Citrus Sinensis ID: 020514

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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-------290-------300-------310-------320-----
Protein Sequence
MDSQLGLIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSIAISPYPKKKSIYMEYVRV
Secondary Structure (PSIPRED)
ccccccHHHHHHccHHHHHHHHHHHHcccEEEEEccccccccEEEEcHHHHHHHcccccccccccccccccccccHHHHHHHHHHHHHcccEEEEEEccccccccEEEEEEEEEEEccccccEEEEEEEEEccccccccccccccccccccccccccEEccccccccccccccHHHHHHcccccccccccccccccHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccHHHHHHHHHHcccccEEEEccccccccEEEEcHHHHHHHccccHHHccccccccccccccHHHHHHHHHHHHccccEEEEEEccccc
Secondary Structure Prediction (SSPRO)
ccccccccHHHHHHHHHHHHHHHHHHcccEEEEEEcccccccEEEEcHHHHHHHcccHHHHccccHHHHccccccHHHHHHHHHHHHHcccEEEEEEEEcccccEEEEEEEEEEEcccccccEEEEEEEEEccHHHHHHHHHccHHHHHcHHHccccHHHHHHHHHHHHHHHHcccccccccccccccccccHHHHHHHHHHHHHccccccccccccccEEEccccccccccHHHHHHHHHHHHHHHHHcccEEEEEEcccccccEEEEcHHHHHHHcccHHHHccccHHHHccccccHHHHHHHHHHHHccccEEEEEEEEccc
Coil and Loop (DISEMBL)
MDSQLGLIEQSFNNRYTLWVHEALdelpdsftitdpsisghpivfasrgflkmsgfsraeiigrngrmfqgprtnrRTIMEIREAIREErpievnllnykkdgtpfWMLFKMSLVfgkedgratHFVAVQVPIvsrkhmrnsgmsysedgggsrlREIVFGScrrevcsdsLLDLDRVlaldsddtgleiedsceaSDLEKRKAATAIDNILSVLTHYSQLtgrlvcgkrcslpgmgfiSSSLYISLGRikqsfvlidphlpdmpmvyASDAFLKltgydrnevvgqncrflngvdtdtTVLYQVSIaispypkkksiyMEYVRV
Flexible Loop (DISEMBL)
MDSQLGLIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEiigrngrmfqgprtnrrTIMEIReaireerpievnllnykkdgtpFWMLFKMSLVFGKEDGRATHFVAVqvpivsrkhmrnsgmsysedgggsrLREIVFGSCRREVCSDSLLDLDRVlaldsddtgleiedsceasdlEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSiaispypkkksiYMEYVRV
Low Complexity Region (SEG)
MDSQLGLIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNrrtimeireaireerpieVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSIAISPYPKKKSIYMEYVRV
Disordered region (IsUnstruct)
******LIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSR******************LREIVFGSCRREVCSDSLLDLDRVLALDSDDTGLEI************KAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSIAISPYPKKKSIYMEY***
Disordered Region (DISOPRED)
***QLGL***********WVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSIAISPYPKKKSIYMEYVRV
Disordered Region (DISEMBL)
MDSQLGLIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNS*********GSRLREIVFGSCRREVCSDSLLDLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSIAISPYPKKKSIYMEYVRV
Disordered Region (DISPRO)
*****GLIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSIAISPYPKKKSIYMEYVRV
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MDSQLGLIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSIAISPYPKKKSIYMEYVRV
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	325	2.2.26 [Sep-21-2011]
O64511	399	Protein TWIN LOV 1 OS=Ara	yes	no	0.910	0.741	0.644	1e-110
P93025	915	Phototropin-2 OS=Arabidop	no	no	0.883	0.313	0.321	2e-35
Q9ST27	907	Phototropin-2 OS=Oryza sa	no	no	0.329	0.117	0.444	3e-21
Q2RBR1	921	Phototropin-1B OS=Oryza s	no	no	0.329	0.116	0.407	2e-19
Q2QYY8	921	Phototropin-1A OS=Oryza s	no	no	0.329	0.116	0.407	3e-19
Q48IV1	534	Blue-light-activated prot	yes	no	0.335	0.204	0.418	4e-19
O48963	996	Phototropin-1 OS=Arabidop	no	no	0.332	0.108	0.394	2e-18
Q4ZSY3	534	Blue-light-activated prot	yes	no	0.32	0.194	0.419	5e-18
O34627	261	Blue-light photoreceptor	yes	no	0.356	0.444	0.361	9e-18
Q9HPU8	674	Bacterioopsin transcripti	yes	no	0.353	0.170	0.362	1e-17

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

 Score =  398 bits (1023), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 194/301 (64%), Positives = 237/301 (78%), Gaps = 5/301 (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 RIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSIA 308
           RIKQSFVL +P LPDMP++YASDAFL LTGY R EV+GQNCRFL+GVDTD++VLY++   
Sbjct: 256 RIKQSFVLTNPCLPDMPIIYASDAFLTLTGYKRQEVLGQNCRFLSGVDTDSSVLYEMKEC 315

Query: 309 I 309
           I
Sbjct: 316 I 316

Arabidopsis thaliana (taxid: 3702)

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

 Score =  150 bits (378), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 108/336 (32%), Positives = 169/336 (50%), Gaps = 49/336 (14%)

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 LKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSIAI 309
           L+LT Y R E++G+NCRFL G +TD   + ++  AI
Sbjct: 411 LELTEYSREEILGRNCRFLQGPETDQATVQKIRDAI 446

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 = 3e-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 = 96.3 bits (238), 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 = 96.3 bits (238), Expect = 3e-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 = 95.5 bits (236), Expect = 4e-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 = 93.2 bits (230), Expect = 2e-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 = 92.0 bits (227), Expect = 5e-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 = 91.3 bits (225), Expect = 9e-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 = 90.5 bits (223), Expect = 1e-17,   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	325
224110804	396	predicted protein [Populus trichocarpa]	0.916	0.752	0.697	1e-122
224102353	396	predicted protein [Populus trichocarpa]	0.96	0.787	0.655	1e-122
255558228	375	twin lov protein, putative [Ricinus comm	0.901	0.781	0.692	1e-118
225424899	397	PREDICTED: protein TWIN LOV 1 [Vitis vin	0.944	0.773	0.687	1e-118
297817884	386	pac motif-containing protein [Arabidopsi	0.904	0.761	0.642	1e-109
18395411	399	protein TWIN LOV 1 [Arabidopsis thaliana	0.910	0.741	0.644	1e-108
30678020	397	protein TWIN LOV 1 [Arabidopsis thaliana	0.96	0.785	0.605	1e-108
42570655	358	protein TWIN LOV 1 [Arabidopsis thaliana	0.96	0.871	0.605	1e-108
350537683	398	LOV/LOV protein [Solanum lycopersicum] g	0.944	0.771	0.589	1e-105
449434827	385	PREDICTED: protein TWIN LOV 1-like [Cucu	0.966	0.815	0.560	1e-104

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

 Score =  445 bits (1144), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 214/307 (69%), Positives = 254/307 (82%), Gaps = 9/307 (2%)

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 GRVIHFIGVQVPILRNKR-------STDDGADAAWNEIVFGSCRREVCSDSLVELGRVLA 173

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

Query: 239 ISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTD 298
           I+SSL ISLGRI QSFVLIDPHLP+MP+VYASDAFLKLTGYDR+EV+G N RFL+GV TD
Sbjct: 234 INSSLNISLGRINQSFVLIDPHLPNMPIVYASDAFLKLTGYDRHEVLGCNWRFLSGVGTD 293

Query: 299 TTVLYQV 305
           ++VL Q+
Sbjct: 294 SSVLNQI 300

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 =  443 bits (1140), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 217/331 (65%), Positives = 264/331 (79%), Gaps = 19/331 (5%)

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 ISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTD 298
           I+SSL ISLGRIKQSFVLIDPHLP+MP+VYASDAFLKLTGYDR+EV+G++  FLNGVDTD
Sbjct: 234 INSSLNISLGRIKQSFVLIDPHLPNMPVVYASDAFLKLTGYDRHEVLGRDWNFLNGVDTD 293

Query: 299 TTVLYQV----------SIAISPYPKKKSIY 319
           +++L+QV          ++ I  Y K KS +
Sbjct: 294 SSILHQVQESIQVEQPCTVCILNYRKDKSTF 324

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

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 =  430 bits (1106), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 207/299 (69%), Positives = 248/299 (82%), Gaps = 6/299 (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 LGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQV 305
           LGRI+QSFVL DPHLPDMP+VYASDAFLKLTGY R+EV+ +NCRFL G+DTD +V+ Q+
Sbjct: 246 LGRIRQSFVLTDPHLPDMPIVYASDAFLKLTGYARHEVLWRNCRFLGGIDTDRSVIEQI 304

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  430 bits (1105), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 216/314 (68%), Positives = 255/314 (81%), Gaps = 7/314 (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 MGFISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGV 295
           +G + +SL ISLGRIKQSFVL DPHLP+MP+VYASDAFLKLTGY R+EV+G  C FL+GV
Sbjct: 239 IGLLGASLIISLGRIKQSFVLTDPHLPEMPIVYASDAFLKLTGYARHEVLGCQCMFLSGV 298

Query: 296 DTDTTVLYQVSIAI 309
           DTD + L QV  +I
Sbjct: 299 DTDPSTLLQVKESI 312

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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 =  399 bits (1025), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 194/302 (64%), Positives = 239/302 (79%), Gaps = 8/302 (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 GRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI 307
           GRIKQSFVL +P LPDMP++YASDAFL LTGY R EV+GQNCRFL+GVDTD++VLY++  
Sbjct: 242 GRIKQSFVLTNPCLPDMPIIYASDAFLTLTGYKRQEVLGQNCRFLSGVDTDSSVLYEIKE 301

Query: 308 AI 309
            I
Sbjct: 302 CI 303

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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 =  398 bits (1023), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 194/301 (64%), Positives = 237/301 (78%), Gaps = 5/301 (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 RIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSIA 308
           RIKQSFVL +P LPDMP++YASDAFL LTGY R EV+GQNCRFL+GVDTD++VLY++   
Sbjct: 256 RIKQSFVLTNPCLPDMPIIYASDAFLTLTGYKRQEVLGQNCRFLSGVDTDSSVLYEMKEC 315

Query: 309 I 309
           I
Sbjct: 316 I 316

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 =  398 bits (1023), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 198/327 (60%), Positives = 246/327 (75%), Gaps = 15/327 (4%)

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 RIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQV--- 305
           RIKQSFVL +P LPDMP++YASDAFL LTGY R EV+GQNCRFL+GVDTD++VLY++   
Sbjct: 256 RIKQSFVLTNPCLPDMPIIYASDAFLTLTGYKRQEVLGQNCRFLSGVDTDSSVLYEMKEC 315

Query: 306 -------SIAISPYPKKKSIYMEYVRV 325
                  ++ I  Y K KS +   + +
Sbjct: 316 ILKGQSCTVQILNYRKDKSSFWNLLHI 342

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

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 =  397 bits (1019), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 198/327 (60%), Positives = 245/327 (74%), Gaps = 15/327 (4%)

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 RIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQV--- 305
           RIKQSFVL +P LPDMP++YASDAFL LTGY R EV+GQNCRFL+GVDTD++VLY++   
Sbjct: 256 RIKQSFVLTNPCLPDMPIIYASDAFLTLTGYKRQEVLGQNCRFLSGVDTDSSVLYEMKEC 315

Query: 306 -------SIAISPYPKKKSIYMEYVRV 325
                  ++ I  Y K KS +   + +
Sbjct: 316 ILKGQSCTVQILNYRKDKSSFWNLLHI 342

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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 =  387 bits (995), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 187/317 (58%), Positives = 242/317 (76%), Gaps = 10/317 (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 LPGMGFISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFL 292
             G   +S+SL IS GRIKQSFVL D HLPDMP+VYASDAFLKL GY R+EV+G+NCRFL
Sbjct: 239 QSGTSLLSASLNISFGRIKQSFVLTDAHLPDMPIVYASDAFLKLIGYLRHEVLGRNCRFL 298

Query: 293 NGVDTDTTVLYQVSIAI 309
           +G DT+    +Q+   I
Sbjct: 299 SGEDTERGTQFQIKQCI 315

Source: Solanum lycopersicum

Species: Solanum lycopersicum

Genus: Solanum

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  384 bits (985), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 189/337 (56%), Positives = 244/337 (72%), Gaps = 23/337 (6%)

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 ISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTD 298
           + SSL  SL RIKQSFVL DP+LPDMP+VYASD FLKLTGY R EV+G+NCRFL+G+DTD
Sbjct: 230 LCSSLNTSLNRIKQSFVLTDPNLPDMPIVYASDEFLKLTGYTRCEVLGRNCRFLSGIDTD 289

Query: 299 TTVLYQV----------SIAISPYPKKKSIYMEYVRV 325
           ++ L+++          ++ I  Y K KS +   + V
Sbjct: 290 SSTLFKIKESLQSEQACTVRILNYRKNKSSFWNDLHV 326

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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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	325
TAIR|locus:2058852	399	PLPB "PAS/LOV PROTEIN C" [Arab	0.916	0.746	0.597	7.3e-91
TAIR|locus:2155821	915	PHOT2 "phototropin 2" [Arabido	0.378	0.134	0.378	1.3e-28
UNIPROTKB|Q2QYY8	921	PHOT1A "Phototropin-1A" [Oryza	0.338	0.119	0.360	2.8e-28
UNIPROTKB|Q2RBR1	921	PHOT1B "Phototropin-1B" [Oryza	0.338	0.119	0.360	4e-28
UNIPROTKB|Q9ST27	907	PHOT2 "Phototropin-2" [Oryza s	0.406	0.145	0.308	5.4e-27
UNIPROTKB|Q8H935	963	Vfphot1a "Phototropin" [Vicia	0.329	0.111	0.361	2.5e-12
TAIR|locus:2102674	996	PHOT1 "phototropin 1" [Arabido	0.827	0.270	0.267	6.4e-13
UNIPROTKB|G4NFS7	961	MGG_08735 "Uncharacterized pro	0.32	0.108	0.371	1.6e-11
UNIPROTKB|Q887F0	425	PSPTO_1346 "Sensory box/GGDEF	0.341	0.261	0.278	0.00035
UNIPROTKB|G4NCS4	225	MGG_01041 "Cellulose signaling	0.147	0.213	0.56	4.2e-07

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

 Score = 906 (324.0 bits), Expect = 7.3e-91, P = 7.3e-91
 Identities = 181/303 (59%), Positives = 221/303 (72%)

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 LGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVS 306
             LGRIKQSFVL +P LPDMP++YASDAFL LTGY R EV+GQNCRFL+GVDTD++VLY++ 
Sbjct:   254 LGRIKQSFVLTNPCLPDMPIIYASDAFLTLTGYKRQEVLGQNCRFLSGVDTDSSVLYEMK 313

Query:   307 IAI 309
               I
Sbjct:   314 ECI 316

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 = 1.3e-28, Sum P(2) = 1.3e-28
 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 = 2.8e-28, Sum P(2) = 2.8e-28
 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 = 4.0e-28, Sum P(2) = 4.0e-28
 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

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

 Score = 196 (74.1 bits), Expect = 5.4e-27, Sum P(2) = 5.4e-27
 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 = 2.5e-12, P = 2.5e-12
 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

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

 Score = 198 (74.8 bits), Expect = 6.4e-13, P = 6.4e-13
 Identities = 78/292 (26%), Positives = 132/292 (45%)

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 EASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCS-LPGMGFISSSLYISLGRIKQS 253
             E+ +L K+ A    +N++      S   GR    +R + +P      SSL   +G IK+ 
Sbjct:   363 ESDELPKKPARRMSENVVPSGRRNSG-GGRRNSMQRINEIPEKKSRKSSLSF-MG-IKKK 419

Query:   254 FVLIDPHLPDMPMVYASDAFLKLTGYD-RNEVVGQNCR---FLNGVDTDTTV 301
                +D  + D  + Y  +   +++  D R E V    R      G+D  TT+
Sbjct:   420 SESLDESIDDGFIEYGEEDD-EISDRDERPESVDDKVRQKEMRKGIDLATTL 470

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

 Score = 186 (70.5 bits), Expect = 1.6e-11, P = 1.6e-11
 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|Q887F0 PSPTO_1346 "Sensory box/GGDEF domain protein" [Pseudomonas syringae pv. tomato str. DC3000 (taxid:223283)]

 Score = 117 (46.2 bits), Expect = 0.00035, P = 0.00035
 Identities = 32/115 (27%), Positives = 55/115 (47%)

Query:    22 EALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNXXXXXX 81
             +AL+   D   ITD + +   IVFA+  F  ++G+S  EIIG+N RM +  + +      
Sbjct:   140 QALNAAFDPIIITDRNST---IVFANEAFQLITGYSAPEIIGQNPRMLRSGKHDALFYAQ 196

Query:    82 XXXXXXXXXXXXVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSR 136
                            +N +KDG+ F+    +S +   E G  TH+V++   + +R
Sbjct:   197 FNESLASGEPFRTTFINKRKDGSLFYAEHSISPLRNVE-GAMTHYVSISQDVTTR 250

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|G4NCS4 MGG_01041 "Cellulose signaling associated protein ENVOY" [Magnaporthe oryzae 70-15 (taxid:242507)]

 Score = 136 (52.9 bits), Expect = 4.2e-07, P = 4.2e-07
 Identities = 28/50 (56%), Positives = 35/50 (70%)

Query:   245 ISLGRIKQS--FVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFL 292
             I LG I  S   +L D  LPD P+VYA++ FL+LTGY   EV+G+NCRFL
Sbjct:    98 IDLGPIDSSCAMILCDLALPDTPIVYATNPFLELTGYSSEEVIGRNCRFL 147

GO:0005575 "cellular_component" evidence=ND

GO:0043581 "mycelium development" evidence=IEP

---

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	0.6445	0.9107	0.7418	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!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: estExt_fgenesh4_pg.C_LG_VIII1581 hypothetical protein (396 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

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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	325
PRK13558	665	PRK13558, PRK13558, bacterio-opsin activator; Prov	2e-30
PRK13557	540	PRK13557, PRK13557, histidine kinase; Provisional	2e-27
PRK13559	361	PRK13559, PRK13559, hypothetical protein; Provisio	3e-27
pfam13426	101	pfam13426, PAS_9, PAS domain	1e-21
PRK13559	361	PRK13559, PRK13559, hypothetical protein; Provisio	3e-15
PRK13557	540	PRK13557, PRK13557, histidine kinase; Provisional	1e-14
PRK13558	665	PRK13558, PRK13558, bacterio-opsin activator; Prov	3e-12
TIGR02938	494	TIGR02938, nifL_nitrog, nitrogen fixation negative	6e-08
TIGR00229	124	TIGR00229, sensory_box, PAS domain S-box	3e-07
pfam13426	101	pfam13426, PAS_9, PAS domain	4e-07
COG2202	232	COG2202, AtoS, FOG: PAS/PAC domain [Signal transdu	2e-04
cd00130	103	cd00130, PAS, PAS domain; PAS motifs appear in arc	7e-04
pfam00989	113	pfam00989, PAS, PAS fold	0.003

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

 Score =  121 bits (304), Expect = 2e-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 =  111 bits (279), 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 =  109 bits (273), Expect = 3e-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|237427 PRK13559, PRK13559, hypothetical protein; Provisional

 Score = 75.2 bits (185), Expect = 3e-15
 Identities = 27/50 (54%), Positives = 35/50 (70%)

Query: 249 RIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTD 298
           + + +  + DPH PD+P+V A+ AFL LTGY   EVVG+NCRFL G  TD
Sbjct: 51  QTRMAMCITDPHQPDLPIVLANQAFLDLTGYAAEEVVGRNCRFLQGAATD 100

Length = 361

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

 Score = 74.3 bits (183), Expect = 1e-14
 Identities = 26/55 (47%), Positives = 39/55 (70%)

Query: 255 VLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSIAI 309
           ++ DP+ PD P+V+A+ AFL++TGY   E++G NCRFL G +TD   + +V  AI
Sbjct: 44  IVTDPNQPDNPIVFANRAFLEMTGYAAEEIIGNNCRFLQGPETDRATVAEVRDAI 98

Length = 540

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

 Score = 66.8 bits (163), Expect = 3e-12
 Identities = 23/41 (56%), Positives = 32/41 (78%)

Query: 258 DPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTD 298
           D  LPD P++Y +DAF ++TGY  +EV+G+NCRFL G DT+
Sbjct: 165 DATLPDEPLIYINDAFERITGYSPDEVLGRNCRFLQGEDTN 205

Length = 665

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

 Score = 53.8 bits (129), 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 = 48.0 bits (115), Expect = 3e-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|222120 pfam13426, PAS_9, PAS domain

 Score = 47.4 bits (113), Expect = 4e-07
 Identities = 19/45 (42%), Positives = 29/45 (64%), Gaps = 3/45 (6%)

Query: 254 FVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTD 298
            +++DP   D  +VYA+DA L+L GY R E++G++ R L G   D
Sbjct: 1   ILVLDP---DGRIVYANDAALRLLGYTREELLGKSIRDLFGPGDD 42

Length = 101

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

 Score = 41.8 bits (96), Expect = 2e-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 = 7e-04
 Identities = 23/107 (21%), Positives = 45/107 (42%), Gaps = 4/107 (3%)

Query: 27  LPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAI 86
           LPD   + D    G  I++A+    ++ G+S  E+IG++      P         +   +
Sbjct: 1   LPDGVIVLDLD--GR-ILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLL 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|216228 pfam00989, PAS, PAS fold

 Score = 36.6 bits (85), Expect = 0.003
 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	325
TIGR02040	442	PpsR-CrtJ transcriptional regulator PpsR. This mod	99.87
PRK13560	807	hypothetical protein; Provisional	99.85
PRK09776	1092	putative diguanylate cyclase; Provisional	99.85
TIGR02040	442	PpsR-CrtJ transcriptional regulator PpsR. This mod	99.82
TIGR02938	494	nifL_nitrog nitrogen fixation negative regulator N	99.8
PRK13560	807	hypothetical protein; Provisional	99.8
PRK11359	799	cyclic-di-GMP phosphodiesterase; Provisional	99.76
PF13426	104	PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_	99.71
PF08448	110	PAS_4: PAS fold; InterPro: IPR013656 The PAS fold	99.64
PF00989	113	PAS: PAS fold; InterPro: IPR013767 PAS domains are	99.63
PRK11091	779	aerobic respiration control sensor protein ArcB; P	99.44
PRK13559	361	hypothetical protein; Provisional	99.41
PRK13557	540	histidine kinase; Provisional	99.38
PF13426	104	PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_	99.34
PF00989	113	PAS: PAS fold; InterPro: IPR013767 PAS domains are	99.34
PRK13558	665	bacterio-opsin activator; Provisional	99.25
PRK10060	663	RNase II stability modulator; Provisional	99.2
PF08447	91	PAS_3: PAS fold; InterPro: IPR013655 The PAS fold	99.17
TIGR00229	124	sensory_box PAS domain S-box. The PAS domain was p	99.17
PRK09776	1092	putative diguanylate cyclase; Provisional	99.07
PRK11359	799	cyclic-di-GMP phosphodiesterase; Provisional	99.04
PRK13557	540	histidine kinase; Provisional	98.99
cd00130	103	PAS PAS domain; PAS motifs appear in archaea, euba	98.97
PF13596	106	PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.	98.88
PRK13559	361	hypothetical protein; Provisional	98.88
PF12860	115	PAS_7: PAS fold	98.85
PF08448	110	PAS_4: PAS fold; InterPro: IPR013656 The PAS fold	98.85
COG3829	560	RocR Transcriptional regulator containing PAS, AAA	98.83
PRK11360	607	sensory histidine kinase AtoS; Provisional	98.79
PRK10060	663	RNase II stability modulator; Provisional	98.79
PF14598	111	PAS_11: PAS domain; PDB: 1P97_A 3F1O_A 2A24_A 3H7W	98.76
KOG3558	768	consensus Hypoxia-inducible factor 1/Neuronal PAS	98.73
TIGR02966	333	phoR_proteo phosphate regulon sensor kinase PhoR.	98.73
PRK11073	348	glnL nitrogen regulation protein NR(II); Provision	98.69
KOG0501	971	consensus K+-channel KCNQ [Inorganic ion transport	98.66
COG3829	560	RocR Transcriptional regulator containing PAS, AAA	98.64
PF08447	91	PAS_3: PAS fold; InterPro: IPR013655 The PAS fold	98.61
PF13188	64	PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.	98.53
PRK11091	779	aerobic respiration control sensor protein ArcB; P	98.51
COG5002	459	VicK Signal transduction histidine kinase [Signal	98.5
PRK13558	665	bacterio-opsin activator; Provisional	98.47
TIGR02938	494	nifL_nitrog nitrogen fixation negative regulator N	98.43
TIGR02966	333	phoR_proteo phosphate regulon sensor kinase PhoR.	98.42
TIGR00229	124	sensory_box PAS domain S-box. The PAS domain was p	98.39
PRK11073	348	glnL nitrogen regulation protein NR(II); Provision	98.35
PRK11006	430	phoR phosphate regulon sensor protein; Provisional	98.29
PF14598	111	PAS_11: PAS domain; PDB: 1P97_A 3F1O_A 2A24_A 3H7W	98.29
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	98.28
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	98.28
PF13188	64	PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.	98.2
cd00130	103	PAS PAS domain; PAS motifs appear in archaea, euba	98.19
COG2202	232	AtoS FOG: PAS/PAC domain [Signal transduction mech	98.0
PRK11086	542	sensory histidine kinase DcuS; Provisional	97.88
COG5000	712	NtrY Signal transduction histidine kinase involved	97.85
PRK11006	430	phoR phosphate regulon sensor protein; Provisional	97.83
PF12860	115	PAS_7: PAS fold	97.82
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	97.81
KOG1229	775	consensus 3'5'-cyclic nucleotide phosphodiesterase	97.75
PF13596	106	PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.	97.61
KOG3559	598	consensus Transcriptional regulator SIM1 [Transcri	97.61
COG2202	232	AtoS FOG: PAS/PAC domain [Signal transduction mech	97.58
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	97.53
smart00091	67	PAS PAS domain. PAS motifs appear in archaea, euba	97.46
KOG0501	971	consensus K+-channel KCNQ [Inorganic ion transport	97.42
PRK15053	545	dpiB sensor histidine kinase DpiB; Provisional	97.41
PRK09959	1197	hybrid sensory histidine kinase in two-component r	97.4
COG3290	537	CitA Signal transduction histidine kinase regulati	97.39
PRK11360	607	sensory histidine kinase AtoS; Provisional	97.34
KOG3558	768	consensus Hypoxia-inducible factor 1/Neuronal PAS	97.27
smart00091	67	PAS PAS domain. PAS motifs appear in archaea, euba	97.27
TIGR02373	124	photo_yellow photoactive yellow protein. Members o	97.19
COG3852	363	NtrB Signal transduction histidine kinase, nitroge	97.08
PRK15053	545	dpiB sensor histidine kinase DpiB; Provisional	97.07
COG2461	409	Uncharacterized conserved protein [Function unknow	97.05
COG3290	537	CitA Signal transduction histidine kinase regulati	97.01
TIGR02373	124	photo_yellow photoactive yellow protein. Members o	96.97
PF08670	148	MEKHLA: MEKHLA domain; InterPro: IPR013978 The MEK	96.91
PF08670	148	MEKHLA: MEKHLA domain; InterPro: IPR013978 The MEK	96.87
KOG1229	775	consensus 3'5'-cyclic nucleotide phosphodiesterase	96.56
KOG3561	803	consensus Aryl-hydrocarbon receptor nuclear transl	96.2
KOG3753	1114	consensus Circadian clock protein period [Signal t	96.16
KOG3560	712	consensus Aryl-hydrocarbon receptor [Transcription	96.07
COG3283	511	TyrR Transcriptional regulator of aromatic amino a	96.06
COG5002	459	VicK Signal transduction histidine kinase [Signal	96.02
smart00086	43	PAC Motif C-terminal to PAS motifs (likely to cont	95.91
PRK11086	542	sensory histidine kinase DcuS; Provisional	95.91
KOG3560	712	consensus Aryl-hydrocarbon receptor [Transcription	95.69
COG3283	511	TyrR Transcriptional regulator of aromatic amino a	95.62
COG3852	363	NtrB Signal transduction histidine kinase, nitroge	95.13
PF07310	137	PAS_5: PAS domain; InterPro: IPR009922 This family	94.61
PF08446	110	PAS_2: PAS fold; InterPro: IPR013654 The PAS fold	94.51
COG5000	712	NtrY Signal transduction histidine kinase involved	93.14
KOG3561	803	consensus Aryl-hydrocarbon receptor nuclear transl	90.82
PRK09959	1197	hybrid sensory histidine kinase in two-component r	90.04
COG3284	606	AcoR Transcriptional activator of acetoin/glycerol	88.92
KOG3559	598	consensus Transcriptional regulator SIM1 [Transcri	87.81
PRK10841	924	hybrid sensory kinase in two-component regulatory	86.99
PF08446	110	PAS_2: PAS fold; InterPro: IPR013654 The PAS fold	84.55

>TIGR02040 PpsR-CrtJ transcriptional regulator PpsR

Probab=99.87  E-value=1.7e-20  Score=167.44  Aligned_cols=202  Identities=18%  Similarity=0.134  Sum_probs=146.3

Q ss_pred             hHHHHHHHHHhhCCCEEEEEcC-CCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeE
Q 020514           15 RYTLWVHEALDELPDSFTITDP-SISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIE   93 (325)
Q Consensus        15 ~~~~~~~~~~~~~~~~i~~~d~-~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~   93 (325)
                      ..+.+++.+++.++++++++|. +   |.++++|++++.++||+.++++|+++..++++.+...+...+......+....
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            3456899999999999999998 7   99999999999999999999999998777777666655666666666665544


Q ss_pred             EEEEEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchhhhhcccCcccCCCCchhhHHHhhhhhhhhcccchh
Q 020514           94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLL  173 (325)
Q Consensus        94 ~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  173 (325)
                      .++.  .++|...| .+.+.++..  ++. ..+++...|||+++++                                  
T Consensus       207 ~~~~--~~~~~~~~-~~~~~~~~~--~~~-~~~l~~~~dit~~~~~----------------------------------  246 (442)
T TIGR02040       207 VRIL--LRRSQKRL-LVVVSVFRQ--DGE-SLFLCQLSPAGATQPV----------------------------------  246 (442)
T ss_pred             eEEE--EcCCCeEE-EEEEEEEEe--CCc-eEEEEEEcccchhhhh----------------------------------
Confidence            4443  33444344 345666654  333 3567788899998773                                  


Q ss_pred             hhhhhccccccCCCCcccchhhhHHHHHHHHhhhhhhHhhhhccceeeccceeeeeecCCCCcccchhhhHhhhhccCCc
Q 020514          174 DLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQS  253 (325)
Q Consensus       174 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  253 (325)
                                              +....                                      +.++.++++++++
T Consensus       247 ------------------------e~~~~--------------------------------------~~~~~l~e~~~d~  264 (442)
T TIGR02040       247 ------------------------GDELS--------------------------------------ENLARLYHEAPDA  264 (442)
T ss_pred             ------------------------hHHHH--------------------------------------HHHHHHHHhCCce
Confidence                                    00000                                      0155688899999


Q ss_pred             eEEecCCCCCCCeEEEehhhHHhhCCC-cccccccccccccCCCCC--hHHHHHHHH-------hhccccCCCceeeEEe
Q 020514          254 FVLIDPHLPDMPMVYASDAFLKLTGYD-RNEVVGQNCRFLNGVDTD--TTVLYQVSI-------AISPYPKKKSIYMEYV  323 (325)
Q Consensus       254 i~~~d~~~~dg~i~~~N~a~~~~~Gy~-~~e~iG~~~~~l~~~~~~--~~~~~~~~~-------e~~~~~kdG~~~~~~~  323 (325)
                      |+++|.   +|+|+++|++|++|+||+ .++++|+++..+.++...  ......+..       +....++||+.+|+++
T Consensus       265 I~v~D~---~G~I~~~N~a~~~l~G~~~~~~l~G~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~G~~~~ve~  341 (442)
T TIGR02040       265 IVFSDA---DGTIRGANEAFLELTDSSSLEAVRGRTLDRWLGRGGVDLRVLLSNVRRTGQVRLYATTLTGEFGAQTEVEI  341 (442)
T ss_pred             EEEEcC---CCcEEehhHHHHHHhCCCChHHHcCCCHHHHhCCCcccHHHHHHHHhhcCceEEEEEEEEcCCCCEEEEEE
Confidence            999998   479999999999999997 578999998776653322  222333332       3345689999999987


Q ss_pred             e
Q 020514          324 R  324 (325)
Q Consensus       324 ~  324 (325)
                      +
T Consensus       342 s  342 (442)
T TIGR02040       342 S  342 (442)
T ss_pred             E
Confidence            6

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).

>PRK13560 hypothetical protein; Provisional

Probab=99.85  E-value=1.1e-19  Score=174.49  Aligned_cols=185  Identities=15%  Similarity=0.156  Sum_probs=145.1

Q ss_pred             HHhhhhhhHHHHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHH
Q 020514            8 IEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIR   87 (325)
Q Consensus         8 ~~~~~~~~~~~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~   87 (325)
                      .++.+. ....+++.++++++++++++|.+   |.++++|++++.++||+.++++|+++..+.++.............+.
T Consensus       195 ae~~l~-~~~~~l~~l~e~~~~~i~~~d~~---g~i~~~N~~~~~~~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~  270 (807)
T PRK13560        195 AEERID-EALHFLQQLLDNIADPAFWKDED---AKVFGCNDAACLACGFRREEIIGMSIHDFAPAQPADDYQEADAAKFD  270 (807)
T ss_pred             HHHHHH-HHHHHHHHHHhhCCCeEEEEcCC---CCEEEEhHHHHHHhCCCHHHHcCCcchhcCCcchhHHHHHHHHHHhc
Confidence            344444 56778999999999999999999   99999999999999999999999998887766544443334444555


Q ss_pred             hCCCeEEEEEEEecCCCeEEEEEEE--EEeecCCCCeeeEEEEEEeccccchhhhhcccCcccCCCCchhhHHHhhhhhh
Q 020514           88 EERPIEVNLLNYKKDGTPFWMLFKM--SLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRR  165 (325)
Q Consensus        88 ~~~~~~~e~~~~~~dg~~~~~~~~~--~~~~~~~~g~~~~~~~~~~DITe~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~  165 (325)
                      .+.....+..+.+++|..+|+.+..  .|+.+ .+|.+.+++++.+|||++|++                          
T Consensus       271 ~~~~~~~e~~~~~~dG~~~~~~~~~~~~~~~~-~~g~~~g~~~~~~DITerk~~--------------------------  323 (807)
T PRK13560        271 ADGSQIIEAEFQNKDGRTRPVDVIFNHAEFDD-KENHCAGLVGAITDISGRRAA--------------------------  323 (807)
T ss_pred             cCCceEEEEEEEcCCCCEEEEEEEecceEEEc-CCCCEEEEEEEEEechHHHHH--------------------------
Confidence            5666677888889999999766554  55667 788999999999999999995                          


Q ss_pred             hhcccchhhhhhhccccccCCCCcccchhhhHHHHHHHHhhhhhhHhhhhccceeeccceeeeeecCCCCcccchhhhHh
Q 020514          166 EVCSDSLLDLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYI  245 (325)
Q Consensus       166 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  245 (325)
                                                      +..++..                                   +..++.
T Consensus       324 --------------------------------e~~L~~s-----------------------------------e~~l~~  336 (807)
T PRK13560        324 --------------------------------ERELLEK-----------------------------------EDMLRA  336 (807)
T ss_pred             --------------------------------HHHHHHH-----------------------------------HHHHHH
Confidence                                            1122222                                   122556


Q ss_pred             hhhccCCceEEecCCCCCCCeEEE-ehhhHHhhCCCccccccccccccc
Q 020514          246 SLGRIKQSFVLIDPHLPDMPMVYA-SDAFLKLTGYDRNEVVGQNCRFLN  293 (325)
Q Consensus       246 ~~~~~~~~i~~~d~~~~dg~i~~~-N~a~~~~~Gy~~~e~iG~~~~~l~  293 (325)
                      ++++++.+++++|.+   |.++++ |+++++++||++++++|+++..+.
T Consensus       337 l~~~~~~~i~~~d~~---g~i~~~nn~~~~~~~G~~~~e~~g~~~~~~~  382 (807)
T PRK13560        337 IIEAAPIAAIGLDAD---GNICFVNNNAAERMLGWSAAEVMGKPLPGMD  382 (807)
T ss_pred             HHHhCcccEEEEcCC---CCEEEecCHHHHHHhCCCHHHHcCCCccccC
Confidence            788899999999984   799987 567788999999999999876654

>PRK09776 putative diguanylate cyclase; Provisional

Probab=99.85  E-value=2.7e-20  Score=184.18  Aligned_cols=283  Identities=14%  Similarity=0.147  Sum_probs=179.2

Q ss_pred             hHHHHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhC-CCeE
Q 020514           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREE-RPIE   93 (325)
Q Consensus        15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~-~~~~   93 (325)
                      ..+.+++.+++.++.+++++|.+   |.++++|+++++++||+.++++|++...+.+|++.......+.....+. ..+.
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            46678999999999999999999   9999999999999999999999999888888877665555555544443 3456


Q ss_pred             EEEEEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchhhhhcccCcccCCCCchhhHHHhhhhhhhhcccchh
Q 020514           94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLL  173 (325)
Q Consensus        94 ~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  173 (325)
                      .+.+..+++|..+|+..+..|+.+ .+|.+.+++++.+|||++|++|+++...          +..++         .+.
T Consensus       357 ~e~~~~~~dG~~~~~~~~~~~~~~-~~g~~~~~i~~~~DITerk~~e~~l~~~----------~~~~~---------~~~  416 (1092)
T PRK09776        357 MEKRYYRRDGEVVWALLAVSLVRD-TDGTPLYFIAQIEDINELKRTEQVNERL----------MERIT---------LAN  416 (1092)
T ss_pred             eeeEEEcCCCCEEEEEEEEEEEEC-CCCCEeeehhhHHhhHHHHHHHHHHHHH----------HHHHH---------HHH
Confidence            778888999999999999999998 8899999999999999999985443221          11111         111


Q ss_pred             hhhhh--ccccccC------------CCCcccchhhh-------HHHHHHHHhhhhhhHhhh------hccceeecccee
Q 020514          174 DLDRV--LALDSDD------------TGLEIEDSCEA-------SDLEKRKAATAIDNILSV------LTHYSQLTGRLV  226 (325)
Q Consensus       174 ~~~~~--~~~~~~~------------~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~  226 (325)
                      +..+.  +.++.+.            .|++.++....       ...+..............      -.+.....| ..
T Consensus       417 ~~~~~~i~~~d~~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~~p~d~~~~~~~~~~~~~~~~~~~~e~r~~~~dG-~~  495 (1092)
T PRK09776        417 EAGGIGIWEWDLKPNIISWDKRMFELYEIPPHIKPTWQVWYACLHPEDRQRVEKEIRDALQGRSPFKLEFRIVVKDG-VR  495 (1092)
T ss_pred             HhcCceEEEEecCCCeEeeCHHHHHHhCCCcccCCCHHHHHHhcCHhHHHHHHHHHHHHHhcCCCeeEEEEEEcCCc-eE
Confidence            11111  1111111            12221111000       000000000001100000      000111122 11


Q ss_pred             e--------------------------eeecCCCCcccchhhhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCC
Q 020514          227 C--------------------------GKRCSLPGMGFISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYD  280 (325)
Q Consensus       227 ~--------------------------~~~~~~~~~~~~~~~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~  280 (325)
                      +                          .++.....+....++++.++++++++++++|.+   |+|+++|+++++++||+
T Consensus       496 w~~~~~~~~~d~~G~~~~~ig~~~DITerk~~e~~L~~~~~~l~~~l~~~~~~i~~~D~~---g~i~~~N~a~~~l~G~~  572 (1092)
T PRK09776        496 HIRALANRVLNKDGEVERLLGINMDMTEVRQLNEALFQEKERLHITLDSIGEAVVCTDMA---MKVTFMNPVAEKMTGWT  572 (1092)
T ss_pred             EEEEeeEEEECCCCCEEEEEeeeeehhHHHHHHHHHHHHHHHHHHHHhccccEEEEECCC---CeEEEEcHHHHHHhCCC
Confidence            1                          111111122233456888999999999999984   79999999999999999


Q ss_pred             cccccccccccccCCCC--ChHHHHHHHH------------hhccccCCCceeeEEee
Q 020514          281 RNEVVGQNCRFLNGVDT--DTTVLYQVSI------------AISPYPKKKSIYMEYVR  324 (325)
Q Consensus       281 ~~e~iG~~~~~l~~~~~--~~~~~~~~~~------------e~~~~~kdG~~~~~~~~  324 (325)
                      .+|++|+++..+.++.+  .......+..            +....++||+.+|+.++
T Consensus       573 ~~e~iG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~  630 (1092)
T PRK09776        573 QEEALGVPLLTVLHITFGDNGPLMENIYSCLTSRSAAYLEQDVVLHCRSGGSYDVHYS  630 (1092)
T ss_pred             HHHHcCCCHHHHcccccCCcchhhHHHHHHHhcCCCccccceEEEEeCCCcEEEEEEE
Confidence            99999999877654321  1112222222            34456789999998764

>TIGR02040 PpsR-CrtJ transcriptional regulator PpsR

Probab=99.82  E-value=1e-19  Score=162.48  Aligned_cols=195  Identities=14%  Similarity=0.086  Sum_probs=138.5

Q ss_pred             HhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCC-CeEEEEEEEecC
Q 020514           24 LDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREER-PIEVNLLNYKKD  102 (325)
Q Consensus        24 ~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~-~~~~e~~~~~~d  102 (325)
                      ++.++++++++|.+   |.++++|++++.++||+.++++|+++..++++++.......+......+. .+..+.....++
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            57789999999999   99999999999999999999999999888887765555555545455543 344455555566


Q ss_pred             CCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchhhhhcccCcccCCCCchhhHHHhhhhhhhhcccchhhhhhhcccc
Q 020514          103 GTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDRVLALD  182 (325)
Q Consensus       103 g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  182 (325)
                      |..+|+.++..++.+   +  .+++++.+|||++++.+++...                                     
T Consensus        79 g~~~~~~~~~~~~~~---~--~~~~~i~rDi~~~~~~~~~l~~-------------------------------------  116 (442)
T TIGR02040        79 SFELPMRFILVRLGA---D--RGVLALGRDLRAVAELQQQLVA-------------------------------------  116 (442)
T ss_pred             CCccCeEEEEEEeCC---C--CeEEEEecccHHHHHHHHHHHH-------------------------------------
Confidence            667777666666543   2  2567889999998874221100                                     


Q ss_pred             ccCCCCcccchhhhHHHHHHHHhhhhhhHhhhhccceeeccceeeeeecCCCCcccchhhhHhhhhccCCceEEecCCCC
Q 020514          183 SDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQSFVLIDPHLP  262 (325)
Q Consensus       183 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~i~~~d~~~~  262 (325)
                                           ....+++-...                     ++..+..++.++++++++++++|..  
T Consensus       117 ---------------------~~~~~e~~~~~---------------------l~~~e~r~~~l~e~~~~~i~~~d~~--  152 (442)
T TIGR02040       117 ---------------------AQQAMERDYWT---------------------LREMETRYRVVLEVSSDAVLLVDMS--  152 (442)
T ss_pred             ---------------------HHHHHHHHHHH---------------------HHHHHHHHHHHHhhCCceEEEEECC--
Confidence                                 00000000000                     0112334777899999999999973  


Q ss_pred             CCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH
Q 020514          263 DMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI  307 (325)
Q Consensus       263 dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~  307 (325)
                      +|+|+++|+++++|+||++++++|+++..+++|+........+.+
T Consensus       153 ~g~i~~~N~a~~~l~G~~~~el~g~~~~~~~~~~~~~~~~~~l~~  197 (442)
T TIGR02040       153 TGRIVEANSAAAALLGGVGQSLVGRAFPQEFEGRRREELMLTLRN  197 (442)
T ss_pred             CCEEEEEcHHHHHHhCcCHHHHcCCCHHHhCCHHHHHHHHHHHHH
Confidence            489999999999999999999999999888877766555555543

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=99.80  E-value=6.5e-19  Score=159.88  Aligned_cols=180  Identities=22%  Similarity=0.340  Sum_probs=145.9

Q ss_pred             HHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEEEE
Q 020514           18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLL   97 (325)
Q Consensus        18 ~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~   97 (325)
                      +.|+.+++.++.+++++|.+   +.++++|++++.++||++++++|++...+.++.........+.+.+..+..+..+..
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            47889999999999999999   999999999999999999999998866666555555556666666777777777777


Q ss_pred             EEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchhhhhcccCcccCCCCchhhHHHhhhhhhhhcccchhhhhh
Q 020514           98 NYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDR  177 (325)
Q Consensus        98 ~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  177 (325)
                      ..+++|..+|+...+.|+.+ .+|.+.+++++.+|||+++++                                      
T Consensus        81 ~~~~~g~~~~~~~~~~~~~~-~~g~~~~~~~~~~DIt~~k~~--------------------------------------  121 (494)
T TIGR02938        81 NRRKDGELYLAELTVAPVLN-EAGETTHFLGMHRDITELHRL--------------------------------------  121 (494)
T ss_pred             ccCCCccchhhheeeEEEEC-CCCCEEEEEEehhhhhHHHHH--------------------------------------
Confidence            78889999999999999998 889999999999999999985                                      


Q ss_pred             hccccccCCCCcccchhhhHHHHHHHHhhhhhhHhhhhccceeeccceeeeeecCCCCcccchhhhHhhhhccCCceEEe
Q 020514          178 VLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQSFVLI  257 (325)
Q Consensus       178 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~i~~~  257 (325)
                                          +..++...                                   ..++.++++++++++++
T Consensus       122 --------------------e~~l~~~~-----------------------------------~~~~~~~~~~~~~i~~~  146 (494)
T TIGR02938       122 --------------------EQVVANQK-----------------------------------LLIESVVDAAPVAFVLL  146 (494)
T ss_pred             --------------------HHHHHHHH-----------------------------------HHHHHHHhcccceEEEE
Confidence                                11111111                                   12455788889999999


Q ss_pred             cCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCC
Q 020514          258 DPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDT  297 (325)
Q Consensus       258 d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~  297 (325)
                      |.   +|.++++|++|++++|+...+..+..+..+.+++.
T Consensus       147 d~---~~~i~~~N~~~~~~~g~~~~~~~~~~~~~~~~~~~  183 (494)
T TIGR02938       147 DP---TGRVILDNQEYKKLATDLRVKEPAHTVLDLLREAW  183 (494)
T ss_pred             cC---CCCEEEechhHHHhhchhhhhHHHHHHHHHhhHHh
Confidence            97   47999999999999999988887776655554443

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.

