpRPHAS--IMFCTVGVLLRKLEAG--IRGISHVIVDEIHERDINTDFLLVVLRDVVLAYPEV 540
Cdd:cd17975     81 PGgknslCGYQIRMES---RTGEAtrLLYCTTGVLLRKLQEDglLSSISHIIVDEVHERSVQSDFLLIILKEILHKRSDL 157

                          170       180
                   ....*....|....*....|....*.
gi 2230809455  541 RIVLMSATIDTTMFCEYFFNCPIIEV 566
Cdd:cd17975    158 HLILMSATVDCEKFSSYFTHCPILRI 183
DEXHc_TDRD9 cd17988
DEXH-box helicase domain of tudor domain containing 9; Tudor domain containing 9 (TDRD9, also ...
 391-558 1.11e-47

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: 168.45  E-value: 1.11e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  391 LPVKKFEAEILEAISSNSVVIIRGATGCGKTTQVPQYILDDFIQndRAAECNIVVTQPRRISAVAVAERVAYERGEEPGK 470
Cdd:cd17988      1 LPIYAKREEILSLIEANSVVIIKGATGCGKTTQLPQFILDHYYK--RGKYCNIVVTQPRRIAAISIARRVSQEREWTLGS 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  471 SCGYSVRFESILPRpHASIMFCTVGVLLRKL--EAGIRGISHVIVDEIHERDINTDFLLVVLRDVVLAYP-EVRIVLMSA 547
Cdd:cd17988     79 LVGYQVGLERPASE-ETRLIYCTTGVLLQKLinNKTLTEYTHIILDEVHERDQELDFLLLVVRRLLRTNSrHVKIILMSA 157

                          170
                   ....*....|.
gi 2230809455  548 TIDTTMFCEYF 558
Cdd:cd17988    158 TISCKEFADYF 168
DSRM_DHX9_rpt2 cd19855
second double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; ...
 181-255 2.02e-44

second double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; DHX9 (EC 3.6.4.13; also known as ATP-dependent RNA helicase A, DExH-box helicase 9 (DDX9), Leukophysin (LKP), nuclear DNA helicase II (NDH II), NDH2, or RNA helicase A) is a multifunctional ATP-dependent nucleic acid helicase that unwinds DNA and RNA in a 3' to 5' direction and plays important roles in many processes, such as DNA replication, transcriptional activation, post-transcriptional RNA regulation, mRNA translation and RNA-mediated gene silencing. It contains two double-stranded RNA binding motifs (DSRMs) at the N-terminal region. This model corresponds to the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380684  Cd Length: 75  Bit Score: 155.07  E-value: 2.02e-44
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2230809455  181 LENAKARLNQYFQKEKIQGEYKYTQVGPDHNRSFIAEMTIYIKQLGRRIFAREHGSNKKLAAQSCALSLVRQLYH 255
Cdd:cd19855      1 LDNAKSRLNEFLQKNKIPAEYKYTSVGPDHNRSFIAELSIFVKQLGKTIYARETGSNKKLASQSCALSLVRQLYH 75
DEXHc_DHX34 cd17979
DEXH-box helicase domain of DEAH-box helicase 34; DEAH-box helicase 34 (DHX34) plays a role in ...
 391-566 5.37e-43

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: 154.52  E-value: 5.37e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  391 LPVKKFEAEILEAISSNSVVIIRGATGCGKTTQVPQYILDdfiqndrAAECNIVVTQPRRISAVAVAERVAYERGEEPGK 470
Cdd:cd17979      1 LPIAQYREKIIELLKTHQVVIVAGDTGCGKSTQVPQYLLA-------AGFRHIACTQPRRIACISLAKRVAFESLNQYGS 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  471 SCGYSVRFESIlPRPHASIMFCTVGVLLRKLE--AGIRGISHVIVDEIHERDINTDFLLVVLRDVVLAYPEVRIVLMSAT 548
Cdd:cd17979     74 KVAYQIRFERT-RTLATKLLFLTEGLLLRQIQrdASLPQYNVLILDEVHERHLHGDFLLGVLRCLLRLRPDLKLILMSAT 152

                          170
                   ....*....|....*...
gi 2230809455  549 IDTTMFCEYFFNCPIIEV 566
Cdd:cd17979    153 INIELFSGYFEGAPVVQV 170
DEXHc_DHX33 cd17978
DEXH-box helicase domain of DEAH-box helicase 33; DEAH-box helicase 33 (DHX33) stimulates RNA ...
 391-564 9.60e-43

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: 154.05  E-value: 9.60e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  391 LPVKKFEAEILEAISSNSVVIIRGATGCGKTTQVPQYILDDFIQNDRAaecnIVVTQPRRISAVAVAERVAYERGEEPGK 470
Cdd:cd17978      1 LPIYSARKRLLEELRKHDTVIIIGETGSGKTTQIPQYLYEAGFARGGM----IGITQPRRVAAVSVAKRVAEEMGVELGQ 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  471 SCGYSVRFESIlPRPHASIMFCTVGVLLRK--LEAGIRGISHVIVDEIHERDINTDF-----LLVVLRDVVLAYPEVRIV 543
Cdd:cd17978     77 LVGYSVRFDDV-TSEETRIKYMTDGMLLREaiGDPLLSKYSVIILDEAHERTVHTDVlfglvKSAQRRRKEQKLSPLKVI 155

