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Conserved domains on  [gi|1907087955|ref|XP_036013353|]
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neuronal PAS domain-containing protein 3 isoform X38 [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PAS_3 pfam08447
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 239-326 1.66e-18

PAS fold; The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya.


:

Pssm-ID: 430001 [Multi-domain]  Cd Length: 89  Bit Score: 80.85  E-value: 1.66e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907087955 239 IIYCENRISDYMDLTPVDIVGK--RCYHFIHAEDVEGIRHSHLDLLNKGQCVTKYYRWMQKNGGYIWIQSSATIaINAKN 316
Cdd:pfam08447   1 IIYWSPRFEEILGYTPEELLGKgeSWLDLVHPDDRERVREALWEALKGGEPYSGEYRIRRKDGEYRWVEARARP-IRDEN 79

                          90
                  ....*....|
gi 1907087955 317 ANEKNIIWVN 326
Cdd:pfam08447  80 GKPVRVIGVA 89
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 48-106 1.59e-11

PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels.


:

Pssm-ID: 214512  Cd Length: 67  Bit Score: 60.49  E-value: 1.59e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1907087955   48 SHILQSLDGFVFALNQEGKFLYISETVSIYLGLSQVELTGSSVFDYVHPGDHVEMAEQL 106
Cdd:smart00091   4 RAILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEAL 62
bHLH_SF super family cl00081
basic Helix Loop Helix (bHLH) domain superfamily; bHLH proteins are transcriptional regulators ...
 1-22 1.17e-08

basic Helix Loop Helix (bHLH) domain superfamily; bHLH proteins are transcriptional regulators that are found in organisms from yeast to humans. Members of the bHLH superfamily have two highly conserved and functionally distinct regions. The basic part is at the amino end of the bHLH that may bind DNA to a consensus hexanucleotide sequence known as the E box (CANNTG). Different families of bHLH proteins recognize different E-box consensus sequences. At the carboxyl-terminal end of the region is the HLH region that interacts with other proteins to form homo- and heterodimers. bHLH proteins function as a diverse set of regulatory factors because they recognize different DNA sequences and dimerize with different proteins. The bHLH proteins can be divided to cell-type specific and widely expressed proteins. The cell-type specific members of bHLH superfamily are involved in cell-fate determination and act in neurogenesis, cardiogenesis, myogenesis, and hematopoiesis.


The actual alignment was detected with superfamily member cd19732:

Pssm-ID: 469605  Cd Length: 78  Bit Score: 52.70  E-value: 1.17e-08
                          10        20
                  ....*....|....*....|..
gi 1907087955   1 MRDFANQGDPPWNLRMEGPPPN 22
Cdd:cd19732    57 MRDFANQGDPPWNLRMEGPPPN 78
KinE super family cl47428
Sporulation sensor histidine kinase E [Cell cycle control, cell division, chromosome ...
 50-309 5.58e-03

Sporulation sensor histidine kinase E [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms];


The actual alignment was detected with superfamily member COG5809:

Pssm-ID: 444511 [Multi-domain]  Cd Length: 489  Bit Score: 39.96  E-value: 5.58e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907087955  50 ILQSLDGFVFALNQEGKFLYISETVSIYLGLSQVELTGSSVFDYVHPGDHVEMAEQlgmklppgRGLLSQGTTEDAASSA 129
Cdd:COG5809    20 LFENAPDAILILDLEGKILKVNPAAERIFGYTEDELLGTNILDFLHPDDEKELREI--------LKLLKEGESRDELEFE 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907087955 130 SSSSQSETPEPVETTSPSLLTTDNTLERSFFIRmksTLTKRgvhIKSSGYkvihitgrlrLRVSLSHGRTVPSQIMGLVV 209
Cdd:COG5809    92 LRHKNGKRLEFSSKLSPIFDQNGDIEGMLAISR---DITER---KRMEEA----------LRESEEKFRLIFNHSPDGII 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907087955 210 VahalppptinevridchmfvtrVNMDLNIIYCENRISDYMDLTPVDIVGKRCYHFIHAEDVEGIRHSHLDLLNKGQCVT 289
Cdd:COG5809   156 V----------------------TDLDGRIIYANPAACKLLGISIEELIGKSILELIHSDDQENVAAFISQLLKDGGIAQ 213