>PRK13560 hypothetical protein; Provisional

Probab=99.80  E-value=3.2e-18  Score=164.54  Aligned_cols=205  Identities=12%  Similarity=0.037  Sum_probs=146.1

Q ss_pred             HHHH-HHHHhhCCCEEEEEcCCCCCCC----EEEechHHHHhcCCChhhhcCCC--CCcccCCCCChHHHH-------HH
Q 020514           17 TLWV-HEALDELPDSFTITDPSISGHP----IVFASRGFLKMSGFSRAEIIGRN--GRMFQGPRTNRRTIM-------EI   82 (325)
Q Consensus        17 ~~~~-~~~~~~~~~~i~~~d~~~~~~~----~~~~N~~~~~~~G~~~~ei~g~~--~~~l~~~~~~~~~~~-------~~   82 (325)
                      .+.+ +.+++++|.+++.++.+   +.    +.+++++...++|+.+.++++..  +..+++|++...+..       .+
T Consensus        66 ~e~~~r~l~~~~p~~i~~~~~~---~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~p~d~~~~~~~~~~~~~~~  142 (807)
T PRK13560         66 REQCERNLKANIPGGMFLFALD---GDGTFSFPSLLDANGELAAIAKHDLMADKGLLAMLIGGDDGDFFFANPFRSAETI  142 (807)
T ss_pred             HHHHHHHHHhcCCceEEEEEEc---CccccccceeeccchhHHHhcCcccCCccchhhhhcCCCcchhhhhChhhHHHHH
Confidence            3444 99999999999998877   55    33477777788888777766533  344667776554432       22


Q ss_pred             HHHHHhCCCeEEEEEEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchhhhhcccCcccCCCCchhhHHHhhh
Q 020514           83 REAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGS  162 (325)
Q Consensus        83 ~~~~~~~~~~~~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~~~~~~~~~~~~~~~~~~~~~~~~  162 (325)
                      ..++..+.....++++.++||+  |+.+...|.++ .+|.+ .+.++..|||++|+++                      
T Consensus       143 ~~~~~~~~~~~~e~r~~~~dg~--~~~~~~~~~~~-~~g~~-~~~g~~~DIT~rk~ae----------------------  196 (807)
T PRK13560        143 AMALQSDDWQEEEGHFRCGDGR--FIDCCLRFERH-AHADD-QVDGFAEDITERKRAE----------------------  196 (807)
T ss_pred             HHHhccCcccceEEEEEeCCcc--EEEEEeeeeec-CCCce-EEEEEEEccchHHHHH----------------------
Confidence            2233344556678888888986  66677778877 66765 6889999999999851                      


Q ss_pred             hhhhhcccchhhhhhhccccccCCCCcccchhhhHHHHHHHHhhhhhhHhhhhccceeeccceeeeeecCCCCcccchhh
Q 020514          163 CRREVCSDSLLDLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSS  242 (325)
Q Consensus       163 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  242 (325)
                                                          ..++..                                   ...
T Consensus       197 ------------------------------------~~l~~~-----------------------------------~~~  205 (807)
T PRK13560        197 ------------------------------------ERIDEA-----------------------------------LHF  205 (807)
T ss_pred             ------------------------------------HHHHHH-----------------------------------HHH
Confidence                                                112221                                   122


Q ss_pred             hHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH----------hhccc
Q 020514          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI----------AISPY  312 (325)
Q Consensus       243 l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~----------e~~~~  312 (325)
                      |+.++++++++++++|.   ||+|+++|+++++++||+++|++|+++.++.++............          +.+++
T Consensus       206 l~~l~e~~~~~i~~~d~---~g~i~~~N~~~~~~~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~  282 (807)
T PRK13560        206 LQQLLDNIADPAFWKDE---DAKVFGCNDAACLACGFRREEIIGMSIHDFAPAQPADDYQEADAAKFDADGSQIIEAEFQ  282 (807)
T ss_pred             HHHHHhhCCCeEEEEcC---CCCEEEEhHHHHHHhCCCHHHHcCCcchhcCCcchhHHHHHHHHHHhccCCceEEEEEEE
Confidence            56688999999999997   579999999999999999999999999998765543332111111          66778


Q ss_pred             cCCCceeeEEee
Q 020514          313 PKKKSIYMEYVR  324 (325)
Q Consensus       313 ~kdG~~~~~~~~  324 (325)
                      ++||+.+|+++.
T Consensus       283 ~~dG~~~~~~~~  294 (807)
T PRK13560        283 NKDGRTRPVDVI  294 (807)
T ss_pred             cCCCCEEEEEEE
Confidence            899999987654

>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional

Probab=99.76  E-value=3.4e-17  Score=157.20  Aligned_cols=201  Identities=18%  Similarity=0.248  Sum_probs=150.0

Q ss_pred             HHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCC----CeE
Q 020514           18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREER----PIE   93 (325)
Q Consensus        18 ~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~----~~~   93 (325)
                      ..+..+++.++.+++++|.+   |.++++|+++++++||++++++|+++..+.++.........+......+.    .+.
T Consensus        12 ~~~~~~le~~~~~i~~~d~~---g~i~~~N~~~~~l~G~s~eeliG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   88 (799)
T PRK11359         12 GIFFPALEQNMMGAVLINEN---DEVLFFNPAAEKLWGYKREEVIGNNIDMLIPRDLRPAHPEYIRHNREGGKARVEGMS   88 (799)
T ss_pred             hhHHHHHHhhcCcEEEEcCC---CeEEEEcHHHHHHhCCCHHHHcCCCHHHhcCccccccchHHHhhhhccCCccccccc
Confidence            35667899999999999999   99999999999999999999999998877776654433333443333332    234


Q ss_pred             EEEEEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchhhhhcccCcccCCCCchhhHHHhhhhhhhhcccchh
Q 020514           94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLL  173 (325)
Q Consensus        94 ~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  173 (325)
                      .+++..+++|..+|+.+...|+..  .|. .+++++.+|||++++.                                  
T Consensus        89 ~e~~~~~~dG~~~~v~~~~~~~~~--~g~-~~~~~~~~DiT~~~~~----------------------------------  131 (799)
T PRK11359         89 RELQLEKKDGSKIWTRFALSKVSA--EGK-VYYLALVRDASVEMAQ----------------------------------  131 (799)
T ss_pred             eeeEEecCCcCEEEEEEEeeeecc--CCc-eEEEEEEeeccchhhh----------------------------------
Confidence            477788899999999999888753  455 4578889999998773                                  


Q ss_pred             hhhhhccccccCCCCcccchhhhHHHHHHHHhhhhhhHhhhhccceeeccceeeeeecCCCCcccchhhhHhhhhccCCc
Q 020514          174 DLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQS  253 (325)
Q Consensus       174 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  253 (325)
                                              +...+                                       .+..++++++++
T Consensus       132 ------------------------~~~~~---------------------------------------~~~~~~~~~~~~  148 (799)
T PRK11359        132 ------------------------KEQTR---------------------------------------QLIIAVDHLDRP  148 (799)
T ss_pred             ------------------------HHHHH---------------------------------------HHHHHHhcCCCc
Confidence                                    00000                                       022356777899


Q ss_pred             eEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCC-CCChHHHHHHHH----------hhccccCCCceeeEE
Q 020514          254 FVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGV-DTDTTVLYQVSI----------AISPYPKKKSIYMEY  322 (325)
Q Consensus       254 i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~-~~~~~~~~~~~~----------e~~~~~kdG~~~~~~  322 (325)
                      ++++|.   +|+++++|+++++++||+.++++|+++..+.++ .........+..          +++..+++|..+|+.
T Consensus       149 i~~~d~---~g~i~~~N~~~~~l~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~  225 (799)
T PRK11359        149 VIVLDP---ERRIVQCNRAFTEMFGYCISEASGMQPDTLLNIPEFPADNRIRLQQLLWKTARDQDEFLLLTRTGEKIWIK  225 (799)
T ss_pred             EEEEcC---CCcEEEEChhhHhhhCCCHHHHCCCChHHhcCCCCCcHHHHHHHHHhhccCCCCcceeEEeCCCCCEEEEE
Confidence            999997   479999999999999999999999998876543 333333333332          556677999999986


Q ss_pred             ee
Q 020514          323 VR  324 (325)
Q Consensus       323 ~~  324 (325)
                      ++
T Consensus       226 ~~  227 (799)
T PRK11359        226 AS  227 (799)
T ss_pred             ee
Confidence            53

>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=99.71  E-value=3.9e-16  Score=110.50  Aligned_cols=104  Identities=27%  Similarity=0.431  Sum_probs=94.9

Q ss_pred             CCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEEEEEEecCCCeEE
Q 020514           28 PDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFW  107 (325)
Q Consensus        28 ~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg~~~~  107 (325)
                      |++++++|.+   |.++++|+++++++|+++++++|+++..++++.........+.+.+..+..+..+.....++|..+|
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            6899999999   9999999999999999999999999988888877778888889999988889999999999999999


Q ss_pred             EEEEEEEeecCCCCeeeEEEEEEecccc
Q 020514          108 MLFKMSLVFGKEDGRATHFVAVQVPIVS  135 (325)
Q Consensus       108 ~~~~~~~~~~~~~g~~~~~~~~~~DITe  135 (325)
                      +.+++.|+.+ ++|.+.+++++++|||+
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

...

>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=99.64  E-value=3.8e-15  Score=106.55  Aligned_cols=110  Identities=26%  Similarity=0.452  Sum_probs=97.3

Q ss_pred             HhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEEEEEEecCC
Q 020514           24 LDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDG  103 (325)
Q Consensus        24 ~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg  103 (325)
                      |+++|++++++|.+   ++++++|+++.+++|++.++++|+++..++++.....+...+.+++.++.....+..... +|
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            67899999999999   999999999999999999999999988888887777778888888888877666555444 89


Q ss_pred             CeEEEEEEEEEeecCCCCeeeEEEEEEeccccchh
Q 020514          104 TPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKH  138 (325)
Q Consensus       104 ~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~  138 (325)
                      ...|+.+++.|+.+ .+|.+.+++++.+|||++|+
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            99999999999999 89999999999999999975

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.

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

Probab=99.63  E-value=1.1e-14  Score=104.65  Aligned_cols=112  Identities=23%  Similarity=0.366  Sum_probs=94.1

Q ss_pred             HHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeE-EEE
Q 020514           18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIE-VNL   96 (325)
Q Consensus        18 ~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~-~e~   96 (325)
                      ++|+.++++++.+++++|.+   |.++++|+++++++|++.++++|+++..++++.+.......+...+..+.... ...
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            37889999999999999999   99999999999999999999999999888877765556677777777766543 334


Q ss_pred             EEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEecc
Q 020514           97 LNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPI  133 (325)
Q Consensus        97 ~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DI  133 (325)
                      ....++|..+|+.++..|+.+ .+|.+.+++++++||
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            344469999999999999999 888899999999997

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=99.44  E-value=3.7e-12  Score=122.04  Aligned_cols=122  Identities=15%  Similarity=0.193  Sum_probs=106.8

Q ss_pred             hHHHHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEE
Q 020514           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV   94 (325)
Q Consensus        15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   94 (325)
                      ....+++.++++++++++++|.+   |.++++|+++++++|++.++++|+++..++++.............+..+.....
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            45567899999999999999999   999999999999999999999999988887766555555555666677777888


Q ss_pred             EEEEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchhhh
Q 020514           95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMR  140 (325)
Q Consensus        95 e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~~  140 (325)
                      +.....++|..+|+.++..|+.+ .+|.+.+++++.+|||++|+++
T Consensus       229 e~~~~~~~G~~~~~~~~~~pi~~-~~g~~~g~v~~~~DITe~k~~e  273 (779)
T PRK11091        229 EQWLDYPDGRKACFELRKVPFYD-RVGKRHGLMGFGRDITERKRYQ  273 (779)
T ss_pred             EEEEEcCCCCEEEEEEEeeeEEc-CCCCEEEEEEEEeehhHHHHHH
Confidence            88888899999999999999998 8899999999999999999973

>PRK13559 hypothetical protein; Provisional

Probab=99.41  E-value=6.9e-12  Score=109.37  Aligned_cols=125  Identities=38%  Similarity=0.676  Sum_probs=105.4

Q ss_pred             hHHHHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEE
Q 020514           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV   94 (325)
Q Consensus        15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   94 (325)
                      .....+..+++.++.+++++|.+..++.++++|+++++++||+.++++|+++..+.++.........+...+..+..+..
T Consensus        40 ~~~~~~~~~~e~~~~~i~i~D~~~~~g~i~~~N~a~~~l~G~~~~e~iG~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~  119 (361)
T PRK13559         40 ASGRLFEQAMEQTRMAMCITDPHQPDLPIVLANQAFLDLTGYAAEEVVGRNCRFLQGAATDPIAVAKIRAAIAAEREIVV  119 (361)
T ss_pred             hhhhHHHHHHHhCCCcEEEecCCCCCCcEEEEchHHHHHhCCCHHHHcCCChhhhcCCCCCHHHHHHHHHHhccCCceEE
Confidence            34567888999999999999974222689999999999999999999999877666665555556666777777777777


Q ss_pred             EEEEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchhhh
Q 020514           95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMR  140 (325)
Q Consensus        95 e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~~  140 (325)
                      +.....++|..+|+.++..|+++ .+|.+.+++++.+|||++|+++
T Consensus       120 e~~~~~~dG~~~~~~~~~~~i~d-~~G~~~~~v~~~~DITerk~~e  164 (361)
T PRK13559        120 ELLNYRKDGEPFWNALHLGPVYG-EDGRLLYFFGSQWDVTDIRAVR  164 (361)
T ss_pred             EEEEEcCCCCEEEEEEEEEEEEc-CCCCEEEeeeeeeehhcchhhH
Confidence            88888899999999999999998 8899999999999999999863

>PRK13557 histidine kinase; Provisional

Probab=99.38  E-value=9.3e-12  Score=114.45  Aligned_cols=128  Identities=37%  Similarity=0.672  Sum_probs=110.1

Q ss_pred             hHHHHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEE
Q 020514           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV   94 (325)
Q Consensus        15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   94 (325)
                      ....+|..+++.++.+++++|....+|.++|+|++|++++||+.++++|+++..+.++.+.......+...+..+..+..
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            45678999999999999999963223899999999999999999999999988888777766667777777777777777


Q ss_pred             EEEEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchhhhhcc
Q 020514           95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG  143 (325)
Q Consensus        95 e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~~~~~  143 (325)
                      +....+++|..+|+.++..|+.+ .+|.+.+++++.+|||++++++++.
T Consensus       107 ~~~~~~~~G~~~~~~~~~~~i~~-~~g~~~~~~~~~~dit~~~~~e~~l  154 (540)
T PRK13557        107 EILNYRKDGSSFWNALFVSPVYN-DAGDLVYFFGSQLDVSRRRDAEDAL  154 (540)
T ss_pred             EEEEEeCCCCEEEEEEEEEEeEC-CCCCEEEEEEEecChHHHHHHHHHH
Confidence            88888899999999999999998 8899999999999999999875443

>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=99.34  E-value=2e-12  Score=91.21  Aligned_cols=71  Identities=21%  Similarity=0.351  Sum_probs=60.8

Q ss_pred             CCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH----------hhccccCCCceee
Q 020514          251 KQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI----------AISPYPKKKSIYM  320 (325)
Q Consensus       251 ~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~----------e~~~~~kdG~~~~  320 (325)
                      |+|++++|.   ||+|+++|++|++++||++++++|+++.++.++.........+.+          ++.+++++|+.+|
T Consensus         1 p~~i~i~d~---~g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~~   77 (104)
T PF13426_consen    1 PDGIFILDP---DGRILYVNPAFERLFGYSREELIGKSISDFFPEEDRPEFEEQIERALEEGGSWSGEVRLRRKDGETFW   77 (104)
T ss_dssp             -SEEEEEET---TSBEEEE-HHHHHHHTS-HHHHTTSBGGGGCSTTSCHHHHHHHHHHHHHTSSEEEEEEEEETTSEEEE
T ss_pred             CEEEEEECC---cCcEEehhHHHHHHHCcCHHHHcCCCcccccCcccchhhHHHHHHHHhcCCceeEEEEEEcCCCCEEE
Confidence            589999998   479999999999999999999999999999988877777776666          7778899999999


Q ss_pred             EEee
Q 020514          321 EYVR  324 (325)
Q Consensus       321 ~~~~  324 (325)
                      +.++
T Consensus        78 ~~~~   81 (104)
T PF13426_consen   78 VEVS   81 (104)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            9886

...

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

Probab=99.34  E-value=1.7e-12  Score=93.14  Aligned_cols=81  Identities=19%  Similarity=0.194  Sum_probs=64.6

Q ss_pred             hhhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH-----------hh
Q 020514          241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI-----------AI  309 (325)
Q Consensus       241 ~~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~-----------e~  309 (325)
                      ++++.+++++++|++++|.   +|+|+++|++++++|||++++++|+++.++.+++........+.+           +.
T Consensus         1 e~~~~i~~~~~~~i~~~d~---~g~I~~~N~a~~~l~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   77 (113)
T PF00989_consen    1 ERYRAILENSPDGIFVIDE---DGRILYVNQAAEELLGYSREELIGKSLFDLIHPEDRRELRERLRQALSQGESGESFEV   77 (113)
T ss_dssp             HHHHHHHHCSSSEEEEEET---TSBEEEECHHHHHHHSS-HHHHTTSBGGGGCSGGGHHHHHHHHHHHHHHCCHECEEEE
T ss_pred             CHHHHHHhcCCceEEEEeC---cCeEEEECHHHHHHHccCHHHHcCCcHHHhcCchhhHHHHHHHHHHHHcCCCceeEEE
Confidence            3578899999999999997   589999999999999999999999999999887754444444443           33


Q ss_pred             ccccCCCceeeEEee
Q 020514          310 SPYPKKKSIYMEYVR  324 (325)
Q Consensus       310 ~~~~kdG~~~~~~~~  324 (325)
                      ....++|+.+|+.++
T Consensus        78 ~~~~~~g~~~~~~~~   92 (113)
T PF00989_consen   78 RFRLRDGRPRWVEVR   92 (113)
T ss_dssp             EEEETTSCEEEEEEE
T ss_pred             EEEecCCcEEEEEEE
Confidence            333469999998765

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 ....

>PRK13558 bacterio-opsin activator; Provisional

Probab=99.25  E-value=3.5e-10  Score=106.58  Aligned_cols=124  Identities=39%  Similarity=0.703  Sum_probs=104.8

Q ss_pred             HHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEEEEE
Q 020514           19 WVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLN   98 (325)
Q Consensus        19 ~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~   98 (325)
                      .+..+++.++.++++.|....++.++++|+++++++||+.++++|+++..+.++.........+...+..+.....+...
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            45778999999999998522238899999999999999999999998877777666555566667777777788888888


Q ss_pred             EecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchhhhhcc
Q 020514           99 YKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG  143 (325)
Q Consensus        99 ~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~~~~~  143 (325)
                      .+++|..+|+.++..|+.+ .+|.+.+++++.+|||++|++++++
T Consensus       229 ~~~dG~~~~~~~~~~pi~d-~~G~~~~~vgi~~DITerk~~E~~L  272 (665)
T PRK13558        229 YRKDGSTFWNQVDIAPIRD-EDGTVTHYVGFQTDVTERKEAELAL  272 (665)
T ss_pred             ECCCCCEEEEEEEEEEEEC-CCCCEEEEEEEEEeCcHHHHHHHHH
Confidence            9999999999999999998 8999999999999999999974443

>PRK10060 RNase II stability modulator; Provisional

Probab=99.20  E-value=3.8e-10  Score=105.76  Aligned_cols=123  Identities=14%  Similarity=0.171  Sum_probs=96.7

Q ss_pred             HHHHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCccc-CCCCChHHHHHHHHHHHhCCCeEE
Q 020514           16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQ-GPRTNRRTIMEIREAIREERPIEV   94 (325)
Q Consensus        16 ~~~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~-~~~~~~~~~~~~~~~~~~~~~~~~   94 (325)
                      ...++..+++.++++++++|.+   |.++++|+++++++||+.++++|+++..++ ++.+.......+...+..+..+..
T Consensus       109 ~~~~~~~v~~~~~~gI~i~D~~---g~I~~~N~a~~~l~Gy~~~eliG~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~  185 (663)
T PRK10060        109 GLSFAEQVVSEANSVIVILDSR---GNIQRFNRLCEEYTGLKEHDVIGQSVFKLFMSRREAAASRRNIRGFFRSGNAYEV  185 (663)
T ss_pred             HHHHHHHHHhhCCceEEEEeCC---CCEEEEcHHHHHHHCcCHHHHcCCCHHHHhCChhhHHHHHHHHHHHHhcCCceEE
Confidence            4457788999999999999999   999999999999999999999999875554 444444445566666777778888


Q ss_pred             EEEEEecCCCeEEEEEEEEEeecCCCC-eeeEEEEEEeccccchhhhhcc
Q 020514           95 NLLNYKKDGTPFWMLFKMSLVFGKEDG-RATHFVAVQVPIVSRKHMRNSG  143 (325)
Q Consensus        95 e~~~~~~dg~~~~~~~~~~~~~~~~~g-~~~~~~~~~~DITe~k~~~~~~  143 (325)
                      +....+++|..+|+.....+. . ..| ...+++++.+|||+++++++++
T Consensus       186 e~~~~~~~G~~~~~~~~~~~~-~-~~g~~~~~~i~~~~DITe~k~~e~~l  233 (663)
T PRK10060        186 ERWIKTRKGQRLFLFRNKFVH-S-GSGKNEIFLICSGTDITEERRAQERL  233 (663)
T ss_pred             EEEEEeCCCCEEEEEeeeEEE-c-CCCCceEEEEEEEEechHHHHHHHHH
Confidence            888899999988876554443 3 344 3456788899999999886655

>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=99.17  E-value=2.9e-10  Score=78.10  Aligned_cols=86  Identities=26%  Similarity=0.464  Sum_probs=71.8

Q ss_pred             EEEechHHHHhcCCChhhhcCCC----CCcccCCCCChHHHHHHHH-HHHhCCCeEEEEEEEecCCCeEEEEEEEEEeec
Q 020514           43 IVFASRGFLKMSGFSRAEIIGRN----GRMFQGPRTNRRTIMEIRE-AIREERPIEVNLLNYKKDGTPFWMLFKMSLVFG  117 (325)
Q Consensus        43 ~~~~N~~~~~~~G~~~~ei~g~~----~~~l~~~~~~~~~~~~~~~-~~~~~~~~~~e~~~~~~dg~~~~~~~~~~~~~~  117 (325)
                      ++++|+.+++++||+++++ +.+    +..+++|++...+...+.. ....+..+..++++.+++|..+|+..++.++++
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            5799999999999999999 665    5667899999988888888 677777899999999999999999999999998


Q ss_pred             CCCCeeeEEEEEE
Q 020514          118 KEDGRATHFVAVQ  130 (325)
Q Consensus       118 ~~~g~~~~~~~~~  130 (325)
                       ++|.+..++|+.
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.

>TIGR00229 sensory_box PAS domain S-box

Probab=99.17  E-value=1e-09  Score=77.74  Aligned_cols=118  Identities=21%  Similarity=0.347  Sum_probs=91.4

Q ss_pred             HHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhC-CCeEEEE
Q 020514           18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREE-RPIEVNL   96 (325)
Q Consensus        18 ~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~-~~~~~e~   96 (325)
                      ..+..+++.++.+++++|.+   +.++++|+++..++|++..+++|.+...++++.........+...+..+ .......
T Consensus         3 ~~~~~~~~~~~~~~~~~d~~---~~i~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   79 (124)
T TIGR00229         3 ERYRAIFESSPDAIIVIDLE---GNILYVNPAFEEIFGYSAEELIGRNVLELIPEEDREEVRERIERLLEGEREPVSEER   79 (124)
T ss_pred             hHHHHHHhhCCceEEEEcCC---CcEEEEchHHHHHhCCChHHhcCcchhhhcChhhhHHHHHHHHHHHcCCCCCcceEe
Confidence            35678999999999999999   9999999999999999999999988776666655544444455555433 2233444


Q ss_pred             EEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchhhh
Q 020514           97 LNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMR  140 (325)
Q Consensus        97 ~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~~  140 (325)
                      .....+|...|+.+...|+..  +|...+++++..|||++++++
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~dit~~~~~~  121 (124)
T TIGR00229        80 RVRRKDGSEIWVEVSVSPIRT--NGGELGVVGIVRDITERKQAE  121 (124)
T ss_pred             eeEcCCCCEEEEEEEEeehhh--CCCeeEEEEEeeehhHHHHHH
Confidence            445778999999988888863  677788999999999998863

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.

>PRK09776 putative diguanylate cyclase; Provisional

Probab=99.07  E-value=2.4e-09  Score=106.71  Aligned_cols=132  Identities=15%  Similarity=0.174  Sum_probs=102.7

Q ss_pred             HhhhhhhHHHHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCC--ChHHHHHHHHHH
Q 020514            9 EQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRT--NRRTIMEIREAI   86 (325)
Q Consensus         9 ~~~~~~~~~~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~--~~~~~~~~~~~~   86 (325)
                      ++.+. ...++++.+++.++++++.+|.+   +.++++|+++++++||+.++++|++...+++..+  .......+....
T Consensus       528 e~~L~-~~~~~l~~~l~~~~~~i~~~D~~---g~i~~~N~a~~~l~G~~~~e~iG~~~~~~~~~~~~~~~~~~~~~~~~~  603 (1092)
T PRK09776        528 NEALF-QEKERLHITLDSIGEAVVCTDMA---MKVTFMNPVAEKMTGWTQEEALGVPLLTVLHITFGDNGPLMENIYSCL  603 (1092)
T ss_pred             HHHHH-HHHHHHHHHHhccccEEEEECCC---CeEEEEcHHHHHHhCCCHHHHcCCCHHHHcccccCCcchhhHHHHHHH
Confidence            44444 56678899999999999999999   9999999999999999999999998665543221  111122234444


Q ss_pred             HhCCC--eEEEEEEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchhhhhcccC
Q 020514           87 REERP--IEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMS  145 (325)
Q Consensus        87 ~~~~~--~~~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~~~~~~~  145 (325)
                      .....  ...+.....++|..+|+..+..|+.+ .+|.+.+++++.+|||++|+.++++..
T Consensus       604 ~~~~~~~~~~~~~~~~~~G~~~~~~~~~~pi~~-~~g~~~g~v~~~~DITe~k~~e~~L~~  663 (1092)
T PRK09776        604 TSRSAAYLEQDVVLHCRSGGSYDVHYSITPLST-LDGENIGSVLVIQDVTESRKMLRQLSY  663 (1092)
T ss_pred             hcCCCccccceEEEEeCCCcEEEEEEEeeeeec-CCCCEEEEEEEEEecchHHHHHHHHHh
Confidence            33333  44566778899999999999999998 899999999999999999998766533

>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional

Probab=99.04  E-value=2.5e-09  Score=103.10  Aligned_cols=120  Identities=19%  Similarity=0.307  Sum_probs=99.7

Q ss_pred             HHHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccC-CCCChHHHHHHHHHHHhCCCeEEE
Q 020514           17 TLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQG-PRTNRRTIMEIREAIREERPIEVN   95 (325)
Q Consensus        17 ~~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~-~~~~~~~~~~~~~~~~~~~~~~~e   95 (325)
                      ...+..+++.++.+++++|.+   +.++++|+++++++||+.++++|.+...+++ +.........+...+..+..+..+
T Consensus       135 ~~~~~~~~~~~~~~i~~~d~~---g~i~~~N~~~~~l~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e  211 (799)
T PRK11359        135 TRQLIIAVDHLDRPVIVLDPE---RRIVQCNRAFTEMFGYCISEASGMQPDTLLNIPEFPADNRIRLQQLLWKTARDQDE  211 (799)
T ss_pred             HHHHHHHHhcCCCcEEEEcCC---CcEEEEChhhHhhhCCCHHHHCCCChHHhcCCCCCcHHHHHHHHHhhccCCCCcce
Confidence            445667899999999999999   9999999999999999999999998765544 444444445555666666666677


Q ss_pred             EEEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchhhh
Q 020514           96 LLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMR  140 (325)
Q Consensus        96 ~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~~  140 (325)
                      .+...++|..+|+.+...|+.+ .+|.+.+++++.+|||++++++
T Consensus       212 ~~~~~~dG~~~~~~~~~~~v~d-~~g~~~~~~~~~~DITerk~~e  255 (799)
T PRK11359        212 FLLLTRTGEKIWIKASISPVYD-VLAHLQNLVMTFSDITEERQIR  255 (799)
T ss_pred             eEEeCCCCCEEEEEeeeeeeec-CCCceeEEEEEeehhhhHHHHH
Confidence            7888899999999999999998 7899999999999999999864

>PRK13557 histidine kinase; Provisional

Probab=98.99  E-value=8.3e-10  Score=101.58  Aligned_cols=84  Identities=33%  Similarity=0.671  Sum_probs=70.8

Q ss_pred             hhhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH----------hhc
Q 020514          241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI----------AIS  310 (325)
Q Consensus       241 ~~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~----------e~~  310 (325)
                      ..|..++++++++|+++|.+..||+|+|+|++|++++||+.+|++|+++.++.+|+........++.          ++.
T Consensus        30 ~~~~~~~~~~~~~i~v~d~~~~~g~i~~~N~a~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~  109 (540)
T PRK13557         30 DIFFAAVETTRMPMIVTDPNQPDNPIVFANRAFLEMTGYAAEEIIGNNCRFLQGPETDRATVAEVRDAIAERREIATEIL  109 (540)
T ss_pred             HHHHHHHHhCcCcEEEEcCCCCCCCEEEEcHHHHHHhCCCHHHhcCCChHhhcCCCCCHHHHHHHHHHHHcCCCceEEEE
Confidence            3477889999999999998655799999999999999999999999999999888777666655554          455


Q ss_pred             cccCCCceeeEEee
Q 020514          311 PYPKKKSIYMEYVR  324 (325)
Q Consensus       311 ~~~kdG~~~~~~~~  324 (325)
                      .+++||+.+|+.++
T Consensus       110 ~~~~~G~~~~~~~~  123 (540)
T PRK13557        110 NYRKDGSSFWNALF  123 (540)
T ss_pred             EEeCCCCEEEEEEE
Confidence            67899999998654

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

Probab=98.97  E-value=4.5e-08  Score=66.02  Aligned_cols=103  Identities=21%  Similarity=0.404  Sum_probs=82.9

Q ss_pred             CCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEEEEEEecCCCeE
Q 020514           27 LPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPF  106 (325)
Q Consensus        27 ~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg~~~  106 (325)
                      ++.+++++|.+   +.+.++|++++.++|++..++.|.....++++.+.......+......+.....+......+|...
T Consensus         1 ~~~~i~~~d~~---~~~~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   77 (103)
T cd00130           1 LPDGVIVLDLD---GRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDGSVI   77 (103)
T ss_pred             CCceEEEECCC---CcEEEECHHHHHHhCCCHHHHcCccHHHhcCCccchHHHHHHHHHHhcCcCeEEEEEEEccCCCEE
Confidence            35788999999   999999999999999999999998877777776665555555555555555666777777889999


Q ss_pred             EEEEEEEEeecCCCCeeeEEEEEEecc
Q 020514          107 WMLFKMSLVFGKEDGRATHFVAVQVPI  133 (325)
Q Consensus       107 ~~~~~~~~~~~~~~g~~~~~~~~~~DI  133 (325)
                      |+.+...++.+ ..|...+++++..||
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.

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

Probab=98.88  E-value=1.8e-08  Score=71.29  Aligned_cols=106  Identities=21%  Similarity=0.272  Sum_probs=71.6

Q ss_pred             HHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEEEEEE
Q 020514           20 VHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNY   99 (325)
Q Consensus        20 ~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~   99 (325)
                      +..++++++.++.++|.+   +.+.+.|+++.++++..+.+ +|+++..+.++.....+...+ +.+..+.....+... 
T Consensus         1 L~~il~s~~~~i~~vD~~---~~I~~~n~~a~~~f~~~~~~-iGr~l~~~~~~~~~~~l~~~i-~~~~~~~~~~~~~~~-   74 (106)
T PF13596_consen    1 LNNILDSMPIGIIFVDRN---LRIRYFNPAAARLFNLSPSD-IGRPLFDIHPPLSYPNLKKII-EQVRSGKEEEFEIVI-   74 (106)
T ss_dssp             HHHHHHHSSSEEEEEETT---SBEEEE-SCGC-SS---GGG-TTSBCCCSS-HHHHHHHHHHH-HHHHTTSBSEEEEEE-
T ss_pred             ChHHHhcCCCCEEEEcCC---CeEEEeChhHhhhcCCChHH-CCCCHHHcCCccchHHHHHHH-HHHHcCCCceEEEEe-
Confidence            357899999999999999   99999999999999977554 699988876654333333333 344444443333332 


Q ss_pred             ecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccc
Q 020514          100 KKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV  134 (325)
Q Consensus       100 ~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIT  134 (325)
                      ..+|  .|+.+.+.|+++ ++|...|++.++.|||
T Consensus        75 ~~~~--~~~~~~~~P~~~-~~g~~~G~v~~~~DIT  106 (106)
T PF13596_consen   75 PNGG--RWYLVRYRPYRD-EDGEYAGAVITFQDIT  106 (106)
T ss_dssp             EETT--EEEEEEEEEEE--TTS-EEEEEEEEEE-G
T ss_pred             cCCC--EEEEEEEEEEEC-CCCCEEEEEEEEEecC
Confidence            2344  467789999998 8999999999999997

>PRK13559 hypothetical protein; Provisional

Probab=98.88  E-value=4.9e-09  Score=91.49  Aligned_cols=83  Identities=35%  Similarity=0.679  Sum_probs=67.6

Q ss_pred             hhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH----------hhcc
Q 020514          242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI----------AISP  311 (325)
Q Consensus       242 ~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~----------e~~~  311 (325)
                      .+..++++++++++++|.+..+|+|+++|++|++++||+.++++|+++.++.++.........+..          +...
T Consensus        44 ~~~~~~e~~~~~i~i~D~~~~~g~i~~~N~a~~~l~G~~~~e~iG~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~  123 (361)
T PRK13559         44 LFEQAMEQTRMAMCITDPHQPDLPIVLANQAFLDLTGYAAEEVVGRNCRFLQGAATDPIAVAKIRAAIAAEREIVVELLN  123 (361)
T ss_pred             HHHHHHHhCCCcEEEecCCCCCCcEEEEchHHHHHhCCCHHHHcCCChhhhcCCCCCHHHHHHHHHHhccCCceEEEEEE
Confidence            467789999999999998655789999999999999999999999999888776665554444443          4556


Q ss_pred             ccCCCceeeEEee
Q 020514          312 YPKKKSIYMEYVR  324 (325)
Q Consensus       312 ~~kdG~~~~~~~~  324 (325)
                      +++||+.+|+.++
T Consensus       124 ~~~dG~~~~~~~~  136 (361)
T PRK13559        124 YRKDGEPFWNALH  136 (361)
T ss_pred             EcCCCCEEEEEEE
Confidence            7899999998764

>PF12860 PAS_7: PAS fold

Probab=98.85  E-value=2.4e-08  Score=71.81  Aligned_cols=104  Identities=20%  Similarity=0.342  Sum_probs=70.9

Q ss_pred             HhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhh-cCCCCCccc---------CCCCChHHHHHHHHHHHhCCCeE
Q 020514           24 LDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEI-IGRNGRMFQ---------GPRTNRRTIMEIREAIREERPIE   93 (325)
Q Consensus        24 ~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei-~g~~~~~l~---------~~~~~~~~~~~~~~~~~~~~~~~   93 (325)
                      +++++.|++++|.+   +.++++|+.|.+++|++.+.+ .|.++..+.         .+.+...................
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 677754432         11222222222222233333333


Q ss_pred             EEEEEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchhhh
Q 020514           94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMR  140 (325)
Q Consensus        94 ~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~~  140 (325)
                      .+  ....+|+  |+.+...|..+   |   |++.+..|||+++++|
T Consensus        78 ~~--~~~~dgr--~l~~~~~~~~~---G---g~v~~~~DVT~~~~~E  114 (115)
T PF12860_consen   78 FE--LRLPDGR--WLEVRAQPLPD---G---GFVLTFTDVTERRRAE  114 (115)
T ss_pred             eE--EECCCCE--EEEEEeEECCC---C---CEEEEEEeCCHHHHhc
Confidence            33  3346665  66778888853   4   5788999999999863

>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=98.85  E-value=3.7e-09  Score=75.22  Aligned_cols=75  Identities=20%  Similarity=0.158  Sum_probs=59.3

Q ss_pred             hhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH---------hhccccCCCc
Q 020514          247 LGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI---------AISPYPKKKS  317 (325)
Q Consensus       247 ~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~---------e~~~~~kdG~  317 (325)
                      |++++++++++|.   ||+|+++|+++++++|+++++++|+++.+++++.........+.+         .......+|.
T Consensus         1 l~~~p~~i~v~D~---~~~i~~~N~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   77 (110)
T PF08448_consen    1 LDSSPDGIFVIDP---DGRIVYANQAAAELFGVSPEELIGRSLFDLLPPEDREEFQAALRRALAGGEPVFFEEILLRDGE   77 (110)
T ss_dssp             HHHCSSEEEEEET---TSBEEEE-HHHHHHHTSTHHHHTTSBHHHHSCCGCHHHHHHHHHHHHHHTSEEEEEEEECTTSC
T ss_pred             CCCCCceeEEECC---CCEEEEEHHHHHHHhCCCHHHHhhccchhccccchhhhhHHHHHHhhccCceEEEEEEEeecCC
Confidence            5778999999998   579999999999999999999999999999888766666666666         1111223788


Q ss_pred             eeeEEee
Q 020514          318 IYMEYVR  324 (325)
Q Consensus       318 ~~~~~~~  324 (325)
                      .+|..++
T Consensus        78 ~~~~~~~   84 (110)
T PF08448_consen   78 ERWFEVS   84 (110)
T ss_dssp             EEEEEEE
T ss_pred             cEEEEEE
Confidence            8887765

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.

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

Probab=98.83  E-value=2.2e-08  Score=87.48  Aligned_cols=163  Identities=20%  Similarity=0.191  Sum_probs=117.7

Q ss_pred             HHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEEEEEEe
Q 020514           21 HEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYK  100 (325)
Q Consensus        21 ~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~  100 (325)
                      ..+++.+++++++++..   ..+..+|..+..+++-....++|++...+.++.......        .+...........
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            34889999999999998   899999999999999999999999877776554433221        1122222222222


Q ss_pred             cCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchhhhhcccCcccCCCCchhhHHHhhhhhhhhcccchhhhhhhcc
Q 020514          101 KDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDRVLA  180 (325)
Q Consensus       101 ~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  180 (325)
                      +  ....+.+...|+.  +.+.+.|++.++.|+++....                                         
T Consensus        73 ~--~~~~~~~~~~~~~--~~~~~~g~~~~~~~~~e~~~~-----------------------------------------  107 (560)
T COG3829          73 K--VKRIVVVGKTPVD--EQGRVVGVLEVFLDISEALEL-----------------------------------------  107 (560)
T ss_pred             c--ceeEEEcCCceee--cCCceeeeehhhhhhHHHHHH-----------------------------------------
Confidence            2  2333434455554  588999999999999996552                                         


Q ss_pred             ccccCCCCcccchhhhHHHHHHHHhhhhhhHhhhhccceeeccceeeeeecCCCCcccchhhhHhhhhccCCceEEecCC
Q 020514          181 LDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQSFVLIDPH  260 (325)
Q Consensus       181 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~i~~~d~~  260 (325)
                                      .+..+...                                   ...|..+++.+.++++++|.+
T Consensus       108 ----------------~~~~l~~~-----------------------------------~~~l~~il~~~~~~l~vvD~~  136 (560)
T COG3829         108 ----------------IEENLRQL-----------------------------------RQRLEAILDSIDDGLLVVDED  136 (560)
T ss_pred             ----------------HHHHHHHH-----------------------------------HHHHHHHHhhccCceEEEcCC
Confidence                            11111111                                   122566888889999999985


Q ss_pred             CCCCCeEEEehhhHHhhCCCccccccccccccc
Q 020514          261 LPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLN  293 (325)
Q Consensus       261 ~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~  293 (325)
                         |.++++|+++.+++|++.++++|+++.++.
T Consensus       137 ---G~~i~~N~~~~~~~gl~~e~~~gk~~~~v~  166 (560)
T COG3829         137 ---GIIIYYNKAYAKLLGLSPEEVLGKHLLDVV  166 (560)
T ss_pred             ---CcEEEEcHHHHHHhCCCHHHHcCCcHHHHH
Confidence               799999999999999999999999998886

>PRK11360 sensory histidine kinase AtoS; Provisional

Probab=98.79  E-value=1e-07  Score=88.92  Aligned_cols=121  Identities=14%  Similarity=0.181  Sum_probs=95.1

Q ss_pred             HHHHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCC-eEE
Q 020514           16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERP-IEV   94 (325)
Q Consensus        16 ~~~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~-~~~   94 (325)
                      ....+..+++.++++++++|.+   +.++++|+++++++|+++++++|+++..++++..  .....+...+..+.. ...
T Consensus       260 ~~~~~~~i~~~~~~~i~~~d~~---g~i~~~N~~~~~l~g~~~~~~~g~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~  334 (607)
T PRK11360        260 TRSLNELILESIADGVIAIDRQ---GKITTMNPAAEVITGLQRHELVGKPYSELFPPNT--PFASPLLDTLEHGTEHVDL  334 (607)
T ss_pred             HHHHHHHHHHhccCeEEEEcCC---CCEEEECHHHHHHhCCChHHhcCCcHHHHcCCch--hHHHHHHHHHhcCCCccce
Confidence            4456788999999999999999   9999999999999999999999998777766532  223344444544433 334


Q ss_pred             EEEEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchhhhhcc
Q 020514           95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG  143 (325)
Q Consensus        95 e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~~~~~  143 (325)
                      ++.....+|... +.++..|+.+ .+|.+.+++++++|||+++++++++
T Consensus       335 ~~~~~~~~~~~~-~~~~~~~i~~-~~g~~~~~i~~~~Dite~~~~e~~l  381 (607)
T PRK11360        335 EISFPGRDRTIE-LSVSTSLLHN-THGEMIGALVIFSDLTERKRLQRRV  381 (607)
T ss_pred             EEEEEcCCCcEE-EEEEEeeEEc-CCCCEEEEEEEEeechHHHHHHHHH
Confidence            555566677665 8899999998 8999999999999999999875444

>PRK10060 RNase II stability modulator; Provisional

Probab=98.79  E-value=1.4e-08  Score=95.25  Aligned_cols=77  Identities=12%  Similarity=0.040  Sum_probs=58.9

Q ss_pred             HhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccC-CCCChHHHHHHHH----------hhccc
Q 020514          244 YISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNG-VDTDTTVLYQVSI----------AISPY  312 (325)
Q Consensus       244 ~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~-~~~~~~~~~~~~~----------e~~~~  312 (325)
                      +.++++++++|+++|.   ||+|+++|++|++++||+.+|++|+++.+++. |.........+..          |++.+
T Consensus       114 ~~v~~~~~~gI~i~D~---~g~I~~~N~a~~~l~Gy~~~eliG~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~  190 (663)
T PRK10060        114 EQVVSEANSVIVILDS---RGNIQRFNRLCEEYTGLKEHDVIGQSVFKLFMSRREAAASRRNIRGFFRSGNAYEVERWIK  190 (663)
T ss_pred             HHHHhhCCceEEEEeC---CCCEEEEcHHHHHHHCcCHHHHcCCCHHHHhCChhhHHHHHHHHHHHHhcCCceEEEEEEE
Confidence            3467888999999998   47999999999999999999999999877654 4333222222222          66778


Q ss_pred             cCCCceeeEEe
Q 020514          313 PKKKSIYMEYV  323 (325)
Q Consensus       313 ~kdG~~~~~~~  323 (325)
                      +++|+.+|+..
T Consensus       191 ~~~G~~~~~~~  201 (663)
T PRK10060        191 TRKGQRLFLFR  201 (663)
T ss_pred             eCCCCEEEEEe
Confidence            89999888754

>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=98.76  E-value=4.5e-07  Score=64.31  Aligned_cols=102  Identities=17%  Similarity=0.261  Sum_probs=83.4

Q ss_pred             EEEcCCCCCCCEEEechH-HHHhcCCChhhhcCCCCCcccCCCCChH-HHHHHHHHHHhCCCeEEEEEEEecCCCeEEEE
Q 020514           32 TITDPSISGHPIVFASRG-FLKMSGFSRAEIIGRNGRMFQGPRTNRR-TIMEIREAIREERPIEVNLLNYKKDGTPFWML  109 (325)
Q Consensus        32 ~~~d~~~~~~~~~~~N~~-~~~~~G~~~~ei~g~~~~~l~~~~~~~~-~~~~~~~~~~~~~~~~~e~~~~~~dg~~~~~~  109 (325)
                      ...+.+   |+++++.+. ...++||.+++++|+++..+++|+|... +.......+..|.....-++...++|..+|+.
T Consensus         6 trhs~d---gki~~~d~~~v~~~lgy~~~eLvG~s~y~~~H~~D~~~~~~~~~~~~~~~g~~~~~~yR~~~k~g~~vwvq   82 (111)
T PF14598_consen    6 TRHSLD---GKITYVDSRAVSSLLGYLPEELVGRSIYDFVHPDDLQRVLKQHHREVLQKGQSVSPYYRFRTKNGGYVWVQ   82 (111)
T ss_dssp             EEEETT---SBEEEEETTHHHHHHSS-HHHHTTSBGGGGBSCCTHHHHHHHHHHHHHHHSSEEEEEEEEE-TTSSEEEEE
T ss_pred             EEECCC---cEEEEEcCccChhhcCCCcHHHcCCchHHhCCHhhhhhHHHHHHHHHhhCCCcCcceEEEEecCCcEEEEE
Confidence            345677   999999999 6999999999999999999999999886 77788888888887666789999999999999


Q ss_pred             EEEEEeecCCCCeeeEEEEEEeccccc
Q 020514          110 FKMSLVFGKEDGRATHFVAVQVPIVSR  136 (325)
Q Consensus       110 ~~~~~~~~~~~g~~~~~~~~~~DITe~  136 (325)
                      ....++.++.++++..++++..=|++.
T Consensus        83 t~~~~~~n~~~~~~~~Iv~~n~vlse~  109 (111)
T PF14598_consen   83 TKATLFYNPWTSKPEFIVCTNTVLSEE  109 (111)
T ss_dssp             EEEEEEEETTTTCEEEEEEEEEEESCE
T ss_pred             EEEEEEECCCCCCccEEEEEEEEeccC
Confidence            999998864566777777766655553

...

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

Probab=98.73  E-value=1.7e-07  Score=83.29  Aligned_cols=69  Identities=19%  Similarity=0.218  Sum_probs=55.3

Q ss_pred             eEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH----------hhccccCCCceeeEEe
Q 020514          254 FVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI----------AISPYPKKKSIYMEYV  323 (325)
Q Consensus       254 i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~----------e~~~~~kdG~~~~~~~  323 (325)
                      .|+.-... |.+|+|+.+.+.++.||+++||+|+++.+|+++.+-..+......          .+++..|.|...|++-
T Consensus       275 ~FvtRhs~-DmkityCedRisdlm~y~PeeLvGrS~Ye~~Ha~Ds~~v~KSh~dL~~KGQv~TgyYR~lak~GGyvWlQT  353 (768)
T KOG3558|consen  275 MFVTRHSL-DMKITYCEDRISDLMDYEPEELVGRSCYEFVHALDSDRVRKSHHDLLTKGQVVTGYYRLLAKNGGYVWLQT  353 (768)
T ss_pred             eeEEeeec-ceeEEEEchhHHHHhcCCHHHhhchhHHHhhhHhhhhHHHHHHHHHHhcCccchhHHHHHHhcCCeEEEEe
Confidence            55554443 789999999999999999999999999999988776555444333          7777789999999863

>TIGR02966 phoR_proteo phosphate regulon sensor kinase PhoR

Probab=98.73  E-value=1.1e-07  Score=81.71  Aligned_cols=108  Identities=13%  Similarity=0.085  Sum_probs=81.9

Q ss_pred             hHHHHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEE
Q 020514           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV   94 (325)
Q Consensus        15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   94 (325)
                      +..+.++.+++.++++++++|.+   |.++++|+++++++|+++++.+|+++..+..+.       .+...+..+.. ..
T Consensus         3 ~~~~~l~~~~~~~~~~i~~~d~~---g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~-------~~~~~l~~~~~-~~   71 (333)
T TIGR02966         3 ALLSRFRAAAQALPDAVVVLDEE---GQIEWCNPAAERLLGLRWPDDLGQRITNLIRHP-------EFVEYLAAGRF-SE   71 (333)
T ss_pred             hHHHHHHHHHHhCcCcEEEECCC---CcEEEEcHHHHHHhCCChHHHcCCcHHHHccCH-------HHHHHHHhccc-CC
Confidence            34567899999999999999999   999999999999999999999998876665432       22333333222 22


Q ss_pred             EEEEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchhh
Q 020514           95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM  139 (325)
Q Consensus        95 e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~  139 (325)
                      ......++|...|+.+...|+.+ . +    .+++.+|||++++.
T Consensus        72 ~~~~~~~~~~~~~~~~~~~p~~~-~-~----~~~~~~dit~~~~~  110 (333)
T TIGR02966        72 PLELPSPINSERVLEIRIAPYGE-E-Q----KLLVARDVTRLRRL  110 (333)
T ss_pred             CeEeecCCCCceEEEEEEEEcCC-C-c----eEEEEeCchHHHHH
Confidence            23344577888899999999865 2 2    67888999998876

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=98.69  E-value=1.7e-07  Score=81.32  Aligned_cols=110  Identities=14%  Similarity=0.141  Sum_probs=84.0

Q ss_pred             HHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEEEEE
Q 020514           19 WVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLN   98 (325)
Q Consensus        19 ~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~   98 (325)
                      .+..++++++++++++|.+   +.++++|+++++++|++..+++|.++..++++...  ....+...+..+.........
T Consensus         8 ~~~~il~~~~~gi~~~d~~---~~i~~~N~a~~~~~g~~~~~~~g~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~   82 (348)
T PRK11073          8 DAGQILNSLINSILLLDDD---LAIHYANPAAQQLLAQSSRKLFGTPLPELLSYFSL--NIELMRESLQAGQGFTDNEVT   82 (348)
T ss_pred             hHHHHHhcCcCeEEEECCC---CeEeeEcHHHHHHhCCCHHHHcCCCHHHHcCcchh--hHHHHHHHHHcCCcccccceE
Confidence            5678999999999999999   99999999999999999999999998777654321  123344455555443333334


Q ss_pred             EecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchhh
Q 020514           99 YKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM  139 (325)
Q Consensus        99 ~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~  139 (325)
                      ...+|..+|+.++..|+..      .+++..++|+|++++.
T Consensus        83 ~~~~g~~~~~~~~~~~~~~------~~~~~~~~dit~~~~~  117 (348)
T PRK11073         83 LVIDGRSHILSLTAQRLPE------GMILLEMAPMDNQRRL  117 (348)
T ss_pred             EEECCceEEEEEEEEEccC------ceeEEEEechhHHHHH
Confidence            4569999999999999853      2456778999998876

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

Probab=98.66  E-value=2.1e-07  Score=81.25  Aligned_cols=123  Identities=26%  Similarity=0.519  Sum_probs=95.7

Q ss_pred             HHHHHHHHHhhCC--C-EEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCC--CCcccCCCCChHHHHHHHHHHHhCC
Q 020514           16 YTLWVHEALDELP--D-SFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRN--GRMFQGPRTNRRTIMEIREAIREER   90 (325)
Q Consensus        16 ~~~~~~~~~~~~~--~-~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~--~~~l~~~~~~~~~~~~~~~~~~~~~   90 (325)
                      ++.+++.++..+.  + .+++.+.+.-|..++|+|.+||++.||.+.+++.++  +....+..........+++.+..-.
T Consensus        12 QNTFLENiiRRsn~~dtsFlL~NAQiVD~PiVY~NdgFcKlsGY~RAevMQKs~tc~FMyGEltdk~ti~k~~~t~eN~~   91 (971)
T KOG0501|consen   12 QNTFLENIIRRSNNADTSFLLANAQIVDWPIVYCNDGFCKLSGYHRAEVMQKSCTCSFMYGELTDKGTIEKVRQTLENYE   91 (971)
T ss_pred             chhHHHHHHhhccCCCcceeeccceeeccceEEecCcchhccCccHHHHhcccceeeeeeccccchhhHHHHHHHHHhhh
Confidence            4455666665444  3 333344433336689999999999999999999987  4445555555555677777787777


Q ss_pred             CeEEEEEEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchhh
Q 020514           91 PIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM  139 (325)
Q Consensus        91 ~~~~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~  139 (325)
                      .-++|+....++...+|+.+.+.|+++ +.+.++.+++.+.|||..|+-
T Consensus        92 ~~qfEillyKKN~TPvW~~vqiAPIrN-e~d~VVLfLctFkDIT~~KQP  139 (971)
T KOG0501|consen   92 TNQFEILLYKKNRTPVWLLVQIAPIRN-EKDKVVLFLCTFKDITALKQP  139 (971)
T ss_pred             hcceeeEeeecCCCceEEEEEeecccC-CCceEEEEEeecccchhhcCC
Confidence            778898899999999999999999999 999999999999999999874

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

Probab=98.64  E-value=1.5e-06  Score=76.23  Aligned_cols=112  Identities=17%  Similarity=0.367  Sum_probs=84.1

Q ss_pred             hHHHHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEE
Q 020514           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV   94 (325)
Q Consensus        15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   94 (325)
                      .....|..+++.+.+++.++|.+   |.++++|+++..++|++.++++|++..+++.....    .....++..+.+...
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            45678999999999999999999   99999999999999999999999986666411110    123455666666555


Q ss_pred             EEEEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchhh
Q 020514           95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM  139 (325)
Q Consensus        95 e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~  139 (325)
                      ....+..+..    .++..|++.  +|.+.|.+++..|+++.+.+
T Consensus       187 ~~~~~~~~~~----i~~~~pv~~--~g~l~G~v~~~~~~~~l~~l  225 (560)
T COG3829         187 VVQTYNGNKI----IVNVAPVYA--DGQLIGVVGISKDVSELERL  225 (560)
T ss_pred             eeeeecCCce----eEeeccEec--CCcEEEEEEeecchHHHHHH
Confidence            4433322222    356677774  78999999999999998876

>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=98.61  E-value=3.2e-08  Score=67.85  Aligned_cols=58  Identities=22%  Similarity=0.228  Sum_probs=46.2

Q ss_pred             eEEEehhhHHhhCCCcccccccc----cccccCCCCChHHHHHHHH-----------hhccccCCCceeeEEee
Q 020514          266 MVYASDAFLKLTGYDRNEVVGQN----CRFLNGVDTDTTVLYQVSI-----------AISPYPKKKSIYMEYVR  324 (325)
Q Consensus       266 i~~~N~a~~~~~Gy~~~e~iG~~----~~~l~~~~~~~~~~~~~~~-----------e~~~~~kdG~~~~~~~~  324 (325)
                      |+|+|+++++|+||+++++ |..    +..+++|++.....+.+.+           +++.+++||+.+|++.+
T Consensus         1 ~i~~s~~~~~i~G~~~~~~-~~~~~~~~~~~ihpdD~~~~~~~~~~~~~~~~~~~~~e~R~~~~~G~~~wi~~~   73 (91)
T PF08447_consen    1 IIYWSDNFYEIFGYSPEEI-GKPDFEEWLERIHPDDRERVRQAIQQAALQNGEPFEIEYRIRRKDGEYRWIEVR   73 (91)
T ss_dssp             -EEE-THHHHHHTS-HHHH-TCBEHHHHHHHB-TTTHHHHHHHHHHHHHHTT-EEEEEEEEEGTTSTEEEEEEE
T ss_pred             CEEEeHHHHHHhCCCHHHh-ccCCHHHHHhhcCHHHHHHHHHHHHHHhhccCcceEEEEEEECCCCCEEEEEEE
Confidence            6899999999999999999 766    7778899988877665555           88889999999999865

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.

