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Conserved domains on  [gi|15234859|ref|NP_193360|]
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phytochrome D [Arabidopsis thaliana]

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 ...
448-622 5.77e-60

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: 203.27  E-value: 5.77e-60
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859    448 VLRMQTLLCDMLLR--DSPAGIVTQRPSIMDLVKCNGAAFLYQGKYYPLGVTPTDSQINDIVEWLVANHsDSTGLSTDSL 525
Cdd:pfam00360    1 LRRIQDRLVEAMARadDLVDGLVDQSPNLLDLVKADGAALCFGGNLLTLGETPPEEAIRDLAQWLGRNH-DSEVFSTDSL 79
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859    526 GDAgYPRAAALGDAVCGMAVACI--TKRDFLFWFRSHTEKEIKWGGAKHHPEDKDD-GQRMNPRSSFQTFLEVVKSRCQP 602
Cdd:pfam00360   80 SQA-YPEAAALADVASGLLAIPIsrKPGNYLLWFRPEVVRTVNWGGDPHKAVEIDPgGVRLSPRKSFDAWKETVRGRSLP 158
                          170       180
                   ....*....|....*....|
gi 15234859    603 WETAEMDAIHSLQLILRDSF 622
Cdd:pfam00360  159 WSEVEIEAARELREALLGVV 178
HATPase_Phy-like cd16932
Histidine kinase-like ATPase domain of plant phytochromes similar to Arabidopsis thaliana ...
1042-1153 9.18e-53

Histidine kinase-like ATPase domain of plant phytochromes similar to Arabidopsis thaliana Phytochrome A, B, C, D and E; This family includes the histidine kinase-like ATPase (HATPase) domains of plant red/far-red photoreceptors, the phytochromes, and includes the Arabidopsis thaliana phytochrome family phyA-phyE. Following red light absorption, biologically inactive forms of phytochromes convert to active forms, which rapidly convert back to inactive forms upon far-red light irradiation. Phytochromes can be considered as having an N-terminal photosensory region to which a bilin chromophore is bound, and a C-terminal output region, which includes the HATPase domain represented here, and is involved in dimerization and presumably contributes to relaying the light signal to downstream signaling events.


:

Pssm-ID: 340409 [Multi-domain]  Cd Length: 113  Bit Score: 180.16  E-value: 9.18e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859 1042 YGDQIRLQQVLAEFLLSIVRYAP-MEGSVELHLCPTLNQMADGFSAVRLEFRMACAGEGVPPEKVQDMFHSSRWTSPEGL 1120
Cdd:cd16932    1 YGDQIRLQQVLADFLLNAVRFTPsPGGWVEIKVSPTKKQIGDGVHVIHLEFRITHPGQGLPEELVQEMFEENQWTTQEGL 80
                         90       100       110
                 ....*....|....*....|....*....|...
gi 15234859 1121 GLSVCRKILKLMNGGVQYIREFERSYFLIVIEL 1153
Cdd:cd16932   81 GLSISRKLVKLMNGDVRYLREAGRSYFLITLEL 113
PAS_2 pfam08446
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
105-222 1.67e-49

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: 170.51  E-value: 1.67e-49
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859    105 AYLSRIQRGGYTQPFGCLIAVEESTFTIIGYSENAREMLGLMSQSVpsiedksevltIGTDLRSLFKSSSYLLLERAFVA 184
Cdd:pfam08446    1 CYLEPIQRPGLIQPHGCLLAVDEPSLRVLQYSENAAEMLGLPAEDL-----------LGTDLRDLFGASSASLLRKALAA 69
                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 15234859    185 REITLLNPIWIHSNNTGKPFYAILHRVDVGILIDLEPA 222
Cdd:pfam08446   70 GEISLLNPILIHSRTSGKPFYAILHRSDGGLVLELEPA 107
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
255-447 1.56e-24

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: 100.53  E-value: 1.56e-24
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859     255 DIKLLCDTVVESVRDLTGYDRVMVYKFHEDEHGEVVAESKRNDLEPYIGLHYPATDipQASRFLFKQNRVRMIVDCYASP 334
Cdd:smart00065    1 DLEELLQTILEELRQLLGADRVLIYLVDENDRGELVLVAADGLTLPTLGIRFPLDE--GLAGRVAETGRPLNIPDVEADP 78
                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859     335 VRvvQDDRLTQFiCLVGSTLRAPhgchaqymtnmgsiaslamavIINGNEedgngvntggrnsmrLWGLVVCHHtsaRCI 414
Cdd:smart00065   79 LF--AEDLLGRY-QGVRSFLAVP---------------------LVADGE---------------LVGVLALHN---KKS 116
                           170       180       190
                    ....*....|....*....|....*....|...
gi 15234859     415 PFPLRYACEFLMQAFGLQLNMELQLALQVSEKR 447
Cdd:smart00065  117 PRPFTEEDEELLQALANQLAIALANAQLYEELR 149
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
658-774 1.99e-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: 99.03  E-value: 1.99e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859    658 REMVRLIETATVPIFAVDIDGCINGWNAKIAELTGLSVEDAMGKSLVRELIYKEYKETVDRLLSCALKGDEGKNVEVKLK 737
Cdd:pfam00989    1 EDLRAILESLPDGIFVVDEDGRILYVNAAAEELLGLSREEVIGKSLLDLIPEEDDAEVAELLRQALLQGEESRGFEVSFR 80
                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 15234859    738 TFgselQGKAMFVVVNACSSKDYLNNIVGVCFVGQDV 774
Cdd:pfam00989   81 VP----DGRPRHVEVRASPVRDAGGEILGFLGVLRDI 113
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
789-909 7.45e-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: 94.79  E-value: 7.45e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859    789 GDYKAIIHSpnpLIPPIFAADENTCCLEWNTAMEKLTGWPRSEVIGKLLVREVFGSYcRLKGPDALTKFMIVLHNAIGGQ 868
Cdd:pfam00989    1 EDLRAILES---LPDGIFVVDEDGRILYVNAAAEELLGLSREEVIGKSLLDLIPEED-DAEVAELLRQALLQGEESRGFE 76
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 15234859    869 DTDKFPfpffdrKGEFIQALLTLNKRVSIDGKIIGAFCFLQ 909
Cdd:pfam00989   77 VSFRVP------DGRPRHVEVRASPVRDAGGEILGFLGVLR 111
KdpD COG2205
K+-sensing histidine kinase KdpD [Signal transduction mechanisms];
914-1155 6.47e-22

K+-sensing histidine kinase KdpD [Signal transduction mechanisms];


:

Pssm-ID: 441807 [Multi-domain]  Cd Length: 239  Bit Score: 96.13  E-value: 6.47e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859  914 ELQQALEVQRRQESeyfsRRKELAYIfqV---IKNPLSGLRFTNSLLEDMD--LNEDQKQLLETSVSCEKQISKIVGDM- 987
Cdd:COG2205    1 ELEEALEELEELER----LKSEFLAN--VsheLRTPLTSILGAAELLLDEEdlSPEERRELLEIIRESAERLLRLIEDLl 74
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859  988 DVKSIDDGSFLLERTEFFIGNVTNAVVSQVMLVVRERNLQLIRNIPTEvkSMAVYGDQIRLQQVLAEFLLSIVRYAPMEG 1067
Cdd:COG2205   75 DLSRLESGKLSLELEPVDLAELLEEAVEELRPLAEEKGIRLELDLPPE--LPLVYADPELLEQVLANLLDNAIKYSPPGG 152
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859 1068 SVELHLCPTLNQmadgfsavrLEFRMACAGEGVPPEKVQDMF------HSSRWTSPEGLGLSVCRKILKLMNGGVQYIRE 1141
Cdd:COG2205  153 TITISARREGDG---------VRISVSDNGPGIPEEELERIFerfyrgDNSRGEGGTGLGLAIVKRIVEAHGGTIWVESE 223
                        250
                 ....*....|....
gi 15234859 1142 fERSYFLIVIELPV 1155
Cdd:COG2205  224 -PGGGTTFTVTLPL 236
 
Name Accession Description Interval E-value
PHY pfam00360
Phytochrome region; Phytochromes are red/far-red photochromic biliprotein photoreceptors which ...
448-622 5.77e-60

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: 203.27  E-value: 5.77e-60
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859    448 VLRMQTLLCDMLLR--DSPAGIVTQRPSIMDLVKCNGAAFLYQGKYYPLGVTPTDSQINDIVEWLVANHsDSTGLSTDSL 525
Cdd:pfam00360    1 LRRIQDRLVEAMARadDLVDGLVDQSPNLLDLVKADGAALCFGGNLLTLGETPPEEAIRDLAQWLGRNH-DSEVFSTDSL 79
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859    526 GDAgYPRAAALGDAVCGMAVACI--TKRDFLFWFRSHTEKEIKWGGAKHHPEDKDD-GQRMNPRSSFQTFLEVVKSRCQP 602
Cdd:pfam00360   80 SQA-YPEAAALADVASGLLAIPIsrKPGNYLLWFRPEVVRTVNWGGDPHKAVEIDPgGVRLSPRKSFDAWKETVRGRSLP 158
                          170       180
                   ....*....|....*....|
gi 15234859    603 WETAEMDAIHSLQLILRDSF 622
Cdd:pfam00360  159 WSEVEIEAARELREALLGVV 178
HATPase_Phy-like cd16932
Histidine kinase-like ATPase domain of plant phytochromes similar to Arabidopsis thaliana ...
1042-1153 9.18e-53

Histidine kinase-like ATPase domain of plant phytochromes similar to Arabidopsis thaliana Phytochrome A, B, C, D and E; This family includes the histidine kinase-like ATPase (HATPase) domains of plant red/far-red photoreceptors, the phytochromes, and includes the Arabidopsis thaliana phytochrome family phyA-phyE. Following red light absorption, biologically inactive forms of phytochromes convert to active forms, which rapidly convert back to inactive forms upon far-red light irradiation. Phytochromes can be considered as having an N-terminal photosensory region to which a bilin chromophore is bound, and a C-terminal output region, which includes the HATPase domain represented here, and is involved in dimerization and presumably contributes to relaying the light signal to downstream signaling events.


