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Conserved domains on  [gi|1198817746|ref|NP_001338741|]
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basic helix-loop-helix ARNT-like protein 1 isoform i [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
bHLH-PAS_ARNTL_PASD3 cd11438
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor ...
50-113 3.30e-42

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: 146.02  E-value: 3.30e-42
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1198817746  50 QGRIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGATN 113
Cdd:cd11438     1 QGRIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGATN 64
PAS_11 super family cl37882
PAS domain; This family includes the PAS-B domain of NCOA1 (Nuclear receptor coactivator 1), ...
322-424 3.60e-26

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: 434060 [Multi-domain]  Cd Length: 110  Bit Score: 103.14  E-value: 3.60e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1198817746 322 EYVSRHAIDGKFVFVDQRATAILAYLPQELLGTSCYEYFHQDDIGHLAECHRQVLQTREKITTNCYKFKIKDGSFITLRS 401
Cdd:pfam14598   3 QFTTRLDIDGKIISCDTRAPFSLGLEKDELVGRSIYDLCHPQDLRTAKSHLREVIQSNGQATELSYRLRLRDGDFVSVHT 82
                          90       100
                  ....*....|....*....|...
gi 1198817746 402 RWFSFMNPWTKEVEYIVSTNTVV 424
Cdd:pfam14598  83 KSKLFLNQNSNQQPFIMCTHTIL 105
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
132-191 7.70e-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.


:

Pssm-ID: 214512  Cd Length: 67  Bit Score: 60.88  E-value: 7.70e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1198817746  132 HLILRAADGFLFVVGCDrGKILFVSESVFKILNYSQNDLIGQSLFDYLHPKDIAKVKEQL 191
Cdd:smart00091   4 RAILESLPDGIFVLDLD-GRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEAL 62
 
Name Accession Description Interval E-value
bHLH-PAS_ARNTL_PASD3 cd11438
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor ...
50-113 3.30e-42

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: 146.02  E-value: 3.30e-42
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1198817746  50 QGRIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGATN 113
Cdd:cd11438     1 QGRIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGATN 64
PAS_11 pfam14598
PAS domain; This family includes the PAS-B domain of NCOA1 (Nuclear receptor coactivator 1), ...
322-424 3.60e-26

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: 434060 [Multi-domain]  Cd Length: 110  Bit Score: 103.14  E-value: 3.60e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1198817746 322 EYVSRHAIDGKFVFVDQRATAILAYLPQELLGTSCYEYFHQDDIGHLAECHRQVLQTREKITTNCYKFKIKDGSFITLRS 401
Cdd:pfam14598   3 QFTTRLDIDGKIISCDTRAPFSLGLEKDELVGRSIYDLCHPQDLRTAKSHLREVIQSNGQATELSYRLRLRDGDFVSVHT 82
                          90       100
                  ....*....|....*....|...
gi 1198817746 402 RWFSFMNPWTKEVEYIVSTNTVV 424
Cdd:pfam14598  83 KSKLFLNQNSNQQPFIMCTHTIL 105
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
324-419 4.17e-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: 74.21  E-value: 4.17e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1198817746 324 VSRHAIDGKFVFVDQRATAILAYLPQELLGTSCYEYFHQDDIGHLAECHRQVLQTREKITTnCYKFKIKDGSFITLRSRW 403
Cdd:cd00130     5 VIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTL-EVRLRRKDGSVIWVLVSL 83
                          90
                  ....*....|....*.
gi 1198817746 404 FSFMNPWTKEVEYIVS 419
Cdd:cd00130    84 TPIRDEGGEVIGLLGV 99
HLH pfam00010
Helix-loop-helix DNA-binding domain;
57-109 8.25e-16

Helix-loop-helix DNA-binding domain;


Pssm-ID: 425419 [Multi-domain]  Cd Length: 53  Bit Score: 71.72  E-value: 8.25e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1198817746  57 REAHSQIEKRRRDKMNSFIDELASLVPTcNAMSRKLDKLTVLRMAVQHMKTLR 109
Cdd:pfam00010   2 RAAHNERERRRRDRINDAFDELRELLPT-LPPDKKLSKAEILRLAIEYIKHLQ 53
HLH smart00353
helix loop helix domain;
63-109 2.83e-14

helix loop helix domain;


Pssm-ID: 197674 [Multi-domain]  Cd Length: 53  Bit Score: 67.24  E-value: 2.83e-14
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1198817746   63 IEKRRRDKMNSFIDELASLVPTCNaMSRKLDKLTVLRMAVQHMKTLR 109
Cdd:smart00353   3 RERRRRRKINEAFDELRSLLPTLP-KNKKLSKAEILRLAIEYIKSLQ 48
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
132-191 7.70e-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.


Pssm-ID: 214512  Cd Length: 67  Bit Score: 60.88  E-value: 7.70e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1198817746  132 HLILRAADGFLFVVGCDrGKILFVSESVFKILNYSQNDLIGQSLFDYLHPKDIAKVKEQL 191
Cdd:smart00091   4 RAILESLPDGIFVLDLD-GRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEAL 62
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
129-236 1.30e-11

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: 395786 [Multi-domain]  Cd Length: 113  Bit Score: 61.66  E-value: 1.30e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1198817746 129 ELKHLILRAADGFLFVVGcDRGKILFVSESVFKILNYSQNDLIGQSLFDYLHPKDIAKVKEQLSS--SDTAPR---ERLI 203
Cdd:pfam00989   1 EDLRAILESLPDGIFVVD-EDGRILYVNAAAEELLGLSREEVIGKSLLDLIPEEDDAEVAELLRQalLQGEESrgfEVSF 79
                          90       100       110
                  ....*....|....*....|....*....|...
gi 1198817746 204 DAKTGLPVKTDITPGPSRLCSGARRSFFCRMKC 236
Cdd:pfam00989  80 RVPDGRPRHVEVRASPVRDAGGEILGFLGVLRD 112
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
138-217 1.84e-11

PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. 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: 60.72  E-value: 1.84e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1198817746 138 ADGFLFVVgCDRGKILFVSESVFKILNYSQNDLIGQSLFDYLHPKDIAKVKEQLSSSDTA----PRERLIDAKTG--LPV 211
Cdd:cd00130     1 LPDGVIVL-DLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGgepvTLEVRLRRKDGsvIWV 79

                  ....*.
gi 1198817746 212 KTDITP 217
Cdd:cd00130    80 LVSLTP 85
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
324-377 1.13e-09

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: 54.71  E-value: 1.13e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1198817746  324 VSRHAIDGKFVFVDQRATAILAYLPQELLGTSCYEYFHQDDIGHLAECHRQVLQ 377
Cdd:smart00091  14 IFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEALQRLLS 67
sensory_box TIGR00229
PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain ...
330-420 4.10e-06

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


Pssm-ID: 272971 [Multi-domain]  Cd Length: 124  Bit Score: 46.13  E-value: 4.10e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1198817746 330 DGKFVFVDQRATAILAYLPQELLGTSCYEYFHQDDIGHLAECHRQVLQTREKITTNCYKFKIKDGSFITLrsRWFSFMNP 409
Cdd:TIGR00229  22 EGNILYVNPAFEEIFGYSAEELIGRNVLELIPEEDREEVRERIERRLEGEPEPVSEERRVRRKDGSEIWV--EVSVSPIR 99
                          90
                  ....*....|.
gi 1198817746 410 WTKEVEYIVST 420
Cdd:TIGR00229 100 TNGGELGVVGI 110
sensory_box TIGR00229
PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain ...
133-192 4.29e-05

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


Pssm-ID: 272971 [Multi-domain]  Cd Length: 124  Bit Score: 43.43  E-value: 4.29e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1198817746 133 LILRAADGFLFVVGcDRGKILFVSESVFKILNYSQNDLIGQSLFDYLHPKDIAKVKEQLS 192
Cdd:TIGR00229   7 AIFESSPDAIIVID-LEGNILYVNPAFEEIFGYSAEELIGRNVLELIPEEDREEVRERIE 65
 
Name Accession Description Interval E-value
bHLH-PAS_ARNTL_PASD3 cd11438
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor ...
50-113 3.30e-42

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: 146.02  E-value: 3.30e-42
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1198817746  50 QGRIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGATN 113
Cdd:cd11438     1 QGRIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGATN 64
bHLH-PAS_cycle_like cd19726
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Drosophila melanogaster protein ...
57-117 1.34e-35

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: 127.60  E-value: 1.34e-35
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1198817746  57 REAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGATNPYTE 117
Cdd:cd19726     2 RQNHSEIEKRRRDKMNTYITELSSMIPMCNAMSRKLDKLTVLRMAVQHMKTLRGSLTSYTE 62
bHLH-PAS_ARNT_like cd11437
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor ...
56-113 3.01e-34

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: 123.69  E-value: 3.01e-34
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1198817746  56 AREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGATN 113
Cdd:cd11437     1 SRSNHSEIEKRRRDKMNAYIQELSALVPACNAMSRKLDKLTVLRMAVQHLKSLRGTGS 58
bHLH-PAS_ARNTL2_PASD9 cd11469
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor ...
57-115 6.23e-30

