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Conserved domains on  [gi|1397992989|ref|WP_110167106|]
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MULTISPECIES: hypothetical protein [Vibrio]

Protein Classification

PAS domain-containing protein( domain architecture ID 1001018)

PAS domain-containing protein binds ligand(s) and may act as sensors for light and oxygen in signal transduction

CATH:  3.30.450.20
Gene Ontology:  GO:0005515|GO:0007165
PubMed:  15009198|33647528|16939366|10357859|9382818|21663441
SCOP:  3000471

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RocR super family cl34674
RocR-type transcriptional regulator, contains PAS, AAA-type ATPase, and DNA-binding Fis ...
 1-65 8.90e-05

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


The actual alignment was detected with superfamily member COG3829:

Pssm-ID: 443041 [Multi-domain]  Cd Length: 448  Bit Score: 40.91  E-value: 8.90e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1397992989   1 MLSLPAEFEQFHWMVDmvqNVDMGLIVLNRDYEIQVWNGFMTHHSGKHGHDVIGKSIFTIFPEIP 65
Cdd:COG3829     3 ELELKELEEELEAILD---SLDDGIIVVDADGRITYVNRAAERILGLPREEVIGKNVTELIPNSP 64
PAS super family cl38023
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 17-134 8.84e-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).


The actual alignment was detected with superfamily member pfam00989:

Pssm-ID: 395786 [Multi-domain]  Cd Length: 113  Bit Score: 36.63  E-value: 8.84e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1397992989  17 MVQNVDMGLIVLNRDYEIQVWNGFMTHHSGKHGHDVIGKSIFTIFPEIPSDWFK------LKTKPVYDLGCRSFITWQQR 90
Cdd:pfam00989   6 ILESLPDGIFVVDEDGRILYVNAAAEELLGLSREEVIGKSLLDLIPEEDDAEVAellrqaLLQGEESRGFEVSFRVPDGR 85

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1397992989  91 PYLFKCRNVrpitqqadfmyqnitlnPMRTPTGKINSLFLSIQD 134
Cdd:pfam00989  86 PRHVEVRAS-----------------PVRDAGGEILGFLGVLRD 112
 
Name Accession Description Interval E-value
RocR COG3829
RocR-type transcriptional regulator, contains PAS, AAA-type ATPase, and DNA-binding Fis ...
 1-65 8.90e-05

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: 40.91  E-value: 8.90e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1397992989   1 MLSLPAEFEQFHWMVDmvqNVDMGLIVLNRDYEIQVWNGFMTHHSGKHGHDVIGKSIFTIFPEIP 65
Cdd:COG3829     3 ELELKELEEELEAILD---SLDDGIIVVDADGRITYVNRAAERILGLPREEVIGKNVTELIPNSP 64
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 17-134 8.84e-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: 36.63  E-value: 8.84e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1397992989  17 MVQNVDMGLIVLNRDYEIQVWNGFMTHHSGKHGHDVIGKSIFTIFPEIPSDWFK------LKTKPVYDLGCRSFITWQQR 90
Cdd:pfam00989   6 ILESLPDGIFVVDEDGRILYVNAAAEELLGLSREEVIGKSLLDLIPEEDDAEVAellrqaLLQGEESRGFEVSFRVPDGR 85

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1397992989  91 PYLFKCRNVrpitqqadfmyqnitlnPMRTPTGKINSLFLSIQD 134
Cdd:pfam00989  86 PRHVEVRAS-----------------PVRDAGGEILGFLGVLRD 112
casE_Cse3 TIGR01907
CRISPR-associated protein Cas6/Cse3/CasE, subtype I-E/ECOLI; CRISPR is a term for Clustered, ...
 57-124 5.95e-03

CRISPR-associated protein Cas6/Cse3/CasE, subtype I-E/ECOLI; CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This model family, represented by CT1974 from Chlorobium tepidum, is found in the Ecoli subtype of CRISPR/Cas regions and is designated Cse3 (CRISPR/Cas Subtype Ecoli protein 3). The representative of this family from Thermus thermophilus HB8 (TTHB192) has been crystallized and found to have a structure consisting of two domains with opposing parallel beta-sheets known as a beta-sheet platform. This structure is similar to those found in the Sex-lethal protein and poly(A)-binding protein. This structure is consistent with an RNA-binding function.


