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Conserved domains on  [gi|1958802412|ref|XP_038939512|]
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neuronal PAS domain-containing protein 2 isoform X1 [Rattus norvegicus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
bHLH-PAS_NPAS2_PASD4 cd19737
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing ...
 1-77 2.42e-45

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: 156.87  E-value: 2.42e-45
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958802412   1 MDEDEKDRAKRASRNKSEKKRRDQFNVLIKELSSMLPGNTRKLDKTTVLEKVIGFLQKHNEVSAQTEICDIQQDWKP 77
Cdd:cd19737     1 MDEDEKDRAKRASRNKSEKKRRDQFNVLIKELSSMLPGNTRKMDKTTVLEKVIGFLQKHNEVSAQTEICDIQQDWKP 77
PAS_11 super family cl37882
PAS domain; This family includes the PAS-B domain of NCOA1 (Nuclear receptor coactivator 1), ...
 288-391 3.23e-22

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


The actual alignment was detected with superfamily member pfam14598:

Pssm-ID: 464214 [Multi-domain]  Cd Length: 110  Bit Score: 92.36  E-value: 3.23e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958802412 288 EEFTSRHSLEWKFLFLDHRAPPIIGYLPFEVLGTSGYDYYHIDDLELLARCHQHLMQF-GKGKSCCYRFLTKGQQWIWLQ 366
Cdd:pfam14598   2 EQFTTRHDIDGKIISCDTRAPFSLGYEKDELVGRSIYDLVHPQDLRTAKSHLREIIQTrGRATSPSYRLRLRDGDFLSVH 81

                          90       100
                  ....*....|....*....|....*
gi 1958802412 367 THYYITYHQWNSKPEFIVCTHSVVS 391
Cdd:pfam14598  82 TKSKLFLNQNSNQQPFIMCTHTILR 106
PAS super family cl38023
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 84-234 7.39e-06

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


The actual alignment was detected with superfamily member pfam00989:

Pssm-ID: 395786 [Multi-domain]  Cd Length: 113  Bit Score: 45.87  E-value: 7.39e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958802412  84 EFTQLMLEALDGFVIVVTTDGSIIYVSDSITPLLGhlpgteeesmkglhrsrtlrlclrsevhpverasfslyfLLQSDV 163
Cdd:pfam00989   1 EDLRAILESLPDGIFVVDEDGRILYVNAAAEELLG---------------------------------------LSREEV 41

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958802412 164 MDQNLLNFLPEQEHSEVYKILSSHMLVTDSPSPE---FLKSDNDlEFYCHLLRgslNPKEFPTYEYIKFVGNFR 234
Cdd:pfam00989  42 IGKSLLDLIPEEDDAEVAELLRQALLQGEESRGFevsFRVPDGR-PRHVEVRA---SPVRDAGGEILGFLGVLR 111
 
Name Accession Description Interval E-value
bHLH-PAS_NPAS2_PASD4 cd19737
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing ...
 1-77 2.42e-45

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: 156.87  E-value: 2.42e-45
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958802412   1 MDEDEKDRAKRASRNKSEKKRRDQFNVLIKELSSMLPGNTRKLDKTTVLEKVIGFLQKHNEVSAQTEICDIQQDWKP 77
Cdd:cd19737     1 MDEDEKDRAKRASRNKSEKKRRDQFNVLIKELSSMLPGNTRKMDKTTVLEKVIGFLQKHNEVSAQTEICDIQQDWKP 77
PAS_11 pfam14598
PAS domain; This family includes the PAS-B domain of NCOA1 (Nuclear receptor coactivator 1), ...
 288-391 3.23e-22

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


Pssm-ID: 464214 [Multi-domain]  Cd Length: 110  Bit Score: 92.36  E-value: 3.23e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958802412 288 EEFTSRHSLEWKFLFLDHRAPPIIGYLPFEVLGTSGYDYYHIDDLELLARCHQHLMQF-GKGKSCCYRFLTKGQQWIWLQ 366
Cdd:pfam14598   2 EQFTTRHDIDGKIISCDTRAPFSLGYEKDELVGRSIYDLVHPQDLRTAKSHLREIIQTrGRATSPSYRLRLRDGDFLSVH 81