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

Probab=98.53  E-value=1.3e-07  Score=60.06  Aligned_cols=45  Identities=22%  Similarity=0.362  Sum_probs=36.3

Q ss_pred             hhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCccccccccccccc
Q 020514          242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLN  293 (325)
Q Consensus       242 ~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~  293 (325)
                      +++.+++++++||+++| .   ++|+++|+++++|+||+   ..|+.+..+.
T Consensus         2 ~~~~l~~~~~~~i~i~d-~---~~i~~~N~~~~~l~g~~---~~~~~~~~~~   46 (64)
T PF13188_consen    2 RYRSLFDNSPDGILIID-G---GRIIYVNPAFEELFGYS---LEGEDIGQLF   46 (64)
T ss_dssp             HHHHHHCCSSSEEEEEE-T---SBEEEE-HHHHHHHCS----HTCCCHHCTS
T ss_pred             HHHHHHHcCccceEEEE-C---CChHHhhHHHHHHhCCC---CCCCCHHHhC
Confidence            57889999999999999 5   49999999999999998   6666664444

>PRK11091 aerobic respiration control sensor protein ArcB; Provisional

Probab=98.51  E-value=9.9e-08  Score=91.78  Aligned_cols=82  Identities=15%  Similarity=-0.013  Sum_probs=66.9

Q ss_pred             hhhhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH----------hh
Q 020514          240 SSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI----------AI  309 (325)
Q Consensus       240 ~~~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~----------e~  309 (325)
                      ...++.++++++++|+++|.   +|+|+++|+++++++||+.++++|+++.++++++...........          +.
T Consensus       154 ~~~l~~il~~~~~~i~~~D~---~g~i~~~N~a~~~l~G~~~~eliG~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~  230 (779)
T PRK11091        154 SSLLRSFLDASPDLVYYRNE---DGEFSGCNRAMELLTGKSEKQLIGLTPKDVYSPEAAEKVIETDEKVFRHNVSLTYEQ  230 (779)
T ss_pred             HHHHHHHHhcCcceEEEECC---CCcEEeEcHHHHHHhCcCHHHHcCCChHHhCCHHHHHHHHHHHHHHHhcCCCeEEEE
Confidence            45588899999999999998   479999999999999999999999999998877655544433332          55


Q ss_pred             ccccCCCceeeEEee
Q 020514          310 SPYPKKKSIYMEYVR  324 (325)
Q Consensus       310 ~~~~kdG~~~~~~~~  324 (325)
                      +..++||+.+|+.++
T Consensus       231 ~~~~~~G~~~~~~~~  245 (779)
T PRK11091        231 WLDYPDGRKACFELR  245 (779)
T ss_pred             EEEcCCCCEEEEEEE
Confidence            567789999988764

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

Probab=98.50  E-value=2.6e-06  Score=70.30  Aligned_cols=114  Identities=15%  Similarity=0.242  Sum_probs=89.2

Q ss_pred             hHHHHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEE
Q 020514           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV   94 (325)
Q Consensus        15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   94 (325)
                      ....++.+++..+.+|++..|..   |.++.+|..+.+++|.+.++++|+++..+..-.+.-.    +...+....+...
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            34567899999999999999999   9999999999999999999999998766654433322    2333344433333


Q ss_pred             EEEEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchhh
Q 020514           95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM  139 (325)
Q Consensus        95 e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~  139 (325)
                      +.   ...++.+.+.+..+.+.. +.|-+.|++.+.+|+|++.+.
T Consensus       181 d~---~~~~E~~~lrv~Fs~i~r-EsGfisGlIaVlhDvTEqek~  221 (459)
T COG5002         181 DS---SDEEEGYVLRVNFSVIQR-ESGFISGLIAVLHDVTEQEKV  221 (459)
T ss_pred             ee---cCCCccEEEEEEEEEEee-cccccceeEEEEecccHHHHH
Confidence            32   236777778888888888 899999999999999999875

>PRK13558 bacterio-opsin activator; Provisional

Probab=98.47  E-value=3.3e-07  Score=86.61  Aligned_cols=82  Identities=34%  Similarity=0.629  Sum_probs=67.1

Q ss_pred             hHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH----------hhccc
Q 020514          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI----------AISPY  312 (325)
Q Consensus       243 l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~----------e~~~~  312 (325)
                      +..+++.++.++++.|...++|.|+++|+++++++||++++++|+++..+.++.........+..          +++.+
T Consensus       150 ~~~~~~~~~~gi~~~d~~~~dg~i~~~N~~~~~l~G~~~eel~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~  229 (665)
T PRK13558        150 KERALDEAPVGITIADATLPDEPLIYINDAFERITGYSPDEVLGRNCRFLQGEDTNEERVAELREAIDEERPTSVELRNY  229 (665)
T ss_pred             HHHHHhcCCccEEEEcCCCCCCcEEEEcHHHHHHhCcCHHHHcCCCHHHhcCCCccHHHHHHHHHHHhcCCCeEEEEEEE
Confidence            35678899999999986545789999999999999999999999999888877766555444433          66778


Q ss_pred             cCCCceeeEEee
Q 020514          313 PKKKSIYMEYVR  324 (325)
Q Consensus       313 ~kdG~~~~~~~~  324 (325)
                      ++||+.+|+.++
T Consensus       230 ~~dG~~~~~~~~  241 (665)
T PRK13558        230 RKDGSTFWNQVD  241 (665)
T ss_pred             CCCCCEEEEEEE
Confidence            899999998764

>TIGR02938 nifL_nitrog nitrogen fixation negative regulator NifL

Probab=98.43  E-value=2.3e-07  Score=84.28  Aligned_cols=80  Identities=21%  Similarity=0.375  Sum_probs=64.1

Q ss_pred             hhhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH----------hhc
Q 020514          241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI----------AIS  310 (325)
Q Consensus       241 ~~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~----------e~~  310 (325)
                      +.++.++++++++++++|.+   |+++++|++|++++||++++++|++...+.++.........+.+          ++.
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            45788999999999999984   79999999999999999999999987777666555544444433          455


Q ss_pred             cccCCCceeeEEe
Q 020514          311 PYPKKKSIYMEYV  323 (325)
Q Consensus       311 ~~~kdG~~~~~~~  323 (325)
                      ..+++|+.+|+.+
T Consensus        81 ~~~~~g~~~~~~~   93 (494)
T TIGR02938        81 NRRKDGELYLAEL   93 (494)
T ss_pred             ccCCCccchhhhe
Confidence            5778999888654

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.

>TIGR02966 phoR_proteo phosphate regulon sensor kinase PhoR

Probab=98.42  E-value=2.3e-07  Score=79.80  Aligned_cols=79  Identities=14%  Similarity=0.106  Sum_probs=60.9

Q ss_pred             hhhhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH-----hhccccC
Q 020514          240 SSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI-----AISPYPK  314 (325)
Q Consensus       240 ~~~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~-----e~~~~~k  314 (325)
                      .+.|+.+++++++|++++|.+   |+|+++|++|++++||++++++|+++..+..+..   ....+..     .+....+
T Consensus         5 ~~~l~~~~~~~~~~i~~~d~~---g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~---~~~~l~~~~~~~~~~~~~~   78 (333)
T TIGR02966         5 LSRFRAAAQALPDAVVVLDEE---GQIEWCNPAAERLLGLRWPDDLGQRITNLIRHPE---FVEYLAAGRFSEPLELPSP   78 (333)
T ss_pred             HHHHHHHHHhCcCcEEEECCC---CcEEEEcHHHHHHhCCChHHHcCCcHHHHccCHH---HHHHHHhcccCCCeEeecC
Confidence            456888999999999999984   7999999999999999999999999988875432   2222222     3444456


Q ss_pred             CCceeeEEee
Q 020514          315 KKSIYMEYVR  324 (325)
Q Consensus       315 dG~~~~~~~~  324 (325)
                      +|..+|+.++
T Consensus        79 ~~~~~~~~~~   88 (333)
T TIGR02966        79 INSERVLEIR   88 (333)
T ss_pred             CCCceEEEEE
Confidence            7777777654

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).

>TIGR00229 sensory_box PAS domain S-box

Probab=98.39  E-value=1.1e-06  Score=61.87  Aligned_cols=80  Identities=19%  Similarity=0.199  Sum_probs=60.4

Q ss_pred             hhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH-----------hhc
Q 020514          242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI-----------AIS  310 (325)
Q Consensus       242 ~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~-----------e~~  310 (325)
                      .++.++++++.+++++|.+   |.++++|+++++++|++..+++|+++..+.++.........+..           ++.
T Consensus         4 ~~~~~~~~~~~~~~~~d~~---~~i~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (124)
T TIGR00229         4 RYRAIFESSPDAIIVIDLE---GNILYVNPAFEEIFGYSAEELIGRNVLELIPEEDREEVRERIERLLEGEREPVSEERR   80 (124)
T ss_pred             HHHHHHhhCCceEEEEcCC---CcEEEEchHHHHHhCCChHHhcCcchhhhcChhhhHHHHHHHHHHHcCCCCCcceEee
Confidence            4677889999999999984   79999999999999999999999998887766655444333322           222


Q ss_pred             cccCCCceeeEEee
Q 020514          311 PYPKKKSIYMEYVR  324 (325)
Q Consensus       311 ~~~kdG~~~~~~~~  324 (325)
                      ...++|..+|+.++
T Consensus        81 ~~~~~~~~~~~~~~   94 (124)
T TIGR00229        81 VRRKDGSEIWVEVS   94 (124)
T ss_pred             eEcCCCCEEEEEEE
Confidence            23678888777643

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.

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

Probab=98.35  E-value=7.6e-07  Score=77.28  Aligned_cols=80  Identities=14%  Similarity=0.081  Sum_probs=59.8

Q ss_pred             hhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCC-hHHH-HHHHH------hhcccc
Q 020514          242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTD-TTVL-YQVSI------AISPYP  313 (325)
Q Consensus       242 ~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~-~~~~-~~~~~------e~~~~~  313 (325)
                      .+..+++++++|++++|.   ||+|+++|+++++++||+.++++|+++.++.++... ...+ ..+..      +.....
T Consensus         8 ~~~~il~~~~~gi~~~d~---~~~i~~~N~a~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   84 (348)
T PRK11073          8 DAGQILNSLINSILLLDD---DLAIHYANPAAQQLLAQSSRKLFGTPLPELLSYFSLNIELMRESLQAGQGFTDNEVTLV   84 (348)
T ss_pred             hHHHHHhcCcCeEEEECC---CCeEeeEcHHHHHHhCCCHHHHcCCCHHHHcCcchhhHHHHHHHHHcCCcccccceEEE
Confidence            467899999999999997   479999999999999999999999999888754321 1111 11211      122245


Q ss_pred             CCCceeeEEee
Q 020514          314 KKKSIYMEYVR  324 (325)
Q Consensus       314 kdG~~~~~~~~  324 (325)
                      +||+.+|+.++
T Consensus        85 ~~g~~~~~~~~   95 (348)
T PRK11073         85 IDGRSHILSLT   95 (348)
T ss_pred             ECCceEEEEEE
Confidence            79999998765

>PRK11006 phoR phosphate regulon sensor protein; Provisional

Probab=98.29  E-value=2.6e-06  Score=76.18  Aligned_cols=112  Identities=13%  Similarity=0.151  Sum_probs=75.4

Q ss_pred             HhhhhhhHHHHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHh
Q 020514            9 EQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIRE   88 (325)
Q Consensus         9 ~~~~~~~~~~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~   88 (325)
                      ++.+. ....+++.++++++++++++|.+   |.++++|+++++++||+.+++.|+++..+..+.   ...    ..+..
T Consensus        90 ~~~l~-~~~~~~~~~~~~~~~~i~~~d~~---g~i~~~N~~a~~l~g~~~~~~~g~~~~~~~~~~---~~~----~~~~~  158 (430)
T PRK11006         90 RRELG-NLIKRFRSGAESLPDAVVLTTEE---GNIFWCNGLAQQLLGFRWPEDNGQNILNLLRYP---EFT----QYLKT  158 (430)
T ss_pred             HHHHH-HHHHHHHHHHHhCCCeEEEEcCC---CceeHHHHHHHHHhCCCChHhCCCcHHHHhcCH---HHH----HHHHh
Confidence            33343 46678999999999999999999   999999999999999999999999876654322   111    11222


Q ss_pred             CCCeEEEEEEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchhhh
Q 020514           89 ERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMR  140 (325)
Q Consensus        89 ~~~~~~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~~  140 (325)
                      ... .........+|.  ++.+...|..+   +   +.+.+.+|||++++++
T Consensus       159 ~~~-~~~~~~~~~~~~--~~~~~~~~~~~---~---~~~~~~~dit~~~~~e  201 (430)
T PRK11006        159 RDF-SRPLTLVLNNGR--HLEIRVMPYTE---G---QLLMVARDVTQMHQLE  201 (430)
T ss_pred             ccc-CCCeEEEcCCCC--EEEEEEEEcCC---C---cEEEEEehhhHHHHHH
Confidence            111 111222234444  45556666543   2   2567789999998863

>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=98.29  E-value=1.2e-06  Score=62.21  Aligned_cols=61  Identities=16%  Similarity=0.072  Sum_probs=49.7

Q ss_pred             CCCeEEEehh-hHHhhCCCcccccccccccccCCCCChH-HHHHHHH----------hhccccCCCceeeEEe
Q 020514          263 DMPMVYASDA-FLKLTGYDRNEVVGQNCRFLNGVDTDTT-VLYQVSI----------AISPYPKKKSIYMEYV  323 (325)
Q Consensus       263 dg~i~~~N~a-~~~~~Gy~~~e~iG~~~~~l~~~~~~~~-~~~~~~~----------e~~~~~kdG~~~~~~~  323 (325)
                      ||+|+++-+. ...++||.++|++|+++.++++|++... ..+..++          -+++..|+|..+|+.-
T Consensus        11 dgki~~~d~~~v~~~lgy~~~eLvG~s~y~~~H~~D~~~~~~~~~~~~~~~g~~~~~~yR~~~k~g~~vwvqt   83 (111)
T PF14598_consen   11 DGKITYVDSRAVSSLLGYLPEELVGRSIYDFVHPDDLQRVLKQHHREVLQKGQSVSPYYRFRTKNGGYVWVQT   83 (111)
T ss_dssp             TSBEEEEETTHHHHHHSS-HHHHTTSBGGGGBSCCTHHHHHHHHHHHHHHHSSEEEEEEEEE-TTSSEEEEEE
T ss_pred             CcEEEEEcCccChhhcCCCcHHHcCCchHHhCCHhhhhhHHHHHHHHHhhCCCcCcceEEEEecCCcEEEEEE
Confidence            7899999999 5999999999999999999999999886 4444443          5677789999888864

...

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=98.28  E-value=1.3e-05  Score=75.31  Aligned_cols=49  Identities=14%  Similarity=0.131  Sum_probs=43.2

Q ss_pred             hHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccC
Q 020514          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNG  294 (325)
Q Consensus       243 l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~  294 (325)
                      +..+++++++||+++|.   +|+|+++|+++++++|++.++++|+++.++++
T Consensus       205 ~~~il~~~~~gVl~vD~---~G~I~~~N~aa~~llg~s~~~l~G~~i~~l~~  253 (638)
T PRK11388        205 LNALLESMDDGVIAWDE---QGNLQFLNAQAARLLRLDATASQGRAITELLT  253 (638)
T ss_pred             HHHHHhccCCcEEEECC---CCeEehhhHHHHHHhCcCHHHHCCCcHHHHhc
Confidence            34467788999999998   47999999999999999999999999988774

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=98.28  E-value=6.1e-06  Score=75.10  Aligned_cols=109  Identities=14%  Similarity=0.137  Sum_probs=78.5

Q ss_pred             hHHHHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEE
Q 020514           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV   94 (325)
Q Consensus        15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   94 (325)
                      +....+..+++++++|++++|.+   |.++++|+++++++|++.++++|+++..+++...       +...+..+.....
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            34567899999999999999999   9999999999999999999999999887765432       2233444433111


Q ss_pred             EEEEEecCCCeEEEEEEEEEee--cCCCCe--eeEEEEEEeccccch
Q 020514           95 NLLNYKKDGTPFWMLFKMSLVF--GKEDGR--ATHFVAVQVPIVSRK  137 (325)
Q Consensus        95 e~~~~~~dg~~~~~~~~~~~~~--~~~~g~--~~~~~~~~~DITe~k  137 (325)
                      . .....+|..++  +...|+.  + ++|.  ..|.+.+++|+++..
T Consensus       147 ~-~~v~~~g~~~~--v~~~PI~~~d-~~g~~~~~GaVivlrd~~~l~  189 (520)
T PRK10820        147 N-EHVVINGQDFL--MEITPVYLQD-ENDQHVLVGAVVMLRSTARMG  189 (520)
T ss_pred             e-EEEEECCEEEE--EEEEeeeecC-CCCceeEEEEEEEeccHHHHH
Confidence            1 12234565444  5667776  4 4454  379999999998754

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

Probab=98.20  E-value=3.7e-06  Score=53.26  Aligned_cols=43  Identities=23%  Similarity=0.421  Sum_probs=36.0

Q ss_pred             HHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCC
Q 020514           18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGR   67 (325)
Q Consensus        18 ~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~   67 (325)
                      ++++.+++++|.+++++| +   ++++++|+++++++||+   ..|....
T Consensus         1 e~~~~l~~~~~~~i~i~d-~---~~i~~~N~~~~~l~g~~---~~~~~~~   43 (64)
T PF13188_consen    1 ERYRSLFDNSPDGILIID-G---GRIIYVNPAFEELFGYS---LEGEDIG   43 (64)
T ss_dssp             HHHHHHHCCSSSEEEEEE-T---SBEEEE-HHHHHHHCS----HTCCCHH
T ss_pred             CHHHHHHHcCccceEEEE-C---CChHHhhHHHHHHhCCC---CCCCCHH
Confidence            368899999999999999 9   89999999999999998   5566543

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

Probab=98.19  E-value=4.8e-06  Score=55.71  Aligned_cols=70  Identities=19%  Similarity=0.243  Sum_probs=53.3

Q ss_pred             CCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH----------hhccccCCCceee
Q 020514          251 KQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI----------AISPYPKKKSIYM  320 (325)
Q Consensus       251 ~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~----------e~~~~~kdG~~~~  320 (325)
                      +++++++|.+   |.++++|+++++++|++..+++|+++..+.++.........+..          ++....++|...|
T Consensus         2 ~~~i~~~d~~---~~~~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (103)
T cd00130           2 PDGVIVLDLD---GRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDGSVIW   78 (103)
T ss_pred             CceEEEECCC---CcEEEECHHHHHHhCCCHHHHcCccHHHhcCCccchHHHHHHHHHHhcCcCeEEEEEEEccCCCEEE
Confidence            5788888874   79999999999999999999999998888877766544443333          4444556787777


Q ss_pred             EEe
Q 020514          321 EYV  323 (325)
Q Consensus       321 ~~~  323 (325)
                      +.+
T Consensus        79 ~~~   81 (103)
T cd00130          79 VLV   81 (103)
T ss_pred             EEE
Confidence            654

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=98.00  E-value=0.00037  Score=54.10  Aligned_cols=117  Identities=25%  Similarity=0.378  Sum_probs=84.2

Q ss_pred             HHHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChH-HHHHHHHHH-HhCCCeEE
Q 020514           17 TLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRR-TIMEIREAI-REERPIEV   94 (325)
Q Consensus        17 ~~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~-~~~~~~~~~-~~~~~~~~   94 (325)
                      ..++..+++..+.+++.+|.+   +.+.++|+++..++|++..+..+.....+........ ......... ........
T Consensus       111 ~~~~~~~~~~~~~~~~~~d~~---~~~~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  187 (232)
T COG2202         111 EERLRALLEASPDGIWVLDED---GRILYANPAAEELLGYSPEEELGRGLSDLIHPEDEERRELELARALAEGRGGPLEI  187 (232)
T ss_pred             HHHHHHHHhhCCceEEEEeCC---CCEEEeCHHHHHHhCCChHHhcCCChhheEecCCCchhhHHHHHHhhccCCCCcce
Confidence            344889999999999999999   9999999999999999988777776544433322211 111222222 22234566


Q ss_pred             EEEEEecCCCe-EEEEEEEEEeecCCCCeeeEEEEEEeccccchh
Q 020514           95 NLLNYKKDGTP-FWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKH  138 (325)
Q Consensus        95 e~~~~~~dg~~-~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~  138 (325)
                      +.....++|.. .+......+...  .|.+..+.....|+++++.
T Consensus       188 ~~~~~~~~g~~~~~~~~~~~~~~~--~~~~~~~~~~~~d~~~~~~  230 (232)
T COG2202         188 EYRVRRKDGERVRWILSRISPVRD--DGEIVGVVGIARDITERKQ  230 (232)
T ss_pred             EEEEEecCCCEEEEEEeeeeEecC--CCceEEEEEEEechHHHhh
Confidence            77778889985 777777777653  6888888899999998876

>PRK11086 sensory histidine kinase DcuS; Provisional

Probab=97.88  E-value=0.00013  Score=67.44  Aligned_cols=110  Identities=10%  Similarity=0.140  Sum_probs=75.7

Q ss_pred             HHHHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCCh---hhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCe
Q 020514           16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSR---AEIIGRNGRMFQGPRTNRRTIMEIREAIREERPI   92 (325)
Q Consensus        16 ~~~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~---~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~   92 (325)
                      ....++.++++++++++++|.+   |+++++|+++++++|++.   .+.+|.....+.++       ..+...+..+...
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   34555554433322       1223344444433


Q ss_pred             EEEEEEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchhhhh
Q 020514           93 EVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRN  141 (325)
Q Consensus        93 ~~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~~~  141 (325)
                      ....  ...+|.  ++.+...|+.+  +|.+.|++.+++|+|+.+++++
T Consensus       289 ~~~~--~~~~g~--~~~~~~~pi~~--~g~~~g~v~~~rDite~~~l~~  331 (542)
T PRK11086        289 RDEE--ININGR--LLLTNTVPVRV--NGEIIGAIATFRDKTEVRQLAQ  331 (542)
T ss_pred             cceE--EEECCE--EEEEEEEEEeE--CCEEEEEEEEEEEchHHHHHHH
Confidence            2211  122443  34566788886  7889999999999999887643

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

Probab=97.85  E-value=0.00022  Score=63.56  Aligned_cols=113  Identities=11%  Similarity=0.015  Sum_probs=77.2

Q ss_pred             hHHHHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhC-CCeE
Q 020514           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREE-RPIE   93 (325)
Q Consensus        15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~-~~~~   93 (325)
                      +..++++.+++....|++.+|.+   |.+..+|++++.|+|.+..++.|.+.+.+.+.     +...+...-..+ ....
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---GCITTVNPSAEQILGKPFDQLLGQSLSAIAPE-----LEEVFAEAGAAARTDKR  438 (712)
T ss_pred             HHHHHHHHHHhcCceeEEEEcCC---CeeEeecchHHHHhcCChhHhhcchhhhhhhH-----HHHHHHHhhhhcCCCcc
Confidence            35567889999999999999999   99999999999999999999999886544321     122222211111 2223


Q ss_pred             EEEEEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchhh
Q 020514           94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM  139 (325)
Q Consensus        94 ~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~  139 (325)
                      .+..+ ...|+...+.+....... +  .-.+++.++.|||+...+
T Consensus       439 ~ev~~-~r~g~~rtl~Vq~t~~~~-d--~~~gyVvt~DDITdLV~A  480 (712)
T COG5000         439 VEVKL-AREGEERTLNVQATREPE-D--NGNGYVVTFDDITDLVIA  480 (712)
T ss_pred             ceeec-ccCCCceeeeeeeeeccc-c--cCCceEEEecchHHHHHH
Confidence            33333 345555556666655543 2  224789999999999886

>PRK11006 phoR phosphate regulon sensor protein; Provisional

Probab=97.83  E-value=1.2e-05  Score=71.94  Aligned_cols=52  Identities=17%  Similarity=0.167  Sum_probs=46.2

Q ss_pred             hhhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCC
Q 020514          241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGV  295 (325)
Q Consensus       241 ~~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~  295 (325)
                      ..++.+++++++|++++|.   +|+|+++|+++++++||+.++++|+++..+..+
T Consensus        98 ~~~~~~~~~~~~~i~~~d~---~g~i~~~N~~a~~l~g~~~~~~~g~~~~~~~~~  149 (430)
T PRK11006         98 KRFRSGAESLPDAVVLTTE---EGNIFWCNGLAQQLLGFRWPEDNGQNILNLLRY  149 (430)
T ss_pred             HHHHHHHHhCCCeEEEEcC---CCceeHHHHHHHHHhCCCChHhCCCcHHHHhcC
Confidence            3477789999999999997   479999999999999999999999998877653

>PF12860 PAS_7: PAS fold

Probab=97.82  E-value=4.1e-05  Score=54.84  Aligned_cols=44  Identities=25%  Similarity=0.349  Sum_probs=38.5

Q ss_pred             hhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccc-ccccccccc
Q 020514          247 LGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEV-VGQNCRFLN  293 (325)
Q Consensus       247 ~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~-iG~~~~~l~  293 (325)
                      +++++.||+++|.   ||+++++|++|.+|+|++++.+ .|.++..+.
T Consensus         1 Ld~l~~Gv~v~D~---~~rl~~~N~~~~~l~~~~~~~~~~G~~~~~l~   45 (115)
T PF12860_consen    1 LDSLPQGVAVFDS---DGRLVFWNQRFRELFGLPPEMLRPGASFRDLL   45 (115)
T ss_pred             CCCcCceEEEEcC---CCeEEeEcHHHHHHhCCCHHHhcCCCCHHHHH
Confidence            4678999999998   4799999999999999999988 788876653

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=97.81  E-value=1.3e-05  Score=72.95  Aligned_cols=52  Identities=17%  Similarity=0.094  Sum_probs=47.2

Q ss_pred             hhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCC
Q 020514          242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVD  296 (325)
Q Consensus       242 ~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~  296 (325)
                      .+..+++++++||+++|.+   |+|+++|++++++||++.++++|+++.++++..
T Consensus        81 ~L~aIL~sm~eGVi~vD~~---G~I~~iN~aA~~Llg~~~eel~Gk~i~eli~~~  132 (520)
T PRK10820         81 ALSALLEALPEPVLSIDMK---GKVELANPASCQLFGQSEEKLRNHTAAQLINGF  132 (520)
T ss_pred             HHHHHHHhCCCcEEEECCC---CeeeHhHHHHHHHHCcCHHHHCCCcHHHHcCcc
Confidence            4778999999999999985   799999999999999999999999999988643

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

Probab=97.75  E-value=1.4e-05  Score=67.76  Aligned_cols=105  Identities=23%  Similarity=0.377  Sum_probs=84.8

Q ss_pred             HHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCC-CChHHHHHHHHHHHhCCCeEEEEEE
Q 020514           20 VHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPR-TNRRTIMEIREAIREERPIEVNLLN   98 (325)
Q Consensus        20 ~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~-~~~~~~~~~~~~~~~~~~~~~e~~~   98 (325)
                      +..+++....++-+.|.+   ..+.|+|++|+.|+|+...+++|++..++...+ ....+...+..+++.|..++++...
T Consensus       159 lFaaLD~c~eAiEI~~dd---hViQYVNpAfE~mmG~hkgEliGke~adlpkkdknradlldtintcikkgke~qG~~~a  235 (775)
T KOG1229|consen  159 LFAALDECDEAIEICDDD---HVIQYVNPAFENMMGCHKGELIGKEEADLPKKDKNRADLLDTINTCIKKGKEAQGEEEA  235 (775)
T ss_pred             HHHHHhhhhhhheeccch---hHHHHhcHHHHhhhcchhhhhcCCchhhccccccchhhhhhhhhHhhhcCccccchHHH
Confidence            346778888899999998   999999999999999999999999977765433 2345677888899999999988777


Q ss_pred             EecCCCeEEEEEEEEEeecCCCCeeeEEEE
Q 020514           99 YKKDGTPFWMLFKMSLVFGKEDGRATHFVA  128 (325)
Q Consensus        99 ~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~  128 (325)
                      +++.|....-.+.+.|+-+ ..|.+..++.
T Consensus       236 RRksgdS~dqh~~itP~~g-qggkirhfvs  264 (775)
T KOG1229|consen  236 RRKSGDSCDQHFIITPFAG-QGGKIRHFVS  264 (775)
T ss_pred             hhccCCcccceEEEeeecC-CCCceeeehh
Confidence            7888877666677889887 6777776653

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

Probab=97.61  E-value=4.9e-05  Score=53.56  Aligned_cols=59  Identities=12%  Similarity=0.121  Sum_probs=41.7

Q ss_pred             hHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHH
Q 020514          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQV  305 (325)
Q Consensus       243 l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~  305 (325)
                      |..++++++.+++++|.+   ++|.++|+++.++|+..+ ..+|+++..++++...+.+...+
T Consensus         1 L~~il~s~~~~i~~vD~~---~~I~~~n~~a~~~f~~~~-~~iGr~l~~~~~~~~~~~l~~~i   59 (106)
T PF13596_consen    1 LNNILDSMPIGIIFVDRN---LRIRYFNPAAARLFNLSP-SDIGRPLFDIHPPLSYPNLKKII   59 (106)
T ss_dssp             HHHHHHHSSSEEEEEETT---SBEEEE-SCGC-SS---G-GGTTSBCCCSS-HHHHHHHHHHH
T ss_pred             ChHHHhcCCCCEEEEcCC---CeEEEeChhHhhhcCCCh-HHCCCCHHHcCCccchHHHHHHH
Confidence            456889999999999985   699999999999999775 55799999998764444433333

>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]

Probab=97.61  E-value=0.00074  Score=56.85  Aligned_cols=55  Identities=18%  Similarity=0.264  Sum_probs=46.1

Q ss_pred             HHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHH
Q 020514           21 HEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRT   78 (325)
Q Consensus        21 ~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~   78 (325)
                      ..+++.+.--+++++++   |.+.|++..+.-.+|++.-|+.|-.+.+.+++.|...+
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            44566666667899999   99999999999999999999999988888888776544

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

Probab=97.58  E-value=0.0054  Score=47.35  Aligned_cols=77  Identities=18%  Similarity=0.160  Sum_probs=53.3

Q ss_pred             hHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCCh----HHHHHHHH--------hhc
Q 020514          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDT----TVLYQVSI--------AIS  310 (325)
Q Consensus       243 l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~----~~~~~~~~--------e~~  310 (325)
                      +..++++++++++++|.   +|.+.++|+++++++||+..+..+.....+.......    ........        ++.
T Consensus       114 ~~~~~~~~~~~~~~~d~---~~~~~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  190 (232)
T COG2202         114 LRALLEASPDGIWVLDE---DGRILYANPAAEELLGYSPEEELGRGLSDLIHPEDEERRELELARALAEGRGGPLEIEYR  190 (232)
T ss_pred             HHHHHhhCCceEEEEeC---CCCEEEeCHHHHHHhCCChHHhcCCChhheEecCCCchhhHHHHHHhhccCCCCcceEEE
Confidence            34467778899999997   4799999999999999998888888776655433332    11111111        555


Q ss_pred             cccCCCce-eeEE
Q 020514          311 PYPKKKSI-YMEY  322 (325)
Q Consensus       311 ~~~kdG~~-~~~~  322 (325)
                      ...++|.. .|..
T Consensus       191 ~~~~~g~~~~~~~  203 (232)
T COG2202         191 VRRKDGERVRWIL  203 (232)
T ss_pred             EEecCCCEEEEEE
Confidence            56688875 5554

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=97.53  E-value=0.00092  Score=62.96  Aligned_cols=108  Identities=12%  Similarity=0.228  Sum_probs=75.2

Q ss_pred             HHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEEEEE
Q 020514           19 WVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLN   98 (325)
Q Consensus        19 ~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~   98 (325)
                      .+..+++.++++++++|.+   |.++++|+++++++|++.++++|+++..+++..      ..+..++..+.........
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            4456889999999999999   999999999999999999999999877665321      1223445555443322222


Q ss_pred             EecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchh
Q 020514           99 YKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKH  138 (325)
Q Consensus        99 ~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~  138 (325)
                      ...+|..+++.+.+.|+.+ ..|.  +++.+..|++..+.
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            3345666678888899865 4443  35555677776544

>smart00091 PAS PAS domain

Probab=97.46  E-value=0.00027  Score=42.78  Aligned_cols=57  Identities=23%  Similarity=0.311  Sum_probs=46.3

Q ss_pred             hHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHH
Q 020514          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVL  302 (325)
Q Consensus       243 l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~  302 (325)
                      ++.+++.+++++++++..   +.+.++|+.+.+++|++..++.|+.+..+.++.......
T Consensus         3 ~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   59 (67)
T smart00091        3 LRAILESLPDGIFVLDLD---GRILYANPAAEELLGYSPEELIGKSLLELIHPEDREEVQ   59 (67)
T ss_pred             HHHHHhhCCceEEEEcCC---CeEEEECHHHHHHhCCCHHHHcCCcHHHhcCcccHHHHH
Confidence            456777888999999974   699999999999999999999999887777666554333

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).

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

Probab=97.42  E-value=0.00015  Score=64.03  Aligned_cols=73  Identities=36%  Similarity=0.620  Sum_probs=57.3

Q ss_pred             CceEEecCCCCCCCeEEEehhhHHhhCCCccccccccc--ccccCCCCChHHHHHHHH----------hhccccCCCcee
Q 020514          252 QSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNC--RFLNGVDTDTTVLYQVSI----------AISPYPKKKSIY  319 (325)
Q Consensus       252 ~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~--~~l~~~~~~~~~~~~~~~----------e~~~~~kdG~~~  319 (325)
                      ..+++.+++-.|.+|+|.|++||++.||.+.|++.+++  .++.....+....+.+++          |+..++|+.++.
T Consensus        28 tsFlL~NAQiVD~PiVY~NdgFcKlsGY~RAevMQKs~tc~FMyGEltdk~ti~k~~~t~eN~~~~qfEillyKKN~TPv  107 (971)
T KOG0501|consen   28 TSFLLANAQIVDWPIVYCNDGFCKLSGYHRAEVMQKSCTCSFMYGELTDKGTIEKVRQTLENYETNQFEILLYKKNRTPV  107 (971)
T ss_pred             cceeeccceeeccceEEecCcchhccCccHHHHhcccceeeeeeccccchhhHHHHHHHHHhhhhcceeeEeeecCCCce
Confidence            45666666667889999999999999999999999965  445555555555566655          888899999999


Q ss_pred             eEEee
Q 020514          320 MEYVR  324 (325)
Q Consensus       320 ~~~~~  324 (325)
                      |..+.
T Consensus       108 W~~vq  112 (971)
T KOG0501|consen  108 WLLVQ  112 (971)
T ss_pred             EEEEE
Confidence            98764

>PRK15053 dpiB sensor histidine kinase DpiB; Provisional

Probab=97.41  E-value=0.001  Score=61.59  Aligned_cols=106  Identities=14%  Similarity=0.108  Sum_probs=73.0

Q ss_pred             HHHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCCh--hhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEE
Q 020514           17 TLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSR--AEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV   94 (325)
Q Consensus        17 ~~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~--~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   94 (325)
                      ...+..+++.+++|++++|.+   |.++++|+++++++|++.  ++++|++...++++...   .   ...... .....
T Consensus       221 ~~~~~~il~~~~egii~~D~~---g~I~~~N~~a~~ll~~~~~~~~~~g~~~~~~~~~~~~---~---~~~~~~-~~~~~  290 (545)
T PRK15053        221 VRQQEALFSSVYEGLIAVDPH---GYITAINRNARKMLGLSSPGRQWLGKPIAEVVRPADF---F---TEQIDE-KRQDV  290 (545)
T ss_pred             HHHHHHHHHHhCceEEEECCC---CeEEeecHHHHHHhCCCCcchhhcCCcHHHhCCCchh---h---hhhcCC-cccce
Confidence            345678999999999999999   999999999999999965  46889886666543211   0   111111 11111


Q ss_pred             EEEEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchhh
Q 020514           95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM  139 (325)
Q Consensus        95 e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~  139 (325)
                      .   ...+|  ..+.+...|+..  .|.+.|.+.+++|+|+.+..
T Consensus       291 ~---~~~~~--~~~~~~~~~i~~--~~~~~G~v~~~~d~te~~~l  328 (545)
T PRK15053        291 V---ANFNG--LSVIANREAIRS--GDDLLGAIISFRSKDEISTL  328 (545)
T ss_pred             E---EEECC--EEEEEEeeeEEE--CCeEEEEEEEEEchHHHHHH
Confidence            1   12234  234467778875  67778999999999998775

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

Probab=97.40  E-value=0.0055  Score=62.34  Aligned_cols=43  Identities=9%  Similarity=0.063  Sum_probs=38.0

Q ss_pred             hHHHHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhh
Q 020514           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAE   60 (325)
Q Consensus        15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~e   60 (325)
                      ....+++.+++.++.+++++|.+   |.++++|++++.++|++...
T Consensus       573 ~~~~~~~~i~~~~~~~i~~~d~~---g~i~~~N~~~~~~~g~~~~~  615 (1197)
T PRK09959        573 NQISFRKALSDSLPNPTYVVNWQ---GNVISHNSAFEHYFTADYYK  615 (1197)
T ss_pred             HHHHHHHHHHhhCCCcEEEEcCC---CcEEEehHHHHHHhCccccc
Confidence            45567889999999999999999   99999999999999986433

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

Probab=97.39  E-value=0.0014  Score=58.01  Aligned_cols=109  Identities=13%  Similarity=0.171  Sum_probs=80.8

Q ss_pred             HHHHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChh--hhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeE
Q 020514           16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRA--EIIGRNGRMFQGPRTNRRTIMEIREAIREERPIE   93 (325)
Q Consensus        16 ~~~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~--ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~   93 (325)
                      .......+++++..|++.+|+.   |.+..+|.++++++|+...  +.+|++...+++|+..      +...+..+.+..
T Consensus       213 l~~er~A~l~si~EGviAvd~~---G~It~~N~~A~~ll~~~~~~~~~ig~~i~~v~~p~~~------l~~vl~~~~~~~  283 (537)
T COG3290         213 LLEERQAMLQSIKEGVIAVDKK---GVITLINQAAQKLLGLRQPSGDPIGRSIVEVLPPDSD------LPEVLETGKPQH  283 (537)
T ss_pred             HHHHHHHHHHHhhceEEEECCC---CeEeehhHHHHHHhcccCcCcccccccceEeeccccC------cHHHHhcCCccc
Confidence            4455678899999999999999   9999999999999999765  6889988888776321      122234444333


Q ss_pred             EEEEEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchhh
Q 020514           94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM  139 (325)
Q Consensus        94 ~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~  139 (325)
                      .+.  ..-+|.  ++.+...|+.-  +|++.|++.+++|-|+-+++
T Consensus       284 ~~e--~~~ng~--~~i~nr~pI~~--~~~~~GaI~tFRdktei~~L  323 (537)
T COG3290         284 DEE--IRINGR--LLVANRVPIRS--GGQIVGAIITFRDKTEIKKL  323 (537)
T ss_pred             chh--hhcCCe--EEEEEeccEEE--CCEEeEEEEEEecHHHHHHH
Confidence            222  122343  45577888885  89999999999999998876

>PRK11360 sensory histidine kinase AtoS; Provisional

Probab=97.34  E-value=0.00035  Score=65.25  Aligned_cols=52  Identities=23%  Similarity=0.215  Sum_probs=46.6

Q ss_pred             hhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCC
Q 020514          242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVD  296 (325)
Q Consensus       242 ~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~  296 (325)
                      .+..++++++++++++|.   +|.++++|+++++++||++++++|+++..++++.
T Consensus       263 ~~~~i~~~~~~~i~~~d~---~g~i~~~N~~~~~l~g~~~~~~~g~~~~~~~~~~  314 (607)
T PRK11360        263 LNELILESIADGVIAIDR---QGKITTMNPAAEVITGLQRHELVGKPYSELFPPN  314 (607)
T ss_pred             HHHHHHHhccCeEEEEcC---CCCEEEECHHHHHHhCCChHHhcCCcHHHHcCCc
Confidence            456788999999999997   4799999999999999999999999999888654

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

Probab=97.27  E-value=0.00071  Score=61.00  Aligned_cols=98  Identities=10%  Similarity=0.245  Sum_probs=80.7

Q ss_pred             EcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEEEEEEecCCCeEEEEEEEE
Q 020514           34 TDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMS  113 (325)
Q Consensus        34 ~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg~~~~~~~~~~  113 (325)
                      .+.+   .+|.|+.+.+..++||.+++++|+++..++++.|...+.......+..|......++...+.|..+|+...++
T Consensus       280 hs~D---mkityCedRisdlm~y~PeeLvGrS~Ye~~Ha~Ds~~v~KSh~dL~~KGQv~TgyYR~lak~GGyvWlQTqAT  356 (768)
T KOG3558|consen  280 HSLD---MKITYCEDRISDLMDYEPEELVGRSCYEFVHALDSDRVRKSHHDLLTKGQVVTGYYRLLAKNGGYVWLQTQAT  356 (768)
T ss_pred             eecc---eeEEEEchhHHHHhcCCHHHhhchhHHHhhhHhhhhHHHHHHHHHHhcCccchhHHHHHHhcCCeEEEEeeeE
Confidence            3455   7899999999999999999999999999999999888888888999999988888899999999999999998


Q ss_pred             EeecCCCCeeeEEEEEEeccc
Q 020514          114 LVFGKEDGRATHFVAVQVPIV  134 (325)
Q Consensus       114 ~~~~~~~g~~~~~~~~~~DIT  134 (325)
                      .+.+..+++...++++.-=|+
T Consensus       357 Vi~~tkn~q~q~IicVnYVlS  377 (768)
T KOG3558|consen  357 VIYNTKNPQEQNIICVNYVLS  377 (768)
T ss_pred             EEecCCCCCcceEEEEEeeec
Confidence            887623344444555443333

>smart00091 PAS PAS domain

Probab=97.27  E-value=0.0013  Score=39.59  Aligned_cols=55  Identities=24%  Similarity=0.412  Sum_probs=45.4

Q ss_pred             HHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCCh
Q 020514           19 WVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNR   76 (325)
Q Consensus        19 ~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~   76 (325)
                      ++..+++.++.++++++..   +.+.++|+.+..++|++..++.|..+..+.++.+..
T Consensus         2 ~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   56 (67)
T smart00091        2 RLRAILESLPDGIFVLDLD---GRILYANPAAEELLGYSPEELIGKSLLELIHPEDRE   56 (67)
T ss_pred             hHHHHHhhCCceEEEEcCC---CeEEEECHHHHHHhCCCHHHHcCCcHHHhcCcccHH
Confidence            3567888999999999999   999999999999999999888887766555555443

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).

>TIGR02373 photo_yellow photoactive yellow protein

Probab=97.19  E-value=0.0012  Score=46.53  Aligned_cols=59  Identities=14%  Similarity=0.072  Sum_probs=48.2

Q ss_pred             hhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccc-cccCCCCChHHHHHHHH
Q 020514          246 SLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCR-FLNGVDTDTTVLYQVSI  307 (325)
Q Consensus       246 ~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~-~l~~~~~~~~~~~~~~~  307 (325)
                      -++..|-|++-.|.+   |+|+..|.+-..+.|++++.++|+++. ++.+=...+.+..++.+
T Consensus        21 elD~lpFGvI~lD~~---G~V~~YN~aE~~~sg~~p~~vlGr~FF~eVAPC~~~~~f~gRF~~   80 (124)
T TIGR02373        21 QFDALPFGAIQLDGS---GVILRYNAAEGRITGRDPERVIGRNFFKEVAPCTDIPEFSGRFME   80 (124)
T ss_pred             HhhcCCcceEEECCC---CEEEEEecchhhhcCCChhhhhchhhhhhcccccCCHHHHHHHHh
Confidence            367778999999984   799999999999999999999999974 55554555666666655

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.

