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Conserved domains on  [gi|528496162|ref|XP_695262|]
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endothelial PAS domain-containing protein 1 isoform X1 [Danio rerio]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
bHLH_SF super family cl00081
basic Helix Loop Helix (bHLH) domain superfamily; bHLH proteins are transcriptional regulators ...
 9-73 6.89e-40

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


The actual alignment was detected with superfamily member cd19728:

Pssm-ID: 469605  Cd Length: 66  Bit Score: 140.99  E-value: 6.89e-40
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 528496162   9 RHPSERRKEKSRDAARCRRSKETEVFYELAHQLPLPHSISSHLDKASIMRLAISFLRTRKLFSSG 73
Cdd:cd19728    1 RSSSERRKEKSRDAARCRRSKETEVFYELAHQLPLPHSVSSHLDKASIMRLAISFLRTHKLLSSV 65
PAS_3 pfam08447
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 253-340 2.16e-23

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: 94.71  E-value: 2.16e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528496162  253 FIYCDERVSSLIGYRPEELLGR--SVYEFCHALDSENMTKSHQNLCNKGQVVSGQYRMLAKNGGYVWVETQATVIYnNRN 330
Cdd:pfam08447   1 IIYWSPRFEEILGYTPEELLGKgeSWLDLVHPDDRERVREALWEALKGGEPYSGEYRIRRKDGEYRWVEARARPIR-DEN 79

                          90
                  ....*....|
gi 528496162  331 SQPQCIICIN 340
Cdd:pfam08447  80 GKPVRVIGVA 89
HIF-1a_CTAD pfam08778
HIF-1 alpha C terminal transactivation domain; Hypoxia inducible factor-1 alpha (HIF-1 alpha) ...
 806-842 1.68e-13

HIF-1 alpha C terminal transactivation domain; Hypoxia inducible factor-1 alpha (HIF-1 alpha) is the regulatory subunit of the heterodimeric transcription factor HIF-1. It plays a key role in cellular response to low oxygen tension. This region corresponds to the C terminal transactivation domain.


:

Pssm-ID: 430212  Cd Length: 37  Bit Score: 65.12  E-value: 1.68e-13
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 528496162  806 SYCLPELTRYDCEVNMPLQGNLHLLQGSDLLRALDQS 842
Cdd:pfam08778   1 LSVLPQLTRYDCEVNAPLQGRSHLLQGEELLRALDQV 37
HIF-1 pfam11413
Hypoxia-inducible factor-1; HIF-1 is a transcriptional complex and controls cellular systemic ...
 522-554 2.58e-11

Hypoxia-inducible factor-1; HIF-1 is a transcriptional complex and controls cellular systemic homeostatic responses to oxygen availability. In the presence of oxygen HIF-1 alpha is targeted for proteasomal degradation by pHVL, a ubiquitination complex.


:

Pssm-ID: 463274  Cd Length: 32  Bit Score: 58.85  E-value: 2.58e-11
                          10        20        30
                  ....*....|....*....|....*....|...
gi 528496162  522 SQLNLSDLDLETLAPYIPMDgEDFQLHPICLEE 554
Cdd:pfam11413   1 TTQDMEDLDLEMLAPYIPMD-DDFQLNPIIPEE 32
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 86-147 3.82e-10

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


:

Pssm-ID: 214512  Cd Length: 67  Bit Score: 56.25  E-value: 3.82e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 528496162    86 QMDNLYLKSLEGFVIVVTSDGDMIFLSENVSKFMGLTQVELTGHSIFDFTHPCDHEEIRENL 147
Cdd:smart00091   1 ERLRAILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEAL 62
 
Name Accession Description Interval E-value
bHLH-PAS_HIF2a_PASD2 cd19728
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in hypoxia-inducible factor ...
 9-73 6.89e-40

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in hypoxia-inducible factor 2-alpha (HIF2a) and similar proteins; HIF2a, also termed HIF-2-alpha, or HIF2-alpha, or endothelial PAS domain-containing protein 1 (EPAS-1), or Basic-helix-loop-helix-PAS protein MOP2, or Class E basic helix-loop-helix protein 73 (bHLHe73), or Member of PAS protein 2, or PAS domain-containing protein 2 (PASD2), or HIF-1-alpha-like factor (HLF), is a bHLH-PAS transcription factor involved in the induction of oxygen regulated genes.