                          90       100
                  ....*....|....*....|....*
gi 1958802412 367 THYYITYHQWNSKPEFIVCTHSVVS 391
Cdd:pfam14598  82 TKSKLFLNQNSNQQPFIMCTHTILR 106
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 289-389 8.54e-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: 73.82  E-value: 8.54e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958802412 289 EFTSRHSLEWKFLFLDHRAPPIIGYLPFEVLGTSGYDYYHIDDLELLARCHQHLMQFGKGKSCCYRFLTKGQQWIWLQTH 368
Cdd:cd00130     3 DGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDGSVIWVLVS 82

                          90       100
                  ....*....|....*....|.
gi 1958802412 369 YYITYHQWNSKPEFIVCTHSV 389
Cdd:cd00130    83 LTPIRDEGGEVIGLLGVVRDI 103
HLH pfam00010
Helix-loop-helix DNA-binding domain;
10-58 3.85e-08

Helix-loop-helix DNA-binding domain;


Pssm-ID: 459628 [Multi-domain]  Cd Length: 53  Bit Score: 50.15  E-value: 3.85e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958802412  10 KRASRNKSEKKRRDQFNVLIKELSSMLP--GNTRKLDKTTVLEKVIGFLQK 58
Cdd:pfam00010   1 RREAHNERERRRRDRINDAFDELRELLPtlPPDKKLSKAEILRLAIEYIKH 51
HLH smart00353
helix loop helix domain;
15-65 7.12e-08

helix loop helix domain;


Pssm-ID: 197674 [Multi-domain]  Cd Length: 53  Bit Score: 49.52  E-value: 7.12e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1958802412   15 NKSEKKRRDQFNVLIKELSSMLPG--NTRKLDKTTVLEKVIGFLQKHNEVSAQ 65
Cdd:smart00353   1 NARERRRRRKINEAFDELRSLLPTlpKNKKLSKAEILRLAIEYIKSLQEELQK 53
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 285-344 3.25e-07

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


Pssm-ID: 214512  Cd Length: 67  Bit Score: 48.16  E-value: 3.25e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958802412  285 EPLEEFTSRHSLEWKFLFLDHRAPPIIGYLPFEVLGTSGYDYYHIDDLELLARCHQHLMQ 344
Cdd:smart00091   8 ESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEALQRLLS 67
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 84-234 7.39e-06

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


Pssm-ID: 395786 [Multi-domain]  Cd Length: 113  Bit Score: 45.87  E-value: 7.39e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958802412  84 EFTQLMLEALDGFVIVVTTDGSIIYVSDSITPLLGhlpgteeesmkglhrsrtlrlclrsevhpverasfslyfLLQSDV 163
Cdd:pfam00989   1 EDLRAILESLPDGIFVVDEDGRILYVNAAAEELLG---------------------------------------LSREEV 41

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958802412 164 MDQNLLNFLPEQEHSEVYKILSSHMLVTDSPSPE---FLKSDNDlEFYCHLLRgslNPKEFPTYEYIKFVGNFR 234
Cdd:pfam00989  42 IGKSLLDLIPEEDDAEVAELLRQALLQGEESRGFevsFRVPDGR-PRHVEVRA---SPVRDAGGEILGFLGVLR 111
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 84-121 4.58e-03

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


Pssm-ID: 214512  Cd Length: 67  Bit Score: 36.61  E-value: 4.58e-03
                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 1958802412   84 EFTQLMLEALDGFVIVVTTDGSIIYVSDSITPLLGHLP 121
Cdd:smart00091   1 ERLRAILESLPDGIFVLDLDGRILYANPAAEELLGYSP 38
PAS COG2202
PAS domain [Signal transduction mechanisms];
285-405 6.41e-03

