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Conserved domains on  [gi|528467758|ref|XP_005168396|]
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clock circadian regulator b isoform X1 [Danio rerio]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
bHLH-PAS_CLOCK cd19734
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Circadian locomotor output ...
19-79 1.27e-34

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: 125.90  E-value: 1.27e-34
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 528467758  19 DEKDKAKRVSRNKSEKKRRDQFNVLIKELGTMLPGNTRKMDKSTILQKSIDYLRKNKENAA 79
Cdd:cd19734    1 DDKDKAKRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKEITA 61
PAS_11 super family cl37882
PAS domain; This family includes the PAS-B domain of NCOA1 (Nuclear receptor coactivator 1), ...
263-366 1.28e-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: 90.43  E-value: 1.28e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528467758  263 EEFTSRHSLEWKFLLLDHRAPPIIGYMPFEVLGTSGYDYYHVDDLHSLAKCHEHLMQF-GKGKSCYYRFLTKGQQWIWLQ 341
Cdd:pfam14598   2 EQFTTRHDIDGKIISCDTRAPFSLGYEKDELVGRSIYDLVHPQDLRTAKSHLREIIQTrGRATSPSYRLRLRDGDFLSVH 81
                          90       100
                  ....*....|....*....|....*
gi 528467758  342 TNYYITYHQWNSRPEFIVCTHTVVS 366
Cdd:pfam14598  82 TKSKLFLNQNSNQQPFIMCTHTILR 106
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
99-160 2.05e-05

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: 43.16  E-value: 2.05e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 528467758    99 EFSQLMLEALDGFFLVMLTDGYIIYISESVTSLLEHLPSDLMDQNLLNFLPVVDHGEVYKAL 160
Cdd:smart00091   1 ERLRAILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEAL 62
 
Name Accession Description Interval E-value
bHLH-PAS_CLOCK cd19734
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Circadian locomotor output ...
19-79 1.27e-34

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: 125.90  E-value: 1.27e-34
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 528467758  19 DEKDKAKRVSRNKSEKKRRDQFNVLIKELGTMLPGNTRKMDKSTILQKSIDYLRKNKENAA 79
Cdd:cd19734    1 DDKDKAKRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKEITA 61
PAS_11 pfam14598
PAS domain; This family includes the PAS-B domain of NCOA1 (Nuclear receptor coactivator 1), ...
263-366 1.28e-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: 90.43  E-value: 1.28e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528467758  263 EEFTSRHSLEWKFLLLDHRAPPIIGYMPFEVLGTSGYDYYHVDDLHSLAKCHEHLMQF-GKGKSCYYRFLTKGQQWIWLQ 341
Cdd:pfam14598   2 EQFTTRHDIDGKIISCDTRAPFSLGYEKDELVGRSIYDLVHPQDLRTAKSHLREIIQTrGRATSPSYRLRLRDGDFLSVH 81
                          90       100
                  ....*....|....*....|....*
gi 528467758  342 TNYYITYHQWNSRPEFIVCTHTVVS 366
Cdd:pfam14598  82 TKSKLFLNQNSNQQPFIMCTHTILR 106
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
264-362 1.41e-12

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: 64.58  E-value: 1.41e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528467758 264 EFTSRHSLEWKFLLLDHRAPPIIGYMPFEVLGTSGYDYYHVDDLHSLAKCHEHLMQFGKGKSCYYRFLTKGQQWIWLQTN 343
Cdd:cd00130    3 DGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDGSVIWVLVS 82
                         90
                 ....*....|....*....
gi 528467758 344 YYITYHQWNSRPEFIVCTH 362
Cdd:cd00130   83 LTPIRDEGGEVIGLLGVVR 101
HLH smart00353
helix loop helix domain;
30-76 1.47e-10

helix loop helix domain;


Pssm-ID: 197674 [Multi-domain]  Cd Length: 53  Bit Score: 57.23  E-value: 1.47e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 528467758    30 NKSEKKRRDQFNVLIKELGTMLPG--NTRKMDKSTILQKSIDYLRKNKE 76
Cdd:smart00353   1 NARERRRRRKINEAFDELRSLLPTlpKNKKLSKAEILRLAIEYIKSLQE 49
HLH pfam00010
Helix-loop-helix DNA-binding domain;
25-73 2.51e-10

Helix-loop-helix DNA-binding domain;


Pssm-ID: 459628 [Multi-domain]  Cd Length: 53  Bit Score: 56.31  E-value: 2.51e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 528467758   25 KRVSRNKSEKKRRDQFNVLIKELGTMLP--GNTRKMDKSTILQKSIDYLRK 73
Cdd:pfam00010   1 RREAHNERERRRRDRINDAFDELRELLPtlPPDKKLSKAEILRLAIEYIKH 51
PAC smart00086
Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); PAC motif ...
325-366 1.90e-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: 42.17  E-value: 1.90e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 528467758   325 SCYYRFLTKGQQWIWLQTNYYITYHqWNSRPEFIVCTHTVVS 366
Cdd:smart00086   1 TVEYRLRRKDGSYIWVLVSASPIRD-EDGEVEGILGVVRDIT 41
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
99-160 2.05e-05

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: 43.16  E-value: 2.05e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 528467758    99 EFSQLMLEALDGFFLVMLTDGYIIYISESVTSLLEHLPSDLMDQNLLNFLPVVDHGEVYKAL 160
Cdd:smart00091   1 ERLRAILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEAL 62
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
108-163 3.02e-04

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: 40.69  E-value: 3.02e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 528467758 108 LDGFFLVMLTDGYIIYISESVTSLLEHLPSDLMDQNLLNFLPVVDHGEVYKALSSQ 163
Cdd:cd00130    1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENL 56
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
102-160 4.02e-04

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: 40.86  E-value: 4.02e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 528467758  102 QLMLEALDGFFLVMLTDGYIIYISESVTSLLEHLPSDLMDQNLLNFLPVVDHGEVYKAL 160
Cdd:pfam00989   4 RAILESLPDGIFVVDEDGRILYVNAAAEELLGLSREEVIGKSLLDLIPEEDDAEVAELL 62
 
Name Accession Description Interval E-value
bHLH-PAS_CLOCK cd19734
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Circadian locomotor output ...
19-79 1.27e-34

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: 125.90  E-value: 1.27e-34
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 528467758  19 DEKDKAKRVSRNKSEKKRRDQFNVLIKELGTMLPGNTRKMDKSTILQKSIDYLRKNKENAA 79
Cdd:cd19734    1 DDKDKAKRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKEITA 61
bHLH-PAS_NPAS2_PASD4 cd19737
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing ...
16-92 2.09e-34

