Citrus Sinensis ID: 022961

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------29
Protein Sequence
MDSQLGLIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRIA
Secondary Structure (PSIPRED)
ccccccHHHHHHHcHHHHHHHHHHHHcccEEEEEccccccccEEEEcHHHHHHHcccccccccccccccccccccHHHHHHHHHHHHHcccEEEEEEcccccccccEEEEEEEEEEccccccEEEEEEEEcccccccccccccccccccccccccHHHHccccccccccccHHHHHHHHcccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccHHHHcccccccEEEEEccccccccEEEEcHHHHHcccccHHHHccccc
Secondary Structure Prediction (SSPRO)
ccccccccHHHHHHHHHHHHHHHHHHcccEEEEEEcccccccEEEEcHHHHHHHcccHHHHccccHHHHccccccHHHHHHHHHHHHHcccEEEEEEEEcccccEEEEEEEEEEEcccccccEEEEEEEEEcccHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccHHHHHHHHHHHHHccccccHHHccccccccccccccccccccHHHHHcHHHHHHHHHHHccEEEEccccccccEEEEcHHHHHHccccEEEEEcccc
Coil and Loop (DISEMBL)
MDSQLGLIEQSFNNRYTLWVHEALdelpdsftitdpsisghpivfasrgflkmsgfsraeiigrngrmfqgprtnrRTIMEIREAIREErpievnllnykkdgtpfWMLFKMSLVfgkedgratHFVAVQVPIvsrkhmrnsgmsysedgggsrlREIVFGScrrevcsdsLLDLDRVlaldsddtgleiedsceaSDLEKRKAATAIDNILSVLTHYSQLtgrlvcgkrcslpgmgfiSSSLYISLGRikqsfvlidphlpdmpmvyASDAFLKLTGAQIFTKITRIA
Flexible Loop (DISEMBL)
MDSQLGLIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEiigrngrmfqgprtnrrTIMEIReaireerpievnllnykkdgtpFWMLFKMSLVFGKEDGRATHFVAVqvpivsrkhmrnsgmsysedgggsrLREIVFGSCRREVCSDSLLDLDRVlaldsddtgleiedsceasdlEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRIA
Low Complexity Region (SEG)
MDSQLGLIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNrrtimeireaireerpieVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRIA
Disordered region (IsUnstruct)
******LIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSR******************LREIVFGSCRREVCSDSLLDLDRVLALDSDDTGLEI************KAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKIT***
Disordered Region (DISOPRED)
***QLGL***********WVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRN*****************VFGSCRREVCSDSLLDLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITR**
Disordered Region (DISEMBL)
MDSQLGLIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNS*********GSRLREIVFGSCRREVCSDSLLDLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRIA
Disordered Region (DISPRO)
*****GLIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDRVLALDSDDTGLEIEDSCEASDLEKRKAAT****I*******************CSLPGMGFISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI*
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MDSQLGLIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRIA
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	289	2.2.26 [Sep-21-2011]
O64511	399	Protein TWIN LOV 1 OS=Ara	yes	no	0.923	0.669	0.639	3e-97
P93025	915	Phototropin-2 OS=Arabidop	no	no	0.882	0.278	0.309	5e-26
Q9ST27	907	Phototropin-2 OS=Oryza sa	no	no	0.370	0.117	0.444	2e-21
Q2RBR1	921	Phototropin-1B OS=Oryza s	no	no	0.370	0.116	0.407	2e-19
Q2QYY8	921	Phototropin-1A OS=Oryza s	no	no	0.370	0.116	0.407	2e-19
Q48IV1	534	Blue-light-activated prot	yes	no	0.377	0.204	0.418	3e-19
O48963	996	Phototropin-1 OS=Arabidop	no	no	0.373	0.108	0.394	1e-18
Q4ZSY3	534	Blue-light-activated prot	yes	no	0.359	0.194	0.419	3e-18
O34627	261	Blue-light photoreceptor	yes	no	0.401	0.444	0.361	4e-18
Q9HPU8	674	Bacterioopsin transcripti	yes	no	0.397	0.170	0.362	7e-18

>sp|O64511|TLOV1_ARATH Protein TWIN LOV 1 OS=Arabidopsis thaliana GN=TLP1 PE=1 SV=2

 Score =  354 bits (909), Expect = 3e-97,   Method: Compositional matrix adjust.
 Identities = 174/272 (63%), Positives = 212/272 (77%), Gaps = 5/272 (1%)

Query: 11  SFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQ 70
           SF+ RYTLW+ EAL+ELP +FTITDP ISGHPIVFAS GFLKM+G+SR E+IGRNG++FQ
Sbjct: 19  SFSGRYTLWIKEALEELPHNFTITDPFISGHPIVFASLGFLKMTGYSREEVIGRNGKVFQ 78

Query: 71  GPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQ 130
           GP+TNRR+IMEIREAIREER ++V+LLNY+K G+PFWMLF M  VFGK+DG+ T+FVAVQ
Sbjct: 79  GPKTNRRSIMEIREAIREERSVQVSLLNYRKSGSPFWMLFHMCPVFGKDDGKVTNFVAVQ 138

Query: 131 VPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDRVLALDSDD--TGL 188
           VPI  R+H R    +    G  S      FGSCRREVC  + +  DR L ++ DD   GL
Sbjct: 139 VPISGREHHRKKLRNV---GDLSSDTSPTFGSCRREVCFGNFVCQDRALPVECDDDEQGL 195

Query: 189 EIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLG 248
           E  + CEAS+ EK KA  AI+N+LS+L HYS+L+GRLVCGKR  L G+  +SSSL ISLG
Sbjct: 196 EDWEQCEASESEKLKATEAINNVLSILVHYSELSGRLVCGKRYCLRGVDCLSSSLVISLG 255

Query: 249 RIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQ 280
           RIKQSFVL +P LPDMP++YASDAFL LTG +
Sbjct: 256 RIKQSFVLTNPCLPDMPIIYASDAFLTLTGYK 287

Arabidopsis thaliana (taxid: 3702)

>sp|P93025|PHOT2_ARATH Phototropin-2 OS=Arabidopsis thaliana GN=PHOT2 PE=1 SV=2

 Score =  118 bits (296), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 94/304 (30%), Positives = 148/304 (48%), Gaps = 49/304 (16%)

Query: 15  RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRT 74
           R +  +  AL  L  +F ++D +    PIV+AS GF  M+G+S  EI+GRN R  QGP T
Sbjct: 119 RVSQELKTALSTLQQTFVVSDATQPHCPIVYASSGFFTMTGYSSKEIVGRNCRFLQGPDT 178

Query: 75  NRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKED-GRATHFVAVQVPI 133
           ++  + +IR+ ++  +     LLNYKKDGTPFW L  ++ +  K+D G    F+ +QV +
Sbjct: 179 DKNEVAKIRDCVKNGKSYCGRLLNYKKDGTPFWNLLTVTPI--KDDQGNTIKFIGMQVEV 236

Query: 134 ------VSRKHMRNSGMSYSEDGGGSRLREIVFGSC---------RREVCSDSLLDLDRV 178
                 V+ K +R +G+S S     +R +E    S          R+    +S+ + D +
Sbjct: 237 SKYTEGVNDKALRPNGLSKSLIRYDARQKEKALDSITEVVQTIRHRKSQVQESVSN-DTM 295

Query: 179 LALDSDDT---GLEIEDSCEASDL------------EKRKAATAIDNILSVLTHYSQLTG 223
           +  DS  T   G +   S EAS               K K++      L  +     +  
Sbjct: 296 VKPDSSTTPTPGRQTRQSDEASKSFRTPGRVSTPTGSKLKSSNNRHEDLLRMEPEELMLS 355

Query: 224 RLVCGKRCSL----------PGMGFISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAF 273
             V G+R S            G+      L  +L RI+++FV+ DP LPD P+++ASD+F
Sbjct: 356 TEVIGQRDSWDLSDRERDIRQGI-----DLATTLERIEKNFVISDPRLPDNPIIFASDSF 410

Query: 274 LKLT 277
           L+LT
Sbjct: 411 LELT 414

Protein kinase that acts as a blue-light photoreceptor in a signal-transduction pathway for photo-induced movements. Mediates calcium spiking of extra- and intracellular origins in response to blue light. Involved in hypocotyl phototropism. Contributes to the chloroplast accumulation in low blue light and mediates their translocation (avoidance response) at high fluence. Regulates stomata opening and photomorphogenesis response of leaf tissue. Not involved in hypocotyl elongation inhibition, anthocyanin accumulation or cotyledon opening.

Arabidopsis thaliana (taxid: 3702)

EC: 2

EC: .

EC: 7

EC: .

EC: 1

EC: 1

EC: .

EC: 1

>sp|Q9ST27|PHOT2_ORYSJ Phototropin-2 OS=Oryza sativa subsp. japonica GN=PHOT2 PE=1 SV=1

 Score =  102 bits (255), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 48/108 (44%), Positives = 73/108 (67%), Gaps = 1/108 (0%)

Query: 24  LDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIR 83
           L+ +  +F ITDP I  +PI+FAS  FL+++ ++R EI+GRN R  QGP T++ T+ +IR
Sbjct: 383 LERIEKNFVITDPRIPDNPIIFASDSFLELTEYTREEILGRNCRFLQGPETDQGTVDKIR 442

Query: 84  EAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQV 131
           EAIRE++ I V L+NY K G  FW LF +  +  ++ G   +F+ VQ+
Sbjct: 443 EAIREQKEITVQLINYTKSGKKFWNLFHLQPMRDQK-GELQYFIGVQL 489

Protein kinase that acts as a blue-light photoreceptor in a signal-transduction pathway for phototropic responses. Regulates a wide range of physiological activities in plants that maximize the efficiency of photosynthesis, such as chloroplast relocations, stomata opening, and leaf expansion.

Oryza sativa subsp. japonica (taxid: 39947)

EC: 2

EC: .

EC: 7

EC: .

EC: 1

EC: 1

EC: .

EC: 1

>sp|Q2RBR1|PHT1B_ORYSJ Phototropin-1B OS=Oryza sativa subsp. japonica GN=PHOT1B PE=1 SV=2

 Score = 96.7 bits (239), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 44/108 (40%), Positives = 70/108 (64%), Gaps = 1/108 (0%)

Query: 24  LDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIR 83
           L+ +  +F ITDP +  +PI+FAS  FL+++ ++R EI+GRN R  QGP T+R T+ +IR
Sbjct: 408 LERIEKNFVITDPRLPDNPIIFASDSFLQLTEYNREEILGRNCRFLQGPETDRATVRKIR 467

Query: 84  EAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQV 131
           +AI  +  + V L+NY K G  FW LF +  +  ++ G   +F+ VQ+
Sbjct: 468 DAIDNQAEVTVQLINYTKSGKKFWNLFHLQPMRDQK-GDVQYFIGVQL 514

Protein kinase that acts as a blue-light photoreceptor in a signal-transduction pathway for phototropic responses. Regulates a wide range of physiological activities in plants that maximize the efficiency of photosynthesis, such as chloroplast relocations, stomata opening, and leaf expansion.

Oryza sativa subsp. japonica (taxid: 39947)

EC: 2

EC: .

EC: 7

EC: .

EC: 1

EC: 1

EC: .

EC: 1

>sp|Q2QYY8|PHT1A_ORYSJ Phototropin-1A OS=Oryza sativa subsp. japonica GN=PHOT1A PE=1 SV=2

 Score = 96.7 bits (239), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 44/108 (40%), Positives = 70/108 (64%), Gaps = 1/108 (0%)

Query: 24  LDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIR 83
           L+ +  +F ITDP +  +PI+FAS  FL+++ ++R EI+GRN R  QGP T+R T+ +IR
Sbjct: 408 LERIEKNFVITDPRLPDNPIIFASDSFLQLTEYNREEILGRNCRFLQGPETDRATVRKIR 467

Query: 84  EAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQV 131
           +AI  +  + V L+NY K G  FW LF +  +  ++ G   +F+ VQ+
Sbjct: 468 DAIDNQAEVTVQLINYTKSGKKFWNLFHLQPMRDQK-GDVQYFIGVQL 514

Protein kinase that acts as a blue-light photoreceptor in a signal-transduction pathway for phototropic responses. Regulates a wide range of physiological activities in plants that maximize the efficiency of photosynthesis, such as chloroplast relocations, stomata opening, and leaf expansion.

Oryza sativa subsp. japonica (taxid: 39947)

EC: 2

EC: .

EC: 7

EC: .

EC: 1

EC: 1

EC: .

EC: 1

>sp|Q48IV1|LOVHK_PSE14 Blue-light-activated protein OS=Pseudomonas syringae pv. phaseolicola (strain 1448A / Race 6) GN=PSPPH_2483 PE=3 SV=2

 Score = 96.3 bits (238), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 46/110 (41%), Positives = 69/110 (62%), Gaps = 1/110 (0%)

Query: 33  ITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPI 92
           +TDP+ + +PI+F++R FL+M+G+S  EIIG N R  QGP T+R  +  IREAI E   I
Sbjct: 37  VTDPNRADNPIIFSNRAFLEMTGYSSEEIIGTNCRFLQGPETDRAVVQSIREAIDERVDI 96

Query: 93  EVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNS 142
              +LNY+KDG+ FW    +S V+  + G   +F A Q+ I  R+   ++
Sbjct: 97  STEILNYRKDGSTFWNALFISPVY-NDAGDLIYFFASQLDISRRRDAEDA 145

Photosensitive kinase and response regulator that is involved in increased bacterial virulence upon exposure to light.

Pseudomonas syringae pv. phaseolicola (strain 1448A / Race 6) (taxid: 264730)

EC: 2

EC: .

EC: 7

EC: .

EC: 1

EC: 3

EC: .

EC: 3

>sp|O48963|PHOT1_ARATH Phototropin-1 OS=Arabidopsis thaliana GN=PHOT1 PE=1 SV=1

 Score = 93.6 bits (231), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 43/109 (39%), Positives = 68/109 (62%), Gaps = 1/109 (0%)

Query: 23  ALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEI 82
            L+ +  +F ITDP +  +PI+FAS  FL+++ +SR EI+GRN R  QGP T+  T+ +I
Sbjct: 469 TLERIEKNFVITDPRLPDNPIIFASDSFLELTEYSREEILGRNCRFLQGPETDLTTVKKI 528

Query: 83  REAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQV 131
           R AI  +  + V L+NY K G  FW +F +  +  ++ G   +F+ VQ+
Sbjct: 529 RNAIDNQTEVTVQLINYTKSGKKFWNIFHLQPMRDQK-GEVQYFIGVQL 576

Protein kinase that acts as a blue-light photoreceptor in a signal-transduction pathway for photo-induced movements. Required for blue-light mediated mRNA destabilization. Mediates calcium spiking of extracellular origin in response to low rate of blue light. Mediates also rapid membrane depolarization and growth inhibition in response to blue light. Necessary for root phototropism. Involved in hypocotyl phototropism under low rate but not under high rate blue light. Contributes to the chloroplast accumulation but seems to be not required for chloroplast translocation. Regulates stomata opening and photomorphogenesis response of leaf tissue. Confers sensitivity to drought. Not involved in hypocotyl elongation inhibition, anthocyanin accumulation or cotyledon opening.

Arabidopsis thaliana (taxid: 3702)

EC: 2

EC: .

EC: 7

EC: .

EC: 1

EC: 1

EC: .

EC: 1

>sp|Q4ZSY3|LOVHK_PSEU2 Blue-light-activated protein OS=Pseudomonas syringae pv. syringae (strain B728a) GN=Psyr_2700 PE=3 SV=1

 Score = 92.4 bits (228), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 44/105 (41%), Positives = 66/105 (62%), Gaps = 1/105 (0%)

Query: 33  ITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPI 92
           +TDP+   +PI+FA+R FL+M+G++  EIIG N R  QGP T+R  +  IR+AI +   I
Sbjct: 37  VTDPNRPDNPIIFANRAFLEMTGYASEEIIGSNCRFLQGPDTDRTAVQSIRDAIDQRVDI 96

Query: 93  EVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRK 137
              +LNY+KDG+ FW    +S V+  + G   +F A Q+ I  R+
Sbjct: 97  STEILNYRKDGSSFWNALFISPVY-NDAGELIYFFASQLDISRRR 140

Photosensitive kinase and response regulator that is involved in increased bacterial virulence upon exposure to light.

Pseudomonas syringae pv. syringae (strain B728a) (taxid: 205918)

EC: 2

EC: .

EC: 7

EC: .

EC: 1

EC: 3

EC: .

EC: 3

>sp|O34627|PHOT_BACSU Blue-light photoreceptor OS=Bacillus subtilis (strain 168) GN=pfyP PE=1 SV=1

 Score = 92.0 bits (227), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 43/119 (36%), Positives = 70/119 (58%), Gaps = 3/119 (2%)

Query: 20  VHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTI 79
           + +ALD +     ITDP++  +PIV+ ++GF++M+G+   EI+G+N R  QG  T+   +
Sbjct: 16  IKKALDHVRVGVVITDPALEDNPIVYVNQGFVQMTGYETEEILGKNCRFLQGKHTDPAEV 75

Query: 80  MEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKH 138
             IR A++ + P+ V + NYKKDGT FW    +  +   E    T+FV +Q  I  +K 
Sbjct: 76  DNIRTALQNKEPVTVQIQNYKKDGTMFWNELNIDPM---EIEDKTYFVGIQNDITKQKE 131

Exhibits the same spectroscopical features and blue-light induced photochemistry as plants phototropins, with the reversible formation of a blue-shifted photoproduct, assigned to an FMN-cysteine thiol adduct. Although it is a positive regulator in the activation of the environmental signaling branch of the general stress transcription factor sigma-B, its precise role is undetermined.

Bacillus subtilis (strain 168) (taxid: 224308)

>sp|Q9HPU8|BAT_HALSA Bacterioopsin transcriptional activator OS=Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) GN=bat PE=1 SV=1

 Score = 91.3 bits (225), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 42/116 (36%), Positives = 67/116 (57%), Gaps = 1/116 (0%)

Query: 21  HEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIM 80
            +ALDE P   TI+D +    PI++ +  F  ++G+S  E++G N R  QGP+TN   + 
Sbjct: 161 EQALDEAPIGITISDATDPEEPIIYINDSFEDITGYSPDEVVGANHRFLQGPKTNEDRVA 220

Query: 81  EIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSR 136
           E   AI E+   +V L NY++DG+ FW    +S ++  EDG  +H+V  Q+ +  R
Sbjct: 221 EFWTAITEDHDTQVVLRNYRRDGSLFWNQVDISPIY-DEDGTVSHYVGFQMDVSER 275

Involved in activating bop (bacterioopsin) and brp gene expression at low-oxygen tension, which naturally occurs in stationary phase.

Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) (taxid: 64091)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	289
224110804	396	predicted protein [Populus trichocarpa]	0.937	0.684	0.703	1e-112
224102353	396	predicted protein [Populus trichocarpa]	0.937	0.684	0.696	1e-110
225424899	397	PREDICTED: protein TWIN LOV 1 [Vitis vin	0.955	0.695	0.703	1e-108
255558228	375	twin lov protein, putative [Ricinus comm	0.920	0.709	0.705	1e-108
350537683	398	LOV/LOV protein [Solanum lycopersicum] g	0.955	0.693	0.601	3e-96
18395411	399	protein TWIN LOV 1 [Arabidopsis thaliana	0.923	0.669	0.639	2e-95
30678020	397	protein TWIN LOV 1 [Arabidopsis thaliana	0.923	0.672	0.639	3e-95
297817884	386	pac motif-containing protein [Arabidopsi	0.916	0.686	0.637	3e-95
42570655	358	protein TWIN LOV 1 [Arabidopsis thaliana	0.923	0.745	0.639	7e-95
449434827	385	PREDICTED: protein TWIN LOV 1-like [Cucu	0.923	0.693	0.6	6e-93

>gi|224110804|ref|XP_002315641.1| predicted protein [Populus trichocarpa] gi|222864681|gb|EEF01812.1| predicted protein [Populus trichocarpa]

 Score =  410 bits (1054), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 197/280 (70%), Positives = 231/280 (82%), Gaps = 9/280 (3%)

Query: 1   MDSQLGLIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAE 60
           M+SQL LIE+SFN RY+ WV EAL+ELP +FTITDP+ISGHPIVFAS GFLKMSGF R +
Sbjct: 1   MESQLALIEKSFNTRYSPWVREALEELPHNFTITDPTISGHPIVFASPGFLKMSGFRRDQ 60

Query: 61  IIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKED 120
           +IG NGRMFQGP+TNR+T+MEIREAIREER ++V+L NY+KDGTPFWMLF+MS VF KED
Sbjct: 61  VIGNNGRMFQGPKTNRKTVMEIREAIREERAVQVSLWNYRKDGTPFWMLFQMSPVFSKED 120

Query: 121 GRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDRVLA 180
           GR  HF+ VQVPI+  K         ++DG  +   EIVFGSCRREVCSDSL++L RVLA
Sbjct: 121 GRVIHFIGVQVPILRNKRS-------TDDGADAAWNEIVFGSCRREVCSDSLVELGRVLA 173

Query: 181 LD--SDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGF 238
           LD  ++  G+E E+  EASDLEK++AAT I+NILSVLTHYS+ TGRL CGKRCS P  G 
Sbjct: 174 LDTYTNCRGVETEEPWEASDLEKQRAATTINNILSVLTHYSESTGRLACGKRCSSPAAGL 233

Query: 239 ISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTG 278
           I+SSL ISLGRI QSFVLIDPHLP+MP+VYASDAFLKLTG
Sbjct: 234 INSSLNISLGRINQSFVLIDPHLPNMPIVYASDAFLKLTG 273

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224102353|ref|XP_002312647.1| predicted protein [Populus trichocarpa] gi|222852467|gb|EEE90014.1| predicted protein [Populus trichocarpa]

 Score =  403 bits (1036), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 195/280 (69%), Positives = 231/280 (82%), Gaps = 9/280 (3%)

Query: 1   MDSQLGLIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAE 60
           M+SQL  IEQS N RY+LWV E LDEL  +FTITDP+I+GHPIVFAS GFLKMSGFSR +
Sbjct: 1   MESQLAPIEQSLNARYSLWVREDLDELRHNFTITDPNITGHPIVFASPGFLKMSGFSREQ 60

Query: 61  IIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKED 120
           ++G NGR+FQGP+TNR+T+MEIREAIREER + V LLNY+KDGTPFWMLF+MS VF KED
Sbjct: 61  VVGNNGRIFQGPKTNRKTVMEIREAIREERAVRVRLLNYRKDGTPFWMLFQMSPVFSKED 120

Query: 121 GRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDRVLA 180
           G   HF+ VQVPI   K +       ++DG  +   EI FGSCRREVCSDSL++L RVLA
Sbjct: 121 GGVVHFIGVQVPIRRNKKL-------TDDGADAACNEIAFGSCRREVCSDSLVELTRVLA 173

Query: 181 LDSDDT--GLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGF 238
           LD+D    G++IE+SCEAS+LEK++AATAI++ILSVLT  S+ TGR+VCGKRCSLP  G 
Sbjct: 174 LDTDTNCKGVKIEESCEASELEKQRAATAINDILSVLTGCSESTGRMVCGKRCSLPAAGL 233

Query: 239 ISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTG 278
           I+SSL ISLGRIKQSFVLIDPHLP+MP+VYASDAFLKLTG
Sbjct: 234 INSSLNISLGRIKQSFVLIDPHLPNMPVVYASDAFLKLTG 273

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225424899|ref|XP_002269901.1| PREDICTED: protein TWIN LOV 1 [Vitis vinifera]

 Score =  396 bits (1018), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 199/283 (70%), Positives = 233/283 (82%), Gaps = 7/283 (2%)

Query: 1   MDSQLGLIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAE 60
           M+SQL LIEQSFN RY++WV EALDELPD+FTITDPSISGHPIVFASRGFLKMSG+S+ E
Sbjct: 1   MESQLALIEQSFNYRYSVWVREALDELPDNFTITDPSISGHPIVFASRGFLKMSGYSKEE 60

Query: 61  IIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKED 120
           +IG+NGR FQGP T+RR+I EI+EAI+EER I+  LLNY+KDGTP WMLF MS VF KED
Sbjct: 61  VIGKNGRAFQGPGTSRRSITEIQEAIQEERTIQTILLNYRKDGTPIWMLFHMSPVFSKED 120

Query: 121 GRATHFVAVQVPIVSRKHMRNSGMSYSEDG---GGSRLREIVFGSCRREVCSDSLLDLDR 177
           GR  HFVAVQVP+ SRK  R SG     DG    G R R+IVFGSCRREVCSDS+L+L+ 
Sbjct: 121 GRVIHFVAVQVPM-SRKP-RWSGSGPGRDGVCEDGCRSRDIVFGSCRREVCSDSVLELEH 178

Query: 178 VLALDS--DDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPG 235
           VLA +S  D    + E+  EASD EKR+AA A++NILS+LTHYS+LTG+LVC KRC+L G
Sbjct: 179 VLAFESLFDSDNRDDEEPREASDQEKRRAAAAVNNILSLLTHYSELTGKLVCEKRCTLSG 238

Query: 236 MGFISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTG 278
           +G + +SL ISLGRIKQSFVL DPHLP+MP+VYASDAFLKLTG
Sbjct: 239 IGLLGASLIISLGRIKQSFVLTDPHLPEMPIVYASDAFLKLTG 281

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255558228|ref|XP_002520141.1| twin lov protein, putative [Ricinus communis] gi|223540633|gb|EEF42196.1| twin lov protein, putative [Ricinus communis]

 Score =  396 bits (1017), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 192/272 (70%), Positives = 226/272 (83%), Gaps = 6/272 (2%)

Query: 7   LIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNG 66
           LI+QSFN RY+    EAL+ LPD FTITDP ISGHPI+FAS GF K+SGF + EIIG+NG
Sbjct: 12  LIQQSFNTRYSFSAREALNGLPDCFTITDPYISGHPIIFASDGFSKLSGFPKDEIIGKNG 71

Query: 67  RMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHF 126
           R+FQGP+TNRR+IMEIREAIREER ++++LLNY+KDGTPFW+LF M+ VF K+DGR  HF
Sbjct: 72  RIFQGPKTNRRSIMEIREAIREERALQISLLNYRKDGTPFWLLFHMTPVFNKKDGRVVHF 131

Query: 127 VAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDRVLALDSDDT 186
           VAVQVPI+ R++    G + SEDG G  LREIVFGSCRREVCSDSL++L RVL+LDSD  
Sbjct: 132 VAVQVPILKRRN----GSALSEDGSG--LREIVFGSCRREVCSDSLVELGRVLSLDSDSR 185

Query: 187 GLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYIS 246
           G  IE+ C AS+ EKRKA TAI++ILSVLT+YS+  G LVC KRC+L G G ISSSL IS
Sbjct: 186 GSNIEEPCVASEAEKRKAVTAINSILSVLTNYSECNGELVCAKRCNLVGAGMISSSLNIS 245

Query: 247 LGRIKQSFVLIDPHLPDMPMVYASDAFLKLTG 278
           LGRI+QSFVL DPHLPDMP+VYASDAFLKLTG
Sbjct: 246 LGRIRQSFVLTDPHLPDMPIVYASDAFLKLTG 277

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|350537683|ref|NP_001234816.1| LOV/LOV protein [Solanum lycopersicum] gi|311692316|dbj|BAJ24889.1| LOV/LOV protein [Solanum lycopersicum]

 Score =  357 bits (916), Expect = 3e-96,   Method: Compositional matrix adjust.
 Identities = 172/286 (60%), Positives = 220/286 (76%), Gaps = 10/286 (3%)

Query: 1   MDSQLGLIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAE 60
           M+SQLGLIE+SFN +Y+  V EALDELPDSFTITDPSISGHPIV+ SRGFLK+ G+S+ E
Sbjct: 1   MESQLGLIEKSFNVKYSDGVREALDELPDSFTITDPSISGHPIVYVSRGFLKVFGYSKNE 60

Query: 61  IIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKED 120
           ++G+NGR+FQGP+TNRR++M IREAIREER I+++LLNY+KDGTPFWMLF M  V+ ++D
Sbjct: 61  VLGKNGRVFQGPKTNRRSVMAIREAIREERGIQISLLNYRKDGTPFWMLFNMCPVYSEKD 120

Query: 121 GRATHFVAVQVPIVSRKH----MRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLD 176
           GR  HF+ +QVPI+ R++              DGG    R  V+  CRREVCS+S++++D
Sbjct: 121 GRVVHFLGIQVPILRRRNSLGGGIGRNGGVCYDGGN--CRGYVYKCCRREVCSNSMMEMD 178

Query: 177 RVLALDS----DDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCS 232
           R L++DS    D T +++E  CEASD EK KA+ A++NI+SVL +YS+L GRLV  +RC 
Sbjct: 179 RALSVDSVSGLDHTEVDVEGPCEASDQEKTKASVAVNNIMSVLANYSELNGRLVIDRRCC 238

Query: 233 LPGMGFISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTG 278
             G   +S+SL IS GRIKQSFVL D HLPDMP+VYASDAFLKL G
Sbjct: 239 QSGTSLLSASLNISFGRIKQSFVLTDAHLPDMPIVYASDAFLKLIG 284

Source: Solanum lycopersicum

Species: Solanum lycopersicum

Genus: Solanum

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18395411|ref|NP_565288.1| protein TWIN LOV 1 [Arabidopsis thaliana] gi|75099072|sp|O64511.2|TLOV1_ARATH RecName: Full=Protein TWIN LOV 1 gi|15010682|gb|AAK74000.1| At2g02710/T20F6.15 [Arabidopsis thaliana] gi|16323302|gb|AAL15406.1| At2g02710/T20F6.15 [Arabidopsis thaliana] gi|20196957|gb|AAC05351.2| putative receptor-like protein kinase [Arabidopsis thaliana] gi|330250520|gb|AEC05614.1| protein TWIN LOV 1 [Arabidopsis thaliana]

 Score =  354 bits (909), Expect = 2e-95,   Method: Compositional matrix adjust.
 Identities = 174/272 (63%), Positives = 212/272 (77%), Gaps = 5/272 (1%)

Query: 11  SFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQ 70
           SF+ RYTLW+ EAL+ELP +FTITDP ISGHPIVFAS GFLKM+G+SR E+IGRNG++FQ
Sbjct: 19  SFSGRYTLWIKEALEELPHNFTITDPFISGHPIVFASLGFLKMTGYSREEVIGRNGKVFQ 78

Query: 71  GPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQ 130
           GP+TNRR+IMEIREAIREER ++V+LLNY+K G+PFWMLF M  VFGK+DG+ T+FVAVQ
Sbjct: 79  GPKTNRRSIMEIREAIREERSVQVSLLNYRKSGSPFWMLFHMCPVFGKDDGKVTNFVAVQ 138

Query: 131 VPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDRVLALDSDD--TGL 188
           VPI  R+H R    +    G  S      FGSCRREVC  + +  DR L ++ DD   GL
Sbjct: 139 VPISGREHHRKKLRNV---GDLSSDTSPTFGSCRREVCFGNFVCQDRALPVECDDDEQGL 195

Query: 189 EIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLG 248
           E  + CEAS+ EK KA  AI+N+LS+L HYS+L+GRLVCGKR  L G+  +SSSL ISLG
Sbjct: 196 EDWEQCEASESEKLKATEAINNVLSILVHYSELSGRLVCGKRYCLRGVDCLSSSLVISLG 255

Query: 249 RIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQ 280
           RIKQSFVL +P LPDMP++YASDAFL LTG +
Sbjct: 256 RIKQSFVLTNPCLPDMPIIYASDAFLTLTGYK 287

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|30678020|ref|NP_849928.1| protein TWIN LOV 1 [Arabidopsis thaliana] gi|18146960|dbj|BAB83170.1| twin LOV protein 1 [Arabidopsis thaliana] gi|330250519|gb|AEC05613.1| protein TWIN LOV 1 [Arabidopsis thaliana]

 Score =  354 bits (908), Expect = 3e-95,   Method: Compositional matrix adjust.
 Identities = 174/272 (63%), Positives = 212/272 (77%), Gaps = 5/272 (1%)

Query: 11  SFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQ 70
           SF+ RYTLW+ EAL+ELP +FTITDP ISGHPIVFAS GFLKM+G+SR E+IGRNG++FQ
Sbjct: 19  SFSGRYTLWIKEALEELPHNFTITDPFISGHPIVFASLGFLKMTGYSREEVIGRNGKVFQ 78

Query: 71  GPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQ 130
           GP+TNRR+IMEIREAIREER ++V+LLNY+K G+PFWMLF M  VFGK+DG+ T+FVAVQ
Sbjct: 79  GPKTNRRSIMEIREAIREERSVQVSLLNYRKSGSPFWMLFHMCPVFGKDDGKVTNFVAVQ 138

Query: 131 VPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDRVLALDSDD--TGL 188
           VPI  R+H R    +    G  S      FGSCRREVC  + +  DR L ++ DD   GL
Sbjct: 139 VPISGREHHRKKLRNV---GDLSSDTSPTFGSCRREVCFGNFVCQDRALPVECDDDEQGL 195

Query: 189 EIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLG 248
           E  + CEAS+ EK KA  AI+N+LS+L HYS+L+GRLVCGKR  L G+  +SSSL ISLG
Sbjct: 196 EDWEQCEASESEKLKATEAINNVLSILVHYSELSGRLVCGKRYCLRGVDCLSSSLVISLG 255

Query: 249 RIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQ 280
           RIKQSFVL +P LPDMP++YASDAFL LTG +
Sbjct: 256 RIKQSFVLTNPCLPDMPIIYASDAFLTLTGYK 287

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297817884|ref|XP_002876825.1| pac motif-containing protein [Arabidopsis lyrata subsp. lyrata] gi|297322663|gb|EFH53084.1| pac motif-containing protein [Arabidopsis lyrata subsp. lyrata]

 Score =  354 bits (908), Expect = 3e-95,   Method: Compositional matrix adjust.
 Identities = 174/273 (63%), Positives = 214/273 (78%), Gaps = 8/273 (2%)

Query: 9   EQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRM 68
           E SFN RYTLW+ EAL+ELP +FTITDP ISGHPIVFAS GFLKM+G+SR E+IGRNG++
Sbjct: 9   EDSFNGRYTLWITEALEELPHNFTITDPFISGHPIVFASLGFLKMTGYSREEVIGRNGKV 68

Query: 69  FQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVA 128
           FQGP+TNRR+IMEIREAIREER + V+LLNY+K G+PFWMLF MS VFG++DG+  +FVA
Sbjct: 69  FQGPKTNRRSIMEIREAIREERSVMVSLLNYRKSGSPFWMLFHMSPVFGRDDGKVINFVA 128

Query: 129 VQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDRVLALDSDD-TG 187
           VQVPI  ++H +   MS       S   E+VFGSCRREVC  S +  +R   ++ DD  G
Sbjct: 129 VQVPISGQEHRKLGVMS-------SDHSELVFGSCRREVCFGSFVHQNRASPVECDDEQG 181

Query: 188 LEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISL 247
           LE  + CEAS+ EK KA  A++N+LS+LT YS+L+GRLVCGKR  L G+  +SSSL ISL
Sbjct: 182 LEDWEHCEASESEKLKAVEAVNNVLSILTRYSELSGRLVCGKRYCLRGVDCLSSSLVISL 241

Query: 248 GRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQ 280
           GRIKQSFVL +P LPDMP++YASDAFL LTG +
Sbjct: 242 GRIKQSFVLTNPCLPDMPIIYASDAFLTLTGYK 274

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|42570655|ref|NP_973401.1| protein TWIN LOV 1 [Arabidopsis thaliana] gi|330250518|gb|AEC05612.1| protein TWIN LOV 1 [Arabidopsis thaliana]

 Score =  353 bits (905), Expect = 7e-95,   Method: Compositional matrix adjust.
 Identities = 174/272 (63%), Positives = 211/272 (77%), Gaps = 5/272 (1%)

Query: 11  SFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQ 70
           SF+ RYTLW+ EAL+ELP +FTITDP ISGHPIVFAS GFLKM+G+SR E+IGRNG++FQ
Sbjct: 19  SFSGRYTLWIKEALEELPHNFTITDPFISGHPIVFASLGFLKMTGYSREEVIGRNGKVFQ 78

Query: 71  GPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQ 130
           GP+TNRR+IMEIREAIREER ++V+LLNY+K G+PFWMLF M  VFGK+DG+ T+FVAVQ
Sbjct: 79  GPKTNRRSIMEIREAIREERSVQVSLLNYRKSGSPFWMLFHMCPVFGKDDGKVTNFVAVQ 138

Query: 131 VPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDRVLALDSDD--TGL 188
           VPI  R+H R         G  S      FGSCRREVC  + +  DR L ++ DD   GL
Sbjct: 139 VPISGREHHRK---KLRNVGDLSSDTSPTFGSCRREVCFGNFVCQDRALPVECDDDEQGL 195

Query: 189 EIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLG 248
           E  + CEAS+ EK KA  AI+N+LS+L HYS+L+GRLVCGKR  L G+  +SSSL ISLG
Sbjct: 196 EDWEQCEASESEKLKATEAINNVLSILVHYSELSGRLVCGKRYCLRGVDCLSSSLVISLG 255

Query: 249 RIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQ 280
           RIKQSFVL +P LPDMP++YASDAFL LTG +
Sbjct: 256 RIKQSFVLTNPCLPDMPIIYASDAFLTLTGYK 287

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449434827|ref|XP_004135197.1| PREDICTED: protein TWIN LOV 1-like [Cucumis sativus]

 Score =  346 bits (888), Expect = 6e-93,   Method: Compositional matrix adjust.
 Identities = 168/280 (60%), Positives = 210/280 (75%), Gaps = 13/280 (4%)

Query: 1   MDSQLGLIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAE 60
           M+  LGLIEQS N+RY+LWV EAL++L D+FTITDP I+GHPIVF S GFLKM+G+++ E
Sbjct: 1   MELPLGLIEQSLNSRYSLWVREALNDLSDNFTITDPCIAGHPIVFVSPGFLKMTGYTKEE 60

Query: 61  IIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKED 120
           +IG+NG+MFQGP T+R ++M IREA+REE+ I++NLLNY+KDGTPFW+ F+M+ VF KED
Sbjct: 61  VIGKNGKMFQGPETSRSSVMLIREAVREEKEIQINLLNYRKDGTPFWVFFQMTPVFSKED 120

Query: 121 GRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDRVLA 180
           G+  HFV VQVPI+        G   S             GSCRRE+ SDS+ +LD  L 
Sbjct: 121 GQIIHFVGVQVPILKNSRKSRCGACKS-----------FLGSCRRELMSDSISELDCTLN 169

Query: 181 LDS--DDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGF 238
            DS  D   +EIE+ CEA D EK++AA AI NIL VLTH+S++TG LVC +RCSLP +G 
Sbjct: 170 RDSQPDSNRVEIEEPCEACDDEKQRAAIAISNILFVLTHHSEVTGGLVCERRCSLPRVGI 229

Query: 239 ISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTG 278
           + SSL  SL RIKQSFVL DP+LPDMP+VYASD FLKLTG
Sbjct: 230 LCSSLNTSLNRIKQSFVLTDPNLPDMPIVYASDEFLKLTG 269

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	289
TAIR|locus:2058852	399	PLPB "PAS/LOV PROTEIN C" [Arab	0.923	0.669	0.591	4.2e-79
TAIR|locus:2155821	915	PHOT2 "phototropin 2" [Arabido	0.425	0.134	0.378	3.5e-23
UNIPROTKB|Q2QYY8	921	PHOT1A "Phototropin-1A" [Oryza	0.380	0.119	0.360	5.9e-23
UNIPROTKB|Q2RBR1	921	PHOT1B "Phototropin-1B" [Oryza	0.380	0.119	0.360	7.5e-23
TAIR|locus:2102674	996	PHOT1 "phototropin 1" [Arabido	0.636	0.184	0.277	4.6e-21
UNIPROTKB|Q9ST27	907	PHOT2 "Phototropin-2" [Oryza s	0.456	0.145	0.308	5.8e-21
UNIPROTKB|Q8H935	963	Vfphot1a "Phototropin" [Vicia	0.370	0.111	0.361	4.9e-13
UNIPROTKB|G4NFS7	961	MGG_08735 "Uncharacterized pro	0.359	0.108	0.371	5.5e-12
UNIPROTKB|Q887E8	763	PSPTO_1348 "Sensory box/GGDEF	0.370	0.140	0.336	1.1e-06
UNIPROTKB|F1SHB2	642	KCNH3 "Uncharacterized protein	0.519	0.233	0.267	1.5e-06

TAIR|locus:2058852 PLPB "PAS/LOV PROTEIN C" [Arabidopsis thaliana (taxid:3702)]

 Score = 795 (284.9 bits), Expect = 4.2e-79, P = 4.2e-79
 Identities = 161/272 (59%), Positives = 195/272 (71%)

Query:     9 EQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRM 68
             E SF+ RYTLW+ EAL+ELP +FTITDP ISGHPIVFAS GFLKM+G+SR E+IGRNG++
Sbjct:    17 EDSFSGRYTLWIKEALEELPHNFTITDPFISGHPIVFASLGFLKMTGYSREEVIGRNGKV 76

Query:    69 FQGPRTNXXXXXXXXXXXXXXXXXXVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVA 128
             FQGP+TN                  V+LLNY+K G+PFWMLF M  VFGK+DG+ T+FVA
Sbjct:    77 FQGPKTNRRSIMEIREAIREERSVQVSLLNYRKSGSPFWMLFHMCPVFGKDDGKVTNFVA 136

Query:   129 VQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDRVLAL--DSDDT 186
             VQVPI  R+H R    +    G  S      FGSCRREVC  + +  DR L +  D D+ 
Sbjct:   137 VQVPISGREHHRKKLRNV---GDLSSDTSPTFGSCRREVCFGNFVCQDRALPVECDDDEQ 193

Query:   187 GLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYIS 246
             GLE  + CEAS+ EK KA  AI+N+LS+L HYS+L+GRLVCGKR  L G+  +SSSL IS
Sbjct:   194 GLEDWEQCEASESEKLKATEAINNVLSILVHYSELSGRLVCGKRYCLRGVDCLSSSLVIS 253

Query:   247 LGRIKQSFVLIDPHLPDMPMVYASDAFLKLTG 278
             LGRIKQSFVL +P LPDMP++YASDAFL LTG
Sbjct:   254 LGRIKQSFVLTNPCLPDMPIIYASDAFLTLTG 285

GO:0000155 "phosphorelay sensor kinase activity" evidence=IEA

GO:0000160 "phosphorelay signal transduction system" evidence=IEA

GO:0004871 "signal transducer activity" evidence=IEA;ISS

GO:0005886 "plasma membrane" evidence=ISM

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA;ISS

GO:0006468 "protein phosphorylation" evidence=IEA

GO:0007165 "signal transduction" evidence=IEA;ISS

GO:0023014 "signal transduction by phosphorylation" evidence=IEA

GO:0010155 "regulation of proton transport" evidence=RCA

GO:0046777 "protein autophosphorylation" evidence=RCA

TAIR|locus:2155821 PHOT2 "phototropin 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 203 (76.5 bits), Expect = 3.5e-23, Sum P(2) = 3.5e-23
 Identities = 50/132 (37%), Positives = 70/132 (53%)

Query:    23 ALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNXXXXXXX 82
             AL  L  +F ++D +    PIV+AS GF  M+G+S  EI+GRN R  QGP T+       
Sbjct:   127 ALSTLQQTFVVSDATQPHCPIVYASSGFFTMTGYSSKEIVGRNCRFLQGPDTDKNEVAKI 186

Query:    83 XXXXXXXXXXXVNLLNYKKDGTPFWMLFKMSLVFGKED-GRATHFVAVQVPI------VS 135
                          LLNYKKDGTPFW L  ++ +  K+D G    F+ +QV +      V+
Sbjct:   187 RDCVKNGKSYCGRLLNYKKDGTPFWNLLTVTPI--KDDQGNTIKFIGMQVEVSKYTEGVN 244

Query:   136 RKHMRNSGMSYS 147
              K +R +G+S S
Sbjct:   245 DKALRPNGLSKS 256

GO:0000155 "phosphorelay sensor kinase activity" evidence=IEA

GO:0000160 "phosphorelay signal transduction system" evidence=IEA

GO:0004672 "protein kinase activity" evidence=IEA

GO:0004674 "protein serine/threonine kinase activity" evidence=IEA;IMP;IDA

GO:0004713 "protein tyrosine kinase activity" evidence=IEA

GO:0004871 "signal transducer activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005886 "plasma membrane" evidence=ISM;IDA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0006468 "protein phosphorylation" evidence=IEA

GO:0007165 "signal transduction" evidence=IEA

GO:0016301 "kinase activity" evidence=ISS

GO:0016772 "transferase activity, transferring phosphorus-containing groups" evidence=IEA

GO:0009638 "phototropism" evidence=IGI;IMP

GO:0010118 "stomatal movement" evidence=IGI;IMP

GO:0009902 "chloroplast relocation" evidence=RCA;TAS

GO:0016020 "membrane" evidence=ISS

GO:0009637 "response to blue light" evidence=IGI;RCA

GO:0010181 "FMN binding" evidence=IDA;TAS

GO:0046777 "protein autophosphorylation" evidence=RCA;TAS

GO:0005794 "Golgi apparatus" evidence=IDA

GO:0009882 "blue light photoreceptor activity" evidence=IMP

GO:0010362 "negative regulation of anion channel activity by blue light" evidence=IMP

GO:0042802 "identical protein binding" evidence=IPI

GO:0000023 "maltose metabolic process" evidence=RCA

GO:0006364 "rRNA processing" evidence=RCA

GO:0009644 "response to high light intensity" evidence=RCA

GO:0009744 "response to sucrose stimulus" evidence=RCA

GO:0010027 "thylakoid membrane organization" evidence=RCA

GO:0010103 "stomatal complex morphogenesis" evidence=RCA

GO:0010114 "response to red light" evidence=RCA

GO:0010155 "regulation of proton transport" evidence=RCA

GO:0010207 "photosystem II assembly" evidence=RCA

GO:0010218 "response to far red light" evidence=RCA

GO:0016556 "mRNA modification" evidence=RCA

GO:0019252 "starch biosynthetic process" evidence=RCA

GO:0019761 "glucosinolate biosynthetic process" evidence=RCA

GO:0034660 "ncRNA metabolic process" evidence=RCA

GO:0035304 "regulation of protein dephosphorylation" evidence=RCA

GO:0042793 "transcription from plastid promoter" evidence=RCA

GO:0043085 "positive regulation of catalytic activity" evidence=RCA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=RCA

UNIPROTKB|Q2QYY8 PHOT1A "Phototropin-1A" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 200 (75.5 bits), Expect = 5.9e-23, Sum P(2) = 5.9e-23
 Identities = 40/111 (36%), Positives = 59/111 (53%)

Query:    23 ALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNXXXXXXX 82
             AL     +F ++D +   HPI++AS GF  M+G++  E++GRN R  QG  T+       
Sbjct:   130 ALSAFQQTFVVSDATHPNHPIMYASAGFFNMTGYTSKEVVGRNCRFLQGSGTDPHEIDKI 189

Query:    83 XXXXXXXXXXXVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPI 133
                          +LNYKKDGTPFW L  ++ +   EDGR   F+ +QV +
Sbjct:   190 RQSLANGSNYCGRILNYKKDGTPFWNLLTIAPI-KDEDGRLLKFIGMQVEV 239

GO:0009785 "blue light signaling pathway" evidence=IDA

GO:0009882 "blue light photoreceptor activity" evidence=IDA

UNIPROTKB|Q2RBR1 PHOT1B "Phototropin-1B" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 199 (75.1 bits), Expect = 7.5e-23, Sum P(2) = 7.5e-23
 Identities = 40/111 (36%), Positives = 59/111 (53%)

Query:    23 ALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNXXXXXXX 82
             AL     +F ++D +   HPI++AS GF  M+G++  E++GRN R  QG  T+       
Sbjct:   130 ALSVFQQTFVVSDATHPNHPIMYASAGFFNMTGYTSKEVVGRNCRFLQGSGTDPHEIDKI 189

Query:    83 XXXXXXXXXXXVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPI 133
                          +LNYKKDGTPFW L  ++ +   EDGR   F+ +QV +
Sbjct:   190 RQSLANGSNYCGRILNYKKDGTPFWNLLTIAPI-KDEDGRLLKFIGMQVEV 239

GO:0009785 "blue light signaling pathway" evidence=IDA

GO:0009882 "blue light photoreceptor activity" evidence=IDA

TAIR|locus:2102674 PHOT1 "phototropin 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 196 (74.1 bits), Expect = 4.6e-21, Sum P(2) = 4.6e-21
 Identities = 55/198 (27%), Positives = 95/198 (47%)

Query:    22 EALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNXXXXXX 81
             +AL     +F ++D +   +PI++AS GF  M+G++  E++GRN R  QG  T+      
Sbjct:   190 DALSTFQQTFVVSDATKPDYPIMYASAGFFNMTGYTSKEVVGRNCRFLQGSGTDADELAK 249

Query:    82 XXXXXXXXXXXXVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRN 141
                           +LNYKKDGT FW L  ++ +   E G+   F+ +QV +   KH   
Sbjct:   250 IRETLAAGNNYCGRILNYKKDGTSFWNLLTIAPI-KDESGKVLKFIGMQVEV--SKHTEG 306

Query:   142 SGMSYSEDGGGSRLRE--IVFGSCRREVCSDSLLDL----DRVLALDSDDTGLE-IEDSC 194
             +        G   L E  I + + ++++ ++S+ +L     R  AL S+ T L       
Sbjct:   307 AKEKALRPNG---LPESLIRYDARQKDMATNSVTELVEAVKRPRAL-SESTNLHPFMTKS 362

Query:   195 EASDLEKRKAATAIDNIL 212
             E+ +L K+ A    +N++
Sbjct:   363 ESDELPKKPARRMSENVV 380

GO:0000160 "phosphorelay signal transduction system" evidence=IEA

GO:0005886 "plasma membrane" evidence=ISM

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0006468 "protein phosphorylation" evidence=IEA

GO:0007165 "signal transduction" evidence=IEA

GO:0016301 "kinase activity" evidence=ISS

GO:0005515 "protein binding" evidence=IPI

GO:0009903 "chloroplast avoidance movement" evidence=IMP

GO:0009904 "chloroplast accumulation movement" evidence=IMP

GO:0010119 "regulation of stomatal movement" evidence=IMP

GO:0005737 "cytoplasm" evidence=IDA

GO:0009898 "internal side of plasma membrane" evidence=IDA

GO:0046777 "protein autophosphorylation" evidence=RCA;IDA;TAS

GO:0005773 "vacuole" evidence=IDA

GO:0009637 "response to blue light" evidence=IGI;RCA

GO:0010155 "regulation of proton transport" evidence=IGI;RCA

GO:0010181 "FMN binding" evidence=IDA;TAS

GO:0010362 "negative regulation of anion channel activity by blue light" evidence=IMP

GO:0042802 "identical protein binding" evidence=IPI

GO:0009986 "cell surface" evidence=IDA

GO:0009644 "response to high light intensity" evidence=RCA

GO:0009744 "response to sucrose stimulus" evidence=RCA

GO:0010114 "response to red light" evidence=RCA

GO:0010218 "response to far red light" evidence=RCA

GO:0004672 "protein kinase activity" evidence=IDA

GO:0009638 "phototropism" evidence=IMP

GO:0004674 "protein serine/threonine kinase activity" evidence=IDA

GO:0009882 "blue light photoreceptor activity" evidence=IDA

UNIPROTKB|Q9ST27 PHOT2 "Phototropin-2" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 196 (74.1 bits), Expect = 5.8e-21, Sum P(2) = 5.8e-21
 Identities = 41/133 (30%), Positives = 67/133 (50%)

Query:     1 MDSQLGLIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAE 60
             +D  +G        R +  + +AL  L  +F ++D +    PI++AS GF  M+G+S  E
Sbjct:    74 VDGGVGRASHDSLPRVSQELKDALSSLQQTFVVSDATRPDCPIIYASEGFFTMTGYSPRE 133

Query:    61 IIGRNGRMFQGPRTNXXXXXXXXXXXXXXXXXXVNLLNYKKDGTPFWMLFKMSLVFGKED 120
             ++GRN R  QGP T+                    LLNY+KDG PFW L  ++ +   ++
Sbjct:   134 VVGRNCRFLQGPDTDAAEVAKIRDAVKHGRSFCGRLLNYRKDGAPFWNLLTVTPI-RDDN 192

Query:   121 GRATHFVAVQVPI 133
             G+   F+ +QV +
Sbjct:   193 GKVIKFIGMQVEV 205

GO:0009785 "blue light signaling pathway" evidence=IDA

GO:0009882 "blue light photoreceptor activity" evidence=IDA

UNIPROTKB|Q8H935 Vfphot1a "Phototropin" [Vicia faba (taxid:3906)]

 Score = 193 (73.0 bits), Expect = 4.9e-13, P = 4.9e-13
 Identities = 39/108 (36%), Positives = 59/108 (54%)

Query:    24 LDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNXXXXXXXX 83
             L+ +  +F ITDP +  +PI+FAS  FL+++ +SR EI+GRN R  QGP T+        
Sbjct:   441 LERIEKNFVITDPRLPDNPIIFASDSFLELTEYSREEILGRNCRFLQGPETDPATVKKIR 500

Query:    84 XXXXXXXXXXVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQV 131
                       V L+NY K G  FW LF +  +  ++ G   +F+ VQ+
Sbjct:   501 YAIDNQTEVTVQLINYTKTGKKFWNLFHLQPMRDQK-GEVQYFIGVQL 547

GO:0005515 "protein binding" evidence=IPI

UNIPROTKB|G4NFS7 MGG_08735 "Uncharacterized protein" [Magnaporthe oryzae 70-15 (taxid:242507)]

 Score = 186 (70.5 bits), Expect = 5.5e-12, P = 5.5e-12
 Identities = 39/105 (37%), Positives = 59/105 (56%)

Query:    27 LPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNXXXXXXXXXXX 86
             L DSFT+TDP ++ +PI+FAS GF  ++G   ++II +N R+ QG +T+           
Sbjct:   612 LGDSFTMTDPRLADNPIIFASDGFASLTGHPLSDIISKNCRVLQGKQTDKQAVARIRAAV 671

Query:    87 XXXXXXXVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQV 131
                      +LNYKK+G PFW L  ++ +F  E G+   F+  QV
Sbjct:   672 REETEVVELVLNYKKNGDPFWNLLYIAPLFD-EQGQLAFFIGGQV 715

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|Q887E8 PSPTO_1348 "Sensory box/GGDEF domain/EAL domain protein" [Pseudomonas syringae pv. tomato str. DC3000 (taxid:223283)]

 Score = 141 (54.7 bits), Expect = 1.1e-06, P = 1.1e-06
 Identities = 38/113 (33%), Positives = 58/113 (51%)

Query:    29 DSFTITD--P-SISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNXXXXXXXXXX 85
             D+  IT+  P  + G  IV+ +  FL ++GF+  E+IGR  R+ Q   T+          
Sbjct:   185 DAILITEAEPIDLPGPRIVYCNPAFLAITGFTEEEVIGRTPRILQCEDTSRETLDVIREA 244

Query:    86 XXXXXXXXVNLLNYKKDGTPFWMLFKMSLV-FGKEDGRATHFVAVQVPIVSRK 137
                     V L+N +KDG+ FW+  ++S+V    E G  TH+V+VQ  I  RK
Sbjct:   245 LTHWRPVEVELINTRKDGSQFWV--ELSIVPVANEKGWFTHWVSVQRDITERK 295

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|F1SHB2 KCNH3 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 139 (54.0 bits), Expect = 1.5e-06, P = 1.5e-06
 Identities = 42/157 (26%), Positives = 65/157 (41%)

Query:     1 MDSQLGLIEQSFNNRYTLWVHEALDELPDSFTITDPSISG-HPIVFASRGFLKMSGFSRA 59
             M +  GL+     N +   +    D    +F + +  ++G  P+V+ S GF  ++GFSRA
Sbjct:     1 MPAMRGLLAPQ--NTFLDTIATRFDGTHSNFVLGNAQVAGLFPVVYCSDGFCDLTGFSRA 58

Query:    60 EIIGRNGR--MFQGPRTNXXXXXXXXXXXXXXXXXXVNLLNYKKDGTPFWMLFKMSLVFG 117
             E++ R        GP T+                    L+ Y+K G PFW L  + +   
Sbjct:    59 EVMQRGCACSFLYGPDTSELVRQQIRKALDEHKEFKAELILYRKSGLPFWCLLDV-IPIK 117

Query:   118 KEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSR 154
              E G    F+     I   K+ R    S+ E GGG R
Sbjct:   118 NEKGEVALFLVSHKDISDTKN-RGGPDSWKERGGGRR 153

GO:0016021 "integral to membrane" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0005249 "voltage-gated potassium channel activity" evidence=IEA

GO:0000155 "phosphorelay sensor kinase activity" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
O64511	TLOV1_ARATH	No assigned EC number	0.6397	0.9238	0.6691	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	2.7.13	LOW CONFIDENCE prediction!
3rd Layer	2.7.13.3	LOW CONFIDENCE prediction!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	289
PRK13558	665	PRK13558, PRK13558, bacterio-opsin activator; Prov	1e-30
PRK13557	540	PRK13557, PRK13557, histidine kinase; Provisional	2e-27
PRK13559	361	PRK13559, PRK13559, hypothetical protein; Provisio	4e-27
pfam13426	101	pfam13426, PAS_9, PAS domain	1e-21
TIGR02938	494	TIGR02938, nifL_nitrog, nitrogen fixation negative	6e-08
TIGR00229	124	TIGR00229, sensory_box, PAS domain S-box	4e-07
COG2202	232	COG2202, AtoS, FOG: PAS/PAC domain [Signal transdu	5e-04
cd00130	103	cd00130, PAS, PAS domain; PAS motifs appear in arc	8e-04
PRK13559	361	PRK13559, PRK13559, hypothetical protein; Provisio	0.001
pfam00989	113	pfam00989, PAS, PAS fold	0.004

>gnl|CDD|237426 PRK13558, PRK13558, bacterio-opsin activator; Provisional

 Score =  120 bits (303), Expect = 1e-30
 Identities = 51/137 (37%), Positives = 75/137 (54%), Gaps = 13/137 (9%)

Query: 1   MDSQLGLIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAE 60
           ++S   L E+            ALDE P   TI D ++   P+++ +  F +++G+S  E
Sbjct: 143 VESDRRLKER------------ALDEAPVGITIADATLPDEPLIYINDAFERITGYSPDE 190

Query: 61  IIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKED 120
           ++GRN R  QG  TN   + E+REAI EERP  V L NY+KDG+ FW    ++ +   ED
Sbjct: 191 VLGRNCRFLQGEDTNEERVAELREAIDEERPTSVELRNYRKDGSTFWNQVDIAPIRD-ED 249

Query: 121 GRATHFVAVQVPIVSRK 137
           G  TH+V  Q  +  RK
Sbjct: 250 GTVTHYVGFQTDVTERK 266

Length = 665

>gnl|CDD|237425 PRK13557, PRK13557, histidine kinase; Provisional

 Score =  110 bits (278), Expect = 2e-27
 Identities = 46/106 (43%), Positives = 68/106 (64%), Gaps = 1/106 (0%)

Query: 32  TITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERP 91
            +TDP+   +PIVFA+R FL+M+G++  EIIG N R  QGP T+R T+ E+R+AI E R 
Sbjct: 44  IVTDPNQPDNPIVFANRAFLEMTGYAAEEIIGNNCRFLQGPETDRATVAEVRDAIAERRE 103

Query: 92  IEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRK 137
           I   +LNY+KDG+ FW    +S V+  + G   +F   Q+ +  R+
Sbjct: 104 IATEILNYRKDGSSFWNALFVSPVY-NDAGDLVYFFGSQLDVSRRR 148

Length = 540

>gnl|CDD|237427 PRK13559, PRK13559, hypothetical protein; Provisional

 Score =  107 bits (270), Expect = 4e-27
 Identities = 45/98 (45%), Positives = 60/98 (61%), Gaps = 1/98 (1%)

Query: 33  ITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPI 92
           ITDP     PIV A++ FL ++G++  E++GRN R  QG  T+   + +IR AI  ER I
Sbjct: 58  ITDPHQPDLPIVLANQAFLDLTGYAAEEVVGRNCRFLQGAATDPIAVAKIRAAIAAEREI 117

Query: 93  EVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQ 130
            V LLNY+KDG PFW    +  V+G EDGR  +F   Q
Sbjct: 118 VVELLNYRKDGEPFWNALHLGPVYG-EDGRLLYFFGSQ 154

Length = 361

>gnl|CDD|222120 pfam13426, PAS_9, PAS domain

 Score = 87.0 bits (216), Expect = 1e-21
 Identities = 33/103 (32%), Positives = 52/103 (50%), Gaps = 4/103 (3%)

Query: 31  FTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREER 90
             + DP      IV+A+   L++ G++R E++G++ R   GP  +   +  +REA+R   
Sbjct: 1   ILVLDPD---GRIVYANDAALRLLGYTREELLGKSIRDLFGPGDDEEAVARLREALRNGG 57

Query: 91  PIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPI 133
            +EV L   +KDG PF +L   S V   EDG     V +   I
Sbjct: 58  EVEVELELRRKDGEPFPVLVSASPVRD-EDGEVVGIVGILRDI 99

Length = 101

>gnl|CDD|131984 TIGR02938, nifL_nitrog, nitrogen fixation negative regulator NifL

 Score = 53.0 bits (127), Expect = 6e-08
 Identities = 29/106 (27%), Positives = 56/106 (52%), Gaps = 4/106 (3%)

Query: 22  EALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIME 81
           + +D+ P + +ITD   +   I++A+  F +++G+++ EIIG+N  +     T       
Sbjct: 8   QTVDQAPLAISITDLKAN---ILYANDAFTRITGYTKEEIIGKNESVLSNHTTPPEVYQA 64

Query: 82  IREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFV 127
           +  ++ E++P    LLN +KDG  +     ++ V   E G  THF+
Sbjct: 65  LWGSLAEQKPWAGKLLNRRKDGELYLAELTVAPVL-NEAGETTHFL 109

NifL is a modulator of the nitrogen fixation positive regulator protein NifA, and is therefore a negative regulator. It binds NifA. NifA and NifL are encoded by adjacent genes [Central intermediary metabolism, Nitrogen fixation, Regulatory functions, Protein interactions]. Length = 494

>gnl|CDD|232884 TIGR00229, sensory_box, PAS domain S-box

 Score = 47.7 bits (114), Expect = 4e-07
 Identities = 29/117 (24%), Positives = 51/117 (43%), Gaps = 8/117 (6%)

Query: 23  ALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIME- 81
             +  PD+  + D  + G+ I++ +  F ++ G+S  E+IGRN      P  +R  + E 
Sbjct: 8   IFESSPDAIIVID--LEGN-ILYVNPAFEEIFGYSAEELIGRNVLELI-PEEDREEVRER 63

Query: 82  IREAIREERPIEVNLLNYK-KDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRK 137
           I   +  ER         + KDG+  W+   +S +    +G     V +   I  RK
Sbjct: 64  IERRLEGEREPVSEERRVRRKDGSEIWVEVSVSPIR--TNGGELGVVGIVRDITERK 118

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]. Length = 124

>gnl|CDD|225112 COG2202, AtoS, FOG: PAS/PAC domain [Signal transduction mechanisms]

 Score = 40.2 bits (92), Expect = 5e-04
 Identities = 26/124 (20%), Positives = 45/124 (36%), Gaps = 6/124 (4%)

Query: 19  WVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRT 78
            +   L+  PD   + D       I++A+    ++ G+S  E +GR       P    R 
Sbjct: 113 RLRALLEASPDGIWVLDE---DGRILYANPAAEELLGYSPEEELGRGLSDLIHPEDEERR 169

Query: 79  IMEIREAIREERPIEVN--LLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSR 136
            +E+  A+ E R   +       +KDG          +   ++DG     V +   I  R
Sbjct: 170 ELELARALAEGRGGPLEIEYRVRRKDGERVR-WILSRISPVRDDGEIVGVVGIARDITER 228

Query: 137 KHMR 140
           K   
Sbjct: 229 KQAE 232

Length = 232

>gnl|CDD|238075 cd00130, PAS, PAS domain; PAS motifs appear in archaea, eubacteria and eukarya

 Score = 38.0 bits (88), Expect = 8e-04
 Identities = 22/107 (20%), Positives = 44/107 (41%), Gaps = 4/107 (3%)

Query: 27  LPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAI 86
           LPD   + D       I++A+    ++ G+S  E+IG++      P         +   +
Sbjct: 1   LPDGVIVLDLD---GRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLL 57

Query: 87  REERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPI 133
               P+ + +   +KDG+  W+L  ++ +   E G     + V   I
Sbjct: 58  SGGEPVTLEVRLRRKDGSVIWVLVSLTPIRD-EGGEVIGLLGVVRDI 103

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. Length = 103

>gnl|CDD|237427 PRK13559, PRK13559, hypothetical protein; Provisional

 Score = 39.8 bits (93), Expect = 0.001
 Identities = 14/30 (46%), Positives = 21/30 (70%)

Query: 249 RIKQSFVLIDPHLPDMPMVYASDAFLKLTG 278
           + + +  + DPH PD+P+V A+ AFL LTG
Sbjct: 51  QTRMAMCITDPHQPDLPIVLANQAFLDLTG 80

Length = 361

>gnl|CDD|216228 pfam00989, PAS, PAS fold

 Score = 36.2 bits (84), Expect = 0.004
 Identities = 19/90 (21%), Positives = 33/90 (36%), Gaps = 6/90 (6%)

Query: 43  IVFASRGFLKMSGFSRAEIIGRNGRMF---QGPRTNRRTIMEIREAIREERPIEVNLLNY 99
           I++ +    ++ G SR E+IG++                + +      E R  EV+    
Sbjct: 23  ILYVNAAAEELLGLSREEVIGKSLLDLIPEDDDAEVAELLRQALLQGEESRGFEVSFR-- 80

Query: 100 KKDGTPFWMLFKMSLVFGKEDGRATHFVAV 129
             DG P  +  + S V     G    F+ V
Sbjct: 81  VPDGRPRHVEVRASPVRD-AGGEVRGFLGV 109

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. Length = 113

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	289
PRK13560	807	hypothetical protein; Provisional	99.83
TIGR02040	442	PpsR-CrtJ transcriptional regulator PpsR. This mod	99.83
TIGR02938	494	nifL_nitrog nitrogen fixation negative regulator N	99.79
PRK09776	1092	putative diguanylate cyclase; Provisional	99.78
PF13426	104	PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_	99.77
TIGR02040	442	PpsR-CrtJ transcriptional regulator PpsR. This mod	99.73
PRK09776	1092	putative diguanylate cyclase; Provisional	99.73
PRK13560	807	hypothetical protein; Provisional	99.7
PF08448	110	PAS_4: PAS fold; InterPro: IPR013656 The PAS fold	99.68
PRK11359	799	cyclic-di-GMP phosphodiesterase; Provisional	99.68
PF00989	113	PAS: PAS fold; InterPro: IPR013767 PAS domains are	99.68
PRK11091	779	aerobic respiration control sensor protein ArcB; P	99.56
PRK13559	361	hypothetical protein; Provisional	99.55
PRK13557	540	histidine kinase; Provisional	99.53
PRK10060	663	RNase II stability modulator; Provisional	99.52
PRK13558	665	bacterio-opsin activator; Provisional	99.44
TIGR00229	124	sensory_box PAS domain S-box. The PAS domain was p	99.35
PF08447	91	PAS_3: PAS fold; InterPro: IPR013655 The PAS fold	99.28
PRK11359	799	cyclic-di-GMP phosphodiesterase; Provisional	99.23
cd00130	103	PAS PAS domain; PAS motifs appear in archaea, euba	99.08
PRK11360	607	sensory histidine kinase AtoS; Provisional	99.01
PF12860	115	PAS_7: PAS fold	98.99
TIGR02966	333	phoR_proteo phosphate regulon sensor kinase PhoR.	98.98
PRK11073	348	glnL nitrogen regulation protein NR(II); Provision	98.94
PF13596	106	PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.	98.92
PF14598	111	PAS_11: PAS domain; PDB: 1P97_A 3F1O_A 2A24_A 3H7W	98.89
KOG0501	971	consensus K+-channel KCNQ [Inorganic ion transport	98.76
COG5002	459	VicK Signal transduction histidine kinase [Signal	98.74
PF00989	113	PAS: PAS fold; InterPro: IPR013767 PAS domains are	98.64
COG3829	560	RocR Transcriptional regulator containing PAS, AAA	98.61
PRK11006	430	phoR phosphate regulon sensor protein; Provisional	98.61
TIGR02938	494	nifL_nitrog nitrogen fixation negative regulator N	98.57
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	98.52
PF13426	104	PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_	98.48
PF13188	64	PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.	98.41
COG2202	232	AtoS FOG: PAS/PAC domain [Signal transduction mech	98.32
PRK11086	542	sensory histidine kinase DcuS; Provisional	98.3
PRK10060	663	RNase II stability modulator; Provisional	98.21
COG3829	560	RocR Transcriptional regulator containing PAS, AAA	98.17
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	98.12
PF13188	64	PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.	98.1
KOG1229	775	consensus 3'5'-cyclic nucleotide phosphodiesterase	98.07
PRK13557	540	histidine kinase; Provisional	97.91
PF08448	110	PAS_4: PAS fold; InterPro: IPR013656 The PAS fold	97.89
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	97.86
PRK15053	545	dpiB sensor histidine kinase DpiB; Provisional	97.83
COG3290	537	CitA Signal transduction histidine kinase regulati	97.78
PRK13559	361	hypothetical protein; Provisional	97.75
COG5000	712	NtrY Signal transduction histidine kinase involved	97.73
PF08670	148	MEKHLA: MEKHLA domain; InterPro: IPR013978 The MEK	97.72
PRK09959	1197	hybrid sensory histidine kinase in two-component r	97.67
KOG3558	768	consensus Hypoxia-inducible factor 1/Neuronal PAS	97.59
KOG3558	768	consensus Hypoxia-inducible factor 1/Neuronal PAS	97.53
smart00091	67	PAS PAS domain. PAS motifs appear in archaea, euba	97.48
COG3852	363	NtrB Signal transduction histidine kinase, nitroge	97.4
PRK11006	430	phoR phosphate regulon sensor protein; Provisional	97.38
PRK11091	779	aerobic respiration control sensor protein ArcB; P	97.32
TIGR00229	124	sensory_box PAS domain S-box. The PAS domain was p	97.3
TIGR02373	124	photo_yellow photoactive yellow protein. Members o	97.17
COG2461	409	Uncharacterized conserved protein [Function unknow	97.14
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	97.05
KOG1229	775	consensus 3'5'-cyclic nucleotide phosphodiesterase	96.99
cd00130	103	PAS PAS domain; PAS motifs appear in archaea, euba	96.98
COG2202	232	AtoS FOG: PAS/PAC domain [Signal transduction mech	96.98
PF12860	115	PAS_7: PAS fold	96.89
COG3283	511	TyrR Transcriptional regulator of aromatic amino a	96.62
smart00091	67	PAS PAS domain. PAS motifs appear in archaea, euba	96.57
PRK13558	665	bacterio-opsin activator; Provisional	96.55
PRK11360	607	sensory histidine kinase AtoS; Provisional	96.32
smart00086	43	PAC Motif C-terminal to PAS motifs (likely to cont	96.28
PF07310	137	PAS_5: PAS domain; InterPro: IPR009922 This family	95.94
KOG3560	712	consensus Aryl-hydrocarbon receptor [Transcription	95.43
PRK15053	545	dpiB sensor histidine kinase DpiB; Provisional	95.08
KOG3559	598	consensus Transcriptional regulator SIM1 [Transcri	95.0
KOG0501	971	consensus K+-channel KCNQ [Inorganic ion transport	94.85
PRK11086	542	sensory histidine kinase DcuS; Provisional	94.03
TIGR02373	124	photo_yellow photoactive yellow protein. Members o	93.84
PF08670	148	MEKHLA: MEKHLA domain; InterPro: IPR013978 The MEK	93.21
PF13596	106	PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.	93.07
KOG3561	803	consensus Aryl-hydrocarbon receptor nuclear transl	92.98
COG5002	459	VicK Signal transduction histidine kinase [Signal	92.66
PRK10841	924	hybrid sensory kinase in two-component regulatory	92.34
COG3290	537	CitA Signal transduction histidine kinase regulati	91.48
KOG3559	598	consensus Transcriptional regulator SIM1 [Transcri	91.28
PF14598	111	PAS_11: PAS domain; PDB: 1P97_A 3F1O_A 2A24_A 3H7W	91.14
COG3283	511	TyrR Transcriptional regulator of aromatic amino a	90.96
PF08446	110	PAS_2: PAS fold; InterPro: IPR013654 The PAS fold	86.96
PRK09959	1197	hybrid sensory histidine kinase in two-component r	85.84
PRK10618	894	phosphotransfer intermediate protein in two-compon	84.2
KOG3561	803	consensus Aryl-hydrocarbon receptor nuclear transl	83.01
COG5388	209	Uncharacterized protein conserved in bacteria [Fun	82.31
KOG3753	1114	consensus Circadian clock protein period [Signal t	81.16
COG5000	712	NtrY Signal transduction histidine kinase involved	80.9

>PRK13560 hypothetical protein; Provisional

Probab=99.83  E-value=3.4e-19  Score=167.20  Aligned_cols=181  Identities=14%  Similarity=0.123  Sum_probs=144.8

Q ss_pred             chHHHhhchHHHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHH
Q 022961            6 GLIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREA   85 (289)
Q Consensus         6 ~~~~~~l~~~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~   85 (289)
                      ++.++.+. +++++++.+++++|+++++.|.+   |+++++|+++++++||++++++|+++..+.++.............
T Consensus       193 k~ae~~l~-~~~~~l~~l~e~~~~~i~~~d~~---g~i~~~N~~~~~~~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~  268 (807)
T PRK13560        193 KRAEERID-EALHFLQQLLDNIADPAFWKDED---AKVFGCNDAACLACGFRREEIIGMSIHDFAPAQPADDYQEADAAK  268 (807)
T ss_pred             HHHHHHHH-HHHHHHHHHHhhCCCeEEEEcCC---CCEEEEhHHHHHHhCCCHHHHcCCcchhcCCcchhHHHHHHHHHH
Confidence            44455565 67789999999999999999999   999999999999999999999999988877654433333334445


Q ss_pred             HHhCCCeEEEEEEEecCCCEEEEEEEE--EEeecCCCCcEEEEEEEEecccccHHHHhcccccccCCCcchhhhhHHhhc
Q 022961           86 IREERPIEVNLLNYKKDGTPFWMLFKM--SLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSC  163 (289)
Q Consensus        86 ~~~~~~~~~e~~~~~~~g~~~~~~~~~--~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l~~~~~~~n~~~~~~~~~~~~  163 (289)
                      +..+.....+..+.+++|..+|+.+..  .|+.+ ..|.+.+++++++|||++|++|+++...                 
T Consensus       269 ~~~~~~~~~e~~~~~~dG~~~~~~~~~~~~~~~~-~~g~~~g~~~~~~DITerk~~e~~L~~s-----------------  330 (807)
T PRK13560        269 FDADGSQIIEAEFQNKDGRTRPVDVIFNHAEFDD-KENHCAGLVGAITDISGRRAAERELLEK-----------------  330 (807)
T ss_pred             hccCCceEEEEEEEcCCCCEEEEEEEecceEEEc-CCCCEEEEEEEEEechHHHHHHHHHHHH-----------------
Confidence            555666677888899999999776655  45567 7889999999999999999996654211                 


Q ss_pred             ccccccccceeccchhcccCCCCCCccccCccccHHHHHHHHHHhhHHHHhhhcccccccceecccccCCCCCCCcchhH
Q 022961          164 RREVCSDSLLDLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSL  243 (289)
Q Consensus       164 ~~~~~~~~l~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~~~~  243 (289)
                                                          ..                                        .+
T Consensus       331 ------------------------------------e~----------------------------------------~l  334 (807)
T PRK13560        331 ------------------------------------ED----------------------------------------ML  334 (807)
T ss_pred             ------------------------------------HH----------------------------------------HH
Confidence                                                00                                        04


Q ss_pred             HHHhhcccccEEEeCCCCCCCCEEEe-cHHHHHhhCCChHhHhhc
Q 022961          244 YISLGRIKQSFVLIDPHLPDMPMVYA-SDAFLKLTGAQIFTKITR  287 (289)
Q Consensus       244 ~~~~e~~~~~i~i~d~~~~~~~i~~v-N~~f~~~tGys~~E~~G~  287 (289)
                      ...++.++.++++.|.   +++|+++ |+++++++||+.+|++|+
T Consensus       335 ~~l~~~~~~~i~~~d~---~g~i~~~nn~~~~~~~G~~~~e~~g~  376 (807)
T PRK13560        335 RAIIEAAPIAAIGLDA---DGNICFVNNNAAERMLGWSAAEVMGK  376 (807)
T ss_pred             HHHHHhCcccEEEEcC---CCCEEEecCHHHHHHhCCCHHHHcCC
Confidence            5578888999999999   9999998 578888999999999996

>TIGR02040 PpsR-CrtJ transcriptional regulator PpsR

Probab=99.83  E-value=1.9e-19  Score=157.45  Aligned_cols=166  Identities=18%  Similarity=0.179  Sum_probs=126.4

Q ss_pred             HHHHHHHHHHhhCCCEEEEEeC-CCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeE
Q 022961           15 RYTLWVHEALDELPDSFTITDP-SISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIE   93 (289)
Q Consensus        15 ~~~~~l~~~~~~~~~~i~~~d~-~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~   93 (289)
                      ..+++++.++++++++++++|. +   |+++++|+++++++||++++++|+++..++++.+.......+......+....
T Consensus       130 ~~e~r~~~l~e~~~~~i~~~d~~~---g~i~~~N~a~~~l~G~~~~el~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~~~  206 (442)
T TIGR02040       130 EMETRYRVVLEVSSDAVLLVDMST---GRIVEANSAAAALLGGVGQSLVGRAFPQEFEGRRREELMLTLRNVRATGSAAP  206 (442)
T ss_pred             HHHHHHHHHHhhCCceEEEEECCC---CEEEEEcHHHHHHhCcCHHHHcCCCHHHhCCHHHHHHHHHHHHHHHhcCCCcc
Confidence            4567899999999999999997 7   99999999999999999999999998777776665555566666665555544


Q ss_pred             EEEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhcccccccCCCcchhhhhHHhhcccccccccce
Q 022961           94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLL  173 (289)
Q Consensus        94 ~e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l~~~~~~~n~~~~~~~~~~~~~~~~~~~~l~  173 (289)
                      .++.  .++|...| .+.+.++..  .+. ..+++..+|||++++.|+++                              
T Consensus       207 ~~~~--~~~~~~~~-~~~~~~~~~--~~~-~~~l~~~~dit~~~~~e~~~------------------------------  250 (442)
T TIGR02040       207 VRIL--LRRSQKRL-LVVVSVFRQ--DGE-SLFLCQLSPAGATQPVGDEL------------------------------  250 (442)
T ss_pred             eEEE--EcCCCeEE-EEEEEEEEe--CCc-eEEEEEEcccchhhhhhHHH------------------------------
Confidence            4443  34444444 345566654  333 35677889999988763321                              


Q ss_pred             eccchhcccCCCCCCccccCccccHHHHHHHHHHhhHHHHhhhcccccccceecccccCCCCCCCcchhHHHHhhccccc
Q 022961          174 DLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQS  253 (289)
Q Consensus       174 e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~  253 (289)
                                                ..                                        .+...++.++++
T Consensus       251 --------------------------~~----------------------------------------~~~~l~e~~~d~  264 (442)
T TIGR02040       251 --------------------------SE----------------------------------------NLARLYHEAPDA  264 (442)
T ss_pred             --------------------------HH----------------------------------------HHHHHHHhCCce
Confidence                                      00                                        156678999999


Q ss_pred             EEEeCCCCCCCCEEEecHHHHHhhCCC-hHhHhhcc
Q 022961          254 FVLIDPHLPDMPMVYASDAFLKLTGAQ-IFTKITRI  288 (289)
Q Consensus       254 i~i~d~~~~~~~i~~vN~~f~~~tGys-~~E~~G~~  288 (289)
                      |+++|.   +|+|+++|++|++++||+ .++++|+-
T Consensus       265 I~v~D~---~G~I~~~N~a~~~l~G~~~~~~l~G~~  297 (442)
T TIGR02040       265 IVFSDA---DGTIRGANEAFLELTDSSSLEAVRGRT  297 (442)
T ss_pred             EEEEcC---CCcEEehhHHHHHHhCCCChHHHcCCC
Confidence            999999   999999999999999997 67899973

This model represents the transcriptional regulator PpsR which is strictly associated with photosynthetic proteobacteria and found in photosynthetic operons. PpsR has been reported to be a repressor. These proteins contain a Helix-Turn_Helix motif of the "fis" type (pfam02954).