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 39.24  E-value: 6.41e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958802412 285 EPLEEFTSRHSLEWKFLFLDHRAPPIIGYLPFEVLGTSGYDYYHIDDLELLARCHQHLMQFGKGK-SCCYRFLTKGQQWI 363
Cdd:COG2202   144 ENAPDGIFVLDLDGRILYVNPAAEELLGYSPEELLGKSLLDLLHPEDRERLLELLRRLLEGGRESyELELRLKDGDGRWV 223

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1958802412 364 WLQTHyyITYHQWNSKPEFIVCTHSvvsyaDVRVERRQELAL 405
Cdd:COG2202   224 WVEAS--AVPLRDGGEVIGVLGIVR-----DITERKRAEEAL 258
 
Name Accession Description Interval E-value
bHLH-PAS_NPAS2_PASD4 cd19737
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing ...
 1-77 2.42e-45

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: 156.87  E-value: 2.42e-45
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958802412   1 MDEDEKDRAKRASRNKSEKKRRDQFNVLIKELSSMLPGNTRKLDKTTVLEKVIGFLQKHNEVSAQTEICDIQQDWKP 77
Cdd:cd19737     1 MDEDEKDRAKRASRNKSEKKRRDQFNVLIKELSSMLPGNTRKMDKTTVLEKVIGFLQKHNEVSAQTEICDIQQDWKP 77
bHLH-PAS_dCLOCK cd19735
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Drosophila melanogaster ...
 2-80 9.09e-37

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: 132.61  E-value: 9.09e-37
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958802412   2 DEDEKDRAKRASRNKSEKKRRDQFNVLIKELSSMLPGNTRKLDKTTVLEKVIGFLQKHNEVSAQTEICDIQQDWKPSFL 80
Cdd:cd19735     2 EEDEKDTIKRKSRNLSEKKRRDQFNVLINELCSMVSTSNRKMDKSTVLKSTIAFLKNHNEVTMQSHQQEIQEDWKPSFL 80
bHLH-PAS_CLOCK cd19734
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Circadian locomotor output ...
 4-64 7.18e-32

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: 118.20  E-value: 7.18e-32
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958802412   4 DEKDRAKRASRNKSEKKRRDQFNVLIKELSSMLPGNTRKLDKTTVLEKVIGFLQKHNEVSA 64
Cdd:cd19734     1 DDKDKAKRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKEITA 61
bHLH-PAS_PASD1 cd19736
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in circadian clock protein PASD1; ...
 1-67 6.24e-31

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


Pssm-ID: 381579  Cd Length: 70  Bit Score: 115.57  E-value: 6.24e-31
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958802412   1 MDEDEKDRAKRASRNKSEKKRRDQFNVLIKELSSMLPGNTR--KLDKTTVLEKVIGFLQKHNEVSAQTE 67
Cdd:cd19736     1 MDEDEKDRAKRASRNKSEKKRRDQFNVLIKELCTMLQGHGHplKMDKSTILQRTIDFLQKQKEITAQTE 69
bHLH-PAS_CLOCK_like cd11441
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Circadian locomotor output ...
 11-64 2.33e-28

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: 107.83  E-value: 2.33e-28
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958802412  11 RASRNKSEKKRRDQFNVLIKELSSMLPGNTRKLDKTTVLEKVIGFLQKHNEVSA 64
Cdd:cd11441     1 RKSRNLSEKKRRDQFNVLINELASMLPGRGRKMDKSTVLKKTIAFLRKHKELTA 54
PAS_11 pfam14598
PAS domain; This family includes the PAS-B domain of NCOA1 (Nuclear receptor coactivator 1), ...
 288-391 3.23e-22

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


Pssm-ID: 464214 [Multi-domain]  Cd Length: 110  Bit Score: 92.36  E-value: 3.23e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958802412 288 EEFTSRHSLEWKFLFLDHRAPPIIGYLPFEVLGTSGYDYYHIDDLELLARCHQHLMQF-GKGKSCCYRFLTKGQQWIWLQ 366
Cdd:pfam14598   2 EQFTTRHDIDGKIISCDTRAPFSLGYEKDELVGRSIYDLVHPQDLRTAKSHLREIIQTrGRATSPSYRLRLRDGDFLSVH 81