                          170       180
                   ....*....|....*....|.
gi 2230809455  544 LMSATIDTTMFCEYFFNCPII 564
Cdd:cd17978    156 IMSATLDADLFSEYFNGAPVL 176
DSRM_DHX9_rpt1 cd19854
first double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; ...
 3-71 3.39e-41

first double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; DHX9 (EC 3.6.4.13; also known as ATP-dependent RNA helicase A, DExH-box helicase 9 (DDX9), Leukophysin (LKP), nuclear DNA helicase II (NDH II), NDH2, or RNA helicase A) is a multifunctional ATP-dependent nucleic acid helicase that unwinds DNA and RNA in a 3' to 5' direction and plays important roles in many processes, such as DNA replication, transcriptional activation, post-transcriptional RNA regulation, mRNA translation, and RNA-mediated gene silencing. It contains two double-stranded RNA binding motifs (DSRMs) at the N-terminal region. This model corresponds to the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380683  Cd Length: 69  Bit Score: 145.49  E-value: 3.39e-41
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2230809455    3 DIKNFLYAWCGKRKMTPAYEIRAVGNKNRQKFMCEVRVEGFNYAGMGNSTNKKDAQSNAARDFVNYLVR 71
Cdd:cd19854      1 EIKAFLYAWCGKKKLTPEYDIKEAGNKHRQRFKCEVRVEGFDYVGTGNATNKKDAQTNAARDFLNYLVR 69
DEXHc_DHX8 cd17971
DEXH-box helicase domain of DEAH-box helicase 8; DEAH-box helicase 8 (DHX8 ,also known as ...
 386-566 2.35e-39

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: 144.55  E-value: 2.35e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  386 QERELLPVKKFEAEILEAISSNSVVIIRGATGCGKTTQVPQYILDDFIQNDRAAECnivvTQPRRISAVAVAERVAYERG 465
Cdd:cd17971      1 EQRESLPIYKLKEQLIQAVHDNQILVVIGETGSGKTTQITQYLAEAGYTSRGKIGC----TQPRRVAAMSVAKRVAEEFG 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  466 EEPGKSCGYSVRFESIlPRPHASIMFCTVGVLLRK--LEAGIRGISHVIVDEIHERDINTDFLLVVLRDVVLAYPEVRIV 543
Cdd:cd17971     77 CCLGQEVGYTIRFEDC-TSPETVIKYMTDGMLLREclIDPDLSQYSVIMLDEAHERTIHTDVLFGLLKKTVQKRPDLKLI 155

                          170       180
                   ....*....|....*....|...
gi 2230809455  544 LMSATIDTTMFCEYFFNCPIIEV 566
Cdd:cd17971    156 VTSATLDAVKFSQYFYEAPIFTI 178
DEXHc_DHX15 cd17973
DEXH-box helicase domain of DEAH-box helicase 15; DEAH-box helicase 15 (DHX15) is a pre-mRNA ...
 382-566 1.20e-37

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: 139.86  E-value: 1.20e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  382 QSVLQERELLPVKKFEAEILEAISSNSVVIIRGATGCGKTTQVPQYILDDFIQNDRAAEcnIVVTQPRRISAVAVAERVA 461
Cdd:cd17973      4 FEILEKRRELPVWEQKEDFLKLLKNNQILVLVGETGSGKTTQIPQFVLDDELPHQPKKL--VACTQPRRVAAMSVAQRVA 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  462 YERGEEPGKSCGYSVRFESiLPRPHASIMFCTVGVLLRKLEAG--IRGISHVIVDEIHERDINTDFLLVVLRDVVLAYPE 539
Cdd:cd17973     82 EEMDVKLGEEVGYSIRFED-CSSAKTILKYMTDGMLLREAMSDplLSRYSVIILDEAHERTLATDILMGLLKEVVRRRPD 160

                          170       180
                   ....*....|....*....|....*..
gi 2230809455  540 VRIVLMSATIDTTMFCEYFFNCPIIEV 566
Cdd:cd17973    161 LKLIVMSATLDAGKFQKYFDNAPLLKV 187
DEXHc_DHX35 cd17980
DEXH-box helicase domain of DEAH-box helicase 35; DHX35 plays a role in colorectal cancers and ...
 391-558 2.21e-37

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: 139.14  E-value: 2.21e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  391 LPVKKFEAEILEAISSNSVVIIRGATGCGKTTQVPQYILD-DFIQNDRAaecnIVVTQPRRISAVAVAERVAYERGEEPG 469
Cdd:cd17980      1 LPVFKLRNHILYLVENYQTIVIVGETGCGKSTQIPQYLAEaGWTAGGRV----VGCTQPRRVAAVTVAGRVAEEMGAVLG 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  470 KSCGYSVRFESILPRPHASIMFCTVGVLLRKLEAG--IRGISHVIVDEIHERDINTDFLLVVLRDVVLAYPEVRIVLMSA 547
Cdd:cd17980     77 HEVGYCIRFDDCTDPQATRIKFLTDGMLVREMMLDplLTKYSVIMLDEAHERTLYTDILIGLLKKIQKKRGDLRLIVASA 156

                          170
                   ....*....|.
gi 2230809455  548 TIDTTMFCEYF 558
Cdd:cd17980    157 TLDAEKFRDFF 167
DEXHc_HrpA cd17989
DEXH-box helicase domain of ATP-dependent RNA helicase HrpA; HrpA is part of the HrpB-HrpA ...
 391-566 2.28e-37

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: 138.74  E-value: 2.28e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  391 LPVKKFEAEILEAISSNSVVIIRGATGCGKTTQVPQYILDdfiqNDRAAECNIVVTQPRRISAVAVAERVAYERGEEPGK 470
Cdd:cd17989      1 LPVSQKRDEIAKAIAENQVVIIAGETGSGKTTQLPKICLE----LGRGIRGLIGHTQPRRLAARSVAERIAEELKTELGG 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  471 SCGYSVRFESILpRPHASIMFCTVGVLLRKLEAG--IRGISHVIVDEIHERDINTDFLLVVLRDVVLAYPEVRIVLMSAT 548
Cdd:cd17989     77 AVGYKVRFTDQT-SDETCVKLMTDGILLAETQTDryLRAYDTIIIDEAHERSLNIDFLLGYLKQLLPRRPDLKVIITSAT 155

                          170
                   ....*....|....*...
gi 2230809455  549 IDTTMFCEYFFNCPIIEV 566
Cdd:cd17989    156 IDAERFSRHFNNAPIIEV 173
DEXHc_DHX37 cd17982
DEXH-box helicase domain of DEAH-box helicase 37; DHX37 plays a role in the development of the ...
 391-556 8.11e-37