Pssm-ID: 381571  Cd Length: 66  Bit Score: 140.99  E-value: 6.89e-40
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 528496162   9 RHPSERRKEKSRDAARCRRSKETEVFYELAHQLPLPHSISSHLDKASIMRLAISFLRTRKLFSSG 73
Cdd:cd19728    1 RSSSERRKEKSRDAARCRRSKETEVFYELAHQLPLPHSVSSHLDKASIMRLAISFLRTHKLLSSV 65
PAS_3 pfam08447
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 253-340 2.16e-23

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: 94.71  E-value: 2.16e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528496162  253 FIYCDERVSSLIGYRPEELLGR--SVYEFCHALDSENMTKSHQNLCNKGQVVSGQYRMLAKNGGYVWVETQATVIYnNRN 330
Cdd:pfam08447   1 IIYWSPRFEEILGYTPEELLGKgeSWLDLVHPDDRERVREALWEALKGGEPYSGEYRIRRKDGEYRWVEARARPIR-DEN 79

                          90
                  ....*....|
gi 528496162  331 SQPQCIICIN 340
Cdd:pfam08447  80 GKPVRVIGVA 89
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 240-339 7.02e-19

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: 82.68  E-value: 7.02e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528496162 240 SKTFMSRHSMDMKFIYCDERVSSLIGYRPEELLGRSVYEFCHALDSENMTKSHQNLCNKGQVVSGQYRMLAKNGGYVWVE 319
Cdd:cd00130    1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDGSVIWVL 80

                         90       100
                 ....*....|....*....|
gi 528496162 320 TQATVIYNNRNSQPQCIICI 339
Cdd:cd00130   81 VSLTPIRDEGGEVIGLLGVV 100
HIF-1a_CTAD pfam08778
HIF-1 alpha C terminal transactivation domain; Hypoxia inducible factor-1 alpha (HIF-1 alpha) ...
 806-842 1.68e-13

HIF-1 alpha C terminal transactivation domain; Hypoxia inducible factor-1 alpha (HIF-1 alpha) is the regulatory subunit of the heterodimeric transcription factor HIF-1. It plays a key role in cellular response to low oxygen tension. This region corresponds to the C terminal transactivation domain.


Pssm-ID: 430212  Cd Length: 37  Bit Score: 65.12  E-value: 1.68e-13
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 528496162  806 SYCLPELTRYDCEVNMPLQGNLHLLQGSDLLRALDQS 842
Cdd:pfam08778   1 LSVLPQLTRYDCEVNAPLQGRSHLLQGEELLRALDQV 37
HIF-1 pfam11413
Hypoxia-inducible factor-1; HIF-1 is a transcriptional complex and controls cellular systemic ...
 522-554 2.58e-11

Hypoxia-inducible factor-1; HIF-1 is a transcriptional complex and controls cellular systemic homeostatic responses to oxygen availability. In the presence of oxygen HIF-1 alpha is targeted for proteasomal degradation by pHVL, a ubiquitination complex.


Pssm-ID: 463274  Cd Length: 32  Bit Score: 58.85  E-value: 2.58e-11
                          10        20        30
                  ....*....|....*....|....*....|...
gi 528496162  522 SQLNLSDLDLETLAPYIPMDgEDFQLHPICLEE 554
Cdd:pfam11413   1 TTQDMEDLDLEMLAPYIPMD-DDFQLNPIIPEE 32
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 86-147 3.82e-10

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


Pssm-ID: 214512  Cd Length: 67  Bit Score: 56.25  E-value: 3.82e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 528496162    86 QMDNLYLKSLEGFVIVVTSDGDMIFLSENVSKFMGLTQVELTGHSIFDFTHPCDHEEIRENL 147
Cdd:smart00091   1 ERLRAILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEAL 62
PAS COG2202
PAS domain [Signal transduction mechanisms];
250-339 8.13e-10

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 60.42  E-value: 8.13e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528496162 250 DMKFIYCDERVSSLIGYRPEELLGRSVYEFCHALDSENMTKSHQNLCNKGQVVSGQYRMLAKNGGYVWVETQATVIYNNR 329
Cdd:COG2202   30 DGRILYVNPAFERLTGYSAEELLGKTLRDLLPPEDDDEFLELLRAALAGGGVWRGELRNRRKDGSLFWVELSISPVRDED 109

                         90
                 ....*....|
gi 528496162 330 NsQPQCIICI 339
Cdd:COG2202  110 G-EITGFVGI 118
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 97-147 2.63e-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. 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: 55.33  E-value: 2.63e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 528496162  97 GFVIVVTSDGDMIFLSENVSKFMGLTQVELTGHSIFDFTHPCDHEEIRENL 147
Cdd:cd00130    3 DGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERL 53
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 240-295 3.58e-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: 53.56  E-value: 3.58e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 528496162   240 SKTFMSRHSMDMKFIYCDERVSSLIGYRPEELLGRSVYEFCHALDSENMTKSHQNL 295
Cdd:smart00091  10 LPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEALQRL 65
HLH smart00353
helix loop helix domain;
20-65 3.14e-08

helix loop helix domain;


