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Conserved domains on  [gi|194239684|ref|NP_033664|]
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single-minded homolog 2 short isoform [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SIM_C super family cl28759
Single-minded protein C-terminus; This family represents the C-terminal region of the ...
 358-530 2.30e-82

Single-minded protein C-terminus; This family represents the C-terminal region of the eukaryotic single-minded (SIM) protein. Drosophila single-minded acts as a positive master gene regulator in central nervous system midline formation. There are two homologs in mammals: SIM1 and SIM2, which are members of the basic-helix-loop-helix PAS family of transcription factors. SIM1 and SIM2 are novel heterodimerization partners for ARNT in vitro, and they may function both as positive and negative transcriptional regulators in vivo, during embryogenesis and in the adult organizm. SIM2 is thought to contribute to some specific Down syndrome phenotypes. This family is found in conjunction with a pfam00989 domain and associated pfam00785 motif.


The actual alignment was detected with superfamily member pfam06621:

Pssm-ID: 461963  Cd Length: 296  Bit Score: 259.39  E-value: 2.30e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194239684  358 TALSTSQETRKLVKPKNTKMKTKLRTNPYPpQQYSSFQMDKLECGQLGNWrASPPASAAAPPELQPHSESSDLLYT-PSY 436
Cdd:pfam06621   1 TSTSTSQENRKLAKSRSTKVKTKLRTSPYP-QQYSSFQTDKSESDQDSPW-GSSPLTDSASPQLLDHSEGSDLLYAyRQY 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194239684  437 SLPFSYHYGHFPLDSHVFSSKKPMLPAKFGQP-QGSPCEVARFFLSTLPASGECQWHYANPLVPSS-SSPAKNPPEP-PA 513
Cdd:pfam06621  79 SDPFSLCYGHFPLDSHVFSSKKPMLSHKFGQPcEGGPCEAARYFLGTPQTGRECWWHTANSLVPLSkSSPEKNLSDPhPA 158

                         170
                  ....*....|....*..
gi 194239684  514 NTARHSLVPSYEGGSGL 530
Cdd:pfam06621 159 NIHRHNGRGHWEEDSVV 175
bHLH-PAS_SIM2 cd19739
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in single-minded homolog 2 (SIM2) ...
 1-74 4.48e-49

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: 164.14  E-value: 4.48e-49
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 194239684   1 MKEKSKNAAKTRREKENGEFYELAKLLPLPSAITSQLDKASIIRLTTSYLKMRAVFPEGLGDAWGQPSRAGPLD 74
Cdd:cd19739    1 MKEKSKNAAKTRREKENGEFYELAKLLPLPSAITSQLDKASIIRLTTSYLKMRAVFPEGLGDAWGQPSRIGPLD 74
PAS_3 pfam08447
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 243-329 6.76e-19

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


:

Pssm-ID: 430001 [Multi-domain]  Cd Length: 89  Bit Score: 81.62  E-value: 6.76e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194239684  243 IFLDSRVTEVTGYEPQDLIEK--TLYHHVHGCDVFHLRYAHHLLLVKGQVTTKYYRLLSKRGGWVWVQSYATVVHNSrSS 320
Cdd:pfam08447   2 IYWSPRFEEILGYTPEELLGKgeSWLDLVHPDDRERVREALWEALKGGEPYSGEYRIRRKDGEYRWVEARARPIRDE-NG 80


                  ....*....
gi 194239684  321 RPHCIVSVN 329
Cdd:pfam08447  81 KPVRVIGVA 89
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 88-158 5.06e-13

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: 65.35  E-value: 5.06e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 194239684  88 LDGFVFVVASDGKIMYISETASVHLGLSQVELTGNSIYEYIHPSDHDEMTAVLTAHQPLHHHLLQEYEIER 158
Cdd:cd00130    1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRR 71
 
Name Accession Description Interval E-value
SIM_C pfam06621
Single-minded protein C-terminus; This family represents the C-terminal region of the ...
 358-530 2.30e-82

Single-minded protein C-terminus; This family represents the C-terminal region of the eukaryotic single-minded (SIM) protein. Drosophila single-minded acts as a positive master gene regulator in central nervous system midline formation. There are two homologs in mammals: SIM1 and SIM2, which are members of the basic-helix-loop-helix PAS family of transcription factors. SIM1 and SIM2 are novel heterodimerization partners for ARNT in vitro, and they may function both as positive and negative transcriptional regulators in vivo, during embryogenesis and in the adult organizm. SIM2 is thought to contribute to some specific Down syndrome phenotypes. This family is found in conjunction with a pfam00989 domain and associated pfam00785 motif.