                         250       260
                  ....*....|....*....|
gi 1907087955 290 KYYRWMQKNGGYIWIQSSAT 309
Cdd:COG5809   214 GEVRFWTKDGRWRLLEASGA 233
MSCRAMM_ClfA super family cl41352
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 360-561 7.06e-03

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


The actual alignment was detected with superfamily member NF033609:

Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 39.89  E-value: 7.06e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907087955 360 SESDSKDTSGITAEDNENSKSDEKGNQSENSEDPEPDRKKSGSACDNDMNCNDDGHSSSNPDSRDSDDSFEHSDFEHPKA 439
Cdd:NF033609  706 SDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD 785

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907087955 440 AEDGFGALGPMQIKVERYVESEADLRLQPCESLTSDSAKDSDSANEAGAQASSKHQKRKRRRKRQKGGSASRRRLSSASS 519
Cdd:NF033609  786 SDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSESDSNSDSE 865

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1907087955 520 PGLDAGLVEPprllSSPHSASVLKIKTEI---AEPI------NFDNDSSIW 561
Cdd:NF033609  866 SGSNNNVVPP----NSPKNGTNASNKNEAkdsKEPLpdtgseDEANTSLIW 912
 
Name Accession Description Interval E-value
PAS_3 pfam08447
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 239-326 1.66e-18

PAS fold; The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya.


Pssm-ID: 430001 [Multi-domain]  Cd Length: 89  Bit Score: 80.85  E-value: 1.66e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907087955 239 IIYCENRISDYMDLTPVDIVGK--RCYHFIHAEDVEGIRHSHLDLLNKGQCVTKYYRWMQKNGGYIWIQSSATIaINAKN 316
Cdd:pfam08447   1 IIYWSPRFEEILGYTPEELLGKgeSWLDLVHPDDRERVREALWEALKGGEPYSGEYRIRRKDGEYRWVEARARP-IRDEN 79

                          90
                  ....*....|
gi 1907087955 317 ANEKNIIWVN 326
Cdd:pfam08447  80 GKPVRVIGVA 89
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 227-309 1.89e-13

PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.


Pssm-ID: 238075 [Multi-domain]  Cd Length: 103  Bit Score: 66.89  E-value: 1.89e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907087955 227 HMFVTRVNMDLNIIYCENRISDYMDLTPVDIVGKRCYHFIHAEDVEGIRHSHLDLLNKGQCVTKYYRWMQKNGGYIWIQS 306
Cdd:cd00130     2 PDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDGSVIWVLV 81


                  ...
gi 1907087955 307 SAT 309
Cdd:cd00130    82 SLT 84
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 48-106 1.59e-11

PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels.


Pssm-ID: 214512  Cd Length: 67  Bit Score: 60.49  E-value: 1.59e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1907087955   48 SHILQSLDGFVFALNQEGKFLYISETVSIYLGLSQVELTGSSVFDYVHPGDHVEMAEQL 106
Cdd:smart00091   4 RAILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEAL 62
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 54-106 3.67e-10

PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.


Pssm-ID: 238075 [Multi-domain]  Cd Length: 103  Bit Score: 57.64  E-value: 3.67e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1907087955  54 LDGFVFALNQEGKFLYISETVSIYLGLSQVELTGSSVFDYVHPGDHVEMAEQL 106
Cdd:cd00130     1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERL 53
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 48-106 7.80e-10

PAS fold; The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya. This domain can bind gases (O2, CO and NO), FAD, 4-hydroxycinnamic acid and NAD+ (Matilla et.al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://0-doi-org.brum.beds.ac.uk/10.1093/femsre/fuab043).