                          90       100
                  ....*....|....*....|....*
gi 1958802412 367 THYYITYHQWNSKPEFIVCTHSVVS 391
Cdd:pfam14598  82 TKSKLFLNQNSNQQPFIMCTHTILR 106
PAS_3 pfam08447
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 300-387 6.59e-17

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: 76.22  E-value: 6.59e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958802412 300 FLFLDHRAPPIIGYLPFEVLGT--SGYDYYHIDDLELLARCHQHLMQFGKGKSCCYRFLTKGQQWIWLQTHYYItYHQWN 377
Cdd:pfam08447   1 IIYWSPRFEEILGYTPEELLGKgeSWLDLVHPDDRERVREALWEALKGGEPYSGEYRIRRKDGEYRWVEARARP-IRDEN 79

                          90
                  ....*....|
gi 1958802412 378 SKPEFIVCTH 387
Cdd:pfam08447  80 GKPVRVIGVA 89
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 289-389 8.54e-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: 73.82  E-value: 8.54e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958802412 289 EFTSRHSLEWKFLFLDHRAPPIIGYLPFEVLGTSGYDYYHIDDLELLARCHQHLMQFGKGKSCCYRFLTKGQQWIWLQTH 368
Cdd:cd00130     3 DGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDGSVIWVLVS 82

                          90       100
                  ....*....|....*....|.
gi 1958802412 369 YYITYHQWNSKPEFIVCTHSV 389
Cdd:cd00130    83 LTPIRDEGGEVIGLLGVVRDI 103
bHLH_PAS cd11391
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain family; bHLH-PAS domain has been found ...
 11-60 1.39e-13

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


Pssm-ID: 381397 [Multi-domain]  Cd Length: 55  Bit Score: 65.68  E-value: 1.39e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958802412  11 RASRNKSEKKRRDQFNVLIKELSSMLPGN---TRKLDKTTVLEKVIGFLQKHN 60
Cdd:cd11391     1 REKSREAAKKRRDKENAEISELASLLPLPpavGSKLDKLSVLRLAVAYLRLKK 53
bHLHzip_scCBP1 cd11398
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Saccharomyces cerevisiae ...
 4-68 7.13e-09

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


Pssm-ID: 381404 [Multi-domain]  Cd Length: 89  Bit Score: 53.50  E-value: 7.13e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958802412   4 DEKDRAKRASRNKSEKKRRDQFNVLIKELSSMLPGNTRKLDKTTVLEKVIGFLQ--KHNEVSAQTEI 68
Cdd:cd11398     1 EEWHRQRRDNHKEVERRRRENINEGINELAALVPGNAREKNKGAILARAVEYIQelQETEAKNIEKW 67
HLH pfam00010
Helix-loop-helix DNA-binding domain;
10-58 3.85e-08

Helix-loop-helix DNA-binding domain;


Pssm-ID: 459628 [Multi-domain]  Cd Length: 53  Bit Score: 50.15  E-value: 3.85e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958802412  10 KRASRNKSEKKRRDQFNVLIKELSSMLP--GNTRKLDKTTVLEKVIGFLQK 58
Cdd:pfam00010   1 RREAHNERERRRRDRINDAFDELRELLPtlPPDKKLSKAEILRLAIEYIKH 51
HLH smart00353
helix loop helix domain;
15-65 7.12e-08

helix loop helix domain;


Pssm-ID: 197674 [Multi-domain]  Cd Length: 53  Bit Score: 49.52  E-value: 7.12e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1958802412   15 NKSEKKRRDQFNVLIKELSSMLPG--NTRKLDKTTVLEKVIGFLQKHNEVSAQ 65
Cdd:smart00353   1 NARERRRRRKINEAFDELRSLLPTlpKNKKLSKAEILRLAIEYIKSLQEELQK 53
bHLH-PAS_cycle_like cd19726
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Drosophila melanogaster protein ...
 10-49 2.40e-07

