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Conserved domains on  [gi|345424346|gb|AEN85277|]
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phytochrome A, partial [Diplotaxis assurgens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PHY pfam00360
Phytochrome region; Phytochromes are red/far-red photochromic biliprotein photoreceptors which ...
 234-408 3.45e-65

Phytochrome region; Phytochromes are red/far-red photochromic biliprotein photoreceptors which regulate plant development. They are widely represented in both photosynthetic and non-photosynthetic bacteria and are known in a variety of fungi. Although sequence similarities are low, this domain is structurally related to pfam01590, which is generally located immediately N-terminal to this domain. Compared with pfam01590, this domain carries an additional tongue-like hairpin loop between the fifth beta-sheet and the sixth alpha-helix which functions to seal the chromophore pocket and stabilize the photoactivated far-red-absorbing state (Pfr). The tongue carries a conserved PRxSF motif, from which an arginine finger points into the chromophore pocket close to ring D forming a salt bridge with a conserved aspartate residue.


:

Pssm-ID: 425635  Cd Length: 178  Bit Score: 211.36  E-value: 3.45e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345424346  234 ILRTQTLLCDMLMR--DAPLGIVSQSPNIMDLVKCDGAALLYKEKVWKLGITPSDYHLQEIATWLCDYHtDSTGLSTDSL 311
Cdd:pfam00360   1 LRRIQDRLVEAMARadDLVDGLVDQSPNLLDLVKADGAALCFGGNLLTLGETPPEEAIRDLAQWLGRNH-DSEVFSTDSL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345424346  312 HDAgFPRALALGDSVCGMAAVRVSSKDM--IFWFRSHTAGEVRWGGAKHDPDDRDDARR-MHPRSSFKAFLEVVKTRSLP 388
Cdd:pfam00360  80 SQA-YPEAAALADVASGLLAIPISRKPGnyLLWFRPEVVRTVNWGGDPHKAVEIDPGGVrLSPRKSFDAWKETVRGRSLP 158

                         170       180
                  ....*....|....*....|
gi 345424346  389 WKDYEMDAIHSLQLILRNAF 408
Cdd:pfam00360 159 WSEVEIEAARELREALLGVV 178
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 443-556 3.43e-24

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: 97.49  E-value: 3.43e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345424346  443 EMVRLIETATVPILAVDSDGLVNGWNTKIAELTGLPVDEAIGKHLLE-IVEDSSVEIVKRMLENALGGTEEQNVQFEIKT 521
Cdd:pfam00989   2 DLRAILESLPDGIFVVDEDGRILYVNAAAEELLGLSREEVIGKSLLDlIPEEDDAEVAELLRQALLQGEESRGFEVSFRV 81

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 345424346  522 hlsrADAGPISLVVNACASRDLHENVVGVCFVAHD 556
Cdd:pfam00989  82 ----PDGRPRHVEVRASPVRDAGGEILGFLGVLRD 112
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 39-225 4.29e-12

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: 63.94  E-value: 4.29e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345424346    39 MERLCDTMVQEVFELTGYDRVMAYKFHDDDHGEVVSEVTKPGLEPYLGLHYPATDipQAARFLFMKNKVRMIVDCNAkhv 118
Cdd:smart00065   2 LEELLQTILEELRQLLGADRVLIYLVDENDRGELVLVAADGLTLPTLGIRFPLDE--GLAGRVAETGRPLNIPDVEA--- 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345424346   119 rvlqddklsfdltlcgstlrAPHSCHLQYMANMDSIASLVMAVVVNEEeddaapdstttaqpqkrkrLWGLVVCHNTTpr 198
Cdd:smart00065  77 --------------------DPLFAEDLLGRYQGVRSFLAVPLVADGE-------------------LVGVLALHNKK-- 115

                          170       180
                   ....*....|....*....|....*..
gi 345424346   199 fVPFPLRYACEFLAQVFAIHVNKEVEL 225
Cdd:smart00065 116 -SPRPFTEEDEELLQALANQLAIALAN 141
PAS super family cl38023
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 572-601 6.06e-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).