Pssm-ID: 395786 [Multi-domain]  Cd Length: 113  Bit Score: 57.04  E-value: 7.80e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1907087955  48 SHILQSLDGFVFALNQEGKFLYISETVSIYLGLSQVELTGSSVFDYVHPGDHVEMAEQL 106
Cdd:pfam00989   4 RAILESLPDGIFVVDEDGRILYVNAAAEELLGLSREEVIGKSLLDLIPEEDDAEVAELL 62
bHLH-PAS_NPAS3_PASD6 cd19732
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing ...
 1-22 1.17e-08

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing protein 3 (NPAS3) and similar proteins; NPAS3, also termed neuronal PAS3, or Basic-helix-loop-helix-PAS protein MOP6, or Class E basic helix-loop-helix protein 12 (bHLHe12), or member of PAS protein 6, or PAS domain-containing protein 6 (PASD6), is a bHLH-PAS brain-enriched transcription factor that is involved in central nervous system development and neurogenesis. It is a replicated genetic risk factor for psychiatric disorders. Human chromosomal rearrangements that affect NPAS3 normal expression are associated with schizophrenia and mental retardation.


Pssm-ID: 381575  Cd Length: 78  Bit Score: 52.70  E-value: 1.17e-08
                          10        20
                  ....*....|....*....|..
gi 1907087955   1 MRDFANQGDPPWNLRMEGPPPN 22
Cdd:cd19732    57 MRDFANQGDPPWNLRMEGPPPN 78
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 227-283 8.62e-06

PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels.


Pssm-ID: 214512  Cd Length: 67  Bit Score: 43.93  E-value: 8.62e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1907087955  227 HMFVTRVNMDLNIIYCENRISDYMDLTPVDIVGKRCYHFIHAEDVEGIRHSHLDLLN 283
Cdd:smart00091  11 PDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEALQRLLS 67
sensory_box TIGR00229
PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain ...
 43-115 1.26e-03

PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include heme in the oxygen sensor FixL, FAD in the redox potential sensor NifL, and a 4-hydroxycinnamyl chromophore in photoactive yellow protein. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator. [Regulatory functions, Small molecule interactions]


Pssm-ID: 272971 [Multi-domain]  Cd Length: 124  Bit Score: 39.58  E-value: 1.26e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1907087955  43 EAHLGShILQSLDGFVFALNQEGKFLYISETVSIYLGLSQVELTGSSVFDYVHPGD---HVEMAEQLGMKLPPGRG 115
Cdd:TIGR00229   2 EERYRA-IFESSPDAIIVIDLEGNILYVNPAFEEIFGYSAEELIGRNVLELIPEEDreeVRERIERRLEGEPEPVS 76
PAS COG2202
PAS domain [Signal transduction mechanisms];
38-106 2.07e-03

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 40.78  E-value: 2.07e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907087955  38 AIEVFEAHLgSHILQSLDGFVFALNQEGKFLYISETVSIYLGLSQVELTGSSVFDYVHPGDHVEMAEQL 106
Cdd:COG2202   131 ALRESEERL-RLLVENAPDGIFVLDLDGRILYVNPAAEELLGYSPEELLGKSLLDLLHPEDRERLLELL 198
PAS COG2202
PAS domain [Signal transduction mechanisms];
230-316 2.73e-03

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 40.39  E-value: 2.73e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907087955 230 VTRVNMDLNIIYCENRISDYMDLTPVDIVGKRCYHFIHAEDVEGIRHSHLDLLNKGQCVTKYYRWMQKNGGYIWIQSSAT 309
Cdd:COG2202    24 IIITDLDGRILYVNPAFERLTGYSAEELLGKTLRDLLPPEDDDEFLELLRAALAGGGVWRGELRNRRKDGSLFWVELSIS 103


                  ....*..
gi 1907087955 310 IAINAKN 316
Cdd:COG2202   104 PVRDEDG 110
KinE COG5809
Sporulation sensor histidine kinase E [Cell cycle control, cell division, chromosome ...
 50-309 5.58e-03