Pssm-ID: 340409 [Multi-domain]  Cd Length: 113  Bit Score: 180.16  E-value: 9.18e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859 1042 YGDQIRLQQVLAEFLLSIVRYAP-MEGSVELHLCPTLNQMADGFSAVRLEFRMACAGEGVPPEKVQDMFHSSRWTSPEGL 1120
Cdd:cd16932    1 YGDQIRLQQVLADFLLNAVRFTPsPGGWVEIKVSPTKKQIGDGVHVIHLEFRITHPGQGLPEELVQEMFEENQWTTQEGL 80
                         90       100       110
                 ....*....|....*....|....*....|...
gi 15234859 1121 GLSVCRKILKLMNGGVQYIREFERSYFLIVIEL 1153
Cdd:cd16932   81 GLSISRKLVKLMNGDVRYLREAGRSYFLITLEL 113
PAS_2 pfam08446
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
105-222 1.67e-49

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: 170.51  E-value: 1.67e-49
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859    105 AYLSRIQRGGYTQPFGCLIAVEESTFTIIGYSENAREMLGLMSQSVpsiedksevltIGTDLRSLFKSSSYLLLERAFVA 184
Cdd:pfam08446    1 CYLEPIQRPGLIQPHGCLLAVDEPSLRVLQYSENAAEMLGLPAEDL-----------LGTDLRDLFGASSASLLRKALAA 69
                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 15234859    185 REITLLNPIWIHSNNTGKPFYAILHRVDVGILIDLEPA 222
Cdd:pfam08446   70 GEISLLNPILIHSRTSGKPFYAILHRSDGGLVLELEPA 107
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
255-447 1.56e-24

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: 100.53  E-value: 1.56e-24
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859     255 DIKLLCDTVVESVRDLTGYDRVMVYKFHEDEHGEVVAESKRNDLEPYIGLHYPATDipQASRFLFKQNRVRMIVDCYASP 334
Cdd:smart00065    1 DLEELLQTILEELRQLLGADRVLIYLVDENDRGELVLVAADGLTLPTLGIRFPLDE--GLAGRVAETGRPLNIPDVEADP 78
                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859     335 VRvvQDDRLTQFiCLVGSTLRAPhgchaqymtnmgsiaslamavIINGNEedgngvntggrnsmrLWGLVVCHHtsaRCI 414
Cdd:smart00065   79 LF--AEDLLGRY-QGVRSFLAVP---------------------LVADGE---------------LVGVLALHN---KKS 116
                           170       180       190
                    ....*....|....*....|....*....|...
gi 15234859     415 PFPLRYACEFLMQAFGLQLNMELQLALQVSEKR 447
Cdd:smart00065  117 PRPFTEEDEELLQALANQLAIALANAQLYEELR 149
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
658-774 1.99e-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: 99.03  E-value: 1.99e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859    658 REMVRLIETATVPIFAVDIDGCINGWNAKIAELTGLSVEDAMGKSLVRELIYKEYKETVDRLLSCALKGDEGKNVEVKLK 737
Cdd:pfam00989    1 EDLRAILESLPDGIFVVDEDGRILYVNAAAEELLGLSREEVIGKSLLDLIPEEDDAEVAELLRQALLQGEESRGFEVSFR 80
                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 15234859    738 TFgselQGKAMFVVVNACSSKDYLNNIVGVCFVGQDV 774
Cdd:pfam00989   81 VP----DGRPRHVEVRASPVRDAGGEILGFLGVLRDI 113
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
789-909 7.45e-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: 94.79  E-value: 7.45e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859    789 GDYKAIIHSpnpLIPPIFAADENTCCLEWNTAMEKLTGWPRSEVIGKLLVREVFGSYcRLKGPDALTKFMIVLHNAIGGQ 868
Cdd:pfam00989    1 EDLRAILES---LPDGIFVVDEDGRILYVNAAAEELLGLSREEVIGKSLLDLIPEED-DAEVAELLRQALLQGEESRGFE 76
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 15234859    869 DTDKFPfpffdrKGEFIQALLTLNKRVSIDGKIIGAFCFLQ 909
Cdd:pfam00989   77 VSFRVP------DGRPRHVEVRASPVRDAGGEILGFLGVLR 111
KdpD COG2205
K+-sensing histidine kinase KdpD [Signal transduction mechanisms];
914-1155 6.47e-22

K+-sensing histidine kinase KdpD [Signal transduction mechanisms];


Pssm-ID: 441807 [Multi-domain]  Cd Length: 239  Bit Score: 96.13  E-value: 6.47e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859  914 ELQQALEVQRRQESeyfsRRKELAYIfqV---IKNPLSGLRFTNSLLEDMD--LNEDQKQLLETSVSCEKQISKIVGDM- 987
Cdd:COG2205    1 ELEEALEELEELER----LKSEFLAN--VsheLRTPLTSILGAAELLLDEEdlSPEERRELLEIIRESAERLLRLIEDLl 74
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859  988 DVKSIDDGSFLLERTEFFIGNVTNAVVSQVMLVVRERNLQLIRNIPTEvkSMAVYGDQIRLQQVLAEFLLSIVRYAPMEG 1067
Cdd:COG2205   75 DLSRLESGKLSLELEPVDLAELLEEAVEELRPLAEEKGIRLELDLPPE--LPLVYADPELLEQVLANLLDNAIKYSPPGG 152
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859 1068 SVELHLCPTLNQmadgfsavrLEFRMACAGEGVPPEKVQDMF------HSSRWTSPEGLGLSVCRKILKLMNGGVQYIRE 1141
Cdd:COG2205  153 TITISARREGDG---------VRISVSDNGPGIPEEELERIFerfyrgDNSRGEGGTGLGLAIVKRIVEAHGGTIWVESE 223
                        250
                 ....*....|....
gi 15234859 1142 fERSYFLIVIELPV 1155
Cdd:COG2205  224 -PGGGTTFTVTLPL 236
HATPase_c smart00387
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases.
1043-1156 6.75e-17

Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases.


Pssm-ID: 214643 [Multi-domain]  Cd Length: 111  Bit Score: 77.69  E-value: 6.75e-17
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859    1043 GDQIRLQQVLAEFLLSIVRYAPMEGSVELHLCPTLNqmadgfsavRLEFRMACAGEGVPPEKVQDMFH-------SSRWT 1115
Cdd:smart00387    1 GDPDRLRQVLSNLLDNAIKYTPEGGRITVTLERDGD---------HVEITVEDNGPGIPPEDLEKIFEpffrtdkRSRKI 71
                            90       100       110       120
                    ....*....|....*....|....*....|....*....|.
gi 15234859    1116 SPEGLGLSVCRKILKLMNGGVQYIREfERSYFLIVIELPVP 1156
Cdd:smart00387   72 GGTGLGLSIVKKLVELHGGEISVESE-PGGGTTFTITLPLE 111
PAS COG2202
PAS domain [Signal transduction mechanisms];
662-909 1.16e-16

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 81.22  E-value: 1.16e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859  662 RLIETATVPIFAVDIDGCINGWNAKIAELTGLSVEDAMGKSLvRELIYKEYKETVDRLLSCALKGDEGKNVEVKLKTfgs 741
Cdd:COG2202   15 ALVESSPDAIIITDLDGRILYVNPAFERLTGYSAEELLGKTL-RDLLPPEDDDEFLELLRAALAGGGVWRGELRNRR--- 90
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859  742 eLQGKAMFVVVNACSSKDYLNNIVGVCFVGQDVTGHKIVMDKFINIQGDYKAIIHSpNPLIppIFAADENTCCLEWNTAM 821
Cdd:COG2202   91 -KDGSLFWVELSISPVRDEDGEITGFVGIARDITERKRAEEALRESEERLRLLVEN-APDG--IFVLDLDGRILYVNPAA 166
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859  822 EKLTGWPRSEVIGKllvrevfgSYCRLKGPDALTKFMIVLHNAIGGQdTDKFPFPFFDRKGEFIQALLTLNKRVSIDG-K 900
Cdd:COG2202  167 EELLGYSPEELLGK--------SLLDLLHPEDRERLLELLRRLLEGG-RESYELELRLKDGDGRWVWVEASAVPLRDGgE 237

                 ....*....
gi 15234859  901 IIGAFCFLQ 909
Cdd:COG2202  238 VIGVLGIVR 246
HATPase_c pfam02518
Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; This family represents the ...
1043-1156 2.07e-13

Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; This family represents the structurally related ATPase domains of histidine kinase, DNA gyrase B and HSP90.


Pssm-ID: 460579 [Multi-domain]  Cd Length: 109  Bit Score: 67.39  E-value: 2.07e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859   1043 GDQIRLQQVLAEFLLSIVRYAPMEGSVELHLCPtlnqmadgfsAVRLEFRMACAGEGVPPEKVQDMFH-----SSRWTSP 1117
Cdd:pfam02518    1 GDELRLRQVLSNLLDNALKHAAKAGEITVTLSE----------GGELTLTVEDNGIGIPPEDLPRIFEpfstaDKRGGGG 70
                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 15234859   1118 EGLGLSVCRKILKLMNGGVQYIREfERSYFLIVIELPVP 1156
Cdd:pfam02518   71 TGLGLSIVRKLVELLGGTITVESE-PGGGTTVTLTLPLA 108
GAF pfam01590
GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl ...
255-437 1.48e-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: 62.88  E-value: 1.48e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859    255 DIKLLCDTVVESVRDLTGYDRVMVYkfhedehgevvaeskrndLEPYIGLHYpatdIPQASRFLfkqnRVRMIVDCYASP 334
Cdd:pfam01590    1 DLEEILQTILEELRELLGADRCALY------------------LPDADGLEY----LPPGARWL----KAAGLEIPPGTG 54
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859    335 VRVVQDDRltqfICLVGSTLRAPHGCH-AQYMTNMGSIASLAMAVIINGneedgngvntggrnsmRLWGLVVCHHTSArc 413
Cdd:pfam01590   55 VTVLRTGR----PLVVPDAAGDPRFLDpLLLLRNFGIRSLLAVPIIDDG----------------ELLGVLVLHHPRP-- 112
                          170       180
                   ....*....|....*....|....
gi 15234859    414 iPFPlRYACEFLmQAFGLQLNMEL 437
Cdd:pfam01590  113 -PFT-EEELELL-EVLADQVAIAL 133
HisKA pfam00512
His Kinase A (phospho-acceptor) domain; dimerization and phospho-acceptor domain of histidine ...
931-995 3.24e-10

His Kinase A (phospho-acceptor) domain; dimerization and phospho-acceptor domain of histidine kinases.