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: 125.67  E-value: 2.09e-34
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 528467758  16 MEEDEKDKAKRVSRNKSEKKRRDQFNVLIKELGTMLPGNTRKMDKSTILQKSIDYLRKNKENAAQSESSDIKQDWKP 92
Cdd:cd19737    1 MDEDEKDRAKRASRNKSEKKRRDQFNVLIKELSSMLPGNTRKMDKTTVLEKVIGFLQKHNEVSAQTEICDIQQDWKP 77
bHLH-PAS_dCLOCK cd19735
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Drosophila melanogaster ...
17-95 2.95e-32

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: 119.90  E-value: 2.95e-32
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 528467758  17 EEDEKDKAKRVSRNKSEKKRRDQFNVLIKELGTMLPGNTRKMDKSTILQKSIDYLRKNKENAAQSESSDIKQDWKPPFL 95
Cdd:cd19735    2 EEDEKDTIKRKSRNLSEKKRRDQFNVLINELCSMVSTSNRKMDKSTVLKSTIAFLKNHNEVTMQSHQQEIQEDWKPSFL 80
bHLH-PAS_PASD1 cd19736
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in circadian clock protein PASD1; ...
16-83 9.46e-29

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: 109.41  E-value: 9.46e-29
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528467758  16 MEEDEKDKAKRVSRNKSEKKRRDQFNVLIKELGTMLPGNTR--KMDKSTILQKSIDYLRKNKENAAQSES 83
Cdd:cd19736    1 MDEDEKDRAKRASRNKSEKKRRDQFNVLIKELCTMLQGHGHplKMDKSTILQRTIDFLQKQKEITAQTEA 70
bHLH-PAS_CLOCK_like cd11441
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Circadian locomotor output ...
26-79 4.26e-27

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: 104.36  E-value: 4.26e-27
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 528467758  26 RVSRNKSEKKRRDQFNVLIKELGTMLPGNTRKMDKSTILQKSIDYLRKNKENAA 79
Cdd:cd11441    1 RKSRNLSEKKRRDQFNVLINELASMLPGRGRKMDKSTVLKKTIAFLRKHKELTA 54
PAS_11 pfam14598
PAS domain; This family includes the PAS-B domain of NCOA1 (Nuclear receptor coactivator 1), ...
263-366 1.28e-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: 90.43  E-value: 1.28e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528467758  263 EEFTSRHSLEWKFLLLDHRAPPIIGYMPFEVLGTSGYDYYHVDDLHSLAKCHEHLMQF-GKGKSCYYRFLTKGQQWIWLQ 341
Cdd:pfam14598   2 EQFTTRHDIDGKIISCDTRAPFSLGYEKDELVGRSIYDLVHPQDLRTAKSHLREIIQTrGRATSPSYRLRLRDGDFLSVH 81
                          90       100
                  ....*....|....*....|....*
gi 528467758  342 TNYYITYHQWNSRPEFIVCTHTVVS 366
Cdd:pfam14598  82 TKSKLFLNQNSNQQPFIMCTHTILR 106
PAS_3 pfam08447
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
275-362 2.21e-15

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: 71.99  E-value: 2.21e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528467758  275 FLLLDHRAPPIIGYMPFEVLGT--SGYDYYHVDDLHSLAKCHEHLMQFGKGKSCYYRFLTKGQQWIWLQTNYYItYHQWN 352
Cdd:pfam08447   1 IIYWSPRFEEILGYTPEELLGKgeSWLDLVHPDDRERVREALWEALKGGEPYSGEYRIRRKDGEYRWVEARARP-IRDEN 79
                          90
                  ....*....|
gi 528467758  353 SRPEFIVCTH 362
Cdd:pfam08447  80 GKPVRVIGVA 89
bHLHzip_scCBP1 cd11398
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Saccharomyces cerevisiae ...
19-81 9.85e-14

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: 67.36  E-value: 9.85e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 528467758  19 DEKDKAKRVSRNKSEKKRRDQFNVLIKELGTMLPGNTRKMDKSTILQKSIDYLRKNKENAAQS 81
Cdd:cd11398    1 EEWHRQRRDNHKEVERRRRENINEGINELAALVPGNAREKNKGAILARAVEYIQELQETEAKN 63
bHLH_PAS cd11391
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain family; bHLH-PAS domain has been found ...
26-75 1.02e-13

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: 66.06  E-value: 1.02e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 528467758  26 RVSRNKSEKKRRDQFNVLIKELGTMLPGN---TRKMDKSTILQKSIDYLRKNK 75
Cdd:cd11391    1 REKSREAAKKRRDKENAEISELASLLPLPpavGSKLDKLSVLRLAVAYLRLKK 53
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
264-362 1.41e-12

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: 64.58  E-value: 1.41e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528467758 264 EFTSRHSLEWKFLLLDHRAPPIIGYMPFEVLGTSGYDYYHVDDLHSLAKCHEHLMQFGKGKSCYYRFLTKGQQWIWLQTN 343
Cdd:cd00130    3 DGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDGSVIWVLVS 82
                         90
                 ....*....|....*....
gi 528467758 344 YYITYHQWNSRPEFIVCTH 362
Cdd:cd00130   83 LTPIRDEGGEVIGLLGVVR 101
HLH smart00353
helix loop helix domain;
30-76 1.47e-10

helix loop helix domain;


Pssm-ID: 197674 [Multi-domain]  Cd Length: 53  Bit Score: 57.23  E-value: 1.47e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 528467758    30 NKSEKKRRDQFNVLIKELGTMLPG--NTRKMDKSTILQKSIDYLRKNKE 76
Cdd:smart00353   1 NARERRRRRKINEAFDELRSLLPTlpKNKKLSKAEILRLAIEYIKSLQE 49
HLH pfam00010
Helix-loop-helix DNA-binding domain;
25-73 2.51e-10

Helix-loop-helix DNA-binding domain;


Pssm-ID: 459628 [Multi-domain]  Cd Length: 53  Bit Score: 56.31  E-value: 2.51e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 528467758   25 KRVSRNKSEKKRRDQFNVLIKELGTMLP--GNTRKMDKSTILQKSIDYLRK 73
Cdd:pfam00010   1 RREAHNERERRRRDRINDAFDELRELLPtlPPDKKLSKAEILRLAIEYIKH 51
bHLHzip_MITF_like cd11397
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in the microphthalmia-associated ...
21-82 5.27e-10