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: 137.87  E-value: 8.11e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  391 LPVKKFEAEILEAISSNSVVIIRGATGCGKTTQVPQYILD-DFIQNDRAAECNIVVTQPRRISAVAVAERVAYERGeEPG 469
Cdd:cd17982      1 LPILAEEQEIMEAINENPVVIICGETGSGKTTQVPQFLYEaGFGSPESDNPGMIGITQPRRVAAVSMAKRVAEELN-VFG 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  470 KSCGYSVRFESILpRPHASIMFCTVGVLLRKLEAG--IRGISHVIVDEIHERDINTD-----------FLLVVLRDVVLA 536
Cdd:cd17982     80 KEVSYQIRYDSTV-SENTKIKFMTDGVLLKEIQTDflLRKYSVIIIDEAHERSVNTDiligmlsrivpLRAKLYLQDQTV 158

                          170       180
                   ....*....|....*....|
gi 2230809455  537 YPeVRIVLMSATIDTTMFCE 556
Cdd:cd17982    159 KP-LKLVIMSATLRVEDFTE 177
DEXHc_DHX16 cd17974
DEXH-box helicase domain of DEAH-box helicase 16; DEAH-box helicase 16 (DHX16) is probably ...
 391-566 6.21e-35

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: 131.86  E-value: 6.21e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  391 LPVKKFEAEILEAISSNSVVIIRGATGCGKTTQVPQYILDDFIQNDRAaecNIVVTQPRRISAVAVAERVAYERGEEPGK 470
Cdd:cd17974      1 LPVYPYRDDLLAAVKEHQVLIIVGETGSGKTTQIPQYLHEAGYTKGGG---KIGCTQPRRVAAMSVAARVAEEMGVKLGN 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  471 SCGYSVRFESIlPRPHASIMFCTVGVLLRKL--EAGIRGISHVIVDEIHERDINTDFLLVVLRDVVLAYPEVRIVLMSAT 548
Cdd:cd17974     78 EVGYSIRFEDC-TSEKTVLKYMTDGMLLREFltEPDLASYSVMIIDEAHERTLHTDILFGLVKDIARFRPDLKLLISSAT 156

                          170
                   ....*....|....*...
gi 2230809455  549 IDTTMFCEYFFNCPIIEV 566
Cdd:cd17974    157 MDAEKFSAFFDDAPIFRI 174
DEXHc_HrpB cd17990
DEXH-box helicase domain of ATP-dependent helicase HrpB; HrpB is part of the HrpB-HrpA ...
 391-566 6.86e-35

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: 131.69  E-value: 6.86e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  391 LPVKKFEAEILEAISSNSVVIIRGATGCGKTTQVPQYILDDFIQNDRaaecNIVVTQPRRISAVAVAERVAYERGEEPGK 470
Cdd:cd17990      1 LPIAAVLPALRAALDAGGQVVLEAPPGAGKTTRVPLALLAELWIAGG----KIIVLEPRRVAARAAARRLATLLGEAPGE 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  471 SCGYSVRFESILPRpHASIMFCTVGVLLRKLEA--GIRGISHVIVDEIHERDINTDFLLVVLRDVVLAY-PEVRIVLMSA 547
Cdd:cd17990     77 TVGYRVRGESRVGR-RTRVEVVTEGVLLRRLQRdpELSGVGAVILDEFHERSLDADLALALLLEVQQLLrDDLRLLAMSA 155

                          170
                   ....*....|....*....
gi 2230809455  548 TIDTTMFCEYFFNCPIIEV 566
Cdd:cd17990    156 TLDGDGLAALLPEAPVVES 174
DEXHc_DHX38 cd17983
DEXH-box helicase domain of DEAH-box helicase 38; DEAH-box helicase 38 (DHX38, also known as ...
 391-566 1.13e-33

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: 127.96  E-value: 1.13e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  391 LPVKKFEAEILEAISSNSVVIIRGATGCGKTTQVPQYILDDFIQNDRAAECnivvTQPRRISAVAVAERVAYERGEEPGK 470
Cdd:cd17983      1 LPIFAVRQELLNVIRDNNVVIVVGETGSGKTTQLTQYLHEDGYTDYGMIGC----TQPRRVAAMSVAKRVSEEMGVELGE 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  471 SCGYSVRFESIlPRPHASIMFCTVGVLLRK--LEAGIRGISHVIVDEIHERDINTDFLLVVLRDVVLAYPEVRIVLMSAT 548
Cdd:cd17983     77 EVGYAIRFEDC-TSENTVIKYMTDGILLREslRDPDLDKYSAIIMDEAHERSLNTDVLFGLLREVVARRRDLKLIVTSAT 155

                          170
                   ....*....|....*...
gi 2230809455  549 IDTTMFCEYFFNCPIIEV 566
Cdd:cd17983    156 MDADKFADFFGNVPIFTI 173
DEXHc_DHX40 cd17984
DEXH-box helicase domain of DEAH-box helicase 40; DEAH-box helicase 40 (DHX40) belongs to the ...
 391-566 2.65e-30

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: 118.42  E-value: 2.65e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  391 LPVKKFEAEILEAISSNSVVIIRGATGCGKTTQVPQYILD-DFIQNDRaaecnIVVTQPRRISAVAVAERVAYERGEEPG 469
Cdd:cd17984      1 LPIQKQRKKLVQAVRDNSFLIVTGNTGSGKTTQLPKYLYEaGFSQHGM-----IGVTQPRRVAAISVAQRVAEEMKCTLG 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  470 KSCGYSVRFESILPRPHAsIMFCTVGVLLRKLEA--GIRGISHVIVDEIHERDINTD-----FLLVVLRDVVLAYPEVRI 542
Cdd:cd17984     76 SKVGYQVRFDDCSSKETA-IKYMTDGCLLRHILAdpNLTKYSVIILDEAHERSLTTDilfglLKKLFQEKSPNRKEHLKV 154

