NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1931773182|gb|QPB77281|]
View 

miRFP670 [Cloning vector (138)_P_EF1a-miRFP670]

Protein Classification

phytochrome family protein( domain architecture ID 1000043)

phytochrome family protein similar to Deinococcus radiodurans bacteriophytochrome, which functions as a light-regulated histidine kinase that helps protect the bacterium from intense visible light

CATH:  3.30.450.40
Gene Ontology:  GO:0009881|GO:0009584
PubMed:  2606345|10617469|31595505

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
PAS_2 super family cl20158
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 20-122 1.28e-18

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.


The actual alignment was detected with superfamily member pfam08446:

Pssm-ID: 400652  Cd Length: 107  Bit Score: 79.61  E-value: 1.28e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1931773182  20 CEHEEIHLAGSIQPHGALLVVSEHDHRVIQASANAAEFLNL--GSVLGVPLAEIDGDLLIKILPH-LDPTAEGM--PVAV 94
Cdd:pfam08446   1 CYLEPIQRPGLIQPHGCLLAVDEPSLRVLQYSENAAEMLGLpaEDLLGTDLRDLFGASSASLLRKaLAAGEISLlnPILI 80

                          90       100
                  ....*....|....*....|....*...
gi 1931773182  95 RCRigNPSTEYCGLMHRpPEGGLIIELE 122
Cdd:pfam08446  81 HSR--TSGKPFYAILHR-SDGGLVLELE 105
GAF pfam01590
GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl ...
 146-310 6.72e-12

GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl cyclases, phytochromes, FhlA and NifA. Adenylyl and guanylyl cyclases catalyze ATP and GTP to the second messengers cAMP and cGMP, respectively, these products up-regulating catalytic activity by binding to the regulatory GAF domain(s). The opposite hydrolysis reaction is catalyzed by phosphodiesterase. cGMP-dependent 3',5'-cyclic phosphodiesterase catalyzes the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. Here too, cGMP regulates catalytic activity by GAF-domain binding. Phytochromes are regulatory photoreceptors in plants and bacteria which exist in two thermally-stable states that are reversibly inter-convertible by light: the Pr state absorbs maximally in the red region of the spectrum, while the Pfr state absorbs maximally in the far-red region. This domain is also found in FhlA (formate hydrogen lyase transcriptional activator) and NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation. NifA interacts with sigma-54. This domain can bind biliverdine and phycocyanobilin (Matilla et al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


:

Pssm-ID: 460259 [Multi-domain]  Cd Length: 133  Bit Score: 62.11  E-value: 6.72e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1931773182 146 SLRALCDDTVLLFQQCTGYDRVMVYRFDEQGHGLVFSEchvpgleSYFGNRYPSSTVPQMARQLYVRQRVRVLVDVTyqp 225
Cdd:pfam01590   1 DLEEILQTILEELRELLGADRCALYLPDADGLEYLPPG-------ARWLKAAGLEIPPGTGVTVLRTGRPLVVPDAA--- 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1931773182 226 vpLEPRLSPltgrdldmsgcflrsmspcHLQFLKDMGVRATLAVSLVVGGKLWGLVVCHHYLPRFIRFELRAIcKRLAER 305
Cdd:pfam01590  71 --GDPRFLD-------------------PLLLLRNFGIRSLLAVPIIDDGELLGVLVLHHPRPPFTEEELELL-EVLADQ 128


                  ....*
gi 1931773182 306 IATRI 310
Cdd:pfam01590 129 VAIAL 133
 
Name Accession Description Interval E-value
PAS_2 pfam08446
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 20-122 1.28e-18

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: 400652  Cd Length: 107  Bit Score: 79.61  E-value: 1.28e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1931773182  20 CEHEEIHLAGSIQPHGALLVVSEHDHRVIQASANAAEFLNL--GSVLGVPLAEIDGDLLIKILPH-LDPTAEGM--PVAV 94
Cdd:pfam08446   1 CYLEPIQRPGLIQPHGCLLAVDEPSLRVLQYSENAAEMLGLpaEDLLGTDLRDLFGASSASLLRKaLAAGEISLlnPILI 80

                          90       100
                  ....*....|....*....|....*...
gi 1931773182  95 RCRigNPSTEYCGLMHRpPEGGLIIELE 122
Cdd:pfam08446  81 HSR--TSGKPFYAILHR-SDGGLVLELE 105
GAF pfam01590
GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl ...
 146-310 6.72e-12

GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl cyclases, phytochromes, FhlA and NifA. Adenylyl and guanylyl cyclases catalyze ATP and GTP to the second messengers cAMP and cGMP, respectively, these products up-regulating catalytic activity by binding to the regulatory GAF domain(s). The opposite hydrolysis reaction is catalyzed by phosphodiesterase. cGMP-dependent 3',5'-cyclic phosphodiesterase catalyzes the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. Here too, cGMP regulates catalytic activity by GAF-domain binding. Phytochromes are regulatory photoreceptors in plants and bacteria which exist in two thermally-stable states that are reversibly inter-convertible by light: the Pr state absorbs maximally in the red region of the spectrum, while the Pfr state absorbs maximally in the far-red region. This domain is also found in FhlA (formate hydrogen lyase transcriptional activator) and NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation. NifA interacts with sigma-54. This domain can bind biliverdine and phycocyanobilin (Matilla et al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 460259 [Multi-domain]  Cd Length: 133  Bit Score: 62.11  E-value: 6.72e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1931773182 146 SLRALCDDTVLLFQQCTGYDRVMVYRFDEQGHGLVFSEchvpgleSYFGNRYPSSTVPQMARQLYVRQRVRVLVDVTyqp 225
Cdd:pfam01590   1 DLEEILQTILEELRELLGADRCALYLPDADGLEYLPPG-------ARWLKAAGLEIPPGTGVTVLRTGRPLVVPDAA--- 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1931773182 226 vpLEPRLSPltgrdldmsgcflrsmspcHLQFLKDMGVRATLAVSLVVGGKLWGLVVCHHYLPRFIRFELRAIcKRLAER 305
Cdd:pfam01590  71 --GDPRFLD-------------------PLLLLRNFGIRSLLAVPIIDDGELLGVLVLHHPRPPFTEEELELL-EVLADQ 128


                  ....*
gi 1931773182 306 IATRI 310
Cdd:pfam01590 129 VAIAL 133
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 147-310 1.04e-09

Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these domains in PDE6B result in autosomal recessive inheritance of retinitis pigmentosa.


Pssm-ID: 214500 [Multi-domain]  Cd Length: 149  Bit Score: 56.24  E-value: 1.04e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1931773182  147 LRALCDDTVLLFQQCTGYDRVMVYRFDEQGHGLVFSE-CHVPGLESYFGNRYPSSTVPQMARQlyvRQRVRVLVDVTYQP 225
Cdd:smart00065   2 LEELLQTILEELRQLLGADRVLIYLVDENDRGELVLVaADGLTLPTLGIRFPLDEGLAGRVAE---TGRPLNIPDVEADP 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1931773182  226 VPLEPRLSPLtgrdldmsgcflrsmspchlqflkdMGVRATLAVSLVVGGKLWGLVVCHH-YLPRFirfeLRAICKRLAE 304
Cdd:smart00065  79 LFAEDLLGRY-------------------------QGVRSFLAVPLVADGELVGVLALHNkKSPRP----FTEEDEELLQ 129


                   ....*.
gi 1931773182  305 RIATRI 310
Cdd:smart00065 130 ALANQL 135
GAF COG2203
GAF domain [Signal transduction mechanisms];
137-310 3.06e-07

GAF domain [Signal transduction mechanisms];


Pssm-ID: 441805 [Multi-domain]  Cd Length: 712  Bit Score: 51.73  E-value: 3.06e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1931773182 137 ALERIRTAGSLRALCDDTVLLFQQCTGYDRVMVYRFDEQGHGLVFseCHVPGLESYFGNRYPSSTvpQMARQLYVRQRVR 216
Cdd:COG2203   198 ISQALRSALDLEELLQRILELAGELLGADRGAILLVDEDGGELEL--VAAPGLPEEELGRLPLGE--GLAGRALRTGEPV 273

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1931773182 217 VLVDVTyqpvpLEPRLSPltgrdldmsgcflrsmspCHLQFLKDMGVRATLAVSLVVGGKLWGLVVCHHYLPRFIRFELR 296
Cdd:COG2203   274 VVNDAS-----TDPRFAP------------------SLRELLLALGIRSLLCVPLLVDGRLIGVLALYSKEPRAFTEEDL 330

                         170
                  ....*....|....
gi 1931773182 297 AICKRLAERIATRI 310
Cdd:COG2203   331 ELLEALADQAAIAI 344
 
Name Accession Description Interval E-value
PAS_2 pfam08446
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 20-122 1.28e-18

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: 400652  Cd Length: 107  Bit Score: 79.61  E-value: 1.28e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1931773182  20 CEHEEIHLAGSIQPHGALLVVSEHDHRVIQASANAAEFLNL--GSVLGVPLAEIDGDLLIKILPH-LDPTAEGM--PVAV 94
Cdd:pfam08446   1 CYLEPIQRPGLIQPHGCLLAVDEPSLRVLQYSENAAEMLGLpaEDLLGTDLRDLFGASSASLLRKaLAAGEISLlnPILI 80