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: 112.05  E-value: 6.23e-30
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1198817746  57 REAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGATNPY 115
Cdd:cd11469     2 REAHSQTEKRRRDKMNNLIEELSAMIPQCNPMARKLDKLTVLRMAVQHLKSLKGSTSSF 60
bHLH-PAS_ARNT cd18947
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor ...
54-114 5.73e-27

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: 103.72  E-value: 5.73e-27
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1198817746  54 KNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGATNP 114
Cdd:cd18947     3 RFARENHSEIERRRRNKMTAYITELSDMVPTCSALARKPDKLTILRMAVSHMKSLRGTGNT 63
PAS_11 pfam14598
PAS domain; This family includes the PAS-B domain of NCOA1 (Nuclear receptor coactivator 1), ...
322-424 3.60e-26

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: 434060 [Multi-domain]  Cd Length: 110  Bit Score: 103.14  E-value: 3.60e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1198817746 322 EYVSRHAIDGKFVFVDQRATAILAYLPQELLGTSCYEYFHQDDIGHLAECHRQVLQTREKITTNCYKFKIKDGSFITLRS 401
Cdd:pfam14598   3 QFTTRLDIDGKIISCDTRAPFSLGLEKDELVGRSIYDLCHPQDLRTAKSHLREVIQSNGQATELSYRLRLRDGDFVSVHT 82
                          90       100
                  ....*....|....*....|...
gi 1198817746 402 RWFSFMNPWTKEVEYIVSTNTVV 424
Cdd:pfam14598  83 KSKLFLNQNSNQQPFIMCTHTIL 105
bHLH_PAS cd11391
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain family; bHLH-PAS domain has been found ...
57-111 2.72e-20

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: 84.55  E-value: 2.72e-20
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1198817746  57 REAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGA 111
Cdd:cd11391     1 REKSREAAKKRRDKENAEISELASLLPLPPAVGSKLDKLSVLRLAVAYLRLKKFL 55
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
324-419 4.17e-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: 74.21  E-value: 4.17e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1198817746 324 VSRHAIDGKFVFVDQRATAILAYLPQELLGTSCYEYFHQDDIGHLAECHRQVLQTREKITTnCYKFKIKDGSFITLRSRW 403
Cdd:cd00130     5 VIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTL-EVRLRRKDGSVIWVLVSL 83
                          90
                  ....*....|....*.
gi 1198817746 404 FSFMNPWTKEVEYIVS 419
Cdd:cd00130    84 TPIRDEGGEVIGLLGV 99
HLH pfam00010
Helix-loop-helix DNA-binding domain;
57-109 8.25e-16

Helix-loop-helix DNA-binding domain;


Pssm-ID: 425419 [Multi-domain]  Cd Length: 53  Bit Score: 71.72  E-value: 8.25e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1198817746  57 REAHSQIEKRRRDKMNSFIDELASLVPTcNAMSRKLDKLTVLRMAVQHMKTLR 109
Cdd:pfam00010   2 RAAHNERERRRRDRINDAFDELRELLPT-LPPDKKLSKAEILRLAIEYIKHLQ 53
bHLH-O_HERP_like cd11389
basic helix-loop-helix-orange (bHLH-O) domain found in hairy and enhancer of split (HES) ...
60-112 5.48e-15

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: 69.27  E-value: 5.48e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1198817746  60 HSQIEKRRRDKMNSFIDELASLVPTCNAM--SRKLDKLTVLRMAVQHMKTLRGAT 112
Cdd:cd11389     1 HKVIEKRRRDRINESLAELRRLVPEARKSkgSGKLEKAEILEMTLQHLKALQSST 55
HLH smart00353
helix loop helix domain;
63-109 2.83e-14

helix loop helix domain;


Pssm-ID: 197674 [Multi-domain]  Cd Length: 53  Bit Score: 67.24  E-value: 2.83e-14
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1198817746   63 IEKRRRDKMNSFIDELASLVPTCNaMSRKLDKLTVLRMAVQHMKTLR 109
Cdd:smart00353   3 RERRRRRKINEAFDELRSLLPTLP-KNKKLSKAEILRLAIEYIKSLQ 48
bHLH_SF cd00083
basic Helix Loop Helix (bHLH) domain superfamily; bHLH proteins are transcriptional regulators ...
64-109 2.65e-12

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: 61.38  E-value: 2.65e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1198817746  64 EKRRRDKMNSFIDELASLVPTCnAMSRKLDKLTVLRMAVQHMKTLR 109
Cdd:cd00083     1 ERRRRDKINDAFEELKRLLPEL-PDSKKLSKASILQKAVEYIRELQ 45
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
132-191 7.70e-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.


Pssm-ID: 214512  Cd Length: 67  Bit Score: 60.88  E-value: 7.70e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1198817746  132 HLILRAADGFLFVVGCDrGKILFVSESVFKILNYSQNDLIGQSLFDYLHPKDIAKVKEQL 191
Cdd:smart00091   4 RAILESLPDGIFVLDLD-GRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEAL 62
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
129-236 1.30e-11

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: 395786 [Multi-domain]  Cd Length: 113  Bit Score: 61.66  E-value: 1.30e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1198817746 129 ELKHLILRAADGFLFVVGcDRGKILFVSESVFKILNYSQNDLIGQSLFDYLHPKDIAKVKEQLSS--SDTAPR---ERLI 203
Cdd:pfam00989   1 EDLRAILESLPDGIFVVD-EDGRILYVNAAAEELLGLSREEVIGKSLLDLIPEEDDAEVAELLRQalLQGEESrgfEVSF 79
                          90       100       110
                  ....*....|....*....|....*....|...
gi 1198817746 204 DAKTGLPVKTDITPGPSRLCSGARRSFFCRMKC 236
Cdd:pfam00989  80 RVPDGRPRHVEVRASPVRDAGGEILGFLGVLRD 112
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
138-217 1.84e-11

PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. 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: 60.72  E-value: 1.84e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1198817746 138 ADGFLFVVgCDRGKILFVSESVFKILNYSQNDLIGQSLFDYLHPKDIAKVKEQLSSSDTA----PRERLIDAKTG--LPV 211
Cdd:cd00130     1 LPDGVIVL-DLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGgepvTLEVRLRRKDGsvIWV 79

                  ....*.
gi 1198817746 212 KTDITP 217
Cdd:cd00130    80 LVSLTP 85
bHLH-PAS_dCLOCK cd19735
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Drosophila melanogaster ...
64-125 2.30e-10

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: 57.11  E-value: 2.30e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1198817746  64 EKRRRDKMNSFIDELASLVPTCNamsRKLDKLTVLRMAVQHMK-----TLRGATNPYTEaNYKPTFL 125
Cdd:cd19735    18 EKKRRDQFNVLINELCSMVSTSN---RKMDKSTVLKSTIAFLKnhnevTMQSHQQEIQE-DWKPSFL 80
PAS_3 pfam08447
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
333-417 4.97e-10

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


Pssm-ID: 430001 [Multi-domain]  Cd Length: 89  Bit Score: 56.19  E-value: 4.97e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1198817746 333 FVFVDQRATAILAYLPQELLGT--SCYEYFHQDDIGHLAECHRQVLQTREKITTNcYKFKIKDGSFITLRSRWFSFMNPW 410
Cdd:pfam08447   1 IIYWSPRFEEILGYTPEELLGKgeSWLDLVHPDDRERVREALWEALKGGEPYSGE-YRIRRKDGEYRWVEARARPIRDEN 79

                  ....*..
gi 1198817746 411 TKEVEYI 417
Cdd:pfam08447  80 GKPVRVI 86
bHLH-O_HERP cd11407
basic helix-loop-helix-orange (bHLH-O) domain found in hairy and enhancer of split (HES) ...
54-111 5.40e-10

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: 55.12  E-value: 5.40e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1198817746  54 KNAREAhsqIEKRRRDKMNSFIDELASLVPTCNAM--SRKLDKLTVLRMAVQHMKTLRGA 111
Cdd:cd11407     2 KKRRGI---IEKRRRDRINNSLAELRRLVPTAFEKqgSAKLEKAEILQMTVDHLKMLHSK 58
bHLH-PAS_AhR_like cd19696
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in the aryl hydrocarbon receptor ...
65-107 5.81e-10

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in the aryl hydrocarbon receptor (AhR) family; The AhR family includes AhR, AhR repressor (AhRR) and Drosophila melanogaster protein spineless. AhR, also termed Ah receptor, or Dioxin receptor (DR), or Class E basic helix-loop-helix protein 76 (bHLHe76), is the only member of bHLH-PAS transcription regulators that bind and be activated by small chemical ligands. It is activated by Dioxin to control the expression of certain genes to influence biological processes such as apoptosis, proliferation, cell growth and differentiation. To form active DNA binding complexes AhR dimerizes with a bHLH-PAS factor ARNT (Aryl hydrocarbon Nuclear Receptor Translocator). AhRR, also termed Class E basic helix-loop-helix protein 77 (bHLHe77), is a member of bHLH-PAS transcription factors that acts as a negative regulator of AhR, playing key roles in development and environmental sensing. AhRR functions by competing with AhR for its partner ARNT. AhRR-ARNT complexes are transcriptionally inactive. Spineless is a bHLH-PAS transcription factor that plays an important role in fly morphogenesis. It is both necessary and sufficient for the formation of the ommatidial mosaic.