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: 56.15  E-value: 5.27e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 528467758  21 KDKAKRVSRNKSEKKRRDQFNVLIKELGTMLPGNTR---KMDKSTILQKSIDY---LRKNKENAAQSE 82
Cdd:cd11397    1 KDRQKKDNHNMIERRRRFNINDRIKELGTLLPKSNDpdmRWNKGTILKASVDYirkLQKEQERLRQLE 68
bHLH_SF cd00083
basic Helix Loop Helix (bHLH) domain superfamily; bHLH proteins are transcriptional regulators ...
33-72 8.51e-09

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: 51.75  E-value: 8.51e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 528467758  33 EKKRRDQFNVLIKELGTMLPG--NTRKMDKSTILQKSIDYLR 72
Cdd:cd00083    1 ERRRRDKINDAFEELKRLLPElpDSKKLSKASILQKAVEYIR 42
bHLHzip_TFE3 cd18928
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in transcription factor E3 (TFE3) and ...
21-88 4.43e-08

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: 51.20  E-value: 4.43e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 528467758  21 KDKAKRVSRNKSEKKRRDQFNVLIKELGTMLPGNT---RKMDKSTILQKSIDYLRKNKENAAQSESSDIKQ 88
Cdd:cd18928    7 KERQKKDNHNLIERRRRFNINDRIKELGTLIPKSTdpeMRWNKGTILKASVDYIRKLQKEQQRSKEIEMRQ 77
bHLHzip_SREBP cd11394
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in sterol regulatory element-binding ...
25-72 3.21e-07

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in sterol regulatory element-binding protein (SREBP) family; The SREBP family includes SREBP1 and SREBP2, which are bHLHzip transcriptional activator of genes encoding proteins essential for cholesterol biosynthesis/uptake and fatty acid biosynthesis. SREBP1 and SREBP2 are principally found in the liver and in adipocytes and made up of an N-terminal transcription factor portion (composed of an activation domain, a bHLHzip domain, and a nuclear localization signal), a hydrophobic region containing two membrane spanning regions, and a C-terminal regulatory segment. They recognize a symmetric sterol regulatory element (TCACNCCAC) instead of E-box.


Pssm-ID: 381400 [Multi-domain]  Cd Length: 73  Bit Score: 48.42  E-value: 3.21e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 528467758  25 KRVSRNKSEKKRRDQFNVLIKELGTMLPGNTRKMDKSTILQKSIDYLR 72
Cdd:cd11394    6 KRSAHNAIEKRYRSSINDRIIELKDLVVGPDAKMNKSAVLRKAIDYIR 53
bHLHzip_MLXIP_like cd11405
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in MLX-interacting protein (MLXIP), ...
25-88 1.01e-06

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in MLX-interacting protein (MLXIP), MLX-interacting protein-like (MLXIPL) and similar proteins; The family includes MLXIP and MLXIPL. MLXIP, also termed Class E basic helix-loop-helix protein 36 (bHLHe36), or transcriptional activator MondoA, is a bHLHZip transcriptional activator that binds DNA as a heterodimer with Mlx. It binds to the canonical E box sequence 5'-CACGTG-3' and plays a role in transcriptional activation of glycolytic target genes. MLXIP is most highly expressed in skeletal muscle and functions as an indirect glucose sensor, by sensing glucose 6-phosphate and shuttling between the nucleus and the cytoplasm. MLXIPL, also termed carbohydrate-responsive element-binding protein (ChREBP), or Class D basic helix-loop-helix protein 14 (bHLHd14), or MLX interactor, or WS basic-helix-loop-helix leucine zipper protein (WS-bHLH), or Williams-Beuren syndrome chromosomal region 14 protein (WBSCR14), is a bHLHZip transcriptional factor integral to the regulation of glycolysis and lipogenesis in the liver. It forms heterodimers with the bHLHZip protein Mlx to bind the DNA sequence 5'-CACGTG-3'.


Pssm-ID: 381411 [Multi-domain]  Cd Length: 74  Bit Score: 46.88  E-value: 1.01e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528467758  25 KRVSRNKSEKKRRDQFNVLIKELGTMLPGNTR----KMDKSTILQKSIDYLRKNK-ENAAQSESSD-IKQ 88
Cdd:cd11405    3 RRLSHISAEQKRRFNIKSGFDTLQSLIPSLGQnpnqKVSKAAMLQKAAEYIKSLKrERQQMQEEAEqLRQ 72
bHLHzip_SREBP2 cd18922
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in sterol regulatory element-binding ...
21-72 1.78e-06

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in sterol regulatory element-binding protein 2 (SREBP2) and similar proteins; SREBP2, also termed Class D basic helix-loop-helix protein 2 (bHLHd2), or sterol regulatory element-binding transcription factor 2 (SREBF2), is a member of a family of bHLHzip transcription factors that recognize sterol regulatory element 1 (SRE-1). It acts as a transcription activator of cholesterol biosynthesis.


Pssm-ID: 381492 [Multi-domain]  Cd Length: 77  Bit Score: 46.49  E-value: 1.78e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 528467758  21 KDKAKRVSRNKSEKKRRDQFNVLIKELGTMLPGNTRKMDKSTILQKSIDYLR 72
Cdd:cd18922    2 KEGERRTTHNIIEKRYRSSINDKIIELKDLVMGTDAKMHKSGVLRKAIDYIK 53
bHLH-PAS_ARNT_like cd11437
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor ...
25-72 2.39e-06

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: 45.49  E-value: 2.39e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 528467758  25 KRVSRNKSEKKRRDQFNVLIKELGTMLP---GNTRKMDKSTILQKSIDYLR 72
Cdd:cd11437    1 SRSNHSEIEKRRRDKMNAYIQELSALVPacnAMSRKLDKLTVLRMAVQHLK 51
bHLHzip_Mlx_like cd11404
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Max-like protein X (Mlx) family; Mlx, ...
25-76 2.61e-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: 45.75  E-value: 2.61e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 528467758  25 KRVSRNKSEKKRRDQFNVLIKELGTMLPG-NTRKMDKSTILQKSIDYLRKNKE 76
Cdd:cd11404    2 RRLNHVRSEKKRRELIKKGYDELCALVPGlDPQKRTKADILQKAADWIQELKE 54
bHLHzip_SREBP1 cd18921
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in sterol regulatory element-binding ...
25-72 3.58e-06

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in sterol regulatory element-binding protein 1 (SREBP1) and similar proteins; SREBP1, also termed Class D basic helix-loop-helix protein 1 (bHLHd1), or sterol regulatory element-binding transcription factor 1 (SREBF1), is a member of a family of bHLHzip transcription factors that recognize sterol regulatory element 1 (SRE-1). It acts as a transcriptional activator required for lipid homeostasis. It may control transcription of the low-density lipoprotein receptor gene as well as the fatty acid. SREBP1 has dual sequence specificity binding to both an E-box motif (5'-ATCACGTGA-3') and to SRE-1 (5'-ATCACCCCAC-3').