Pssm-ID: 273869  Cd Length: 206  Bit Score: 35.27  E-value: 5.95e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1397992989  57 IFTIFPEIPSD----WFKLKTKPVYDlGCRSFITWQQRP-----YLFKCRNVRPITQQADFMYQNITLNPMRTPTGK 124
Cdd:TIGR01907  28 LWHLFPNRPDEarqfLFRVEKRNAPG-GCHFLLLSAQPPlqavaFVIETKQVEPQLQVGVPLYFRLRANPTITINGK 103
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 12-63 7.59e-03

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


Pssm-ID: 214512  Cd Length: 67  Bit Score: 33.14  E-value: 7.59e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1397992989   12 HWMVDMVQNVDMGLIVLNRDYEIQVWNGFMTHHSGKHGHDVIGKSIFTIFPE 63
Cdd:smart00091   1 ERLRAILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHP 52
 
Name Accession Description Interval E-value
RocR COG3829
RocR-type transcriptional regulator, contains PAS, AAA-type ATPase, and DNA-binding Fis ...
 1-65 8.90e-05

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: 40.91  E-value: 8.90e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1397992989   1 MLSLPAEFEQFHWMVDmvqNVDMGLIVLNRDYEIQVWNGFMTHHSGKHGHDVIGKSIFTIFPEIP 65
Cdd:COG3829     3 ELELKELEEELEAILD---SLDDGIIVVDADGRITYVNRAAERILGLPREEVIGKNVTELIPNSP 64
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 17-134 8.84e-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: 36.63  E-value: 8.84e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1397992989  17 MVQNVDMGLIVLNRDYEIQVWNGFMTHHSGKHGHDVIGKSIFTIFPEIPSDWFK------LKTKPVYDLGCRSFITWQQR 90
Cdd:pfam00989   6 ILESLPDGIFVVDEDGRILYVNAAAEELLGLSREEVIGKSLLDLIPEEDDAEVAellrqaLLQGEESRGFEVSFRVPDGR 85

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1397992989  91 PYLFKCRNVrpitqqadfmyqnitlnPMRTPTGKINSLFLSIQD 134
Cdd:pfam00989  86 PRHVEVRAS-----------------PVRDAGGEILGFLGVLRD 112
NtrY COG5000
Signal transduction histidine kinase NtrY involved in nitrogen fixation and metabolism ...
 17-65 4.41e-03

Signal transduction histidine kinase NtrY involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms];


Pssm-ID: 444024 [Multi-domain]  Cd Length: 422  Bit Score: 36.09  E-value: 4.41e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1397992989  17 MVQNVDMGLIVLNRDYEIQVWNGFMTHHSGKHGHDVIGKSIFTIFPEIP 65
Cdd:COG5000    95 ILENLPAGVIVLDADGRITLANPAAERLLGIPLEELIGKPLEELLPELD 143
casE_Cse3 TIGR01907
CRISPR-associated protein Cas6/Cse3/CasE, subtype I-E/ECOLI; CRISPR is a term for Clustered, ...
 57-124 5.95e-03

CRISPR-associated protein Cas6/Cse3/CasE, subtype I-E/ECOLI; CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This model family, represented by CT1974 from Chlorobium tepidum, is found in the Ecoli subtype of CRISPR/Cas regions and is designated Cse3 (CRISPR/Cas Subtype Ecoli protein 3). The representative of this family from Thermus thermophilus HB8 (TTHB192) has been crystallized and found to have a structure consisting of two domains with opposing parallel beta-sheets known as a beta-sheet platform. This structure is similar to those found in the Sex-lethal protein and poly(A)-binding protein. This structure is consistent with an RNA-binding function.


Pssm-ID: 273869  Cd Length: 206  Bit Score: 35.27  E-value: 5.95e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1397992989  57 IFTIFPEIPSD----WFKLKTKPVYDlGCRSFITWQQRP-----YLFKCRNVRPITQQADFMYQNITLNPMRTPTGK 124
Cdd:TIGR01907  28 LWHLFPNRPDEarqfLFRVEKRNAPG-GCHFLLLSAQPPlqavaFVIETKQVEPQLQVGVPLYFRLRANPTITINGK 103
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 12-63 7.59e-03

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


Pssm-ID: 214512  Cd Length: 67  Bit Score: 33.14  E-value: 7.59e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1397992989   12 HWMVDMVQNVDMGLIVLNRDYEIQVWNGFMTHHSGKHGHDVIGKSIFTIFPE 63
Cdd:smart00091   1 ERLRAILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHP 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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