Pssm-ID: 381539  Cd Length: 59  Bit Score: 54.99  E-value: 5.81e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1198817746  65 KRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKT 107
Cdd:cd19696     9 KRHRDRLNSELDELASLLPFPEDVISKLDKLSVLRLSVSYLRT 51
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
324-377 1.13e-09

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: 54.71  E-value: 1.13e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1198817746  324 VSRHAIDGKFVFVDQRATAILAYLPQELLGTSCYEYFHQDDIGHLAECHRQVLQ 377
Cdd:smart00091  14 IFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEALQRLLS 67
bHLHzip_USF2 cd18923
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in upstream stimulatory factor 2 (USF2) ...
52-121 2.58e-09

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in upstream stimulatory factor 2 (USF2) and similar proteins; USF2, also termed Class B basic helix-loop-helix protein 12 (bHLHb12), or major late transcription factor 2, or FOS-interacting protein (FIP), or upstream transcription factor 2, is a bHLHzip transcription factor that binds to a symmetrical DNA sequence (E-boxes) (5'-CACGTG-3') that is found in a variety of viral and cellular promoters.


Pssm-ID: 381493  Cd Length: 80  Bit Score: 53.94  E-value: 2.58e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1198817746  52 RIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKL--DKLTVLRMAVQHMKTLRgATNPYTEANYK 121
Cdd:cd18923     4 RDERRRAQHNEVERRRRDKINNWIVQLSKIIPDCNTDNSKTgaSKGGILSKACDYIRELR-QTNQRMQETYK 74
bHLH_O_HES cd11410
basic helix-loop-helix-orange (bHLH-O) domain found in hairy and enhancer of split (HES) ...
63-109 2.86e-09

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: 52.85  E-value: 2.86e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1198817746  63 IEKRRRDKMNSFIDELASLVPTC----NAMSRKLDKLTVLRMAVQHMKTLR 109
Cdd:cd11410     1 MEKKRRARINKSLEQLKTLVLEAlnkdNTRYSKLEKADILEMTVKYLKQLQ 51
bHLH-O_HEYL cd11447
basic helix-loop-helix-orange (bHLH-O) domain found in hairy/enhancer-of-split related with ...
56-108 3.15e-09

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: 53.56  E-value: 3.15e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1198817746  56 AREAHSQI-EKRRRDKMNSFIDELASLVPTC--NAMSRKLDKLTVLRMAVQHMKTL 108
Cdd:cd11447     8 ARKKRRGIiEKRRRDRINSSLSELRRLVPTAfeKQGSSKLEKAEILQMTVDHLKML 63
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
330-418 3.31e-09

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: 395786 [Multi-domain]  Cd Length: 113  Bit Score: 54.73  E-value: 3.31e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1198817746 330 DGKFVFVDQRATAILAYLPQELLGTSCYEYFHQDDIGHLAECHRQVLQTREKITTNCYKFKIKDGSFITLRSRWFSFMNP 409
Cdd:pfam00989  20 DGRILYVNAAAEELLGLSREEVIGKSLLDLIPEEDDAEVAELLRQALLQGEESRGFEVSFRVPDGRPRHVEVRASPVRDA 99

                  ....*....
gi 1198817746 410 WTKEVEYIV 418
Cdd:pfam00989 100 GGEILGFLG 108
bHLH_AtbHLH_like cd11393
basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana genes coding transcription ...
60-109 1.85e-08

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  Cd Length: 53  Bit Score: 50.64  E-value: 1.85e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1198817746  60 HSQIEKRRRDKMNSFIDELASLVPTCNamsrKLDKLTVLRMAVQHMKTLR 109
Cdd:cd11393     1 HSIAERKRREKINERIRALRSLVPNGG----KTDKASILDEAIEYIKFLQ 46
bHLH-PAS_CLOCK_like cd11441
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Circadian locomotor output ...
57-106 2.10e-08

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: 50.43  E-value: 2.10e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1198817746  57 REAHSQIEKRRRDKMNSFIDELASLVPTcnaMSRKLDKLTVLRMAVQHMK 106
Cdd:cd11441     1 RKSRNLSEKKRRDQFNVLINELASMLPG---RGRKMDKSTVLKKTIAFLR 47
bHLH-O_HEY1 cd19748
basic helix-loop-helix-orange (bHLH-O) domain found in hairy/enhancer-of-split related with ...
63-111 2.32e-08

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: 51.11  E-value: 2.32e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1198817746  63 IEKRRRDKMNSFIDELASLVPTC--NAMSRKLDKLTVLRMAVQHMKTLRGA 111
Cdd:cd19748    16 IEKRRRDRINNSLSELRRLVPSAfeKQGSAKLEKAEILQMTVDHLKMLHAA 66
bHLH-O_HELT cd11408
basic helix-loop-helix-orange (bHLH-O) domain found in hairy and enhancer of split-related ...
59-111 2.34e-08

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: 50.76  E-value: 2.34e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1198817746  59 AHSQIEKRRRDKMNSFIDELASLVPTCNA--MSRKLDKLTVLRMAVQHMKTLRGA 111
Cdd:cd11408     1 SHKVIEKRRRDRINRCLNELGKTVPMALAkqTSGKLEKAEILEMTVQYLRALHSA 55
bHLH-O_HERP_HES cd19685
basic helix-loop-helix-orange (bHLH-O) domain found in HERP/HES-like family; The HERP/HES-like ...
63-111 2.77e-08

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: 50.12  E-value: 2.77e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1198817746  63 IEKRRRDKMNSFIDELASLVPTCNAM--SRKLDKLTVLRMAVQHMKTLRGA 111
Cdd:cd19685     1 SEKRRRQRINDKLNQLKELLPPNLSKqsRSKLSKAEILEMAITELRRLQQE 51
bHLH-PAS_AhR cd11436
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor (AhR) ...
56-106 3.35e-08

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor (AhR) and similar proteins; AhR, also termed Ah receptor, or Dioxin receptor (DR), or Class E basic helix-loop-helix protein 76 (bHLHe76), is the only member of bHLH-PAS transcription regulators that bind and be activated by small chemical ligands. It is activated by Dioxin to control the expression of certain genes to influence biological processes such as apoptosis, proliferation, cell growth and differentiation. To form active DNA binding complexes AhR dimerize with a bHLH-PAS factor ARNT (Aryl hydrocarbon Nuclear Receptor Translocator).


Pssm-ID: 381442  Cd Length: 61  Bit Score: 50.31  E-value: 3.35e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1198817746  56 AREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMK 106
Cdd:cd11436     1 AEGVKSNPSKRHRDRLNTELDRLASLLPFPQDVISKLDKLSVLRLSVSYLR 51
bHLHzip_USF cd11396
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in upstream stimulatory factors, USF1, ...
60-109 3.38e-08

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: 49.99  E-value: 3.38e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1198817746  60 HSQIEKRRRDKMNSFIDELASLVPTCN--AMSRKLDKLTVLRMAVQHMKTLR 109
Cdd:cd11396     2 HNEVERRRRDKINNWIVKLAKIVPDCEkdNSKQGQSKGGILSKACDYIQELR 53
bHLHzip_Mlx cd19687
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Max-like protein X (Mlx) and similar ...
57-108 4.18e-08

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: 50.50  E-value: 4.18e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1198817746  57 REAHSQIEKRRRDKMNSFIDELASLVPTC----NAMSRKLDKLTVLRMAVQHMKTL 108
Cdd:cd19687     3 REAHTQAEQKRRDAIKKGYDDLQDIVPTCqqqdDIGSQKLSKATILQRSIDYIQFL 58
bHLH-PAS_AhRR cd11435
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor ...
61-106 4.48e-08

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor repressor (AhRR) and similar proteins; AhRR, also termed AhR repressor, or Class E basic helix-loop-helix protein 77 (bHLHe77), is a member of bHLH-PAS transcription factors that acts as a negative regulator of AhR (or Dioxin Receptor), playing key roles in development and environmental sensing. AhR is activated by Dioxin to control the expression of certain genes to influence biological processes such as apoptosis, proliferation, cell growth and differentiation. To form active DNA binding complexes, AhR dimerizes with a bHLH-PAS factor ARNT (Aryl hydrocarbon Nuclear Receptor Translocator). AhRR functions by competing with AhR for its partner ARNT. AhRR-ARNT complexes are transcriptionally inactive.


