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Conserved domains on  [gi|62472069|ref|NP_001014574|]
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clock, isoform F [Drosophila melanogaster]

Protein Classification

helix-loop-helix domain-containing protein( domain architecture ID 15361122)

helix-loop-helix (HLH) domain-containing protein with PAS domains

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PAS_11 super family cl37882
PAS domain; This family includes the PAS-B domain of NCOA1 (Nuclear receptor coactivator 1), ...
 199-302 2.84e-20

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


The actual alignment was detected with superfamily member pfam14598:

Pssm-ID: 464214 [Multi-domain]  Cd Length: 110  Bit Score: 86.96  E-value: 2.84e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472069   199 NEFTSKHSMEWKFLFLDHRAPPIIGYMPFEVLGTSGYDYYHFDDL-DSIVACHEELRQTGEGKSCYYRFLTKGQQWIWLQ 277
Cdd:pfam14598   2 EQFTTRHDIDGKIISCDTRAPFSLGYEKDELVGRSIYDLVHPQDLrTAKSHLREIIQTRGRATSPSYRLRLRDGDFLSVH 81

                          90       100
                  ....*....|....*....|....*
gi 62472069   278 TDYYVSYHQFNSKPDYVVCTHKVVS 302
Cdd:pfam14598  82 TKSKLFLNQNSNQQPFIMCTHTILR 106
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 27-87 9.00e-05

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


:

Pssm-ID: 214512  Cd Length: 67  Bit Score: 41.23  E-value: 9.00e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 62472069     27 HLMLESLDGFMMVFSSMGSIFYASESITSQLGYLPQDLYNMTIYDLAYEMDHEALLNIFMN 87
Cdd:smart00091   4 RAILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEALQR 64
bHLH_SF super family cl00081
basic Helix Loop Helix (bHLH) domain superfamily; bHLH proteins are transcriptional regulators ...
 2-20 2.96e-03

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 cd19735:

Pssm-ID: 469605  Cd Length: 80  Bit Score: 37.47  E-value: 2.96e-03
                        10
                ....*....|....*....
gi 62472069   2 ATDRSKVFEIQQDWKPAFL 20
Cdd:cd19735  62 VTMQSHQQEIQEDWKPSFL 80
 
Name Accession Description Interval E-value
PAS_11 pfam14598
PAS domain; This family includes the PAS-B domain of NCOA1 (Nuclear receptor coactivator 1), ...
 199-302 2.84e-20

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: 86.96  E-value: 2.84e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472069   199 NEFTSKHSMEWKFLFLDHRAPPIIGYMPFEVLGTSGYDYYHFDDL-DSIVACHEELRQTGEGKSCYYRFLTKGQQWIWLQ 277
Cdd:pfam14598   2 EQFTTRHDIDGKIISCDTRAPFSLGYEKDELVGRSIYDLVHPQDLrTAKSHLREIIQTRGRATSPSYRLRLRDGDFLSVH 81

                          90       100
                  ....*....|....*....|....*
gi 62472069   278 TDYYVSYHQFNSKPDYVVCTHKVVS 302
Cdd:pfam14598  82 TKSKLFLNQNSNQQPFIMCTHTILR 106
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 198-300 5.94e-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: 5.94e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472069 198 SNEFTSKHSMEWKFLFLDHRAPPIIGYMPFEVLGTSGYDYYHFDDLDSIVACHEELRQTGEGKSCYYRFLTKGQQWIWLQ 277
Cdd:cd00130   1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDGSVIWVL 80

                        90       100
                ....*....|....*....|...
gi 62472069 278 TDYYVSYHQFNSKPDYVVCTHKV 300
Cdd:cd00130  81 VSLTPIRDEGGEVIGLLGVVRDI 103
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 27-87 9.00e-05

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


Pssm-ID: 214512  Cd Length: 67  Bit Score: 41.23  E-value: 9.00e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 62472069     27 HLMLESLDGFMMVFSSMGSIFYASESITSQLGYLPQDLYNMTIYDLAYEMDHEALLNIFMN 87
Cdd:smart00091   4 RAILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEALQR 64
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 192-255 1.94e-04

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


Pssm-ID: 214512  Cd Length: 67  Bit Score: 40.46  E-value: 1.94e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 62472069    192 SIIDpTSNEFTSKHSMEWKFLFLDHRAPPIIGYMPFEVLGTSGYDYYHFDDLDSIVACHEELRQ 255
Cdd:smart00091   5 AILE-SLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEALQRLLS 67
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 33-100 1.78e-03

PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. 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: 38.77  E-value: 1.78e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 62472069  33 LDGFMMVFSSMGSIFYASESITSQLGYLPQDLYNMTIYDLAYEMDHEALLNIFMNPTPVIEPRQTDIS 100
Cdd:cd00130   1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVR 68
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 29-97 2.47e-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: 2.47e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 62472069    29 MLESLDGFMMVFSSMGSIFYASESITSQLGYLPQDLYNMTIYDLAYEMDHEALLNIFMNPTPVIEPRQT 97
Cdd:pfam00989   6 ILESLPDGIFVVDEDGRILYVNAAAEELLGLSREEVIGKSLLDLIPEEDDAEVAELLRQALLQGEESRG 74
bHLH-PAS_dCLOCK cd19735
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Drosophila melanogaster ...
 2-20 2.96e-03

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Drosophila melanogaster Circadian locomotor output cycles protein kaput (dCLOCK) and similar proteins; dCLOCK, also termed dPAS1, is a bHLH-PAS Circadian regulator that acts as a transcription factor and generates a rhythmic output with a period of about 24 hours.