Pssm-ID: 461963  Cd Length: 296  Bit Score: 259.39  E-value: 2.30e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194239684  358 TALSTSQETRKLVKPKNTKMKTKLRTNPYPpQQYSSFQMDKLECGQLGNWrASPPASAAAPPELQPHSESSDLLYT-PSY 436
Cdd:pfam06621   1 TSTSTSQENRKLAKSRSTKVKTKLRTSPYP-QQYSSFQTDKSESDQDSPW-GSSPLTDSASPQLLDHSEGSDLLYAyRQY 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194239684  437 SLPFSYHYGHFPLDSHVFSSKKPMLPAKFGQP-QGSPCEVARFFLSTLPASGECQWHYANPLVPSS-SSPAKNPPEP-PA 513
Cdd:pfam06621  79 SDPFSLCYGHFPLDSHVFSSKKPMLSHKFGQPcEGGPCEAARYFLGTPQTGRECWWHTANSLVPLSkSSPEKNLSDPhPA 158

                         170
                  ....*....|....*..
gi 194239684  514 NTARHSLVPSYEGGSGL 530
Cdd:pfam06621 159 NIHRHNGRGHWEEDSVV 175
bHLH-PAS_SIM2 cd19739
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in single-minded homolog 2 (SIM2) ...
 1-74 4.48e-49

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: 164.14  E-value: 4.48e-49
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 194239684   1 MKEKSKNAAKTRREKENGEFYELAKLLPLPSAITSQLDKASIIRLTTSYLKMRAVFPEGLGDAWGQPSRAGPLD 74
Cdd:cd19739    1 MKEKSKNAAKTRREKENGEFYELAKLLPLPSAITSQLDKASIIRLTTSYLKMRAVFPEGLGDAWGQPSRIGPLD 74
PAS_3 pfam08447
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 243-329 6.76e-19

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


Pssm-ID: 430001 [Multi-domain]  Cd Length: 89  Bit Score: 81.62  E-value: 6.76e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194239684  243 IFLDSRVTEVTGYEPQDLIEK--TLYHHVHGCDVFHLRYAHHLLLVKGQVTTKYYRLLSKRGGWVWVQSYATVVHNSrSS 320
Cdd:pfam08447   2 IYWSPRFEEILGYTPEELLGKgeSWLDLVHPDDRERVREALWEALKGGEPYSGEYRIRRKDGEYRWVEARARPIRDE-NG 80


                  ....*....
gi 194239684  321 RPHCIVSVN 329
Cdd:pfam08447  81 KPVRVIGVA 89
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 229-328 4.00e-13

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: 65.73  E-value: 4.00e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194239684 229 SNMFMFRASLDLKLIFLDSRVTEVTGYEPQDLIEKTLYHHVHGCDVFHLRYAHHLLLVKGQVTTKYYRLLSKRGGWVWVQ 308
Cdd:cd00130    1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDGSVIWVL 80

                         90       100
                 ....*....|....*....|
gi 194239684 309 SYATVVHNSRSSRPHCIVSV 328
Cdd:cd00130   81 VSLTPIRDEGGEVIGLLGVV 100
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 88-158 5.06e-13

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: 65.35  E-value: 5.06e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 194239684  88 LDGFVFVVASDGKIMYISETASVHLGLSQVELTGNSIYEYIHPSDHDEMTAVLTAHQPLHHHLLQEYEIER 158
Cdd:cd00130    1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRR 71
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 79-140 5.06e-13

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: 63.96  E-value: 5.06e-13
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 194239684    79 ELGSHLLQTLDGFVFVVASDGKIMYISETASVHLGLSQVELTGNSIYEYIHPSDHDEMTAVL 140
Cdd:smart00091   1 ERLRAILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEAL 62
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 79-159 1.92e-12

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: 63.98  E-value: 1.92e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194239684   79 ELGSHLLQTLDGFVFVVASDGKIMYISETASVHLGLSQVELTGNSIYEYIHPSDHDEM-TAVLTAHQPLHHHLLQEYEIE 157
Cdd:pfam00989   1 EDLRAILESLPDGIFVVDEDGRILYVNAAAEELLGLSREEVIGKSLLDLIPEEDDAEVaELLRQALLQGEESRGFEVSFR 80


                  ..
gi 194239684  158 RS 159
Cdd:pfam00989  81 VP 82
HLH smart00353
helix loop helix domain;
8-51 1.86e-08

helix loop helix domain;


Pssm-ID: 197674 [Multi-domain]  Cd Length: 53  Bit Score: 50.68  E-value: 1.86e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 194239684     8 AAKTRREKENGEFYELAKLLPlPSAITSQLDKASIIRLTTSYLK 51
Cdd:smart00353   3 RERRRRRKINEAFDELRSLLP-TLPKNKKLSKAEILRLAIEYIK 45
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 224-285 8.62e-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: 46.62  E-value: 8.62e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 194239684   224 EIKLYSNMFMFRASLDLKLIFLDSRVTEVTGYEPQDLIEKTLYHHVHGCDVFHLRYAHHLLL 285
Cdd:smart00091   5 AILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEALQRLL 66
PAS COG2202
PAS domain [Signal transduction mechanisms];
229-365 5.82e-05