Pssm-ID: 381441  Cd Length: 60  Bit Score: 49.97  E-value: 4.48e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1198817746  61 SQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMK 106
Cdd:cd11435     5 SNPSKRHRDRLNAELDHLASLLPFPPDIISKLDKLSVLRLSVSYLR 50
bHLH_AtPIF_like cd11445
basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana phytochrome interacting ...
56-108 6.22e-08

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: 49.68  E-value: 6.22e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1198817746  56 AREAHSQIEKRRRDKMNSFIDELASLVPTCNamsrKLDKLTVLRMAVQHMKTL 108
Cdd:cd11445     2 AAEVHNLSERRRRDRINEKMKALQELIPNCN----KTDKASMLDEAIEYLKSL 50
bHLH_SOHLH_like cd19683
basic helix-loop-helix (bHLH) domain found in the spermatogenesis- and oogenesis-specific ...
57-111 7.71e-08

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: 49.27  E-value: 7.71e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1198817746  57 REAHSQIEKRRRDKMNSFIDELASLVPTCnamSRKLDKLTVLRMAVQHMKTLRGA 111
Cdd:cd19683     3 RERHNAKERQRRERIKIACDQLRKLVPGC---SRKTDKATVFEFTVAYIKFLREK 54
bHLHzip_scCBP1 cd11398
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Saccharomyces cerevisiae ...
57-108 8.85e-08

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: 50.03  E-value: 8.85e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1198817746  57 REAHSQIEKRRRDKMNSFIDELASLVPTCNamsRKLDKLTVLRMAVQHMKTL 108
Cdd:cd11398     8 RDNHKEVERRRRENINEGINELAALVPGNA---REKNKGAILARAVEYIQEL 56
bHLHzip_SREBP_like cd11395
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in sterol regulatory element-binding ...
54-108 1.20e-07

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: 49.64  E-value: 1.20e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1198817746  54 KNAREAHSQIEKRRRDKMNSFIDELASLVPTCN--------------AMSRKLDKLTVLRMAVQHMKTL 108
Cdd:cd11395     1 PRKRLPHNAIEKRYRSNLNTKIERLRDAIPSLRspegksddgglgglAPTTKLSKATILTKAIEYIRHL 69
bHLHzip_USF3 cd18910
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in basic helix-loop-helix ...
54-109 1.26e-07

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: 48.84  E-value: 1.26e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1198817746  54 KNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAmsRKLDKLTVLRMAVQHMKTLR 109
Cdd:cd18910     3 EKKRESHNEVERRRKDKINAGINKIGELLPDRDA--KKQSKNMILEQAYKYIVELK 56
bHLH_AtAIG1_like cd11455
basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein AIG1 and similar ...
60-124 2.56e-07

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: 48.44  E-value: 2.56e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1198817746  60 HSQIEKRRRDKMNSFIDELASLVPTcnamSRKLDKLTVLRMAVQHMKTLRG----ATNPYTEANYKPTF 124
Cdd:cd11455    11 HSEAERRRRERINSHLATLRTLLPN----LSKTDKASLLAEVVQHVKELKRqaaeITTPPDVPTEDEED 75
bHLHzip_MITF_like cd11397
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in the microphthalmia-associated ...
52-109 3.12e-07

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: 47.67  E-value: 3.12e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1198817746  52 RIKnaREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLR 109
Cdd:cd11397     3 RQK--KDNHNMIERRRRFNINDRIKELGTLLPKSNDPDMRWNKGTILKASVDYIRKLQ 58
bHLH-O_HEY2 cd18920
basic helix-loop-helix-orange (bHLH-O) domain found in hairy/enhancer-of-split related with ...
63-110 3.37e-07

basic helix-loop-helix-orange (bHLH-O) domain found in hairy/enhancer-of-split related with YRPW motif protein 2 (HEY2) and similar proteins; HEY2, also termed cardiovascular helix-loop-helix factor 1 (CHF-1), or Class B basic helix-loop-helix protein 32 (bHLHb32), or HES-related repressor protein 2, or hairy and enhancer of split-related protein 2 (HESR-2), or hairy-related transcription factor 2 (HRT-2), or protein gridlock homolog, is a bHLH-O transcriptional repressor expressed preferentially in the developing and adult cardiovascular system. As a downstream effector of Notch signaling, HEY2 may be required for cardiovascular development. It also plays an important role in neurologic development, as well as in the progression of human cancers.


Pssm-ID: 381490 [Multi-domain]  Cd Length: 82  Bit Score: 48.21  E-value: 3.37e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1198817746  63 IEKRRRDKMNSFIDELASLVPTC--NAMSRKLDKLTVLRMAVQHMKTLRG 110
Cdd:cd18920    17 IEKRRRDRINNSLSELRRLVPTAfeKQGSAKLEKAEILQMTVDHLKMLQA 66
bHLH-PAS_spineless_like cd19730
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Drosophila melanogaster protein ...
61-107 3.69e-07

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Drosophila melanogaster protein spineless and similar proteins; Spineless is a bHLH-PAS transcription factor that plays an important role in fly morphogenesis. It is both necessary and sufficient for the formation of the ommatidial mosaic.


Pssm-ID: 381573  Cd Length: 64  Bit Score: 47.54  E-value: 3.69e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1198817746  61 SQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKT 107
Cdd:cd19730     8 SNPSKRHRERLNAELDHLASLLPFEQSVISKLDKLSILRLSVSYLRT 54
bHLHzip_USF_MITF cd11387
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in USF/MITF family; The USF (upstream ...
60-109 5.86e-07

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: 46.48  E-value: 5.86e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1198817746  60 HSQIEKRRRDKMNSFIDELASLVPTCN--AMSRKLDKLTVLRMAVQHMKTLR 109
Cdd:cd11387     2 HNAVERRRRDNINEKIQELGSLVPPSRleTKDLKPNKGSILSKAVEYIRELQ 53
bHLH-O_Cwo_like cd11440
basic helix-loop-helix-orange (bHLH-O) domain found in Drosophila melanogaster protein ...
59-109 1.17e-06

basic helix-loop-helix-orange (bHLH-O) domain found in Drosophila melanogaster protein clockwork orange (Cwo) and similar proteins; Cwo is a bHLH-O transcriptional regulator involved in the regulation of Drosophila circadian rhythms. It functions as both an activator and a repressor of clock gene expression.


Pssm-ID: 381446 [Multi-domain]  Cd Length: 60  Bit Score: 45.94  E-value: 1.17e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1198817746  59 AHSQIEKRRRDKMNSFIDELASLVPTcNAMSR---KLDKLTVLRMAVQHMKTLR 109
Cdd:cd11440     5 SHRIIEKRRRDRMNNCLADLSRLIPP-TYLKKgrgRIEKTEIIEMAIKHIKHLQ 57
bHLHzip_USF1 cd18924
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in upstream stimulatory factor 1 (USF1) ...
52-109 1.55e-06

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in upstream stimulatory factor 1 (USF1) and similar proteins; USF1, also termed Class B basic helix-loop-helix protein 11 (bHLHb11), or major late transcription factor 1, is a bHLHzip transcription factor that binds to a symmetrical DNA sequence (E-boxes) (5'-CACGTG-3') that is found in a variety of viral and cellular promoters. It is ubiquitously expressed and involved in the transcription activation of various functional genes implicated in lipid and glucose metabolism, stress response, immune response, cell cycle control and tumour suppression. USF-1 recruits chromatin remodeling enzymes and interact with co-activators and the members of the transcription pre-initiation complex. Genetic polymorphisms of USF1 are associated with some metabolic and cardiovascular diseases, like diabetes, atherosclerosis, coronary artery calcifications and familial combined hyperlipidaemia (FCHL).


Pssm-ID: 381494  Cd Length: 65  Bit Score: 45.83  E-value: 1.55e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1198817746  52 RIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKL--DKLTVLRMAVQHMKTLR 109
Cdd:cd18924     1 RDEKRRAQHNEVERRRRDKINNWIVQLSKIIPDCSMESTKSgqSKGGILSKACDYIQELR 60
bHLHzip_Mlx_like cd11404
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Max-like protein X (Mlx) family; Mlx, ...
57-108 2.20e-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: 45.37  E-value: 2.20e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1198817746  57 REAHSQIEKRRRDKMNSFIDELASLVPTCNamSRKLDKLTVLRMAVQHMKTL 108
Cdd:cd11404     3 RLNHVRSEKKRRELIKKGYDELCALVPGLD--PQKRTKADILQKAADWIQEL 52
bHLHzip_TFEB cd18927
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in transcription factor EB (TFEB) and ...
54-109 3.50e-06

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: 45.36  E-value: 3.50e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1198817746  54 KNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLR 109
Cdd:cd18927     9 RQKKDNHNLIERRRRFNINDRIKELGTLIPKTNDLDVRWNKGTILKASVDYIKRMQ 64
sensory_box TIGR00229
PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain ...
330-420 4.10e-06

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


Pssm-ID: 272971 [Multi-domain]  Cd Length: 124  Bit Score: 46.13  E-value: 4.10e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1198817746 330 DGKFVFVDQRATAILAYLPQELLGTSCYEYFHQDDIGHLAECHRQVLQTREKITTNCYKFKIKDGSFITLrsRWFSFMNP 409
Cdd:TIGR00229  22 EGNILYVNPAFEEIFGYSAEELIGRNVLELIPEEDREEVRERIERRLEGEPEPVSEERRVRRKDGSEIWV--EVSVSPIR 99
                          90
                  ....*....|.
gi 1198817746 410 WTKEVEYIVST 420
Cdd:TIGR00229 100 TNGGELGVVGI 110
bHLH-PAS_CLOCK cd19734
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Circadian locomotor output ...
54-106 4.18e-06

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: 44.24  E-value: 4.18e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1198817746  54 KNAREAHSQIEKRRRDKMNSFIDELASLVPtcnAMSRKLDKLTVLRMAVQHMK 106
Cdd:cd19734     5 KAKRVSRNKSEKKRRDQFNVLIKELGSMLP---GNARKMDKSTVLQKSIDFLR 54
bHLH_TCFL5 cd18909
basic helix-loop-helix (bHLH) domain found in transcription factor-like 5 protein (TCFL5) and ...
57-110 5.25e-06

basic helix-loop-helix (bHLH) domain found in 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: 381479  Cd Length: 60  Bit Score: 44.16  E-value: 5.25e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1198817746  57 REAHSQIEKRRRDKMNSFIDELASLVPTCNAMSrklDKLTVLRMAVQHMKTLRG 110
Cdd:cd18909     3 RERHNRMERDRRRRIRICCDELNLLVPFCNAET---DKATTLQWTTAFLKYIQE 53
bHLH-O_ESMB_like cd19741
basic helix-loop-helix-orange (bHLH-O) domain found in Drosophila melanogaster enhancer of ...
63-109 7.38e-06

basic helix-loop-helix-orange (bHLH-O) domain found in Drosophila melanogaster enhancer of split mbeta protein (ESMB) and similar proteins; ESMB, also termed E(spl)mbeta, or HLH-mbeta, or split locus enhancer protein mA, is a bHLH-O transcriptional repressor of genes that require a bHLH protein for their transcription. It is involved in the neural-epidermal lineage decision during early neurogenesis. The family also includes Enhancer of split m7 protein (also known as E(spl)m7), which acts as a transcriptional repressor that participates in the control of cell fate choice by uncommitted neuroectodermal cells in the embryo.