Pssm-ID: 197674 [Multi-domain]  Cd Length: 53  Bit Score: 50.68  E-value: 3.14e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 528496162    20 RDAARCRRSKETEVFYELAHQLPlPHSISSHLDKASIMRLAISFLR 65
Cdd:smart00353   1 NARERRRRRKINEAFDELRSLLP-TLPKNKKLSKAEILRLAIEYIK 45
KinA COG5805
Sporulation sensor histidine kinase A (Stage II sporulation protein SpoIIF/SpoIIJ) [Cell cycle ...
 89-167 9.20e-05

Sporulation sensor histidine kinase A (Stage II sporulation protein SpoIIF/SpoIIJ) [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms];


Pssm-ID: 444507 [Multi-domain]  Cd Length: 496  Bit Score: 45.88  E-value: 9.20e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528496162  89 NLYLKSLEGFVIVVTSDGDMIFLSENVSKFMGLTQVELTGHSIFDFTHPCDHEEIRENL--------------------- 147
Cdd:COG5805  160 QTLIENSPDLICVIDTDGRILFINESIERLFGAPREELIGKNLLELLHPCDKEEFKERIesitevwqefiiereiitkdg 239

                         90       100
                 ....*....|....*....|....*...
gi 528496162 148 -----SIKSGPVYGRKGKE---MSTSRD 167
Cdd:COG5805  240 riryfEAVIVPLIDTDGSVkgiLVILRD 267
sensory_box TIGR00229
PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain ...
 252-330 2.56e-03

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


Pssm-ID: 272971 [Multi-domain]  Cd Length: 124  Bit Score: 38.81  E-value: 2.56e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528496162  252 KFIYCDERVSSLIGYRPEELLGRSVYEFCHALDSE-NMTKSHQNLCNKGQVVSGQYRMLAKNGGYVWVETQATVIYNNRN 330
Cdd:TIGR00229  24 NILYVNPAFEEIFGYSAEELIGRNVLELIPEEDREeVRERIERRLEGEPEPVSEERRVRRKDGSEIWVEVSVSPIRTNGG 103
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 94-183 2.61e-03

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: 38.55  E-value: 2.61e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528496162   94 SLEGFVIVVTSDGDMIFLSENVSKFMGLTQVELTGHSIFDFTHPCDHEEIRENLSiksgpvygrkgKEMSTSRDFFMRMK 173
Cdd:pfam00989   9 SLPDGIFVVDEDGRILYVNAAAEELLGLSREEVIGKSLLDLIPEEDDAEVAELLR-----------QALLQGEESRGFEV 77

                          90
                  ....*....|
gi 528496162  174 CTVTNRGRTV 183
Cdd:pfam00989  78 SFRVPDGRPR 87
sensory_box TIGR00229
PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain ...
 100-148 3.73e-03

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


Pssm-ID: 272971 [Multi-domain]  Cd Length: 124  Bit Score: 38.04  E-value: 3.73e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 528496162  100 IVVTSDGDMIFLSENVSKFMGLTQVELTGHSIFDFTHPCDHEEIRENLS 148
Cdd:TIGR00229  17 IVIDLEGNILYVNPAFEEIFGYSAEELIGRNVLELIPEEDREEVRERIE 65
 
Name Accession Description Interval E-value
bHLH-PAS_HIF2a_PASD2 cd19728
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in hypoxia-inducible factor ...
 9-73 6.89e-40

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in hypoxia-inducible factor 2-alpha (HIF2a) and similar proteins; HIF2a, also termed HIF-2-alpha, or HIF2-alpha, or endothelial PAS domain-containing protein 1 (EPAS-1), or Basic-helix-loop-helix-PAS protein MOP2, or Class E basic helix-loop-helix protein 73 (bHLHe73), or Member of PAS protein 2, or PAS domain-containing protein 2 (PASD2), or HIF-1-alpha-like factor (HLF), is a bHLH-PAS transcription factor involved in the induction of oxygen regulated genes.


Pssm-ID: 381571  Cd Length: 66  Bit Score: 140.99  E-value: 6.89e-40
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 528496162   9 RHPSERRKEKSRDAARCRRSKETEVFYELAHQLPLPHSISSHLDKASIMRLAISFLRTRKLFSSG 73
Cdd:cd19728    1 RSSSERRKEKSRDAARCRRSKETEVFYELAHQLPLPHSVSSHLDKASIMRLAISFLRTHKLLSSV 65
bHLH-PAS_HIF1a_PASD8 cd19727
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in hypoxia-inducible factor ...
 12-73 2.61e-36

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in hypoxia-inducible factor 1-alpha (HIF1a) and similar proteins; HIF1a, also termed HIF-1-alpha, or HIF1-alpha, or ARNT-interacting protein, or Basic-helix-loop-helix-PAS protein MOP1, or Class E basic helix-loop-helix protein 78 (bHLHe78), or Member of PAS protein 1, or PAS domain-containing protein 8 (PASD8), functions as a master transcriptional regulator of the adaptive response to hypoxia.