Pssm-ID: 381491  Cd Length: 75  Bit Score: 45.27  E-value: 3.58e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 528467758  25 KRVSRNKSEKKRRDQFNVLIKELGTMLPGNTRKMDKSTILQKSIDYLR 72
Cdd:cd18921    6 KRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIR 53
bHLHzip_MITF cd18926
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in microphthalmia-associated ...
21-88 4.98e-06

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in microphthalmia-associated transcription factor (MITF) and similar proteins; MITF, also termed Class E basic helix-loop-helix protein 32 (bHLHe32), is a bHLHzip transcription factor that is involved in neural crest melanocytes development as well as the pigmented retinal epithelium. It regulates the expression of genes with essential roles in cell differentiation, proliferation and survival. It binds to M-boxes (5'-TCATGTG-3') and symmetrical DNA sequences (E-boxes) (5'-CACGTG-3') found in the promoters of target genes, such as BCL2 and tyrosinase (TYR).


Pssm-ID: 381496  Cd Length: 104  Bit Score: 45.85  E-value: 4.98e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 528467758  21 KDKAKRVSRNKSEKKRRDQFNVLIKELGTMLPGNT---RKMDKSTILQKSIDYLRKNKENAAQSESSDIKQ 88
Cdd:cd18926    9 KERQKKDNHNLIERRRRFNINDRIKELGTLIPKSNdpdMRWNKGTILKASVDYIRKLQREQQRAKELENRQ 79
bHLHzip_USF3 cd18910
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in basic helix-loop-helix ...
20-73 5.34e-06

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in basic helix-loop-helix domain-containing protein USF3 and similar proteins; USF3, also termed upstream transcription factor 3, is a bHLHzip protein that is involved in the negative regulation of epithelial-mesenchymal transition, the process by which epithelial cells lose their polarity and adhesion properties to become mesenchymal cells with enhanced migration and invasive properties.


Pssm-ID: 381480  Cd Length: 65  Bit Score: 44.60  E-value: 5.34e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 528467758  20 EKDKaKRVSRNKSEKKRRDQFNVLIKELGTMLPG-NTRKMDKSTILQKS---IDYLRK 73
Cdd:cd18910    1 RREK-KRESHNEVERRRKDKINAGINKIGELLPDrDAKKQSKNMILEQAykyIVELKK 57
bHLH_AtILR3_like cd11446
basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein IAA-leucine ...
23-89 5.64e-06

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: 45.02  E-value: 5.64e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 528467758  23 KAKRvsrnksEKKRRDQFNVLIKELGTML-PGNTRKMDKSTILQKSIDYL--------RKNKENAA-QSESSDIKQD 89
Cdd:cd11446    1 KACR------EKLRRDKLNERFMELSNVLePGRPPKTDKATILGDAIRMLkqlrgevqKLKEENSSlQEESKELKAE 71
bHLHzip_USF_MITF cd11387
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in USF/MITF family; The USF (upstream ...
28-73 5.71e-06

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in USF/MITF family; The USF (upstream stimulatory factor)/MITF (microphthalmia-associated transcription factor) family includes two bHLHzip transcription factor subfamilies. USFs are ubiquitously expressed and key regulators of a wide number of gene regulation networks, including the stress and immune responses, cell cycle and proliferation, lipid and glucid metabolism. USFs recruit chromatin remodeling enzymes and interact with co-activators and the members of the transcription pre-initiation complex. USFs interact with high affinity to E-box regulatory elements. The MITF (also known as microphthalmia-TFE, or MiT) subfamily 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 subfamily proteins can form homodimers or heterodimers with each other but not with other bHLH or bHLHzip proteins.


Pssm-ID: 381393 [Multi-domain]  Cd Length: 58  Bit Score: 44.17  E-value: 5.71e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 528467758  28 SRNKSEKKRRDQFNVLIKELGTMLP-----GNTRKMDKSTILQKSIDYLRK 73
Cdd:cd11387    1 SHNAVERRRRDNINEKIQELGSLVPpsrleTKDLKPNKGSILSKAVEYIRE 51
bHLH-PAS_ARNTL2_PASD9 cd11469
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor ...
26-75 6.25e-06

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: 44.25  E-value: 6.25e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 528467758  26 RVSRNKSEKKRRDQFNVLIKELGTMLPGNT---RKMDKSTILQKSIDYLRKNK 75
Cdd:cd11469    2 REAHSQTEKRRRDKMNNLIEELSAMIPQCNpmaRKLDKLTVLRMAVQHLKSLK 54
bHLH_AtAIG1_like cd11455
basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein AIG1 and similar ...
22-89 9.97e-06

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: 44.21  E-value: 9.97e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528467758  22 DKAKRVSRNKS--EKKRRDQFNVLIKELGTMLPGNTrKMDKSTILQKSIDYLRKNKENAAQSESSDIKQD 89
Cdd:cd11455    2 DKALAASKSHSeaERRRRERINSHLATLRTLLPNLS-KTDKASLLAEVVQHVKELKRQAAEITTPPDVPT 70
bHLHzip_TFEB cd18927
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in transcription factor EB (TFEB) and ...
21-81 1.04e-05

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: 44.58  E-value: 1.04e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 528467758  21 KDKAKRVSRNKSEKKRRDQFNVLIKELGTMLPgNTRKMD----KSTILQKSIDYLRKNKENAAQS 81
Cdd:cd18927    7 KERQKKDNHNLIERRRRFNINDRIKELGTLIP-KTNDLDvrwnKGTILKASVDYIKRMQKDLQRS 70
bHLH-PAS_ARNTL_PASD3 cd11438
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor ...
19-72 1.06e-05

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor nuclear translocator-like protein 1 (ARNTL) and similar proteins; 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.


Pssm-ID: 381444  Cd Length: 64  Bit Score: 43.94  E-value: 1.06e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 528467758  19 DEKDKAKRVSRNKSEKKRRDQFNVLIKELGTMLP---GNTRKMDKSTILQKSIDYLR 72
Cdd:cd11438    1 QGRIKNAREAHSQIEKRRRDKMNSFIDELASLVPtcnAMSRKLDKLTVLRMAVQHMK 57
bHLH-PAS_cycle_like cd19726
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Drosophila melanogaster protein ...
25-72 1.58e-05

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Drosophila melanogaster protein cycle and similar proteins; 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: 381569  Cd Length: 62  Bit Score: 43.24  E-value: 1.58e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 528467758  25 KRVSRNKSEKKRRDQFNVLIKELGTMLP---GNTRKMDKSTILQKSIDYLR 72
Cdd:cd19726    1 RRQNHSEIEKRRRDKMNTYITELSSMIPmcnAMSRKLDKLTVLRMAVQHMK 51
bHLH_AtbHLH_like cd11393
basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana genes coding transcription ...
32-72 1.75e-05

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana genes coding transcription factors and similar proteins; bHLH proteins are the second largest class of plant transcription factors that regulate transcription of genes that are involve in many essential physiological and developmental process. bHLH proteins are transcriptional regulators that are found in organisms from yeast to humans. The Arabidopsis bHLH proteins that have been characterized so far have roles in regulation of fruit dehiscence, cell development (carpel, anther and epidermal), phytochrome signaling, flavonoid biosynthesis, hormone signaling and stress responses.