Pssm-ID: 381578  Cd Length: 80  Bit Score: 37.47  E-value: 2.96e-03
                        10
                ....*....|....*....
gi 62472069   2 ATDRSKVFEIQQDWKPAFL 20
Cdd:cd19735  62 VTMQSHQQEIQEDWKPSFL 80
 
Name Accession Description Interval E-value
PAS_11 pfam14598
PAS domain; This family includes the PAS-B domain of NCOA1 (Nuclear receptor coactivator 1), ...
 199-302 2.84e-20

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: 86.96  E-value: 2.84e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472069   199 NEFTSKHSMEWKFLFLDHRAPPIIGYMPFEVLGTSGYDYYHFDDL-DSIVACHEELRQTGEGKSCYYRFLTKGQQWIWLQ 277
Cdd:pfam14598   2 EQFTTRHDIDGKIISCDTRAPFSLGYEKDELVGRSIYDLVHPQDLrTAKSHLREIIQTRGRATSPSYRLRLRDGDFLSVH 81

                          90       100
                  ....*....|....*....|....*
gi 62472069   278 TDYYVSYHQFNSKPDYVVCTHKVVS 302
Cdd:pfam14598  82 TKSKLFLNQNSNQQPFIMCTHTILR 106
PAS_3 pfam08447
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 211-298 2.34e-15

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


Pssm-ID: 430001 [Multi-domain]  Cd Length: 89  Bit Score: 71.99  E-value: 2.34e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472069   211 FLFLDHRAPPIIGYMPFEVLGT--SGYDYYHFDDLDSIVACHEELRQTGEGKSCYYRFLTKGQQWIWLQtDYYVSYHQFN 288
Cdd:pfam08447   1 IIYWSPRFEEILGYTPEELLGKgeSWLDLVHPDDRERVREALWEALKGGEPYSGEYRIRRKDGEYRWVE-ARARPIRDEN 79

                          90
                  ....*....|
gi 62472069   289 SKPDYVVCTH 298
Cdd:pfam08447  80 GKPVRVIGVA 89
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 198-300 5.94e-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: 5.94e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472069 198 SNEFTSKHSMEWKFLFLDHRAPPIIGYMPFEVLGTSGYDYYHFDDLDSIVACHEELRQTGEGKSCYYRFLTKGQQWIWLQ 277
Cdd:cd00130   1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDGSVIWVL 80

                        90       100
                ....*....|....*....|...
gi 62472069 278 TDYYVSYHQFNSKPDYVVCTHKV 300
Cdd:cd00130  81 VSLTPIRDEGGEVIGLLGVVRDI 103
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 27-87 9.00e-05

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


Pssm-ID: 214512  Cd Length: 67  Bit Score: 41.23  E-value: 9.00e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 62472069     27 HLMLESLDGFMMVFSSMGSIFYASESITSQLGYLPQDLYNMTIYDLAYEMDHEALLNIFMN 87
Cdd:smart00091   4 RAILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEALQR 64
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 192-255 1.94e-04

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


Pssm-ID: 214512  Cd Length: 67  Bit Score: 40.46  E-value: 1.94e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 62472069    192 SIIDpTSNEFTSKHSMEWKFLFLDHRAPPIIGYMPFEVLGTSGYDYYHFDDLDSIVACHEELRQ 255
Cdd:smart00091   5 AILE-SLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEALQRLLS 67
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 33-100 1.78e-03

PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. 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: 38.77  E-value: 1.78e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 62472069  33 LDGFMMVFSSMGSIFYASESITSQLGYLPQDLYNMTIYDLAYEMDHEALLNIFMNPTPVIEPRQTDIS 100
Cdd:cd00130   1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVR 68
PAC smart00086
Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); PAC motif ...
 261-302 2.16e-03

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: 36.78  E-value: 2.16e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 62472069    261 SCYYRFLTKGQQWIWLQTDYYVSYHQfNSKPDYVVCTHKVVS 302
Cdd:smart00086   1 TVEYRLRRKDGSYIWVLVSASPIRDE-DGEVEGILGVVRDIT 41
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 29-97 2.47e-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: 2.47e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 62472069    29 MLESLDGFMMVFSSMGSIFYASESITSQLGYLPQDLYNMTIYDLAYEMDHEALLNIFMNPTPVIEPRQT 97
Cdd:pfam00989   6 ILESLPDGIFVVDEDGRILYVNAAAEELLGLSREEVIGKSLLDLIPEEDDAEVAELLRQALLQGEESRG 74
bHLH-PAS_dCLOCK cd19735
basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Drosophila melanogaster ...
 2-20 2.96e-03

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Drosophila melanogaster Circadian locomotor output cycles protein kaput (dCLOCK) and similar proteins; dCLOCK, also termed dPAS1, is a bHLH-PAS Circadian regulator that acts as a transcription factor and generates a rhythmic output with a period of about 24 hours.


Pssm-ID: 381578  Cd Length: 80  Bit Score: 37.47  E-value: 2.96e-03
                        10
                ....*....|....*....
gi 62472069   2 ATDRSKVFEIQQDWKPAFL 20
Cdd:cd19735  62 VTMQSHQQEIQEDWKPSFL 80
 
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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