Pssm-ID: 459839 [Multi-domain]  Cd Length: 66  Bit Score: 56.84  E-value: 3.24e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15234859    931 SRRKELAYIFQVIKNPLSGLRFTNSLLEDMDLNEDQKQLLETSVSCEKQISKIVGDM-DVKSIDDG 995
Cdd:pfam00512    1 AKSEFLANLSHELRTPLTAIRGYLELLRDEKLDEEQREYLETILRSAERLLRLINDLlDLSRIEAG 66
PRK09303 PRK09303
histidine kinase;
913-1128 7.94e-10

histidine kinase;


Pssm-ID: 236462 [Multi-domain]  Cd Length: 380  Bit Score: 62.28  E-value: 7.94e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859   913 PELQQALEVQR-RQESEYFSRR---KE--LAYIFQVIKNPLSGLRF---TNSLLEDMDLNEDQKQLLEtsvSCEKQISKI 983
Cdd:PRK09303  126 ELLQLSDELFVlRQENETLLEQlkfKDrvLAMLAHDLRTPLTAASLaleTLELGQIDEDTELKPALIE---QLQDQARRQ 202
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859   984 VGDMDVKSID--------DGSFLLERTEFFIGNVTNAVVSQVMLVVRERNLQLIRNIPTEVKSmaVYGDQIRLQQVLAEF 1055
Cdd:PRK09303  203 LEEIERLITDllevgrtrWEALRFNPQKLDLGSLCQEVILELEKRWLAKSLEIQTDIPSDLPS--VYADQERIRQVLLNL 280
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15234859  1056 LLSIVRYAPMEGSVELHLCPTLNQmadgfsavRLEFRMACAGEGVPPEKVQDMFHS------SRWTSPEGLGLSVCRKI 1128
Cdd:PRK09303  281 LDNAIKYTPEGGTITLSMLHRTTQ--------KVQVSICDTGPGIPEEEQERIFEDrvrlprDEGTEGYGIGLSVCRRI 351
HisKA smart00388
His Kinase A (phosphoacceptor) domain; Dimerisation and phosphoacceptor domain of histidine ...
931-995 8.29e-10

His Kinase A (phosphoacceptor) domain; Dimerisation and phosphoacceptor domain of histidine kinases.


Pssm-ID: 214644 [Multi-domain]  Cd Length: 66  Bit Score: 55.65  E-value: 8.29e-10
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15234859     931 SRRKELAYIFQVIKNPLSGLRFTNSLLEDMDLNEDQKQLLETSVSCEKQISKIVGDM-DVKSIDDG 995
Cdd:smart00388    1 AKREFLANLSHELRTPLTAIRGYLELLLDTELSEEQREYLETILREAERLLRLINDLlDLSRIEAG 66
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
662-725 4.87e-08

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: 50.86  E-value: 4.87e-08
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15234859     662 RLIETATVPIFAVDIDGCINGWNAKIAELTGLSVEDAMGKSLvRELIYKEYKETVDRLLSCALK 725
Cdd:smart00091    5 AILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSL-LELIHPEDRERVQEALQRLLS 67
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
801-909 3.07e-07

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: 49.94  E-value: 3.07e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859  801 LIPPIFAADENTCCLEWNTAMEKLTGWPRSEVIGKLLVREVFgsycrlkgPDALTKFMIVLHNAIGGQDTDKFPFPFFDR 880
Cdd:cd00130    1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIH--------PEDREELRERLENLLSGGEPVTLEVRLRRK 72
                         90       100
                 ....*....|....*....|....*....
gi 15234859  881 KGEFIQALLTLNKRVSIDGKIIGAFCFLQ 909
Cdd:cd00130   73 DGSVIWVLVSLTPIRDEGGEVIGLLGVVR 101
sensory_box TIGR00229
PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain ...
659-778 1.07e-06

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: 48.83  E-value: 1.07e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859    659 EMVRLI-ETATVPIFAVDIDGCINGWNAKIAELTGLSVEDAMGKSlVRELIYKEYKETVDRLLSCALKGDE---GKNVEV 734
Cdd:TIGR00229    3 ERYRAIfESSPDAIIVIDLEGNILYVNPAFEEIFGYSAEELIGRN-VLELIPEEDREEVRERIERRLEGEPepvSEERRV 81
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 15234859    735 KLKtfgselQGKAMFVVVNAcSSKDYLNNIVGVCFVGQDVTGHK 778
Cdd:TIGR00229   82 RRK------DGSEIWVEVSV-SPIRTNGGELGVVGIVRDITERK 118
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
667-738 2.80e-06

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: 47.24  E-value: 2.80e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15234859  667 ATVPIFAVDIDGCINGWNAKIAELTGLSVEDAMGKSLvRELIYKEYKETVDRLLSCALKGDEGKNVEVKLKT 738
Cdd:cd00130    1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSL-LDLIHPEDREELRERLENLLSGGEPVTLEVRLRR 71
PAS COG2202
PAS domain [Signal transduction mechanisms];
662-778 5.10e-06

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 49.25  E-value: 5.10e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859  662 RLIETATVPIFAVDIDGCINGWNAKIAELTGLSVEDAMGKSlVRELIYKEYKETVDRLLSCALKGdEGKNVEVKLKTFGS 741
Cdd:COG2202  141 LLVENAPDGIFVLDLDGRILYVNPAAEELLGYSPEELLGKS-LLDLLHPEDRERLLELLRRLLEG-GRESYELELRLKDG 218
                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 15234859  742 ELQgkaMFVVVNACSSKDYLNNIVGVCFVGQDVTGHK 778
Cdd:COG2202  219 DGR---WVWVEASAVPLRDGGEVIGVLGIVRDITERK 252
PRK13560 PRK13560
hypothetical protein; Provisional
573-837 1.17e-05

hypothetical protein; Provisional


Pssm-ID: 106506 [Multi-domain]  Cd Length: 807  Bit Score: 49.67  E-value: 1.17e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859   573 HPEDKDDgQRMNPRSSFQTFLEVVKSrcQPWETAEMDAIHslqlilrdsfKESEAMDSkaAAAGAVQPHGDDMVQQGMQE 652
Cdd:PRK13560  124 GGDDGDF-FFANPFRSAETIAMALQS--DDWQEEEGHFRC----------GDGRFIDC--CLRFERHAHADDQVDGFAED 188
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859   653 IGAVAREMVRL----------IETATVPIFAVDIDGCINGWNAKIAELTGLSVEDAMGKSlVRELIYKEYKETVDRLLSC 722
Cdd:PRK13560  189 ITERKRAEERIdealhflqqlLDNIADPAFWKDEDAKVFGCNDAACLACGFRREEIIGMS-IHDFAPAQPADDYQEADAA 267
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859   723 ALKGDEGKNVEVKLKTFGSELqgKAMFVVVNACSSKDYLNNIVGVCFVGQDVTGHKIVMDKFINIQGDYKAIIHSPnPLI 802
Cdd:PRK13560  268 KFDADGSQIIEAEFQNKDGRT--RPVDVIFNHAEFDDKENHCAGLVGAITDISGRRAAERELLEKEDMLRAIIEAA-PIA 344
                         250       260       270
                  ....*....|....*....|....*....|....*
gi 15234859   803 PPIFAADENTCCLeWNTAMEKLTGWPRSEVIGKLL 837
Cdd:PRK13560  345 AIGLDADGNICFV-NNNAAERMLGWSAAEVMGKPL 378
HisKA cd00082
Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed ...
931-987 1.32e-05

Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-autophosphorylation by the catalytic domain of the histidine kinase. They subsequently transfer the phosphoryl group to the Asp acceptor residue of a response regulator protein. Two-component signalling systems, consisting of a histidine protein kinase that senses a signal input and a response regulator that mediates the output, are ancient and evolutionarily conserved signaling mechanisms in prokaryotes and eukaryotes.


Pssm-ID: 119399 [Multi-domain]  Cd Length: 65  Bit Score: 43.74  E-value: 1.32e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 15234859  931 SRRKELAYIFQVIKNPLSGLRFTNSLLED-MDLNEDQKQLLETSVSCEKQISKIVGDM 987
Cdd:cd00082    3 AKGEFLANVSHELRTPLTAIRGALELLEEeLLDDEEQREYLERIREEAERLLRLINDL 60
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
790-837 4.26e-05

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


Pssm-ID: 214512  Cd Length: 67  Bit Score: 42.39  E-value: 4.26e-05
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*...
gi 15234859     790 DYKAIIHSpnpLIPPIFAADENTCCLEWNTAMEKLTGWPRSEVIGKLL 837
Cdd:smart00091    2 RLRAILES---LPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSL 46
RocR COG3829
RocR-type transcriptional regulator, contains PAS, AAA-type ATPase, and DNA-binding Fis ...
791-943 2.21e-04

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: 45.15  E-value: 2.21e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859  791 YKAIIHSpnplIP-PIFAADENTCCLEWNTAMEKLTGWPRSEVIGKlLVREVFGSycrlkgpdalTKFMIVLHNaiGGQD 869
Cdd:COG3829   13 LEAILDS----LDdGIIVVDADGRITYVNRAAERILGLPREEVIGK-NVTELIPN----------SPLLEVLKT--GKPV 75
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15234859  870 TDKfpfpFFDRKGEFIQALLTLNkRVSIDGKIIGAFCFLQipspELQQALEVQRRQESEYFSRRKELAYIFQVI 943
Cdd:COG3829   76 TGV----IQKTGGKGKTVIVTAI-PIFEDGEVIGAVETFR----DITELKRLERKLREEELERGLSAKYTFDDI 140
sensory_box TIGR00229
PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain ...
791-835 1.39e-03

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: 39.97  E-value: 1.39e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 15234859    791 YKAIIHSPNPlipPIFAADENTCCLEWNTAMEKLTGWPRSEVIGK 835
Cdd:TIGR00229    5 YRAIFESSPD---AIIVIDLEGNILYVNPAFEEIFGYSAEELIGR 46
 
Name Accession Description Interval E-value
PHY pfam00360
Phytochrome region; Phytochromes are red/far-red photochromic biliprotein photoreceptors which ...
448-622 5.77e-60