Pssm-ID: 381399 [Multi-domain]  Cd Length: 53  Bit Score: 42.55  E-value: 1.75e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 528467758  32 SEKKRRDQFNVLIKELGTMLPgNTRKMDKSTILQKSIDYLR 72
Cdd:cd11393    4 AERKRREKINERIRALRSLVP-NGGKTDKASILDEAIEYIK 43
PAC smart00086
Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); PAC motif ...
325-366 1.90e-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: 42.17  E-value: 1.90e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 528467758   325 SCYYRFLTKGQQWIWLQTNYYITYHqWNSRPEFIVCTHTVVS 366
Cdd:smart00086   1 TVEYRLRRKDGSYIWVLVSASPIRD-EDGEVEGILGVVRDIT 41
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
99-160 2.05e-05

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: 43.16  E-value: 2.05e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 528467758    99 EFSQLMLEALDGFFLVMLTDGYIIYISESVTSLLEHLPSDLMDQNLLNFLPVVDHGEVYKAL 160
Cdd:smart00091   1 ERLRAILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEAL 62
bHLH_SOHLH_like cd19683
basic helix-loop-helix (bHLH) domain found in the spermatogenesis- and oogenesis-specific ...
25-71 6.11e-05

basic helix-loop-helix (bHLH) domain found in the spermatogenesis- and oogenesis-specific basic helix-loop-helix-containing protein (SOHLH) family and similar proteins; The SOHLH family includes two bHLH transcription factors, SOHLH1 and SOHLH2. They are specifically in spermatogonia and oocytes and essential for early spermatogonial and oocyte differentiation. The family also includes transcription factor-like 5 protein (TCFL5) and similar proteins. TCFL5, also termed Cha transcription factor, or HPV-16 E2-binding protein 1 (E2BP-1), is a bHLH transcription factor that plays a crucial role in spermatogenesis. It regulates cell proliferation or differentiation of cells through binding to a specific DNA sequence like other bHLH molecules.


Pssm-ID: 381526  Cd Length: 58  Bit Score: 41.57  E-value: 6.11e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 528467758  25 KRVSRNKSEKKRRDQFNVLIKELGTMLPGNTRKMDKSTILQKSIDYL 71
Cdd:cd19683    2 SRERHNAKERQRRERIKIACDQLRKLVPGCSRKTDKATVFEFTVAYI 48
bHLH-O_HERP cd11407
basic helix-loop-helix-orange (bHLH-O) domain found in hairy and enhancer of split (HES) ...
25-72 6.24e-05

basic helix-loop-helix-orange (bHLH-O) domain found in hairy and enhancer of split (HES)-related repressor protein (HERP) family; HERP (also called Hey/Hesr/HRT/CHF/gridlock) proteins corresponds to a family of bHLH-O transcriptional repressors that are related to the Drosophila hairy and Enhancer-of-split proteins and act as downstream effectors of Notch signaling. 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 are involved in cardiovascular development and have roles in somitogenesis, myogenesis and gliogenesis.


Pssm-ID: 381413 [Multi-domain]  Cd Length: 59  Bit Score: 41.26  E-value: 6.24e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 528467758  25 KRVSRNKSEKKRRDQFNVLIKELGTMLPG-----NTRKMDKSTILQKSIDYLR 72
Cdd:cd11407    1 RKKRRGIIEKRRRDRINNSLAELRRLVPTafekqGSAKLEKAEILQMTVDHLK 53
bHLH-O_HELT cd11408
basic helix-loop-helix-orange (bHLH-O) domain found in hairy and enhancer of split-related ...
33-72 9.00e-05

basic helix-loop-helix-orange (bHLH-O) domain found in hairy and enhancer of split-related protein HELT and similar proteins; HELT, also termed HES/HEY-like transcription factor, is a bHLH-O 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. HELT could homodimerize and heterodimerize with other bHLH-O protein such as HES-5 or HEY-2 and bound to E box to repress gene transcription.


Pssm-ID: 381414 [Multi-domain]  Cd Length: 56  Bit Score: 40.74  E-value: 9.00e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 528467758  33 EKKRRDQFNVLIKELGTMLPG-----NTRKMDKSTILQKSIDYLR 72
Cdd:cd11408    6 EKRRRDRINRCLNELGKTVPMalakqTSGKLEKAEILEMTVQYLR 50
bHLH_ScINO2_like cd11388
basic helix-loop-helix (bHLH) domain found in Saccharomyces cerevisiae protein INO2 and ...
23-83 9.96e-05

basic helix-loop-helix (bHLH) domain found in Saccharomyces cerevisiae protein INO2 and similar proteins; INO2 is a positive regulatory factor required for depression of the co-regulated phospholipid biosynthetic enzymes in Saccharomyces cerevisiae. It is also involved in the expression of ITR1.


Pssm-ID: 381394  Cd Length: 68  Bit Score: 41.18  E-value: 9.96e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 528467758  23 KAKRVSRNKSEKKRRDQ----FNVLIKELGTMLPGNTRKMDKSTILQKSIDYLRKNKENAAQSES 83
Cdd:cd11388    1 PVKKWKHVEAEKKRRNQikkgFEDLINLINYPRNNNEKRISKSELLNKAVDDIRGLLKANEQLQE 65
bHLHzip_MGA_like cd19682
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in MAX gene-associated protein (MGA) ...
26-73 1.02e-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: 41.11  E-value: 1.02e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 528467758  26 RVSRNKSEKKRRDQFNVLIKELGTMLPGNTR-KMDKSTILQKS---IDYLRK 73
Cdd:cd19682    1 RLRHKKRERERRSELRELFDKLKQLLGLDSDeKASKLAVLTEAieeIQQLKR 52
bHLHzip_TFEC cd18925
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in transcription factor EC (TFEC) and ...
21-87 1.16e-04

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in transcription factor EC (TFEC) and similar proteins; TFEC, also termed Class E basic helix-loop-helix protein 34 (bHLHe34), or transcription factor EC-like (TFEC-L), is a bHLHzip transcriptional regulator that acts as a repressor or an activator and regulates gene expression in macrophages. It plays an important role in the niche to expand hematopoietic progenitors through the modulation of several cytokines.