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

Probab=97.08  E-value=0.0061  Score=50.14  Aligned_cols=109  Identities=12%  Similarity=0.106  Sum_probs=79.2

Q ss_pred             HHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEEEEEEe
Q 020514           21 HEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYK  100 (325)
Q Consensus        21 ~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~  100 (325)
                      ..++++++..++++|.+   +.+.|+|++++.+||.+...+.|.+++.+++..  ......+.+....+......-....
T Consensus        10 ~~~Ln~~~~pVl~vd~~---~~i~yaN~aAe~~~~~Sa~~L~~~~l~~l~~~g--s~ll~ll~q~~~~~~~~~~~~v~l~   84 (363)
T COG3852          10 GAILNNLINPVLLVDDE---LAIHYANPAAEQLLAVSARRLAGTRLSELLPFG--SLLLSLLDQVLERGQPVTEYEVTLV   84 (363)
T ss_pred             HhHHhccCCceEEEcCC---CcEEecCHHHHHHHHHHHHHHhcCChHHHcCCC--cHHHHHHHHHHHhcCCcccceeeee
Confidence            36889999999999999   999999999999999999999999887776543  2345556666666655432222223


Q ss_pred             cCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchh
Q 020514          101 KDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKH  138 (325)
Q Consensus       101 ~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~  138 (325)
                      .+|....+...+.|+.. ..|.+   +..+..+....+
T Consensus        85 ~~g~~~~v~~~v~~v~~-~~G~v---lle~~~~~~~~r  118 (363)
T COG3852          85 ILGRSHIVDLTVAPVPE-EPGSV---LLEFHPRDMQRR  118 (363)
T ss_pred             ecCccceEEEEEeeccC-CCCeE---EEEechhHHHhH
Confidence            68888899999999976 56643   444455444443

>PRK15053 dpiB sensor histidine kinase DpiB; Provisional

Probab=97.07  E-value=0.0036  Score=57.94  Aligned_cols=52  Identities=12%  Similarity=0.151  Sum_probs=44.3

Q ss_pred             hhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCc--ccccccccccccCCC
Q 020514          242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDR--NEVVGQNCRFLNGVD  296 (325)
Q Consensus       242 ~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~--~e~iG~~~~~l~~~~  296 (325)
                      .+..+++++++|++++|.+   |+|+++|+++++++|++.  ++++|+++.++.++.
T Consensus       223 ~~~~il~~~~egii~~D~~---g~I~~~N~~a~~ll~~~~~~~~~~g~~~~~~~~~~  276 (545)
T PRK15053        223 QQEALFSSVYEGLIAVDPH---GYITAINRNARKMLGLSSPGRQWLGKPIAEVVRPA  276 (545)
T ss_pred             HHHHHHHHhCceEEEECCC---CeEEeecHHHHHHhCCCCcchhhcCCcHHHhCCCc
Confidence            3566889999999999984   799999999999999975  479999988877543

>COG2461 Uncharacterized conserved protein [Function unknown]

Probab=97.05  E-value=0.0028  Score=53.57  Aligned_cols=114  Identities=17%  Similarity=0.175  Sum_probs=85.8

Q ss_pred             HHHHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEE
Q 020514           16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVN   95 (325)
Q Consensus        16 ~~~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e   95 (325)
                      ..+.+..+++..|.-+..+|.+   +.+.+.|+. .++|-.++.. +|++...- +|.........+.+...+|..-..+
T Consensus       288 ~~~e~naif~~lP~Ditfvdk~---diV~ffs~~-~rif~rt~sv-iGr~v~~c-hpPksv~iv~ki~~~fksG~kd~~e  361 (409)
T COG2461         288 SLEELNAIFKHLPVDITFVDKN---DIVRFFSGG-ERIFPRTPSV-IGRRVQLC-HPPKSVHIVEKILKDFKSGEKDFAE  361 (409)
T ss_pred             eHHHHHHHHhhCCCceEEeccc---ceEEecCCc-ceecccChHh-hCCcccCC-CCCchHHHHHHHHHHhhcCCcchHH
Confidence            3457889999999888889999   999999998 7777766554 68886644 4444455566667777777665555


Q ss_pred             EEEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchhh
Q 020514           96 LLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM  139 (325)
Q Consensus        96 ~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~  139 (325)
                      +..  ..| ...+.++..++++ ++|...|.+.+.+|||..+..
T Consensus       362 fw~--~~~-~~~i~i~Y~av~d-e~ge~~g~le~~qdi~~i~~l  401 (409)
T COG2461         362 FWI--NMG-DKFIHIRYFAVKD-EEGEYLGTLEVVQDITRIKEL  401 (409)
T ss_pred             Hhc--cCC-CceEEEEEEEEEc-CCCceeeeehhhhhhHHHHhc
Confidence            542  122 2356688999999 899999999999999999875

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

Probab=97.01  E-value=0.0037  Score=55.51  Aligned_cols=53  Identities=21%  Similarity=0.238  Sum_probs=46.2

Q ss_pred             hHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcc--cccccccccccCCCCC
Q 020514          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRN--EVVGQNCRFLNGVDTD  298 (325)
Q Consensus       243 l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~--e~iG~~~~~l~~~~~~  298 (325)
                      ...+++++.+|++.+|..   |.|+.+|.++++|+|+...  +.+|+++.++.+|+.+
T Consensus       217 r~A~l~si~EGviAvd~~---G~It~~N~~A~~ll~~~~~~~~~ig~~i~~v~~p~~~  271 (537)
T COG3290         217 RQAMLQSIKEGVIAVDKK---GVITLINQAAQKLLGLRQPSGDPIGRSIVEVLPPDSD  271 (537)
T ss_pred             HHHHHHHhhceEEEECCC---CeEeehhHHHHHHhcccCcCcccccccceEeeccccC
Confidence            456788899999999986   6999999999999999775  7999999999987544

>TIGR02373 photo_yellow photoactive yellow protein

Probab=96.97  E-value=0.013  Score=41.45  Aligned_cols=67  Identities=18%  Similarity=0.076  Sum_probs=54.6

Q ss_pred             HHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCC-cccCCCCChHHHHHHHHHHHhCC
Q 020514           21 HEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGR-MFQGPRTNRRTIMEIREAIREER   90 (325)
Q Consensus        21 ~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~-~l~~~~~~~~~~~~~~~~~~~~~   90 (325)
                      ..-++.+|.|++-+|.+   |.++..|.+=..+.|++++.++|++.. ++.|......+...+.+....+.
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            35589999999999999   999999999999999999999999844 45555555667777777666554

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=96.91  E-value=0.05  Score=40.31  Aligned_cols=112  Identities=11%  Similarity=0.105  Sum_probs=72.7

Q ss_pred             HHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEEEE
Q 020514           18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLL   97 (325)
Q Consensus        18 ~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~   97 (325)
                      ..++.++. .|.+|+-.+.+ .+=.++|.|.++.++++++-+++++.|...-..+.........+.++...|-.....=.
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            34555555 88888877665 22468999999999999999999999876655554444445556666666643333323


Q ss_pred             EEecCCCeEEEE-EEEEEeecCCCCeeeEEEEEEec
Q 020514           98 NYKKDGTPFWML-FKMSLVFGKEDGRATHFVAVQVP  132 (325)
Q Consensus        98 ~~~~dg~~~~~~-~~~~~~~~~~~g~~~~~~~~~~D  132 (325)
                      -+.+.|+.+++. ..+--+.+ ++|...|.-..+.+
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            356778777664 23444556 67777665544443

>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=96.87  E-value=0.0028  Score=46.79  Aligned_cols=79  Identities=16%  Similarity=0.094  Sum_probs=55.3

Q ss_pred             hHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH-----hhc-----cc
Q 020514          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI-----AIS-----PY  312 (325)
Q Consensus       243 l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~-----e~~-----~~  312 (325)
                      +...+-+.|.+|+.-+.. +|-.++|+|.++.+||+|+-+|++|.+.+--..+..+......+.+     -..     ..
T Consensus        33 ~~~~L~~ap~ailsh~~~-~dP~f~yaN~aaL~l~e~~w~el~~lPsr~sae~~~r~er~~lL~~v~~qG~~~~y~GiRi  111 (148)
T PF08670_consen   33 LAKALWHAPFAILSHGTK-ADPIFIYANQAALDLFETTWDELVGLPSRLSAEEPERKERQSLLAQVMQQGYIDNYSGIRI  111 (148)
T ss_pred             HHHHHHcCCCEEEEcCCC-CCCEEEehhHHHHHHhcCCHHHHhcCcHhhccChhhHHHHHHHHHHHHHhCCccCCCeEEE
Confidence            444555588888888766 4778999999999999999999999987765555544444333333     111     13


Q ss_pred             cCCCceeeEE
Q 020514          313 PKKKSIYMEY  322 (325)
Q Consensus       313 ~kdG~~~~~~  322 (325)
                      .+.|..++++
T Consensus       112 ss~Grrf~ie  121 (148)
T PF08670_consen  112 SSTGRRFRIE  121 (148)
T ss_pred             cCCCCeEEEe
Confidence            4788877664

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

Probab=96.56  E-value=0.0011  Score=56.78  Aligned_cols=72  Identities=19%  Similarity=0.332  Sum_probs=53.3

Q ss_pred             hHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCCh-HHHHHHHH----------hhcc
Q 020514          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDT-TVLYQVSI----------AISP  311 (325)
Q Consensus       243 l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~-~~~~~~~~----------e~~~  311 (325)
                      +..+++....+|-++|.   |..|.|||++|+.|+||-+.|++|+...++...+..+ ..++.+..          +...
T Consensus       159 lFaaLD~c~eAiEI~~d---dhViQYVNpAfE~mmG~hkgEliGke~adlpkkdknradlldtintcikkgke~qG~~~a  235 (775)
T KOG1229|consen  159 LFAALDECDEAIEICDD---DHVIQYVNPAFENMMGCHKGELIGKEEADLPKKDKNRADLLDTINTCIKKGKEAQGEEEA  235 (775)
T ss_pred             HHHHHhhhhhhheeccc---hhHHHHhcHHHHhhhcchhhhhcCCchhhccccccchhhhhhhhhHhhhcCccccchHHH
Confidence            55677788889999987   4689999999999999999999999998887554332 33333332          4455


Q ss_pred             ccCCCc
Q 020514          312 YPKKKS  317 (325)
Q Consensus       312 ~~kdG~  317 (325)
                      +||.|.
T Consensus       236 RRksgd  241 (775)
T KOG1229|consen  236 RRKSGD  241 (775)
T ss_pred             hhccCC
Confidence            666654

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

Probab=96.20  E-value=0.0025  Score=59.66  Aligned_cols=64  Identities=19%  Similarity=0.211  Sum_probs=48.5

Q ss_pred             hhhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHH
Q 020514          241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVS  306 (325)
Q Consensus       241 ~~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~  306 (325)
                      ..|..++=.+.||++++-..  ||+|+||+.+.+.++||..+|++|+++.++++|.+....+..+-
T Consensus        94 ~eL~~LmLeAlDGF~fvV~c--dG~IvyVSeSVT~~L~y~QsDL~~qSly~ilhp~d~~~~~~ql~  157 (803)
T KOG3561|consen   94 DELTHLILEALDGFLFVVNC--DGRIVYVSESVTSVLGYLQSDLMGQSLYDILHPLDNDKPREQLS  157 (803)
T ss_pred             HHHHHHHHHHhcCeEEEEec--CceEEEEecchHHhhCcCHHHHhcchHHHhcCccccCccccccc
Confidence            34554444444666554443  69999999999999999999999999999998887766655544

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

Probab=96.16  E-value=0.017  Score=53.80  Aligned_cols=67  Identities=13%  Similarity=0.113  Sum_probs=49.8

Q ss_pred             eEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHH---HHH----------hhccccCCCceee
Q 020514          254 FVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQ---VSI----------AISPYPKKKSIYM  320 (325)
Q Consensus       254 i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~---~~~----------e~~~~~kdG~~~~  320 (325)
                      ||++-.. +.+.|..|..++..++||-+.++||+++..++++++.....+.   +.+          .+++..++|.++-
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            5555443 5788999999999999999999999999888888776544332   222          5566678888764


Q ss_pred             E
Q 020514          321 E  321 (325)
Q Consensus       321 ~  321 (325)
                      +
T Consensus       411 l  411 (1114)
T KOG3753|consen  411 L  411 (1114)
T ss_pred             E
Confidence            4

>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]

Probab=96.07  E-value=0.086  Score=46.73  Aligned_cols=59  Identities=12%  Similarity=0.147  Sum_probs=49.4

Q ss_pred             HHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHH
Q 020514           22 EALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIR   83 (325)
Q Consensus        22 ~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~   83 (325)
                      -++..++--++++..+   |.|.|++......+|+...+++-.++.++++.+|...+...+.
T Consensus       115 ~lLqsLnGF~lVvt~e---g~ifyAS~tIedYLGFhQSDV~HQsVYdlIHseDR~dfqrQLh  173 (712)
T KOG3560|consen  115 LLLQSLNGFALVVTAE---GEIFYASATIEDYLGFHQSDVMHQSVYDLIHSEDRQDFQRQLH  173 (712)
T ss_pred             HHHHhcCCeEEEEecC---ceEEEehhhHHhhhcccccchhhhhHHHHhhhhhHHHHHHHHh
Confidence            3456666667888898   9999999999999999999999999999999888777655543

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

Probab=96.06  E-value=0.0083  Score=50.60  Aligned_cols=55  Identities=16%  Similarity=0.088  Sum_probs=47.9

Q ss_pred             hhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCCh
Q 020514          242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDT  299 (325)
Q Consensus       242 ~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~  299 (325)
                      .|..++++++++++-+|..   |.+..+|+|+++++|.+.+++.|+....++....-.
T Consensus        81 ~L~aLL~al~~pVlsvd~k---g~v~~aNpAa~~l~~~~~~~~~g~~~~~l~~~~nf~  135 (511)
T COG3283          81 ALSALLEALPEPVLSVDMK---GKVDMANPAACQLFGRKEDRLRGHTAAQLINGFNFL  135 (511)
T ss_pred             HHHHHHHhCCCceEEeccc---CceeecCHHHHHHhCCChhhhcCccHHHhcCcCCHH
Confidence            3777899999999999985   799999999999999999999999988877554433

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

Probab=96.02  E-value=0.012  Score=49.25  Aligned_cols=62  Identities=16%  Similarity=0.197  Sum_probs=51.9

Q ss_pred             hHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH
Q 020514          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI  307 (325)
Q Consensus       243 l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~  307 (325)
                      |..++--+.+|++-+|..   |+|+.+|..+.+|+|.+.++++|+++.++..-.+.-.+.+.+.+
T Consensus       113 L~SvlayMtDGViATdRr---G~iI~iN~~A~k~L~~~~E~~~~~~i~elL~i~d~y~~~dL~e~  174 (459)
T COG5002         113 LDSVLAYMTDGVIATDRR---GKIILINKPALKMLGVSKEDALGRSILELLKIEDTYTFEDLVEK  174 (459)
T ss_pred             HHHHHHHHcCceEeecCC---CcEEEeccHHHHHhCcCHHHHhcccHHHHhCCccceeHHHHHhc
Confidence            555666667999999986   79999999999999999999999999999877776666655544

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

Probab=95.91  E-value=0.086  Score=27.63  Aligned_cols=40  Identities=30%  Similarity=0.452  Sum_probs=32.4

Q ss_pred             EEEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccc
Q 020514           96 LLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSR  136 (325)
Q Consensus        96 ~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~  136 (325)
                      +.....+|...|+.....++.+ ..+.+.++++...|+|++
T Consensus         4 ~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~di~~~   43 (43)
T smart00086        4 YRLRRKDGSYIWVLVSASPIRD-EDGEVEGILGVVRDITER   43 (43)
T ss_pred             EEEEecCCCEEEEEEEeEEEEC-CCCCEEEEEEEEEeccCC
Confidence            3455678888899888888887 678888999999999863

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

>PRK11086 sensory histidine kinase DcuS; Provisional

Probab=95.91  E-value=0.0097  Score=54.98  Aligned_cols=52  Identities=15%  Similarity=0.199  Sum_probs=42.7

Q ss_pred             hhhhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCC---cccccccccccccC
Q 020514          240 SSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYD---RNEVVGQNCRFLNG  294 (325)
Q Consensus       240 ~~~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~---~~e~iG~~~~~l~~  294 (325)
                      ...++.+++++++||+++|.   +|+|+++|+++++++|++   ..+.+|+.+..+.+
T Consensus       220 ~~~~~~il~~~~~gIi~~D~---~g~I~~~N~~a~~llg~~~~~~~~~~~~~~~~~~~  274 (542)
T PRK11086        220 FEQRQAMLQSIKEGVIAVDD---RGEVTLINDEAKRLFNYKKGLEDDPLGTDVESWMP  274 (542)
T ss_pred             HHHHHHHHHHhcCcEEEECC---CCeEEEEhHHHHHHhCCCcCCcccccCCcHHHhCC
Confidence            34567889999999999998   479999999999999875   35677887766654

>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]

Probab=95.69  E-value=0.052  Score=48.01  Aligned_cols=93  Identities=14%  Similarity=0.162  Sum_probs=75.8

Q ss_pred             CCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEEEEEEecCCCeEEEEEEEEEeecCCC
Q 020514           41 HPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKED  120 (325)
Q Consensus        41 ~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg~~~~~~~~~~~~~~~~~  120 (325)
                      +..+.+......++||...|+.|.+...+++.+|..-......+.+++|.+.-.-++..+++|++.|+..++..++.  +
T Consensus       293 fa~vs~Dak~k~~lgy~eaEL~~m~gY~lvH~~D~~y~Aeah~e~iktgeSGmlvyR~qtk~grw~wvqssarllyk--n  370 (712)
T KOG3560|consen  293 FALVSMDAKVKATLGYCEAELHGMPGYNLVHVEDKVYMAEAHSEGIKTGESGMLVYREQTKAGRWAWVQSSARLLYK--N  370 (712)
T ss_pred             cceeccchhhhhhhccchhhccCCCccceeehhhhhhhhHHHHHHhhcCCcceEEEEEeecCCcEEEeeccceeeee--c
Confidence            55667778888999999999999888888888776655666778888888888888889999999999988888874  7


Q ss_pred             CeeeEEEEEEecccc
Q 020514          121 GRATHFVAVQVPIVS  135 (325)
Q Consensus       121 g~~~~~~~~~~DITe  135 (325)
                      |.+-.++...+-.++
T Consensus       371 gkPD~vi~thr~l~D  385 (712)
T KOG3560|consen  371 GKPDLVIDTHRGLGD  385 (712)
T ss_pred             CCCCEEEecCCCccc
Confidence            887777776665555

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

Probab=95.62  E-value=0.049  Score=46.17  Aligned_cols=56  Identities=14%  Similarity=0.158  Sum_probs=49.7

Q ss_pred             HHHHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCC
Q 020514           16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRT   74 (325)
Q Consensus        16 ~~~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~   74 (325)
                      ....+..++++++++++-+|..   |.+..+|++++.++|.+.+.+.|.+...+++...
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            4456889999999999999999   9999999999999999999999998777765543

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

Probab=95.13  E-value=0.028  Score=46.40  Aligned_cols=49  Identities=18%  Similarity=0.259  Sum_probs=43.7

Q ss_pred             hhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCC
Q 020514          245 ISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVD  296 (325)
Q Consensus       245 ~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~  296 (325)
                      .+++++..+++++|.   +|.|.|+|++++.+||-|..-+.|+.+..+++..
T Consensus        11 ~~Ln~~~~pVl~vd~---~~~i~yaN~aAe~~~~~Sa~~L~~~~l~~l~~~g   59 (363)
T COG3852          11 AILNNLINPVLLVDD---ELAIHYANPAAEQLLAVSARRLAGTRLSELLPFG   59 (363)
T ss_pred             hHHhccCCceEEEcC---CCcEEecCHHHHHHHHHHHHHHhcCChHHHcCCC
Confidence            478888999999998   4799999999999999999999999999888543

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

Probab=94.61  E-value=0.69  Score=34.08  Aligned_cols=86  Identities=13%  Similarity=0.156  Sum_probs=68.6

Q ss_pred             CCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEEEEEEecCCCeEEEEEEEEEeecCCC
Q 020514           41 HPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKED  120 (325)
Q Consensus        41 ~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg~~~~~~~~~~~~~~~~~  120 (325)
                      .++..+-...+.++|+   ++.|+++..++.+.....+...+..++..+.+..........+|....+..-.-|+.+ .+
T Consensus        51 ~r~RLaGt~i~~~~G~---d~tG~~~~el~~~~~~~~~~~~~~~v~~~~~p~~~~~~~~~~~g~~~~~e~l~LPL~~-~~  126 (137)
T PF07310_consen   51 FRYRLAGTRIVELFGR---DLTGRRLSELFPPEDRERVRRAYRAVVERPAPVRARGRAEDADGRYLEYERLLLPLRS-DG  126 (137)
T ss_pred             eEEEEecHHHHHHhCC---CCCCCCHHHhcChHhHHHHHHHHHHHHcCCceEEEEEEEecCCCCeeEEEEEEcccCC-CC
Confidence            4456789999999997   5679988888888777777778888888877777777777788888888888999988 67


Q ss_pred             CeeeEEEEEE
Q 020514          121 GRATHFVAVQ  130 (325)
Q Consensus       121 g~~~~~~~~~  130 (325)
                      |.+..++|..
T Consensus       127 ~~v~rilG~~  136 (137)
T PF07310_consen  127 GTVDRILGAL  136 (137)
T ss_pred             CCccEEEEec
Confidence            7777777754

>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=94.51  E-value=0.045  Score=38.66  Aligned_cols=46  Identities=26%  Similarity=0.484  Sum_probs=36.9

Q ss_pred             eEEecCCCCCCCeEEEehhhHHhhCCC---cccccccccccccCCCCChHH
Q 020514          254 FVLIDPHLPDMPMVYASDAFLKLTGYD---RNEVVGQNCRFLNGVDTDTTV  301 (325)
Q Consensus       254 i~~~d~~~~dg~i~~~N~a~~~~~Gy~---~~e~iG~~~~~l~~~~~~~~~  301 (325)
                      ++++|..  |++|+.++..+.+++|.+   +++++|+++..++++.....+
T Consensus        18 LLa~d~~--~~~I~~~S~N~~~~lg~~~~~~~~llG~~l~~ll~~~~~~~l   66 (110)
T PF08446_consen   18 LLALDPD--DLRIVQASENIAELLGIPPELPEELLGRPLSELLGAESAERL   66 (110)
T ss_dssp             EEEEETT--TTBEEEEETTHHHHHSS----HHHHTTCBHHHHSCCCCHHHH
T ss_pred             EEEEECC--CCEEEEEcCCHHHHhCCccccchhhcccCHHHHhCHHHHHHH
Confidence            3456664  689999999999999999   999999999999976654433

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 ....

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

Probab=93.14  E-value=0.087  Score=47.76  Aligned_cols=48  Identities=13%  Similarity=0.143  Sum_probs=42.4

Q ss_pred             hHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCccccccccccccc
Q 020514          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLN  293 (325)
Q Consensus       243 l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~  293 (325)
                      +...++.+..|++.+|.+   |+|.-+|+++++|+|.+-++++|+++..+.
T Consensus       372 ~E~VLsgvtaGVi~~d~~---g~i~t~N~~ae~~l~~~~~~~~G~~lsa~a  419 (712)
T COG5000         372 LEAVLSGLTAGVIGFDNR---GCITTVNPSAEQILGKPFDQLLGQSLSAIA  419 (712)
T ss_pred             HHHHHhcCceeEEEEcCC---CeeEeecchHHHHhcCChhHhhcchhhhhh
Confidence            455788889999999985   799999999999999999999999977655

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

Probab=90.82  E-value=0.23  Score=47.05  Aligned_cols=57  Identities=18%  Similarity=0.294  Sum_probs=47.8

Q ss_pred             HHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChH
Q 020514           18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRR   77 (325)
Q Consensus        18 ~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~   77 (325)
                      ++-..+++++.--++++..+   |.|+||+.+...++||..++++|.++..+.+|++...
T Consensus        95 eL~~LmLeAlDGF~fvV~cd---G~IvyVSeSVT~~L~y~QsDL~~qSly~ilhp~d~~~  151 (803)
T KOG3561|consen   95 ELTHLILEALDGFLFVVNCD---GRIVYVSESVTSVLGYLQSDLMGQSLYDILHPLDNDK  151 (803)
T ss_pred             HHHHHHHHHhcCeEEEEecC---ceEEEEecchHHhhCcCHHHHhcchHHHhcCccccCc
Confidence            34456677777677899999   9999999999999999999999999888888776544

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

Probab=90.04  E-value=0.43  Score=48.93  Aligned_cols=40  Identities=8%  Similarity=-0.062  Sum_probs=34.2

Q ss_pred             hhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccc
Q 020514          242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEV  284 (325)
Q Consensus       242 ~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~  284 (325)
                      .++.++++++++|+++|.+   |+|+++|+++++++|++....
T Consensus       577 ~~~~i~~~~~~~i~~~d~~---g~i~~~N~~~~~~~g~~~~~~  616 (1197)
T PRK09959        577 FRKALSDSLPNPTYVVNWQ---GNVISHNSAFEHYFTADYYKN  616 (1197)
T ss_pred             HHHHHHhhCCCcEEEEcCC---CcEEEehHHHHHHhCcccccc
Confidence            4667889999999999984   799999999999999875443

>COG3284 AcoR Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]

Probab=88.92  E-value=8.5  Score=35.67  Aligned_cols=41  Identities=20%  Similarity=0.254  Sum_probs=32.2

Q ss_pred             cCCceEEecCCCCCCCeEEEehhhHHhhCCC-ccccccccccccc
Q 020514          250 IKQSFVLIDPHLPDMPMVYASDAFLKLTGYD-RNEVVGQNCRFLN  293 (325)
Q Consensus       250 ~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~-~~e~iG~~~~~l~  293 (325)
                      .+.+.+++|.   ||+|+.+|+++..+++.+ ..-++|.+...+.
T Consensus       231 ~~~~~lavd~---~grvl~at~aA~~~La~~~~~~l~g~p~~~~~  272 (606)
T COG3284         231 QSEALLAVDQ---DGRVLGATRAARQLLALTDRQRLIGQPVEDFL  272 (606)
T ss_pred             ccceeeeecC---cchhhhccHHHHHhhccchhhHhhcCCccccc
Confidence            3577888887   579999999999999988 5566677665554

>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]

Probab=87.81  E-value=1.5  Score=37.77  Aligned_cols=85  Identities=8%  Similarity=0.051  Sum_probs=59.5

Q ss_pred             EEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEEEEEEecCCCeEEEE
Q 020514           30 SFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWML  109 (325)
Q Consensus        30 ~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg~~~~~~  109 (325)
                      -++....+   ..+++.......++||.+.+++++.+...++..|...+...-.-.+..|..-.--+++..+.|.++|+.
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            34555666   788999999999999999999999877666665554444443444555554444455667888888887


Q ss_pred             EEEEEeec
Q 020514          110 FKMSLVFG  117 (325)
Q Consensus       110 ~~~~~~~~  117 (325)
                      -....+.+
T Consensus       304 syat~vHn  311 (598)
T KOG3559|consen  304 SYATFVHN  311 (598)
T ss_pred             EeeEEEec
Confidence            66666654

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

Probab=86.99  E-value=35  Score=34.23  Aligned_cols=42  Identities=7%  Similarity=0.025  Sum_probs=34.6

Q ss_pred             hHHHHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCCh
Q 020514           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSR   58 (325)
Q Consensus        15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~   58 (325)
                      ....+++.+++.+|.++++++..  ++.++..|+.+..++|+..
T Consensus       331 e~e~~~r~iv~~~p~gi~i~~~~--~g~~~~~N~~a~~~~~l~~  372 (924)
T PRK10841        331 EHEQFNRKIVASAPVGICILRTS--DGTNILSNELAHNYLNMLT  372 (924)
T ss_pred             HHHHHHHHHHHhCCccEEEEEcC--CCcEEEehHHHHHHhccCC
Confidence            45567889999999999999743  3999999999999888643

>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=84.55  E-value=1.4  Score=31.02  Aligned_cols=42  Identities=26%  Similarity=0.397  Sum_probs=33.7

Q ss_pred             EEEEcCCCCCCCEEEechHHHHhcCCC---hhhhcCCCCCcccCCCC
Q 020514           31 FTITDPSISGHPIVFASRGFLKMSGFS---RAEIIGRNGRMFQGPRT   74 (325)
Q Consensus        31 i~~~d~~~~~~~~~~~N~~~~~~~G~~---~~ei~g~~~~~l~~~~~   74 (325)
                      ++++|.+  +++++.++.....++|.+   .++++|+++..++++..
T Consensus        18 LLa~d~~--~~~I~~~S~N~~~~lg~~~~~~~~llG~~l~~ll~~~~   62 (110)
T PF08446_consen   18 LLALDPD--DLRIVQASENIAELLGIPPELPEELLGRPLSELLGAES   62 (110)
T ss_dssp             EEEEETT--TTBEEEEETTHHHHHSS----HHHHTTCBHHHHSCCCC
T ss_pred             EEEEECC--CCEEEEEcCCHHHHhCCccccchhhcccCHHHHhCHHH
Confidence            3456553  489999999999999999   99999999888876553

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 ....

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	325
3ue6_A	166	The Dark Structure Of The Blue-light Photoreceptor		1e-16
3ue6_A	166	The Dark Structure Of The Blue-light Photoreceptor		6e-12
3ulf_A	170	The Light State Structure Of The Blue-light Photore		1e-16
3ulf_A	170	The Light State Structure Of The Blue-light Photore		5e-12
2z6d_A	130	Crystal Structure Of Lov1 Domain Of Phototropin2 Fr		1e-16
2z6d_A	130	Crystal Structure Of Lov1 Domain Of Phototropin2 Fr		1e-11
2wkq_A	332	Structure Of A Photoactivatable Rac1 Containing The		2e-16
2wkq_A	332	Structure Of A Photoactivatable Rac1 Containing The		3e-14
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		3e-15
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		3e-15
2wkp_A	332	Structure Of A Photoactivatable Rac1 Containing Lov		4e-16
2wkp_A	332	Structure Of A Photoactivatable Rac1 Containing Lov		3e-15
4eeu_A	118	Crystal Structure Of Philov2.1 Length = 118		4e-16
4eeu_A	118	Crystal Structure Of Philov2.1 Length = 118		4e-13
4ees_A	115	Crystal Structure Of Ilov Length = 115		4e-16
4ees_A	115	Crystal Structure Of Ilov Length = 115		1e-12
2wkr_A	332	Structure Of A Photoactivatable Rac1 Containing The		4e-16
2wkr_A	332	Structure Of A Photoactivatable Rac1 Containing The		5e-14
1n9l_A	109	Crystal Structure Of The Phot-lov1 Domain From Chla		3e-15
1n9l_A	109	Crystal Structure Of The Phot-lov1 Domain From Chla		9e-11
4eer_A	115	Crystal Structure Of Lov2 Domain Of Arabidopsis Tha		4e-15
4eer_A	115	Crystal Structure Of Lov2 Domain Of Arabidopsis Tha		1e-12
4eep_A	115	Crystal Structure Of Lov2 Domain Of Arabidopsis Tha		8e-15
4eep_A	115	Crystal Structure Of Lov2 Domain Of Arabidopsis Tha		2e-13
2z6c_A	129	Crystal Structure Of Lov1 Domain Of Phototropin1 Fr		2e-14
2z6c_A	129	Crystal Structure Of Lov1 Domain Of Phototropin1 Fr		2e-11
2pr5_A	132	Structural Basis For Light-dependent Signaling In T		9e-14
2pr5_A	132	Structural Basis For Light-dependent Signaling In T		4e-09
1g28_A	104	Structure Of A Flavin-Binding Domain, Lov2, From Th		2e-13
1g28_A	104	Structure Of A Flavin-Binding Domain, Lov2, From Th		4e-12
3t50_A	128	X-Ray Structure Of The Lov Domain From The Lov-Hk S		1e-12
3t50_A	128	X-Ray Structure Of The Lov Domain From The Lov-Hk S		7e-12
3p7n_A	258	Crystal Structure Of Light Activated Transcription		4e-10
3p7n_A	258	Crystal Structure Of Light Activated Transcription		2e-06
3hjk_A	154	2.0 Angstrom Structure Of The Ile74val Variant Of V		2e-07
3d72_A	149	1.65 Angstrom Crystal Structure Of The Cys71val Var		2e-07
3hji_A	154	1.8 Angstrom Crystal Structure Of The I74v:i85v Var		2e-07
3is2_A	154	2.3 Angstrom Crystal Structure Of A Cys71 Sulfenic		2e-07
3is2_B	154	2.3 Angstrom Crystal Structure Of A Cys71 Sulfenic		3e-07
2pd7_A	149	2.0 Angstrom Crystal Structure Of The Fungal Blue-L		3e-07
2pd8_A	149	1.8 Angstrom Crystal Structure Of The Cys71ser Muta		3e-07
3rh8_B	148	Crystal Structure Of The Light-State Dimer Of Funga		3e-07
4hj4_A	177	Crystal Structure Of Rhodobacter Sphaeroides Lov Pr		5e-06
4hj6_A	178	Crystal Structure Of Rhodobacter Sphaeroides Lov Pr		5e-06
4hj3_A	176	Crystal Structure Of Rhodobacter Sphaeroides Lov Pr		6e-06
4hia_A	176	Crystal Structure Of Rhodobacter Sphaeroides Lov Pr		8e-06
2l1m_A	150	Solution Structure Of The Eag Domain Of The Herg (K		1e-04
2l4r_A	135	Nmr Solution Structure Of The N-Terminal Pas Domain		1e-04
2l0w_A	138	Solution Nmr Structure Of The N-Terminal Pas Domain		2e-04
3sw1_A	162	Structure Of A Full-Length Bacterial Lov Protein Le		3e-04
1byw_A	110	Structure Of The N-Terminal Domain Of The Human-Erg		4e-04

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

Iteration: 1
 Score = 84.0 bits (206), Expect = 1e-16,   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 = 68.2 bits (165), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 32/69 (46%), Positives = 47/69 (68%)
Query: 242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTV 301
           SL  +L   +Q+FV+ D  LPD P+VYAS  FL LTGY  ++++G+NCRFL G +TD   
Sbjct: 36  SLVKALQMAQQNFVITDASLPDNPIVYASRGFLTLTGYSLDQILGRNCRFLQGPETDPRA 95
Query: 302 LYQVSIAIS 310
           + ++  AI+
Sbjct: 96  VDKIRNAIT 104

>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 = 1e-16,   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 = 68.2 bits (165), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 32/69 (46%), Positives = 47/69 (68%)
Query: 242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTV 301
           SL  +L   +Q+FV+ D  LPD P+VYAS  FL LTGY  ++++G+NCRFL G +TD   
Sbjct: 40  SLVKALQMAQQNFVITDASLPDNPIVYASRGFLTLTGYSLDQILGRNCRFLQGPETDPRA 99
Query: 302 LYQVSIAIS 310
           + ++  AI+
Sbjct: 100 VDKIRNAIT 108

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

Iteration: 1
 Score = 67.4 bits (163), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 29/60 (48%), Positives = 39/60 (65%)
Query: 239 ISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTD 298
           +S  L  +L  ++Q+FV+ D   P  P+VYAS  F  +TGY   E+VG+NCRFL G DTD
Sbjct: 4   VSQELKTALSTLQQTFVVSDATQPHCPIVYASSGFFTMTGYSSKEIVGRNCRFLQGPDTD 63

>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 = 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: 16  TLERIEKNFVITDPRLPDNPIIFASDSFLQLTEYSREEILGRNARFLQGPETDRATVRKI 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|2WKQ|A Chain A, Structure Of A Photoactivatable Rac1 Containing The Lov2 C450a Mutant Length = 332

Iteration: 1
 Score = 75.9 bits (185), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 33/68 (48%), Positives = 50/68 (73%)
Query: 242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTV 301
           SL  +L RI+++FV+ DP LPD P+++ASD+FL+LT Y R E++G+N RFL G +TD   
Sbjct: 12  SLATTLERIEKNFVITDPRLPDNPIIFASDSFLQLTEYSREEILGRNARFLQGPETDRAT 71
Query: 302 LYQVSIAI 309
           + ++  AI
Sbjct: 72  VRKIRDAI 79

>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 = 82.8 bits (203), 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 = 79.3 bits (194), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 33/67 (49%), Positives = 50/67 (74%)
Query: 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVL 302
           L  +L RI+++FV+ DP LPD P+++ASD+FL+LT Y R E++G+NCRFL G +TD   +
Sbjct: 2   LATTLERIEKNFVITDPRLPDNPIIFASDSFLQLTEYSREEILGRNCRFLQGPETDRATV 61
Query: 303 YQVSIAI 309
            ++  AI
Sbjct: 62  RKIRDAI 68

>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 = 82.8 bits (203), 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 = 79.3 bits (194), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 33/67 (49%), Positives = 50/67 (74%)
Query: 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVL 302
           L  +L RI+++FV+ DP LPD P+++ASD+FL+LT Y R E++G+NCRFL G +TD   +
Sbjct: 4   LATTLERIEKNFVITDPRLPDNPIIFASDSFLQLTEYSREEILGRNCRFLQGPETDRATV 63
Query: 303 YQVSIAI 309
            ++  AI
Sbjct: 64  RKIRDAI 70

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

Iteration: 1
 Score = 82.0 bits (201), Expect = 4e-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 = 79.3 bits (194), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 34/68 (50%), Positives = 51/68 (75%)
Query: 242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTV 301
           SL  +L RI+++FV+ DP LPD P+++ASD+FL+LT Y R E++G+NCRFL G +TD   
Sbjct: 12  SLATTLERIEKNFVITDPRLPDNPIIFASDSFLQLTEYSREEILGRNCRFLQGPETDRAT 71
Query: 302 LYQVSIAI 309
           + ++  AI
Sbjct: 72  VRKIRDAI 79

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

Iteration: 1
 Score = 82.0 bits (201), Expect = 4e-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 = 72.0 bits (175), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 30/60 (50%), Positives = 44/60 (73%)
Query: 250 IKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSIAI 309
           I++SFV+ DP LPD P+++ASD FL+LT Y R E++G+N RFL G +TD   + ++  AI
Sbjct: 9   IEKSFVITDPRLPDYPIIFASDGFLELTEYSREEIMGRNARFLQGPETDQATVQKIRDAI 68

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

Iteration: 1
 Score = 82.0 bits (201), Expect = 4e-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 = 70.5 bits (171), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 29/60 (48%), Positives = 44/60 (73%)
Query: 250 IKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSIAI 309
           I+++FV+ DP LPD P+++ASD FL+LT Y R E++G+N RFL G +TD   + ++  AI
Sbjct: 6   IEKNFVITDPRLPDNPIIFASDGFLELTEYSREEILGRNARFLQGPETDQATVQKIRDAI 65

>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 = 4e-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 = 75.1 bits (183), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 33/68 (48%), Positives = 50/68 (73%)
Query: 242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTV 301
           SL  +L RI+++FV+ DP LPD P+++ASD+FL+LT Y R E++G+N RFL G +TD   
Sbjct: 12  SLATTLERIEKNFVITDPRLPDNPIIFASDSFLQLTEYSREEILGRNMRFLQGPETDRAT 71
Query: 302 LYQVSIAI 309
           + ++  AI
Sbjct: 72  VRKIRDAI 79

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

Iteration: 1
 Score = 79.0 bits (193), Expect = 3e-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|1N9L|A Chain A, Crystal Structure Of The Phot-lov1 Domain From Chlamydomonas Reinhardtii In The Dark State. Length = 109

Iteration: 1
 Score = 64.3 bits (155), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 28/60 (46%), Positives = 40/60 (66%)
Query: 250 IKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSIAI 309
           ++ +FV+ D  LPD P+VYAS+ F  +TGY  +EV+G NCRFL G  TD   + ++  AI
Sbjct: 2   LRHTFVVADATLPDCPLVYASEGFYAMTGYGPDEVLGHNCRFLQGEGTDPKEVQKIRDAI 61

>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 = 4e-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 = 70.1 bits (170), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 29/60 (48%), Positives = 45/60 (75%)
Query: 250 IKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSIAI 309
           I+++FV+ DP LPD P+++ASD+FL+LT Y R E++G+N RFL G +TD   + ++  AI
Sbjct: 6   IEKNFVISDPRLPDNPIIFASDSFLELTEYSREEILGRNARFLQGPETDQATVQKIRDAI 65

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

Iteration: 1
 Score = 77.8 bits (190), Expect = 8e-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 = 73.6 bits (179), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 30/60 (50%), Positives = 46/60 (76%)
Query: 250 IKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSIAI 309
           I+++FV+ DP LPD P+++ASD+FL+LT Y R E++G+NCRFL G +TD   + ++  AI
Sbjct: 6   IEKNFVISDPRLPDNPIIFASDSFLELTEYSREEILGRNCRFLQGPETDQATVQKIRDAI 65

>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 = 38/123 (30%), Positives = 62/123 (50%), Gaps = 3/123 (2%)
Query: 20  VHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNXXXX 79
           + +AL     +F ++D +   +PI++AS GF  M+G++  E++GRN R  QG  T+    
Sbjct: 9   LKDALSTFQQTFVVSDATKPDYPIMYASAGFFNMTGYTSKEVVGRNCRFLQGSGTDADEL 68
Query: 80  XXXXXXXXXXXXXXVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM 139
                           +LNYKKDGT FW L  ++ +   E G+   F+ +QV +   KH 
Sbjct: 69  AKIRETLAAGNNYCGRILNYKKDGTSFWNLLTIAPI-KDESGKVLKFIGMQVEV--SKHT 125
Query: 140 RNS 142
             +
Sbjct: 126 EGA 128

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

Iteration: 1
 Score = 66.2 bits (160), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 31/71 (43%), Positives = 43/71 (60%)
Query: 235 GMGFISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNG 294
           G+  +S  L  +L   +Q+FV+ D   PD P++YAS  F  +TGY   EVVG+NCRFL G
Sbjct: 1   GIPRVSEDLKDALSTFQQTFVVSDATKPDYPIMYASAGFFNMTGYTSKEVVGRNCRFLQG 60
Query: 295 VDTDTTVLYQV 305
             TD   L ++
Sbjct: 61  SGTDADELAKI 71

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

Iteration: 1
 Score = 74.3 bits (181), Expect = 9e-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|2PR5|A Chain A, Structural Basis For Light-dependent Signaling In The Dimeric Lov Photosensor Ytva (dark Structure) Length = 132

Iteration: 1
 Score = 58.9 bits (141), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 24/64 (37%), Positives = 39/64 (60%)
Query: 247 LGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVS 306
           L  ++   V+ DP L D P+VY +  F+++TGY+  E++G+NCRFL G  TD   +  + 
Sbjct: 5   LDHVRVGVVITDPALEDNPIVYVNQGFVQMTGYETEEILGKNCRFLQGKHTDPAEVDNIR 64
Query: 307 IAIS 310
            A+ 
Sbjct: 65  TALQ 68

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

Iteration: 1
 Score = 73.2 bits (178), Expect = 2e-13,   Method: Composition-based stats.
 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 = 68.9 bits (167), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 30/58 (51%), Positives = 40/58 (68%)
Query: 252 QSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSIAI 309
           +SFV+ DP LPD P+++ASD FL+LT Y R EV+G NCRFL G  TD   +  +  A+
Sbjct: 1   KSFVITDPRLPDNPIIFASDRFLELTEYTREEVLGNNCRFLQGRGTDRKAVQLIRDAV 58

>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 = 70.5 bits (171), Expect = 1e-12,   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|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 = 67.8 bits (164), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 29/56 (51%), Positives = 42/56 (75%)
Query: 255 VLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSIAIS 310
           ++ +PHLPD P+V+A+ AFLKLTGY+ +EV+G+NCRFL G  TD   +  +  AI+
Sbjct: 11  LITNPHLPDNPIVFANPAFLKLTGYEADEVMGRNCRFLQGHGTDPAHVRAIKSAIA 66

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

Iteration: 1
 Score = 62.4 bits (150), Expect = 4e-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|3P7N|A Chain A, Crystal Structure Of Light Activated Transcription Factor El222 From Erythrobacter Litoralis Length = 258

Iteration: 1
 Score = 50.1 bits (118), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 22/44 (50%), Positives = 28/44 (63%)
Query: 255 VLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTD 298
           V+ DP L D P++  + AF  LTGY   E VG+NCRFL G  T+
Sbjct: 77  VVSDPRLADNPLIAINQAFTDLTGYSEEECVGRNCRFLAGSGTE 120

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

Iteration: 1
 Score = 53.1 bits (126), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 27/54 (50%), Positives = 34/54 (62%), Gaps = 2/54 (3%)
Query: 245 ISLGRIKQS--FVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVD 296
           + LG +  S   VL D    D P+VYAS+AFL +TGY   EV+G+NCRFL   D
Sbjct: 30  VELGPVDTSCALVLCDLKQKDTPIVYASEAFLYMTGYSNAEVLGRNCRFLQSPD 83

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

Iteration: 1
 Score = 53.1 bits (126), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 27/54 (50%), Positives = 34/54 (62%), Gaps = 2/54 (3%)
Query: 245 ISLGRIKQSFVLI--DPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVD 296
           + LG +  S  LI  D    D P+VYAS+AFL +TGY   EV+G+NCRFL   D
Sbjct: 27  VELGPVDTSVALILCDLKQKDTPIVYASEAFLYMTGYSNAEVLGRNCRFLQSPD 80

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

Iteration: 1
 Score = 53.1 bits (126), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 27/54 (50%), Positives = 34/54 (62%), Gaps = 2/54 (3%)
Query: 245 ISLGRIKQS--FVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVD 296
           + LG +  S   VL D    D P+VYAS+AFL +TGY   EV+G+NCRFL   D
Sbjct: 30  VELGPVDTSCALVLCDLKQKDTPVVYASEAFLYMTGYSNAEVLGRNCRFLQSPD 83

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

Iteration: 1
 Score = 53.1 bits (126), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 27/54 (50%), Positives = 34/54 (62%), Gaps = 2/54 (3%)
Query: 245 ISLGRIKQSFVLI--DPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVD 296
           + LG +  S  LI  D    D P+VYAS+AFL +TGY   EV+G+NCRFL   D
Sbjct: 30  VELGPVDTSXALILCDLKQKDTPIVYASEAFLYMTGYSNAEVLGRNCRFLQSPD 83

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 26/54 (48%), Positives = 34/54 (62%), Gaps = 2/54 (3%)
Query: 245 ISLGRIKQS--FVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVD 296
           + LG +  S   +L D    D P+VYAS+AFL +TGY   EV+G+NCRFL   D
Sbjct: 30  VELGPVDTSCALILCDLKQKDTPIVYASEAFLYMTGYSNAEVLGRNCRFLQSPD 83

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 26/54 (48%), Positives = 34/54 (62%), Gaps = 2/54 (3%)
Query: 245 ISLGRIKQS--FVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVD 296
           + LG +  S   +L D    D P+VYAS+AFL +TGY   EV+G+NCRFL   D
Sbjct: 27  VELGPVDTSCALILCDLKQKDTPIVYASEAFLYMTGYSNAEVLGRNCRFLQSPD 80

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 26/54 (48%), Positives = 34/54 (62%), Gaps = 2/54 (3%)
Query: 245 ISLGRIKQS--FVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVD 296
           + LG +  S   +L D    D P+VYAS+AFL +TGY   EV+G+NCRFL   D
Sbjct: 27  VELGPVDTSSALILCDLKQKDTPIVYASEAFLYMTGYSNAEVLGRNCRFLQSPD 80

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 26/54 (48%), Positives = 34/54 (62%), Gaps = 2/54 (3%)
Query: 245 ISLGRIKQS--FVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVD 296
           + LG +  S   +L D    D P+VYAS+AFL +TGY   EV+G+NCRFL   D
Sbjct: 26  VELGPVDTSCALILCDLKQKDTPIVYASEAFLYMTGYSNAEVLGRNCRFLQSPD 79

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

Iteration: 1
 Score = 48.5 bits (114), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 20/58 (34%), Positives = 33/58 (56%)
Query: 253 SFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSIAIS 310
           +  L+D  LP+ P+V A+  FL++TGY   +++G NCRFL   D +      +  A+ 
Sbjct: 20  ALTLVDMSLPEQPLVLANPPFLRMTGYTEGQILGFNCRFLQRGDENAQARADIRDALK 77

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

Iteration: 1
 Score = 48.5 bits (114), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 20/58 (34%), Positives = 33/58 (56%)
Query: 253 SFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSIAIS 310
           +  L+D  LP+ P+V A+  FL++TGY   +++G NCRFL   D +      +  A+ 
Sbjct: 21  ALTLVDMSLPEQPLVLANPPFLRMTGYTEGQILGFNCRFLQRGDENAQARADIRDALK 78

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

Iteration: 1
 Score = 48.1 bits (113), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 20/58 (34%), Positives = 33/58 (56%)
Query: 253 SFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSIAIS 310
           +  L+D  LP+ P+V A+  FL++TGY   +++G NCRFL   D +      +  A+ 
Sbjct: 19  ALTLVDMSLPEQPLVLANPPFLRMTGYTEGQILGFNCRFLQRGDENAQARADIRDALK 76

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

Iteration: 1
 Score = 47.8 bits (112), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 20/58 (34%), Positives = 33/58 (56%)
Query: 253 SFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSIAIS 310
           +  L+D  LP+ P+V A+  FL++TGY   +++G NCRFL   D +      +  A+ 
Sbjct: 19  ALTLVDMSLPEQPVVLANPPFLRMTGYTEGQILGFNCRFLQRGDENAQARADIRDALK 76

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

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: 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 = 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: 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 = 43.5 bits (101), Expect = 2e-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|3SW1|A Chain A, Structure Of A Full-Length Bacterial Lov Protein Length = 162

Iteration: 1
 Score = 42.7 bits (99), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 20/57 (35%), Positives = 33/57 (57%)
Query: 254 FVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSIAIS 310
            V+ +    D  ++Y + AF  LTGY R+E++ Q+CRFL G D D     ++  A++
Sbjct: 38  IVVAEKEGDDTILIYVNAAFEYLTGYSRDEILYQDCRFLQGDDRDQLGRARIRKAMA 94

>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 = 4e-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

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	325
2z6d_A	130	Phototropin-2; PAS-fold, LOV-fold, alternative spl	2e-50
2z6d_A	130	Phototropin-2; PAS-fold, LOV-fold, alternative spl	5e-22
4eet_B	115	Phototropin-2; LOV, blue light photoreceptor, sign	2e-49
4eet_B	115	Phototropin-2; LOV, blue light photoreceptor, sign	8e-24
2v0u_A	146	NPH1-1, LOV2; kinase, transferase, ATP-binding, se	4e-49
2v0u_A	146	NPH1-1, LOV2; kinase, transferase, ATP-binding, se	5e-23
3t50_A	128	Blue-light-activated histidine kinase; PAS superfa	3e-48
3t50_A	128	Blue-light-activated histidine kinase; PAS superfa	2e-21
3ue6_A	166	Aureochrome1; PAS/LOV domain, FMN-binding blue-lig	6e-48
3ue6_A	166	Aureochrome1; PAS/LOV domain, FMN-binding blue-lig	1e-21
2pr5_A	132	Blue-light photoreceptor; light-oxygen-voltage, LO	3e-47
2pr5_A	132	Blue-light photoreceptor; light-oxygen-voltage, LO	9e-21
3p7n_A	258	Sensor histidine kinase; LOV domain, light-activat	4e-47
3p7n_A	258	Sensor histidine kinase; LOV domain, light-activat	3e-19
1n9l_A	109	PHOT-LOV1, putative blue light receptor; phototrop	5e-47
1n9l_A	109	PHOT-LOV1, putative blue light receptor; phototrop	2e-23
2l0w_A	138	Potassium voltage-gated channel, subfamily H (EAG	9e-46
2l0w_A	138	Potassium voltage-gated channel, subfamily H (EAG	3e-20
3sw1_A	162	Sensory box protein; light-oxygen-voltage, LOV, PA	3e-45
3sw1_A	162	Sensory box protein; light-oxygen-voltage, LOV, PA	2e-19
1byw_A	110	Protein (human ERG potassium channel); PAS domain,	6e-43
1byw_A	110	Protein (human ERG potassium channel); PAS domain,	1e-21
3d72_A	149	Vivid PAS protein VVD; circadian, photoreceptor, b	2e-42
3d72_A	149	Vivid PAS protein VVD; circadian, photoreceptor, b	3e-19
2wkq_A	332	NPH1-1, RAS-related C3 botulinum toxin substrate 1	2e-35
2wkq_A	332	NPH1-1, RAS-related C3 botulinum toxin substrate 1	2e-22
3lyx_A	124	Sensory BOX/ggdef domain protein; structural genom	1e-18
3ewk_A	227	Sensor protein; PAS domain, alpha/beta fold, kinas	2e-18
3ewk_A	227	Sensor protein; PAS domain, alpha/beta fold, kinas	2e-16
3ewk_A	227	Sensor protein; PAS domain, alpha/beta fold, kinas	2e-05
3ewk_A	227	Sensor protein; PAS domain, alpha/beta fold, kinas	2e-05
2gj3_A	120	Nitrogen fixation regulatory protein; PAS domain,	2e-13
2gj3_A	120	Nitrogen fixation regulatory protein; PAS domain,	3e-05
3mqq_A	120	Transcriptional regulator, LUXR family; PAS domain	3e-10
3mjq_A	126	Uncharacterized protein; NESG, structural genomics	2e-07
3bwl_A	126	Sensor protein; structural genomics, APC87707.1, P	2e-07
2r78_A	117	Sensor protein; sensory box sensor histidine kinas	2e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	9e-05
3olo_A	118	Two-component sensor histidine kinase; structural	1e-04
3mfx_A	129	Sensory BOX/ggdef family protein; alpha-beta prote	4e-04
3fc7_A	125	HTR-like protein, sensor protein; APC87712.1, HTR-	4e-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 = 2e-50
 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 = 88.8 bits (221), Expect = 5e-22
 Identities = 28/67 (41%), Positives = 41/67 (61%)

Query: 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVL 302
           L  +L  ++Q+FV+ D   P  P+VYAS  F  +TGY   E+VG+NCRFL G DTD   +
Sbjct: 8   LKTALSTLQQTFVVSDATQPHCPIVYASSGFFTMTGYSSKEIVGRNCRFLQGPDTDKNEV 67

Query: 303 YQVSIAI 309
            ++   +
Sbjct: 68  AKIRDCV 74

>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 =  159 bits (406), Expect = 2e-49
 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 = 93.0 bits (232), Expect = 8e-24
 Identities = 29/61 (47%), Positives = 44/61 (72%)

Query: 249 RIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSIA 308
            I+++FV+ DP LPD P+++ASD FL+LT Y R E++G+N RFL G +TD   + ++  A
Sbjct: 5   FIEKNFVITDPRLPDNPIIFASDGFLELTEYSREEILGRNARFLQGPETDQATVQKIRDA 64

Query: 309 I 309
           I
Sbjct: 65  I 65

>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 =  160 bits (406), Expect = 4e-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 = 91.9 bits (229), Expect = 5e-23
 Identities = 33/67 (49%), Positives = 50/67 (74%)

Query: 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVL 302
           L  +L RI+++FV+ DP LPD P+++ASD+FL+LT Y R E++G+NCRFL G +TD   +
Sbjct: 4   LATTLERIEKNFVITDPRLPDNPIIFASDSFLQLTEYSREEILGRNCRFLQGPETDRATV 63

Query: 303 YQVSIAI 309
            ++  AI
Sbjct: 64  RKIRDAI 70

>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 = 3e-48
 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 = 86.8 bits (216), Expect = 2e-21
 Identities = 29/59 (49%), Positives = 42/59 (71%)

Query: 252 QSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSIAIS 310
              ++ +PHLPD P+V+A+ AFLKLTGY+ +EV+G+NCRFL G  TD   +  +  AI+
Sbjct: 8   MPMLITNPHLPDNPIVFANPAFLKLTGYEADEVMGRNCRFLQGHGTDPAHVRAIKSAIA 66

>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 (400), Expect = 6e-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 = 88.5 bits (220), Expect = 1e-21
 Identities = 31/68 (45%), Positives = 46/68 (67%)

Query: 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVL 302
           L  +L   +Q+FV+ D  LPD P+VYAS  FL LTGY  ++++G+NCRFL G +TD   +
Sbjct: 37  LVKALQMAQQNFVITDASLPDNPIVYASRGFLTLTGYSLDQILGRNCRFLQGPETDPRAV 96

Query: 303 YQVSIAIS 310
            ++  AI+
Sbjct: 97  DKIRNAIT 104

>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 (393), Expect = 3e-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 = 85.7 bits (213), Expect = 9e-21
 Identities = 23/59 (38%), Positives = 36/59 (61%)

Query: 252 QSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSIAIS 310
              V+ DP L D P+VY +  F+++TGY+  E++G+NCRFL G  TD   +  +  A+ 
Sbjct: 10  VGVVITDPALEDNPIVYVNQGFVQMTGYETEEILGKNCRFLQGKHTDPAEVDNIRTALQ 68

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

 Score =  158 bits (401), 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 = 84.7 bits (209), Expect = 3e-19
 Identities = 22/58 (37%), Positives = 33/58 (56%)