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: 203.27  E-value: 5.77e-60
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859    448 VLRMQTLLCDMLLR--DSPAGIVTQRPSIMDLVKCNGAAFLYQGKYYPLGVTPTDSQINDIVEWLVANHsDSTGLSTDSL 525
Cdd:pfam00360    1 LRRIQDRLVEAMARadDLVDGLVDQSPNLLDLVKADGAALCFGGNLLTLGETPPEEAIRDLAQWLGRNH-DSEVFSTDSL 79
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859    526 GDAgYPRAAALGDAVCGMAVACI--TKRDFLFWFRSHTEKEIKWGGAKHHPEDKDD-GQRMNPRSSFQTFLEVVKSRCQP 602
Cdd:pfam00360   80 SQA-YPEAAALADVASGLLAIPIsrKPGNYLLWFRPEVVRTVNWGGDPHKAVEIDPgGVRLSPRKSFDAWKETVRGRSLP 158
                          170       180
                   ....*....|....*....|
gi 15234859    603 WETAEMDAIHSLQLILRDSF 622
Cdd:pfam00360  159 WSEVEIEAARELREALLGVV 178
HATPase_Phy-like cd16932
Histidine kinase-like ATPase domain of plant phytochromes similar to Arabidopsis thaliana ...
1042-1153 9.18e-53

Histidine kinase-like ATPase domain of plant phytochromes similar to Arabidopsis thaliana Phytochrome A, B, C, D and E; This family includes the histidine kinase-like ATPase (HATPase) domains of plant red/far-red photoreceptors, the phytochromes, and includes the Arabidopsis thaliana phytochrome family phyA-phyE. Following red light absorption, biologically inactive forms of phytochromes convert to active forms, which rapidly convert back to inactive forms upon far-red light irradiation. Phytochromes can be considered as having an N-terminal photosensory region to which a bilin chromophore is bound, and a C-terminal output region, which includes the HATPase domain represented here, and is involved in dimerization and presumably contributes to relaying the light signal to downstream signaling events.


Pssm-ID: 340409 [Multi-domain]  Cd Length: 113  Bit Score: 180.16  E-value: 9.18e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859 1042 YGDQIRLQQVLAEFLLSIVRYAP-MEGSVELHLCPTLNQMADGFSAVRLEFRMACAGEGVPPEKVQDMFHSSRWTSPEGL 1120
Cdd:cd16932    1 YGDQIRLQQVLADFLLNAVRFTPsPGGWVEIKVSPTKKQIGDGVHVIHLEFRITHPGQGLPEELVQEMFEENQWTTQEGL 80
                         90       100       110
                 ....*....|....*....|....*....|...
gi 15234859 1121 GLSVCRKILKLMNGGVQYIREFERSYFLIVIEL 1153
Cdd:cd16932   81 GLSISRKLVKLMNGDVRYLREAGRSYFLITLEL 113
PAS_2 pfam08446
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
105-222 1.67e-49

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: 170.51  E-value: 1.67e-49
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859    105 AYLSRIQRGGYTQPFGCLIAVEESTFTIIGYSENAREMLGLMSQSVpsiedksevltIGTDLRSLFKSSSYLLLERAFVA 184
Cdd:pfam08446    1 CYLEPIQRPGLIQPHGCLLAVDEPSLRVLQYSENAAEMLGLPAEDL-----------LGTDLRDLFGASSASLLRKALAA 69
                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 15234859    185 REITLLNPIWIHSNNTGKPFYAILHRVDVGILIDLEPA 222
Cdd:pfam08446   70 GEISLLNPILIHSRTSGKPFYAILHRSDGGLVLELEPA 107
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
255-447 1.56e-24

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: 100.53  E-value: 1.56e-24
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859     255 DIKLLCDTVVESVRDLTGYDRVMVYKFHEDEHGEVVAESKRNDLEPYIGLHYPATDipQASRFLFKQNRVRMIVDCYASP 334
Cdd:smart00065    1 DLEELLQTILEELRQLLGADRVLIYLVDENDRGELVLVAADGLTLPTLGIRFPLDE--GLAGRVAETGRPLNIPDVEADP 78
                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859     335 VRvvQDDRLTQFiCLVGSTLRAPhgchaqymtnmgsiaslamavIINGNEedgngvntggrnsmrLWGLVVCHHtsaRCI 414
Cdd:smart00065   79 LF--AEDLLGRY-QGVRSFLAVP---------------------LVADGE---------------LVGVLALHN---KKS 116
                           170       180       190
                    ....*....|....*....|....*....|...
gi 15234859     415 PFPLRYACEFLMQAFGLQLNMELQLALQVSEKR 447
Cdd:smart00065  117 PRPFTEEDEELLQALANQLAIALANAQLYEELR 149
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
658-774 1.99e-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: 99.03  E-value: 1.99e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859    658 REMVRLIETATVPIFAVDIDGCINGWNAKIAELTGLSVEDAMGKSLVRELIYKEYKETVDRLLSCALKGDEGKNVEVKLK 737
Cdd:pfam00989    1 EDLRAILESLPDGIFVVDEDGRILYVNAAAEELLGLSREEVIGKSLLDLIPEEDDAEVAELLRQALLQGEESRGFEVSFR 80
                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 15234859    738 TFgselQGKAMFVVVNACSSKDYLNNIVGVCFVGQDV 774
Cdd:pfam00989   81 VP----DGRPRHVEVRASPVRDAGGEILGFLGVLRDI 113
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
789-909 7.45e-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: 94.79  E-value: 7.45e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859    789 GDYKAIIHSpnpLIPPIFAADENTCCLEWNTAMEKLTGWPRSEVIGKLLVREVFGSYcRLKGPDALTKFMIVLHNAIGGQ 868
Cdd:pfam00989    1 EDLRAILES---LPDGIFVVDEDGRILYVNAAAEELLGLSREEVIGKSLLDLIPEED-DAEVAELLRQALLQGEESRGFE 76
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 15234859    869 DTDKFPfpffdrKGEFIQALLTLNKRVSIDGKIIGAFCFLQ 909
Cdd:pfam00989   77 VSFRVP------DGRPRHVEVRASPVRDAGGEILGFLGVLR 111
KdpD COG2205
K+-sensing histidine kinase KdpD [Signal transduction mechanisms];
914-1155 6.47e-22

K+-sensing histidine kinase KdpD [Signal transduction mechanisms];


Pssm-ID: 441807 [Multi-domain]  Cd Length: 239  Bit Score: 96.13  E-value: 6.47e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859  914 ELQQALEVQRRQESeyfsRRKELAYIfqV---IKNPLSGLRFTNSLLEDMD--LNEDQKQLLETSVSCEKQISKIVGDM- 987
Cdd:COG2205    1 ELEEALEELEELER----LKSEFLAN--VsheLRTPLTSILGAAELLLDEEdlSPEERRELLEIIRESAERLLRLIEDLl 74
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859  988 DVKSIDDGSFLLERTEFFIGNVTNAVVSQVMLVVRERNLQLIRNIPTEvkSMAVYGDQIRLQQVLAEFLLSIVRYAPMEG 1067
Cdd:COG2205   75 DLSRLESGKLSLELEPVDLAELLEEAVEELRPLAEEKGIRLELDLPPE--LPLVYADPELLEQVLANLLDNAIKYSPPGG 152
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859 1068 SVELHLCPTLNQmadgfsavrLEFRMACAGEGVPPEKVQDMF------HSSRWTSPEGLGLSVCRKILKLMNGGVQYIRE 1141
Cdd:COG2205  153 TITISARREGDG---------VRISVSDNGPGIPEEELERIFerfyrgDNSRGEGGTGLGLAIVKRIVEAHGGTIWVESE 223
                        250
                 ....*....|....
gi 15234859 1142 fERSYFLIVIELPV 1155
Cdd:COG2205  224 -PGGGTTFTVTLPL 236
BaeS COG0642
Signal transduction histidine kinase [Signal transduction mechanisms];
943-1134 2.90e-19

Signal transduction histidine kinase [Signal transduction mechanisms];


Pssm-ID: 440407 [Multi-domain]  Cd Length: 328  Bit Score: 90.35  E-value: 2.90e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859  943 IKNPLSGLRFTNSLLEDmDLNEDQKQLLETSVSCEKQISKIVGDM-DVKSIDDGSFLLERTEFFIGNVTNAVVSQVMLVV 1021
Cdd:COG0642  121 LRTPLTAIRGYLELLLE-ELDEEQREYLETILRSADRLLRLINDLlDLSRLEAGKLELEPEPVDLAELLEEVVELFRPLA 199
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859 1022 RERNLQLIRNIPTEVksMAVYGDQIRLQQVLAEFLLSIVRYAPMEGSVELHLCPTlnqmadgfsAVRLEFRMACAGEGVP 1101
Cdd:COG0642  200 EEKGIELELDLPDDL--PTVRGDPDRLRQVLLNLLSNAIKYTPEGGTVTVSVRRE---------GDRVRISVEDTGPGIP 268
                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 15234859 1102 PEKVQDMF------HSSRWTSPEGLGLSVCRKILKLMNG 1134
Cdd:COG0642  269 PEDLERIFepffrtDPSRRGGGTGLGLAIVKRIVELHGG 307
HATPase_c smart00387
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases.
1043-1156 6.75e-17

Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases.