                          170       180
                   ....*....|....*....|....
gi 2230809455  543 VLMSATIDTTMFCEYFFNCPIIEV 566
Cdd:cd17984    155 VVMSATLELAKLSAFFGNCPVFDI 178
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 407-548 1.13e-22

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: 95.55  E-value: 1.13e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  407 NSVVIIRGATGCGKTTQVPQYILDDFIQndraAECNIVVTQPRRISAVAVAERVAYERGeePGKSCGYSVRFESILPR-- 484
Cdd:cd00046      1 GENVLITAPTGSGKTLAALLAALLLLLK----KGKKVLVLVPTKALALQTAERLRELFG--PGIRVAVLVGGSSAEERek 74

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2230809455  485 ---PHASIMFCTVGVLLRKLEA----GIRGISHVIVDEIHERDINTDFLLVVLRDVVLA-YPEVRIVLMSAT 548
Cdd:cd00046     75 nklGDADIIIATPDMLLNLLLRedrlFLKDLKLIIVDEAHALLIDSRGALILDLAVRKAgLKNAQVILLSAT 146
DEXDc smart00487
DEAD-like helicases superfamily;
400-572 1.87e-22

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 96.79  E-value: 1.87e-22
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455   400 ILEAISSNSVVIIRGATGCGKTTQVPQYILDDFIQNDRaaeCNIVVTQPRRISAVAVAERVAYERGEEPGKSCGYSVRFE 479
Cdd:smart00487   17 IEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKG---GRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGGDS 93

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455   480 SI-----LPRPHASIMFCTVGVLLRKLEAG---IRGISHVIVDEIHERDiNTDFLLVVLRDVVLAYPEVRIVLMSATI-- 549
Cdd:smart00487   94 KReqlrkLESGKTDILVTTPGRLLDLLENDklsLSNVDLVILDEAHRLL-DGGFGDQLEKLLKLLPKNVQLLLLSATPpe 172

                           170       180
                    ....*....|....*....|...
gi 2230809455   550 DTTMFCEYFFNCPIIEVYGRTFP 572
Cdd:smart00487  173 EIENLLELFLNDPVFIDVGFTPL 195
HA2 smart00847
Helicase associated domain (HA2) Add an annotation; This presumed domain is about 90 amino ...
 841-922 6.31e-21

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: 88.09  E-value: 6.31e-21
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455   841 ELDALDANDELTPLGRILAKLPIEPRFGKMMIMGCIFYVGDAVCTISAATCFPEPFISE-GKRLGYIHRNFAGNRfSDHV 919
Cdd:smart00847    1 ELGALDDDGRLTPLGRKMAELPLDPRLAKMLLAAAEFGCLDEILTIVAMLSVGDPRPKEkREDADAARRRFADPE-SDHL 79


                    ...
gi 2230809455   920 ALL 922
Cdd:smart00847   80 TLL 82
HA2 pfam04408
Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in ...
 835-921 7.05e-20

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: 86.14  E-value: 7.05e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  835 AEHTLRELDALDANDELTPLGRILAKLPIEPRFGKMMIMGCIFYVGDAVCTISAATCFPEPFISEG-------------- 900
Cdd:pfam04408    1 ALELLYYLGALDEDGELTPLGRKMAELPLDPRLAKMLLAAAELGCLDEVLTIVAALSVRDPFVQPNfldprsaakaarrr 80

                           90       100
                   ....*....|....*....|....
gi 2230809455  901 --KRLGYIHRNFAGNRF-SDHVAL 921
Cdd:pfam04408   81 rrAADEKARAKFARLDLeGDHLTL 104
OB_NTP_bind pfam07717
Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus ...
 997-1076 2.31e-19

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: 83.84  E-value: 2.31e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  997 LLAFGVYPNVCYHKEKRKILTT--EGRNALIHKSSVNCpfssQDMKYPSPFFVFGEKIRTRAISAKGMTLVTPLQLLLFA 1074
Cdd:pfam07717    4 ALAAGLYPNVARRDPKGKGYTTlsDNQRVFIHPSSVLF----NEKTFPPEWVVYQELVETTKVYIRTVTAISPEWLLLFA 79


                   ..
gi 2230809455 1075 SK 1076
Cdd:pfam07717   80 PH 81
DEXHc_DHX32 cd17977
DEXH-box helicase domain of DEAH-box helicase 32; DEAH-box helicase 32 (DHX32) belongs to the ...
 391-566 1.58e-18

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: 84.49  E-value: 1.58e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  391 LPVKKFEAEILEAISSNSVVIIRGATGCGKTTQVPQ----YILDDFIQNDraaecNIVVTQPRRISAVAVAERVAYERGE 466
Cdd:cd17977      1 LPVWEAKYEFMESLAHNQIVIVSGDAKTGKSSQIPQwcaeYCLSAHYQHG-----VVVCTQVHKQTAVWLALRVADEMDV 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  467 EPGKSCGYSVRFESILPRpHASIMFCTVGVLLRKLEA----GIRGIshVIVDEIHERDINTDFLLVVLRDVVLAYPEVRI 542
Cdd:cd17977     76 NIGHEVGYVIPFENCCTN-ETILRYCTDDMLLREMMSdpllESYGV--IILDDAHERTVSTDVLLGLLKDVLLSRPELKL 152

                          170       180
                   ....*....|....*....|....
gi 2230809455  543 VLMSATIDTTMFCEYFFNCPIIEV 566
Cdd:cd17977    153 VIITCPHLSSKLLSYYGNVPLIEV 176
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 638-771 5.17e-17

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: 78.02  E-value: 5.17e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  638 ELIEALLKYIETLNvPGAVLVFLPgwnliytMQKHLENNSHFGSHRYQILPLHSQIPREEQRKVFDPVPDGVTKVILSTN 717
Cdd:pfam00271    1 EKLEALLELLKKER-GGKVLIFSQ-------TKKTLEAELLLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATD 72