Pssm-ID: 381584 [Multi-domain]  Cd Length: 69  Bit Score: 43.91  E-value: 7.38e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1198817746  63 IEKRRRDKMNSFIDELASLVPTCNAMSR----KLDKLTVLRMAVQHMKTLR 109
Cdd:cd19741    15 LERKRRARINKCLDELKDLMVEALATEAenvsKLEKADILELTVRHLKKLR 65
bHLH_SOHLH1_2 cd18908
basic helix-loop-helix (bHLH) domain found in the spermatogenesis- and oogenesis-specific ...
60-109 8.33e-06

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: 43.48  E-value: 8.33e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1198817746  60 HSQIEKRRRDKMNSFIDELASLVPtcNAMSRKLDKLTVLRMAVQHMKTLR 109
Cdd:cd18908     6 HSLKERLRRERIKSSCDQLRDLLP--YIKGRKLDMASVLEMTVKYIRYIQ 53
bHLHzip_MITF cd18926
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in microphthalmia-associated ...
54-136 1.34e-05

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: 44.31  E-value: 1.34e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1198817746  54 KNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGATNPYTEANYKPTFLSDDElKHL 133
Cdd:cd18926    11 RQKKDNHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKELENRQKKLEHAN-RHL 89

                  ...
gi 1198817746 134 ILR 136
Cdd:cd18926    90 LLR 92
bHLHzip_TFEC cd18925
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in transcription factor EC (TFEC) and ...
54-109 1.62e-05

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: 43.53  E-value: 1.62e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1198817746  54 KNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLR 109
Cdd:cd18925     3 RQKKDNHNLIERRRRYNINYRIKELGTLIPKSNDPDMRWNKGTILKASVEYIKWLQ 58
bHLHzip_SREBP1 cd18921
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in sterol regulatory element-binding ...
57-119 2.24e-05

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: 42.57  E-value: 2.24e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1198817746  57 REAHSQIEKRRRDKMNSFIDELASLVPTCNAmsrKLDKLTVLRMAVQHMKTLRGATNPYTEAN 119
Cdd:cd18921     7 RTAHNAIEKRYRSSINDKIIELKDLVVGTEA---KLNKSAVLRKAIDYIRFLQQSNQKLKQEN 66
bHLH_TS_FERD3L_like cd19686
basic helix-loop-helix (bHLH) domain found in Fer3-like protein (FERD3L), pancreas ...
57-108 2.32e-05

basic helix-loop-helix (bHLH) domain found in Fer3-like protein (FERD3L), pancreas transcription factor 1 subunit alpha (PTF1A) and similar proteins; The family corresponds to a group of bHLH transcription factors, including FERD3L and PTF1A. FERD3L, also termed basic helix-loop-helix protein N-twist, or Class A basic helix-loop-helix protein 31 (bHLHa31), or nephew of atonal 3 (NATO3), or Neuronal twist (NTWIST), is expressed in the developing central nervous system (CNS). It regulates floor plate (FP) cells development. FP is a critical organizing center located at the ventral-most midline of the neural tube. FERD3L binds to the E-box and functions as inhibitor of transcription. PTF1A, also termed Class A basic helix-loop-helix protein 29 (bHLHa29), or pancreas-specific transcription factor 1a, or bHLH transcription factor p48, or p48 DNA-binding subunit of transcription factor PTF1 (PTF1-p48), is implicated in the cell fate determination in various organs. It binds to the E-box consensus sequence 5'-CANNTG-3' and plays a role in early and late pancreas development and differentiation.


Pssm-ID: 381529 [Multi-domain]  Cd Length: 56  Bit Score: 42.03  E-value: 2.32e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1198817746  57 REAHSQIEKRRRDKMNSFIDELASLVPTcNAMSRKLDKLTVLRMAVQHMKTL 108
Cdd:cd19686     2 RQAANIRERKRMRSINDAFDGLRRHIPT-FPYEKRLSKVDTLRLAIQYINFL 52
bHLHzip_TFE3 cd18928
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in transcription factor E3 (TFE3) and ...
54-109 3.06e-05

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: 42.73  E-value: 3.06e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1198817746  54 KNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLR 109
Cdd:cd18928     9 RQKKDNHNLIERRRRFNINDRIKELGTLIPKSTDPEMRWNKGTILKASVDYIRKLQ 64
bHLH-O_HES5 cd11461
basic helix-loop-helix-orange (bHLH-O) domain found in transcription factor HES-5 and similar ...
62-106 3.29e-05

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: 41.56  E-value: 3.29e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1198817746  62 QIEKRRRDKMNSFIDELASLVPTCNAMSR---KLDKLTVLRMAVQHMK 106
Cdd:cd11461     6 VVEKTRRDRINSSIEQLKTLLEKEFQRHQpnsKLEKADILEMTVSFLK 53
bHLHzip_scHMS1_like cd11399
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Saccharomyces cerevisiae transcription ...
57-119 3.34e-05

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Saccharomyces cerevisiae transcription factor HMS1 and similar proteins; HMS1, also termed high-copy MEP suppressor protein 1, is a putative bHLHzip transcription factor involved in exit from mitosis and pseudohyphal differentiation.


Pssm-ID: 381405 [Multi-domain]  Cd Length: 96  Bit Score: 42.85  E-value: 3.34e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1198817746  57 REAHSQIEKRRRDKMNSFIDELASLVPTCNAMS-------------------RKLDKLTVLRMAVQHMKTLRGATNPYTE 117
Cdd:cd11399     4 KTAHNMIEKRYRSNINDRIAELRDSVPALREAYksargededeedlggltpaTKLNKATILSKATEYIRHLEKKNKRLSR 83

                  ..
gi 1198817746 118 AN 119
Cdd:cd11399    84 EN 85
bHLH_AtILR3_like cd11446
basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein IAA-leucine ...
64-133 3.39e-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: 42.32  E-value: 3.39e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1198817746  64 EKRRRDKMNSFIDELASLV-PTcnaMSRKLDKLTVLRMAVQHMKTLRGATNPYTEANykpTFLSdDELKHL 133
Cdd:cd11446     5 EKLRRDKLNERFMELSNVLePG---RPPKTDKATILGDAIRMLKQLRGEVQKLKEEN---SSLQ-EESKEL 68
sensory_box TIGR00229
PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain ...
133-192 4.29e-05

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


Pssm-ID: 272971 [Multi-domain]  Cd Length: 124  Bit Score: 43.43  E-value: 4.29e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1198817746 133 LILRAADGFLFVVGcDRGKILFVSESVFKILNYSQNDLIGQSLFDYLHPKDIAKVKEQLS 192
Cdd:TIGR00229   7 AIFESSPDAIIVID-LEGNILYVNPAFEEIFGYSAEELIGRNVLELIPEEDREEVRERIE 65
bHLHzip_SREBP cd11394
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in sterol regulatory element-binding ...
57-109 6.09e-05

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  Cd Length: 73  Bit Score: 41.49  E-value: 6.09e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1198817746  57 REAHSQIEKRRRDKMNSFIDELASLVPTCNAmsrKLDKLTVLRMAVQHMKTLR 109
Cdd:cd11394     7 RSAHNAIEKRYRSSINDRIIELKDLVVGPDA---KMNKSAVLRKAIDYIRYLQ 56
bHLHzip_MLXIP_like cd11405
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in MLX-interacting protein (MLXIP), ...
57-109 8.53e-05

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: 41.11  E-value: 8.53e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1198817746  57 REAHSQIEKRRRDKMNSFIDELASLVPTCNAM-SRKLDKLTVLRMAVQHMKTLR 109
Cdd:cd11405     4 RLSHISAEQKRRFNIKSGFDTLQSLIPSLGQNpNQKVSKAAMLQKAAEYIKSLK 57
bHLH-O_DEC2 cd19750
basic helix-loop-helix-orange (bHLH-O) domain found in differentially expressed in ...
60-112 8.76e-05

basic helix-loop-helix-orange (bHLH-O) domain found in differentially expressed in chondrocytes protein 2 (DEC2) and similar proteins; DEC2, also termed Class E basic helix-loop-helix protein 41 (bHLHe41), or Class B basic helix-loop-helix protein 3 (bHLHb3), or enhancer-of-split and hairy-related protein 1 (SHARP-1), is a bHLH-O transcriptional repressor involved in the regulation of the circadian rhythm by negatively regulating the activity of the clock genes and clock-controlled genes.