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 45.02  E-value: 5.82e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194239684 229 SNMFMFRASLDLKLIFLDSRVTEVTGYEPQDLIEKTLYHHVHGCDVFHLRYAHHLLLVKGQVTTKYYRLLSKRGGWVWVQ 308
Cdd:COG2202   20 SPDAIIITDLDGRILYVNPAFERLTGYSAEELLGKTLRDLLPPEDDDEFLELLRAALAGGGVWRGELRNRRKDGSLFWVE 99

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 194239684 309 SYATVVHNSRSSRPHCIVsvnyVLTEI-EYKELQLSLEQvstakSQDSWRTALSTSQE 365
Cdd:COG2202  100 LSISPVRDEDGEITGFVG----IARDItERKRAEEALRE-----SEERLRLLVENAPD 148
PAS COG2202
PAS domain [Signal transduction mechanisms];
83-157 9.29e-04

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 41.16  E-value: 9.29e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 194239684  83 HLLQTLDGFVFVVASDGKIMYISETASVHLGLSQVELTGNSIYEYIHPSDHDEMTAVLtahQPLHHHLLQEYEIE 157
Cdd:COG2202  141 LLVENAPDGIFVLDLDGRILYVNPAAEELLGYSPEELLGKSLLDLLHPEDRERLLELL---RRLLEGGRESYELE 212
HLH pfam00010
Helix-loop-helix DNA-binding domain;
2-52 3.26e-03

Helix-loop-helix DNA-binding domain;


Pssm-ID: 459628 [Multi-domain]  Cd Length: 53  Bit Score: 35.90  E-value: 3.26e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 194239684    2 KEKSKNAA-KTRREKENGEFYELAKLLPLpSAITSQLDKASIIRLTTSYLKM 52
Cdd:pfam00010   1 RREAHNEReRRRRDRINDAFDELRELLPT-LPPDKKLSKAEILRLAIEYIKH 51
sensory_box TIGR00229
PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain ...
 221-308 8.96e-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: 36.50  E-value: 8.96e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194239684  221 AITEiklYSNMFMFRASLDLKLIFLDSRVTEVTGYEPQDLIEKTL--YHHVHGCDVFHLRYAHHlLLVKGQVTTKYYRLL 298
Cdd:TIGR00229   7 AIFE---SSPDAIIVIDLEGNILYVNPAFEEIFGYSAEELIGRNVleLIPEEDREEVRERIERR-LEGEPEPVSEERRVR 82

                          90
                  ....*....|
gi 194239684  299 SKRGGWVWVQ 308
Cdd:TIGR00229  83 RKDGSEIWVE 92
 
Name Accession Description Interval E-value
SIM_C pfam06621
Single-minded protein C-terminus; This family represents the C-terminal region of the ...
 358-530 2.30e-82

Single-minded protein C-terminus; This family represents the C-terminal region of the eukaryotic single-minded (SIM) protein. Drosophila single-minded acts as a positive master gene regulator in central nervous system midline formation. There are two homologs in mammals: SIM1 and SIM2, which are members of the basic-helix-loop-helix PAS family of transcription factors. SIM1 and SIM2 are novel heterodimerization partners for ARNT in vitro, and they may function both as positive and negative transcriptional regulators in vivo, during embryogenesis and in the adult organizm. SIM2 is thought to contribute to some specific Down syndrome phenotypes. This family is found in conjunction with a pfam00989 domain and associated pfam00785 motif.


Pssm-ID: 461963  Cd Length: 296  Bit Score: 259.39  E-value: 2.30e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194239684  358 TALSTSQETRKLVKPKNTKMKTKLRTNPYPpQQYSSFQMDKLECGQLGNWrASPPASAAAPPELQPHSESSDLLYT-PSY 436
Cdd:pfam06621   1 TSTSTSQENRKLAKSRSTKVKTKLRTSPYP-QQYSSFQTDKSESDQDSPW-GSSPLTDSASPQLLDHSEGSDLLYAyRQY 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194239684  437 SLPFSYHYGHFPLDSHVFSSKKPMLPAKFGQP-QGSPCEVARFFLSTLPASGECQWHYANPLVPSS-SSPAKNPPEP-PA 513
Cdd:pfam06621  79 SDPFSLCYGHFPLDSHVFSSKKPMLSHKFGQPcEGGPCEAARYFLGTPQTGRECWWHTANSLVPLSkSSPEKNLSDPhPA 158