Pssm-ID: 214643 [Multi-domain]  Cd Length: 111  Bit Score: 77.69  E-value: 6.75e-17
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859    1043 GDQIRLQQVLAEFLLSIVRYAPMEGSVELHLCPTLNqmadgfsavRLEFRMACAGEGVPPEKVQDMFH-------SSRWT 1115
Cdd:smart00387    1 GDPDRLRQVLSNLLDNAIKYTPEGGRITVTLERDGD---------HVEITVEDNGPGIPPEDLEKIFEpffrtdkRSRKI 71
                            90       100       110       120
                    ....*....|....*....|....*....|....*....|.
gi 15234859    1116 SPEGLGLSVCRKILKLMNGGVQYIREfERSYFLIVIELPVP 1156
Cdd:smart00387   72 GGTGLGLSIVKKLVELHGGEISVESE-PGGGTTFTITLPLE 111
PAS COG2202
PAS domain [Signal transduction mechanisms];
662-909 1.16e-16

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 81.22  E-value: 1.16e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859  662 RLIETATVPIFAVDIDGCINGWNAKIAELTGLSVEDAMGKSLvRELIYKEYKETVDRLLSCALKGDEGKNVEVKLKTfgs 741
Cdd:COG2202   15 ALVESSPDAIIITDLDGRILYVNPAFERLTGYSAEELLGKTL-RDLLPPEDDDEFLELLRAALAGGGVWRGELRNRR--- 90
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859  742 eLQGKAMFVVVNACSSKDYLNNIVGVCFVGQDVTGHKIVMDKFINIQGDYKAIIHSpNPLIppIFAADENTCCLEWNTAM 821
Cdd:COG2202   91 -KDGSLFWVELSISPVRDEDGEITGFVGIARDITERKRAEEALRESEERLRLLVEN-APDG--IFVLDLDGRILYVNPAA 166
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859  822 EKLTGWPRSEVIGKllvrevfgSYCRLKGPDALTKFMIVLHNAIGGQdTDKFPFPFFDRKGEFIQALLTLNKRVSIDG-K 900
Cdd:COG2202  167 EELLGYSPEELLGK--------SLLDLLHPEDRERLLELLRRLLEGG-RESYELELRLKDGDGRWVWVEASAVPLRDGgE 237

                 ....*....
gi 15234859  901 IIGAFCFLQ 909
Cdd:COG2202  238 VIGVLGIVR 246
KinE COG5809
Sporulation sensor histidine kinase E [Cell cycle control, cell division, chromosome ...
645-1134 3.44e-14

Sporulation sensor histidine kinase E [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms];


Pssm-ID: 444511 [Multi-domain]  Cd Length: 489  Bit Score: 76.55  E-value: 3.44e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859  645 MVQQGMQEIGAVAREMVR-LIETATVPIFAVDIDGCINGWNAKIAELTGLSVEDAMGKSLvRELIYKEYKETVDRLLSCA 723
Cdd:COG5809    1 MKSSKMELQLRKSEQRFRsLFENAPDAILILDLEGKILKVNPAAERIFGYTEDELLGTNI-LDFLHPDDEKELREILKLL 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859  724 LKGDEGKNVEVKLKT-FGSELQGKAMFVVVnacssKDYLNNIVGVCFVGQDVTGHKIVMDKFINIQGDYKAII-HSPNPL 801
Cdd:COG5809   80 KEGESRDELEFELRHkNGKRLEFSSKLSPI-----FDQNGDIEGMLAISRDITERKRMEEALRESEEKFRLIFnHSPDGI 154
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859  802 IppIFAADENTccLEWNTAMEKLTGWPRSEVIGKllvrevfgSYCRLKGPDALTKFMIVLHNAIGGQDTDKFPFPFFDRK 881
Cdd:COG5809  155 I--VTDLDGRI--IYANPAACKLLGISIEELIGK--------SILELIHSDDQENVAAFISQLLKDGGIAQGEVRFWTKD 222
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859  882 GEFIQALLTLNKRVSiDGKIIGAFCFLQIPSpELQQALEVQRRQESeyFSRRKELAY-IFQVIKNPLSGLR-FTNSLLED 959
Cdd:COG5809  223 GRWRLLEASGAPIKK-NGEVDGIVIIFRDIT-ERKKLEELLRKSEK--LSVVGELAAgIAHEIRNPLTSLKgFIQLLKDT 298
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859  960 MDlnEDQKQLLETSVSCEKQISKIVGD-MDVKSIDDGSFllERTEF--FIGNVTNAVVSQVMLvvreRNLQLIRNIPTEV 1036
Cdd:COG5809  299 ID--EEQKTYLDIMLSELDRIESIISEfLVLAKPQAIKY--EPKDLntLIEEVIPLLQPQALL----KNVQIELELEDDI 370
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859 1037 KSmaVYGDQIRLQQVLaeflLSIVRYA----PMEGSVELHLCPTLNQmadgfsavRLEFRMACAGEGVPPEKVQDMFH-- 1110
Cdd:COG5809  371 PD--ILGDENQLKQVF----INLLKNAieamPEGGNITIETKAEDDD--------KVVISVTDEGCGIPEERLKKLGEpf 436
                        490       500
                 ....*....|....*....|....*..
gi 15234859 1111 ---SSRWTspeGLGLSVCRKILKLMNG 1134
Cdd:COG5809  437 yttKEKGT---GLGLMVSYKIIEEHGG 460
WalK COG5002
Sensor histidine kinase WalK [Signal transduction mechanisms];
943-1134 5.88e-14

Sensor histidine kinase WalK [Signal transduction mechanisms];


Pssm-ID: 444026 [Multi-domain]  Cd Length: 390  Bit Score: 75.36  E-value: 5.88e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859  943 IKNPLSGLRFTNSLLED--MDLNEDQKQLLETSVSCEKQISKIVGDM-DVKSIDDGSFLLERTEFFIGNVTNAVVSQVML 1019
Cdd:COG5002  176 LRTPLTSIRGYLELLLDgaADDPEERREYLEIILEEAERLSRLVNDLlDLSRLESGELKLEKEPVDLAELLEEVVEELRP 255
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859 1020 VVRERNLQLIRNIPTEvkSMAVYGDQIRLQQVLAEFLLSIVRYAPMEGSVELHLcptlnQMADGfsavRLEFRMACAGEG 1099
Cdd:COG5002  256 LAEEKGIELELDLPED--PLLVLGDPDRLEQVLTNLLDNAIKYTPEGGTITVSL-----REEDD----QVRISVRDTGIG 324
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 15234859 1100 VPPEKVQ---DMFH---SSRWTSPE--GLGLSVCRKILKLMNG 1134
Cdd:COG5002  325 IPEEDLPrifERFYrvdKSRSRETGgtGLGLAIVKHIVEAHGG 367
HATPase_c pfam02518
Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; This family represents the ...
1043-1156 2.07e-13

Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; This family represents the structurally related ATPase domains of histidine kinase, DNA gyrase B and HSP90.


Pssm-ID: 460579 [Multi-domain]  Cd Length: 109  Bit Score: 67.39  E-value: 2.07e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859   1043 GDQIRLQQVLAEFLLSIVRYAPMEGSVELHLCPtlnqmadgfsAVRLEFRMACAGEGVPPEKVQDMFH-----SSRWTSP 1117
Cdd:pfam02518    1 GDELRLRQVLSNLLDNALKHAAKAGEITVTLSE----------GGELTLTVEDNGIGIPPEDLPRIFEpfstaDKRGGGG 70
                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 15234859   1118 EGLGLSVCRKILKLMNGGVQYIREfERSYFLIVIELPVP 1156
Cdd:pfam02518   71 TGLGLSIVRKLVELLGGTITVESE-PGGGTTVTLTLPLA 108
NtrB COG3852
Signal transduction histidine kinase NtrB, nitrogen specific [Signal transduction mechanisms];
804-1134 4.12e-13

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


Pssm-ID: 443061 [Multi-domain]  Cd Length: 361  Bit Score: 72.19  E-value: 4.12e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859  804 PIFAADENTCCLEWNTAMEKLTGWPRSEVIGKLLvREVFGSYCRLKGPdaltkfmivLHNAI-GGQDTDKFPFPFFDRKG 882
Cdd:COG3852   19 AVIVLDADGRITYVNPAAERLLGLSAEELLGRPL-AELFPEDSPLREL---------LERALaEGQPVTEREVTLRRKDG 88
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859  883 EFIQALLTLNkRVSIDGKIIGAFCFLQipspelqqALEVQRRQESEyFSRRKELAYIFQV-------IKNPLSGLRFTNS 955
Cdd:COG3852   89 EERPVDVSVS-PLRDAEGEGGVLLVLR--------DITERKRLERE-LRRAEKLAAVGELaaglaheIRNPLTGIRGAAQ 158
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859  956 LLEDMDLNEDQKQLLETSVSCEKQISKIVGDMdvKSIDDGSfLLERTEFfigNVtNAVVSQVMLVVRE---RNLQLIRNI 1032
Cdd:COG3852  159 LLERELPDDELREYTQLIIEEADRLNNLVDRL--LSFSRPR-PPEREPV---NL-HEVLERVLELLRAeapKNIRIVRDY 231
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859 1033 PTEVKsmAVYGDQIRLQQVLaeflLSIVRYA----PMEGSVELHLCpTLNQMADGFSAVRLEFRMACA--GEGVPPEKVQ 1106
Cdd:COG3852  232 DPSLP--EVLGDPDQLIQVL----LNLVRNAaeamPEGGTITIRTR-VERQVTLGGLRPRLYVRIEVIdnGPGIPEEILD 304
                        330       340       350
                 ....*....|....*....|....*....|...
gi 15234859 1107 DMFH---SSRwtsPE--GLGLSVCRKILKLMNG 1134
Cdd:COG3852  305 RIFEpffTTK---EKgtGLGLAIVQKIVEQHGG 334
KinA COG5805
Sporulation sensor histidine kinase A (Stage II sporulation protein SpoIIF/SpoIIJ) [Cell cycle ...
659-1156 6.49e-13