Pssm-ID: 381593  Cd Length: 92  Bit Score: 41.51  E-value: 8.76e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1198817746  60 HSQIEKRRRDKMNSFIDELASLVPTCNAMSR--KLDKLTVLRMAVQHMKTLRGAT 112
Cdd:cd19750    19 HRLIEKKRRDRINECIAQLKDLLPEHLKLTTlgHLEKAVVLELTLKHLKALTALT 73
bHLH-O_DEC cd11409
basic helix-loop-helix-orange (bHLH-O) domain found in differentially expressed in ...
60-108 9.43e-05

basic helix-loop-helix-orange (bHLH-O) domain found in differentially expressed in chondrocytes protein (DEC) family; The DEC family includes two bHLH-O transcriptional repressors, DEC1 and DEC2, which 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. They mediate the circadian rhythm by negatively regulating the activity of the clock genes and clock-controlled genes. They are induced by CLOCK:BMAL1 heterodimer via the CACGTG E-box in the promoter.


Pssm-ID: 381415 [Multi-domain]  Cd Length: 75  Bit Score: 41.18  E-value: 9.43e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1198817746  60 HSQIEKRRRDKMNSFIDELASLVPTCNAMSR--KLDKLTVLRMAVQHMKTL 108
Cdd:cd11409     8 HRLIEKKRRDRINECIAQLKDLLPEHLKLTTlgHLEKAVVLELTLKHLKAL 58
bHLH-PAS_NPAS2_PASD4 cd19737
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing ...
54-106 1.01e-04

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: 40.93  E-value: 1.01e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1198817746  54 KNAREAHSQIEKRRRDKMNSFIDELASLVPtcnAMSRKLDKLTVLRMAVQHMK 106
Cdd:cd19737     8 RAKRASRNKSEKKRRDQFNVLIKELSSMLP---GNTRKMDKTTVLEKVIGFLQ 57
bHLH-PAS_SIM1 cd19738
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in single-minded homolog 1 (SIM1) ...
57-106 1.09e-04

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in single-minded homolog 1 (SIM1) and similar proteins; SIM1, also termed Class E basic helix-loop-helix protein 14 (bHLHe14), is a bHLH-PAS transcription factor that may have pleiotropic effects during embryogenesis and in the adult.


Pssm-ID: 381581  Cd Length: 71  Bit Score: 40.53  E-value: 1.09e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1198817746  57 REAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMK 106
Cdd:cd19738     2 KEKSKNAARTRREKENSEFYELAKLLPLPSAITSQLDKASIIRLTTSYLK 51
bHLHzip_SREBP2 cd18922
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in sterol regulatory element-binding ...
57-119 1.62e-04

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: 40.32  E-value: 1.62e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1198817746  57 REAHSQIEKRRRDKMNSFIDELASLVPTCNAmsrKLDKLTVLRMAVQHMKTLRGATNPYTEAN 119
Cdd:cd18922     7 RTTHNIIEKRYRSSINDKIIELKDLVMGTDA---KMHKSGVLRKAIDYIKYLQQVNHKLRQEN 66
bHLH-PAS_SIM cd11434
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in single-minded (SIM) family; The ...
57-106 1.85e-04

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in single-minded (SIM) family; The SIM family includes Drosophila melanogaster protein SIM and its homologs from vertebrates, single-minded homolog 1 (SIM1) and single-minded homolog 2 (SIM2). SIM is a nuclear bHLH-PAS transcription factor that functions as a master developmental regulator controlling midline development of the ventral nerve cord in Drosophila. SIM1, also termed Class E basic helix-loop-helix protein 14 (bHLHe14), is a bHLH-PAS transcription factor that may have pleiotropic effects during embryogenesis and in the adult. SIM2, also termed Class E basic helix-loop-helix protein 15 (bHLHe15), is a bHLH-PAS transcription factor that may be a master gene of central nervous system (CNS) development in cooperation with ARNT. It may have pleiotropic effects in the tissues expressed during development.


Pssm-ID: 381440  Cd Length: 61  Bit Score: 39.58  E-value: 1.85e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1198817746  57 REAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMK 106
Cdd:cd11434     2 KEKSKNAARTRREKENAEFYELAKLLPLPSAITSQLDKASIIRLTTSYLK 51
bHLH-PAS_SIM2 cd19739
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in single-minded homolog 2 (SIM2) ...
57-106 1.91e-04

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in single-minded homolog 2 (SIM2) and similar proteins; SIM2, also termed Class E basic helix-loop-helix protein 15 (bHLHe15), is a bHLH-PAS transcription factor that may be a master gene of central nervous system (CNS) development in cooperation with ARNT. It may have pleiotropic effects in the tissues expressed during development.


Pssm-ID: 381582  Cd Length: 74  Bit Score: 40.10  E-value: 1.91e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1198817746  57 REAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMK 106
Cdd:cd19739     2 KEKSKNAAKTRREKENGEFYELAKLLPLPSAITSQLDKASIIRLTTSYLK 51
bHLHzip_Mnt cd11402
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Max-binding protein Mnt and similar ...
57-109 1.93e-04

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Max-binding protein Mnt and similar proteins; Mnt, also termed Class D basic helix-loop-helix protein 3 (bHLHd3), or Myc antagonist MNT, or protein ROX, is a bHLHZip transcriptional repressor that binds DNA as a heterodimer with MAX. It binds to the canonical E box sequence 5'-CACGTG-3' and, with higher affinity, to 5'-CACGCG-3'. Mnt has an important role as an antagonist and regulator of Myc activities and it is a potential tumor suppressor. Mnt is ubiquitously expressed. Mnt-deficient mice shown to exhibit early postnatal lethality.


Pssm-ID: 381408 [Multi-domain]  Cd Length: 77  Bit Score: 40.00  E-value: 1.93e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1198817746  57 REAHSQIEKRRRDKMNSFIDELASLVPTCNamSRKLDKLTVLRMAVQHMKTLR 109
Cdd:cd11402     3 REVHNKLEKNRRAHLKECFETLKRQIPNLD--DKKTSNLNILRSALRYIQILK 53
bHLH-PAS_dSIM_like cd19740
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Drosophila melanogaster protein ...
57-106 1.97e-04

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Drosophila melanogaster protein single-minded (SIM) and similar proteins; SIM is a nuclear bHLH-PAS transcription factor that functions as a master developmental regulator controlling midline development of the ventral nerve cord in Drosophila.


Pssm-ID: 381583  Cd Length: 62  Bit Score: 39.67  E-value: 1.97e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1198817746  57 REAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMK 106
Cdd:cd19740     2 KEKSKNAARSRREKENAEFLELAKLLPLPAAITSQLDKASIIRLTTSYLK 51
bHLHzip_MGA_like cd19682
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in MAX gene-associated protein (MGA) ...
57-109 2.05e-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: 39.56  E-value: 2.05e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1198817746  57 REAHSQIEKRRRDKMNSFIDELASLVPTcnAMSRKLDKLTVLRMAVQHMKTLR 109
Cdd:cd19682     1 RLRHKKRERERRSELRELFDKLKQLLGL--DSDEKASKLAVLTEAIEEIQQLK 51
bHLH-O_HES3 cd18933
basic helix-loop-helix-orange (bHLH-O) domain found in transcription factor HES-3 and similar ...
63-109 2.22e-04

basic helix-loop-helix-orange (bHLH-O) domain found in transcription factor HES-3 and similar proteins; HES-3, also termed Class B basic helix-loop-helix protein 43 (bHLHb43), or hairy and enhancer of split 3, is a bHLH-O transcription factor expressed in neural stem and progenitor cells that is involved in tissue regeneration. It regulates gene expression, cell growth, and insulin release. HES-3 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: 381503 [Multi-domain]  Cd Length: 55  Bit Score: 39.18  E-value: 2.22e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1198817746  63 IEKRRRDKMNSFIDELASLVP---TCNAMSRKLDKLTVLRMAVQHMKTLR 109
Cdd:cd18933     1 MEKKRRARINVSLEQLKSLLEkhySNNIRKRKLEKADILELTVKYLRSLQ 50
bHLHzip_Mad4 cd18929
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Max-associated protein 4 (Mad4) and ...
55-108 2.67e-04

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Max-associated protein 4 (Mad4) and similar proteins; Mad4, also termed Max dimerization protein 4, or Max dimerizer 4 (MXD4), or Class C basic helix-loop-helix protein 12 (bHLHc12), or Max-interacting transcriptional repressor MAD4, is a bHLHZip Max-interacting transcriptional repressor that suppresses c-myc dependent transformation and is expressed during neural and epidermal differentiation. It is regulated by a transcriptional repressor complex that contains Miz-1 and c-Myc.