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2230809455  718 IAETSITINDVVYVIDsckqkvklFTAHNNMTNYatvwasktnlEQRKGRAGRV 771
Cdd:pfam00271   73 VAERGLDLPDVDLVIN--------YDLPWNPASY----------IQRIGRAGRA 108
DEXQc_DQX1 cd17986
DEXQ-box helicase domain of DEAQ-box RNA dependent ATPase 1; DEAQ-box RNA dependent ATPase 1 ...
 391-566 1.14e-15

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: 76.47  E-value: 1.14e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  391 LPVKKFEAEILEAISSNS-VVIIRGATGCGKTTQVPQYILdDFIQNDRAAECNIVVTQPRRISAVAVAERVAYERGEEPG 469
Cdd:cd17986      1 LPIWAAKFTFLEQLESPSgIVLVSGEPGSGKSTQVPQWCA-EFALSRGFQKGQVTVTQPHPLAARSLALRVADEMDLNLG 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  470 KSCGYSVRFESILPrPHASIMFCTVGVLLRKLEA--GIRGISHVIVDEIHERDINTDFLLVVLRDVVLAYPEVRIVLMSA 547
Cdd:cd17986     80 HEVGYSIPQEDCTG-PNTILRFCWDRLLLQEMTStpLLGAWGVVVLDEAQERSVASDSLLGLLKDVRLQRPELRVVVVTS 158

                          170
                   ....*....|....*....
gi 2230809455  548 TIDTTMFCEYFFNCPIIEV 566
Cdd:cd17986    159 PALEPKLRAFWGNPPVVHV 177
DSRM smart00358
Double-stranded RNA binding motif;
5-69 2.13e-15

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 71.91  E-value: 2.13e-15
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2230809455     5 KNFLYAWCGKRKMTPAYE-IRAVGNKNRQKFMCEVRVEGFNYaGMGNSTNKKDAQSNAARDFVNYL 69
Cdd:smart00358    2 KSLLQELAQKRKLPPEYElVKEEGPDHAPRFTVTVKVGGKRT-GEGEGSSKKEAKQRAAEAALRSL 66
PHA02653 PHA02653
RNA helicase NPH-II; Provisional
 397-774 5.33e-15

RNA helicase NPH-II; Provisional


Pssm-ID: 177443 [Multi-domain]  Cd Length: 675  Bit Score: 80.02  E-value: 5.33e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  397 EAEILEAISSNSVVIIRGATGCGKTTQVPQ------YILDDFIQNDR----AAECNIVVTQPRrisavavaerVAYER-- 464
Cdd:PHA02653   169 QLKIFEAWISRKPVVLTGGTGVGKTSQVPKlllwfnYLFGGFDNLDKidpnFIERPIVLSLPR----------VALVRlh 238

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  465 GEEPGKSCGY--------SVRFESIL-------PRPHAsIMFCTVGVLLRKLeagiRGISHVIVDEIHERDINTDFLLVV 529
Cdd:PHA02653   239 SITLLKSLGFdeidgspiSLKYGSIPdelintnPKPYG-LVFSTHKLTLNKL----FDYGTVIIDEVHEHDQIGDIIIAV 313

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  530 LRDVVLaypEVR-IVLMSATI--DTTMFCEYFFNCPIIEVYGRT-FPVQEYFLEDCIQmtqfipPPKDKkkkdkeddgge 605
Cdd:PHA02653   314 ARKHID---KIRsLFLMTATLedDRDRIKEFFPNPAFVHIPGGTlFPISEVYVKNKYN------PKNKR----------- 373

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  606 dddancnlicgdEYGPETKLSMSQlneketpfelieALLKYieTLNVPGAVLVFLPGWNLIYTMQKHLEnNSHFGshrYQ 685
Cdd:PHA02653   374 ------------AYIEEEKKNIVT------------ALKKY--TPPKGSSGIVFVASVSQCEEYKKYLE-KRLPI---YD 423

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  686 ILPLHSQIPREEQ--RKVFDpvPDGVTkVILSTNIAETSITINDVVYVIDSCKQKVKLFTAHNNMtnyatvWASKTNLEQ 763
Cdd:PHA02653   424 FYIIHGKVPNIDEilEKVYS--SKNPS-IIISTPYLESSVTIRNATHVYDTGRVYVPEPFGGKEM------FISKSMRTQ 494

                          410
                   ....*....|.
gi 2230809455  764 RKGRAGRVRPG 774
Cdd:PHA02653   495 RKGRVGRVSPG 505
HELICc smart00490
helicase superfamily c-terminal domain;
678-770 1.06e-14

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 70.32  E-value: 1.06e-14
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455   678 HFGSHRYQILPLHSQIPREEQRKVFDPVPDGVTKVILSTNIAETSITINDVVYVIDSCkqkvklftahnnmtnyatVWAS 757
Cdd:smart00490    6 LLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYD------------------LPWS 67

                            90
                    ....*....|...
gi 2230809455   758 KTNLEQRKGRAGR 770
Cdd:smart00490   68 PASYIQRIGRAGR 80
DSRM smart00358
Double-stranded RNA binding motif;
184-254 2.52e-14

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 68.83  E-value: 2.52e-14
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2230809455   184 AKARLNQYFQKEKIQGEYKYT-QVGPDHNRSFIAEMTIyikqlGRRIFAREHGSNKKLAAQSCALSLVRQLY 254
Cdd:smart00358    1 PKSLLQELAQKRKLPPEYELVkEEGPDHAPRFTVTVKV-----GGKRTGEGEGSSKKEAKQRAAEAALRSLK 67
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 184-253 5.63e-13

Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training Putative motif shared by proteins that bind to dsRNA. At least some DSRM proteins seem to bind to specific RNA targets. Exemplified by Staufen, which is involved in localization of at least five different mRNAs in the early Drosophila embryo. Also by interferon-induced protein kinase in humans, which is part of the cellular response to dsRNA.