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: 48.24  E-value: 2.40e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1958802412  10 KRASRNKSEKKRRDQFNVLIKELSSMLP---GNTRKLDKTTVL 49
Cdd:cd19726     1 RRQNHSEIEKRRRDKMNTYITELSSMIPmcnAMSRKLDKLTVL 43
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 285-344 3.25e-07

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


Pssm-ID: 214512  Cd Length: 67  Bit Score: 48.16  E-value: 3.25e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958802412  285 EPLEEFTSRHSLEWKFLFLDHRAPPIIGYLPFEVLGTSGYDYYHIDDLELLARCHQHLMQ 344
Cdd:smart00091   8 ESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEALQRLLS 67
bHLH-PAS_ARNT_like cd11437
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor ...
 10-49 6.76e-07

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: 47.03  E-value: 6.76e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1958802412  10 KRASRNKSEKKRRDQFNVLIKELSSMLP---GNTRKLDKTTVL 49
Cdd:cd11437     1 SRSNHSEIEKRRRDKMNAYIQELSALVPacnAMSRKLDKLTVL 43
bHLH-PAS_ARNTL_PASD3 cd11438
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor ...
 4-53 2.21e-06

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: 45.87  E-value: 2.21e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958802412   4 DEKDRAKRASRNKSEKKRRDQFNVLIKELSSMLP---GNTRKLDKTTVLEKVI 53
Cdd:cd11438     1 QGRIKNAREAHSQIEKRRRDKMNSFIDELASLVPtcnAMSRKLDKLTVLRMAV 53
bHLH-PAS_ARNTL2_PASD9 cd11469
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor ...
 11-57 4.40e-06

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


Pssm-ID: 381475  Cd Length: 60  Bit Score: 44.64  E-value: 4.40e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958802412  11 RASRNKSEKKRRDQFNVLIKELSSMLPGNT---RKLDKTTVLEKVIGFLQ 57
Cdd:cd11469     2 REAHSQTEKRRRDKMNNLIEELSAMIPQCNpmaRKLDKLTVLRMAVQHLK 51
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 84-234 7.39e-06

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


Pssm-ID: 395786 [Multi-domain]  Cd Length: 113  Bit Score: 45.87  E-value: 7.39e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958802412  84 EFTQLMLEALDGFVIVVTTDGSIIYVSDSITPLLGhlpgteeesmkglhrsrtlrlclrsevhpverasfslyfLLQSDV 163
Cdd:pfam00989   1 EDLRAILESLPDGIFVVDEDGRILYVNAAAEELLG---------------------------------------LSREEV 41

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958802412 164 MDQNLLNFLPEQEHSEVYKILSSHMLVTDSPSPE---FLKSDNDlEFYCHLLRgslNPKEFPTYEYIKFVGNFR 234
Cdd:pfam00989  42 IGKSLLDLIPEEDDAEVAELLRQALLQGEESRGFevsFRVPDGR-PRHVEVRA---SPVRDAGGEILGFLGVLR 111
PAC smart00086
Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); PAC motif ...
 350-391 1.85e-05

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


Pssm-ID: 197509  Cd Length: 43  Bit Score: 42.56  E-value: 1.85e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1958802412  350 SCCYRFLTKGQQWIWLQTHYYITYHqWNSKPEFIVCTHSVVS 391
Cdd:smart00086   1 TVEYRLRRKDGSYIWVLVSASPIRD-EDGEVEGILGVVRDIT 41
bHLHzip_MITF_like cd11397
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in the microphthalmia-associated ...
 6-67 3.10e-05