Pssm-ID: 381499 [Multi-domain]  Cd Length: 88  Bit Score: 39.99  E-value: 2.67e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1198817746  55 NAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKlDKLTVLRMAVQHMKTL 108
Cdd:cd18929     1 NNRSSHNELEKHRRAKLRLYLEQLKQLVPLGPDSTRH-TTLSLLKRAKMHIKKL 53
bHLH-O_DEC1 cd19749
basic helix-loop-helix-orange (bHLH-O) domain found in differentially expressed in ...
60-108 2.89e-04

basic helix-loop-helix-orange (bHLH-O) domain found in differentially expressed in chondrocytes protein 1 (DEC1) and similar proteins; DEC1, also termed Class E basic helix-loop-helix protein 40 (bHLHe40), or Class B basic helix-loop-helix protein 2 (bHLHb2), or enhancer-of-split and hairy-related protein 2 (SHARP-2), or stimulated by retinoic acid gene 13 protein (STRA13), is a bHLH-O transcriptional repressor involved in the regulation of the circadian rhythm by negatively regulating the activity of the clock genes and clock-controlled genes.


Pssm-ID: 381592  Cd Length: 90  Bit Score: 39.96  E-value: 2.89e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1198817746  60 HSQIEKRRRDKMNSFIDELASLVPTCNAMSR--KLDKLTVLRMAVQHMKTL 108
Cdd:cd19749    18 HRLIEKKRRDRINECIAQLKDLLPEHLKLTTlgHLEKAVVLELTLKHVKAL 68
bHLH-O_HES7 cd11462
basic helix-loop-helix-orange (bHLH-O) domain found in hairy and enhancer of split 7 (HES-7) ...
61-107 3.06e-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: 39.25  E-value: 3.06e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1198817746  61 SQIEKRRRDKMNSFIDELASLV----PTCNAMSRKLDKLTVLRMAVQHMKT 107
Cdd:cd11462     6 PLVEKRRRDRINRSLEELRVLLlqntQDEKLKNPKVEKAEILELTVQFLRN 56
bHLH-O_hairy_like cd18913
basic helix-loop-helix-orange (bHLH-O) domain found in Drosophila melanogaster protein hairy, ...
63-109 3.74e-04

basic helix-loop-helix-orange (bHLH-O) domain found in Drosophila melanogaster protein hairy, protein deadpan and similar proteins; Protein hairy is a bHLH transcriptional repressor of genes that require a bHLH-O protein for their transcription. It acts as a pair-rule protein that regulates embryonic segmentation and adult bristle patterning. Protein deadpan is closely related to the product of the segmentation gene hairy. It is a direct target of Notch signaling and regulates neuroblast self-renewal in Drosophila.


Pssm-ID: 381483 [Multi-domain]  Cd Length: 67  Bit Score: 39.06  E-value: 3.74e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1198817746  63 IEKRRRDKMNSFIDELASLVPTC----NAMSRKLDKLTVLRMAVQHMKTLR 109
Cdd:cd18913    10 MEKRRRARINASLNELKSLLLDAlkkdGTRHSKLEKADILEMTVKHLRQVQ 60
bHLH_AtBIM_like cd11453
basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana BES1-interacting Myc-like ...
57-117 4.96e-04

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana BES1-interacting Myc-like proteins (BIMs) and similar proteins; The family includes Arabidopsis thaliana BIM1 and its homologs (BIM2 and BIM3), which are bHLH transcription factors that interact with BES1 to regulate transcription of Brassinosteroid (BR)-induced gene. BR regulates many growth and developmental processes such as cell elongation, vascular development, senescence stress responses, and photomorphogenesis. BIM1 heterodimerize with BES1 and bind to E-box sequences present in many BR-induced promoters to regulated BR-induced genes.


Pssm-ID: 381459  Cd Length: 77  Bit Score: 38.99  E-value: 4.96e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1198817746  57 REAHSQIEKRRRDKMNSFIDELASLVPTCNAmsrKLDKLTVLRMAVQHMKTLRGATNPYTE 117
Cdd:cd11453     4 RSKHSATEQRRRSKINERLQALRDLIPHSDQ---KRDKASFLLEVIEYIQALQEKVAKLEE 61
bHLH_AtNAI1_like cd11452
basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein NAI1 and similar ...
55-109 5.35e-04

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein NAI1 and similar proteins; NAI1, also termed AtbHLH20, or EN 27, is a bHLH transcription activator that regulates the expression of at least NAI2, PYK10 and PBP1. It is required for and mediates the formation of endoplasmic reticulum bodies (ER bodies). It plays a role in the symbiotic interactions with the endophytes of the Sebacinaceae fungus family, such as Piriformospora indica and Sebacina.


Pssm-ID: 381458 [Multi-domain]  Cd Length: 75  Bit Score: 38.98  E-value: 5.35e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1198817746  55 NAREaHSQIEKRRRDKMNSFIDELASLVPTCnamsRKLDKLTVLRMAVQHMKTLR 109
Cdd:cd11452     2 LAQD-HILAERKRREKLSQRFIALSALVPGL----KKMDKASVLGDAIKHIKQLQ 51
bHLH-PAS_NPAS1_3_like cd11432
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing ...
65-106 6.08e-04

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing proteins, NPAS1, NPAS3 and similar proteins; The family includes neuronal PAS domain proteins NPAS1 and NPAS3, both of which are master regulators of neuropsychiatric function. NPAS1, also termed neuronal PAS1, or Basic-helix-loop-helix-PAS protein MOP5, or Class E basic helix-loop-helix protein 11 (bHLHe11), or member of PAS protein 5, or PAS domain-containing protein 5 (PASD5), is a bHLH-PAS transcriptional repressor expressed in the central nervous system and involved in neuronal differentiation. It is active during late embryogenesis and postnatal development. NPAS3, also termed neuronal PAS3, or Basic-helix-loop-helix-PAS protein MOP6, or Class E basic helix-loop-helix protein 12 (bHLHe12), or member of PAS protein 6, or PAS domain-containing protein 6 (PASD6), is a bHLH-PAS brain-enriched transcription factor that is involved in central nervous system development and neurogenesis. It is a replicated genetic risk factor for psychiatric disorders. Human chromosomal rearrangements that affect NPAS3 normal expression are associated with schizophrenia and mental retardation.


Pssm-ID: 381438  Cd Length: 55  Bit Score: 37.94  E-value: 6.08e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1198817746  65 KRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMK 106
Cdd:cd11432     9 RSRRGKENYEFYELAKLLPLPAAISSQLDKASIVRLTISYLK 50
bHLH-PAS_SRC cd11439
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in steroid receptor coactivator ...
64-109 6.96e-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: 6.96e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1198817746  64 EKRRRDKMNSFIDELASL----VPTCNAMSRKLDKLTVLRMAVQHMKTLR 109
Cdd:cd11439     6 EKRRREQENKYIEELAELisasISDMDSLSVKPDKCAILQETVKQIRQIK 55
bHLH_TS_ASCL cd11418
basic helix-loop-helix (bHLH) domain found in achaete-scute complex-like (ASCL) family; The ...
54-110 9.21e-04

basic helix-loop-helix (bHLH) domain found in achaete-scute complex-like (ASCL) family; The achaete-scute complex-like (ASCL, also known as achaete-scute complex homolog or ASH) family of bHLH transcription factors, ASCL1-5, have been implicated in cell fate specification and differentiation. They are critical for proper development of the nervous system. The deregulation of ASCL plays a key role in psychiatric and neurological disorders. ASCL-1, also termed Class A basic helix-loop-helix protein 46 (bHLHa46), or achaete-scute homolog 1 (ASH-1), or mammalian achaete-scute homolog 1 (Mash1), is a neural-specific bHLH transcription factor that is expressed in subsets of neural progenitors in both the central and peripheral nervous system. It plays a key role in neuronal differentiation and specification in the nervous system. ASCL-2, also termed achaete-scute homolog 2 (ASH-2), or Class A basic helix-loop-helix protein 45 (bHLHa45), or mammalian achaete-scute homolog 2 (Mash2), is a bHLH transcription factor that is involved in Schwann cell differentiation and control of proliferation in adult peripheral nerves. ASCL-3, also termed Class A basic helix-loop-helix protein 42 (bHLHa42), or bHLH transcriptional regulator Sgn-1, or achaete-scute homolog 3 (ASH-3), is a bHLH transcription factor specifically localized in the duct cells of the salivary glands. It may act as transcriptional repressor that inhibits myogenesis. The family also includes Drosophila melanogaster achaete-scute complex (AS-C) proteins, which consists of lethal of scute (also known as achaete-scute complex protein T3 or AST3), scute (also known as achaete-scute complex protein T4 or AST4), achaete (also known as achaete-scute complex protein T5 or AST5), and asense (also known as achaete-scute complex protein T8 or AST8). They are involved in the determination of the neuronal precursors in the peripheral nervous system and the central nervous system, as well as in sex determination and dosage compensation.


Pssm-ID: 381424 [Multi-domain]  Cd Length: 56  Bit Score: 37.59  E-value: 9.21e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1198817746  54 KNAREahsqiekRRRDKM-NSFIDELASLVPTCNAmSRKLDKLTVLRMAVQHMKTLRG 110
Cdd:cd11418     5 RNERE-------RRRVQAvNDAFDRLRQHVPYLKR-RKKLSKVKTLRRAIEYIRHLQK 54
PAS_3 pfam08447
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
152-191 9.52e-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.


