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Conserved domains on  [gi|1721875558|ref|XP_030217046|]
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neuronal PAS domain-containing protein 2-like isoform X1 [Gadus morhua]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
bHLH-PAS_PASD1 cd19736
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in circadian clock protein PASD1; ...
 28-97 7.85e-36

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in circadian clock protein PASD1; PASD1, also termed PAS domain-containing protein 1, is evolutionarily related to Circadian locomotor output cycles protein kaput (CLOCK)and functions as a suppressor of the biological clock that drives the daily circadian rhythms of cells throughout the body. Mammalian PASD1 doesn't harbor the bHLH-PAS domain and is not included in this family.


:

Pssm-ID: 381579  Cd Length: 70  Bit Score: 129.83  E-value: 7.85e-36
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721875558  28 LEEDEKDRAKRASRNKSEKKRRDQFNVLIKELCTMLQVQGLPCKMDKSTILQRTIGFLQKQKDMSAQNDS 97
Cdd:cd19736     1 MDEDEKDRAKRASRNKSEKKRRDQFNVLIKELCTMLQGHGHPLKMDKSTILQRTIDFLQKQKEITAQTEA 70
PAS_11 super family cl37882
PAS domain; This family includes the PAS-B domain of NCOA1 (Nuclear receptor coactivator 1), ...
 279-381 4.96e-21

PAS domain; This family includes the PAS-B domain of NCOA1 (Nuclear receptor coactivator 1), which binds to an LXXLL motif in the C-terminal region of STAT6 (Signal transducer and activator of transcription 6).


The actual alignment was detected with superfamily member pfam14598:

Pssm-ID: 464214 [Multi-domain]  Cd Length: 110  Bit Score: 88.89  E-value: 4.96e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721875558 279 EFTSRHSLEWKFLFLDHRASPIIGYLPFEVLGTSGYDYYHVDDLELIAQCHKHLMQ-LGKGKSCYYRFLTKGQQWIWLQT 357
Cdd:pfam14598   3 QFTTRHDIDGKIISCDTRAPFSLGYEKDELVGRSIYDLVHPQDLRTAKSHLREIIQtRGRATSPSYRLRLRDGDFLSVHT 82

                          90       100
                  ....*....|....*....|....
gi 1721875558 358 HYYITYHQWNSKPEFIVCTHTVVS 381
Cdd:pfam14598  83 KSKLFLNQNSNQQPFIMCTHTILR 106
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 113-178 7.41e-08

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: 50.09  E-value: 7.41e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1721875558  113 EFTQLMLEALDGFLVALTTDGNIIYVSDSVSSLIGHLPPDMVDQNILNFLPEREHSDVYKLLSSHM 178
Cdd:smart00091   1 ERLRAILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEALQRLL 66
 
Name Accession Description Interval E-value
bHLH-PAS_PASD1 cd19736
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in circadian clock protein PASD1; ...
 28-97 7.85e-36

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in circadian clock protein PASD1; PASD1, also termed PAS domain-containing protein 1, is evolutionarily related to Circadian locomotor output cycles protein kaput (CLOCK)and functions as a suppressor of the biological clock that drives the daily circadian rhythms of cells throughout the body. Mammalian PASD1 doesn't harbor the bHLH-PAS domain and is not included in this family.


Pssm-ID: 381579  Cd Length: 70  Bit Score: 129.83  E-value: 7.85e-36
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721875558  28 LEEDEKDRAKRASRNKSEKKRRDQFNVLIKELCTMLQVQGLPCKMDKSTILQRTIGFLQKQKDMSAQNDS 97
Cdd:cd19736     1 MDEDEKDRAKRASRNKSEKKRRDQFNVLIKELCTMLQGHGHPLKMDKSTILQRTIDFLQKQKEITAQTEA 70
PAS_11 pfam14598
PAS domain; This family includes the PAS-B domain of NCOA1 (Nuclear receptor coactivator 1), ...
 279-381 4.96e-21

PAS domain; This family includes the PAS-B domain of NCOA1 (Nuclear receptor coactivator 1), which binds to an LXXLL motif in the C-terminal region of STAT6 (Signal transducer and activator of transcription 6).


Pssm-ID: 464214 [Multi-domain]  Cd Length: 110  Bit Score: 88.89  E-value: 4.96e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721875558 279 EFTSRHSLEWKFLFLDHRASPIIGYLPFEVLGTSGYDYYHVDDLELIAQCHKHLMQ-LGKGKSCYYRFLTKGQQWIWLQT 357
Cdd:pfam14598   3 QFTTRHDIDGKIISCDTRAPFSLGYEKDELVGRSIYDLVHPQDLRTAKSHLREIIQtRGRATSPSYRLRLRDGDFLSVHT 82

                          90       100
                  ....*....|....*....|....
gi 1721875558 358 HYYITYHQWNSKPEFIVCTHTVVS 381
Cdd:pfam14598  83 KSKLFLNQNSNQQPFIMCTHTILR 106
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 278-377 3.78e-16

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: 74.98  E-value: 3.78e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721875558 278 DEFTSRHSLEWKFLFLDHRASPIIGYLPFEVLGTSGYDYYHVDDLELIAQCHKHLMQLGKGKSCYYRFLTKGQQWIWLQT 357
Cdd:cd00130     2 PDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDGSVIWVLV 81

                          90       100
                  ....*....|....*....|
gi 1721875558 358 HYYITYHQWNSKPEFIVCTH 377
Cdd:cd00130    82 SLTPIRDEGGEVIGLLGVVR 101
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 113-178 7.41e-08

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: 50.09  E-value: 7.41e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1721875558  113 EFTQLMLEALDGFLVALTTDGNIIYVSDSVSSLIGHLPPDMVDQNILNFLPEREHSDVYKLLSSHM 178
Cdd:smart00091   1 ERLRAILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEALQRLL 66
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 269-334 1.36e-07