Pssm-ID: 425434 [Multi-domain]  Cd Length: 66  Bit Score: 64.94  E-value: 5.63e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2230809455  184 AKARLNQYFQKEKIQGEYKYT-QVGPDHNRSFIAEMTIyikqlGRRIFAREHGSNKKLAAQSCALSLVRQL 253
Cdd:pfam00035    1 PKSLLQEYAQKNGKPPPYEYVsEEGPPHSPKFTVTVKV-----DGKLYGSGTGSSKKEAEQLAAEKALEKL 66
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 5-69 1.17e-12

Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training Putative motif shared by proteins that bind to dsRNA. At least some DSRM proteins seem to bind to specific RNA targets. Exemplified by Staufen, which is involved in localization of at least five different mRNAs in the early Drosophila embryo. Also by interferon-induced protein kinase in humans, which is part of the cellular response to dsRNA.


Pssm-ID: 425434 [Multi-domain]  Cd Length: 66  Bit Score: 64.17  E-value: 1.17e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2230809455    5 KNFLYAWCGKRKMTPAYEIRAV-GNKNRQKFMCEVRVEGFNYaGMGNSTNKKDAQSNAARDFVNYL 69
Cdd:pfam00035    2 KSLLQEYAQKNGKPPPYEYVSEeGPPHSPKFTVTVKVDGKLY-GSGTGSSKKEAEQLAAEKALEKL 66
DSRM_EIF2AK2-like cd19875
double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 ...
 188-253 1.22e-08

double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 (EIF2AK2) and similar proteins; The family includes EIF2AK2 and adenosine deaminase domain-containing proteins, ADAD1 and ADAD2. EIF2AK2 (EC 2.7.11.1/EC 2.7.10.2; also known as interferon-induced, double-stranded RNA-activated protein kinase, eIF-2A protein kinase 2, interferon-inducible RNA-dependent protein kinase, P1/eIF-2A protein kinase, protein kinase RNA-activated (PKR), protein kinase R, tyrosine-protein kinase EIF2AK2, or p68 kinase) acts as an IFN-induced dsRNA-dependent serine/threonine-protein kinase which plays a key role in the innate immune response to viral infection and is also involved in the regulation of signal transduction, apoptosis, cell proliferation and differentiation. ADAD1 (also called testis nuclear RNA-binding protein (TENR)) and ADAD2 (also called testis nuclear RNA-binding protein-like (TENRL)) are phylogenetically related to a family of adenosine deaminases involved in RNA editing. ADAD1 plays an essential function in spermatid morphogenesis. It may be involved in testis-specific nuclear post-transcriptional processes such as heterogeneous nuclear RNA (hnRNA) packaging, alternative splicing, or nuclear/cytoplasmic transport of mRNAs. ADAD2 is a double-stranded RNA binding protein with unclear biological function. Members of this group contains varying numbers of double-stranded RNA binding motifs (DSRMs). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380704  Cd Length: 67  Bit Score: 52.65  E-value: 1.22e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2230809455  188 LNQYFQKEKIQGEYKYTQVGPDHNRSFIAEMTIyikqlGRRIFAREHGSNKKLAAQSCALSLVRQL 253
Cdd:cd19875      7 LNEYCQKRGLSLEFVDVSVGPDHCPGFTASATI-----DGIVFASATGTSKKEAKRAAAKLALKKL 67
DSRM_RNAse_III_family cd10845
double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase ...
 183-253 9.03e-07

double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase III (EC 3.1.26.3; also known as ribonuclease 3) digests double-stranded RNA formed within single-strand substrates, but not RNA-DNA hybrids. It is involved in the processing of rRNA precursors, viral transcripts, some mRNAs, and at least 1 tRNA (metY, a minor form of tRNA-init-Met). It cleaves the 30S primary rRNA transcript to yield the immediate precursors to the 16S and 23S rRNAs. The cleavage can occur in assembled 30S, 50S, and even 70S subunits and is influenced by the presence of ribosomal proteins. The RNase III family also includes the mitochondrion-specific ribosomal protein mL44 subfamily, which is composed of mitochondrial 54S ribosomal protein L3 (MRPL3) and mitochondrial 39S ribosomal protein L44 (MRPL44). Members of this family contain an RNase III domain and a C-terminal double-stranded RNA binding motif (DSRM). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380682 [Multi-domain]  Cd Length: 69  Bit Score: 47.49  E-value: 9.03e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2230809455  183 NAKARLNQYFQKEKIQG-EYKYT-QVGPDHNRSFIAEMTIyikqlGRRIFAREHGSNKKLAAQSCALSLVRQL 253
Cdd:cd10845      2 DYKTALQEYLQKRGLPLpEYELVeEEGPDHNKTFTVEVKV-----NGKVIGEGTGRSKKEAEQAAAKAALEKL 69
DSRM_SF cd00048
double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...
 189-246 1.01e-06

double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 amino acid domain that adopts an alpha-beta-beta-beta-alpha fold. It is not sequence specific, but highly specific for double-stranded RNAs (dsRNAs) of various origin and structure. The DSRM domains are found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila Staufen protein, E. coli RNase III, RNase H1, and dsRNA dependent adenosine deaminases. They are involved in numerous cellular mechanisms ranging from localization and transport of messenger RNAs, through maturation and degradation of RNAs, to viral response and signal transduction. Some members harbor tandem DSRMs that act in small RNA biogenesis.


Pssm-ID: 380679 [Multi-domain]  Cd Length: 57  Bit Score: 46.89  E-value: 1.01e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2230809455  189 NQYFQKEKIQG-EYKYTQVGPDHNRSFIAEMTIYIkqlgrrIFAREHGSNKKLAAQSCA 246
Cdd:cd00048      1 NELCQKNKWPPpEYETVEEGGPHNPRFTCTVTVNG------QTFEGEGKSKKEAKQAAA 53
DSRM_SF cd00048
double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...
 11-63 1.07e-06

double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 amino acid domain that adopts an alpha-beta-beta-beta-alpha fold. It is not sequence specific, but highly specific for double-stranded RNAs (dsRNAs) of various origin and structure. The DSRM domains are found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila Staufen protein, E. coli RNase III, RNase H1, and dsRNA dependent adenosine deaminases. They are involved in numerous cellular mechanisms ranging from localization and transport of messenger RNAs, through maturation and degradation of RNAs, to viral response and signal transduction. Some members harbor tandem DSRMs that act in small RNA biogenesis.