                         170
                  ....*....|....*..
gi 194239684  514 NTARHSLVPSYEGGSGL 530
Cdd:pfam06621 159 NIHRHNGRGHWEEDSVV 175
bHLH-PAS_SIM2 cd19739
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in single-minded homolog 2 (SIM2) ...
 1-74 4.48e-49

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: 164.14  E-value: 4.48e-49
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 194239684   1 MKEKSKNAAKTRREKENGEFYELAKLLPLPSAITSQLDKASIIRLTTSYLKMRAVFPEGLGDAWGQPSRAGPLD 74
Cdd:cd19739    1 MKEKSKNAAKTRREKENGEFYELAKLLPLPSAITSQLDKASIIRLTTSYLKMRAVFPEGLGDAWGQPSRIGPLD 74
bHLH-PAS_SIM1 cd19738
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in single-minded homolog 1 (SIM1) ...
 1-69 8.00e-43

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: 147.62  E-value: 8.00e-43
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 194239684   1 MKEKSKNAAKTRREKENGEFYELAKLLPLPSAITSQLDKASIIRLTTSYLKMRAVFPEGLGDAWGQPSR 69
Cdd:cd19738    1 MKEKSKNAARTRREKENSEFYELAKLLPLPSAITSQLDKASIIRLTTSYLKMRVVFPEGLGEAWGHSSR 69
bHLH-PAS_SIM cd11434
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in single-minded (SIM) family; The ...
 1-61 1.97e-38

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: 135.11  E-value: 1.97e-38
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 194239684   1 MKEKSKNAAKTRREKENGEFYELAKLLPLPSAITSQLDKASIIRLTTSYLKMRAVFPEGLG 61
Cdd:cd11434    1 MKEKSKNAARTRREKENAEFYELAKLLPLPSAITSQLDKASIIRLTTSYLKMRAVFPEGLG 61
bHLH-PAS_dSIM_like cd19740
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Drosophila melanogaster protein ...
 1-62 1.44e-37

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: 132.89  E-value: 1.44e-37
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 194239684   1 MKEKSKNAAKTRREKENGEFYELAKLLPLPSAITSQLDKASIIRLTTSYLKMRAVFPEGLGD 62
Cdd:cd19740    1 MKEKSKNAARSRREKENAEFLELAKLLPLPAAITSQLDKASIIRLTTSYLKMRQVFPDGLGD 62
bHLH-PAS_NPAS1_PASD5 cd19731
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing ...
 2-53 7.06e-28

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: 106.54  E-value: 7.06e-28
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 194239684   2 KEKSKNAAKTRREKENGEFYELAKLLPLPSAITSQLDKASIIRLTTSYLKMR 53
Cdd:cd19731    5 KEKSRNAARSRRGKENFEFYELAKMLPLPGAITSQLDKASIVRLTISYLKMR 56
bHLH-PAS_NPAS3_PASD6 cd19732
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing ...
 2-53 2.83e-27

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: 105.08  E-value: 2.83e-27
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 194239684   2 KEKSKNAAKTRREKENGEFYELAKLLPLPSAITSQLDKASIIRLTTSYLKMR 53
Cdd:cd19732    7 KEKSRDAARSRRGKENFEFYELAKLLPLPAAITSQLDKASIIRLTISYLKMR 58
bHLH-PAS_trachealess_like cd19733
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Drosophila melanogaster protein ...
 2-53 3.83e-27

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: 104.63  E-value: 3.83e-27
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 194239684   2 KEKSKNAAKTRREKENGEFYELAKLLPLPSAITSQLDKASIIRLTTSYLKMR 53
Cdd:cd19733    6 KEKSRDAARSRRGKENYEFYELAKMLPLPAAITSQLDKASIIRLTISYLKLR 57
bHLH-PAS_NPAS1_3_like cd11432
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing ...
 2-53 1.60e-26

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: 101.88  E-value: 1.60e-26
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 194239684   2 KEKSKNAAKTRREKENGEFYELAKLLPLPSAITSQLDKASIIRLTTSYLKMR 53
Cdd:cd11432    1 KEKSRNAARSRRGKENYEFYELAKLLPLPAAISSQLDKASIVRLTISYLKLR 52
bHLH_PAS cd11391
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain family; bHLH-PAS domain has been found ...
 2-56 9.80e-24

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: 94.18  E-value: 9.80e-24
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 194239684   2 KEKSKNAAKTRREKENGEFYELAKLLPLPSAITSQLDKASIIRLTTSYLKMRAVF 56
Cdd:cd11391    1 REKSREAAKKRRDKENAEISELASLLPLPPAVGSKLDKLSVLRLAVAYLRLKKFL 55
bHLH-PAS_HIF cd11433
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in hypoxia-inducible factor (HIF) ...
 2-57 1.71e-22