Pssm-ID: 430001 [Multi-domain]  Cd Length: 89  Bit Score: 38.47  E-value: 9.52e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1198817746 152 ILFVSESVFKILNYSQNDLIG--QSLFDYLHPKDIAKVKEQL 191
Cdd:pfam08447   1 IIYWSPRFEEILGYTPEELLGkgESWLDLVHPDDRERVREAL 42
bHLH-O_ESM5_like cd18916
basic helix-loop-helix-orange (bHLH-O) domain found in Drosophila melanogaster Enhancer of ...
63-113 1.73e-03

basic helix-loop-helix-orange (bHLH-O) domain found in Drosophila melanogaster Enhancer of split proteins, E(spl)m5, E(spl)m8 and similar proteins; The family includes two bHLH-O transcriptional repressors, E(spl)m5 and E(spl)m8, which participate in the control of cell fate choice by uncommitted neuroectodermal cells in the embryo. They bind DNA on N-box motifs, 5'-CACNAG-3'.


Pssm-ID: 381486 [Multi-domain]  Cd Length: 59  Bit Score: 36.74  E-value: 1.73e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1198817746  63 IEKRRRDKMNSFIDELASLVPTC--NAMSRKLDKLTVLRMAVQHMKTLRGATN 113
Cdd:cd18916     7 LERQRRARINKCLSELKTLVAECsgDDGCLRMDKAEMLETAVAFMRQQQTAKN 59
bHLH_ScPHO4_like cd11392
basic helix-loop-helix (bHLH) domain found in Saccharomyces cerevisiae phosphate system ...
57-109 1.74e-03

basic helix-loop-helix (bHLH) domain found in Saccharomyces cerevisiae phosphate system positive regulatory protein PHO4 and similar proteins; PHO4 is a transcriptional activator that regulates the expression of repressible phosphatase under phosphate starvation conditions in Saccharomyces cerevisiae. The PHO4 protein has four functional domains with the bHLH domain at its carboxyl-terminal region. It regulates transcription by binding to promoter of the genes as a homodimer.


Pssm-ID: 381398  Cd Length: 80  Bit Score: 37.43  E-value: 1.74e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1198817746  57 REAHSQIEKRRRDKMNSFIDELASLVP--------------------TCNAMSRKLDKLTVLRMAVQHMKTLR 109
Cdd:cd11392     3 RTAHKVAERGRRDRLNAALKELASLMPaefvegkmgadgsasdsndkEKAAASAAGSKAATVEMAIDYIKHLQ 75
PAS_9 pfam13426
PAS domain;
139-232 1.93e-03

PAS domain;


Pssm-ID: 433196 [Multi-domain]  Cd Length: 102  Bit Score: 37.85  E-value: 1.93e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1198817746 139 DGFLFVVgcDRGKILFVSESVFKILNYSQNDLIGQSLFDYLHPKDIAKVKEQLSSSDTAPRERLIDA--KTGLPVKTDIT 216
Cdd:pfam13426   2 DGILITD--EDGRIIYVNDAALRLLGYSREEVLGKSITDLFTEPEDSERLREALREGREVRELEVILyrKDGEPFPVLVS 79
                          90
                  ....*....|....*.
gi 1198817746 217 PGPSRLCSGARRSFFC 232
Cdd:pfam13426  80 IAPIRDDGGELVGIIA 95
bHLH_AtTT8_like cd11451
basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein transparent testa 8 ...
59-109 2.43e-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: 37.01  E-value: 2.43e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1198817746  59 AHSQIEKRRRDKMNSFIDELASLVPTCNamsrKLDKLTVLRMAVQHMKTLR 109
Cdd:cd11451     5 SHAMAERRRREKLNERFITLRSMVPFVT----KMDKVSILGDAIEYLKQLQ 51
bHLHzip_Mad3 cd18932
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Max-associated protein 3 (Mad3) and ...
55-109 3.70e-03

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Max-associated protein 3 (Mad3) and similar proteins; Mad3, also termed Max dimerization protein 3, or Max dimerizer 3 (MXD3), or Class C basic helix-loop-helix protein 13 (bHLHc13), or Max-interacting transcriptional repressor MAD3, or Myx, is a bHLHZip Max-interacting transcriptional repressor that plays an important role in cellular proliferation. It suppresses c-myc dependent transformation and is expressed during neural and epidermal differentiation.


Pssm-ID: 381502 [Multi-domain]  Cd Length: 85  Bit Score: 36.70  E-value: 3.70e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1198817746  55 NAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKlDKLTVLRMAVQHMKTLR 109
Cdd:cd18932     5 SGRSVHNELEKHRRAQLRRCLEQLKQQVPLGADCSRY-TTLSLLRRARLHIQKLE 58
bHLH-O_HES1_4 cd11459
basic helix-loop-helix-orange (bHLH-O) domain found in hairy and enhancer of split HES-1, ...
62-109 6.41e-03

basic helix-loop-helix-orange (bHLH-O) domain found in hairy and enhancer of split HES-1, HES-4 and similar proteins; The family includes two bHLH-O transcriptional repressors, HES-1 and HES-4. HES-1, also termed Class B basic helix-loop-helix protein 39 (bHLHb39), or hairy homolog, or hairy-like protein (HL), plays an essential role in development of both compartment and boundary cells of the central nervous system. It regulates the maintenance of neural stem/progenitor cells by inhibiting proneural gene expression via Notch signaling. HES-4, also termed Class B basic helix-loop-helix protein 42 (bHLHb42), or bHLH factor Hes4, antagonizes the function of Twist-1 to regulate lineage commitment of bone marrow stromal/stem cells (BMSC). Epigenetic dysregulation of HES-4 is associated with striatal degeneration in postmortem Huntington brains. Both HES-1 and HES-4 are mammalian counterparts 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: 381465 [Multi-domain]  Cd Length: 63  Bit Score: 35.50  E-value: 6.41e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1198817746  62 QIEKRRRDKMNSFIDELASLVptCNAMSR------KLDKLTVLRMAVQHMKTLR 109
Cdd:cd11459     9 IMEKRRRARINESLSQLKTLI--LDALKKdssrhsKLEKADILEMTVKHLRNLQ 60
bHLH_TS_ATOH1_like cd11430
basic helix-loop-helix (bHLH) domain found in protein atonal homologs ATOH1, ATOH7 and similar ...
56-108 6.42e-03

basic helix-loop-helix (bHLH) domain found in protein atonal homologs ATOH1, ATOH7 and similar proteins; The family includes ATOH1 and ATOH7. ATOH1, also termed Class A basic helix-loop-helix protein 14 (bHLHa14), or helix-loop-helix protein hATH-1 (hATH1), or Math1, or Cath1, is a proneural bHLH transcription factor that is essential for inner ear hair cell differentiation. It dimerizes with E47 and activates E-box (CANNTG) dependent transcription. ATOH1 is a mammalian homolog of the Drosophila melanogaster gene atonal and mouse atonal homolog 1 (Math1). ATOH7, also termed Class A basic helix-loop-helix protein 13 (bHLHa13), or helix-loop-helix protein hATH-5 (hATH5), or Math5, is a bHLH transcription factor involved in the differentiation of retinal ganglion cells. The family also includes protein Amos (also termed absent MD neurons and olfactory sensilla protein, or reduced olfactory organs protein, or rough eye protein). It is a bHLH transcription factor that promotes multiple dendritic neuron formation in the Drosophila peripheral nervous system.


Pssm-ID: 381436 [Multi-domain]  Cd Length: 56  Bit Score: 35.10  E-value: 6.42e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1198817746  56 AREAHSQIEKRRRDKMNSFIDELASLVPTCNAmSRKLDKLTVLRMAVQHMKTL 108
Cdd:cd11430     1 RRLAANARERRRMNGLNRAFDQLRSVVPSIGN-DKKLSKYETLQMAQIYIETL 52
bHLH_AtAMS_like cd11443
basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein aborted microspores ...
64-108 7.07e-03

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein aborted microspores (AMS) and similar proteins; The family includes several bHLH transcription factors from Arabidopsis thaliana, such as AMS, ICE1 and SCREAM2. AMS, also termed AtbHLH21, or EN 48, plays a crucial role in tapetum development and it is required for male fertility and pollen differentiation. ICE1, also termed inducer of CBF expression 1, or AtbHLH116, or EN 45, or SCREAM, acts as a transcriptional activator that regulates the cold-induced transcription of CBF/DREB1 genes. It binds specifically to the MYC recognition sites (5'-CANNTG-3') found in the CBF3/DREB1A promoter. SCREAM2, also termed AtbHLH33, or EN 44, mediates stomatal differentiation in the epidermis probably by controlling successive roles of SPCH, MUTE, and FAMA.


Pssm-ID: 381449 [Multi-domain]  Cd Length: 72  Bit Score: 35.43  E-value: 7.07e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1198817746  64 EKRRRDKMNSFIDELASLVPTCNamsrKLDKLTVLRMAVQHMKTL 108
Cdd:cd11443     7 ERRRRKKLNDRLYMLRSVVPKIT----KMDRASILGDAIDYVKEL 47
bHLH_AtMEE8_like cd19698
basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein maternal effect ...
60-109 7.19e-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: 35.50  E-value: 7.19e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1198817746  60 HSQIEKRRRDKMNSFIDELASLVPTCnamSRKLDKLTVLRMAVQHMKTLR 109
Cdd:cd19698     1 HNLLEKKRRERIKDKIEILKGLTPNC---TPKSDIASILSCVIDYIKSLL 47
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.20
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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