Pssm-ID: 381570  Cd Length: 71  Bit Score: 130.92  E-value: 2.61e-36
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 528496162  12 SERRKEKSRDAARCRRSKETEVFYELAHQLPLPHSISSHLDKASIMRLAISFLRTRKLFSSG 73
Cdd:cd19727    3 SERRKEKSRDAARSRRSKESEVFYELAHQLPLPHNVSSHLDKASIMRLTISYLRMRKLLDAG 64
bHLH-PAS_HIF cd11433
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in hypoxia-inducible factor (HIF) ...
 15-72 3.47e-35

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in hypoxia-inducible factor (HIF) family; The HIF family contains bHLH-PAS transcription regulators involved in oxygen homeostasis, including HIF1a, HIF2a, and HIF3a. They have been implicated in development, postnatal physiology as well as disease pathogenesis. HIF1a, also termed HIF-1-alpha, or HIF1-alpha, or ARNT-interacting protein, or Basic-helix-loop-helix-PAS protein MOP1, or Class E basic helix-loop-helix protein 78 (bHLHe78), or Member of PAS protein 1, or PAS domain-containing protein 8 (PASD8), functions as a master transcriptional regulator of the adaptive response to hypoxia. HIF2a, also termed HIF-2-alpha, or HIF2-alpha, or endothelial PAS domain-containing protein 1 (EPAS-1), or Basic-helix-loop-helix-PAS protein MOP2, or Class E basic helix-loop-helix protein 73 (bHLHe73), or Member of PAS protein 2, or PAS domain-containing protein 2 (PASD2), or HIF-1-alpha-like factor (HLF), is a bHLH-PAS transcription factor involved in the induction of oxygen regulated genes. HIF3a, also termed HIF-3-alpha, or HIF3-alpha, or endothelial PAS domain-containing protein 1 (EPAS-1), or Basic-helix-loop-helix-PAS protein MOP7, or Class E basic helix-loop-helix protein 17 (bHLHe17), or Member of PAS protein 7, or PAS domain-containing protein 7 (PASD7), or HIF3-alpha-1, or inhibitory PAS domain protein (IPAS), is a bHLH-PAS transcriptional regulator in adaptive response to low oxygen tension. It plays a role in the regulation of hypoxia-inducible gene expression.


Pssm-ID: 381439  Cd Length: 58  Bit Score: 127.36  E-value: 3.47e-35
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 528496162  15 RKEKSRDAARCRRSKETEVFYELAHQLPLPHSISSHLDKASIMRLAISFLRTRKLFSS 72
Cdd:cd11433    1 RKEKSRDAARCRRGKESEIFYELAHQLPLPHSVSSQLDKASIMRLTISYLKLRKLLSA 58
bHLH-PAS_HIF3a_PASD7 cd19729
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in hypoxia-inducible factor ...
 12-73 3.22e-32

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in hypoxia-inducible factor 3-alpha (HIF3a) and similar proteins; HIF3a, also termed HIF-3-alpha, or HIF3-alpha, or endothelial PAS domain-containing protein 1 (EPAS-1), or Basic-helix-loop-helix-PAS protein MOP7, or Class E basic helix-loop-helix protein 17 (bHLHe17), or Member of PAS protein 7, or PAS domain-containing protein 7 (PASD7), or HIF3-alpha-1, or inhibitory PAS domain protein (IPAS), is a bHLH-PAS transcriptional regulator in adaptive response to low oxygen tension. It plays a role in the regulation of hypoxia-inducible gene expression.


Pssm-ID: 381572  Cd Length: 63  Bit Score: 118.96  E-value: 3.22e-32
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 528496162  12 SERRKEKSRDAARCRRSKETEVFYELAHQLPLPHSISSHLDKASIMRLAISFLRTRKLFSSG 73
Cdd:cd19729    1 TEQRKEKSRDAARCRRSQETEVFYELAHTLPFPRGVSSHLDKASIMRLTISYLRMHRLIASG 62
PAS_3 pfam08447
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 253-340 2.16e-23

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: 94.71  E-value: 2.16e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528496162  253 FIYCDERVSSLIGYRPEELLGR--SVYEFCHALDSENMTKSHQNLCNKGQVVSGQYRMLAKNGGYVWVETQATVIYnNRN 330
Cdd:pfam08447   1 IIYWSPRFEEILGYTPEELLGKgeSWLDLVHPDDRERVREALWEALKGGEPYSGEYRIRRKDGEYRWVEARARPIR-DEN 79

                          90
                  ....*....|
gi 528496162  331 SQPQCIICIN 340
Cdd:pfam08447  80 GKPVRVIGVA 89
bHLH-PAS_NPAS3_PASD6 cd19732
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing ...
 13-83 1.07e-22