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: 49.32  E-value: 1.36e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1721875558  269 DLCNVQDPCDEFTSRHSLEWKFLFLDHRASPIIGYLPFEVLGTSGYDYYHVDDLELIAQCHKHLMQ 334
Cdd:smart00091   2 RLRAILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEALQRLLS 67
HLH pfam00010
Helix-loop-helix DNA-binding domain;
37-87 2.95e-07

Helix-loop-helix DNA-binding domain;


Pssm-ID: 459628 [Multi-domain]  Cd Length: 53  Bit Score: 47.84  E-value: 2.95e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1721875558  37 KRASRNKSEKKRRDQFNVLIKELCTMLQVQGLPCKMDKSTILQRTIGFLQK 87
Cdd:pfam00010   1 RREAHNERERRRRDRINDAFDELRELLPTLPPDKKLSKAEILRLAIEYIKH 51
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 113-186 3.10e-07

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://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 395786 [Multi-domain]  Cd Length: 113  Bit Score: 49.72  E-value: 3.10e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1721875558 113 EFTQLMLEALDGFLVALTTDGNIIYVSDSVSSLIGHLPPDMVDQNILNFLPEREHSDVYKLLSSHMLSSDPASS 186
Cdd:pfam00989   1 EDLRAILESLPDGIFVVDEDGRILYVNAAAEELLGLSREEVIGKSLLDLIPEEDDAEVAELLRQALLQGEESRG 74
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 122-188 4.70e-07

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: 48.78  E-value: 4.70e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1721875558 122 LDGFLVALTTDGNIIYVSDSVSSLIGHLPPDMVDQNILNFLPEREHSDVYKLLSSHMLSSDPASSDF 188
Cdd:cd00130     1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEV 67
HLH smart00353
helix loop helix domain;
42-94 6.16e-06

helix loop helix domain;


Pssm-ID: 197674 [Multi-domain]  Cd Length: 53  Bit Score: 44.13  E-value: 6.16e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1721875558   42 NKSEKKRRDQFNVLIKELCTMLqVQGLPC-KMDKSTILQRTIGFLQKQKDMSAQ 94
Cdd:smart00353   1 NARERRRRRKINEAFDELRSLL-PTLPKNkKLSKAEILRLAIEYIKSLQEELQK 53
PAS COG2202
PAS domain [Signal transduction mechanisms];
109-392 3.64e-04

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 43.47  E-value: 3.64e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721875558 109 LSNEEFTQLMLEALDGFLVALTTDGNIIYVSDSVSSLIGHLPPDMVDQNILNFLPEREHSDVYKLLSSHMLSSDPAssdf 188
Cdd:COG2202     7 EESERRLRALVESSPDAIIITDLDGRILYVNPAFERLTGYSAEELLGKTLRDLLPPEDDDEFLELLRAALAGGGVW---- 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721875558 189 ldsesHVEFCCHLARGnmdlKEPPVYEYVKFIGDfkfhnnvptsscnglelalprtlqsSLEEQLCLIATVRLVTPQ--- 265
Cdd:COG2202    83 -----RGELRNRRKDG----SLFWVELSISPVRD-------------------------EDGEITGFVGIARDITERkra 128

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721875558 266 ---------FLKDLcnvQDPCDEFTSRHSLEWKFLFLDHRASPIIGYLPFEVLGTSGYDYYHVDDLELIAQCHKHLMQLG 336
Cdd:COG2202   129 eealreseeRLRLL---VENAPDGIFVLDLDGRILYVNPAAEELLGYSPEELLGKSLLDLLHPEDRERLLELLRRLLEGG 205

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1721875558 337 KGKSCY-YRFLTKGQQWIWLQTHyyITYHQWNSKPEFIVCTHTVVSyaevraERRRA 392
Cdd:COG2202   206 RESYELeLRLKDGDGRWVWVEAS--AVPLRDGGEVIGVLGIVRDIT------ERKRA 254
 
Name Accession Description Interval E-value
bHLH-PAS_PASD1 cd19736
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in circadian clock protein PASD1; ...
 28-97 7.85e-36

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in circadian clock protein PASD1; PASD1, also termed PAS domain-containing protein 1, is evolutionarily related to Circadian locomotor output cycles protein kaput (CLOCK)and functions as a suppressor of the biological clock that drives the daily circadian rhythms of cells throughout the body. Mammalian PASD1 doesn't harbor the bHLH-PAS domain and is not included in this family.


Pssm-ID: 381579  Cd Length: 70  Bit Score: 129.83  E-value: 7.85e-36
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721875558  28 LEEDEKDRAKRASRNKSEKKRRDQFNVLIKELCTMLQVQGLPCKMDKSTILQRTIGFLQKQKDMSAQNDS 97
Cdd:cd19736     1 MDEDEKDRAKRASRNKSEKKRRDQFNVLIKELCTMLQGHGHPLKMDKSTILQRTIDFLQKQKEITAQTEA 70
bHLH-PAS_NPAS2_PASD4 cd19737
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing ...
 28-106 8.91e-31

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing protein 2 (NPAS2) and similar proteins; NPAS2, also termed neuronal PAS2, or basic-helix-loop-helix-PAS protein MOP4, or Class E basic helix-loop-helix protein 9 (bHLHe9), or member of PAS protein 4, or PAS domain-containing protein 4 (PASD4), is a bHLH-PAS transcriptional activator which forms a core component of the circadian clock.