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: 72.46  E-value: 6.49e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859  659 EMVRLIETATVPIFAVDIDGCINGWNAKIAELTGLSVEDAMGKSlVRELIYKEYKETVDRLLSCALKGDEGKNVEVKLKt 738
Cdd:COG5805   35 ELETILENLPDAIIAVNREGKVIYINPAMEKLLGYTSEEIIGKT-IFDFLEKEYHYRVKTRIERLQKGYDVVMIEQIYC- 112
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859  739 fgseLQGKAMFVVVNACSSKDYLNNIVGVCFVgqDVTGHKIvMDKFINIQGD-YKAIIHSPNPLIppiFAADENTCCLEW 817
Cdd:COG5805  113 ----KDGELIYVEVKLFPIYNQNGQAAILALR--DITKKKK-IEEILQEQEErLQTLIENSPDLI---CVIDTDGRILFI 182
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859  818 NTAMEKLTGWPRSEVIGKLLVRevFGSYCrlkgpDALTKFMIVLHNAIGGQDTdKFPFPFFDRKGEFIQALLTLNKRVSI 897
Cdd:COG5805  183 NESIERLFGAPREELIGKNLLE--LLHPC-----DKEEFKERIESITEVWQEF-IIEREIITKDGRIRYFEAVIVPLIDT 254
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859  898 DGKIIGAFCFLQIPSpELQQALEVQRRqeSEYFSRRKELAY-IFQVIKNPLSGLR-FTNSLLEDMDLNEDQKQLLETSVS 975
Cdd:COG5805  255 DGSVKGILVILRDIT-EKKEAEELMAR--SEKLSIAGQLAAgIAHEIRNPLTSIKgFLQLLQPGIEDKEEYFDIMLSELD 331
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859  976 cekQISKIVGDMDVKSIDDgSFLLERTeffigNVTNAVVSQVMLVVRERNLQLIrNIPTEV--KSMAVYGDQIRLQQVla 1053
Cdd:COG5805  332 ---RIESIISEFLALAKPQ-AVNKEKE-----NINELIQDVVTLLETEAILHNI-QIRLELldEDPFIYCDENQIKQV-- 399
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859 1054 efLLSIVRYA----PMEGSVELHLCPtlnqmADGFSAVRLEFRmacaGEGVPPE---KVQDMFHSSRwTSPEGLGLSVCR 1126
Cdd:COG5805  400 --FINLIKNAieamPNGGTITIHTEE-----EDNSVIIRVIDE----GIGIPEErlkKLGEPFFTTK-EKGTGLGLMVSY 467
                        490       500       510
                 ....*....|....*....|....*....|.
gi 15234859 1127 KILKLMNGGVQYIREFER-SYFliVIELPVP 1156
Cdd:COG5805  468 KIIENHNGTIDIDSKVGKgTTF--TITLPLS 496
GAF pfam01590
GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl ...
255-437 1.48e-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: 62.88  E-value: 1.48e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859    255 DIKLLCDTVVESVRDLTGYDRVMVYkfhedehgevvaeskrndLEPYIGLHYpatdIPQASRFLfkqnRVRMIVDCYASP 334
Cdd:pfam01590    1 DLEEILQTILEELRELLGADRCALY------------------LPDADGLEY----LPPGARWL----KAAGLEIPPGTG 54
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859    335 VRVVQDDRltqfICLVGSTLRAPHGCH-AQYMTNMGSIASLAMAVIINGneedgngvntggrnsmRLWGLVVCHHTSArc 413
Cdd:pfam01590   55 VTVLRTGR----PLVVPDAAGDPRFLDpLLLLRNFGIRSLLAVPIIDDG----------------ELLGVLVLHHPRP-- 112
                          170       180
                   ....*....|....*....|....
gi 15234859    414 iPFPlRYACEFLmQAFGLQLNMEL 437
Cdd:pfam01590  113 -PFT-EEELELL-EVLADQVAIAL 133
HisKA pfam00512
His Kinase A (phospho-acceptor) domain; dimerization and phospho-acceptor domain of histidine ...
931-995 3.24e-10

His Kinase A (phospho-acceptor) domain; dimerization and phospho-acceptor domain of histidine kinases.


Pssm-ID: 459839 [Multi-domain]  Cd Length: 66  Bit Score: 56.84  E-value: 3.24e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15234859    931 SRRKELAYIFQVIKNPLSGLRFTNSLLEDMDLNEDQKQLLETSVSCEKQISKIVGDM-DVKSIDDG 995
Cdd:pfam00512    1 AKSEFLANLSHELRTPLTAIRGYLELLRDEKLDEEQREYLETILRSAERLLRLINDLlDLSRIEAG 66
PRK09303 PRK09303
histidine kinase;
913-1128 7.94e-10

histidine kinase;


Pssm-ID: 236462 [Multi-domain]  Cd Length: 380  Bit Score: 62.28  E-value: 7.94e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859   913 PELQQALEVQR-RQESEYFSRR---KE--LAYIFQVIKNPLSGLRF---TNSLLEDMDLNEDQKQLLEtsvSCEKQISKI 983
Cdd:PRK09303  126 ELLQLSDELFVlRQENETLLEQlkfKDrvLAMLAHDLRTPLTAASLaleTLELGQIDEDTELKPALIE---QLQDQARRQ 202
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859   984 VGDMDVKSID--------DGSFLLERTEFFIGNVTNAVVSQVMLVVRERNLQLIRNIPTEVKSmaVYGDQIRLQQVLAEF 1055
Cdd:PRK09303  203 LEEIERLITDllevgrtrWEALRFNPQKLDLGSLCQEVILELEKRWLAKSLEIQTDIPSDLPS--VYADQERIRQVLLNL 280
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15234859  1056 LLSIVRYAPMEGSVELHLCPTLNQmadgfsavRLEFRMACAGEGVPPEKVQDMFHS------SRWTSPEGLGLSVCRKI 1128
Cdd:PRK09303  281 LDNAIKYTPEGGTITLSMLHRTTQ--------KVQVSICDTGPGIPEEEQERIFEDrvrlprDEGTEGYGIGLSVCRRI 351
HisKA smart00388
His Kinase A (phosphoacceptor) domain; Dimerisation and phosphoacceptor domain of histidine ...
931-995 8.29e-10

His Kinase A (phosphoacceptor) domain; Dimerisation and phosphoacceptor domain of histidine kinases.


Pssm-ID: 214644 [Multi-domain]  Cd Length: 66  Bit Score: 55.65  E-value: 8.29e-10
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15234859     931 SRRKELAYIFQVIKNPLSGLRFTNSLLEDMDLNEDQKQLLETSVSCEKQISKIVGDM-DVKSIDDG 995
Cdd:smart00388    1 AKREFLANLSHELRTPLTAIRGYLELLLDTELSEEQREYLETILREAERLLRLINDLlDLSRIEAG 66
PRK15347 PRK15347
two component system sensor kinase;
917-1134 1.50e-09

two component system sensor kinase;


Pssm-ID: 237951 [Multi-domain]  Cd Length: 921  Bit Score: 62.35  E-value: 1.50e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859   917 QALEvQRRQESEYFSRRK--ELAYIFQVIKNPLSGLRFTNSLLEDMDLNEDQKQLLETSVSCEKQISKIVGDM-DVKSID 993
Cdd:PRK15347  382 QALA-EAKQRAEQANKRKseHLTTISHEIRTPLNGVLGALELLQNTPLTAEQMDLADTARQCTLSLLAIINNLlDFSRIE 460
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859   994 DGSFLL--ERTEFFignvtnAVVSQVMLVVR----ERNLQL----IRNIPTEVksmavYGDQIRLQQVLAEFLLSIVRYA 1063
Cdd:PRK15347  461 SGQMTLslEETALL------PLLDQAMLTIQgpaqSKSLTLrtfvGAHVPLYL-----HLDSLRLRQILVNLLGNAVKFT 529
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15234859  1064 PmEGSVELHLcPTLNQMadgfsavrLEFRMACAGEGVPPEKVQDMF-------HSSRWTspeGLGLSVCRKILKLMNG 1134
Cdd:PRK15347  530 E-TGGIRLRV-KRHEQQ--------LCFTVEDTGCGIDIQQQQQIFtpfyqadTHSQGT---GLGLTIASSLAKMMGG 594
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
662-725 4.87e-08

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: 50.86  E-value: 4.87e-08
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15234859     662 RLIETATVPIFAVDIDGCINGWNAKIAELTGLSVEDAMGKSLvRELIYKEYKETVDRLLSCALK 725
Cdd:smart00091    5 AILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSL-LELIHPEDRERVQEALQRLLS 67
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
801-909 3.07e-07

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: 49.94  E-value: 3.07e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859  801 LIPPIFAADENTCCLEWNTAMEKLTGWPRSEVIGKLLVREVFgsycrlkgPDALTKFMIVLHNAIGGQDTDKFPFPFFDR 880
Cdd:cd00130    1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIH--------PEDREELRERLENLLSGGEPVTLEVRLRRK 72
                         90       100
                 ....*....|....*....|....*....
gi 15234859  881 KGEFIQALLTLNKRVSIDGKIIGAFCFLQ 909
Cdd:cd00130   73 DGSVIWVLVSLTPIRDEGGEVIGLLGVVR 101
sensory_box TIGR00229
PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain ...
659-778 1.07e-06

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: 48.83  E-value: 1.07e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859    659 EMVRLI-ETATVPIFAVDIDGCINGWNAKIAELTGLSVEDAMGKSlVRELIYKEYKETVDRLLSCALKGDE---GKNVEV 734
Cdd:TIGR00229    3 ERYRAIfESSPDAIIVIDLEGNILYVNPAFEEIFGYSAEELIGRN-VLELIPEEDREEVRERIERRLEGEPepvSEERRV 81
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 15234859    735 KLKtfgselQGKAMFVVVNAcSSKDYLNNIVGVCFVGQDVTGHK 778
Cdd:TIGR00229   82 RRK------DGSEIWVEVSV-SPIRTNGGELGVVGIVRDITERK 118
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
667-738 2.80e-06

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: 47.24  E-value: 2.80e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15234859  667 ATVPIFAVDIDGCINGWNAKIAELTGLSVEDAMGKSLvRELIYKEYKETVDRLLSCALKGDEGKNVEVKLKT 738
Cdd:cd00130    1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSL-LDLIHPEDREELRERLENLLSGGEPVTLEVRLRR 71
PAS COG2202
PAS domain [Signal transduction mechanisms];
662-778 5.10e-06

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 49.25  E-value: 5.10e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859  662 RLIETATVPIFAVDIDGCINGWNAKIAELTGLSVEDAMGKSlVRELIYKEYKETVDRLLSCALKGdEGKNVEVKLKTFGS 741
Cdd:COG2202  141 LLVENAPDGIFVLDLDGRILYVNPAAEELLGYSPEELLGKS-LLDLLHPEDRERLLELLRRLLEG-GRESYELELRLKDG 218
                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 15234859  742 ELQgkaMFVVVNACSSKDYLNNIVGVCFVGQDVTGHK 778
Cdd:COG2202  219 DGR---WVWVEASAVPLRDGGEVIGVLGIVRDITERK 252
NtrB COG3852
Signal transduction histidine kinase NtrB, nitrogen specific [Signal transduction mechanisms];
662-778 1.11e-05