Pssm-ID: 381495  Cd Length: 85  Bit Score: 41.60  E-value: 1.16e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 528467758  21 KDKAKRVSRNKSEKKRRDQFNVLIKELGTMLPGNT---RKMDKSTILQKSIDY---LRKNKENAAQSESSDIK 87
Cdd:cd18925    1 KERQKKDNHNLIERRRRYNINYRIKELGTLIPKSNdpdMRWNKGTILKASVEYikwLQKEQQRARELEHRQKK 73
bHLHzip_USF cd11396
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in upstream stimulatory factors, USF1, ...
30-73 1.31e-04

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in upstream stimulatory factors, USF1, USF2 and similar proteins; Upstream stimulatory factor 1 and 2 (USF-1 and USF-2) are members of bHLHzip transcription factor family. USFs are ubiquitously expressed and key regulators of a wide number of gene regulation networks, including the stress and immune responses, cell cycle and proliferation, lipid and glucid metabolism. USFs recruit chromatin remodeling enzymes and interact with co-activators and the members of the transcription pre-initiation complex. USFs interact with high affinity to E-box regulatory elements.


Pssm-ID: 381402  Cd Length: 58  Bit Score: 40.36  E-value: 1.31e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 528467758  30 NKSEKKRRDQFNVLIKELGTMLPGN-----TRKMDKSTILQKSIDYLRK 73
Cdd:cd11396    3 NEVERRRRDKINNWIVKLAKIVPDCekdnsKQGQSKGGILSKACDYIQE 51
bHLH-PAS_ARNT cd18947
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor ...
21-82 1.43e-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: 40.55  E-value: 1.43e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 528467758  21 KDKAKRVSRNKSEKKRRDQFNVLIKELGTMLP---GNTRKMDKSTILQKSIDYLRKNKENAAQSE 82
Cdd:cd18947    1 KERFARENHSEIERRRRNKMTAYITELSDMVPtcsALARKPDKLTILRMAVSHMKSLRGTGNTST 65
bHLH-O_HERP_like cd11389
basic helix-loop-helix-orange (bHLH-O) domain found in hairy and enhancer of split (HES) ...
33-73 2.92e-04

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: 39.23  E-value: 2.92e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 528467758  33 EKKRRDQFNVLIKELGTMLP-----GNTRKMDKSTILQKSIDYLRK 73
Cdd:cd11389    5 EKRRRDRINESLAELRRLVPearksKGSGKLEKAEILEMTLQHLKA 50
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
108-163 3.02e-04

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: 40.69  E-value: 3.02e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 528467758 108 LDGFFLVMLTDGYIIYISESVTSLLEHLPSDLMDQNLLNFLPVVDHGEVYKALSSQ 163
Cdd:cd00130    1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENL 56
bHLH_AtPIF_like cd11445
basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana phytochrome interacting ...
30-73 3.25e-04

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana phytochrome interacting factors (PIFs) and similar proteins; The family includes several bHLH transcription factors from Arabidopsis thaliana, such as PIFs, ALC, PIL1, SPATULA, and UNE10. PIFs (PIF1, PIF3, PIF4, PIF5, PIF6 and PIF7) have been shown to control light-regulated gene expression. They directly bind to the photoactivated phytochromes and are degraded in response to light signals. ALC, also termed AtbHLH73, or protein ALCATRAZ, or EN 98, is required for the dehiscence of fruit, especially for the separation of the valve cells from the replum. It promotes the differentiation of a strip of labile non-lignified cells sandwiched between layers of lignified cells. PIL1, also termed AtbHLH124, or protein phytochrome interacting factor 3-like 1, or EN 110, is involved in responses to transient and long-term shade. It is required for the light-mediated inhibition of hypocotyl elongation and necessary for rapid light-induced expression of the photomorphogenesis- and circadian-related gene APRR9. PIL1 seems to play a role in multiple PHYB responses, such as flowering transition and petiole elongation. SPATULA, also termed AtbHLH24, or EN 99, plays a role in floral organogenesis. It promotes the growth of carpel margins and of pollen tract tissues derived from them. UNE10, also termed AtbHLH16, or protein UNFERTILIZED EMBRYO SAC 10, or EN 99, is required during the fertilization of ovules by pollen.


Pssm-ID: 381451  Cd Length: 64  Bit Score: 39.66  E-value: 3.25e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 528467758  30 NKSEKKRRDQFNVLIKELGTMLPgNTRKMDKSTILQKSIDYLRK 73
Cdd:cd11445    7 NLSERRRRDRINEKMKALQELIP-NCNKTDKASMLDEAIEYLKS 49
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
102-160 4.02e-04

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: 40.86  E-value: 4.02e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 528467758  102 QLMLEALDGFFLVMLTDGYIIYISESVTSLLEHLPSDLMDQNLLNFLPVVDHGEVYKAL 160
Cdd:pfam00989   4 RAILESLPDGIFVVDEDGRILYVNAAAEELLGLSREEVIGKSLLDLIPEEDDAEVAELL 62
bHLH_AtMYC1_like cd18918
basic Helix-Loop-Helix (bHLH) domain found in Arabidopsis thaliana MYC1 and similar proteins; ...
30-73 4.59e-04

basic Helix-Loop-Helix (bHLH) domain found in Arabidopsis thaliana MYC1 and similar proteins; MYC1, also termed AtbHLH12, or EN 58, acts as a transcription activator, when associated with MYB75/PAP1 or MYB90/PAP2.