Sporulation sensor histidine kinase E [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms];


Pssm-ID: 444511 [Multi-domain]  Cd Length: 489  Bit Score: 39.96  E-value: 5.58e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907087955  50 ILQSLDGFVFALNQEGKFLYISETVSIYLGLSQVELTGSSVFDYVHPGDHVEMAEQlgmklppgRGLLSQGTTEDAASSA 129
Cdd:COG5809    20 LFENAPDAILILDLEGKILKVNPAAERIFGYTEDELLGTNILDFLHPDDEKELREI--------LKLLKEGESRDELEFE 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907087955 130 SSSSQSETPEPVETTSPSLLTTDNTLERSFFIRmksTLTKRgvhIKSSGYkvihitgrlrLRVSLSHGRTVPSQIMGLVV 209
Cdd:COG5809    92 LRHKNGKRLEFSSKLSPIFDQNGDIEGMLAISR---DITER---KRMEEA----------LRESEEKFRLIFNHSPDGII 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907087955 210 VahalppptinevridchmfvtrVNMDLNIIYCENRISDYMDLTPVDIVGKRCYHFIHAEDVEGIRHSHLDLLNKGQCVT 289
Cdd:COG5809   156 V----------------------TDLDGRIIYANPAACKLLGISIEELIGKSILELIHSDDQENVAAFISQLLKDGGIAQ 213

                         250       260
                  ....*....|....*....|
gi 1907087955 290 KYYRWMQKNGGYIWIQSSAT 309
Cdd:COG5809   214 GEVRFWTKDGRWRLLEASGA 233
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 360-561 7.06e-03

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 39.89  E-value: 7.06e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907087955 360 SESDSKDTSGITAEDNENSKSDEKGNQSENSEDPEPDRKKSGSACDNDMNCNDDGHSSSNPDSRDSDDSFEHSDFEHPKA 439
Cdd:NF033609  706 SDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD 785

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907087955 440 AEDGFGALGPMQIKVERYVESEADLRLQPCESLTSDSAKDSDSANEAGAQASSKHQKRKRRRKRQKGGSASRRRLSSASS 519
Cdd:NF033609  786 SDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSESDSNSDSE 865

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1907087955 520 PGLDAGLVEPprllSSPHSASVLKIKTEI---AEPI------NFDNDSSIW 561
Cdd:NF033609  866 SGSNNNVVPP----NSPKNGTNASNKNEAkdsKEPLpdtgseDEANTSLIW 912
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 368-566 7.24e-03

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 39.89  E-value: 7.24e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907087955 368 SGITAEDNENSKSDEKGNQSENSEDPEPDRKKSGSACDNDMNCNDDGHSSSNPDSRDSDDSFEHSDFEHPKAAEDGFGAL 447
Cdd:NF033609  676 SDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD 755

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907087955 448 GPMQIKVERYVESEADLRLQPCESLTSDSAKDSDSANEAGAQASSKHQKRKRRRKRQKGGSASRRRLSSASSPGLDAGLV 527
Cdd:NF033609  756 SDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD 835

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1907087955 528 EPPRLLSSPHSASVLKIKTEIAEPINFDNDSSIWN--YPPN 566
Cdd:NF033609  836 SDSDSDSDSDSDSDSDSDSDSESDSNSDSESGSNNnvVPPN 876
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 360-492 9.19e-03

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 39.51  E-value: 9.19e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907087955 360 SESDSKDTSGITAEDNENSKSDEKGNQSENSEDPEPDRKKSGSACDNDMNCNDDGHSSSNPDSRDSDDSFEHSDFEHPKA 439
Cdd:NF033609  646 SDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD 725

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1907087955 440 AEDGFGALGPMQIKVERYVESEADLRLQPCESLTSDSAKDSDSANEAGAQASS 492
Cdd:NF033609  726 SDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDS 778
 
Name Accession Description Interval E-value
PAS_3 pfam08447
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 239-326 1.66e-18

PAS fold; The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya.