Pssm-ID: 381580  Cd Length: 77  Bit Score: 115.66  E-value: 8.91e-31
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1721875558  28 LEEDEKDRAKRASRNKSEKKRRDQFNVLIKELCTMLqvQGLPCKMDKSTILQRTIGFLQKQKDMSAQNDSCDVRQDWKP 106
Cdd:cd19737     1 MDEDEKDRAKRASRNKSEKKRRDQFNVLIKELSSML--PGNTRKMDKTTVLEKVIGFLQKHNEVSAQTEICDIQQDWKP 77
bHLH-PAS_dCLOCK cd19735
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Drosophila melanogaster ...
 29-109 2.44e-30

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Drosophila melanogaster Circadian locomotor output cycles protein kaput (dCLOCK) and similar proteins; dCLOCK, also termed dPAS1, is a bHLH-PAS Circadian regulator that acts as a transcription factor and generates a rhythmic output with a period of about 24 hours.


Pssm-ID: 381578  Cd Length: 80  Bit Score: 114.51  E-value: 2.44e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721875558  29 EEDEKDRAKRASRNKSEKKRRDQFNVLIKELCTMlqVQGLPCKMDKSTILQRTIGFLQKQKDMSAQNDSCDVRQDWKPSF 108
Cdd:cd19735     2 EEDEKDTIKRKSRNLSEKKRRDQFNVLINELCSM--VSTSNRKMDKSTVLKSTIAFLKNHNEVTMQSHQQEIQEDWKPSF 79


                  .
gi 1721875558 109 L 109
Cdd:cd19735    80 L 80
bHLH-PAS_CLOCK_like cd11441
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Circadian locomotor output ...
 38-93 2.44e-25

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Circadian locomotor output cycles protein kaput (CLOCK) and similar proteins; The family includes CLOCK, neuronal PAS domain-containing protein 2 (NPAS2) and non-mammalian circadian clock protein PASD1. CLOCK, also termed Class E basic helix-loop-helix protein 8 (bHLHe8), is a transcriptional activator which forms a core component of the circadian clock. NPAS2, also termed neuronal PAS2, or basic-helix-loop-helix-PAS protein MOP4, or Class E basic helix-loop-helix protein 9 (bHLHe9), or member of PAS protein 4, or PAS domain-containing protein 4, is a transcriptional activator which forms a core component of the circadian clock. PASD1 is evolutionarily related to Circadian locomotor output cycles protein kaput (CLOCK)and functions as a suppressor of the biological clock that drives the daily circadian rhythms of cells throughout the body.


Pssm-ID: 381447  Cd Length: 54  Bit Score: 99.35  E-value: 2.44e-25
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1721875558  38 RASRNKSEKKRRDQFNVLIKELCTMLQVQGLpcKMDKSTILQRTIGFLQKQKDMSA 93
Cdd:cd11441     1 RKSRNLSEKKRRDQFNVLINELASMLPGRGR--KMDKSTVLKKTIAFLRKHKELTA 54
bHLH-PAS_CLOCK cd19734
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Circadian locomotor output ...
 31-93 2.67e-25

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Circadian locomotor output cycles protein kaput (CLOCK) and similar proteins; CLOCK, also termed Class E basic helix-loop-helix protein 8 (bHLHe8), is a bHLH-PAS transcriptional activator which forms a core component of the circadian clock. It forms heterodimers with another bHLH-PAS protein, Brain-Muscle-Arnt-Like (also known as BMAL or ARNT3 or mop3), which regulates circadian rhythm. BMAL1-CLOCK heterodimer complex activates transcription from E-box (CANNTG) elements found in the promoter of circadian responsive genes.


Pssm-ID: 381577  Cd Length: 61  Bit Score: 99.32  E-value: 2.67e-25
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1721875558  31 DEKDRAKRASRNKSEKKRRDQFNVLIKELCTMLqvQGLPCKMDKSTILQRTIGFLQKQKDMSA 93
Cdd:cd19734     1 DDKDKAKRVSRNKSEKKRRDQFNVLIKELGSML--PGNARKMDKSTVLQKSIDFLRKHKEITA 61
PAS_11 pfam14598
PAS domain; This family includes the PAS-B domain of NCOA1 (Nuclear receptor coactivator 1), ...
 279-381 4.96e-21

PAS domain; This family includes the PAS-B domain of NCOA1 (Nuclear receptor coactivator 1), which binds to an LXXLL motif in the C-terminal region of STAT6 (Signal transducer and activator of transcription 6).


Pssm-ID: 464214 [Multi-domain]  Cd Length: 110  Bit Score: 88.89  E-value: 4.96e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721875558 279 EFTSRHSLEWKFLFLDHRASPIIGYLPFEVLGTSGYDYYHVDDLELIAQCHKHLMQ-LGKGKSCYYRFLTKGQQWIWLQT 357
Cdd:pfam14598   3 QFTTRHDIDGKIISCDTRAPFSLGYEKDELVGRSIYDLVHPQDLRTAKSHLREIIQtRGRATSPSYRLRLRDGDFLSVHT 82

                          90       100
                  ....*....|....*....|....
gi 1721875558 358 HYYITYHQWNSKPEFIVCTHTVVS 381
Cdd:pfam14598  83 KSKLFLNQNSNQQPFIMCTHTILR 106
PAS_3 pfam08447
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 290-377 1.35e-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: 81.23  E-value: 1.35e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721875558 290 FLFLDHRASPIIGYLPFEVLGT--SGYDYYHVDDLELIAQCHKHLMQLGKGKSCYYRFLTKGQQWIWLQTHYYItYHQWN 367
Cdd:pfam08447   1 IIYWSPRFEEILGYTPEELLGKgeSWLDLVHPDDRERVREALWEALKGGEPYSGEYRIRRKDGEYRWVEARARP-IRDEN 79

                          90
                  ....*....|
gi 1721875558 368 SKPEFIVCTH 377
Cdd:pfam08447  80 GKPVRVIGVA 89
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 278-377 3.78e-16