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


Pssm-ID: 381575  Cd Length: 78  Bit Score: 92.37  E-value: 1.07e-22
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 528496162  13 ERRKEKSRDAARCRRSKETEVFYELAHQLPLPHSISSHLDKASIMRLAISFLRTRKLFSSGHTVQQMRSQN 83
Cdd:cd19732    4 ALRKEKSRDAARSRRGKENFEFYELAKLLPLPAAITSQLDKASIIRLTISYLKMRDFANQGDPPWNLRMEG 74
bHLH-PAS_trachealess_like cd19733
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Drosophila melanogaster protein ...
 13-73 1.65e-22

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


Pssm-ID: 381576  Cd Length: 79  Bit Score: 91.92  E-value: 1.65e-22
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 528496162  13 ERRKEKSRDAARCRRSKETEVFYELAHQLPLPHSISSHLDKASIMRLAISFLRTRKLFSSG 73
Cdd:cd19733    3 ELRKEKSRDAARSRRGKENYEFYELAKMLPLPAAITSQLDKASIIRLTISYLKLRDFSGHG 63
bHLH_PAS cd11391
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain family; bHLH-PAS domain has been found ...
 16-70 1.39e-21

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: 88.41  E-value: 1.39e-21
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 528496162  16 KEKSRDAARCRRSKETEVFYELAHQLPLPHSISSHLDKASIMRLAISFLRTRKLF 70
Cdd:cd11391    1 REKSREAAKKRRDKENAEISELASLLPLPPAVGSKLDKLSVLRLAVAYLRLKKFL 55
bHLH-PAS_NPAS1_PASD5 cd19731
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing ...
 15-73 1.54e-21

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


Pssm-ID: 381574  Cd Length: 74  Bit Score: 89.20  E-value: 1.54e-21
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 528496162  15 RKEKSRDAARCRRSKETEVFYELAHQLPLPHSISSHLDKASIMRLAISFLRTRKLFSSG 73
Cdd:cd19731    4 RKEKSRNAARSRRGKENFEFYELAKMLPLPGAITSQLDKASIVRLTISYLKMRDFASHG 62
bHLH-PAS_NPAS1_3_like cd11432
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing ...
 16-68 1.36e-19

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: 83.01  E-value: 1.36e-19
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 528496162  16 KEKSRDAARCRRSKETEVFYELAHQLPLPHSISSHLDKASIMRLAISFLRTRK 68
Cdd:cd11432    1 KEKSRNAARSRRGKENYEFYELAKLLPLPAAISSQLDKASIVRLTISYLKLRD 53
bHLH-PAS_SIM cd11434
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in single-minded (SIM) family; The ...
 16-73 2.55e-19

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: 82.34  E-value: 2.55e-19
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 528496162  16 KEKSRDAARCRRSKETEVFYELAHQLPLPHSISSHLDKASIMRLAISFLRTRKLFSSG 73
Cdd:cd11434    2 KEKSKNAARTRREKENAEFYELAKLLPLPSAITSQLDKASIIRLTTSYLKMRAVFPEG 59
bHLH-PAS_dSIM_like cd19740
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Drosophila melanogaster protein ...
 16-73 5.48e-19

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: 81.27  E-value: 5.48e-19
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 528496162  16 KEKSRDAARCRRSKETEVFYELAHQLPLPHSISSHLDKASIMRLAISFLRTRKLFSSG 73
Cdd:cd19740    2 KEKSKNAARSRREKENAEFLELAKLLPLPAAITSQLDKASIIRLTTSYLKMRQVFPDG 59
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 240-339 7.02e-19

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: 82.68  E-value: 7.02e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528496162 240 SKTFMSRHSMDMKFIYCDERVSSLIGYRPEELLGRSVYEFCHALDSENMTKSHQNLCNKGQVVSGQYRMLAKNGGYVWVE 319
Cdd:cd00130    1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDGSVIWVL 80

                         90       100
                 ....*....|....*....|
gi 528496162 320 TQATVIYNNRNSQPQCIICI 339
Cdd:cd00130   81 VSLTPIRDEGGEVIGLLGVV 100
bHLH-PAS_SIM1 cd19738
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in single-minded homolog 1 (SIM1) ...
 16-73 3.54e-18

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: 79.44  E-value: 3.54e-18
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 528496162  16 KEKSRDAARCRRSKETEVFYELAHQLPLPHSISSHLDKASIMRLAISFLRTRKLFSSG 73
Cdd:cd19738    2 KEKSKNAARTRREKENSEFYELAKLLPLPSAITSQLDKASIIRLTTSYLKMRVVFPEG 59
PAS_11 pfam14598
PAS domain; This family includes the PAS-B domain of NCOA1 (Nuclear receptor coactivator 1), ...
 243-348 5.07e-18