>TIGR02938 nifL_nitrog nitrogen fixation negative regulator NifL

Probab=99.79  E-value=2.3e-18  Score=152.74  Aligned_cols=170  Identities=22%  Similarity=0.384  Sum_probs=142.9

Q ss_pred             HHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEEEE
Q 022961           18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLL   97 (289)
Q Consensus        18 ~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~   97 (289)
                      +.++.++++++++++++|.+   |+++++|+++++++||++++++|++...+.++.........+...+..+..+..+..
T Consensus         4 ~~~~~i~~~~~~~i~~~d~~---g~~~~~N~~~~~~~G~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (494)
T TIGR02938         4 EAYRQTVDQAPLAISITDLK---ANILYANDAFTRITGYTKEEIIGKNESVLSNHTTPPEVYQALWGSLAEQKPWAGKLL   80 (494)
T ss_pred             HHHHHHHHhCCceEEEECCC---CcEEEEchhheeecCCCHHHHhCCCchhhcCCCCCHHHHHHHHHHHHhCCcccceee
Confidence            46889999999999999999   999999999999999999999999876666665566666666777777777777777


Q ss_pred             EEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhcccccccCCCcchhhhhHHhhcccccccccceeccc
Q 022961           98 NYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDR  177 (289)
Q Consensus        98 ~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l~~~~~~~n~~~~~~~~~~~~~~~~~~~~l~e~~~  177 (289)
                      ..+++|..+|+.....|+.+ .+|.+.+++++.+|||++|++++++...                               
T Consensus        81 ~~~~~g~~~~~~~~~~~~~~-~~g~~~~~~~~~~DIt~~k~~e~~l~~~-------------------------------  128 (494)
T TIGR02938        81 NRRKDGELYLAELTVAPVLN-EAGETTHFLGMHRDITELHRLEQVVANQ-------------------------------  128 (494)
T ss_pred             ccCCCccchhhheeeEEEEC-CCCCEEEEEEehhhhhHHHHHHHHHHHH-------------------------------
Confidence            78899999999999999998 8999999999999999999985543110                               


Q ss_pred             hhcccCCCCCCccccCccccHHHHHHHHHHhhHHHHhhhcccccccceecccccCCCCCCCcchhHHHHhhcccccEEEe
Q 022961          178 VLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQSFVLI  257 (289)
Q Consensus       178 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~i~i~  257 (289)
                                            ..                                        .+...++.++.++++.
T Consensus       129 ----------------------~~----------------------------------------~~~~~~~~~~~~i~~~  146 (494)
T TIGR02938       129 ----------------------KL----------------------------------------LIESVVDAAPVAFVLL  146 (494)
T ss_pred             ----------------------HH----------------------------------------HHHHHHhcccceEEEE
Confidence                                  00                                        0455778889999999


Q ss_pred             CCCCCCCCEEEecHHHHHhhCCChHhHhhc
Q 022961          258 DPHLPDMPMVYASDAFLKLTGAQIFTKITR  287 (289)
Q Consensus       258 d~~~~~~~i~~vN~~f~~~tGys~~E~~G~  287 (289)
                      |.   +++|+++|++|++++||...+..+.
T Consensus       147 d~---~~~i~~~N~~~~~~~g~~~~~~~~~  173 (494)
T TIGR02938       147 DP---TGRVILDNQEYKKLATDLRVKEPAH  173 (494)
T ss_pred             cC---CCCEEEechhHHHhhchhhhhHHHH
Confidence            99   9999999999999999998876653

NifL is a modulator of the nitrogen fixation positive regulator protein NifA, and is therefore a negative regulator. It binds NifA. NifA and NifL are encoded by adjacent genes.

>PRK09776 putative diguanylate cyclase; Provisional

Probab=99.78  E-value=5.4e-18  Score=163.97  Aligned_cols=180  Identities=16%  Similarity=0.145  Sum_probs=147.7

Q ss_pred             chHHHhhchHHHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCC-CCCccCCCCCHHHHHHHHH
Q 022961            6 GLIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRN-GRMFQGPRTNRRTIMEIRE   84 (289)
Q Consensus         6 ~~~~~~l~~~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~-~~~l~~~~~~~~~~~~~~~   84 (289)
                      ++.++.+. +.+++++.+++..+++++.+|.+   +.++++|+++++++||++++..+.. +....+|++.......+..
T Consensus       399 k~~e~~l~-~~~~~~~~~~~~~~~~i~~~d~~---~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~~p~d~~~~~~~~~~  474 (1092)
T PRK09776        399 KRTEQVNE-RLMERITLANEAGGIGIWEWDLK---PNIISWDKRMFELYEIPPHIKPTWQVWYACLHPEDRQRVEKEIRD  474 (1092)
T ss_pred             HHHHHHHH-HHHHHHHHHHHhcCceEEEEecC---CCeEeeCHHHHHHhCCCcccCCCHHHHHHhcCHhHHHHHHHHHHH
Confidence            34455554 66778899999999999999999   9999999999999999988844322 2334456655556666677


Q ss_pred             HHHhCCCeEEEEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhcccccccCCCcchhhhhHHhhcc
Q 022961           85 AIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCR  164 (289)
Q Consensus        85 ~~~~~~~~~~e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l~~~~~~~n~~~~~~~~~~~~~  164 (289)
                      ....+..+..+++..+++| ..|+.....|+.+ .+|.+.+++++.+|||++|++|+++...                  
T Consensus       475 ~~~~~~~~~~e~r~~~~dG-~~w~~~~~~~~~d-~~G~~~~~ig~~~DITerk~~e~~L~~~------------------  534 (1092)
T PRK09776        475 ALQGRSPFKLEFRIVVKDG-VRHIRALANRVLN-KDGEVERLLGINMDMTEVRQLNEALFQE------------------  534 (1092)
T ss_pred             HHhcCCCeeEEEEEEcCCc-eEEEEEeeEEEEC-CCCCEEEEEeeeeehhHHHHHHHHHHHH------------------
Confidence            7777888889999999999 9999999999998 8999999999999999999996554110                  


Q ss_pred             cccccccceeccchhcccCCCCCCccccCccccHHHHHHHHHHhhHHHHhhhcccccccceecccccCCCCCCCcchhHH
Q 022961          165 REVCSDSLLDLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLY  244 (289)
Q Consensus       165 ~~~~~~~l~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~~~~~  244 (289)
                                                         ..                                        .+.
T Consensus       535 -----------------------------------~~----------------------------------------~l~  539 (1092)
T PRK09776        535 -----------------------------------KE----------------------------------------RLH  539 (1092)
T ss_pred             -----------------------------------HH----------------------------------------HHH
Confidence                                               00                                        045


Q ss_pred             HHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhc
Q 022961          245 ISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITR  287 (289)
Q Consensus       245 ~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~  287 (289)
                      ..++.++++++++|.   +++|+++|+++++++||+.+|++|+
T Consensus       540 ~~l~~~~~~i~~~D~---~g~i~~~N~a~~~l~G~~~~e~iG~  579 (1092)
T PRK09776        540 ITLDSIGEAVVCTDM---AMKVTFMNPVAEKMTGWTQEEALGV  579 (1092)
T ss_pred             HHHhccccEEEEECC---CCeEEEEcHHHHHHhCCCHHHHcCC
Confidence            567888999999999   9999999999999999999999997

>PF13426 PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_B 3P7N_B 1LL8_A 3MJQ_A 3BWL_A 4EET_B 4EEP_A

Probab=99.77  E-value=2.1e-17  Score=114.87  Aligned_cols=104  Identities=27%  Similarity=0.431  Sum_probs=95.1

Q ss_pred             CCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEEEEEEecCCCEEE
Q 022961           28 PDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFW  107 (289)
Q Consensus        28 ~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~~  107 (289)
                      |++++++|.+   |+|+++|+++++++||++++++|+++..++++.........+.+.+..+..+..+..+.+++|..+|
T Consensus         1 p~~i~i~d~~---g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~~   77 (104)
T PF13426_consen    1 PDGIFILDPD---GRILYVNPAFERLFGYSREELIGKSISDFFPEEDRPEFEEQIERALEEGGSWSGEVRLRRKDGETFW   77 (104)
T ss_dssp             -SEEEEEETT---SBEEEE-HHHHHHHTS-HHHHTTSBGGGGCSTTSCHHHHHHHHHHHHHTSSEEEEEEEEETTSEEEE
T ss_pred             CEEEEEECCc---CcEEehhHHHHHHHCcCHHHHcCCCcccccCcccchhhHHHHHHHHhcCCceeEEEEEEcCCCCEEE
Confidence            7899999999   9999999999999999999999999988888777788888899999888889999999999999999


Q ss_pred             EEEEEEEeecCCCCcEEEEEEEEecccc
Q 022961          108 MLFKMSLVFGKEDGRATHFVAVQVPIVS  135 (289)
Q Consensus       108 ~~~~~~~~~~~~~g~~~~~~~~~~DITe  135 (289)
                      +.+++.|+.+ ++|.+.+++++++|||+
T Consensus        78 ~~~~~~~i~~-~~g~~~~~i~~~~DiTe  104 (104)
T PF13426_consen   78 VEVSASPIRD-EDGEITGIIGIFRDITE  104 (104)
T ss_dssp             EEEEEEEEEE-TTSSEEEEEEEEEEEHH
T ss_pred             EEEEEEEEEC-CCCCEEEEEEEEEECCC
Confidence            9999999999 89999999999999996

...

>TIGR02040 PpsR-CrtJ transcriptional regulator PpsR

Probab=99.73  E-value=1.1e-17  Score=146.44  Aligned_cols=175  Identities=14%  Similarity=0.095  Sum_probs=124.1

Q ss_pred             HhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCC-CeEEEEEEEecC
Q 022961           24 LDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREER-PIEVNLLNYKKD  102 (289)
Q Consensus        24 ~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~-~~~~e~~~~~~~  102 (289)
                      +++++++++++|.+   |+++++|+.++.++||+.++++|+++..+++|++.+.....+......+. .+..+.....++
T Consensus         2 ~~~~~d~~~~~d~~---g~i~~~n~~~~~~~g~~~~el~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~   78 (442)
T TIGR02040         2 LATAADVTLLLDAE---GVVREVAANPHHPSFEQLSEWEGRRWEEIVTAESVEKFELRLSEALRTGRGAVRVELNHIDPS   78 (442)
T ss_pred             CcccCcEEEEECCC---CcEEEEEECCCcccccccccCCCCcHhHhhCcchHHHHHHHHHHHhccCCCcceEeeccCCCC
Confidence            57889999999999   99999999999999999999999999888887665555444545554443 355555555666


Q ss_pred             CCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhcccccccCCCcchhhhhHHhhcccccccccceeccchhccc
Q 022961          103 GTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDRVLALD  182 (289)
Q Consensus       103 g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l~~~~~~~n~~~~~~~~~~~~~~~~~~~~l~e~~~~~~~~  182 (289)
                      |..+|+.++..++.+   +  .+++++.+|||++++.++++...          ..++.                     
T Consensus        79 g~~~~~~~~~~~~~~---~--~~~~~i~rDi~~~~~~~~~l~~~----------~~~~e---------------------  122 (442)
T TIGR02040        79 SFELPMRFILVRLGA---D--RGVLALGRDLRAVAELQQQLVAA----------QQAME---------------------  122 (442)
T ss_pred             CCccCeEEEEEEeCC---C--CeEEEEecccHHHHHHHHHHHHH----------HHHHH---------------------
Confidence            767777777666643   2  25678899999988875443110          00000                     


Q ss_pred             CCCCCCccccCccccHHHHHHHHHHhhHHHHhhhcccccccceecccccCCCCCCCcchhHHHHhhcccccEEEeCCCCC
Q 022961          183 SDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQSFVLIDPHLP  262 (289)
Q Consensus       183 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~i~i~d~~~~  262 (289)
                                       .....+...+                               ..+...++.+++++++.|.  .
T Consensus       123 -----------------~~~~~l~~~e-------------------------------~r~~~l~e~~~~~i~~~d~--~  152 (442)
T TIGR02040       123 -----------------RDYWTLREME-------------------------------TRYRVVLEVSSDAVLLVDM--S  152 (442)
T ss_pred             -----------------HHHHHHHHHH-------------------------------HHHHHHHhhCCceEEEEEC--C
Confidence                             0000000000                               0156678899999999995  2


Q ss_pred             CCCEEEecHHHHHhhCCChHhHhhc
Q 022961          263 DMPMVYASDAFLKLTGAQIFTKITR  287 (289)
Q Consensus       263 ~~~i~~vN~~f~~~tGys~~E~~G~  287 (289)
                      +|+|+++|++|++++||+.+|++|+
T Consensus       153 ~g~i~~~N~a~~~l~G~~~~el~g~  177 (442)
T TIGR02040       153 TGRIVEANSAAAALLGGVGQSLVGR  177 (442)
T ss_pred             CCEEEEEcHHHHHHhCcCHHHHcCC
Confidence            5899999999999999999999997

This model represents the transcriptional regulator PpsR which is strictly associated with photosynthetic proteobacteria and found in photosynthetic operons. PpsR has been reported to be a repressor. These proteins contain a Helix-Turn_Helix motif of the "fis" type (pfam02954).

>PRK09776 putative diguanylate cyclase; Provisional

Probab=99.73  E-value=7.5e-17  Score=156.09  Aligned_cols=170  Identities=14%  Similarity=0.190  Sum_probs=140.8

Q ss_pred             HHHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhC-CCeE
Q 022961           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREE-RPIE   93 (289)
Q Consensus        15 ~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~-~~~~   93 (289)
                      +++++++.++++++++++++|.+   |+++++|+++++++||++++++|++...+.+|++.......+....... ..+.
T Consensus       280 ~~e~r~~~l~e~~~~~i~~~d~d---G~i~~~N~~~~~l~G~~~~el~g~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~  356 (1092)
T PRK09776        280 ESETRFRNAMEYSAIGMALVGTE---GQWLQVNKALCQFLGYSQEELRGLTFQQLTWPEDLNKDLQQVEKLLSGEINSYS  356 (1092)
T ss_pred             HHHHHHHHHHHhCCceEEEEcCC---CcEEehhHHHHHHhCCCHHHHccCCceeccCcchhHhHHHHHHHHHcCCcccee
Confidence            57788999999999999999999   9999999999999999999999999888877776555544444444332 3466


Q ss_pred             EEEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhcccccccCCCcchhhhhHHhhcccccccccce
Q 022961           94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLL  173 (289)
Q Consensus        94 ~e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l~~~~~~~n~~~~~~~~~~~~~~~~~~~~l~  173 (289)
                      .+.+..+++|..+|+.....|+.+ .+|.+.+++++.+|||++|++|+++...                           
T Consensus       357 ~e~~~~~~dG~~~~~~~~~~~~~~-~~g~~~~~i~~~~DITerk~~e~~l~~~---------------------------  408 (1092)
T PRK09776        357 MEKRYYRRDGEVVWALLAVSLVRD-TDGTPLYFIAQIEDINELKRTEQVNERL---------------------------  408 (1092)
T ss_pred             eeeEEEcCCCCEEEEEEEEEEEEC-CCCCEeeehhhHHhhHHHHHHHHHHHHH---------------------------
Confidence            788889999999999999999998 7899999999999999999996654111                           


Q ss_pred             eccchhcccCCCCCCccccCccccHHHHHHHHHHhhHHHHhhhcccccccceecccccCCCCCCCcchhHHHHhhccccc
Q 022961          174 DLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQS  253 (289)
Q Consensus       174 e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~  253 (289)
                                                ..                                        .+...++..+.+
T Consensus       409 --------------------------~~----------------------------------------~~~~~~~~~~~~  422 (1092)
T PRK09776        409 --------------------------ME----------------------------------------RITLANEAGGIG  422 (1092)
T ss_pred             --------------------------HH----------------------------------------HHHHHHHhcCce
Confidence                                      00                                        033456667789


Q ss_pred             EEEeCCCCCCCCEEEecHHHHHhhCCChHhH
Q 022961          254 FVLIDPHLPDMPMVYASDAFLKLTGAQIFTK  284 (289)
Q Consensus       254 i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~  284 (289)
                      ++..|.   +++++++|+++++++||+.+|.
T Consensus       423 i~~~d~---~~~~~~~n~~~~~l~G~~~~~~  450 (1092)
T PRK09776        423 IWEWDL---KPNIISWDKRMFELYEIPPHIK  450 (1092)
T ss_pred             EEEEec---CCCeEeeCHHHHHHhCCCcccC
Confidence            999999   9999999999999999998874

>PRK13560 hypothetical protein; Provisional

Probab=99.70  E-value=6.9e-16  Score=144.97  Aligned_cols=177  Identities=11%  Similarity=0.006  Sum_probs=126.9

Q ss_pred             HhhchHHHHHH-HHHHhhCCCEEEEEeCCCCCcc--EEEccHHHHHHhCCCccccCCCC--CCCccCCCCCHHHHH----
Q 022961           10 QSFNNRYTLWV-HEALDELPDSFTITDPSISGHP--IVFASRGFLKMSGFSRAEIIGRN--GRMFQGPRTNRRTIM----   80 (289)
Q Consensus        10 ~~l~~~~~~~l-~~~~~~~~~~i~~~d~~~~~g~--i~~~N~~~~~~~G~~~~e~~g~~--~~~l~~~~~~~~~~~----   80 (289)
                      ..+. ..++++ +.+++++|.+++.++.+ ++|.  +.+++++...++||.+.++++..  +..+.+|++......    
T Consensus        60 ~~l~-~~~e~~~r~l~~~~p~~i~~~~~~-~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~p~d~~~~~~~~~~  137 (807)
T PRK13560         60 AEAQ-DCREQCERNLKANIPGGMFLFALD-GDGTFSFPSLLDANGELAAIAKHDLMADKGLLAMLIGGDDGDFFFANPFR  137 (807)
T ss_pred             HHHH-HHHHHHHHHHHhcCCceEEEEEEc-CccccccceeeccchhHHHhcCcccCCccchhhhhcCCCcchhhhhChhh
Confidence            4444 334445 99999999999998876 1133  33477777888888887766543  344566666554332    


Q ss_pred             ---HHHHHHHhCCCeEEEEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhcccccccCCCcchhhh
Q 022961           81 ---EIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLRE  157 (289)
Q Consensus        81 ---~~~~~~~~~~~~~~e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l~~~~~~~n~~~~~~  157 (289)
                         .+..++..+.....++++++++|.  |+.....|..+ .+|.. .+.+++.|||++|++|+++...           
T Consensus       138 ~~~~~~~~~~~~~~~~~e~r~~~~dg~--~~~~~~~~~~~-~~g~~-~~~g~~~DIT~rk~ae~~l~~~-----------  202 (807)
T PRK13560        138 SAETIAMALQSDDWQEEEGHFRCGDGR--FIDCCLRFERH-AHADD-QVDGFAEDITERKRAEERIDEA-----------  202 (807)
T ss_pred             HHHHHHHHhccCcccceEEEEEeCCcc--EEEEEeeeeec-CCCce-EEEEEEEccchHHHHHHHHHHH-----------
Confidence               222233334455678888999996  55566777777 56764 6899999999999996654111           


Q ss_pred             hHHhhcccccccccceeccchhcccCCCCCCccccCccccHHHHHHHHHHhhHHHHhhhcccccccceecccccCCCCCC
Q 022961          158 IVFGSCRREVCSDSLLDLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMG  237 (289)
Q Consensus       158 ~~~~~~~~~~~~~~l~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~  237 (289)
                                                                ..                                    
T Consensus       203 ------------------------------------------~~------------------------------------  204 (807)
T PRK13560        203 ------------------------------------------LH------------------------------------  204 (807)
T ss_pred             ------------------------------------------HH------------------------------------
Confidence                                                      00                                    


Q ss_pred             CcchhHHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          238 FISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       238 ~~~~~~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                          .+...++++++++++.|.   +|+|+++|++|++++||+.+|++|+.
T Consensus       205 ----~l~~l~e~~~~~i~~~d~---~g~i~~~N~~~~~~~G~~~~e~~g~~  248 (807)
T PRK13560        205 ----FLQQLLDNIADPAFWKDE---DAKVFGCNDAACLACGFRREEIIGMS  248 (807)
T ss_pred             ----HHHHHHhhCCCeEEEEcC---CCCEEEEhHHHHHHhCCCHHHHcCCc
Confidence                056678999999999999   99999999999999999999999973

>PF08448 PAS_4: PAS fold; InterPro: IPR013656 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []

Probab=99.68  E-value=7.4e-16  Score=108.23  Aligned_cols=110  Identities=26%  Similarity=0.452  Sum_probs=96.8

Q ss_pred             HhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEEEEEEecCC
Q 022961           24 LDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDG  103 (289)
Q Consensus        24 ~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g  103 (289)
                      ++++|++++++|.+   |+++++|+++.+++|++.++++|+++..++++...+.....+.+++..+.....+..... +|
T Consensus         1 l~~~p~~i~v~D~~---~~i~~~N~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~   76 (110)
T PF08448_consen    1 LDSSPDGIFVIDPD---GRIVYANQAAAELFGVSPEELIGRSLFDLLPPEDREEFQAALRRALAGGEPVFFEEILLR-DG   76 (110)
T ss_dssp             HHHCSSEEEEEETT---SBEEEE-HHHHHHHTSTHHHHTTSBHHHHSCCGCHHHHHHHHHHHHHHTSEEEEEEEECT-TS
T ss_pred             CCCCCceeEEECCC---CEEEEEHHHHHHHhCCCHHHHhhccchhccccchhhhhHHHHHHhhccCceEEEEEEEee-cC
Confidence            68899999999999   999999999999999999999999988888777777777788888888777666555444 89


Q ss_pred             CEEEEEEEEEEeecCCCCcEEEEEEEEecccccHH
Q 022961          104 TPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKH  138 (289)
Q Consensus       104 ~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~  138 (289)
                      ...|+.+++.|+.+ .+|.+.+++++.+|||++|+
T Consensus        77 ~~~~~~~~~~Pi~~-~~g~~~g~~~~~~DiT~~rr  110 (110)
T PF08448_consen   77 EERWFEVSISPIFD-EDGEVVGVLVIIRDITERRR  110 (110)
T ss_dssp             CEEEEEEEEEEEEC-TTTCEEEEEEEEEEECCHHH
T ss_pred             CcEEEEEEEEEeEc-CCCCEEEEEEEEEECchhhC
Confidence            99999999999998 89999999999999999985

The PAS fold appears in archaea, eubacteria and eukarya. ; PDB: 3K3D_A 3K3C_B 3KX0_X 3FC7_B 3LUQ_D 3MXQ_A 3BWL_C 3FG8_A.

>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional

Probab=99.68  E-value=1.3e-15  Score=142.96  Aligned_cols=166  Identities=20%  Similarity=0.288  Sum_probs=130.3

Q ss_pred             HHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCC----Ce
Q 022961           17 TLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREER----PI   92 (289)
Q Consensus        17 ~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~----~~   92 (289)
                      +..+..+++.++++++++|.+   |+++++|+++++++||++++++|++...+.++.........+......+.    .+
T Consensus        11 ~~~~~~~le~~~~~i~~~d~~---g~i~~~N~~~~~l~G~s~eeliG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   87 (799)
T PRK11359         11 DGIFFPALEQNMMGAVLINEN---DEVLFFNPAAEKLWGYKREEVIGNNIDMLIPRDLRPAHPEYIRHNREGGKARVEGM   87 (799)
T ss_pred             hhhHHHHHHhhcCcEEEEcCC---CeEEEEcHHHHHHhCCCHHHHcCCCHHHhcCccccccchHHHhhhhccCCcccccc
Confidence            345667899999999999999   99999999999999999999999998877776654444444444333322    23


Q ss_pred             EEEEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhcccccccCCCcchhhhhHHhhcccccccccc
Q 022961           93 EVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSL  172 (289)
Q Consensus        93 ~~e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l~~~~~~~n~~~~~~~~~~~~~~~~~~~~l  172 (289)
                      ..+.+..+++|..+|+.....|+..  .|. ..++++.+|||++++.+++.                             
T Consensus        88 ~~e~~~~~~dG~~~~v~~~~~~~~~--~g~-~~~~~~~~DiT~~~~~~~~~-----------------------------  135 (799)
T PRK11359         88 SRELQLEKKDGSKIWTRFALSKVSA--EGK-VYYLALVRDASVEMAQKEQT-----------------------------  135 (799)
T ss_pred             ceeeEEecCCcCEEEEEEEeeeecc--CCc-eEEEEEEeeccchhhhHHHH-----------------------------
Confidence            4577888999999999999888753  555 45788899999987763321                             


Q ss_pred             eeccchhcccCCCCCCccccCccccHHHHHHHHHHhhHHHHhhhcccccccceecccccCCCCCCCcchhHHHHhhcccc
Q 022961          173 LDLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQ  252 (289)
Q Consensus       173 ~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~e~~~~  252 (289)
                                                  +.                                        +...++..++
T Consensus       136 ----------------------------~~----------------------------------------~~~~~~~~~~  147 (799)
T PRK11359        136 ----------------------------RQ----------------------------------------LIIAVDHLDR  147 (799)
T ss_pred             ----------------------------HH----------------------------------------HHHHHhcCCC
Confidence                                        00                                        2335677889


Q ss_pred             cEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          253 SFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       253 ~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      +++++|.   +++|+++|++|++++||+.+|++|+.
T Consensus       148 ~i~~~d~---~g~i~~~N~~~~~l~G~~~~e~~g~~  180 (799)
T PRK11359        148 PVIVLDP---ERRIVQCNRAFTEMFGYCISEASGMQ  180 (799)
T ss_pred             cEEEEcC---CCcEEEEChhhHhhhCCCHHHHCCCC
Confidence            9999999   99999999999999999999999973

>PF00989 PAS: PAS fold; InterPro: IPR013767 PAS domains are involved in many signalling proteins where they are used as a signal sensor domain []

Probab=99.68  E-value=1.3e-15  Score=107.46  Aligned_cols=112  Identities=23%  Similarity=0.366  Sum_probs=93.9

Q ss_pred             HHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeE-EEE
Q 022961           18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIE-VNL   96 (289)
Q Consensus        18 ~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~-~e~   96 (289)
                      ++++.++++++++++++|.+   |+|+++|+++++++||++++++|+++..++++.+.......+...+..+.... ...
T Consensus         1 e~~~~i~~~~~~~i~~~d~~---g~I~~~N~a~~~l~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   77 (113)
T PF00989_consen    1 ERYRAILENSPDGIFVIDED---GRILYVNQAAEELLGYSREELIGKSLFDLIHPEDRRELRERLRQALSQGESGESFEV   77 (113)
T ss_dssp             HHHHHHHHCSSSEEEEEETT---SBEEEECHHHHHHHSS-HHHHTTSBGGGGCSGGGHHHHHHHHHHHHHHCCHECEEEE
T ss_pred             CHHHHHHhcCCceEEEEeCc---CeEEEECHHHHHHHccCHHHHcCCcHHHhcCchhhHHHHHHHHHHHHcCCCceeEEE
Confidence            46889999999999999999   99999999999999999999999998888877655556667777777666543 344


Q ss_pred             EEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecc
Q 022961           97 LNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPI  133 (289)
Q Consensus        97 ~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DI  133 (289)
                      ....++|+.+|+.+...|+.+ .+|.+.+++++++||
T Consensus        78 ~~~~~~g~~~~~~~~~~~~~~-~~~~~~~~~~~~~DI  113 (113)
T PF00989_consen   78 RFRLRDGRPRWVEVRASPVRD-EDGQIIGILVIFRDI  113 (113)
T ss_dssp             EEEETTSCEEEEEEEEEEEEE-TTEEEEEEEEEEEE-
T ss_pred             EEEecCCcEEEEEEEEEEEEe-CCCCEEEEEEEEEeC
Confidence            444469999999999999999 788888999999997

PAS domains appear in archaea, bacteria and eukaryotes. Several PAS-domain proteins are known to detect their signal by way of an associated cofactor. Haeme, flavin, and a 4-hydroxycinnamyl chromophore are used in different proteins. The PAS domain was named after three proteins that it occurs in: Per- period circadian protein Arnt- Ah receptor nuclear translocator protein Sim- single-minded protein. PAS domains are often associated with PAC domains IPR001610 from INTERPRO. It appears that these domains are directly linked, and that together they form the conserved 3D PAS fold. The division between the PAS and PAC domains is caused by major differences in sequences in the region connecting these two motifs []. In human PAS kinase, this region has been shown to be very flexible, and adopts different conformations depending on the bound ligand []. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels [].; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 2GJ3_A 4F3L_B 1XFN_A 1OTD_A 2PYR_A 1KOU_A 1XFQ_A 2ZOI_A 2ZOH_A 1OTA_A ....

>PRK11091 aerobic respiration control sensor protein ArcB; Provisional

Probab=99.56  E-value=5e-14  Score=131.81  Aligned_cols=125  Identities=14%  Similarity=0.186  Sum_probs=108.9

Q ss_pred             HHHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEE
Q 022961           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV   94 (289)
Q Consensus        15 ~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   94 (289)
                      +.+++++.+++++|++++++|.+   |+++++|+++++++||+.++++|+++..++++.............+..+..+..
T Consensus       152 ~~~~~l~~il~~~~~~i~~~D~~---g~i~~~N~a~~~l~G~~~~eliG~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~  228 (779)
T PRK11091        152 QQSSLLRSFLDASPDLVYYRNED---GEFSGCNRAMELLTGKSEKQLIGLTPKDVYSPEAAEKVIETDEKVFRHNVSLTY  228 (779)
T ss_pred             HHHHHHHHHHhcCcceEEEECCC---CcEEeEcHHHHHHhCcCHHHHcCCChHHhCCHHHHHHHHHHHHHHHhcCCCeEE
Confidence            45678899999999999999999   999999999999999999999999988777665444455555566667777888


Q ss_pred             EEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhcc
Q 022961           95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG  143 (289)
Q Consensus        95 e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l  143 (289)
                      +.....++|..+|+.++..|+.+ .+|.+.+++++.+|||++|++|+++
T Consensus       229 e~~~~~~~G~~~~~~~~~~pi~~-~~g~~~g~v~~~~DITe~k~~e~~l  276 (779)
T PRK11091        229 EQWLDYPDGRKACFELRKVPFYD-RVGKRHGLMGFGRDITERKRYQDAL  276 (779)
T ss_pred             EEEEEcCCCCEEEEEEEeeeEEc-CCCCEEEEEEEEeehhHHHHHHHHH
Confidence            88888999999999999999998 7899999999999999999997765

>PRK13559 hypothetical protein; Provisional

Probab=99.55  E-value=2.2e-13  Score=116.29  Aligned_cols=126  Identities=37%  Similarity=0.666  Sum_probs=107.0

Q ss_pred             HHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEE
Q 022961           16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVN   95 (289)
Q Consensus        16 ~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e   95 (289)
                      ..+.++.++++++++++++|.+..+|.++++|+++++++||+.++++|+++..+.++.........+...+..+..+..+
T Consensus        41 ~~~~~~~~~e~~~~~i~i~D~~~~~g~i~~~N~a~~~l~G~~~~e~iG~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e  120 (361)
T PRK13559         41 SGRLFEQAMEQTRMAMCITDPHQPDLPIVLANQAFLDLTGYAAEEVVGRNCRFLQGAATDPIAVAKIRAAIAAEREIVVE  120 (361)
T ss_pred             hhhHHHHHHHhCCCcEEEecCCCCCCcEEEEchHHHHHhCCCHHHHcCCChhhhcCCCCCHHHHHHHHHHhccCCceEEE
Confidence            45678889999999999999742237899999999999999999999999877766666666666677777777778788


Q ss_pred             EEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhc
Q 022961           96 LLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNS  142 (289)
Q Consensus        96 ~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~  142 (289)
                      ....+++|..+|+.....|+.+ .+|.+.+++++.+|||++|++|+.
T Consensus       121 ~~~~~~dG~~~~~~~~~~~i~d-~~G~~~~~v~~~~DITerk~~e~~  166 (361)
T PRK13559        121 LLNYRKDGEPFWNALHLGPVYG-EDGRLLYFFGSQWDVTDIRAVRAL  166 (361)
T ss_pred             EEEEcCCCCEEEEEEEEEEEEc-CCCCEEEeeeeeeehhcchhhHHH
Confidence            8888999999999999999998 789999999999999999987543

>PRK13557 histidine kinase; Provisional

Probab=99.53  E-value=2.1e-13  Score=122.57  Aligned_cols=128  Identities=37%  Similarity=0.672  Sum_probs=112.0

Q ss_pred             HHHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEE
Q 022961           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV   94 (289)
Q Consensus        15 ~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   94 (289)
                      .....|+.+++.++++++++|.+..+|+|+|+|++|++++||+.++++|+++..+.++.........++..+..+..+..
T Consensus        27 ~~~~~~~~~~~~~~~~i~v~d~~~~~g~i~~~N~a~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~  106 (540)
T PRK13557         27 HRSDIFFAAVETTRMPMIVTDPNQPDNPIVFANRAFLEMTGYAAEEIIGNNCRFLQGPETDRATVAEVRDAIAERREIAT  106 (540)
T ss_pred             hhhHHHHHHHHhCcCcEEEEcCCCCCCCEEEEcHHHHHHhCCCHHHhcCCChHhhcCCCCCHHHHHHHHHHHHcCCCceE
Confidence            45678999999999999999963233899999999999999999999999988888777777777777888877777777


Q ss_pred             EEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhcc
Q 022961           95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG  143 (289)
Q Consensus        95 e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l  143 (289)
                      +.+..+++|..+|+.....|+.+ .+|.+.+++++.+|||+++++|+++
T Consensus       107 ~~~~~~~~G~~~~~~~~~~~i~~-~~g~~~~~~~~~~dit~~~~~e~~l  154 (540)
T PRK13557        107 EILNYRKDGSSFWNALFVSPVYN-DAGDLVYFFGSQLDVSRRRDAEDAL  154 (540)
T ss_pred             EEEEEeCCCCEEEEEEEEEEeEC-CCCCEEEEEEEecChHHHHHHHHHH
Confidence            88888999999999999999998 7899999999999999999887655

>PRK10060 RNase II stability modulator; Provisional

Probab=99.52  E-value=3.7e-13  Score=123.24  Aligned_cols=137  Identities=13%  Similarity=0.208  Sum_probs=108.0

Q ss_pred             HHHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCcc-CCCCCHHHHHHHHHHHHhCCCeE
Q 022961           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQ-GPRTNRRTIMEIREAIREERPIE   93 (289)
Q Consensus        15 ~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~-~~~~~~~~~~~~~~~~~~~~~~~   93 (289)
                      ....+++.+++.++++++++|.+   |+|+++|+++++++||+.++++|+++..++ ++.+.......+...+..+..+.
T Consensus       108 ~~~~~~~~v~~~~~~gI~i~D~~---g~I~~~N~a~~~l~Gy~~~eliG~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~  184 (663)
T PRK10060        108 HGLSFAEQVVSEANSVIVILDSR---GNIQRFNRLCEEYTGLKEHDVIGQSVFKLFMSRREAAASRRNIRGFFRSGNAYE  184 (663)
T ss_pred             HHHHHHHHHHhhCCceEEEEeCC---CCEEEEcHHHHHHHCcCHHHHcCCCHHHHhCChhhHHHHHHHHHHHHhcCCceE
Confidence            34457788999999999999999   999999999999999999999999965544 44444445556667777888888


Q ss_pred             EEEEEEecCCCEEEEEEEEEEeecCCCCc-EEEEEEEEecccccHHHHhcc--cccccC--C--Ccchhh
Q 022961           94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGR-ATHFVAVQVPIVSRKHMRNSG--MSYSED--G--GGSRLR  156 (289)
Q Consensus        94 ~e~~~~~~~g~~~~~~~~~~~~~~~~~g~-~~~~~~~~~DITe~k~~e~~l--~~~~~~--~--n~~~~~  156 (289)
                      .+.+..+++|..+|+.....+ .+ ..|. ...++++.+|||++|++++++  ++.+|.  |  ||..|.
T Consensus       185 ~e~~~~~~~G~~~~~~~~~~~-~~-~~g~~~~~~i~~~~DITe~k~~e~~l~~~a~~D~LTGL~NR~~f~  252 (663)
T PRK10060        185 VERWIKTRKGQRLFLFRNKFV-HS-GSGKNEIFLICSGTDITEERRAQERLRILANTDSITGLPNRNAIQ  252 (663)
T ss_pred             EEEEEEeCCCCEEEEEeeeEE-Ec-CCCCceEEEEEEEEechHHHHHHHHHHHHhhcCccCCCcCHHHHH
Confidence            999999999998887655444 33 3443 456788999999999999888  455555  4  998888

>PRK13558 bacterio-opsin activator; Provisional

Probab=99.44  E-value=3.4e-12  Score=117.50  Aligned_cols=125  Identities=38%  Similarity=0.695  Sum_probs=107.6

Q ss_pred             HHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEEEEE
Q 022961           19 WVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLN   98 (289)
Q Consensus        19 ~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~   98 (289)
                      .++.+++.++.++++.|...++|.++++|+++++++||++++++|+++..+.++.........+...+..+..+..+++.
T Consensus       149 ~~~~~~~~~~~gi~~~d~~~~dg~i~~~N~~~~~l~G~~~eel~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~  228 (665)
T PRK13558        149 LKERALDEAPVGITIADATLPDEPLIYINDAFERITGYSPDEVLGRNCRFLQGEDTNEERVAELREAIDEERPTSVELRN  228 (665)
T ss_pred             HHHHHHhcCCccEEEEcCCCCCCcEEEEcHHHHHHhCcCHHHHcCCCHHHhcCCCccHHHHHHHHHHHhcCCCeEEEEEE
Confidence            45678999999999998532338999999999999999999999999877777666666666667777777788889999


Q ss_pred             EecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhccc
Q 022961           99 YKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGM  144 (289)
Q Consensus        99 ~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l~  144 (289)
                      ++++|..+|+.....|+.+ .+|.+.+++++.+|||++|++|+++.
T Consensus       229 ~~~dG~~~~~~~~~~pi~d-~~G~~~~~vgi~~DITerk~~E~~L~  273 (665)
T PRK13558        229 YRKDGSTFWNQVDIAPIRD-EDGTVTHYVGFQTDVTERKEAELALQ  273 (665)
T ss_pred             ECCCCCEEEEEEEEEEEEC-CCCCEEEEEEEEEeCcHHHHHHHHHH
Confidence            9999999999999999998 79999999999999999999988773

>TIGR00229 sensory_box PAS domain S-box

Probab=99.35  E-value=3.2e-11  Score=83.84  Aligned_cols=120  Identities=21%  Similarity=0.347  Sum_probs=93.4

Q ss_pred             HHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhC-CCeEEEE
Q 022961           18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREE-RPIEVNL   96 (289)
Q Consensus        18 ~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~-~~~~~e~   96 (289)
                      +.++.+++.++.+++++|.+   +.++++|+++.+++|++..+++|.+...+.++.........+....... .......
T Consensus         3 ~~~~~~~~~~~~~~~~~d~~---~~i~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   79 (124)
T TIGR00229         3 ERYRAIFESSPDAIIVIDLE---GNILYVNPAFEEIFGYSAEELIGRNVLELIPEEDREEVRERIERLLEGEREPVSEER   79 (124)
T ss_pred             hHHHHHHhhCCceEEEEcCC---CcEEEEchHHHHHhCCChHHhcCcchhhhcChhhhHHHHHHHHHHHcCCCCCcceEe
Confidence            45778999999999999999   9999999999999999999999988776666555444444444544422 2233444


Q ss_pred             EEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhc
Q 022961           97 LNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNS  142 (289)
Q Consensus        97 ~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~  142 (289)
                      .+...+|...|+.....|+..  +|...+++++..|||++++++++
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~dit~~~~~~~~  123 (124)
T TIGR00229        80 RVRRKDGSEIWVEVSVSPIRT--NGGELGVVGIVRDITERKQAEEA  123 (124)
T ss_pred             eeEcCCCCEEEEEEEEeehhh--CCCeeEEEEEeeehhHHHHHHhc
Confidence            555788999999988888863  67778889999999999998664

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.

>PF08447 PAS_3: PAS fold; InterPro: IPR013655 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []

Probab=99.28  E-value=3.4e-11  Score=81.38  Aligned_cols=86  Identities=26%  Similarity=0.464  Sum_probs=71.7

Q ss_pred             EEEccHHHHHHhCCCccccCCCC----CCCccCCCCCHHHHHHHHH-HHHhCCCeEEEEEEEecCCCEEEEEEEEEEeec
Q 022961           43 IVFASRGFLKMSGFSRAEIIGRN----GRMFQGPRTNRRTIMEIRE-AIREERPIEVNLLNYKKDGTPFWMLFKMSLVFG  117 (289)
Q Consensus        43 i~~~N~~~~~~~G~~~~e~~g~~----~~~l~~~~~~~~~~~~~~~-~~~~~~~~~~e~~~~~~~g~~~~~~~~~~~~~~  117 (289)
                      ++++|+.+++++||+++++ +.+    +..+++|++.......+.. ....+..+..++++++++|...|+...+.++.+
T Consensus         1 ~i~~s~~~~~i~G~~~~~~-~~~~~~~~~~~ihpdD~~~~~~~~~~~~~~~~~~~~~e~R~~~~~G~~~wi~~~~~~~~d   79 (91)
T PF08447_consen    1 IIYWSDNFYEIFGYSPEEI-GKPDFEEWLERIHPDDRERVRQAIQQAALQNGEPFEIEYRIRRKDGEYRWIEVRGRPIFD   79 (91)
T ss_dssp             -EEE-THHHHHHTS-HHHH-TCBEHHHHHHHB-TTTHHHHHHHHHHHHHHTT-EEEEEEEEEGTTSTEEEEEEEEEEEET
T ss_pred             CEEEeHHHHHHhCCCHHHh-ccCCHHHHHhhcCHHHHHHHHHHHHHHhhccCcceEEEEEEECCCCCEEEEEEEEEEEEC
Confidence            5899999999999999999 665    6667889998888888888 677777899999999999999999999999998


Q ss_pred             CCCCcEEEEEEEE
Q 022961          118 KEDGRATHFVAVQ  130 (289)
Q Consensus       118 ~~~g~~~~~~~~~  130 (289)
                       .+|.+..++|++
T Consensus        80 -~~g~~~~~~Gv~   91 (91)
T PF08447_consen   80 -ENGKPIRIIGVI   91 (91)
T ss_dssp             -TTS-EEEEEEEE
T ss_pred             -CCCCEEEEEEEC
Confidence             899999998874

The PAS fold appears in archaea, eubacteria and eukarya. The PAS domain contains a sensory box, or S-box domain that 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 haem 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. This domain has been found in the gene product of the madA gene of the filamentous zygomycete fungus Phycomyces blakesleeanus. It has been shown that MadA encodes a blue-light photoreceptor for phototropism and other light responses. The gene is involved in the phototropic responses associated with sporangiophore growth; they exhibit phototropism by bending toward near-UV and blue wavelengths and away from far-UV wavelengths in a manner that is physiologically similar to plant phototropic responses [].; GO: 0005515 protein binding; PDB: 3NJA_D 3H9W_A 3GDI_B 3ICY_A 3EEH_A 3MR0_B.

>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional

Probab=99.23  E-value=1.3e-10  Score=109.40  Aligned_cols=123  Identities=19%  Similarity=0.291  Sum_probs=102.0

Q ss_pred             HHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccC-CCCCHHHHHHHHHHHHhCCCeEE
Q 022961           16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQG-PRTNRRTIMEIREAIREERPIEV   94 (289)
Q Consensus        16 ~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~-~~~~~~~~~~~~~~~~~~~~~~~   94 (289)
                      .++.+..+++.++++++++|.+   |+++++|+++++++||+.++++|++...+.+ +.........+...+..+..+..
T Consensus       134 ~~~~~~~~~~~~~~~i~~~d~~---g~i~~~N~~~~~l~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  210 (799)
T PRK11359        134 QTRQLIIAVDHLDRPVIVLDPE---RRIVQCNRAFTEMFGYCISEASGMQPDTLLNIPEFPADNRIRLQQLLWKTARDQD  210 (799)
T ss_pred             HHHHHHHHHhcCCCcEEEEcCC---CcEEEEChhhHhhhCCCHHHHCCCChHHhcCCCCCcHHHHHHHHHhhccCCCCcc
Confidence            4456667899999999999999   9999999999999999999999998665543 44444455555666666666777


Q ss_pred             EEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhc
Q 022961           95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNS  142 (289)
Q Consensus        95 e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~  142 (289)
                      +.+..+++|..+|+.....|+.+ ..|.+.+++++.+|||++|++++.
T Consensus       211 e~~~~~~dG~~~~~~~~~~~v~d-~~g~~~~~~~~~~DITerk~~e~~  257 (799)
T PRK11359        211 EFLLLTRTGEKIWIKASISPVYD-VLAHLQNLVMTFSDITEERQIRQL  257 (799)
T ss_pred             eeEEeCCCCCEEEEEeeeeeeec-CCCceeEEEEEeehhhhHHHHHHH
Confidence            88888999999999999999998 789999999999999999987543

>cd00130 PAS PAS domain; PAS motifs appear in archaea, eubacteria and eukarya

Probab=99.08  E-value=9e-09  Score=68.05  Aligned_cols=103  Identities=21%  Similarity=0.404  Sum_probs=82.9

Q ss_pred             CCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEEEEEEecCCCEE
Q 022961           27 LPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPF  106 (289)
Q Consensus        27 ~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~  106 (289)
                      ++++++++|.+   +.++++|+.++.++|++..+++|.+...+.++.........+......+..+..+......+|...
T Consensus         1 ~~~~i~~~d~~---~~~~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   77 (103)
T cd00130           1 LPDGVIVLDLD---GRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDGSVI   77 (103)
T ss_pred             CCceEEEECCC---CcEEEECHHHHHHhCCCHHHHcCccHHHhcCCccchHHHHHHHHHHhcCcCeEEEEEEEccCCCEE
Confidence            36789999999   999999999999999999999998877677666655555555555555555667777778889999


Q ss_pred             EEEEEEEEeecCCCCcEEEEEEEEecc
Q 022961          107 WMLFKMSLVFGKEDGRATHFVAVQVPI  133 (289)
Q Consensus       107 ~~~~~~~~~~~~~~g~~~~~~~~~~DI  133 (289)
                      |+.....++.+ ..|...+++++..||
T Consensus        78 ~~~~~~~~~~~-~~~~~~~~~~~~~di  103 (103)
T cd00130          78 WVLVSLTPIRD-EGGEVIGLLGVVRDI  103 (103)
T ss_pred             EEEEEEEEEec-CCCCEEEEEEEEecC
Confidence            99999999887 677888888888875

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.

>PRK11360 sensory histidine kinase AtoS; Provisional

Probab=99.01  E-value=6.7e-09  Score=94.55  Aligned_cols=122  Identities=14%  Similarity=0.181  Sum_probs=97.7

Q ss_pred             HHHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCC-eE
Q 022961           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERP-IE   93 (289)
Q Consensus        15 ~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~-~~   93 (289)
                      ..+..++.++++++++++++|.+   |.++++|+++++++||++++++|++...++++..  .....+.+.+..+.. ..
T Consensus       259 ~~~~~~~~i~~~~~~~i~~~d~~---g~i~~~N~~~~~l~g~~~~~~~g~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~  333 (607)
T PRK11360        259 ETRSLNELILESIADGVIAIDRQ---GKITTMNPAAEVITGLQRHELVGKPYSELFPPNT--PFASPLLDTLEHGTEHVD  333 (607)
T ss_pred             HHHHHHHHHHHhccCeEEEEcCC---CCEEEECHHHHHHhCCChHHhcCCcHHHHcCCch--hHHHHHHHHHhcCCCccc
Confidence            44567788999999999999999   9999999999999999999999999777765432  233344455554443 33


Q ss_pred             EEEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhcc
Q 022961           94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG  143 (289)
Q Consensus        94 ~e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l  143 (289)
                      .+.....++|... +.++..|+.+ .+|.+.+++++.+|||+++++|+++
T Consensus       334 ~~~~~~~~~~~~~-~~~~~~~i~~-~~g~~~~~i~~~~Dite~~~~e~~l  381 (607)
T PRK11360        334 LEISFPGRDRTIE-LSVSTSLLHN-THGEMIGALVIFSDLTERKRLQRRV  381 (607)
T ss_pred             eEEEEEcCCCcEE-EEEEEeeEEc-CCCCEEEEEEEEeechHHHHHHHHH
Confidence            4566667777766 8899999998 7999999999999999999998776

>PF12860 PAS_7: PAS fold

Probab=98.99  E-value=3.1e-09  Score=75.16  Aligned_cols=105  Identities=21%  Similarity=0.356  Sum_probs=71.8

Q ss_pred             HhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCcccc-CCCCCCCcc---------CCCCCHHHHHHHHHHHHhCCCeE
Q 022961           24 LDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEI-IGRNGRMFQ---------GPRTNRRTIMEIREAIREERPIE   93 (289)
Q Consensus        24 ~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~-~g~~~~~l~---------~~~~~~~~~~~~~~~~~~~~~~~   93 (289)
                      +++++.|+++.|.+   ++++++|+.|.+++|++.+.+ .|.++..+.         .+.....................
T Consensus         1 Ld~l~~Gv~v~D~~---~rl~~~N~~~~~l~~~~~~~~~~G~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~   77 (115)
T PF12860_consen    1 LDSLPQGVAVFDSD---GRLVFWNQRFRELFGLPPEMLRPGASFRDLLRRLAERGEFPPGDPEAWVRQRLARLRRRQPRS   77 (115)
T ss_pred             CCCcCceEEEEcCC---CeEEeEcHHHHHHhCCCHHHhcCCCCHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHhcCCCce
Confidence            47899999999999   999999999999999999887 677755442         11222222222222233333333


Q ss_pred             EEEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHh
Q 022961           94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRN  141 (289)
Q Consensus        94 ~e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~  141 (289)
                      .+  ....+|.  |+.+...|..   +|   +++.+..|||+++++|+
T Consensus        78 ~~--~~~~dgr--~l~~~~~~~~---~G---g~v~~~~DVT~~~~~E~  115 (115)
T PF12860_consen   78 FE--LRLPDGR--WLEVRAQPLP---DG---GFVLTFTDVTERRRAEE  115 (115)
T ss_pred             eE--EECCCCE--EEEEEeEECC---CC---CEEEEEEeCCHHHHhcC
Confidence            33  3456775  5677788885   34   46788999999999864

>TIGR02966 phoR_proteo phosphate regulon sensor kinase PhoR

Probab=98.98  E-value=5.1e-09  Score=88.07  Aligned_cols=111  Identities=12%  Similarity=0.073  Sum_probs=84.6

Q ss_pred             HHHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEE
Q 022961           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV   94 (289)
Q Consensus        15 ~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   94 (289)
                      +..+.++.++++++++++++|.+   |+++++|+++++++||++++.+|+++..+..+   +.    +...+..+.. ..
T Consensus         3 ~~~~~l~~~~~~~~~~i~~~d~~---g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~---~~----~~~~l~~~~~-~~   71 (333)
T TIGR02966         3 ALLSRFRAAAQALPDAVVVLDEE---GQIEWCNPAAERLLGLRWPDDLGQRITNLIRH---PE----FVEYLAAGRF-SE   71 (333)
T ss_pred             hHHHHHHHHHHhCcCcEEEECCC---CcEEEEcHHHHHHhCCChHHHcCCcHHHHccC---HH----HHHHHHhccc-CC
Confidence            45567899999999999999999   99999999999999999999999987666543   22    2333333222 22


Q ss_pred             EEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhc
Q 022961           95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNS  142 (289)
Q Consensus        95 e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~  142 (289)
                      ......++|...|+.+...|+.+ . +    ++++.+|||++++.++.
T Consensus        72 ~~~~~~~~~~~~~~~~~~~p~~~-~-~----~~~~~~dit~~~~~~~~  113 (333)
T TIGR02966        72 PLELPSPINSERVLEIRIAPYGE-E-Q----KLLVARDVTRLRRLEQM  113 (333)
T ss_pred             CeEeecCCCCceEEEEEEEEcCC-C-c----eEEEEeCchHHHHHHHH
Confidence            34445578888899999999875 2 2    67888999999887654

Members of this protein family are the regulatory histidine kinase PhoR associated with the phosphate ABC transporter in most Proteobacteria. Related proteins from Gram-positive organisms are not included in this model. The phoR gene usually is adjacent to the response regulator phoB gene (TIGR02154).

>PRK11073 glnL nitrogen regulation protein NR(II); Provisional

Probab=98.94  E-value=7.5e-09  Score=87.94  Aligned_cols=114  Identities=13%  Similarity=0.138  Sum_probs=85.9

Q ss_pred             HHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEEEEE
Q 022961           19 WVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLN   98 (289)
Q Consensus        19 ~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~   98 (289)
                      .+..++++++++++++|.+   |+|+++|+++++++||+.++++|+++..+.++..  .....+...+..+..+......
T Consensus         8 ~~~~il~~~~~gi~~~d~~---~~i~~~N~a~~~~~g~~~~~~~g~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~   82 (348)
T PRK11073          8 DAGQILNSLINSILLLDDD---LAIHYANPAAQQLLAQSSRKLFGTPLPELLSYFS--LNIELMRESLQAGQGFTDNEVT   82 (348)
T ss_pred             hHHHHHhcCcCeEEEECCC---CeEeeEcHHHHHHhCCCHHHHcCCCHHHHcCcch--hhHHHHHHHHHcCCcccccceE
Confidence            5678999999999999999   9999999999999999999999999777765322  2223344555555444333334


Q ss_pred             EecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhcc
Q 022961           99 YKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG  143 (289)
Q Consensus        99 ~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l  143 (289)
                      ...+|..+|+.++..|+..      .+++...+|+|++++.++++
T Consensus        83 ~~~~g~~~~~~~~~~~~~~------~~~~~~~~dit~~~~~~~~~  121 (348)
T PRK11073         83 LVIDGRSHILSLTAQRLPE------GMILLEMAPMDNQRRLSQEQ  121 (348)
T ss_pred             EEECCceEEEEEEEEEccC------ceeEEEEechhHHHHHHHHH
Confidence            4579999999999998853      23567789999998875544

>PF13596 PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D

Probab=98.92  E-value=1.4e-08  Score=70.72  Aligned_cols=106  Identities=21%  Similarity=0.259  Sum_probs=71.2

Q ss_pred             HHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEEEEEE
Q 022961           20 VHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNY   99 (289)
Q Consensus        20 l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~   99 (289)
                      +..++++++.++.++|.+   +++.+.|+++.++++..+ ..+|++...+.++...+.... +.+.+..+.....+... 
T Consensus         1 L~~il~s~~~~i~~vD~~---~~I~~~n~~a~~~f~~~~-~~iGr~l~~~~~~~~~~~l~~-~i~~~~~~~~~~~~~~~-   74 (106)
T PF13596_consen    1 LNNILDSMPIGIIFVDRN---LRIRYFNPAAARLFNLSP-SDIGRPLFDIHPPLSYPNLKK-IIEQVRSGKEEEFEIVI-   74 (106)
T ss_dssp             HHHHHHHSSSEEEEEETT---SBEEEE-SCGC-SS---G-GGTTSBCCCSS-HHHHHHHHH-HHHHHHTTSBSEEEEEE-
T ss_pred             ChHHHhcCCCCEEEEcCC---CeEEEeChhHhhhcCCCh-HHCCCCHHHcCCccchHHHHH-HHHHHHcCCCceEEEEe-
Confidence            467899999999999999   999999999999999775 457999887765432233333 33444555543333333 


Q ss_pred             ecCCCEEEEEEEEEEeecCCCCcEEEEEEEEeccc
Q 022961          100 KKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV  134 (289)
Q Consensus       100 ~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIT  134 (289)
                      ..+|.  |+.+...|+.+ .+|...|++.+..|||
T Consensus        75 ~~~~~--~~~~~~~P~~~-~~g~~~G~v~~~~DIT  106 (106)
T PF13596_consen   75 PNGGR--WYLVRYRPYRD-EDGEYAGAVITFQDIT  106 (106)
T ss_dssp             EETTE--EEEEEEEEEE--TTS-EEEEEEEEEE-G
T ss_pred             cCCCE--EEEEEEEEEEC-CCCCEEEEEEEEEecC
Confidence            24443  56789999998 7999999999999998

>PF14598 PAS_11: PAS domain; PDB: 1P97_A 3F1O_A 2A24_A 3H7W_A 3F1P_A 3H82_A 3F1N_A 4F3L_B 4DJ3_A 2KDK_A

Probab=98.89  E-value=8.6e-08  Score=66.93  Aligned_cols=100  Identities=16%  Similarity=0.257  Sum_probs=82.0

Q ss_pred             EEeCCCCCccEEEccHH-HHHHhCCCccccCCCCCCCccCCCCCHH-HHHHHHHHHHhCCCeEEEEEEEecCCCEEEEEE
Q 022961           33 ITDPSISGHPIVFASRG-FLKMSGFSRAEIIGRNGRMFQGPRTNRR-TIMEIREAIREERPIEVNLLNYKKDGTPFWMLF  110 (289)
Q Consensus        33 ~~d~~~~~g~i~~~N~~-~~~~~G~~~~e~~g~~~~~l~~~~~~~~-~~~~~~~~~~~~~~~~~e~~~~~~~g~~~~~~~  110 (289)
                      -.+.+   |+|+++.+. ...++||.+++++|+++..+++|++... ........+..|.....-+++..++|...|+..
T Consensus         7 rhs~d---gki~~~d~~~v~~~lgy~~~eLvG~s~y~~~H~~D~~~~~~~~~~~~~~~g~~~~~~yR~~~k~g~~vwvqt   83 (111)
T PF14598_consen    7 RHSLD---GKITYVDSRAVSSLLGYLPEELVGRSIYDFVHPDDLQRVLKQHHREVLQKGQSVSPYYRFRTKNGGYVWVQT   83 (111)
T ss_dssp             EEETT---SBEEEEETTHHHHHHSS-HHHHTTSBGGGGBSCCTHHHHHHHHHHHHHHHSSEEEEEEEEE-TTSSEEEEEE
T ss_pred             EECCC---cEEEEEcCccChhhcCCCcHHHcCCchHHhCCHhhhhhHHHHHHHHHhhCCCcCcceEEEEecCCcEEEEEE
Confidence            45677   999999999 6999999999999999999999998886 667778888888877777999999999999999


Q ss_pred             EEEEeecCCCCcEEEEEEEEecccc
Q 022961          111 KMSLVFGKEDGRATHFVAVQVPIVS  135 (289)
Q Consensus       111 ~~~~~~~~~~g~~~~~~~~~~DITe  135 (289)
                      ...++.+|..+.+..++++-+=|++
T Consensus        84 ~~~~~~n~~~~~~~~Iv~~n~vlse  108 (111)
T PF14598_consen   84 KATLFYNPWTSKPEFIVCTNTVLSE  108 (111)
T ss_dssp             EEEEEEETTTTCEEEEEEEEEEESC
T ss_pred             EEEEEECCCCCCccEEEEEEEEecc
Confidence            9999886456677777776655554

...

>KOG0501 consensus K+-channel KCNQ [Inorganic ion transport and metabolism]

Probab=98.76  E-value=4.6e-08  Score=83.92  Aligned_cols=122  Identities=25%  Similarity=0.526  Sum_probs=99.1

Q ss_pred             HHHHHHHHhhCC--CE-EEEEeCCCCCccEEEccHHHHHHhCCCccccCCCC--CCCccCCCCCHHHHHHHHHHHHhCCC
Q 022961           17 TLWVHEALDELP--DS-FTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRN--GRMFQGPRTNRRTIMEIREAIREERP   91 (289)
Q Consensus        17 ~~~l~~~~~~~~--~~-i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~--~~~l~~~~~~~~~~~~~~~~~~~~~~   91 (289)
                      +-+++.++..+.  +. ++..+.+..|..|+|+|+.||++.||.+.|++.++  +.+++....+....+.+.+.+.+.+.
T Consensus        13 NTFLENiiRRsn~~dtsFlL~NAQiVD~PiVY~NdgFcKlsGY~RAevMQKs~tc~FMyGEltdk~ti~k~~~t~eN~~~   92 (971)
T KOG0501|consen   13 NTFLENIIRRSNNADTSFLLANAQIVDWPIVYCNDGFCKLSGYHRAEVMQKSCTCSFMYGELTDKGTIEKVRQTLENYET   92 (971)
T ss_pred             hhHHHHHHhhccCCCcceeeccceeeccceEEecCcchhccCccHHHHhcccceeeeeeccccchhhHHHHHHHHHhhhh
Confidence            345666666555  43 33344444457899999999999999999999987  45566666667777888888888888


Q ss_pred             eEEEEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHH
Q 022961           92 IEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM  139 (289)
Q Consensus        92 ~~~e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~  139 (289)
                      -++|+.++.++..+.|+.+.+.|+++ +...++.+++...|||..|+-
T Consensus        93 ~qfEillyKKN~TPvW~~vqiAPIrN-e~d~VVLfLctFkDIT~~KQP  139 (971)
T KOG0501|consen   93 NQFEILLYKKNRTPVWLLVQIAPIRN-EKDKVVLFLCTFKDITALKQP  139 (971)
T ss_pred             cceeeEeeecCCCceEEEEEeecccC-CCceEEEEEeecccchhhcCC
Confidence            88999999999999999999999998 888899999999999988864

>COG5002 VicK Signal transduction histidine kinase [Signal transduction mechanisms]

Probab=98.74  E-value=1.3e-07  Score=76.58  Aligned_cols=118  Identities=14%  Similarity=0.233  Sum_probs=92.4

Q ss_pred             HHHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEE
Q 022961           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV   94 (289)
Q Consensus        15 ~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   94 (289)
                      ...+++.+++.++.||++.+|..   |+|+.+|..+.+++|.+.++++|++...+..-.+.-.    +.+.+....+...
T Consensus       108 ~Er~kL~SvlayMtDGViATdRr---G~iI~iN~~A~k~L~~~~E~~~~~~i~elL~i~d~y~----~~dL~e~~~s~ll  180 (459)
T COG5002         108 QERRKLDSVLAYMTDGVIATDRR---GKIILINKPALKMLGVSKEDALGRSILELLKIEDTYT----FEDLVEKNDSLLL  180 (459)
T ss_pred             HHHHHHHHHHHHHcCceEeecCC---CcEEEeccHHHHHhCcCHHHHhcccHHHHhCCcccee----HHHHHhcCCcEEE
Confidence            45678999999999999999999   9999999999999999999999999766654433222    2333333333333


Q ss_pred             EEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhcc
Q 022961           95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG  143 (289)
Q Consensus        95 e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l  143 (289)
                      +.   +..++.+.+++..+.+.. +.|-+.|++++..|+|++.+.|++.
T Consensus       181 d~---~~~~E~~~lrv~Fs~i~r-EsGfisGlIaVlhDvTEqek~e~Er  225 (459)
T COG5002         181 DS---SDEEEGYVLRVNFSVIQR-ESGFISGLIAVLHDVTEQEKVERER  225 (459)
T ss_pred             ee---cCCCccEEEEEEEEEEee-cccccceeEEEEecccHHHHHHHHH
Confidence            32   226777778888899988 8999999999999999999887765

>PF00989 PAS: PAS fold; InterPro: IPR013767 PAS domains are involved in many signalling proteins where they are used as a signal sensor domain []

Probab=98.64  E-value=4.1e-08  Score=68.79  Aligned_cols=43  Identities=21%  Similarity=0.192  Sum_probs=39.6

Q ss_pred             HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      +...+++++++++++|.   +|+|+++|++|++++||+.+|++|+.
T Consensus         3 ~~~i~~~~~~~i~~~d~---~g~I~~~N~a~~~l~g~~~~~~~g~~   45 (113)
T PF00989_consen    3 YRAILENSPDGIFVIDE---DGRILYVNQAAEELLGYSREELIGKS   45 (113)
T ss_dssp             HHHHHHCSSSEEEEEET---TSBEEEECHHHHHHHSS-HHHHTTSB
T ss_pred             HHHHHhcCCceEEEEeC---cCeEEEECHHHHHHHccCHHHHcCCc
Confidence            56789999999999999   99999999999999999999999974

PAS domains appear in archaea, bacteria and eukaryotes. Several PAS-domain proteins are known to detect their signal by way of an associated cofactor. Haeme, flavin, and a 4-hydroxycinnamyl chromophore are used in different proteins. The PAS domain was named after three proteins that it occurs in: Per- period circadian protein Arnt- Ah receptor nuclear translocator protein Sim- single-minded protein. PAS domains are often associated with PAC domains IPR001610 from INTERPRO. It appears that these domains are directly linked, and that together they form the conserved 3D PAS fold. The division between the PAS and PAC domains is caused by major differences in sequences in the region connecting these two motifs []. In human PAS kinase, this region has been shown to be very flexible, and adopts different conformations depending on the bound ligand []. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels [].; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 2GJ3_A 4F3L_B 1XFN_A 1OTD_A 2PYR_A 1KOU_A 1XFQ_A 2ZOI_A 2ZOH_A 1OTA_A ....