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


Pssm-ID: 381403  Cd Length: 69  Bit Score: 42.67  E-value: 3.10e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1958802412   6 KDRAKRASRNKSEKKRRDQFNVLIKELSSMLPGNTR---KLDKTTVLEKVIGF---LQKHNEVSAQTE 67
Cdd:cd11397     1 KDRQKKDNHNMIERRRRFNINDRIKELGTLLPKSNDpdmRWNKGTILKASVDYirkLQKEQERLRQLE 68
bHLH_SF cd00083
basic Helix Loop Helix (bHLH) domain superfamily; bHLH proteins are transcriptional regulators ...
 18-53 5.12e-05

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: 41.35  E-value: 5.12e-05
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1958802412  18 EKKRRDQFNVLIKELSSMLPG--NTRKLDKTTVLEKVI 53
Cdd:cd00083     1 ERRRRDKINDAFEELKRLLPElpDSKKLSKASILQKAV 38
bHLHzip_Mlx_like cd11404
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Max-like protein X (Mlx) family; Mlx, ...
 10-58 9.60e-05

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: 41.13  E-value: 9.60e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958802412  10 KRASRNKSEKKRRDQFNVLIKELSSMLPG-NTRKLDKTTVLEKVIGFLQK 58
Cdd:cd11404     2 RRLNHVRSEKKRRELIKKGYDELCALVPGlDPQKRTKADILQKAADWIQE 51
bHLH_AtAIG1_like cd11455
basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein AIG1 and similar ...
 7-74 1.11e-04

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: 41.51  E-value: 1.11e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958802412   7 DRAKRASRNKS--EKKRRDQFNVLIKELSSMLPGNTrKLDKTTVLEKVIGFLQK-HNEVSAQTEICDIQQD 74
Cdd:cd11455     2 DKALAASKSHSeaERRRRERINSHLATLRTLLPNLS-KTDKASLLAEVVQHVKElKRQAAEITTPPDVPTE 71
bHLHzip_SREBP1 cd18921
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in sterol regulatory element-binding ...
 10-61 1.17e-04

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: 41.03  E-value: 1.17e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958802412  10 KRASRNKSEKKRRDQFNVLIKELSSMLPGNTRKLDKTTVLEKVIG---FLQKHNE 61
Cdd:cd18921     6 KRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDyirFLQQSNQ 60
bHLH-PAS_ARNT cd18947
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor ...
 6-49 1.51e-04

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


Pssm-ID: 381517  Cd Length: 65  Bit Score: 40.55  E-value: 1.51e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1958802412   6 KDRAKRASRNKSEKKRRDQFNVLIKELSSMLP---GNTRKLDKTTVL 49
Cdd:cd18947     1 KERFARENHSEIERRRRNKMTAYITELSDMVPtcsALARKPDKLTIL 47
bHLH_AtILR3_like cd11446
basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein IAA-leucine ...
 18-74 2.28e-04

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: 40.39  E-value: 2.28e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958802412  18 EKKRRDQFNVLIKELSSML-PGNTRKLDKTTVLEKVIGFL-QKHNEV--------SAQTEICDIQQD 74
Cdd:cd11446     5 EKLRRDKLNERFMELSNVLePGRPPKTDKATILGDAIRMLkQLRGEVqklkeensSLQEESKELKAE 71
bHLH_AtPIF_like cd11445
basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana phytochrome interacting ...
 15-56 3.42e-04

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


Pssm-ID: 381451  Cd Length: 64  Bit Score: 39.66  E-value: 3.42e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1958802412  15 NKSEKKRRDQFNVLIKELSSMLPgNTRKLDKTTVLEKVIGFL 56
Cdd:cd11445     7 NLSERRRRDRINEKMKALQELIP-NCNKTDKASMLDEAIEYL 47
bHLHzip_SREBP cd11394
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in sterol regulatory element-binding ...
 10-60 3.89e-04

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


Pssm-ID: 381400 [Multi-domain]  Cd Length: 73  Bit Score: 39.56  E-value: 3.89e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958802412  10 KRASRNKSEKKRRDQFNVLIKELSSMLPGNTRKLDKTTVLEKVIG---FLQKHN 60
Cdd:cd11394     6 KRSAHNAIEKRYRSSINDRIIELKDLVVGPDAKMNKSAVLRKAIDyirYLQKVN 59
bHLHzip_USF3 cd18910
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in basic helix-loop-helix ...
 5-61 4.11e-04