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: 90.77  E-value: 1.71e-22
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 194239684   2 KEKSKNAAKTRREKENGEFYELAKLLPLPSAITSQLDKASIIRLTTSYLKMRAVFP 57
Cdd:cd11433    2 KEKSRDAARCRRGKESEIFYELAHQLPLPHSVSSQLDKASIMRLTISYLKLRKLLS 57
bHLH-PAS_HIF1a_PASD8 cd19727
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in hypoxia-inducible factor ...
 2-59 6.29e-19

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: 81.23  E-value: 6.29e-19
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 194239684   2 KEKSKNAAKTRREKENGEFYELAKLLPLPSAITSQLDKASIIRLTTSYLKMRAVFPEG 59
Cdd:cd19727    7 KEKSRDAARSRRSKESEVFYELAHQLPLPHNVSSHLDKASIMRLTISYLRMRKLLDAG 64
PAS_3 pfam08447
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 243-329 6.76e-19

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


Pssm-ID: 430001 [Multi-domain]  Cd Length: 89  Bit Score: 81.62  E-value: 6.76e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194239684  243 IFLDSRVTEVTGYEPQDLIEK--TLYHHVHGCDVFHLRYAHHLLLVKGQVTTKYYRLLSKRGGWVWVQSYATVVHNSrSS 320
Cdd:pfam08447   2 IYWSPRFEEILGYTPEELLGKgeSWLDLVHPDDRERVREALWEALKGGEPYSGEYRIRRKDGEYRWVEARARPIRDE-NG 80


                  ....*....
gi 194239684  321 RPHCIVSVN 329
Cdd:pfam08447  81 KPVRVIGVA 89
bHLH-PAS_HIF3a_PASD7 cd19729
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in hypoxia-inducible factor ...
 2-59 6.30e-18

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: 78.13  E-value: 6.30e-18
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 194239684   2 KEKSKNAAKTRREKENGEFYELAKLLPLPSAITSQLDKASIIRLTTSYLKMRAVFPEG 59
Cdd:cd19729    5 KEKSRDAARCRRSQETEVFYELAHTLPFPRGVSSHLDKASIMRLTISYLRMHRLIASG 62
bHLH-PAS_HIF2a_PASD2 cd19728
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in hypoxia-inducible factor ...
 2-60 4.44e-17

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: 75.50  E-value: 4.44e-17
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 194239684   2 KEKSKNAAKTRREKENGEFYELAKLLPLPSAITSQLDKASIIRLTTSYLKMRAVFPEGL 60
Cdd:cd19728    8 KEKSRDAARCRRSKETEVFYELAHQLPLPHSVSSHLDKASIMRLAISFLRTHKLLSSVC 66
PAS_11 pfam14598
PAS domain; This family includes the PAS-B domain of NCOA1 (Nuclear receptor coactivator 1), ...
 232-334 4.12e-14

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: 68.48  E-value: 4.12e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194239684  232 FMFRASLDLKLIFLDSRVTEVTGYEPQDLIEKTLYHHVHGCDVFHLRYAHHLLLVK-GQVTTKYYRLLSKRGGWVWVQSY 310
Cdd:pfam14598   4 FTTRHDIDGKIISCDTRAPFSLGYEKDELVGRSIYDLVHPQDLRTAKSHLREIIQTrGRATSPSYRLRLRDGDFLSVHTK 83

                          90       100
                  ....*....|....*....|....
gi 194239684  311 ATVVHNSRSSRPHCIVSVNYVLTE 334
Cdd:pfam14598  84 SKLFLNQNSNQQPFIMCTHTILRE 107
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 229-328 4.00e-13

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: 65.73  E-value: 4.00e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194239684 229 SNMFMFRASLDLKLIFLDSRVTEVTGYEPQDLIEKTLYHHVHGCDVFHLRYAHHLLLVKGQVTTKYYRLLSKRGGWVWVQ 308
Cdd:cd00130    1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDGSVIWVL 80

                         90       100
                 ....*....|....*....|
gi 194239684 309 SYATVVHNSRSSRPHCIVSV 328
Cdd:cd00130   81 VSLTPIRDEGGEVIGLLGVV 100
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 88-158 5.06e-13

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: 65.35  E-value: 5.06e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 194239684  88 LDGFVFVVASDGKIMYISETASVHLGLSQVELTGNSIYEYIHPSDHDEMTAVLTAHQPLHHHLLQEYEIER 158
Cdd:cd00130    1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRR 71
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 79-140 5.06e-13

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: 63.96  E-value: 5.06e-13
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 194239684    79 ELGSHLLQTLDGFVFVVASDGKIMYISETASVHLGLSQVELTGNSIYEYIHPSDHDEMTAVL 140
Cdd:smart00091   1 ERLRAILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEAL 62
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 79-159 1.92e-12