>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]

Probab=98.61  E-value=4.6e-07  Score=78.08  Aligned_cols=157  Identities=19%  Similarity=0.175  Sum_probs=112.3

Q ss_pred             HHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEEEEEEe
Q 022961           21 HEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYK  100 (289)
Q Consensus        21 ~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~  100 (289)
                      ..+++.+++++++++..   ..+..+|..+..+++-....++|++...+.++...+...        .+..+........
T Consensus         4 ~~~l~~~~~~~~vi~~~---~~~~~~~~~a~~~~~~~~~~~i~~~~~~i~~~~~~~~v~--------~~~~~~~~~~~~~   72 (560)
T COG3829           4 EGILKSILDGPVVIDKN---TGIDVANALALAKRQKNAEAVIGRPLREILETLGMERVE--------QSRDKELTERLKL   72 (560)
T ss_pred             hhhhhhcccceEEEEcC---CceeeechHHHHhhhcceEEEecccceeeccccCcceee--------ccCccceeeeeec
Confidence            34899999999999998   999999999999999999999999877776554332221        2222222223333


Q ss_pred             cCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhcccccccCCCcchhhhhHHhhcccccccccceeccchhc
Q 022961          101 KDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDRVLA  180 (289)
Q Consensus       101 ~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l~~~~~~~n~~~~~~~~~~~~~~~~~~~~l~e~~~~~~  180 (289)
                      + + ...+.....|+.  +.+++.+++.+..|+++....-++.+                                    
T Consensus        73 ~-~-~~~~~~~~~~~~--~~~~~~g~~~~~~~~~e~~~~~~~~l------------------------------------  112 (560)
T COG3829          73 K-V-KRIVVVGKTPVD--EQGRVVGVLEVFLDISEALELIEENL------------------------------------  112 (560)
T ss_pred             c-c-eeEEEcCCceee--cCCceeeeehhhhhhHHHHHHHHHHH------------------------------------
Confidence            3 2 223333344444  58899999999999998555411100                                    


Q ss_pred             ccCCCCCCccccCccccHHHHHHHHHHhhHHHHhhhcccccccceecccccCCCCCCCcchhHHHHhhcccccEEEeCCC
Q 022961          181 LDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQSFVLIDPH  260 (289)
Q Consensus       181 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~i~i~d~~  260 (289)
                                          +                                    .....+...++.+.++++++|. 
T Consensus       113 --------------------~------------------------------------~~~~~l~~il~~~~~~l~vvD~-  135 (560)
T COG3829         113 --------------------R------------------------------------QLRQRLEAILDSIDDGLLVVDE-  135 (560)
T ss_pred             --------------------H------------------------------------HHHHHHHHHHhhccCceEEEcC-
Confidence                                0                                    0000156678889999999999 


Q ss_pred             CCCCCEEEecHHHHHhhCCChHhHhhc
Q 022961          261 LPDMPMVYASDAFLKLTGAQIFTKITR  287 (289)
Q Consensus       261 ~~~~~i~~vN~~f~~~tGys~~E~~G~  287 (289)
                        +|++++.|++..+++|++.++++|+
T Consensus       136 --~G~~i~~N~~~~~~~gl~~e~~~gk  160 (560)
T COG3829         136 --DGIIIYYNKAYAKLLGLSPEEVLGK  160 (560)
T ss_pred             --CCcEEEEcHHHHHHhCCCHHHHcCC
Confidence              9999999999999999999999997

>PRK11006 phoR phosphate regulon sensor protein; Provisional

Probab=98.61  E-value=1.2e-07  Score=82.99  Aligned_cols=110  Identities=13%  Similarity=0.147  Sum_probs=75.9

Q ss_pred             HHHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEE
Q 022961           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV   94 (289)
Q Consensus        15 ~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   94 (289)
                      ..+++++.+++++|++++++|.+   |+|+++|+++++++||+.++..|++...+..+.   ....    .+... ....
T Consensus        95 ~~~~~~~~~~~~~~~~i~~~d~~---g~i~~~N~~a~~l~g~~~~~~~g~~~~~~~~~~---~~~~----~~~~~-~~~~  163 (430)
T PRK11006         95 NLIKRFRSGAESLPDAVVLTTEE---GNIFWCNGLAQQLLGFRWPEDNGQNILNLLRYP---EFTQ----YLKTR-DFSR  163 (430)
T ss_pred             HHHHHHHHHHHhCCCeEEEEcCC---CceeHHHHHHHHHhCCCChHhCCCcHHHHhcCH---HHHH----HHHhc-ccCC
Confidence            45678999999999999999999   999999999999999999999999866554322   2211    11111 1111


Q ss_pred             EEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhcc
Q 022961           95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG  143 (289)
Q Consensus        95 e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l  143 (289)
                      .......+|.  ++.+...|..+   +   .++.+.+|||++++.|+..
T Consensus       164 ~~~~~~~~~~--~~~~~~~~~~~---~---~~~~~~~dit~~~~~e~~~  204 (430)
T PRK11006        164 PLTLVLNNGR--HLEIRVMPYTE---G---QLLMVARDVTQMHQLEGAR  204 (430)
T ss_pred             CeEEEcCCCC--EEEEEEEEcCC---C---cEEEEEehhhHHHHHHHHH
Confidence            2223344554  44556666643   2   2467789999999886543

>TIGR02938 nifL_nitrog nitrogen fixation negative regulator NifL

Probab=98.57  E-value=4.2e-08  Score=87.16  Aligned_cols=128  Identities=13%  Similarity=0.161  Sum_probs=82.4

Q ss_pred             hHHHhhchHHHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHH
Q 022961            7 LIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAI   86 (289)
Q Consensus         7 ~~~~~l~~~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~   86 (289)
                      +.++.+. +.+..++.++++++++++++|.+   |+++++|+++++++|+...+..+.......++....    .+....
T Consensus       120 ~~e~~l~-~~~~~~~~~~~~~~~~i~~~d~~---~~i~~~N~~~~~~~g~~~~~~~~~~~~~~~~~~~~~----~~~~~~  191 (494)
T TIGR02938       120 RLEQVVA-NQKLLIESVVDAAPVAFVLLDPT---GRVILDNQEYKKLATDLRVKEPAHTVLDLLREAWRE----ALAENW  191 (494)
T ss_pred             HHHHHHH-HHHHHHHHHHhcccceEEEEcCC---CCEEEechhHHHhhchhhhhHHHHHHHHHhhHHhhh----hhhhcc
Confidence            3344444 56678899999999999999999   999999999999999987766655433222222111    111111


Q ss_pred             HhCCCeE-EEEEEEecCCC-EEEEEEEEEEeecCCCCcE---------EEEEEEEecccccHHHHhcc
Q 022961           87 REERPIE-VNLLNYKKDGT-PFWMLFKMSLVFGKEDGRA---------THFVAVQVPIVSRKHMRNSG  143 (289)
Q Consensus        87 ~~~~~~~-~e~~~~~~~g~-~~~~~~~~~~~~~~~~g~~---------~~~~~~~~DITe~k~~e~~l  143 (289)
                      ..+..+. .+......+|. .+|+.....|+.. ..|..         .+++++++|||++|++|+++
T Consensus       192 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~DITe~k~~ee~l  258 (494)
T TIGR02938       192 PQQLAFSNREARFDRGGGRPARWLSCTGSVIGM-ESDCADSFFCAAEQPYLLLTIADISNLREEQERA  258 (494)
T ss_pred             hhhhccccceeeeccCCCceeeEEEecCceEEe-ecchhhheeccCCCchheehHHHHHHHHHHHHHH
Confidence            1111111 23334444544 6888888777765 44433         34566789999999987764

NifL is a modulator of the nitrogen fixation positive regulator protein NifA, and is therefore a negative regulator. It binds NifA. NifA and NifL are encoded by adjacent genes.

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=98.52  E-value=7.2e-07  Score=79.47  Aligned_cols=110  Identities=14%  Similarity=0.139  Sum_probs=78.6

Q ss_pred             HHHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEE
Q 022961           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV   94 (289)
Q Consensus        15 ~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   94 (289)
                      +....+..+++++++||+++|.+   |+|+++|+++++++|++.++++|+++..+++...       +...+..+.....
T Consensus        77 ~e~~~L~aIL~sm~eGVi~vD~~---G~I~~iN~aA~~Llg~~~eel~Gk~i~eli~~~~-------l~~~le~~~~~~~  146 (520)
T PRK10820         77 REHRALSALLEALPEPVLSIDMK---GKVELANPASCQLFGQSEEKLRNHTAAQLINGFN-------FLRWLESEPQDSH  146 (520)
T ss_pred             HHHHHHHHHHHhCCCcEEEECCC---CeeeHhHHHHHHHHCcCHHHHCCCcHHHHcCcch-------HHHHHHcCCCccc
Confidence            44567899999999999999999   9999999999999999999999999887765422       2233444433111


Q ss_pred             EEEEEecCCCEEEEEEEEEEee--cCCCCcE--EEEEEEEecccccHH
Q 022961           95 NLLNYKKDGTPFWMLFKMSLVF--GKEDGRA--THFVAVQVPIVSRKH  138 (289)
Q Consensus        95 e~~~~~~~g~~~~~~~~~~~~~--~~~~g~~--~~~~~~~~DITe~k~  138 (289)
                      . .....+|..++  +...|+.  + +.|..  .|.+.+.+|+++..+
T Consensus       147 ~-~~v~~~g~~~~--v~~~PI~~~d-~~g~~~~~GaVivlrd~~~l~~  190 (520)
T PRK10820        147 N-EHVVINGQDFL--MEITPVYLQD-ENDQHVLVGAVVMLRSTARMGR  190 (520)
T ss_pred             e-EEEEECCEEEE--EEEEeeeecC-CCCceeEEEEEEEeccHHHHHH
Confidence            1 12234566555  5556765  5 45543  788999999987643

>PF13426 PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_B 3P7N_B 1LL8_A 3MJQ_A 3BWL_A 4EET_B 4EEP_A

Probab=98.48  E-value=1.3e-07  Score=65.03  Aligned_cols=34  Identities=26%  Similarity=0.444  Sum_probs=30.1

Q ss_pred             cccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhc
Q 022961          251 KQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITR  287 (289)
Q Consensus       251 ~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~  287 (289)
                      |+|+++.|+   +|+|+++|++|++++||+++|++|+
T Consensus         1 p~~i~i~d~---~g~i~~~N~~~~~~~g~~~~~~~g~   34 (104)
T PF13426_consen    1 PDGIFILDP---DGRILYVNPAFERLFGYSREELIGK   34 (104)
T ss_dssp             -SEEEEEET---TSBEEEE-HHHHHHHTS-HHHHTTS
T ss_pred             CEEEEEECC---cCcEEehhHHHHHHHCcCHHHHcCC
Confidence            579999999   9999999999999999999999997

...

>PF13188 PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A

Probab=98.41  E-value=5.9e-07  Score=56.11  Aligned_cols=42  Identities=24%  Similarity=0.438  Sum_probs=35.5

Q ss_pred             HHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCC
Q 022961           18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNG   66 (289)
Q Consensus        18 ~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~   66 (289)
                      ++++.+++++|.+++++| +   ++|+++|+++++++||+   ..|+..
T Consensus         1 e~~~~l~~~~~~~i~i~d-~---~~i~~~N~~~~~l~g~~---~~~~~~   42 (64)
T PF13188_consen    1 ERYRSLFDNSPDGILIID-G---GRIIYVNPAFEELFGYS---LEGEDI   42 (64)
T ss_dssp             HHHHHHHCCSSSEEEEEE-T---SBEEEE-HHHHHHHCS----HTCCCH
T ss_pred             CHHHHHHHcCccceEEEE-C---CChHHhhHHHHHHhCCC---CCCCCH
Confidence            468899999999999999 9   99999999999999998   555554

>COG2202 AtoS FOG: PAS/PAC domain [Signal transduction mechanisms]

Probab=98.32  E-value=2.6e-05  Score=59.25  Aligned_cols=119  Identities=24%  Similarity=0.365  Sum_probs=85.4

Q ss_pred             HHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHH-HHHHHHHHH-HhCCCeE
Q 022961           16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRR-TIMEIREAI-REERPIE   93 (289)
Q Consensus        16 ~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~-~~~~~~~~~-~~~~~~~   93 (289)
                      ...++..+++..+++++..|.+   +.+.++|+.+..++|++..+..+.....+........ ......... .......
T Consensus       110 ~~~~~~~~~~~~~~~~~~~d~~---~~~~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  186 (232)
T COG2202         110 SEERLRALLEASPDGIWVLDED---GRILYANPAAEELLGYSPEEELGRGLSDLIHPEDEERRELELARALAEGRGGPLE  186 (232)
T ss_pred             HHHHHHHHHhhCCceEEEEeCC---CCEEEeCHHHHHHhCCChHHhcCCChhheEecCCCchhhHHHHHHhhccCCCCcc
Confidence            4445888999999999999999   9999999999999999987777776554443322221 111112222 2223456


Q ss_pred             EEEEEEecCCCE-EEEEEEEEEeecCCCCcEEEEEEEEecccccHHH
Q 022961           94 VNLLNYKKDGTP-FWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM  139 (289)
Q Consensus        94 ~e~~~~~~~g~~-~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~  139 (289)
                      .+.....++|.. .+......+...  .|.+..+.....|+++++..
T Consensus       187 ~~~~~~~~~g~~~~~~~~~~~~~~~--~~~~~~~~~~~~d~~~~~~~  231 (232)
T COG2202         187 IEYRVRRKDGERVRWILSRISPVRD--DGEIVGVVGIARDITERKQA  231 (232)
T ss_pred             eEEEEEecCCCEEEEEEeeeeEecC--CCceEEEEEEEechHHHhhc
Confidence            777788899986 777777776653  67888888999999988764

>PRK11086 sensory histidine kinase DcuS; Provisional

Probab=98.30  E-value=5.9e-06  Score=74.54  Aligned_cols=112  Identities=10%  Similarity=0.124  Sum_probs=78.1

Q ss_pred             HHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCc---cccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCe
Q 022961           16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSR---AEIIGRNGRMFQGPRTNRRTIMEIREAIREERPI   92 (289)
Q Consensus        16 ~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~---~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~   92 (289)
                      ..+.++.++++++++++++|.+   |+|+++|+++++++|++.   .+.+|+....+.++       ..+...+..+...
T Consensus       219 l~~~~~~il~~~~~gIi~~D~~---g~I~~~N~~a~~llg~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~  288 (542)
T PRK11086        219 LFEQRQAMLQSIKEGVIAVDDR---GEVTLINDEAKRLFNYKKGLEDDPLGTDVESWMPV-------SRLKEVLRTGTPR  288 (542)
T ss_pred             HHHHHHHHHHHhcCcEEEECCC---CeEEEEhHHHHHHhCCCcCCcccccCCcHHHhCCc-------hhHHHHHhcCCCc
Confidence            3456688999999999999999   999999999999998753   35556554443321       1233444444433


Q ss_pred             EEEEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhcc
Q 022961           93 EVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG  143 (289)
Q Consensus        93 ~~e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l  143 (289)
                      ....  ...+|.  ++.+...|+.+  +|.+.+++.+.+|+|+.++.++++
T Consensus       289 ~~~~--~~~~g~--~~~~~~~pi~~--~g~~~g~v~~~rDite~~~l~~~l  333 (542)
T PRK11086        289 RDEE--ININGR--LLLTNTVPVRV--NGEIIGAIATFRDKTEVRQLAQRL  333 (542)
T ss_pred             cceE--EEECCE--EEEEEEEEEeE--CCEEEEEEEEEEEchHHHHHHHHH
Confidence            2211  122444  34566778886  788899999999999999886665

>PRK10060 RNase II stability modulator; Provisional

Probab=98.21  E-value=1.9e-06  Score=79.52  Aligned_cols=43  Identities=12%  Similarity=0.055  Sum_probs=39.3

Q ss_pred             HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      +..+++.++++|+++|.   +|+|+++|++|+++|||+.+|++|+-
T Consensus       113 ~~~v~~~~~~gI~i~D~---~g~I~~~N~a~~~l~Gy~~~eliG~~  155 (663)
T PRK10060        113 AEQVVSEANSVIVILDS---RGNIQRFNRLCEEYTGLKEHDVIGQS  155 (663)
T ss_pred             HHHHHhhCCceEEEEeC---CCCEEEEcHHHHHHHCcCHHHHcCCC
Confidence            44578888999999999   99999999999999999999999973

>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]

Probab=98.17  E-value=6.9e-06  Score=71.04  Aligned_cols=116  Identities=16%  Similarity=0.342  Sum_probs=86.1

Q ss_pred             HHHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEE
Q 022961           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV   94 (289)
Q Consensus        15 ~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   94 (289)
                      +..+.|..+++.+.++++++|.+   |.++++|.+...++|++.++++|++...+.....+    ....+++..+.+...
T Consensus       114 ~~~~~l~~il~~~~~~l~vvD~~---G~~i~~N~~~~~~~gl~~e~~~gk~~~~v~~~~~~----s~~l~vl~~~kp~~~  186 (560)
T COG3829         114 QLRQRLEAILDSIDDGLLVVDED---GIIIYYNKAYAKLLGLSPEEVLGKHLLDVVSAGED----STLLEVLRTGKPIRD  186 (560)
T ss_pred             HHHHHHHHHHhhccCceEEEcCC---CcEEEEcHHHHHHhCCCHHHHcCCcHHHHHhccCC----ceehhhhhcCCccee
Confidence            45578899999999999999999   99999999999999999999999986665411111    123456667776555


Q ss_pred             EEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhcc
Q 022961           95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG  143 (289)
Q Consensus        95 e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l  143 (289)
                      ....+..+..    .....|+..  +|.+.+.+++..|+++.+....++
T Consensus       187 ~~~~~~~~~~----i~~~~pv~~--~g~l~G~v~~~~~~~~l~~l~~~~  229 (560)
T COG3829         187 VVQTYNGNKI----IVNVAPVYA--DGQLIGVVGISKDVSELERLTREL  229 (560)
T ss_pred             eeeeecCCce----eEeeccEec--CCcEEEEEEeecchHHHHHHHHHH
Confidence            4433332222    355566764  779999999999999888775555

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=98.12  E-value=4e-05  Score=70.53  Aligned_cols=42  Identities=10%  Similarity=0.071  Sum_probs=37.8

Q ss_pred             HHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          244 YISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       244 ~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      ...++...++|++.|.   +|+|+++|+++++++|++.++++|+.
T Consensus       206 ~~il~~~~~gVl~vD~---~G~I~~~N~aa~~llg~s~~~l~G~~  247 (638)
T PRK11388        206 NALLESMDDGVIAWDE---QGNLQFLNAQAARLLRLDATASQGRA  247 (638)
T ss_pred             HHHHhccCCcEEEECC---CCeEehhhHHHHHHhCcCHHHHCCCc
Confidence            3456777899999999   99999999999999999999999974

>PF13188 PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A

Probab=98.10  E-value=4.7e-06  Score=51.96  Aligned_cols=34  Identities=21%  Similarity=0.330  Sum_probs=29.0

Q ss_pred             HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCC
Q 022961          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQ  280 (289)
Q Consensus       243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys  280 (289)
                      +...++++++||++.|    +++|+++|++|++++||+
T Consensus         3 ~~~l~~~~~~~i~i~d----~~~i~~~N~~~~~l~g~~   36 (64)
T PF13188_consen    3 YRSLFDNSPDGILIID----GGRIIYVNPAFEELFGYS   36 (64)
T ss_dssp             HHHHHCCSSSEEEEEE----TSBEEEE-HHHHHHHCS-
T ss_pred             HHHHHHcCccceEEEE----CCChHHhhHHHHHHhCCC
Confidence            5678999999999999    348999999999999999

>KOG1229 consensus 3'5'-cyclic nucleotide phosphodiesterases [Signal transduction mechanisms]

Probab=98.07  E-value=2.5e-06  Score=71.18  Aligned_cols=106  Identities=23%  Similarity=0.362  Sum_probs=86.4

Q ss_pred             HHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCC-CCHHHHHHHHHHHHhCCCeEEEEE
Q 022961           19 WVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPR-TNRRTIMEIREAIREERPIEVNLL   97 (289)
Q Consensus        19 ~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~-~~~~~~~~~~~~~~~~~~~~~e~~   97 (289)
                      .+..+++....++-+.|.+   ..|.|+|++|+.|+||-..|++|++..++...+ ....+.+.+...++.|..|+++..
T Consensus       158 alFaaLD~c~eAiEI~~dd---hViQYVNpAfE~mmG~hkgEliGke~adlpkkdknradlldtintcikkgke~qG~~~  234 (775)
T KOG1229|consen  158 ALFAALDECDEAIEICDDD---HVIQYVNPAFENMMGCHKGELIGKEEADLPKKDKNRADLLDTINTCIKKGKEAQGEEE  234 (775)
T ss_pred             HHHHHHhhhhhhheeccch---hHHHHhcHHHHhhhcchhhhhcCCchhhccccccchhhhhhhhhHhhhcCccccchHH
Confidence            3445788888999999998   999999999999999999999999988776433 234566777788888999999888


Q ss_pred             EEecCCCEEEEEEEEEEeecCCCCcEEEEEE
Q 022961           98 NYKKDGTPFWMLFKMSLVFGKEDGRATHFVA  128 (289)
Q Consensus        98 ~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~  128 (289)
                      .+++.|......+.+.|+.. ..|.+..++.
T Consensus       235 aRRksgdS~dqh~~itP~~g-qggkirhfvs  264 (775)
T KOG1229|consen  235 ARRKSGDSCDQHFIITPFAG-QGGKIRHFVS  264 (775)
T ss_pred             HhhccCCcccceEEEeeecC-CCCceeeehh
Confidence            88888888777788899987 6777766653

>PRK13557 histidine kinase; Provisional

Probab=97.91  E-value=1.5e-05  Score=71.85  Aligned_cols=46  Identities=28%  Similarity=0.557  Sum_probs=41.8

Q ss_pred             HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      +...++.++++++++|+..++|+|+|+|++|++++||+.+|++|+.
T Consensus        32 ~~~~~~~~~~~i~v~d~~~~~g~i~~~N~a~~~~~G~~~~e~~g~~   77 (540)
T PRK13557         32 FFAAVETTRMPMIVTDPNQPDNPIVFANRAFLEMTGYAAEEIIGNN   77 (540)
T ss_pred             HHHHHHhCcCcEEEEcCCCCCCCEEEEcHHHHHHhCCCHHHhcCCC
Confidence            6778999999999999755689999999999999999999999973

>PF08448 PAS_4: PAS fold; InterPro: IPR013656 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []

Probab=97.89  E-value=1.5e-05  Score=55.28  Aligned_cols=39  Identities=33%  Similarity=0.395  Sum_probs=35.4

Q ss_pred             hhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          247 LGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       247 ~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      ++++++++++.|.   +++|+++|+++.+++|++.++++|+-
T Consensus         1 l~~~p~~i~v~D~---~~~i~~~N~~~~~~~~~~~~~~~G~~   39 (110)
T PF08448_consen    1 LDSSPDGIFVIDP---DGRIVYANQAAAELFGVSPEELIGRS   39 (110)
T ss_dssp             HHHCSSEEEEEET---TSBEEEE-HHHHHHHTSTHHHHTTSB
T ss_pred             CCCCCceeEEECC---CCEEEEEHHHHHHHhCCCHHHHhhcc
Confidence            4678999999999   99999999999999999999999973

The PAS fold appears in archaea, eubacteria and eukarya. ; PDB: 3K3D_A 3K3C_B 3KX0_X 3FC7_B 3LUQ_D 3MXQ_A 3BWL_C 3FG8_A.

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=97.86  E-value=0.00017  Score=66.41  Aligned_cols=108  Identities=12%  Similarity=0.228  Sum_probs=75.7

Q ss_pred             HHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEEEEE
Q 022961           19 WVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLN   98 (289)
Q Consensus        19 ~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~   98 (289)
                      .+..++++++++++++|.+   |+|+++|+++++++|++.++++|++...+++..      ..+..++..+..+......
T Consensus       204 ~~~~il~~~~~gVl~vD~~---G~I~~~N~aa~~llg~s~~~l~G~~i~~l~~~~------~~l~~vl~~~~~~~~~~~~  274 (638)
T PRK11388        204 QLNALLESMDDGVIAWDEQ---GNLQFLNAQAARLLRLDATASQGRAITELLTLP------AVLQQAIKQAHPLKHVEVT  274 (638)
T ss_pred             HHHHHHhccCCcEEEECCC---CeEehhhHHHHHHhCcCHHHHCCCcHHHHhccc------hHHHHHHhcCCceeeEEEE
Confidence            3455899999999999999   999999999999999999999999877665321      1233455555544332222


Q ss_pred             EecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHH
Q 022961           99 YKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKH  138 (289)
Q Consensus        99 ~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~  138 (289)
                      ...+|..+++.+...|+.+ ..|.  +++.+..|++..++
T Consensus       275 l~~~g~~~~~~v~~~Pi~~-~~g~--~~v~~l~~~~~~~~  311 (638)
T PRK11388        275 FESQGQFIDAVITLKPIIE-GQGT--SFILLLHPVEQMRQ  311 (638)
T ss_pred             EecCCceEEEEEEEEeecc-cCce--EEEEEehhhHHHHH
Confidence            3345777788888899865 3443  24555678776544

>PRK15053 dpiB sensor histidine kinase DpiB; Provisional

Probab=97.83  E-value=0.00012  Score=66.19  Aligned_cols=110  Identities=14%  Similarity=0.072  Sum_probs=75.1

Q ss_pred             HHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCc--cccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEE
Q 022961           17 TLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSR--AEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV   94 (289)
Q Consensus        17 ~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~--~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   94 (289)
                      ...+..+++++++|++++|.+   |+|+++|+++++++|++.  ++++|++...+.++...  .    ..... ......
T Consensus       221 ~~~~~~il~~~~egii~~D~~---g~I~~~N~~a~~ll~~~~~~~~~~g~~~~~~~~~~~~--~----~~~~~-~~~~~~  290 (545)
T PRK15053        221 VRQQEALFSSVYEGLIAVDPH---GYITAINRNARKMLGLSSPGRQWLGKPIAEVVRPADF--F----TEQID-EKRQDV  290 (545)
T ss_pred             HHHHHHHHHHhCceEEEECCC---CeEEeecHHHHHHhCCCCcchhhcCCcHHHhCCCchh--h----hhhcC-Ccccce
Confidence            345678999999999999999   999999999999999965  46889886666543211  1    11111 111111


Q ss_pred             EEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhcc
Q 022961           95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG  143 (289)
Q Consensus        95 e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l  143 (289)
                      .   ...+|.  .+.....|+..  .+.+.+.+...+|+|+.++.++++
T Consensus       291 ~---~~~~~~--~~~~~~~~i~~--~~~~~G~v~~~~d~te~~~l~~~l  332 (545)
T PRK15053        291 V---ANFNGL--SVIANREAIRS--GDDLLGAIISFRSKDEISTLNAQL  332 (545)
T ss_pred             E---EEECCE--EEEEEeeeEEE--CCeEEEEEEEEEchHHHHHHHHHH
Confidence            1   122443  34466777775  667788999999999988776555

>COG3290 CitA Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]

Probab=97.78  E-value=0.00012  Score=63.46  Aligned_cols=112  Identities=13%  Similarity=0.156  Sum_probs=83.8

Q ss_pred             HHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCcc--ccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEE
Q 022961           17 TLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRA--EIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV   94 (289)
Q Consensus        17 ~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~--e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   94 (289)
                      -+.-..+++++..|++.+|..   |.+..+|.++++|+|+...  +.+|++...+.+|+..      +...++.+++...
T Consensus       214 ~~er~A~l~si~EGviAvd~~---G~It~~N~~A~~ll~~~~~~~~~ig~~i~~v~~p~~~------l~~vl~~~~~~~~  284 (537)
T COG3290         214 LEERQAMLQSIKEGVIAVDKK---GVITLINQAAQKLLGLRQPSGDPIGRSIVEVLPPDSD------LPEVLETGKPQHD  284 (537)
T ss_pred             HHHHHHHHHHhhceEEEECCC---CeEeehhHHHHHHhcccCcCcccccccceEeeccccC------cHHHHhcCCcccc
Confidence            344567899999999999999   9999999999999999765  6889988887776221      2233445544332


Q ss_pred             EEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhcc
Q 022961           95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG  143 (289)
Q Consensus        95 e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l  143 (289)
                      +.  .+-+|.  ++.+...|+..  .|++.+.+.+++|-|+-++.-++|
T Consensus       285 ~e--~~~ng~--~~i~nr~pI~~--~~~~~GaI~tFRdktei~~L~eqL  327 (537)
T COG3290         285 EE--IRINGR--LLVANRVPIRS--GGQIVGAIITFRDKTEIKKLTEQL  327 (537)
T ss_pred             hh--hhcCCe--EEEEEeccEEE--CCEEeEEEEEEecHHHHHHHHHHH
Confidence            22  223454  45577788886  889999999999999998886666

>PRK13559 hypothetical protein; Provisional

Probab=97.75  E-value=4.3e-05  Score=65.31  Aligned_cols=46  Identities=33%  Similarity=0.577  Sum_probs=40.7

Q ss_pred             HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      +...++.++++++++|...++++|+++|++|++++||+.+|++|+.
T Consensus        45 ~~~~~e~~~~~i~i~D~~~~~g~i~~~N~a~~~l~G~~~~e~iG~~   90 (361)
T PRK13559         45 FEQAMEQTRMAMCITDPHQPDLPIVLANQAFLDLTGYAAEEVVGRN   90 (361)
T ss_pred             HHHHHHhCCCcEEEecCCCCCCcEEEEchHHHHHhCCCHHHHcCCC
Confidence            5667899999999999744567899999999999999999999974

>COG5000 NtrY Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]

Probab=97.73  E-value=0.00035  Score=61.35  Aligned_cols=115  Identities=11%  Similarity=0.046  Sum_probs=78.7

Q ss_pred             HHHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhC-CCeE
Q 022961           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREE-RPIE   93 (289)
Q Consensus        15 ~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~-~~~~   93 (289)
                      +..+.++.+++..+.|++..|.+   |.+.-+|++.++|+|.+.++++|.+.+.+.+     .+...+...-..+ ....
T Consensus       367 ~rr~f~E~VLsgvtaGVi~~d~~---g~i~t~N~~ae~~l~~~~~~~~G~~lsa~ap-----~~~~vf~~~~a~~~~~~~  438 (712)
T COG5000         367 QRRRFLEAVLSGLTAGVIGFDNR---GCITTVNPSAEQILGKPFDQLLGQSLSAIAP-----ELEEVFAEAGAAARTDKR  438 (712)
T ss_pred             HHHHHHHHHHhcCceeEEEEcCC---CeeEeecchHHHHhcCChhHhhcchhhhhhh-----HHHHHHHHhhhhcCCCcc
Confidence            34567788999999999999999   9999999999999999999999998665532     1222222222221 2223


Q ss_pred             EEEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHh
Q 022961           94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRN  141 (289)
Q Consensus        94 ~e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~  141 (289)
                      .+..+ ...|+...+.+..+.... ++|  .+++.++-|||+...+|.
T Consensus       439 ~ev~~-~r~g~~rtl~Vq~t~~~~-d~~--~gyVvt~DDITdLV~AQR  482 (712)
T COG5000         439 VEVKL-AREGEERTLNVQATREPE-DNG--NGYVVTFDDITDLVIAQR  482 (712)
T ss_pred             ceeec-ccCCCceeeeeeeeeccc-ccC--CceEEEecchHHHHHHHH
Confidence            34333 344555566666555544 322  468889999999988854

>PF08670 MEKHLA: MEKHLA domain; InterPro: IPR013978 The MEKHLA domain shares similarity with the PAS domain and is found in the 3' end of plant HD-ZIP III homeobox genes, and bacterial proteins

Probab=97.72  E-value=0.0016  Score=47.34  Aligned_cols=112  Identities=11%  Similarity=0.102  Sum_probs=77.3

Q ss_pred             HHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEEEE
Q 022961           18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLL   97 (289)
Q Consensus        18 ~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~   97 (289)
                      ..++.++. .|.+|+-.+.. ++-.++|.|.++.+|++++-+++.+.+.+.-..+.........+.++.+.|-.....-.
T Consensus        32 ~~~~~L~~-ap~ailsh~~~-~dP~f~yaN~aaL~l~e~~w~el~~lPsr~sae~~~r~er~~lL~~v~~qG~~~~y~Gi  109 (148)
T PF08670_consen   32 ELAKALWH-APFAILSHGTK-ADPIFIYANQAALDLFETTWDELVGLPSRLSAEEPERKERQSLLAQVMQQGYIDNYSGI  109 (148)
T ss_pred             HHHHHHHc-CCCEEEEcCCC-CCCEEEehhHHHHHHhcCCHHHHhcCcHhhccChhhHHHHHHHHHHHHHhCCccCCCeE
Confidence            44555555 88888877654 44789999999999999999999999877655555555555666666666654333333


Q ss_pred             EEecCCCEEEEEE-EEEEeecCCCCcEEEEEEEEec
Q 022961           98 NYKKDGTPFWMLF-KMSLVFGKEDGRATHFVAVQVP  132 (289)
Q Consensus        98 ~~~~~g~~~~~~~-~~~~~~~~~~g~~~~~~~~~~D  132 (289)
                      -..+.|+.++++- ++-.+.| ++|...+.-.+..+
T Consensus       110 Riss~Grrf~ie~a~vW~l~D-~~g~~~GqAa~F~~  144 (148)
T PF08670_consen  110 RISSTGRRFRIERATVWNLID-EDGNYCGQAAMFSN  144 (148)
T ss_pred             EEcCCCCeEEEeceEEEEEEc-CCCCEEEEEEEEee
Confidence            4578898887763 4455666 68877766554443

>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional

Probab=97.67  E-value=0.00065  Score=67.38  Aligned_cols=44  Identities=9%  Similarity=0.041  Sum_probs=38.3

Q ss_pred             HHHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCcccc
Q 022961           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEI   61 (289)
Q Consensus        15 ~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~   61 (289)
                      ....+++.+++++|++++++|.+   |+++++|+++++++|++....
T Consensus       573 ~~~~~~~~i~~~~~~~i~~~d~~---g~i~~~N~~~~~~~g~~~~~~  616 (1197)
T PRK09959        573 NQISFRKALSDSLPNPTYVVNWQ---GNVISHNSAFEHYFTADYYKN  616 (1197)
T ss_pred             HHHHHHHHHHhhCCCcEEEEcCC---CcEEEehHHHHHHhCcccccc
Confidence            45567788999999999999999   999999999999999875433

>KOG3558 consensus Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms; Transcription]

Probab=97.59  E-value=0.00078  Score=59.77  Aligned_cols=59  Identities=15%  Similarity=0.173  Sum_probs=50.2

Q ss_pred             HHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHH
Q 022961           22 EALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIR   83 (289)
Q Consensus        22 ~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~   83 (289)
                      .+++++..-+++++.+   |.++|+++.....+|++.-|+.|.++.+++||.+...+.+.+.
T Consensus       123 ~iLqsLDGFVm~l~~d---G~~lYiSEtVS~yLGLSQvELTG~SvFDfiHP~DheE~~eqL~  181 (768)
T KOG3558|consen  123 HILQSLDGFVMALTQD---GDFLYISETVSIYLGLSQVELTGSSVFDFIHPCDHEEIAEQLG  181 (768)
T ss_pred             hHHhhccceEEEEccC---CCEEEEechhHhhhCccceeeecchhhhccCccCHHHHHHHhc
Confidence            3566666667888999   9999999999999999999999999999999998877665543

>KOG3558 consensus Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms; Transcription]

Probab=97.53  E-value=0.00016  Score=63.89  Aligned_cols=89  Identities=11%  Similarity=0.277  Sum_probs=75.6

Q ss_pred             ccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEEEEEEecCCCEEEEEEEEEEeecCCC
Q 022961           41 HPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKED  120 (289)
Q Consensus        41 g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~~~~~~~~~~~~~~~  120 (289)
                      -+|.|+.+.+..++||.+++++|+++..++|+.+...+.....+.+..|.....-+++..++|...|+...++.+....+
T Consensus       284 mkityCedRisdlm~y~PeeLvGrS~Ye~~Ha~Ds~~v~KSh~dL~~KGQv~TgyYR~lak~GGyvWlQTqATVi~~tkn  363 (768)
T KOG3558|consen  284 MKITYCEDRISDLMDYEPEELVGRSCYEFVHALDSDRVRKSHHDLLTKGQVVTGYYRLLAKNGGYVWLQTQATVIYNTKN  363 (768)
T ss_pred             eeEEEEchhHHHHhcCCHHHhhchhHHHhhhHhhhhHHHHHHHHHHhcCccchhHHHHHHhcCCeEEEEeeeEEEecCCC
Confidence            78999999999999999999999999999999888888888888888888888889999999999999999888865223


Q ss_pred             CcEEEEEEE
Q 022961          121 GRATHFVAV  129 (289)
Q Consensus       121 g~~~~~~~~  129 (289)
                      ++-..++++
T Consensus       364 ~q~q~IicV  372 (768)
T KOG3558|consen  364 PQEQNIICV  372 (768)
T ss_pred             CCcceEEEE
Confidence            333344443

>smart00091 PAS PAS domain

Probab=97.48  E-value=0.00038  Score=41.26  Aligned_cols=54  Identities=24%  Similarity=0.417  Sum_probs=44.8

Q ss_pred             HHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCC
Q 022961           19 WVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTN   75 (289)
Q Consensus        19 ~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~   75 (289)
                      +++.+++.+++++++++..   +.+.++|+.+..++|++..++.+..+..+.++.+.
T Consensus         2 ~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   55 (67)
T smart00091        2 RLRAILESLPDGIFVLDLD---GRILYANPAAEELLGYSPEELIGKSLLELIHPEDR   55 (67)
T ss_pred             hHHHHHhhCCceEEEEcCC---CeEEEECHHHHHHhCCCHHHHcCCcHHHhcCcccH
Confidence            3566888999999999998   99999999999999999988888776555555443

PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels ([1]; Ponting & Aravind, in press).

>COG3852 NtrB Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]

Probab=97.40  E-value=0.0014  Score=52.91  Aligned_cols=96  Identities=13%  Similarity=0.124  Sum_probs=74.5

Q ss_pred             HHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeE-EEEEEE
Q 022961           21 HEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIE-VNLLNY   99 (289)
Q Consensus        21 ~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~-~e~~~~   99 (289)
                      ..++++.+..++++|.+   +.|.|+|++++.+||.+...+.+.+.+.+++..  ......+.+....+..+. .+..+ 
T Consensus        10 ~~~Ln~~~~pVl~vd~~---~~i~yaN~aAe~~~~~Sa~~L~~~~l~~l~~~g--s~ll~ll~q~~~~~~~~~~~~v~l-   83 (363)
T COG3852          10 GAILNNLINPVLLVDDE---LAIHYANPAAEQLLAVSARRLAGTRLSELLPFG--SLLLSLLDQVLERGQPVTEYEVTL-   83 (363)
T ss_pred             HhHHhccCCceEEEcCC---CcEEecCHHHHHHHHHHHHHHhcCChHHHcCCC--cHHHHHHHHHHHhcCCcccceeee-
Confidence            46899999999999999   999999999999999999999999988877543  344555666666665543 23333 


Q ss_pred             ecCCCEEEEEEEEEEeecCCCCcE
Q 022961          100 KKDGTPFWMLFKMSLVFGKEDGRA  123 (289)
Q Consensus       100 ~~~g~~~~~~~~~~~~~~~~~g~~  123 (289)
                      ..+|....+...+.|+.. ..|.+
T Consensus        84 ~~~g~~~~v~~~v~~v~~-~~G~v  106 (363)
T COG3852          84 VILGRSHIVDLTVAPVPE-EPGSV  106 (363)
T ss_pred             eecCccceEEEEEeeccC-CCCeE
Confidence            268888899999999986 56654

>PRK11006 phoR phosphate regulon sensor protein; Provisional

Probab=97.38  E-value=0.00014  Score=63.78  Aligned_cols=42  Identities=10%  Similarity=0.090  Sum_probs=39.3

Q ss_pred             HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhc
Q 022961          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITR  287 (289)
Q Consensus       243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~  287 (289)
                      +...++.+++++++.|.   +|+|+++|+++++++||+.+|++|+
T Consensus       100 ~~~~~~~~~~~i~~~d~---~g~i~~~N~~a~~l~g~~~~~~~g~  141 (430)
T PRK11006        100 FRSGAESLPDAVVLTTE---EGNIFWCNGLAQQLLGFRWPEDNGQ  141 (430)
T ss_pred             HHHHHHhCCCeEEEEcC---CCceeHHHHHHHHHhCCCChHhCCC
Confidence            56678999999999999   9999999999999999999999886

>PRK11091 aerobic respiration control sensor protein ArcB; Provisional

Probab=97.32  E-value=0.00028  Score=66.73  Aligned_cols=43  Identities=19%  Similarity=-0.011  Sum_probs=40.3

Q ss_pred             HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      +...++.++++|++.|.   +|+|+++|++|++++||+.+|++|+.
T Consensus       157 l~~il~~~~~~i~~~D~---~g~i~~~N~a~~~l~G~~~~eliG~~  199 (779)
T PRK11091        157 LRSFLDASPDLVYYRNE---DGEFSGCNRAMELLTGKSEKQLIGLT  199 (779)
T ss_pred             HHHHHhcCcceEEEECC---CCcEEeEcHHHHHHhCcCHHHHcCCC
Confidence            66788999999999999   99999999999999999999999973

>TIGR00229 sensory_box PAS domain S-box

Probab=97.30  E-value=0.00045  Score=46.92  Aligned_cols=42  Identities=19%  Similarity=0.263  Sum_probs=38.2

Q ss_pred             HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhc
Q 022961          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITR  287 (289)
Q Consensus       243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~  287 (289)
                      +...++.++.+++++|.   +++|+++|++|++++||+.++++|+
T Consensus         5 ~~~~~~~~~~~~~~~d~---~~~i~~~n~~~~~~~g~~~~~~~~~   46 (124)
T TIGR00229         5 YRAIFESSPDAIIVIDL---EGNILYVNPAFEEIFGYSAEELIGR   46 (124)
T ss_pred             HHHHHhhCCceEEEEcC---CCcEEEEchHHHHHhCCChHHhcCc
Confidence            45678888999999999   9999999999999999999998875

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.

>TIGR02373 photo_yellow photoactive yellow protein

Probab=97.17  E-value=0.006  Score=42.55  Aligned_cols=67  Identities=18%  Similarity=0.076  Sum_probs=52.9

Q ss_pred             HHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCC-CccCCCCCHHHHHHHHHHHHhCC
Q 022961           21 HEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGR-MFQGPRTNRRTIMEIREAIREER   90 (289)
Q Consensus        21 ~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~-~l~~~~~~~~~~~~~~~~~~~~~   90 (289)
                      ..-++..|-|++-+|.+   |.|+..|.+-..+.|++++.++|+++. ++-+.-..+.+...+.+..+.+.
T Consensus        19 ~eelD~lpFGvI~lD~~---G~V~~YN~aE~~~sg~~p~~vlGr~FF~eVAPC~~~~~f~gRF~~g~~~g~   86 (124)
T TIGR02373        19 DAQFDALPFGAIQLDGS---GVILRYNAAEGRITGRDPERVIGRNFFKEVAPCTDIPEFSGRFMEGVASGT   86 (124)
T ss_pred             HhHhhcCCcceEEECCC---CEEEEEecchhhhcCCChhhhhchhhhhhcccccCCHHHHHHHHhhhhcCC
Confidence            34589999999999999   999999999999999999999999844 44443444556666666555554

Members of this family are photoactive yellow protein, a cytosolic, 14-kDa light-sensing protein which has a 4-hydroxycinnamyl (p-coumaric acid) chromophore covalently linked to a Cys residue. The enzyme 4-coumarate--CoA ligase as described by TIGR02372 is required for its biosynthesis. The modified Cys is in a PAS (pfam00989) domain, frequently found in signal transducing proteins. Members are known in alpha and gamma Proteobacteria that include Rhodobacter capsulatus, Halorhodospira halophila, Rhodospirillum centenum, etc.

>COG2461 Uncharacterized conserved protein [Function unknown]

Probab=97.14  E-value=0.0018  Score=53.82  Aligned_cols=114  Identities=16%  Similarity=0.187  Sum_probs=86.6

Q ss_pred             HHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEEE
Q 022961           17 TLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNL   96 (289)
Q Consensus        17 ~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~   96 (289)
                      .+.+..++.+.|.-+..+|.+   +.+.+.|+. .++|-.++. .+|++.. +.+|.........+.+.+++|..-..++
T Consensus       289 ~~e~naif~~lP~Ditfvdk~---diV~ffs~~-~rif~rt~s-viGr~v~-~chpPksv~iv~ki~~~fksG~kd~~ef  362 (409)
T COG2461         289 LEELNAIFKHLPVDITFVDKN---DIVRFFSGG-ERIFPRTPS-VIGRRVQ-LCHPPKSVHIVEKILKDFKSGEKDFAEF  362 (409)
T ss_pred             HHHHHHHHhhCCCceEEeccc---ceEEecCCc-ceecccChH-hhCCccc-CCCCCchHHHHHHHHHHhhcCCcchHHH
Confidence            456888999999777788999   999999997 777877765 4688755 3455556666677777778877655565


Q ss_pred             EEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHH
Q 022961           97 LNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMR  140 (289)
Q Consensus        97 ~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e  140 (289)
                      .. ...+.  .+.++..+++| +.|...|.+.+++|||..|+.+
T Consensus       363 w~-~~~~~--~i~i~Y~av~d-e~ge~~g~le~~qdi~~i~~l~  402 (409)
T COG2461         363 WI-NMGDK--FIHIRYFAVKD-EEGEYLGTLEVVQDITRIKELE  402 (409)
T ss_pred             hc-cCCCc--eEEEEEEEEEc-CCCceeeeehhhhhhHHHHhcc
Confidence            52 22222  45688889999 8999999999999999998874

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=97.05  E-value=0.00055  Score=61.32  Aligned_cols=43  Identities=19%  Similarity=0.067  Sum_probs=40.6

Q ss_pred             HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      +...++.+++||+++|.   +|+|+++|+++++++|++.++++|+.
T Consensus        82 L~aIL~sm~eGVi~vD~---~G~I~~iN~aA~~Llg~~~eel~Gk~  124 (520)
T PRK10820         82 LSALLEALPEPVLSIDM---KGKVELANPASCQLFGQSEEKLRNHT  124 (520)
T ss_pred             HHHHHHhCCCcEEEECC---CCeeeHhHHHHHHHHCcCHHHHCCCc
Confidence            77889999999999999   99999999999999999999999973

>KOG1229 consensus 3'5'-cyclic nucleotide phosphodiesterases [Signal transduction mechanisms]

Probab=96.99  E-value=0.00019  Score=60.24  Aligned_cols=42  Identities=21%  Similarity=0.363  Sum_probs=38.7

Q ss_pred             HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhc
Q 022961          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITR  287 (289)
Q Consensus       243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~  287 (289)
                      +-.+++...++|-|+|.   +..|.||||||++|+||-+.|+|||
T Consensus       159 lFaaLD~c~eAiEI~~d---dhViQYVNpAfE~mmG~hkgEliGk  200 (775)
T KOG1229|consen  159 LFAALDECDEAIEICDD---DHVIQYVNPAFENMMGCHKGELIGK  200 (775)
T ss_pred             HHHHHhhhhhhheeccc---hhHHHHhcHHHHhhhcchhhhhcCC
Confidence            55677888899999999   8899999999999999999999997

>cd00130 PAS PAS domain; PAS motifs appear in archaea, eubacteria and eukarya

Probab=96.98  E-value=0.0012  Score=42.48  Aligned_cols=34  Identities=24%  Similarity=0.285  Sum_probs=31.2

Q ss_pred             cccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhc
Q 022961          251 KQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITR  287 (289)
Q Consensus       251 ~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~  287 (289)
                      +.++++.|.   ++.++++|+++++++||+.++++|+
T Consensus         2 ~~~i~~~d~---~~~~~~~n~~~~~~~g~~~~~~~~~   35 (103)
T cd00130           2 PDGVIVLDL---DGRILYANPAAEQLLGYSPEELIGK   35 (103)
T ss_pred             CceEEEECC---CCcEEEECHHHHHHhCCCHHHHcCc
Confidence            467889999   9999999999999999999999886

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.

>COG2202 AtoS FOG: PAS/PAC domain [Signal transduction mechanisms]

Probab=96.98  E-value=0.019  Score=43.05  Aligned_cols=42  Identities=24%  Similarity=0.238  Sum_probs=36.2

Q ss_pred             HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhc
Q 022961          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITR  287 (289)
Q Consensus       243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~  287 (289)
                      +...++..++++++.|.   ++.++++|+++++++||+..+.+++
T Consensus       114 ~~~~~~~~~~~~~~~d~---~~~~~~~n~~~~~~~g~~~~~~~~~  155 (232)
T COG2202         114 LRALLEASPDGIWVLDE---DGRILYANPAAEELLGYSPEEELGR  155 (232)
T ss_pred             HHHHHhhCCceEEEEeC---CCCEEEeCHHHHHHhCCChHHhcCC
Confidence            34567777899999999   9999999999999999998877654

>PF12860 PAS_7: PAS fold

Probab=96.89  E-value=0.0013  Score=46.19  Aligned_cols=37  Identities=22%  Similarity=0.241  Sum_probs=33.5

Q ss_pred             hhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhH-hh
Q 022961          247 LGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTK-IT  286 (289)
Q Consensus       247 ~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~-~G  286 (289)
                      ++++++||++-|+   +++++++|++|.+++|++.+.+ .|
T Consensus         1 Ld~l~~Gv~v~D~---~~rl~~~N~~~~~l~~~~~~~~~~G   38 (115)
T PF12860_consen    1 LDSLPQGVAVFDS---DGRLVFWNQRFRELFGLPPEMLRPG   38 (115)
T ss_pred             CCCcCceEEEEcC---CCeEEeEcHHHHHHhCCCHHHhcCC
Confidence            3678899999999   9999999999999999999887 45

>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]

Probab=96.62  E-value=0.0057  Score=50.80  Aligned_cols=56  Identities=14%  Similarity=0.158  Sum_probs=49.3

Q ss_pred             HHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCC
Q 022961           16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRT   74 (289)
Q Consensus        16 ~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~   74 (289)
                      ..-.+..+++++|++++.+|..   |.+..+|++++.++|.+++.+.|.+...++...+
T Consensus        78 ~hl~L~aLL~al~~pVlsvd~k---g~v~~aNpAa~~l~~~~~~~~~g~~~~~l~~~~n  133 (511)
T COG3283          78 EHLALSALLEALPEPVLSVDMK---GKVDMANPAACQLFGRKEDRLRGHTAAQLINGFN  133 (511)
T ss_pred             HhHHHHHHHHhCCCceEEeccc---CceeecCHHHHHHhCCChhhhcCccHHHhcCcCC
Confidence            3446788999999999999999   9999999999999999999999999777765443

>smart00091 PAS PAS domain

Probab=96.57  E-value=0.0059  Score=35.73  Aligned_cols=41  Identities=22%  Similarity=0.229  Sum_probs=36.0

Q ss_pred             HHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhc
Q 022961          244 YISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITR  287 (289)
Q Consensus       244 ~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~  287 (289)
                      ...++..+.+++++|.   ++.++++|+.+.+++||+..++.|+
T Consensus         4 ~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~   44 (67)
T smart00091        4 RAILESLPDGIFVLDL---DGRILYANPAAEELLGYSPEELIGK   44 (67)
T ss_pred             HHHHhhCCceEEEEcC---CCeEEEECHHHHHHhCCCHHHHcCC
Confidence            4456778889999998   9999999999999999999888875

PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels ([1]; Ponting & Aravind, in press).

>PRK13558 bacterio-opsin activator; Provisional

Probab=96.55  E-value=0.0036  Score=58.19  Aligned_cols=45  Identities=29%  Similarity=0.445  Sum_probs=39.4

Q ss_pred             HHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          244 YISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       244 ~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      ...++..+.++++.|...++++|+++|++|++++||+.+|++|+.
T Consensus       151 ~~~~~~~~~gi~~~d~~~~dg~i~~~N~~~~~l~G~~~eel~g~~  195 (665)
T PRK13558        151 ERALDEAPVGITIADATLPDEPLIYINDAFERITGYSPDEVLGRN  195 (665)
T ss_pred             HHHHhcCCccEEEEcCCCCCCcEEEEcHHHHHHhCcCHHHHcCCC
Confidence            456788899999998655689999999999999999999999973

>PRK11360 sensory histidine kinase AtoS; Provisional

Probab=96.32  E-value=0.0056  Score=55.89  Aligned_cols=43  Identities=19%  Similarity=0.128  Sum_probs=38.8

Q ss_pred             HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      +...++.++++++++|.   +++|+++|+++++++||+.++++|+.
T Consensus       264 ~~~i~~~~~~~i~~~d~---~g~i~~~N~~~~~l~g~~~~~~~g~~  306 (607)
T PRK11360        264 NELILESIADGVIAIDR---QGKITTMNPAAEVITGLQRHELVGKP  306 (607)
T ss_pred             HHHHHHhccCeEEEEcC---CCCEEEECHHHHHHhCCChHHhcCCc
Confidence            44567889999999999   99999999999999999999999873

>smart00086 PAC Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain)

Probab=96.28  E-value=0.049  Score=28.11  Aligned_cols=41  Identities=29%  Similarity=0.448  Sum_probs=33.2

Q ss_pred             EEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEeccccc
Q 022961           95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSR  136 (289)
Q Consensus        95 e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~  136 (289)
                      ++.....+|..+|+.....++.+ ..+.+.+++++..|||++
T Consensus         3 ~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~di~~~   43 (43)
T smart00086        3 EYRLRRKDGSYIWVLVSASPIRD-EDGEVEGILGVVRDITER   43 (43)
T ss_pred             EEEEEecCCCEEEEEEEeEEEEC-CCCCEEEEEEEEEeccCC
Confidence            34556778888899888888887 678888899999999863

PAC motif occurs C-terminal to a subset of all known PAS motifs. It is proposed to contribute to the PAS domain fold.

>PF07310 PAS_5: PAS domain; InterPro: IPR009922 This family contains a number of hypothetical bacterial proteins of unknown function approximately 200 residues long

Probab=95.94  E-value=0.2  Score=36.37  Aligned_cols=86  Identities=13%  Similarity=0.147  Sum_probs=69.1

Q ss_pred             ccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEEEEEEecCCCEEEEEEEEEEeecCCC
Q 022961           41 HPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKED  120 (289)
Q Consensus        41 g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~~~~~~~~~~~~~~~  120 (289)
                      -++..+=..+++++|++   +-|+++..++.+.........+..++....+..........+|....++....|+.+ +.
T Consensus        51 ~r~RLaGt~i~~~~G~d---~tG~~~~el~~~~~~~~~~~~~~~v~~~~~p~~~~~~~~~~~g~~~~~e~l~LPL~~-~~  126 (137)
T PF07310_consen   51 FRYRLAGTRIVELFGRD---LTGRRLSELFPPEDRERVRRAYRAVVERPAPVRARGRAEDADGRYLEYERLLLPLRS-DG  126 (137)
T ss_pred             eEEEEecHHHHHHhCCC---CCCCCHHHhcChHhHHHHHHHHHHHHcCCceEEEEEEEecCCCCeeEEEEEEcccCC-CC
Confidence            45667889999999984   568988888777776667777777777777777777777888988888999999998 77


Q ss_pred             CcEEEEEEEE
Q 022961          121 GRATHFVAVQ  130 (289)
Q Consensus       121 g~~~~~~~~~  130 (289)
                      |.+..++|..
T Consensus       127 ~~v~rilG~~  136 (137)
T PF07310_consen  127 GTVDRILGAL  136 (137)
T ss_pred             CCccEEEEec
Confidence            8888888764

>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]

Probab=95.43  E-value=0.071  Score=46.50  Aligned_cols=93  Identities=14%  Similarity=0.170  Sum_probs=73.1

Q ss_pred             ccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEEEEEEecCCCEEEEEEEEEEeecCCC
Q 022961           41 HPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKED  120 (289)
Q Consensus        41 g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~~~~~~~~~~~~~~~  120 (289)
                      +..+.+......++||...|+.|++...+++.++..-....-.+.+++|.+--..++..+++|++.|+..+...+.  .+
T Consensus       293 fa~vs~Dak~k~~lgy~eaEL~~m~gY~lvH~~D~~y~Aeah~e~iktgeSGmlvyR~qtk~grw~wvqssarlly--kn  370 (712)
T KOG3560|consen  293 FALVSMDAKVKATLGYCEAELHGMPGYNLVHVEDKVYMAEAHSEGIKTGESGMLVYREQTKAGRWAWVQSSARLLY--KN  370 (712)
T ss_pred             cceeccchhhhhhhccchhhccCCCccceeehhhhhhhhHHHHHHhhcCCcceEEEEEeecCCcEEEeeccceeee--ec
Confidence            5666677778899999999999988777777666554555566778888887788889999999999987766665  48


Q ss_pred             CcEEEEEEEEecccc
Q 022961          121 GRATHFVAVQVPIVS  135 (289)
Q Consensus       121 g~~~~~~~~~~DITe  135 (289)
                      |+...++...+-.++
T Consensus       371 gkPD~vi~thr~l~D  385 (712)
T KOG3560|consen  371 GKPDLVIDTHRGLGD  385 (712)
T ss_pred             CCCCEEEecCCCccc
Confidence            888877777766665

>PRK15053 dpiB sensor histidine kinase DpiB; Provisional

Probab=95.08  E-value=0.025  Score=51.25  Aligned_cols=42  Identities=10%  Similarity=0.103  Sum_probs=36.9

Q ss_pred             HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCCh--HhHhhc
Q 022961          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQI--FTKITR  287 (289)
Q Consensus       243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~--~E~~G~  287 (289)
                      +...++...+|+++.|.   +|+|+++|+++++++|+..  ++++|+
T Consensus       224 ~~~il~~~~egii~~D~---~g~I~~~N~~a~~ll~~~~~~~~~~g~  267 (545)
T PRK15053        224 QEALFSSVYEGLIAVDP---HGYITAINRNARKMLGLSSPGRQWLGK  267 (545)
T ss_pred             HHHHHHHhCceEEEECC---CCeEEeecHHHHHHhCCCCcchhhcCC
Confidence            45578888999999999   9999999999999999975  468886

>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]

Probab=95.00  E-value=0.26  Score=41.51  Aligned_cols=55  Identities=18%  Similarity=0.264  Sum_probs=46.1

Q ss_pred             HHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHH
Q 022961           21 HEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRT   78 (289)
Q Consensus        21 ~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~   78 (289)
                      ..+++.+..-+++++++   |.|.|+++.+.--+|++.-|+.|....+.+++.+....
T Consensus        82 shlLqtLDGF~fvva~d---GkimYISETaSvhLGLSQVElTGNsi~eYIH~~D~dem  136 (598)
T KOG3559|consen   82 SHLLQTLDGFIFVVAPD---GKIMYISETASVHLGLSQVELTGNSIYEYIHPQDHDEM  136 (598)
T ss_pred             HhHHHhhcceEEEEeCC---CCEEEEecceeeeecceeeEeecchhhhhhcccchHHH
Confidence            34566666678889999   99999999999999999999999998888888776544

>KOG0501 consensus K+-channel KCNQ [Inorganic ion transport and metabolism]

Probab=94.85  E-value=0.016  Score=50.91  Aligned_cols=35  Identities=34%  Similarity=0.657  Sum_probs=28.8

Q ss_pred             cEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhc
Q 022961          253 SFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITR  287 (289)
Q Consensus       253 ~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~  287 (289)
                      ++++..+..-|.+|+|.|++||+++||.+.|+..|
T Consensus        29 sFlL~NAQiVD~PiVY~NdgFcKlsGY~RAevMQK   63 (971)
T KOG0501|consen   29 SFLLANAQIVDWPIVYCNDGFCKLSGYHRAEVMQK   63 (971)
T ss_pred             ceeeccceeeccceEEecCcchhccCccHHHHhcc
Confidence            34555555558899999999999999999999876

>PRK11086 sensory histidine kinase DcuS; Provisional

Probab=94.03  E-value=0.057  Score=48.81  Aligned_cols=42  Identities=14%  Similarity=0.092  Sum_probs=35.2

Q ss_pred             HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCCh---HhHhhc
Q 022961          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQI---FTKITR  287 (289)
Q Consensus       243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~---~E~~G~  287 (289)
                      ....++.+++||+++|.   +|+|+++|+++++++||..   .+.+|+
T Consensus       223 ~~~il~~~~~gIi~~D~---~g~I~~~N~~a~~llg~~~~~~~~~~~~  267 (542)
T PRK11086        223 RQAMLQSIKEGVIAVDD---RGEVTLINDEAKRLFNYKKGLEDDPLGT  267 (542)
T ss_pred             HHHHHHHhcCcEEEECC---CCeEEEEhHHHHHHhCCCcCCcccccCC
Confidence            45678899999999999   9999999999999998763   345543

>TIGR02373 photo_yellow photoactive yellow protein

Probab=93.84  E-value=0.081  Score=37.04  Aligned_cols=40  Identities=15%  Similarity=0.071  Sum_probs=36.5

Q ss_pred             HhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          246 SLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       246 ~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      .++..+-|++-.|.   +|.|+.-|.+=.+++|++++.++||.
T Consensus        21 elD~lpFGvI~lD~---~G~V~~YN~aE~~~sg~~p~~vlGr~   60 (124)
T TIGR02373        21 QFDALPFGAIQLDG---SGVILRYNAAEGRITGRDPERVIGRN   60 (124)
T ss_pred             HhhcCCcceEEECC---CCEEEEEecchhhhcCCChhhhhchh
Confidence            36677889999999   99999999999999999999999983

Members of this family are photoactive yellow protein, a cytosolic, 14-kDa light-sensing protein which has a 4-hydroxycinnamyl (p-coumaric acid) chromophore covalently linked to a Cys residue. The enzyme 4-coumarate--CoA ligase as described by TIGR02372 is required for its biosynthesis. The modified Cys is in a PAS (pfam00989) domain, frequently found in signal transducing proteins. Members are known in alpha and gamma Proteobacteria that include Rhodobacter capsulatus, Halorhodospira halophila, Rhodospirillum centenum, etc.

>PF08670 MEKHLA: MEKHLA domain; InterPro: IPR013978 The MEKHLA domain shares similarity with the PAS domain and is found in the 3' end of plant HD-ZIP III homeobox genes, and bacterial proteins

Probab=93.21  E-value=0.19  Score=36.75  Aligned_cols=43  Identities=19%  Similarity=0.091  Sum_probs=36.4

Q ss_pred             HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhh
Q 022961          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKIT  286 (289)
Q Consensus       243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G  286 (289)
                      ....+-+.+.+|+..+. .+|=..+|+|.+.++|++|+.+|++|
T Consensus        33 ~~~~L~~ap~ailsh~~-~~dP~f~yaN~aaL~l~e~~w~el~~   75 (148)
T PF08670_consen   33 LAKALWHAPFAILSHGT-KADPIFIYANQAALDLFETTWDELVG   75 (148)
T ss_pred             HHHHHHcCCCEEEEcCC-CCCCEEEehhHHHHHHhcCCHHHHhc
Confidence            55666668899988886 55667999999999999999999987

>PF13596 PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D

Probab=93.07  E-value=0.074  Score=36.50  Aligned_cols=40  Identities=18%  Similarity=0.263  Sum_probs=29.9

Q ss_pred             HHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhc
Q 022961          244 YISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITR  287 (289)
Q Consensus       244 ~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~  287 (289)
                      ...++..+.++++.|.   +++|.++|++..++++.+. ..+||
T Consensus         2 ~~il~s~~~~i~~vD~---~~~I~~~n~~a~~~f~~~~-~~iGr   41 (106)
T PF13596_consen    2 NNILDSMPIGIIFVDR---NLRIRYFNPAAARLFNLSP-SDIGR   41 (106)
T ss_dssp             HHHHHHSSSEEEEEET---TSBEEEE-SCGC-SS---G-GGTTS
T ss_pred             hHHHhcCCCCEEEEcC---CCeEEEeChhHhhhcCCCh-HHCCC
Confidence            4567888999999999   9999999999999999765 44676

>KOG3561 consensus Aryl-hydrocarbon receptor nuclear translocator [Transcription]

Probab=92.98  E-value=0.078  Score=49.22  Aligned_cols=53  Identities=17%  Similarity=0.300  Sum_probs=45.1

Q ss_pred             HHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHH
Q 022961           22 EALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRR   77 (289)
Q Consensus        22 ~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~   77 (289)
                      .+++++..-++++.-+   |+|+||++....++||..++++|+++..+.+|.+...
T Consensus        99 LmLeAlDGF~fvV~cd---G~IvyVSeSVT~~L~y~QsDL~~qSly~ilhp~d~~~  151 (803)
T KOG3561|consen   99 LILEALDGFLFVVNCD---GRIVYVSESVTSVLGYLQSDLMGQSLYDILHPLDNDK  151 (803)
T ss_pred             HHHHHhcCeEEEEecC---ceEEEEecchHHhhCcCHHHHhcchHHHhcCccccCc
Confidence            4567776677888999   9999999999999999999999999888887766443

>COG5002 VicK Signal transduction histidine kinase [Signal transduction mechanisms]

Probab=92.66  E-value=0.19  Score=41.89  Aligned_cols=43  Identities=16%  Similarity=0.186  Sum_probs=39.3

Q ss_pred             HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      |..++.-..+|++-||.   .|+|+.+|..++++.|-+.++++|+.
T Consensus       113 L~SvlayMtDGViATdR---rG~iI~iN~~A~k~L~~~~E~~~~~~  155 (459)
T COG5002         113 LDSVLAYMTDGVIATDR---RGKIILINKPALKMLGVSKEDALGRS  155 (459)
T ss_pred             HHHHHHHHcCceEeecC---CCcEEEeccHHHHHhCcCHHHHhccc
Confidence            66677778899999999   99999999999999999999999974

>PRK10841 hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional

Probab=92.34  E-value=3  Score=40.68  Aligned_cols=102  Identities=10%  Similarity=0.044  Sum_probs=61.3

Q ss_pred             HHHHHHHHHHhhCCCEEEEEe-CCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeE
Q 022961           15 RYTLWVHEALDELPDSFTITD-PSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIE   93 (289)
Q Consensus        15 ~~~~~l~~~~~~~~~~i~~~d-~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~   93 (289)
                      ..+++++.+++.+|.++++++ .+   |.++++|+.+..++|+...+.             .    ..+......... .
T Consensus       331 e~e~~~r~iv~~~p~gi~i~~~~~---g~~~~~N~~a~~~~~l~~~~~-------------~----~~~~~~~~~~~~-~  389 (924)
T PRK10841        331 EHEQFNRKIVASAPVGICILRTSD---GTNILSNELAHNYLNMLTHED-------------R----QRLTQIICGQQV-N  389 (924)
T ss_pred             HHHHHHHHHHHhCCccEEEEEcCC---CcEEEehHHHHHHhccCChhH-------------H----HHHHHHHhcccc-c
Confidence            566788999999999999997 45   999999999999887643211             0    111111111111 1


Q ss_pred             EEEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhcc
Q 022961           94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG  143 (289)
Q Consensus        94 ~e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l  143 (289)
                      . ......++....  +...+...  .+. ...+++..|||+++++|+++
T Consensus       390 ~-~~~~~~~~~~~~--i~~~~~~~--~~~-~~~i~~~~Dit~r~~~e~~L  433 (924)
T PRK10841        390 F-VDVLTSNNTNLQ--ISFVHSRY--RNE-NVAICVLVDVSARVKMEESL  433 (924)
T ss_pred             e-eeEEcCCCcEEE--EEEEeeee--cCc-eEEEEEEEEhhHHHHHHHHH
Confidence            1 112234444433  33333332  222 34578889999999987766

>COG3290 CitA Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]

Probab=91.48  E-value=0.22  Score=43.94  Aligned_cols=42  Identities=24%  Similarity=0.212  Sum_probs=36.3

Q ss_pred             HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChH--hHhhc
Q 022961          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIF--TKITR  287 (289)
Q Consensus       243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~--E~~G~  287 (289)
                      ....++.+.+||+..|.   .|.|..+|.++++|.|+...  +.+|+
T Consensus       217 r~A~l~si~EGviAvd~---~G~It~~N~~A~~ll~~~~~~~~~ig~  260 (537)
T COG3290         217 RQAMLQSIKEGVIAVDK---KGVITLINQAAQKLLGLRQPSGDPIGR  260 (537)
T ss_pred             HHHHHHHhhceEEEECC---CCeEeehhHHHHHHhcccCcCcccccc
Confidence            34567888999999999   99999999999999999876  46664

>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]

Probab=91.28  E-value=0.46  Score=40.13  Aligned_cols=84  Identities=8%  Similarity=0.050  Sum_probs=56.9

Q ss_pred             EEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEEEEEEecCCCEEEEE
Q 022961           30 SFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWML  109 (289)
Q Consensus        30 ~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~~~~  109 (289)
                      -++....+   -.+++.......++||.+.++++++.-.+++..+.......-...+..|....--+++..+.|.+.|+.
T Consensus       227 FmfraslD---lkliF~D~rv~qltgYepqdliektLY~~ih~~D~~~lr~~H~~ll~kGqvtTkYYR~l~k~ggwvwvq  303 (598)
T KOG3559|consen  227 FMFRASLD---LKLIFLDSRVHQLTGYEPQDLIEKTLYHHIHGCDSFHLRCAHHLLLVKGQVTTKYYRFLLKQGGWVWVQ  303 (598)
T ss_pred             EEEEeecc---eEEEeehhhHHHhhCCCchhhhhHHHHHHhhhhhHHHHHHHHHHHHhccccccHHHHHHHcCCceEEEE
Confidence            34555667   889999999999999999999999866666555443333332333444443333456777888888887


Q ss_pred             EEEEEee
Q 022961          110 FKMSLVF  116 (289)
Q Consensus       110 ~~~~~~~  116 (289)
                      -....+.
T Consensus       304 syat~vH  310 (598)
T KOG3559|consen  304 SYATFVH  310 (598)
T ss_pred             EeeEEEe
Confidence            6655554

>PF14598 PAS_11: PAS domain; PDB: 1P97_A 3F1O_A 2A24_A 3H7W_A 3F1P_A 3H82_A 3F1N_A 4F3L_B 4DJ3_A 2KDK_A

Probab=91.14  E-value=0.25  Score=34.32  Aligned_cols=26  Identities=19%  Similarity=0.146  Sum_probs=23.4

Q ss_pred             CCCEEEecHH-HHHhhCCChHhHhhcc
Q 022961          263 DMPMVYASDA-FLKLTGAQIFTKITRI  288 (289)
Q Consensus       263 ~~~i~~vN~~-f~~~tGys~~E~~G~~  288 (289)
                      ||+|+++-+. ...++||..+|++|+.
T Consensus        11 dgki~~~d~~~v~~~lgy~~~eLvG~s   37 (111)
T PF14598_consen   11 DGKITYVDSRAVSSLLGYLPEELVGRS   37 (111)
T ss_dssp             TSBEEEEETTHHHHHHSS-HHHHTTSB
T ss_pred             CcEEEEEcCccChhhcCCCcHHHcCCc
Confidence            9999999999 6999999999999985

...

>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]

Probab=90.96  E-value=0.33  Score=40.82  Aligned_cols=44  Identities=16%  Similarity=0.050  Sum_probs=40.7

Q ss_pred             hHHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       242 ~~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      .+...++..++.+.-.|.   .|.|..+|||++..+|-+.+++.|+-
T Consensus        81 ~L~aLL~al~~pVlsvd~---kg~v~~aNpAa~~l~~~~~~~~~g~~  124 (511)
T COG3283          81 ALSALLEALPEPVLSVDM---KGKVDMANPAACQLFGRKEDRLRGHT  124 (511)
T ss_pred             HHHHHHHhCCCceEEecc---cCceeecCHHHHHHhCCChhhhcCcc
Confidence            377889999999999999   99999999999999999999999864

>PF08446 PAS_2: PAS fold; InterPro: IPR013654 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []

Probab=86.96  E-value=0.67  Score=32.14  Aligned_cols=42  Identities=26%  Similarity=0.394  Sum_probs=33.9

Q ss_pred             EEEEEeCCCCCccEEEccHHHHHHhCCC---ccccCCCCCCCccCCC
Q 022961           30 SFTITDPSISGHPIVFASRGFLKMSGFS---RAEIIGRNGRMFQGPR   73 (289)
Q Consensus        30 ~i~~~d~~~~~g~i~~~N~~~~~~~G~~---~~e~~g~~~~~l~~~~   73 (289)
                      .++++|.+  +++|+.++..+..++|.+   .++++|++...++.+.
T Consensus        17 ~LLa~d~~--~~~I~~~S~N~~~~lg~~~~~~~~llG~~l~~ll~~~   61 (110)
T PF08446_consen   17 ALLALDPD--DLRIVQASENIAELLGIPPELPEELLGRPLSELLGAE   61 (110)
T ss_dssp             EEEEEETT--TTBEEEEETTHHHHHSS----HHHHTTCBHHHHSCCC
T ss_pred             EEEEEECC--CCEEEEEcCCHHHHhCCccccchhhcccCHHHHhCHH
Confidence            45566653  389999999999999999   9999999988887654

The PAS fold appears in archaea, eubacteria and eukarya. ; GO: 0008020 G-protein coupled photoreceptor activity, 0006355 regulation of transcription, DNA-dependent, 0009584 detection of visible light, 0018298 protein-chromophore linkage; PDB: 3S7O_A 2O9B_A 3S7P_A 1ZTU_A 3S7N_A 3S7Q_A 2O9C_A 2OOL_A 3C2W_G 3NHQ_B ....