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: 74.98  E-value: 3.78e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721875558 278 DEFTSRHSLEWKFLFLDHRASPIIGYLPFEVLGTSGYDYYHVDDLELIAQCHKHLMQLGKGKSCYYRFLTKGQQWIWLQT 357
Cdd:cd00130     2 PDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDGSVIWVLV 81

                          90       100
                  ....*....|....*....|
gi 1721875558 358 HYYITYHQWNSKPEFIVCTH 377
Cdd:cd00130    82 SLTPIRDEGGEVIGLLGVVR 101
bHLH_PAS cd11391
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain family; bHLH-PAS domain has been found ...
 38-89 2.11e-09

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain family; bHLH-PAS domain has been found in a large group of bHLH transcription regulators that are involved in gene expression responding to environmental change and controlling aspects of neural development, including proteins from aryl hydrocarbon receptor nuclear translocator (ARNT) family, hypoxia-inducible factor (HIF) family, aryl hydrocarbon receptor (AhR) family, neuronal PAS domain-containing protein (NPAS) family, Circadian locomotor output cycles protein kaput (CLOCK)-like family, and single-minded (SIM) family. bHLH-PAS transcriptional regulatory factors have a bHLH DNA-binding domain followed by two PAS domains and a C-terminal activation or repression domain. bHLH-PAS family members can be divided into class I and class II based on their dimerization partner. bHLH-PAS class I factors include AhR, HIF and SIM. The best characterized bHLH-PAS Class II protein is the ubiquitous ARNT. Some members of bHLH-PAS family act as transcriptional coactivators (such as NCoA) that lack the ability to dimerize and bind DNA.


Pssm-ID: 381397 [Multi-domain]  Cd Length: 55  Bit Score: 54.12  E-value: 2.11e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1721875558  38 RASRNKSEKKRRDQFNVLIKELCTMLQVQGLPC-KMDKSTILQRTIGFLQKQK 89
Cdd:cd11391     1 REKSREAAKKRRDKENAEISELASLLPLPPAVGsKLDKLSVLRLAVAYLRLKK 53
bHLHzip_scCBP1 cd11398
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Saccharomyces cerevisiae ...
 31-97 7.42e-09

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Saccharomyces cerevisiae centromere-binding protein 1 (CBP-1) and similar proteins; CBP-1, also termed centromere promoter factor 1 (CPF1), or centromere-binding factor 1 (CBF1), is a bHLHzip protein that is required for chromosome stability and methionine prototrophy. It binds as a homodimer to the centromere DNA elements I (CDEI, GTCACATG) region of the centromere that is required for optimal centromere function.


Pssm-ID: 381404 [Multi-domain]  Cd Length: 89  Bit Score: 53.50  E-value: 7.42e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1721875558  31 DEKDRAKRASRNKSEKKRRDQFNVLIKELCTMlqVQGLPCKMDKSTILQRTIGFLQKQKDMSAQNDS 97
Cdd:cd11398     1 EEWHRQRRDNHKEVERRRRENINEGINELAAL--VPGNAREKNKGAILARAVEYIQELQETEAKNIE 65
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 113-178 7.41e-08

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: 50.09  E-value: 7.41e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1721875558  113 EFTQLMLEALDGFLVALTTDGNIIYVSDSVSSLIGHLPPDMVDQNILNFLPEREHSDVYKLLSSHM 178
Cdd:smart00091   1 ERLRAILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEALQRLL 66
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 269-334 1.36e-07

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: 49.32  E-value: 1.36e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1721875558  269 DLCNVQDPCDEFTSRHSLEWKFLFLDHRASPIIGYLPFEVLGTSGYDYYHVDDLELIAQCHKHLMQ 334
Cdd:smart00091   2 RLRAILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEALQRLLS 67
HLH pfam00010
Helix-loop-helix DNA-binding domain;
37-87 2.95e-07

Helix-loop-helix DNA-binding domain;


Pssm-ID: 459628 [Multi-domain]  Cd Length: 53  Bit Score: 47.84  E-value: 2.95e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1721875558  37 KRASRNKSEKKRRDQFNVLIKELCTMLQVQGLPCKMDKSTILQRTIGFLQK 87
Cdd:pfam00010   1 RREAHNERERRRRDRINDAFDELRELLPTLPPDKKLSKAEILRLAIEYIKH 51
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 113-186 3.10e-07

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://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 395786 [Multi-domain]  Cd Length: 113  Bit Score: 49.72  E-value: 3.10e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1721875558 113 EFTQLMLEALDGFLVALTTDGNIIYVSDSVSSLIGHLPPDMVDQNILNFLPEREHSDVYKLLSSHMLSSDPASS 186
Cdd:pfam00989   1 EDLRAILESLPDGIFVVDEDGRILYVNAAAEELLGLSREEVIGKSLLDLIPEEDDAEVAELLRQALLQGEESRG 74
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 122-188 4.70e-07

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: 48.78  E-value: 4.70e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1721875558 122 LDGFLVALTTDGNIIYVSDSVSSLIGHLPPDMVDQNILNFLPEREHSDVYKLLSSHMLSSDPASSDF 188
Cdd:cd00130     1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEV 67
HLH smart00353
helix loop helix domain;
42-94 6.16e-06

helix loop helix domain;


Pssm-ID: 197674 [Multi-domain]  Cd Length: 53  Bit Score: 44.13  E-value: 6.16e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1721875558   42 NKSEKKRRDQFNVLIKELCTMLqVQGLPC-KMDKSTILQRTIGFLQKQKDMSAQ 94
Cdd:smart00353   1 NARERRRRRKINEAFDELRSLL-PTLPKNkKLSKAEILRLAIEYIKSLQEELQK 53
bHLHzip_Mlx_like cd11404
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Max-like protein X (Mlx) family; Mlx, ...
 37-90 6.65e-06

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Max-like protein X (Mlx) family; Mlx, also termed Class D basic helix-loop-helix protein 13 (bHLHd13), or Max-like bHLHZip protein, or protein BigMax, or transcription factor-like protein 4, is a Max-like bHLHZip transcription regulator that interacts with the Max network of transcription factors. It forms a sequence-specific DNA-binding protein complex with some member of Mad family (Mad1 and Mad4) and Mondo family but not the Myc family and bind the E-box DNA to control transcription. The family also includes Saccharomyces cerevisiae INO4, which is a bHLH transcriptional activator of phospholipid synthetic genes (such as INO1, CHO1/PSS, CHO2/PEM1, OPI3/PEM2, etc.). It is required for de-repression of phospholipid biosynthetic gene expression in response to inositol deprivation in yeast.