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: 63.98  E-value: 1.92e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194239684   79 ELGSHLLQTLDGFVFVVASDGKIMYISETASVHLGLSQVELTGNSIYEYIHPSDHDEM-TAVLTAHQPLHHHLLQEYEIE 157
Cdd:pfam00989   1 EDLRAILESLPDGIFVVDEDGRILYVNAAAEELLGLSREEVIGKSLLDLIPEEDDAEVaELLRQALLQGEESRGFEVSFR 80


                  ..
gi 194239684  158 RS 159
Cdd:pfam00989  81 VP 82
bHLH-PAS_AhR_like cd19696
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in the aryl hydrocarbon receptor ...
 7-56 8.71e-12

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: 60.38  E-value: 8.71e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 194239684   7 NAAKTRREKENGEFYELAKLLPLPSAITSQLDKASIIRLTTSYLKMRAVF 56
Cdd:cd19696    6 NPSKRHRDRLNSELDELASLLPFPEDVISKLDKLSVLRLSVSYLRTKNYF 55
bHLH-PAS_AhRR cd11435
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor ...
 3-56 5.26e-11

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: 58.06  E-value: 5.26e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 194239684   3 EKSkNAAKTRREKENGEFYELAKLLPLPSAITSQLDKASIIRLTTSYLKMRAVF 56
Cdd:cd11435    3 EKS-NPSKRHRDRLNAELDHLASLLPFPPDIISKLDKLSVLRLSVSYLRVKSFF 55
bHLH-PAS_AhR cd11436
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor (AhR) ...
 7-56 3.25e-10

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: 56.09  E-value: 3.25e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 194239684   7 NAAKTRREKENGEFYELAKLLPLPSAITSQLDKASIIRLTTSYLKMRAVF 56
Cdd:cd11436    7 NPSKRHRDRLNTELDRLASLLPFPQDVISKLDKLSVLRLSVSYLRAKSFF 56
bHLH-PAS_spineless_like cd19730
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Drosophila melanogaster protein ...
 7-56 1.20e-08

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: 51.78  E-value: 1.20e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 194239684   7 NAAKTRREKENGEFYELAKLLPLPSAITSQLDKASIIRLTTSYLKMRAVF 56
Cdd:cd19730    9 NPSKRHRERLNAELDHLASLLPFEQSVISKLDKLSILRLSVSYLRTKSYF 58
HLH smart00353
helix loop helix domain;
8-51 1.86e-08

helix loop helix domain;


Pssm-ID: 197674 [Multi-domain]  Cd Length: 53  Bit Score: 50.68  E-value: 1.86e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 194239684     8 AAKTRREKENGEFYELAKLLPlPSAITSQLDKASIIRLTTSYLK 51
Cdd:smart00353   3 RERRRRRKINEAFDELRSLLP-TLPKNKKLSKAEILRLAIEYIK 45
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 224-285 8.62e-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: 46.62  E-value: 8.62e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 194239684   224 EIKLYSNMFMFRASLDLKLIFLDSRVTEVTGYEPQDLIEKTLYHHVHGCDVFHLRYAHHLLL 285
Cdd:smart00091   5 AILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEALQRLL 66
bHLH-PAS_ARNT_like cd11437
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor ...
 10-51 1.59e-05

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: 42.41  E-value: 1.59e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 194239684  10 KTRREKENGEFYELAKLLPLPSAITSQLDKASIIRLTTSYLK 51
Cdd:cd11437   10 KRRRDKMNAYIQELSALVPACNAMSRKLDKLTVLRMAVQHLK 51
PAC smart00086
Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); PAC motif ...
 292-334 2.45e-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: 41.40  E-value: 2.45e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 194239684   292 TKYYRLLSKRGGWVWVQSYATVVHNsRSSRPHCIVSVNYVLTE 334
Cdd:smart00086   1 TVEYRLRRKDGSYIWVLVSASPIRD-EDGEVEGILGVVRDITE 42
bHLH-PAS_NPAS4_PASD10 cd19697
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing ...
 5-58 4.37e-05

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing protein 4 (NPAS4) and similar proteins; NPAS4, also termed neuronal Per-Arnt-Sim homology (PAS) factor 4, or neuronal PAS4, or Class E basic helix-loop-helix protein 79 (bHLHe79), or HLH-PAS transcription factor NXF, or PAS domain-containing protein 10 (PASD10), is a bHLH-PAS neuronal activity-dependent transcription factor which heterodimerizes with ARNT2 to regulate genes involved in inhibitory synapse formation.