Query: 252 QSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSIAI 309
            + V+ DP L D P++  + AF  LTGY   E VG+NCRFL G  T+  +  ++   +
Sbjct: 74  IASVVSDPRLADNPLIAINQAFTDLTGYSEEECVGRNCRFLAGSGTEPWLTDKIRQGV 131

>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 (389), Expect = 5e-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 = 92.2 bits (230), Expect = 2e-23
 Identities = 28/60 (46%), Positives = 40/60 (66%)

Query: 250 IKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSIAI 309
           ++ +FV+ D  LPD P+VYAS+ F  +TGY  +EV+G NCRFL G  TD   + ++  AI
Sbjct: 2   LRHTFVVADATLPDCPLVYASEGFYAMTGYGPDEVLGHNCRFLQGEGTDPKEVQKIRDAI 61

>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 =  151 bits (383), Expect = 9e-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 = 84.2 bits (209), Expect = 3e-20
 Identities = 17/60 (28%), Positives = 33/60 (55%), Gaps = 2/60 (3%)

Query: 252 QSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQ--NCRFLNGVDTDTTVLYQVSIAI 309
           + F++ +  + +  ++Y +D F +L GY R EV+ +   C FL+G  T      Q++ A+
Sbjct: 30  RKFIIANARVENCAVIYCNDGFCELCGYSRAEVMQRPCTCDFLHGPRTQRRAAAQIAQAL 89

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

 Score =  150 bits (382), Expect = 3e-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 = 82.7 bits (205), Expect = 2e-19
 Identities = 20/59 (33%), Positives = 33/59 (55%)

Query: 252 QSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSIAIS 310
              V+ +    D  ++Y + AF  LTGY R+E++ Q+CRFL G D D     ++  A++
Sbjct: 36  DGIVVAEKEGDDTILIYVNAAFEYLTGYSRDEILYQDCRFLQGDDRDQLGRARIRKAMA 94

>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 =  142 bits (361), Expect = 6e-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 = 86.8 bits (216), Expect = 1e-21
 Identities = 17/60 (28%), Positives = 33/60 (55%), Gaps = 2/60 (3%)

Query: 252 QSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQ--NCRFLNGVDTDTTVLYQVSIAI 309
           + F++ +  + +  ++Y +D F +L GY R EV+ +   C FL+G  T      Q++ A+
Sbjct: 2   RKFIIANARVENCAVIYCNDGFCELCGYSRAEVMQRPCTCDFLHGPCTQRRAAAQIAQAL 61

>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 =  142 bits (361), Expect = 2e-42
 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 = 82.0 bits (203), Expect = 3e-19
 Identities = 23/48 (47%), Positives = 30/48 (62%)

Query: 253 SFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTT 300
           + +L D    D P+VYAS+AFL +TGY   EV+G+NCRFL   D    
Sbjct: 37  ALILCDLKQKDTPIVYASEAFLYMTGYSNAEVLGRNCRFLQSPDGMVK 84

>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 =  129 bits (326), Expect = 2e-35
 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 = 94.7 bits (235), Expect = 2e-22
 Identities = 33/70 (47%), Positives = 50/70 (71%)

Query: 240 SSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDT 299
             SL  +L RI+++FV+ DP LPD P+++ASD+FL+LT Y R E++G+N RFL G +TD 
Sbjct: 10  HGSLATTLERIEKNFVITDPRLPDNPIIFASDSFLQLTEYSREEILGRNARFLQGPETDR 69

Query: 300 TVLYQVSIAI 309
             + ++  AI
Sbjct: 70  ATVRKIRDAI 79

>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 = 79.4 bits (197), 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 = 2e-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 = 2e-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

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

 Score = 43.9 bits (104), Expect = 2e-05
 Identities = 9/32 (28%), Positives = 17/32 (53%)

Query: 267 VYASDAFLKLTGYDRNEVVGQNCRFLNGVDTD 298
           +YA+ A  + +G    E++GQ+   L+    D
Sbjct: 134 IYANPALCRFSGMAEGELLGQSPSILDSPLAD 165

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

 Score = 43.9 bits (104), Expect = 2e-05
 Identities = 12/32 (37%), Positives = 19/32 (59%)

Query: 267 VYASDAFLKLTGYDRNEVVGQNCRFLNGVDTD 298
           +YA+D F  ++ Y R E+VGQ+ R +N     
Sbjct: 12  LYANDNFCAVSRYGREELVGQDHRIVNSGYHG 43

>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 = 2e-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

>2gj3_A Nitrogen fixation regulatory protein; PAS domain, FAD, redox sensor, atomic resolution, transferase; HET: FAD; 1.04A {Azotobacter vinelandii} Length = 120

 Score = 41.7 bits (99), Expect = 3e-05
 Identities = 12/27 (44%), Positives = 18/27 (66%)

Query: 267 VYASDAFLKLTGYDRNEVVGQNCRFLN 293
           +YA+ AF  +TGY   EV+G+N   L+
Sbjct: 28  LYANRAFRTITGYGSEEVLGKNESILS 54

>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 = 56.4 bits (137), 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 = 48.4 bits (116), Expect = 2e-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 = 47.9 bits (115), Expect = 2e-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 = 44.8 bits (107), Expect = 2e-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

>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 = 43.3 bits (101), Expect = 9e-05
 Identities = 44/360 (12%), Positives = 96/360 (26%), Gaps = 98/360 (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 -------HLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTT-VLYQVSIAISP 311
                   + D    +  D +  +       ++      LN ++      ++   +++ P
Sbjct: 329 RLSIIAESIRDGLATW--DNWKHVNCDKLTTIIE---SSLNVLEPAEYRKMFD-RLSVFP 382

>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 = 40.3 bits (95), 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

>3mfx_A Sensory BOX/ggdef family protein; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.40A {Shewanella oneidensis} Length = 129

 Score = 39.0 bits (91), Expect = 4e-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

>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 = 38.8 bits (91), Expect = 4e-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

>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	325
3ewk_A	227	Sensor protein; PAS domain, alpha/beta fold, kinas	99.97
2gj3_A	120	Nitrogen fixation regulatory protein; PAS domain,	99.81
4f3l_A	361	Mclock, circadian locomoter output cycles protein	99.76
4hia_A	176	LOV protein; PAS, HTH, signaling protein; HET: FMN	99.76
3f1p_B	121	ARYL hydrocarbon receptor nuclear translocator; PA	99.75
2pr5_A	132	Blue-light photoreceptor; light-oxygen-voltage, LO	99.75
3mr0_A	142	Sensory box histidine kinase/response regulator; P	99.74
1n9l_A	109	PHOT-LOV1, putative blue light receptor; phototrop	99.74
3ue6_A	166	Aureochrome1; PAS/LOV domain, FMN-binding blue-lig	99.73
3t50_A	128	Blue-light-activated histidine kinase; PAS superfa	99.71
3f1p_A	117	Endothelial PAS domain-containing protein 1; PAS d	99.7
3p7n_A	258	Sensor histidine kinase; LOV domain, light-activat	99.7
3rty_A	339	Period circadian protein; PAS domain, signalling,	99.7
4eet_B	115	Phototropin-2; LOV, blue light photoreceptor, sign	99.7
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	99.7
3nja_A	125	Probable ggdef family protein; structural genomics	99.68
3mqq_A	120	Transcriptional regulator, LUXR family; PAS domain	99.67
3lyx_A	124	Sensory BOX/ggdef domain protein; structural genom	99.67
2z6d_A	130	Phototropin-2; PAS-fold, LOV-fold, alternative spl	99.66
1d06_A	130	Nitrogen fixation regulatory protein FIXL; oxygen	99.65
3sw1_A	162	Sensory box protein; light-oxygen-voltage, LOV, PA	99.64
3mxq_A	152	Sensor protein; PSI2, MCSG, structural genomics, p	99.64
3h9w_A	115	Diguanylate cyclase with PAS/PAC sensor; alpha-bet	99.63
2vv6_A	119	FIXL, sensor protein FIXL; signaling protein, tran	99.63
2r78_A	117	Sensor protein; sensory box sensor histidine kinas	99.62
3luq_A	114	Sensor protein; PAS, histidine, kinase, PSI, MCSG,	99.62
2wkq_A	332	NPH1-1, RAS-related C3 botulinum toxin substrate 1	99.61
3k3c_A	158	Protein RV1364C/MT1410; sensor, PAS, signal transd	99.6
3ewk_A	227	Sensor protein; PAS domain, alpha/beta fold, kinas	99.59
3icy_A	118	Sensor protein; sensory box histidine kinase/respo	99.58
1n9l_A	109	PHOT-LOV1, putative blue light receptor; phototrop	99.57
3kx0_X	185	Uncharacterized protein RV1364C/MT1410; PAS domain	99.57
2v0u_A	146	NPH1-1, LOV2; kinase, transferase, ATP-binding, se	99.56
2kdk_A	121	ARYL hydrocarbon receptor nuclear translocator-LI	99.56
2gj3_A	120	Nitrogen fixation regulatory protein; PAS domain,	99.53
2r78_A	117	Sensor protein; sensory box sensor histidine kinas	99.52
4dj2_A	320	Period circadian protein homolog 1; PAS domains, c	99.52
3olo_A	118	Two-component sensor histidine kinase; structural	99.52
3mjq_A	126	Uncharacterized protein; NESG, structural genomics	99.52
4dj3_A	317	Period circadian protein homolog 3; PAS domain, ci	99.51
2pr5_A	132	Blue-light photoreceptor; light-oxygen-voltage, LO	99.51
3bwl_A	126	Sensor protein; structural genomics, APC87707.1, P	99.51
2vlg_A	111	Sporulation kinase A; histidine kinase, two-compon	99.51
3eeh_A	125	Putative light and redox sensing histidine kinase;	99.5
2l0w_A	138	Potassium voltage-gated channel, subfamily H (EAG	99.5
3gdi_A	309	Period circadian protein homolog 2; tandem PAS dom	99.48
1d06_A	130	Nitrogen fixation regulatory protein FIXL; oxygen	99.48
1byw_A	110	Protein (human ERG potassium channel); PAS domain,	99.46
1v9y_A	167	Heme PAS sensor protein; signaling protein; HET: H	99.46
3f1p_B	121	ARYL hydrocarbon receptor nuclear translocator; PA	99.44
4eho_A	635	Bacteriophytochrome, PAS/PAC sensor; photoreceptor	99.43
3d72_A	149	Vivid PAS protein VVD; circadian, photoreceptor, b	99.43
3mfx_A	129	Sensory BOX/ggdef family protein; alpha-beta prote	99.42
3mfx_A	129	Sensory BOX/ggdef family protein; alpha-beta prote	99.41
3fc7_A	125	HTR-like protein, sensor protein; APC87712.1, HTR-	99.41
4hia_A	176	LOV protein; PAS, HTH, signaling protein; HET: FMN	99.39
3p7n_A	258	Sensor histidine kinase; LOV domain, light-activat	99.37
3vol_A	233	Aerotaxis transducer AER2; heme, oxygen sensor pro	99.36
2kdk_A	121	ARYL hydrocarbon receptor nuclear translocator-LI	99.35
3bwl_A	126	Sensor protein; structural genomics, APC87707.1, P	99.35
3fg8_A	118	Uncharacterized protein RHA05790; PAS domain, stru	99.34
2vv6_A	119	FIXL, sensor protein FIXL; signaling protein, tran	99.33
4f3l_A	361	Mclock, circadian locomoter output cycles protein	99.33
2qkp_A	151	Uncharacterized protein; structural genomics, unkn	99.32
3f1p_A	117	Endothelial PAS domain-containing protein 1; PAS d	99.32
2vlg_A	111	Sporulation kinase A; histidine kinase, two-compon	99.32
4hi4_A	121	Aerotaxis transducer AER2; PAS domain, diatomic GA	99.31
4eet_B	115	Phototropin-2; LOV, blue light photoreceptor, sign	99.3
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	99.29
3olo_A	118	Two-component sensor histidine kinase; structural	99.29
3ue6_A	166	Aureochrome1; PAS/LOV domain, FMN-binding blue-lig	99.29
3mqq_A	120	Transcriptional regulator, LUXR family; PAS domain	99.29
3t50_A	128	Blue-light-activated histidine kinase; PAS superfa	99.26
1ll8_A	114	PAS kinase; PAS domain, ligand binding, ligand scr	99.23
3b33_A	115	Sensor protein; structural genomics, PAS domain, n	99.22
3luq_A	114	Sensor protein; PAS, histidine, kinase, PSI, MCSG,	99.19
2wkq_A	332	NPH1-1, RAS-related C3 botulinum toxin substrate 1	99.18
3d72_A	149	Vivid PAS protein VVD; circadian, photoreceptor, b	99.16
3cax_A	369	Uncharacterized protein PF0695; structural genomic	99.09
3mjq_A	126	Uncharacterized protein; NESG, structural genomics	99.07
2z6d_A	130	Phototropin-2; PAS-fold, LOV-fold, alternative spl	99.07
3nja_A	125	Probable ggdef family protein; structural genomics	99.06
3icy_A	118	Sensor protein; sensory box histidine kinase/respo	99.05
3lyx_A	124	Sensory BOX/ggdef domain protein; structural genom	99.04
1nwz_A	125	PYP, photoactive yellow protein; PAS, LOV, GAF, do	99.04
3mr0_A	142	Sensory box histidine kinase/response regulator; P	99.04
3rty_A	339	Period circadian protein; PAS domain, signalling,	99.02
1mzu_A	129	PPR; photoactive yellow protein, PAS, PYP, signali	99.02
3a0r_A	349	Sensor protein; four helix bundle, PAS fold, kinas	99.0
1ll8_A	114	PAS kinase; PAS domain, ligand binding, ligand scr	99.0
1byw_A	110	Protein (human ERG potassium channel); PAS domain,	98.99
3a0s_A	96	Sensor protein; PAS-fold, kinase, phosphoprotein,	98.99
1nwz_A	125	PYP, photoactive yellow protein; PAS, LOV, GAF, do	98.98
3sw1_A	162	Sensory box protein; light-oxygen-voltage, LOV, PA	98.98
3eeh_A	125	Putative light and redox sensing histidine kinase;	98.97
2jhe_A	190	Transcription regulator TYRR; aromatic hydrocarbon	98.97
3mxq_A	152	Sensor protein; PSI2, MCSG, structural genomics, p	98.96
2v0u_A	146	NPH1-1, LOV2; kinase, transferase, ATP-binding, se	98.96
2w0n_A	118	Sensor protein DCUS; signal transduction, two-comp	98.96
2l0w_A	138	Potassium voltage-gated channel, subfamily H (EAG	98.95
1mzu_A	129	PPR; photoactive yellow protein, PAS, PYP, signali	98.95
3fc7_A	125	HTR-like protein, sensor protein; APC87712.1, HTR-	98.92
3h9w_A	115	Diguanylate cyclase with PAS/PAC sensor; alpha-bet	98.91
3b33_A	115	Sensor protein; structural genomics, PAS domain, n	98.9
3fg8_A	118	Uncharacterized protein RHA05790; PAS domain, stru	98.89
4dj3_A	317	Period circadian protein homolog 3; PAS domain, ci	98.87
1v9y_A	167	Heme PAS sensor protein; signaling protein; HET: H	98.82
3gdi_A	309	Period circadian protein homolog 2; tandem PAS dom	98.76
3k3c_A	158	Protein RV1364C/MT1410; sensor, PAS, signal transd	98.75
4eho_A	635	Bacteriophytochrome, PAS/PAC sensor; photoreceptor	98.72
4dj2_A	320	Period circadian protein homolog 1; PAS domains, c	98.72
3kx0_X	185	Uncharacterized protein RV1364C/MT1410; PAS domain	98.72
4hi4_A	121	Aerotaxis transducer AER2; PAS domain, diatomic GA	98.66
3a0s_A	96	Sensor protein; PAS-fold, kinase, phosphoprotein,	98.61
3vol_A	233	Aerotaxis transducer AER2; heme, oxygen sensor pro	98.46
3a0r_A	349	Sensor protein; four helix bundle, PAS fold, kinas	98.44
2w0n_A	118	Sensor protein DCUS; signal transduction, two-comp	98.43
2ykf_A	305	Pdtas, probable sensor histidine kinase pdtas; tra	97.66
2jhe_A	190	Transcription regulator TYRR; aromatic hydrocarbon	98.3
2qkp_A	151	Uncharacterized protein; structural genomics, unkn	98.24
2ykf_A	305	Pdtas, probable sensor histidine kinase pdtas; tra	97.38
3cax_A	369	Uncharacterized protein PF0695; structural genomic	97.76
1oj5_A	132	Steroid receptor coactivator 1A; transcriptional c	97.7
1oj5_A	132	Steroid receptor coactivator 1A; transcriptional c	97.41
2ool_A	337	Sensor protein; bacteriophytochrome, photoconversi	96.38
4ew7_A	127	Conjugative transfer: regulation; alpha-beta-alpha	90.86
2ool_A	337	Sensor protein; bacteriophytochrome, photoconversi	89.64
3s7o_A	343	Bacteriophytochrome; biliverdin, PAS, GAF, photore	85.2
4e04_A	327	Bacteriophytochrome (light-regulated signal trans	81.41

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

Probab=99.97  E-value=2.4e-29  Score=203.71  Aligned_cols=190  Identities=19%  Similarity=0.361  Sum_probs=163.9

Q ss_pred             EEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEEEEEEecCCCeEEEEE
Q 020514           31 FTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLF  110 (325)
Q Consensus        31 i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg~~~~~~~  110 (325)
                      ++++|.+   |.++++|++|++++||++++++|++...+.++.........+.+.+..+..+..++...++||..+|+.+
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   9999999999999999999999999877776666666667777888888889999999999999999999


Q ss_pred             EEEEeecCCCCeeeEEEEEEeccccchhhhhcccCcccCCCCchhhHHHhhhhhhhhcccchhhhhhhccccccCCCCcc
Q 020514          111 KMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDRVLALDSDDTGLEI  190 (325)
Q Consensus       111 ~~~~~~~~~~g~~~~~~~~~~DITe~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  190 (325)
                      ++.|+.+ .+|.+.+++++.+|||++|++                                                   
T Consensus        79 ~~~p~~d-~~g~~~~~~~~~~DIT~~k~~---------------------------------------------------  106 (227)
T 3ewk_A           79 TIVPLMD-NAGKPRQYISIRRDITAQKEA---------------------------------------------------  106 (227)
T ss_dssp             EEEEEEC-SSSCEEEEEEEEEECTTTTHH---------------------------------------------------
T ss_pred             EEEEEEc-CCCCEEEEEEEEEehhhHHHH---------------------------------------------------
Confidence            9999998 899999999999999999985                                                   


Q ss_pred             cchhhhHHHHHHHHhhhhhhHhhhhccceeeccceeeeeecCCCCcccchhhhHhhhhccCCceEEecCCCCCCCeEEEe
Q 020514          191 EDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQSFVLIDPHLPDMPMVYAS  270 (325)
Q Consensus       191 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~i~~~d~~~~dg~i~~~N  270 (325)
                             +.+++.                                       +..++++++++|+++|.   +|+|+++|
T Consensus       107 -------e~~l~~---------------------------------------~~~~~~~~~~~i~~~d~---~g~i~~~N  137 (227)
T 3ewk_A          107 -------EAQLAR---------------------------------------LKQAMDANSEMILLTDR---AGRIIYAN  137 (227)
T ss_dssp             -------HHHHHH---------------------------------------HHHHHHTCCSEEEEECT---TSCEEEEC
T ss_pred             -------HHHHHH---------------------------------------HHHHHhcCcCeEEEEcC---CCcEEEEc
Confidence                   111111                                       23356778899999997   57999999


Q ss_pred             hhhHHhhCCCcccccccccccccCCCCChHHHHHHHH----------hhccccCCCc------eeeEEee
Q 020514          271 DAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI----------AISPYPKKKS------IYMEYVR  324 (325)
Q Consensus       271 ~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~----------e~~~~~kdG~------~~~~~~~  324 (325)
                      ++|++++||+++|++|+++..+.+|.........+++          |++.++|||+      .+|++++
T Consensus       138 ~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~k~G~~~~dg~~~~~~~~  207 (227)
T 3ewk_A          138 PALCRFSGMAEGELLGQSPSILDSPLADQETLAAMQEALQAGQPWSGRLLNRRRTGPAPHDAEDYWAEIS  207 (227)
T ss_dssp             HHHHHHHTCCTHHHHSSCGGGGBCTTSCHHHHHHHHHHHHHTCCEECCEEEEEECCSSSSCEEEEEEEEE
T ss_pred             hHHHHHhCCCHHHHcCCChhhccCCCCCHHHHHHHHHHHHcCCceeEEEEEECCCCCcCcccceEEEEEE
Confidence            9999999999999999999999988888887777765          7777888886      8998875

>2gj3_A Nitrogen fixation regulatory protein; PAS domain, FAD, redox sensor, atomic resolution, transferase; HET: FAD; 1.04A {Azotobacter vinelandii}

Probab=99.81  E-value=1.6e-18  Score=125.21  Aligned_cols=117  Identities=20%  Similarity=0.377  Sum_probs=104.8

Q ss_pred             HHHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEEE
Q 020514           17 TLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNL   96 (325)
Q Consensus        17 ~~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~   96 (325)
                      ..+++.++++++++++++|.+   |.++++|++|++++||+.++++|++...+.++.........+...+..+..+..++
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            357889999999999999999   99999999999999999999999988777776666555666777778888888888


Q ss_pred             EEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccch
Q 020514           97 LNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRK  137 (325)
Q Consensus        97 ~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k  137 (325)
                      ...+++|..+|+.+++.|+.+ .+|.+.+++++.+|||++|
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            889999999999999999998 8999999999999999986

>4f3l_A Mclock, circadian locomoter output cycles protein kaput; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus}

Probab=99.76  E-value=1.2e-17  Score=143.62  Aligned_cols=65  Identities=9%  Similarity=0.109  Sum_probs=56.4

Q ss_pred             HHHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHH
Q 020514           17 TLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIRE   84 (325)
Q Consensus        17 ~~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~   84 (325)
                      ..+...++++++..+++++.+   |.++|+|+++..++||++++++|+++.++++|++...+...+..
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            445667889999999999999   99999999999999999999999999999999887766555543

>4hia_A LOV protein; PAS, HTH, signaling protein; HET: FMN; 1.95A {Rhodobacter sphaeroides} PDB: 4hnb_A* 4hj4_A* 4hj6_A* 4hj3_A*

Probab=99.76  E-value=2.5e-17  Score=127.18  Aligned_cols=126  Identities=25%  Similarity=0.409  Sum_probs=113.2

Q ss_pred             HHHHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEE
Q 020514           16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVN   95 (325)
Q Consensus        16 ~~~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e   95 (325)
                      ...+++.++++++++++++|.+.++|.++++|+++++++||+.++++|+++..++++.+.......+...+..+..+..+
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            44578899999999999999865558999999999999999999999999888888888777778888888888888888


Q ss_pred             EEEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchhhhhc
Q 020514           96 LLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNS  142 (325)
Q Consensus        96 ~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~~~~  142 (325)
                      +...+++|..+|+.+++.|+.+ .+|.+.+++++.+|||++|+++++
T Consensus        85 ~~~~~~dG~~~~~~~~~~pi~~-~~g~~~~~~~~~~DITe~k~~e~~  130 (176)
T 4hia_A           85 LRNYRANDEPFDNLLFLHPVGG-RPDAPDYFLGSQFELGRSGNSEEA  130 (176)
T ss_dssp             EEEECTTCCEEEEEEEEEEESS-BTTBCSEEEEEEEEESSSGGGHHH
T ss_pred             EEEEcCCCCEEEEEEEEEEeeC-CCCCeEEEEEEEEECcHhhHHHHH
Confidence            8889999999999999999998 799999999999999999998544

>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=99.75  E-value=1.2e-17  Score=120.77  Aligned_cols=116  Identities=9%  Similarity=0.137  Sum_probs=98.7

Q ss_pred             HHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHH-hCCCeEEEEE
Q 020514           19 WVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIR-EERPIEVNLL   97 (325)
Q Consensus        19 ~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~-~~~~~~~e~~   97 (325)
                      ++..+++++++.+++.|.+   |.++++|+++++++||++++++|+++..+++|++.......+.+.+. .+..+..+++
T Consensus         3 ~~~ll~e~~~d~i~~~d~~---g~i~~~n~~~~~~~G~~~~el~g~~~~~~i~p~d~~~~~~~~~~~~~~~~~~~~~e~r   79 (121)
T 3f1p_B            3 FKGLNVCQPTRFISRHNIE---GIFTFVDHRCVATVGYQPQELLGKNIVEFCHPEDQQLLRDSFQQVVKLKGQVLSVMFR   79 (121)
T ss_dssp             -----CCCCCEEEEEECTT---SBEEEECTTHHHHHSCCGGGTTTSBGGGGBCTTTHHHHHHHHHHHTTSTTCCEEEEEE
T ss_pred             cccceecCCCceEEEECCC---ceEEEECcchhhhhCCChHHHcCCCHHHeECHHHHHHHHHHHHHHHhcCCCcccEEEE
Confidence            4557889999999999999   99999999999999999999999998889999888777777777664 4456788999


Q ss_pred             EEecCCCeEEEEEEEEEeecCC-CCeeeEEEEEEeccccchh
Q 020514           98 NYKKDGTPFWMLFKMSLVFGKE-DGRATHFVAVQVPIVSRKH  138 (325)
Q Consensus        98 ~~~~dg~~~~~~~~~~~~~~~~-~g~~~~~~~~~~DITe~k~  138 (325)
                      +.+++|..+|+.++..|+.+ . +|.+.+++++.+|||++|+
T Consensus        80 ~~~~dG~~~w~~~~~~~~~~-~~~g~~~~iv~~~~DIT~~kq  120 (121)
T 3f1p_B           80 FRSKNQEWLWMRTSSFTFQN-PYSDEIEYIICTNTNVKNSSQ  120 (121)
T ss_dssp             EECTTSCEEEEEEEEEEECC-TTCCCCCEEEEEEEECCCC--
T ss_pred             EEecCCCEEEEEEEEEEEEC-CCCCceeEEEEEeEEcccccC
Confidence            99999999999999999987 5 7888999999999999986

>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=99.75  E-value=8.5e-17  Score=118.14  Aligned_cols=117  Identities=36%  Similarity=0.668  Sum_probs=96.7

Q ss_pred             HHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEEEEEEe
Q 020514           21 HEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYK  100 (325)
Q Consensus        21 ~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~  100 (325)
                      +.++++++++++++|.+..++.++++|++|++++||+.++++|+++..+.++.........+...+..+..+..++...+
T Consensus         2 ~~~~~~~~~~i~~~d~~g~~~~i~~~N~a~~~~~G~~~~el~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~   81 (132)
T 2pr5_A            2 SHMLDHVRVGVVITDPALEDNPIVYVNQGFVQMTGYETEEILGKNCRFLQGKHTDPAEVDNIRTALQNKEPVTVQIQNYK   81 (132)
T ss_dssp             ----CCCCCEEEEECTTSTTCCEEEECHHHHHHHSCCHHHHTTSCGGGGCCTTCCHHHHHHHHHHHHHTCCEEEEEEEEC
T ss_pred             hhHHhcCCCcEEEEeCCCCCCcEEEECHHHHHHhCcCHHHHcCCChhhhCCCCCCHHHHHHHHHHHHcCCCeEEEEEEEe
Confidence            35789999999999997111399999999999999999999999887777666666656677777788888888888899


Q ss_pred             cCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchhhh
Q 020514          101 KDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMR  140 (325)
Q Consensus       101 ~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~~  140 (325)
                      +||..+|+.+++.|+.+ . + +.+++++.+|||++|++|
T Consensus        82 kdG~~~~~~~~~~~~~~-~-~-~~~~~~~~~DITe~k~~e  118 (132)
T 2pr5_A           82 KDGTMFWNELNIDPMEI-E-D-KTYFVGIQNDITKQKEYE  118 (132)
T ss_dssp             TTSCEEEEEEEEEEEEE-T-T-EEEEEEEEEECHHHHHHH
T ss_pred             cCCCeeeeEEEEEeccC-C-C-eeEEEEEEEeCcHHHHHH
Confidence            99999999999999987 4 3 788999999999999963

>3mr0_A Sensory box histidine kinase/response regulator; PAS fold, structural genomics, PSI-2; HET: PG5; 1.49A {Burkholderia thailandensis}

Probab=99.74  E-value=8.3e-17  Score=119.84  Aligned_cols=121  Identities=14%  Similarity=0.214  Sum_probs=105.7

Q ss_pred             hHHHHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCC--CCCcccCCCCChHHHHHHHHHHHhCCCe
Q 020514           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGR--NGRMFQGPRTNRRTIMEIREAIREERPI   92 (325)
Q Consensus        15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~--~~~~l~~~~~~~~~~~~~~~~~~~~~~~   92 (325)
                      .++.+|+.+++.++.++|.+|..   +..+++|++++.++||+++++.+.  .+..+++|++...+...+...+..+..+
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            34557888999999999999999   999999999999999999988763  3556788988888888888888888888


Q ss_pred             EEEEEEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchhh
Q 020514           93 EVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM  139 (325)
Q Consensus        93 ~~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~  139 (325)
                      ..++++.+++|..+|+...+.|+.+ .+|.+.+++|+..|||++|++
T Consensus        83 ~~e~r~~~~~G~~~w~~~~~~~~~d-~~g~~~~~~G~~~DITerk~~  128 (142)
T 3mr0_A           83 DVEYRVRTRSGDFRWIQSRGQALWN-SAGEPYRMVGWIMDVTDRKRD  128 (142)
T ss_dssp             EEEEEEECTTSCEEEEEEEEEEEEC-TTSCEEEEEEEEEECHHHHHH
T ss_pred             EEEEEEECCCCCEEEEEEEEEEEEC-CCCCEEEEEEEEEcCchHHHH
Confidence            9999999999999999999999998 899999999999999999997

>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=99.74  E-value=1.5e-16  Score=112.73  Aligned_cols=108  Identities=41%  Similarity=0.805  Sum_probs=94.7

Q ss_pred             CCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEEEEEEecCCCeE
Q 020514           27 LPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPF  106 (325)
Q Consensus        27 ~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg~~~  106 (325)
                      ++++++++|....++.++++|++|++++||+.++++|++...+.++.........+++.+..+..+..++..+++||..+
T Consensus         2 ~~~~i~i~d~~~~~g~i~~~N~a~~~l~Gy~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~kdG~~~   81 (109)
T 1n9l_A            2 LRHTFVVADATLPDCPLVYASEGFYAMTGYGPDEVLGHNCRFLQGEGTDPKEVQKIRDAIKKGEACSVRLLNYRKDGTPF   81 (109)
T ss_dssp             CSCEEEEEETTSTTCCEEEECHHHHHHHCCCHHHHTTSCGGGGCCTTCCHHHHHHHHHHHHHTCCEEEEEEEECTTSCEE
T ss_pred             CccEEEEEcCCCCCCeEEEEchHHHHHHCcCHHHHcCCCchhcCCCCCCHHHHHHHHHHHHcCCcEEEEEEEEcCCCCEE
Confidence            57899999952122999999999999999999999999977777776666666778888888889999999999999999


Q ss_pred             EEEEEEEEeecCCCCeeeEEEEEEecccc
Q 020514          107 WMLFKMSLVFGKEDGRATHFVAVQVPIVS  135 (325)
Q Consensus       107 ~~~~~~~~~~~~~~g~~~~~~~~~~DITe  135 (325)
                      |+.+++.|+++ ++|.+.+++++.+|||+
T Consensus        82 ~~~~~~~pi~d-~~G~~~~~v~~~~DITe  109 (109)
T 1n9l_A           82 WNLLTVTPIKT-PDGRVSKFVGVQVDVTS  109 (109)
T ss_dssp             EEEEEEEEEEC-TTSCEEEEEEEEEECCC
T ss_pred             EEEEEEEEEEC-CCCCEEEEEEEEEeCCC
Confidence            99999999998 89999999999999996

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

Probab=99.73  E-value=6.8e-17  Score=123.21  Aligned_cols=120  Identities=39%  Similarity=0.656  Sum_probs=109.4

Q ss_pred             HHHHHHHHHhhCCCEEEEEcC---CCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCe
Q 020514           16 YTLWVHEALDELPDSFTITDP---SISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPI   92 (325)
Q Consensus        16 ~~~~~~~~~~~~~~~i~~~d~---~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~   92 (325)
                      ...++..++++++++++++|.   +   |.++++|+++++++||+.++++|+++..++++.........+...+..+..+
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   8   9999999999999999999999999888888877777777788888888888


Q ss_pred             EEEEEEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchhh
Q 020514           93 EVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM  139 (325)
Q Consensus        93 ~~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~  139 (325)
                      ..+.....++|..+|+.+++.|+.+ .+|.+.+++++++|||++|.+
T Consensus       110 ~~e~~~~~~~g~~~~~~~~~~~i~~-~~g~~~~~~~~~~DITe~k~~  155 (166)
T 3ue6_A          110 SVCLLNYRQDGTTFWNLFFVAGLRD-SKGNIVNYVGVQSKVSEDYAK  155 (166)
T ss_dssp             EEEEEEECTTSCEEEEEEEEEEEEC-TTSCEEEEEEECCBCCHHHHH
T ss_pred             EEEEEEEcCCCCEEEEEEEEEeeeC-CCCCEEEEEEEEEechHHHHH
Confidence            8888889999999999999999998 889999999999999999985

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

Probab=99.71  E-value=1.5e-16  Score=115.73  Aligned_cols=117  Identities=38%  Similarity=0.664  Sum_probs=102.6

Q ss_pred             HHhhCCCEEEEEcC---CCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEEEEEE
Q 020514           23 ALDELPDSFTITDP---SISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNY   99 (325)
Q Consensus        23 ~~~~~~~~i~~~d~---~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~   99 (325)
                      ++++++.+++++|.   +   |.++++|++++.++|++.++++|+++..++++.........+...+..+..+..+....
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            57889999999999   7   89999999999999999999999998888877777777777888888888888888889


Q ss_pred             ecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchhhhhcc
Q 020514          100 KKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG  143 (325)
Q Consensus       100 ~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~~~~~  143 (325)
                      .++|..+|+.+++.|+.+ .+|.+.+++++++|||++|+++++.
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 8899999999999999999985443

>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=99.70  E-value=9.2e-17  Score=115.21  Aligned_cols=108  Identities=8%  Similarity=0.170  Sum_probs=97.5

Q ss_pred             CCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEEEEEEecCCCeE
Q 020514           27 LPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPF  106 (325)
Q Consensus        27 ~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg~~~  106 (325)
                      +++.+++.|.+   |.++++|+++++++||++++++|+++..+++|++.......+...+..+..+..++++.+++|..+
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            45678899999   999999999999999999999999988899998887777778888887777777889999999999


Q ss_pred             EEEEEEEEeecCC-CCeeeEEEEEEeccccchh
Q 020514          107 WMLFKMSLVFGKE-DGRATHFVAVQVPIVSRKH  138 (325)
Q Consensus       107 ~~~~~~~~~~~~~-~g~~~~~~~~~~DITe~k~  138 (325)
                      |+.++..|+.+ . +|.+.+++++.+|||++|+
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 7899999999999999986

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

Probab=99.70  E-value=3.6e-16  Score=128.58  Aligned_cols=120  Identities=30%  Similarity=0.597  Sum_probs=105.9

Q ss_pred             hHHHHHHHHHhhCCCEEEEEcC---CCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCC
Q 020514           15 RYTLWVHEALDELPDSFTITDP---SISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERP   91 (325)
Q Consensus        15 ~~~~~~~~~~~~~~~~i~~~d~---~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~   91 (325)
                      ....+|+.++++++++++++|.   +   |.++++|++|++++||++++++|+++..+.++.+.......+...+..+..
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            3456789999999999999999   7   889999999999999999999999988888888888888888888888888


Q ss_pred             eEEEEEEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchh
Q 020514           92 IEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKH  138 (325)
Q Consensus        92 ~~~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~  138 (325)
                      +..+....+++|..+|+.+++.|+.+ .+|.+.+++++++|||++|.
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 89999999999999999954

>3rty_A Period circadian protein; PAS domain, signalling, timeless, circadian clock protein; 2.85A {Drosophila melanogaster} PDB: 1wa9_A 3gec_A

Probab=99.70  E-value=2.4e-16  Score=133.14  Aligned_cols=70  Identities=6%  Similarity=-0.037  Sum_probs=56.1

Q ss_pred             CceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH---------------hhccccCCC
Q 020514          252 QSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI---------------AISPYPKKK  316 (325)
Q Consensus       252 ~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~---------------e~~~~~kdG  316 (325)
                      +.+...++   ||+++|+|+++..++||+++|++|+++.++++|++.....+.+.+               ++++++|||
T Consensus       155 ~fi~r~~~---dG~~~yvn~~~~~lLGY~peELiG~s~~~~vHPdD~~~~~~~~~~~l~~G~~~~~~~~s~~yR~~~kdG  231 (339)
T 3rty_A          155 KFAIRHTA---TGIISHVDSAAVSALGYLPQDLIGRSIMDFYHHEDLSVMKETYETVMKKGQTAGASFCSKPYRFLIQNG  231 (339)
T ss_dssp             EEEEEEET---TCBEEEECTTHHHHHCCCHHHHTTSBGGGGBCGGGHHHHHHHHHHHHHHTTSTTCCCBCCCEEEECTTS
T ss_pred             eEEEEECC---CCeEEEcChhhhcccCCCHHHHcCCcHHHEECHHHHHHHHHHHHHHHHcCCcccccccceEEEEEccCC
Confidence            34455555   689999999999999999999999999999999987765544433               256678999


Q ss_pred             ceeeEEee
Q 020514          317 SIYMEYVR  324 (325)
Q Consensus       317 ~~~~~~~~  324 (325)
                      +.+|++.+
T Consensus       232 ~~vWlet~  239 (339)
T 3rty_A          232 CYVLLETE  239 (339)
T ss_dssp             CEEEEEEE
T ss_pred             CEEEEEEE
Confidence            99999753

>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=99.70  E-value=8.9e-16  Score=109.03  Aligned_cols=111  Identities=41%  Similarity=0.778  Sum_probs=98.9

Q ss_pred             HHhhCCCEEEEEcC---CCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEEEEEE
Q 020514           23 ALDELPDSFTITDP---SISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNY   99 (325)
Q Consensus        23 ~~~~~~~~i~~~d~---~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~   99 (325)
                      .+++++.+++++|.   +   +.++++|+++++++|++.++++|+++..+.++.........+...+..+..+..+....
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            57889999999999   8   99999999999999999999999998888877777777777888888888888888888


Q ss_pred             ecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccch
Q 020514          100 KKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRK  137 (325)
Q Consensus       100 ~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k  137 (325)
                      .++|..+|+.++..|+.+ .+|.+.+++++.+|||+++
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 8899999999999999974

>4f3l_B BMAL1B; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus}

Probab=99.70  E-value=2.5e-16  Score=136.55  Aligned_cols=70  Identities=14%  Similarity=0.027  Sum_probs=58.5

Q ss_pred             CceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH-----------hhccccCCCceee
Q 020514          252 QSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI-----------AISPYPKKKSIYM  320 (325)
Q Consensus       252 ~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~-----------e~~~~~kdG~~~~  320 (325)
                      +.++..+.   ||+++|+|++++.++||+++|++|+++.++++|++.......+.+           ++++++|||+.+|
T Consensus       279 ~fi~~~~~---dg~~~~vn~~~~~ilGY~~eEl~g~~~~~~iHpdD~~~~~~~~~~~l~~~~~~~~~eyR~~~kdG~~vW  355 (387)
T 4f3l_B          279 EYVSRHAI---DGKFVFVDQRATAILAYLPQELLGTSCYEYFHQDDIGHLAECHRQVLQTREKITTNCYKFKIKDGSFIT  355 (387)
T ss_dssp             EEEEEECT---TSBEEEECTHHHHHHCCCHHHHTTSBGGGTBCHHHHHHHHHHHHHHTTCSSCEECCCEEEECTTSCEEE
T ss_pred             eEEEEECC---CCEEEEECCCcccccCCCHHHHcCCcHHHeeCHHHHHHHHHHHHHHHhcCCCeeeEEEEEEccCCCEEE
Confidence            34455555   689999999999999999999999999999999887776665544           7888899999999


Q ss_pred             EEee
Q 020514          321 EYVR  324 (325)
Q Consensus       321 ~~~~  324 (325)
                      ++.+
T Consensus       356 v~~~  359 (387)
T 4f3l_B          356 LRSR  359 (387)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            9753

>3nja_A Probable ggdef family protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; 2.37A {Chromobacterium violaceum}

Probab=99.68  E-value=3.3e-16  Score=113.09  Aligned_cols=120  Identities=14%  Similarity=0.090  Sum_probs=93.1

Q ss_pred             hHHHHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcC--CCCCcccCCCCChHHHHHHHHHHHhCCCe
Q 020514           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIG--RNGRMFQGPRTNRRTIMEIREAIREERPI   92 (325)
Q Consensus        15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g--~~~~~l~~~~~~~~~~~~~~~~~~~~~~~   92 (325)
                      ....+++.+++.++.+++++|.+   +.++++|++++.++|++++++.|  ..+..+++|++...+...+...+..+...
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            34557889999999999999999   99999999999999999999988  33445677877777777778888888888


Q ss_pred             EEEEEEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchh
Q 020514           93 EVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKH  138 (325)
Q Consensus        93 ~~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~  138 (325)
                      ..+++...++|..+|+.+.+.|+.+ .+|.+.+++++.+|||++|+
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 89999999999999999974

>3mqq_A Transcriptional regulator, LUXR family; PAS domain, PSI, MCSG, structural genomics, center for structural genomics; 1.65A {Burkholderia thailandensis} PDB: 3mqo_A

Probab=99.67  E-value=3.6e-16  Score=112.66  Aligned_cols=115  Identities=12%  Similarity=0.093  Sum_probs=91.3

Q ss_pred             HHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCC-hHHHHHHHHHHHhCCCeEEEEE
Q 020514           19 WVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTN-RRTIMEIREAIREERPIEVNLL   97 (325)
Q Consensus        19 ~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~-~~~~~~~~~~~~~~~~~~~e~~   97 (325)
                      .|+.++++++.+++ ++.+   |.++++|+++++++||++++++|+++..++++... ......+...+..+..+..+..
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 5778   99999999999999999999999997776654322 2334445566667777888889


Q ss_pred             EEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchhh
Q 020514           98 NYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM  139 (325)
Q Consensus        98 ~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~  139 (325)
                      ..+++|..+|+.++..|+.  .++...+++++++|||++|++
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  466667889999999999974

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

Probab=99.67  E-value=3.4e-15  Score=106.90  Aligned_cols=119  Identities=20%  Similarity=0.264  Sum_probs=103.7

Q ss_pred             HHHHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEE
Q 020514           16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVN   95 (325)
Q Consensus        16 ~~~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e   95 (325)
                      ....++.+++.++.+++++|.+   +.++++|+++++++|++.++++|++...+.++.........+...+..+..+..+
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   9999999999999999999999998776666655555566677778888888888


Q ss_pred             EEEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchh
Q 020514           96 LLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKH  138 (325)
Q Consensus        96 ~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~  138 (325)
                      .....++|..+|+.++..|+.+ .+|.+.+++++.+|||++|+
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            8888999999999999999998 88999999999999999986

>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=99.66  E-value=6.8e-15  Score=106.15  Aligned_cols=121  Identities=37%  Similarity=0.725  Sum_probs=103.8

Q ss_pred             HHHHHHHHHhhCCCEEEEEc---CCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCe
Q 020514           16 YTLWVHEALDELPDSFTITD---PSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPI   92 (325)
Q Consensus        16 ~~~~~~~~~~~~~~~i~~~d---~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~   92 (325)
                      ....++.+++.++.+++++|   .+   +.++++|++++.++|++.++++|+++..+.++.........+...+..+...
T Consensus         4 ~~~~~~~~~~~~~~~i~~~d~~d~~---~~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (130)
T 2z6d_A            4 VSQELKTALSTLQQTFVVSDATQPH---CPIVYASSGFFTMTGYSSKEIVGRNCRFLQGPDTDKNEVAKIRDCVKNGKSY   80 (130)
T ss_dssp             ---CHHHHHHHTTCEEEEEETTSTT---CCEEEECHHHHHHHCCCHHHHTTSCGGGGCCTTSCHHHHHHHHHHHHTTCCE
T ss_pred             HHHHHHHHHHhcccceeeeeccCCC---CcEEEecHHHHHHhCcCHHHHcCCChhhccCCCCCchHHHHHHHHHHcCCcc
Confidence            34567889999999999999   88   9999999999999999999999999888877777766667777778888888


Q ss_pred             EEEEEEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchhhh
Q 020514           93 EVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMR  140 (325)
Q Consensus        93 ~~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~~  140 (325)
                      ..+.....++|..+|+.+...|+.+ .+|.+.+++++++|||++++++
T Consensus        81 ~~~~~~~~~~g~~~~~~~~~~~~~~-~~g~~~~~~~~~~Dit~~~~~e  127 (130)
T 2z6d_A           81 CGRLLNYKKDGTPFWNLLTVTPIKD-DQGNTIKFIGMQVEVSKYTEGV  127 (130)
T ss_dssp             EEEEEEECTTSCEEEEEEEEEEEEC-TTSCEEEEEEEEEECCTTC---
T ss_pred             eeEEEEEcCCCcEEEEEEEEEEEEC-CCCCeeEEEEEEecchHHHHhh
Confidence            8888888899999999999999998 7899999999999999999863

>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=99.65  E-value=3.2e-15  Score=109.27  Aligned_cols=123  Identities=17%  Similarity=0.240  Sum_probs=93.8

Q ss_pred             hhhHHhhhhhhHHHHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHH
Q 020514            5 LGLIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIRE   84 (325)
Q Consensus         5 ~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~   84 (325)
                      +...++++. ....+++.++++++++++++|.+   |.++++|+++++++||++++++|+++..++++.........+..
T Consensus         4 ~~~~e~~l~-~~~~~~~~l~~~~~d~i~~~d~~---g~i~~~N~a~~~l~Gy~~~eliG~~~~~l~~~~~~~~~~~~~~~   79 (130)
T 1d06_A            4 MLETEDVVR-ARDAHLRSILDTVPDATVVSATD---GTIVSFNAAAVRQFGYAEEEVIGQNLRILMPEPYRHEHDGYLQR   79 (130)
T ss_dssp             HHHHHHHHH-HHTSCHHHHHTTCSSEEEEEETT---SBEEEECHHHHHHHCCCHHHHTTSBGGGGSCTTHHHHHHHHHHH
T ss_pred             HHHHHHHHH-HHHHHHHHHHhhCcCeEEEECCC---CeEEEEcHHHHHHHCCCHHHHcCCcHHHHCCchhHHHHHHHHHH
Confidence            344555555 55567899999999999999999   99999999999999999999999998777766543333333334


Q ss_pred             HHHhCCC----eEEEEEEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccc
Q 020514           85 AIREERP----IEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV  134 (325)
Q Consensus        85 ~~~~~~~----~~~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIT  134 (325)
                      ....+..    ...++...++||..+|+.+++.|+.+  .+. .+++++++|||
T Consensus        80 ~~~~~~~~~~~~~~e~~~~~kdG~~~~~~~~~~~~~~--~~~-~~~~~~~~DIT  130 (130)
T 1d06_A           80 YMATGEKRIIGIDRVVSGQRKDGSTFPMKLAVGEMRS--GGE-RFFTGFIRDLT  130 (130)
T ss_dssp             HHHHCCCSSTTSCEEEEEECTTSCEEEEEEEEEEEEE--TTE-EEEEEEEEECC
T ss_pred             HHhcCCccccCCeeEEEEEeCCCCEEEEEEEEEEEEE--CCe-EEEEEEEEECc
Confidence            3433332    23466778999999999999999976  333 45888999997

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

Probab=99.64  E-value=4.4e-15  Score=112.63  Aligned_cols=124  Identities=23%  Similarity=0.437  Sum_probs=110.5

Q ss_pred             HHHHHHHHHhhCCCEEEEEcCCCCCC---CEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCe
Q 020514           16 YTLWVHEALDELPDSFTITDPSISGH---PIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPI   92 (325)
Q Consensus        16 ~~~~~~~~~~~~~~~i~~~d~~~~~~---~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~   92 (325)
                      ...+++.+++.++.+++++|.+   +   .++++|++++.++|++.++++|+++..++++.........+...+..+..+
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            4467899999999999999999   9   999999999999999999999999888877776667777778888888888


Q ss_pred             EEEEEEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchhhhhcc
Q 020514           93 EVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG  143 (325)
Q Consensus        93 ~~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~~~~~  143 (325)
                      ..+......+|..+|+.+++.|+.+ .+|.+.+++++++|||+++++++++
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 7899999999999999999984443

>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=99.64  E-value=1.4e-15  Score=113.82  Aligned_cols=120  Identities=16%  Similarity=0.129  Sum_probs=94.0

Q ss_pred             hHHHHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEE
Q 020514           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV   94 (325)
Q Consensus        15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   94 (325)
                      .....+..+++++++|++++|.+   |+++++|+++++++|+++++++|+++.++++. ....+...+.+++..|.+...
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            45567899999999999999999   99999999999999999999999998888776 445556667778877754322


Q ss_pred             E---------EE---EEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchhh
Q 020514           95 N---------LL---NYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM  139 (325)
Q Consensus        95 e---------~~---~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~  139 (325)
                      .         +.   ....+|...|..+++.|+.+ .+|.+.+++.+++|||+++.+
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            1         11   12245677888999999999 899999999999999999875

>3h9w_A Diguanylate cyclase with PAS/PAC sensor; alpha-beta protein., structural genomics, PSI-2, protein STR initiative; 1.90A {Marinobacter aquaeolei}

Probab=99.63  E-value=1.2e-15  Score=108.99  Aligned_cols=111  Identities=9%  Similarity=0.058  Sum_probs=94.4

Q ss_pred             CCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCC-CCcccCCCCChHHHHHHHHHHHhCCCeEEEEEEEecCCCe
Q 020514           27 LPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRN-GRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTP  105 (325)
Q Consensus        27 ~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~-~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg~~  105 (325)
                      +++++|.+|..  ++.+.++|+++++++||+++++.|.. +..+++|++...+...+...+..+..+..++++.+++|..
T Consensus         2 a~~giw~~d~~--~~~~~~~n~~~~~l~G~~~~e~~~~~~~~~~ihpdd~~~~~~~~~~~~~~~~~~~~e~r~~~~dG~~   79 (115)
T 3h9w_A            2 TKAIPWKINWQ--TMAFEYIGPQIEALLGWPQGSWKSVEDWATRMHPEDQEWVVNFCVKQSECGVDHEADYRALHRDGHY   79 (115)
T ss_dssp             -CCEEEEEETT--TTEEEEECTHHHHHHCSCGGGCCBHHHHHHSBCHHHHHHHHHHHHHHHHTTCCEEEEEEEECTTSCE
T ss_pred             cceEEEEEEcC--CCcEEEEChhHHHHhCCChHHccCHHHHHHhcCHHHHHHHHHHHHHHHhcCCcccEEEEEEcCCCCE
Confidence            56789999943  28889999999999999999998832 3456778877777778888888888888999999999999