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: 80.42  E-value: 5.07e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528496162  243 FMSRHSMDMKFIYCDERVSSLIGYRPEELLGRSVYEFCHALD-SENMTKSHQNLCNKGQVVSGQYRMLAKNGGYVWVETQ 321
Cdd:pfam14598   4 FTTRHDIDGKIISCDTRAPFSLGYEKDELVGRSIYDLVHPQDlRTAKSHLREIIQTRGRATSPSYRLRLRDGDFLSVHTK 83

                          90       100
                  ....*....|....*....|....*..
gi 528496162  322 ATVIYNNRNSQPQCIICINYILSSVEE 348
Cdd:pfam14598  84 SKLFLNQNSNQQPFIMCTHTILREENA 110
bHLH-PAS_SIM2 cd19739
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in single-minded homolog 2 (SIM2) ...
 16-73 1.06e-17

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: 78.24  E-value: 1.06e-17
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 528496162  16 KEKSRDAARCRRSKETEVFYELAHQLPLPHSISSHLDKASIMRLAISFLRTRKLFSSG 73
Cdd:cd19739    2 KEKSKNAAKTRREKENGEFYELAKLLPLPSAITSQLDKASIIRLTTSYLKMRAVFPEG 59
HIF-1a_CTAD pfam08778
HIF-1 alpha C terminal transactivation domain; Hypoxia inducible factor-1 alpha (HIF-1 alpha) ...
 806-842 1.68e-13

HIF-1 alpha C terminal transactivation domain; Hypoxia inducible factor-1 alpha (HIF-1 alpha) is the regulatory subunit of the heterodimeric transcription factor HIF-1. It plays a key role in cellular response to low oxygen tension. This region corresponds to the C terminal transactivation domain.


Pssm-ID: 430212  Cd Length: 37  Bit Score: 65.12  E-value: 1.68e-13
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 528496162  806 SYCLPELTRYDCEVNMPLQGNLHLLQGSDLLRALDQS 842
Cdd:pfam08778   1 LSVLPQLTRYDCEVNAPLQGRSHLLQGEELLRALDQV 37
HIF-1 pfam11413
Hypoxia-inducible factor-1; HIF-1 is a transcriptional complex and controls cellular systemic ...
 522-554 2.58e-11

Hypoxia-inducible factor-1; HIF-1 is a transcriptional complex and controls cellular systemic homeostatic responses to oxygen availability. In the presence of oxygen HIF-1 alpha is targeted for proteasomal degradation by pHVL, a ubiquitination complex.


Pssm-ID: 463274  Cd Length: 32  Bit Score: 58.85  E-value: 2.58e-11
                          10        20        30
                  ....*....|....*....|....*....|...
gi 528496162  522 SQLNLSDLDLETLAPYIPMDgEDFQLHPICLEE 554
Cdd:pfam11413   1 TTQDMEDLDLEMLAPYIPMD-DDFQLNPIIPEE 32
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 86-147 3.82e-10

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


Pssm-ID: 214512  Cd Length: 67  Bit Score: 56.25  E-value: 3.82e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 528496162    86 QMDNLYLKSLEGFVIVVTSDGDMIFLSENVSKFMGLTQVELTGHSIFDFTHPCDHEEIRENL 147
Cdd:smart00091   1 ERLRAILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEAL 62
PAS COG2202
PAS domain [Signal transduction mechanisms];
250-339 8.13e-10

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 60.42  E-value: 8.13e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528496162 250 DMKFIYCDERVSSLIGYRPEELLGRSVYEFCHALDSENMTKSHQNLCNKGQVVSGQYRMLAKNGGYVWVETQATVIYNNR 329
Cdd:COG2202   30 DGRILYVNPAFERLTGYSAEELLGKTLRDLLPPEDDDEFLELLRAALAGGGVWRGELRNRRKDGSLFWVELSISPVRDED 109

                         90
                 ....*....|
gi 528496162 330 NsQPQCIICI 339
Cdd:COG2202  110 G-EITGFVGI 118
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 97-147 2.63e-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. 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: 55.33  E-value: 2.63e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 528496162  97 GFVIVVTSDGDMIFLSENVSKFMGLTQVELTGHSIFDFTHPCDHEEIRENL 147
Cdd:cd00130    3 DGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERL 53
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 240-295 3.58e-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: 53.56  E-value: 3.58e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 528496162   240 SKTFMSRHSMDMKFIYCDERVSSLIGYRPEELLGRSVYEFCHALDSENMTKSHQNL 295
Cdd:smart00091  10 LPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEALQRL 65
HLH smart00353
helix loop helix domain;
20-65 3.14e-08

helix loop helix domain;