Pssm-ID: 381540  Cd Length: 57  Bit Score: 41.14  E-value: 4.37e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 194239684   5 SKNAAKTRREKENGEFYELAKLLPLPSAITSQLDKASIIRLTTSYLKMRAVFPE 58
Cdd:cd19697    4 TKGASKQRRDLINAEIRELRDLLPLPESTRQRLSQLQIMSLACVYIRKSNFFSQ 57
PAS COG2202
PAS domain [Signal transduction mechanisms];
229-365 5.82e-05

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 45.02  E-value: 5.82e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194239684 229 SNMFMFRASLDLKLIFLDSRVTEVTGYEPQDLIEKTLYHHVHGCDVFHLRYAHHLLLVKGQVTTKYYRLLSKRGGWVWVQ 308
Cdd:COG2202   20 SPDAIIITDLDGRILYVNPAFERLTGYSAEELLGKTLRDLLPPEDDDEFLELLRAALAGGGVWRGELRNRRKDGSLFWVE 99

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 194239684 309 SYATVVHNSRSSRPHCIVsvnyVLTEI-EYKELQLSLEQvstakSQDSWRTALSTSQE 365
Cdd:COG2202  100 LSISPVRDEDGEITGFVG----IARDItERKRAEEALRE-----SEERLRLLVENAPD 148
bHLH_SF cd00083
basic Helix Loop Helix (bHLH) domain superfamily; bHLH proteins are transcriptional regulators ...
 12-52 7.20e-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: 40.20  E-value: 7.20e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 194239684  12 RREKENGEFYELAKLLPLPSAItSQLDKASIIRLTTSYLKM 52
Cdd:cd00083    4 RRDKINDAFEELKRLLPELPDS-KKLSKASILQKAVEYIRE 43
bHLH-PAS_ARNTL_PASD3 cd11438
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor ...
 2-51 1.63e-04

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: 40.09  E-value: 1.63e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 194239684   2 KEKSKNAAKTRREKENGEFYELAKLLPLPSAITSQLDKASIIRLTTSYLK 51
Cdd:cd11438    8 REAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMK 57
PAS_11 pfam14598
PAS domain; This family includes the PAS-B domain of NCOA1 (Nuclear receptor coactivator 1), ...
 91-194 5.21e-04

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: 39.97  E-value: 5.21e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194239684   91 FVFVVASDGKIMYISETASVHLGLSQVELTGNSIYEYIHPSDhdemtaVLTAHQpLHHHLLQEYEIERSFFLRMKcvlak 170
Cdd:pfam14598   4 FTTRHDIDGKIISCDTRAPFSLGYEKDELVGRSIYDLVHPQD------LRTAKS-HLREIIQTRGRATSPSYRLR----- 71

                          90       100
                  ....*....|....*....|....
gi 194239684  171 rnagLTCSGYKVIHCSGYLKIRQY 194
Cdd:pfam14598  72 ----LRDGDFLSVHTKSKLFLNQN 91
bHLH-O_HERP_like cd11389
basic helix-loop-helix-orange (bHLH-O) domain found in hairy and enhancer of split (HES) ...
 6-52 9.02e-04

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


Pssm-ID: 381395 [Multi-domain]  Cd Length: 55  Bit Score: 37.69  E-value: 9.02e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 194239684   6 KNAAKTRREKENGEFYELAKLLP--LPSAITSQLDKASIIRLTTSYLKM 52
Cdd:cd11389    2 KVIEKRRRDRINESLAELRRLVPeaRKSKGSGKLEKAEILEMTLQHLKA 50
PAS COG2202
PAS domain [Signal transduction mechanisms];
83-157 9.29e-04

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 41.16  E-value: 9.29e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 194239684  83 HLLQTLDGFVFVVASDGKIMYISETASVHLGLSQVELTGNSIYEYIHPSDHDEMTAVLtahQPLHHHLLQEYEIE 157
Cdd:COG2202  141 LLVENAPDGIFVLDLDGRILYVNPAAEELLGYSPEELLGKSLLDLLHPEDRERLLELL---RRLLEGGRESYELE 212
bHLH-O_HERP cd11407
basic helix-loop-helix-orange (bHLH-O) domain found in hairy and enhancer of split (HES) ...
 10-52 9.45e-04

basic helix-loop-helix-orange (bHLH-O) domain found in hairy and enhancer of split (HES)-related repressor protein (HERP) family; HERP (also called Hey/Hesr/HRT/CHF/gridlock) proteins corresponds to a family of bHLH-O transcriptional repressors that are related to the Drosophila hairy and Enhancer-of-split proteins and act as downstream effectors of Notch signaling. They contain a basic helix-loop-helix (bHLH) domain with an invariant glycine residue in its basic region, an orange domain in the central region and YXXW sequence motif at its C-terminal region. HERP proteins are involved in cardiovascular development and have roles in somitogenesis, myogenesis and gliogenesis.