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: 39.21  E-value: 4.11e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958802412   5 EKDRaKRASRNKSEKKRRDQFNVLIKELSSMLPG-NTRKLDKTTVLEKV---IGFLQKHNE 61
Cdd:cd18910     1 RREK-KRESHNEVERRRKDKINAGINKIGELLPDrDAKKQSKNMILEQAykyIVELKKKND 60
bHLHzip_USF1 cd18924
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in upstream stimulatory factor 1 (USF1) ...
 6-58 6.42e-04

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: 38.90  E-value: 6.42e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1958802412   6 KDRAKRASRNKSEKKRRDQFNVLIKELSSMLPGNTRKLDKTT-----VLEKVIGFLQK 58
Cdd:cd18924     1 RDEKRRAQHNEVERRRRDKINNWIVQLSKIIPDCSMESTKSGqskggILSKACDYIQE 58
bHLH_SOHLH_like cd19683
basic helix-loop-helix (bHLH) domain found in the spermatogenesis- and oogenesis-specific ...
 10-58 7.45e-04

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: 38.49  E-value: 7.45e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958802412  10 KRASRNKSEKKRRDQFNVLIKELSSMLPGNTRKLDKTTVLE---KVIGFLQK 58
Cdd:cd19683     2 SRERHNAKERQRRERIKIACDQLRKLVPGCSRKTDKATVFEftvAYIKFLRE 53
bHLHzip_USF cd11396
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in upstream stimulatory factors, USF1, ...
 15-58 1.08e-03

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: 38.05  E-value: 1.08e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1958802412  15 NKSEKKRRDQFNVLIKELSSMLPGN-----TRKLDKTTVLEKVIGFLQK 58
Cdd:cd11396     3 NEVERRRRDKINNWIVKLAKIVPDCekdnsKQGQSKGGILSKACDYIQE 51
bHLHzip_TFE3 cd18928
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in transcription factor E3 (TFE3) and ...
 6-68 1.54e-03

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: 38.49  E-value: 1.54e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958802412   6 KDRAKRASRNKSEKKRRDQFNVLIKELSSMLPGNT---RKLDKTTVLEKVIGF---LQKHNEVSAQTEI 68
Cdd:cd18928     7 KERQKKDNHNLIERRRRFNINDRIKELGTLIPKSTdpeMRWNKGTILKASVDYirkLQKEQQRSKEIEM 75
bHLH-O_HERP_like cd11389
basic helix-loop-helix-orange (bHLH-O) domain found in hairy and enhancer of split (HES) ...
 18-58 1.63e-03

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


Pssm-ID: 381395 [Multi-domain]  Cd Length: 55  Bit Score: 37.30  E-value: 1.63e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1958802412  18 EKKRRDQFNVLIKELSSMLP-----GNTRKLDKTTVLEKVIGFLQK 58
Cdd:cd11389     5 EKRRRDRINESLAELRRLVPearksKGSGKLEKAEILEMTLQHLKA 50
bHLH_AtbHLH_like cd11393
basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana genes coding transcription ...
 17-58 1.74e-03

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


Pssm-ID: 381399 [Multi-domain]  Cd Length: 53  Bit Score: 37.16  E-value: 1.74e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1958802412  17 SEKKRRDQFNVLIKELSSMLPgNTRKLDKTTVLEKVIG---FLQK 58
Cdd:cd11393     4 AERKRREKINERIRALRSLVP-NGGKTDKASILDEAIEyikFLQE 47
bHLH-O_HES7 cd11462
basic helix-loop-helix-orange (bHLH-O) domain found in hairy and enhancer of split 7 (HES-7) ...
 18-58 3.82e-03