Pssm-ID: 380679 [Multi-domain]  Cd Length: 57  Bit Score: 46.89  E-value: 1.07e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2230809455   11 WCGKRKM-TPAYEIRAVGNKNRQKFMCEVRVEGFNYagMGNSTNKKDAQSNAAR 63
Cdd:cd00048      3 LCQKNKWpPPEYETVEEGGPHNPRFTCTVTVNGQTF--EGEGKSKKEAKQAAAE 54
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 398-552 1.19e-06

DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.


Pssm-ID: 425570 [Multi-domain]  Cd Length: 165  Bit Score: 49.93  E-value: 1.19e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  398 AEILEAISSNSVVIIRGATGCGKTT--QVPqyILDDFIQNDRAAECnIVVTqPRRISAVAVAERVayergEEPGKSCGYS 475
Cdd:pfam00270    5 AEAIPAILEGRDVLVQAPTGSGKTLafLLP--ALEALDKLDNGPQA-LVLA-PTRELAEQIYEEL-----KKLGKGLGLK 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  476 VRFE----------SILPRPHasIMFCTVGVLLR--KLEAGIRGISHVIVDEIHeRDINTDFLLVVLRDVVLAYPEVRIV 543
Cdd:pfam00270   76 VASLlggdsrkeqlEKLKGPD--ILVGTPGRLLDllQERKLLKNLKLLVLDEAH-RLLDMGFGPDLEEILRRLPKKRQIL 152


                   ....*....
gi 2230809455  544 LMSATIDTT 552
Cdd:pfam00270  153 LLSATLPRN 161
DSRM_RNAse_III_family cd10845
double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase ...
 3-69 3.17e-05

double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase III (EC 3.1.26.3; also known as ribonuclease 3) digests double-stranded RNA formed within single-strand substrates, but not RNA-DNA hybrids. It is involved in the processing of rRNA precursors, viral transcripts, some mRNAs, and at least 1 tRNA (metY, a minor form of tRNA-init-Met). It cleaves the 30S primary rRNA transcript to yield the immediate precursors to the 16S and 23S rRNAs. The cleavage can occur in assembled 30S, 50S, and even 70S subunits and is influenced by the presence of ribosomal proteins. The RNase III family also includes the mitochondrion-specific ribosomal protein mL44 subfamily, which is composed of mitochondrial 54S ribosomal protein L3 (MRPL3) and mitochondrial 39S ribosomal protein L44 (MRPL44). Members of this family contain an RNase III domain and a C-terminal double-stranded RNA binding motif (DSRM). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380682 [Multi-domain]  Cd Length: 69  Bit Score: 43.25  E-value: 3.17e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2230809455    3 DIKNFLYAWCGKRKM-TPAYE-IRAVGNKNRQKFMCEVRVEGfNYAGMGNSTNKKDAQSNAARDFVNYL 69
Cdd:cd10845      2 DYKTALQEYLQKRGLpLPEYElVEEEGPDHNKTFTVEVKVNG-KVIGEGTGRSKKEAEQAAAKAALEKL 69
DSRM_SON-like cd19870
double-stranded RNA binding motif of protein SON and similar proteins; Protein SON (also known ...
 12-63 2.87e-04

double-stranded RNA binding motif of protein SON and similar proteins; Protein SON (also known as Bax antagonist selected in saccharomyces 1 (BASS1), negative regulatory element-binding protein (NRE-binding protein), or protein DBP-5, or SON3) is an RNA-binding protein which acts as an mRNA splicing cofactor by promoting efficient splicing of transcripts that possess weak splice sites. It specifically promotes splicing of many cell-cycle and DNA-repair transcripts that possess weak splice sites, such as TUBG1, KATNB1, TUBGCP2, AURKB, PCNT, AKT1, RAD23A, and FANCG. Members of this group contain a double-stranded RNA binding motif (DSRM) at the C-terminus. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380699  Cd Length: 75  Bit Score: 40.73  E-value: 2.87e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2230809455   12 CGKRK-MTPAYE-IRAVGNKNRQKFMCEVRVEGFNYAGMGNSTNKKDAQSNAAR 63
Cdd:cd19870     12 CNKRKwGPPEFRlVEESGPPHRKHFLFKVVVNGVEYQPSVASGNKKDAKAQAAT 65
DSRM_Kanadaptin cd19856
double-stranded RNA binding motif of Kanadaptin and similar proteins; Kanadaptin (also known ...
 181-258 4.20e-04

double-stranded RNA binding motif of Kanadaptin and similar proteins; Kanadaptin (also known as human lung cancer oncogene 3 protein (HLC-3), kidney anion exchanger adapter protein, or solute carrier family 4 anion exchanger member 1 adapter protein (SLC4A1AP)) is a nuclear protein widely expressed in mammalian tissues. It was originally isolated as a kidney Cl-/HCO3- anion exchanger 1 (kAE1)-binding protein. It is a highly mobile nucleocytoplasmic shuttling and multilocalizing protein. Its role in mammalian cells remains unclear. The double-stranded RNA binding motif (DSRM) is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380685  Cd Length: 86  Bit Score: 40.68  E-value: 4.20e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  181 LENAKARLNQYFQKEKIQGEYKYTQVGPDHNRSFIA--EMTIYIkQLGRRIFAREHGSNKKLAAQ-SCALSLVRQLYHLG 257
Cdd:cd19856      5 LKDPKKALKGFFDREGEELEYEVEEQGSGRTRKYVCriELPLDD-ASGGPIVAEASVSGKKKEAVvACALEACRILDRHG 83