Pssm-ID: 381410 [Multi-domain]  Cd Length: 70  Bit Score: 44.60  E-value: 6.65e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1721875558  37 KRASRNKSEKKRRDQFNVLIKELCTMlqVQGL-PCKMDKSTILQRTIGFLQKQKD 90
Cdd:cd11404     2 RRLNHVRSEKKRRELIKKGYDELCAL--VPGLdPQKRTKADILQKAADWIQELKE 54
PAC smart00086
Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); PAC motif ...
 340-381 1.53e-05

Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); PAC motif occurs C-terminal to a subset of all known PAS motifs. It is proposed to contribute to the PAS domain fold.


Pssm-ID: 197509  Cd Length: 43  Bit Score: 42.56  E-value: 1.53e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1721875558  340 SCYYRFLTKGQQWIWLQTHYYITYHqWNSKPEFIVCTHTVVS 381
Cdd:smart00086   1 TVEYRLRRKDGSYIWVLVSASPIRD-EDGEVEGILGVVRDIT 41
bHLHzip_MITF_like cd11397
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in the microphthalmia-associated ...
 33-90 2.92e-05

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in the microphthalmia-associated transcription factor family (MITF) family; The MITF (also known as microphthalmia-TFE, or MiT) family is a small family that contain a basic helix loop helix domain associated with a leucine zipper (bHLHZip). The MITF family comprises four genes in mammals (MITF, TFE3, TFEB, and TFEC); each gene has different functions. MITF is involved in neural crest melanocytes development as well as the pigmented retinal epithelium. TFEB is required for vascularization of the mouse placenta. TFE3 is involved in B cell function. TFEC regulates gene expression in macrophages. The MITF family can form homodimers or heterodimers with each other but not with other bHLH or bHLHzip proteins.


Pssm-ID: 381403  Cd Length: 69  Bit Score: 42.67  E-value: 2.92e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721875558  33 KDRAKRASRNKSEKKRRDQFNVLIKELCTMLQVQGLP-CKMDKSTILQRTIGFLQK-QKD 90
Cdd:cd11397     1 KDRQKKDNHNMIERRRRFNINDRIKELGTLLPKSNDPdMRWNKGTILKASVDYIRKlQKE 60
bHLH-PAS_ARNTL2_PASD9 cd11469
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor ...
 38-92 8.29e-05

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor nuclear translocator-like protein 2 (ARNTL2) and similar proteins; ARNTL2, also termed Basic-helix-loop-helix-PAS protein MOP9, or brain and muscle ARNT-like 2 (BMAL2), or CYCLE-like factor (CLIF), or Class E basic helix-loop-helix protein 6 (bHLHe6), or member of PAS protein 9, or PAS domain-containing protein 9 (PASD9), is a neuronal bHLH-PAS transcriptional factor, regulating cell cycle progression and preventing cell death, whose sustained expression might ensure brain neuron survival. It also plays important roles in tumor angiogenesis. ARNT-2 heterodimerize with other bHLH-PAS proteins such as aryl hydrocarbon receptor (AhR), hypoxia-inducible factor (HIF), and single-minded (SIM).


Pssm-ID: 381475  Cd Length: 60  Bit Score: 41.17  E-value: 8.29e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1721875558  38 RASRNKSEKKRRDQFNVLIKELCTML-QVQGLPCKMDKSTILQRTIGFLQKQKDMS 92
Cdd:cd11469     2 REAHSQTEKRRRDKMNNLIEELSAMIpQCNPMARKLDKLTVLRMAVQHLKSLKGST 57
bHLH_AtILR3_like cd11446
basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein IAA-leucine ...
 45-103 8.80e-05

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein IAA-leucine resistant 3 (ILR3) and similar proteins; ILR3, also termed AtbHLH105, or EN 133, is a bHLH transcription factor that plays a role in resistance to amide-linked indole-3-acetic acid (IAA) conjugates such as IAA-Leu and IAA-Phe. It may regulate gene expression in response to metal homeostasis changes.


Pssm-ID: 381452 [Multi-domain]  Cd Length: 76  Bit Score: 41.55  E-value: 8.80e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1721875558  45 EKKRRDQFNVLIKELCTMLQVQGLPcKMDKSTILQRTIGFLQ---------KQKDMSAQNDSCDVRQD 103
Cdd:cd11446     5 EKLRRDKLNERFMELSNVLEPGRPP-KTDKATILGDAIRMLKqlrgevqklKEENSSLQEESKELKAE 71
bHLH-PAS_ARNT cd18947
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor ...
 33-79 2.88e-04

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor nuclear translocator (ARNT) and similar proteins; ARNT, also termed Class E basic helix-loop-helix protein 2 (bHLHe2), or Dioxin receptor, nuclear translocator, or hypoxia-inducible factor 1-beta (HIF1b), or HIF-1-beta, or HIF1-beta, is a member of bHLH-PAS transcription regulators that acts as the heterodimeric partner for bHLH-PAS proteins such as aryl hydrocarbon receptor (AhR), hypoxia-inducible factor (HIF), and single-minded (SIM). These bHLH-PAS transcription complexes are involved in transcriptional responses to xenobiotic, hypoxia, and developmental pathways. Heterodimerization of bHLH-PAS proteins with ARNT is mediated by contacts between both the bHLH and the tandem PAS domains. ARNT use bHLH and/or PAS domains to interact with several transcriptional coactivators. It is required for activity of the aryl hydrocarbon (dioxin) receptor.