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


Pssm-ID: 443061 [Multi-domain]  Cd Length: 361  Bit Score: 49.07  E-value: 1.11e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859  662 RLIETATVPIFAVDIDGCINGWNAKIAELTGLSVEDAMGKSLvRELIyKEYKETVDRLLSCALKGDEGKNVEVKLKTfgs 741
Cdd:COG3852   11 AILDSLPDAVIVLDADGRITYVNPAAERLLGLSAEELLGRPL-AELF-PEDSPLRELLERALAEGQPVTEREVTLRR--- 85
                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 15234859  742 eLQGKAMFVVVNACSSKDYlNNIVGVCFVGQDVTGHK 778
Cdd:COG3852   86 -KDGEERPVDVSVSPLRDA-EGEGGVLLVLRDITERK 120
PRK13560 PRK13560
hypothetical protein; Provisional
573-837 1.17e-05

hypothetical protein; Provisional


Pssm-ID: 106506 [Multi-domain]  Cd Length: 807  Bit Score: 49.67  E-value: 1.17e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859   573 HPEDKDDgQRMNPRSSFQTFLEVVKSrcQPWETAEMDAIHslqlilrdsfKESEAMDSkaAAAGAVQPHGDDMVQQGMQE 652
Cdd:PRK13560  124 GGDDGDF-FFANPFRSAETIAMALQS--DDWQEEEGHFRC----------GDGRFIDC--CLRFERHAHADDQVDGFAED 188
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859   653 IGAVAREMVRL----------IETATVPIFAVDIDGCINGWNAKIAELTGLSVEDAMGKSlVRELIYKEYKETVDRLLSC 722
Cdd:PRK13560  189 ITERKRAEERIdealhflqqlLDNIADPAFWKDEDAKVFGCNDAACLACGFRREEIIGMS-IHDFAPAQPADDYQEADAA 267
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859   723 ALKGDEGKNVEVKLKTFGSELqgKAMFVVVNACSSKDYLNNIVGVCFVGQDVTGHKIVMDKFINIQGDYKAIIHSPnPLI 802
Cdd:PRK13560  268 KFDADGSQIIEAEFQNKDGRT--RPVDVIFNHAEFDDKENHCAGLVGAITDISGRRAAERELLEKEDMLRAIIEAA-PIA 344
                         250       260       270
                  ....*....|....*....|....*....|....*
gi 15234859   803 PPIFAADENTCCLeWNTAMEKLTGWPRSEVIGKLL 837
Cdd:PRK13560  345 AIGLDADGNICFV-NNNAAERMLGWSAAEVMGKPL 378
HisKA cd00082
Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed ...
931-987 1.32e-05

Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-autophosphorylation by the catalytic domain of the histidine kinase. They subsequently transfer the phosphoryl group to the Asp acceptor residue of a response regulator protein. Two-component signalling systems, consisting of a histidine protein kinase that senses a signal input and a response regulator that mediates the output, are ancient and evolutionarily conserved signaling mechanisms in prokaryotes and eukaryotes.


Pssm-ID: 119399 [Multi-domain]  Cd Length: 65  Bit Score: 43.74  E-value: 1.32e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 15234859  931 SRRKELAYIFQVIKNPLSGLRFTNSLLED-MDLNEDQKQLLETSVSCEKQISKIVGDM 987
Cdd:cd00082    3 AKGEFLANVSHELRTPLTAIRGALELLEEeLLDDEEQREYLERIREEAERLLRLINDL 60
COG4191 COG4191
Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal ...
943-1134 2.01e-05

Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms];


Pssm-ID: 443345 [Multi-domain]  Cd Length: 361  Bit Score: 48.26  E-value: 2.01e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859  943 IKNPLSGLR-FTNSLLEDMDLNEDQKQLLETSVSCEKQ---ISKIVGDMDvksiddgSFL----LERTEFFIGNVTNAVV 1014
Cdd:COG4191  153 INNPLAAILgNAELLRRRLEDEPDPEELREALERILEGaerAAEIVRSLR-------AFSrrdeEEREPVDLNELIDEAL 225
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859 1015 SQVMLVVRERNLQLIRNIPTEVksMAVYGDQIRLQQVLaeflLSIV---RYApME----GSVELHLCPTLNQmadgfsaV 1087
Cdd:COG4191  226 ELLRPRLKARGIEVELDLPPDL--PPVLGDPGQLEQVL----LNLLinaIDA-MEegegGRITISTRREGDY-------V 291
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 15234859 1088 RLEFRMAcaGEGVPPE---KVQDMFHSsrwTSPE----GLGLSVCRKILKLMNG 1134
Cdd:COG4191  292 VISVRDN--GPGIPPEvleRIFEPFFT---TKPVgkgtGLGLSISYGIVEKHGG 340
RocR COG3829
RocR-type transcriptional regulator, contains PAS, AAA-type ATPase, and DNA-binding Fis ...
650-775 3.65e-05

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


Pssm-ID: 443041 [Multi-domain]  Cd Length: 448  Bit Score: 47.46  E-value: 3.65e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859  650 MQEIGAVAREMVRLIETATVPIFAVDIDGCINGWNAKIAELTGLSVEDAMGKSlVRELIYKEyketvdRLLSCALKGDEG 729
Cdd:COG3829    3 ELELKELEEELEAILDSLDDGIIVVDADGRITYVNRAAERILGLPREEVIGKN-VTELIPNS------PLLEVLKTGKPV 75
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 15234859  730 KNVEVKLKTFGSELQGKAMFVVVNacsskdylNNIVGVCFVGQDVT 775
Cdd:COG3829   76 TGVIQKTGGKGKTVIVTAIPIFED--------GEVIGAVETFRDIT 113
PRK10841 PRK10841
two-component system sensor histidine kinase RcsC;
914-1141 3.70e-05

two-component system sensor histidine kinase RcsC;


Pssm-ID: 182772 [Multi-domain]  Cd Length: 924  Bit Score: 48.05  E-value: 3.70e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859   914 ELQQALEvQRRQESEYFsrrkeLAYIFQVIKNPLSGLRFTNSLLEDMDLNEDQKQLLETSVSCEKQISKIVGD-MDVKSI 992
Cdd:PRK10841  435 EMAQAAE-QASQSKSMF-----LATVSHELRTPLYGIIGNLDLLQTKELPKGVDRLVTAMNNSSSLLLKIISDiLDFSKI 508
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859   993 DDGSFLLERTEFFIGNVTNAVVSQVM-LVVRERnLQLIRNIPTEVkSMAVYGDQIRLQQVLAEFLLSIVRYAPMeGSVEL 1071
Cdd:PRK10841  509 ESEQLKIEPREFSPREVINHITANYLpLVVKKR-LGLYCFIEPDV-PVALNGDPMRLQQVISNLLSNAIKFTDT-GCIVL 585
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859  1072 HLCptlnqMADGFsavrLEFRMACAGEGVPPEKVQDMF-----------HSSRWTspeGLGLSVCRKILKLMNGGVQYIR 1140
Cdd:PRK10841  586 HVR-----VDGDY----LSFRVRDTGVGIPAKEVVRLFdpffqvgtgvqRNFQGT---GLGLAICEKLINMMDGDISVDS 653

                  .
gi 15234859  1141 E 1141
Cdd:PRK10841  654 E 654
HATPase_BaeS-like cd16946
Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to ...
1044-1154 3.85e-05

Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Escherichia coli BasS; This family includes the histidine kinase-like ATPase (HATPase) domains of various two-component sensor histidine kinase (HKs) similar to Escherichia coli BaeS HK of the BaeS/BaeR two-component regulatory system (TCS), which responds to envelope stress. Proteins having this HATPase domain also contain a histidine kinase dimerization and phosphoacceptor domain (HisKA), and a HAMP sensory domain.


Pssm-ID: 340422 [Multi-domain]  Cd Length: 109  Bit Score: 43.99  E-value: 3.85e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859 1044 DQIRLQQVLAEFLLSIVRYAPMEGSVELHlCPTLNQmadgfsAVRLEFrmACAGEGVPPEKVQDMFH--------SSRWT 1115
Cdd:cd16946    1 DRDRLQQLFVNLLENSLRYTDTGGKLRIR-AAQTPQ------EVRLDV--EDSAPGVSDDQLARLFErfyrvessRNRAS 71
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 15234859 1116 SPEGLGLSVCRKILKLMNGGVQyireFERSYF---LIVIELP 1154
Cdd:cd16946   72 GGSGLGLAICHNIALAHGGTIS----AEHSPLgglRLVLTLP 109
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
790-837 4.26e-05

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


Pssm-ID: 214512  Cd Length: 67  Bit Score: 42.39  E-value: 4.26e-05
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*...
gi 15234859     790 DYKAIIHSpnpLIPPIFAADENTCCLEWNTAMEKLTGWPRSEVIGKLL 837
Cdd:smart00091    2 RLRAILES---LPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSL 46
PRK09959 PRK09959
acid-sensing system histidine kinase EvgS;
914-1134 6.75e-05

acid-sensing system histidine kinase EvgS;


Pssm-ID: 182169 [Multi-domain]  Cd Length: 1197  Bit Score: 47.42  E-value: 6.75e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859   914 ELQQALEVQRRQE-SEYFSRRKELAYIFQVIKNPLSGLRFTNSLLEDMDLNEDQK-QLLETSVSCEKQISKIVGD-MDVK 990
Cdd:PRK09959  693 DLIHALEVERNKAiNATVAKSQFLATMSHEIRTPISSIMGFLELLSGSGLSKEQRvEAISLAYATGQSLLGLIGEiLDVD 772
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859   991 SIDDGSFLLERTEFFIGNVTNAVVSQVMLVVRERNLQLIRNiPTEVKSMAVYGDQIRLQQVLAEFLLSIVRYApMEGSVE 1070
Cdd:PRK09959  773 KIESGNYQLQPQWVDIPTLVQNTCHSFGAIAASKSIALSCS-STFPDHYLVKIDPQAFKQVLSNLLSNALKFT-TEGAVK 850
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859  1071 LhlCPTLNQMADGFSAVRLEfrMACAGEGVPPEKVQDMFH------SSRWTSPEGLGLSVCRKILKLMNG 1134
Cdd:PRK09959  851 I--TTSLGHIDDNHAVIKMT--IMDSGSGLSQEEQQQLFKrysqtsAGRQQTGSGLGLMICKELIKNMQG 916
RocR COG3829
RocR-type transcriptional regulator, contains PAS, AAA-type ATPase, and DNA-binding Fis ...
791-943 2.21e-04

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: 45.15  E-value: 2.21e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859  791 YKAIIHSpnplIP-PIFAADENTCCLEWNTAMEKLTGWPRSEVIGKlLVREVFGSycrlkgpdalTKFMIVLHNaiGGQD 869
Cdd:COG3829   13 LEAILDS----LDdGIIVVDADGRITYVNRAAERILGLPREEVIGK-NVTELIPN----------SPLLEVLKT--GKPV 75
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15234859  870 TDKfpfpFFDRKGEFIQALLTLNkRVSIDGKIIGAFCFLQipspELQQALEVQRRQESEYFSRRKELAYIFQVI 943
Cdd:COG3829   76 TGV----IQKTGGKGKTVIVTAI-PIFEDGEVIGAVETFR----DITELKRLERKLREEELERGLSAKYTFDDI 140
HATPase_EvgS-ArcB-TorS-like cd16922
Histidine kinase-like ATPase domain of two-component sensor histidine kinases, many are hybrid ...
1048-1137 2.29e-04

Histidine kinase-like ATPase domain of two-component sensor histidine kinases, many are hybrid sensor histidine kinases, similar to Escherichia coli EvgS, ArcB, TorS, BarA, RcsC; This family contains the histidine kinase-like ATPase (HATPase) domains of various two-component hybrid sensor histidine kinases (HKs), including the following Escherichia coli HKs: EvgS, a HK of the EvgS-EvgA two-component system (TCS) that confers acid resistance; ArcB, a HK of the ArcB-ArcA TCS that modulates the expression of numerous genes in response to respiratory growth conditions; TorS, a HK of the TorS-TorR TCS which is involved in the anaerobic utilization of trimethylamine-N-oxide; BarA, a HK of the BarA-UvrY TCS involved in the regulation of carbon metabolism; and RcsC, a HK of the RcsB-RcsC TCS which regulates the expression of the capsule operon and of the cell division gene ftsZ. Proteins having this HATPase domain also contain a histidine kinase dimerization and phosphoacceptor domain (HisKA), with most having accessory sensor domain(s) such as GAF, PAS and CHASE; many are hybrid sensor histidine kinases as they also contain a REC signal receiver domain.