The actual alignment was detected with superfamily member pfam00989:

Pssm-ID: 395786 [Multi-domain]  Cd Length: 113  Bit Score: 37.01  E-value: 6.06e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 345424346  572 GDYKAIVQNpnpLIPPIFGTDEFGWCSEWN 601
Cdd:pfam00989   1 EDLRAILES---LPDGIFVVDEDGRILYVN 27
 
Name Accession Description Interval E-value
PHY pfam00360
Phytochrome region; Phytochromes are red/far-red photochromic biliprotein photoreceptors which ...
 234-408 3.45e-65

Phytochrome region; Phytochromes are red/far-red photochromic biliprotein photoreceptors which regulate plant development. They are widely represented in both photosynthetic and non-photosynthetic bacteria and are known in a variety of fungi. Although sequence similarities are low, this domain is structurally related to pfam01590, which is generally located immediately N-terminal to this domain. Compared with pfam01590, this domain carries an additional tongue-like hairpin loop between the fifth beta-sheet and the sixth alpha-helix which functions to seal the chromophore pocket and stabilize the photoactivated far-red-absorbing state (Pfr). The tongue carries a conserved PRxSF motif, from which an arginine finger points into the chromophore pocket close to ring D forming a salt bridge with a conserved aspartate residue.


Pssm-ID: 425635  Cd Length: 178  Bit Score: 211.36  E-value: 3.45e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345424346  234 ILRTQTLLCDMLMR--DAPLGIVSQSPNIMDLVKCDGAALLYKEKVWKLGITPSDYHLQEIATWLCDYHtDSTGLSTDSL 311
Cdd:pfam00360   1 LRRIQDRLVEAMARadDLVDGLVDQSPNLLDLVKADGAALCFGGNLLTLGETPPEEAIRDLAQWLGRNH-DSEVFSTDSL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345424346  312 HDAgFPRALALGDSVCGMAAVRVSSKDM--IFWFRSHTAGEVRWGGAKHDPDDRDDARR-MHPRSSFKAFLEVVKTRSLP 388
Cdd:pfam00360  80 SQA-YPEAAALADVASGLLAIPISRKPGnyLLWFRPEVVRTVNWGGDPHKAVEIDPGGVrLSPRKSFDAWKETVRGRSLP 158

                         170       180
                  ....*....|....*....|
gi 345424346  389 WKDYEMDAIHSLQLILRNAF 408
Cdd:pfam00360 159 WSEVEIEAARELREALLGVV 178
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 443-556 3.43e-24

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: 97.49  E-value: 3.43e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345424346  443 EMVRLIETATVPILAVDSDGLVNGWNTKIAELTGLPVDEAIGKHLLE-IVEDSSVEIVKRMLENALGGTEEQNVQFEIKT 521
Cdd:pfam00989   2 DLRAILESLPDGIFVVDEDGRILYVNAAAEELLGLSREEVIGKSLLDlIPEEDDAEVAELLRQALLQGEESRGFEVSFRV 81

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 345424346  522 hlsrADAGPISLVVNACASRDLHENVVGVCFVAHD 556
Cdd:pfam00989  82 ----PDGRPRHVEVRASPVRDAGGEILGFLGVLRD 112
PAS COG2202
PAS domain [Signal transduction mechanisms];
435-601 1.35e-13

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 71.21  E-value: 1.35e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345424346 435 QELEAVTSEMVRLIETATVPILAVDSDGLVNGWNTKIAELTGLPVDEAIGKHLLEIVEDSSVEIVKRMLENALGGTEEQN 514
Cdd:COG2202    4 EALEESERRLRALVESSPDAIIITDLDGRILYVNPAFERLTGYSAEELLGKTLRDLLPPEDDDEFLELLRAALAGGGVWR 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345424346 515 VQFEIKthlsRADAGPISLVVNACASRDLHENVVGVCFVAHDLTGQKTVMDKFTRIEGDYKAIVQNpNPLIppIFGTDEF 594
Cdd:COG2202   84 GELRNR----RKDGSLFWVELSISPVRDEDGEITGFVGIARDITERKRAEEALRESEERLRLLVEN-APDG--IFVLDLD 156


                 ....*..
gi 345424346 595 GWCSEWN 601
Cdd:COG2202  157 GRILYVN 163
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 39-225 4.29e-12

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: 63.94  E-value: 4.29e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345424346    39 MERLCDTMVQEVFELTGYDRVMAYKFHDDDHGEVVSEVTKPGLEPYLGLHYPATDipQAARFLFMKNKVRMIVDCNAkhv 118
Cdd:smart00065   2 LEELLQTILEELRQLLGADRVLIYLVDENDRGELVLVAADGLTLPTLGIRFPLDE--GLAGRVAETGRPLNIPDVEA--- 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345424346   119 rvlqddklsfdltlcgstlrAPHSCHLQYMANMDSIASLVMAVVVNEEeddaapdstttaqpqkrkrLWGLVVCHNTTpr 198
Cdd:smart00065  77 --------------------DPLFAEDLLGRYQGVRSFLAVPLVADGE-------------------LVGVLALHNKK-- 115

                          170       180
                   ....*....|....*....|....*..
gi 345424346   199 fVPFPLRYACEFLAQVFAIHVNKEVEL 225
Cdd:smart00065 116 -SPRPFTEEDEELLQALANQLAIALAN 141
GAF pfam01590
GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl ...
 38-223 1.17e-10

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: 59.41  E-value: 1.17e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345424346   38 SMERLCDTMVQEVFELTGYDRVMAYkfhdddhgevvsevtkpgLEPYLGLHYpatdIPQAARFLfmknKVRMIVDCNAKH 117
Cdd:pfam01590   1 DLEEILQTILEELRELLGADRCALY------------------LPDADGLEY----LPPGARWL----KAAGLEIPPGTG 54

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345424346  118 VRVLQDDKlsfDLTLCGStlrAPHSCHLQ---YMANMDSIASLVMAVVVNEeeddaapdstttaqpqkrkRLWGLVVCHN 194
Cdd:pfam01590  55 VTVLRTGR---PLVVPDA---AGDPRFLDpllLLRNFGIRSLLAVPIIDDG-------------------ELLGVLVLHH 109

                         170       180
                  ....*....|....*....|....*....
gi 345424346  195 TTPRFvpfpLRYACEFLaQVFAIHVNKEV 223
Cdd:pfam01590 110 PRPPF----TEEELELL-EVLADQVAIAL 133
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 451-557 1.01e-09

PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.


Pssm-ID: 238075 [Multi-domain]  Cd Length: 103  Bit Score: 56.10  E-value: 1.01e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345424346 451 ATVPILAVDSDGLVNGWNTKIAELTGLPVDEAIGKHLLEIVEDSSVEIVKRMLENALGGTEEQNVQFEIKTHlsraDAGP 530
Cdd:cd00130    1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRK----DGSV 76

                         90       100
                 ....*....|....*....|....*..
gi 345424346 531 ISLVVNACASRDLHENVVGVCFVAHDL 557
Cdd:cd00130   77 IWVLVSLTPIRDEGGEVIGLLGVVRDI 103
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 446-507 8.52e-09

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


Pssm-ID: 214512  Cd Length: 67  Bit Score: 52.02  E-value: 8.52e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 345424346   446 RLIETATVPILAVDSDGLVNGWNTKIAELTGLPVDEAIGKHLLEIVEDSSVEIVKRMLENAL 507
Cdd:smart00091   5 AILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEALQRLL 66
sensory_box TIGR00229
PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain ...
 443-562 1.32e-08

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: 53.45  E-value: 1.32e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345424346  443 EMVRLI-ETATVPILAVDSDGLVNGWNTKIAELTGLPVDEAIGKHLLEIVEDSSVEIVKRMLENALGGTEEQNVQFEIKT 521
Cdd:TIGR00229   3 ERYRAIfESSPDAIIVIDLEGNILYVNPAFEEIFGYSAEELIGRNVLELIPEEDREEVRERIERRLEGEPEPVSEERRVR 82

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 345424346  522 hlsRADAGPISLVVNAcASRDLHENVVGVCFVAHDLTGQKT 562
Cdd:TIGR00229  83 ---RKDGSEIWVEVSV-SPIRTNGGELGVVGIVRDITERKE 119
PRK11360 PRK11360
two-component system sensor histidine kinase AtoS;
448-571 8.59e-08

two-component system sensor histidine kinase AtoS;


Pssm-ID: 236901 [Multi-domain]  Cd Length: 607  Bit Score: 54.97  E-value: 8.59e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345424346 448 IETATVPILAVDSDGLVNGWNTKIAELTGLPVDEAIGKHLLEIVEDSS--VEIVKRMLENalgGTEEqnVQFEIKTHlsr 525
Cdd:PRK11360 268 LESIADGVIAIDRQGKITTMNPAAEVITGLQRHELVGKPYSELFPPNTpfASPLLDTLEH---GTEH--VDLEISFP--- 339

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 345424346 526 ADAGPISLVVNACASRDLHENVVGVCFVAHDLTGQKTVMDKFTRIE 571
Cdd:PRK11360 340 GRDRTIELSVSTSLLHNTHGEMIGALVIFSDLTERKRLQRRVARQE 385
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 572-601 6.06e-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: 37.01  E-value: 6.06e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 345424346  572 GDYKAIVQNpnpLIPPIFGTDEFGWCSEWN 601
Cdd:pfam00989   1 EDLRAILES---LPDGIFVVDEDGRILYVN 27
 
Name Accession Description Interval E-value
PHY pfam00360
Phytochrome region; Phytochromes are red/far-red photochromic biliprotein photoreceptors which ...
 234-408 3.45e-65

Phytochrome region; Phytochromes are red/far-red photochromic biliprotein photoreceptors which regulate plant development. They are widely represented in both photosynthetic and non-photosynthetic bacteria and are known in a variety of fungi. Although sequence similarities are low, this domain is structurally related to pfam01590, which is generally located immediately N-terminal to this domain. Compared with pfam01590, this domain carries an additional tongue-like hairpin loop between the fifth beta-sheet and the sixth alpha-helix which functions to seal the chromophore pocket and stabilize the photoactivated far-red-absorbing state (Pfr). The tongue carries a conserved PRxSF motif, from which an arginine finger points into the chromophore pocket close to ring D forming a salt bridge with a conserved aspartate residue.


Pssm-ID: 425635  Cd Length: 178  Bit Score: 211.36  E-value: 3.45e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345424346  234 ILRTQTLLCDMLMR--DAPLGIVSQSPNIMDLVKCDGAALLYKEKVWKLGITPSDYHLQEIATWLCDYHtDSTGLSTDSL 311
Cdd:pfam00360   1 LRRIQDRLVEAMARadDLVDGLVDQSPNLLDLVKADGAALCFGGNLLTLGETPPEEAIRDLAQWLGRNH-DSEVFSTDSL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345424346  312 HDAgFPRALALGDSVCGMAAVRVSSKDM--IFWFRSHTAGEVRWGGAKHDPDDRDDARR-MHPRSSFKAFLEVVKTRSLP 388
Cdd:pfam00360  80 SQA-YPEAAALADVASGLLAIPISRKPGnyLLWFRPEVVRTVNWGGDPHKAVEIDPGGVrLSPRKSFDAWKETVRGRSLP 158

                         170       180
                  ....*....|....*....|
gi 345424346  389 WKDYEMDAIHSLQLILRNAF 408
Cdd:pfam00360 159 WSEVEIEAARELREALLGVV 178
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 443-556 3.43e-24

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: 97.49  E-value: 3.43e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345424346  443 EMVRLIETATVPILAVDSDGLVNGWNTKIAELTGLPVDEAIGKHLLE-IVEDSSVEIVKRMLENALGGTEEQNVQFEIKT 521
Cdd:pfam00989   2 DLRAILESLPDGIFVVDEDGRILYVNAAAEELLGLSREEVIGKSLLDlIPEEDDAEVAELLRQALLQGEESRGFEVSFRV 81

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 345424346  522 hlsrADAGPISLVVNACASRDLHENVVGVCFVAHD 556
Cdd:pfam00989  82 ----PDGRPRHVEVRASPVRDAGGEILGFLGVLRD 112
PAS COG2202
PAS domain [Signal transduction mechanisms];
435-601 1.35e-13

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 71.21  E-value: 1.35e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345424346 435 QELEAVTSEMVRLIETATVPILAVDSDGLVNGWNTKIAELTGLPVDEAIGKHLLEIVEDSSVEIVKRMLENALGGTEEQN 514
Cdd:COG2202    4 EALEESERRLRALVESSPDAIIITDLDGRILYVNPAFERLTGYSAEELLGKTLRDLLPPEDDDEFLELLRAALAGGGVWR 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345424346 515 VQFEIKthlsRADAGPISLVVNACASRDLHENVVGVCFVAHDLTGQKTVMDKFTRIEGDYKAIVQNpNPLIppIFGTDEF 594
Cdd:COG2202   84 GELRNR----RKDGSLFWVELSISPVRDEDGEITGFVGIARDITERKRAEEALRESEERLRLLVEN-APDG--IFVLDLD 156


                 ....*..
gi 345424346 595 GWCSEWN 601
Cdd:COG2202  157 GRILYVN 163
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 39-225 4.29e-12

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: 63.94  E-value: 4.29e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345424346    39 MERLCDTMVQEVFELTGYDRVMAYKFHDDDHGEVVSEVTKPGLEPYLGLHYPATDipQAARFLFMKNKVRMIVDCNAkhv 118
Cdd:smart00065   2 LEELLQTILEELRQLLGADRVLIYLVDENDRGELVLVAADGLTLPTLGIRFPLDE--GLAGRVAETGRPLNIPDVEA--- 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345424346   119 rvlqddklsfdltlcgstlrAPHSCHLQYMANMDSIASLVMAVVVNEEeddaapdstttaqpqkrkrLWGLVVCHNTTpr 198
Cdd:smart00065  77 --------------------DPLFAEDLLGRYQGVRSFLAVPLVADGE-------------------LVGVLALHNKK-- 115

                          170       180
                   ....*....|....*....|....*..
gi 345424346   199 fVPFPLRYACEFLAQVFAIHVNKEVEL 225
Cdd:smart00065 116 -SPRPFTEEDEELLQALANQLAIALAN 141
GAF pfam01590
GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl ...
 38-223 1.17e-10

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: 59.41  E-value: 1.17e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345424346   38 SMERLCDTMVQEVFELTGYDRVMAYkfhdddhgevvsevtkpgLEPYLGLHYpatdIPQAARFLfmknKVRMIVDCNAKH 117
Cdd:pfam01590   1 DLEEILQTILEELRELLGADRCALY------------------LPDADGLEY----LPPGARWL----KAAGLEIPPGTG 54

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345424346  118 VRVLQDDKlsfDLTLCGStlrAPHSCHLQ---YMANMDSIASLVMAVVVNEeeddaapdstttaqpqkrkRLWGLVVCHN 194
Cdd:pfam01590  55 VTVLRTGR---PLVVPDA---AGDPRFLDpllLLRNFGIRSLLAVPIIDDG-------------------ELLGVLVLHH 109

                         170       180
                  ....*....|....*....|....*....
gi 345424346  195 TTPRFvpfpLRYACEFLaQVFAIHVNKEV 223
Cdd:pfam01590 110 PRPPF----TEEELELL-EVLADQVAIAL 133
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 451-557 1.01e-09

PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.


Pssm-ID: 238075 [Multi-domain]  Cd Length: 103  Bit Score: 56.10  E-value: 1.01e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345424346 451 ATVPILAVDSDGLVNGWNTKIAELTGLPVDEAIGKHLLEIVEDSSVEIVKRMLENALGGTEEQNVQFEIKTHlsraDAGP 530
Cdd:cd00130    1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRK----DGSV 76

                         90       100
                 ....*....|....*....|....*..
gi 345424346 531 ISLVVNACASRDLHENVVGVCFVAHDL 557
Cdd:cd00130   77 IWVLVSLTPIRDEGGEVIGLLGVVRDI 103
PAS COG2202
PAS domain [Signal transduction mechanisms];
435-561 3.61e-09

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 57.73  E-value: 3.61e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345424346 435 QELEAVTSEMVRLIETATVPILAVDSDGLVNGWNTKIAELTGLPVDEAIGKHLLEIVEDSSVEIVKRMLENALGGTEEqn 514
Cdd:COG2202  130 EALRESEERLRLLVENAPDGIFVLDLDGRILYVNPAAEELLGYSPEELLGKSLLDLLHPEDRERLLELLRRLLEGGRE-- 207

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 345424346 515 vQFEIKTHLSRADAGPISLVVNAcASRDLHENVVGVCFVAHDLTGQK 561
Cdd:COG2202  208 -SYELELRLKDGDGRWVWVEASA-VPLRDGGEVIGVLGIVRDITERK 252
NtrB COG3852
Signal transduction histidine kinase NtrB, nitrogen specific [Signal transduction mechanisms];
436-561 4.91e-09

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


Pssm-ID: 443061 [Multi-domain]  Cd Length: 361  Bit Score: 58.32  E-value: 4.91e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345424346 436 ELEAVTSEMVRLIETATVPILAVDSDGLVNGWNTKIAELTGLPVDEAIGKHLLEIVEDSSveIVKRMLENALggtEEQNV 515
Cdd:COG3852    1 ALRESEELLRAILDSLPDAVIVLDADGRITYVNPAAERLLGLSAEELLGRPLAELFPEDS--PLRELLERAL---AEGQP 75

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 345424346 516 QFEIKTHLSRADAGPISLVVNACASRDlHENVVGVCFVAHDLTGQK 561
Cdd:COG3852   76 VTEREVTLRRKDGEERPVDVSVSPLRD-AEGEGGVLLVLRDITERK 120
RocR COG3829
RocR-type transcriptional regulator, contains PAS, AAA-type ATPase, and DNA-binding Fis ...
 434-571 7.06e-09

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: 58.24  E-value: 7.06e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345424346 434 IQELEAVTSEMVRLIETATVPILAVDSDGLVNGWNTKIAELTGLPVDEAIGKHLLEIVEDSSVEIVkrmLENalgGTEEQ 513
Cdd:COG3829    3 ELELKELEEELEAILDSLDDGIIVVDADGRITYVNRAAERILGLPREEVIGKNVTELIPNSPLLEV---LKT---GKPVT 76

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 345424346 514 NVQFEIKThlsradaGPISLVVNACASRDlHENVVGVCFVAHDLTGQKTVMDKFTRIE 571
Cdd:COG3829   77 GVIQKTGG-------KGKTVIVTAIPIFE-DGEVIGAVETFRDITELKRLERKLREEE 126
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 446-507 8.52e-09

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


Pssm-ID: 214512  Cd Length: 67  Bit Score: 52.02  E-value: 8.52e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 345424346   446 RLIETATVPILAVDSDGLVNGWNTKIAELTGLPVDEAIGKHLLEIVEDSSVEIVKRMLENAL 507
Cdd:smart00091   5 AILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEALQRLL 66
sensory_box TIGR00229
PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain ...
 443-562 1.32e-08

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: 53.45  E-value: 1.32e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345424346  443 EMVRLI-ETATVPILAVDSDGLVNGWNTKIAELTGLPVDEAIGKHLLEIVEDSSVEIVKRMLENALGGTEEQNVQFEIKT 521
Cdd:TIGR00229   3 ERYRAIfESSPDAIIVIDLEGNILYVNPAFEEIFGYSAEELIGRNVLELIPEEDREEVRERIERRLEGEPEPVSEERRVR 82

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 345424346  522 hlsRADAGPISLVVNAcASRDLHENVVGVCFVAHDLTGQKT 562
Cdd:TIGR00229  83 ---RKDGSEIWVEVSV-SPIRTNGGELGVVGIVRDITERKE 119
PAS_4 pfam08448
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 453-558 4.96e-08

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 is associated to signalling systems and works as a signal sensor domain. It recognizes differently substituted aromatic hydrocarbons, oxygen, different dodecanoic acids, autoinducers, 3,5-dimethyl-pyrazin-2-ol and N-alanyl-aminoacetone (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 312075 [Multi-domain]  Cd Length: 110  Bit Score: 51.26  E-value: 4.96e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345424346  453 VPILAVDSDGLVNGWNTKIAELTGLPVDEAIGKHLLEIVEDSSVEIVKRMLENALggTEEQNVQFEIKTHLSRADAgpiS 532
Cdd:pfam08448   6 DALAVLDPDGRVRYANAAAAELFGLPPEELLGKTLAELLPPEDAARLERALRRAL--EGEEPIDFLEELLLNGEER---H 80

                          90       100
                  ....*....|....*....|....*.
gi 345424346  533 LVVNACASRDLHENVVGVCFVAHDLT 558
Cdd:pfam08448  81 YELRLTPLRDPDGEVIGVLVISRDIT 106
PRK11360 PRK11360
two-component system sensor histidine kinase AtoS;
448-571 8.59e-08

two-component system sensor histidine kinase AtoS;


Pssm-ID: 236901 [Multi-domain]  Cd Length: 607  Bit Score: 54.97  E-value: 8.59e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345424346 448 IETATVPILAVDSDGLVNGWNTKIAELTGLPVDEAIGKHLLEIVEDSS--VEIVKRMLENalgGTEEqnVQFEIKTHlsr 525
Cdd:PRK11360 268 LESIADGVIAIDRQGKITTMNPAAEVITGLQRHELVGKPYSELFPPNTpfASPLLDTLEH---GTEH--VDLEISFP--- 339

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 345424346 526 ADAGPISLVVNACASRDLHENVVGVCFVAHDLTGQKTVMDKFTRIE 571
Cdd:PRK11360 340 GRDRTIELSVSTSLLHNTHGEMIGALVIFSDLTERKRLQRRVARQE 385
PAS_9 pfam13426
PAS domain; This domain is found in many signalling proteins in which it functions as a sensor ...
 467-558 1.20e-05

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


Pssm-ID: 463873 [Multi-domain]  Cd Length: 93  Bit Score: 43.99  E-value: 1.20e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345424346  467 WNTKIAELTGLPVDEAIGKHLLEIVEDSSVEIVKRMLENALGGTEEQNVQFEikthlsRADAGPISLVVNACASRDLHEN 546
Cdd:pfam13426   7 VNDAALRLLGYTREELLGKSITDLFAEPEDSERLREALREGKAVREFEVVLY------RKDGEPFPVLVSLAPIRDDGGE 80

                          90
                  ....*....|..
gi 345424346  547 VVGVCFVAHDLT 558
Cdd:pfam13426  81 LVGIIAILRDIT 92
NtrY COG5000
Signal transduction histidine kinase NtrY involved in nitrogen fixation and metabolism ...
 435-524 2.98e-04

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: 43.41  E-value: 2.98e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 345424346 435 QELEAVTSEMVRLIETATVPILAVDSDGLVNGWNTKIAELTGLPVDEAIGKHLLEIVEDSSVEivkRMLENALGGTEEQN 514
Cdd:COG5000   83 EELEERRRYLETILENLPAGVIVLDADGRITLANPAAERLLGIPLEELIGKPLEELLPELDLA---ELLREALERGWQEE 159

                         90
                 ....*....|
gi 345424346 515 VQFEIKTHLS 524
Cdd:COG5000  160 IELTRDGRRT 169
KinA COG5805
Sporulation sensor histidine kinase A (Stage II sporulation protein SpoIIF/SpoIIJ) [Cell cycle ...
 441-512 1.78e-03

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


Pssm-ID: 444507 [Multi-domain]  Cd Length: 496  Bit Score: 41.26  E-value: 1.78e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 345424346 441 TSEMVRLIETATVPILAVDSDGLVNGWNTKIAELTGLPVDEAIGKHLLEIVEDSSVEIVKRMLENALGGTEE 512
Cdd:COG5805   33 TEELETILENLPDAIIAVNREGKVIYINPAMEKLLGYTSEEIIGKTIFDFLEKEYHYRVKTRIERLQKGYDV 104
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 572-601 6.06e-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: 37.01  E-value: 6.06e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 345424346  572 GDYKAIVQNpnpLIPPIFGTDEFGWCSEWN 601
Cdd:pfam00989   1 EDLRAILES---LPDGIFVVDEDGRILYVN 27
 
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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