Pssm-ID: 430001 [Multi-domain]  Cd Length: 89  Bit Score: 80.85  E-value: 1.66e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907087955 239 IIYCENRISDYMDLTPVDIVGK--RCYHFIHAEDVEGIRHSHLDLLNKGQCVTKYYRWMQKNGGYIWIQSSATIaINAKN 316
Cdd:pfam08447   1 IIYWSPRFEEILGYTPEELLGKgeSWLDLVHPDDRERVREALWEALKGGEPYSGEYRIRRKDGEYRWVEARARP-IRDEN 79

                          90
                  ....*....|
gi 1907087955 317 ANEKNIIWVN 326
Cdd:pfam08447  80 GKPVRVIGVA 89
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 227-309 1.89e-13

PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.


Pssm-ID: 238075 [Multi-domain]  Cd Length: 103  Bit Score: 66.89  E-value: 1.89e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907087955 227 HMFVTRVNMDLNIIYCENRISDYMDLTPVDIVGKRCYHFIHAEDVEGIRHSHLDLLNKGQCVTKYYRWMQKNGGYIWIQS 306
Cdd:cd00130     2 PDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDGSVIWVLV 81


                  ...
gi 1907087955 307 SAT 309
Cdd:cd00130    82 SLT 84
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 48-106 1.59e-11

PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels.


Pssm-ID: 214512  Cd Length: 67  Bit Score: 60.49  E-value: 1.59e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1907087955   48 SHILQSLDGFVFALNQEGKFLYISETVSIYLGLSQVELTGSSVFDYVHPGDHVEMAEQL 106
Cdd:smart00091   4 RAILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEAL 62
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 54-106 3.67e-10

PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.


Pssm-ID: 238075 [Multi-domain]  Cd Length: 103  Bit Score: 57.64  E-value: 3.67e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1907087955  54 LDGFVFALNQEGKFLYISETVSIYLGLSQVELTGSSVFDYVHPGDHVEMAEQL 106
Cdd:cd00130     1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERL 53
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 48-106 7.80e-10

PAS fold; The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya. This domain can bind gases (O2, CO and NO), FAD, 4-hydroxycinnamic acid and NAD+ (Matilla et.al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://0-doi-org.brum.beds.ac.uk/10.1093/femsre/fuab043).


Pssm-ID: 395786 [Multi-domain]  Cd Length: 113  Bit Score: 57.04  E-value: 7.80e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1907087955  48 SHILQSLDGFVFALNQEGKFLYISETVSIYLGLSQVELTGSSVFDYVHPGDHVEMAEQL 106
Cdd:pfam00989   4 RAILESLPDGIFVVDEDGRILYVNAAAEELLGLSREEVIGKSLLDLIPEEDDAEVAELL 62
bHLH-PAS_NPAS3_PASD6 cd19732
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing ...
 1-22 1.17e-08

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing protein 3 (NPAS3) and similar proteins; NPAS3, also termed neuronal PAS3, or Basic-helix-loop-helix-PAS protein MOP6, or Class E basic helix-loop-helix protein 12 (bHLHe12), or member of PAS protein 6, or PAS domain-containing protein 6 (PASD6), is a bHLH-PAS brain-enriched transcription factor that is involved in central nervous system development and neurogenesis. It is a replicated genetic risk factor for psychiatric disorders. Human chromosomal rearrangements that affect NPAS3 normal expression are associated with schizophrenia and mental retardation.


Pssm-ID: 381575  Cd Length: 78  Bit Score: 52.70  E-value: 1.17e-08
                          10        20
                  ....*....|....*....|..
gi 1907087955   1 MRDFANQGDPPWNLRMEGPPPN 22
Cdd:cd19732    57 MRDFANQGDPPWNLRMEGPPPN 78
bHLH-PAS_NPAS1_PASD5 cd19731
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing ...
 1-20 3.42e-07

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing protein 1 (NPAS1) and similar proteins; NPAS1, also termed neuronal PAS1, or Basic-helix-loop-helix-PAS protein MOP5, or Class E basic helix-loop-helix protein 11 (bHLHe11), or member of PAS protein 5, or PAS domain-containing protein 5 (PASD5), is a bHLH-PAS transcriptional repressor expressed in the central nervous system and involved in neuronal differentiation. It is active during late embryogenesis and postnatal development.


Pssm-ID: 381574  Cd Length: 74  Bit Score: 48.37  E-value: 3.42e-07
                          10        20
                  ....*....|....*....|
gi 1907087955   1 MRDFANQGDPPWNLRMEGPP 20
Cdd:cd19731    55 MRDFASHGDPPWSLRAEGPP 74
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 227-283 8.62e-06

PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels.


Pssm-ID: 214512  Cd Length: 67  Bit Score: 43.93  E-value: 8.62e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1907087955  227 HMFVTRVNMDLNIIYCENRISDYMDLTPVDIVGKRCYHFIHAEDVEGIRHSHLDLLN 283
Cdd:smart00091  11 PDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEALQRLLS 67
bHLH-PAS_trachealess_like cd19733
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Drosophila melanogaster protein ...
 1-24 1.14e-05

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Drosophila melanogaster protein trachealess and similar proteins; Protein trachealess is a bHLH-PAS transcription factor that acts as an inducer of tracheal cell fates in Drosophila. It is necessary for the development of the salivary gland duct and the posterior spiracles.


Pssm-ID: 381576  Cd Length: 79  Bit Score: 44.15  E-value: 1.14e-05
                          10        20
                  ....*....|....*....|....
gi 1907087955   1 MRDFANQGDPPWNLRMEGPPPNTS 24
Cdd:cd19733    56 LRDFSGHGDPPWNRESLSSPPSTS 79
sensory_box TIGR00229
PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain ...
 43-115 1.26e-03

PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include heme in the oxygen sensor FixL, FAD in the redox potential sensor NifL, and a 4-hydroxycinnamyl chromophore in photoactive yellow protein. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator. [Regulatory functions, Small molecule interactions]


Pssm-ID: 272971 [Multi-domain]  Cd Length: 124  Bit Score: 39.58  E-value: 1.26e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1907087955  43 EAHLGShILQSLDGFVFALNQEGKFLYISETVSIYLGLSQVELTGSSVFDYVHPGD---HVEMAEQLGMKLPPGRG 115
Cdd:TIGR00229   2 EERYRA-IFESSPDAIIVIDLEGNILYVNPAFEEIFGYSAEELIGRNVLELIPEEDreeVRERIERRLEGEPEPVS 76
PAS COG2202
PAS domain [Signal transduction mechanisms];
38-106 2.07e-03

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 40.78  E-value: 2.07e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907087955  38 AIEVFEAHLgSHILQSLDGFVFALNQEGKFLYISETVSIYLGLSQVELTGSSVFDYVHPGDHVEMAEQL 106
Cdd:COG2202   131 ALRESEERL-RLLVENAPDGIFVLDLDGRILYVNPAAEELLGYSPEELLGKSLLDLLHPEDRERLLELL 198
PAS COG2202
PAS domain [Signal transduction mechanisms];
230-316 2.73e-03

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 40.39  E-value: 2.73e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907087955 230 VTRVNMDLNIIYCENRISDYMDLTPVDIVGKRCYHFIHAEDVEGIRHSHLDLLNKGQCVTKYYRWMQKNGGYIWIQSSAT 309
Cdd:COG2202    24 IIITDLDGRILYVNPAFERLTGYSAEELLGKTLRDLLPPEDDDEFLELLRAALAGGGVWRGELRNRRKDGSLFWVELSIS 103


                  ....*..
gi 1907087955 310 IAINAKN 316
Cdd:COG2202   104 PVRDEDG 110
KinE COG5809
Sporulation sensor histidine kinase E [Cell cycle control, cell division, chromosome ...
 50-309 5.58e-03

Sporulation sensor histidine kinase E [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms];


Pssm-ID: 444511 [Multi-domain]  Cd Length: 489  Bit Score: 39.96  E-value: 5.58e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907087955  50 ILQSLDGFVFALNQEGKFLYISETVSIYLGLSQVELTGSSVFDYVHPGDHVEMAEQlgmklppgRGLLSQGTTEDAASSA 129
Cdd:COG5809    20 LFENAPDAILILDLEGKILKVNPAAERIFGYTEDELLGTNILDFLHPDDEKELREI--------LKLLKEGESRDELEFE 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907087955 130 SSSSQSETPEPVETTSPSLLTTDNTLERSFFIRmksTLTKRgvhIKSSGYkvihitgrlrLRVSLSHGRTVPSQIMGLVV 209
Cdd:COG5809    92 LRHKNGKRLEFSSKLSPIFDQNGDIEGMLAISR---DITER---KRMEEA----------LRESEEKFRLIFNHSPDGII 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907087955 210 VahalppptinevridchmfvtrVNMDLNIIYCENRISDYMDLTPVDIVGKRCYHFIHAEDVEGIRHSHLDLLNKGQCVT 289
Cdd:COG5809   156 V----------------------TDLDGRIIYANPAACKLLGISIEELIGKSILELIHSDDQENVAAFISQLLKDGGIAQ 213

                         250       260
                  ....*....|....*....|
gi 1907087955 290 KYYRWMQKNGGYIWIQSSAT 309
Cdd:COG5809   214 GEVRFWTKDGRWRLLEASGA 233
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 360-561 7.06e-03

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 39.89  E-value: 7.06e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907087955 360 SESDSKDTSGITAEDNENSKSDEKGNQSENSEDPEPDRKKSGSACDNDMNCNDDGHSSSNPDSRDSDDSFEHSDFEHPKA 439
Cdd:NF033609  706 SDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD 785

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907087955 440 AEDGFGALGPMQIKVERYVESEADLRLQPCESLTSDSAKDSDSANEAGAQASSKHQKRKRRRKRQKGGSASRRRLSSASS 519
Cdd:NF033609  786 SDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSESDSNSDSE 865

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1907087955 520 PGLDAGLVEPprllSSPHSASVLKIKTEI---AEPI------NFDNDSSIW 561
Cdd:NF033609  866 SGSNNNVVPP----NSPKNGTNASNKNEAkdsKEPLpdtgseDEANTSLIW 912
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 368-566 7.24e-03

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 39.89  E-value: 7.24e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907087955 368 SGITAEDNENSKSDEKGNQSENSEDPEPDRKKSGSACDNDMNCNDDGHSSSNPDSRDSDDSFEHSDFEHPKAAEDGFGAL 447
Cdd:NF033609  676 SDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD 755

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907087955 448 GPMQIKVERYVESEADLRLQPCESLTSDSAKDSDSANEAGAQASSKHQKRKRRRKRQKGGSASRRRLSSASSPGLDAGLV 527
Cdd:NF033609  756 SDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD 835

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1907087955 528 EPPRLLSSPHSASVLKIKTEIAEPINFDNDSSIWN--YPPN 566
Cdd:NF033609  836 SDSDSDSDSDSDSDSDSDSDSESDSNSDSESGSNNnvVPPN 876
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 360-492 9.19e-03

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 39.51  E-value: 9.19e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907087955 360 SESDSKDTSGITAEDNENSKSDEKGNQSENSEDPEPDRKKSGSACDNDMNCNDDGHSSSNPDSRDSDDSFEHSDFEHPKA 439
Cdd:NF033609  646 SDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD 725

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1907087955 440 AEDGFGALGPMQIKVERYVESEADLRLQPCESLTSDSAKDSDSANEAGAQASS 492
Cdd:NF033609  726 SDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDS 778
 
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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