>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional

Probab=85.84  E-value=0.98  Score=45.33  Aligned_cols=36  Identities=8%  Similarity=-0.006  Sum_probs=32.0

Q ss_pred             HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCCh
Q 022961          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQI  281 (289)
Q Consensus       243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~  281 (289)
                      ....++.++.+|++.|.   +|+|+++|++|++++|+..
T Consensus       578 ~~~i~~~~~~~i~~~d~---~g~i~~~N~~~~~~~g~~~  613 (1197)
T PRK09959        578 RKALSDSLPNPTYVVNW---QGNVISHNSAFEHYFTADY  613 (1197)
T ss_pred             HHHHHhhCCCcEEEEcC---CCcEEEehHHHHHHhCccc
Confidence            34567889999999999   9999999999999999874

>PRK10618 phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional

Probab=84.20  E-value=2.6  Score=40.85  Aligned_cols=39  Identities=15%  Similarity=0.118  Sum_probs=34.7

Q ss_pred             HHHHHHHHHHhhCCCEEEEEe-CCCCCccEEEccHHHHHHhCC
Q 022961           15 RYTLWVHEALDELPDSFTITD-PSISGHPIVFASRGFLKMSGF   56 (289)
Q Consensus        15 ~~~~~l~~~~~~~~~~i~~~d-~~~~~g~i~~~N~~~~~~~G~   56 (289)
                      ..+...+.+++++|+|++++| .+   |+++++|+++.+++|+
T Consensus       340 ~~~~l~~~Ii~~lp~Gilv~D~~~---~~Ii~~N~aA~~ll~~  379 (894)
T PRK10618        340 ILRALNEEIVSNLPLGLLVYDFES---NRTVISNKIADHLLPH  379 (894)
T ss_pred             HHHHHHHHHHHhCCceEEEEECCC---CeEEEEhHHHHHHhCc
Confidence            566788899999999999999 45   8999999999999975

>KOG3561 consensus Aryl-hydrocarbon receptor nuclear translocator [Transcription]

Probab=83.01  E-value=1.3  Score=41.58  Aligned_cols=38  Identities=16%  Similarity=0.235  Sum_probs=30.9

Q ss_pred             hhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhc
Q 022961          247 LGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITR  287 (289)
Q Consensus       247 ~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~  287 (289)
                      +|.....+++..-   +|+|+||.+.-+.++||..+|++|+
T Consensus       101 LeAlDGF~fvV~c---dG~IvyVSeSVT~~L~y~QsDL~~q  138 (803)
T KOG3561|consen  101 LEALDGFLFVVNC---DGRIVYVSESVTSVLGYLQSDLMGQ  138 (803)
T ss_pred             HHHhcCeEEEEec---CceEEEEecchHHhhCcCHHHHhcc
Confidence            4545444555566   7999999999999999999999996

>COG5388 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=82.31  E-value=11  Score=28.71  Aligned_cols=107  Identities=17%  Similarity=0.220  Sum_probs=72.1

Q ss_pred             HHHhhCCCEEEEEeCC-CCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEEEEEEe
Q 022961           22 EALDELPDSFTITDPS-ISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYK  100 (289)
Q Consensus        22 ~~~~~~~~~i~~~d~~-~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~  100 (289)
                      .+-...++.++ +..+ ..+-.+..+-...|.+||-   |+-|.++..+..+.+.......+..+.....+.-.......
T Consensus        52 ~l~slL~d~Fi-L~~~~~G~~~FRLAGTriC~LfGR---ELr~~~F~sLW~~~~~~~~~r~~~~v~~~~tPvl~~~dg~s  127 (209)
T COG5388          52 KLKSLLPDVFI-LERDGRGKLPFRLAGTRICDLFGR---ELRGRDFLSLWAEADRLELKRAADGVRKRRTPVLVTADGRS  127 (209)
T ss_pred             HHHhhcCceEE-EeccCCCCceEEecccchhhhhch---hhcCCchhHhccccchHHHHHHHHHHhhccCceEEecchhh
Confidence            34556666544 4433 1112345577778888884   67788888787777666666666666666666666666667


Q ss_pred             cCCCEEEEEEEEEEeecCCCCcEEEEEEEEecc
Q 022961          101 KDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPI  133 (289)
Q Consensus       101 ~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DI  133 (289)
                      ..|...-+++-..|+.. ..|+...++|...-+
T Consensus       128 ~~G~sl~fEmLl~PL~~-~~g~~~R~LGais~~  159 (209)
T COG5388         128 HGGRSLGFEMLLAPLQG-ASGETDRFLGAISPI  159 (209)
T ss_pred             ccCcccceeeeeecccC-CCCCccchhhhcccc
Confidence            77888888999999988 788767777766544

>KOG3753 consensus Circadian clock protein period [Signal transduction mechanisms]

Probab=81.16  E-value=4.1  Score=38.30  Aligned_cols=82  Identities=10%  Similarity=0.124  Sum_probs=59.4

Q ss_pred             EEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCC--e-EEEEEEEecCCCEEE
Q 022961           31 FTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERP--I-EVNLLNYKKDGTPFW  107 (289)
Q Consensus        31 i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~--~-~~e~~~~~~~g~~~~  107 (289)
                      +|.+... +++.+..|..++..++||-+.++||+++-.++++.+.....+....+++.+..  + ...+++...+|....
T Consensus       332 iFtT~HT-ptClf~hVDeaAVp~LGyLPqDLIG~sil~f~H~eDr~vm~q~H~~v~q~~G~p~F~~sp~Rf~aqNG~yv~  410 (1114)
T KOG3753|consen  332 IFTTTHT-PTCLFQHVDEAAVPLLGYLPQDLIGTSILAFVHPEDRHVMVQIHQKVLQSGGKPVFSHSPIRFCAQNGSYVR  410 (1114)
T ss_pred             eeEeccC-CcceeeecchhhhhhhccCchhhhccchhhhhcCCchHHHHHHHHHHHHhCCCCcccccceeeeecCCcEEE
Confidence            4444332 34788899999999999999999999988888888877766666666665532  2 235778888998776


Q ss_pred             EEEEEE
Q 022961          108 MLFKMS  113 (289)
Q Consensus       108 ~~~~~~  113 (289)
                      +.....
T Consensus       411 ldTeWS  416 (1114)
T KOG3753|consen  411 LDTEWS  416 (1114)
T ss_pred             Eechhh
Confidence            554433

>COG5000 NtrY Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]

Probab=80.90  E-value=2.5  Score=38.28  Aligned_cols=42  Identities=10%  Similarity=0.052  Sum_probs=37.8

Q ss_pred             HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhc
Q 022961          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITR  287 (289)
Q Consensus       243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~  287 (289)
                      +..+++...-|++..|.   +|+|.-+||+.++|+|-+.++++|+
T Consensus       372 ~E~VLsgvtaGVi~~d~---~g~i~t~N~~ae~~l~~~~~~~~G~  413 (712)
T COG5000         372 LEAVLSGLTAGVIGFDN---RGCITTVNPSAEQILGKPFDQLLGQ  413 (712)
T ss_pred             HHHHHhcCceeEEEEcC---CCeeEeecchHHHHhcCChhHhhcc
Confidence            44567778899999999   9999999999999999999999995

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	289
3ue6_A	166	The Dark Structure Of The Blue-light Photoreceptor		8e-17
3ue6_A	166	The Dark Structure Of The Blue-light Photoreceptor		5e-04
3ulf_A	170	The Light State Structure Of The Blue-light Photore		8e-17
3ulf_A	170	The Light State Structure Of The Blue-light Photore		5e-04
2z6d_A	130	Crystal Structure Of Lov1 Domain Of Phototropin2 Fr		1e-16
2wkq_A	332	Structure Of A Photoactivatable Rac1 Containing The		1e-16
2wkq_A	332	Structure Of A Photoactivatable Rac1 Containing The		5e-06
2v1a_A	144	N- And C-Terminal Helices Of Oat Lov2 (404-546) Are		2e-16
2v1a_A	144	N- And C-Terminal Helices Of Oat Lov2 (404-546) Are		6e-06
2v0u_A	146	N- And C-terminal Helices Of Oat Lov2 (404-546) Are		2e-16
2v0u_A	146	N- And C-terminal Helices Of Oat Lov2 (404-546) Are		5e-06
4eeu_A	118	Crystal Structure Of Philov2.1 Length = 118		3e-16
4eeu_A	118	Crystal Structure Of Philov2.1 Length = 118		1e-04
4ees_A	115	Crystal Structure Of Ilov Length = 115		3e-16
4ees_A	115	Crystal Structure Of Ilov Length = 115		3e-04
2wkp_A	332	Structure Of A Photoactivatable Rac1 Containing Lov		3e-16
2wkp_A	332	Structure Of A Photoactivatable Rac1 Containing Lov		5e-06
2wkr_A	332	Structure Of A Photoactivatable Rac1 Containing The		3e-16
2wkr_A	332	Structure Of A Photoactivatable Rac1 Containing The		5e-06
1n9l_A	109	Crystal Structure Of The Phot-lov1 Domain From Chla		2e-15
4eer_A	115	Crystal Structure Of Lov2 Domain Of Arabidopsis Tha		3e-15
4eer_A	115	Crystal Structure Of Lov2 Domain Of Arabidopsis Tha		4e-04
4eep_A	115	Crystal Structure Of Lov2 Domain Of Arabidopsis Tha		6e-15
4eep_A	115	Crystal Structure Of Lov2 Domain Of Arabidopsis Tha		5e-04
2z6c_A	129	Crystal Structure Of Lov1 Domain Of Phototropin1 Fr		2e-14
2pr5_A	132	Structural Basis For Light-dependent Signaling In T		5e-14
1g28_A	104	Structure Of A Flavin-Binding Domain, Lov2, From Th		1e-13
1g28_A	104	Structure Of A Flavin-Binding Domain, Lov2, From Th		6e-04
3t50_A	128	X-Ray Structure Of The Lov Domain From The Lov-Hk S		8e-13
3p7n_A	258	Crystal Structure Of Light Activated Transcription		2e-10
4hia_A	176	Crystal Structure Of Rhodobacter Sphaeroides Lov Pr		3e-05
2pd7_A	149	2.0 Angstrom Crystal Structure Of The Fungal Blue-L		3e-05
3rh8_B	148	Crystal Structure Of The Light-State Dimer Of Funga		3e-05
3hjk_A	154	2.0 Angstrom Structure Of The Ile74val Variant Of V		3e-05
3is2_B	154	2.3 Angstrom Crystal Structure Of A Cys71 Sulfenic		3e-05
2pd8_A	149	1.8 Angstrom Crystal Structure Of The Cys71ser Muta		4e-05
3d72_A	149	1.65 Angstrom Crystal Structure Of The Cys71val Var		4e-05
3is2_A	154	2.3 Angstrom Crystal Structure Of A Cys71 Sulfenic		4e-05
4hj6_A	178	Crystal Structure Of Rhodobacter Sphaeroides Lov Pr		4e-05
4hj4_A	177	Crystal Structure Of Rhodobacter Sphaeroides Lov Pr		4e-05
4hj3_A	176	Crystal Structure Of Rhodobacter Sphaeroides Lov Pr		4e-05
3hji_A	154	1.8 Angstrom Crystal Structure Of The I74v:i85v Var		5e-05
2l1m_A	150	Solution Structure Of The Eag Domain Of The Herg (K		8e-05
2l4r_A	135	Nmr Solution Structure Of The N-Terminal Pas Domain		8e-05
2l0w_A	138	Solution Nmr Structure Of The N-Terminal Pas Domain		1e-04
1byw_A	110	Structure Of The N-Terminal Domain Of The Human-Erg		3e-04
3sw1_A	162	Structure Of A Full-Length Bacterial Lov Protein Le		4e-04

>pdb|3UE6|A Chain A, The Dark Structure Of The Blue-light Photoreceptor Aureochrome1 Lov Length = 166

Iteration: 1
 Score = 84.3 bits (207), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 46/111 (41%), Positives = 61/111 (54%), Gaps = 5/111 (4%)
Query: 22  EALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNXXXXXX 81
           +AL     +F ITD S+  +PIV+ASRGFL ++G+S  +I+GRN R  QGP T+      
Sbjct: 39  KALQMAQQNFVITDASLPDNPIVYASRGFLTLTGYSLDQILGRNCRFLQGPETDPRAVDK 98
Query: 82  XXXXXXXXXXXXVNLLNYKKDGTPFWMLFKMSLVFGKED--GRATHFVAVQ 130
                       V LLNY++DGT FW LF    V G  D  G   ++V VQ
Sbjct: 99  IRNAITKGVDTSVCLLNYRQDGTTFWNLF---FVAGLRDSKGNIVNYVGVQ 146

>pdb|3UE6|A Chain A, The Dark Structure Of The Blue-light Photoreceptor Aureochrome1 Lov Length = 166

Iteration: 1
 Score = 41.6 bits (96), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 20/37 (54%), Positives = 25/37 (67%)
Query: 242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTG 278
           SL  +L   +Q+FV+ D  LPD P+VYAS  FL LTG
Sbjct: 36  SLVKALQMAQQNFVITDASLPDNPIVYASRGFLTLTG 72

>pdb|3ULF|A Chain A, The Light State Structure Of The Blue-light Photoreceptor Aureochrome1 Lov Length = 170

Iteration: 1
 Score = 84.0 bits (206), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 46/111 (41%), Positives = 61/111 (54%), Gaps = 5/111 (4%)
Query: 22  EALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNXXXXXX 81
           +AL     +F ITD S+  +PIV+ASRGFL ++G+S  +I+GRN R  QGP T+      
Sbjct: 43  KALQMAQQNFVITDASLPDNPIVYASRGFLTLTGYSLDQILGRNCRFLQGPETDPRAVDK 102
Query: 82  XXXXXXXXXXXXVNLLNYKKDGTPFWMLFKMSLVFGKED--GRATHFVAVQ 130
                       V LLNY++DGT FW LF    V G  D  G   ++V VQ
Sbjct: 103 IRNAITKGVDTSVCLLNYRQDGTTFWNLF---FVAGLRDSKGNIVNYVGVQ 150

>pdb|3ULF|A Chain A, The Light State Structure Of The Blue-light Photoreceptor Aureochrome1 Lov Length = 170

Iteration: 1
 Score = 41.6 bits (96), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 20/37 (54%), Positives = 25/37 (67%)
Query: 242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTG 278
           SL  +L   +Q+FV+ D  LPD P+VYAS  FL LTG
Sbjct: 40  SLVKALQMAQQNFVITDASLPDNPIVYASRGFLTLTG 76

>pdb|2Z6D|A Chain A, Crystal Structure Of Lov1 Domain Of Phototropin2 From Arabidopsis Thaliana Length = 130

Iteration: 1
 Score = 83.6 bits (205), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 45/120 (37%), Positives = 63/120 (52%), Gaps = 3/120 (2%)
Query: 15  RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRT 74
           R +  +  AL  L  +F ++D +    PIV+AS GF  M+G+S  EI+GRN R  QGP T
Sbjct: 3   RVSQELKTALSTLQQTFVVSDATQPHCPIVYASSGFFTMTGYSSKEIVGRNCRFLQGPDT 62
Query: 75  NXXXXXXXXXXXXXXXXXXVNLLNYKKDGTPFWMLFKMSLVFGKED-GRATHFVAVQVPI 133
           +                    LLNYKKDGTPFW L  ++ +  K+D G    F+ +QV +
Sbjct: 63  DKNEVAKIRDCVKNGKSYCGRLLNYKKDGTPFWNLLTVTPI--KDDQGNTIKFIGMQVEV 120

>pdb|2WKQ|A Chain A, Structure Of A Photoactivatable Rac1 Containing The Lov2 C450a Mutant Length = 332

Iteration: 1
 Score = 83.2 bits (204), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 41/120 (34%), Positives = 65/120 (54%), Gaps = 3/120 (2%)
Query: 24  LDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNXXXXXXXX 83
           L+ +  +F ITDP +  +PI+FAS  FL+++ +SR EI+GRN R  QGP T+        
Sbjct: 17  LERIEKNFVITDPRLPDNPIIFASDSFLQLTEYSREEILGRNARFLQGPETDRATVRKIR 76
Query: 84  XXXXXXXXXXVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG 143
                     V L+NY K G  FW LF +  +  ++ G   +F+ VQ+     +H+R++ 
Sbjct: 77  DAIDNQTEVTVQLINYTKSGKKFWNLFHLQPMRDQK-GDVQYFIGVQLD--GTEHVRDAA 133

>pdb|2WKQ|A Chain A, Structure Of A Photoactivatable Rac1 Containing The Lov2 C450a Mutant Length = 332

Iteration: 1
 Score = 48.1 bits (113), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 20/36 (55%), Positives = 30/36 (83%)
Query: 242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLT 277
           SL  +L RI+++FV+ DP LPD P+++ASD+FL+LT
Sbjct: 12  SLATTLERIEKNFVITDPRLPDNPIIFASDSFLQLT 47

>pdb|2V1A|A Chain A, N- And C-Terminal Helices Of Oat Lov2 (404-546) Are Involved In Light-Induced Signal Transduction (Room Temperature (293k) Dark Structure Of Lov2 (404-546)) Length = 144

Iteration: 1
 Score = 83.2 bits (204), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 41/121 (33%), Positives = 65/121 (53%), Gaps = 3/121 (2%)
Query: 23  ALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNXXXXXXX 82
            L+ +  +F ITDP +  +PI+FAS  FL+++ +SR EI+GRN R  QGP T+       
Sbjct: 5   TLERIEKNFVITDPRLPDNPIIFASDSFLQLTEYSREEILGRNCRFLQGPETDRATVRKI 64
Query: 83  XXXXXXXXXXXVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNS 142
                      V L+NY K G  FW LF +  +  ++ G   +F+ VQ+     +H+R++
Sbjct: 65  RDAIDNQTEVTVQLINYTKSGKKFWNLFHLQPMRDQK-GDVQYFIGVQLD--GTEHVRDA 121
Query: 143 G 143
Sbjct: 122 A 122

>pdb|2V1A|A Chain A, N- And C-Terminal Helices Of Oat Lov2 (404-546) Are Involved In Light-Induced Signal Transduction (Room Temperature (293k) Dark Structure Of Lov2 (404-546)) Length = 144

Iteration: 1
 Score = 48.1 bits (113), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 19/35 (54%), Positives = 29/35 (82%)
Query: 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLT 277
           L  +L RI+++FV+ DP LPD P+++ASD+FL+LT
Sbjct: 2   LATTLERIEKNFVITDPRLPDNPIIFASDSFLQLT 36

>pdb|2V0U|A Chain A, N- And C-terminal Helices Of Oat Lov2 (404-546) Are Involved In Light-induced Signal Transduction (cryo Dark Structure Of Lov2 (404-546)) Length = 146

Iteration: 1
 Score = 83.2 bits (204), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 41/121 (33%), Positives = 65/121 (53%), Gaps = 3/121 (2%)
Query: 23  ALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNXXXXXXX 82
            L+ +  +F ITDP +  +PI+FAS  FL+++ +SR EI+GRN R  QGP T+       
Sbjct: 7   TLERIEKNFVITDPRLPDNPIIFASDSFLQLTEYSREEILGRNCRFLQGPETDRATVRKI 66
Query: 83  XXXXXXXXXXXVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNS 142
                      V L+NY K G  FW LF +  +  ++ G   +F+ VQ+     +H+R++
Sbjct: 67  RDAIDNQTEVTVQLINYTKSGKKFWNLFHLQPMRDQK-GDVQYFIGVQLD--GTEHVRDA 123
Query: 143 G 143
Sbjct: 124 A 124

>pdb|2V0U|A Chain A, N- And C-terminal Helices Of Oat Lov2 (404-546) Are Involved In Light-induced Signal Transduction (cryo Dark Structure Of Lov2 (404-546)) Length = 146

Iteration: 1
 Score = 48.1 bits (113), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 19/35 (54%), Positives = 29/35 (82%)
Query: 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLT 277
           L  +L RI+++FV+ DP LPD P+++ASD+FL+LT
Sbjct: 4   LATTLERIEKNFVITDPRLPDNPIIFASDSFLQLT 38

>pdb|4EEU|A Chain A, Crystal Structure Of Philov2.1 Length = 118

Iteration: 1
 Score = 82.4 bits (202), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 40/102 (39%), Positives = 56/102 (54%), Gaps = 1/102 (0%)
Query: 30  SFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNXXXXXXXXXXXXXX 89
           SF ITDP +  +PI+FAS GFL+++ +SR EI+GRN R  QGP T+              
Sbjct: 12  SFVITDPRLPDYPIIFASDGFLELTEYSREEIMGRNARFLQGPETDQATVQKIRDAIRDQ 71
Query: 90  XXXXVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQV 131
               V L+NY K G  FW L  +  V  ++ G   +F+ VQ+
Sbjct: 72  RETTVQLINYTKSGKKFWNLLHLQPVRDRKGG-LQYFIGVQL 112

>pdb|4EEU|A Chain A, Crystal Structure Of Philov2.1 Length = 118

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 17/28 (60%), Positives = 24/28 (85%)
Query: 250 IKQSFVLIDPHLPDMPMVYASDAFLKLT 277
           I++SFV+ DP LPD P+++ASD FL+LT
Sbjct: 9   IEKSFVITDPRLPDYPIIFASDGFLELT 36

>pdb|4EES|A Chain A, Crystal Structure Of Ilov Length = 115

Iteration: 1
 Score = 82.4 bits (202), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 39/102 (38%), Positives = 56/102 (54%), Gaps = 1/102 (0%)
Query: 30  SFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNXXXXXXXXXXXXXX 89
           +F ITDP +  +PI+FAS GFL+++ +SR EI+GRN R  QGP T+              
Sbjct: 9   NFVITDPRLPDNPIIFASDGFLELTEYSREEILGRNARFLQGPETDQATVQKIRDAIRDQ 68
Query: 90  XXXXVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQV 131
               V L+NY K G  FW L  +  V  ++ G   +F+ VQ+
Sbjct: 69  RETTVQLINYTKSGKKFWNLLHLQPVRDQK-GELQYFIGVQL 109

>pdb|4EES|A Chain A, Crystal Structure Of Ilov Length = 115

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 16/28 (57%), Positives = 24/28 (85%)
Query: 250 IKQSFVLIDPHLPDMPMVYASDAFLKLT 277
           I+++FV+ DP LPD P+++ASD FL+LT
Sbjct: 6   IEKNFVITDPRLPDNPIIFASDGFLELT 33

>pdb|2WKP|A Chain A, Structure Of A Photoactivatable Rac1 Containing Lov2 Wildtype Length = 332

Iteration: 1
 Score = 82.4 bits (202), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 41/121 (33%), Positives = 65/121 (53%), Gaps = 3/121 (2%)
Query: 23  ALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNXXXXXXX 82
            L+ +  +F ITDP +  +PI+FAS  FL+++ +SR EI+GRN R  QGP T+       
Sbjct: 16  TLERIEKNFVITDPRLPDNPIIFASDSFLQLTEYSREEILGRNCRFLQGPETDRATVRKI 75
Query: 83  XXXXXXXXXXXVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNS 142
                      V L+NY K G  FW LF +  +  ++ G   +F+ VQ+     +H+R++
Sbjct: 76  RDAIDNQTEVTVQLINYTKSGKKFWNLFHLQPMRDQK-GDVQYFIGVQLD--GTEHVRDA 132
Query: 143 G 143
Sbjct: 133 A 133

>pdb|2WKP|A Chain A, Structure Of A Photoactivatable Rac1 Containing Lov2 Wildtype Length = 332

Iteration: 1
 Score = 48.1 bits (113), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 20/36 (55%), Positives = 30/36 (83%)
Query: 242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLT 277
           SL  +L RI+++FV+ DP LPD P+++ASD+FL+LT
Sbjct: 12  SLATTLERIEKNFVITDPRLPDNPIIFASDSFLQLT 47

>pdb|2WKR|A Chain A, Structure Of A Photoactivatable Rac1 Containing The Lov2 C450m Mutant Length = 332

Iteration: 1
 Score = 82.0 bits (201), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 41/121 (33%), Positives = 65/121 (53%), Gaps = 3/121 (2%)
Query: 23  ALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNXXXXXXX 82
            L+ +  +F ITDP +  +PI+FAS  FL+++ +SR EI+GRN R  QGP T+       
Sbjct: 16  TLERIEKNFVITDPRLPDNPIIFASDSFLQLTEYSREEILGRNMRFLQGPETDRATVRKI 75
Query: 83  XXXXXXXXXXXVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNS 142
                      V L+NY K G  FW LF +  +  ++ G   +F+ VQ+     +H+R++
Sbjct: 76  RDAIDNQTEVTVQLINYTKSGKKFWNLFHLQPMRDQK-GDVQYFIGVQLD--GTEHVRDA 132
Query: 143 G 143
Sbjct: 133 A 133

>pdb|2WKR|A Chain A, Structure Of A Photoactivatable Rac1 Containing The Lov2 C450m Mutant Length = 332

Iteration: 1
 Score = 48.1 bits (113), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 20/36 (55%), Positives = 30/36 (83%)
Query: 242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLT 277
           SL  +L RI+++FV+ DP LPD P+++ASD+FL+LT
Sbjct: 12  SLATTLERIEKNFVITDPRLPDNPIIFASDSFLQLT 47

>pdb|1N9L|A Chain A, Crystal Structure Of The Phot-lov1 Domain From Chlamydomonas Reinhardtii In The Dark State. Length = 109

Iteration: 1
 Score = 79.3 bits (194), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 39/106 (36%), Positives = 56/106 (52%), Gaps = 1/106 (0%)
Query: 30  SFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNXXXXXXXXXXXXXX 89
           +F + D ++   P+V+AS GF  M+G+   E++G N R  QG  T+              
Sbjct: 5   TFVVADATLPDCPLVYASEGFYAMTGYGPDEVLGHNCRFLQGEGTDPKEVQKIRDAIKKG 64
Query: 90  XXXXVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVS 135
               V LLNY+KDGTPFW L  ++ +    DGR + FV VQV + S
Sbjct: 65  EACSVRLLNYRKDGTPFWNLLTVTPI-KTPDGRVSKFVGVQVDVTS 109

>pdb|4EER|A Chain A, Crystal Structure Of Lov2 Domain Of Arabidopsis Thaliana Phototropin 2 C426a Mutant Length = 115

Iteration: 1
 Score = 79.0 bits (193), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 37/102 (36%), Positives = 56/102 (54%), Gaps = 1/102 (0%)
Query: 30  SFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNXXXXXXXXXXXXXX 89
           +F I+DP +  +PI+FAS  FL+++ +SR EI+GRN R  QGP T+              
Sbjct: 9   NFVISDPRLPDNPIIFASDSFLELTEYSREEILGRNARFLQGPETDQATVQKIRDAIRDQ 68
Query: 90  XXXXVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQV 131
               V L+NY K G  FW LF +  +  ++ G   +F+ VQ+
Sbjct: 69  REITVQLINYTKSGKKFWNLFHLQPMRDQK-GELQYFIGVQL 109

>pdb|4EER|A Chain A, Crystal Structure Of Lov2 Domain Of Arabidopsis Thaliana Phototropin 2 C426a Mutant Length = 115

Iteration: 1
 Score = 42.0 bits (97), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 16/28 (57%), Positives = 25/28 (89%)
Query: 250 IKQSFVLIDPHLPDMPMVYASDAFLKLT 277
           I+++FV+ DP LPD P+++ASD+FL+LT
Sbjct: 6   IEKNFVISDPRLPDNPIIFASDSFLELT 33

>pdb|4EEP|A Chain A, Crystal Structure Of Lov2 Domain Of Arabidopsis Thaliana Phototropin 2 Length = 115

Iteration: 1
 Score = 78.2 bits (191), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 37/102 (36%), Positives = 56/102 (54%), Gaps = 1/102 (0%)
Query: 30  SFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNXXXXXXXXXXXXXX 89
           +F I+DP +  +PI+FAS  FL+++ +SR EI+GRN R  QGP T+              
Sbjct: 9   NFVISDPRLPDNPIIFASDSFLELTEYSREEILGRNCRFLQGPETDQATVQKIRDAIRDQ 68
Query: 90  XXXXVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQV 131
               V L+NY K G  FW LF +  +  ++ G   +F+ VQ+
Sbjct: 69  REITVQLINYTKSGKKFWNLFHLQPMRDQK-GELQYFIGVQL 109

>pdb|4EEP|A Chain A, Crystal Structure Of Lov2 Domain Of Arabidopsis Thaliana Phototropin 2 Length = 115

Iteration: 1
 Score = 41.6 bits (96), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 16/28 (57%), Positives = 25/28 (89%)
Query: 250 IKQSFVLIDPHLPDMPMVYASDAFLKLT 277
           I+++FV+ DP LPD P+++ASD+FL+LT
Sbjct: 6   IEKNFVISDPRLPDNPIIFASDSFLELT 33

>pdb|2Z6C|A Chain A, Crystal Structure Of Lov1 Domain Of Phototropin1 From Arabidopsis Thaliana Length = 129

Iteration: 1
 Score = 76.3 bits (186), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 36/114 (31%), Positives = 59/114 (51%), Gaps = 1/114 (0%)
Query: 20  VHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNXXXX 79
           + +AL     +F ++D +   +PI++AS GF  M+G++  E++GRN R  QG  T+    
Sbjct: 9   LKDALSTFQQTFVVSDATKPDYPIMYASAGFFNMTGYTSKEVVGRNCRFLQGSGTDADEL 68
Query: 80  XXXXXXXXXXXXXXVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPI 133
                           +LNYKKDGT FW L  ++ +   E G+   F+ +QV +
Sbjct: 69  AKIRETLAAGNNYCGRILNYKKDGTSFWNLLTIAPI-KDESGKVLKFIGMQVEV 121

>pdb|2PR5|A Chain A, Structural Basis For Light-dependent Signaling In The Dimeric Lov Photosensor Ytva (dark Structure) Length = 132

Iteration: 1
 Score = 74.7 bits (182), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 38/115 (33%), Positives = 58/115 (50%), Gaps = 3/115 (2%)
Query: 24  LDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNXXXXXXXX 83
           LD +     ITDP++  +PIV+ ++GF++M+G+   EI+G+N R  QG  T+        
Sbjct: 5   LDHVRVGVVITDPALEDNPIVYVNQGFVQMTGYETEEILGKNCRFLQGKHTDPAEVDNIR 64
Query: 84  XXXXXXXXXXVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKH 138
                     V + NYKKDGT FW    +  +   E    T+FV +Q  I  +K 
Sbjct: 65  TALQNKEPVTVQIQNYKKDGTMFWNELNIDPM---EIEDKTYFVGIQNDITKQKE 116

>pdb|1G28|A Chain A, Structure Of A Flavin-Binding Domain, Lov2, From The Chimeric PhytochromePHOTOTROPIN PHOTORECEPTOR PHY3 Length = 104

Iteration: 1
 Score = 73.9 bits (180), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 37/101 (36%), Positives = 53/101 (52%), Gaps = 1/101 (0%)
Query: 30  SFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNXXXXXXXXXXXXXX 89
           SF ITDP +  +PI+FAS  FL+++ ++R E++G N R  QG  T+              
Sbjct: 2   SFVITDPRLPDNPIIFASDRFLELTEYTREEVLGNNCRFLQGRGTDRKAVQLIRDAVKEQ 61
Query: 90  XXXXVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQ 130
               V +LNY K G  FW LF +  V   E+G   +F+ VQ
Sbjct: 62  RDVTVQVLNYTKGGRAFWNLFHLQ-VMRDENGDVQYFIGVQ 101

>pdb|1G28|A Chain A, Structure Of A Flavin-Binding Domain, Lov2, From The Chimeric PhytochromePHOTOTROPIN PHOTORECEPTOR PHY3 Length = 104

Iteration: 1
 Score = 41.2 bits (95), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 16/26 (61%), Positives = 22/26 (84%)
Query: 252 QSFVLIDPHLPDMPMVYASDAFLKLT 277
           +SFV+ DP LPD P+++ASD FL+LT
Sbjct: 1   KSFVITDPRLPDNPIIFASDRFLELT 26

>pdb|3T50|A Chain A, X-Ray Structure Of The Lov Domain From The Lov-Hk Sensory Protein From Brucella Abortus (Dark State). Length = 128

Iteration: 1
 Score = 70.9 bits (172), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 35/99 (35%), Positives = 53/99 (53%), Gaps = 1/99 (1%)
Query: 33  ITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNXXXXXXXXXXXXXXXXX 92
           IT+P +  +PIVFA+  FLK++G+   E++GRN R  QG  T+                 
Sbjct: 12  ITNPHLPDNPIVFANPAFLKLTGYEADEVMGRNCRFLQGHGTDPAHVRAIKSAIAAEKPI 71
Query: 93  XVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQV 131
            ++++NYKK G  FW    +S V    +GR  HFV+ Q+
Sbjct: 72  DIDIINYKKSGEAFWNRLHISPVHNA-NGRLQHFVSSQL 109

>pdb|3P7N|A Chain A, Crystal Structure Of Light Activated Transcription Factor El222 From Erythrobacter Litoralis Length = 258

Iteration: 1
 Score = 62.8 bits (151), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 35/130 (26%), Positives = 63/130 (48%), Gaps = 3/130 (2%)
Query: 19  WVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNXXX 78
           WV + ++  P +  ++DP ++ +P++  ++ F  ++G+S  E +GRN R   G  T    
Sbjct: 64  WVLDLIEASPIASVVSDPRLADNPLIAINQAFTDLTGYSEEECVGRNCRFLAGSGTEPWL 123
Query: 79  XXXXXXXXXXXXXXXVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKH 138
                          V +LNYKKDGTPF     ++ ++  +D    +F+  QV +   + 
Sbjct: 124 TDKIRQGVREHKPVLVEILNYKKDGTPFRNAVLVAPIY-DDDDELLYFLGSQVEVDDDQP 182
Query: 139 MRNSGMSYSE 148
             N GM+  E
Sbjct: 183 --NMGMARRE 190

>pdb|4HIA|A Chain A, Crystal Structure Of Rhodobacter Sphaeroides Lov Protein Length = 176

Iteration: 1
 Score = 45.8 bits (107), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 28/101 (27%), Positives = 45/101 (44%), Gaps = 1/101 (0%)
Query: 30  SFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNXXXXXXXXXXXXXX 89
           + T+ D S+   P+V A+  FL+M+G++  +I+G N R  Q    N              
Sbjct: 19  ALTLVDMSLPEQPVVLANPPFLRMTGYTEGQILGFNCRFLQRGDENAQARADIRDALKLG 78
Query: 90  XXXXVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQ 130
               V L NY+ +  PF  L  +  V G+ D    +F+  Q
Sbjct: 79  RELQVVLRNYRANDEPFDNLLFLHPVGGRPDA-PDYFLGSQ 118

>pdb|2PD7|A Chain A, 2.0 Angstrom Crystal Structure Of The Fungal Blue-Light Photoreceptor Vivid Length = 149

Iteration: 1
 Score = 45.4 bits (106), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 18/31 (58%), Positives = 23/31 (74%)
Query: 42 PIVFASRGFLKMSGFSRAEIIGRNGRMFQGP 72
          PIV+AS  FL M+G+S AE++GRN R  Q P
Sbjct: 49 PIVYASEAFLYMTGYSNAEVLGRNCRFLQSP 79

>pdb|3RH8|B Chain B, Crystal Structure Of The Light-State Dimer Of Fungal Blue-Light Photoreceptor Vivid Length = 148

Iteration: 1
 Score = 45.4 bits (106), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 18/31 (58%), Positives = 23/31 (74%)
Query: 42 PIVFASRGFLKMSGFSRAEIIGRNGRMFQGP 72
          PIV+AS  FL M+G+S AE++GRN R  Q P
Sbjct: 48 PIVYASEAFLYMTGYSNAEVLGRNCRFLQSP 78

>pdb|3HJK|A Chain A, 2.0 Angstrom Structure Of The Ile74val Variant Of Vivid (Vvd). Length = 154

Iteration: 1
 Score = 45.4 bits (106), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 18/31 (58%), Positives = 23/31 (74%)
Query: 42 PIVFASRGFLKMSGFSRAEIIGRNGRMFQGP 72
          PIV+AS  FL M+G+S AE++GRN R  Q P
Sbjct: 52 PIVYASEAFLYMTGYSNAEVLGRNCRFLQSP 82

>pdb|3IS2|B Chain B, 2.3 Angstrom Crystal Structure Of A Cys71 Sulfenic Acid Form Of Vivid Length = 154

Iteration: 1
 Score = 45.4 bits (106), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 18/31 (58%), Positives = 23/31 (74%)
Query: 42 PIVFASRGFLKMSGFSRAEIIGRNGRMFQGP 72
          PIV+AS  FL M+G+S AE++GRN R  Q P
Sbjct: 52 PIVYASEAFLYMTGYSNAEVLGRNCRFLQSP 82

>pdb|2PD8|A Chain A, 1.8 Angstrom Crystal Structure Of The Cys71ser Mutant Of Vivid Length = 149

Iteration: 1
 Score = 45.4 bits (106), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 18/31 (58%), Positives = 23/31 (74%)
Query: 42 PIVFASRGFLKMSGFSRAEIIGRNGRMFQGP 72
          PIV+AS  FL M+G+S AE++GRN R  Q P
Sbjct: 49 PIVYASEAFLYMTGYSNAEVLGRNCRFLQSP 79

>pdb|3D72|A Chain A, 1.65 Angstrom Crystal Structure Of The Cys71val Variant In The Fungal Photoreceptor Vvd Length = 149

Iteration: 1
 Score = 45.4 bits (106), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 18/31 (58%), Positives = 23/31 (74%)
Query: 42 PIVFASRGFLKMSGFSRAEIIGRNGRMFQGP 72
          PIV+AS  FL M+G+S AE++GRN R  Q P
Sbjct: 49 PIVYASEAFLYMTGYSNAEVLGRNCRFLQSP 79

>pdb|3IS2|A Chain A, 2.3 Angstrom Crystal Structure Of A Cys71 Sulfenic Acid Form Of Vivid Length = 154

Iteration: 1
 Score = 45.4 bits (106), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 18/31 (58%), Positives = 23/31 (74%)
Query: 42 PIVFASRGFLKMSGFSRAEIIGRNGRMFQGP 72
          PIV+AS  FL M+G+S AE++GRN R  Q P
Sbjct: 52 PIVYASEAFLYMTGYSNAEVLGRNCRFLQSP 82

>pdb|4HJ6|A Chain A, Crystal Structure Of Rhodobacter Sphaeroides Lov Protein Length = 178

Iteration: 1
 Score = 45.4 bits (106), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 28/101 (27%), Positives = 45/101 (44%), Gaps = 1/101 (0%)
Query: 30  SFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNXXXXXXXXXXXXXX 89
           + T+ D S+   P+V A+  FL+M+G++  +I+G N R  Q    N              
Sbjct: 21  ALTLVDMSLPEQPLVLANPPFLRMTGYTEGQILGFNCRFLQRGDENAQARADIRDALKLG 80
Query: 90  XXXXVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQ 130
               V L NY+ +  PF  L  +  V G+ D    +F+  Q
Sbjct: 81  RELQVVLRNYRANDEPFDNLLFLHPVGGRPDA-PDYFLGSQ 120

>pdb|4HJ4|A Chain A, Crystal Structure Of Rhodobacter Sphaeroides Lov Protein Length = 177

Iteration: 1
 Score = 45.4 bits (106), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 28/101 (27%), Positives = 45/101 (44%), Gaps = 1/101 (0%)
Query: 30  SFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNXXXXXXXXXXXXXX 89
           + T+ D S+   P+V A+  FL+M+G++  +I+G N R  Q    N              
Sbjct: 20  ALTLVDMSLPEQPLVLANPPFLRMTGYTEGQILGFNCRFLQRGDENAQARADIRDALKLG 79
Query: 90  XXXXVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQ 130
               V L NY+ +  PF  L  +  V G+ D    +F+  Q
Sbjct: 80  RELQVVLRNYRANDEPFDNLLFLHPVGGRPDA-PDYFLGSQ 119

>pdb|4HJ3|A Chain A, Crystal Structure Of Rhodobacter Sphaeroides Lov Protein Length = 176

Iteration: 1
 Score = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 28/101 (27%), Positives = 45/101 (44%), Gaps = 1/101 (0%)
Query: 30  SFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNXXXXXXXXXXXXXX 89
           + T+ D S+   P+V A+  FL+M+G++  +I+G N R  Q    N              
Sbjct: 19  ALTLVDMSLPEQPLVLANPPFLRMTGYTEGQILGFNCRFLQRGDENAQARADIRDALKLG 78
Query: 90  XXXXVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQ 130
               V L NY+ +  PF  L  +  V G+ D    +F+  Q
Sbjct: 79  RELQVVLRNYRANDEPFDNLLFLHPVGGRPDA-PDYFLGSQ 118

>pdb|3HJI|A Chain A, 1.8 Angstrom Crystal Structure Of The I74v:i85v Variant Of Vivid (Vvd). Length = 154

Iteration: 1
 Score = 45.1 bits (105), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 17/31 (54%), Positives = 23/31 (74%)
Query: 42 PIVFASRGFLKMSGFSRAEIIGRNGRMFQGP 72
          P+V+AS  FL M+G+S AE++GRN R  Q P
Sbjct: 52 PVVYASEAFLYMTGYSNAEVLGRNCRFLQSP 82

>pdb|2L1M|A Chain A, Solution Structure Of The Eag Domain Of The Herg (Kv11.1) K+ Channel Length = 150

Iteration: 1
 Score = 44.3 bits (103), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 26/100 (26%), Positives = 42/100 (42%), Gaps = 3/100 (3%)
Query: 30  SFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGR--NGRMFQGPRTNXXXXXXXXXXXX 87
            F I +  +    +++ + GF ++ G+SRAE++ R        GPRT             
Sbjct: 28  KFIIANARVENCAVIYCNDGFCELCGYSRAEVMQRPCTCDFLHGPRTQRRAAAQIAQALL 87
Query: 88  XXXXXXVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFV 127
                 V +  Y+KDG+ F  L  +  V   EDG    F+
Sbjct: 88  GAEERKVEIAFYRKDGSCFLCLVDVVPV-KNEDGAVIMFI 126

>pdb|2L4R|A Chain A, Nmr Solution Structure Of The N-Terminal Pas Domain Of Herg Length = 135

Iteration: 1
 Score = 44.3 bits (103), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 26/100 (26%), Positives = 42/100 (42%), Gaps = 3/100 (3%)
Query: 30  SFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGR--NGRMFQGPRTNXXXXXXXXXXXX 87
            F I +  +    +++ + GF ++ G+SRAE++ R        GPRT             
Sbjct: 28  KFIIANARVENCAVIYCNDGFCELCGYSRAEVMQRPCTCDFLHGPRTQRRAAAQIAQALL 87
Query: 88  XXXXXXVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFV 127
                 V +  Y+KDG+ F  L  +  V   EDG    F+
Sbjct: 88  GAEERKVEIAFYRKDGSCFLCLVDVVPV-KNEDGAVIMFI 126

>pdb|2L0W|A Chain A, Solution Nmr Structure Of The N-Terminal Pas Domain Of Herg Potassium Channel Length = 138

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 26/100 (26%), Positives = 42/100 (42%), Gaps = 3/100 (3%)
Query: 30  SFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGR--NGRMFQGPRTNXXXXXXXXXXXX 87
            F I +  +    +++ + GF ++ G+SRAE++ R        GPRT             
Sbjct: 31  KFIIANARVENCAVIYCNDGFCELCGYSRAEVMQRPCTCDFLHGPRTQRRAAAQIAQALL 90
Query: 88  XXXXXXVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFV 127
                 V +  Y+KDG+ F  L  +  V   EDG    F+
Sbjct: 91  GAEERKVEIAFYRKDGSCFLCLVDVVPV-KNEDGAVIMFI 129

>pdb|1BYW|A Chain A, Structure Of The N-Terminal Domain Of The Human-Erg Potassium Channel Length = 110

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 25/100 (25%), Positives = 41/100 (41%), Gaps = 3/100 (3%)
Query: 30  SFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGR--NGRMFQGPRTNXXXXXXXXXXXX 87
            F I +  +    +++ + GF ++ G+SRAE++ R        GP T             
Sbjct: 3   KFIIANARVENCAVIYCNDGFCELCGYSRAEVMQRPCTCDFLHGPCTQRRAAAQIAQALL 62
Query: 88  XXXXXXVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFV 127
                 V +  Y+KDG+ F  L  +  V   EDG    F+
Sbjct: 63  GAEERKVEIAFYRKDGSCFLCLVDVVPV-KNEDGAVIMFI 101

>pdb|3SW1|A Chain A, Structure Of A Full-Length Bacterial Lov Protein Length = 162

Iteration: 1
 Score = 42.0 bits (97), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 25/107 (23%), Positives = 46/107 (42%), Gaps = 1/107 (0%)
Query: 24  LDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNXXXXXXXX 83
           +D   D   + +       +++ +  F  ++G+SR EI+ ++ R  QG   +        
Sbjct: 31  VDASNDGIVVAEKEGDDTILIYVNAAFEYLTGYSRDEILYQDCRFLQGDDRDQLGRARIR 90
Query: 84  XXXXXXXXXXVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQ 130
                       L NY+KDG+ FW    ++ V    D R T+F+ +Q
Sbjct: 91  KAMAEGRPCREVLRNYRKDGSAFWNELSITPVKSDFDQR-TYFIGIQ 136

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	289
2z6d_A	130	Phototropin-2; PAS-fold, LOV-fold, alternative spl	5e-51
2z6d_A	130	Phototropin-2; PAS-fold, LOV-fold, alternative spl	3e-07
4eet_B	115	Phototropin-2; LOV, blue light photoreceptor, sign	4e-50
4eet_B	115	Phototropin-2; LOV, blue light photoreceptor, sign	2e-08
2v0u_A	146	NPH1-1, LOV2; kinase, transferase, ATP-binding, se	2e-49
2v0u_A	146	NPH1-1, LOV2; kinase, transferase, ATP-binding, se	8e-08
3t50_A	128	Blue-light-activated histidine kinase; PAS superfa	9e-49
3t50_A	128	Blue-light-activated histidine kinase; PAS superfa	9e-07
3ue6_A	166	Aureochrome1; PAS/LOV domain, FMN-binding blue-lig	3e-48
3ue6_A	166	Aureochrome1; PAS/LOV domain, FMN-binding blue-lig	5e-07
2pr5_A	132	Blue-light photoreceptor; light-oxygen-voltage, LO	1e-47
2pr5_A	132	Blue-light photoreceptor; light-oxygen-voltage, LO	3e-06
1n9l_A	109	PHOT-LOV1, putative blue light receptor; phototrop	1e-47
1n9l_A	109	PHOT-LOV1, putative blue light receptor; phototrop	2e-08
3p7n_A	258	Sensor histidine kinase; LOV domain, light-activat	4e-47
3p7n_A	258	Sensor histidine kinase; LOV domain, light-activat	5e-06
2l0w_A	138	Potassium voltage-gated channel, subfamily H (EAG	4e-46
2l0w_A	138	Potassium voltage-gated channel, subfamily H (EAG	2e-07
3sw1_A	162	Sensory box protein; light-oxygen-voltage, LOV, PA	2e-45
3sw1_A	162	Sensory box protein; light-oxygen-voltage, LOV, PA	2e-05
1byw_A	110	Protein (human ERG potassium channel); PAS domain,	1e-43
1byw_A	110	Protein (human ERG potassium channel); PAS domain,	2e-08
3d72_A	149	Vivid PAS protein VVD; circadian, photoreceptor, b	6e-43
3d72_A	149	Vivid PAS protein VVD; circadian, photoreceptor, b	3e-07
2wkq_A	332	NPH1-1, RAS-related C3 botulinum toxin substrate 1	6e-36
2wkq_A	332	NPH1-1, RAS-related C3 botulinum toxin substrate 1	2e-09
3lyx_A	124	Sensory BOX/ggdef domain protein; structural genom	1e-18
3ewk_A	227	Sensor protein; PAS domain, alpha/beta fold, kinas	1e-18
3ewk_A	227	Sensor protein; PAS domain, alpha/beta fold, kinas	1e-16
2gj3_A	120	Nitrogen fixation regulatory protein; PAS domain,	1e-13
3mqq_A	120	Transcriptional regulator, LUXR family; PAS domain	3e-10
3mjq_A	126	Uncharacterized protein; NESG, structural genomics	3e-07
3bwl_A	126	Sensor protein; structural genomics, APC87707.1, P	3e-07
2r78_A	117	Sensor protein; sensory box sensor histidine kinas	3e-06
3olo_A	118	Two-component sensor histidine kinase; structural	1e-04
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-04
3fc7_A	125	HTR-like protein, sensor protein; APC87712.1, HTR-	5e-04
3mfx_A	129	Sensory BOX/ggdef family protein; alpha-beta prote	6e-04
3luq_A	114	Sensor protein; PAS, histidine, kinase, PSI, MCSG,	7e-04

>2z6d_A Phototropin-2; PAS-fold, LOV-fold, alternative splicing, ATP-binding, chromophore, flavoprotein, FMN, kinase, membrane, nucleotide-binding; HET: FMN; 2.00A {Arabidopsis thaliana} PDB: 2z6c_A* Length = 130

 Score =  163 bits (414), Expect = 5e-51
 Identities = 46/127 (36%), Positives = 71/127 (55%), Gaps = 1/127 (0%)

Query: 15  RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRT 74
           R +  +  AL  L  +F ++D +    PIV+AS GF  M+G+S  EI+GRN R  QGP T
Sbjct: 3   RVSQELKTALSTLQQTFVVSDATQPHCPIVYASSGFFTMTGYSSKEIVGRNCRFLQGPDT 62

Query: 75  NRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV 134
           ++  + +IR+ ++  +     LLNYKKDGTPFW L  ++ +   + G    F+ +QV + 
Sbjct: 63  DKNEVAKIRDCVKNGKSYCGRLLNYKKDGTPFWNLLTVTPIKD-DQGNTIKFIGMQVEVS 121

Query: 135 SRKHMRN 141
                 N
Sbjct: 122 KYTEGVN 128

>2z6d_A Phototropin-2; PAS-fold, LOV-fold, alternative splicing, ATP-binding, chromophore, flavoprotein, FMN, kinase, membrane, nucleotide-binding; HET: FMN; 2.00A {Arabidopsis thaliana} PDB: 2z6c_A* Length = 130

 Score = 47.6 bits (114), Expect = 3e-07
 Identities = 15/36 (41%), Positives = 22/36 (61%)

Query: 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTG 278
           L  +L  ++Q+FV+ D   P  P+VYAS  F  +TG
Sbjct: 8   LKTALSTLQQTFVVSDATQPHCPIVYASSGFFTMTG 43

>4eet_B Phototropin-2; LOV, blue light photoreceptor, signaling protein, flavoprote; HET: FMN; 1.20A {Arabidopsis thaliana} PDB: 4ees_A* 4eer_A* 4eep_A* 4eeu_A* 1jnu_A* 1g28_A* Length = 115

 Score =  160 bits (407), Expect = 4e-50
 Identities = 46/114 (40%), Positives = 71/114 (62%), Gaps = 1/114 (0%)

Query: 23  ALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEI 82
           + + +  +F ITDP +  +PI+FAS GFL+++ +SR EI+GRN R  QGP T++ T+ +I
Sbjct: 2   SPEFIEKNFVITDPRLPDNPIIFASDGFLELTEYSREEILGRNARFLQGPETDQATVQKI 61

Query: 83  REAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSR 136
           R+AIR++R   V L+NY K G  FW L  +  V   + G   +F+ VQ+     
Sbjct: 62  RDAIRDQRETTVQLINYTKSGKKFWNLLHLQPVRD-QKGELQYFIGVQLDGSDH 114

>4eet_B Phototropin-2; LOV, blue light photoreceptor, signaling protein, flavoprote; HET: FMN; 1.20A {Arabidopsis thaliana} PDB: 4ees_A* 4eer_A* 4eep_A* 4eeu_A* 1jnu_A* 1g28_A* Length = 115

 Score = 50.6 bits (122), Expect = 2e-08
 Identities = 16/30 (53%), Positives = 24/30 (80%)

Query: 249 RIKQSFVLIDPHLPDMPMVYASDAFLKLTG 278
            I+++FV+ DP LPD P+++ASD FL+LT 
Sbjct: 5   FIEKNFVITDPRLPDNPIIFASDGFLELTE 34

>2v0u_A NPH1-1, LOV2; kinase, transferase, ATP-binding, serine/threonine-protein kinase, light-induced signal trans phototropin1, nucleotide-binding; HET: FMN; 1.40A {Avena sativa} PDB: 2v0w_A* 2v1b_A* 2v1a_A* 1jnu_A* 1g28_A* Length = 146

 Score =  159 bits (405), Expect = 2e-49
 Identities = 45/121 (37%), Positives = 71/121 (58%), Gaps = 1/121 (0%)

Query: 19  WVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRT 78
           ++   L+ +  +F ITDP +  +PI+FAS  FL+++ +SR EI+GRN R  QGP T+R T
Sbjct: 3   FLATTLERIEKNFVITDPRLPDNPIIFASDSFLQLTEYSREEILGRNCRFLQGPETDRAT 62

Query: 79  IMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKH 138
           + +IR+AI  +  + V L+NY K G  FW LF +  +   + G   +F+ VQ+       
Sbjct: 63  VRKIRDAIDNQTEVTVQLINYTKSGKKFWNLFHLQPMRD-QKGDVQYFIGVQLDGTEHVR 121

Query: 139 M 139
            
Sbjct: 122 D 122

>2v0u_A NPH1-1, LOV2; kinase, transferase, ATP-binding, serine/threonine-protein kinase, light-induced signal trans phototropin1, nucleotide-binding; HET: FMN; 1.40A {Avena sativa} PDB: 2v0w_A* 2v1b_A* 2v1a_A* 1jnu_A* 1g28_A* Length = 146

 Score = 49.6 bits (119), Expect = 8e-08
 Identities = 19/36 (52%), Positives = 29/36 (80%)

Query: 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTG 278
           L  +L RI+++FV+ DP LPD P+++ASD+FL+LT 
Sbjct: 4   LATTLERIEKNFVITDPRLPDNPIIFASDSFLQLTE 39

>3t50_A Blue-light-activated histidine kinase; PAS superfamily, blue-light photoreceptor, FMN binding, TRAN; HET: FMN; 1.64A {Brucella melitensis} Length = 128

 Score =  157 bits (399), Expect = 9e-49
 Identities = 43/118 (36%), Positives = 67/118 (56%), Gaps = 1/118 (0%)

Query: 23  ALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEI 82
           A +       IT+P +  +PIVFA+  FLK++G+   E++GRN R  QG  T+   +  I
Sbjct: 2   ASEFTLMPMLITNPHLPDNPIVFANPAFLKLTGYEADEVMGRNCRFLQGHGTDPAHVRAI 61

Query: 83  REAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMR 140
           + AI  E+PI+++++NYKK G  FW    +S V    +GR  HFV+ Q+ +      R
Sbjct: 62  KSAIAAEKPIDIDIINYKKSGEAFWNRLHISPVHN-ANGRLQHFVSSQLDVTLELVPR 118

>3t50_A Blue-light-activated histidine kinase; PAS superfamily, blue-light photoreceptor, FMN binding, TRAN; HET: FMN; 1.64A {Brucella melitensis} Length = 128

 Score = 46.0 bits (110), Expect = 9e-07
 Identities = 15/27 (55%), Positives = 21/27 (77%)

Query: 252 QSFVLIDPHLPDMPMVYASDAFLKLTG 278
              ++ +PHLPD P+V+A+ AFLKLTG
Sbjct: 8   MPMLITNPHLPDNPIVFANPAFLKLTG 34

>3ue6_A Aureochrome1; PAS/LOV domain, FMN-binding blue-light photoreceptor, signal protein; HET: FMN; 2.75A {Vaucheria frigida} PDB: 3ulf_A* Length = 166

 Score =  157 bits (399), Expect = 3e-48
 Identities = 48/116 (41%), Positives = 70/116 (60%), Gaps = 1/116 (0%)

Query: 22  EALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIME 81
           +AL     +F ITD S+  +PIV+ASRGFL ++G+S  +I+GRN R  QGP T+ R + +
Sbjct: 39  KALQMAQQNFVITDASLPDNPIVYASRGFLTLTGYSLDQILGRNCRFLQGPETDPRAVDK 98

Query: 82  IREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRK 137
           IR AI +     V LLNY++DGT FW LF ++ +     G   ++V VQ  +    
Sbjct: 99  IRNAITKGVDTSVCLLNYRQDGTTFWNLFFVAGLRD-SKGNIVNYVGVQSKVSEDY 153

>3ue6_A Aureochrome1; PAS/LOV domain, FMN-binding blue-light photoreceptor, signal protein; HET: FMN; 2.75A {Vaucheria frigida} PDB: 3ulf_A* Length = 166

 Score = 47.7 bits (114), Expect = 5e-07
 Identities = 19/36 (52%), Positives = 24/36 (66%)

Query: 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTG 278
           L  +L   +Q+FV+ D  LPD P+VYAS  FL LTG
Sbjct: 37  LVKALQMAQQNFVITDASLPDNPIVYASRGFLTLTG 72

>2pr5_A Blue-light photoreceptor; light-oxygen-voltage, LOV, PER-ARNT-SIM, PAS, flavoprotein, protein; HET: FMN; 1.45A {Bacillus subtilis} PDB: 2pr6_A* Length = 132

 Score =  154 bits (392), Expect = 1e-47
 Identities = 41/119 (34%), Positives = 66/119 (55%), Gaps = 3/119 (2%)

Query: 22  EALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIME 81
             LD +     ITDP++  +PIV+ ++GF++M+G+   EI+G+N R  QG  T+   +  
Sbjct: 3   HMLDHVRVGVVITDPALEDNPIVYVNQGFVQMTGYETEEILGKNCRFLQGKHTDPAEVDN 62

Query: 82  IREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMR 140
           IR A++ + P+ V + NYKKDGT FW    +  +        T+FV +Q  I  +K   
Sbjct: 63  IRTALQNKEPVTVQIQNYKKDGTMFWNELNIDPME---IEDKTYFVGIQNDITKQKEYE 118

>2pr5_A Blue-light photoreceptor; light-oxygen-voltage, LOV, PER-ARNT-SIM, PAS, flavoprotein, protein; HET: FMN; 1.45A {Bacillus subtilis} PDB: 2pr6_A* Length = 132

 Score = 44.8 bits (107), Expect = 3e-06
 Identities = 11/27 (40%), Positives = 17/27 (62%)

Query: 252 QSFVLIDPHLPDMPMVYASDAFLKLTG 278
              V+ DP L D P+VY +  F+++TG
Sbjct: 10  VGVVITDPALEDNPIVYVNQGFVQMTG 36

>1n9l_A PHOT-LOV1, putative blue light receptor; phototropin, flavin, electron transport; HET: FMN; 1.90A {Chlamydomonas reinhardtii} SCOP: d.110.3.6 PDB: 1n9n_A* 1n9o_A* Length = 109

 Score =  153 bits (390), Expect = 1e-47
 Identities = 43/107 (40%), Positives = 66/107 (61%), Gaps = 1/107 (0%)

Query: 27  LPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAI 86
           L  +F + D ++   P+V+AS GF  M+G+   E++G N R  QG  T+ + + +IR+AI
Sbjct: 2   LRHTFVVADATLPDCPLVYASEGFYAMTGYGPDEVLGHNCRFLQGEGTDPKEVQKIRDAI 61

Query: 87  REERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPI 133
           ++     V LLNY+KDGTPFW L  ++ +    DGR + FV VQV +
Sbjct: 62  KKGEACSVRLLNYRKDGTPFWNLLTVTPIKT-PDGRVSKFVGVQVDV 107

>1n9l_A PHOT-LOV1, putative blue light receptor; phototropin, flavin, electron transport; HET: FMN; 1.90A {Chlamydomonas reinhardtii} SCOP: d.110.3.6 PDB: 1n9n_A* 1n9o_A* Length = 109

 Score = 50.2 bits (121), Expect = 2e-08
 Identities = 14/29 (48%), Positives = 21/29 (72%)

Query: 250 IKQSFVLIDPHLPDMPMVYASDAFLKLTG 278
           ++ +FV+ D  LPD P+VYAS+ F  +TG
Sbjct: 2   LRHTFVVADATLPDCPLVYASEGFYAMTG 30

>3p7n_A Sensor histidine kinase; LOV domain, light-activated transcription factor, DNA bindin; HET: FMN; 2.10A {Erythrobacter litoralis} Length = 258

 Score =  157 bits (398), Expect = 4e-47
 Identities = 39/168 (23%), Positives = 73/168 (43%), Gaps = 1/168 (0%)

Query: 19  WVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRT 78
           WV + ++  P +  ++DP ++ +P++  ++ F  ++G+S  E +GRN R   G  T    
Sbjct: 64  WVLDLIEASPIASVVSDPRLADNPLIAINQAFTDLTGYSEEECVGRNCRFLAGSGTEPWL 123

Query: 79  IMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKH 138
             +IR+ +RE +P+ V +LNYKKDGTPF     ++ ++  +D    +F+  QV +   + 
Sbjct: 124 TDKIRQGVREHKPVLVEILNYKKDGTPFRNAVLVAPIYD-DDDELLYFLGSQVEVDDDQP 182

Query: 139 MRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDRVLALDSDDT 186
                           L                  ++   L L     
Sbjct: 183 NMGMARRERAAEMLKTLSPRQLEVTTLVASGLRNKEVAARLGLSEKTV 230

>3p7n_A Sensor histidine kinase; LOV domain, light-activated transcription factor, DNA bindin; HET: FMN; 2.10A {Erythrobacter litoralis} Length = 258

 Score = 46.1 bits (109), Expect = 5e-06
 Identities = 11/27 (40%), Positives = 16/27 (59%)

Query: 252 QSFVLIDPHLPDMPMVYASDAFLKLTG 278
            + V+ DP L D P++  + AF  LTG
Sbjct: 74  IASVVSDPRLADNPLIAINQAFTDLTG 100

>2l0w_A Potassium voltage-gated channel, subfamily H (EAG member 2, isoform CRA_B; HERG, PAS domain, voltage-gated potassium channel, membrane; NMR {Homo sapiens} PDB: 2l1m_A 2l4r_A Length = 138

 Score =  150 bits (382), Expect = 4e-46
 Identities = 33/138 (23%), Positives = 61/138 (44%), Gaps = 5/138 (3%)

Query: 1   MDSQLGLIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAE 60
           M  + G +     N +   +    +     F I +  +    +++ + GF ++ G+SRAE
Sbjct: 4   MPVRRGHVAPQ--NTFLDTIIRKFEGQSRKFIIANARVENCAVIYCNDGFCELCGYSRAE 61

Query: 61  IIGR--NGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGK 118
           ++ R        GPRT RR   +I +A+      +V +  Y+KDG+ F  L  +  V   
Sbjct: 62  VMQRPCTCDFLHGPRTQRRAAAQIAQALLGAEERKVEIAFYRKDGSCFLCLVDVVPVKN- 120

Query: 119 EDGRATHFVAVQVPIVSR 136
           EDG    F+     ++ +
Sbjct: 121 EDGAVIMFILNFEVVMEK 138

>2l0w_A Potassium voltage-gated channel, subfamily H (EAG member 2, isoform CRA_B; HERG, PAS domain, voltage-gated potassium channel, membrane; NMR {Homo sapiens} PDB: 2l1m_A 2l4r_A Length = 138

 Score = 48.4 bits (116), Expect = 2e-07
 Identities = 6/27 (22%), Positives = 16/27 (59%)

Query: 252 QSFVLIDPHLPDMPMVYASDAFLKLTG 278
           + F++ +  + +  ++Y +D F +L G
Sbjct: 30  RKFIIANARVENCAVIYCNDGFCELCG 56

>3sw1_A Sensory box protein; light-oxygen-voltage, LOV, PAS, signaling protein; HET: FMN; 2.63A {Pseudomonas putida} Length = 162

 Score =  150 bits (380), Expect = 2e-45
 Identities = 29/118 (24%), Positives = 58/118 (49%), Gaps = 1/118 (0%)

Query: 23  ALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEI 82
            +D   D   + +       +++ +  F  ++G+SR EI+ ++ R  QG   ++     I
Sbjct: 30  MVDASNDGIVVAEKEGDDTILIYVNAAFEYLTGYSRDEILYQDCRFLQGDDRDQLGRARI 89

Query: 83  REAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMR 140
           R+A+ E RP    L NY+KDG+ FW    ++ V   +  + T+F+ +Q  +  +  + 
Sbjct: 90  RKAMAEGRPCREVLRNYRKDGSAFWNELSITPVKS-DFDQRTYFIGIQKDVSRQVELE 146

>3sw1_A Sensory box protein; light-oxygen-voltage, LOV, PAS, signaling protein; HET: FMN; 2.63A {Pseudomonas putida} Length = 162

 Score = 43.4 bits (103), Expect = 2e-05
 Identities = 8/27 (29%), Positives = 13/27 (48%)

Query: 252 QSFVLIDPHLPDMPMVYASDAFLKLTG 278
              V+ +    D  ++Y + AF  LTG
Sbjct: 36  DGIVVAEKEGDDTILIYVNAAFEYLTG 62

>1byw_A Protein (human ERG potassium channel); PAS domain, potassium channel domain, membrane protein; 2.60A {Homo sapiens} SCOP: d.110.3.6 Length = 110

 Score =  143 bits (363), Expect = 1e-43
 Identities = 29/110 (26%), Positives = 52/110 (47%), Gaps = 3/110 (2%)

Query: 29  DSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGR--NGRMFQGPRTNRRTIMEIREAI 86
             F I +  +    +++ + GF ++ G+SRAE++ R        GP T RR   +I +A+
Sbjct: 2   RKFIIANARVENCAVIYCNDGFCELCGYSRAEVMQRPCTCDFLHGPCTQRRAAAQIAQAL 61

Query: 87  REERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSR 136
                 +V +  Y+KDG+ F  L  +  V   EDG    F+     ++ +
Sbjct: 62  LGAEERKVEIAFYRKDGSCFLCLVDVVPVKN-EDGAVIMFILNFEVVMEK 110

>1byw_A Protein (human ERG potassium channel); PAS domain, potassium channel domain, membrane protein; 2.60A {Homo sapiens} SCOP: d.110.3.6 Length = 110

 Score = 50.6 bits (122), Expect = 2e-08
 Identities = 6/27 (22%), Positives = 16/27 (59%)

Query: 252 QSFVLIDPHLPDMPMVYASDAFLKLTG 278
           + F++ +  + +  ++Y +D F +L G
Sbjct: 2   RKFIIANARVENCAVIYCNDGFCELCG 28

>3d72_A Vivid PAS protein VVD; circadian, photoreceptor, blue-light, LOV, signaling protein; HET: FAD; 1.65A {Neurospora crassa} PDB: 3is2_A* 2pd8_A* 3hjk_A* 2pdr_A* 2pd7_A* 2pdt_A* 3hji_A* 3rh8_B* Length = 149

 Score =  143 bits (362), Expect = 6e-43
 Identities = 38/129 (29%), Positives = 57/129 (44%), Gaps = 12/129 (9%)

Query: 14  NRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGP- 72
           NR    V     +   +  + D      PIV+AS  FL M+G+S AE++GRN R  Q P 
Sbjct: 21  NRPNPQVELGPVDTSVALILCDLKQKDTPIVYASEAFLYMTGYSNAEVLGRNCRFLQSPD 80

Query: 73  ----------RTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGR 122
                       +  TI  +R+AI     ++V ++N+KK+G  F     M  V   E G 
Sbjct: 81  GMVKPKSTRKYVDSNTINTMRKAIDRNAEVQVEVVNFKKNGQRFVNFLTMIPVRD-ETGE 139

Query: 123 ATHFVAVQV 131
             + +  Q 
Sbjct: 140 YRYSMGFQC 148

>3d72_A Vivid PAS protein VVD; circadian, photoreceptor, blue-light, LOV, signaling protein; HET: FAD; 1.65A {Neurospora crassa} PDB: 3is2_A* 2pd8_A* 3hjk_A* 2pdr_A* 2pd7_A* 2pdt_A* 3hji_A* 3rh8_B* Length = 149

 Score = 48.1 bits (115), Expect = 3e-07
 Identities = 13/26 (50%), Positives = 18/26 (69%)

Query: 253 SFVLIDPHLPDMPMVYASDAFLKLTG 278
           + +L D    D P+VYAS+AFL +TG
Sbjct: 37  ALILCDLKQKDTPIVYASEAFLYMTG 62

>2wkq_A NPH1-1, RAS-related C3 botulinum toxin substrate 1; transferase, cell adhesion, nucleotide-binding, protein engineering, RAS superfamily LOV2; HET: GTP FMN; 1.60A {Avena sativa} PDB: 2wkr_A* 2wkp_A* Length = 332

 Score =  130 bits (328), Expect = 6e-36
 Identities = 46/129 (35%), Positives = 75/129 (58%), Gaps = 1/129 (0%)

Query: 8   IEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGR 67
           +  S ++ +   +   L+ +  +F ITDP +  +PI+FAS  FL+++ +SR EI+GRN R
Sbjct: 1   MRGSHHHHHHGSLATTLERIEKNFVITDPRLPDNPIIFASDSFLQLTEYSREEILGRNAR 60

Query: 68  MFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFV 127
             QGP T+R T+ +IR+AI  +  + V L+NY K G  FW LF +  +   + G   +F+
Sbjct: 61  FLQGPETDRATVRKIRDAIDNQTEVTVQLINYTKSGKKFWNLFHLQPMRD-QKGDVQYFI 119

Query: 128 AVQVPIVSR 136
            VQ+     
Sbjct: 120 GVQLDGTEH 128

>2wkq_A NPH1-1, RAS-related C3 botulinum toxin substrate 1; transferase, cell adhesion, nucleotide-binding, protein engineering, RAS superfamily LOV2; HET: GTP FMN; 1.60A {Avena sativa} PDB: 2wkr_A* 2wkp_A* Length = 332

 Score = 56.5 bits (136), Expect = 2e-09
 Identities = 20/39 (51%), Positives = 30/39 (76%)

Query: 240 SSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTG 278
             SL  +L RI+++FV+ DP LPD P+++ASD+FL+LT 
Sbjct: 10  HGSLATTLERIEKNFVITDPRLPDNPIIFASDSFLQLTE 48

>3lyx_A Sensory BOX/ggdef domain protein; structural genomics, PSI- 2, protein structure initiative, northeast structural genomics consortium; 2.00A {Colwellia psychrerythraea} Length = 124

 Score = 78.7 bits (195), Expect = 1e-18
 Identities = 25/116 (21%), Positives = 48/116 (41%), Gaps = 4/116 (3%)

Query: 22  EALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIME 81
           +A D + D+  +TD    G  I+  ++G   + G+S+ + IG+   M   P        E
Sbjct: 11  KAFDYVFDAIVVTDLQ--GF-IIDWNKGSETLYGYSKEQAIGQPVNMLHVPGDTEHITSE 67

Query: 82  IREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRK 137
           +  A+  +      +    KDG   W+      ++G E+ +    + +   I  RK
Sbjct: 68  VISAVENQGKWTGEIRMLHKDGHIGWIESMCVPIYG-ENYQMVGALGINRDITKRK 122

>3ewk_A Sensor protein; PAS domain, alpha/beta fold, kinase, phosphoprotein, transfe flavoprotein; HET: FAD; 2.34A {Methylococcus capsulatus} Length = 227

 Score = 81.7 bits (202), Expect = 1e-18
 Identities = 23/128 (17%), Positives = 54/128 (42%), Gaps = 4/128 (3%)

Query: 33  ITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPI 92
           ITD    G  I++A+  F  +S + R E++G++ R+       +  I ++   I      
Sbjct: 4   ITDLQ--GR-ILYANDNFCAVSRYGREELVGQDHRIVNSGYHGKAYIRDMWRTISRGNIW 60

Query: 93  EVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGG 152
           +    N +KDGT +W+   +  +     G+   +++++  I ++K          +    
Sbjct: 61  QGEFCNRRKDGTRYWVDSTIVPLMD-NAGKPRQYISIRRDITAQKEAEAQLARLKQAMDA 119

Query: 153 SRLREIVF 160
           +    ++ 
Sbjct: 120 NSEMILLT 127

>3ewk_A Sensor protein; PAS domain, alpha/beta fold, kinase, phosphoprotein, transfe flavoprotein; HET: FAD; 2.34A {Methylococcus capsulatus} Length = 227