                   .
gi 2230809455  258 V 258
Cdd:cd19856     84 L 84
DSRM_AtDRB-like cd19878
double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding proteins ...
 185-246 4.49e-04

double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding proteins (AtDRBs)and similar proteins; This family includes a group of Arabidopsis thaliana double-stranded RNA-binding proteins (AtDRB1-5). They bind double-stranded RNA (dsRNA) and may be involved in RNA-mediated silencing. Members of this family contain two to three double-stranded RNA binding motifs (DSRMs). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380707 [Multi-domain]  Cd Length: 67  Bit Score: 39.81  E-value: 4.49e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2230809455  185 KARLNQYFQKEKIQ-GEYKYTQVGPDHNRSFIAEMTIyikqLGRRiFAREHGSNKKLAAQSCA 246
Cdd:cd19878      2 KNLLQEYAQKKKIPlPKYESAKSGPSHQPTFVSTVIV----LGVR-FSSEGAKNKKQAEQSAA 59
DSRM_EIF2AK2-like cd19875
double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 ...
 8-69 6.12e-04

double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 (EIF2AK2) and similar proteins; The family includes EIF2AK2 and adenosine deaminase domain-containing proteins, ADAD1 and ADAD2. EIF2AK2 (EC 2.7.11.1/EC 2.7.10.2; also known as interferon-induced, double-stranded RNA-activated protein kinase, eIF-2A protein kinase 2, interferon-inducible RNA-dependent protein kinase, P1/eIF-2A protein kinase, protein kinase RNA-activated (PKR), protein kinase R, tyrosine-protein kinase EIF2AK2, or p68 kinase) acts as an IFN-induced dsRNA-dependent serine/threonine-protein kinase which plays a key role in the innate immune response to viral infection and is also involved in the regulation of signal transduction, apoptosis, cell proliferation and differentiation. ADAD1 (also called testis nuclear RNA-binding protein (TENR)) and ADAD2 (also called testis nuclear RNA-binding protein-like (TENRL)) are phylogenetically related to a family of adenosine deaminases involved in RNA editing. ADAD1 plays an essential function in spermatid morphogenesis. It may be involved in testis-specific nuclear post-transcriptional processes such as heterogeneous nuclear RNA (hnRNA) packaging, alternative splicing, or nuclear/cytoplasmic transport of mRNAs. ADAD2 is a double-stranded RNA binding protein with unclear biological function. Members of this group contains varying numbers of double-stranded RNA binding motifs (DSRMs). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380704  Cd Length: 67  Bit Score: 39.56  E-value: 6.12e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2230809455    8 LYAWCGKRKMTPAYEIRAVGNKNRQKFMCEVRVEGFNYAGmGNSTNKKDAQSNAARDFVNYL 69
Cdd:cd19875      7 LNEYCQKRGLSLEFVDVSVGPDHCPGFTASATIDGIVFAS-ATGTSKKEAKRAAAKLALKKL 67
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
183-253 1.03e-03

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 42.39  E-value: 1.03e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2230809455  183 NAKARLNQYFQKEKIQG-EYKYTQV-GPDHNRSFIAEMTIyikqlGRRIFAREHGSNKKLAAQSCALSLVRQL 253
Cdd:COG0571    158 DYKTALQEWLQARGLPLpEYEVVEEeGPDHAKTFTVEVLV-----GGKVLGEGTGRSKKEAEQAAAKAALEKL 225
DEXHc_Ski2 cd17921
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ...
 395-550 2.33e-03

DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases play an important role in RNA degradation, processing, and splicing pathways. They belong to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350679 [Multi-domain]  Cd Length: 181  Bit Score: 40.71  E-value: 2.33e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  395 KFEAEILEAI--SSNSVVIirGA-TGCGKTTQVPQYILDDFIQNDRaaecNIVVTQPRRisavAVAERVAY---ERGEEP 468
Cdd:cd17921      4 PIQREALRALylSGDSVLV--SApTSSGKTLIAELAILRALATSGG----KAVYIAPTR----ALVNQKEAdlrERFGPL 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2230809455  469 GKSCG--YSVRFESILPRPHASIMFCT---VGVLLRKL-EAGIRGISHVIVDEIH-----------ERDINTdfllvvlr 531
Cdd:cd17921     74 GKNVGllTGDPSVNKLLLAEADILVATpekLDLLLRNGgERLIQDVRLVVVDEAHligdgergvvlELLLSR-------- 145

                          170
                   ....*....|....*....
gi 2230809455  532 dVVLAYPEVRIVLMSATID 550
Cdd:cd17921    146 -LLRINKNARFVGLSATLP 163
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
13-69 5.29e-03

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 40.08  E-value: 5.29e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2230809455   13 GKRKMTPAYEIRAV-GNKNRQKFMCEVRVEGFNYA-GMGNStnKKDAQSNAARDFVNYL 69
Cdd:COG0571    169 ARGLPLPEYEVVEEeGPDHAKTFTVEVLVGGKVLGeGTGRS--KKEAEQAAAKAALEKL 225
DSRM_DUS2L cd19871
double-stranded RNA binding motif of tRNA-dihydrouridine(20) synthase [NAD(P)+]-like (DUS2L) ...
 5-62 9.54e-03

double-stranded RNA binding motif of tRNA-dihydrouridine(20) synthase [NAD(P)+]-like (DUS2L) and similar proteins; DUS2L (also known as dihydrouridine synthase 2 (DUS2), up-regulated in lung cancer protein 8 (URLC8), or tRNA-dihydrouridine synthase 2-like) catalyzes the synthesis of dihydrouridine, a modified base found in the D-loop of most tRNAs. It negatively regulates the activation of EIF2AK2/PKR. DUS2L contains an N-terminal FMN-binding domain and a C-terminal double-stranded RNA binding motif (DSRM) that is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380700  Cd Length: 68  Bit Score: 36.10  E-value: 9.54e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2230809455    5 KNFLYAWCGKRKMT-PAYEirAVGNKNRQKFMCEVRVEGFNYAGMGNSTNKKDAQSNAA 62
Cdd:cd19871      3 KMILNEWCRKNKLPqPVYE--TVQRPSDRLFQSVVTVDGKKYTSSLWEKSKKLAEQAAA 59
 
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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