Pssm-ID: 381517  Cd Length: 65  Bit Score: 39.78  E-value: 2.88e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1721875558  33 KDRAKRASRNKSEKKRRDQFNVLIKELCTML-QVQGLPCKMDKSTILQ 79
Cdd:cd18947     1 KERFARENHSEIERRRRNKMTAYITELSDMVpTCSALARKPDKLTILR 48
PAS COG2202
PAS domain [Signal transduction mechanisms];
109-392 3.64e-04

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 43.47  E-value: 3.64e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721875558 109 LSNEEFTQLMLEALDGFLVALTTDGNIIYVSDSVSSLIGHLPPDMVDQNILNFLPEREHSDVYKLLSSHMLSSDPAssdf 188
Cdd:COG2202     7 EESERRLRALVESSPDAIIITDLDGRILYVNPAFERLTGYSAEELLGKTLRDLLPPEDDDEFLELLRAALAGGGVW---- 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721875558 189 ldsesHVEFCCHLARGnmdlKEPPVYEYVKFIGDfkfhnnvptsscnglelalprtlqsSLEEQLCLIATVRLVTPQ--- 265
Cdd:COG2202    83 -----RGELRNRRKDG----SLFWVELSISPVRD-------------------------EDGEITGFVGIARDITERkra 128

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721875558 266 ---------FLKDLcnvQDPCDEFTSRHSLEWKFLFLDHRASPIIGYLPFEVLGTSGYDYYHVDDLELIAQCHKHLMQLG 336
Cdd:COG2202   129 eealreseeRLRLL---VENAPDGIFVLDLDGRILYVNPAAEELLGYSPEELLGKSLLDLLHPEDRERLLELLRRLLEGG 205

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1721875558 337 KGKSCY-YRFLTKGQQWIWLQTHyyITYHQWNSKPEFIVCTHTVVSyaevraERRRA 392
Cdd:COG2202   206 RESYELeLRLKDGDGRWVWVEAS--AVPLRDGGEVIGVLGIVRDIT------ERKRA 254
bHLH_SF cd00083
basic Helix Loop Helix (bHLH) domain superfamily; bHLH proteins are transcriptional regulators ...
 45-90 4.41e-04

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.


Pssm-ID: 381392 [Multi-domain]  Cd Length: 46  Bit Score: 38.66  E-value: 4.41e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1721875558  45 EKKRRDQFNVLIKELCTMLQVQGLPCKMDKSTILQRTIGFLQKQKD 90
Cdd:cd00083     1 ERRRRDKINDAFEELKRLLPELPDSKKLSKASILQKAVEYIRELQS 46
bHLHzip_TFEB cd18927
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in transcription factor EB (TFEB) and ...
 33-91 6.20e-04

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in transcription factor EB (TFEB) and similar proteins; TFEB, also termed Class E basic helix-loop-helix protein 35 (bHLHe35), is a bHLHzip transcription factor that is required for vascularization of the mouse placenta. It specifically recognizes and binds E-box sequences (5'-CANNTG-3'). Its efficient DNA-binding requires dimerization with itself or with another MiT/TFE family member such as TFE3 or MITF.


Pssm-ID: 381497  Cd Length: 91  Bit Score: 39.58  E-value: 6.20e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1721875558  33 KDRAKRASRNKSEKKRRDQFNVLIKELCTML-QVQGLPCKMDKSTILQRTIGFLQK-QKDM 91
Cdd:cd18927     7 KERQKKDNHNLIERRRRFNINDRIKELGTLIpKTNDLDVRWNKGTILKASVDYIKRmQKDL 67
bHLH-O_HES7 cd11462
basic helix-loop-helix-orange (bHLH-O) domain found in hairy and enhancer of split 7 (HES-7) ...
 45-89 7.45e-04

basic helix-loop-helix-orange (bHLH-O) domain found in hairy and enhancer of split 7 (HES-7) and similar proteins; HES-7, also termed Class B basic helix-loop-helix protein 37 (bHLHb37), or bHLH factor Hes7, is a bHLH-O transcriptional repressor that is expressed in an oscillatory manner and acts as a key regulator of the pace of the segmentation clock. It is regulated by the Notch and Fgf/Mapk pathways. HES-7 is one mammalian counterpart of the Hairy and Enhancer of split proteins that play a critical role in many physiological processes including cellular differentiation, cell cycle arrest, apoptosis and self-renewal ability.


Pssm-ID: 381468 [Multi-domain]  Cd Length: 61  Bit Score: 38.48  E-value: 7.45e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1721875558  45 EKKRRDQFNVLIKELCTML----QVQGL--PcKMDKSTILQRTIGFLQKQK 89
Cdd:cd11462     9 EKRRRDRINRSLEELRVLLlqntQDEKLknP-KVEKAEILELTVQFLRNSS 58
bHLH-O_HES5 cd11461
basic helix-loop-helix-orange (bHLH-O) domain found in transcription factor HES-5 and similar ...
 45-89 8.05e-04

basic helix-loop-helix-orange (bHLH-O) domain found in transcription factor HES-5 and similar proteins; HES-5, also termed Class B basic helix-loop-helix protein 38 (bHLHb38), or hairy and enhancer of split 5, is a bHLH-O transcription factor that is involved in cell differentiation and proliferation in a variety of tissues. HES-5 is an essential effector for Notch signaling. It acts as a transducer of Notch signals in brain vascular development. It also acts as a key mediator of Wnt-3a-induced neuronal differentiation and plays a crucial role in normal inner ear hair cell development. HES-5 is one mammalian counterpart of the Hairy and Enhancer of split proteins that play a critical role in many physiological processes including cellular differentiation, cell cycle arrest, apoptosis and self-renewal ability.