 Score = 76.3 bits (188), Expect = 1e-16
 Identities = 24/128 (18%), Positives = 56/128 (43%), Gaps = 10/128 (7%)

Query: 9   EQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRM 68
            Q         + +A+D   +   +TD +  G  I++A+    + SG +  E++G++  +
Sbjct: 102 AQKEAEAQLARLKQAMDANSEMILLTDRA--GR-IIYANPALCRFSGMAEGELLGQSPSI 158

Query: 69  FQGPRTNRRTIMEIREAIREERPIEVNLLNYKK------DGTPFWMLFKMSLVFGKEDGR 122
              P  ++ T+  ++EA++  +P    LLN ++      D   +W     + +   +   
Sbjct: 159 LDSPLADQETLAAMQEALQAGQPWSGRLLNRRRTGPAPHDAEDYWAEISTTPIHT-DGNG 217

Query: 123 ATHFVAVQ 130
              +V +Q
Sbjct: 218 LVGYVQIQ 225

>2gj3_A Nitrogen fixation regulatory protein; PAS domain, FAD, redox sensor, atomic resolution, transferase; HET: FAD; 1.04A {Azotobacter vinelandii} Length = 120

 Score = 65.2 bits (160), Expect = 1e-13
 Identities = 23/108 (21%), Positives = 52/108 (48%), Gaps = 4/108 (3%)

Query: 23  ALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEI 82
            ++  P + +ITD     + I++A+R F  ++G+   E++G+N  +     T R     +
Sbjct: 10  TVEHAPIAISITDLK--AN-ILYANRAFRTITGYGSEEVLGKNESILSNGTTPRLVYQAL 66

Query: 83  REAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQ 130
              + +++P    L+N +KD T +     ++ V   E G   +++ + 
Sbjct: 67  WGRLAQKKPWSGVLVNRRKDKTLYLAELTVAPVLN-EAGETIYYLGMH 113

>3mqq_A Transcriptional regulator, LUXR family; PAS domain, PSI, MCSG, structural genomics, center for structural genomics; 1.65A {Burkholderia thailandensis} PDB: 3mqo_A Length = 120

 Score = 55.6 bits (135), Expect = 3e-10
 Identities = 12/88 (13%), Positives = 24/88 (27%), Gaps = 3/88 (3%)

Query: 43  IVFASRGFLKMSGFSRAEIIGRNGRMFQ-GPRTNRRTIMEIREAIREERPIEVNLLNYKK 101
           I   +     +   +RA++IGR+  +         R    I   +        + +  + 
Sbjct: 24  IEDCNDELAAIFRCARADLIGRSFEVLYPSSDEFERIGERISPVMIAHGSYADDRIMKRA 83

Query: 102 DGTPFWMLFKMSLVFGKEDGRATHFVAV 129
            G  FW       +           V  
Sbjct: 84  GGELFWCHVTGRAL--DRTAPLAAGVWT 109

>3mjq_A Uncharacterized protein; NESG, structural genomics, PSI-2, protein structure initiati northeast structural genomics consortium; 2.60A {Desulfitobacterium hafniense} Length = 126

 Score = 47.6 bits (114), Expect = 3e-07
 Identities = 18/106 (16%), Positives = 37/106 (34%), Gaps = 7/106 (6%)

Query: 24  LDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIR 83
           L+ + D   I +    G  +++A+    K  G++  E++  +               +I 
Sbjct: 5   LETIEDMILIINRE--GR-LLYANTAVPKKLGYTHEELMSMHILTIT-SAGKMAEGEKIL 60

Query: 84  EAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAV 129
             +   +   + L   KK+GT      K  +  GK         A+
Sbjct: 61  AELFAGKKESLPLSLEKKEGTSIPA--KARIWQGKWHNE-PCLFAI 103

>3bwl_A Sensor protein; structural genomics, APC87707.1, PAS domain, HTR-like protei protein structure initiative; HET: MSE I3A; 1.73A {Haloarcula marismortui atcc 43049} Length = 126

 Score = 47.6 bits (114), Expect = 3e-07
 Identities = 17/102 (16%), Positives = 37/102 (36%), Gaps = 7/102 (6%)

Query: 28  PDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIR 87
           PD   + D    G  I   ++ F    G+  +E++GR+   F     +   +        
Sbjct: 27  PDMIDVLDAD--GT-ICEVNQRFCAELGYDESEVLGRSIWEF-DLMFDAEDVQTQLSGFS 82

Query: 88  EERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAV 129
            +   +   L  ++DG+   +   +       +G    F+A+
Sbjct: 83  VDERRKFEGLYERRDGSTMSVEVHLLRF--NLEGE-DRFLAI 121

>2r78_A Sensor protein; sensory box sensor histidine kinase/response regulator, structural genomics, PSI, MCSG; 1.60A {Geobacter sulfurreducens pca} Length = 117

 Score = 44.5 bits (106), Expect = 3e-06
 Identities = 14/102 (13%), Positives = 31/102 (30%), Gaps = 10/102 (9%)

Query: 28  PDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIR 87
            D   I D    GH  +  +       G++R E +  +  +      +          I 
Sbjct: 21  IDGIFIMDAE--GH-YLDVNPAICSAIGYTRDEFLALDWGVLSRG-VDSGWAAASLARIV 76

Query: 88  EERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAV 129
              P+      + ++G    +     L+    DG+    + +
Sbjct: 77  GGEPLREERTVWTRNGDQLTVELSAHLL---PDGK---ILGI 112

>3olo_A Two-component sensor histidine kinase; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG, TRA; 2.09A {Nostoc SP} Length = 118

 Score = 39.9 bits (94), Expect = 1e-04
 Identities = 12/109 (11%), Positives = 36/109 (33%), Gaps = 11/109 (10%)

Query: 21  HEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIM 80
           H  ++   ++      +      ++ +    +M+ +SR +++  N +       +    +
Sbjct: 16  HYLINNAVEASFCLGDN--WQ-FLYVNDATCRMTEYSREQLLSMNLQDI-----DVDFAL 67

Query: 81  EIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAV 129
              E IR++           + G  F +   ++ +   ED         
Sbjct: 68  HDWEEIRQKNNYTFKTRYRSQSGRIFLVEMSLTFL---EDQERRFSCVF 113

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 41.4 bits (96), Expect = 3e-04
 Identities = 43/333 (12%), Positives = 88/333 (26%), Gaps = 93/333 (27%)

Query: 5   LGLIEQSFNNRYTLWVHEALDE----LPDSFTITDPSISGHPIVFASRGFLKMSGFSRAE 60
              +          +V E L      L           S    ++            R  
Sbjct: 68  FWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIE---------QRDR 118

Query: 61  IIGRNGRMFQGPRTNRRTIMEIREAIREERP------------------IEVNLLNYK-- 100
           +   N    +   +  +  +++R+A+ E RP                  ++V  L+YK  
Sbjct: 119 LYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDV-CLSYKVQ 177

Query: 101 --KDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMS---YSEDGGGSRL 155
              D   FW+  K        +        +   I      R+   S          + L
Sbjct: 178 CKMDFKIFWLNLKNC---NSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAEL 234

Query: 156 REIVFGSCRREVCSDSLLDLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDN---IL 212
           R ++    + +   + LL L                      +++  KA  A +    IL
Sbjct: 235 RRLL----KSKPYENCLLVLL---------------------NVQNAKAWNAFNLSCKIL 269

Query: 213 SVLTHYSQLTGRLVCGKRCSLP------------GMGFISSSLYISLGRIKQSFVLIDP- 259
            + T + Q+T  L       +                 +   L      + +  +  +P 
Sbjct: 270 -LTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPR 328

Query: 260 -------HLPDMPMVYASDAFLKLTGAQIFTKI 285
                   + D    +  D +  +   ++ T I
Sbjct: 329 RLSIIAESIRDGLATW--DNWKHVNCDKLTTII 359

>3fc7_A HTR-like protein, sensor protein; APC87712.1, HTR-like protein,haloarcula marismortui ATCC 430 structural genomics, PSI-2; 2.65A {Haloarcula marismortui} Length = 125

 Score = 38.1 bits (89), Expect = 5e-04
 Identities = 7/70 (10%), Positives = 19/70 (27%), Gaps = 3/70 (4%)

Query: 24 LDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIR 83
          + + PD       +  G  I+  +       G     ++G+            + +   +
Sbjct: 25 VSDSPDGIVHLTTN--GT-ILSVNPSMAGRLGADPDTLVGQQLSAVMDSEAANQRLEAGK 81

Query: 84 EAIREERPIE 93
           A+       
Sbjct: 82 SAVENGTATR 91

>3mfx_A Sensory BOX/ggdef family protein; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.40A {Shewanella oneidensis} Length = 129

 Score = 38.2 bits (89), Expect = 6e-04
 Identities = 14/115 (12%), Positives = 36/115 (31%), Gaps = 18/115 (15%)

Query: 24  LDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMF---------QGPRT 74
           +  L ++  + + +     I   ++   ++    +  + G++ R F             +
Sbjct: 13  IQHLTEAMILVNAN---GFIRSCNQRSAELLDCPQVSLKGQDWRNFLTEHHQARYDNLLS 69

Query: 75  NRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAV 129
           +   +        +    E  L+     G    +   +S + G E      FV V
Sbjct: 70  HDVQLGTNCGQPVQHPAQETTLI--CASGKAKDVELSISYIPGHE----PMFVMV 118

>3luq_A Sensor protein; PAS, histidine, kinase, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: PGE; 2.49A {Geobacter sulfurreducens} Length = 114

 Score = 37.6 bits (88), Expect = 7e-04
 Identities = 17/107 (15%), Positives = 35/107 (32%), Gaps = 7/107 (6%)

Query: 24  LDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGR-MFQGPRTNRRTIMEI 82
            +  P +  + D        +  SR + +  G    +I+G +   +F  P          
Sbjct: 9   TEHAPAALAMFDRE--MR-YLAVSRRWREDYGLGDGDILGMSHYDIF--PEIGEEWKSVH 63

Query: 83  REAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAV 129
           R  +  E          + DG   W+ +++   +   +GR    V  
Sbjct: 64  RRGLAGEVIRVEEDCFVRADGRTQWLRWEVRPWYE-GEGRVGGVVIF 109

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	289
3ewk_A	227	Sensor protein; PAS domain, alpha/beta fold, kinas	99.95
2gj3_A	120	Nitrogen fixation regulatory protein; PAS domain,	99.86
2pr5_A	132	Blue-light photoreceptor; light-oxygen-voltage, LO	99.82
4hia_A	176	LOV protein; PAS, HTH, signaling protein; HET: FMN	99.82
3mr0_A	142	Sensory box histidine kinase/response regulator; P	99.81
1n9l_A	109	PHOT-LOV1, putative blue light receptor; phototrop	99.81
3ue6_A	166	Aureochrome1; PAS/LOV domain, FMN-binding blue-lig	99.8
3f1p_B	121	ARYL hydrocarbon receptor nuclear translocator; PA	99.8
3p7n_A	258	Sensor histidine kinase; LOV domain, light-activat	99.78
3t50_A	128	Blue-light-activated histidine kinase; PAS superfa	99.78
3f1p_A	117	Endothelial PAS domain-containing protein 1; PAS d	99.76
4eet_B	115	Phototropin-2; LOV, blue light photoreceptor, sign	99.75
3nja_A	125	Probable ggdef family protein; structural genomics	99.75
3mqq_A	120	Transcriptional regulator, LUXR family; PAS domain	99.74
2z6d_A	130	Phototropin-2; PAS-fold, LOV-fold, alternative spl	99.74
1d06_A	130	Nitrogen fixation regulatory protein FIXL; oxygen	99.73
3lyx_A	124	Sensory BOX/ggdef domain protein; structural genom	99.73
3sw1_A	162	Sensory box protein; light-oxygen-voltage, LOV, PA	99.73
2r78_A	117	Sensor protein; sensory box sensor histidine kinas	99.73
2vv6_A	119	FIXL, sensor protein FIXL; signaling protein, tran	99.72
3h9w_A	115	Diguanylate cyclase with PAS/PAC sensor; alpha-bet	99.71
2wkq_A	332	NPH1-1, RAS-related C3 botulinum toxin substrate 1	99.7
3k3c_A	158	Protein RV1364C/MT1410; sensor, PAS, signal transd	99.69
3mxq_A	152	Sensor protein; PSI2, MCSG, structural genomics, p	99.69
3luq_A	114	Sensor protein; PAS, histidine, kinase, PSI, MCSG,	99.69
3ewk_A	227	Sensor protein; PAS domain, alpha/beta fold, kinas	99.67
3kx0_X	185	Uncharacterized protein RV1364C/MT1410; PAS domain	99.66
3icy_A	118	Sensor protein; sensory box histidine kinase/respo	99.65
2v0u_A	146	NPH1-1, LOV2; kinase, transferase, ATP-binding, se	99.64
3bwl_A	126	Sensor protein; structural genomics, APC87707.1, P	99.64
2kdk_A	121	ARYL hydrocarbon receptor nuclear translocator-LI	99.64
3olo_A	118	Two-component sensor histidine kinase; structural	99.62
3mjq_A	126	Uncharacterized protein; NESG, structural genomics	99.6
1v9y_A	167	Heme PAS sensor protein; signaling protein; HET: H	99.59
2l0w_A	138	Potassium voltage-gated channel, subfamily H (EAG	99.59
3eeh_A	125	Putative light and redox sensing histidine kinase;	99.58
1byw_A	110	Protein (human ERG potassium channel); PAS domain,	99.58
3vol_A	233	Aerotaxis transducer AER2; heme, oxygen sensor pro	99.56
4eho_A	635	Bacteriophytochrome, PAS/PAC sensor; photoreceptor	99.55
3mfx_A	129	Sensory BOX/ggdef family protein; alpha-beta prote	99.54
3d72_A	149	Vivid PAS protein VVD; circadian, photoreceptor, b	99.53
3fc7_A	125	HTR-like protein, sensor protein; APC87712.1, HTR-	99.48
4f3l_A	361	Mclock, circadian locomoter output cycles protein	99.47
4f3l_A	361	Mclock, circadian locomoter output cycles protein	99.44
4hi4_A	121	Aerotaxis transducer AER2; PAS domain, diatomic GA	99.43
2vlg_A	111	Sporulation kinase A; histidine kinase, two-compon	99.43
3fg8_A	118	Uncharacterized protein RHA05790; PAS domain, stru	99.42
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	99.4
2qkp_A	151	Uncharacterized protein; structural genomics, unkn	99.4
3rty_A	339	Period circadian protein; PAS domain, signalling,	99.38
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	99.36
3b33_A	115	Sensor protein; structural genomics, PAS domain, n	99.32
3a0r_A	349	Sensor protein; four helix bundle, PAS fold, kinas	99.22
3cax_A	369	Uncharacterized protein PF0695; structural genomic	99.2
1ll8_A	114	PAS kinase; PAS domain, ligand binding, ligand scr	99.17
3rty_A	339	Period circadian protein; PAS domain, signalling,	99.16
2w0n_A	118	Sensor protein DCUS; signal transduction, two-comp	99.13
3a0s_A	96	Sensor protein; PAS-fold, kinase, phosphoprotein,	99.13
1nwz_A	125	PYP, photoactive yellow protein; PAS, LOV, GAF, do	99.09
1mzu_A	129	PPR; photoactive yellow protein, PAS, PYP, signali	99.07
2jhe_A	190	Transcription regulator TYRR; aromatic hydrocarbon	99.05
4dj3_A	317	Period circadian protein homolog 3; PAS domain, ci	99.0
4dj2_A	320	Period circadian protein homolog 1; PAS domains, c	98.98
2r78_A	117	Sensor protein; sensory box sensor histidine kinas	98.94
3gdi_A	309	Period circadian protein homolog 2; tandem PAS dom	98.92
3gdi_A	309	Period circadian protein homolog 2; tandem PAS dom	98.91
2gj3_A	120	Nitrogen fixation regulatory protein; PAS domain,	98.9
4dj3_A	317	Period circadian protein homolog 3; PAS domain, ci	98.9
1n9l_A	109	PHOT-LOV1, putative blue light receptor; phototrop	98.9
4dj2_A	320	Period circadian protein homolog 1; PAS domains, c	98.88
1d06_A	130	Nitrogen fixation regulatory protein FIXL; oxygen	98.83
3bwl_A	126	Sensor protein; structural genomics, APC87707.1, P	98.76
3mfx_A	129	Sensory BOX/ggdef family protein; alpha-beta prote	98.75
2pr5_A	132	Blue-light photoreceptor; light-oxygen-voltage, LO	98.73
3olo_A	118	Two-component sensor histidine kinase; structural	98.63
2ykf_A	305	Pdtas, probable sensor histidine kinase pdtas; tra	97.97
3mxq_A	152	Sensor protein; PSI2, MCSG, structural genomics, p	98.55
2vlg_A	111	Sporulation kinase A; histidine kinase, two-compon	98.54
1ll8_A	114	PAS kinase; PAS domain, ligand binding, ligand scr	98.53
1nwz_A	125	PYP, photoactive yellow protein; PAS, LOV, GAF, do	98.5
1mzu_A	129	PPR; photoactive yellow protein, PAS, PYP, signali	98.48
3mqq_A	120	Transcriptional regulator, LUXR family; PAS domain	98.47
4eet_B	115	Phototropin-2; LOV, blue light photoreceptor, sign	98.45
3f1p_B	121	ARYL hydrocarbon receptor nuclear translocator; PA	98.45
3fg8_A	118	Uncharacterized protein RHA05790; PAS domain, stru	98.44
4hi4_A	121	Aerotaxis transducer AER2; PAS domain, diatomic GA	98.42
3b33_A	115	Sensor protein; structural genomics, PAS domain, n	98.4
3fc7_A	125	HTR-like protein, sensor protein; APC87712.1, HTR-	98.4
3ue6_A	166	Aureochrome1; PAS/LOV domain, FMN-binding blue-lig	98.33
2kdk_A	121	ARYL hydrocarbon receptor nuclear translocator-LI	98.33
3luq_A	114	Sensor protein; PAS, histidine, kinase, PSI, MCSG,	98.31
3p7n_A	258	Sensor histidine kinase; LOV domain, light-activat	98.3
3f1p_A	117	Endothelial PAS domain-containing protein 1; PAS d	98.3
3t50_A	128	Blue-light-activated histidine kinase; PAS superfa	98.27
3a0s_A	96	Sensor protein; PAS-fold, kinase, phosphoprotein,	98.24
3vol_A	233	Aerotaxis transducer AER2; heme, oxygen sensor pro	98.2
1byw_A	110	Protein (human ERG potassium channel); PAS domain,	98.2
3d72_A	149	Vivid PAS protein VVD; circadian, photoreceptor, b	98.19
3mjq_A	126	Uncharacterized protein; NESG, structural genomics	98.16
3lyx_A	124	Sensory BOX/ggdef domain protein; structural genom	98.09
2z6d_A	130	Phototropin-2; PAS-fold, LOV-fold, alternative spl	98.03
2jhe_A	190	Transcription regulator TYRR; aromatic hydrocarbon	98.01
2w0n_A	118	Sensor protein DCUS; signal transduction, two-comp	97.97
2l0w_A	138	Potassium voltage-gated channel, subfamily H (EAG	97.96
3eeh_A	125	Putative light and redox sensing histidine kinase;	97.92
3sw1_A	162	Sensory box protein; light-oxygen-voltage, LOV, PA	97.88
3k3c_A	158	Protein RV1364C/MT1410; sensor, PAS, signal transd	97.88
1v9y_A	167	Heme PAS sensor protein; signaling protein; HET: H	97.87
3kx0_X	185	Uncharacterized protein RV1364C/MT1410; PAS domain	97.82
2ykf_A	305	Pdtas, probable sensor histidine kinase pdtas; tra	97.0
1oj5_A	132	Steroid receptor coactivator 1A; transcriptional c	97.77
2v0u_A	146	NPH1-1, LOV2; kinase, transferase, ATP-binding, se	97.75
2qkp_A	151	Uncharacterized protein; structural genomics, unkn	97.66
3nja_A	125	Probable ggdef family protein; structural genomics	97.61
3icy_A	118	Sensor protein; sensory box histidine kinase/respo	97.57
4eho_A	635	Bacteriophytochrome, PAS/PAC sensor; photoreceptor	97.37
3h9w_A	115	Diguanylate cyclase with PAS/PAC sensor; alpha-bet	97.23
3mr0_A	142	Sensory box histidine kinase/response regulator; P	97.12
3cax_A	369	Uncharacterized protein PF0695; structural genomic	96.94
2ool_A	337	Sensor protein; bacteriophytochrome, photoconversi	91.83
4ew7_A	127	Conjugative transfer: regulation; alpha-beta-alpha	89.42
2ool_A	337	Sensor protein; bacteriophytochrome, photoconversi	86.64

>3ewk_A Sensor protein; PAS domain, alpha/beta fold, kinase, phosphoprotein, transfe flavoprotein; HET: FAD; 2.34A {Methylococcus capsulatus}

Probab=99.95  E-value=3.2e-27  Score=187.38  Aligned_cols=154  Identities=19%  Similarity=0.355  Sum_probs=137.9

Q ss_pred             EEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEEEEEEecCCCEEEEEE
Q 022961           31 FTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLF  110 (289)
Q Consensus        31 i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~~~~~  110 (289)
                      |+++|.+   |+++++|++|++++||++++++|++...+.++.........++..+..+..+..++..++++|..+|+..
T Consensus         2 i~i~D~~---g~i~~~N~a~~~l~Gy~~~el~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~   78 (227)
T 3ewk_A            2 VSITDLQ---GRILYANDNFCAVSRYGREELVGQDHRIVNSGYHGKAYIRDMWRTISRGNIWQGEFCNRRKDGTRYWVDS   78 (227)
T ss_dssp             EEEEETT---CBEEEECHHHHHHTTCCHHHHTTSBGGGGCCSCSCHHHHHHHHHHHTTTCCEEEEEEEECSSSCEEEEEE
T ss_pred             EEEECCC---CcEEehHHHHHHHHCcCHHHHcCCCHHHcCCCCCCHHHHHHHHHHHHcCCeEEEEEEEEcCCCCEEeeee
Confidence            6788999   9999999999999999999999999887777766777777788888888899999999999999999999


Q ss_pred             EEEEeecCCCCcEEEEEEEEecccccHHHHhcccccccCCCcchhhhhHHhhcccccccccceeccchhcccCCCCCCcc
Q 022961          111 KMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDRVLALDSDDTGLEI  190 (289)
Q Consensus       111 ~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l~~~~~~~n~~~~~~~~~~~~~~~~~~~~l~e~~~~~~~~~~~~~~~~  190 (289)
                      +..|+.+ .+|.+.+++++.+|||++|++|+++..                                             
T Consensus        79 ~~~p~~d-~~g~~~~~~~~~~DIT~~k~~e~~l~~---------------------------------------------  112 (227)
T 3ewk_A           79 TIVPLMD-NAGKPRQYISIRRDITAQKEAEAQLAR---------------------------------------------  112 (227)
T ss_dssp             EEEEEEC-SSSCEEEEEEEEEECTTTTHHHHHHHH---------------------------------------------
T ss_pred             EEEEEEc-CCCCEEEEEEEEEehhhHHHHHHHHHH---------------------------------------------
Confidence            9999998 899999999999999999999554310                                             


Q ss_pred             ccCccccHHHHHHHHHHhhHHHHhhhcccccccceecccccCCCCCCCcchhHHHHhhcccccEEEeCCCCCCCCEEEec
Q 022961          191 EDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQSFVLIDPHLPDMPMVYAS  270 (289)
Q Consensus       191 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~i~i~d~~~~~~~i~~vN  270 (289)
                                                                          +...++.++++|+++|.   +|+|+++|
T Consensus       113 ----------------------------------------------------~~~~~~~~~~~i~~~d~---~g~i~~~N  137 (227)
T 3ewk_A          113 ----------------------------------------------------LKQAMDANSEMILLTDR---AGRIIYAN  137 (227)
T ss_dssp             ----------------------------------------------------HHHHHHTCCSEEEEECT---TSCEEEEC
T ss_pred             ----------------------------------------------------HHHHHhcCcCeEEEEcC---CCcEEEEc
Confidence                                                                34467788899999999   99999999


Q ss_pred             HHHHHhhCCChHhHhhcc
Q 022961          271 DAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       271 ~~f~~~tGys~~E~~G~~  288 (289)
                      ++|++++||+.+|++|+.
T Consensus       138 ~~~~~~~G~~~~e~~g~~  155 (227)
T 3ewk_A          138 PALCRFSGMAEGELLGQS  155 (227)
T ss_dssp             HHHHHHHTCCTHHHHSSC
T ss_pred             hHHHHHhCCCHHHHcCCC
Confidence            999999999999999974

>2gj3_A Nitrogen fixation regulatory protein; PAS domain, FAD, redox sensor, atomic resolution, transferase; HET: FAD; 1.04A {Azotobacter vinelandii}

Probab=99.86  E-value=1.7e-20  Score=133.17  Aligned_cols=117  Identities=20%  Similarity=0.377  Sum_probs=105.7

Q ss_pred             HHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEEE
Q 022961           17 TLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNL   96 (289)
Q Consensus        17 ~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~   96 (289)
                      +++++.++++++++++++|.+   |+|+++|++|++++||++++++|++...+.++.........++..+..+..+..++
T Consensus         4 ~~~~~~~~~~~~~~i~~~d~~---g~i~~~N~a~~~~~G~~~~elig~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~   80 (120)
T 2gj3_A            4 PEIFRQTVEHAPIAISITDLK---ANILYANRAFRTITGYGSEEVLGKNESILSNGTTPRLVYQALWGRLAQKKPWSGVL   80 (120)
T ss_dssp             HHHHHHHHHHCSSEEEEECTT---CBEEEECHHHHHHHCCCTTGGGGCBGGGGCCTTSCHHHHHHHHHHHHTTCCEEEEE
T ss_pred             HHHHHHHHHhCCCeEEEECCC---CCEEeehHHHHHHHCcCHHHHcCCCHHHcCCCCCCHHHHHHHHHHHHcCCCEEEEE
Confidence            457889999999999999999   99999999999999999999999998877776666666667778888888899999


Q ss_pred             EEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccH
Q 022961           97 LNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRK  137 (289)
Q Consensus        97 ~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k  137 (289)
                      ..++++|..+|+.+++.|+.+ .+|.+.+++++.+|||++|
T Consensus        81 ~~~~~dG~~~~~~~~~~pi~~-~~g~~~~~v~~~~DITe~k  120 (120)
T 2gj3_A           81 VNRRKDKTLYLAELTVAPVLN-EAGETIYYLGMHRDTSELH  120 (120)
T ss_dssp             EEECTTSCEEEEEEEEEEEEC-TTSCEEEEEEEEEECCSCC
T ss_pred             EEEcCCCCEEEEEEEEEEEEC-CCCCEEEEEEEeccCcccC
Confidence            999999999999999999998 8999999999999999986

>2pr5_A Blue-light photoreceptor; light-oxygen-voltage, LOV, PER-ARNT-SIM, PAS, flavoprotein, protein; HET: FMN; 1.45A {Bacillus subtilis} PDB: 2pr6_A*

Probab=99.82  E-value=2.8e-19  Score=129.03  Aligned_cols=119  Identities=36%  Similarity=0.654  Sum_probs=100.6

Q ss_pred             HHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEEEEEEec
Q 022961           22 EALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKK  101 (289)
Q Consensus        22 ~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~  101 (289)
                      .++++++++++++|.+.++|+|+++|++|++++||++++++|+++..+.++.........+...+..+..+..+...+++
T Consensus         3 ~~~~~~~~~i~~~d~~g~~~~i~~~N~a~~~~~G~~~~el~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~k   82 (132)
T 2pr5_A            3 HMLDHVRVGVVITDPALEDNPIVYVNQGFVQMTGYETEEILGKNCRFLQGKHTDPAEVDNIRTALQNKEPVTVQIQNYKK   82 (132)
T ss_dssp             ---CCCCCEEEEECTTSTTCCEEEECHHHHHHHSCCHHHHTTSCGGGGCCTTCCHHHHHHHHHHHHHTCCEEEEEEEECT
T ss_pred             hHHhcCCCcEEEEeCCCCCCcEEEECHHHHHHhCcCHHHHcCCChhhhCCCCCCHHHHHHHHHHHHcCCCeEEEEEEEec
Confidence            57899999999999871113999999999999999999999999877777766666666777778888888889999999


Q ss_pred             CCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhcc
Q 022961          102 DGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG  143 (289)
Q Consensus       102 ~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l  143 (289)
                      +|..+|+.+++.|+.+ .+  +.+++++.+|||++|++|+++
T Consensus        83 dG~~~~~~~~~~~~~~-~~--~~~~~~~~~DITe~k~~e~~l  121 (132)
T 2pr5_A           83 DGTMFWNELNIDPMEI-ED--KTYFVGIQNDITKQKEYEKLL  121 (132)
T ss_dssp             TSCEEEEEEEEEEEEE-TT--EEEEEEEEEECHHHHHHHHHH
T ss_pred             CCCeeeeEEEEEeccC-CC--eeEEEEEEEeCcHHHHHHHHH
Confidence            9999999999999987 43  778999999999999998776

>4hia_A LOV protein; PAS, HTH, signaling protein; HET: FMN; 1.95A {Rhodobacter sphaeroides} PDB: 4hnb_A* 4hj4_A* 4hj6_A* 4hj3_A*

Probab=99.82  E-value=4.7e-19  Score=134.20  Aligned_cols=127  Identities=25%  Similarity=0.407  Sum_probs=114.9

Q ss_pred             HHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEE
Q 022961           16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVN   95 (289)
Q Consensus        16 ~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e   95 (289)
                      ..++++.++++++++++++|.+.++|+|+++|+++++++||++++++|+++..+.++.........+...+..+..+..+
T Consensus         5 ~~~~~~~~~~~~~~~i~~~d~~~~~g~i~~~N~a~~~~~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e   84 (176)
T 4hia_A            5 QFEKIRAVFDRSGVALTLVDMSLPEQPVVLANPPFLRMTGYTEGQILGFNCRFLQRGDENAQARADIRDALKLGRELQVV   84 (176)
T ss_dssp             HHHHHHHHHHHCSSCCEEEETTSTTCCEEEECHHHHHHHTCCHHHHTTSCGGGGCCTTCCHHHHHHHHHHHHHTCCEEEE
T ss_pred             HHHHHHHHHhcCCCcEEEEecCCCCCcEEEECHHHHHHHCcCHHHHcCCCcceeeCCCCCHHHHHHHHHHHHcCCceEEE
Confidence            44578899999999999999765569999999999999999999999999888888888888888888888888889889


Q ss_pred             EEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhcc
Q 022961           96 LLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG  143 (289)
Q Consensus        96 ~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l  143 (289)
                      +...+++|..+|+.+++.|+.+ .+|.+.+++++++|||++|++|+++
T Consensus        85 ~~~~~~dG~~~~~~~~~~pi~~-~~g~~~~~~~~~~DITe~k~~e~~~  131 (176)
T 4hia_A           85 LRNYRANDEPFDNLLFLHPVGG-RPDAPDYFLGSQFELGRSGNSEEAA  131 (176)
T ss_dssp             EEEECTTCCEEEEEEEEEEESS-BTTBCSEEEEEEEEESSSGGGHHHH
T ss_pred             EEEEcCCCCEEEEEEEEEEeeC-CCCCeEEEEEEEEECcHhhHHHHHH
Confidence            9899999999999999999998 7899999999999999999998774

>3mr0_A Sensory box histidine kinase/response regulator; PAS fold, structural genomics, PSI-2; HET: PG5; 1.49A {Burkholderia thailandensis}

Probab=99.81  E-value=8.1e-19  Score=128.35  Aligned_cols=125  Identities=14%  Similarity=0.205  Sum_probs=109.1

Q ss_pred             HHHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCC--CCCCccCCCCCHHHHHHHHHHHHhCCCe
Q 022961           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGR--NGRMFQGPRTNRRTIMEIREAIREERPI   92 (289)
Q Consensus        15 ~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~--~~~~l~~~~~~~~~~~~~~~~~~~~~~~   92 (289)
                      .++++|+.+++.+++++|.+|..   +.++++|+++.+++||+++++.+.  .+..+++|++.......+...+..+..+
T Consensus         6 ~se~rl~~~~~~~~~g~w~~d~~---~~~~~~s~~~~~~~G~~~~~~~~~~~~~~~~ihpdD~~~~~~~~~~~~~~~~~~   82 (142)
T 3mr0_A            6 ASEERFQLAVSGASAGLWDWNPK---TGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAALKAHLEHRDTY   82 (142)
T ss_dssp             ---CCHHHHHHHTTCEEEEECTT---TCCEEECHHHHHHTTCCGGGSCSEEC---CCBCTTTHHHHHHHHHHHHHHCCCE
T ss_pred             HHHHHHHHHHHhCCcEEEEEEcC---CCeEEECHHHHHHhCCCccccCCCHHHHHhhcCHHHHHHHHHHHHHHHhCCCce
Confidence            56677889999999999999999   999999999999999999988763  3556778888888878888888888889


Q ss_pred             EEEEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhcc
Q 022961           93 EVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG  143 (289)
Q Consensus        93 ~~e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l  143 (289)
                      ..++++.+++|..+|+...+.|+.+ .+|.+.+++|+++|||++|++|++|
T Consensus        83 ~~e~r~~~~~G~~~w~~~~~~~~~d-~~g~~~~~~G~~~DITerk~~E~~L  132 (142)
T 3mr0_A           83 DVEYRVRTRSGDFRWIQSRGQALWN-SAGEPYRMVGWIMDVTDRKRDEDAL  132 (142)
T ss_dssp             EEEEEEECTTSCEEEEEEEEEEEEC-TTSCEEEEEEEEEECHHHHHHHHHH
T ss_pred             EEEEEEECCCCCEEEEEEEEEEEEC-CCCCEEEEEEEEEcCchHHHHHHHH
Confidence            9999999999999999999999998 8999999999999999999998776

>1n9l_A PHOT-LOV1, putative blue light receptor; phototropin, flavin, electron transport; HET: FMN; 1.90A {Chlamydomonas reinhardtii} SCOP: d.110.3.6 PDB: 1n9n_A* 1n9o_A*

Probab=99.81  E-value=1.9e-18  Score=120.52  Aligned_cols=109  Identities=40%  Similarity=0.795  Sum_probs=97.1

Q ss_pred             hCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEEEEEEecCCCE
Q 022961           26 ELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTP  105 (289)
Q Consensus        26 ~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~  105 (289)
                      +++++++++|...++|+|+++|++|++++||++++++|++...+.++.........++..+..+..+..++..++++|+.
T Consensus         1 ~~~~~i~i~d~~~~~g~i~~~N~a~~~l~Gy~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~kdG~~   80 (109)
T 1n9l_A            1 GLRHTFVVADATLPDCPLVYASEGFYAMTGYGPDEVLGHNCRFLQGEGTDPKEVQKIRDAIKKGEACSVRLLNYRKDGTP   80 (109)
T ss_dssp             CCSCEEEEEETTSTTCCEEEECHHHHHHHCCCHHHHTTSCGGGGCCTTCCHHHHHHHHHHHHHTCCEEEEEEEECTTSCE
T ss_pred             CCccEEEEEcCCCCCCeEEEEchHHHHHHCcCHHHHcCCCchhcCCCCCCHHHHHHHHHHHHcCCcEEEEEEEEcCCCCE
Confidence            36789999995323399999999999999999999999998877777776677778888888999999999999999999


Q ss_pred             EEEEEEEEEeecCCCCcEEEEEEEEecccc
Q 022961          106 FWMLFKMSLVFGKEDGRATHFVAVQVPIVS  135 (289)
Q Consensus       106 ~~~~~~~~~~~~~~~g~~~~~~~~~~DITe  135 (289)
                      +|+.+++.|+.+ ++|.+.+++++.+|||+
T Consensus        81 ~~~~~~~~pi~d-~~G~~~~~v~~~~DITe  109 (109)
T 1n9l_A           81 FWNLLTVTPIKT-PDGRVSKFVGVQVDVTS  109 (109)
T ss_dssp             EEEEEEEEEEEC-TTSCEEEEEEEEEECCC
T ss_pred             EEEEEEEEEEEC-CCCCEEEEEEEEEeCCC
Confidence            999999999998 89999999999999996

>3ue6_A Aureochrome1; PAS/LOV domain, FMN-binding blue-light photoreceptor, signal protein; HET: FMN; 2.75A {Vaucheria frigida} PDB: 3ulf_A*

Probab=99.80  E-value=1e-18  Score=130.64  Aligned_cols=123  Identities=38%  Similarity=0.624  Sum_probs=111.4

Q ss_pred             HHHHHHHHHhhCCCEEEEEeC---CCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCe
Q 022961           16 YTLWVHEALDELPDSFTITDP---SISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPI   92 (289)
Q Consensus        16 ~~~~l~~~~~~~~~~i~~~d~---~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~   92 (289)
                      ...++..++++++++++++|.   +   |+++++|+++++++||++++++|+++..+.++.........+...+..+..+
T Consensus        33 ~~~~~~~~~~~~~~~i~~~d~~~~~---g~i~~~N~~~~~l~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~  109 (166)
T 3ue6_A           33 PDYSLVKALQMAQQNFVITDASLPD---NPIVYASRGFLTLTGYSLDQILGRNCRFLQGPETDPRAVDKIRNAITKGVDT  109 (166)
T ss_dssp             CCCHHHHHHHHTTSCEEEEETTSTT---CCEEEECHHHHHHHCCCHHHHTTSCGGGGCCTTSCHHHHHHHHHHHHHTCCE
T ss_pred             HHHHHHHHHhcCCceEEEEEccCCC---CcEEEECHHHHHHhCcCHHHHcCCCHhheeCCCCCHHHHHHHHHHHhcCCce
Confidence            445788999999999999999   7   9999999999999999999999999888888777777777888888888889


Q ss_pred             EEEEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhc
Q 022961           93 EVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNS  142 (289)
Q Consensus        93 ~~e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~  142 (289)
                      ..+....+++|..+|+.+.+.|+.+ .+|.+.+++++++|||++|+++..
T Consensus       110 ~~e~~~~~~~g~~~~~~~~~~~i~~-~~g~~~~~~~~~~DITe~k~~~~~  158 (166)
T 3ue6_A          110 SVCLLNYRQDGTTFWNLFFVAGLRD-SKGNIVNYVGVQSKVSEDYAKLLV  158 (166)
T ss_dssp             EEEEEEECTTSCEEEEEEEEEEEEC-TTSCEEEEEEECCBCCHHHHHHHH
T ss_pred             EEEEEEEcCCCCEEEEEEEEEeeeC-CCCCEEEEEEEEEechHHHHHHHH
Confidence            8899999999999999999999998 799999999999999999988443

>3f1p_B ARYL hydrocarbon receptor nuclear translocator; PAS domain, heterodimer, internal cavity, activator, angiogenesis, congenital erythrocytosis; 1.17A {Homo sapiens} SCOP: d.110.3.0 PDB: 3f1o_B* 3f1n_B 3h7w_B* 3h82_B* 1x0o_A 2hv1_A 4h6j_B 2b02_A* 2k7s_A 2a24_B

Probab=99.80  E-value=5.2e-19  Score=125.54  Aligned_cols=115  Identities=10%  Similarity=0.128  Sum_probs=98.2

Q ss_pred             HHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHH-hCCCeEEEEEE
Q 022961           20 VHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIR-EERPIEVNLLN   98 (289)
Q Consensus        20 l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~-~~~~~~~e~~~   98 (289)
                      ...+++++++.+++.|.+   |+++++|+++++++||++++++|+++..+++|++.+.....+...+. .+..+..++++
T Consensus         4 ~~ll~e~~~d~i~~~d~~---g~i~~~n~~~~~~~G~~~~el~g~~~~~~i~p~d~~~~~~~~~~~~~~~~~~~~~e~r~   80 (121)
T 3f1p_B            4 KGLNVCQPTRFISRHNIE---GIFTFVDHRCVATVGYQPQELLGKNIVEFCHPEDQQLLRDSFQQVVKLKGQVLSVMFRF   80 (121)
T ss_dssp             ----CCCCCEEEEEECTT---SBEEEECTTHHHHHSCCGGGTTTSBGGGGBCTTTHHHHHHHHHHHTTSTTCCEEEEEEE
T ss_pred             ccceecCCCceEEEECCC---ceEEEECcchhhhhCCChHHHcCCCHHHeECHHHHHHHHHHHHHHHhcCCCcccEEEEE
Confidence            445789999999999999   99999999999999999999999998888888887777767766664 44568889999


Q ss_pred             EecCCCEEEEEEEEEEeecCC-CCcEEEEEEEEecccccHH
Q 022961           99 YKKDGTPFWMLFKMSLVFGKE-DGRATHFVAVQVPIVSRKH  138 (289)
Q Consensus        99 ~~~~g~~~~~~~~~~~~~~~~-~g~~~~~~~~~~DITe~k~  138 (289)
                      ++++|..+|+..+..|+.+ . +|.+.+++++.+|||++|+
T Consensus        81 ~~~dG~~~w~~~~~~~~~~-~~~g~~~~iv~~~~DIT~~kq  120 (121)
T 3f1p_B           81 RSKNQEWLWMRTSSFTFQN-PYSDEIEYIICTNTNVKNSSQ  120 (121)
T ss_dssp             ECTTSCEEEEEEEEEEECC-TTCCCCCEEEEEEEECCCC--
T ss_pred             EecCCCEEEEEEEEEEEEC-CCCCceeEEEEEeEEcccccC
Confidence            9999999999999999987 5 7888899999999999986

>3p7n_A Sensor histidine kinase; LOV domain, light-activated transcription factor, DNA bindin; HET: FMN; 2.10A {Erythrobacter litoralis}

Probab=99.78  E-value=3.6e-18  Score=137.69  Aligned_cols=120  Identities=30%  Similarity=0.597  Sum_probs=106.5

Q ss_pred             HHHHHHHHHHhhCCCEEEEEeC---CCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCC
Q 022961           15 RYTLWVHEALDELPDSFTITDP---SISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERP   91 (289)
Q Consensus        15 ~~~~~l~~~~~~~~~~i~~~d~---~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~   91 (289)
                      ..+++++.+++++|++++++|.   +   |+|+++|++|++++||++++++|+++..+.++.........+...+..+..
T Consensus        60 ~~~~~~~~i~~~~~~~i~~~d~~~~~---g~i~~~N~a~~~l~G~~~~el~g~~~~~l~~~~~~~~~~~~~~~~l~~~~~  136 (258)
T 3p7n_A           60 PPAQWVLDLIEASPIASVVSDPRLAD---NPLIAINQAFTDLTGYSEEECVGRNCRFLAGSGTEPWLTDKIRQGVREHKP  136 (258)
T ss_dssp             -CCHHHHHHHHTCSSEEEEECTTSTT---CCEEEECHHHHHHHCCCGGGTTTSCGGGGCCTTCCHHHHHHHHHHHHHTCC
T ss_pred             hHHHHHHHHHhcCCccEEEEcCCCCC---CcEEEEhHHHHHHcCCCHHHHCCCChhhccCCCCchhHHHHHHHHHHcCCC
Confidence            4456899999999999999999   7   899999999999999999999999998888888888888888888889999


Q ss_pred             eEEEEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHH
Q 022961           92 IEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKH  138 (289)
Q Consensus        92 ~~~e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~  138 (289)
                      +..+....+++|..+|+.+.+.|+.+ .+|.+.+++++++|||++|.
T Consensus       137 ~~~e~~~~~~dG~~~~~~~~~~pi~d-~~g~~~~~v~~~~DITerk~  182 (258)
T 3p7n_A          137 VLVEILNYKKDGTPFRNAVLVAPIYD-DDDELLYFLGSQVEVDDDQP  182 (258)
T ss_dssp             EEEEEEEECTTSCEEEEEEEEEEEEC-TTSCSEEEEEEEEEC-----
T ss_pred             eEEEEEEEcCCCCEEEEeeEEEEEEc-CCCCEEEEEEEeeecchhhh
Confidence            99999999999999999999999998 89999999999999999943

>3t50_A Blue-light-activated histidine kinase; PAS superfamily, blue-light photoreceptor, FMN binding, TRAN; HET: FMN; 1.64A {Brucella melitensis}

Probab=99.78  E-value=3.7e-18  Score=121.96  Aligned_cols=117  Identities=38%  Similarity=0.664  Sum_probs=103.2

Q ss_pred             HHhhCCCEEEEEeC---CCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEEEEEE
Q 022961           23 ALDELPDSFTITDP---SISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNY   99 (289)
Q Consensus        23 ~~~~~~~~i~~~d~---~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~   99 (289)
                      ++++++++++++|.   +   |+++++|+++++++||++++++|+++..+.++.........+...+..+..+..+....
T Consensus         2 ~~~~~~~~i~~~d~~~~~---g~i~~~N~~~~~l~g~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~   78 (128)
T 3t50_A            2 ASEFTLMPMLITNPHLPD---NPIVFANPAFLKLTGYEADEVMGRNCRFLQGHGTDPAHVRAIKSAIAAEKPIDIDIINY   78 (128)
T ss_dssp             CCCCCSSCEEEECTTSTT---CCEEEECHHHHHHHCCCHHHHTTSCGGGGCCTTSCHHHHHHHHHHHHTTCCEEEEEEEE
T ss_pred             ccccCcccEEEecCCCCC---CcEEEEcHHHHHHhCcCHHHHcCCCHhhhcCCccCHHHHHHHHHHHHcCCCceeEEEEE
Confidence            47889999999999   7   99999999999999999999999998888877777777778888888888888899999


Q ss_pred             ecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhcc
Q 022961          100 KKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG  143 (289)
Q Consensus       100 ~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l  143 (289)
                      +++|..+|+.+++.|+.+ .+|.+.+++++++|||++|++|++.
T Consensus        79 ~~~g~~~~~~~~~~~i~~-~~g~~~~~~~~~~DITe~k~~e~~~  121 (128)
T 3t50_A           79 KKSGEAFWNRLHISPVHN-ANGRLQHFVSSQLDVTLELVPRGSL  121 (128)
T ss_dssp             CTTCCEEEEEEEEEEEEC-TTSCEEEEEEEEEECHHHHC-----
T ss_pred             cCCCCEEEEEEEEEEEEC-CCCCEEEEEEEEEEcchhhhhhhhh
Confidence            999999999999999998 7899999999999999999997765

>3f1p_A Endothelial PAS domain-containing protein 1; PAS domain, heterodimer, internal cavity, activator, angiogenesis, congenital erythrocytosis; 1.17A {Homo sapiens} SCOP: d.110.3.7 PDB: 3f1o_A* 3f1n_A 3h7w_A* 3h82_A* 1p97_A 2a24_A 4h6j_A

Probab=99.76  E-value=2.4e-18  Score=121.22  Aligned_cols=108  Identities=8%  Similarity=0.170  Sum_probs=97.2

Q ss_pred             CCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEEEEEEecCCCEE
Q 022961           27 LPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPF  106 (289)
Q Consensus        27 ~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~  106 (289)
                      +++.+++.|.+   |+++++|+++++++||++++++|+++..+++|++.+.....+...+..+..+..++++++++|..+
T Consensus         8 ~~~~i~~~d~~---g~i~~~n~~~~~~~Gy~~~el~g~~~~~~~~p~d~~~~~~~~~~~~~~~~~~~~e~r~~~~dG~~~   84 (117)
T 3f1p_A            8 SKTFLSEHSMD---MKFTYCDDRITELIGYHPEELLGRSAYEFYHALDSENMTKSHQNLCTKGQVVSGQYRMLAKHGGYV   84 (117)
T ss_dssp             GGEEEEEECTT---CBEEEECTHHHHHHCCCHHHHTTSBGGGGBCGGGHHHHHHHHHHHHHHSEEECCCEEEECTTSSEE
T ss_pred             CccEEEEECCC---ceEEEECcChhhhhCCCHHHHcCCchhheECHHHHHHHHHHHHHHHhCCCeeeeEEEEEecCCCEE
Confidence            45788889999   999999999999999999999999988888888877777777788777777778899999999999


Q ss_pred             EEEEEEEEeecCC-CCcEEEEEEEEecccccHH
Q 022961          107 WMLFKMSLVFGKE-DGRATHFVAVQVPIVSRKH  138 (289)
Q Consensus       107 ~~~~~~~~~~~~~-~g~~~~~~~~~~DITe~k~  138 (289)
                      |+.....|+.+ . +|.+.+++++.+|||++|+
T Consensus        85 w~~~~~~~~~d-~~~g~~~~iv~~~~DITer~~  116 (117)
T 3f1p_A           85 WLETQGTVIYN-PRNLQPQCIMCVNYVLSEIEK  116 (117)
T ss_dssp             EEEEEEEEEEE-TTTTEEEEEEEEEEECSCCBC
T ss_pred             EEEEeeEEEEC-CCCCCceEEEEEeeecccccc
Confidence            99999999998 6 7888999999999999986

>4eet_B Phototropin-2; LOV, blue light photoreceptor, signaling protein, flavoprote; HET: FMN; 1.20A {Arabidopsis thaliana} PDB: 4ees_A* 4eer_A* 4eep_A* 4eeu_A* 1jnu_A* 1g28_A*

Probab=99.75  E-value=4.2e-17  Score=113.71  Aligned_cols=111  Identities=41%  Similarity=0.778  Sum_probs=99.3

Q ss_pred             HHhhCCCEEEEEeC---CCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEEEEEE
Q 022961           23 ALDELPDSFTITDP---SISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNY   99 (289)
Q Consensus        23 ~~~~~~~~i~~~d~---~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~   99 (289)
                      .+++++++++++|.   +   |+++++|+++++++||++++++|+++..+.++.........+...+..+..+..+.+..
T Consensus         2 ~l~~~~~~i~~~d~~~~~---g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (115)
T 4eet_B            2 SPEFIEKNFVITDPRLPD---NPIIFASDGFLELTEYSREEILGRNARFLQGPETDQATVQKIRDAIRDQRETTVQLINY   78 (115)
T ss_dssp             ---CCCCSEEEECTTSTT---CCEEEECHHHHHHHCCCHHHHTTSCGGGGCCTTSCHHHHHHHHHHHHTTCCEEEEEEEE
T ss_pred             ccccCCCcEEEEcCCCCC---CcEEEEcHHHHHHHCcCHHHHhCCCHHHhcCCCCChHHHHHHHHHHHcCCCcceEEEEe
Confidence            57899999999999   8   99999999999999999999999998888877777777777888888888888898889


Q ss_pred             ecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccH
Q 022961          100 KKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRK  137 (289)
Q Consensus       100 ~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k  137 (289)
                      +++|..+|+.++..|+.+ .+|.+.+++++.+|||+++
T Consensus        79 ~~~g~~~~~~~~~~~~~~-~~g~~~~~~~~~~DITer~  115 (115)
T 4eet_B           79 TKSGKKFWNLLHLQPVRD-QKGELQYFIGVQLDGSDHV  115 (115)
T ss_dssp             CTTCCEEEEEEEEEEEEC-TTSCEEEEEEEEEECSCCC
T ss_pred             cCCCCEEEEEEEEEEEEC-CCCCEEEEEEEEEeecccC
Confidence            999999999999999998 7899999999999999874

>3nja_A Probable ggdef family protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; 2.37A {Chromobacterium violaceum}

Probab=99.75  E-value=1.3e-17  Score=118.04  Aligned_cols=120  Identities=14%  Similarity=0.090  Sum_probs=92.4

Q ss_pred             HHHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCC--CCCCCccCCCCCHHHHHHHHHHHHhCCCe
Q 022961           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIG--RNGRMFQGPRTNRRTIMEIREAIREERPI   92 (289)
Q Consensus        15 ~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g--~~~~~l~~~~~~~~~~~~~~~~~~~~~~~   92 (289)
                      +++++++.++++++++++.+|.+   +.++++|+++++++||++++++|  ..+..+.+|++.......+...+..+..+
T Consensus         4 ~~~~~l~~~~~~~~~~i~~~d~~---~~~~~~n~~~~~~~G~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~   80 (125)
T 3nja_A            4 MAEKLLHTAESDAGIGSWVLHME---SGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDRPF   80 (125)
T ss_dssp             -------------CCEEEEEETT---TTEEEECHHHHHHHTCCTTTCCCBHHHHHHHBCTTTHHHHHHHHHHHHHSCCCE
T ss_pred             HHHHHHHHHHHhCCeeEEEEEcC---CCcEEECHHHHHHhCCCcccccccHHHHHhhcChhHHHHHHHHHHHHHhcCCCc
Confidence            45667889999999999999999   99999999999999999999988  33445567777677777777777888888


Q ss_pred             EEEEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHH
Q 022961           93 EVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKH  138 (289)
Q Consensus        93 ~~e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~  138 (289)
                      ..++++.+++|..+|+.+...|+.+ .+|.+.+++++++|||++|+
T Consensus        81 ~~e~~~~~~~g~~~~~~~~~~~~~~-~~g~~~~~~g~~~DITe~k~  125 (125)
T 3nja_A           81 DVEYRIVRPDGQVRELLERNHIQRQ-ASGQVDHLWGTVIDMTEHKQ  125 (125)
T ss_dssp             EEEEEEECTTSCEEEEEEEEEEEEC-TTSCEEEEEEEEEECCC---
T ss_pred             eEEEEEECCCCCEEEEEEeeEEEEC-CCCCEEEEEEEEEecccccC
Confidence            8899999999999999999999998 79999999999999999985

>3mqq_A Transcriptional regulator, LUXR family; PAS domain, PSI, MCSG, structural genomics, center for structural genomics; 1.65A {Burkholderia thailandensis} PDB: 3mqo_A

Probab=99.74  E-value=8.7e-18  Score=118.96  Aligned_cols=115  Identities=12%  Similarity=0.093  Sum_probs=90.9

Q ss_pred             HHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCC-HHHHHHHHHHHHhCCCeEEEEE
Q 022961           19 WVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTN-RRTIMEIREAIREERPIEVNLL   97 (289)
Q Consensus        19 ~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~-~~~~~~~~~~~~~~~~~~~e~~   97 (289)
                      .|+.+++++|++++ ++.+   |+|+++|+++++++||++++++|+++..+.++... ......+...+..+..+..+.+
T Consensus         4 ~~~~~~~~~~~~i~-~~~~---g~i~~~N~a~~~l~G~~~~el~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~   79 (120)
T 3mqq_A            4 DYKTAFHLAPIGLV-LSRD---RVIEDCNDELAAIFRCARADLIGRSFEVLYPSSDEFERIGERISPVMIAHGSYADDRI   79 (120)
T ss_dssp             CHHHHHHHCSSEEE-EEET---TEEEEECHHHHHHTTSCHHHHTTCBGGGGSSSHHHHHHHHHHHHHHHHHHSCEEEEEE
T ss_pred             hHHHHHhcCCceEE-EecC---CEEHHHHHHHHHHhCcCHHHhCCCchhhccCChhhHHHHHHHHHHHHhcCCcceEEEE
Confidence            36789999999996 4778   99999999999999999999999998776654322 2334445556667778888999


Q ss_pred             EEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHH
Q 022961           98 NYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM  139 (289)
Q Consensus        98 ~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~  139 (289)
                      +.+++|..+|+.++..|+.  ..+...+++++++|||++|++
T Consensus        80 ~~~~dG~~~~~~~~~~~~~--~~~~~~~~v~~~~DITerk~~  119 (120)
T 3mqq_A           80 MKRAGGELFWCHVTGRALD--RTAPLAAGVWTFEDLSATRRV  119 (120)
T ss_dssp             EECTTSCEEEEEEEEEESS--TTSTTSSEEEEEEESCC----
T ss_pred             EEeCCCCEEEEEEEEEECC--CCCCceeEEEEEEcccHhhcc
Confidence            9999999999999999994  356566789999999999986

>2z6d_A Phototropin-2; PAS-fold, LOV-fold, alternative splicing, ATP-binding, chromophore, flavoprotein, FMN, kinase, membrane, nucleotide-binding; HET: FMN; 2.00A {Arabidopsis thaliana} PDB: 2z6c_A*

Probab=99.74  E-value=1.6e-16  Score=112.46  Aligned_cols=124  Identities=38%  Similarity=0.732  Sum_probs=104.4

Q ss_pred             HHHHHHHHHHhhCCCEEEEEe---CCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCC
Q 022961           15 RYTLWVHEALDELPDSFTITD---PSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERP   91 (289)
Q Consensus        15 ~~~~~l~~~~~~~~~~i~~~d---~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~   91 (289)
                      +.++.++.++++++++++++|   .+   |.++++|+++++++|++.++++|+++..+.++.........+...+..+..
T Consensus         3 ~~~~~~~~~~~~~~~~i~~~d~~d~~---~~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~   79 (130)
T 2z6d_A            3 RVSQELKTALSTLQQTFVVSDATQPH---CPIVYASSGFFTMTGYSSKEIVGRNCRFLQGPDTDKNEVAKIRDCVKNGKS   79 (130)
T ss_dssp             ----CHHHHHHHTTCEEEEEETTSTT---CCEEEECHHHHHHHCCCHHHHTTSCGGGGCCTTSCHHHHHHHHHHHHTTCC
T ss_pred             hHHHHHHHHHHhcccceeeeeccCCC---CcEEEecHHHHHHhCcCHHHHcCCChhhccCCCCCchHHHHHHHHHHcCCc
Confidence            345568889999999999999   88   999999999999999999999999988887777777777777777888888


Q ss_pred             eEEEEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhc
Q 022961           92 IEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNS  142 (289)
Q Consensus        92 ~~~e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~  142 (289)
                      +..+....+++|..+|+.+...|+.+ ..|.+.+++++.+|||++|++|++
T Consensus        80 ~~~~~~~~~~~g~~~~~~~~~~~~~~-~~g~~~~~~~~~~Dit~~~~~e~e  129 (130)
T 2z6d_A           80 YCGRLLNYKKDGTPFWNLLTVTPIKD-DQGNTIKFIGMQVEVSKYTEGVND  129 (130)
T ss_dssp             EEEEEEEECTTSCEEEEEEEEEEEEC-TTSCEEEEEEEEEECCTTC-----
T ss_pred             ceeEEEEEcCCCcEEEEEEEEEEEEC-CCCCeeEEEEEEecchHHHHhhcc
Confidence            88888888999999999999999998 789999999999999999988653

>1d06_A Nitrogen fixation regulatory protein FIXL; oxygen sensor, histidine kinase, PAS, high-resolution, two-C system, signaling protein; HET: HEM; 1.40A {Sinorhizobium meliloti} SCOP: d.110.3.2 PDB: 1ew0_A*

Probab=99.73  E-value=3.9e-17  Score=117.36  Aligned_cols=124  Identities=17%  Similarity=0.239  Sum_probs=96.2

Q ss_pred             ccchHHHhhchHHHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHH
Q 022961            4 QLGLIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIR   83 (289)
Q Consensus         4 ~l~~~~~~l~~~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~   83 (289)
                      ++...++.+. +.+.+++.++++++++++++|.+   |+|+++|+++++++||++++++|+++..+.++.........+.
T Consensus         3 ~~~~~e~~l~-~~~~~~~~l~~~~~d~i~~~d~~---g~i~~~N~a~~~l~Gy~~~eliG~~~~~l~~~~~~~~~~~~~~   78 (130)
T 1d06_A            3 HMLETEDVVR-ARDAHLRSILDTVPDATVVSATD---GTIVSFNAAAVRQFGYAEEEVIGQNLRILMPEPYRHEHDGYLQ   78 (130)
T ss_dssp             HHHHHHHHHH-HHTSCHHHHHTTCSSEEEEEETT---SBEEEECHHHHHHHCCCHHHHTTSBGGGGSCTTHHHHHHHHHH
T ss_pred             hHHHHHHHHH-HHHHHHHHHHhhCcCeEEEECCC---CeEEEEcHHHHHHHCCCHHHHcCCcHHHHCCchhHHHHHHHHH
Confidence            4556677776 66778999999999999999999   9999999999999999999999999887776554333333333


Q ss_pred             HHHHhCCC----eEEEEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEeccc
Q 022961           84 EAIREERP----IEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV  134 (289)
Q Consensus        84 ~~~~~~~~----~~~e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIT  134 (289)
                      .....+..    ...++..+++||..+|+.+++.|+.+ + +. ..++++++|||
T Consensus        79 ~~~~~~~~~~~~~~~e~~~~~kdG~~~~~~~~~~~~~~-~-~~-~~~~~~~~DIT  130 (130)
T 1d06_A           79 RYMATGEKRIIGIDRVVSGQRKDGSTFPMKLAVGEMRS-G-GE-RFFTGFIRDLT  130 (130)
T ss_dssp             HHHHHCCCSSTTSCEEEEEECTTSCEEEEEEEEEEEEE-T-TE-EEEEEEEEECC
T ss_pred             HHHhcCCccccCCeeEEEEEeCCCCEEEEEEEEEEEEE-C-Ce-EEEEEEEEECc
Confidence            43333332    23466778999999999999999976 3 33 45889999997

>3lyx_A Sensory BOX/ggdef domain protein; structural genomics, PSI- 2, protein structure initiative, northeast structural genomics consortium; 2.00A {Colwellia psychrerythraea}

Probab=99.73  E-value=1.9e-16  Score=111.21  Aligned_cols=119  Identities=20%  Similarity=0.264  Sum_probs=103.9

Q ss_pred             HHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEE
Q 022961           16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVN   95 (289)
Q Consensus        16 ~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e   95 (289)
                      ..++++.++++++++++++|.+   |.++++|+++++++|++.++++|++...+.++.........+...+..+..+..+
T Consensus         5 ~~~~~~~~~~~~~~~i~~~d~~---~~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (124)
T 3lyx_A            5 ILKQRAKAFDYVFDAIVVTDLQ---GFIIDWNKGSETLYGYSKEQAIGQPVNMLHVPGDTEHITSEVISAVENQGKWTGE   81 (124)
T ss_dssp             HHHHHHHGGGTCSSEEEEEETT---CBEEEECHHHHHHHCCCHHHHTTSBGGGGSCTTTHHHHHHHHHHHHHHTSCEEEE
T ss_pred             HHHHHHHHHhhcCceEEEECCC---CcEeehhhHHHHHhCCCHHHHcCCCHHHhcCcchhhHHHHHHHHHHHcCCcccce
Confidence            4567889999999999999999   9999999999999999999999998776665555555566677778888888888


Q ss_pred             EEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHH
Q 022961           96 LLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKH  138 (289)
Q Consensus        96 ~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~  138 (289)
                      .....++|..+|+.+...|+.+ ..|.+.+++++.+|||++|+
T Consensus        82 ~~~~~~~g~~~~~~~~~~~~~~-~~g~~~~~~~~~~Dit~~~~  123 (124)
T 3lyx_A           82 IRMLHKDGHIGWIESMCVPIYG-ENYQMVGALGINRDITKRKK  123 (124)
T ss_dssp             EEEECTTSCEEEEEEEEEEEEC-STTCEEEEEEEEEECSCC--
T ss_pred             EEEEccCCCEEEEEEEEEEEEC-CCCCEEEEEEEEecchhhhc
Confidence            8889999999999999999998 79999999999999999986

>3sw1_A Sensory box protein; light-oxygen-voltage, LOV, PAS, signaling protein; HET: FMN; 2.63A {Pseudomonas putida}

Probab=99.73  E-value=1e-16  Score=119.34  Aligned_cols=124  Identities=23%  Similarity=0.437  Sum_probs=112.4

Q ss_pred             HHHHHHHHHhhCCCEEEEEeCCCCCc---cEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCe
Q 022961           16 YTLWVHEALDELPDSFTITDPSISGH---PIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPI   92 (289)
Q Consensus        16 ~~~~l~~~~~~~~~~i~~~d~~~~~g---~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~   92 (289)
                      .+++++.++++++++++++|.+   |   +++++|+++++++|++.++++|+++..+.++.........+...+..+..+
T Consensus        23 ~~~~~~~i~~~~~~~i~~~d~~---~~~~~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   99 (162)
T 3sw1_A           23 NAQLLQSMVDASNDGIVVAEKE---GDDTILIYVNAAFEYLTGYSRDEILYQDCRFLQGDDRDQLGRARIRKAMAEGRPC   99 (162)
T ss_dssp             CHHHHHHHHHTCSSEEEEEEEE---TTEEEEEEECHHHHHHHTCCHHHHTTSBGGGGTTTCCCCHHHHHHHHHHHHTCCE
T ss_pred             hHHHHHHHHhhccCcEEEEeCC---CCccEEEEECHHHHHHHCCCHHHHcCCCcceecCCCcCHHHHHHHHHHHhcCCCC
Confidence            4567899999999999999999   9   999999999999999999999999888877777777777778888888888


Q ss_pred             EEEEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhcc
Q 022961           93 EVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG  143 (289)
Q Consensus        93 ~~e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l  143 (289)
                      ..+....+++|..+|+.+.+.|+.+ .+|.+.+++++++|||++|++|+++
T Consensus       100 ~~~~~~~~~~g~~~~~~~~~~~i~~-~~g~~~~~~~~~~DiTe~k~~e~~l  149 (162)
T 3sw1_A          100 REVLRNYRKDGSAFWNELSITPVKS-DFDQRTYFIGIQKDVSRQVELEREL  149 (162)
T ss_dssp             EEEEEEECTTCCEEEEEEEEEEEEC-SSSSCEEEEEEEEECHHHHHHHHHH
T ss_pred             cceEEEECCCCCEEEEEEEEEEeec-CCCCEEEEEEEEEeCcHHHHHHHHH
Confidence            8888888999999999999999998 7899999999999999999998776

>2r78_A Sensor protein; sensory box sensor histidine kinase/response regulator, structural genomics, PSI, MCSG; 1.60A {Geobacter sulfurreducens pca}

Probab=99.73  E-value=1.9e-16  Score=111.70  Aligned_cols=110  Identities=11%  Similarity=0.137  Sum_probs=87.8

Q ss_pred             HHHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEE
Q 022961           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV   94 (289)
Q Consensus        15 ~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   94 (289)
                      .++++++.++++++++++++|.+   |+++++|+++++++||++++++|+++..+.++.... ........+..+..+..
T Consensus         8 ~se~~~~~l~e~~~d~i~~~d~~---g~i~~vN~a~~~l~Gy~~~el~g~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~   83 (117)
T 2r78_A            8 FQSNAYRALFEHAIDGIFIMDAE---GHYLDVNPAICSAIGYTRDEFLALDWGVLSRGVDSG-WAAASLARIVGGEPLRE   83 (117)
T ss_dssp             HHHHHHHHHHHHCSSEEEEECTT---SBEEEECHHHHHHHCCCHHHHTTCBTTTTTTCSTTS-HHHHHHHHHHTTCCEEE
T ss_pred             HhHHHHHHHHhcCCceEEEECCC---CCEEEecHHHHHHHCcCHHHHcCCCHHHhCCccchh-HHHHHHHHHHcCCcEEE
Confidence            66788999999999999999999   999999999999999999999999876664433222 22234455566677888


Q ss_pred             EEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEeccc
Q 022961           95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV  134 (289)
Q Consensus        95 e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIT  134 (289)
                      +.+.++++|..+|+.++..|+.   +|.   ++++++|||
T Consensus        84 e~~~~~kdG~~~~v~~~~~~~~---~g~---~~~i~~DIT  117 (117)
T 2r78_A           84 ERTVWTRNGDQLTVELSAHLLP---DGK---ILGIARDVS  117 (117)
T ss_dssp             EEEEECTTSCEEEEEEEEEECT---TSC---EEEEEEC--
T ss_pred             EEEEEecCCCEEEEEEEEEEec---CCe---EEEEEEeCC
Confidence            8889999999999999999884   344   678889997

>2vv6_A FIXL, sensor protein FIXL; signaling protein, transferase, phosphoprotein, nitrogen FIX PER-ARNT-SIM, metal-binding, PAS, iron, heme; HET: HEM; 1.5A {Bradyrhizobium japonicum} PDB: 1xj6_A* 1xj4_A* 2vv7_A* 2vv8_A* 1lsw_A* 1dp8_A* 1dp9_A* 1drm_A* 1lsv_A* 1dp6_A* 1lsx_A* 1lt0_A* 1y28_A* 2cmn_A* 1xj3_A* 1xj2_A* 2owh_A* 2owj_A*

Probab=99.72  E-value=7e-17  Score=114.08  Aligned_cols=112  Identities=20%  Similarity=0.253  Sum_probs=78.8

Q ss_pred             hCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCC----eEEEEEEEec
Q 022961           26 ELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERP----IEVNLLNYKK  101 (289)
Q Consensus        26 ~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~----~~~e~~~~~~  101 (289)
                      +++++++++|.+   |+|+++|+++++++||++++++|++...+.++.........+......+..    ...+...+++
T Consensus         1 ~~~d~i~~~d~~---g~i~~~N~a~~~l~G~~~~el~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   77 (119)
T 2vv6_A            1 TIPDAMIVIDGH---GIIQLFSTAAERLFGWSELEAIGQNVNILMPEPDRSRHDSYISRYRTTSDPHIIGIGRIVTGKRR   77 (119)
T ss_dssp             -CCCEEEEEETT---SBEEEECHHHHHHHCCCHHHHTTSBGGGGSCTTHHHHHHHHHHHHHHHCCCSSTTTCEEEEEECT
T ss_pred             CCcceEEEECCC---CeEEEEhHHHHHHhCCCHHHHcCCCHHHhCCchHHHHHHHHHHHHhcCCCcccCCCceEEEEEeC
Confidence            368999999999   999999999999999999999999987776554433333333333333332    2346677899


Q ss_pred             CCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhcc
Q 022961          102 DGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG  143 (289)
Q Consensus       102 ~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l  143 (289)
                      ||..+|+.+++.|+.+ . +. ..++++++|||++|++|++|
T Consensus        78 dG~~~~~~~~~~~~~~-~-~~-~~~~~~~~DITerk~~e~~l  116 (119)
T 2vv6_A           78 DGTTFPMHLSIGEMQS-G-GE-PYFTGFVRDLTEHQQTQARL  116 (119)
T ss_dssp             TSCEEEEEEEEEEEEE-T-TE-EEEEEEEEECC---------
T ss_pred             CCCEEEEEEEEEEEEE-C-Ce-EEEEEEEEEcHHHHHHHHHH
Confidence            9999999999999976 3 33 46889999999999998876

>3h9w_A Diguanylate cyclase with PAS/PAC sensor; alpha-beta protein., structural genomics, PSI-2, protein STR initiative; 1.90A {Marinobacter aquaeolei}

Probab=99.71  E-value=4.3e-17  Score=114.40  Aligned_cols=111  Identities=9%  Similarity=0.083  Sum_probs=93.9

Q ss_pred             CCCEEEEEe-CCCCCccEEEccHHHHHHhCCCccccCCCC-CCCccCCCCCHHHHHHHHHHHHhCCCeEEEEEEEecCCC
Q 022961           27 LPDSFTITD-PSISGHPIVFASRGFLKMSGFSRAEIIGRN-GRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGT  104 (289)
Q Consensus        27 ~~~~i~~~d-~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~-~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~  104 (289)
                      +++++|.+| ..   ++++|+|+++++++||+++++.+.. +..+++|++.+.....+...+..+..+..++++++++|.
T Consensus         2 a~~giw~~d~~~---~~~~~~n~~~~~l~G~~~~e~~~~~~~~~~ihpdd~~~~~~~~~~~~~~~~~~~~e~r~~~~dG~   78 (115)
T 3h9w_A            2 TKAIPWKINWQT---MAFEYIGPQIEALLGWPQGSWKSVEDWATRMHPEDQEWVVNFCVKQSECGVDHEADYRALHRDGH   78 (115)
T ss_dssp             -CCEEEEEETTT---TEEEEECTHHHHHHCSCGGGCCBHHHHHHSBCHHHHHHHHHHHHHHHHTTCCEEEEEEEECTTSC
T ss_pred             cceEEEEEEcCC---CcEEEEChhHHHHhCCChHHccCHHHHHHhcCHHHHHHHHHHHHHHHhcCCcccEEEEEEcCCCC
Confidence            568999999 55   8899999999999999999998832 334667777677777777888888888999999999999


Q ss_pred             EEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHh
Q 022961          105 PFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRN  141 (289)
Q Consensus       105 ~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~  141 (289)
                      .+|+...+.|+.+ .+|.+.+++|+.+|||++|++|+
T Consensus        79 ~~w~~~~~~~~~d-~~G~~~~~~G~~~Dit~~k~~~~  114 (115)
T 3h9w_A           79 YVWIRDVVHVVRD-DSGEVEALIGFMFDISLEHHHHH  114 (115)
T ss_dssp             EEEEEEEEEEEEC-TTSCEEEEEEEEEECGGGGC---
T ss_pred             EEEEEEEEEEEEC-CCCCEEEEEEEEeccCccccccc
Confidence            9999999999998 89999999999999999999864