Pssm-ID: 197674 [Multi-domain]  Cd Length: 53  Bit Score: 50.68  E-value: 3.14e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 528496162    20 RDAARCRRSKETEVFYELAHQLPlPHSISSHLDKASIMRLAISFLR 65
Cdd:smart00353   1 NARERRRRRKINEAFDELRSLLP-TLPKNKKLSKAEILRLAIEYIK 45
PAC smart00086
Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); PAC motif ...
 303-344 6.75e-08

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: 49.10  E-value: 6.75e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 528496162   303 SGQYRMLAKNGGYVWVETQATVIYnNRNSQPQCIICINYILS 344
Cdd:smart00086   1 TVEYRLRRKDGSYIWVLVSASPIR-DEDGEVEGILGVVRDIT 41
PAS_9 pfam13426
PAS domain; This domain is found in many signalling proteins in which it functions as a sensor ...
 250-342 7.09e-08

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


Pssm-ID: 463873 [Multi-domain]  Cd Length: 93  Bit Score: 50.92  E-value: 7.09e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528496162  250 DMKFIYCDERVSSLIGYRPEELLGRSVYEFCHalDSENMTKSHQNLCNKGQVVSGQYRMLAKNGGYVWVETQATVIYNNR 329
Cdd:pfam13426   1 DGRIIYVNDAALRLLGYTREELLGKSITDLFA--EPEDSERLREALREGKAVREFEVVLYRKDGEPFPVLVSLAPIRDDG 78

                          90
                  ....*....|...
gi 528496162  330 NSQPQCIICINYI 342
Cdd:pfam13426  79 GELVGIIAILRDI 91
bHLH-PAS_AhR_like cd19696
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in the aryl hydrocarbon receptor ...
 8-73 1.26e-07

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: 49.21  E-value: 1.26e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 528496162   8 KRHPSERRKEksrdaarcRRSKETEvfyELAHQLPLPHSISSHLDKASIMRLAISFLRTRKLFSSG 73
Cdd:cd19696    4 KSNPSKRHRD--------RLNSELD---ELASLLPFPEDVISKLDKLSVLRLSVSYLRTKNYFQAV 58
bHLH-PAS_AhR cd11436
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor (AhR) ...
 8-71 6.61e-07

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: 47.23  E-value: 6.61e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 528496162   8 KRHPSERRKEksrdaarcRRSKETEvfyELAHQLPLPHSISSHLDKASIMRLAISFLRTRKLFS 71
Cdd:cd11436    5 KSNPSKRHRD--------RLNTELD---RLASLLPFPQDVISKLDKLSVLRLSVSYLRAKSFFD 57
bHLH-PAS_AhRR cd11435
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor ...
 17-72 5.87e-06

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: 44.58  E-value: 5.87e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 528496162  17 EKSRDAARCRRSKETEVfYELAHQLPLPHSISSHLDKASIMRLAISFLRTRKLFSS 72
Cdd:cd11435    3 EKSNPSKRHRDRLNAEL-DHLASLLPFPPDIISKLDKLSVLRLSVSYLRVKSFFQA 57
PAS COG2202
PAS domain [Signal transduction mechanisms];
250-339 8.05e-06

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 48.10  E-value: 8.05e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528496162 250 DMKFIYCDERVSSLIGYRPEELLGRSVYEFCHALDSENMTKSHQNLCNKG-QVVSGQYRMLAKNGGYVWVETQATVIYNN 328
Cdd:COG2202  156 DGRILYVNPAAEELLGYSPEELLGKSLLDLLHPEDRERLLELLRRLLEGGrESYELELRLKDGDGRWVWVEASAVPLRDG 235

                         90
                 ....*....|.
gi 528496162 329 RnsQPQCIICI 339
Cdd:COG2202  236 G--EVIGVLGI 244
bHLH-PAS_spineless_like cd19730
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Drosophila melanogaster protein ...
 8-72 1.13e-05

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: 43.69  E-value: 1.13e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 528496162   8 KRHPSERRKEksrdaarcRRSKETEvfyELAHQLPLPHSISSHLDKASIMRLAISFLRTRKLFSS 72
Cdd:cd19730    7 KSNPSKRHRE--------RLNAELD---HLASLLPFEQSVISKLDKLSILRLSVSYLRTKSYFQA 60
KinA COG5805
Sporulation sensor histidine kinase A (Stage II sporulation protein SpoIIF/SpoIIJ) [Cell cycle ...
 89-167 9.20e-05

Sporulation sensor histidine kinase A (Stage II sporulation protein SpoIIF/SpoIIJ) [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms];


Pssm-ID: 444507 [Multi-domain]  Cd Length: 496  Bit Score: 45.88  E-value: 9.20e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528496162  89 NLYLKSLEGFVIVVTSDGDMIFLSENVSKFMGLTQVELTGHSIFDFTHPCDHEEIRENL--------------------- 147
Cdd:COG5805  160 QTLIENSPDLICVIDTDGRILFINESIERLFGAPREELIGKNLLELLHPCDKEEFKERIesitevwqefiiereiitkdg 239