Q ss_pred             EEEEEEEEEeecCCCCeeeEEEEEEeccccchhhh
Q 020514          106 FWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMR  140 (325)
Q Consensus       106 ~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~~  140 (325)
                      +|+...+.|+++ ++|.+.+++|+..|||++|.+|
T Consensus        80 ~w~~~~~~~~~d-~~G~~~~~~G~~~Dit~~k~~~  113 (115)
T 3h9w_A           80 VWIRDVVHVVRD-DSGEVEALIGFMFDISLEHHHH  113 (115)
T ss_dssp             EEEEEEEEEEEC-TTSCEEEEEEEEEECGGGGC--
T ss_pred             EEEEEEEEEEEC-CCCCEEEEEEEEeccCcccccc
Confidence            999999999998 8999999999999999999863

>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=99.63  E-value=6.6e-15  Score=105.82  Aligned_cols=111  Identities=20%  Similarity=0.255  Sum_probs=78.6

Q ss_pred             CCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCC----eEEEEEEEecC
Q 020514           27 LPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERP----IEVNLLNYKKD  102 (325)
Q Consensus        27 ~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~----~~~e~~~~~~d  102 (325)
                      ++++++++|.+   |.++++|+++++++||++++++|+++..++++.........+......+..    ...++...++|
T Consensus         2 ~~d~i~~~d~~---g~i~~~N~a~~~l~G~~~~el~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d   78 (119)
T 2vv6_A            2 IPDAMIVIDGH---GIIQLFSTAAERLFGWSELEAIGQNVNILMPEPDRSRHDSYISRYRTTSDPHIIGIGRIVTGKRRD   78 (119)
T ss_dssp             CCCEEEEEETT---SBEEEECHHHHHHHCCCHHHHTTSBGGGGSCTTHHHHHHHHHHHHHHHCCCSSTTTCEEEEEECTT
T ss_pred             CcceEEEECCC---CeEEEEhHHHHHHhCCCHHHHcCCCHHHhCCchHHHHHHHHHHHHhcCCCcccCCCceEEEEEeCC
Confidence            67899999999   999999999999999999999999887776654433323333333333332    23566778999


Q ss_pred             CCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchhhhhcc
Q 020514          103 GTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG  143 (325)
Q Consensus       103 g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~~~~~  143 (325)
                      |..+|+.+++.|+.+ . +. .+++++++|||++|++|+++
T Consensus        79 G~~~~~~~~~~~~~~-~-~~-~~~~~~~~DITerk~~e~~l  116 (119)
T 2vv6_A           79 GTTFPMHLSIGEMQS-G-GE-PYFTGFVRDLTEHQQTQARL  116 (119)
T ss_dssp             SCEEEEEEEEEEEEE-T-TE-EEEEEEEEECC---------
T ss_pred             CCEEEEEEEEEEEEE-C-Ce-EEEEEEEEEcHHHHHHHHHH
Confidence            999999999999976 3 33 46889999999999985544

>2r78_A Sensor protein; sensory box sensor histidine kinase/response regulator, structural genomics, PSI, MCSG; 1.60A {Geobacter sulfurreducens pca}

Probab=99.62  E-value=2.6e-14  Score=102.48  Aligned_cols=110  Identities=11%  Similarity=0.137  Sum_probs=86.6

Q ss_pred             hHHHHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEE
Q 020514           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV   94 (325)
Q Consensus        15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   94 (325)
                      .++.+|+.++++++++++++|.+   |.++++|+++++++||++++++|+++..+.++.... ........+..+..+..
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            45668999999999999999999   999999999999999999999999876654433322 22233445566667778


Q ss_pred             EEEEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccc
Q 020514           95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV  134 (325)
Q Consensus        95 e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIT  134 (325)
                      +....++||..+|+.++..|+.   +|.   ++++++|||
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            8888999999999999999885   344   578889997

>3luq_A Sensor protein; PAS, histidine, kinase, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: PGE; 2.49A {Geobacter sulfurreducens}

Probab=99.62  E-value=8.6e-15  Score=103.75  Aligned_cols=112  Identities=15%  Similarity=0.182  Sum_probs=90.8

Q ss_pred             HHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEEEE
Q 020514           18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLL   97 (325)
Q Consensus        18 ~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~   97 (325)
                      ++++.++++++.+++++|.+   +.++++|+++++++|+++++++|+++..++ |.+.......+...+.++.....+..
T Consensus         3 ~~~~~~~~~~~~~i~~~d~~---g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (114)
T 3luq_A            3 ERLRLFTEHAPAALAMFDRE---MRYLAVSRRWREDYGLGDGDILGMSHYDIF-PEIGEEWKSVHRRGLAGEVIRVEEDC   78 (114)
T ss_dssp             HHHHHHHHTCSSEEEEEETT---CBEEEECHHHHHHTTCCSSCCTTCBHHHHC-TTCCHHHHHHHHHHHTTCCEEEEEEE
T ss_pred             HHHHHHHhcCCceEEEEcCC---cEEEEECHHHHHHHCCCHHHHcCCcHHHHC-CccHHHHHHHHHHHhcCCcceeeeeE
Confidence            46788999999999999999   999999999999999999999999877776 55555555555555543333333336


Q ss_pred             EEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccc
Q 020514           98 NYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV  134 (325)
Q Consensus        98 ~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIT  134 (325)
                      ...++|..+|+.++..|+.+ .+|.+.+++++.+|||
T Consensus        79 ~~~~~g~~~~~~~~~~p~~~-~~g~~~~~~~~~~DIT  114 (114)
T 3luq_A           79 FVRADGRTQWLRWEVRPWYE-GEGRVGGVVIFTEDIT  114 (114)
T ss_dssp             EEC--CCEEEEEEEEEEEEC-TTSCEEEEEEEEEECC
T ss_pred             EEcCCCcEEEEEEEEEEeEC-CCCCEEEEEEEEeeCC
Confidence            77889999999999999998 8999999999999997

>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=99.61  E-value=1.4e-14  Score=123.48  Aligned_cols=116  Identities=39%  Similarity=0.744  Sum_probs=106.2

Q ss_pred             HHHhhCCCEEEEEcC---CCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEEEEE
Q 020514           22 EALDELPDSFTITDP---SISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLN   98 (325)
Q Consensus        22 ~~~~~~~~~i~~~d~---~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~   98 (325)
                      .+++.++++++++|.   +   |.++++|+++++++||++++++|+++..+.++.+.......+...+..+..+..+...
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            468899999999999   8   9999999999999999999999999888888777777777888888888888899999


Q ss_pred             EecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchhhhh
Q 020514           99 YKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRN  141 (325)
Q Consensus        99 ~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~~~  141 (325)
                      .+++|..+|+.+++.|+.+ .+|.+.+++++.+|||+++++++
T Consensus        92 ~~~dG~~~~~~~~~~pi~d-~~g~~~~~v~~~~DITe~k~~e~  133 (332)
T 2wkq_A           92 YTKSGKKFWNLFHLQPMRD-QKGDVQYFIGVQLDGTEHVRDAA  133 (332)
T ss_dssp             ECTTCCEEEEEEEEEEEEC-TTSCEEEEEEEEEEESSCCCHHH
T ss_pred             EcCCCCEEEEeeEEEEeEc-CCCCEEEEEEEeccCchhhhhhh
Confidence            9999999999999999998 88999999999999999998743

>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=99.60  E-value=4.9e-15  Score=112.01  Aligned_cols=122  Identities=12%  Similarity=0.115  Sum_probs=99.4

Q ss_pred             hHHHHHHHHHhhCCCEEEEEc-CCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeE
Q 020514           15 RYTLWVHEALDELPDSFTITD-PSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIE   93 (325)
Q Consensus        15 ~~~~~~~~~~~~~~~~i~~~d-~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~   93 (325)
                      ....+|+.++++++.+++++| .+   +.++++|++++.++|++  +++|+++..++++.........+.+++..+.+..
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            345688999999999999999 99   99999999999999999  8899998777776655556667777787777654


Q ss_pred             EEEE-E--Ee-cC-CCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchhhhhc
Q 020514           94 VNLL-N--YK-KD-GTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNS  142 (325)
Q Consensus        94 ~e~~-~--~~-~d-g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~~~~  142 (325)
                      .... .  .. .+ |..+|+.++..|+.+ .+|.+.+++++++|||++|+++++
T Consensus        89 ~~~~~~~~~~~~~~g~~~~~~~~~~pi~~-~~g~~~g~~~~~~DITe~k~~e~~  141 (158)
T 3k3c_A           89 GSEWRLQTDYDGSGVEERYFDFVVTPRRR-ADGSIEGVQLIVDDVTSRVRARQA  141 (158)
T ss_dssp             EEEEEEEEESSSSCEEEEEEEEEEEEEEC-TTSCEEEEEEEEEECHHHHHHHHH
T ss_pred             ccceeEEeccCCCCcceEEEEEEEEEeEC-CCCCEEEEEEEEEehhHHHHHHHH
Confidence            4322 2  21 22 677899999999998 899999999999999999998444

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

Probab=99.59  E-value=5.8e-14  Score=113.05  Aligned_cols=111  Identities=20%  Similarity=0.465  Sum_probs=102.3

Q ss_pred             HHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEEEE
Q 020514           18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLL   97 (325)
Q Consensus        18 ~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~   97 (325)
                      ..+..++++++++++++|.+   |.++++|++|++++||++++++|+++..+.++.........+++.+..+..+..++.
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   999999999999999999999999988888888888888888899999999999998


Q ss_pred             EEecCCC------eEEEEEEEEEeecCCCCeeeEEEEEEec
Q 020514           98 NYKKDGT------PFWMLFKMSLVFGKEDGRATHFVAVQVP  132 (325)
Q Consensus        98 ~~~~dg~------~~~~~~~~~~~~~~~~g~~~~~~~~~~D  132 (325)
                      .++++|.      .+|+.+++.|+++ .+|.+.+++++.+|
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            8899886      8999999999999 89999999999887

>3icy_A Sensor protein; sensory box histidine kinase/response regulator domain, kinase, chlorobium tepidum TLS, PSI-2; 2.68A {Chlorobaculum tepidum}

Probab=99.58  E-value=7.2e-15  Score=104.97  Aligned_cols=114  Identities=10%  Similarity=0.061  Sum_probs=101.5

Q ss_pred             HHHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCC--CCcccCCCCChHHHHHHHHHHHhCCCeEE
Q 020514           17 TLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRN--GRMFQGPRTNRRTIMEIREAIREERPIEV   94 (325)
Q Consensus        17 ~~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~--~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   94 (325)
                      .++|+.++++++.+++.+|.+   +.++++|+++++++||+++++.+.+  +..+++|++...+...+...+..+..+..
T Consensus         3 ~~~~~~l~~~~~~~i~~~d~~---~~~~~~n~~~~~~~G~~~~~~~~~~~~~~~~i~p~d~~~~~~~~~~~~~~~~~~~~   79 (118)
T 3icy_A            3 AEELQALVDNIPAAIYHLDVS---GQATIRFRPPAFLKTLVSEHAGTTRLNTLSMIHHDDRHMLSNAYSKLREAKHSLTL   79 (118)
T ss_dssp             HHHHHHHHTTCCCCCEEECTT---SCEEECCCCCGGGGGGEEEETTEEEEGGGGGBCGGGHHHHHHHHHHHHHSCCEEEE
T ss_pred             HHHHHHHHhcCCceEEEEEcC---CCceEEechhHhhcCCCHHHccCChhHHHHHcCHHHHHHHHHHHHHHHhcCCCceE
Confidence            457889999999999999999   9999999999999999999987764  34567888777777777887788888888


Q ss_pred             EEEEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccc
Q 020514           95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV  134 (325)
Q Consensus        95 e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIT  134 (325)
                      ++++.+++|..+|+.....|+.+ .+|.+.+++++.+|||
T Consensus        80 e~r~~~~~g~~~w~~~~~~~~~~-~~g~~~~~~g~~~DIT  118 (118)
T 3icy_A           80 VYRIVTPEGKLHWIEDHMRSSFS-DDGLFSGIDGILCEVT  118 (118)
T ss_dssp             EEEEECTTCCEEEEEEEEEEEEC-TTSCEEEEEEEEEECC
T ss_pred             EEEEECCCCCEEEEEEEEEEEEC-CCCCEEEEEEEEEecC
Confidence            99999999999999999999998 8999999999999998

>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=99.57  E-value=5e-15  Score=104.80  Aligned_cols=75  Identities=37%  Similarity=0.757  Sum_probs=64.2

Q ss_pred             cCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH----------hhccccCCCcee
Q 020514          250 IKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI----------AISPYPKKKSIY  319 (325)
Q Consensus       250 ~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~----------e~~~~~kdG~~~  319 (325)
                      ++++|+++|.+.+||+|+|+|++|++|+||+++|++|+++..+.+|......+..+++          +++.++|||+.+
T Consensus         2 ~~~~i~i~d~~~~~g~i~~~N~a~~~l~Gy~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~kdG~~~   81 (109)
T 1n9l_A            2 LRHTFVVADATLPDCPLVYASEGFYAMTGYGPDEVLGHNCRFLQGEGTDPKEVQKIRDAIKKGEACSVRLLNYRKDGTPF   81 (109)
T ss_dssp             CSCEEEEEETTSTTCCEEEECHHHHHHHCCCHHHHTTSCGGGGCCTTCCHHHHHHHHHHHHHTCCEEEEEEEECTTSCEE
T ss_pred             CccEEEEEcCCCCCCeEEEEchHHHHHHCcCHHHHcCCCchhcCCCCCCHHHHHHHHHHHHcCCcEEEEEEEEcCCCCEE
Confidence            5789999997655799999999999999999999999999888888777666655554          677889999999


Q ss_pred             eEEee
Q 020514          320 MEYVR  324 (325)
Q Consensus       320 ~~~~~  324 (325)
                      |++++
T Consensus        82 ~~~~~   86 (109)
T 1n9l_A           82 WNLLT   86 (109)
T ss_dssp             EEEEE
T ss_pred             EEEEE
Confidence            99875

>3kx0_X Uncharacterized protein RV1364C/MT1410; PAS domain, sensory domain, mycobacteium tuberculos molecule binding domain; 2.30A {Mycobacterium tuberculosis}

Probab=99.57  E-value=2.5e-14  Score=111.39  Aligned_cols=122  Identities=12%  Similarity=0.121  Sum_probs=98.3

Q ss_pred             hHHHHHHHHHhhCCCEEEEEc-CCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeE
Q 020514           15 RYTLWVHEALDELPDSFTITD-PSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIE   93 (325)
Q Consensus        15 ~~~~~~~~~~~~~~~~i~~~d-~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~   93 (325)
                      +...+|+.++++++++++++| .+   +.++++|++++.++|++  +++|+++..++++.........+..++..+....
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            355689999999999999999 99   99999999999999999  8999998888777665555566777777777655


Q ss_pred             EE-EEE--Eec-C-CCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchhhhhc
Q 020514           94 VN-LLN--YKK-D-GTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNS  142 (325)
Q Consensus        94 ~e-~~~--~~~-d-g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~~~~  142 (325)
                      .. ...  ..+ + |..+|+.++..|+.+ .+|.+.+++++++|||++|+++++
T Consensus       109 ~~~~~~~~~~~~~gg~~~~~~~~~~pi~~-~~g~~~g~~~~~~DITerk~~e~~  161 (185)
T 3kx0_X          109 GSEWRLQTDYDGSGVEERYFDFVVTPRRR-ADGSIEGVQLIVDDVTSRVRARQA  161 (185)
T ss_dssp             EEEEEEC--------CCEEEEEEEEEEEC-TTSCEEEEEEEEEECHHHHTTCC-
T ss_pred             ccceeEEeeccCCCCccEEEEEEEEEEEC-CCCCEEEEEEEEEeCCHHHHHHHH
Confidence            43 222  111 2 778999999999998 899999999999999999998666

>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=99.56  E-value=7.1e-14  Score=103.07  Aligned_cols=116  Identities=39%  Similarity=0.742  Sum_probs=103.9

Q ss_pred             HHHHHhhCCCEEEEEcC---CCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEEE
Q 020514           20 VHEALDELPDSFTITDP---SISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNL   96 (325)
Q Consensus        20 ~~~~~~~~~~~i~~~d~---~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~   96 (325)
                      +..+++.++.+++++|.   +   +.++++|++++.++|++.++++|+++..+.++.........+...+..+..+..+.
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             EEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchhh
Q 020514           97 LNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM  139 (325)
Q Consensus        97 ~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~  139 (325)
                      ....++|..+|+.++..|+.+ .+|.+.+++++.+|||++++.
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 789999999999999999874

>2kdk_A ARYL hydrocarbon receptor nuclear translocator-LI 2; circadian clock, PAS domain, transcription, activator, biolo rhythms, DNA-binding, nucleus; NMR {Homo sapiens}

Probab=99.56  E-value=6.6e-14  Score=100.66  Aligned_cols=112  Identities=11%  Similarity=0.085  Sum_probs=94.0

Q ss_pred             HHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCC-CeEEEEEEEe
Q 020514           22 EALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREER-PIEVNLLNYK  100 (325)
Q Consensus        22 ~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~-~~~~e~~~~~  100 (325)
                      .++++++++++++|.+   |.++++|+++++++||++++++|+++..+++|++.......+.+.+..+. ....+++..+
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            4677899999999999   99999999999999999999999998888888877666666666665433 4567888899


Q ss_pred             cCCCeEEEEEEEEEeecCCC-CeeeEEEEEEeccccch
Q 020514          101 KDGTPFWMLFKMSLVFGKED-GRATHFVAVQVPIVSRK  137 (325)
Q Consensus       101 ~dg~~~~~~~~~~~~~~~~~-g~~~~~~~~~~DITe~k  137 (325)
                      ++|..+|+.++..|+.+ .. +.+.+++++.+||++.+
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 56677889999999865

>2gj3_A Nitrogen fixation regulatory protein; PAS domain, FAD, redox sensor, atomic resolution, transferase; HET: FAD; 1.04A {Azotobacter vinelandii}

Probab=99.53  E-value=2.9e-14  Score=102.59  Aligned_cols=81  Identities=22%  Similarity=0.328  Sum_probs=68.6

Q ss_pred             hhhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH----------hhc
Q 020514          241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI----------AIS  310 (325)
Q Consensus       241 ~~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~----------e~~  310 (325)
                      ..++.++++++++|+++|.   +|+|+|+|++|++++||+++|++|+++..+.++.........+.+          ++.
T Consensus         5 ~~~~~~~~~~~~~i~~~d~---~g~i~~~N~a~~~~~G~~~~elig~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~   81 (120)
T 2gj3_A            5 EIFRQTVEHAPIAISITDL---KANILYANRAFRTITGYGSEEVLGKNESILSNGTTPRLVYQALWGRLAQKKPWSGVLV   81 (120)
T ss_dssp             HHHHHHHHHCSSEEEEECT---TCBEEEECHHHHHHHCCCTTGGGGCBGGGGCCTTSCHHHHHHHHHHHHTTCCEEEEEE
T ss_pred             HHHHHHHHhCCCeEEEECC---CCCEEeehHHHHHHHCcCHHHHcCCCHHHcCCCCCCHHHHHHHHHHHHcCCCEEEEEE
Confidence            4578899999999999998   479999999999999999999999999988877766555544443          567


Q ss_pred             cccCCCceeeEEee
Q 020514          311 PYPKKKSIYMEYVR  324 (325)
Q Consensus       311 ~~~kdG~~~~~~~~  324 (325)
                      .++|||+.+|++++
T Consensus        82 ~~~~dG~~~~~~~~   95 (120)
T 2gj3_A           82 NRRKDKTLYLAELT   95 (120)
T ss_dssp             EECTTSCEEEEEEE
T ss_pred             EEcCCCCEEEEEEE
Confidence            78999999999865

>2r78_A Sensor protein; sensory box sensor histidine kinase/response regulator, structural genomics, PSI, MCSG; 1.60A {Geobacter sulfurreducens pca}

Probab=99.52  E-value=1.9e-14  Score=103.14  Aligned_cols=85  Identities=12%  Similarity=0.112  Sum_probs=66.4

Q ss_pred             ccchhhhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChH---HHHHHHH------
Q 020514          237 GFISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTT---VLYQVSI------  307 (325)
Q Consensus       237 ~~~~~~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~---~~~~~~~------  307 (325)
                      ...+..++.++++++++|+++|.   +|+|+++|+++++|+||+++|++|+++..+.++.....   ....+..      
T Consensus         7 ~~se~~~~~l~e~~~d~i~~~d~---~g~i~~vN~a~~~l~Gy~~~el~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   83 (117)
T 2r78_A            7 YFQSNAYRALFEHAIDGIFIMDA---EGHYLDVNPAICSAIGYTRDEFLALDWGVLSRGVDSGWAAASLARIVGGEPLRE   83 (117)
T ss_dssp             HHHHHHHHHHHHHCSSEEEEECT---TSBEEEECHHHHHHHCCCHHHHTTCBTTTTTTCSTTSHHHHHHHHHHTTCCEEE
T ss_pred             HHhHHHHHHHHhcCCceEEEECC---CCCEEEecHHHHHHHCcCHHHHcCCCHHHhCCccchhHHHHHHHHHHcCCcEEE
Confidence            34456788999999999999998   47999999999999999999999999877654433221   2222222      


Q ss_pred             hhccccCCCceeeEEee
Q 020514          308 AISPYPKKKSIYMEYVR  324 (325)
Q Consensus       308 e~~~~~kdG~~~~~~~~  324 (325)
                      |.+.++|||+.+|++++
T Consensus        84 e~~~~~kdG~~~~v~~~  100 (117)
T 2r78_A           84 ERTVWTRNGDQLTVELS  100 (117)
T ss_dssp             EEEEECTTSCEEEEEEE
T ss_pred             EEEEEecCCCEEEEEEE
Confidence            66778999999999875

>4dj2_A Period circadian protein homolog 1; PAS domains, circadian clock protein, protein binding; 2.75A {Mus musculus}

Probab=99.52  E-value=1.4e-13  Score=115.21  Aligned_cols=61  Identities=10%  Similarity=0.044  Sum_probs=52.4

Q ss_pred             CCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH------------hhccccCCCceeeEEe
Q 020514          263 DMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI------------AISPYPKKKSIYMEYV  323 (325)
Q Consensus       263 dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~------------e~~~~~kdG~~~~~~~  323 (325)
                      ||+++|+|+++..++||+++|++|+++.++++|++.....+.+.+            ++++++|||+.+|++.
T Consensus       185 dG~~~yvd~~~~~lLGY~peELig~s~~~~vHPdD~~~~~~~~~~~l~~~g~~~~~~~yR~~~kdG~~vwvet  257 (320)
T 4dj2_A          185 SCLFQDVDERAAPLLGYLPQDLLGAPVLLFLHPEDRPLMLAIHKKILQLAGQPFDHSPIRFCARNGEYVTMDT  257 (320)
T ss_dssp             TCBEEEECTTHHHHHSCCHHHHTTSBGGGGBCGGGHHHHHHHHHHHTTSSSCCEECCCEEEECSSSCEEEEEC
T ss_pred             CceEEEcCcceeccCCcChHHHcCCcHHHhCCHHHHHHHHHHHHHHHhcCCCcccceEEEEEccCCCEEEEEE
Confidence            799999999999999999999999999999999987766554443            5566789999999864

>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=99.52  E-value=3.1e-13  Score=96.31  Aligned_cols=108  Identities=10%  Similarity=0.117  Sum_probs=86.0

Q ss_pred             HHHHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEE
Q 020514           16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVN   95 (325)
Q Consensus        16 ~~~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e   95 (325)
                      ...+++.++++++++++++|.+   |.++++|+++++++||++++++|+++..+.++.....     ...+..+.....+
T Consensus        11 ~~~~~~~~~~~~~~~i~~~d~~---g~i~~~N~~~~~l~G~~~~el~g~~~~~~~~~~~~~~-----~~~~~~~~~~~~e   82 (118)
T 3olo_A           11 EFKFAHYLINNAVEASFCLGDN---WQFLYVNDATCRMTEYSREQLLSMNLQDIDVDFALHD-----WEEIRQKNNYTFK   82 (118)
T ss_dssp             HHHHHHHHHHHCSSEEEEECTT---SBEEEECHHHHHHHCCCHHHHTTCBGGGTBTTGGGSC-----HHHHHHHSEEEEE
T ss_pred             HHHHHHHHHhcCCceEEEECCC---CcEEEEHHHHHHHHCCCHHHHhCCChhhcccccCHHH-----HHHHHhcCcEEEE
Confidence            3346788999999999999999   9999999999999999999999999877765432222     2233445566778


Q ss_pred             EEEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccc
Q 020514           96 LLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV  134 (325)
Q Consensus        96 ~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIT  134 (325)
                      ....+++|..+|+.++..|+..  .+. .+++++++|||
T Consensus        83 ~~~~~~~g~~~~~~~~~~~~~~--~~~-~~~~~~~~DIT  118 (118)
T 3olo_A           83 TRYRSQSGRIFLVEMSLTFLED--QER-RFSCVFVREKS  118 (118)
T ss_dssp             EEEECTTCCEEEEEEEEEEEEE--TTE-EEEEEEEEEC-
T ss_pred             EEEEccCCCEEEEEEEEEEEEE--CCc-cEEEEEEEeCC
Confidence            8888999999999999999976  343 35678999997

>3mjq_A Uncharacterized protein; NESG, structural genomics, PSI-2, protein structure initiati northeast structural genomics consortium; 2.60A {Desulfitobacterium hafniense}

Probab=99.52  E-value=8.1e-14  Score=100.59  Aligned_cols=116  Identities=12%  Similarity=0.112  Sum_probs=88.2

Q ss_pred             HHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEEEEEEe
Q 020514           21 HEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYK  100 (325)
Q Consensus        21 ~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~  100 (325)
                      +.+++.++++++++|.+   |.++++|+++++++|++.++++|+++..++++.+.......+......+.. ..++....
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   999999999999999999999999887777776665555555555555544 67777888


Q ss_pred             cCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchhhhhcc
Q 020514          101 KDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG  143 (325)
Q Consensus       101 ~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~~~~~  143 (325)
                      ++|..+|+.+...|...   +...+++++++|||++++++++.
T Consensus        78 ~~g~~~~~~~~~~~~~~---~~~~~~~~~~~DITe~k~a~~~~  117 (126)
T 3mjq_A           78 KEGTSIPAKARIWQGKW---HNEPCLFAIIKDLSKEERASSPP  117 (126)
T ss_dssp             TTSCEEEEEEEEEEEES---SSSEEEEEEEEECC---------
T ss_pred             cCCCEEEEEEEEEeeeE---CCceEEEEEEEechHHHHhhccc
Confidence            99999999999887754   33567899999999999985443

>4dj3_A Period circadian protein homolog 3; PAS domain, circadian rhythm, protein binding; 2.50A {Mus musculus}

Probab=99.51  E-value=8.2e-13  Score=110.41  Aligned_cols=62  Identities=8%  Similarity=0.081  Sum_probs=52.8

Q ss_pred             CCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH-------------hhccccCCCceeeEEe
Q 020514          262 PDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI-------------AISPYPKKKSIYMEYV  323 (325)
Q Consensus       262 ~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~-------------e~~~~~kdG~~~~~~~  323 (325)
                      .||+++|+|+++..++||+++|++|+++.++++|++.....+.+.+             ++++++|||+.+|++.
T Consensus       182 ~dG~~~yvs~~~~~lLGY~peELig~s~~~~vHPdD~~~~~~~~~~~l~~~~~~~f~s~~yR~~~kdG~~vwvet  256 (317)
T 4dj3_A          182 PGCVFLEVDERAVPLLGYLPQDLIGTSILTYLHPEDRPLMVAIHQKVLKYAGHPPFEHSPVRFCTQNGEYVILDS  256 (317)
T ss_dssp             TTSBEEEECTTHHHHHSCCHHHHTTSBGGGGBCTTTTTHHHHHHHHHHHTTTSCCEECCCEEEECTTSCEEEEEE
T ss_pred             CCCeEEEEChHHhhhcCcChHHHcCCCHHHeECHHHHHHHHHHHHHHHHcCCCccccceEEEEEccCCCEEEEEE
Confidence            3799999999999999999999999999999999988766554433             3466789999999974

>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=99.51  E-value=2.8e-14  Score=104.54  Aligned_cols=80  Identities=33%  Similarity=0.704  Sum_probs=64.7

Q ss_pred             hhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH----------hhccccC
Q 020514          245 ISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI----------AISPYPK  314 (325)
Q Consensus       245 ~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~----------e~~~~~k  314 (325)
                      .++++++++|+++|.+++||+|+|+|++|++|+||+++|++|+++..+.+|.........+.+          +++.++|
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            468889999999998644569999999999999999999999999888877776655554443          5667889


Q ss_pred             CCceeeEEee
Q 020514          315 KKSIYMEYVR  324 (325)
Q Consensus       315 dG~~~~~~~~  324 (325)
                      ||+.+|++++
T Consensus        83 dG~~~~~~~~   92 (132)
T 2pr5_A           83 DGTMFWNELN   92 (132)
T ss_dssp             TSCEEEEEEE
T ss_pred             CCCeeeeEEE
Confidence            9999999875

>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=99.51  E-value=6.8e-13  Score=95.97  Aligned_cols=119  Identities=13%  Similarity=0.170  Sum_probs=85.3

Q ss_pred             hhHHhhhhhhHHHHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhc--CCCCCcccCCCCChHHHHHHH
Q 020514            6 GLIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEII--GRNGRMFQGPRTNRRTIMEIR   83 (325)
Q Consensus         6 ~~~~~~~~~~~~~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~--g~~~~~l~~~~~~~~~~~~~~   83 (325)
                      ...++++. ....+|+.++++++++++++|.+   |.++++|+++++++||++++++  |++...+++  +.......+.
T Consensus         6 ~~~e~~L~-~~~~~~~~l~e~~~~~i~~~d~~---g~i~~~N~a~~~~~G~~~~el~g~g~~~~~~~~--~~~~~~~~~~   79 (126)
T 3bwl_A            6 KRREKRLE-ETSSRLEALFENSPDMIDVLDAD---GTICEVNQRFCAELGYDESEVLGRSIWEFDLMF--DAEDVQTQLS   79 (126)
T ss_dssp             HHHHHHHH-HHHHHHHHHHHHCSSEEEEECTT---CBEEEECHHHHHHHTCCGGGTTTSBGGGTBTTC--CHHHHHHHHH
T ss_pred             HHHHHHHH-HHHHHHHHHHhhCCcEEEEEcCC---CCEEEEcHHHHHHhCCCHHHHhhCCCchhhccC--CHHHHHHHHH
Confidence            44555565 66778999999999999999999   9999999999999999999994  565555554  2222211111


Q ss_pred             HHHHhCCCeEEEEEEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccc
Q 020514           84 EAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV  134 (325)
Q Consensus        84 ~~~~~~~~~~~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIT  134 (325)
                      . ...+.....+..+.+++|..+|+.++..++..  +|.. .++++.+|||
T Consensus        80 ~-~~~~~~~~~e~~~~~~dG~~~~~~~~~~~~~~--~~~~-~~~~~~~DIT  126 (126)
T 3bwl_A           80 G-FSVDERRKFEGLYERRDGSTMSVEVHLLRFNL--EGED-RFLAISRDIT  126 (126)
T ss_dssp             T-CCTTCEEEEEEEEECTTSCEEEEEEEEEEEEE--TTEE-EEEEEEEEC-
T ss_pred             H-HhcCCCcceEEEEEeCCCCEEEEEEEeEEEec--CCcE-EEEEEEEeCC
Confidence            1 11223344566677899999999988888754  4554 5678899997

>2vlg_A Sporulation kinase A; histidine kinase, two-component regulatory system, two-component signal transduction, transferase, phosphorylation, SCOD; 1.7A {Bacillus subtilis}

Probab=99.51  E-value=1.1e-14  Score=103.12  Aligned_cols=76  Identities=13%  Similarity=0.078  Sum_probs=62.8

Q ss_pred             hhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH-------hhccccCCCce
Q 020514          246 SLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI-------AISPYPKKKSI  318 (325)
Q Consensus       246 ~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~-------e~~~~~kdG~~  318 (325)
                      ++++++++|+++|.   ||+|+|+|+++++++||+++|++|+++.++++|++.......+..       +++.++|||+.
T Consensus         4 lle~~~d~i~v~d~---~G~i~yvn~~~~~~lGy~~~el~G~~~~~~ihp~D~~~~~~~~~~~~~~~~~e~r~~~kdG~~   80 (111)
T 2vlg_A            4 PLQTKTDIHAVLAS---NGRIIYISANSKLHLGYLQGEMIGSFLKTFLHEEDQFLVESYFYNEHHLMPCTFRFIKKDHTI   80 (111)
T ss_dssp             -----CCEEEEECT---TSBEEEECTTHHHHHSCCHHHHTTSBGGGGBCGGGHHHHHHHHHCSCCSSCEEEEEECTTSCE
T ss_pred             hhhcCCCEEEEEcC---CCeEEEEChHHHHHhCCCHHHHcCCcHHHeECHhHHHHHHHHHhccCCCccEEEEEEcCCCCE
Confidence            67888999999997   589999999999999999999999999999999988776665543       67778999999


Q ss_pred             eeEEee
Q 020514          319 YMEYVR  324 (325)
Q Consensus       319 ~~~~~~  324 (325)
                      +|++++
T Consensus        81 ~wve~~   86 (111)
T 2vlg_A           81 VWVEAA   86 (111)
T ss_dssp             EEEEEE
T ss_pred             EEEEEE
Confidence            999875

>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=99.50  E-value=1.6e-13  Score=98.30  Aligned_cols=116  Identities=9%  Similarity=0.060  Sum_probs=95.0

Q ss_pred             hHHHHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCC--CCcccCCCCChHHHHHHHHHHHhCCCe
Q 020514           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRN--GRMFQGPRTNRRTIMEIREAIREERPI   92 (325)
Q Consensus        15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~--~~~l~~~~~~~~~~~~~~~~~~~~~~~   92 (325)
                      ....+++.+++.++.+++++|.+  ++.++++|++++.++|++.+++.|.+  +..++++++...+...+.. +..+...
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            44568899999999999999976  47899999999999999999999876  4445555554444444444 5566777


Q ss_pred             EEEEEEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccc
Q 020514           93 EVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV  134 (325)
Q Consensus        93 ~~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIT  134 (325)
                      ..++....++|...|+.+...|+.+ .+|.+.+++++.+|||
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            8888888899999999999999998 8999999999999997

>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=99.50  E-value=1e-12  Score=95.80  Aligned_cols=115  Identities=26%  Similarity=0.486  Sum_probs=96.9

Q ss_pred             HHHHHHHhhCCCEEEEEcC---CCCCCCEEEechHHHHhcCCChhhhcCCC--CCcccCCCCChHHHHHHHHHHHhCCCe
Q 020514           18 LWVHEALDELPDSFTITDP---SISGHPIVFASRGFLKMSGFSRAEIIGRN--GRMFQGPRTNRRTIMEIREAIREERPI   92 (325)
Q Consensus        18 ~~~~~~~~~~~~~i~~~d~---~~~~~~~~~~N~~~~~~~G~~~~ei~g~~--~~~l~~~~~~~~~~~~~~~~~~~~~~~   92 (325)
                      ..+...++.++.+++++|.   +   +.++++|+++++++|++.++++|++  ...+.++.........+...+..+..+
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            3455677889999999999   8   9999999999999999999999998  455555555555556666667777777


Q ss_pred             EEEEEEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccc
Q 020514           93 EVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSR  136 (325)
Q Consensus        93 ~~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~  136 (325)
                      ..+.....++|..+|+.++..|+.+ .+|.+.+++++.+|||++
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            7788888899999999999999998 789999999999999975

>3gdi_A Period circadian protein homolog 2; tandem PAS domains, biological rhythms, cytoplasm, nucleus, phosphoprotein, transcription; 2.40A {Mus musculus}

Probab=99.48  E-value=4.2e-13  Score=111.86  Aligned_cols=62  Identities=10%  Similarity=0.030  Sum_probs=52.1

Q ss_pred             CCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH------------hhccccCCCceeeEEe
Q 020514          262 PDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI------------AISPYPKKKSIYMEYV  323 (325)
Q Consensus       262 ~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~------------e~~~~~kdG~~~~~~~  323 (325)
                      .||+++|+|+++..++||.++|++|+++.++++|++.....+.+.+            ++++++|||+.+|++.
T Consensus       173 ~dG~~~yvd~~~~~lLGY~peELig~s~~~~iHpdD~~~~~~~~~~~l~~~g~~~~~~~yR~~~kdG~~vwvet  246 (309)
T 3gdi_A          173 PNCLFQAVDERAVPLLGYLPQDLIETPVLVQLHPSDRPLMLAIHKKILQAGGQPFDYSPIRFRTRNGEYITLDT  246 (309)
T ss_dssp             TTCBEEEECTTHHHHHSCCHHHHTTSBHHHHBCTTSHHHHHHHHHHHHHTTTCCEEEEEEEEECTTSCEEEEEE
T ss_pred             CCCeEEEECcccccccCcCHHHHcCCCHHHhCCHHHHHHHHHHHHHHHhcCCceeeceEEEEEccCCCEEEEEE
Confidence            3799999999999999999999999999999999987655444433            3666789999999864

>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=99.48  E-value=2.9e-14  Score=104.12  Aligned_cols=80  Identities=23%  Similarity=0.181  Sum_probs=63.5

Q ss_pred             hhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHH---HH-----------
Q 020514          242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQV---SI-----------  307 (325)
Q Consensus       242 ~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~---~~-----------  307 (325)
                      .++.++++++++|+++|.   +|+|+++|+++++|+||+++|++|+++..+.+++........+   ..           
T Consensus        17 ~~~~l~~~~~d~i~~~d~---~g~i~~~N~a~~~l~Gy~~~eliG~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   93 (130)
T 1d06_A           17 HLRSILDTVPDATVVSAT---DGTIVSFNAAAVRQFGYAEEEVIGQNLRILMPEPYRHEHDGYLQRYMATGEKRIIGIDR   93 (130)
T ss_dssp             CHHHHHTTCSSEEEEEET---TSBEEEECHHHHHHHCCCHHHHTTSBGGGGSCTTHHHHHHHHHHHHHHHCCCSSTTSCE
T ss_pred             HHHHHHhhCcCeEEEECC---CCeEEEEcHHHHHHHCCCHHHHcCCcHHHHCCchhHHHHHHHHHHHHhcCCccccCCee
Confidence            467789999999999998   4799999999999999999999999999888665433222222   11           


Q ss_pred             hhccccCCCceeeEEee
Q 020514          308 AISPYPKKKSIYMEYVR  324 (325)
Q Consensus       308 e~~~~~kdG~~~~~~~~  324 (325)
                      ++..++|||+.+|++++
T Consensus        94 e~~~~~kdG~~~~~~~~  110 (130)
T 1d06_A           94 VVSGQRKDGSTFPMKLA  110 (130)
T ss_dssp             EEEEECTTSCEEEEEEE
T ss_pred             EEEEEeCCCCEEEEEEE
Confidence            34457899999999875

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

Probab=99.46  E-value=3.2e-12  Score=89.00  Aligned_cols=107  Identities=27%  Similarity=0.520  Sum_probs=88.0

Q ss_pred             CEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCC--CCcccCCCCChHHHHHHHHHHHhCCCeEEEEEEEecCCCeE
Q 020514           29 DSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRN--GRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPF  106 (325)
Q Consensus        29 ~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~--~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg~~~  106 (325)
                      .+++++|....++.++++|+++++++|++.++++|++  ...+.++.........+...+..+.....+.....++|..+
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            5788888632238999999999999999999999998  44455555555556666777777777888888888999999


Q ss_pred             EEEEEEEEeecCCCCeeeEEEEEEeccccc
Q 020514          107 WMLFKMSLVFGKEDGRATHFVAVQVPIVSR  136 (325)
Q Consensus       107 ~~~~~~~~~~~~~~g~~~~~~~~~~DITe~  136 (325)
                      |+.++..|+.+ .+|.+.+++++.+|||++
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 789999999999999985

>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=99.46  E-value=4.3e-13  Score=101.78  Aligned_cols=122  Identities=20%  Similarity=0.248  Sum_probs=85.3

Q ss_pred             HHHHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCC----
Q 020514           16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERP----   91 (325)
Q Consensus        16 ~~~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~----   91 (325)
                      ....+..+++.++.+++++|.+   |.++++|++++.++|++.++++|+++..++++.........+......+..    
T Consensus        38 ~~~~~~~~l~~~~~~i~~~d~~---g~i~~~N~~~~~l~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  114 (167)
T 1v9y_A           38 ADGIFFPALEQNMMGAVLINEN---DEVMFFNPAAEKLWGYKREEVIGNNIDMLIPRDLRPAHPEYIRHNREGGKARVEG  114 (167)
T ss_dssp             --CCHHHHHHTCSSEEEEECTT---SBEEEECHHHHHHHSCCGGGTTTSBGGGGSCGGGTTTHHHHHHHHHC--------
T ss_pred             hhHHHHHHHHhCCCCEEEECCC---CcEEEECHHHHHHhCCCHHHHcCCChhhccCccccchHHHHHHHHhhcCCCcccc
Confidence            4457889999999999999999   999999999999999999999999887777665554444444444444322    


Q ss_pred             eEEEEEEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchhhhhcc
Q 020514           92 IEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG  143 (325)
Q Consensus        92 ~~~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~~~~~  143 (325)
                      +..+.....++|..+|+.+...|+.  .+|.+. ++++++|||+++++++++
T Consensus       115 ~~~~~~~~~~~g~~~~~~~~~~~~~--~~g~~~-~~~~~~DiT~~~~~e~~l  163 (167)
T 1v9y_A          115 MSRELQLEKKDGSKIWTRFALSKVS--AEGKVY-YLALVRDASVEMAQKEQT  163 (167)
T ss_dssp             --CEEEEECTTSCEEEEEEEEEEEE--ETTEEE-EEEEEEC-----------
T ss_pred             cceEEEEEcCCCcEEEEEEEEEEEe--cCCCEE-EEEEEecCcHHHHHHHHH
Confidence            3446677788999999999999995  467664 889999999999875443

>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=99.44  E-value=1.4e-13  Score=99.09  Aligned_cols=78  Identities=8%  Similarity=0.050  Sum_probs=66.3

Q ss_pred             HhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH-----------hhccc
Q 020514          244 YISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI-----------AISPY  312 (325)
Q Consensus       244 ~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~-----------e~~~~  312 (325)
                      ..+++++++.|++.|.   ||+|+|+|+++++++||+++|++|+++..+++|++.......+.+           +++.+
T Consensus         5 ~ll~e~~~d~i~~~d~---~g~i~~~n~~~~~~~G~~~~el~g~~~~~~i~p~d~~~~~~~~~~~~~~~~~~~~~e~r~~   81 (121)
T 3f1p_B            5 GLNVCQPTRFISRHNI---EGIFTFVDHRCVATVGYQPQELLGKNIVEFCHPEDQQLLRDSFQQVVKLKGQVLSVMFRFR   81 (121)
T ss_dssp             ---CCCCCEEEEEECT---TSBEEEECTTHHHHHSCCGGGTTTSBGGGGBCTTTHHHHHHHHHHHTTSTTCCEEEEEEEE
T ss_pred             cceecCCCceEEEECC---CceEEEECcchhhhhCCChHHHcCCCHHHeECHHHHHHHHHHHHHHHhcCCCcccEEEEEE
Confidence            3478889999999998   579999999999999999999999999999999988776665544           77788


Q ss_pred             cCCCceeeEEee
Q 020514          313 PKKKSIYMEYVR  324 (325)
Q Consensus       313 ~kdG~~~~~~~~  324 (325)
                      ++||+.+|++.+
T Consensus        82 ~~dG~~~w~~~~   93 (121)
T 3f1p_B           82 SKNQEWLWMRTS   93 (121)
T ss_dssp             CTTSCEEEEEEE
T ss_pred             ecCCCEEEEEEE
Confidence            999999999865

>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=99.43  E-value=2.9e-12  Score=95.50  Aligned_cols=106  Identities=34%  Similarity=0.562  Sum_probs=91.0

Q ss_pred             HHHhhCCCEEEEEc---CCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCC-----------ChHHHHHHHHHHH
Q 020514           22 EALDELPDSFTITD---PSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRT-----------NRRTIMEIREAIR   87 (325)
Q Consensus        22 ~~~~~~~~~i~~~d---~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~-----------~~~~~~~~~~~~~   87 (325)
                      .+++.. .+++++|   .+   |.++++|+++++++||+.++++|+++..+.++..           .......+...+.
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   68   9999999999999999999999999887777663           5555667777788


Q ss_pred             hCCCeEEEEEEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEec
Q 020514           88 EERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVP  132 (325)
Q Consensus        88 ~~~~~~~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~D  132 (325)
                      .+..+..+....+++|..+|+.++..|+.+ .+|.+.+++++.+|
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            888888888888999999999999999998 88999999998876

>3mfx_A Sensory BOX/ggdef family protein; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.40A {Shewanella oneidensis}

Probab=99.42  E-value=1.8e-12  Score=94.34  Aligned_cols=113  Identities=11%  Similarity=0.065  Sum_probs=83.3

Q ss_pred             HHHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCC------
Q 020514           17 TLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREER------   90 (325)
Q Consensus        17 ~~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~------   90 (325)
                      ...+..++++++++++++|.+   |.++++|+++++++||++++++|+++..++++.+.......+......+.      
T Consensus         6 ~~~l~~i~~~~~d~i~~~D~~---g~I~~~N~aa~~l~G~~~~el~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (129)
T 3mfx_A            6 LETIELFIQHLTEAMILVNAN---GFIRSCNQRSAELLDCPQVSLKGQDWRNFLTEHHQARYDNLLSHDVQLGTNCGQPV   82 (129)
T ss_dssp             HHHHHHHHTTCSSEEEEEETT---SBEEEECHHHHHHTTSCHHHHTTSBGGGGBCTTCCGGGGCTTC----------CCS
T ss_pred             HHHHHHHHhcCCceEEEECCC---CEEEeEhHHHHHHHCcCHHHHcCCcHHHHcChHhHHHHHHHHHHHHhcCccccccc
Confidence            346888999999999999999   99999999999999999999999998888877654432211111111111      


Q ss_pred             -CeEEEEEEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccc
Q 020514           91 -PIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSR  136 (325)
Q Consensus        91 -~~~~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~  136 (325)
                       ....++...++||..+|+.++++|+.+  ++.  .++++++|+...
T Consensus        83 ~~~~~E~~~~rkdG~~~~velsis~i~~--~~~--~~v~~~~~~~~~  125 (129)
T 3mfx_A           83 QHPAQETTLICASGKAKDVELSISYIPG--HEP--MFVMVMHDLEHH  125 (129)
T ss_dssp             CEEEEEEEEECTTSCEEEEEEEEEEECS--SSC--EEEEEEEEC---
T ss_pred             CCCceEEEEEcCCCCEEEEEEEEEEecC--CCc--EEEEEEechhhh
Confidence             234678888999999999999999974  222  367888887543

>3mfx_A Sensory BOX/ggdef family protein; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.40A {Shewanella oneidensis}

Probab=99.41  E-value=1.1e-13  Score=100.76  Aligned_cols=82  Identities=6%  Similarity=0.017  Sum_probs=65.9

Q ss_pred             hhhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHH---H----H-------
Q 020514          241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQ---V----S-------  306 (325)
Q Consensus       241 ~~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~---~----~-------  306 (325)
                      ..|..+++++++||+++|.   +|+|+++|+++++|+||++++++|+++.++++++........   +    .       
T Consensus         7 ~~l~~i~~~~~d~i~~~D~---~g~I~~~N~aa~~l~G~~~~el~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~   83 (129)
T 3mfx_A            7 ETIELFIQHLTEAMILVNA---NGFIRSCNQRSAELLDCPQVSLKGQDWRNFLTEHHQARYDNLLSHDVQLGTNCGQPVQ   83 (129)
T ss_dssp             HHHHHHHTTCSSEEEEEET---TSBEEEECHHHHHHTTSCHHHHTTSBGGGGBCTTCCGGGGCTTC----------CCSC
T ss_pred             HHHHHHHhcCCceEEEECC---CCEEEeEhHHHHHHHCcCHHHHcCCcHHHHcChHhHHHHHHHHHHHHhcCcccccccC
Confidence            3477899999999999998   479999999999999999999999999999877654321110   0    0       


Q ss_pred             ---HhhccccCCCceeeEEeeC
Q 020514          307 ---IAISPYPKKKSIYMEYVRV  325 (325)
Q Consensus       307 ---~e~~~~~kdG~~~~~~~~~  325 (325)
                         .|+..++|||+.+|+++++
T Consensus        84 ~~~~E~~~~rkdG~~~~velsi  105 (129)
T 3mfx_A           84 HPAQETTLICASGKAKDVELSI  105 (129)
T ss_dssp             EEEEEEEEECTTSCEEEEEEEE
T ss_pred             CCceEEEEEcCCCCEEEEEEEE
Confidence               1666788999999998863

>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=99.41  E-value=5.1e-13  Score=96.28  Aligned_cols=108  Identities=10%  Similarity=0.081  Sum_probs=74.4

Q ss_pred             HHHHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEE
Q 020514           16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVN   95 (325)
Q Consensus        16 ~~~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e   95 (325)
                      ...+++.+++.++++++++|.+   |.++++|+++++++|+++++++|+++..++++................+...   
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            5568899999999999999999   9999999999999999999999999887773222222222223444444433   


Q ss_pred             EEEEecCCC-eEEEEEEEEEeecCCCCeeeEEEEEEeccc
Q 020514           96 LLNYKKDGT-PFWMLFKMSLVFGKEDGRATHFVAVQVPIV  134 (325)
Q Consensus        96 ~~~~~~dg~-~~~~~~~~~~~~~~~~g~~~~~~~~~~DIT  134 (325)
                         ...+|. ..|+.++..|+.+  +|...+++++++|||
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 6788999999876  566788999999997

>4hia_A LOV protein; PAS, HTH, signaling protein; HET: FMN; 1.95A {Rhodobacter sphaeroides} PDB: 4hnb_A* 4hj4_A* 4hj6_A* 4hj3_A*

Probab=99.39  E-value=7e-13  Score=101.97  Aligned_cols=84  Identities=25%  Similarity=0.505  Sum_probs=71.9

Q ss_pred             hhhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH----------hhc
Q 020514          241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI----------AIS  310 (325)
Q Consensus       241 ~~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~----------e~~  310 (325)
                      ..++.++++++++|+++|.+.+||+|+++|++|++++||++++++|+++..+.++.........+.+          ++.
T Consensus         7 ~~~~~~~~~~~~~i~~~d~~~~~g~i~~~N~a~~~~~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~   86 (176)
T 4hia_A            7 EKIRAVFDRSGVALTLVDMSLPEQPVVLANPPFLRMTGYTEGQILGFNCRFLQRGDENAQARADIRDALKLGRELQVVLR   86 (176)
T ss_dssp             HHHHHHHHHCSSCCEEEETTSTTCCEEEECHHHHHHHTCCHHHHTTSCGGGGCCTTCCHHHHHHHHHHHHHTCCEEEEEE
T ss_pred             HHHHHHHhcCCCcEEEEecCCCCCcEEEECHHHHHHHCcCHHHHcCCCcceeeCCCCCHHHHHHHHHHHHcCCceEEEEE
Confidence            3477889999999999998644589999999999999999999999999999988887776666554          666