Pssm-ID: 381488 [Multi-domain]  Cd Length: 70  Bit Score: 39.24  E-value: 4.59e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 528467758  30 NKSEKKRRDQFNVLIKELGTMLPgNTRKMDKSTILQKSIDYLRK 73
Cdd:cd18918    2 FATERERREKLNEKFSDLRNLIP-NPTKNDRASILSDAIKYINE 44
bHLH-O_HERP_HES cd19685
basic helix-loop-helix-orange (bHLH-O) domain found in HERP/HES-like family; The HERP/HES-like ...
32-72 5.44e-04

basic helix-loop-helix-orange (bHLH-O) domain found in HERP/HES-like family; The HERP/HES-like family includes bHLH-O transcriptional regulators that are related to the Drosophila hairy and Enhancer-of-split (HES) proteins. The HERP (HES-related repressor protein) subfamily proteins 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. Hairy and enhancer of split (HES)-related repressor protein (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 subfamily. It is involved in the regulation of Drosophila circadian rhythms. It functions as both an activator and a repressor of clock gene expression. The HES subfamily proteins 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. They 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: 381528 [Multi-domain]  Cd Length: 52  Bit Score: 38.56  E-value: 5.44e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 528467758  32 SEKKRRDQFNVLIKELGTMLPGN-----TRKMDKSTILQKSIDYLR 72
Cdd:cd19685    1 SEKRRRQRINDKLNQLKELLPPNlskqsRSKLSKAEILEMAITELR 46
bHLH-O_HES7 cd11462
basic helix-loop-helix-orange (bHLH-O) domain found in hairy and enhancer of split 7 (HES-7) ...
33-75 9.32e-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: 38.09  E-value: 9.32e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 528467758  33 EKKRRDQFNVLIKELGTMLPGNTR-------KMDKSTILQKSIDYLRKNK 75
Cdd:cd11462    9 EKRRRDRINRSLEELRVLLLQNTQdeklknpKVEKAEILELTVQFLRNSS 58
bHLH-O_HEYL cd11447
basic helix-loop-helix-orange (bHLH-O) domain found in hairy/enhancer-of-split related with ...
23-72 1.19e-03

basic helix-loop-helix-orange (bHLH-O) domain found in hairy/enhancer-of-split related with YRPW motif-like protein (HEYL) and similar proteins; HEYL, also termed Class B basic helix-loop-helix protein 33 (bHLHb33), or hairy-related transcription factor 3 (HRT-3), is a bHLH-O transcriptional repressor that is strongly expressed in the presomitic mesoderm, the somites, the peripheral nervous system and smooth muscle of all arteries and is a downstream effector of the Notch and transforming growth factor-beta pathways. It promotes neuronal differentiation by activating proneural genes and inhibiting other hairy and enhancer of split (HES) and hairy/enhancer-of-split related with YRPW motif protein (HEY) proteins. HEYL also functions as a tumor suppressor involved in the progression of human cancers.


Pssm-ID: 381453 [Multi-domain]  Cd Length: 74  Bit Score: 38.15  E-value: 1.19e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 528467758  23 KAKRVSRNKSEKKRRDQFNVLIKELGTMLPG-----NTRKMDKSTILQKSIDYLR 72
Cdd:cd11447    7 QARKKRRGIIEKRRRDRINSSLSELRRLVPTafekqGSSKLEKAEILQMTVDHLK 61
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
264-319 1.79e-03

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: 37.38  E-value: 1.79e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 528467758   264 EFTSRHSLEWKFLLLDHRAPPIIGYMPFEVLGTSGYDYYHVDDLHSLAKCHEHLMQ 319
Cdd:smart00091  12 DGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEALQRLLS 67
bHLH_AtTT8_like cd11451
basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein transparent testa 8 ...
32-92 1.99e-03

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein transparent testa 8 (TT8) and similar proteins; The family includes several bHLH transcription factors from Arabidopsis thaliana, such as TT8, EGL1, and GL3. TT8, also termed AtbHLH42, or EN 32, is involved in the control of flavonoid pigmentation and plays a key role in regulating leucoanthocyanidin reductase (BANYULS) and dihydroflavonol-4-reductase (DFR). EGL1, also termed AtbHLH2, or EN 30, or AtMYC146, or protein enhancer of GLABRA 3, is involved in epidermal cell fate specification and regulates negatively stomata formation but promotes trichome formation. GL3, also termed AtbHLH1, or AtMYC6, or protein shapeshifter, or EN 31, is involved in epidermal cell fate specification. It regulates negatively stomata formation, but, in association with TTG1 and MYB0/GL1, promotes trichome formation, branching and endoreplication.


Pssm-ID: 381457  Cd Length: 75  Bit Score: 37.79  E-value: 1.99e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 528467758  32 SEKKRRDQFNVLIKELGTMLPGNTrKMDKSTILQKSIDYLRKNKENAAQSESSDIKQDWKP 92
Cdd:cd11451    9 AERRRREKLNERFITLRSMVPFVT-KMDKVSILGDAIEYLKQLQRRVEELESRRKSSDTET 68
bHLH-PAS_SRC cd11439
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in steroid receptor coactivator ...
33-77 2.46e-03

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: 37.02  E-value: 2.46e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 528467758  33 EKKRRDQFNVLIKELGTMLPGN-------TRKMDKSTILQKSIDYLRKNKEN 77
Cdd:cd11439    6 EKRRREQENKYIEELAELISASisdmdslSVKPDKCAILQETVKQIRQIKEQ 57
bHLH_AtFIT_like cd11450
basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana Fe-deficiency induced ...
28-98 3.64e-03

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana Fe-deficiency induced transcription factor 1 (FIT) and similar proteins; The family includes bHLH transcription factors from Arabidopsis thaliana, such as FIT and DYT1. FIT, also termed FER-like iron deficiency-induced transcription factor, or FER-like regulator of iron uptake, or AtbHLH29, or EN 43, is a bHLH transcription factor that is required for the iron deficiency response in plant. It regulates FRO2 at the level of mRNA accumulation and IRT1 at the level of protein accumulation. DYT1, also termed AtbHLH22, or protein dysfunctional tapetum 1, or EN 49, is a bHLH transcription factor involved in the control of tapetum development. It is required for male fertility and pollen differentiation, especially during callose deposition.


Pssm-ID: 381456 [Multi-domain]  Cd Length: 76  Bit Score: 37.12  E-value: 3.64e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 528467758  28 SRN-KSEKKRRDQFNVLIKELGTMLPgNTRKMDKSTILQKSIDYLRKNKENAAQSESSDIKQDWKPPFLSNE 98
Cdd:cd11450    5 SKNlVSERNRRQKLNQRLFALRSVVP-NITKMDKASIIKDAISYIQELQYQEKKLEAEIRELESRPPSTLSF 75
bHLHzip_spESC1_like cd19690
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Schizosaccharomyces pombe ESC1 (spESC1) ...
26-83 3.93e-03

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Schizosaccharomyces pombe ESC1 (spESC1) and similar proteins; 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: 381533  Cd Length: 65  Bit Score: 36.67  E-value: 3.93e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 528467758  26 RVSRNKSEKKRRDQFNVLIKELGTMLPGN-TRKMDKSTILQKSIDYLRKNKENAAQSES 83
Cdd:cd19690    1 RVSHKLAERKRRKEMKELFEDLRDALPQErGTKASKWEILTKAISYIQQLKRHIRELRS 59
bHLH_SOHLH1_2 cd18908
basic helix-loop-helix (bHLH) domain found in the spermatogenesis- and oogenesis-specific ...
28-77 4.30e-03

basic helix-loop-helix (bHLH) domain found in the spermatogenesis- and oogenesis-specific basic helix-loop-helix-containing protein (SOHLH) family; The SOHLH family includes two bHLH transcription factors, SOHLH1 and SOHLH2. They are specifically in spermatogonia and oocytes and essential for early spermatogonial and oocyte differentiation.