Pssm-ID: 381413 [Multi-domain]  Cd Length: 59  Bit Score: 37.79  E-value: 9.45e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 194239684  10 KTRREKENGEFYELAKLLPlpSAI----TSQLDKASIIRLTTSYLKM 52
Cdd:cd11407   10 KRRRDRINNSLAELRRLVP--TAFekqgSAKLEKAEILQMTVDHLKM 54
bHLH-PAS_cycle_like cd19726
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Drosophila melanogaster protein ...
 10-52 9.81e-04

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: 37.84  E-value: 9.81e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 194239684  10 KTRREKENGEFYELAKLLPLPSAITSQLDKASIIRLTTSYLKM 52
Cdd:cd19726   10 KRRRDKMNTYITELSSMIPMCNAMSRKLDKLTVLRMAVQHMKT 52
bHLH-PAS_ARNTL2_PASD9 cd11469
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor ...
 2-51 1.48e-03

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: 37.32  E-value: 1.48e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 194239684   2 KEKSKNAAKTRREKENGEFYELAKLLPLPSAITSQLDKASIIRLTTSYLK 51
Cdd:cd11469    2 REAHSQTEKRRRDKMNNLIEELSAMIPQCNPMARKLDKLTVLRMAVQHLK 51
HLH pfam00010
Helix-loop-helix DNA-binding domain;
2-52 3.26e-03

Helix-loop-helix DNA-binding domain;


Pssm-ID: 459628 [Multi-domain]  Cd Length: 53  Bit Score: 35.90  E-value: 3.26e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 194239684    2 KEKSKNAA-KTRREKENGEFYELAKLLPLpSAITSQLDKASIIRLTTSYLKM 52
Cdd:pfam00010   1 RREAHNEReRRRRDRINDAFDELRELLPT-LPPDKKLSKAEILRLAIEYIKH 51
RocR COG3829
RocR-type transcriptional regulator, contains PAS, AAA-type ATPase, and DNA-binding Fis ...
 83-152 3.29e-03

RocR-type transcriptional regulator, contains PAS, AAA-type ATPase, and DNA-binding Fis domains [Transcription, Signal transduction mechanisms];


Pssm-ID: 443041 [Multi-domain]  Cd Length: 448  Bit Score: 40.14  E-value: 3.29e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194239684  83 HLLQTLDGFVFVVASDGKIMYISETASVHLGLSQVELTGNSIYEYIHPSDHDEmtaVLTAHQPLHHHLLQ 152
Cdd:COG3829   15 AILDSLDDGIIVVDADGRITYVNRAAERILGLPREEVIGKNVTELIPNSPLLE---VLKTGKPVTGVIQK 81
bHLH_AtbHLH_like cd11393
basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana genes coding transcription ...
 8-51 3.95e-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: 35.62  E-value: 3.95e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 194239684   8 AAKTRREKENGEFYELAKLLPlPSAitsQLDKASIIRLTTSYLK 51
Cdd:cd11393    4 AERKRREKINERIRALRSLVP-NGG---KTDKASILDEAIEYIK 43
NtrB COG3852
Signal transduction histidine kinase NtrB, nitrogen specific [Signal transduction mechanisms];
77-158 8.60e-03

Signal transduction histidine kinase NtrB, nitrogen specific [Signal transduction mechanisms];


Pssm-ID: 443061 [Multi-domain]  Cd Length: 361  Bit Score: 38.67  E-value: 8.60e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194239684  77 AKELGSHLLQTLDGFVFVVASDGKIMYISETASVHLGLSQVELTGNSIYEYIHPSD--HDEMTAVLTAHQPLHHHllqEY 154
Cdd:COG3852    5 SEELLRAILDSLPDAVIVLDADGRITYVNPAAERLLGLSAEELLGRPLAELFPEDSplRELLERALAEGQPVTER---EV 81


                 ....
gi 194239684 155 EIER 158
Cdd:COG3852   82 TLRR 85
sensory_box TIGR00229
PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain ...
 221-308 8.96e-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: 36.50  E-value: 8.96e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194239684  221 AITEiklYSNMFMFRASLDLKLIFLDSRVTEVTGYEPQDLIEKTL--YHHVHGCDVFHLRYAHHlLLVKGQVTTKYYRLL 298
Cdd:TIGR00229   7 AIFE---SSPDAIIVIDLEGNILYVNPAFEEIFGYSAEELIGRNVleLIPEEDREEVRERIERR-LEGEPEPVSEERRVR 82

                          90
                  ....*....|
gi 194239684  299 SKRGGWVWVQ 308
Cdd:TIGR00229  83 RKDGSEIWVE 92
 
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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