Q ss_pred             cccCCCceeeEEee
Q 020514          311 PYPKKKSIYMEYVR  324 (325)
Q Consensus       311 ~~~kdG~~~~~~~~  324 (325)
                      .+++||+.+|+.++
T Consensus        87 ~~~~dG~~~~~~~~  100 (176)
T 4hia_A           87 NYRANDEPFDNLLF  100 (176)
T ss_dssp             EECTTCCEEEEEEE
T ss_pred             EEcCCCCEEEEEEE
Confidence            78899999999865

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

Probab=99.37  E-value=1.6e-12  Score=106.71  Aligned_cols=85  Identities=31%  Similarity=0.481  Sum_probs=72.9

Q ss_pred             hhhhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH----------hh
Q 020514          240 SSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI----------AI  309 (325)
Q Consensus       240 ~~~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~----------e~  309 (325)
                      ...|+.++++++++|+++|....||+|+++|++|++++||+++|++|+++.++.+|.........+.+          ++
T Consensus        62 ~~~~~~i~~~~~~~i~~~d~~~~~g~i~~~N~a~~~l~G~~~~el~g~~~~~l~~~~~~~~~~~~~~~~l~~~~~~~~e~  141 (258)
T 3p7n_A           62 AQWVLDLIEASPIASVVSDPRLADNPLIAINQAFTDLTGYSEEECVGRNCRFLAGSGTEPWLTDKIRQGVREHKPVLVEI  141 (258)
T ss_dssp             CHHHHHHHHTCSSEEEEECTTSTTCCEEEECHHHHHHHCCCGGGTTTSCGGGGCCTTCCHHHHHHHHHHHHHTCCEEEEE
T ss_pred             HHHHHHHHhcCCccEEEEcCCCCCCcEEEEhHHHHHHcCCCHHHHCCCChhhccCCCCchhHHHHHHHHHHcCCCeEEEE
Confidence            34578899999999999998433579999999999999999999999999999988888777666654          67


Q ss_pred             ccccCCCceeeEEee
Q 020514          310 SPYPKKKSIYMEYVR  324 (325)
Q Consensus       310 ~~~~kdG~~~~~~~~  324 (325)
                      +.+++||+.+|+.++
T Consensus       142 ~~~~~dG~~~~~~~~  156 (258)
T 3p7n_A          142 LNYKKDGTPFRNAVL  156 (258)
T ss_dssp             EEECTTSCEEEEEEE
T ss_pred             EEEcCCCCEEEEeeE
Confidence            778999999999875

>3vol_A Aerotaxis transducer AER2; heme, oxygen sensor protein, PAS, HAMP, cyanoMet, CN-bound, protein; HET: HEM; 2.40A {Pseudomonas aeruginosa}

Probab=99.36  E-value=1.1e-11  Score=99.95  Aligned_cols=110  Identities=15%  Similarity=0.197  Sum_probs=84.6

Q ss_pred             HHHHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhc------------CCChhhhcCCCCCcccCCCCChHHHHHHH
Q 020514           16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMS------------GFSRAEIIGRNGRMFQGPRTNRRTIMEIR   83 (325)
Q Consensus        16 ~~~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~------------G~~~~ei~g~~~~~l~~~~~~~~~~~~~~   83 (325)
                      ...++..++++++.+++++|.+   |+++++|+++++++            ||++++++|+++..+++.   +.....+.
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            3457889999999999999999   99999999999998            899999999998776643   22222222


Q ss_pred             HHHHhCCCeEEEEEEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchhh
Q 020514           84 EAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM  139 (325)
Q Consensus        84 ~~~~~~~~~~~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~  139 (325)
                      ..+.  ..+..++   ..+|  .|+.+++.|+.+ .+|.+.|++++++|||+++++
T Consensus        94 ~~~~--~~~~~~~---~~~g--~~~~~~~~Pi~d-~~G~~~g~v~~~~DITe~~~~  141 (233)
T 3vol_A           94 ANLT--GVHKAEL---NLGG--RRFSLDVVPVFN-DANERLGSAVQWTDRTEEHRA  141 (233)
T ss_dssp             HTCC--SCEEEEE---EETT--EEEEEEEEEEEC-TTCCEEEEEEEEEECHHHHHH
T ss_pred             Hhcc--cceeEEE---EECC--EEEEEEEEEEEC-CCCCEEEEEEEEehhhHHHHH
Confidence            2211  2233332   2345  367899999998 899999999999999999985

>2kdk_A ARYL hydrocarbon receptor nuclear translocator-LI 2; circadian clock, PAS domain, transcription, activator, biolo rhythms, DNA-binding, nucleus; NMR {Homo sapiens}

Probab=99.35  E-value=8.3e-13  Score=94.80  Aligned_cols=79  Identities=13%  Similarity=0.050  Sum_probs=65.7

Q ss_pred             hHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH-----------hhcc
Q 020514          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI-----------AISP  311 (325)
Q Consensus       243 l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~-----------e~~~  311 (325)
                      ...++++++++|+++|.   ||+|+++|+++++++||+++|++|+++..+++|++.......+.+           +++.
T Consensus         5 ~~~~~~~~~~~i~~~d~---~g~i~~~N~~~~~~~G~~~~el~g~~~~~~~~p~d~~~~~~~~~~~~~~~~~~~~~e~r~   81 (121)
T 2kdk_A            5 SGEINVKPTEFITRFAV---NGKFVYVDQRATAILGYLPQELLGTSCYEYFHQDDHNNLTDKHKAVLQSKEKILTDSYKF   81 (121)
T ss_dssp             TTCCCCCSSEEEEEECT---TSBEEEECTHHHHHTCCCTTTSBTSBTTTTBCSSSHHHHHHHHHHHHTSSSCEEEEEEEE
T ss_pred             ccccccCCccEEEEECC---CeeEEEEChhHHHHHCCCHHHHcCCcHHHeeCHHHHHHHHHHHHHHHhCCCCCccEEEEE
Confidence            34567888999999998   479999999999999999999999999999888876655544443           5667


Q ss_pred             ccCCCceeeEEee
Q 020514          312 YPKKKSIYMEYVR  324 (325)
Q Consensus       312 ~~kdG~~~~~~~~  324 (325)
                      ++|||+.+|++++
T Consensus        82 ~~~dG~~~~~~~~   94 (121)
T 2kdk_A           82 RAKDGSFVTLKSQ   94 (121)
T ss_dssp             ECSSSCEEEEEEE
T ss_pred             EEcCCCEEEEEEE
Confidence            7899999999764

>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=99.35  E-value=2.1e-12  Score=93.31  Aligned_cols=78  Identities=19%  Similarity=0.020  Sum_probs=59.7

Q ss_pred             hhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccc--cccccccccCCCCChHHHHHHHH---------hhc
Q 020514          242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEV--VGQNCRFLNGVDTDTTVLYQVSI---------AIS  310 (325)
Q Consensus       242 ~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~--iG~~~~~l~~~~~~~~~~~~~~~---------e~~  310 (325)
                      .++.++++++++|+++|.   ||+|+++|+++++++||+++|+  +|+++..+.+  ........+..         +..
T Consensus        18 ~~~~l~e~~~~~i~~~d~---~g~i~~~N~a~~~~~G~~~~el~g~g~~~~~~~~--~~~~~~~~~~~~~~~~~~~~e~~   92 (126)
T 3bwl_A           18 RLEALFENSPDMIDVLDA---DGTICEVNQRFCAELGYDESEVLGRSIWEFDLMF--DAEDVQTQLSGFSVDERRKFEGL   92 (126)
T ss_dssp             HHHHHHHHCSSEEEEECT---TCBEEEECHHHHHHHTCCGGGTTTSBGGGTBTTC--CHHHHHHHHHTCCTTCEEEEEEE
T ss_pred             HHHHHHhhCCcEEEEEcC---CCCEEEEcHHHHHHhCCCHHHHhhCCCchhhccC--CHHHHHHHHHHHhcCCCcceEEE
Confidence            366688999999999997   5799999999999999999999  5677777665  22223333222         445


Q ss_pred             cccCCCceeeEEee
Q 020514          311 PYPKKKSIYMEYVR  324 (325)
Q Consensus       311 ~~~kdG~~~~~~~~  324 (325)
                      ..+|||+.+|++++
T Consensus        93 ~~~~dG~~~~~~~~  106 (126)
T 3bwl_A           93 YERRDGSTMSVEVH  106 (126)
T ss_dssp             EECTTSCEEEEEEE
T ss_pred             EEeCCCCEEEEEEE
Confidence            56899999999764

>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=99.34  E-value=5.1e-12  Score=90.48  Aligned_cols=108  Identities=14%  Similarity=0.076  Sum_probs=84.8

Q ss_pred             HHHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEEE
Q 020514           17 TLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNL   96 (325)
Q Consensus        17 ~~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~   96 (325)
                      ....+.++++++++++++|.+   |+++++|+++++++|+++++++|+++..++++.........+..++..+.....++
T Consensus        11 ~~~~~~il~~~~~~i~~~D~~---g~i~~~N~a~~~l~g~~~~e~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   87 (118)
T 3fg8_A           11 SSGRENLYFQGGLGFMALDED---LRIIYVNSGCLRHVRRSRDELLGRVVTEVLPETQGSYFDALCRKVLATGREQQTRV   87 (118)
T ss_dssp             --CCCCSSSCTTCEEEEECTT---CBEEEECHHHHHHHTCCHHHHTTSBHHHHCGGGTTSHHHHHHHHHHHHCCCEEEEE
T ss_pred             cchHHHHHhhCCceEEEECCC---CeEEEECHHHHHHhCCCHHHHcCCcHHHHcCccchHHHHHHHHHHHHcCCceEEEE
Confidence            345667899999999999999   99999999999999999999999998877766655566667778888887776643


Q ss_pred             EEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccc
Q 020514           97 LNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSR  136 (325)
Q Consensus        97 ~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~  136 (325)
                      .....+|  .|+.++..|+.+       +++++++|||++
T Consensus        88 ~~~~~~g--~~~~~~~~p~~~-------g~v~~~~DITer  118 (118)
T 3fg8_A           88 DSLYSPG--MTIEVTAAADSG-------ALVVHFRDVTAE  118 (118)
T ss_dssp             ECSSSTT--CEEEEEEEEETT-------EEEEEEEECSCC
T ss_pred             EEEcCCC--eEEEEEEEEcCC-------cEEEEEEeccCC
Confidence            3333355  577788888753       377889999986

>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=99.33  E-value=1.1e-12  Score=93.93  Aligned_cols=72  Identities=17%  Similarity=0.180  Sum_probs=55.9

Q ss_pred             cCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHH---HHHH-----------hhccccCC
Q 020514          250 IKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLY---QVSI-----------AISPYPKK  315 (325)
Q Consensus       250 ~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~---~~~~-----------e~~~~~kd  315 (325)
                      ++++|+++|.   +|+|+++|+++++|+||+++|++|+++..+.++........   .+..           ++..++||
T Consensus         2 ~~d~i~~~d~---~g~i~~~N~a~~~l~G~~~~el~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d   78 (119)
T 2vv6_A            2 IPDAMIVIDG---HGIIQLFSTAAERLFGWSELEAIGQNVNILMPEPDRSRHDSYISRYRTTSDPHIIGIGRIVTGKRRD   78 (119)
T ss_dssp             CCCEEEEEET---TSBEEEECHHHHHHHCCCHHHHTTSBGGGGSCTTHHHHHHHHHHHHHHHCCCSSTTTCEEEEEECTT
T ss_pred             CcceEEEECC---CCeEEEEhHHHHHHhCCCHHHHcCCCHHHhCCchHHHHHHHHHHHHhcCCCcccCCCceEEEEEeCC
Confidence            5789999997   47999999999999999999999999988876554322221   2211           34557899


Q ss_pred             CceeeEEee
Q 020514          316 KSIYMEYVR  324 (325)
Q Consensus       316 G~~~~~~~~  324 (325)
                      |+.+|++++
T Consensus        79 G~~~~~~~~   87 (119)
T 2vv6_A           79 GTTFPMHLS   87 (119)
T ss_dssp             SCEEEEEEE
T ss_pred             CCEEEEEEE
Confidence            999999875

>4f3l_A Mclock, circadian locomoter output cycles protein kaput; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus}

Probab=99.33  E-value=2.7e-12  Score=110.27  Aligned_cols=108  Identities=8%  Similarity=0.097  Sum_probs=95.7

Q ss_pred             CCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEEEEEEecCCCeEE
Q 020514           28 PDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFW  107 (325)
Q Consensus        28 ~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg~~~~  107 (325)
                      ...++..+.+   |.++++|+++..++||++++++|+++..+++|++...+...+...+..+.....++++.+++|..+|
T Consensus       251 ~~f~~~~~~d---g~~~~vn~~~~~ilGY~~eEl~g~~~~~~iHpdD~~~~~~~~~~~l~~g~~~~~eyR~~~kdG~~vW  327 (361)
T 4f3l_A          251 EEFTSRHSLE---WKFLFLDHRAPPIIGYLPFEVLGTSGYDYYHVDDLENLAKCHEHLMQYGKGKSCYYRFLTKGQQWIW  327 (361)
T ss_dssp             CEEEEEECTT---SBEEEECTTSHHHHCCCHHHHTTSBGGGGBCHHHHHHHHHHHHHHHHHSEEECCCEEEECTTSEEEE
T ss_pred             ceeEEEEcCC---ceEEEECChhhhhhCcCHHHHcCCCHHHeECHHHHHHHHHHHHHHHhCCCcceEEEEEEecCCCEEE
Confidence            3455667888   9999999999999999999999999999999988887777788888887766678899999999999


Q ss_pred             EEEEEEEeecCC-CCeeeEEEEEEeccccchhh
Q 020514          108 MLFKMSLVFGKE-DGRATHFVAVQVPIVSRKHM  139 (325)
Q Consensus       108 ~~~~~~~~~~~~-~g~~~~~~~~~~DITe~k~~  139 (325)
                      +..+..|+.+ . +|.+.+++++.+|||+++..
T Consensus       328 v~~~~~~v~~-~~~g~~~~iv~~~~dITe~~~~  359 (361)
T 4f3l_A          328 LQTHYYITYH-QWNSRPEFIVCTHTVVSYAEVR  359 (361)
T ss_dssp             EEEEEEEEEC-TTTCCEEEEEEEEEECCHHHHH
T ss_pred             EEEEEEEEEc-CCCCCeeEEEEEEEECChhHhh
Confidence            9999999998 5 79999999999999999764

>2qkp_A Uncharacterized protein; structural genomics, unknown function, PSI-2, protein struct initiative; 1.75A {Streptococcus mutans}

Probab=99.32  E-value=2.5e-11  Score=90.61  Aligned_cols=115  Identities=13%  Similarity=0.127  Sum_probs=88.8

Q ss_pred             HHHHHHHhhCCCEEEEEcCCCCCCCEEEechH---HHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEE
Q 020514           18 LWVHEALDELPDSFTITDPSISGHPIVFASRG---FLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV   94 (325)
Q Consensus        18 ~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~---~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   94 (325)
                      ..+..++++++.++.++|.+   |.++++|++   +++++| ..++++|+++..+.++. .......+...+..+.....
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            46889999999999999999   999999999   999999 56789999987765432 22223445566666766555


Q ss_pred             EEEEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchhh
Q 020514           95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM  139 (325)
Q Consensus        95 e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~  139 (325)
                      ++.... .+...++.++..|+++ ++|.+.|.+.+++|||+.++.
T Consensus        94 ~~~~~~-~~~~~~v~v~~~Pi~d-~~G~~~G~vev~~Dit~l~~l  136 (151)
T 2qkp_A           94 NMWFQS-ERLGKFVYVTYAAVRD-QAGDFQGVLEYVQDIKPFFEL  136 (151)
T ss_dssp             EEEEEE-TTTTEEEEEEEEEEEC-TTCCEEEEEEEEEECGGGGGG
T ss_pred             EEEEec-CCCCeEEEEEEEEEEC-CCCCEEEEEEEEEECHHHHhh
Confidence            544432 3223567889999998 789999999999999999875

>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=99.32  E-value=1.4e-12  Score=93.10  Aligned_cols=71  Identities=15%  Similarity=0.146  Sum_probs=60.9

Q ss_pred             CCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH----------hhccccCCCceee
Q 020514          251 KQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI----------AISPYPKKKSIYM  320 (325)
Q Consensus       251 ~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~----------e~~~~~kdG~~~~  320 (325)
                      ++.|++.|+   ||+|+|+|+++++++||+++|++|+++..+++|++.......+.+          +++.++|||+.+|
T Consensus         9 ~~~i~~~d~---~g~i~~~n~~~~~~~Gy~~~el~g~~~~~~~~p~d~~~~~~~~~~~~~~~~~~~~e~r~~~~dG~~~w   85 (117)
T 3f1p_A            9 KTFLSEHSM---DMKFTYCDDRITELIGYHPEELLGRSAYEFYHALDSENMTKSHQNLCTKGQVVSGQYRMLAKHGGYVW   85 (117)
T ss_dssp             GEEEEEECT---TCBEEEECTHHHHHHCCCHHHHTTSBGGGGBCGGGHHHHHHHHHHHHHHSEEECCCEEEECTTSSEEE
T ss_pred             ccEEEEECC---CceEEEECcChhhhhCCCHHHHcCCchhheECHHHHHHHHHHHHHHHhCCCeeeeEEEEEecCCCEEE
Confidence            567778887   589999999999999999999999999999999887766655544          7788899999999


Q ss_pred             EEee
Q 020514          321 EYVR  324 (325)
Q Consensus       321 ~~~~  324 (325)
                      ++++
T Consensus        86 ~~~~   89 (117)
T 3f1p_A           86 LETQ   89 (117)
T ss_dssp             EEEE
T ss_pred             EEEe
Confidence            9765

>2vlg_A Sporulation kinase A; histidine kinase, two-component regulatory system, two-component signal transduction, transferase, phosphorylation, SCOD; 1.7A {Bacillus subtilis}

Probab=99.32  E-value=6.7e-12  Score=88.64  Aligned_cols=90  Identities=18%  Similarity=0.173  Sum_probs=69.1

Q ss_pred             HHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEEEEEEec
Q 020514           22 EALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKK  101 (325)
Q Consensus        22 ~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~  101 (325)
                      .++++++++++++|.+   |.++|+|+++.+++||++++++|+++..+++|++.......+.   ..+.....++++.++
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            4788999999999999   9999999999999999999999999888888887655443321   223334567888899


Q ss_pred             CCCeEEEEEEEEEeec
Q 020514          102 DGTPFWMLFKMSLVFG  117 (325)
Q Consensus       102 dg~~~~~~~~~~~~~~  117 (325)
                      ||..+|+.+++.++.+
T Consensus        77 dG~~~wve~~~~~v~~   92 (111)
T 2vlg_A           77 DHTIVWVEAAVEIVTT   92 (111)
T ss_dssp             TSCEEEEEEEEEEC--
T ss_pred             CCCEEEEEEEEEEEec
Confidence            9999999999999987

>4hi4_A Aerotaxis transducer AER2; PAS domain, diatomic GAS sensor, signaling protein; HET: HEM GOL; 2.30A {Pseudomonas aeruginosa}

Probab=99.31  E-value=5.1e-11  Score=85.62  Aligned_cols=104  Identities=17%  Similarity=0.233  Sum_probs=77.6

Q ss_pred             HHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcC------------CChhhhcCCCCCcccCCCCChHHHHHHHHH
Q 020514           18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSG------------FSRAEIIGRNGRMFQGPRTNRRTIMEIREA   85 (325)
Q Consensus        18 ~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G------------~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~   85 (325)
                      .+++.++++++++++++|.+   |+++++|+++++++|            ++.++++|+++..+++.   ....   ...
T Consensus         5 ~rl~~il~~~~~gviv~D~~---g~I~~~N~a~~~llg~~~~~i~~~~~g~~~~~~~G~~~~~~~~~---~~~~---~~~   75 (121)
T 4hi4_A            5 ARIASALDNVSANVMIADND---LNIIYMNRTVSEMLGRAEADIRKQLPNFDAGRLMGANIDVFHKN---PAHQ---RHL   75 (121)
T ss_dssp             HHHHHHHTTSSSEEEEEETT---CBEEEECHHHHHHHHHTHHHHHHHCTTCCGGGCTTCBGGGGCSS---HHHH---HHH
T ss_pred             HHHHHHHhcCCccEEEEcCC---CeEEEecHHHHHHHHHHHHHHHHhcCCCChHHhcCCCHHHhcCC---HHHH---HHH
Confidence            47889999999999999999   999999999999996            88899999987776642   1111   122


Q ss_pred             HHhC-CCeEEEEEEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccc
Q 020514           86 IREE-RPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSR  136 (325)
Q Consensus        86 ~~~~-~~~~~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~  136 (325)
                      +... ..+..++.   .+|.  ++.+++.|+.+ .+|.+.|++++++|||++
T Consensus        76 ~~~~~~~~~~~~~---~~~~--~~~~~~~pi~~-~~g~~~g~v~~~~DiTee  121 (121)
T 4hi4_A           76 LANLTGVHKAELN---LGGR--RFSLDVVPVFN-DANARLGSAVQWTDRTEE  121 (121)
T ss_dssp             HHHCSSCEEEEEE---ETTE--EEEEEEEEEEC-TTSCEEEEEEEEEECC--
T ss_pred             HhCcCCCcEEEEE---ECCE--EEEEEEEEEEC-CCCCEEEEEEEEEEecCC
Confidence            2222 23333322   2443  45788999998 789999999999999974

>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=99.30  E-value=6.3e-12  Score=88.75  Aligned_cols=79  Identities=38%  Similarity=0.725  Sum_probs=63.9

Q ss_pred             hhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH----------hhccccCC
Q 020514          246 SLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI----------AISPYPKK  315 (325)
Q Consensus       246 ~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~----------e~~~~~kd  315 (325)
                      ++++++++++++|...++|+|+++|++|++++||++++++|+++..+.++.........+.+          ++...+++
T Consensus         2 ~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (115)
T 4eet_B            2 SPEFIEKNFVITDPRLPDNPIIFASDGFLELTEYSREEILGRNARFLQGPETDQATVQKIRDAIRDQRETTVQLINYTKS   81 (115)
T ss_dssp             ---CCCCSEEEECTTSTTCCEEEECHHHHHHHCCCHHHHTTSCGGGGCCTTSCHHHHHHHHHHHHTTCCEEEEEEEECTT
T ss_pred             ccccCCCcEEEEcCCCCCCcEEEEcHHHHHHHCcCHHHHhCCCHHHhcCCCCChHHHHHHHHHHHcCCCcceEEEEecCC
Confidence            46788999999998322479999999999999999999999999988888877766555544          66667899


Q ss_pred             CceeeEEee
Q 020514          316 KSIYMEYVR  324 (325)
Q Consensus       316 G~~~~~~~~  324 (325)
                      |+.+|+.++
T Consensus        82 g~~~~~~~~   90 (115)
T 4eet_B           82 GKKFWNLLH   90 (115)
T ss_dssp             CCEEEEEEE
T ss_pred             CCEEEEEEE
Confidence            999998765

>4f3l_B BMAL1B; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus}

Probab=99.29  E-value=9.7e-12  Score=107.73  Aligned_cols=107  Identities=8%  Similarity=0.027  Sum_probs=88.8

Q ss_pred             CEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCC-eEEEEEEEecCCCeEE
Q 020514           29 DSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERP-IEVNLLNYKKDGTPFW  107 (325)
Q Consensus        29 ~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~-~~~e~~~~~~dg~~~~  107 (325)
                      ..++..+.+   |.++|+|+++..++||++++++|+++..+++|+|...+...+.+.+..+.. ...++++.+++|..+|
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            356677888   999999999999999999999999998999998877777777776655443 4568899999999999


Q ss_pred             EEEEEEEeecCCCCeeeEEEEEEeccccchh
Q 020514          108 MLFKMSLVFGKEDGRATHFVAVQVPIVSRKH  138 (325)
Q Consensus       108 ~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~  138 (325)
                      +..+..++.+..+|.+.+++++.+|||++|.
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

>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=99.29  E-value=2.9e-12  Score=91.18  Aligned_cols=78  Identities=10%  Similarity=0.132  Sum_probs=63.2

Q ss_pred             hHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH------hhccccCCC
Q 020514          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI------AISPYPKKK  316 (325)
Q Consensus       243 l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~------e~~~~~kdG  316 (325)
                      ++.++++++++|+++|.   +|+|+++|+++++++||++++++|+++.++.++..... +..+..      +....++||
T Consensus        15 ~~~~~~~~~~~i~~~d~---~g~i~~~N~~~~~l~G~~~~el~g~~~~~~~~~~~~~~-~~~~~~~~~~~~e~~~~~~~g   90 (118)
T 3olo_A           15 AHYLINNAVEASFCLGD---NWQFLYVNDATCRMTEYSREQLLSMNLQDIDVDFALHD-WEEIRQKNNYTFKTRYRSQSG   90 (118)
T ss_dssp             HHHHHHHCSSEEEEECT---TSBEEEECHHHHHHHCCCHHHHTTCBGGGTBTTGGGSC-HHHHHHHSEEEEEEEEECTTC
T ss_pred             HHHHHhcCCceEEEECC---CCcEEEEHHHHHHHHCCCHHHHhCCChhhcccccCHHH-HHHHHhcCcEEEEEEEEccCC
Confidence            55688999999999997   57999999999999999999999999988875433222 444444      677788999


Q ss_pred             ceeeEEee
Q 020514          317 SIYMEYVR  324 (325)
Q Consensus       317 ~~~~~~~~  324 (325)
                      +.+|+.++
T Consensus        91 ~~~~~~~~   98 (118)
T 3olo_A           91 RIFLVEMS   98 (118)
T ss_dssp             CEEEEEEE
T ss_pred             CEEEEEEE
Confidence            99998765

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

Probab=99.29  E-value=7.1e-12  Score=95.04  Aligned_cols=88  Identities=35%  Similarity=0.618  Sum_probs=73.2

Q ss_pred             ccchhhhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH---------
Q 020514          237 GFISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI---------  307 (325)
Q Consensus       237 ~~~~~~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~---------  307 (325)
                      ......+..++++++++|+++|...+||+|+++|++|++++||++++++|+++..+.++.........+..         
T Consensus        31 ~~~~~~~~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  110 (166)
T 3ue6_A           31 EDPDYSLVKALQMAQQNFVITDASLPDNPIVYASRGFLTLTGYSLDQILGRNCRFLQGPETDPRAVDKIRNAITKGVDTS  110 (166)
T ss_dssp             CCCCCHHHHHHHHTTSCEEEEETTSTTCCEEEECHHHHHHHCCCHHHHTTSCGGGGCCTTSCHHHHHHHHHHHHHTCCEE
T ss_pred             HHHHHHHHHHHhcCCceEEEEEccCCCCcEEEECHHHHHHhCcCHHHHcCCCHhheeCCCCCHHHHHHHHHHHhcCCceE
Confidence            34456788999999999999998423589999999999999999999999999988888877766665544         


Q ss_pred             -hhccccCCCceeeEEee
Q 020514          308 -AISPYPKKKSIYMEYVR  324 (325)
Q Consensus       308 -e~~~~~kdG~~~~~~~~  324 (325)
                       ++...++||+.+|+.++
T Consensus       111 ~e~~~~~~~g~~~~~~~~  128 (166)
T 3ue6_A          111 VCLLNYRQDGTTFWNLFF  128 (166)
T ss_dssp             EEEEEECTTSCEEEEEEE
T ss_pred             EEEEEEcCCCCEEEEEEE
Confidence             66667899999998765

>3mqq_A Transcriptional regulator, LUXR family; PAS domain, PSI, MCSG, structural genomics, center for structural genomics; 1.65A {Burkholderia thailandensis} PDB: 3mqo_A

Probab=99.29  E-value=2.1e-12  Score=92.60  Aligned_cols=79  Identities=11%  Similarity=0.104  Sum_probs=61.9

Q ss_pred             hhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCC-hHHHHHHHH----------hhc
Q 020514          242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTD-TTVLYQVSI----------AIS  310 (325)
Q Consensus       242 ~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~-~~~~~~~~~----------e~~  310 (325)
                      .|+.++++++++|++ +.   +|+|+++|++|++|+||++++++|+++..+++++.. ......+.+          |+.
T Consensus         4 ~~~~~~~~~~~~i~~-~~---~g~i~~~N~a~~~l~G~~~~el~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~   79 (120)
T 3mqq_A            4 DYKTAFHLAPIGLVL-SR---DRVIEDCNDELAAIFRCARADLIGRSFEVLYPSSDEFERIGERISPVMIAHGSYADDRI   79 (120)
T ss_dssp             CHHHHHHHCSSEEEE-EE---TTEEEEECHHHHHHTTSCHHHHTTCBGGGGSSSHHHHHHHHHHHHHHHHHHSCEEEEEE
T ss_pred             hHHHHHhcCCceEEE-ec---CCEEHHHHHHHHHHhCcCHHHhCCCchhhccCChhhHHHHHHHHHHHHhcCCcceEEEE
Confidence            377899999999964 54   589999999999999999999999999887755332 222222222          677


Q ss_pred             cccCCCceeeEEee
Q 020514          311 PYPKKKSIYMEYVR  324 (325)
Q Consensus       311 ~~~kdG~~~~~~~~  324 (325)
                      .+++||+.+|+.++
T Consensus        80 ~~~~dG~~~~~~~~   93 (120)
T 3mqq_A           80 MKRAGGELFWCHVT   93 (120)
T ss_dssp             EECTTSCEEEEEEE
T ss_pred             EEeCCCCEEEEEEE
Confidence            78999999999875

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

Probab=99.26  E-value=1.2e-11  Score=89.49  Aligned_cols=79  Identities=38%  Similarity=0.700  Sum_probs=66.2

Q ss_pred             hhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH----------hhccccCC
Q 020514          246 SLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI----------AISPYPKK  315 (325)
Q Consensus       246 ~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~----------e~~~~~kd  315 (325)
                      ++++++++|+++|...+||+|+++|++|++++||++++++|+++..+.++.........+..          ++...+++
T Consensus         2 ~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~g~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~   81 (128)
T 3t50_A            2 ASEFTLMPMLITNPHLPDNPIVFANPAFLKLTGYEADEVMGRNCRFLQGHGTDPAHVRAIKSAIAAEKPIDIDIINYKKS   81 (128)
T ss_dssp             CCCCCSSCEEEECTTSTTCCEEEECHHHHHHHCCCHHHHTTSCGGGGCCTTSCHHHHHHHHHHHHTTCCEEEEEEEECTT
T ss_pred             ccccCcccEEEecCCCCCCcEEEEcHHHHHHhCcCHHHHcCCCHhhhcCCccCHHHHHHHHHHHHcCCCceeEEEEEcCC
Confidence            46788999999998422579999999999999999999999999999888877766665544          66667899


Q ss_pred             CceeeEEee
Q 020514          316 KSIYMEYVR  324 (325)
Q Consensus       316 G~~~~~~~~  324 (325)
                      |..+|+.++
T Consensus        82 g~~~~~~~~   90 (128)
T 3t50_A           82 GEAFWNRLH   90 (128)
T ss_dssp             CCEEEEEEE
T ss_pred             CCEEEEEEE
Confidence            999998765

>1ll8_A PAS kinase; PAS domain, ligand binding, ligand screening, kinase regulation, transferase; NMR {Homo sapiens} SCOP: d.110.3.5

Probab=99.23  E-value=7.5e-12  Score=88.86  Aligned_cols=72  Identities=14%  Similarity=0.180  Sum_probs=55.9

Q ss_pred             cCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH---------------hhccccC
Q 020514          250 IKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI---------------AISPYPK  314 (325)
Q Consensus       250 ~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~---------------e~~~~~k  314 (325)
                      .+++|+++|.+  +|+|+++|+++++||||+++|++|+++.+++++..... ...+.+               ++..++|
T Consensus         7 ~~~~i~~~d~~--~g~I~~~N~aa~~l~G~~~~el~g~~~~~l~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~   83 (114)
T 1ll8_A            7 FNKAIFTVDAK--TTEILVANDKACGLLGYSSQDLIGQKLTQFFLRSDSDV-VEALSEEHMEADGHAAVVFGTVVDIISR   83 (114)
T ss_dssp             TTCEEEEEETT--TCBEEEECTTHHHHHTCCTTTTTTSBGGGGSSCTTTHH-HHHTTSSTTSSSSCSSCCCSSSEEECCT
T ss_pred             CCceEEEEECC--CCeEEEehHHHHHHhCCCHHHHcCCCHHHhcCcchhHH-HHHHHHHhhccCCcceeccCcEEEEEec
Confidence            45799999973  27999999999999999999999999999987764432 222211               2445679


Q ss_pred             CCceeeEEee
Q 020514          315 KKSIYMEYVR  324 (325)
Q Consensus       315 dG~~~~~~~~  324 (325)
                      ||+.+|++++
T Consensus        84 dG~~~~v~~~   93 (114)
T 1ll8_A           84 SGEKIPVSVW   93 (114)
T ss_dssp             TCCCEEEECC
T ss_pred             CCCEEEEEEE
Confidence            9999999875

>3b33_A Sensor protein; structural genomics, PAS domain, nitrogen regulation protein APC91440.4, PSI-2; HET: MSE; 1.83A {Vibrio parahaemolyticus rimd 2210633}

Probab=99.22  E-value=1.6e-10  Score=81.93  Aligned_cols=107  Identities=12%  Similarity=0.119  Sum_probs=81.2

Q ss_pred             HHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCe-EEEEE
Q 020514           19 WVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPI-EVNLL   97 (325)
Q Consensus        19 ~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~-~~e~~   97 (325)
                      ....+++.++++++++|.+   |.++++|+++++++|++.++++|+++..++++...  ....+.+.+..+... ..+..
T Consensus         8 l~~~il~~~~~~i~~~D~~---g~I~~~N~aa~~l~g~~~~~~~g~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~   82 (115)
T 3b33_A            8 LPSAILNNMVTATLILDDG---LAIRYANPAAELLFSQSAKRIVEQSLSQLIQHASL--DLALLTQPLQSGQSITDSDVT   82 (115)
T ss_dssp             HHHHHHHHCSSEEEEECTT---CBEEEECHHHHHHTTSCHHHHTTCBHHHHCSEEEC--CTHHHHHHHHHCCCEEEEEEE
T ss_pred             cHHHHHhhcCceEEEECCC---CcEEEECHHHHHHhCCCHHHHhCCCHHHHhCccch--hhHHHHHHHHcCCcccCCceE
Confidence            3456899999999999999   99999999999999999999999987766543221  122344455555543 34555


Q ss_pred             EEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccc
Q 020514           98 NYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV  134 (325)
Q Consensus        98 ~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIT  134 (325)
                      .. ++|..+|+.+++.|+.+  +|. .+++.+++||+
T Consensus        83 ~~-~~g~~~~~~~~~~pi~~--~g~-~~~l~~~~Di~  115 (115)
T 3b33_A           83 FV-VDGRPLMLEVTVSPITW--QRQ-LMLLVEMRKID  115 (115)
T ss_dssp             EE-ETTEEEEEEEEEEEEEE--TTE-EEEEEEEEEC-
T ss_pred             Ee-cCCCEEEEEEEEEEeec--CCc-eEEEEEEEeCC
Confidence            54 78988999999999975  455 57888999985

>3luq_A Sensor protein; PAS, histidine, kinase, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: PGE; 2.49A {Geobacter sulfurreducens}

Probab=99.19  E-value=3.7e-11  Score=84.62  Aligned_cols=80  Identities=8%  Similarity=-0.026  Sum_probs=62.7

Q ss_pred             hhhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH----------hhc
Q 020514          241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI----------AIS  310 (325)
Q Consensus       241 ~~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~----------e~~  310 (325)
                      +.++.++++++++++++|.   +|+|+++|+++++++||++++++|+++.+++ |+........+.+          +..
T Consensus         3 ~~~~~~~~~~~~~i~~~d~---~g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (114)
T 3luq_A            3 ERLRLFTEHAPAALAMFDR---EMRYLAVSRRWREDYGLGDGDILGMSHYDIF-PEIGEEWKSVHRRGLAGEVIRVEEDC   78 (114)
T ss_dssp             HHHHHHHHTCSSEEEEEET---TCBEEEECHHHHHHTTCCSSCCTTCBHHHHC-TTCCHHHHHHHHHHHTTCCEEEEEEE
T ss_pred             HHHHHHHhcCCceEEEEcC---CcEEEEECHHHHHHHCCCHHHHcCCcHHHHC-CccHHHHHHHHHHHhcCCcceeeeeE
Confidence            4578899999999999997   5799999999999999999999999999888 5555444333333          235


Q ss_pred             cccCCCceeeEEee
Q 020514          311 PYPKKKSIYMEYVR  324 (325)
Q Consensus       311 ~~~kdG~~~~~~~~  324 (325)
                      ..+++|+.+|+.++
T Consensus        79 ~~~~~g~~~~~~~~   92 (114)
T 3luq_A           79 FVRADGRTQWLRWE   92 (114)
T ss_dssp             EEC--CCEEEEEEE
T ss_pred             EEcCCCcEEEEEEE
Confidence            67789999998764

>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=99.18  E-value=3.3e-11  Score=102.58  Aligned_cols=81  Identities=38%  Similarity=0.746  Sum_probs=68.4

Q ss_pred             HhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH----------hhcccc
Q 020514          244 YISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI----------AISPYP  313 (325)
Q Consensus       244 ~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~----------e~~~~~  313 (325)
                      ..++++++++|+++|.+.+||+|+++|++|++++||+++|++|+++.++.+|+........+.+          +++.++
T Consensus        14 ~~~~~~~~~~i~~~D~~~~~g~i~~~N~a~~~l~G~~~~el~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~   93 (332)
T 2wkq_A           14 ATTLERIEKNFVITDPRLPDNPIIFASDSFLQLTEYSREEILGRNARFLQGPETDRATVRKIRDAIDNQTEVTVQLINYT   93 (332)
T ss_dssp             CCCGGGCCSEEEEECTTSTTCCEEEECHHHHHHHCCCHHHHTTSCGGGGCCTTCCHHHHHHHHHHHHTTCCEEEEEEEEC
T ss_pred             HhHhhcCCCcEEEecCCCCCCCEEEeehHHHHHhCCCHHHHcCCCchhhcCCCCCHHHHHHHHHHHHcCCeeEEEEEEEc
Confidence            3468889999999998433589999999999999999999999999999888877766555554          667788


Q ss_pred             CCCceeeEEee
Q 020514          314 KKKSIYMEYVR  324 (325)
Q Consensus       314 kdG~~~~~~~~  324 (325)
                      +||+.+|++++
T Consensus        94 ~dG~~~~~~~~  104 (332)
T 2wkq_A           94 KSGKKFWNLFH  104 (332)
T ss_dssp             TTCCEEEEEEE
T ss_pred             CCCCEEEEeeE
Confidence            99999999765

>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=99.16  E-value=4.4e-11  Score=89.02  Aligned_cols=78  Identities=32%  Similarity=0.657  Sum_probs=61.0

Q ss_pred             hhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCC-----------ChHHHHHHHH-------
Q 020514          246 SLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDT-----------DTTVLYQVSI-------  307 (325)
Q Consensus       246 ~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~-----------~~~~~~~~~~-------  307 (325)
                      ++++ +++|+++|...++|+|+++|+++++++||+++|++|+++..+.+++.           .......+.+       
T Consensus        31 ~~~~-~~~i~~~d~~d~~g~i~~~N~a~~~l~G~~~~el~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  109 (149)
T 3d72_A           31 PVDT-SVALILCDLKQKDTPIVYASEAFLYMTGYSNAEVLGRNCRFLQSPDGMVKPKSTRKYVDSNTINTMRKAIDRNAE  109 (149)
T ss_dssp             SCCT-TSCEEEEETTSTTCCEEEECHHHHHHHCCCHHHHTTSCGGGGGSTTSCCCTTCCCSSSCHHHHHHHHHHHHHTCC
T ss_pred             hhcC-CccEEEEeccCCCCcEEEECHHHHHHHCcCHHHHcCCChhHhCCccccccccccccccChHHHHHHHHHHHCCCc
Confidence            4555 48999998422258999999999999999999999999998887763           5544444443       


Q ss_pred             ---hhccccCCCceeeEEee
Q 020514          308 ---AISPYPKKKSIYMEYVR  324 (325)
Q Consensus       308 ---e~~~~~kdG~~~~~~~~  324 (325)
                         ++..+++||+.+|+.++
T Consensus       110 ~~~e~~~~~~dG~~~~~~~~  129 (149)
T 3d72_A          110 VQVEVVNFKKNGQRFVNFLT  129 (149)
T ss_dssp             EEEEEEEECTTCCEEEEEEE
T ss_pred             eEEEEEEECCCCCEEEEEEE
Confidence               56667899999999765

>3cax_A Uncharacterized protein PF0695; structural genomics, unknown function, PSI-2, protein struct initiative; 2.43A {Pyrococcus furiosus dsm 3638}

Probab=99.09  E-value=8.5e-10  Score=94.91  Aligned_cols=115  Identities=18%  Similarity=0.282  Sum_probs=91.4

Q ss_pred             HHHHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEE
Q 020514           16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVN   95 (325)
Q Consensus        16 ~~~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e   95 (325)
                      ....+..+++++++|++++|.+   |+++++|++ ++++ ++.++++|+++..++++. .......+..++..+.....+
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            4457889999999999999999   999999999 9999 889999999988776543 223334455666777665444


Q ss_pred             EEEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchhhh
Q 020514           96 LLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMR  140 (325)
Q Consensus        96 ~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~~  140 (325)
                      ... ..+|  .++.++..|+++ .+|.+.|++.+++|||+.++++
T Consensus       311 ~~~-~~~g--~~v~v~~~PI~d-~~G~~~G~v~v~~DITe~~~le  351 (369)
T 3cax_A          311 FWL-RLRE--KYVYIKYVPLFN-EKGEYIGTLEMTMDIAPYKKIE  351 (369)
T ss_dssp             EEE-EETT--EEEEEEEEEEEC-TTSCEEEEEEEEEECHHHHTCC
T ss_pred             EEE-eeCC--EEEEEEEEEEEC-CCCCEEEEEEEEEcCHHHHHHH
Confidence            443 3355  578889999998 8999999999999999998863

>3mjq_A Uncharacterized protein; NESG, structural genomics, PSI-2, protein structure initiati northeast structural genomics consortium; 2.60A {Desulfitobacterium hafniense}

Probab=99.07  E-value=9.2e-11  Score=84.20  Aligned_cols=78  Identities=17%  Similarity=0.159  Sum_probs=63.9

Q ss_pred             HhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH---------hhccccC
Q 020514          244 YISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI---------AISPYPK  314 (325)
Q Consensus       244 ~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~---------e~~~~~k  314 (325)
                      +.++++++++++++|.   +|+|+++|+++++++||++++++|+++.++.++.........+..         ++...++
T Consensus         2 ~~l~~~~~~~i~~~d~---~g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (126)
T 3mjq_A            2 KNFLETIEDMILIINR---EGRLLYANTAVPKKLGYTHEELMSMHILTITSAGKMAEGEKILAELFAGKKESLPLSLEKK   78 (126)
T ss_dssp             CTTGGGCSSEEEEEET---TSBEEEECTHHHHHHSCCHHHHHHSBHHHHHCTTCHHHHHHHHHHHHHTCCSEEEEEEECT
T ss_pred             hhHHhhCCceEEEEeC---CCcEEEEcHHHHHHHCCCHHHHcCCCHHHHcCchhHHHHHHHHHHHHhCCCceeEEEEEcc
Confidence            4578899999999998   479999999999999999999999999998877765544444433         5556788


Q ss_pred             CCceeeEEee
Q 020514          315 KKSIYMEYVR  324 (325)
Q Consensus       315 dG~~~~~~~~  324 (325)
                      +|..+|+.++
T Consensus        79 ~g~~~~~~~~   88 (126)
T 3mjq_A           79 EGTSIPAKAR   88 (126)
T ss_dssp             TSCEEEEEEE
T ss_pred             CCCEEEEEEE
Confidence            9999998764

>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=99.07  E-value=3.1e-10  Score=81.13  Aligned_cols=85  Identities=36%  Similarity=0.687  Sum_probs=67.2

Q ss_pred             hhhhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH----------hh
Q 020514          240 SSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI----------AI  309 (325)
Q Consensus       240 ~~~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~----------e~  309 (325)
                      ...++.++++++++++++|....+|+|+++|+++++++||+.++++|+++..+.++.........+..          ++
T Consensus         5 ~~~~~~~~~~~~~~i~~~d~~d~~~~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   84 (130)
T 2z6d_A            5 SQELKTALSTLQQTFVVSDATQPHCPIVYASSGFFTMTGYSSKEIVGRNCRFLQGPDTDKNEVAKIRDCVKNGKSYCGRL   84 (130)
T ss_dssp             --CHHHHHHHTTCEEEEEETTSTTCCEEEECHHHHHHHCCCHHHHTTSCGGGGCCTTSCHHHHHHHHHHHHTTCCEEEEE
T ss_pred             HHHHHHHHHhcccceeeeeccCCCCcEEEecHHHHHHhCcCHHHHcCCChhhccCCCCCchHHHHHHHHHHcCCcceeEE
Confidence            45578899999999999992111579999999999999999999999999988888777665554443          55


Q ss_pred             ccccCCCceeeEEee
Q 020514          310 SPYPKKKSIYMEYVR  324 (325)
Q Consensus       310 ~~~~kdG~~~~~~~~  324 (325)
                      ...+++|+.+|+.++
T Consensus        85 ~~~~~~g~~~~~~~~   99 (130)
T 2z6d_A           85 LNYKKDGTPFWNLLT   99 (130)
T ss_dssp             EEECTTSCEEEEEEE
T ss_pred             EEEcCCCcEEEEEEE
Confidence            566789999888754

>3nja_A Probable ggdef family protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; 2.37A {Chromobacterium violaceum}

Probab=99.06  E-value=1.5e-10  Score=82.74  Aligned_cols=83  Identities=10%  Similarity=-0.083  Sum_probs=59.1

Q ss_pred             chhhhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccc--cccccccCCCCChHHHHHHHH---------
Q 020514          239 ISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVG--QNCRFLNGVDTDTTVLYQVSI---------  307 (325)
Q Consensus       239 ~~~~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG--~~~~~l~~~~~~~~~~~~~~~---------  307 (325)
                      .+..|+.++++++++++++|.+   +.++++|+++++++||++++++|  ..+..+++|++.......+.+         
T Consensus         5 ~~~~l~~~~~~~~~~i~~~d~~---~~~~~~n~~~~~~~G~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~   81 (125)
T 3nja_A            5 AEKLLHTAESDAGIGSWVLHME---SGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDRPFD   81 (125)
T ss_dssp             ------------CCEEEEEETT---TTEEEECHHHHHHHTCCTTTCCCBHHHHHHHBCTTTHHHHHHHHHHHHHSCCCEE
T ss_pred             HHHHHHHHHHhCCeeEEEEEcC---CCcEEECHHHHHHhCCCcccccccHHHHHhhcChhHHHHHHHHHHHHHhcCCCce
Confidence            3456788999999999999985   69999999999999999999999  556677778877666555544         


Q ss_pred             -hhccccCCCceeeEEee
Q 020514          308 -AISPYPKKKSIYMEYVR  324 (325)
Q Consensus       308 -e~~~~~kdG~~~~~~~~  324 (325)
                       +++..+++|+.+|+.++
T Consensus        82 ~e~~~~~~~g~~~~~~~~   99 (125)
T 3nja_A           82 VEYRIVRPDGQVRELLER   99 (125)
T ss_dssp             EEEEEECTTSCEEEEEEE
T ss_pred             EEEEEECCCCCEEEEEEe
Confidence             67777899999998764

>3icy_A Sensor protein; sensory box histidine kinase/response regulator domain, kinase, chlorobium tepidum TLS, PSI-2; 2.68A {Chlorobaculum tepidum}

Probab=99.05  E-value=9.8e-11  Score=83.08  Aligned_cols=82  Identities=7%  Similarity=-0.123  Sum_probs=68.1

Q ss_pred             hhhhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCccccccccc--ccccCCCCChHHHHHHHH----------
Q 020514          240 SSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNC--RFLNGVDTDTTVLYQVSI----------  307 (325)
Q Consensus       240 ~~~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~--~~l~~~~~~~~~~~~~~~----------  307 (325)
                      +++|+.++++++++++.+|.+   |.++++|+++++++||++++++|+..  ..+++|++.......+.+          
T Consensus         3 ~~~~~~l~~~~~~~i~~~d~~---~~~~~~n~~~~~~~G~~~~~~~~~~~~~~~~i~p~d~~~~~~~~~~~~~~~~~~~~   79 (118)
T 3icy_A            3 AEELQALVDNIPAAIYHLDVS---GQATIRFRPPAFLKTLVSEHAGTTRLNTLSMIHHDDRHMLSNAYSKLREAKHSLTL   79 (118)
T ss_dssp             HHHHHHHHTTCCCCCEEECTT---SCEEECCCCCGGGGGGEEEETTEEEEGGGGGBCGGGHHHHHHHHHHHHHSCCEEEE
T ss_pred             HHHHHHHHhcCCceEEEEEcC---CCceEEechhHhhcCCCHHHccCChhHHHHHcCHHHHHHHHHHHHHHHhcCCCceE
Confidence            356888999999999999984   69999999999999999999988754  567788877766655554          


Q ss_pred             hhccccCCCceeeEEee
Q 020514          308 AISPYPKKKSIYMEYVR  324 (325)
Q Consensus       308 e~~~~~kdG~~~~~~~~  324 (325)
                      |++..++||+.+|+..+
T Consensus        80 e~r~~~~~g~~~w~~~~   96 (118)
T 3icy_A           80 VYRIVTPEGKLHWIEDH   96 (118)
T ss_dssp             EEEEECTTCCEEEEEEE
T ss_pred             EEEEECCCCCEEEEEEE
Confidence            77778899999998764

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

Probab=99.04  E-value=4.3e-10  Score=79.74  Aligned_cols=81  Identities=15%  Similarity=0.104  Sum_probs=65.1

Q ss_pred             hhhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH----------hhc
Q 020514          241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI----------AIS  310 (325)
Q Consensus       241 ~~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~----------e~~  310 (325)
                      ..++.++++++++++++|.   +|+|+++|+++++++|+++++++|+++..+.++.........+.+          ++.
T Consensus         7 ~~~~~~~~~~~~~i~~~d~---~~~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   83 (124)
T 3lyx_A            7 KQRAKAFDYVFDAIVVTDL---QGFIIDWNKGSETLYGYSKEQAIGQPVNMLHVPGDTEHITSEVISAVENQGKWTGEIR   83 (124)
T ss_dssp             HHHHHGGGTCSSEEEEEET---TCBEEEECHHHHHHHCCCHHHHTTSBGGGGSCTTTHHHHHHHHHHHHHHTSCEEEEEE
T ss_pred             HHHHHHHhhcCceEEEECC---CCcEeehhhHHHHHhCCCHHHHcCCCHHHhcCcchhhHHHHHHHHHHHcCCcccceEE
Confidence            4578899999999999997   479999999999999999999999999866666555444433333          556