Pssm-ID: 340399 [Multi-domain]  Cd Length: 110  Bit Score: 41.71  E-value: 2.29e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859 1048 LQQVLAEFLLSIVRYAPmEGSVELHLcptlNQMADGFSAVRLEFRMACAGEGVPPEKVQDMFHS--------SRWTSPEG 1119
Cdd:cd16922    1 LRQILLNLLGNAIKFTE-EGEVTLRV----SLEEEEEDGVQLRFSVEDTGIGIPEEQQARLFEPfsqadsstTRKYGGTG 75
                         90
                 ....*....|....*...
gi 15234859 1120 LGLSVCRKILKLMNGGVQ 1137
Cdd:cd16922   76 LGLAISKKLVELMGGDIS 93
PRK11360 PRK11360
two-component system sensor histidine kinase AtoS;
805-1137 3.48e-04

two-component system sensor histidine kinase AtoS;


Pssm-ID: 236901 [Multi-domain]  Cd Length: 607  Bit Score: 44.57  E-value: 3.48e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859   805 IFAADENTCCLEWNTAMEKLTGWPRSEVIGKlLVREVFgsycrlkgpDALTKFMIVLHNAI--GGQDTDKFP-FPFFDRK 881
Cdd:PRK11360  275 VIAIDRQGKITTMNPAAEVITGLQRHELVGK-PYSELF---------PPNTPFASPLLDTLehGTEHVDLEIsFPGRDRT 344
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859   882 gefIQALLTLNKRVSIDGKIIGAFCFLQipspELQQALEVQRR-QESEYFSRRKEL-AYIFQVIKNPLSGLR-------- 951
Cdd:PRK11360  345 ---IELSVSTSLLHNTHGEMIGALVIFS----DLTERKRLQRRvARQERLAALGELvAGVAHEIRNPLTAIRgyvqiwrq 417
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859   952 ---------FTNSLLEDMD-LNEDQKQLLETSVSCEKQISKIvgdmdvkSIDdgsFLLERTEFFIGNVTNAVVSQVmlvv 1021
Cdd:PRK11360  418 qtsdppsqeYLSVVLREVDrLNKVIDQLLEFSRPRESQWQPV-------SLN---ALVEEVLQLFQTAGVQARVDF---- 483
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859  1022 rERNLQliRNIPtevksmAVYGDQIRLQQVLAEFLLSIVRYAPMEGSVELhlcpTLNQMADGFSAVRLEfrmaCAGEGVP 1101
Cdd:PRK11360  484 -ETELD--NELP------PIWADPELLKQVLLNILINAVQAISARGKIRI----RTWQYSDGQVAVSIE----DNGCGID 546
                         330       340       350
                  ....*....|....*....|....*....|....*...
gi 15234859  1102 PEKVQDMFHSSRWTSPE--GLGLSVCRKILKLMNGGVQ 1137
Cdd:PRK11360  547 PELLKKIFDPFFTTKAKgtGLGLALSQRIINAHGGDIE 584
HATPase_BasS-like cd16940
Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to ...
1041-1136 5.60e-04

Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Escherichia coli BasS; This family includes the histidine kinase-like ATPase (HATPase) domains of various two-component sensor histidine kinase (HKs) similar to Escherichia coli BasS HK of the BasS-BasR two-component regulatory system (TCS). Proteins having this HATPase domain also contain a histidine kinase dimerization and phosphoacceptor domain (HisKA); some contain a HAMP sensory domain, while some an N-terminal two-component sensor kinase domain.


Pssm-ID: 340417 [Multi-domain]  Cd Length: 113  Bit Score: 40.85  E-value: 5.60e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859 1041 VYGDQIRLQQVLAEFLLSIVRYAPMEGSVELhlcpTLNQMADGFSAVRLEfrmacaGEGVPPEKVQDMFH-----SSRWT 1115
Cdd:cd16940    7 VQGDALLLFLLLRNLVDNAVRYSPQGSRVEI----KLSADDGAVIRVEDN------GPGIDEEELEALFErfyrsDGQNY 76
                         90       100
                 ....*....|....*....|.
gi 15234859 1116 SPEGLGLSVCRKILKLMNGGV 1136
Cdd:cd16940   77 GGSGLGLSIVKRIVELHGGQI 97
PAS_4 pfam08448
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
669-775 5.87e-04

PAS fold; The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya. This domain 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: 40.48  E-value: 5.87e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859    669 VPIFAVDIDGCINGWNAKIAELTGLSVEDAMGKSLvRELIYKEYKETVDRLLSCALKGDEGKNVEVKLKTFGSELqgkam 748
Cdd:pfam08448    6 DALAVLDPDGRVRYANAAAAELFGLPPEELLGKTL-AELLPPEDAARLERALRRALEGEEPIDFLEELLLNGEER----- 79
                           90       100
                   ....*....|....*....|....*..
gi 15234859    749 FVVVNACSSKDYLNNIVGVCFVGQDVT 775
Cdd:pfam08448   80 HYELRLTPLRDPDGEVIGVLVISRDIT 106
PRK11466 PRK11466
hybrid sensory histidine kinase TorS; Provisional
908-1134 1.19e-03

hybrid sensory histidine kinase TorS; Provisional


Pssm-ID: 236914 [Multi-domain]  Cd Length: 914  Bit Score: 42.97  E-value: 1.19e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859   908 LQIPSPELQqALEVQRRQ---ESEYFSRRKE--LAYIFQVIKNPLSGLRFTNSLLEDMDLNEDQKQLLETSVSCEKQISK 982
Cdd:PRK11466  416 VKARTAELQ-ELVIEHRQaraEAEKASQAKSafLAAMSHEIRTPLYGILGTAQLLADNPALNAQRDDLRAITDSGESLLT 494
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859   983 IVGD-MDVKSIDDG--SFLLERTEFFIGNVTNAVVSQVMLVVRERNLQLIRNIPTEVKSmAVYGDQIRLQQVLAEFLLSI 1059
Cdd:PRK11466  495 ILNDiLDYSAIEAGgkNVSVSDEPFEPRPLLESTLQLMSGRVKGRPIRLATDIADDLPT-ALMGDPRRIRQVITNLLSNA 573
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15234859  1060 VRYAPmEGSVELHlCPTLNQmaDGFSAVRlefrmaCAGEGVPPEKVQDMFHSSRWTSPE----GLGLSVCRKILKLMNG 1134
Cdd:PRK11466  574 LRFTD-EGSIVLR-SRTDGE--QWLVEVE------DSGCGIDPAKLAEIFQPFVQVSGKrggtGLGLTISSRLAQAMGG 642
sensory_box TIGR00229
PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain ...
791-835 1.39e-03

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: 39.97  E-value: 1.39e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 15234859    791 YKAIIHSPNPlipPIFAADENTCCLEWNTAMEKLTGWPRSEVIGK 835
Cdd:TIGR00229    5 YRAIFESSPD---AIIVIDLEGNILYVNPAFEEIFGYSAEELIGR 46
HATPase_EnvZ-like cd16950
Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to ...
1048-1154 3.84e-03

Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Escherichia coli EnvZ and Pseudomonas aeruginosa BfmS; This family includes the histidine kinase-like ATPase (HATPase) domains of various two-component sensor histidine kinase (HKs) such as Escherichia coli EnvZ of the EnvZ-OmpR two-component regulatory system (TCS), which functions in osmoregulation. It also contains the HATPase domain of Pseudomonas aeruginosa BfmS, the HK of the BfmSR TCS, which functions in the regulation of the rhl quorum-sensing system and bacterial virulence in P. aeruginosa. Proteins having this HATPase domain also contain a histidine kinase dimerization and phosphoacceptor domain (HisKA) and a HAMP sensor domain; some also contain a periplasmic domain.


Pssm-ID: 340426 [Multi-domain]  Cd Length: 101  Bit Score: 38.20  E-value: 3.84e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234859 1048 LQQVLAEFLLSIVRYApmEGSVELHlcptlnqmaDGFSAVRLEFRMACAGEGVPPEKVQDMFH------SSRWTSPEGLG 1121
Cdd:cd16950    1 LKRVLSNLVDNALRYG--GGWVEVS---------SDGEGNRTRIQVLDNGPGIAPEEVDELFQpfyrgdNARGTSGTGLG 69
                         90       100       110
                 ....*....|....*....|....*....|...
gi 15234859 1122 LSVCRKILKLMNGGVQyIREFERSYFLIVIELP 1154
Cdd:cd16950   70 LAIVQRISDAHGGSLT-LANRAGGGLCARIELP 101
KinA COG5805
Sporulation sensor histidine kinase A (Stage II sporulation protein SpoIIF/SpoIIJ) [Cell cycle ...
777-835 5.52e-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: 40.87  E-value: 5.52e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 15234859  777 HKIVMDKFINIQGDYKAIIHSpnpLIPPIFAADENTCCLEWNTAMEKLTGWPRSEVIGK 835
Cdd:COG5805   22 NNEVLRMAIEITEELETILEN---LPDAIIAVNREGKVIYINPAMEKLLGYTSEEIIGK 77
 
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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