                         90       100
                 ....*....|....*....|....*...
gi 528496162 148 -----SIKSGPVYGRKGKE---MSTSRD 167
Cdd:COG5805  240 riryfEAVIVPLIDTDGSVkgiLVILRD 267
KinA COG5805
Sporulation sensor histidine kinase A (Stage II sporulation protein SpoIIF/SpoIIJ) [Cell cycle ...
 248-330 9.77e-05

Sporulation sensor histidine kinase A (Stage II sporulation protein SpoIIF/SpoIIJ) [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms];


Pssm-ID: 444507 [Multi-domain]  Cd Length: 496  Bit Score: 45.88  E-value: 9.77e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528496162 248 SMDMKFIYCDERVSSLIGYRPEELLGRSVYEFCHALDSENMTKSHQNLcNKGQVVSGQYRMLAKNGGYVWVETQATVIYN 327
Cdd:COG5805   51 NREGKVIYINPAMEKLLGYTSEEIIGKTIFDFLEKEYHYRVKTRIERL-QKGYDVVMIEQIYCKDGELIYVEVKLFPIYN 129


                 ...
gi 528496162 328 NRN 330
Cdd:COG5805  130 QNG 132
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 252-339 1.72e-04

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


Pssm-ID: 395786 [Multi-domain]  Cd Length: 113  Bit Score: 41.63  E-value: 1.72e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528496162  252 KFIYCDERVSSLIGYRPEELLGRSVYEFCHALDSENMTKSHQNLCN-KGQVVSGQYRMLAKNGGYVWVETQATVIYnNRN 330
Cdd:pfam00989  22 RILYVNAAAEELLGLSREEVIGKSLLDLIPEEDDAEVAELLRQALLqGEESRGFEVSFRVPDGRPRHVEVRASPVR-DAG 100


                  ....*....
gi 528496162  331 SQPQCIICI 339
Cdd:pfam00989 101 GEILGFLGV 109
sensory_box TIGR00229
PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain ...
 252-330 2.56e-03

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


Pssm-ID: 272971 [Multi-domain]  Cd Length: 124  Bit Score: 38.81  E-value: 2.56e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528496162  252 KFIYCDERVSSLIGYRPEELLGRSVYEFCHALDSE-NMTKSHQNLCNKGQVVSGQYRMLAKNGGYVWVETQATVIYNNRN 330
Cdd:TIGR00229  24 NILYVNPAFEEIFGYSAEELIGRNVLELIPEEDREeVRERIERRLEGEPEPVSEERRVRRKDGSEIWVEVSVSPIRTNGG 103
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 94-183 2.61e-03

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: 38.55  E-value: 2.61e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528496162   94 SLEGFVIVVTSDGDMIFLSENVSKFMGLTQVELTGHSIFDFTHPCDHEEIRENLSiksgpvygrkgKEMSTSRDFFMRMK 173
Cdd:pfam00989   9 SLPDGIFVVDEDGRILYVNAAAEELLGLSREEVIGKSLLDLIPEEDDAEVAELLR-----------QALLQGEESRGFEV 77

                          90
                  ....*....|
gi 528496162  174 CTVTNRGRTV 183
Cdd:pfam00989  78 SFRVPDGRPR 87
sensory_box TIGR00229
PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain ...
 100-148 3.73e-03

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


Pssm-ID: 272971 [Multi-domain]  Cd Length: 124  Bit Score: 38.04  E-value: 3.73e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 528496162  100 IVVTSDGDMIFLSENVSKFMGLTQVELTGHSIFDFTHPCDHEEIRENLS 148
Cdd:TIGR00229  17 IVIDLEGNILYVNPAFEEIFGYSAEELIGRNVLELIPEEDREEVRERIE 65
PAS COG2202
PAS domain [Signal transduction mechanisms];
86-147 5.14e-03

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 39.62  E-value: 5.14e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 528496162  86 QMDNLYLKSLEGFVIVVTSDGDMIFLSENVSKFMGLTQVELTGHSIFDFTHPCDHEEIRENL 147
Cdd:COG2202  137 ERLRLLVENAPDGIFVLDLDGRILYVNPAAEELLGYSPEELLGKSLLDLLHPEDRERLLELL 198
bHLH-PAS_ARNT_like cd11437
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor ...
 26-66 9.61e-03

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


Pssm-ID: 381443  Cd Length: 58  Bit Score: 35.09  E-value: 9.61e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 528496162  26 RRSKETEVFYELAHQLPLPHSISSHLDKASIMRLAISFLRT 66
Cdd:cd11437   12 RRDKMNAYIQELSALVPACNAMSRKLDKLTVLRMAVQHLKS 52
 
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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