Pssm-ID: 381478 [Multi-domain]  Cd Length: 59  Bit Score: 36.16  E-value: 4.30e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 528467758  28 SRNKSEKKRRDQFNVLIKELGTMLPG-NTRKMDKSTILQKSIDYLRKNKEN 77
Cdd:cd18908    5 SHSLKERLRRERIKSSCDQLRDLLPYiKGRKLDMASVLEMTVKYIRYIQER 55
bHLH-O_HEY1 cd19748
basic helix-loop-helix-orange (bHLH-O) domain found in hairy/enhancer-of-split related with ...
24-72 5.08e-03

basic helix-loop-helix-orange (bHLH-O) domain found in hairy/enhancer-of-split related with YRPW motif protein 1 (HEY1) and similar proteins; HEY1, also termed cardiovascular helix-loop-helix factor 2 (CHF-2), or Class B basic helix-loop-helix protein 31 (bHLHb31), or HES-related repressor protein 1, or hairy and enhancer of split-related protein 1 (HESR-1), or hairy-related transcription factor 1 (HRT-1), is a bHLH-O transcriptional repressor that acts as an essential downstream effector of the Notch signaling pathway and may play a fundamental role in vascular development. HEY1 also participates several cancer-related pathways. It acts as a positive regulator of the tumor suppressor p53.


Pssm-ID: 381591 [Multi-domain]  Cd Length: 71  Bit Score: 36.47  E-value: 5.08e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 528467758  24 AKRVSRNKSEKKRRDQFNVLIKELGTMLPG-----NTRKMDKSTILQKSIDYLR 72
Cdd:cd19748    8 ARKRRRGIIEKRRRDRINNSLSELRRLVPSafekqGSAKLEKAEILQMTVDHLK 61
bHLHzip_Mlx cd19687
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Max-like protein X (Mlx) and similar ...
25-71 7.17e-03

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Max-like protein X (Mlx) and similar proteins; 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.


Pssm-ID: 381530 [Multi-domain]  Cd Length: 76  Bit Score: 36.24  E-value: 7.17e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 528467758  25 KRVSRNKSEKKRRDQFNVLIKELGTMLP-------GNTRKMDKSTILQKSIDYL 71
Cdd:cd19687    2 RREAHTQAEQKRRDAIKKGYDDLQDIVPtcqqqddIGSQKLSKATILQRSIDYI 55
bHLHzip_Max cd11406
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in protein Max and similar proteins; Max, ...
25-87 7.73e-03

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in protein Max and similar proteins; Max, also termed Class D basic helix-loop-helix protein 4 (bHLHd4), or Myc-associated factor X, is a bHLHZip transcription regulator that forms a sequence-specific DNA-binding protein complex with MYC or MAD which recognizes the core sequence 5'-CAC[GA]TG-3'. The MYC:MAX complex is a transcriptional activator, whereas the MAD:MAX complex is a transcriptional repressor. Max homodimer bind DNA but is transcriptionally inactive. Targeted deletion of max results in early embryonic lethality in mice.


Pssm-ID: 381412  Cd Length: 69  Bit Score: 35.79  E-value: 7.73e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528467758  25 KRVSRNKSEKKRRDQfnvlIKELGTML----PG-NTRKMDKSTILQKSIDYLR--KNKENAAQSESSDIK 87
Cdd:cd11406    1 KRAHHNALERKRRDH----IKDSFHSLrdsvPSlQGEKASRAQILKKATEYIQymRRKNHTHQQDIDDLK 66
bHLHzip_SREBP_like cd11395
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in sterol regulatory element-binding ...
25-89 7.73e-03

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in sterol regulatory element-binding protein (SREBP) family and similar proteins; The SREBP family includes SREBP1 and SREBP2, which are bHLHzip transcriptional activator of genes encoding proteins essential for cholesterol biosynthesis/uptake and fatty acid biosynthesis. SREBP1 and SREBP2 are principally found in the liver and in adipocytes and made up of an N-terminal transcription factor portion (composed of an activation domain, a bHLHzip domain, and a nuclear localization signal), a hydrophobic region containing two membrane spanning regions, and a C-terminal regulatory segment. They recognize a symmetric sterol regulatory element (TCACNCCAC) instead of E-box. The family also includes Saccharomyces cerevisiae transcription factor HMS1 (also termed high-copy MEP suppressor protein 1) and serine-rich protein TYE7. HMS1 is a putative bHLHzip transcription factor involved in exit from mitosis and pseudohyphal differentiation. TYE7, also termed basic-helix-loop-helix protein SGC1, is a putative bHLHzip transcription activator required for Ty1-mediated glycolytic gene expression. TYE7 N-terminal is extremely rich in serine residues. It binds DNA on E-box motifs, 5'-CANNTG-3'. TYE7 is not essential for growth.


Pssm-ID: 381401 [Multi-domain]  Cd Length: 87  Bit Score: 36.16  E-value: 7.73e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528467758  25 KRVSRNKSEKKRRDQFNVLIKELGTMLP-----------------GNTRKMDKSTILQKSIDYLR--KNKENAAQSESSD 85
Cdd:cd11395    3 KRLPHNAIEKRYRSNLNTKIERLRDAIPslrspegksddgglgglAPTTKLSKATILTKAIEYIRhlEQENERLEEENEE 82

                 ....
gi 528467758  86 IKQD 89
Cdd:cd11395   83 LRQQ 86
bHLH_AtMEE8_like cd19698
basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein maternal effect ...
29-94 8.64e-03

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein maternal effect embryo arrest 8 (AtMEE8) and similar proteins; AtMEE8, also termed AtbHLH108, or EN 132, is a bHLH transcription factor required during early embryo development, for the endosperm formation.


Pssm-ID: 381541  Cd Length: 71  Bit Score: 35.88  E-value: 8.64e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 528467758  29 RNKSEKKRRDQFNVLIKELGTMLPGNTRKMDKSTILQKSIDYLrKNKENAAQSESSDIKQDW--KPPF 94
Cdd:cd19698    1 HNLLEKKRRERIKDKIEILKGLTPNCTPKSDIASILSCVIDYI-KSLLLQVEKLSMGICDDWrlFTPF 67
 
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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