                          90       100
                  ....*....|....*....|....*...
gi 1931773182  95 RCRigNPSTEYCGLMHRpPEGGLIIELE 122
Cdd:pfam08446  81 HSR--TSGKPFYAILHR-SDGGLVLELE 105
GAF pfam01590
GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl ...
 146-310 6.72e-12

GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl cyclases, phytochromes, FhlA and NifA. Adenylyl and guanylyl cyclases catalyze ATP and GTP to the second messengers cAMP and cGMP, respectively, these products up-regulating catalytic activity by binding to the regulatory GAF domain(s). The opposite hydrolysis reaction is catalyzed by phosphodiesterase. cGMP-dependent 3',5'-cyclic phosphodiesterase catalyzes the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. Here too, cGMP regulates catalytic activity by GAF-domain binding. Phytochromes are regulatory photoreceptors in plants and bacteria which exist in two thermally-stable states that are reversibly inter-convertible by light: the Pr state absorbs maximally in the red region of the spectrum, while the Pfr state absorbs maximally in the far-red region. This domain is also found in FhlA (formate hydrogen lyase transcriptional activator) and NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation. NifA interacts with sigma-54. This domain can bind biliverdine and phycocyanobilin (Matilla et al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 460259 [Multi-domain]  Cd Length: 133  Bit Score: 62.11  E-value: 6.72e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1931773182 146 SLRALCDDTVLLFQQCTGYDRVMVYRFDEQGHGLVFSEchvpgleSYFGNRYPSSTVPQMARQLYVRQRVRVLVDVTyqp 225
Cdd:pfam01590   1 DLEEILQTILEELRELLGADRCALYLPDADGLEYLPPG-------ARWLKAAGLEIPPGTGVTVLRTGRPLVVPDAA--- 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1931773182 226 vpLEPRLSPltgrdldmsgcflrsmspcHLQFLKDMGVRATLAVSLVVGGKLWGLVVCHHYLPRFIRFELRAIcKRLAER 305
Cdd:pfam01590  71 --GDPRFLD-------------------PLLLLRNFGIRSLLAVPIIDDGELLGVLVLHHPRPPFTEEELELL-EVLADQ 128


                  ....*
gi 1931773182 306 IATRI 310
Cdd:pfam01590 129 VAIAL 133
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 147-310 1.04e-09

Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these domains in PDE6B result in autosomal recessive inheritance of retinitis pigmentosa.


Pssm-ID: 214500 [Multi-domain]  Cd Length: 149  Bit Score: 56.24  E-value: 1.04e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1931773182  147 LRALCDDTVLLFQQCTGYDRVMVYRFDEQGHGLVFSE-CHVPGLESYFGNRYPSSTVPQMARQlyvRQRVRVLVDVTYQP 225
Cdd:smart00065   2 LEELLQTILEELRQLLGADRVLIYLVDENDRGELVLVaADGLTLPTLGIRFPLDEGLAGRVAE---TGRPLNIPDVEADP 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1931773182  226 VPLEPRLSPLtgrdldmsgcflrsmspchlqflkdMGVRATLAVSLVVGGKLWGLVVCHH-YLPRFirfeLRAICKRLAE 304
Cdd:smart00065  79 LFAEDLLGRY-------------------------QGVRSFLAVPLVADGELVGVLALHNkKSPRP----FTEEDEELLQ 129


                   ....*.
gi 1931773182  305 RIATRI 310
Cdd:smart00065 130 ALANQL 135
GAF COG2203
GAF domain [Signal transduction mechanisms];
137-310 3.06e-07

GAF domain [Signal transduction mechanisms];


Pssm-ID: 441805 [Multi-domain]  Cd Length: 712  Bit Score: 51.73  E-value: 3.06e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1931773182 137 ALERIRTAGSLRALCDDTVLLFQQCTGYDRVMVYRFDEQGHGLVFseCHVPGLESYFGNRYPSSTvpQMARQLYVRQRVR 216
Cdd:COG2203   198 ISQALRSALDLEELLQRILELAGELLGADRGAILLVDEDGGELEL--VAAPGLPEEELGRLPLGE--GLAGRALRTGEPV 273

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1931773182 217 VLVDVTyqpvpLEPRLSPltgrdldmsgcflrsmspCHLQFLKDMGVRATLAVSLVVGGKLWGLVVCHHYLPRFIRFELR 296
Cdd:COG2203   274 VVNDAS-----TDPRFAP------------------SLRELLLALGIRSLLCVPLLVDGRLIGVLALYSKEPRAFTEEDL 330

                         170
                  ....*....|....
gi 1931773182 297 AICKRLAERIATRI 310
Cdd:COG2203   331 ELLEALADQAAIAI 344
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH