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Conserved domains on  [gi|315377385|gb|ADU05530|]
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phytochrome A, partial [Neslia paniculata]

Protein Classification

PAS domain-containing sensor histidine kinase( domain architecture ID 13406978)

two-component sensor histidine kinase with a PAS sensor and/or ligand binding domain, similar to Zea mays phytochrome B1 that mediates physiological responses to light cues

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 ...
 234-407 2.97e-66

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: 214.05  E-value: 2.97e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315377385  234 LRTQTLLCDMLMR--DAPLGIVSQSPNIMDLVKCDGAALLYKDKIWKLGTTPSEFHLQEIASWLCEYHtDSTGLSTDSLH 311
Cdd:pfam00360   2 RRIQDRLVEAMARadDLVDGLVDQSPNLLDLVKADGAALCFGGNLLTLGETPPEEAIRDLAQWLGRNH-DSEVFSTDSLS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315377385  312 DAgFSRALSLGDSVCGMAAVRISSKDM--IFWFRSHTAGEVRWGGAKHDPDDRDDARR-MHPRSSFKAFLEVVKTRSLPW 388
Cdd:pfam00360  81 QA-YPEAAALADVASGLLAIPISRKPGnyLLWFRPEVVRTVNWGGDPHKAVEIDPGGVrLSPRKSFDAWKETVRGRSLPW 159

                         170
                  ....*....|....*....
gi 315377385  389 KDYEMDAIHSLQLILRNAF 407
Cdd:pfam00360 160 SEVEIEAARELREALLGVV 178
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 441-554 1.25e-23

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: 95.95  E-value: 1.25e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315377385  441 EMVRLIETATVPILAVDSDGLVNGWNTKIAELTGLSVDEAIGKHLLTLV-EDSSVEIVKRMLENALEGTEEQNVQFEIKT 519
Cdd:pfam00989   2 DLRAILESLPDGIFVVDEDGRILYVNAAAEELLGLSREEVIGKSLLDLIpEEDDAEVAELLRQALLQGEESRGFEVSFRV 81

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 315377385  520 QltraDAGPISLVVNACASRDLHENVVGVCFVAHD 554
Cdd:pfam00989  82 P----DGRPRHVEVRASPVRDAGGEILGFLGVLRD 112
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 39-224 9.59e-13

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: 65.87  E-value: 9.59e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315377385    39 MERLCDTMVQEVFELTGYDRVMAYKFHEDDHGEVVSEVTKPGLEPYLGLHYPATDipQAARFLFMKNKVRMIVDCNAkha 118
Cdd:smart00065   2 LEELLQTILEELRQLLGADRVLIYLVDENDRGELVLVAADGLTLPTLGIRFPLDE--GLAGRVAETGRPLNIPDVEA--- 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315377385   119 rvlqdeklsfdltlcgstlrAPHSCHLQYMANMDSIASLVMAVVVNEEdgegdapdstaqpqkrkrLWGLVVCHNTTprf 198
Cdd:smart00065  77 --------------------DPLFAEDLLGRYQGVRSFLAVPLVADGE------------------LVGVLALHNKK--- 115

                          170       180
                   ....*....|....*....|....*.
gi 315377385   199 VPFPLRYACEFLAQVFAIHVNKEVEL 224
Cdd:smart00065 116 SPRPFTEEDEELLQALANQLAIALAN 141
PAS super family cl38023
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 570-599 3.79e-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: 37.40  E-value: 3.79e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 315377385  570 GDYKAIIQNpnpLIPPIFGTDEFGWCTEWN 599
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 ...
 234-407 2.97e-66

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: 214.05  E-value: 2.97e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315377385  234 LRTQTLLCDMLMR--DAPLGIVSQSPNIMDLVKCDGAALLYKDKIWKLGTTPSEFHLQEIASWLCEYHtDSTGLSTDSLH 311
Cdd:pfam00360   2 RRIQDRLVEAMARadDLVDGLVDQSPNLLDLVKADGAALCFGGNLLTLGETPPEEAIRDLAQWLGRNH-DSEVFSTDSLS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315377385  312 DAgFSRALSLGDSVCGMAAVRISSKDM--IFWFRSHTAGEVRWGGAKHDPDDRDDARR-MHPRSSFKAFLEVVKTRSLPW 388
Cdd:pfam00360  81 QA-YPEAAALADVASGLLAIPISRKPGnyLLWFRPEVVRTVNWGGDPHKAVEIDPGGVrLSPRKSFDAWKETVRGRSLPW 159

                         170
                  ....*....|....*....
gi 315377385  389 KDYEMDAIHSLQLILRNAF 407
Cdd:pfam00360 160 SEVEIEAARELREALLGVV 178
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 441-554 1.25e-23

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: 95.95  E-value: 1.25e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315377385  441 EMVRLIETATVPILAVDSDGLVNGWNTKIAELTGLSVDEAIGKHLLTLV-EDSSVEIVKRMLENALEGTEEQNVQFEIKT 519
Cdd:pfam00989   2 DLRAILESLPDGIFVVDEDGRILYVNAAAEELLGLSREEVIGKSLLDLIpEEDDAEVAELLRQALLQGEESRGFEVSFRV 81

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 315377385  520 QltraDAGPISLVVNACASRDLHENVVGVCFVAHD 554
Cdd:pfam00989  82 P----DGRPRHVEVRASPVRDAGGEILGFLGVLRD 112
PAS COG2202
PAS domain [Signal transduction mechanisms];
433-599 2.64e-14

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 73.14  E-value: 2.64e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315377385 433 QELEAVTSEMVRLIETATVPILAVDSDGLVNGWNTKIAELTGLSVDEAIGKHLLTLVEDSSVEIVKRMLENALEGTEEQN 512
Cdd:COG2202    4 EALEESERRLRALVESSPDAIIITDLDGRILYVNPAFERLTGYSAEELLGKTLRDLLPPEDDDEFLELLRAALAGGGVWR 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315377385 513 VQFEIKtqltRADAGPISLVVNACASRDLHENVVGVCFVAHDLTGQKTVMDKFTRIEGDYKAIIQNpNPLIppIFGTDEF 592
Cdd:COG2202   84 GELRNR----RKDGSLFWVELSISPVRDEDGEITGFVGIARDITERKRAEEALRESEERLRLLVEN-APDG--IFVLDLD 156


                 ....*..
gi 315377385 593 GWCTEWN 599
Cdd:COG2202  157 GRILYVN 163
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 39-224 9.59e-13

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: 65.87  E-value: 9.59e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315377385    39 MERLCDTMVQEVFELTGYDRVMAYKFHEDDHGEVVSEVTKPGLEPYLGLHYPATDipQAARFLFMKNKVRMIVDCNAkha 118
Cdd:smart00065   2 LEELLQTILEELRQLLGADRVLIYLVDENDRGELVLVAADGLTLPTLGIRFPLDE--GLAGRVAETGRPLNIPDVEA--- 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315377385   119 rvlqdeklsfdltlcgstlrAPHSCHLQYMANMDSIASLVMAVVVNEEdgegdapdstaqpqkrkrLWGLVVCHNTTprf 198
Cdd:smart00065  77 --------------------DPLFAEDLLGRYQGVRSFLAVPLVADGE------------------LVGVLALHNKK--- 115

                          170       180
                   ....*....|....*....|....*.
gi 315377385   199 VPFPLRYACEFLAQVFAIHVNKEVEL 224
Cdd:smart00065 116 SPRPFTEEDEELLQALANQLAIALAN 141
GAF pfam01590
GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl ...
 38-222 9.27e-11

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: 59.80  E-value: 9.27e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315377385   38 SMERLCDTMVQEVFELTGYDRVMAYkfheddhgevvsevtkpgLEPYLGLHYpatdIPQAARFLfmknKVRMIVDCNAKH 117
Cdd:pfam01590   1 DLEEILQTILEELRELLGADRCALY------------------LPDADGLEY----LPPGARWL----KAAGLEIPPGTG 54

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315377385  118 ARVLQDEKlsfDLTLCGStlrAPHSCHLQ---YMANMDSIASLVMAVVVNEedgegdapdstaqpqkrkRLWGLVVCHNT 194
Cdd:pfam01590  55 VTVLRTGR---PLVVPDA---AGDPRFLDpllLLRNFGIRSLLAVPIIDDG------------------ELLGVLVLHHP 110

                         170       180
                  ....*....|....*....|....*...
gi 315377385  195 TPRFvpfpLRYACEFLaQVFAIHVNKEV 222
Cdd:pfam01590 111 RPPF----TEEELELL-EVLADQVAIAL 133
sensory_box TIGR00229
PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain ...
 441-560 4.34e-10

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: 57.69  E-value: 4.34e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315377385  441 EMVRLI-ETATVPILAVDSDGLVNGWNTKIAELTGLSVDEAIGKHLLTLVEDSSVEIVKRMLENALEGTEEQNvqfEIKT 519
Cdd:TIGR00229   3 ERYRAIfESSPDAIIVIDLEGNILYVNPAFEEIFGYSAEELIGRNVLELIPEEDREEVRERIERRLEGEPEPV---SEER 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 315377385  520 QLTRADAGPISLVVNAcASRDLHENVVGVCFVAHDLTGQKT 560
Cdd:TIGR00229  80 RVRRKDGSEIWVEVSV-SPIRTNGGELGVVGIVRDITERKE 119
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 449-555 8.05e-10

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: 8.05e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315377385 449 ATVPILAVDSDGLVNGWNTKIAELTGLSVDEAIGKHLLTLVEDSSVEIVKRMLENALEGTEEQNVQFEiktqLTRADAGP 528
Cdd:cd00130    1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVR----LRRKDGSV 76

                         90       100
                 ....*....|....*....|....*..
gi 315377385 529 ISLVVNACASRDLHENVVGVCFVAHDL 555
Cdd:cd00130   77 IWVLVSLTPIRDEGGEVIGLLGVVRDI 103
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 444-506 7.26e-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: 52.40  E-value: 7.26e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 315377385   444 RLIETATVPILAVDSDGLVNGWNTKIAELTGLSVDEAIGKHLLTLVEDSSVEIVKRMLENALE 506
Cdd:smart00091   5 AILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEALQRLLS 67
PRK11360 PRK11360
two-component system sensor histidine kinase AtoS;
446-569 4.45e-07

two-component system sensor histidine kinase AtoS;


Pssm-ID: 236901 [Multi-domain]  Cd Length: 607  Bit Score: 52.66  E-value: 4.45e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315377385 446 IETATVPILAVDSDGLVNGWNTKIAELTGLSVDEAIGKHLLTLVEDSS--VEIVKRMLENaleGTEEqnVQFEIKTQltr 523
Cdd:PRK11360 268 LESIADGVIAIDRQGKITTMNPAAEVITGLQRHELVGKPYSELFPPNTpfASPLLDTLEH---GTEH--VDLEISFP--- 339

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 315377385 524 ADAGPISLVVNACASRDLHENVVGVCFVAHDLTGQKTVMDKFTRIE 569
Cdd:PRK11360 340 GRDRTIELSVSTSLLHNTHGEMIGALVIFSDLTERKRLQRRVARQE 385
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 570-599 3.79e-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: 37.40  E-value: 3.79e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 315377385  570 GDYKAIIQNpnpLIPPIFGTDEFGWCTEWN 599
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 ...
 234-407 2.97e-66

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: 214.05  E-value: 2.97e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315377385  234 LRTQTLLCDMLMR--DAPLGIVSQSPNIMDLVKCDGAALLYKDKIWKLGTTPSEFHLQEIASWLCEYHtDSTGLSTDSLH 311
Cdd:pfam00360   2 RRIQDRLVEAMARadDLVDGLVDQSPNLLDLVKADGAALCFGGNLLTLGETPPEEAIRDLAQWLGRNH-DSEVFSTDSLS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315377385  312 DAgFSRALSLGDSVCGMAAVRISSKDM--IFWFRSHTAGEVRWGGAKHDPDDRDDARR-MHPRSSFKAFLEVVKTRSLPW 388
Cdd:pfam00360  81 QA-YPEAAALADVASGLLAIPISRKPGnyLLWFRPEVVRTVNWGGDPHKAVEIDPGGVrLSPRKSFDAWKETVRGRSLPW 159

                         170
                  ....*....|....*....
gi 315377385  389 KDYEMDAIHSLQLILRNAF 407
Cdd:pfam00360 160 SEVEIEAARELREALLGVV 178
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 441-554 1.25e-23

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: 95.95  E-value: 1.25e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315377385  441 EMVRLIETATVPILAVDSDGLVNGWNTKIAELTGLSVDEAIGKHLLTLV-EDSSVEIVKRMLENALEGTEEQNVQFEIKT 519
Cdd:pfam00989   2 DLRAILESLPDGIFVVDEDGRILYVNAAAEELLGLSREEVIGKSLLDLIpEEDDAEVAELLRQALLQGEESRGFEVSFRV 81

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 315377385  520 QltraDAGPISLVVNACASRDLHENVVGVCFVAHD 554
Cdd:pfam00989  82 P----DGRPRHVEVRASPVRDAGGEILGFLGVLRD 112
PAS COG2202
PAS domain [Signal transduction mechanisms];
433-599 2.64e-14

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 73.14  E-value: 2.64e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315377385 433 QELEAVTSEMVRLIETATVPILAVDSDGLVNGWNTKIAELTGLSVDEAIGKHLLTLVEDSSVEIVKRMLENALEGTEEQN 512
Cdd:COG2202    4 EALEESERRLRALVESSPDAIIITDLDGRILYVNPAFERLTGYSAEELLGKTLRDLLPPEDDDEFLELLRAALAGGGVWR 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315377385 513 VQFEIKtqltRADAGPISLVVNACASRDLHENVVGVCFVAHDLTGQKTVMDKFTRIEGDYKAIIQNpNPLIppIFGTDEF 592
Cdd:COG2202   84 GELRNR----RKDGSLFWVELSISPVRDEDGEITGFVGIARDITERKRAEEALRESEERLRLLVEN-APDG--IFVLDLD 156


                 ....*..
gi 315377385 593 GWCTEWN 599
Cdd:COG2202  157 GRILYVN 163
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 39-224 9.59e-13

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: 65.87  E-value: 9.59e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315377385    39 MERLCDTMVQEVFELTGYDRVMAYKFHEDDHGEVVSEVTKPGLEPYLGLHYPATDipQAARFLFMKNKVRMIVDCNAkha 118
Cdd:smart00065   2 LEELLQTILEELRQLLGADRVLIYLVDENDRGELVLVAADGLTLPTLGIRFPLDE--GLAGRVAETGRPLNIPDVEA--- 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315377385   119 rvlqdeklsfdltlcgstlrAPHSCHLQYMANMDSIASLVMAVVVNEEdgegdapdstaqpqkrkrLWGLVVCHNTTprf 198
Cdd:smart00065  77 --------------------DPLFAEDLLGRYQGVRSFLAVPLVADGE------------------LVGVLALHNKK--- 115

                          170       180
                   ....*....|....*....|....*.
gi 315377385   199 VPFPLRYACEFLAQVFAIHVNKEVEL 224
Cdd:smart00065 116 SPRPFTEEDEELLQALANQLAIALAN 141
GAF pfam01590
GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl ...
 38-222 9.27e-11

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: 59.80  E-value: 9.27e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315377385   38 SMERLCDTMVQEVFELTGYDRVMAYkfheddhgevvsevtkpgLEPYLGLHYpatdIPQAARFLfmknKVRMIVDCNAKH 117
Cdd:pfam01590   1 DLEEILQTILEELRELLGADRCALY------------------LPDADGLEY----LPPGARWL----KAAGLEIPPGTG 54

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315377385  118 ARVLQDEKlsfDLTLCGStlrAPHSCHLQ---YMANMDSIASLVMAVVVNEedgegdapdstaqpqkrkRLWGLVVCHNT 194
Cdd:pfam01590  55 VTVLRTGR---PLVVPDA---AGDPRFLDpllLLRNFGIRSLLAVPIIDDG------------------ELLGVLVLHHP 110

                         170       180
                  ....*....|....*....|....*...
gi 315377385  195 TPRFvpfpLRYACEFLaQVFAIHVNKEV 222
Cdd:pfam01590 111 RPPF----TEEELELL-EVLADQVAIAL 133
PAS COG2202
PAS domain [Signal transduction mechanisms];
400-559 3.11e-10

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 61.19  E-value: 3.11e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315377385 400 QLILRNAFKDGETTDVNTKVIHSKLNDLKIDGI--------------QELEAVTSEMVRLIETATVPILAVDSDGLVNGW 465
Cdd:COG2202   83 RGELRNRRKDGSLFWVELSISPVRDEDGEITGFvgiarditerkraeEALRESEERLRLLVENAPDGIFVLDLDGRILYV 162

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315377385 466 NTKIAELTGLSVDEAIGKHLLTLVEDSSVEIVKRMLENALEGTEEqnvQFEIKTQLTRADAGPISLVVNAcASRDLHENV 545
Cdd:COG2202  163 NPAAEELLGYSPEELLGKSLLDLLHPEDRERLLELLRRLLEGGRE---SYELELRLKDGDGRWVWVEASA-VPLRDGGEV 238

                        170
                 ....*....|....
gi 315377385 546 VGVCFVAHDLTGQK 559
Cdd:COG2202  239 IGVLGIVRDITERK 252
sensory_box TIGR00229
PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain ...
 441-560 4.34e-10

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: 57.69  E-value: 4.34e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315377385  441 EMVRLI-ETATVPILAVDSDGLVNGWNTKIAELTGLSVDEAIGKHLLTLVEDSSVEIVKRMLENALEGTEEQNvqfEIKT 519
Cdd:TIGR00229   3 ERYRAIfESSPDAIIVIDLEGNILYVNPAFEEIFGYSAEELIGRNVLELIPEEDREEVRERIERRLEGEPEPV---SEER 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 315377385  520 QLTRADAGPISLVVNAcASRDLHENVVGVCFVAHDLTGQKT 560
Cdd:TIGR00229  80 RVRRKDGSEIWVEVSV-SPIRTNGGELGVVGIVRDITERKE 119
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 449-555 8.05e-10

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: 8.05e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315377385 449 ATVPILAVDSDGLVNGWNTKIAELTGLSVDEAIGKHLLTLVEDSSVEIVKRMLENALEGTEEQNVQFEiktqLTRADAGP 528
Cdd:cd00130    1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVR----LRRKDGSV 76

                         90       100
                 ....*....|....*....|....*..
gi 315377385 529 ISLVVNACASRDLHENVVGVCFVAHDL 555
Cdd:cd00130   77 IWVLVSLTPIRDEGGEVIGLLGVVRDI 103
NtrB COG3852
Signal transduction histidine kinase NtrB, nitrogen specific [Signal transduction mechanisms];
434-559 2.48e-09

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


Pssm-ID: 443061 [Multi-domain]  Cd Length: 361  Bit Score: 59.47  E-value: 2.48e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315377385 434 ELEAVTSEMVRLIETATVPILAVDSDGLVNGWNTKIAELTGLSVDEAIGKHLLTLVEDSSveIVKRMLENALegtEEQNV 513
Cdd:COG3852    1 ALRESEELLRAILDSLPDAVIVLDADGRITYVNPAAERLLGLSAEELLGRPLAELFPEDS--PLRELLERAL---AEGQP 75

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 315377385 514 QFEIKTQLTRADAGPISLVVNACASRDlHENVVGVCFVAHDLTGQK 559
Cdd:COG3852   76 VTEREVTLRRKDGEERPVDVSVSPLRD-AEGEGGVLLVLRDITERK 120
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 444-506 7.26e-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: 52.40  E-value: 7.26e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 315377385   444 RLIETATVPILAVDSDGLVNGWNTKIAELTGLSVDEAIGKHLLTLVEDSSVEIVKRMLENALE 506
Cdd:smart00091   5 AILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEALQRLLS 67
RocR COG3829
RocR-type transcriptional regulator, contains PAS, AAA-type ATPase, and DNA-binding Fis ...
 432-569 3.22e-08

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: 56.32  E-value: 3.22e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315377385 432 IQELEAVTSEMVRLIETATVPILAVDSDGLVNGWNTKIAELTGLSVDEAIGKHLLTLVEDSSVEIVKRmlenalEGTEEQ 511
Cdd:COG3829    3 ELELKELEEELEAILDSLDDGIIVVDADGRITYVNRAAERILGLPREEVIGKNVTELIPNSPLLEVLK------TGKPVT 76

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 315377385 512 NVQFEIKTqltradaGPISLVVNACASRDlHENVVGVCFVAHDLTGQKTVMDKFTRIE 569
Cdd:COG3829   77 GVIQKTGG-------KGKTVIVTAIPIFE-DGEVIGAVETFRDITELKRLERKLREEE 126
PRK11360 PRK11360
two-component system sensor histidine kinase AtoS;
446-569 4.45e-07

two-component system sensor histidine kinase AtoS;


Pssm-ID: 236901 [Multi-domain]  Cd Length: 607  Bit Score: 52.66  E-value: 4.45e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315377385 446 IETATVPILAVDSDGLVNGWNTKIAELTGLSVDEAIGKHLLTLVEDSS--VEIVKRMLENaleGTEEqnVQFEIKTQltr 523
Cdd:PRK11360 268 LESIADGVIAIDRQGKITTMNPAAEVITGLQRHELVGKPYSELFPPNTpfASPLLDTLEH---GTEH--VDLEISFP--- 339

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 315377385 524 ADAGPISLVVNACASRDLHENVVGVCFVAHDLTGQKTVMDKFTRIE 569
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 ...
 465-556 9.49e-07

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: 47.07  E-value: 9.49e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315377385  465 WNTKIAELTGLSVDEAIGKHLLTLVEDSSVEivkRMLENALegtEEQNVQFEIKTQLTRADAGPISLVVNACASRDLHEN 544
Cdd:pfam13426   7 VNDAALRLLGYTREELLGKSITDLFAEPEDS---ERLREAL---REGKAVREFEVVLYRKDGEPFPVLVSLAPIRDDGGE 80

                          90
                  ....*....|..
gi 315377385  545 VVGVCFVAHDLT 556
Cdd:pfam13426  81 LVGIIAILRDIT 92
PAS_4 pfam08448
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 451-556 1.45e-06

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: 47.02  E-value: 1.45e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315377385  451 VPILAVDSDGLVNGWNTKIAELTGLSVDEAIGKHLLTLVEDSSVEIVKRMLENALEGTEEQNVQFEiktqlTRADAGPIS 530
Cdd:pfam08448   6 DALAVLDPDGRVRYANAAAAELFGLPPEELLGKTLAELLPPEDAARLERALRRALEGEEPIDFLEE-----LLLNGEERH 80

                          90       100
                  ....*....|....*....|....*.
gi 315377385  531 LVVNACASRDLHENVVGVCFVAHDLT 556
Cdd:pfam08448  81 YELRLTPLRDPDGEVIGVLVISRDIT 106
NtrY COG5000
Signal transduction histidine kinase NtrY involved in nitrogen fixation and metabolism ...
 433-522 1.66e-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: 44.18  E-value: 1.66e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315377385 433 QELEAVTSEMVRLIETATVPILAVDSDGLVNGWNTKIAELTGLSVDEAIGKHLLTLVEDSSVEivkRMLENALEGTEEQN 512
Cdd:COG5000   83 EELEERRRYLETILENLPAGVIVLDADGRITLANPAAERLLGIPLEELIGKPLEELLPELDLA---ELLREALERGWQEE 159

                         90
                 ....*....|
gi 315377385 513 VQFEIKTQLT 522
Cdd:COG5000  160 IELTRDGRRT 169
KinA COG5805
Sporulation sensor histidine kinase A (Stage II sporulation protein SpoIIF/SpoIIJ) [Cell cycle ...
 439-583 3.28e-04

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: 43.57  E-value: 3.28e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315377385 439 TSEMVRLIETATVPILAVDSDGLVNGWNTKIAELTGLSVDEAIGKHLLTLVEDSSVEIVKRMLENALEGTeeqnvQFEIK 518
Cdd:COG5805   33 TEELETILENLPDAIIAVNREGKVIYINPAMEKLLGYTSEEIIGKTIFDFLEKEYHYRVKTRIERLQKGY-----DVVMI 107

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 315377385 519 TQLTRADAGPISLVVNACASRDLHENVVGVCFVahDLTGQKTVMDKFTRIEGDYKAIIQNPNPLI 583
Cdd:COG5805  108 EQIYCKDGELIYVEVKLFPIYNQNGQAAILALR--DITKKKKIEEILQEQEERLQTLIENSPDLI 170
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 570-599 3.79e-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: 37.40  E-value: 3.79e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 315377385  570 GDYKAIIQNpnpLIPPIFGTDEFGWCTEWN 599
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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