Pssm-ID: 381467 [Multi-domain]  Cd Length: 59  Bit Score: 38.48  E-value: 8.05e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1721875558  45 EKKRRDQFNVLIKELCTML----QVQGLPCKMDKSTILQRTIGFLQKQK 89
Cdd:cd11461     8 EKTRRDRINSSIEQLKTLLekefQRHQPNSKLEKADILEMTVSFLKQSA 56
bHLH-PAS_SRC cd11439
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in steroid receptor coactivator ...
 42-92 9.02e-04

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in steroid receptor coactivator (SRC) family; The SRC family of coactivators includes SRC-1 (NcoA-1/p160), SRC-2(TIF2/GRIP1/NcoA-2) and SRC-3(NcoA-3/pCIP/RAC3/ACTR/pCIP/AIB1/TRAM1), which are critical mediators of steroid receptor action. They contain bHLH-PAS domain at the N-terminal that is followed by receptor interacting domain and C-terminal transcriptional activation domain. SRC coactivators interact with nuclear receptors in a ligand-dependent manner and enhance transcriptional activation by the receptor via histone acetylation/methylation.


Pssm-ID: 381445  Cd Length: 58  Bit Score: 38.18  E-value: 9.02e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1721875558  42 NKS--EKKRRDQFNVLIKELCTMLQVQG-----LPCKMDKSTILQRTIGFLQKQKDMS 92
Cdd:cd11439     1 NKClnEKRRREQENKYIEELAELISASIsdmdsLSVKPDKCAILQETVKQIRQIKEQE 58
bHLHzip_TFE3 cd18928
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in transcription factor E3 (TFE3) and ...
 33-102 9.17e-04

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in transcription factor E3 (TFE3) and similar proteins; TFE3, also termed Class E basic helix-loop-helix protein 33 (bHLHe33), is a bHLHzip transcription factor that is involved in B cell function. It specifically recognizes and binds E-box sequences (5'-CANNTG-3'). Its efficient DNA-binding requires dimerization with itself or with another MiT/TFE family member such as TFEB or MITF.


Pssm-ID: 381498 [Multi-domain]  Cd Length: 91  Bit Score: 39.26  E-value: 9.17e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1721875558  33 KDRAKRASRNKSEKKRRDQFNVLIKELCTMLQVQGLP-CKMDKSTILQRTIGFLQKQKDMSAQNDSCDVRQ 102
Cdd:cd18928     7 KERQKKDNHNLIERRRRFNINDRIKELGTLIPKSTDPeMRWNKGTILKASVDYIRKLQKEQQRSKEIEMRQ 77
bHLHzip_MGA_like cd19682
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in MAX gene-associated protein (MGA) ...
 38-90 9.18e-04

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in MAX gene-associated protein (MGA) family; The MGA family includes MGA, Schizosaccharomyces pombe ESC1 (spESC1) and similar proteins. MGA, also termed MAX dimerization protein 5 (MAD5), is a dual specificity T-box/ bHLHzip transcription factor that regulates the expression of both Max-network and T-box family target genes. It contains a Myc-like bHLHZip motif and requires heterodimerization with Max for binding to the preferred Myc-Max-binding site CACGTG. In addition to the bHLHZip domain, MGA harbors a second DNA-binding domain, the T-box or T-domain. It thus binds the preferred Brachyury-binding sequence and represses transcription of reporter genes containing promoter-proximal Brachyury-binding sites. spESC1 is a bHLHzip protein with homology to human MyoD and Myf-5 myogenic differentiation inducers. It is involved in the sexual differentiation process.


Pssm-ID: 381525 [Multi-domain]  Cd Length: 65  Bit Score: 38.41  E-value: 9.18e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1721875558  38 RASRNKSEKKRRDQFNVLIKELCTMLQVQGLPcKMDKSTI----------LQRTIGFLQKQKD 90
Cdd:cd19682     1 RLRHKKRERERRSELRELFDKLKQLLGLDSDE-KASKLAVlteaieeiqqLKREEDELQKEKA 62
bHLH_AtAIG1_like cd11455
basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein AIG1 and similar ...
 34-94 2.35e-03

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein AIG1 and similar proteins; AIG1, also termed AtbHLH32, or EN 54, or protein target of MOOPTEROS 5, is a transcription factor required for MONOPTEROS-dependent root initiation in embryo.


Pssm-ID: 381461  Cd Length: 80  Bit Score: 37.66  E-value: 2.35e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1721875558  34 DRAKRASRNKS--EKKRRDQFNvliKELCTMLQVqgLPC--KMDKSTILQRTIGFLQKQKDMSAQ 94
Cdd:cd11455     2 DKALAASKSHSeaERRRRERIN---SHLATLRTL--LPNlsKTDKASLLAEVVQHVKELKRQAAE 61
bHLH_O_HES cd11410
basic helix-loop-helix-orange (bHLH-O) domain found in hairy and enhancer of split (HES) ...
 45-89 2.75e-03

basic helix-loop-helix-orange (bHLH-O) domain found in hairy and enhancer of split (HES) family; The HES family includes bHLH-O transcriptional regulators that are related to the Drosophila hairy and Enhancer-of-split (HES) proteins. They contain a basic helix-loop-helix (bHLH) domain with an invariant proline residue in its basic region, an orange domain in the central region and a conserved tetrapeptide motif, WRPW, at its C-terminal region. HES family proteins form heterodimers or homodimers via their HLH domain and bind DNA to repress gene transcription that play an essential role in development of both compartment and boundary cells of the central nervous system.


Pssm-ID: 381416 [Multi-domain]  Cd Length: 54  Bit Score: 36.68  E-value: 2.75e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1721875558  45 EKKRRDQFNVLIKELCTML-----QVQGLPCKMDKSTILQRTIGFLQKQK 89
Cdd:cd11410     2 EKKRRARINKSLEQLKTLVlealnKDNTRYSKLEKADILEMTVKYLKQLQ 51
PAS_9 pfam13426
PAS domain; This domain is found in many signalling proteins in which it functions as a sensor ...
 132-169 6.57e-03

PAS domain; This domain is found in many signalling proteins in which it functions as a sensor domain. It recognizes FMN, Zn(II), FAD and riboflavin (MAtilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 463873 [Multi-domain]  Cd Length: 93  Bit Score: 36.67  E-value: 6.57e-03
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1721875558 132 DGNIIYVSDSVSSLIGHLPPDMVDQNILNFLPEREHSD 169
Cdd:pfam13426   1 DGRIIYVNDAALRLLGYTREELLGKSITDLFAEPEDSE 38
bHLH-O_HERP_like cd11389
basic helix-loop-helix-orange (bHLH-O) domain found in hairy and enhancer of split (HES) ...
 45-88 7.71e-03

basic helix-loop-helix-orange (bHLH-O) domain found in hairy and enhancer of split (HES)-related repressor protein (HERP)-like family; The HERP-like family includes bHLH-O transcriptional regulators that are related to the Drosophila hairy and Enhancer-of-split proteins. They contain a basic helix-loop-helix (bHLH) domain with an invariant glycine residue in its basic region, an orange domain in the central region and YXXW sequence motif at its C-terminal region. HERP proteins (HEY1, HEY2 and HEYL) act as downstream effectors of Notch signaling. They are involved in cardiovascular development and have roles in somitogenesis, myogenesis and gliogenesis. Hairy and enhancer of split-related protein HELT is a transcriptional repressor expressed in the developing central nervous system. It binds preferentially to the canonical E box sequence 5'-CACGCG-3' and regulates neuronal differentiation and/or identity. Differentially expressed in chondrocytes proteins, DEC1 and DEC2, are widely expressed in both embryonic and adult tissues and have been implicated in apoptosis, cell proliferation, and circadian rhythms, as well as malignancy in various cancers. Drosophila melanogaster protein clockwork orange (Cwo) is also included in this family. It is involved in the regulation of Drosophila circadian rhythms. It functions as both an activator and a repressor of clock gene expression.


Pssm-ID: 381395 [Multi-domain]  Cd Length: 55  Bit Score: 35.38  E-value: 7.71e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1721875558  45 EKKRRDQFNVLIKELCTML------QVQGlpcKMDKSTILQRTIGFLQKQ 88
Cdd:cd11389     5 EKRRRDRINESLAELRRLVpearksKGSG---KLEKAEILEMTLQHLKAL 51
bHLH-PAS_ARNT_like cd11437
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor ...
 37-78 8.48e-03

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor nuclear translocator (ARNT) family; The ARNT family of bHLH-PAS transcription regulators includes ARNT, ARNT-like proteins (ARNTL and ARNTL2), and Drosophila melanogaster protein cycle. They act as the heterodimeric partner for bHLH-PAS proteins such as aryl hydrocarbon receptor (AhR), hypoxia-inducible factor (HIF), and single-minded (SIM). These bHLH-PAS transcription complexes are involved in transcriptional responses to xenobiotic, hypoxia, and developmental pathways. Heterodimerization of bHLH-PAS proteins with ARNT is mediated by contacts between both the bHLH and the tandem PAS domains. ARNT use bHLH and/or PAS domains to interact with several transcriptional coactivators. It is required for activity of the aryl hydrocarbon (dioxin) receptor. ARNTL, also termed Basic-helix-loop-helix-PAS protein MOP3, or brain and muscle ARNT-like 1 (BMAL1), or Class E basic helix-loop-helix protein 5 (bHLHe5), or member of PAS protein 3, or PAS domain-containing protein 3 (PASD3), or bHLH-PAS protein JAP3, is a member of the bHLH-PAS transcription factor family that forms heterodimers with another bHLH-PAS protein, CLOCK (circadian locomotor output cycle kaput), which regulates circadian rhythm. ARNTL-CLOCK heterodimer complex activates transcription from E-box (CANNTG) elements found in the promoter of circadian responsive genes. ARNTL is highly homologous to ARNT. ARNTL2, also termed Basic-helix-loop-helix-PAS protein MOP9, or brain and muscle ARNT-like 2 (BMAL2), or CYCLE-like factor (CLIF), or Class E basic helix-loop-helix protein 6 (bHLHe6), or member of PAS protein 9, or PAS domain-containing protein 9 (PASD9), is a neuronal bHLH-PAS transcriptional factor, regulating cell cycle progression and preventing cell death, whose sustained expression might ensure brain neuron survival. It also plays important roles in tumor angiogenesis. Protein cycle, also termed brain and muscle ARNT-like 1 (BMAL1), or MOP3, is a putative bHLH-PAS transcription factor involved in the generation of biological rhythms in Drosophila. It activates cycling transcription of Period (PER) and Timeless (TIM) by binding to the E-box (5'-CACGTG-3') present in their promoters.


Pssm-ID: 381443  Cd Length: 58  Bit Score: 35.47  E-value: 8.48e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1721875558  37 KRASRNKSEKKRRDQFNVLIKELCTML-QVQGLPCKMDKSTIL 78
Cdd:cd11437     1 SRSNHSEIEKRRRDKMNAYIQELSALVpACNAMSRKLDKLTVL 43
 
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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