>2wkq_A NPH1-1, RAS-related C3 botulinum toxin substrate 1; transferase, cell adhesion, nucleotide-binding, protein engineering, RAS superfamily LOV2; HET: GTP FMN; 1.60A {Avena sativa} PDB: 2wkr_A* 2wkp_A*

Probab=99.70  E-value=2.7e-16  Score=131.34  Aligned_cols=118  Identities=38%  Similarity=0.729  Sum_probs=108.4

Q ss_pred             HHHhhCCCEEEEEeC---CCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEEEEE
Q 022961           22 EALDELPDSFTITDP---SISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLN   98 (289)
Q Consensus        22 ~~~~~~~~~i~~~d~---~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~   98 (289)
                      .++++++++++++|.   +   |+++++|+++++++||++++++|+++..+.++.........+...+..+..+..+.+.
T Consensus        15 ~~~~~~~~~i~~~D~~~~~---g~i~~~N~a~~~l~G~~~~el~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~   91 (332)
T 2wkq_A           15 TTLERIEKNFVITDPRLPD---NPIIFASDSFLQLTEYSREEILGRNARFLQGPETDRATVRKIRDAIDNQTEVTVQLIN   91 (332)
T ss_dssp             CCGGGCCSEEEEECTTSTT---CCEEEECHHHHHHHCCCHHHHTTSCGGGGCCTTCCHHHHHHHHHHHHTTCCEEEEEEE
T ss_pred             hHhhcCCCcEEEecCCCCC---CCEEEeehHHHHHhCCCHHHHcCCCchhhcCCCCCHHHHHHHHHHHHcCCeeEEEEEE
Confidence            468999999999999   8   9999999999999999999999999888888887777778888888888889999999


Q ss_pred             EecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhcc
Q 022961           99 YKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG  143 (289)
Q Consensus        99 ~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l  143 (289)
                      .+++|..+|+.+++.|+.+ ..|.+.+++++.+|||++++.|++.
T Consensus        92 ~~~dG~~~~~~~~~~pi~d-~~g~~~~~v~~~~DITe~k~~e~~~  135 (332)
T 2wkq_A           92 YTKSGKKFWNLFHLQPMRD-QKGDVQYFIGVQLDGTEHVRDAAER  135 (332)
T ss_dssp             ECTTCCEEEEEEEEEEEEC-TTSCEEEEEEEEEEESSCCCHHHHH
T ss_pred             EcCCCCEEEEeeEEEEeEc-CCCCEEEEEEEeccCchhhhhhhhc
Confidence            9999999999999999998 7899999999999999998886655

>3k3c_A Protein RV1364C/MT1410; sensor, PAS, signal transduction, fatty-acid binding, sigma regulator, signaling protein; HET: PLM; 1.62A {Mycobacterium tuberculosis} PDB: 3k3d_A

Probab=99.69  E-value=1.7e-16  Score=117.74  Aligned_cols=123  Identities=12%  Similarity=0.117  Sum_probs=101.3

Q ss_pred             HHHHHHHHHHhhCCCEEEEEe-CCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeE
Q 022961           15 RYTLWVHEALDELPDSFTITD-PSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIE   93 (289)
Q Consensus        15 ~~~~~l~~~~~~~~~~i~~~d-~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~   93 (289)
                      ...++|+.+++++|++++++| .+   |+++++|+++++++|++  +++|+++..++++.........+..++..+.+..
T Consensus        14 ~~~~~~~~~~~~~~~~i~~~d~~~---~~i~~~N~~~~~~~g~~--~~~G~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~   88 (158)
T 3k3c_A           14 GAAEDVRRIFEHIPAILVGLEGPD---HRFVAVNAAYRGFSPLL--DTVGQPAREVYPELEGQQIYEMLDRVYQTGEPQS   88 (158)
T ss_dssp             CCHHHHHHHHHHCSSEEEEEETTT---TEEEEECHHHHHHCTTC--CSTTSBHHHHSGGGGGTTHHHHHHHHHHHCCCEE
T ss_pred             HHHHHHHHHHhcCCceEEEEECCC---cEeHHHHHHHHHHcCCc--hhcCCcHHHhCCchhHHHHHHHHHHHHHhCCccc
Confidence            345689999999999999999 99   99999999999999999  8999998777766555556667777777777754


Q ss_pred             EE-EEE--Ee-cC-CCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhcc
Q 022961           94 VN-LLN--YK-KD-GTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG  143 (289)
Q Consensus        94 ~e-~~~--~~-~~-g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l  143 (289)
                      .+ ...  .+ .+ |..+|+.+...|+.+ .+|.+.+++++++|||++|++|+++
T Consensus        89 ~~~~~~~~~~~~~~g~~~~~~~~~~pi~~-~~g~~~g~~~~~~DITe~k~~e~~l  142 (158)
T 3k3c_A           89 GSEWRLQTDYDGSGVEERYFDFVVTPRRR-ADGSIEGVQLIVDDVTSRVRARQAA  142 (158)
T ss_dssp             EEEEEEEEESSSSCEEEEEEEEEEEEEEC-TTSCEEEEEEEEEECHHHHHHHHHH
T ss_pred             ccceeEEeccCCCCcceEEEEEEEEEeEC-CCCCEEEEEEEEEehhHHHHHHHHH
Confidence            43 222  22 22 677899999999998 7999999999999999999998776

>3mxq_A Sensor protein; PSI2, MCSG, structural genomics, protein structure initiativ midwest center for structural genomics; 2.78A {Vibrio cholerae o1 biovar el tor}

Probab=99.69  E-value=8.7e-17  Score=118.35  Aligned_cols=120  Identities=16%  Similarity=0.121  Sum_probs=93.8

Q ss_pred             HHHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEE
Q 022961           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV   94 (289)
Q Consensus        15 ~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   94 (289)
                      +.+..+..+++++++|++++|.+   |+|++||+++++++|+++++++|+++..+++. ....+...+..++..+.+...
T Consensus        19 ~~~~~l~~il~~~~~gi~v~D~~---g~I~~~N~a~~~~~G~~~~eviG~~~~~~~p~-~~~~~~~~l~~vl~~G~~~~~   94 (152)
T 3mxq_A           19 KSRLLLSELLDQLSFALCIVRND---YVIVKVNEYFESRVIFDGETMQGKNILELFPE-SADYLKRKIDTALVIESSSFS   94 (152)
T ss_dssp             HHHHHHHHHHHHHCCEEEEEETT---SBEEEECHHHHHTSSSCHHHHTTSBHHHHSGG-GHHHHHHHHHHHHHHTSCEEE
T ss_pred             HHHHHHHHHHhcCCCCEEEEcCC---CEEEEECHHHHHHHCcCHHHHCCCCHHHhcCC-hHHHHHHHHHHHHhcCCceee
Confidence            55667899999999999999999   99999999999999999999999998888766 444555667777877765322


Q ss_pred             EE---------E---EEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHH
Q 022961           95 NL---------L---NYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM  139 (289)
Q Consensus        95 e~---------~---~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~  139 (289)
                      ..         .   ...++|...|..+++.|+.+ .+|.+.+++.+++|||+++.+
T Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ti~Pl~d-~~G~v~gv~~ii~DVTe~~~a  150 (152)
T 3mxq_A           95 SWEQKPHLLPFKSSRPVSGEEEQMYQNLEVIPIHS-EDGTIEHVCLCVYDVTIQASQ  150 (152)
T ss_dssp             ECCSSSCSSCC----------CCEEEEEEEEEEEC-TTSCEEEEEEEEEEEECC---
T ss_pred             ecccccccccccccCCCCCCCcEEEEEEEEEEEEC-CCCCEEEEEEEEEECCHHHhc
Confidence            11         1   12345677888999999999 899999999999999999876

>3luq_A Sensor protein; PAS, histidine, kinase, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: PGE; 2.49A {Geobacter sulfurreducens}

Probab=99.69  E-value=6.7e-16  Score=107.39  Aligned_cols=111  Identities=16%  Similarity=0.225  Sum_probs=90.8

Q ss_pred             HHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEE-E
Q 022961           18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVN-L   96 (289)
Q Consensus        18 ~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e-~   96 (289)
                      ++++.+++++|++++++|.+   |+++++|+++++++|+++++++|++...++ |.........+...+. +.....+ .
T Consensus         3 ~~~~~~~~~~~~~i~~~d~~---g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~-~~~~~~~~~~~~~~~~-~~~~~~~~~   77 (114)
T 3luq_A            3 ERLRLFTEHAPAALAMFDRE---MRYLAVSRRWREDYGLGDGDILGMSHYDIF-PEIGEEWKSVHRRGLA-GEVIRVEED   77 (114)
T ss_dssp             HHHHHHHHTCSSEEEEEETT---CBEEEECHHHHHHTTCCSSCCTTCBHHHHC-TTCCHHHHHHHHHHHT-TCCEEEEEE
T ss_pred             HHHHHHHhcCCceEEEEcCC---cEEEEECHHHHHHHCCCHHHHcCCcHHHHC-CccHHHHHHHHHHHhc-CCcceeeee
Confidence            56888999999999999999   999999999999999999999999977776 5555555444444444 4544443 3


Q ss_pred             EEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEeccc
Q 022961           97 LNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV  134 (289)
Q Consensus        97 ~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIT  134 (289)
                      ...+++|..+|+.+...|+.+ .+|.+.+++++.+|||
T Consensus        78 ~~~~~~g~~~~~~~~~~p~~~-~~g~~~~~~~~~~DIT  114 (114)
T 3luq_A           78 CFVRADGRTQWLRWEVRPWYE-GEGRVGGVVIFTEDIT  114 (114)
T ss_dssp             EEEC--CCEEEEEEEEEEEEC-TTSCEEEEEEEEEECC
T ss_pred             EEEcCCCcEEEEEEEEEEeEC-CCCCEEEEEEEEeeCC
Confidence            778899999999999999998 7999999999999997

>3ewk_A Sensor protein; PAS domain, alpha/beta fold, kinase, phosphoprotein, transfe flavoprotein; HET: FAD; 2.34A {Methylococcus capsulatus}

Probab=99.67  E-value=1.4e-15  Score=120.06  Aligned_cols=111  Identities=20%  Similarity=0.465  Sum_probs=103.1

Q ss_pred             HHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEEEE
Q 022961           18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLL   97 (289)
Q Consensus        18 ~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~   97 (289)
                      ++++.++++++++++++|.+   |+|+++|++|++++||++++++|+++..+.++.........+++.+..+..|..++.
T Consensus       111 ~~~~~~~~~~~~~i~~~d~~---g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~  187 (227)
T 3ewk_A          111 ARLKQAMDANSEMILLTDRA---GRIIYANPALCRFSGMAEGELLGQSPSILDSPLADQETLAAMQEALQAGQPWSGRLL  187 (227)
T ss_dssp             HHHHHHHHTCCSEEEEECTT---SCEEEECHHHHHHHTCCTHHHHSSCGGGGBCTTSCHHHHHHHHHHHHHTCCEECCEE
T ss_pred             HHHHHHHhcCcCeEEEEcCC---CcEEEEchHHHHHhCCCHHHHcCCChhhccCCCCCHHHHHHHHHHHHcCCceeEEEE
Confidence            46778999999999999999   999999999999999999999999998888888888888889999999999999999


Q ss_pred             EEecCCC------EEEEEEEEEEeecCCCCcEEEEEEEEec
Q 022961           98 NYKKDGT------PFWMLFKMSLVFGKEDGRATHFVAVQVP  132 (289)
Q Consensus        98 ~~~~~g~------~~~~~~~~~~~~~~~~g~~~~~~~~~~D  132 (289)
                      .++++|.      .+|+.+++.|+.+ .+|.+.+++++.+|
T Consensus       188 ~~~k~G~~~~dg~~~~~~~~~~pi~d-~~g~~~~~v~i~~D  227 (227)
T 3ewk_A          188 NRRRTGPAPHDAEDYWAEISTTPIHT-DGNGLVGYVQIQHD  227 (227)
T ss_dssp             EEEECCSSSSCEEEEEEEEEEEEEEC-SSSCEEEEEEEEEC
T ss_pred             EECCCCCcCcccceEEEEEEEEEEEC-CCCCEEEEEEEecC
Confidence            9999987      8999999999998 89999999999887

>3kx0_X Uncharacterized protein RV1364C/MT1410; PAS domain, sensory domain, mycobacteium tuberculos molecule binding domain; 2.30A {Mycobacterium tuberculosis}

Probab=99.66  E-value=9.4e-16  Score=117.17  Aligned_cols=123  Identities=12%  Similarity=0.121  Sum_probs=98.8

Q ss_pred             HHHHHHHHHHhhCCCEEEEEe-CCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeE
Q 022961           15 RYTLWVHEALDELPDSFTITD-PSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIE   93 (289)
Q Consensus        15 ~~~~~l~~~~~~~~~~i~~~d-~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~   93 (289)
                      +.+++|+.+++++|++++++| .+   |+++++|+++++++|++  +++|+++..++++.........+..++..+....
T Consensus        34 ~~~~~l~~l~~~~~~~i~~~d~~~---g~i~~~N~a~~~l~G~~--~~~G~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~  108 (185)
T 3kx0_X           34 GAAEDVRRIFEHIPAILVGLEGPD---HRFVAVNAAYRGFSPLL--DTVGQPAREVYPELEGQQIYEMLDRVYQTGEPQS  108 (185)
T ss_dssp             CCHHHHHHHHHHCSSEEEEEETTT---TEEEEECHHHHHHCCCC--SCTTSBHHHHCTTSCSSSSHHHHHHHHHHCCCEE
T ss_pred             hhHHHHHHHHhcCCceEEEEECCC---cEEEEEcHHHHHHcCCc--cccCCcHHHHCCchhhhhHHHHHHHHHHcCCccc
Confidence            355789999999999999999 99   99999999999999999  8999998877776655555566677777777755


Q ss_pred             EE-EEE--Eec-C-CCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhcc
Q 022961           94 VN-LLN--YKK-D-GTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG  143 (289)
Q Consensus        94 ~e-~~~--~~~-~-g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l  143 (289)
                      .+ ...  .++ + |...|+.+...|+.+ .+|.+.+++++++|||++|++|+++
T Consensus       109 ~~~~~~~~~~~~~gg~~~~~~~~~~pi~~-~~g~~~g~~~~~~DITerk~~e~~~  162 (185)
T 3kx0_X          109 GSEWRLQTDYDGSGVEERYFDFVVTPRRR-ADGSIEGVQLIVDDVTSRVRARQAA  162 (185)
T ss_dssp             EEEEEEC--------CCEEEEEEEEEEEC-TTSCEEEEEEEEEECHHHHTTCC--
T ss_pred             ccceeEEeeccCCCCccEEEEEEEEEEEC-CCCCEEEEEEEEEeCCHHHHHHHHH
Confidence            44 222  222 2 778999999999998 7999999999999999999998773

>3icy_A Sensor protein; sensory box histidine kinase/response regulator domain, kinase, chlorobium tepidum TLS, PSI-2; 2.68A {Chlorobaculum tepidum}

Probab=99.65  E-value=4.9e-16  Score=108.97  Aligned_cols=115  Identities=10%  Similarity=0.047  Sum_probs=101.3

Q ss_pred             HHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCC--CCccCCCCCHHHHHHHHHHHHhCCCeE
Q 022961           16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNG--RMFQGPRTNRRTIMEIREAIREERPIE   93 (289)
Q Consensus        16 ~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~--~~l~~~~~~~~~~~~~~~~~~~~~~~~   93 (289)
                      ++++|+.++++++++++.+|.+   +.++++|+++.+++||+++++.+.+.  ..+++|++.......+...+..+..+.
T Consensus         2 s~~~~~~l~~~~~~~i~~~d~~---~~~~~~n~~~~~~~G~~~~~~~~~~~~~~~~i~p~d~~~~~~~~~~~~~~~~~~~   78 (118)
T 3icy_A            2 NAEELQALVDNIPAAIYHLDVS---GQATIRFRPPAFLKTLVSEHAGTTRLNTLSMIHHDDRHMLSNAYSKLREAKHSLT   78 (118)
T ss_dssp             HHHHHHHHHTTCCCCCEEECTT---SCEEECCCCCGGGGGGEEEETTEEEEGGGGGBCGGGHHHHHHHHHHHHHSCCEEE
T ss_pred             cHHHHHHHHhcCCceEEEEEcC---CCceEEechhHhhcCCCHHHccCChhHHHHHcCHHHHHHHHHHHHHHHhcCCCce
Confidence            3567899999999999999999   99999999999999999999887653  456677777777777777777778888


Q ss_pred             EEEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEeccc
Q 022961           94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV  134 (289)
Q Consensus        94 ~e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIT  134 (289)
                      .++++.+++|...|+.....|+.+ ++|.+.+++++++|||
T Consensus        79 ~e~r~~~~~g~~~w~~~~~~~~~~-~~g~~~~~~g~~~DIT  118 (118)
T 3icy_A           79 LVYRIVTPEGKLHWIEDHMRSSFS-DDGLFSGIDGILCEVT  118 (118)
T ss_dssp             EEEEEECTTCCEEEEEEEEEEEEC-TTSCEEEEEEEEEECC
T ss_pred             EEEEEECCCCCEEEEEEEEEEEEC-CCCCEEEEEEEEEecC
Confidence            899999999999999999999998 8999999999999998

>2v0u_A NPH1-1, LOV2; kinase, transferase, ATP-binding, serine/threonine-protein kinase, light-induced signal trans phototropin1, nucleotide-binding; HET: FMN; 1.40A {Avena sativa} PDB: 2v0w_A* 2v1b_A* 2v1a_A* 1jnu_A* 1g28_A*

Probab=99.64  E-value=2.3e-15  Score=108.81  Aligned_cols=116  Identities=39%  Similarity=0.742  Sum_probs=104.4

Q ss_pred             HHHHHhhCCCEEEEEeC---CCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEEE
Q 022961           20 VHEALDELPDSFTITDP---SISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNL   96 (289)
Q Consensus        20 l~~~~~~~~~~i~~~d~---~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~   96 (289)
                      ++.++++++++++++|.   +   |.++++|+++++++|++.++++|+++..+.++.........+...+..+..+..+.
T Consensus         4 l~~~~~~~~~~i~~~d~~~~~---~~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (146)
T 2v0u_A            4 LATTLERIEKNFVITDPRLPD---NPIIFASDSFLQLTEYSREEILGRNCRFLQGPETDRATVRKIRDAIDNQTEVTVQL   80 (146)
T ss_dssp             CCCTGGGSSSCEEEECTTSTT---CCEEEECHHHHHHHCCCHHHHTTSCGGGGCCTTSCHHHHHHHHHHHHTTCCEEEEE
T ss_pred             HHHHHhcCCCcEEEEcCCCCC---ceEEEEcHHHHHHHCcCHHHHcCCCHHHhcCCcCChHHHHHHHHHHhcCCCcceEE
Confidence            34578999999999999   8   99999999999999999999999998888777777777777788888888888888


Q ss_pred             EEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHH
Q 022961           97 LNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM  139 (289)
Q Consensus        97 ~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~  139 (289)
                      ...+++|..+|+.+...|+.+ .+|.+.+++++.+|||++|+.
T Consensus        81 ~~~~~~g~~~~~~~~~~~~~~-~~g~~~~~~~~~~Dit~~~~~  122 (146)
T 2v0u_A           81 INYTKSGKKFWNLFHLQPMRD-QKGDVQYFIGVQLDGTEHVRD  122 (146)
T ss_dssp             EEECTTCCEEEEEEEEEEEEC-TTSCEEEEEEEEEEESSCCCH
T ss_pred             EEEecCCcEEEEEEEEEEeEC-CCCCEEEEEEEEeechHHHHH
Confidence            888999999999999999998 789999999999999999984

>3bwl_A Sensor protein; structural genomics, APC87707.1, PAS domain, HTR-like protei protein structure initiative; HET: MSE I3A; 1.73A {Haloarcula marismortui atcc 43049}

Probab=99.64  E-value=8.9e-15  Score=104.01  Aligned_cols=120  Identities=13%  Similarity=0.163  Sum_probs=87.3

Q ss_pred             cchHHHhhchHHHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccC--CCCCCCccCCCCCHHHHHHH
Q 022961            5 LGLIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEII--GRNGRMFQGPRTNRRTIMEI   82 (289)
Q Consensus         5 l~~~~~~l~~~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~--g~~~~~l~~~~~~~~~~~~~   82 (289)
                      .++.++.+. +++++++.+++++|++++++|.+   |+++++|+++++++||++++++  |++...+.+  +.......+
T Consensus         5 r~~~e~~L~-~~~~~~~~l~e~~~~~i~~~d~~---g~i~~~N~a~~~~~G~~~~el~g~g~~~~~~~~--~~~~~~~~~   78 (126)
T 3bwl_A            5 RKRREKRLE-ETSSRLEALFENSPDMIDVLDAD---GTICEVNQRFCAELGYDESEVLGRSIWEFDLMF--DAEDVQTQL   78 (126)
T ss_dssp             HHHHHHHHH-HHHHHHHHHHHHCSSEEEEECTT---CBEEEECHHHHHHHTCCGGGTTTSBGGGTBTTC--CHHHHHHHH
T ss_pred             HHHHHHHHH-HHHHHHHHHHhhCCcEEEEEcCC---CCEEEEcHHHHHHhCCCHHHHhhCCCchhhccC--CHHHHHHHH
Confidence            455666666 77889999999999999999999   9999999999999999999994  566555544  222221111


Q ss_pred             HHHHHhCCCeEEEEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEeccc
Q 022961           83 REAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV  134 (289)
Q Consensus        83 ~~~~~~~~~~~~e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIT  134 (289)
                      .. ...+.....+..+.+++|..+|+.++..|+..  .|.. .++++++|||
T Consensus        79 ~~-~~~~~~~~~e~~~~~~dG~~~~~~~~~~~~~~--~~~~-~~~~~~~DIT  126 (126)
T 3bwl_A           79 SG-FSVDERRKFEGLYERRDGSTMSVEVHLLRFNL--EGED-RFLAISRDIT  126 (126)
T ss_dssp             HT-CCTTCEEEEEEEEECTTSCEEEEEEEEEEEEE--TTEE-EEEEEEEEC-
T ss_pred             HH-HhcCCCcceEEEEEeCCCCEEEEEEEeEEEec--CCcE-EEEEEEEeCC
Confidence            11 11233345566778999999999988888754  4543 5778899997

>2kdk_A ARYL hydrocarbon receptor nuclear translocator-LI 2; circadian clock, PAS domain, transcription, activator, biolo rhythms, DNA-binding, nucleus; NMR {Homo sapiens}

Probab=99.64  E-value=3.1e-15  Score=105.62  Aligned_cols=112  Identities=11%  Similarity=0.085  Sum_probs=93.7

Q ss_pred             HHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCC-CeEEEEEEEe
Q 022961           22 EALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREER-PIEVNLLNYK  100 (289)
Q Consensus        22 ~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~-~~~~e~~~~~  100 (289)
                      .+++++++++++.|.+   |+++++|+++++++||++++++|+++..+.+|++.......+...+..+. ....++++++
T Consensus         7 ~~~~~~~~~i~~~d~~---g~i~~~N~~~~~~~G~~~~el~g~~~~~~~~p~d~~~~~~~~~~~~~~~~~~~~~e~r~~~   83 (121)
T 2kdk_A            7 EINVKPTEFITRFAVN---GKFVYVDQRATAILGYLPQELLGTSCYEYFHQDDHNNLTDKHKAVLQSKEKILTDSYKFRA   83 (121)
T ss_dssp             CCCCCSSEEEEEECTT---SBEEEECTHHHHHTCCCTTTSBTSBTTTTBCSSSHHHHHHHHHHHHTSSSCEEEEEEEEEC
T ss_pred             ccccCCccEEEEECCC---eeEEEEChhHHHHHCCCHHHHcCCcHHHeeCHHHHHHHHHHHHHHHhCCCCCccEEEEEEE
Confidence            3678899999999999   99999999999999999999999998888888776666555566555433 3577888999


Q ss_pred             cCCCEEEEEEEEEEeecCCC-CcEEEEEEEEecccccH
Q 022961          101 KDGTPFWMLFKMSLVFGKED-GRATHFVAVQVPIVSRK  137 (289)
Q Consensus       101 ~~g~~~~~~~~~~~~~~~~~-g~~~~~~~~~~DITe~k  137 (289)
                      ++|..+|+.....|+.+ .. +.+..++++.+||++.+
T Consensus        84 ~dG~~~~~~~~~~~~~d-~~~~~~~~~v~~~~~i~~~~  120 (121)
T 2kdk_A           84 KDGSFVTLKSQWFSFTN-PDTKELEYIVSVNTLVLGHS  120 (121)
T ss_dssp             SSSCEEEEEEEEEEEEC-CSSSCEEEEEEEEECCSSCC
T ss_pred             cCCCEEEEEEEEEEEEC-CCCCeeeEEEEEEEeccccC
Confidence            99999999999999987 54 56777899999999864

>3olo_A Two-component sensor histidine kinase; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG, TRA; 2.09A {Nostoc SP}

Probab=99.62  E-value=7.5e-15  Score=102.80  Aligned_cols=109  Identities=10%  Similarity=0.109  Sum_probs=86.8

Q ss_pred             HHHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEE
Q 022961           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV   94 (289)
Q Consensus        15 ~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   94 (289)
                      +..++++.++++++++++++|.+   |+++++|+++++++||++++++|+++..+.++.....     +..+..+..+..
T Consensus        10 ~~~~~~~~~~~~~~~~i~~~d~~---g~i~~~N~~~~~l~G~~~~el~g~~~~~~~~~~~~~~-----~~~~~~~~~~~~   81 (118)
T 3olo_A           10 LEFKFAHYLINNAVEASFCLGDN---WQFLYVNDATCRMTEYSREQLLSMNLQDIDVDFALHD-----WEEIRQKNNYTF   81 (118)
T ss_dssp             HHHHHHHHHHHHCSSEEEEECTT---SBEEEECHHHHHHHCCCHHHHTTCBGGGTBTTGGGSC-----HHHHHHHSEEEE
T ss_pred             HHHHHHHHHHhcCCceEEEECCC---CcEEEEHHHHHHHHCCCHHHHhCCChhhcccccCHHH-----HHHHHhcCcEEE
Confidence            34456788999999999999999   9999999999999999999999999877764332222     233344556778


Q ss_pred             EEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEeccc
Q 022961           95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV  134 (289)
Q Consensus        95 e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIT  134 (289)
                      +....+++|..+|+.++..|+..  .+. ..++++++|||
T Consensus        82 e~~~~~~~g~~~~~~~~~~~~~~--~~~-~~~~~~~~DIT  118 (118)
T 3olo_A           82 KTRYRSQSGRIFLVEMSLTFLED--QER-RFSCVFVREKS  118 (118)
T ss_dssp             EEEEECTTCCEEEEEEEEEEEEE--TTE-EEEEEEEEEC-
T ss_pred             EEEEEccCCCEEEEEEEEEEEEE--CCc-cEEEEEEEeCC
Confidence            88889999999999999999976  343 46778999997

>3mjq_A Uncharacterized protein; NESG, structural genomics, PSI-2, protein structure initiati northeast structural genomics consortium; 2.60A {Desulfitobacterium hafniense}

Probab=99.60  E-value=2.7e-15  Score=106.29  Aligned_cols=116  Identities=12%  Similarity=0.118  Sum_probs=87.1

Q ss_pred             HHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEEEEEEe
Q 022961           21 HEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYK  100 (289)
Q Consensus        21 ~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~  100 (289)
                      +.++++++++++++|.+   |+++++|+++++++|+++++++|+++..+.++.+.......+......+.. ..++...+
T Consensus         2 ~~l~~~~~~~i~~~d~~---g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~   77 (126)
T 3mjq_A            2 KNFLETIEDMILIINRE---GRLLYANTAVPKKLGYTHEELMSMHILTITSAGKMAEGEKILAELFAGKKE-SLPLSLEK   77 (126)
T ss_dssp             CTTGGGCSSEEEEEETT---SBEEEECTHHHHHHSCCHHHHHHSBHHHHHCTTCHHHHHHHHHHHHHTCCS-EEEEEEEC
T ss_pred             hhHHhhCCceEEEEeCC---CcEEEEcHHHHHHHCCCHHHHcCCCHHHHcCchhHHHHHHHHHHHHhCCCc-eeEEEEEc
Confidence            45789999999999999   999999999999999999999999877777766555555555555544444 67788888


Q ss_pred             cCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhcc
Q 022961          101 KDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG  143 (289)
Q Consensus       101 ~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l  143 (289)
                      ++|..+|+.+...|...  .+ ..+++++++|||++|+++++.
T Consensus        78 ~~g~~~~~~~~~~~~~~--~~-~~~~~~~~~DITe~k~a~~~~  117 (126)
T 3mjq_A           78 KEGTSIPAKARIWQGKW--HN-EPCLFAIIKDLSKEERASSPP  117 (126)
T ss_dssp             TTSCEEEEEEEEEEEES--SS-SEEEEEEEEECC---------
T ss_pred             cCCCEEEEEEEEEeeeE--CC-ceEEEEEEEechHHHHhhccc
Confidence            99999999999887754  33 467889999999999997776

>1v9y_A Heme PAS sensor protein; signaling protein; HET: HEM; 1.32A {Escherichia coli} SCOP: d.110.3.2 PDB: 1v9z_A* 1vb6_A* 1s67_L* 1s66_L*

Probab=99.59  E-value=8.3e-15  Score=109.09  Aligned_cols=123  Identities=20%  Similarity=0.245  Sum_probs=85.3

Q ss_pred             HHHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCC---
Q 022961           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERP---   91 (289)
Q Consensus        15 ~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~---   91 (289)
                      ..++++..++++++++++++|.+   |.++++|++++.++|++.++++|+++..++++.........+......+..   
T Consensus        37 ~~~~~~~~~l~~~~~~i~~~d~~---g~i~~~N~~~~~l~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  113 (167)
T 1v9y_A           37 AADGIFFPALEQNMMGAVLINEN---DEVMFFNPAAEKLWGYKREEVIGNNIDMLIPRDLRPAHPEYIRHNREGGKARVE  113 (167)
T ss_dssp             ---CCHHHHHHTCSSEEEEECTT---SBEEEECHHHHHHHSCCGGGTTTSBGGGGSCGGGTTTHHHHHHHHHC-------
T ss_pred             hhhHHHHHHHHhCCCCEEEECCC---CcEEEECHHHHHHhCCCHHHHcCCChhhccCccccchHHHHHHHHhhcCCCccc
Confidence            45567889999999999999999   999999999999999999999999887777665544444444444433322   


Q ss_pred             -eEEEEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhcc
Q 022961           92 -IEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG  143 (289)
Q Consensus        92 -~~~e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l  143 (289)
                       +..+.....++|..+|+.+...|+..  .|.. .++++++|||+++++|+++
T Consensus       114 ~~~~~~~~~~~~g~~~~~~~~~~~~~~--~g~~-~~~~~~~DiT~~~~~e~~l  163 (167)
T 1v9y_A          114 GMSRELQLEKKDGSKIWTRFALSKVSA--EGKV-YYLALVRDASVEMAQKEQT  163 (167)
T ss_dssp             ---CEEEEECTTSCEEEEEEEEEEEEE--TTEE-EEEEEEEC-----------
T ss_pred             ccceEEEEEcCCCcEEEEEEEEEEEec--CCCE-EEEEEEecCcHHHHHHHHH
Confidence             44567778899999999999999953  6665 4899999999999997776

>2l0w_A Potassium voltage-gated channel, subfamily H (EAG member 2, isoform CRA_B; HERG, PAS domain, voltage-gated potassium channel, membrane; NMR {Homo sapiens} PDB: 2l1m_A 2l4r_A

Probab=99.59  E-value=6.1e-14  Score=100.31  Aligned_cols=115  Identities=26%  Similarity=0.486  Sum_probs=97.6

Q ss_pred             HHHHHHHhhCCCEEEEEeC---CCCCccEEEccHHHHHHhCCCccccCCCC--CCCccCCCCCHHHHHHHHHHHHhCCCe
Q 022961           18 LWVHEALDELPDSFTITDP---SISGHPIVFASRGFLKMSGFSRAEIIGRN--GRMFQGPRTNRRTIMEIREAIREERPI   92 (289)
Q Consensus        18 ~~l~~~~~~~~~~i~~~d~---~~~~g~i~~~N~~~~~~~G~~~~e~~g~~--~~~l~~~~~~~~~~~~~~~~~~~~~~~   92 (289)
                      +.+...+++++++++++|.   +   |+++++|+++++++|++.++++|++  ...+.++.........+...+..+..+
T Consensus        19 ~~~~~~~~~~~~~i~~~d~~~~~---g~i~~~N~~~~~l~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   95 (138)
T 2l0w_A           19 DTIIRKFEGQSRKFIIANARVEN---CAVIYCNDGFCELCGYSRAEVMQRPCTCDFLHGPRTQRRAAAQIAQALLGAEER   95 (138)
T ss_dssp             HHHHHHHTTTTSEEEEEESSSTT---CBEEEECSHHHHHHSCCHHHHTTSBTTCGGGCCTTCCHHHHHHHHHHTTCSSCE
T ss_pred             HHHHHHHhcCCCCEEEEecCCCC---CEEEEeCHHHHHHhCCCHHHHcCCCCcccccCCcccchhHHHHHHHHHhhcCCc
Confidence            3455667889999999999   8   9999999999999999999999998  555666665565566666777677777


Q ss_pred             EEEEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEeccccc
Q 022961           93 EVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSR  136 (289)
Q Consensus        93 ~~e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~  136 (289)
                      ..+....+++|..+|+.+...|+.+ .+|.+.+++++.+|||++
T Consensus        96 ~~~~~~~~~~g~~~~~~~~~~~~~~-~~g~~~~~~~~~~Dit~~  138 (138)
T 2l0w_A           96 KVEIAFYRKDGSCFLCLVDVVPVKN-EDGAVIMFILNFEVVMEK  138 (138)
T ss_dssp             EEEEEEECTTSCEEEEEEEEEEEEC-TTSCEEEEEEEEEEEEEC
T ss_pred             eeEEEEECCCCCEEEEEEEEEEEeC-CCCCEEEEEEEEEeccCC
Confidence            8888888999999999999999998 789999999999999975

>3eeh_A Putative light and redox sensing histidine kinase; structural genomic MCSG, protein structure initiative, midwest center for STRU genomics; HET: PG5; 1.95A {Haloarcula marismortui}

Probab=99.58  E-value=9.7e-15  Score=102.68  Aligned_cols=116  Identities=9%  Similarity=0.060  Sum_probs=94.2

Q ss_pred             HHHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCC--CCCccCCCCCHHHHHHHHHHHHhCCCe
Q 022961           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRN--GRMFQGPRTNRRTIMEIREAIREERPI   92 (289)
Q Consensus        15 ~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~--~~~l~~~~~~~~~~~~~~~~~~~~~~~   92 (289)
                      +.+++++.++++++++++++|.+  +|.++++|+++++++|+++++++|.+  +..+.+|++.......+.. +..+..+
T Consensus         8 ~~~~~~~~~~~~~~~~i~~~d~~--~~~i~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~   84 (125)
T 3eeh_A            8 KSERRVRELTEATNDILWEFTAD--LSEVLVINSAYEDIWGRSVAKLRENPHDFLNGIHPEDRELMKDTMQS-LMDGESA   84 (125)
T ss_dssp             --CHHHHHHHSCCCCEEEEEETT--SSCEEEECTHHHHHHSSCHHHHHHCGGGGGGGBCHHHHHHHHHHHHH-HHTTCCE
T ss_pred             HHHHHHHHHHhcCCceEEEEEcC--CCcEEEecHHHHHHHCCCHHHHccCcHHHHHhcCHHHHHHHHHHHHH-HHcCCCc
Confidence            55678899999999999999975  37999999999999999999998876  3444555444444444333 5567778


Q ss_pred             EEEEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEeccc
Q 022961           93 EVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV  134 (289)
Q Consensus        93 ~~e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIT  134 (289)
                      ..++++.+++|...|+.+...|+.+ ..|.+.+++++.+|||
T Consensus        85 ~~e~~~~~~~g~~~~~~~~~~~~~~-~~g~~~~~~~~~~DIT  125 (125)
T 3eeh_A           85 DVECRVNATEEYQRWVWIQGEPITN-DAGETVRVAGFARDIT  125 (125)
T ss_dssp             EEEEEECGGGTTCEEEEEEEEEEEC-TTSCEEEEEEEEEECC
T ss_pred             cEEEEEEcCCCCEEEEEEecEEEEC-CCCCEEEEEEEEEecC
Confidence            8888889999999999999999998 7999999999999997

>1byw_A Protein (human ERG potassium channel); PAS domain, potassium channel domain, membrane protein; 2.60A {Homo sapiens} SCOP: d.110.3.6

Probab=99.58  E-value=1.2e-13  Score=94.54  Aligned_cols=107  Identities=27%  Similarity=0.520  Sum_probs=89.5

Q ss_pred             CEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCC--CCCccCCCCCHHHHHHHHHHHHhCCCeEEEEEEEecCCCEE
Q 022961           29 DSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRN--GRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPF  106 (289)
Q Consensus        29 ~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~--~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~  106 (289)
                      .+++++|....+|+++++|+++++++||++++++|++  ...+.++.........+...+..+..+..+....+++|..+
T Consensus         2 ~~i~i~d~~~~~g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~   81 (110)
T 1byw_A            2 RKFIIANARVENCAVIYCNDGFCELCGYSRAEVMQRPCTCDFLHGPCTQRRAAAQIAQALLGAEERKVEIAFYRKDGSCF   81 (110)
T ss_dssp             CEEEEEETTSSSCBEEEECHHHHHHHTCCHHHHTTSBTTCGGGCCTTCCHHHHHHHHHHHHTTCCEEEEEEEECTTSCEE
T ss_pred             CCEEEEeccCCCCcEEEECHHHHHHhCCCHHHHccCCCccccccCCcCCHHHHHHHHHHHhcCCCceEEEEEEcCCCCEE
Confidence            5788888743349999999999999999999999998  45555555555556667777777788888888889999999


Q ss_pred             EEEEEEEEeecCCCCcEEEEEEEEeccccc
Q 022961          107 WMLFKMSLVFGKEDGRATHFVAVQVPIVSR  136 (289)
Q Consensus       107 ~~~~~~~~~~~~~~g~~~~~~~~~~DITe~  136 (289)
                      |+.+...|+.+ ..|.+.+++++.+|||++
T Consensus        82 ~~~~~~~~~~~-~~g~~~~~~~~~~DiTe~  110 (110)
T 1byw_A           82 LCLVDVVPVKN-EDGAVIMFILNFEVVMEK  110 (110)
T ss_dssp             EEEEEEEEEEC-TTCCEEEEEEEEEEEEEC
T ss_pred             EEEEEEEEeec-CCCCEEEEEEEEEeccCC
Confidence            99999999998 789999999999999975

>3vol_A Aerotaxis transducer AER2; heme, oxygen sensor protein, PAS, HAMP, cyanoMet, CN-bound, protein; HET: HEM; 2.40A {Pseudomonas aeruginosa}

Probab=99.56  E-value=5.7e-14  Score=111.21  Aligned_cols=114  Identities=14%  Similarity=0.182  Sum_probs=89.5

Q ss_pred             HHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHh------------CCCccccCCCCCCCccCCCCCHHHHHHHH
Q 022961           16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMS------------GFSRAEIIGRNGRMFQGPRTNRRTIMEIR   83 (289)
Q Consensus        16 ~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~------------G~~~~e~~g~~~~~l~~~~~~~~~~~~~~   83 (289)
                      ...+++.++++++++++++|.+   |+|+|+|+++++++            ||++++++|+++..+.+.   +.....++
T Consensus        20 e~~~l~~iLd~~~~~vii~D~~---g~I~~~N~a~~~ll~~~~~~~~~~l~G~~~~eliG~~~~~~~~~---~~~~~~~~   93 (233)
T 3vol_A           20 HMARIKSALDNVSANVMIADND---LNIIYMNRTVSEMLGRAEADIRKQLPNFDAGRLMGANIDVFHKN---PAHQRHLL   93 (233)
T ss_dssp             HHHHHHHHHTTSSSEEEEEETT---SBEEEECHHHHHHHHHTHHHHHTTCTTCCTTSCTTCBGGGGSSS---HHHHHHHH
T ss_pred             HHHHHHHHHhcCCCcEEEECCC---CcEEEecHHHHHHHHHHHHHHHhhcCCCCHHHHcCCCHHHHcCC---HHHHHHHH
Confidence            4467889999999999999999   99999999999999            899999999998877642   23333333


Q ss_pred             HHHHhCCCeEEEEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhcc
Q 022961           84 EAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG  143 (289)
Q Consensus        84 ~~~~~~~~~~~e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l  143 (289)
                      ..+.  ..+..++.   .+|.  |+.++..|+.+ .+|.+.+++++++|||+++++|+++
T Consensus        94 ~~~~--~~~~~~~~---~~g~--~~~~~~~Pi~d-~~G~~~g~v~~~~DITe~~~~e~ei  145 (233)
T 3vol_A           94 ANLT--GVHKAELN---LGGR--RFSLDVVPVFN-DANERLGSAVQWTDRTEEHRAEQEV  145 (233)
T ss_dssp             HTCC--SCEEEEEE---ETTE--EEEEEEEEEEC-TTCCEEEEEEEEEECHHHHHHHHHH
T ss_pred             Hhcc--cceeEEEE---ECCE--EEEEEEEEEEC-CCCCEEEEEEEEehhhHHHHHHHHH
Confidence            3221  23444432   3453  67899999998 8999999999999999999997765

>3mfx_A Sensory BOX/ggdef family protein; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.40A {Shewanella oneidensis}

Probab=99.54  E-value=5.2e-14  Score=100.79  Aligned_cols=112  Identities=11%  Similarity=0.075  Sum_probs=83.5

Q ss_pred             HHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhC-------C
Q 022961           18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREE-------R   90 (289)
Q Consensus        18 ~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~-------~   90 (289)
                      ..+..++++++++++++|.+   |+|+++|+++++++||++++++|+++..++++.........+......+       .
T Consensus         7 ~~l~~i~~~~~d~i~~~D~~---g~I~~~N~aa~~l~G~~~~el~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~   83 (129)
T 3mfx_A            7 ETIELFIQHLTEAMILVNAN---GFIRSCNQRSAELLDCPQVSLKGQDWRNFLTEHHQARYDNLLSHDVQLGTNCGQPVQ   83 (129)
T ss_dssp             HHHHHHHTTCSSEEEEEETT---SBEEEECHHHHHHTTSCHHHHTTSBGGGGBCTTCCGGGGCTTC----------CCSC
T ss_pred             HHHHHHHhcCCceEEEECCC---CEEEeEhHHHHHHHCcCHHHHcCCcHHHHcChHhHHHHHHHHHHHHhcCcccccccC
Confidence            46888999999999999999   9999999999999999999999999888887665443221111111111       1


Q ss_pred             CeEEEEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEeccccc
Q 022961           91 PIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSR  136 (289)
Q Consensus        91 ~~~~e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~  136 (289)
                      .+..++...++||+.+|+.++++|+.+  ++.  .++++++|+...
T Consensus        84 ~~~~E~~~~rkdG~~~~velsis~i~~--~~~--~~v~~~~~~~~~  125 (129)
T 3mfx_A           84 HPAQETTLICASGKAKDVELSISYIPG--HEP--MFVMVMHDLEHH  125 (129)
T ss_dssp             EEEEEEEEECTTSCEEEEEEEEEEECS--SSC--EEEEEEEEC---
T ss_pred             CCceEEEEEcCCCCEEEEEEEEEEecC--CCc--EEEEEEechhhh
Confidence            235688889999999999999999975  222  467888887643

>3d72_A Vivid PAS protein VVD; circadian, photoreceptor, blue-light, LOV, signaling protein; HET: FAD; 1.65A {Neurospora crassa} PDB: 3is2_A* 2pd8_A* 3hjk_A* 2pdr_A* 2pd7_A* 2pdt_A* 3hji_A* 3rh8_B*

Probab=99.53  E-value=1.9e-13  Score=100.06  Aligned_cols=106  Identities=34%  Similarity=0.562  Sum_probs=91.5

Q ss_pred             HHHhhCCCEEEEEe---CCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCC-----------CHHHHHHHHHHHH
Q 022961           22 EALDELPDSFTITD---PSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRT-----------NRRTIMEIREAIR   87 (289)
Q Consensus        22 ~~~~~~~~~i~~~d---~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~-----------~~~~~~~~~~~~~   87 (289)
                      .++++. ++++++|   .+   |+++++|+++++++||++++++|+++..+.++..           .......+...+.
T Consensus        30 ~~~~~~-~~i~~~d~~d~~---g~i~~~N~a~~~l~G~~~~el~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  105 (149)
T 3d72_A           30 GPVDTS-VALILCDLKQKD---TPIVYASEAFLYMTGYSNAEVLGRNCRFLQSPDGMVKPKSTRKYVDSNTINTMRKAID  105 (149)
T ss_dssp             CSCCTT-SCEEEEETTSTT---CCEEEECHHHHHHHCCCHHHHTTSCGGGGGSTTSCCCTTCCCSSSCHHHHHHHHHHHH
T ss_pred             HhhcCC-ccEEEEeccCCC---CcEEEECHHHHHHHCcCHHHHcCCChhHhCCccccccccccccccChHHHHHHHHHHH
Confidence            456664 8999999   67   9999999999999999999999999887776653           5666667777788


Q ss_pred             hCCCeEEEEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEec
Q 022961           88 EERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVP  132 (289)
Q Consensus        88 ~~~~~~~e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~D  132 (289)
                      .+..+..+....+++|..+|+.++..|+.+ .+|.+.+++++.+|
T Consensus       106 ~~~~~~~e~~~~~~dG~~~~~~~~~~~i~~-~~g~~~~~v~~~~D  149 (149)
T 3d72_A          106 RNAEVQVEVVNFKKNGQRFVNFLTMIPVRD-ETGEYRYSMGFQCE  149 (149)
T ss_dssp             HTCCEEEEEEEECTTCCEEEEEEEEEEEEC-TTSSEEEEEEECCC
T ss_pred             CCCceEEEEEEECCCCCEEEEEEEEEEEEc-CCCCEEEEEEEEeC
Confidence            888888898889999999999999999998 89999999998876

>3fc7_A HTR-like protein, sensor protein; APC87712.1, HTR-like protein,haloarcula marismortui ATCC 430 structural genomics, PSI-2; 2.65A {Haloarcula marismortui}

Probab=99.48  E-value=5.2e-14  Score=99.57  Aligned_cols=108  Identities=10%  Similarity=0.081  Sum_probs=73.9

Q ss_pred             HHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEE
Q 022961           16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVN   95 (289)
Q Consensus        16 ~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e   95 (289)
                      .+++++.++++++++++++|.+   |+++++|+++++++||++++++|+++..++++................+...   
T Consensus        17 ~~~~~~~i~~~~~~~i~~~d~~---g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---   90 (125)
T 3fc7_A           17 TRKKFESLVSDSPDGIVHLTTN---GTILSVNPSMAGRLGADPDTLVGQQLSAVMDSEAANQRLEAGKSAVENGTAT---   90 (125)
T ss_dssp             ---------CCSCCEEEEEETT---SBEEEECHHHHHHHTSCHHHHTTSBGGGSSCHHHHHHHHHHHHHHHHHTSCE---
T ss_pred             HHHHHHHHHhcCCCeEEEEcCC---CeEEEECHHHHHHhCCCHHHHcCccHHHhCCHHHHHHHHHHHHHHhcCCCeE---
Confidence            5678899999999999999999   9999999999999999999999999887763222122222223444455433   


Q ss_pred             EEEEecCCC-EEEEEEEEEEeecCCCCcEEEEEEEEeccc
Q 022961           96 LLNYKKDGT-PFWMLFKMSLVFGKEDGRATHFVAVQVPIV  134 (289)
Q Consensus        96 ~~~~~~~g~-~~~~~~~~~~~~~~~~g~~~~~~~~~~DIT  134 (289)
                         ...+|. ..|+.+...|+.+  +|...+++++++|||
T Consensus        91 ---~~~~~~~~~~~~~~~~p~~~--~~~~~~~~~~~~DIT  125 (125)
T 3fc7_A           91 ---RSEDAVGGRHYHNQYIPVDS--HRKSDTFQLVSRDIT  125 (125)
T ss_dssp             ---EEEEEETTEEEEEEEEESST--TTTTTEEEEEEEECC
T ss_pred             ---EeEcCCCcEEEEEEEEeEec--CCCeEEEEEEEecCC
Confidence               123344 6788899999876  466678899999997

>4f3l_A Mclock, circadian locomoter output cycles protein kaput; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus}

Probab=99.47  E-value=4.9e-13  Score=112.71  Aligned_cols=65  Identities=9%  Similarity=0.109  Sum_probs=56.0

Q ss_pred             HHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHH
Q 022961           17 TLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIRE   84 (289)
Q Consensus        17 ~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~   84 (289)
                      +++...+++++++.+++++.+   |+|+|+|+++..++||++++++|+++..+++|++.......+..
T Consensus        85 ~~~~~~~l~a~~~~i~v~~~~---G~i~yvs~~~~~~lGy~~~el~g~~~~~~ihp~D~~~~~~~l~~  149 (361)
T 4f3l_A           85 EEFTQLMLEALDGFFLAIMTD---GSIIYVSESVTSLLEHLPSDLVDQSIFNFIPEGEHSEVYKILST  149 (361)
T ss_dssp             HHHHHHHHHHTTEEEEEEETT---SBEEEECTTHHHHHCCCHHHHTTSBGGGGSCGGGHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCceEEEEcCC---ccEEEEechhhhhcCCCHHHhcCCcHHHhcCHHHHHHHHHHhcc
Confidence            445566889999999999999   99999999999999999999999999999998887666555443

>4f3l_A Mclock, circadian locomoter output cycles protein kaput; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus}

Probab=99.44  E-value=1.8e-13  Score=115.37  Aligned_cols=108  Identities=8%  Similarity=0.097  Sum_probs=94.6

Q ss_pred             CEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEEEEEEecCCCEEEE
Q 022961           29 DSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWM  108 (289)
Q Consensus        29 ~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~~~  108 (289)
                      ..++..+.+   |.++|+|+++..++||++++++|+++..+++|++.+.....++..+..+..+..++++++++|..+|+
T Consensus       252 ~f~~~~~~d---g~~~~vn~~~~~ilGY~~eEl~g~~~~~~iHpdD~~~~~~~~~~~l~~g~~~~~eyR~~~kdG~~vWv  328 (361)
T 4f3l_A          252 EFTSRHSLE---WKFLFLDHRAPPIIGYLPFEVLGTSGYDYYHVDDLENLAKCHEHLMQYGKGKSCYYRFLTKGQQWIWL  328 (361)
T ss_dssp             EEEEEECTT---SBEEEECTTSHHHHCCCHHHHTTSBGGGGBCHHHHHHHHHHHHHHHHHSEEECCCEEEECTTSEEEEE
T ss_pred             eeEEEEcCC---ceEEEECChhhhhhCcCHHHHcCCCHHHeECHHHHHHHHHHHHHHHhCCCcceEEEEEEecCCCEEEE
Confidence            344556677   99999999999999999999999999899998887777777788887777667789999999999999


Q ss_pred             EEEEEEeecCC-CCcEEEEEEEEecccccHHHH
Q 022961          109 LFKMSLVFGKE-DGRATHFVAVQVPIVSRKHMR  140 (289)
Q Consensus       109 ~~~~~~~~~~~-~g~~~~~~~~~~DITe~k~~e  140 (289)
                      .....|+.+ . +|.+..++++.+|||+++..+
T Consensus       329 ~~~~~~v~~-~~~g~~~~iv~~~~dITe~~~~~  360 (361)
T 4f3l_A          329 QTHYYITYH-QWNSRPEFIVCTHTVVSYAEVRA  360 (361)
T ss_dssp             EEEEEEEEC-TTTCCEEEEEEEEEECCHHHHHH
T ss_pred             EEEEEEEEc-CCCCCeeEEEEEEEECChhHhhc
Confidence            999999998 5 799999999999999998764

>4hi4_A Aerotaxis transducer AER2; PAS domain, diatomic GAS sensor, signaling protein; HET: HEM GOL; 2.30A {Pseudomonas aeruginosa}

Probab=99.43  E-value=3.8e-12  Score=89.90  Aligned_cols=106  Identities=16%  Similarity=0.219  Sum_probs=78.7

Q ss_pred             HHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhC------------CCccccCCCCCCCccCCCCCHHHHHHHHH
Q 022961           17 TLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSG------------FSRAEIIGRNGRMFQGPRTNRRTIMEIRE   84 (289)
Q Consensus        17 ~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G------------~~~~e~~g~~~~~l~~~~~~~~~~~~~~~   84 (289)
                      ..+++.++++++++++++|.+   |+|+++|+++++++|            |++++++|++...+.+.   +.....+..
T Consensus         4 ~~rl~~il~~~~~gviv~D~~---g~I~~~N~a~~~llg~~~~~i~~~~~g~~~~~~~G~~~~~~~~~---~~~~~~~~~   77 (121)
T 4hi4_A            4 MARIASALDNVSANVMIADND---LNIIYMNRTVSEMLGRAEADIRKQLPNFDAGRLMGANIDVFHKN---PAHQRHLLA   77 (121)
T ss_dssp             HHHHHHHHTTSSSEEEEEETT---CBEEEECHHHHHHHHHTHHHHHHHCTTCCGGGCTTCBGGGGCSS---HHHHHHHHH
T ss_pred             HHHHHHHHhcCCccEEEEcCC---CeEEEecHHHHHHHHHHHHHHHHhcCCCChHHhcCCCHHHhcCC---HHHHHHHHh
Confidence            357889999999999999999   999999999999995            89999999997776532   222222222


Q ss_pred             HHHhCCCeEEEEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEeccccc
Q 022961           85 AIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSR  136 (289)
Q Consensus        85 ~~~~~~~~~~e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~  136 (289)
                      ...  ..+..++.   .+|.  ++.+...|+.+ .+|.+.+++++.+|||++
T Consensus        78 ~~~--~~~~~~~~---~~~~--~~~~~~~pi~~-~~g~~~g~v~~~~DiTee  121 (121)
T 4hi4_A           78 NLT--GVHKAELN---LGGR--RFSLDVVPVFN-DANARLGSAVQWTDRTEE  121 (121)
T ss_dssp             HCS--SCEEEEEE---ETTE--EEEEEEEEEEC-TTSCEEEEEEEEEECC--
T ss_pred             CcC--CCcEEEEE---ECCE--EEEEEEEEEEC-CCCCEEEEEEEEEEecCC
Confidence            211  33443332   2444  45788999998 789999999999999974

>2vlg_A Sporulation kinase A; histidine kinase, two-component regulatory system, two-component signal transduction, transferase, phosphorylation, SCOD; 1.7A {Bacillus subtilis}

Probab=99.43  E-value=3.7e-13  Score=93.61  Aligned_cols=93  Identities=17%  Similarity=0.165  Sum_probs=68.6

Q ss_pred             HHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEEEEEEec
Q 022961           22 EALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKK  101 (289)
Q Consensus        22 ~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~  101 (289)
                      .+++++++.++++|.+   |+++|+|+++++++||++++++|+++..+.+|++.+.....+.   ........+++++++
T Consensus         3 ~lle~~~d~i~v~d~~---G~i~yvn~~~~~~lGy~~~el~G~~~~~~ihp~D~~~~~~~~~---~~~~~~~~e~r~~~k   76 (111)
T 2vlg_A            3 FPLQTKTDIHAVLASN---GRIIYISANSKLHLGYLQGEMIGSFLKTFLHEEDQFLVESYFY---NEHHLMPCTFRFIKK   76 (111)
T ss_dssp             ------CCEEEEECTT---SBEEEECTTHHHHHSCCHHHHTTSBGGGGBCGGGHHHHHHHHH---CSCCSSCEEEEEECT
T ss_pred             chhhcCCCEEEEEcCC---CeEEEEChHHHHHhCCCHHHHcCCcHHHeECHhHHHHHHHHHh---ccCCCccEEEEEEcC
Confidence            4789999999999999   9999999999999999999999999888888877655433221   222334567888999


Q ss_pred             CCCEEEEEEEEEEeecCCCC
Q 022961          102 DGTPFWMLFKMSLVFGKEDG  121 (289)
Q Consensus       102 ~g~~~~~~~~~~~~~~~~~g  121 (289)
                      ||+.+|+..++.++.+ ..+
T Consensus        77 dG~~~wve~~~~~v~~-~~~   95 (111)
T 2vlg_A           77 DHTIVWVEAAVEIVTT-RAE   95 (111)
T ss_dssp             TSCEEEEEEEEEEC------
T ss_pred             CCCEEEEEEEEEEEec-ccC
Confidence            9999999999999987 443

>3fg8_A Uncharacterized protein RHA05790; PAS domain, structural genomics, PS protein structure initiative, midwest center for structural genomics, MCSG; HET: 3PB; 1.80A {Rhodococcus SP}

Probab=99.42  E-value=6.2e-13  Score=93.55  Aligned_cols=109  Identities=14%  Similarity=0.073  Sum_probs=84.2

Q ss_pred             HHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEE
Q 022961           16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVN   95 (289)
Q Consensus        16 ~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e   95 (289)
                      .....+.+++++|++++++|.+   |+|+++|+++++++|+++++++|+++..++++.........+..++..+.....+
T Consensus        10 ~~~~~~~il~~~~~~i~~~D~~---g~i~~~N~a~~~l~g~~~~e~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   86 (118)
T 3fg8_A           10 HSSGRENLYFQGGLGFMALDED---LRIIYVNSGCLRHVRRSRDELLGRVVTEVLPETQGSYFDALCRKVLATGREQQTR   86 (118)
T ss_dssp             ---CCCCSSSCTTCEEEEECTT---CBEEEECHHHHHHHTCCHHHHTTSBHHHHCGGGTTSHHHHHHHHHHHHCCCEEEE
T ss_pred             ccchHHHHHhhCCceEEEECCC---CeEEEECHHHHHHhCCCHHHHcCCcHHHHcCccchHHHHHHHHHHHHcCCceEEE
Confidence            3445567899999999999999   9999999999999999999999999877776555556666777888888877764


Q ss_pred             EEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEeccccc
Q 022961           96 LLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSR  136 (289)
Q Consensus        96 ~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~  136 (289)
                      +.....+|  .|+.+...|+.+   |    ++++++|||++
T Consensus        87 ~~~~~~~g--~~~~~~~~p~~~---g----~v~~~~DITer  118 (118)
T 3fg8_A           87 VDSLYSPG--MTIEVTAAADSG---A----LVVHFRDVTAE  118 (118)
T ss_dssp             EECSSSTT--CEEEEEEEEETT---E----EEEEEEECSCC
T ss_pred             EEEEcCCC--eEEEEEEEEcCC---c----EEEEEEeccCC
Confidence            33333355  467777888743   2    67889999985

>4f3l_B BMAL1B; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus}

Probab=99.40  E-value=7.6e-13  Score=112.43  Aligned_cols=107  Identities=8%  Similarity=0.027  Sum_probs=87.3

Q ss_pred             CEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCC-eEEEEEEEecCCCEEE
Q 022961           29 DSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERP-IEVNLLNYKKDGTPFW  107 (289)
Q Consensus        29 ~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~-~~~e~~~~~~~g~~~~  107 (289)
                      +.++..+.+   |+++|+|+++..++||++++++|+++..+++|++.+.....+...+..+.. ...++++++++|..+|
T Consensus       279 ~fi~~~~~d---g~~~~vn~~~~~ilGY~~eEl~g~~~~~~iHpdD~~~~~~~~~~~l~~~~~~~~~eyR~~~kdG~~vW  355 (387)
T 4f3l_B          279 EYVSRHAID---GKFVFVDQRATAILAYLPQELLGTSCYEYFHQDDIGHLAECHRQVLQTREKITTNCYKFKIKDGSFIT  355 (387)
T ss_dssp             EEEEEECTT---SBEEEECTHHHHHHCCCHHHHTTSBGGGTBCHHHHHHHHHHHHHHTTCSSCEECCCEEEECTTSCEEE
T ss_pred             eEEEEECCC---CEEEEECCCcccccCCCHHHHcCCcHHHeeCHHHHHHHHHHHHHHHhcCCCeeeEEEEEEccCCCEEE
Confidence            355566777   999999999999999999999999988898888777666666666655544 4568999999999999


Q ss_pred             EEEEEEEeecCCCCcEEEEEEEEecccccHH
Q 022961          108 MLFKMSLVFGKEDGRATHFVAVQVPIVSRKH  138 (289)
Q Consensus       108 ~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~  138 (289)
                      +.....++.++.+|.+.+++++.+|||++|.
T Consensus       356 v~~~~~~~~~~~~g~~~~ivg~~~dIT~Rk~  386 (387)
T 4f3l_B          356 LRSRWFSFMNPWTKEVEYIVSTNTVVLANVL  386 (387)
T ss_dssp             EEEEEEEEEETTTTEEEEEEEEEEECC----
T ss_pred             EEEEEEEEECCCCCCEEEEEEEEEEcchhhc
Confidence            9999999988237899999999999999985

>2qkp_A Uncharacterized protein; structural genomics, unknown function, PSI-2, protein struct initiative; 1.75A {Streptococcus mutans}

Probab=99.40  E-value=2.9e-12  Score=94.10  Aligned_cols=118  Identities=13%  Similarity=0.124  Sum_probs=90.9

Q ss_pred             HHHHHHHhhCCCEEEEEeCCCCCccEEEccHH---HHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEE
Q 022961           18 LWVHEALDELPDSFTITDPSISGHPIVFASRG---FLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV   94 (289)
Q Consensus        18 ~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~---~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   94 (289)
                      .++..++++++++++++|.+   |+|+|+|++   +++++| ..++++|+++..+.++. .......+...++.+.....
T Consensus        19 ~~l~~IL~~~~~gI~~vD~~---g~I~~~N~a~~~~~~i~g-~~~~~iGr~v~~~~~~~-~~~~v~~i~~~l~~g~~~~~   93 (151)
T 2qkp_A           19 EQANLILNHLPLEITFVNKD---DIFQYYNDSVPAAEMVFK-RTPSQVGRNVELCHPPK-VLDKVKKVFELLRNGQRDKV   93 (151)
T ss_dssp             HHHHHHHHHSSSEEEEEETT---SBEEEECCCSCGGGCSSC-CCGGGTTSBGGGSSCHH-HHHHHHHHHHHHHTTSBSEE
T ss_pred             HHHHHHHHhCCCceEEEcCC---CeEEEEeCCCchhhhhcC-CCHHHcCCCHHHhCCHH-HHHHHHHHHHHHHcCCccEE
Confidence            56889999999999999999   999999999   999999 56789999987665422 22223445566677776655


Q ss_pred             EEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhc
Q 022961           95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNS  142 (289)
Q Consensus        95 e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~  142 (289)
                      ++.....+ ...++.++..|+.+ ++|.+.+++.+++|||+.++.+++
T Consensus        94 ~~~~~~~~-~~~~v~v~~~Pi~d-~~G~~~G~vev~~Dit~l~~le~~  139 (151)
T 2qkp_A           94 NMWFQSER-LGKFVYVTYAAVRD-QAGDFQGVLEYVQDIKPFFELDSE  139 (151)
T ss_dssp             EEEEEETT-TTEEEEEEEEEEEC-TTCCEEEEEEEEEECGGGGGGGGC
T ss_pred             EEEEecCC-CCeEEEEEEEEEEC-CCCCEEEEEEEEEECHHHHhhhhh
Confidence            55543332 12456788999998 789999999999999999988655

>3rty_A Period circadian protein; PAS domain, signalling, timeless, circadian clock protein; 2.85A {Drosophila melanogaster} PDB: 1wa9_A 3gec_A

Probab=99.38  E-value=3.3e-12  Score=105.88  Aligned_cols=47  Identities=11%  Similarity=0.180  Sum_probs=39.8

Q ss_pred             EEEEe-CCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHH
Q 022961           31 FTITD-PSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIM   80 (289)
Q Consensus        31 i~~~d-~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~   80 (289)
                      +++++ .+   |+|+|+|+.+..++||++++++|+++..+.+|++...+..
T Consensus         6 ~~vv~~~~---G~i~yvS~~~~~~LGy~~~el~G~s~~d~ihp~D~~~f~~   53 (339)
T 3rty_A            6 CCVISMHD---GIVLYTTPSITDVLGYPRDMWLGRSFIDFVHLKDRATFAS   53 (339)
T ss_dssp             EEEEETTT---CBEEEECTTHHHHHCCCTTSSTTSBGGGGBCHHHHHHHHH
T ss_pred             EEEEECCC---cEEEEEChHHHHHcCCCHHHHCCCcHHHhcCHHHHHHHHH
Confidence            45667 57   9999999999999999999999999988988776555443

>4f3l_B BMAL1B; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus}

Probab=99.36  E-value=9.5e-12  Score=105.68  Aligned_cols=62  Identities=16%  Similarity=0.241  Sum_probs=52.5

Q ss_pred             HHHHHHHhhCCCEEEEEeC-CCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHH
Q 022961           18 LWVHEALDELPDSFTITDP-SISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEI   82 (289)
Q Consensus        18 ~~l~~~~~~~~~~i~~~d~-~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~   82 (289)
                      ++...++++++..+++++. .   |+|+|+|++++.++||++++++|+++..+++|++...+...+
T Consensus        86 ~~~~~ll~~~~gfi~v~~~~~---G~i~yvs~~~~~~lG~~~~el~g~~~~~~ihp~D~~~~~~~L  148 (387)
T 4f3l_B           86 ELKHLILRAADGFLFVVGCDR---GKILFVSESVFKILNYSQNDLIGQSLFDYLHPKDIAKVKEQL  148 (387)
T ss_dssp             HHHHHHHHTCCSEEEEEETTT---CBEEEECTTHHHHHSCCHHHHTTSBGGGGBCGGGHHHHHHHH
T ss_pred             HHHHHHHhcCCCEEEEEecCC---eEEEEEchhhHHHcCCCHHHHCCCcHHHhcCCCCHHHHHHHh
Confidence            3445678888888888886 5   999999999999999999999999999999998776655444

>3b33_A Sensor protein; structural genomics, PAS domain, nitrogen regulation protein APC91440.4, PSI-2; HET: MSE; 1.83A {Vibrio parahaemolyticus rimd 2210633}

Probab=99.32  E-value=1.5e-11  Score=85.67  Aligned_cols=106  Identities=12%  Similarity=0.122  Sum_probs=80.7

Q ss_pred             HHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCe-EEEEEE
Q 022961           20 VHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPI-EVNLLN   98 (289)
Q Consensus        20 l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~-~~e~~~   98 (289)
                      ...++++++++++++|.+   |+|+++|+++++++|++.++++|+++..+.++...  ....+...+..+... ..+..+
T Consensus         9 ~~~il~~~~~~i~~~D~~---g~I~~~N~aa~~l~g~~~~~~~g~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~   83 (115)
T 3b33_A            9 PSAILNNMVTATLILDDG---LAIRYANPAAELLFSQSAKRIVEQSLSQLIQHASL--DLALLTQPLQSGQSITDSDVTF   83 (115)
T ss_dssp             HHHHHHHCSSEEEEECTT---CBEEEECHHHHHHTTSCHHHHTTCBHHHHCSEEEC--CTHHHHHHHHHCCCEEEEEEEE
T ss_pred             HHHHHhhcCceEEEECCC---CcEEEECHHHHHHhCCCHHHHhCCCHHHHhCccch--hhHHHHHHHHcCCcccCCceEE
Confidence            456899999999999999   99999999999999999999999987666543211  112344555566553 345555


Q ss_pred             EecCCCEEEEEEEEEEeecCCCCcEEEEEEEEeccc
Q 022961           99 YKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV  134 (289)
Q Consensus        99 ~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIT  134 (289)
                      . ++|..+|+.+++.|+.+  .|. .+++.+++||+
T Consensus        84 ~-~~g~~~~~~~~~~pi~~--~g~-~~~l~~~~Di~  115 (115)
T 3b33_A           84 V-VDGRPLMLEVTVSPITW--QRQ-LMLLVEMRKID  115 (115)
T ss_dssp             E-ETTEEEEEEEEEEEEEE--TTE-EEEEEEEEEC-
T ss_pred             e-cCCCEEEEEEEEEEeec--CCc-eEEEEEEEeCC
Confidence            5 78999999999999975  454 57888899985

>3a0r_A Sensor protein; four helix bundle, PAS fold, kinase, phosphoprotein, transfe two-component regulatory system; 3.80A {Thermotoga maritima}

Probab=99.22  E-value=8.7e-12  Score=104.57  Aligned_cols=118  Identities=8%  Similarity=0.075  Sum_probs=86.9

Q ss_pred             HHHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEE
Q 022961           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV   94 (289)
Q Consensus        15 ~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   94 (289)
                      +++++++.++++++++++++|.+   |+|+++|+++++++||++++++|+++..+..+   ......+......+.....
T Consensus         5 ~~~~~~~~i~~~~~~~i~~~d~~---g~i~~~N~a~~~l~G~~~~e~~G~~~~~~~~~---~~~~~~~~~~~~~~~~~~~   78 (349)
T 3a0r_A            5 HLRNFSESILESLETAIITLSKD---GRITEWNKKAEQLFGLKKENVLGRRLKDLPDF---EEIGSVAESVFENKEPVFL   78 (349)
T ss_dssp             ----CCCSSGGGSSSEEEEEESS---SBCSCBCHHHHHHHSCCSTTTTTCBSTTSTTT---THHHHHHHHHHHHCCCCEE
T ss_pred             HHHHHHHHHHhhhcCeEEEECCC---CCEEeeHHHHHHHhCCCHHHHcCcCHHHCcCh---hHHHHHHHHHHhcCCceee
Confidence            44456778999999999999999   99999999999999999999999998777322   2333344555555554433


Q ss_pred             EEEEEecCCCEEEEEEEEEEeecCCCCcE-EEEEEEEecccccHHHHhcc
Q 022961           95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRA-THFVAVQVPIVSRKHMRNSG  143 (289)
Q Consensus        95 e~~~~~~~g~~~~~~~~~~~~~~~~~g~~-~~~~~~~~DITe~k~~e~~l  143 (289)
                      ..    ..+...|+.+...|+.+ ..|.. .+++++.+|||++|++|+++
T Consensus        79 ~~----~~~~~~~~~~~~~~~~~-~~~~~~~g~~~~~~DiTe~~~~e~~~  123 (349)
T 3a0r_A           79 NF----YKFGERYFNIRFSPFRN-AKTQLLEGVIITIDDVTELYKYEEER  123 (349)
T ss_dssp             EC----CCBTTBCCEEEEEEECC-TTTTSSCEEEEEEECCSTTTTTTTTT
T ss_pred             cc----cccCceEEEEEEEEEEc-CCCceeeEEEEEEEechHHHHHHHHH
Confidence            21    12233477888899987 56654 58899999999999987766

>3cax_A Uncharacterized protein PF0695; structural genomics, unknown function, PSI-2, protein struct initiative; 2.43A {Pyrococcus furiosus dsm 3638}

Probab=99.20  E-value=8.6e-11  Score=99.13  Aligned_cols=117  Identities=18%  Similarity=0.267  Sum_probs=92.7

Q ss_pred             HHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEE
Q 022961           16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVN   95 (289)
Q Consensus        16 ~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e   95 (289)
                      ....+..+++++++||+++|.+   |+|+++|++ ++++ ++.++++|+++..+.++. .......+...+.++.....+
T Consensus       237 ~~~~l~~IL~~l~dgIivvD~~---g~I~~~N~a-e~i~-~~~~e~iGr~v~~~~p~~-~~~~~~~l~~~l~~g~~~~~~  310 (369)
T 3cax_A          237 NIEELKAIFEALPVDVTFIDKD---DRVRFFSPG-ERIF-TRTPSVLGRPVQLCHPPK-SVYVVNKILKAFKEGRKKEAT  310 (369)
T ss_dssp             CHHHHHHHHHHSSSEEEEECTT---SBEEEECCS-SCSS-CCCGGGTTCBTTTSSCGG-GHHHHHHHHHHHHHTSCSCEE
T ss_pred             hHHHHHHHHHhCCCcEEEECCC---CcEEEEcCH-HHcc-CChHHHcCCcHHHHCChh-hHHHHHHHHHHHHcCCceEEE
Confidence            3457889999999999999999   999999999 9999 899999999988776532 223334456667777655444


Q ss_pred             EEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhc
Q 022961           96 LLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNS  142 (289)
Q Consensus        96 ~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~  142 (289)
                      .... .+|  .++.++..|+.+ .+|.+.|++.+++|||+.++.+++
T Consensus       311 ~~~~-~~g--~~v~v~~~PI~d-~~G~~~G~v~v~~DITe~~~le~~  353 (369)
T 3cax_A          311 FWLR-LRE--KYVYIKYVPLFN-EKGEYIGTLEMTMDIAPYKKIEGE  353 (369)
T ss_dssp             EEEE-ETT--EEEEEEEEEEEC-TTSCEEEEEEEEEECHHHHTCCSC
T ss_pred             EEEe-eCC--EEEEEEEEEEEC-CCCCEEEEEEEEEcCHHHHHHHHH
Confidence            4433 355  477889999998 799999999999999999987544

>1ll8_A PAS kinase; PAS domain, ligand binding, ligand screening, kinase regulation, transferase; NMR {Homo sapiens} SCOP: d.110.3.5

Probab=99.17  E-value=2.6e-11  Score=84.37  Aligned_cols=103  Identities=16%  Similarity=0.154  Sum_probs=73.3

Q ss_pred             hCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHH-HHHh-CCCe---EEEEEEEe
Q 022961           26 ELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIRE-AIRE-ERPI---EVNLLNYK  100 (289)
Q Consensus        26 ~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~-~~~~-~~~~---~~e~~~~~  100 (289)
                      +.+++++++|.+  +|+|+++|+++++++||++++++|+++..++++..... ...+.. .... +...   ..+....+
T Consensus         6 ~~~~~i~~~d~~--~g~I~~~N~aa~~l~G~~~~el~g~~~~~l~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (114)
T 1ll8_A            6 EFNKAIFTVDAK--TTEILVANDKACGLLGYSSQDLIGQKLTQFFLRSDSDV-VEALSEEHMEADGHAAVVFGTVVDIIS   82 (114)
T ss_dssp             TTTCEEEEEETT--TCBEEEECTTHHHHHTCCTTTTTTSBGGGGSSCTTTHH-HHHTTSSTTSSSSCSSCCCSSSEEECC
T ss_pred             CCCceEEEEECC--CCeEEEehHHHHHHhCCCHHHHcCCCHHHhcCcchhHH-HHHHHHHhhccCCcceeccCcEEEEEe
Confidence            355799999963  28999999999999999999999999888877654332 222211 1111 1111   23456678


Q ss_pred             cCCCEEEEEEEEEEeecCCCCcEEEEEEEEeccc
Q 022961          101 KDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV  134 (289)
Q Consensus       101 ~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIT  134 (289)
                      ++|..+|+.+++.|+.+ ..+  ..++++++|++
T Consensus        83 ~dG~~~~v~~~~~~~~~-~~~--~~~v~~~~~~~  113 (114)
T 1ll8_A           83 RSGEKIPVSVWMKRMRQ-ERR--LCCVVVLEPVE  113 (114)
T ss_dssp             TTCCCEEEECCEECCBS-SSS--BEEEEEEEECC
T ss_pred             cCCCEEEEEEEEEeecc-CCc--cEEEEEEeecC
Confidence            99999999999999986 333  35778888875

>3rty_A Period circadian protein; PAS domain, signalling, timeless, circadian clock protein; 2.85A {Drosophila melanogaster} PDB: 1wa9_A 3gec_A

Probab=99.16  E-value=1.7e-10  Score=95.67  Aligned_cols=108  Identities=9%  Similarity=0.037  Sum_probs=91.1

Q ss_pred             CCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCC-----eEEEEEEEecC
Q 022961           28 PDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERP-----IEVNLLNYKKD  102 (289)
Q Consensus        28 ~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~-----~~~e~~~~~~~  102 (289)
                      .+.++..+.+   |.++|+|+++..++||++++++|+++..+++|++.+.....+...+..|..     ...++++++++
T Consensus       154 ~~fi~r~~~d---G~~~yvn~~~~~lLGY~peELiG~s~~~~vHPdD~~~~~~~~~~~l~~G~~~~~~~~s~~yR~~~kd  230 (339)
T 3rty_A          154 PKFAIRHTAT---GIISHVDSAAVSALGYLPQDLIGRSIMDFYHHEDLSVMKETYETVMKKGQTAGASFCSKPYRFLIQN  230 (339)
T ss_dssp             CEEEEEEETT---CBEEEECTTHHHHHCCCHHHHTTSBGGGGBCGGGHHHHHHHHHHHHHHTTSTTCCCBCCCEEEECTT
T ss_pred             ceEEEEECCC---CeEEEcChhhhcccCCCHHHHcCCcHHHEECHHHHHHHHHHHHHHHHcCCcccccccceEEEEEccC
Confidence            4567777888   999999999999999999999999999999998887777777777776654     34688999999


Q ss_pred             CCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHH
Q 022961          103 GTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKH  138 (289)
Q Consensus       103 g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~  138 (289)
                      |..+|++....++.+|.++.+..++++.+.|+....
T Consensus       231 G~~vWlet~~~~~~np~s~~~~~II~~h~vi~~p~~  266 (339)
T 3rty_A          231 GCYVLLETEWTSFVNPWSRKLEFVVGHHRVFQGPKQ  266 (339)
T ss_dssp             SCEEEEEEEEEEEECTTTCSEEEEEEEEEEEECCSS
T ss_pred             CCEEEEEEEEEEEECCCCCCeeEEEEEEEECCCCCC
Confidence            999999999999987445677788888888886553

>2w0n_A Sensor protein DCUS; signal transduction, two-component regulatory system, PAS, kinase, membrane, transferase, solid state cell inner membrane; NMR {Escherichia coli}

Probab=99.13  E-value=2.7e-11  Score=84.27  Aligned_cols=104  Identities=9%  Similarity=0.083  Sum_probs=78.0

Q ss_pred             HHHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCC---CccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCC
Q 022961           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGF---SRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERP   91 (289)
Q Consensus        15 ~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~---~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~   91 (289)
                      +..+.++.++++++++++++|.+   |+|+++|+++++++||   +.++++|+++..+.++..       +...+..+..
T Consensus        12 ~~~~~~~~il~~~~~~i~~~d~~---g~i~~~N~~~~~~~g~~~~~~~~~~g~~~~~~~~~~~-------~~~~~~~~~~   81 (118)
T 2w0n_A           12 TLFEQRQAMLQSIKEGVVAVDDR---GEVTLINDAAQELLNYRKSQDDEKLSTLSHSWSQVVD-------VSEVLRDGTP   81 (118)
T ss_dssp             TTHHHHHHHHHCCCCCCEEEBTT---TBCCCBCHHHHHHHCSCTTTTTSSCCCTTCCCSCTHH-------HHHHHHTTCC
T ss_pred             HHHHHHHHHHhhccccEEEECCC---CcEeehhHHHHHHhCCCccChhhhhccCcccccCchh-------HHHHhccCce
Confidence            45567889999999999999999   9999999999999997   789999998877764421       3444444443


Q ss_pred             eEEEEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEeccc
Q 022961           92 IEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV  134 (289)
Q Consensus        92 ~~~e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIT  134 (289)
                      .....  ...+|  .|+.+...|+.+  .|...+++++.+|||
T Consensus        82 ~~~~~--~~~~~--~~~~~~~~p~~~--~g~~~g~v~~~~DiT  118 (118)
T 2w0n_A           82 RRDEE--ITIKD--RLLLINTVPVRS--NGVIIGAISTFRDKT  118 (118)
T ss_dssp             CCCCC--EESSS--CEECCCEECCCC--SSCCCCEEECCCCCC
T ss_pred             eccEE--EEECC--EEEEEeeceeee--CCEEEEEEEEEEeCC
Confidence            22111  12345  366778888875  677778889999997

>3a0s_A Sensor protein; PAS-fold, kinase, phosphoprotein, transferase, two-component regulatory system; HET: PG4 PGE; 1.47A {Thermotoga maritima} PDB: 3a0v_A*

Probab=99.13  E-value=1.5e-09  Score=71.77  Aligned_cols=95  Identities=8%  Similarity=0.076  Sum_probs=70.5

Q ss_pred             CCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEEEEEEecCCCEE
Q 022961           27 LPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPF  106 (289)
Q Consensus        27 ~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~  106 (289)
                      ++++++++|.+   |+++++|+++++++|++.++++|++...+  +. .......+...+..+..+...  .  .++...
T Consensus         1 ~~~~i~~~d~~---g~i~~~N~~~~~l~g~~~~~~~g~~~~~~--~~-~~~~~~~~~~~~~~~~~~~~~--~--~~~~~~   70 (96)
T 3a0s_A            1 METAIITLSKD---GRITEWNKKAEQLFGLKKENVLGRRLKDL--PD-FEEIGSVAESVFENKEPVFLN--F--YKFGER   70 (96)
T ss_dssp             CCCEEEEEETT---SBEEEECHHHHHHHCCCHHHHTTSBGGGS--TT-CHHHHHHHHHHHHHTCCEEEE--E--EEETTE
T ss_pred             CCceEEEEcCC---CCEeehhHHHHHHhCCCHHHhcCCCHHHC--cc-hHHHHHHHHHHhccCCeEEEE--E--EcCCcE
Confidence            47899999999   99999999999999999999999987766  22 234444555566666655332  2  234446


Q ss_pred             EEEEEEEEeecCCCCc-EEEEEEEEec
Q 022961          107 WMLFKMSLVFGKEDGR-ATHFVAVQVP  132 (289)
Q Consensus       107 ~~~~~~~~~~~~~~g~-~~~~~~~~~D  132 (289)
                      |+.+...|+.+ .+|. +.+++++.+|
T Consensus        71 ~~~~~~~p~~~-~~~~~~~g~v~~~~D   96 (96)
T 3a0s_A           71 YFNIRFSPFRN-AKTQLLEGVIITIDD   96 (96)
T ss_dssp             EEEEEEEEEEC-TTTCCEEEEEEEEEC
T ss_pred             EEEEEEEEeEc-CCCCeeeEEEEEecC
Confidence            88899999987 5554 5688888776

>1nwz_A PYP, photoactive yellow protein; PAS, LOV, GAF, domains fold, signaling protein; HET: HC4; 0.82A {Halorhodospira halophila} SCOP: d.110.3.1 PDB: 1kou_A* 1ot9_A* 1otb_A* 1s4r_A* 1s4s_A* 1ts0_A* 1ts6_A* 1ts7_A* 1ts8_A* 1uwn_X* 1uwp_X* 2d01_A* 2phy_A* 2pyp_A* 2pyr_A* 2qj5_A* 2qj7_A* 2qws_A* 2zoh_A* 2zoi_A* ...