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: 36.55  E-value: 3.82e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1958802412  18 EKKRRDQFNVLIKELSSMLPGNTR-------KLDKTTVLEKVIGFLQK 58
Cdd:cd11462     9 EKRRRDRINRSLEELRVLLLQNTQdeklknpKVEKAEILELTVQFLRN 56
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 84-121 4.58e-03

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


Pssm-ID: 214512  Cd Length: 67  Bit Score: 36.61  E-value: 4.58e-03
                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 1958802412   84 EFTQLMLEALDGFVIVVTTDGSIIYVSDSITPLLGHLP 121
Cdd:smart00091   1 ERLRAILESLPDGIFVLDLDGRILYANPAAEELLGYSP 38
bHLHzip_MLXIP_like cd11405
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in MLX-interacting protein (MLXIP), ...
 10-67 5.44e-03

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: 36.48  E-value: 5.44e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958802412  10 KRASRNKSEKKRRDQFNVLIKELSSMLPGNTR----KLDKTTVLEKVIGFLQK-HNEVSAQTE 67
Cdd:cd11405     3 RRLSHISAEQKRRFNIKSGFDTLQSLIPSLGQnpnqKVSKAAMLQKAAEYIKSlKRERQQMQE 65
PAS COG2202
PAS domain [Signal transduction mechanisms];
285-405 6.41e-03

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 39.24  E-value: 6.41e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958802412 285 EPLEEFTSRHSLEWKFLFLDHRAPPIIGYLPFEVLGTSGYDYYHIDDLELLARCHQHLMQFGKGK-SCCYRFLTKGQQWI 363
Cdd:COG2202   144 ENAPDGIFVLDLDGRILYVNPAAEELLGYSPEELLGKSLLDLLHPEDRERLLELLRRLLEGGRESyELELRLKDGDGRWV 223

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1958802412 364 WLQTHyyITYHQWNSKPEFIVCTHSvvsyaDVRVERRQELAL 405
Cdd:COG2202   224 WVEAS--AVPLRDGGEVIGVLGIVR-----DITERKRAEEAL 258
bHLH_O_HES cd11410
basic helix-loop-helix-orange (bHLH-O) domain found in hairy and enhancer of split (HES) ...
 18-60 6.55e-03

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


Pssm-ID: 381416 [Multi-domain]  Cd Length: 54  Bit Score: 35.52  E-value: 6.55e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958802412  18 EKKRRDQFNVLIKELSSMLPGNTR-------KLDKTTVLEKVIGFLQKHN 60
Cdd:cd11410     2 EKKRRARINKSLEQLKTLVLEALNkdntrysKLEKADILEMTVKYLKQLQ 51
bHLHzip_MGA_like cd19682
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in MAX gene-associated protein (MGA) ...
 11-58 7.05e-03

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: 35.71  E-value: 7.05e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1958802412  11 RASRNKSEKKRRDQFNVLIKELSSMLPGNTR-KLDKTTVLEKVIGFLQK 58
Cdd:cd19682     1 RLRHKKRERERRSELRELFDKLKQLLGLDSDeKASKLAVLTEAIEEIQQ 49
bHLHzip_USF_MITF cd11387
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in USF/MITF family; The USF (upstream ...
 13-61 7.38e-03

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: 35.69  E-value: 7.38e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958802412  13 SRNKSEKKRRDQFNVLIKELSSMLP-----GNTRKLDKTTVLEKVIGF---LQKHNE 61
Cdd:cd11387     1 SHNAVERRRRDNINEKIQELGSLVPpsrleTKDLKPNKGSILSKAVEYireLQNQNQ 57
bHLH_AtBIM_like cd11453
basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana BES1-interacting Myc-like ...
 9-57 9.28e-03

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: 35.91  E-value: 9.28e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1958802412   9 AKRASRNKSEKKRRDQFNVLIKELSSMLPGNTRKLDKTTVLEKVIGFLQ 57
Cdd:cd11453     2 TPRSKHSATEQRRRSKINERLQALRDLIPHSDQKRDKASFLLEVIEYIQ 50
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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