Probab=99.09  E-value=2.7e-09  Score=74.43  Aligned_cols=99  Identities=14%  Similarity=0.085  Sum_probs=74.3

Q ss_pred             HHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCc-cCCCCCHHHHHHHHHHHHhCCCeEEEE-EE
Q 022961           21 HEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMF-QGPRTNRRTIMEIREAIREERPIEVNL-LN   98 (289)
Q Consensus        21 ~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l-~~~~~~~~~~~~~~~~~~~~~~~~~e~-~~   98 (289)
                      ..++++++.|++++|.+   |+|++||.+++++.||++++++|+++... .+......+...+.+.+..+. +.... ..
T Consensus        20 ~~~ld~l~~Gii~lD~~---g~I~~~N~~~e~~sG~~~~eviGk~~f~~~~~~~~~~~f~~rf~~~~~~g~-l~~~~~~v   95 (125)
T 1nwz_A           20 DGQLDGLAFGAIQLDGD---GNILQYNAAEGDITGRDPKQVIGKNFFKDVAPCTDSPEFYGKFKEGVASGN-LNTMFEYT   95 (125)
T ss_dssp             HHHHTTCSSEEEEEETT---CBEEEECHHHHHHHCCCHHHHTTSBCCCCCCGGGCSTTTHHHHHHHHHHTC-CEEEEEEE
T ss_pred             HHHHhccCceEEEECCC---CEEEEEHHHHHHHhCCCHHHHcCCchhhhccchhcccHHHHHHHHHHhcCc-eeEEEEEE
Confidence            45799999999999999   99999999999999999999999997654 333455566777788777766 44333 34


Q ss_pred             EecCCCEEEEEEEEEEeecCCCCcEEEE
Q 022961           99 YKKDGTPFWMLFKMSLVFGKEDGRATHF  126 (289)
Q Consensus        99 ~~~~g~~~~~~~~~~~~~~~~~g~~~~~  126 (289)
                      .+.+|.++++.++..  .. .+|...++
T Consensus        96 ~~~~~~p~~v~i~l~--~~-~~~~~~~i  120 (125)
T 1nwz_A           96 FDYQMTPTKVKVHMK--KA-LSGDSYWV  120 (125)
T ss_dssp             ECTTSCCEEEEEEEE--EC-SSSSEEEE
T ss_pred             EcCCCCEEEEEEEEE--Ec-CCCCEEEE
Confidence            588898666555544  44 46655443

>1mzu_A PPR; photoactive yellow protein, PAS, PYP, signaling protein; HET: HC4; 2.00A {Rhodospirillum centenum} SCOP: d.110.3.1

Probab=99.07  E-value=4e-09  Score=73.71  Aligned_cols=98  Identities=14%  Similarity=0.082  Sum_probs=73.2

Q ss_pred             HHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCc-cCCCCCHHHHHHHHHHHHhCCCeEEEE-EEE
Q 022961           22 EALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMF-QGPRTNRRTIMEIREAIREERPIEVNL-LNY   99 (289)
Q Consensus        22 ~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l-~~~~~~~~~~~~~~~~~~~~~~~~~e~-~~~   99 (289)
                      .++++++.|++++|.+   |+|++||.+++++.||++++++|+++... .+......+...+.+.+..+. +.... ...
T Consensus        26 ~~ld~l~~GiivlD~d---g~I~~~N~~~e~isG~s~eeviGk~~f~~~~p~~~~~~f~grf~~~~~~G~-l~~~~~yv~  101 (129)
T 1mzu_A           26 AEFDALPVGAIQVDGS---GVIHRYNRTESRLSGRIPERVIGRNFFTEVAPCTNIPAFSGRFMDGVTSGT-LDARFDFVF  101 (129)
T ss_dssp             TTGGGCSSEEEEEETT---CBEEEECHHHHHHHCCCHHHHTTSBCCCCCCGGGCSTTTHHHHHHHHHTSC-CEEEEEEEE
T ss_pred             HHHhccCceEEEECCC---CeEEEEHHHHHHHhCCCHHHHcCCchhhhccchhcccHHHHHHHHHHhcCc-eeEEEEEEE
Confidence            4699999999999999   99999999999999999999999997654 333455566777788877666 44333 344


Q ss_pred             ecCCCEEEEEEEEEEeecCCCCcEEEE
Q 022961          100 KKDGTPFWMLFKMSLVFGKEDGRATHF  126 (289)
Q Consensus       100 ~~~g~~~~~~~~~~~~~~~~~g~~~~~  126 (289)
                      +.+|.++++.++  +... .+|...++
T Consensus       102 ~~~~~p~~v~i~--l~~~-~~~~~~~i  125 (129)
T 1mzu_A          102 DFQMAPVRVQIR--MQNA-GVPDRYWI  125 (129)
T ss_dssp             ECSSCEEEEEEE--EEEC-SSTTEEEE
T ss_pred             cCCCCEEEEEEE--EEEc-CCCCEEEE
Confidence            888886665555  4444 46665443

>2jhe_A Transcription regulator TYRR; aromatic hydrocarbons catabolism, TYRR protei nucleotide-binding, transcription regulation, activator; HET: PG4; 2.30A {Escherichia coli}

Probab=99.05  E-value=2.8e-10  Score=86.79  Aligned_cols=107  Identities=14%  Similarity=0.162  Sum_probs=78.8

Q ss_pred             HHHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCC--Ce
Q 022961           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREER--PI   92 (289)
Q Consensus        15 ~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~--~~   92 (289)
                      +....++.+++++++|++++|.+   |+|+++|+++++++|++.++++|+++..+.++..       +...+..+.  ..
T Consensus        77 ~~~~~l~~il~~~~~gvi~~D~~---g~I~~~N~aa~~llg~~~~~~~g~~~~~~~~~~~-------~~~~~~~~~~~~~  146 (190)
T 2jhe_A           77 REHLALSALLEALPEPVLSVDMK---SKVDMANPASCQLFGQKLDRLRNHTAAQLINGFN-------FLRWLESEPQDSH  146 (190)
T ss_dssp             HHHHHHHHHHHHCSSCEEEECTT---CBEEEECHHHHHHHTSCHHHHTTSBGGGTSTTCC-------HHHHHHTCCCSCE
T ss_pred             HHHHHHHHHHHhCCCcEEEEcCC---CCEEEEcHHHHHHhCCCHHHhcCccHHHHhCCCC-------HHHHHhcCCCCCc
Confidence            45567899999999999999999   9999999999999999999999999887765432       122333333  23


Q ss_pred             EEEEEEEecCCCEEEEEEEEEEeecCCCCc----EEEEEEEEecccccH
Q 022961           93 EVNLLNYKKDGTPFWMLFKMSLVFGKEDGR----ATHFVAVQVPIVSRK  137 (289)
Q Consensus        93 ~~e~~~~~~~g~~~~~~~~~~~~~~~~~g~----~~~~~~~~~DITe~k  137 (289)
                      ..++..   +|..  +.+...|+.+ .+|.    +.+++.+.+|||+.+
T Consensus       147 ~~~~~~---~g~~--~~~~~~pi~~-~~~~~~~~~~g~v~~~~DiTe~~  189 (190)
T 2jhe_A          147 NEHVVI---NGQN--FLMEITPVYL-QDENDQHVLTGAVVMLRSTIRMG  189 (190)
T ss_dssp             EEEEEE---TTEE--EEEEEEEETT-TTEEEEEEEE-HHHHHHHHTTTC
T ss_pred             ceEEEE---CCeE--EEEEEEEEEe-cCCCCcceEEeEEEEEeccchhc
Confidence            333322   6643  5577888875 4554    677778889999876

>4dj3_A Period circadian protein homolog 3; PAS domain, circadian rhythm, protein binding; 2.50A {Mus musculus}

Probab=99.00  E-value=3.9e-09  Score=86.62  Aligned_cols=105  Identities=9%  Similarity=0.044  Sum_probs=85.5

Q ss_pred             CEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCC---eEEEEEEEecCCCE
Q 022961           29 DSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERP---IEVNLLNYKKDGTP  105 (289)
Q Consensus        29 ~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~---~~~e~~~~~~~g~~  105 (289)
                      .-+...+.+   |+++|+|+++..++||.+++++|+++..+++|++.......+...+..+..   ...+++++++||..
T Consensus       175 ~Fitrh~~d---G~~~yvs~~~~~lLGY~peELig~s~~~~vHPdD~~~~~~~~~~~l~~~~~~~f~s~~yR~~~kdG~~  251 (317)
T 4dj3_A          175 IFTTTHTPG---CVFLEVDERAVPLLGYLPQDLIGTSILTYLHPEDRPLMVAIHQKVLKYAGHPPFEHSPVRFCTQNGEY  251 (317)
T ss_dssp             EEEEEECTT---SBEEEECTTHHHHHSCCHHHHTTSBGGGGBCTTTTTHHHHHHHHHHHTTTSCCEECCCEEEECTTSCE
T ss_pred             ceEEEecCC---CeEEEEChHHhhhcCcChHHHcCCCHHHeECHHHHHHHHHHHHHHHHcCCCccccceEEEEEccCCCE
Confidence            345555677   999999999999999999999999999999999988887777777776554   34689999999999


Q ss_pred             EEEEEEEEEeecCCCCcEEEEEEEEeccccc
Q 022961          106 FWMLFKMSLVFGKEDGRATHFVAVQVPIVSR  136 (289)
Q Consensus       106 ~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~  136 (289)
                      +|++....++.+|.++.+..+++...-++..
T Consensus       252 vwvet~~~~~~np~s~~~e~II~~h~v~~~p  282 (317)
T 4dj3_A          252 VILDSSWSSFVNPWSRKVSFIIGRHKVRTSP  282 (317)
T ss_dssp             EEEEEEEEEEECSSSCCEEEEEEEEEECCCC
T ss_pred             EEEEEEEEEEECCCCCcccEEEEEEEeccCC
Confidence            9999999999873456676777766655544

>4dj2_A Period circadian protein homolog 1; PAS domains, circadian clock protein, protein binding; 2.75A {Mus musculus}

Probab=98.98  E-value=2.5e-09  Score=87.86  Aligned_cols=55  Identities=13%  Similarity=-0.032  Sum_probs=45.1

Q ss_pred             HhhCCCEEEEEeC-CCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHH
Q 022961           24 LDELPDSFTITDP-SISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIME   81 (289)
Q Consensus        24 ~~~~~~~i~~~d~-~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~   81 (289)
                      ++++..-++++.. +   |+|+|+|+.+..++||++++++|+++.++++|+|...+...
T Consensus        32 LqaldGF~~vvs~~~---G~i~yvS~sv~~~Lg~~~~~l~g~s~~d~iHp~D~~~f~~q   87 (320)
T 4dj2_A           32 LRNQDTFSVAVSFLT---GRIVYISEQAGVLLRCKRDVFRGARFSELLAPQDVGVFYGS   87 (320)
T ss_dssp             TSCSSEEEEEEETTT---CBEEEECTHHHHHHTSCSTTTTTSBGGGGBCHHHHHHHHHH
T ss_pred             HhccCCEEEEEECCC---ceEEEECcHHHHHhCcCHHHHcCCcHHHhcCHHHHHHHHHh
Confidence            6666555666775 6   99999999999999999999999999999988776655543

>2r78_A Sensor protein; sensory box sensor histidine kinase/response regulator, structural genomics, PSI, MCSG; 1.60A {Geobacter sulfurreducens pca}

Probab=98.94  E-value=8e-10  Score=77.23  Aligned_cols=42  Identities=7%  Similarity=-0.001  Sum_probs=40.1

Q ss_pred             HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhc
Q 022961          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITR  287 (289)
Q Consensus       243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~  287 (289)
                      +...++.++++|+++|.   +|+|++||++|++++||+++|++|+
T Consensus        13 ~~~l~e~~~d~i~~~d~---~g~i~~vN~a~~~l~Gy~~~el~g~   54 (117)
T 2r78_A           13 YRALFEHAIDGIFIMDA---EGHYLDVNPAICSAIGYTRDEFLAL   54 (117)
T ss_dssp             HHHHHHHCSSEEEEECT---TSBEEEECHHHHHHHCCCHHHHTTC
T ss_pred             HHHHHhcCCceEEEECC---CCCEEEecHHHHHHHCcCHHHHcCC
Confidence            66789999999999999   9999999999999999999999997

>3gdi_A Period circadian protein homolog 2; tandem PAS domains, biological rhythms, cytoplasm, nucleus, phosphoprotein, transcription; 2.40A {Mus musculus}

Probab=98.92  E-value=8.5e-09  Score=84.35  Aligned_cols=105  Identities=8%  Similarity=0.030  Sum_probs=85.9

Q ss_pred             EEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCC-eE-EEEEEEecCCCEEE
Q 022961           30 SFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERP-IE-VNLLNYKKDGTPFW  107 (289)
Q Consensus        30 ~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~-~~-~e~~~~~~~g~~~~  107 (289)
                      .+...+.+   |+++|+|+++..++||.+++++|+++..+++|++.......+...+..+.. .. .++++++++|..+|
T Consensus       167 Fitrh~~d---G~~~yvd~~~~~lLGY~peELig~s~~~~iHpdD~~~~~~~~~~~l~~~g~~~~~~~yR~~~kdG~~vw  243 (309)
T 3gdi_A          167 FTTTHTPN---CLFQAVDERAVPLLGYLPQDLIETPVLVQLHPSDRPLMLAIHKKILQAGGQPFDYSPIRFRTRNGEYIT  243 (309)
T ss_dssp             EEEEECTT---CBEEEECTTHHHHHSCCHHHHTTSBHHHHBCTTSHHHHHHHHHHHHHTTTCCEEEEEEEEECTTSCEEE
T ss_pred             EEEEecCC---CeEEEECcccccccCcCHHHHcCCCHHHhCCHHHHHHHHHHHHHHHhcCCceeeceEEEEEccCCCEEE
Confidence            45556677   999999999999999999999999988899998877777777777765543 54 58999999999999


Q ss_pred             EEEEEEEeecCCCCcEEEEEEEEecccccH
Q 022961          108 MLFKMSLVFGKEDGRATHFVAVQVPIVSRK  137 (289)
Q Consensus       108 ~~~~~~~~~~~~~g~~~~~~~~~~DITe~k  137 (289)
                      ++....++.+|.++.+..+++.-+-++...
T Consensus       244 vet~~~~~~np~s~~~e~ii~~h~v~~gp~  273 (309)
T 3gdi_A          244 LDTSWSSFINPWSRKISFIIGRHKVRVGPL  273 (309)
T ss_dssp             EEEEEEEEECTTTCCEEEEEEEEEEEECCS
T ss_pred             EEEEEEEEECCCCCcccEEEEEEEEccCCC
Confidence            999999888634677878888877776543

>3gdi_A Period circadian protein homolog 2; tandem PAS domains, biological rhythms, cytoplasm, nucleus, phosphoprotein, transcription; 2.40A {Mus musculus}

Probab=98.91  E-value=3.7e-09  Score=86.44  Aligned_cols=58  Identities=7%  Similarity=-0.062  Sum_probs=38.9

Q ss_pred             HHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHH
Q 022961           23 ALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEI   82 (289)
Q Consensus        23 ~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~   82 (289)
                      +++++..-+++++.+  +|+|+|+|+++..++||++++++|+++..+.+|+|...+...+
T Consensus        20 ll~a~dgF~~vvs~~--~G~i~yvS~s~~~~Lg~~~~el~g~s~~d~iHp~D~~~~~~~L   77 (309)
T 3gdi_A           20 IVKNADMFAVAVSLV--SGKILYISNQVASIFHCKKDAFSDAKFVEFLAPHDVSVFHSYT   77 (309)
T ss_dssp             ---CTTEEEEEECTT--TCBEEEECTTTTTTC-------CCSBGGGGBCTTTHHHHHHHT
T ss_pred             HHHhcCCEEEEEECC--CceEEEECCHHHHHcCCCHHHHcCCchhhccCHhHHHHHHHhc
Confidence            566666666777752  2999999999999999999999999999999998876665543

>2gj3_A Nitrogen fixation regulatory protein; PAS domain, FAD, redox sensor, atomic resolution, transferase; HET: FAD; 1.04A {Azotobacter vinelandii}

Probab=98.90  E-value=1.2e-09  Score=76.56  Aligned_cols=43  Identities=16%  Similarity=0.218  Sum_probs=40.5

Q ss_pred             HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      +..+++.++++|+++|.   +|+|+++|++|++++||+.+|++|+.
T Consensus         7 ~~~~~~~~~~~i~~~d~---~g~i~~~N~a~~~~~G~~~~elig~~   49 (120)
T 2gj3_A            7 FRQTVEHAPIAISITDL---KANILYANRAFRTITGYGSEEVLGKN   49 (120)
T ss_dssp             HHHHHHHCSSEEEEECT---TCBEEEECHHHHHHHCCCTTGGGGCB
T ss_pred             HHHHHHhCCCeEEEECC---CCCEEeehHHHHHHHCcCHHHHcCCC
Confidence            66789999999999999   99999999999999999999999973

>4dj3_A Period circadian protein homolog 3; PAS domain, circadian rhythm, protein binding; 2.50A {Mus musculus}

Probab=98.90  E-value=1.6e-08  Score=83.00  Aligned_cols=57  Identities=11%  Similarity=-0.057  Sum_probs=47.6

Q ss_pred             HHhhCCCEEEEEeC-CCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHH
Q 022961           23 ALDELPDSFTITDP-SISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEI   82 (289)
Q Consensus        23 ~~~~~~~~i~~~d~-~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~   82 (289)
                      +++++..-+++++. +   |+|+|+|+++..++||++++++|+++.++++|.|...+...+
T Consensus        31 ~L~aldgF~~vvs~~~---G~i~yvS~~~~~~Lg~~~~el~g~s~~d~ihp~D~~~f~~ql   88 (317)
T 4dj3_A           31 TSKNTDTFAAVFSFLS---GRLVHISEQAALILNSKRGFLKSVHFVDLLAPQDVRAFYAHT   88 (317)
T ss_dssp             HTSCTTEEEEEEETTT---CBEEEECTTHHHHTTCCHHHHHTSBGGGGBCGGGHHHHHHHT
T ss_pred             HHhccCCEEEEEEcCC---cEEEEECCHHHHHcCCCHHHHcCCchhhhcChhhHHHHHHhh
Confidence            46666666677775 5   999999999999999999999999999999998877665543

>1n9l_A PHOT-LOV1, putative blue light receptor; phototropin, flavin, electron transport; HET: FMN; 1.90A {Chlamydomonas reinhardtii} SCOP: d.110.3.6 PDB: 1n9n_A* 1n9o_A*

Probab=98.90  E-value=1.2e-09  Score=75.30  Aligned_cols=39  Identities=36%  Similarity=0.641  Sum_probs=35.2

Q ss_pred             ccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          250 IKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       250 ~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      ++++|+|+|+..++++|+++|++|+++|||+.+|++|+.
T Consensus         2 ~~~~i~i~d~~~~~g~i~~~N~a~~~l~Gy~~~e~~G~~   40 (109)
T 1n9l_A            2 LRHTFVVADATLPDCPLVYASEGFYAMTGYGPDEVLGHN   40 (109)
T ss_dssp             CSCEEEEEETTSTTCCEEEECHHHHHHHCCCHHHHTTSC
T ss_pred             CccEEEEEcCCCCCCeEEEEchHHHHHHCcCHHHHcCCC
Confidence            468999999755689999999999999999999999973

>4dj2_A Period circadian protein homolog 1; PAS domains, circadian clock protein, protein binding; 2.75A {Mus musculus}

Probab=98.88  E-value=6.8e-09  Score=85.28  Aligned_cols=106  Identities=9%  Similarity=0.043  Sum_probs=85.4

Q ss_pred             CEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhC-CCe-EEEEEEEecCCCEE
Q 022961           29 DSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREE-RPI-EVNLLNYKKDGTPF  106 (289)
Q Consensus        29 ~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~-~~~-~~e~~~~~~~g~~~  106 (289)
                      ..+...+.+   |+++|+|+++..++||.++|++|+++..+++|++.......+...+..+ ... ..++++++++|..+
T Consensus       177 ~Fitrh~~d---G~~~yvd~~~~~lLGY~peELig~s~~~~vHPdD~~~~~~~~~~~l~~~g~~~~~~~yR~~~kdG~~v  253 (320)
T 4dj2_A          177 IFTTRHTPS---CLFQDVDERAAPLLGYLPQDLLGAPVLLFLHPEDRPLMLAIHKKILQLAGQPFDHSPIRFCARNGEYV  253 (320)
T ss_dssp             EEEEEECTT---CBEEEECTTHHHHHSCCHHHHTTSBGGGGBCGGGHHHHHHHHHHHTTSSSCCEECCCEEEECSSSCEE
T ss_pred             eEEEEecCC---ceEEEcCcceeccCCcChHHHcCCcHHHhCCHHHHHHHHHHHHHHHhcCCCcccceEEEEEccCCCEE
Confidence            345556777   9999999999999999999999999999999988776666666666643 344 35899999999999


Q ss_pred             EEEEEEEEeecCCCCcEEEEEEEEecccccH
Q 022961          107 WMLFKMSLVFGKEDGRATHFVAVQVPIVSRK  137 (289)
Q Consensus       107 ~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k  137 (289)
                      |++....++.+|-++.+..+++.-.-++...
T Consensus       254 wvet~~~~~~np~s~~~e~II~~h~v~~gp~  284 (320)
T 4dj2_A          254 TMDTSWAGFVHPWSRKVAFVLGRHKVRTAPL  284 (320)
T ss_dssp             EEECEEEEEECTTTCSEEEEEEEEEESSCCS
T ss_pred             EEEEEEEEEECCCCCCccEEEEEEEEccCCC
Confidence            9999999988744677888888877777644

>1d06_A Nitrogen fixation regulatory protein FIXL; oxygen sensor, histidine kinase, PAS, high-resolution, two-C system, signaling protein; HET: HEM; 1.40A {Sinorhizobium meliloti} SCOP: d.110.3.2 PDB: 1ew0_A*

Probab=98.83  E-value=3.2e-09  Score=75.49  Aligned_cols=43  Identities=19%  Similarity=0.078  Sum_probs=40.5

Q ss_pred             HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      +...++.++++|+++|.   +|+|+++|++|++++||+.+|++|+.
T Consensus        18 ~~~l~~~~~d~i~~~d~---~g~i~~~N~a~~~l~Gy~~~eliG~~   60 (130)
T 1d06_A           18 LRSILDTVPDATVVSAT---DGTIVSFNAAAVRQFGYAEEEVIGQN   60 (130)
T ss_dssp             HHHHHTTCSSEEEEEET---TSBEEEECHHHHHHHCCCHHHHTTSB
T ss_pred             HHHHHhhCcCeEEEECC---CCeEEEEcHHHHHHHCCCHHHHcCCc
Confidence            66789999999999999   99999999999999999999999973

>3bwl_A Sensor protein; structural genomics, APC87707.1, PAS domain, HTR-like protei protein structure initiative; HET: MSE I3A; 1.73A {Haloarcula marismortui atcc 43049}

Probab=98.76  E-value=6.2e-09  Score=73.27  Aligned_cols=41  Identities=12%  Similarity=0.066  Sum_probs=37.6

Q ss_pred             HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhh
Q 022961          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKIT  286 (289)
Q Consensus       243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G  286 (289)
                      +...++.++++|+++|.   +|+|+++|++|++++||+.+|++|
T Consensus        19 ~~~l~e~~~~~i~~~d~---~g~i~~~N~a~~~~~G~~~~el~g   59 (126)
T 3bwl_A           19 LEALFENSPDMIDVLDA---DGTICEVNQRFCAELGYDESEVLG   59 (126)
T ss_dssp             HHHHHHHCSSEEEEECT---TCBEEEECHHHHHHHTCCGGGTTT
T ss_pred             HHHHHhhCCcEEEEEcC---CCCEEEEcHHHHHHhCCCHHHHhh
Confidence            55678999999999999   999999999999999999999953

>3mfx_A Sensory BOX/ggdef family protein; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.40A {Shewanella oneidensis}

Probab=98.75  E-value=8.8e-09  Score=73.36  Aligned_cols=43  Identities=5%  Similarity=0.081  Sum_probs=40.7

Q ss_pred             HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      +...++.++++|+++|.   +|+|+++|+++++++||+++|++|+-
T Consensus         9 l~~i~~~~~d~i~~~D~---~g~I~~~N~aa~~l~G~~~~el~G~~   51 (129)
T 3mfx_A            9 IELFIQHLTEAMILVNA---NGFIRSCNQRSAELLDCPQVSLKGQD   51 (129)
T ss_dssp             HHHHHTTCSSEEEEEET---TSBEEEECHHHHHHTTSCHHHHTTSB
T ss_pred             HHHHHhcCCceEEEECC---CCEEEeEhHHHHHHHCcCHHHHcCCc
Confidence            67789999999999999   99999999999999999999999973

>2pr5_A Blue-light photoreceptor; light-oxygen-voltage, LOV, PER-ARNT-SIM, PAS, flavoprotein, protein; HET: FMN; 1.45A {Bacillus subtilis} PDB: 2pr6_A*

Probab=98.73  E-value=8.8e-09  Score=73.35  Aligned_cols=44  Identities=27%  Similarity=0.526  Sum_probs=35.8

Q ss_pred             HHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          245 ISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       245 ~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      ..++.++++|+++|...++++|+++|++|++++||+.+|++|+.
T Consensus         3 ~~~~~~~~~i~~~d~~g~~~~i~~~N~a~~~~~G~~~~el~g~~   46 (132)
T 2pr5_A            3 HMLDHVRVGVVITDPALEDNPIVYVNQGFVQMTGYETEEILGKN   46 (132)
T ss_dssp             ---CCCCCEEEEECTTSTTCCEEEECHHHHHHHSCCHHHHTTSC
T ss_pred             hHHhcCCCcEEEEeCCCCCCcEEEECHHHHHHhCcCHHHHcCCC
Confidence            46788999999999822234999999999999999999999973

>3olo_A Two-component sensor histidine kinase; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG, TRA; 2.09A {Nostoc SP}

Probab=98.63  E-value=3.5e-08  Score=68.19  Aligned_cols=43  Identities=9%  Similarity=0.070  Sum_probs=39.5

Q ss_pred             HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      +...++.++++|++.|.   +|+|+++|++|++++||+++|++|+.
T Consensus        15 ~~~~~~~~~~~i~~~d~---~g~i~~~N~~~~~l~G~~~~el~g~~   57 (118)
T 3olo_A           15 AHYLINNAVEASFCLGD---NWQFLYVNDATCRMTEYSREQLLSMN   57 (118)
T ss_dssp             HHHHHHHCSSEEEEECT---TSBEEEECHHHHHHHCCCHHHHTTCB
T ss_pred             HHHHHhcCCceEEEECC---CCcEEEEHHHHHHHHCCCHHHHhCCC
Confidence            45678999999999999   99999999999999999999999973

>2ykf_A Pdtas, probable sensor histidine kinase pdtas; transferase, two-component system, GAF domain, PAS domain; 2.00A {Mycobacterium tuberculosis} PDB: 2ykh_A

Probab=97.97  E-value=7.9e-09  Score=84.69  Aligned_cols=111  Identities=14%  Similarity=0.108  Sum_probs=75.9

Q ss_pred             HHhhCCCEEEEEeCCCCCccEEEccHHHHHHhC---CCccccCCCCCCCccCCC---CCH--HHHHHHHHHHHh-CCCeE
Q 022961           23 ALDELPDSFTITDPSISGHPIVFASRGFLKMSG---FSRAEIIGRNGRMFQGPR---TNR--RTIMEIREAIRE-ERPIE   93 (289)
Q Consensus        23 ~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G---~~~~e~~g~~~~~l~~~~---~~~--~~~~~~~~~~~~-~~~~~   93 (289)
                      +++++++|++++|.+   |+|+++|++++++++   ++ ++++|+++..+.+..   ...  .+...+...+.. +....
T Consensus       175 ~~~~~~dGIivvD~~---G~Ii~~N~aA~~ll~~lG~~-~~~iGk~l~el~~~~~~~~~~~~~~~~~l~~vl~~~~~~~~  250 (305)
T 2ykf_A          175 SSPRAGDGFIRLDVD---GVVSYASPNALSAYHRMGLT-TELEGVNLIDATRPLISDPFEAHEVDEHVQDLLAGDGKGMR  250 (305)
Confidence            356899999999999   999999999999985   44 688999877776432   100  111222223332 22222


Q ss_pred             EEEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhccc
Q 022961           94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGM  144 (289)
Q Consensus        94 ~e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l~  144 (289)
                      .+..   .+|  .++.++..|+.+  .|.+.+++.+++|||+.++.|++|.
T Consensus       251 ~ei~---~~~--~~l~v~~~Pi~~--~g~~~G~Vvv~rDITE~~~lE~eL~  294 (305)
T 2ykf_A          251 MEVD---AGG--ATVLLRTLPLVV--AGRNVGAAILIRDVTEVKRRDRALI  294 (305)
Confidence            2221   122  456677889876  5777888999999999999988874

>3mxq_A Sensor protein; PSI2, MCSG, structural genomics, protein structure initiativ midwest center for structural genomics; 2.78A {Vibrio cholerae o1 biovar el tor}

Probab=98.55  E-value=5.1e-08  Score=71.36  Aligned_cols=43  Identities=14%  Similarity=0.040  Sum_probs=40.4

Q ss_pred             HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      +..+++.+++||+++|.   +|+|+++|+++++++||+++|++||.
T Consensus        24 l~~il~~~~~gi~v~D~---~g~I~~~N~a~~~~~G~~~~eviG~~   66 (152)
T 3mxq_A           24 LSELLDQLSFALCIVRN---DYVIVKVNEYFESRVIFDGETMQGKN   66 (152)
T ss_dssp             HHHHHHHHCCEEEEEET---TSBEEEECHHHHHTSSSCHHHHTTSB
T ss_pred             HHHHHhcCCCCEEEEcC---CCEEEEECHHHHHHHCcCHHHHCCCC
Confidence            56788999999999999   99999999999999999999999984

>2vlg_A Sporulation kinase A; histidine kinase, two-component regulatory system, two-component signal transduction, transferase, phosphorylation, SCOD; 1.7A {Bacillus subtilis}

Probab=98.54  E-value=5.1e-08  Score=67.36  Aligned_cols=40  Identities=13%  Similarity=0.042  Sum_probs=33.4

Q ss_pred             HhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          246 SLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       246 ~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      .++.++++|++.|.   +|+|+|+|+++++++||+++|++|+-
T Consensus         4 lle~~~d~i~v~d~---~G~i~yvn~~~~~~lGy~~~el~G~~   43 (111)
T 2vlg_A            4 PLQTKTDIHAVLAS---NGRIIYISANSKLHLGYLQGEMIGSF   43 (111)
T ss_dssp             -----CCEEEEECT---TSBEEEECTTHHHHHSCCHHHHTTSB
T ss_pred             hhhcCCCEEEEEcC---CCeEEEEChHHHHHhCCCHHHHcCCc
Confidence            56788899999999   99999999999999999999999973

>1ll8_A PAS kinase; PAS domain, ligand binding, ligand screening, kinase regulation, transferase; NMR {Homo sapiens} SCOP: d.110.3.5

Probab=98.53  E-value=3.9e-08  Score=67.94  Aligned_cols=36  Identities=17%  Similarity=0.194  Sum_probs=33.2

Q ss_pred             ccccEEEeCCCCCC-CCEEEecHHHHHhhCCChHhHhhcc
Q 022961          250 IKQSFVLIDPHLPD-MPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       250 ~~~~i~i~d~~~~~-~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      ..++|+++|.   + |+|+++|+++++++||+++|++|+-
T Consensus         7 ~~~~i~~~d~---~~g~I~~~N~aa~~l~G~~~~el~g~~   43 (114)
T 1ll8_A            7 FNKAIFTVDA---KTTEILVANDKACGLLGYSSQDLIGQK   43 (114)
T ss_dssp             TTCEEEEEET---TTCBEEEECTTHHHHHTCCTTTTTTSB
T ss_pred             CCceEEEEEC---CCCeEEEehHHHHHHhCCCHHHHcCCC
Confidence            4579999999   9 9999999999999999999999973

>1nwz_A PYP, photoactive yellow protein; PAS, LOV, GAF, domains fold, signaling protein; HET: HC4; 0.82A {Halorhodospira halophila} SCOP: d.110.3.1 PDB: 1kou_A* 1ot9_A* 1otb_A* 1s4r_A* 1s4s_A* 1ts0_A* 1ts6_A* 1ts7_A* 1ts8_A* 1uwn_X* 1uwp_X* 2d01_A* 2phy_A* 2pyp_A* 2pyr_A* 2qj5_A* 2qj7_A* 2qws_A* 2zoh_A* 2zoi_A* ...

Probab=98.50  E-value=1.2e-07  Score=66.21  Aligned_cols=42  Identities=17%  Similarity=0.039  Sum_probs=39.0

Q ss_pred             HHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          244 YISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       244 ~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      ...++.++.|+++.|.   +++|+++|++.++++||+++|++||.
T Consensus        20 ~~~ld~l~~Gii~lD~---~g~I~~~N~~~e~~sG~~~~eviGk~   61 (125)
T 1nwz_A           20 DGQLDGLAFGAIQLDG---DGNILQYNAAEGDITGRDPKQVIGKN   61 (125)
T ss_dssp             HHHHTTCSSEEEEEET---TCBEEEECHHHHHHHCCCHHHHTTSB
T ss_pred             HHHHhccCceEEEECC---CCEEEEEHHHHHHHhCCCHHHHcCCc
Confidence            3468899999999999   99999999999999999999999984

>1mzu_A PPR; photoactive yellow protein, PAS, PYP, signaling protein; HET: HC4; 2.00A {Rhodospirillum centenum} SCOP: d.110.3.1

Probab=98.48  E-value=1.2e-07  Score=66.21  Aligned_cols=40  Identities=13%  Similarity=0.034  Sum_probs=38.1

Q ss_pred             HhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          246 SLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       246 ~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      .++.++.||++.|.   +++|+++|++.++++||+++|++||.
T Consensus        27 ~ld~l~~GiivlD~---dg~I~~~N~~~e~isG~s~eeviGk~   66 (129)
T 1mzu_A           27 EFDALPVGAIQVDG---SGVIHRYNRTESRLSGRIPERVIGRN   66 (129)
T ss_dssp             TGGGCSSEEEEEET---TCBEEEECHHHHHHHCCCHHHHTTSB
T ss_pred             HHhccCceEEEECC---CCeEEEEHHHHHHHhCCCHHHHcCCc
Confidence            58889999999999   99999999999999999999999984

>3mqq_A Transcriptional regulator, LUXR family; PAS domain, PSI, MCSG, structural genomics, center for structural genomics; 1.65A {Burkholderia thailandensis} PDB: 3mqo_A

Probab=98.47  E-value=9.1e-08  Score=66.66  Aligned_cols=42  Identities=14%  Similarity=0.060  Sum_probs=37.8

Q ss_pred             HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      +..+++.++++|++ |.   +|+|+++|++|++++||+.+|++|+.
T Consensus         5 ~~~~~~~~~~~i~~-~~---~g~i~~~N~a~~~l~G~~~~el~g~~   46 (120)
T 3mqq_A            5 YKTAFHLAPIGLVL-SR---DRVIEDCNDELAAIFRCARADLIGRS   46 (120)
T ss_dssp             HHHHHHHCSSEEEE-EE---TTEEEEECHHHHHHTTSCHHHHTTCB
T ss_pred             HHHHHhcCCceEEE-ec---CCEEHHHHHHHHHHhCcCHHHhCCCc
Confidence            56789999999965 66   89999999999999999999999973

>4eet_B Phototropin-2; LOV, blue light photoreceptor, signaling protein, flavoprote; HET: FMN; 1.20A {Arabidopsis thaliana} PDB: 4ees_A* 4eer_A* 4eep_A* 4eeu_A* 1jnu_A* 1g28_A*

Probab=98.45  E-value=2e-07  Score=63.71  Aligned_cols=43  Identities=42%  Similarity=0.637  Sum_probs=36.9

Q ss_pred             HhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          246 SLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       246 ~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      .++.++++++++|...++++|+++|++|++++||+.+|++|+.
T Consensus         2 ~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~~~~g~~   44 (115)
T 4eet_B            2 SPEFIEKNFVITDPRLPDNPIIFASDGFLELTEYSREEILGRN   44 (115)
T ss_dssp             ---CCCCSEEEECTTSTTCCEEEECHHHHHHHCCCHHHHTTSC
T ss_pred             ccccCCCcEEEEcCCCCCCcEEEEcHHHHHHHCcCHHHHhCCC
Confidence            4678899999999866689999999999999999999999973

>3f1p_B ARYL hydrocarbon receptor nuclear translocator; PAS domain, heterodimer, internal cavity, activator, angiogenesis, congenital erythrocytosis; 1.17A {Homo sapiens} SCOP: d.110.3.0 PDB: 3f1o_B* 3f1n_B 3h7w_B* 3h82_B* 1x0o_A 2hv1_A 4h6j_B 2b02_A* 2k7s_A 2a24_B

Probab=98.45  E-value=1e-07  Score=66.56  Aligned_cols=41  Identities=5%  Similarity=0.008  Sum_probs=37.0

Q ss_pred             HHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          245 ISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       245 ~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      ..++++++.|++.|+   +|+|+|+|+++++++||+++|++|+.
T Consensus         6 ll~e~~~d~i~~~d~---~g~i~~~n~~~~~~~G~~~~el~g~~   46 (121)
T 3f1p_B            6 LNVCQPTRFISRHNI---EGIFTFVDHRCVATVGYQPQELLGKN   46 (121)
T ss_dssp             --CCCCCEEEEEECT---TSBEEEECTTHHHHHSCCGGGTTTSB
T ss_pred             ceecCCCceEEEECC---CceEEEECcchhhhhCCChHHHcCCC
Confidence            467889999999999   99999999999999999999999973

>3fg8_A Uncharacterized protein RHA05790; PAS domain, structural genomics, PS protein structure initiative, midwest center for structural genomics, MCSG; HET: 3PB; 1.80A {Rhodococcus SP}

Probab=98.44  E-value=1.5e-07  Score=65.61  Aligned_cols=42  Identities=14%  Similarity=0.171  Sum_probs=38.6

Q ss_pred             HHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          244 YISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       244 ~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      ..+++.++++|++.|.   +|+|+++|+++++++||+.+|++|+.
T Consensus        15 ~~il~~~~~~i~~~D~---~g~i~~~N~a~~~l~g~~~~e~~G~~   56 (118)
T 3fg8_A           15 ENLYFQGGLGFMALDE---DLRIIYVNSGCLRHVRRSRDELLGRV   56 (118)
T ss_dssp             CCSSSCTTCEEEEECT---TCBEEEECHHHHHHHTCCHHHHTTSB
T ss_pred             HHHHhhCCceEEEECC---CCeEEEECHHHHHHhCCCHHHHcCCc
Confidence            3467889999999999   99999999999999999999999973

>4hi4_A Aerotaxis transducer AER2; PAS domain, diatomic GAS sensor, signaling protein; HET: HEM GOL; 2.30A {Pseudomonas aeruginosa}

Probab=98.42  E-value=1.5e-07  Score=65.83  Aligned_cols=43  Identities=12%  Similarity=0.248  Sum_probs=39.8

Q ss_pred             HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhC------------CChHhHhhcc
Q 022961          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTG------------AQIFTKITRI  288 (289)
Q Consensus       243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tG------------ys~~E~~G~~  288 (289)
                      +..+++.++++|+++|.   +|+|+++|++|++++|            |+.++++|+.
T Consensus         7 l~~il~~~~~gviv~D~---~g~I~~~N~a~~~llg~~~~~i~~~~~g~~~~~~~G~~   61 (121)
T 4hi4_A            7 IASALDNVSANVMIADN---DLNIIYMNRTVSEMLGRAEADIRKQLPNFDAGRLMGAN   61 (121)
T ss_dssp             HHHHHTTSSSEEEEEET---TCBEEEECHHHHHHHHHTHHHHHHHCTTCCGGGCTTCB
T ss_pred             HHHHHhcCCccEEEEcC---CCeEEEecHHHHHHHHHHHHHHHHhcCCCChHHhcCCC
Confidence            67789999999999999   9999999999999985            9999999973

>3b33_A Sensor protein; structural genomics, PAS domain, nitrogen regulation protein APC91440.4, PSI-2; HET: MSE; 1.83A {Vibrio parahaemolyticus rimd 2210633}

Probab=98.40  E-value=3.3e-07  Score=63.14  Aligned_cols=41  Identities=15%  Similarity=0.172  Sum_probs=38.7

Q ss_pred             HHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhc
Q 022961          244 YISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITR  287 (289)
Q Consensus       244 ~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~  287 (289)
                      ...++.++++|+++|.   +|+|+++|+++++++||+.++++|+
T Consensus        10 ~~il~~~~~~i~~~D~---~g~I~~~N~aa~~l~g~~~~~~~g~   50 (115)
T 3b33_A           10 SAILNNMVTATLILDD---GLAIRYANPAAELLFSQSAKRIVEQ   50 (115)
T ss_dssp             HHHHHHCSSEEEEECT---TCBEEEECHHHHHHTTSCHHHHTTC
T ss_pred             HHHHhhcCceEEEECC---CCcEEEECHHHHHHhCCCHHHHhCC
Confidence            4578999999999999   9999999999999999999999997

>3fc7_A HTR-like protein, sensor protein; APC87712.1, HTR-like protein,haloarcula marismortui ATCC 430 structural genomics, PSI-2; 2.65A {Haloarcula marismortui}

Probab=98.40  E-value=1.9e-07  Score=65.08  Aligned_cols=43  Identities=9%  Similarity=0.040  Sum_probs=36.5

Q ss_pred             HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      +...++.++++|+++|.   +|+|+++|++|++++||+.++++|+.
T Consensus        21 ~~~i~~~~~~~i~~~d~---~g~i~~~N~~~~~~~g~~~~~~~g~~   63 (125)
T 3fc7_A           21 FESLVSDSPDGIVHLTT---NGTILSVNPSMAGRLGADPDTLVGQQ   63 (125)
T ss_dssp             -----CCSCCEEEEEET---TSBEEEECHHHHHHHTSCHHHHTTSB
T ss_pred             HHHHHhcCCCeEEEEcC---CCeEEEECHHHHHHhCCCHHHHcCcc
Confidence            56688999999999999   99999999999999999999999973

>3ue6_A Aureochrome1; PAS/LOV domain, FMN-binding blue-light photoreceptor, signal protein; HET: FMN; 2.75A {Vaucheria frigida} PDB: 3ulf_A*

Probab=98.33  E-value=5.5e-07  Score=66.17  Aligned_cols=46  Identities=43%  Similarity=0.631  Sum_probs=41.6

Q ss_pred             HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      +...++.++++|+++|...++++|+++|++|++++||+.+|++|+.
T Consensus        37 ~~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~g~~   82 (166)
T 3ue6_A           37 LVKALQMAQQNFVITDASLPDNPIVYASRGFLTLTGYSLDQILGRN   82 (166)
T ss_dssp             HHHHHHHTTSCEEEEETTSTTCCEEEECHHHHHHHCCCHHHHTTSC
T ss_pred             HHHHHhcCCceEEEEEccCCCCcEEEECHHHHHHhCcCHHHHcCCC
Confidence            7788999999999999844569999999999999999999999973

>2kdk_A ARYL hydrocarbon receptor nuclear translocator-LI 2; circadian clock, PAS domain, transcription, activator, biolo rhythms, DNA-binding, nucleus; NMR {Homo sapiens}

Probab=98.33  E-value=2.1e-07  Score=64.68  Aligned_cols=40  Identities=8%  Similarity=-0.055  Sum_probs=37.1

Q ss_pred             HhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          246 SLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       246 ~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      .+++++++|++.|.   +|+|+++|++|++++||+.+|++|+.
T Consensus         8 ~~~~~~~~i~~~d~---~g~i~~~N~~~~~~~G~~~~el~g~~   47 (121)
T 2kdk_A            8 INVKPTEFITRFAV---NGKFVYVDQRATAILGYLPQELLGTS   47 (121)
T ss_dssp             CCCCSSEEEEEECT---TSBEEEECTHHHHHTCCCTTTSBTSB
T ss_pred             cccCCccEEEEECC---CeeEEEEChhHHHHHCCCHHHHcCCc
Confidence            56788899999999   99999999999999999999999973

>3luq_A Sensor protein; PAS, histidine, kinase, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: PGE; 2.49A {Geobacter sulfurreducens}

Probab=98.31  E-value=3.8e-07  Score=62.25  Aligned_cols=43  Identities=12%  Similarity=0.041  Sum_probs=40.0

Q ss_pred             HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      +...++.+++++++.|.   +++|+++|++|++++||+.++++|+.
T Consensus         5 ~~~~~~~~~~~i~~~d~---~g~i~~~N~~~~~~~g~~~~~~~g~~   47 (114)
T 3luq_A            5 LRLFTEHAPAALAMFDR---EMRYLAVSRRWREDYGLGDGDILGMS   47 (114)
T ss_dssp             HHHHHHTCSSEEEEEET---TCBEEEECHHHHHHTTCCSSCCTTCB
T ss_pred             HHHHHhcCCceEEEEcC---CcEEEEECHHHHHHHCCCHHHHcCCc
Confidence            56788999999999999   99999999999999999999999973

>3p7n_A Sensor histidine kinase; LOV domain, light-activated transcription factor, DNA bindin; HET: FMN; 2.10A {Erythrobacter litoralis}

Probab=98.30  E-value=6.6e-07  Score=71.40  Aligned_cols=46  Identities=26%  Similarity=0.297  Sum_probs=41.0

Q ss_pred             HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      +..+++.++++|+++|....+|+|+++|++|++++||+.+|++|+.
T Consensus        65 ~~~i~~~~~~~i~~~d~~~~~g~i~~~N~a~~~l~G~~~~el~g~~  110 (258)
T 3p7n_A           65 VLDLIEASPIASVVSDPRLADNPLIAINQAFTDLTGYSEEECVGRN  110 (258)
T ss_dssp             HHHHHHTCSSEEEEECTTSTTCCEEEECHHHHHHHCCCGGGTTTSC
T ss_pred             HHHHHhcCCccEEEEcCCCCCCcEEEEhHHHHHHcCCCHHHHCCCC
Confidence            7788999999999999843366799999999999999999999973

>3f1p_A Endothelial PAS domain-containing protein 1; PAS domain, heterodimer, internal cavity, activator, angiogenesis, congenital erythrocytosis; 1.17A {Homo sapiens} SCOP: d.110.3.7 PDB: 3f1o_A* 3f1n_A 3h7w_A* 3h82_A* 1p97_A 2a24_A 4h6j_A

Probab=98.30  E-value=5.5e-07  Score=62.24  Aligned_cols=36  Identities=22%  Similarity=0.200  Sum_probs=32.9

Q ss_pred             ccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          250 IKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       250 ~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      +.+.|+++|+   +|+|+++|++|++++||+.+|++|+.
T Consensus         8 ~~~~i~~~d~---~g~i~~~n~~~~~~~Gy~~~el~g~~   43 (117)
T 3f1p_A            8 SKTFLSEHSM---DMKFTYCDDRITELIGYHPEELLGRS   43 (117)
T ss_dssp             GGEEEEEECT---TCBEEEECTHHHHHHCCCHHHHTTSB
T ss_pred             CccEEEEECC---CceEEEECcChhhhhCCCHHHHcCCc
Confidence            3578899999   99999999999999999999999973

>3t50_A Blue-light-activated histidine kinase; PAS superfamily, blue-light photoreceptor, FMN binding, TRAN; HET: FMN; 1.64A {Brucella melitensis}

Probab=98.27  E-value=7.3e-07  Score=62.41  Aligned_cols=43  Identities=37%  Similarity=0.573  Sum_probs=37.4

Q ss_pred             HhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          246 SLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       246 ~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      +++.++++++++|...++|+|+++|++|++++||+.+|++|+.
T Consensus         2 ~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~g~~~~e~~g~~   44 (128)
T 3t50_A            2 ASEFTLMPMLITNPHLPDNPIVFANPAFLKLTGYEADEVMGRN   44 (128)
T ss_dssp             CCCCCSSCEEEECTTSTTCCEEEECHHHHHHHCCCHHHHTTSC
T ss_pred             ccccCcccEEEecCCCCCCcEEEEcHHHHHHhCcCHHHHcCCC
Confidence            3677889999999833477999999999999999999999973

>3a0s_A Sensor protein; PAS-fold, kinase, phosphoprotein, transferase, two-component regulatory system; HET: PG4 PGE; 1.47A {Thermotoga maritima} PDB: 3a0v_A*

Probab=98.24  E-value=8.8e-07  Score=57.92  Aligned_cols=35  Identities=11%  Similarity=0.071  Sum_probs=32.8

Q ss_pred             cccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          251 KQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       251 ~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      +++|+++|.   +++|+++|+++++++||+.+|++|+.
T Consensus         2 ~~~i~~~d~---~g~i~~~N~~~~~l~g~~~~~~~g~~   36 (96)
T 3a0s_A            2 ETAIITLSK---DGRITEWNKKAEQLFGLKKENVLGRR   36 (96)
T ss_dssp             CCEEEEEET---TSBEEEECHHHHHHHCCCHHHHTTSB
T ss_pred             CceEEEEcC---CCCEeehhHHHHHHhCCCHHHhcCCC
Confidence            578999999   99999999999999999999999973

>3vol_A Aerotaxis transducer AER2; heme, oxygen sensor protein, PAS, HAMP, cyanoMet, CN-bound, protein; HET: HEM; 2.40A {Pseudomonas aeruginosa}

Probab=98.20  E-value=8.2e-07  Score=69.88  Aligned_cols=43  Identities=9%  Similarity=0.201  Sum_probs=39.9

Q ss_pred             HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhh------------CCChHhHhhcc
Q 022961          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLT------------GAQIFTKITRI  288 (289)
Q Consensus       243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~t------------Gys~~E~~G~~  288 (289)
                      +..+++.++++|+++|+   +|+|+|+|++|++++            ||+.+|++|+.
T Consensus        24 l~~iLd~~~~~vii~D~---~g~I~~~N~a~~~ll~~~~~~~~~~l~G~~~~eliG~~   78 (233)
T 3vol_A           24 IKSALDNVSANVMIADN---DLNIIYMNRTVSEMLGRAEADIRKQLPNFDAGRLMGAN   78 (233)
T ss_dssp             HHHHHTTSSSEEEEEET---TSBEEEECHHHHHHHHHTHHHHHTTCTTCCTTSCTTCB
T ss_pred             HHHHHhcCCCcEEEECC---CCcEEEecHHHHHHHHHHHHHHHhhcCCCCHHHHcCCC
Confidence            67789999999999999   999999999999988            89999999973

>1byw_A Protein (human ERG potassium channel); PAS domain, potassium channel domain, membrane protein; 2.60A {Homo sapiens} SCOP: d.110.3.6

Probab=98.20  E-value=1.3e-06  Score=58.53  Aligned_cols=37  Identities=19%  Similarity=0.467  Sum_probs=33.5

Q ss_pred             ccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          252 QSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       252 ~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      .+|+++|...++++|+++|++|++++||+.+|++|+.
T Consensus         2 ~~i~i~d~~~~~g~i~~~N~~~~~~~g~~~~~~~g~~   38 (110)
T 1byw_A            2 RKFIIANARVENCAVIYCNDGFCELCGYSRAEVMQRP   38 (110)
T ss_dssp             CEEEEEETTSSSCBEEEECHHHHHHHTCCHHHHTTSB
T ss_pred             CCEEEEeccCCCCcEEEECHHHHHHhCCCHHHHccCC
Confidence            5889999866679999999999999999999999973

>3d72_A Vivid PAS protein VVD; circadian, photoreceptor, blue-light, LOV, signaling protein; HET: FAD; 1.65A {Neurospora crassa} PDB: 3is2_A* 2pd8_A* 3hjk_A* 2pdr_A* 2pd7_A* 2pdt_A* 3hji_A* 3rh8_B*

Probab=98.19  E-value=9.3e-07  Score=63.82  Aligned_cols=41  Identities=34%  Similarity=0.480  Sum_probs=34.5

Q ss_pred             hhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          247 LGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       247 ~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      ++.. ++|+++|...++|+|+++|++|++++||+.+|++|+.
T Consensus        32 ~~~~-~~i~~~d~~d~~g~i~~~N~a~~~l~G~~~~el~g~~   72 (149)
T 3d72_A           32 VDTS-VALILCDLKQKDTPIVYASEAFLYMTGYSNAEVLGRN   72 (149)
T ss_dssp             CCTT-SCEEEEETTSTTCCEEEECHHHHHHHCCCHHHHTTSC
T ss_pred             hcCC-ccEEEEeccCCCCcEEEECHHHHHHHCcCHHHHcCCC
Confidence            3443 8999999333399999999999999999999999973

>3mjq_A Uncharacterized protein; NESG, structural genomics, PSI-2, protein structure initiati northeast structural genomics consortium; 2.60A {Desulfitobacterium hafniense}

Probab=98.16  E-value=1e-06  Score=61.24  Aligned_cols=40  Identities=20%  Similarity=0.213  Sum_probs=37.3

Q ss_pred             HHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhc
Q 022961          245 ISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITR  287 (289)
Q Consensus       245 ~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~  287 (289)
                      ..++.+++++++.|.   +|+|+++|+++++++||+.++++|+
T Consensus         3 ~l~~~~~~~i~~~d~---~g~i~~~N~~~~~~~g~~~~~~~g~   42 (126)
T 3mjq_A            3 NFLETIEDMILIINR---EGRLLYANTAVPKKLGYTHEELMSM   42 (126)
T ss_dssp             TTGGGCSSEEEEEET---TSBEEEECTHHHHHHSCCHHHHHHS
T ss_pred             hHHhhCCceEEEEeC---CCcEEEEcHHHHHHHCCCHHHHcCC
Confidence            357888999999999   9999999999999999999999986

>3lyx_A Sensory BOX/ggdef domain protein; structural genomics, PSI- 2, protein structure initiative, northeast structural genomics consortium; 2.00A {Colwellia psychrerythraea}

Probab=98.09  E-value=3.9e-06  Score=57.46  Aligned_cols=43  Identities=12%  Similarity=-0.028  Sum_probs=39.9

Q ss_pred             HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      +...++.+++++++.|.   +++|+++|++|++++||+.++++|+.
T Consensus         9 ~~~~~~~~~~~i~~~d~---~~~i~~~N~~~~~~~g~~~~~~~g~~   51 (124)
T 3lyx_A            9 RAKAFDYVFDAIVVTDL---QGFIIDWNKGSETLYGYSKEQAIGQP   51 (124)
T ss_dssp             HHHGGGTCSSEEEEEET---TCBEEEECHHHHHHHCCCHHHHTTSB
T ss_pred             HHHHHhhcCceEEEECC---CCcEeehhhHHHHHhCCCHHHHcCCC
Confidence            56788999999999999   99999999999999999999999863

>2z6d_A Phototropin-2; PAS-fold, LOV-fold, alternative splicing, ATP-binding, chromophore, flavoprotein, FMN, kinase, membrane, nucleotide-binding; HET: FMN; 2.00A {Arabidopsis thaliana} PDB: 2z6c_A*

Probab=98.03  E-value=5.4e-06  Score=57.17  Aligned_cols=45  Identities=36%  Similarity=0.600  Sum_probs=39.4

Q ss_pred             HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhc
Q 022961          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITR  287 (289)
Q Consensus       243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~  287 (289)
                      +...++.++++++++|...++++|+++|++|++++||+.++++|+
T Consensus         8 ~~~~~~~~~~~i~~~d~~d~~~~i~~~N~~~~~~~g~~~~~~~g~   52 (130)
T 2z6d_A            8 LKTALSTLQQTFVVSDATQPHCPIVYASSGFFTMTGYSSKEIVGR   52 (130)
T ss_dssp             HHHHHHHTTCEEEEEETTSTTCCEEEECHHHHHHHCCCHHHHTTS
T ss_pred             HHHHHHhcccceeeeeccCCCCcEEEecHHHHHHhCcCHHHHcCC
Confidence            667889999999999921129999999999999999999999986

>2jhe_A Transcription regulator TYRR; aromatic hydrocarbons catabolism, TYRR protei nucleotide-binding, transcription regulation, activator; HET: PG4; 2.30A {Escherichia coli}

Probab=98.01  E-value=6.2e-06  Score=62.39  Aligned_cols=43  Identities=16%  Similarity=0.113  Sum_probs=40.4

Q ss_pred             HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      +...++.+++||+++|.   +|+|+++|+++++++||+.++++|+-
T Consensus        82 l~~il~~~~~gvi~~D~---~g~I~~~N~aa~~llg~~~~~~~g~~  124 (190)
T 2jhe_A           82 LSALLEALPEPVLSVDM---KSKVDMANPASCQLFGQKLDRLRNHT  124 (190)
T ss_dssp             HHHHHHHCSSCEEEECT---TCBEEEECHHHHHHHTSCHHHHTTSB
T ss_pred             HHHHHHhCCCcEEEEcC---CCCEEEEcHHHHHHhCCCHHHhcCcc
Confidence            67789999999999999   99999999999999999999999973

>2w0n_A Sensor protein DCUS; signal transduction, two-component regulatory system, PAS, kinase, membrane, transferase, solid state cell inner membrane; NMR {Escherichia coli}

Probab=97.97  E-value=2.3e-06  Score=58.65  Aligned_cols=42  Identities=24%  Similarity=0.158  Sum_probs=39.0

Q ss_pred             HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCC---ChHhHhhc
Q 022961          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGA---QIFTKITR  287 (289)
Q Consensus       243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGy---s~~E~~G~  287 (289)
                      +...++.++++|++.|.   +|+|+++|++|++++||   +.++++|+
T Consensus        17 ~~~il~~~~~~i~~~d~---~g~i~~~N~~~~~~~g~~~~~~~~~~g~   61 (118)
T 2w0n_A           17 RQAMLQSIKEGVVAVDD---RGEVTLINDAAQELLNYRKSQDDEKLST   61 (118)
T ss_dssp             HHHHHHCCCCCCEEEBT---TTBCCCBCHHHHHHHCSCTTTTTSSCCC
T ss_pred             HHHHHhhccccEEEECC---CCcEeehhHHHHHHhCCCccChhhhhcc
Confidence            56788999999999999   99999999999999998   88999886

>2l0w_A Potassium voltage-gated channel, subfamily H (EAG member 2, isoform CRA_B; HERG, PAS domain, voltage-gated potassium channel, membrane; NMR {Homo sapiens} PDB: 2l1m_A 2l4r_A

Probab=97.96  E-value=8.7e-06  Score=56.99  Aligned_cols=46  Identities=15%  Similarity=0.363  Sum_probs=39.9

Q ss_pred             HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      +...++.++++++++|...++++|+++|++|++++||+.++++|+.
T Consensus        21 ~~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~g~~~~~~~g~~   66 (138)
T 2l0w_A           21 IIRKFEGQSRKFIIANARVENCAVIYCNDGFCELCGYSRAEVMQRP   66 (138)
T ss_dssp             HHHHHTTTTSEEEEEESSSTTCBEEEECSHHHHHHSCCHHHHTTSB
T ss_pred             HHHHHhcCCCCEEEEecCCCCCEEEEeCHHHHHHhCCCHHHHcCCC
Confidence            4556677999999999755579999999999999999999999973

>3eeh_A Putative light and redox sensing histidine kinase; structural genomic MCSG, protein structure initiative, midwest center for STRU genomics; HET: PG5; 1.95A {Haloarcula marismortui}

Probab=97.92  E-value=1.1e-05  Score=55.46  Aligned_cols=42  Identities=7%  Similarity=0.024  Sum_probs=39.5

Q ss_pred             HHHHhhcccccEEEeCCCCCC-CCEEEecHHHHHhhCCChHhHhhc
Q 022961          243 LYISLGRIKQSFVLIDPHLPD-MPMVYASDAFLKLTGAQIFTKITR  287 (289)
Q Consensus       243 ~~~~~e~~~~~i~i~d~~~~~-~~i~~vN~~f~~~tGys~~E~~G~  287 (289)
                      +...++.+++++++.|.   + ++|+++|++|++++||+.++++|+
T Consensus        13 ~~~~~~~~~~~i~~~d~---~~~~i~~~n~~~~~~~g~~~~~~~~~   55 (125)
T 3eeh_A           13 VRELTEATNDILWEFTA---DLSEVLVINSAYEDIWGRSVAKLREN   55 (125)
T ss_dssp             HHHHHSCCCCEEEEEET---TSSCEEEECTHHHHHHSSCHHHHHHC
T ss_pred             HHHHHhcCCceEEEEEc---CCCcEEEecHHHHHHHCCCHHHHccC
Confidence            67789999999999999   8 999999999999999999999886

>3sw1_A Sensory box protein; light-oxygen-voltage, LOV, PAS, signaling protein; HET: FMN; 2.63A {Pseudomonas putida}

Probab=97.88  E-value=8.2e-06  Score=59.54  Aligned_cols=43  Identities=19%  Similarity=0.190  Sum_probs=40.1

Q ss_pred             HHHHhhcccccEEEeCCCCCCC---CEEEecHHHHHhhCCChHhHhhcc
Q 022961          243 LYISLGRIKQSFVLIDPHLPDM---PMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       243 ~~~~~e~~~~~i~i~d~~~~~~---~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      +...++.++++++++|.   ++   +|+++|++|++++||+.++++|+.
T Consensus        27 ~~~i~~~~~~~i~~~d~---~~~~~~i~~~N~~~~~~~g~~~~~~~g~~   72 (162)
T 3sw1_A           27 LQSMVDASNDGIVVAEK---EGDDTILIYVNAAFEYLTGYSRDEILYQD   72 (162)
T ss_dssp             HHHHHHTCSSEEEEEEE---ETTEEEEEEECHHHHHHHTCCHHHHTTSB
T ss_pred             HHHHHhhccCcEEEEeC---CCCccEEEEECHHHHHHHCCCHHHHcCCC
Confidence            67789999999999999   99   999999999999999999999973

>3k3c_A Protein RV1364C/MT1410; sensor, PAS, signal transduction, fatty-acid binding, sigma regulator, signaling protein; HET: PLM; 1.62A {Mycobacterium tuberculosis} PDB: 3k3d_A

Probab=97.88  E-value=7.4e-06  Score=59.64  Aligned_cols=40  Identities=15%  Similarity=0.218  Sum_probs=37.4

Q ss_pred             HHHHhhcccccEEEeC-CCCCCCCEEEecHHHHHhhCCChHhHhhc
Q 022961          243 LYISLGRIKQSFVLID-PHLPDMPMVYASDAFLKLTGAQIFTKITR  287 (289)
Q Consensus       243 ~~~~~e~~~~~i~i~d-~~~~~~~i~~vN~~f~~~tGys~~E~~G~  287 (289)
                      +...++.++.++++.| .   +++|+++|++|++++||+  +++|+
T Consensus        19 ~~~~~~~~~~~i~~~d~~---~~~i~~~N~~~~~~~g~~--~~~G~   59 (158)
T 3k3c_A           19 VRRIFEHIPAILVGLEGP---DHRFVAVNAAYRGFSPLL--DTVGQ   59 (158)
T ss_dssp             HHHHHHHCSSEEEEEETT---TTEEEEECHHHHHHCTTC--CSTTS
T ss_pred             HHHHHhcCCceEEEEECC---CcEeHHHHHHHHHHcCCc--hhcCC
Confidence            6778999999999999 8   999999999999999999  88886

>1v9y_A Heme PAS sensor protein; signaling protein; HET: HEM; 1.32A {Escherichia coli} SCOP: d.110.3.2 PDB: 1v9z_A* 1vb6_A* 1s67_L* 1s66_L*

Probab=97.87  E-value=1.5e-05  Score=58.14  Aligned_cols=43  Identities=21%  Similarity=0.160  Sum_probs=40.1

Q ss_pred             HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      +...++.+++++++.|.   +++|+++|++|++++||+.++++|+.
T Consensus        42 ~~~~l~~~~~~i~~~d~---~g~i~~~N~~~~~l~g~~~~~~~g~~   84 (167)
T 1v9y_A           42 FFPALEQNMMGAVLINE---NDEVMFFNPAAEKLWGYKREEVIGNN   84 (167)
T ss_dssp             HHHHHHTCSSEEEEECT---TSBEEEECHHHHHHHSCCGGGTTTSB
T ss_pred             HHHHHHhCCCCEEEECC---CCcEEEECHHHHHHhCCCHHHHcCCC
Confidence            67789999999999999   99999999999999999999999873

>3kx0_X Uncharacterized protein RV1364C/MT1410; PAS domain, sensory domain, mycobacteium tuberculos molecule binding domain; 2.30A {Mycobacterium tuberculosis}

Probab=97.82  E-value=1e-05  Score=60.87  Aligned_cols=41  Identities=15%  Similarity=0.192  Sum_probs=37.9

Q ss_pred             HHHHhhcccccEEEeC-CCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          243 LYISLGRIKQSFVLID-PHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       243 ~~~~~e~~~~~i~i~d-~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      +...++.+++++++.| .   +++|+++|++|++++||+  +++|+-
T Consensus        39 l~~l~~~~~~~i~~~d~~---~g~i~~~N~a~~~l~G~~--~~~G~~   80 (185)
T 3kx0_X           39 VRRIFEHIPAILVGLEGP---DHRFVAVNAAYRGFSPLL--DTVGQP   80 (185)
T ss_dssp             HHHHHHHCSSEEEEEETT---TTEEEEECHHHHHHCCCC--SCTTSB
T ss_pred             HHHHHhcCCceEEEEECC---CcEEEEEcHHHHHHcCCc--cccCCc
Confidence            6778999999999999 8   999999999999999999  888873

>2ykf_A Pdtas, probable sensor histidine kinase pdtas; transferase, two-component system, GAF domain, PAS domain; 2.00A {Mycobacterium tuberculosis} PDB: 2ykh_A

Probab=97.00  E-value=2.9e-06  Score=69.42  Aligned_cols=39  Identities=26%  Similarity=0.165  Sum_probs=34.1

Q ss_pred             HHhhcccccEEEeCCCCCCCCEEEecHHHHHhh---CCChHhHhhc
Q 022961          245 ISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLT---GAQIFTKITR  287 (289)
Q Consensus       245 ~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~t---Gys~~E~~G~  287 (289)
                      ..++++.+||+++|.   +|+|+++|+++++++   |+. ++++|+
T Consensus       174 ~~~~~~~dGIivvD~---~G~Ii~~N~aA~~ll~~lG~~-~~~iGk  215 (305)
T 2ykf_A          174 RSSPRAGDGFIRLDV---DGVVSYASPNALSAYHRMGLT-TELEGV  215 (305)
Confidence            357888999999999   999999999999997   565 788886

>1oj5_A Steroid receptor coactivator 1A; transcriptional coactivator, complex, LXXLL motif, transcriptional regulation; 2.2A {Mus musculus} SCOP: d.110.3.8

Probab=97.77  E-value=3.8e-05  Score=53.35  Aligned_cols=100  Identities=11%  Similarity=0.091  Sum_probs=75.2

Q ss_pred             EEEEeCCCCCccEEEccHHHHHHhCCCc--cccCCCCCCCccCCCCCH--HHHHHHHHHHHhCCCeEEEEEEEecCCCEE
Q 022961           31 FTITDPSISGHPIVFASRGFLKMSGFSR--AEIIGRNGRMFQGPRTNR--RTIMEIREAIREERPIEVNLLNYKKDGTPF  106 (289)
Q Consensus        31 i~~~d~~~~~g~i~~~N~~~~~~~G~~~--~e~~g~~~~~l~~~~~~~--~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~  106 (289)
                      +.-.|.+   |+|+++..... ..+|.+  ++++|+++.+++++.+..  .......+++..|.....-++++.++|..+
T Consensus        10 ~sRh~~d---GKf~~vDq~~~-r~~~~~g~qdLlGrsiy~f~H~~D~~~s~l~~h~~~vl~~Gq~~S~~YRfr~k~g~~V   85 (132)
T 1oj5_A           10 MTKQDTT---GKIISIDTSSL-RAAGRTGWEDLVRKCIYAFFQPQGREPSYARQLFQEVMTRGTASSPSYRFILNDGTML   85 (132)
T ss_dssp             EEEECTT---CCEEEEECHHH-HTTCCSCHHHHHHHHHHHHTSCBTTBCCHHHHHHHHHHHHSEEECCCEEEECTTSCEE
T ss_pred             EEeecCC---CcEEEEecccc-cccccccHHHHHHHHHHHHhCcccchHHHHHHHHHHHHHcCCccccceEEEecCCcEE
Confidence            3445777   99999999887 477888  899999999999988854  677777788877776667789999999999


Q ss_pred             EEEEEEEEeecCCCCcEEEEEEEEeccc
Q 022961          107 WMLFKMSLVFGKEDGRATHFVAVQVPIV  134 (289)
Q Consensus       107 ~~~~~~~~~~~~~~g~~~~~~~~~~DIT  134 (289)
                      |+......+.+|-...+..++++-.=+.
T Consensus        86 ~~qT~sk~f~np~t~e~e~Ivs~n~v~r  113 (132)
T 1oj5_A           86 SAHTRCKLCYPQSPDMQPFIMGIHIIDR  113 (132)
T ss_dssp             EEEEEEEEECC----CCCEEEEEEEEEC
T ss_pred             EEEEEEEEecCCCCCCCCEEEEEEEEEc
Confidence            9998888887633445555555544333

>2v0u_A NPH1-1, LOV2; kinase, transferase, ATP-binding, serine/threonine-protein kinase, light-induced signal trans phototropin1, nucleotide-binding; HET: FMN; 1.40A {Avena sativa} PDB: 2v0w_A* 2v1b_A* 2v1a_A* 1jnu_A* 1g28_A*

Probab=97.75  E-value=3.5e-05  Score=54.26  Aligned_cols=44  Identities=43%  Similarity=0.727  Sum_probs=38.5

Q ss_pred             HHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          245 ISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       245 ~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      ..++.+++++++.|...++++|+++|++|++++||+.++++|+.
T Consensus         6 ~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~~~~~g~~   49 (146)
T 2v0u_A            6 TTLERIEKNFVITDPRLPDNPIIFASDSFLQLTEYSREEILGRN   49 (146)
T ss_dssp             CTGGGSSSCEEEECTTSTTCCEEEECHHHHHHHCCCHHHHTTSC
T ss_pred             HHHhcCCCcEEEEcCCCCCceEEEEcHHHHHHHCcCHHHHcCCC
Confidence            45788899999999744578999999999999999999999873

>2qkp_A Uncharacterized protein; structural genomics, unknown function, PSI-2, protein struct initiative; 1.75A {Streptococcus mutans}

Probab=97.66  E-value=1.8e-05  Score=57.69  Aligned_cols=42  Identities=12%  Similarity=0.156  Sum_probs=38.6

Q ss_pred             HHHHhhcccccEEEeCCCCCCCCEEEecHH---HHHhhCCChHhHhhcc
Q 022961          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDA---FLKLTGAQIFTKITRI  288 (289)
Q Consensus       243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~---f~~~tGys~~E~~G~~  288 (289)
                      +...++.++++|+++|.   +|+|+|+|++   +++++| ..++++||-
T Consensus        21 l~~IL~~~~~gI~~vD~---~g~I~~~N~a~~~~~~i~g-~~~~~iGr~   65 (151)
T 2qkp_A           21 ANLILNHLPLEITFVNK---DDIFQYYNDSVPAAEMVFK-RTPSQVGRN   65 (151)
T ss_dssp             HHHHHHHSSSEEEEEET---TSBEEEECCCSCGGGCSSC-CCGGGTTSB
T ss_pred             HHHHHHhCCCceEEEcC---CCeEEEEeCCCchhhhhcC-CCHHHcCCC
Confidence            67789999999999999   9999999999   999999 567899984

>3nja_A Probable ggdef family protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; 2.37A {Chromobacterium violaceum}

Probab=97.61  E-value=2.9e-05  Score=53.40  Aligned_cols=41  Identities=12%  Similarity=-0.065  Sum_probs=31.9

Q ss_pred             HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhh
Q 022961          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKIT  286 (289)
Q Consensus       243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G  286 (289)
                      +..+++.++.++++.|.   ++.++++|++|++++||+.++++|
T Consensus         9 l~~~~~~~~~~i~~~d~---~~~~~~~n~~~~~~~G~~~~~~~~   49 (125)
T 3nja_A            9 LHTAESDAGIGSWVLHM---ESGRLEWSQAVHDIFGTDSATFDA   49 (125)
T ss_dssp             --------CCEEEEEET---TTTEEEECHHHHHHHTCCTTTCCC
T ss_pred             HHHHHHhCCeeEEEEEc---CCCcEEECHHHHHHhCCCcccccc
Confidence            55678889999999999   999999999999999999999887

>3icy_A Sensor protein; sensory box histidine kinase/response regulator domain, kinase, chlorobium tepidum TLS, PSI-2; 2.68A {Chlorobaculum tepidum}

Probab=97.57  E-value=1.5e-05  Score=54.53  Aligned_cols=42  Identities=12%  Similarity=-0.116  Sum_probs=38.7

Q ss_pred             HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhc
Q 022961          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITR  287 (289)
Q Consensus       243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~  287 (289)
                      +...++.+++++++.|.   +++++++|+++++++||+.+|++|+
T Consensus         6 ~~~l~~~~~~~i~~~d~---~~~~~~~n~~~~~~~G~~~~~~~~~   47 (118)
T 3icy_A            6 LQALVDNIPAAIYHLDV---SGQATIRFRPPAFLKTLVSEHAGTT   47 (118)
T ss_dssp             HHHHHTTCCCCCEEECT---TSCEEECCCCCGGGGGGEEEETTEE
T ss_pred             HHHHHhcCCceEEEEEc---CCCceEEechhHhhcCCCHHHccCC
Confidence            56788999999999999   9999999999999999999998775

>3h9w_A Diguanylate cyclase with PAS/PAC sensor; alpha-beta protein., structural genomics, PSI-2, protein STR initiative; 1.90A {Marinobacter aquaeolei}

Probab=97.23  E-value=0.00016  Score=49.37  Aligned_cols=34  Identities=18%  Similarity=-0.016  Sum_probs=29.1

Q ss_pred             cccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhh
Q 022961          251 KQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKIT  286 (289)
Q Consensus       251 ~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G  286 (289)
                      +++++..|.  ++++++|+|+++++++||+.+|++|
T Consensus         3 ~~giw~~d~--~~~~~~~~n~~~~~l~G~~~~e~~~   36 (115)
T 3h9w_A            3 KAIPWKINW--QTMAFEYIGPQIEALLGWPQGSWKS   36 (115)
T ss_dssp             CCEEEEEET--TTTEEEEECTHHHHHHCSCGGGCCB
T ss_pred             ceEEEEEEc--CCCcEEEEChhHHHHhCCChHHccC
Confidence            567888883  2778999999999999999999876

>3mr0_A Sensory box histidine kinase/response regulator; PAS fold, structural genomics, PSI-2; HET: PG5; 1.49A {Burkholderia thailandensis}

Probab=97.12  E-value=0.00039  Score=49.52  Aligned_cols=42  Identities=14%  Similarity=0.184  Sum_probs=38.1

Q ss_pred             HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhc
Q 022961          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITR  287 (289)
Q Consensus       243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~  287 (289)
                      +..+++.++.+++..|+   ++.++++|++|.+++||+.+++.|.
T Consensus        11 l~~~~~~~~~g~w~~d~---~~~~~~~s~~~~~~~G~~~~~~~~~   52 (142)
T 3mr0_A           11 FQLAVSGASAGLWDWNP---KTGAMYLSPHFKKIMGYEDHELPDE   52 (142)
T ss_dssp             HHHHHHHTTCEEEEECT---TTCCEEECHHHHHHTTCCGGGSCSE
T ss_pred             HHHHHHhCCcEEEEEEc---CCCeEEECHHHHHHhCCCccccCCC
Confidence            67788899999999999   9999999999999999999987764

>3cax_A Uncharacterized protein PF0695; structural genomics, unknown function, PSI-2, protein struct initiative; 2.43A {Pyrococcus furiosus dsm 3638}

Probab=96.94  E-value=0.00032  Score=58.94  Aligned_cols=42  Identities=14%  Similarity=0.149  Sum_probs=39.2

Q ss_pred             hHHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       242 ~~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      .+..+++.+++||+++|.   +|+|+++|++ ++++ |+.++++||-
T Consensus       240 ~l~~IL~~l~dgIivvD~---~g~I~~~N~a-e~i~-~~~~e~iGr~  281 (369)
T 3cax_A          240 ELKAIFEALPVDVTFIDK---DDRVRFFSPG-ERIF-TRTPSVLGRP  281 (369)
T ss_dssp             HHHHHHHHSSSEEEEECT---TSBEEEECCS-SCSS-CCCGGGTTCB
T ss_pred             HHHHHHHhCCCcEEEECC---CCcEEEEcCH-HHcc-CChHHHcCCc
Confidence            377889999999999999   9999999999 9999 9999999983

>2ool_A Sensor protein; bacteriophytochrome, photoconversion, photoreceptor, biliver signaling protein; HET: LBV; 2.20A {Rhodopseudomonas palustris} SCOP: d.110.2.1 d.110.3.9

Probab=91.83  E-value=0.17  Score=41.56  Aligned_cols=40  Identities=8%  Similarity=0.015  Sum_probs=33.2

Q ss_pred             EEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCC
Q 022961           31 FTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGP   72 (289)
Q Consensus        31 i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~   72 (289)
                      +++++.+  +++|+.+|..+.+++|+++++++|++...++++
T Consensus        45 Ll~~~~~--~~~i~~~S~N~~~~lg~~~~~llG~~l~~ll~~   84 (337)
T 2ool_A           45 LFVVSET--DLRIASVSANVEDLLRQPPASLLNVPIAHYLTA   84 (337)
T ss_dssp             EEEECTT--TCBEEEEETTHHHHHSSCGGGGTTCBGGGGBCH
T ss_pred             EEEEECC--CCEEEEEehhHHHHHCcCHHHHcCCCHHHHcCH
Confidence            3445532  389999999999999999999999998888765

>4ew7_A Conjugative transfer: regulation; alpha-beta-alpha structure, structural genomics, midwest CEN structural genomics (MCSG), PSI-biology; 1.67A {Salmonella enterica subsp}

Probab=89.42  E-value=3.1  Score=27.12  Aligned_cols=92  Identities=10%  Similarity=0.141  Sum_probs=53.4

Q ss_pred             HHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHH-HHHHhCCCeEEEE
Q 022961           18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIR-EAIREERPIEVNL   96 (289)
Q Consensus        18 ~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~-~~~~~~~~~~~e~   96 (289)
                      --.+.+..++|..+.+-+..   ..|+|+|.+|.+||--....+-|.+.....    -+.....+. +...-|.... -.
T Consensus        20 L~iq~iY~nSPVpVCVRNq~---RkilYaN~aF~elF~Ked~~~sg~S~~~~~----vE~~LS~LELeCqsLGhG~a-f~   91 (127)
T 4ew7_A           20 LSIQDIYKNSPVPVCVRNQS---RKIIYANGAFIELFSKEDQPLSGDSYNRYG----VEVFLSSLELECQSLGHGAA-FC   91 (127)
T ss_dssp             HHHHHHHTTCSSCEEEECTT---SCEEEECHHHHHHTTSCCCGGGCTTSSHHH----HHHHHHHHHHHHHHHCTTCE-EE
T ss_pred             HhHHhhhcCCCccEEEeccc---ceEEEecchHHHHhhcccCcccCcccceee----ehhhHHHHHHHHHhhcCCce-EE
Confidence            34577899999999999999   999999999999975444333333322110    011111121 1122233322 23


Q ss_pred             EEEecCCCEEEEEEEEEEeec
Q 022961           97 LNYKKDGTPFWMLFKMSLVFG  117 (289)
Q Consensus        97 ~~~~~~g~~~~~~~~~~~~~~  117 (289)
                      +...-.|..+.+++....+.+
T Consensus        92 r~Fn~~~e~yQIRmE~iSf~~  112 (127)
T 4ew7_A           92 RRFNFHGEIYQIRMENISFDN  112 (127)
T ss_dssp             EEEEETTEEEEEEEEEEECTT
T ss_pred             EEeecCCceEEEEEEEeeecC
Confidence            344566777776666555543

>2ool_A Sensor protein; bacteriophytochrome, photoconversion, photoreceptor, biliver signaling protein; HET: LBV; 2.20A {Rhodopseudomonas palustris} SCOP: d.110.2.1 d.110.3.9

Probab=86.64  E-value=0.48  Score=38.92  Aligned_cols=25  Identities=12%  Similarity=0.054  Sum_probs=24.0

Q ss_pred             CCCEEEecHHHHHhhCCChHhHhhc
Q 022961          263 DMPMVYASDAFLKLTGAQIFTKITR  287 (289)
Q Consensus       263 ~~~i~~vN~~f~~~tGys~~E~~G~  287 (289)
                      +++|+++|..+.+++|++.++++|+
T Consensus        52 ~~~i~~~S~N~~~~lg~~~~~llG~   76 (337)
T 2ool_A           52 DLRIASVSANVEDLLRQPPASLLNV   76 (337)
T ss_dssp             TCBEEEEETTHHHHHSSCGGGGTTC
T ss_pred             CCEEEEEehhHHHHHCcCHHHHcCC
Confidence            6899999999999999999999997

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	289
d1n9la_	109	d.110.3.6 (A:) Putative blue light receptor, phot-	4e-18
d1n9la_	109	d.110.3.6 (A:) Putative blue light receptor, phot-	3e-06
d1jnua_	104	d.110.3.6 (A:) Photoreceptor phy3 flavin-binding d	7e-16
d1jnua_	104	d.110.3.6 (A:) Photoreceptor phy3 flavin-binding d	3e-06
d1bywa_	110	d.110.3.6 (A:) Erg potassium channel, N-terminal d	4e-10
d1bywa_	110	d.110.3.6 (A:) Erg potassium channel, N-terminal d	6e-06
d1mzua_	110	d.110.3.1 (A:) PYP domain of sensor histidine kina	4e-04
d1p97a_	114	d.110.3.7 (A:) Hypoxia-inducible factor Hif2a, C-t	0.002

>d1n9la_ d.110.3.6 (A:) Putative blue light receptor, phot-lov1 domain {Green algae (Chlamydomonas reinhardtii) [TaxId: 3055]} Length = 109

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Flavin-binding PAS domain
domain: Putative blue light receptor, phot-lov1 domain
species: Green algae (Chlamydomonas reinhardtii) [TaxId: 3055]

 Score = 76.1 bits (186), Expect = 4e-18
 Identities = 43/107 (40%), Positives = 66/107 (61%), Gaps = 1/107 (0%)

Query: 27  LPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAI 86
           L  +F + D ++   P+V+AS GF  M+G+   E++G N R  QG  T+ + + +IR+AI
Sbjct: 2   LRHTFVVADATLPDCPLVYASEGFYAMTGYGPDEVLGHNCRFLQGEGTDPKEVQKIRDAI 61

Query: 87  REERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPI 133
           ++     V LLNY+KDGTPFW L  ++ +    DGR + FV VQV +
Sbjct: 62  KKGEACSVRLLNYRKDGTPFWNLLTVTPIKT-PDGRVSKFVGVQVDV 107

>d1n9la_ d.110.3.6 (A:) Putative blue light receptor, phot-lov1 domain {Green algae (Chlamydomonas reinhardtii) [TaxId: 3055]} Length = 109

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Flavin-binding PAS domain
domain: Putative blue light receptor, phot-lov1 domain
species: Green algae (Chlamydomonas reinhardtii) [TaxId: 3055]

 Score = 42.9 bits (100), Expect = 3e-06
 Identities = 14/29 (48%), Positives = 21/29 (72%)

Query: 250 IKQSFVLIDPHLPDMPMVYASDAFLKLTG 278
           ++ +FV+ D  LPD P+VYAS+ F  +TG
Sbjct: 2   LRHTFVVADATLPDCPLVYASEGFYAMTG 30

>d1jnua_ d.110.3.6 (A:) Photoreceptor phy3 flavin-binding domain, lov2 {Maidenhair fern (Adiantum capillus-veneris) [TaxId: 13818]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Flavin-binding PAS domain
domain: Photoreceptor phy3 flavin-binding domain, lov2
species: Maidenhair fern (Adiantum capillus-veneris) [TaxId: 13818]

 Score = 70.0 bits (170), Expect = 7e-16
 Identities = 42/104 (40%), Positives = 68/104 (65%), Gaps = 1/104 (0%)

Query: 30  SFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREE 89
           SF ITDP +  +PI+FAS  FL+++ ++R E++G N R  QG  T+R+ +  IR+A++E+
Sbjct: 2   SFVITDPRLPDNPIIFASDRFLELTEYTREEVLGNNCRFLQGRGTDRKAVQLIRDAVKEQ 61

Query: 90  RPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPI 133
           R + V +LNY K G  FW LF + ++   E+G   +F+ VQ  +
Sbjct: 62  RDVTVQVLNYTKGGRAFWNLFHLQVMRD-ENGDVQYFIGVQQEM 104

>d1jnua_ d.110.3.6 (A:) Photoreceptor phy3 flavin-binding domain, lov2 {Maidenhair fern (Adiantum capillus-veneris) [TaxId: 13818]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Flavin-binding PAS domain
domain: Photoreceptor phy3 flavin-binding domain, lov2
species: Maidenhair fern (Adiantum capillus-veneris) [TaxId: 13818]

 Score = 43.0 bits (100), Expect = 3e-06
 Identities = 16/27 (59%), Positives = 22/27 (81%)

Query: 252 QSFVLIDPHLPDMPMVYASDAFLKLTG 278
           +SFV+ DP LPD P+++ASD FL+LT 
Sbjct: 1   KSFVITDPRLPDNPIIFASDRFLELTE 27

>d1bywa_ d.110.3.6 (A:) Erg potassium channel, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 110

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Flavin-binding PAS domain
domain: Erg potassium channel, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.9 bits (128), Expect = 4e-10
 Identities = 19/108 (17%), Positives = 39/108 (36%), Gaps = 1/108 (0%)

Query: 30  SFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREE 89
            F I +  +    +++ + GF ++ G+SRAE++ R            +     + A    
Sbjct: 3   KFIIANARVENCAVIYCNDGFCELCGYSRAEVMQRPCTCDFLHGPCTQRRAAAQIAQALL 62

Query: 90  RPIEVNLLNYKKDGTPFWMLFKMSLVFGK-EDGRATHFVAVQVPIVSR 136
              E  +            L  + +V  K EDG    F+     ++ +
Sbjct: 63  GAEERKVEIAFYRKDGSCFLCLVDVVPVKNEDGAVIMFILNFEVVMEK 110

>d1bywa_ d.110.3.6 (A:) Erg potassium channel, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 110

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Flavin-binding PAS domain
domain: Erg potassium channel, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.4 bits (98), Expect = 6e-06
 Identities = 6/27 (22%), Positives = 16/27 (59%)

Query: 252 QSFVLIDPHLPDMPMVYASDAFLKLTG 278
           + F++ +  + +  ++Y +D F +L G
Sbjct: 2   RKFIIANARVENCAVIYCNDGFCELCG 28

>d1mzua_ d.110.3.1 (A:) PYP domain of sensor histidine kinase Ppr {Rhodospirillum centenum [TaxId: 34018]} Length = 110

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: PYP-like
domain: PYP domain of sensor histidine kinase Ppr
species: Rhodospirillum centenum [TaxId: 34018]

 Score = 37.0 bits (85), Expect = 4e-04
 Identities = 20/107 (18%), Positives = 30/107 (28%), Gaps = 6/107 (5%)

Query: 23  ALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIME- 81
             D LP      D S     I   +R   ++SG     +IGRN      P TN       
Sbjct: 8   EFDALPVGAIQVDGS---GVIHRYNRTESRLSGRIPERVIGRNFFTEVAPCTNIPAFSGR 64

Query: 82  IREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVA 128
             + +            +     P     ++ +       R   FV 
Sbjct: 65  FMDGVTSGTLDARFDFVFDFQMAPVR--VQIRMQNAGVPDRYWIFVR 109

>d1p97a_ d.110.3.7 (A:) Hypoxia-inducible factor Hif2a, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Hypoxia-inducible factor Hif2a, C-terminal domain
domain: Hypoxia-inducible factor Hif2a, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.0 bits (79), Expect = 0.002
 Identities = 13/115 (11%), Positives = 41/115 (35%), Gaps = 4/115 (3%)

Query: 23  ALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEI 82
           A+D    +F ++  S+      +      ++ G+   E++GR+   F     +       
Sbjct: 2   AMDS--KTF-LSRHSMDMK-FTYCDDRITELIGYHPEELLGRSAYEFYHALDSENMTKSH 57

Query: 83  REAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRK 137
           +    + + +        K G   W+  + ++++   + +    + V   +   +
Sbjct: 58  QNLCTKGQVVSGQYRMLAKHGGYVWLETQGTVIYNPRNLQPQCIMCVNYVLSEIE 112

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	289
d1n9la_	109	Putative blue light receptor, phot-lov1 domain {Gr	99.87
d1bywa_	110	Erg potassium channel, N-terminal domain {Human (H	99.8
d1jnua_	104	Photoreceptor phy3 flavin-binding domain, lov2 {Ma	99.8
d1ew0a_	130	Histidine kinase FixL heme domain {Rhizobium melil	99.79
d1p97a_	114	Hypoxia-inducible factor Hif2a, C-terminal domain	99.71
d1v9ya_	113	Direct oxygen sensor protein, DOS {Escherichia col	99.64
d1xj3a1	106	Histidine kinase FixL heme domain {Bradyrhizobium	99.63
d1nwza_	125	Photoactive yellow protein, PYP {Ectothiorhodospir	99.56
d1mzua_	110	PYP domain of sensor histidine kinase Ppr {Rhodosp	99.5
d1ll8a_	114	N-terminal PAS domain of Pas kinase {Human (Homo s	99.37
d1n9la_	109	Putative blue light receptor, phot-lov1 domain {Gr	99.23
d1oj5a_	109	PAS domain of steroid receptor coactivator 1A, NCo	99.14
d1jnua_	104	Photoreceptor phy3 flavin-binding domain, lov2 {Ma	99.13
d1v9ya_	113	Direct oxygen sensor protein, DOS {Escherichia col	98.97
d1mzua_	110	PYP domain of sensor histidine kinase Ppr {Rhodosp	98.94
d1bywa_	110	Erg potassium channel, N-terminal domain {Human (H	98.81
d1ew0a_	130	Histidine kinase FixL heme domain {Rhizobium melil	98.8
d1nwza_	125	Photoactive yellow protein, PYP {Ectothiorhodospir	98.74
d1ll8a_	114	N-terminal PAS domain of Pas kinase {Human (Homo s	98.44
d1p97a_	114	Hypoxia-inducible factor Hif2a, C-terminal domain	98.02
d2oola2	114	Sensor protein PhyB2 {Rhodopseudomonas palustris [	97.27
d1oj5a_	109	PAS domain of steroid receptor coactivator 1A, NCo	97.14
d2oola2	114	Sensor protein PhyB2 {Rhodopseudomonas palustris [	95.32
d2veaa3	127	Phytochrome-like protein Cph1 {Synechocystis sp. p	94.85
d2o9ca2	127	Bacteriophytochrome BphP {Deinococcus radiodurans	92.14
d2o9ca2	127	Bacteriophytochrome BphP {Deinococcus radiodurans	85.56
d3c2wa3	113	Bacteriophytochrome BphP {Pseudomonas aeruginosa [	82.35

>d1n9la_ d.110.3.6 (A:) Putative blue light receptor, phot-lov1 domain {Green algae (Chlamydomonas reinhardtii) [TaxId: 3055]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Flavin-binding PAS domain
domain: Putative blue light receptor, phot-lov1 domain
species: Green algae (Chlamydomonas reinhardtii) [TaxId: 3055]

Probab=99.87  E-value=5e-21  Score=131.94  Aligned_cols=108  Identities=41%  Similarity=0.805  Sum_probs=99.4

Q ss_pred             CCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEEEEEEecCCCEE
Q 022961           27 LPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPF  106 (289)
Q Consensus        27 ~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~  106 (289)
                      ++++++++|...++|+|+|+|++|++++||+++|++|+++..+.++...+.....+...+..+..+..++..+++||+.+
T Consensus         2 i~~~~vi~Da~~pdg~Ii~vN~a~~~~~Gy~~~El~G~~~~~l~~~~~~~~~~~~~~~~l~~~~~~~~e~~~~~kdG~~~   81 (109)
T d1n9la_           2 LRHTFVVADATLPDCPLVYASEGFYAMTGYGPDEVLGHNCRFLQGEGTDPKEVQKIRDAIKKGEACSVRLLNYRKDGTPF   81 (109)
T ss_dssp             CSCEEEEEETTSTTCCEEEECHHHHHHHCCCHHHHTTSCGGGGCCTTCCHHHHHHHHHHHHHTCCEEEEEEEECTTSCEE
T ss_pred             ccceEEEEeCCCCCCeEEEEcHHHHHHHCcCHHHHcCCcceeeecccCCHHHhhhhhhHhhcCCceeeeEEEEecCCeEE
Confidence            46889999965455999999999999999999999999998888888888888889999999999999999999999999


Q ss_pred             EEEEEEEEeecCCCCcEEEEEEEEecccc
Q 022961          107 WMLFKMSLVFGKEDGRATHFVAVQVPIVS  135 (289)
Q Consensus       107 ~~~~~~~~~~~~~~g~~~~~~~~~~DITe  135 (289)
                      |+.+++.|+++ ++|.+.+++++.+|||.
T Consensus        82 w~~~~~~pi~d-~~G~v~~~v~~~~DITa  109 (109)
T d1n9la_          82 WNLLTVTPIKT-PDGRVSKFVGVQVDVTS  109 (109)
T ss_dssp             EEEEEEEEEEC-TTSCEEEEEEEEEECCC
T ss_pred             EEEEEEEEEEC-CCCCEEEEEEEEEECCC
Confidence            99999999999 89999999999999994

>d1bywa_ d.110.3.6 (A:) Erg potassium channel, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Flavin-binding PAS domain
domain: Erg potassium channel, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=9.3e-19  Score=120.60  Aligned_cols=106  Identities=27%  Similarity=0.519  Sum_probs=93.3

Q ss_pred             EEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCC--ccCCCCCHHHHHHHHHHHHhCCCeEEEEEEEecCCCEEE
Q 022961           30 SFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRM--FQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFW  107 (289)
Q Consensus        30 ~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~--l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~~  107 (289)
                      .++++|.+.+|..|+|+|++|++++||++++++|+++..  +.+++..+.....+...+..+..+..+++.++++|+.+|
T Consensus         3 ~f~i~~~~~~d~~I~~~N~a~~~l~G~~~~eiiG~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~e~~~~~~~g~~~w   82 (110)
T d1bywa_           3 KFIIANARVENCAVIYCNDGFCELCGYSRAEVMQRPCTCDFLHGPCTQRRAAAQIAQALLGAEERKVEIAFYRKDGSCFL   82 (110)
T ss_dssp             EEEEEETTSSSCBEEEECHHHHHHHTCCHHHHTTSBTTCGGGCCTTCCHHHHHHHHHHHHTTCCEEEEEEEECTTSCEEE
T ss_pred             eEEEEcCCCCCCEEEEEcHHHHHHhCCCHHHhcccCcccccceeeheecccccccchhhcccccccceeeeeecccceee
Confidence            356778654558899999999999999999999998654  335666777888888999999999999999999999999


Q ss_pred             EEEEEEEeecCCCCcEEEEEEEEeccccc
Q 022961          108 MLFKMSLVFGKEDGRATHFVAVQVPIVSR  136 (289)
Q Consensus       108 ~~~~~~~~~~~~~g~~~~~~~~~~DITe~  136 (289)
                      +.+++.|+.+ ++|.+.+++++++|||+|
T Consensus        83 ~~~~~~pi~d-~~G~v~~~i~~~~DITer  110 (110)
T d1bywa_          83 CLVDVVPVKN-EDGAVIMFILNFEVVMEK  110 (110)
T ss_dssp             EEEEEEEEEC-TTCCEEEEEEEEEEEEEC
T ss_pred             eeeeEEEEEC-CCCCEEEEEEEEEECCCC
Confidence            9999999999 899999999999999986

>d1jnua_ d.110.3.6 (A:) Photoreceptor phy3 flavin-binding domain, lov2 {Maidenhair fern (Adiantum capillus-veneris) [TaxId: 13818]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Flavin-binding PAS domain
domain: Photoreceptor phy3 flavin-binding domain, lov2
species: Maidenhair fern (Adiantum capillus-veneris) [TaxId: 13818]

Probab=99.80  E-value=7.9e-19  Score=119.70  Aligned_cols=103  Identities=41%  Similarity=0.824  Sum_probs=95.4

Q ss_pred             EEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEEEEEEecCCCEEEEE
Q 022961           30 SFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWML  109 (289)
Q Consensus        30 ~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~~~~  109 (289)
                      .++++|+..++|+|+|+|++|++++||++++++|+++..+.++...+.....+...+..+..+..+++.++++|+.+|+.
T Consensus         2 ~fvi~d~~~pd~~I~y~N~a~~~~~G~s~~e~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg~~~~~~   81 (104)
T d1jnua_           2 SFVITDPRLPDNPIIFASDRFLELTEYTREEVLGNNCRFLQGRGTDRKAVQLIRDAVKEQRDVTVQVLNYTKGGRAFWNL   81 (104)
T ss_dssp             EEEEECTTSTTCCEEEECHHHHHHHTCCHHHHTTSCGGGGCCTTSCHHHHHHHHHHHHHTCCEEEEEEEECTTSCEEEEE
T ss_pred             eEEEEcCCCCCCEEEEEcHHHHHHHCcCHHHHCCccceeccccccchHHHhhhhhhhhcCceeEeEEEEEecccceEEEE
Confidence            36778865456999999999999999999999999998888888888899999999999999999999999999999999


Q ss_pred             EEEEEeecCCCCcEEEEEEEEecc
Q 022961          110 FKMSLVFGKEDGRATHFVAVQVPI  133 (289)
Q Consensus       110 ~~~~~~~~~~~g~~~~~~~~~~DI  133 (289)
                      +++.|+++ ++|++.+++++.+||
T Consensus        82 ~~~~pi~d-~~G~v~~~i~i~~DI  104 (104)
T d1jnua_          82 FHLQVMRD-ENGDVQYFIGVQQEM  104 (104)
T ss_dssp             EEEEEECT-TTSSCCEEEEEEEEC
T ss_pred             EEEEEEEC-CCCCEEEEEEEEEcC
Confidence            99999999 899999999999997

>d1ew0a_ d.110.3.2 (A:) Histidine kinase FixL heme domain {Rhizobium meliloti [TaxId: 382]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Heme-binding PAS domain
domain: Histidine kinase FixL heme domain
species: Rhizobium meliloti [TaxId: 382]

Probab=99.79  E-value=8.8e-19  Score=124.51  Aligned_cols=124  Identities=16%  Similarity=0.222  Sum_probs=102.4

Q ss_pred             ccchHHHhhchHHHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHH
Q 022961            4 QLGLIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIR   83 (289)
Q Consensus         4 ~l~~~~~~l~~~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~   83 (289)
                      ++.+.++.+. +++++++.++++++++++++|.+   |+|+++|+++++++||++++++|+++..+.++.........+.
T Consensus         3 ~l~~~e~~l~-~~e~~~~~i~~~~~~~i~~~d~~---g~i~~~N~~~~~l~Gy~~~el~g~~~~~~~~~~~~~~~~~~~~   78 (130)
T d1ew0a_           3 HMLETEDVVR-ARDAHLRSILDTVPDATVVSATD---GTIVSFNAAAVRQFGYAEEEVIGQNLRILMPEPYRHEHDGYLQ   78 (130)
T ss_dssp             HHHHHHHHHH-HHTSCHHHHHTTCSSEEEEEETT---SBEEEECHHHHHHHCCCHHHHTTSBGGGGSCTTTGGGHHHHHH
T ss_pred             hHHHHHHHHH-HHHHHHHHHHHcCCCeEEEEeCC---ccEEEEHHHHHHhhcCCHHHhcCCccccccccchhHHHHHHHH
Confidence            3455666666 77788999999999999999999   9999999999999999999999999888887776666666666


Q ss_pred             HHHHhCCC----eEEEEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEeccc
Q 022961           84 EAIREERP----IEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV  134 (289)
Q Consensus        84 ~~~~~~~~----~~~e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIT  134 (289)
                      ..+..+..    ...++...++||..+|+.+++.|+.+ +. . ..++++++|||
T Consensus        79 ~~~~~~~~~~~~~~~e~~~~~~dG~~~~v~~~~~~i~~-~~-~-~~~~~i~rDIT  130 (130)
T d1ew0a_          79 RYMATGEKRIIGIDRVVSGQRKDGSTFPMKLAVGEMRS-GG-E-RFFTGFIRDLT  130 (130)
T ss_dssp             HHHHHCCCSSTTSCEEEEEECTTSCEEEEEEEEEEEEE-TT-E-EEEEEEEEECC
T ss_pred             HHHHhCCCccccceeeEEEEcCCCCEEEEEEEEEEEEE-CC-e-EEEEEEEEECC
Confidence            66655433    45678888999999999999999987 33 3 34788999998

>d1p97a_ d.110.3.7 (A:) Hypoxia-inducible factor Hif2a, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Hypoxia-inducible factor Hif2a, C-terminal domain
domain: Hypoxia-inducible factor Hif2a, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=7.8e-18  Score=116.66  Aligned_cols=108  Identities=8%  Similarity=0.180  Sum_probs=92.3

Q ss_pred             CCEEEE--EeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEEEEEEecCCCE
Q 022961           28 PDSFTI--TDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTP  105 (289)
Q Consensus        28 ~~~i~~--~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~  105 (289)
                      ....++  .+.+   |+++|+|+++++++||++++++|+++..+.+|++.+.....+...+..+..+..+++++++||+.
T Consensus         4 d~~~fi~r~~~d---G~i~~~N~~~~~~~G~~~~el~g~~~~~~~~~ed~~~~~~~~~~~~~~~~~~~~e~~~~~kdG~~   80 (114)
T d1p97a_           4 DSKTFLSRHSMD---MKFTYCDDRITELIGYHPEELLGRSAYEFYHALDSENMTKSHQNLCTKGQVVSGQYRMLAKHGGY   80 (114)
T ss_dssp             CCEEEEEEECTT---TSCSEECTTHHHHTSSCHHHHTTSCHHHHSCSSSHHHHHHHHHHHTTTSEEEEEEEEEECTTSCE
T ss_pred             CcCEEEEEECCC---CcEEEECHHHHHHcCCCccccccccccccccccccccceeeeeecccccceeecceeeeeecCcc
Confidence            334444  5888   99999999999999999999999998888888877776666666666666678899999999999


Q ss_pred             EEEEEEEEEeecCCCCcEEEEEEEEecccccHH
Q 022961          106 FWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKH  138 (289)
Q Consensus       106 ~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~  138 (289)
                      +|+.++..|+.++.+|.+.+++++.+|||++|+
T Consensus        81 ~wv~~~~~~~~~~~~~~~~~ii~~~~dite~k~  113 (114)
T d1p97a_          81 VWLETQGTVIYNPRNLQPQCIMCVNYVLSEIEK  113 (114)
T ss_dssp             EEEEEEEEEEECTTTCSEEEEEEEEEEEEEEEC
T ss_pred             eEEEEEEEEEEeCCCCCEEEEEEEEEECChhhc
Confidence            999999999997236899999999999999986

>d1v9ya_ d.110.3.2 (A:) Direct oxygen sensor protein, DOS {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Heme-binding PAS domain
domain: Direct oxygen sensor protein, DOS
species: Escherichia coli [TaxId: 562]

Probab=99.64  E-value=1.6e-15  Score=104.34  Aligned_cols=107  Identities=22%  Similarity=0.276  Sum_probs=82.7

Q ss_pred             HHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhC----CCeEEE
Q 022961           20 VHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREE----RPIEVN   95 (289)
Q Consensus        20 l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~----~~~~~e   95 (289)
                      |..++++++++++++|.+   |+|+++|+++++++||++++++|++...+.++.........+.......    .....+
T Consensus         3 ~~~~~e~~~d~i~~~d~~---g~i~~~N~~~~~l~Gy~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e   79 (113)
T d1v9ya_           3 FFPALEQNMMGAVLINEN---DEVMFFNPAAEKLWGYKREEVIGNNIDMLIPRDLRPAHPEYIRHNREGGKARVEGMSRE   79 (113)
T ss_dssp             HHHHHHTCSSEEEEECTT---SBEEEECHHHHHHHSCCGGGTTTSBGGGGSCGGGTTTHHHHHHHHHC----------CE
T ss_pred             HHHHHHcCcCcEEEEeCC---CCEEEEchhHhhhhccchhhhcCcceeccccccccccccccccccccccccccccccee
Confidence            678999999999999999   9999999999999999999999999877776555444444434333222    234557


Q ss_pred             EEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEec
Q 022961           96 LLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVP  132 (289)
Q Consensus        96 ~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~D  132 (289)
                      ...++++|+.+|+.+++.|+.+ +.+  ..++++++|
T Consensus        80 ~~~~~~dG~~~~v~~~~~~i~~-~~~--~~~~~v~rD  113 (113)
T d1v9ya_          80 LQLEKKDGSKIWTRFALSKVSA-EGK--VYYLALVRD  113 (113)
T ss_dssp             EEEECTTSCEEEEEEEEEEEEE-TTE--EEEEEEEEC
T ss_pred             eeeccccceeEEEEEEEEEEEE-CCe--EEEEEEEEC
Confidence            7789999999999999999997 444  347788877

>d1xj3a1 d.110.3.2 (A:154-259) Histidine kinase FixL heme domain {Bradyrhizobium japonicum [TaxId: 375]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Heme-binding PAS domain
domain: Histidine kinase FixL heme domain
species: Bradyrhizobium japonicum [TaxId: 375]

Probab=99.63  E-value=9.4e-16  Score=104.29  Aligned_cols=102  Identities=19%  Similarity=0.193  Sum_probs=82.3

Q ss_pred             CEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCC----CeEEEEEEEecCCC
Q 022961           29 DSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREER----PIEVNLLNYKKDGT  104 (289)
Q Consensus        29 ~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~----~~~~e~~~~~~~g~  104 (289)
                      +||+++|.+   |+|+++|+++++++||+.++++|+++..+.++.........+........    ....+....+++|.
T Consensus         1 dgi~~~D~~---G~I~~~N~a~~~l~Gy~~~el~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg~   77 (106)
T d1xj3a1           1 DAMIVIDGH---GIIQLFSTAAERLFGWSELEAIGQNVNILMPEPDRSRHDSYISRYRTTSDPHIIGIGRIVTGKRRDGT   77 (106)
T ss_dssp             CCEEEEETT---SBEEEECHHHHHHHCCCHHHHTTSBGGGGSCTTHHHHHHHHHHHHHHHCCCSSTTTCEEEEEECTTSC
T ss_pred             CEEEEECCC---CcEEEEcHHHHHHhhhchHhhcCCCcccccccccccchhhhhhhhhhhcccccccccceeeeeeccce
Confidence            589999999   99999999999999999999999998888777655555544444444332    24567888999999


Q ss_pred             EEEEEEEEEEeecCCCCcEEEEEEEEeccccc
Q 022961          105 PFWMLFKMSLVFGKEDGRATHFVAVQVPIVSR  136 (289)
Q Consensus       105 ~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~  136 (289)
                      .+|+.+++.|+.+ +++  ..++++++||||.
T Consensus        78 ~~~v~~~~~~~~~-~~~--~~~~~~~~DITE~  106 (106)
T d1xj3a1          78 TFPMHLSIGEMQS-GGE--PYFTGFVRDLTEH  106 (106)
T ss_dssp             EEEEEEEEEEEEE-TTE--EEEEEEEEECHHH
T ss_pred             EEEEEEEEEEEEE-CCe--EEEEEEEEeCCCC
Confidence            9999999999987 443  4578999999973

>d1nwza_ d.110.3.1 (A:) Photoactive yellow protein, PYP {Ectothiorhodospira halophila [TaxId: 1053]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: PYP-like
domain: Photoactive yellow protein, PYP
species: Ectothiorhodospira halophila [TaxId: 1053]

Probab=99.56  E-value=1.6e-14  Score=101.21  Aligned_cols=109  Identities=14%  Similarity=0.082  Sum_probs=86.7

Q ss_pred             HHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCC-CCCHHHHHHHHHHHHhCCCeEEE
Q 022961           17 TLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGP-RTNRRTIMEIREAIREERPIEVN   95 (289)
Q Consensus        17 ~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~-~~~~~~~~~~~~~~~~~~~~~~e   95 (289)
                      .+++..+++++|+|++++|.+   |+|+++|+++++++||++++++|+++..++.| ...+.+...+.+.+..+.....+
T Consensus        16 ~~~~d~~ld~~p~gi~~lD~~---G~i~~~N~a~~~l~G~~~~e~iG~~~~~~~~p~~~~~~~~~~~~~~~~~g~~~~~~   92 (125)
T d1nwza_          16 AKMDDGQLDGLAFGAIQLDGD---GNILQYNAAEGDITGRDPKQVIGKNFFKDVAPCTDSPEFYGKFKEGVASGNLNTMF   92 (125)
T ss_dssp             TTCCHHHHTTCSSEEEEEETT---CBEEEECHHHHHHHCCCHHHHTTSBCCCCCCGGGCSTTTHHHHHHHHHHTCCEEEE
T ss_pred             HHHHHHHHhCCCccEEEEeCC---CCEEEEcHHHHHhhccchHhhcCCCHHHccCchhhhhheeeeceeeeecCCcceEE
Confidence            355678999999999999999   99999999999999999999999997655544 44455666778888888876666


Q ss_pred             EEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecc
Q 022961           96 LLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPI  133 (289)
Q Consensus        96 ~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DI  133 (289)
                      ....+++|+.+|+.+++.+..+   |.  .+..+++||
T Consensus        93 ~~~~~~~G~~~~v~v~l~~~~~---g~--~~~v~V~di  125 (125)
T d1nwza_          93 EYTFDYQMTPTKVKVHMKKALS---GD--SYWVFVKRV  125 (125)
T ss_dssp             EEEECTTSCCEEEEEEEEECSS---SS--EEEEEEEEC
T ss_pred             EEEeccCCcEEEEEEEEEEecC---CC--EEEEEEEEC
Confidence            5667899999999999888754   33  233456665

>d1mzua_ d.110.3.1 (A:) PYP domain of sensor histidine kinase Ppr {Rhodospirillum centenum [TaxId: 34018]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: PYP-like
domain: PYP domain of sensor histidine kinase Ppr
species: Rhodospirillum centenum [TaxId: 34018]

Probab=99.50  E-value=1.1e-13  Score=94.49  Aligned_cols=94  Identities=16%  Similarity=0.057  Sum_probs=76.2

Q ss_pred             HHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccC-CCCCHHHHHHHHHHHHhCCCeE-EEEE
Q 022961           20 VHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQG-PRTNRRTIMEIREAIREERPIE-VNLL   97 (289)
Q Consensus        20 l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~-~~~~~~~~~~~~~~~~~~~~~~-~e~~   97 (289)
                      +.++++++|++++++|.+   |+|+++|+++++|+||++++++|+++..++. +...+.+...+.+.+.++.... .++.
T Consensus         5 ~~A~ld~~p~gvi~~D~~---G~I~~~N~aa~~~~G~~~eellG~~~~~~~~p~~~~~~~~~~~~~~~~~g~~~~~~~~~   81 (110)
T d1mzua_           5 GTAEFDALPVGAIQVDGS---GVIHRYNRTESRLSGRIPERVIGRNFFTEVAPCTNIPAFSGRFMDGVTSGTLDARFDFV   81 (110)
T ss_dssp             -CTTGGGCSSEEEEEETT---CBEEEECHHHHHHHCCCHHHHTTSBCCCCCCGGGCSTTTHHHHHHHHHTSCCEEEEEEE
T ss_pred             HHHHHhCCCcEEEEEcCC---CCEEEeHHHHHHHHcCCHHHHcCCCHHHhcCChhhhHHHHHHHHHHHhccccCcceEEE
Confidence            456899999999999999   9999999999999999999999999755444 4445566777788888877543 4443


Q ss_pred             EEecCCCEEEEEEEEEEeec
Q 022961           98 NYKKDGTPFWMLFKMSLVFG  117 (289)
Q Consensus        98 ~~~~~g~~~~~~~~~~~~~~  117 (289)
                       .+++|..+++.++..+...
T Consensus        82 -l~~~G~~~~v~v~~~~~~~  100 (110)
T d1mzua_          82 -FDFQMAPVRVQIRMQNAGV  100 (110)
T ss_dssp             -EECSSCEEEEEEEEEECSS
T ss_pred             -EecCCceEEEEEEEEEecC
Confidence             5789999999999888754

>d1ll8a_ d.110.3.5 (A:) N-terminal PAS domain of Pas kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: N-terminal PAS domain of Pas kinase
domain: N-terminal PAS domain of Pas kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.37  E-value=2.2e-13  Score=93.73  Aligned_cols=104  Identities=15%  Similarity=0.141  Sum_probs=81.3

Q ss_pred             hhCCCEEEEEeC-CCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCC----CeEEEEEEE
Q 022961           25 DELPDSFTITDP-SISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREER----PIEVNLLNY   99 (289)
Q Consensus        25 ~~~~~~i~~~d~-~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~----~~~~e~~~~   99 (289)
                      +.+.++|+++|. +   |.|+++|+++++++||++++++|+++..+.++.+.......+...+..+.    .+..++...
T Consensus         5 ~~~n~AI~~id~~~---G~I~~~N~a~~~l~Gy~~~el~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~   81 (114)
T d1ll8a_           5 PEFNKAIFTVDAKT---TEILVANDKACGLLGYSSQDLIGQKLTQFFLRSDSDVVEALSEEHMEADGHAAVVFGTVVDII   81 (114)
T ss_dssp             TTTTCEEEEEETTT---CBEEEECTTHHHHHTCCTTTTTTSBGGGGSSCTTTHHHHHTTSSTTSSSSCSSCCCSSSEEEC
T ss_pred             hhcCcEEEEEECCC---CEEEEECHHHHHhhcCCHHHHcCCCeeeecCcccHHHHHHHHHHHHhcCCCccceeeEEEEEE
Confidence            457789999994 6   99999999999999999999999999999887776655443334443332    122356778


Q ss_pred             ecCCCEEEEEEEEEEeecCCCCcEEEEEEEEeccc
Q 022961          100 KKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV  134 (289)
Q Consensus       100 ~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIT  134 (289)
                      +++|..+|+.+++.++..  +|.. .++++++||+
T Consensus        82 ~~~G~~~pvevs~~~i~~--~~~~-~~l~vi~dV~  113 (114)
T d1ll8a_          82 SRSGEKIPVSVWMKRMRQ--ERRL-CCVVVLEPVE  113 (114)
T ss_dssp             CTTCCCEEEECCEECCBS--SSSB-EEEEEEEECC
T ss_pred             ccCCcEEEEEEEEEEEEE--CCeE-EEEEEEEECc
Confidence            999999999999999976  4554 4689999994

>d1n9la_ d.110.3.6 (A:) Putative blue light receptor, phot-lov1 domain {Green algae (Chlamydomonas reinhardtii) [TaxId: 3055]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Flavin-binding PAS domain
domain: Putative blue light receptor, phot-lov1 domain
species: Green algae (Chlamydomonas reinhardtii) [TaxId: 3055]

Probab=99.23  E-value=3.3e-12  Score=86.89  Aligned_cols=39  Identities=36%  Similarity=0.641  Sum_probs=36.4

Q ss_pred             ccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          250 IKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       250 ~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      ++++|+|+|++.||++|+|||++|+++|||+++|++||-
T Consensus         2 i~~~~vi~Da~~pdg~Ii~vN~a~~~~~Gy~~~El~G~~   40 (109)
T d1n9la_           2 LRHTFVVADATLPDCPLVYASEGFYAMTGYGPDEVLGHN   40 (109)
T ss_dssp             CSCEEEEEETTSTTCCEEEECHHHHHHHCCCHHHHTTSC
T ss_pred             ccceEEEEeCCCCCCeEEEEcHHHHHHHCcCHHHHcCCc
Confidence            468999999988899999999999999999999999984

>d1oj5a_ d.110.3.8 (A:) PAS domain of steroid receptor coactivator 1A, NCo-A1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: PAS domain of steroid receptor coactivator 1A, NCo-A1
domain: PAS domain of steroid receptor coactivator 1A, NCo-A1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.14  E-value=1.4e-11  Score=83.38  Aligned_cols=95  Identities=13%  Similarity=0.152  Sum_probs=73.6

Q ss_pred             EEEeCCCCCccEEEccHHHHHHhCCCc-cccCCCCCCCccCCCCCHH--HHHHHHHHHHhCCCeEEEEEEEecCCCEEEE
Q 022961           32 TITDPSISGHPIVFASRGFLKMSGFSR-AEIIGRNGRMFQGPRTNRR--TIMEIREAIREERPIEVNLLNYKKDGTPFWM  108 (289)
Q Consensus        32 ~~~d~~~~~g~i~~~N~~~~~~~G~~~-~e~~g~~~~~l~~~~~~~~--~~~~~~~~~~~~~~~~~e~~~~~~~g~~~~~  108 (289)
                      .-.|.+   |+++++|+++++++||.+ ++++|+++..+++|++.+.  ...........+.....+++++++||..+|+
T Consensus         6 trh~~~---g~~~~vd~~~~~~~gy~~~eelig~s~~~f~HPeD~~~~~~~~~~~~~~~~g~~~~~~yR~~~kdG~~vWv   82 (109)
T d1oj5a_           6 TKQDTT---GKIISIDTSSLRAAGRTGWEDLVRKCIYAFFQPQGREPSYARQLFQEVMTRGTASSPSYRFILNDGTMLSA   82 (109)
T ss_dssp             EEECTT---CCEEEEECHHHHTTCCSCHHHHHHHHHHHHTSCBTTBCCHHHHHHHHHHHHSEEECCCEEEECTTSCEEEE
T ss_pred             EEECCC---ceEEEECHHHhhHhhcCCHHHHcCCcHHHeECcccchHHHhhHHHHHHHhhcccchhhhhhhhccCcEEEE
Confidence            345777   999999999999999985 8999999999999988542  3333456667777788889999999999999


Q ss_pred             EEEEEEeecCCCCcEEEEEEE
Q 022961          109 LFKMSLVFGKEDGRATHFVAV  129 (289)
Q Consensus       109 ~~~~~~~~~~~~g~~~~~~~~  129 (289)
                      ..+..++.++..+.+..++++
T Consensus        83 ~t~~~~~~~~~~~~~~~Ii~~  103 (109)
T d1oj5a_          83 HTRCKLCYPQSPDMQPFIMGI  103 (109)
T ss_dssp             EEEEEEECC----CCCEEEEE
T ss_pred             EEEEEEEECCCCCcccEEEEE
Confidence            999999987223444444443

>d1jnua_ d.110.3.6 (A:) Photoreceptor phy3 flavin-binding domain, lov2 {Maidenhair fern (Adiantum capillus-veneris) [TaxId: 13818]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Flavin-binding PAS domain
domain: Photoreceptor phy3 flavin-binding domain, lov2
species: Maidenhair fern (Adiantum capillus-veneris) [TaxId: 13818]

Probab=99.13  E-value=1.9e-11  Score=82.18  Aligned_cols=37  Identities=43%  Similarity=0.695  Sum_probs=34.4

Q ss_pred             ccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          252 QSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       252 ~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      ++++|||+..||++|+|+|++|+++|||+.+|++|+.
T Consensus         1 ~~fvi~d~~~pd~~I~y~N~a~~~~~G~s~~e~~G~~   37 (104)
T d1jnua_           1 KSFVITDPRLPDNPIIFASDRFLELTEYTREEVLGNN   37 (104)
T ss_dssp             CEEEEECTTSTTCCEEEECHHHHHHHTCCHHHHTTSC
T ss_pred             CeEEEEcCCCCCCEEEEEcHHHHHHHCcCHHHHCCcc
Confidence            4689999988899999999999999999999999984

>d1v9ya_ d.110.3.2 (A:) Direct oxygen sensor protein, DOS {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Heme-binding PAS domain
domain: Direct oxygen sensor protein, DOS
species: Escherichia coli [TaxId: 562]

Probab=98.97  E-value=2.6e-10  Score=77.46  Aligned_cols=43  Identities=21%  Similarity=0.160  Sum_probs=40.4

Q ss_pred             HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      +..++++++++|+++|.   +|+|+++|++|++++||+.+|++|+.
T Consensus         3 ~~~~~e~~~d~i~~~d~---~g~i~~~N~~~~~l~Gy~~~e~~g~~   45 (113)
T d1v9ya_           3 FFPALEQNMMGAVLINE---NDEVMFFNPAAEKLWGYKREEVIGNN   45 (113)
T ss_dssp             HHHHHHTCSSEEEEECT---TSBEEEECHHHHHHHSCCGGGTTTSB
T ss_pred             HHHHHHcCcCcEEEEeC---CCCEEEEchhHhhhhccchhhhcCcc
Confidence            56789999999999999   99999999999999999999999973

>d1mzua_ d.110.3.1 (A:) PYP domain of sensor histidine kinase Ppr {Rhodospirillum centenum [TaxId: 34018]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: PYP-like
domain: PYP domain of sensor histidine kinase Ppr
species: Rhodospirillum centenum [TaxId: 34018]

Probab=98.94  E-value=3.1e-10  Score=76.89  Aligned_cols=42  Identities=12%  Similarity=0.011  Sum_probs=39.4

Q ss_pred             HHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          244 YISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       244 ~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      ..+++.+++||+++|.   +|+|+++|+++++|+||+++|++||.
T Consensus         6 ~A~ld~~p~gvi~~D~---~G~I~~~N~aa~~~~G~~~eellG~~   47 (110)
T d1mzua_           6 TAEFDALPVGAIQVDG---SGVIHRYNRTESRLSGRIPERVIGRN   47 (110)
T ss_dssp             CTTGGGCSSEEEEEET---TCBEEEECHHHHHHHCCCHHHHTTSB
T ss_pred             HHHHhCCCcEEEEEcC---CCCEEEeHHHHHHHHcCCHHHHcCCC
Confidence            4578999999999999   99999999999999999999999984

>d1bywa_ d.110.3.6 (A:) Erg potassium channel, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Flavin-binding PAS domain
domain: Erg potassium channel, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.81  E-value=1.4e-09  Score=73.55  Aligned_cols=37  Identities=19%  Similarity=0.467  Sum_probs=33.7

Q ss_pred             ccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          252 QSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       252 ~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      ..++|+|+..+|.+|+|+|++|++||||+.+|++||.
T Consensus         2 ~~f~i~~~~~~d~~I~~~N~a~~~l~G~~~~eiiG~~   38 (110)
T d1bywa_           2 RKFIIANARVENCAVIYCNDGFCELCGYSRAEVMQRP   38 (110)
T ss_dssp             CEEEEEETTSSSCBEEEECHHHHHHHTCCHHHHTTSB
T ss_pred             ceEEEEcCCCCCCEEEEEcHHHHHHhCCCHHHhcccC
Confidence            3578999877899999999999999999999999984

>d1ew0a_ d.110.3.2 (A:) Histidine kinase FixL heme domain {Rhizobium meliloti [TaxId: 382]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Heme-binding PAS domain
domain: Histidine kinase FixL heme domain
species: Rhizobium meliloti [TaxId: 382]

Probab=98.80  E-value=2.2e-09  Score=74.84  Aligned_cols=43  Identities=19%  Similarity=0.078  Sum_probs=40.8

Q ss_pred             HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      +..++++++++|+++|.   +|+|+++|++|++++||+.+|++|+-
T Consensus        18 ~~~i~~~~~~~i~~~d~---~g~i~~~N~~~~~l~Gy~~~el~g~~   60 (130)
T d1ew0a_          18 LRSILDTVPDATVVSAT---DGTIVSFNAAAVRQFGYAEEEVIGQN   60 (130)
T ss_dssp             HHHHHTTCSSEEEEEET---TSBEEEECHHHHHHHCCCHHHHTTSB
T ss_pred             HHHHHHcCCCeEEEEeC---CccEEEEHHHHHHhhcCCHHHhcCCc
Confidence            67889999999999999   99999999999999999999999973

>d1nwza_ d.110.3.1 (A:) Photoactive yellow protein, PYP {Ectothiorhodospira halophila [TaxId: 1053]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: PYP-like
domain: Photoactive yellow protein, PYP
species: Ectothiorhodospira halophila [TaxId: 1053]

Probab=98.74  E-value=3.9e-09  Score=73.07  Aligned_cols=43  Identities=16%  Similarity=0.007  Sum_probs=40.0

Q ss_pred             HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      +...++..++||++.|.   +|+|+++|++|++++||+++|++||.
T Consensus        19 ~d~~ld~~p~gi~~lD~---~G~i~~~N~a~~~l~G~~~~e~iG~~   61 (125)
T d1nwza_          19 DDGQLDGLAFGAIQLDG---DGNILQYNAAEGDITGRDPKQVIGKN   61 (125)
T ss_dssp             CHHHHTTCSSEEEEEET---TCBEEEECHHHHHHHCCCHHHHTTSB
T ss_pred             HHHHHhCCCccEEEEeC---CCCEEEEcHHHHHhhccchHhhcCCC
Confidence            35678999999999999   99999999999999999999999984

>d1ll8a_ d.110.3.5 (A:) N-terminal PAS domain of Pas kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: N-terminal PAS domain of Pas kinase
domain: N-terminal PAS domain of Pas kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.44  E-value=4.3e-08  Score=66.43  Aligned_cols=38  Identities=16%  Similarity=0.177  Sum_probs=33.3

Q ss_pred             cccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          249 RIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       249 ~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      ...++|+++|+  .+|+|+++|+++++++||+++|++|+.
T Consensus         6 ~~n~AI~~id~--~~G~I~~~N~a~~~l~Gy~~~el~g~~   43 (114)
T d1ll8a_           6 EFNKAIFTVDA--KTTEILVANDKACGLLGYSSQDLIGQK   43 (114)
T ss_dssp             TTTCEEEEEET--TTCBEEEECTTHHHHHTCCTTTTTTSB
T ss_pred             hcCcEEEEEEC--CCCEEEEECHHHHHhhcCCHHHHcCCC
Confidence            45688999995  169999999999999999999999984

>d1p97a_ d.110.3.7 (A:) Hypoxia-inducible factor Hif2a, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Hypoxia-inducible factor Hif2a, C-terminal domain
domain: Hypoxia-inducible factor Hif2a, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.02  E-value=1e-06  Score=59.20  Aligned_cols=33  Identities=21%  Similarity=0.210  Sum_probs=28.8

Q ss_pred             cEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          253 SFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       253 ~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      .|+..|.   +|+|+|+|+++++++||+.+|++|+.
T Consensus         8 fi~r~~~---dG~i~~~N~~~~~~~G~~~~el~g~~   40 (114)
T d1p97a_           8 FLSRHSM---DMKFTYCDDRITELIGYHPEELLGRS   40 (114)
T ss_dssp             EEEEECT---TTSCSEECTTHHHHTSSCHHHHTTSC
T ss_pred             EEEEECC---CCcEEEECHHHHHHcCCCcccccccc
Confidence            3444577   99999999999999999999999973

>d2oola2 d.110.3.9 (A:26-139) Sensor protein PhyB2 {Rhodopseudomonas palustris [TaxId: 1076]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: BphP N-terminal domain-like
domain: Sensor protein PhyB2
species: Rhodopseudomonas palustris [TaxId: 1076]

Probab=97.27  E-value=0.00019  Score=47.78  Aligned_cols=42  Identities=7%  Similarity=-0.002  Sum_probs=35.6

Q ss_pred             EEEEEeC-CCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCC
Q 022961           30 SFTITDP-SISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRT   74 (289)
Q Consensus        30 ~i~~~d~-~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~   74 (289)
                      .++++|. +   ++|+++++....++|+++++++|+++..++++.+
T Consensus        19 ~Llvld~~d---~~I~~vS~N~~~lLG~~~~~llG~~l~dll~~~~   61 (114)
T d2oola2          19 YLFVVSETD---LRIASVSANVEDLLRQPPASLLNVPIAHYLTAAS   61 (114)
T ss_dssp             EEEEECTTT---CBEEEEETTHHHHHSSCGGGGTTCBGGGGBCHHH
T ss_pred             EEEEEECCC---CEEEEEcCCHHHHhCCChHHHcCCCHHHhCCHHH
Confidence            3455664 5   9999999999999999999999999988887644

>d1oj5a_ d.110.3.8 (A:) PAS domain of steroid receptor coactivator 1A, NCo-A1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: PAS domain of steroid receptor coactivator 1A, NCo-A1
domain: PAS domain of steroid receptor coactivator 1A, NCo-A1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.14  E-value=0.00017  Score=47.50  Aligned_cols=32  Identities=9%  Similarity=0.094  Sum_probs=27.6

Q ss_pred             EEEeCCCCCCCCEEEecHHHHHhhCCC-hHhHhhcc
Q 022961          254 FVLIDPHLPDMPMVYASDAFLKLTGAQ-IFTKITRI  288 (289)
Q Consensus       254 i~i~d~~~~~~~i~~vN~~f~~~tGys-~~E~~G~~  288 (289)
                      +.-.|.   +|+|+++|++..+++||. .+|++|+.
T Consensus         5 ~trh~~---~g~~~~vd~~~~~~~gy~~~eelig~s   37 (109)
T d1oj5a_           5 MTKQDT---TGKIISIDTSSLRAAGRTGWEDLVRKC   37 (109)
T ss_dssp             EEEECT---TCCEEEEECHHHHTTCCSCHHHHHHHH
T ss_pred             EEEECC---CceEEEECHHHhhHhhcCCHHHHcCCc
Confidence            344567   999999999999999999 49999984

>d2oola2 d.110.3.9 (A:26-139) Sensor protein PhyB2 {Rhodopseudomonas palustris [TaxId: 1076]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: BphP N-terminal domain-like
domain: Sensor protein PhyB2
species: Rhodopseudomonas palustris [TaxId: 1076]

Probab=95.32  E-value=0.0061  Score=40.00  Aligned_cols=26  Identities=12%  Similarity=0.019  Sum_probs=24.7

Q ss_pred             CCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          263 DMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       263 ~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      +++|+|+.+...+++||+.++++|+-
T Consensus        27 d~~I~~vS~N~~~lLG~~~~~llG~~   52 (114)
T d2oola2          27 DLRIASVSANVEDLLRQPPASLLNVP   52 (114)
T ss_dssp             TCBEEEEETTHHHHHSSCGGGGTTCB
T ss_pred             CCEEEEEcCCHHHHhCCChHHHcCCC
Confidence            79999999999999999999999973

>d2veaa3 d.110.3.9 (A:4-130) Phytochrome-like protein Cph1 {Synechocystis sp. pcc 6803 [TaxId: 1148]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: BphP N-terminal domain-like
domain: Phytochrome-like protein Cph1
species: Synechocystis sp. pcc 6803 [TaxId: 1148]

Probab=94.85  E-value=0.019  Score=38.33  Aligned_cols=43  Identities=14%  Similarity=0.057  Sum_probs=34.9

Q ss_pred             EEEEEeC-CCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCC
Q 022961           30 SFTITDP-SISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTN   75 (289)
Q Consensus        30 ~i~~~d~-~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~   75 (289)
                      .++++|. +   ++|..++.....++|+++++++|+++..++.+...
T Consensus        28 ~LLald~~~---~~I~~aS~N~~~~lG~~~~~lLG~~l~~ll~~~~~   71 (127)
T d2veaa3          28 LVVVLQEPD---LTISQISANCTGILGRSPEDLLGRTLGEVFDSFQI   71 (127)
T ss_dssp             EEEEEETTT---TEEEEEETTHHHHTSCCTTTSSTTTTTTTSBCC--
T ss_pred             EEEEEECCC---CEEEEEcCCHHHHhCcChHHHcCCCHHHHCCHHHH
Confidence            3455664 5   89999999999999999999999999888865543

>d2o9ca2 d.110.3.9 (A:4-130) Bacteriophytochrome BphP {Deinococcus radiodurans [TaxId: 1299]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: BphP N-terminal domain-like
domain: Bacteriophytochrome BphP
species: Deinococcus radiodurans [TaxId: 1299]

Probab=92.14  E-value=0.085  Score=34.99  Aligned_cols=39  Identities=13%  Similarity=0.066  Sum_probs=33.4

Q ss_pred             EEEEEeC-CCCCccEEEccHHHHHHhCCCccccCCCCCCCccC
Q 022961           30 SFTITDP-SISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQG   71 (289)
Q Consensus        30 ~i~~~d~-~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~   71 (289)
                      .++++|. +   +.|+.++.....++|+++++++|++...+++
T Consensus        37 ~LLald~~~---~~I~~~S~N~~~~lG~~~~~llG~~l~~ll~   76 (127)
T d2o9ca2          37 ALLTADGHS---GEVLQMSLNAATFLGQEPTVLRGQTLAALLP   76 (127)
T ss_dssp             EEEEEETTT---CBEEEEETTHHHHHSSCHHHHTTCBHHHHCT
T ss_pred             EEEEEECCC---CEEEEECCCHHHHhCCChHHHcCCCHHHHCC
Confidence            3455564 5   9999999999999999999999999888874

>d2o9ca2 d.110.3.9 (A:4-130) Bacteriophytochrome BphP {Deinococcus radiodurans [TaxId: 1299]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: BphP N-terminal domain-like
domain: Bacteriophytochrome BphP
species: Deinococcus radiodurans [TaxId: 1299]

Probab=85.56  E-value=0.39  Score=31.57  Aligned_cols=26  Identities=8%  Similarity=-0.109  Sum_probs=24.5

Q ss_pred             CCCEEEecHHHHHhhCCChHhHhhcc
Q 022961          263 DMPMVYASDAFLKLTGAQIFTKITRI  288 (289)
Q Consensus       263 ~~~i~~vN~~f~~~tGys~~E~~G~~  288 (289)
                      +++|++++....+++|++.++++|+-
T Consensus        45 ~~~I~~~S~N~~~~lG~~~~~llG~~   70 (127)
T d2o9ca2          45 SGEVLQMSLNAATFLGQEPTVLRGQT   70 (127)
T ss_dssp             TCBEEEEETTHHHHHSSCHHHHTTCB
T ss_pred             CCEEEEECCCHHHHhCCChHHHcCCC
Confidence            79999999999999999999999973

>d3c2wa3 d.110.3.9 (A:5-117) Bacteriophytochrome BphP {Pseudomonas aeruginosa [TaxId: 287]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: BphP N-terminal domain-like
domain: Bacteriophytochrome BphP
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=82.35  E-value=1.9  Score=27.42  Aligned_cols=70  Identities=11%  Similarity=0.108  Sum_probs=41.1

Q ss_pred             EEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEEEEEEecCCCEEEEE
Q 022961           31 FTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWML  109 (289)
Q Consensus        31 i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~~~~  109 (289)
                      ++++|.+   +.|+.++.....++|++++ .+|+....++.    ......+...+.....+...... ..+|..+++.
T Consensus        25 LLald~~---~~I~~~S~N~~~~lg~~~~-~L~~~~~~~~~----~~~~~~l~~~~~~~~~~~~~~~~-~~~~~~~d~~   94 (113)
T d3c2wa3          25 LVTLRAD---GMVLAASENIQALLGFVAS-PGSYLTQEQVG----PEVLRMLEEGLTGNGPWSNSVET-RIGEHLFDVI   94 (113)
T ss_dssp             EEEECTT---SBEEEEETTHHHHTSSCCC-TTCBCCHHHHH----HHHHHHHHHHHSCSSCCCCEEEE-CCSSSCEEEE
T ss_pred             EEEEcCC---CeEEEEcCCHHHHhCCChh-HhcccHHHHhC----HHHHHHHHhhhhcCCCceeEEEe-ccCCeEEEEE
Confidence            4556777   9999999999999999865 45665444332    22333444444444433333322 3456655543