Q ss_pred             cccCCCceeeEEee
Q 020514          311 PYPKKKSIYMEYVR  324 (325)
Q Consensus       311 ~~~kdG~~~~~~~~  324 (325)
                      ..+++|..+|+.++
T Consensus        84 ~~~~~g~~~~~~~~   97 (124)
T 3lyx_A           84 MLHKDGHIGWIESM   97 (124)
T ss_dssp             EECTTSCEEEEEEE
T ss_pred             EEccCCCEEEEEEE
Confidence            67789999998764

>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=99.04  E-value=2.3e-10  Score=81.03  Aligned_cols=78  Identities=14%  Similarity=0.014  Sum_probs=58.4

Q ss_pred             HhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccc-cCCCCChHHHHHHHH---------hhccc-
Q 020514          244 YISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFL-NGVDTDTTVLYQVSI---------AISPY-  312 (325)
Q Consensus       244 ~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l-~~~~~~~~~~~~~~~---------e~~~~-  312 (325)
                      ..++++++.|++++|.   ||+|+++|+++++++||++++++|+++.+. .+....+.+..++.+         ++... 
T Consensus        20 ~~~ld~l~~Gii~lD~---~g~I~~~N~~~e~~sG~~~~eviGk~~f~~~~~~~~~~~f~~rf~~~~~~g~l~~~~~~v~   96 (125)
T 1nwz_A           20 DGQLDGLAFGAIQLDG---DGNILQYNAAEGDITGRDPKQVIGKNFFKDVAPCTDSPEFYGKFKEGVASGNLNTMFEYTF   96 (125)
T ss_dssp             HHHHTTCSSEEEEEET---TCBEEEECHHHHHHHCCCHHHHTTSBCCCCCCGGGCSTTTHHHHHHHHHHTCCEEEEEEEE
T ss_pred             HHHHhccCceEEEECC---CCEEEEEHHHHHHHhCCCHHHHcCCchhhhccchhcccHHHHHHHHHHhcCceeEEEEEEE
Confidence            3468999999999998   479999999999999999999999999774 444455564555544         33333 


Q ss_pred             cCCCceeeEEee
Q 020514          313 PKKKSIYMEYVR  324 (325)
Q Consensus       313 ~kdG~~~~~~~~  324 (325)
                      +++|+++++.++
T Consensus        97 ~~~~~p~~v~i~  108 (125)
T 1nwz_A           97 DYQMTPTKVKVH  108 (125)
T ss_dssp             CTTSCCEEEEEE
T ss_pred             cCCCCEEEEEEE
Confidence            666666665543

>3mr0_A Sensory box histidine kinase/response regulator; PAS fold, structural genomics, PSI-2; HET: PG5; 1.49A {Burkholderia thailandensis}

Probab=99.04  E-value=4.1e-10  Score=83.20  Aligned_cols=85  Identities=15%  Similarity=0.171  Sum_probs=66.7

Q ss_pred             ccchhhhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCccccccc--ccccccCCCCChHHHHHHHH-------
Q 020514          237 GFISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQ--NCRFLNGVDTDTTVLYQVSI-------  307 (325)
Q Consensus       237 ~~~~~~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~--~~~~l~~~~~~~~~~~~~~~-------  307 (325)
                      ...+++|+.++++++.|++.+|+.   +.++++|+++++++||+++++.+.  .+..+++|++...+...+..       
T Consensus         5 ~~se~rl~~~~~~~~~g~w~~d~~---~~~~~~s~~~~~~~G~~~~~~~~~~~~~~~~ihpdD~~~~~~~~~~~~~~~~~   81 (142)
T 3mr0_A            5 SASEERFQLAVSGASAGLWDWNPK---TGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAALKAHLEHRDT   81 (142)
T ss_dssp             ----CCHHHHHHHTTCEEEEECTT---TCCEEECHHHHHHTTCCGGGSCSEEC---CCBCTTTHHHHHHHHHHHHHHCCC
T ss_pred             HHHHHHHHHHHHhCCcEEEEEEcC---CCeEEECHHHHHHhCCCccccCCCHHHHHhhcCHHHHHHHHHHHHHHHhCCCc
Confidence            344567899999999999999985   588999999999999999998874  45677889888776666654       


Q ss_pred             ---hhccccCCCceeeEEee
Q 020514          308 ---AISPYPKKKSIYMEYVR  324 (325)
Q Consensus       308 ---e~~~~~kdG~~~~~~~~  324 (325)
                         |++.+++||+.+|+...
T Consensus        82 ~~~e~r~~~~~G~~~w~~~~  101 (142)
T 3mr0_A           82 YDVEYRVRTRSGDFRWIQSR  101 (142)
T ss_dssp             EEEEEEEECTTSCEEEEEEE
T ss_pred             eEEEEEEECCCCCEEEEEEE
Confidence               77888999999998753

>3rty_A Period circadian protein; PAS domain, signalling, timeless, circadian clock protein; 2.85A {Drosophila melanogaster} PDB: 1wa9_A 3gec_A

Probab=99.02  E-value=2e-09  Score=90.94  Aligned_cols=108  Identities=9%  Similarity=0.037  Sum_probs=92.2

Q ss_pred             CCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCC-----eEEEEEEEecC
Q 020514           28 PDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERP-----IEVNLLNYKKD  102 (325)
Q Consensus        28 ~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~-----~~~e~~~~~~d  102 (325)
                      ...+...+.+   |.++|+|+++..++||.+++++|+++..+++|+|.......+...+..|..     ...++++++++
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            4567788899   999999999999999999999999999999999888777778887876654     34678999999


Q ss_pred             CCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchh
Q 020514          103 GTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKH  138 (325)
Q Consensus       103 g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~  138 (325)
                      |..+|+..+..++.++..+.+..++++.+.++....
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            999999999999987345677788888888888755

>1mzu_A PPR; photoactive yellow protein, PAS, PYP, signaling protein; HET: HC4; 2.00A {Rhodospirillum centenum} SCOP: d.110.3.1

Probab=99.02  E-value=3.3e-10  Score=80.35  Aligned_cols=76  Identities=9%  Similarity=-0.032  Sum_probs=57.9

Q ss_pred             hhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccc-cCCCCChHHHHHHHH---------hhccc-cC
Q 020514          246 SLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFL-NGVDTDTTVLYQVSI---------AISPY-PK  314 (325)
Q Consensus       246 ~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l-~~~~~~~~~~~~~~~---------e~~~~-~k  314 (325)
                      ++++++.|++++|.   ||+|+++|+++++++||++++++|+++.+. .+....+.+..++.+         ++... ++
T Consensus        27 ~ld~l~~GiivlD~---dg~I~~~N~~~e~isG~s~eeviGk~~f~~~~p~~~~~~f~grf~~~~~~G~l~~~~~yv~~~  103 (129)
T 1mzu_A           27 EFDALPVGAIQVDG---SGVIHRYNRTESRLSGRIPERVIGRNFFTEVAPCTNIPAFSGRFMDGVTSGTLDARFDFVFDF  103 (129)
T ss_dssp             TGGGCSSEEEEEET---TCBEEEECHHHHHHHCCCHHHHTTSBCCCCCCGGGCSTTTHHHHHHHHHTSCCEEEEEEEEEC
T ss_pred             HHhccCceEEEECC---CCeEEEEHHHHHHHhCCCHHHHcCCchhhhccchhcccHHHHHHHHHHhcCceeEEEEEEEcC
Confidence            68899999999998   479999999999999999999999999774 444455565555554         33333 66


Q ss_pred             CCceeeEEee
Q 020514          315 KKSIYMEYVR  324 (325)
Q Consensus       315 dG~~~~~~~~  324 (325)
                      +|+++++.++
T Consensus       104 ~~~p~~v~i~  113 (129)
T 1mzu_A          104 QMAPVRVQIR  113 (129)
T ss_dssp             SSCEEEEEEE
T ss_pred             CCCEEEEEEE
Confidence            7776666543

>3a0r_A Sensor protein; four helix bundle, PAS fold, kinase, phosphoprotein, transfe two-component regulatory system; 3.80A {Thermotoga maritima}

Probab=99.00  E-value=2.9e-10  Score=97.39  Aligned_cols=117  Identities=8%  Similarity=0.074  Sum_probs=85.8

Q ss_pred             HHHHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEE
Q 020514           16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVN   95 (325)
Q Consensus        16 ~~~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e   95 (325)
                      +..+++.++++++++++++|.+   |.++++|+++++++||++++++|+++..+.++   ..........+..+......
T Consensus         6 ~~~~~~~i~~~~~~~i~~~d~~---g~i~~~N~a~~~l~G~~~~e~~G~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~   79 (349)
T 3a0r_A            6 LRNFSESILESLETAIITLSKD---GRITEWNKKAEQLFGLKKENVLGRRLKDLPDF---EEIGSVAESVFENKEPVFLN   79 (349)
T ss_dssp             ---CCCSSGGGSSSEEEEEESS---SBCSCBCHHHHHHHSCCSTTTTTCBSTTSTTT---THHHHHHHHHHHHCCCCEEE
T ss_pred             HHHHHHHHHhhhcCeEEEECCC---CCEEeeHHHHHHHhCCCHHHHcCcCHHHCcCh---hHHHHHHHHHHhcCCceeec
Confidence            4456778999999999999999   99999999999999999999999988776322   22334444555555544332


Q ss_pred             EEEEecCCCeEEEEEEEEEeecCCCCee-eEEEEEEeccccchhhhhcc
Q 020514           96 LLNYKKDGTPFWMLFKMSLVFGKEDGRA-THFVAVQVPIVSRKHMRNSG  143 (325)
Q Consensus        96 ~~~~~~dg~~~~~~~~~~~~~~~~~g~~-~~~~~~~~DITe~k~~~~~~  143 (325)
                      .    ..+...|+.++..|+.+ ..|.. .+++++++|||++++++++.
T Consensus        80 ~----~~~~~~~~~~~~~~~~~-~~~~~~~g~~~~~~DiTe~~~~e~~~  123 (349)
T 3a0r_A           80 F----YKFGERYFNIRFSPFRN-AKTQLLEGVIITIDDVTELYKYEEER  123 (349)
T ss_dssp             C----CCBTTBCCEEEEEEECC-TTTTSSCEEEEEEECCSTTTTTTTTT
T ss_pred             c----cccCceEEEEEEEEEEc-CCCceeeEEEEEEEechHHHHHHHHH
Confidence            1    22234577888999987 56654 58999999999999875544

>1ll8_A PAS kinase; PAS domain, ligand binding, ligand screening, kinase regulation, transferase; NMR {Homo sapiens} SCOP: d.110.3.5

Probab=99.00  E-value=4.7e-10  Score=79.38  Aligned_cols=103  Identities=16%  Similarity=0.154  Sum_probs=73.0

Q ss_pred             hCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHH-HHHh-CCCe---EEEEEEEe
Q 020514           26 ELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIRE-AIRE-ERPI---EVNLLNYK  100 (325)
Q Consensus        26 ~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~-~~~~-~~~~---~~e~~~~~  100 (325)
                      +.+++++++|.+  +|.++++|+++++++||++++++|+++..++++..... ...+.. .... +...   ..+....+
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            345799999973  28999999999999999999999999888887754432 122111 1111 1111   23455678


Q ss_pred             cCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccc
Q 020514          101 KDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV  134 (325)
Q Consensus       101 ~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIT  134 (325)
                      ++|..+|+.+++.|+.+ ..+  .+++++++|++
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            99999999999999976 333  36788888875

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

Probab=98.99  E-value=1e-09  Score=75.95  Aligned_cols=73  Identities=29%  Similarity=0.576  Sum_probs=56.1

Q ss_pred             CceEEecCCCCCCCeEEEehhhHHhhCCCcccccccc--cccccCCCCChHHHHHHHH----------hhccccCCCcee
Q 020514          252 QSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQN--CRFLNGVDTDTTVLYQVSI----------AISPYPKKKSIY  319 (325)
Q Consensus       252 ~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~--~~~l~~~~~~~~~~~~~~~----------e~~~~~kdG~~~  319 (325)
                      .+|+++|...+||+|+++|+++++++||++++++|++  ...+.++.........+.+          ++...+++|+.+
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            5889999864578999999999999999999999998  4555555555544444433          555678899999


Q ss_pred             eEEee
Q 020514          320 MEYVR  324 (325)
Q Consensus       320 ~~~~~  324 (325)
                      |+.++
T Consensus        82 ~~~~~   86 (110)
T 1byw_A           82 LCLVD   86 (110)
T ss_dssp             EEEEE
T ss_pred             EEEEE
Confidence            98764

>3a0s_A Sensor protein; PAS-fold, kinase, phosphoprotein, transferase, two-component regulatory system; HET: PG4 PGE; 1.47A {Thermotoga maritima} PDB: 3a0v_A*

Probab=98.99  E-value=1.3e-08  Score=68.39  Aligned_cols=95  Identities=7%  Similarity=0.052  Sum_probs=69.9

Q ss_pred             CCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEEEEEEecCCCeE
Q 020514           27 LPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPF  106 (325)
Q Consensus        27 ~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg~~~  106 (325)
                      ++++++++|.+   |.++++|+++++++|++.++++|+++..+  +. .......+...+..+.....  ..  .++...
T Consensus         1 ~~~~i~~~d~~---g~i~~~N~~~~~l~g~~~~~~~g~~~~~~--~~-~~~~~~~~~~~~~~~~~~~~--~~--~~~~~~   70 (96)
T 3a0s_A            1 METAIITLSKD---GRITEWNKKAEQLFGLKKENVLGRRLKDL--PD-FEEIGSVAESVFENKEPVFL--NF--YKFGER   70 (96)
T ss_dssp             CCCEEEEEETT---SBEEEECHHHHHHHCCCHHHHTTSBGGGS--TT-CHHHHHHHHHHHHHTCCEEE--EE--EEETTE
T ss_pred             CCceEEEEcCC---CCEeehhHHHHHHhCCCHHHhcCCCHHHC--cc-hHHHHHHHHHHhccCCeEEE--EE--EcCCcE
Confidence            46899999999   99999999999999999999999987766  22 23334445555555555432  22  234456


Q ss_pred             EEEEEEEEeecCCCCe-eeEEEEEEec
Q 020514          107 WMLFKMSLVFGKEDGR-ATHFVAVQVP  132 (325)
Q Consensus       107 ~~~~~~~~~~~~~~g~-~~~~~~~~~D  132 (325)
                      |+.++..|+.+ .+|. +.+++++++|
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            88999999987 5554 5788888776

>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=98.98  E-value=1.5e-08  Score=71.81  Aligned_cols=100  Identities=13%  Similarity=0.073  Sum_probs=75.4

Q ss_pred             HHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCc-ccCCCCChHHHHHHHHHHHhCCCeEEEEEE-
Q 020514           21 HEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRM-FQGPRTNRRTIMEIREAIREERPIEVNLLN-   98 (325)
Q Consensus        21 ~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~-l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~-   98 (325)
                      ..+++.++.|++++|.+   +++++||++++++.|+++++++|+++.. +.+......+...+.+.+..|. ......+ 
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   9999999999999999999999999865 4444555666777888777766 4434333 


Q ss_pred             EecCCCeEEEEEEEEEeecCCCCeeeEEE
Q 020514           99 YKKDGTPFWMLFKMSLVFGKEDGRATHFV  127 (325)
Q Consensus        99 ~~~dg~~~~~~~~~~~~~~~~~g~~~~~~  127 (325)
                      .+.+|+++++.++  +... ++|...+++
T Consensus        96 ~~~~~~p~~v~i~--l~~~-~~~~~~~i~  121 (125)
T 1nwz_A           96 FDYQMTPTKVKVH--MKKA-LSGDSYWVF  121 (125)
T ss_dssp             ECTTSCCEEEEEE--EEEC-SSSSEEEEE
T ss_pred             EcCCCCEEEEEEE--EEEc-CCCCEEEEE
Confidence            4888886665554  4545 566655543

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

Probab=98.98  E-value=7.1e-10  Score=83.52  Aligned_cols=82  Identities=27%  Similarity=0.453  Sum_probs=68.5

Q ss_pred             hhhhHhhhhccCCceEEecCCCCCC---CeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH---------
Q 020514          240 SSSLYISLGRIKQSFVLIDPHLPDM---PMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI---------  307 (325)
Q Consensus       240 ~~~l~~~~~~~~~~i~~~d~~~~dg---~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~---------  307 (325)
                      ...++.++++++++|+++|.   +|   +|+++|+++++++||+.++++|+++..+.++.........+..         
T Consensus        24 ~~~~~~i~~~~~~~i~~~d~---~~~~~~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  100 (162)
T 3sw1_A           24 AQLLQSMVDASNDGIVVAEK---EGDDTILIYVNAAFEYLTGYSRDEILYQDCRFLQGDDRDQLGRARIRKAMAEGRPCR  100 (162)
T ss_dssp             HHHHHHHHHTCSSEEEEEEE---ETTEEEEEEECHHHHHHHTCCHHHHTTSBGGGGTTTCCCCHHHHHHHHHHHHTCCEE
T ss_pred             HHHHHHHHhhccCcEEEEeC---CCCccEEEEECHHHHHHHCCCHHHHcCCCcceecCCCcCHHHHHHHHHHHhcCCCCc
Confidence            34578899999999999998   47   9999999999999999999999999988877766665555544         


Q ss_pred             -hhccccCCCceeeEEee
Q 020514          308 -AISPYPKKKSIYMEYVR  324 (325)
Q Consensus       308 -e~~~~~kdG~~~~~~~~  324 (325)
                       ++...+++|..+|+.++
T Consensus       101 ~~~~~~~~~g~~~~~~~~  118 (162)
T 3sw1_A          101 EVLRNYRKDGSAFWNELS  118 (162)
T ss_dssp             EEEEEECTTCCEEEEEEE
T ss_pred             ceEEEECCCCCEEEEEEE
Confidence             56667899999998764

>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=98.97  E-value=3e-10  Score=80.87  Aligned_cols=86  Identities=2%  Similarity=-0.115  Sum_probs=66.1

Q ss_pred             ccchhhhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccc--cccccCCCCChHHHHHHHH-------
Q 020514          237 GFISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQN--CRFLNGVDTDTTVLYQVSI-------  307 (325)
Q Consensus       237 ~~~~~~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~--~~~l~~~~~~~~~~~~~~~-------  307 (325)
                      ......++.++++++++++++|.+  +|.++++|+++++++||++++++|++  +..+.+|+........+..       
T Consensus         7 ~~~~~~~~~~~~~~~~~i~~~d~~--~~~i~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   84 (125)
T 3eeh_A            7 AKSERRVRELTEATNDILWEFTAD--LSEVLVINSAYEDIWGRSVAKLRENPHDFLNGIHPEDRELMKDTMQSLMDGESA   84 (125)
T ss_dssp             ---CHHHHHHHSCCCCEEEEEETT--SSCEEEECTHHHHHHSSCHHHHHHCGGGGGGGBCHHHHHHHHHHHHHHHTTCCE
T ss_pred             HHHHHHHHHHHhcCCceEEEEEcC--CCcEEEecHHHHHHHCCCHHHHccCcHHHHHhcCHHHHHHHHHHHHHHHcCCCc
Confidence            334567889999999999999984  27999999999999999999999987  4556666655544444433       


Q ss_pred             --hhccccCCCceeeEEee
Q 020514          308 --AISPYPKKKSIYMEYVR  324 (325)
Q Consensus       308 --e~~~~~kdG~~~~~~~~  324 (325)
                        +++..+++|+.+|+.++
T Consensus        85 ~~e~~~~~~~g~~~~~~~~  103 (125)
T 3eeh_A           85 DVECRVNATEEYQRWVWIQ  103 (125)
T ss_dssp             EEEEEECGGGTTCEEEEEE
T ss_pred             cEEEEEEcCCCCEEEEEEe
Confidence              66667889999998764

>2jhe_A Transcription regulator TYRR; aromatic hydrocarbons catabolism, TYRR protei nucleotide-binding, transcription regulation, activator; HET: PG4; 2.30A {Escherichia coli}

Probab=98.97  E-value=1.7e-09  Score=84.06  Aligned_cols=108  Identities=14%  Similarity=0.140  Sum_probs=79.8

Q ss_pred             hHHHHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCC-C-e
Q 020514           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREER-P-I   92 (325)
Q Consensus        15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~-~-~   92 (325)
                      +....++.+++++++|++++|.+   |.++++|+++++++|++.++++|+++..++++...       ...+..+. . .
T Consensus        77 ~~~~~l~~il~~~~~gvi~~D~~---g~I~~~N~aa~~llg~~~~~~~g~~~~~~~~~~~~-------~~~~~~~~~~~~  146 (190)
T 2jhe_A           77 REHLALSALLEALPEPVLSVDMK---SKVDMANPASCQLFGQKLDRLRNHTAAQLINGFNF-------LRWLESEPQDSH  146 (190)
T ss_dssp             HHHHHHHHHHHHCSSCEEEECTT---CBEEEECHHHHHHHTSCHHHHTTSBGGGTSTTCCH-------HHHHHTCCCSCE
T ss_pred             HHHHHHHHHHHhCCCcEEEEcCC---CCEEEEcHHHHHHhCCCHHHhcCccHHHHhCCCCH-------HHHHhcCCCCCc
Confidence            34567899999999999999999   99999999999999999999999998877655321       22333333 2 2


Q ss_pred             EEEEEEEecCCCeEEEEEEEEEeecCCCCe----eeEEEEEEeccccchh
Q 020514           93 EVNLLNYKKDGTPFWMLFKMSLVFGKEDGR----ATHFVAVQVPIVSRKH  138 (325)
Q Consensus        93 ~~e~~~~~~dg~~~~~~~~~~~~~~~~~g~----~~~~~~~~~DITe~k~  138 (325)
                      ..++.   .+|.  ++.+++.|+.+ .+|.    +.|++.+++|||++++
T Consensus       147 ~~~~~---~~g~--~~~~~~~pi~~-~~~~~~~~~~g~v~~~~DiTe~~~  190 (190)
T 2jhe_A          147 NEHVV---INGQ--NFLMEITPVYL-QDENDQHVLTGAVVMLRSTIRMGR  190 (190)
T ss_dssp             EEEEE---ETTE--EEEEEEEEETT-TTEEEEEEEE-HHHHHHHHTTTCC
T ss_pred             ceEEE---ECCe--EEEEEEEEEEe-cCCCCcceEEeEEEEEeccchhcC
Confidence            22222   2564  45678889875 4555    6788888999999763

>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=98.96  E-value=3.2e-10  Score=84.56  Aligned_cols=61  Identities=15%  Similarity=0.166  Sum_probs=50.9

Q ss_pred             hHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH
Q 020514          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI  307 (325)
Q Consensus       243 l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~  307 (325)
                      |..+++++++||+++|.   ||+|+++|+++++++|++++|++|+++.+++++ ....+.+.+++
T Consensus        24 l~~il~~~~~gi~v~D~---~g~I~~~N~a~~~~~G~~~~eviG~~~~~~~p~-~~~~~~~~l~~   84 (152)
T 3mxq_A           24 LSELLDQLSFALCIVRN---DYVIVKVNEYFESRVIFDGETMQGKNILELFPE-SADYLKRKIDT   84 (152)
T ss_dssp             HHHHHHHHCCEEEEEET---TSBEEEECHHHHHTSSSCHHHHTTSBHHHHSGG-GHHHHHHHHHH
T ss_pred             HHHHHhcCCCCEEEEcC---CCEEEEECHHHHHHHCcCHHHHCCCCHHHhcCC-hHHHHHHHHHH
Confidence            56688999999999998   579999999999999999999999999999876 43333344444

>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=98.96  E-value=1.2e-09  Score=80.00  Aligned_cols=82  Identities=40%  Similarity=0.798  Sum_probs=66.7

Q ss_pred             hHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH----------hhccc
Q 020514          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI----------AISPY  312 (325)
Q Consensus       243 l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~----------e~~~~  312 (325)
                      ++.++++++++++++|...++|.|+++|+++++++||++++++|+++..+.++.........+..          ++...
T Consensus         4 l~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   83 (146)
T 2v0u_A            4 LATTLERIEKNFVITDPRLPDNPIIFASDSFLQLTEYSREEILGRNCRFLQGPETDRATVRKIRDAIDNQTEVTVQLINY   83 (146)
T ss_dssp             CCCTGGGSSSCEEEECTTSTTCCEEEECHHHHHHHCCCHHHHTTSCGGGGCCTTSCHHHHHHHHHHHHTTCCEEEEEEEE
T ss_pred             HHHHHhcCCCcEEEEcCCCCCceEEEEcHHHHHHHCcCHHHHcCCCHHHhcCCcCChHHHHHHHHHHhcCCCcceEEEEE
Confidence            55688999999999997211479999999999999999999999999998888877665555544          55667


Q ss_pred             cCCCceeeEEee
Q 020514          313 PKKKSIYMEYVR  324 (325)
Q Consensus       313 ~kdG~~~~~~~~  324 (325)
                      +++|..+|+.++
T Consensus        84 ~~~g~~~~~~~~   95 (146)
T 2v0u_A           84 TKSGKKFWNLFH   95 (146)
T ss_dssp             CTTCCEEEEEEE
T ss_pred             ecCCcEEEEEEE
Confidence            789998888764

>2w0n_A Sensor protein DCUS; signal transduction, two-component regulatory system, PAS, kinase, membrane, transferase, solid state cell inner membrane; NMR {Escherichia coli}

Probab=98.96  E-value=2.6e-10  Score=80.74  Aligned_cols=104  Identities=9%  Similarity=0.083  Sum_probs=78.1

Q ss_pred             hHHHHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCC---ChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCC
Q 020514           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGF---SRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERP   91 (325)
Q Consensus        15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~---~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~   91 (325)
                      .....++.++++++++++++|.+   |.++++|+++++++|+   +.++++|+++..++++..       +...+..+..
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   788999998877665421       3344445443


Q ss_pred             eEEEEEEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccc
Q 020514           92 IEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV  134 (325)
Q Consensus        92 ~~~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIT  134 (325)
                      .....  ...+|  .|+.++..|+.+  +|.+.+++++++|||
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  467778889875  677788999999997

>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=98.95  E-value=2e-09  Score=77.92  Aligned_cols=83  Identities=25%  Similarity=0.518  Sum_probs=63.8

Q ss_pred             hhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccc--cccccCCCCChHHHHHHHH----------hh
Q 020514          242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQN--CRFLNGVDTDTTVLYQVSI----------AI  309 (325)
Q Consensus       242 ~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~--~~~l~~~~~~~~~~~~~~~----------e~  309 (325)
                      .+...+++++++++++|...++|+|+++|+++++++||+.++++|++  ...+.++.........+.+          ++
T Consensus        20 ~~~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   99 (138)
T 2l0w_A           20 TIIRKFEGQSRKFIIANARVENCAVIYCNDGFCELCGYSRAEVMQRPCTCDFLHGPRTQRRAAAQIAQALLGAEERKVEI   99 (138)
T ss_dssp             HHHHHHTTTTSEEEEEESSSTTCBEEEECSHHHHHHSCCHHHHTTSBTTCGGGCCTTCCHHHHHHHHHHTTCSSCEEEEE
T ss_pred             HHHHHHhcCCCCEEEEecCCCCCEEEEeCHHHHHHhCCCHHHHcCCCCcccccCCcccchhHHHHHHHHHhhcCCceeEE
Confidence            35556777999999999832247999999999999999999999998  5666666666555555544          55


Q ss_pred             ccccCCCceeeEEee
Q 020514          310 SPYPKKKSIYMEYVR  324 (325)
Q Consensus       310 ~~~~kdG~~~~~~~~  324 (325)
                      ...+++|+.+|+.++
T Consensus       100 ~~~~~~g~~~~~~~~  114 (138)
T 2l0w_A          100 AFYRKDGSCFLCLVD  114 (138)
T ss_dssp             EEECTTSCEEEEEEE
T ss_pred             EEECCCCCEEEEEEE
Confidence            566789999888764

>1mzu_A PPR; photoactive yellow protein, PAS, PYP, signaling protein; HET: HC4; 2.00A {Rhodospirillum centenum} SCOP: d.110.3.1

Probab=98.95  E-value=2.2e-08  Score=70.99  Aligned_cols=100  Identities=14%  Similarity=0.061  Sum_probs=74.7

Q ss_pred             HHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCc-ccCCCCChHHHHHHHHHHHhCCCeEEEEEE-
Q 020514           21 HEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRM-FQGPRTNRRTIMEIREAIREERPIEVNLLN-   98 (325)
Q Consensus        21 ~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~-l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~-   98 (325)
                      ..+++.++.|++++|.+   +++++||++++++.|+++++++|+++.. +.+......+...+.+.+..+. ......+ 
T Consensus        25 ~~~ld~l~~GiivlD~d---g~I~~~N~~~e~isG~s~eeviGk~~f~~~~p~~~~~~f~grf~~~~~~G~-l~~~~~yv  100 (129)
T 1mzu_A           25 TAEFDALPVGAIQVDGS---GVIHRYNRTESRLSGRIPERVIGRNFFTEVAPCTNIPAFSGRFMDGVTSGT-LDARFDFV  100 (129)
T ss_dssp             CTTGGGCSSEEEEEETT---CBEEEECHHHHHHHCCCHHHHTTSBCCCCCCGGGCSTTTHHHHHHHHHTSC-CEEEEEEE
T ss_pred             HHHHhccCceEEEECCC---CeEEEEHHHHHHHhCCCHHHHcCCchhhhccchhcccHHHHHHHHHHhcCc-eeEEEEEE
Confidence            34699999999999999   9999999999999999999999999865 3444555666777888888666 4433333 


Q ss_pred             EecCCCeEEEEEEEEEeecCCCCeeeEEE
Q 020514           99 YKKDGTPFWMLFKMSLVFGKEDGRATHFV  127 (325)
Q Consensus        99 ~~~dg~~~~~~~~~~~~~~~~~g~~~~~~  127 (325)
                      .+.+|..+.+.+  ++... ++|...+++
T Consensus       101 ~~~~~~p~~v~i--~l~~~-~~~~~~~i~  126 (129)
T 1mzu_A          101 FDFQMAPVRVQI--RMQNA-GVPDRYWIF  126 (129)
T ss_dssp             EECSSCEEEEEE--EEEEC-SSTTEEEEE
T ss_pred             EcCCCCEEEEEE--EEEEc-CCCCEEEEE
Confidence            478888655554  45555 566655443

>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=98.92  E-value=3.9e-10  Score=80.86  Aligned_cols=51  Identities=12%  Similarity=0.140  Sum_probs=41.1

Q ss_pred             hhhhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCccccccccccccc
Q 020514          240 SSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLN  293 (325)
Q Consensus       240 ~~~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~  293 (325)
                      ...++.++++++++|+++|.   +|+|+++|+++++++||++++++|+++.+++
T Consensus        18 ~~~~~~i~~~~~~~i~~~d~---~g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~   68 (125)
T 3fc7_A           18 RKKFESLVSDSPDGIVHLTT---NGTILSVNPSMAGRLGADPDTLVGQQLSAVM   68 (125)
T ss_dssp             --------CCSCCEEEEEET---TSBEEEECHHHHHHHTSCHHHHTTSBGGGSS
T ss_pred             HHHHHHHHhcCCCeEEEEcC---CCeEEEECHHHHHHhCCCHHHHcCccHHHhC
Confidence            34577899999999999998   4799999999999999999999999999988

>3h9w_A Diguanylate cyclase with PAS/PAC sensor; alpha-beta protein., structural genomics, PSI-2, protein STR initiative; 1.90A {Marinobacter aquaeolei}

Probab=98.91  E-value=5.7e-10  Score=79.03  Aligned_cols=73  Identities=10%  Similarity=-0.047  Sum_probs=58.4

Q ss_pred             cCCceEEecCCCCCCCeEEEehhhHHhhCCCccccccc-ccccccCCCCChHHHHHHHH----------hhccccCCCce
Q 020514          250 IKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQ-NCRFLNGVDTDTTVLYQVSI----------AISPYPKKKSI  318 (325)
Q Consensus       250 ~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~-~~~~l~~~~~~~~~~~~~~~----------e~~~~~kdG~~  318 (325)
                      ++++++.+|..  +|+++|+|+++++|+||++++++|. .+..+++|++.....+.+.+          |++.+++||+.
T Consensus         2 a~~giw~~d~~--~~~~~~~n~~~~~l~G~~~~e~~~~~~~~~~ihpdd~~~~~~~~~~~~~~~~~~~~e~r~~~~dG~~   79 (115)
T 3h9w_A            2 TKAIPWKINWQ--TMAFEYIGPQIEALLGWPQGSWKSVEDWATRMHPEDQEWVVNFCVKQSECGVDHEADYRALHRDGHY   79 (115)
T ss_dssp             -CCEEEEEETT--TTEEEEECTHHHHHHCSCGGGCCBHHHHHHSBCHHHHHHHHHHHHHHHHTTCCEEEEEEEECTTSCE
T ss_pred             cceEEEEEEcC--CCcEEEEChhHHHHhCCChHHccCHHHHHHhcCHHHHHHHHHHHHHHHhcCCcccEEEEEEcCCCCE
Confidence            36789999974  5899999999999999999999994 23457778877666655554          77888999999


Q ss_pred             eeEEee
Q 020514          319 YMEYVR  324 (325)
Q Consensus       319 ~~~~~~  324 (325)
                      +|+..+
T Consensus        80 ~w~~~~   85 (115)
T 3h9w_A           80 VWIRDV   85 (115)
T ss_dssp             EEEEEE
T ss_pred             EEEEEE
Confidence            999764

>3b33_A Sensor protein; structural genomics, PAS domain, nitrogen regulation protein APC91440.4, PSI-2; HET: MSE; 1.83A {Vibrio parahaemolyticus rimd 2210633}

Probab=98.90  E-value=1.5e-09  Score=76.78  Aligned_cols=78  Identities=15%  Similarity=0.088  Sum_probs=58.1

Q ss_pred             hHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCC-Ch-HHHHHHHH-------hhcccc
Q 020514          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDT-DT-TVLYQVSI-------AISPYP  313 (325)
Q Consensus       243 l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~-~~-~~~~~~~~-------e~~~~~  313 (325)
                      ...+++++++|++++|.+   |+|+++|+++++++||++++++|+++.++.++.. .. .....+..       ++... 
T Consensus         9 ~~~il~~~~~~i~~~D~~---g~I~~~N~aa~~l~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-   84 (115)
T 3b33_A            9 PSAILNNMVTATLILDDG---LAIRYANPAAELLFSQSAKRIVEQSLSQLIQHASLDLALLTQPLQSGQSITDSDVTFV-   84 (115)
T ss_dssp             HHHHHHHCSSEEEEECTT---CBEEEECHHHHHHTTSCHHHHTTCBHHHHCSEEECCTHHHHHHHHHCCCEEEEEEEEE-
T ss_pred             HHHHHhhcCceEEEECCC---CcEEEECHHHHHHhCCCHHHHhCCCHHHHhCccchhhHHHHHHHHcCCcccCCceEEe-
Confidence            345899999999999984   7999999999999999999999999988765432 22 22222222       33333 


Q ss_pred             CCCceeeEEee
Q 020514          314 KKKSIYMEYVR  324 (325)
Q Consensus       314 kdG~~~~~~~~  324 (325)
                      ++|+.+|+.++
T Consensus        85 ~~g~~~~~~~~   95 (115)
T 3b33_A           85 VDGRPLMLEVT   95 (115)
T ss_dssp             ETTEEEEEEEE
T ss_pred             cCCCEEEEEEE
Confidence            68988887664

>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=98.89  E-value=1.2e-09  Score=77.82  Aligned_cols=62  Identities=13%  Similarity=0.116  Sum_probs=51.9

Q ss_pred             hhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHH
Q 020514          242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVS  306 (325)
Q Consensus       242 ~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~  306 (325)
                      ..+.+++++++||+++|.   ||+|+++|+++++++||++++++|+++.+++++.........+.
T Consensus        13 ~~~~il~~~~~~i~~~D~---~g~i~~~N~a~~~l~g~~~~e~~G~~~~~~~~~~~~~~~~~~~~   74 (118)
T 3fg8_A           13 GRENLYFQGGLGFMALDE---DLRIIYVNSGCLRHVRRSRDELLGRVVTEVLPETQGSYFDALCR   74 (118)
T ss_dssp             CCCCSSSCTTCEEEEECT---TCBEEEECHHHHHHHTCCHHHHTTSBHHHHCGGGTTSHHHHHHH
T ss_pred             hHHHHHhhCCceEEEECC---CCeEEEECHHHHHHhCCCHHHHcCCcHHHHcCccchHHHHHHHH
Confidence            356689999999999997   57999999999999999999999999999887665554444443

>4dj3_A Period circadian protein homolog 3; PAS domain, circadian rhythm, protein binding; 2.50A {Mus musculus}

Probab=98.87  E-value=3.2e-08  Score=82.70  Aligned_cols=107  Identities=8%  Similarity=0.040  Sum_probs=88.2

Q ss_pred             CEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCC---eEEEEEEEecCCCe
Q 020514           29 DSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERP---IEVNLLNYKKDGTP  105 (325)
Q Consensus        29 ~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~---~~~e~~~~~~dg~~  105 (325)
                      .-+...+.+   |.++++|+++..++||.+++++|+++..+++|+|...+...+.+.+..+..   ...+++++++||..
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            455667888   999999999999999999999999999999999988888888888876554   34678999999999


Q ss_pred             EEEEEEEEEeecCCCCeeeEEEEEEeccccchh
Q 020514          106 FWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKH  138 (325)
Q Consensus       106 ~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~  138 (325)
                      +|+.....++.+..++.+..+++...-++....
T Consensus       252 vwvet~~~~~~np~s~~~e~II~~h~v~~~p~~  284 (317)
T 4dj3_A          252 VILDSSWSSFVNPWSRKVSFIIGRHKVRTSPLN  284 (317)
T ss_dssp             EEEEEEEEEEECSSSCCEEEEEEEEEECCCCSS
T ss_pred             EEEEEEEEEEECCCCCcccEEEEEEEeccCCCC
Confidence            999999999887335677777777766665543

>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=98.82  E-value=7.3e-09  Score=78.02  Aligned_cols=82  Identities=22%  Similarity=0.216  Sum_probs=63.7

Q ss_pred             hhhhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH------------
Q 020514          240 SSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI------------  307 (325)
Q Consensus       240 ~~~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~------------  307 (325)
                      ...+..++++++++++++|.   +|.|+++|+++++++||+.++++|+++..++++.........+..            
T Consensus        39 ~~~~~~~l~~~~~~i~~~d~---~g~i~~~N~~~~~l~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  115 (167)
T 1v9y_A           39 DGIFFPALEQNMMGAVLINE---NDEVMFFNPAAEKLWGYKREEVIGNNIDMLIPRDLRPAHPEYIRHNREGGKARVEGM  115 (167)
T ss_dssp             -CCHHHHHHTCSSEEEEECT---TSBEEEECHHHHHHHSCCGGGTTTSBGGGGSCGGGTTTHHHHHHHHHC---------
T ss_pred             hHHHHHHHHhCCCCEEEECC---CCcEEEECHHHHHHhCCCHHHHcCCChhhccCccccchHHHHHHHHhhcCCCccccc
Confidence            34578899999999999997   479999999999999999999999999988876654433332222            


Q ss_pred             --hhccccCCCceeeEEee
Q 020514          308 --AISPYPKKKSIYMEYVR  324 (325)
Q Consensus       308 --e~~~~~kdG~~~~~~~~  324 (325)
                        ++...+++|..+|+.++
T Consensus       116 ~~~~~~~~~~g~~~~~~~~  134 (167)
T 1v9y_A          116 SRELQLEKKDGSKIWTRFA  134 (167)
T ss_dssp             -CEEEEECTTSCEEEEEEE
T ss_pred             ceEEEEEcCCCcEEEEEEE
Confidence              33446789999888764

>3gdi_A Period circadian protein homolog 2; tandem PAS domains, biological rhythms, cytoplasm, nucleus, phosphoprotein, transcription; 2.40A {Mus musculus}

Probab=98.76  E-value=7.8e-08  Score=80.09  Aligned_cols=106  Identities=8%  Similarity=0.034  Sum_probs=88.2

Q ss_pred             EEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCC-eE-EEEEEEecCCCeEE
Q 020514           30 SFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERP-IE-VNLLNYKKDGTPFW  107 (325)
Q Consensus        30 ~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~-~~-~e~~~~~~dg~~~~  107 (325)
                      .+...+.+   |.++++|+++..++||.+++++|+++..+++|+|...+...+.+.+..+.. .. .++++.+++|..+|
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            56667888   999999999999999999999999988999999987777777777775443 44 58899999999999


Q ss_pred             EEEEEEEeecCCCCeeeEEEEEEeccccchh
Q 020514          108 MLFKMSLVFGKEDGRATHFVAVQVPIVSRKH  138 (325)
Q Consensus       108 ~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~  138 (325)
                      +.....++.+..++++..+++...-++....
T Consensus       244 vet~~~~~~np~s~~~e~ii~~h~v~~gp~~  274 (309)
T 3gdi_A          244 LDTSWSSFINPWSRKISFIIGRHKVRVGPLN  274 (309)
T ss_dssp             EEEEEEEEECTTTCCEEEEEEEEEEEECCSS
T ss_pred             EEEEEEEEECCCCCcccEEEEEEEEccCCCC
Confidence            9999988877346778888888887777544

>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=98.75  E-value=7e-09  Score=77.73  Aligned_cols=59  Identities=17%  Similarity=0.171  Sum_probs=49.5

Q ss_pred             hhhHhhhhccCCceEEec-CCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHH
Q 020514          241 SSLYISLGRIKQSFVLID-PHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQ  304 (325)
Q Consensus       241 ~~l~~~~~~~~~~i~~~d-~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~  304 (325)
                      +.|+.++++++++++++| .   ||+|+++|+++++++||+  +++|+++.+++++.........
T Consensus        17 ~~~~~~~~~~~~~i~~~d~~---~~~i~~~N~~~~~~~g~~--~~~G~~~~~~~~~~~~~~~~~~   76 (158)
T 3k3c_A           17 EDVRRIFEHIPAILVGLEGP---DHRFVAVNAAYRGFSPLL--DTVGQPAREVYPELEGQQIYEM   76 (158)
T ss_dssp             HHHHHHHHHCSSEEEEEETT---TTEEEEECHHHHHHCTTC--CSTTSBHHHHSGGGGGTTHHHH
T ss_pred             HHHHHHHhcCCceEEEEECC---CcEeHHHHHHHHHHcCCc--hhcCCcHHHhCCchhHHHHHHH
Confidence            458889999999999999 6   579999999999999999  9999999998876654333333

>4dj2_A Period circadian protein homolog 1; PAS domains, circadian clock protein, protein binding; 2.75A {Mus musculus}

Probab=98.72  E-value=6e-08  Score=81.14  Aligned_cols=107  Identities=9%  Similarity=0.046  Sum_probs=88.0

Q ss_pred             CEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhC-CCe-EEEEEEEecCCCeE
Q 020514           29 DSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREE-RPI-EVNLLNYKKDGTPF  106 (325)
Q Consensus        29 ~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~-~~~-~~e~~~~~~dg~~~  106 (325)
                      .-+...+.+   |.++++|+++..++||.+++++|+++..+++|+|...+...+.+.+..+ ... ..++++.+++|..+
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            456667888   9999999999999999999999999999999998877777777776643 344 35789999999999


Q ss_pred             EEEEEEEEeecCCCCeeeEEEEEEeccccchh
Q 020514          107 WMLFKMSLVFGKEDGRATHFVAVQVPIVSRKH  138 (325)
Q Consensus       107 ~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~  138 (325)
                      |+.....++.++.++++..+++...-++....
T Consensus       254 wvet~~~~~~np~s~~~e~II~~h~v~~gp~~  285 (320)
T 4dj2_A          254 TMDTSWAGFVHPWSRKVAFVLGRHKVRTAPLN  285 (320)
T ss_dssp             EEECEEEEEECTTTCSEEEEEEEEEESSCCSS
T ss_pred             EEEEEEEEEECCCCCCccEEEEEEEEccCCCC
Confidence            99999988887346778888888887777654

>3kx0_X Uncharacterized protein RV1364C/MT1410; PAS domain, sensory domain, mycobacteium tuberculos molecule binding domain; 2.30A {Mycobacterium tuberculosis}

Probab=98.72  E-value=9.3e-09  Score=79.53  Aligned_cols=54  Identities=19%  Similarity=0.191  Sum_probs=47.5

Q ss_pred             hhhHhhhhccCCceEEec-CCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCCh
Q 020514          241 SSLYISLGRIKQSFVLID-PHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDT  299 (325)
Q Consensus       241 ~~l~~~~~~~~~~i~~~d-~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~  299 (325)
                      +.|+.++++++++++++| .   ||+|+++|++|++++||+  +++|+++.+++++....
T Consensus        37 ~~l~~l~~~~~~~i~~~d~~---~g~i~~~N~a~~~l~G~~--~~~G~~~~~~~~~~~~~   91 (185)
T 3kx0_X           37 EDVRRIFEHIPAILVGLEGP---DHRFVAVNAAYRGFSPLL--DTVGQPAREVYPELEGQ   91 (185)
T ss_dssp             HHHHHHHHHCSSEEEEEETT---TTEEEEECHHHHHHCCCC--SCTTSBHHHHCTTSCSS
T ss_pred             HHHHHHHhcCCceEEEEECC---CcEEEEEcHHHHHHcCCc--cccCCcHHHHCCchhhh
Confidence            457889999999999999 6   589999999999999999  99999999988766543

>4hi4_A Aerotaxis transducer AER2; PAS domain, diatomic GAS sensor, signaling protein; HET: HEM GOL; 2.30A {Pseudomonas aeruginosa}

Probab=98.66  E-value=2.4e-08  Score=71.34  Aligned_cols=51  Identities=14%  Similarity=0.423  Sum_probs=46.2

Q ss_pred             hhhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhC------------CCcccccccccccccC
Q 020514          241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTG------------YDRNEVVGQNCRFLNG  294 (325)
Q Consensus       241 ~~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~G------------y~~~e~iG~~~~~l~~  294 (325)
                      .+++.+++++++||+++|.+   |+|+++|++|++|+|            |++++++|+++..+++
T Consensus         5 ~rl~~il~~~~~gviv~D~~---g~I~~~N~a~~~llg~~~~~i~~~~~g~~~~~~~G~~~~~~~~   67 (121)
T 4hi4_A            5 ARIASALDNVSANVMIADND---LNIIYMNRTVSEMLGRAEADIRKQLPNFDAGRLMGANIDVFHK   67 (121)
T ss_dssp             HHHHHHHTTSSSEEEEEETT---CBEEEECHHHHHHHHHTHHHHHHHCTTCCGGGCTTCBGGGGCS
T ss_pred             HHHHHHHhcCCccEEEEcCC---CeEEEecHHHHHHHHHHHHHHHHhcCCCChHHhcCCCHHHhcC
Confidence            45788999999999999984   799999999999995            9999999999988874

>3a0s_A Sensor protein; PAS-fold, kinase, phosphoprotein, transferase, two-component regulatory system; HET: PG4 PGE; 1.47A {Thermotoga maritima} PDB: 3a0v_A*

Probab=98.61  E-value=4.2e-08  Score=65.84  Aligned_cols=39  Identities=15%  Similarity=0.253  Sum_probs=36.3

Q ss_pred             CCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccc
Q 020514          251 KQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFL  292 (325)
Q Consensus       251 ~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l  292 (325)
                      +++|+++|.   +|+|+++|+++++++||++++++|+++..+
T Consensus         2 ~~~i~~~d~---~g~i~~~N~~~~~l~g~~~~~~~g~~~~~~   40 (96)
T 3a0s_A            2 ETAIITLSK---DGRITEWNKKAEQLFGLKKENVLGRRLKDL   40 (96)
T ss_dssp             CCEEEEEET---TSBEEEECHHHHHHHCCCHHHHTTSBGGGS
T ss_pred             CceEEEEcC---CCCEeehhHHHHHHhCCCHHHhcCCCHHHC
Confidence            689999997   479999999999999999999999999887

>3vol_A Aerotaxis transducer AER2; heme, oxygen sensor protein, PAS, HAMP, cyanoMet, CN-bound, protein; HET: HEM; 2.40A {Pseudomonas aeruginosa}

Probab=98.46  E-value=1.8e-07  Score=75.10  Aligned_cols=51  Identities=14%  Similarity=0.411  Sum_probs=46.4

Q ss_pred             hhhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhh------------CCCcccccccccccccC
Q 020514          241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLT------------GYDRNEVVGQNCRFLNG  294 (325)
Q Consensus       241 ~~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~------------Gy~~~e~iG~~~~~l~~  294 (325)
                      .++..++++++++|+++|+   ||+|+|+|++|++|+            ||++++++|+++..+++
T Consensus        22 ~~l~~iLd~~~~~vii~D~---~g~I~~~N~a~~~ll~~~~~~~~~~l~G~~~~eliG~~~~~~~~   84 (233)
T 3vol_A           22 ARIKSALDNVSANVMIADN---DLNIIYMNRTVSEMLGRAEADIRKQLPNFDAGRLMGANIDVFHK   84 (233)
T ss_dssp             HHHHHHHTTSSSEEEEEET---TSBEEEECHHHHHHHHHTHHHHHTTCTTCCTTSCTTCBGGGGSS
T ss_pred             HHHHHHHhcCCCcEEEECC---CCcEEEecHHHHHHHHHHHHHHHhhcCCCCHHHHcCCCHHHHcC
Confidence            4577899999999999998   579999999999998            89999999999998874

>3a0r_A Sensor protein; four helix bundle, PAS fold, kinase, phosphoprotein, transfe two-component regulatory system; 3.80A {Thermotoga maritima}

Probab=98.44  E-value=6e-08  Score=82.85  Aligned_cols=52  Identities=13%  Similarity=0.157  Sum_probs=45.8

Q ss_pred             hhhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCC
Q 020514          241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGV  295 (325)
Q Consensus       241 ~~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~  295 (325)
                      ..++.++++++++|+++|.   ||+|+++|+++++++||++++++|+++.++.++
T Consensus         8 ~~~~~i~~~~~~~i~~~d~---~g~i~~~N~a~~~l~G~~~~e~~G~~~~~~~~~   59 (349)
T 3a0r_A            8 NFSESILESLETAIITLSK---DGRITEWNKKAEQLFGLKKENVLGRRLKDLPDF   59 (349)
T ss_dssp             -CCCSSGGGSSSEEEEEES---SSBCSCBCHHHHHHHSCCSTTTTTCBSTTSTTT
T ss_pred             HHHHHHHhhhcCeEEEECC---CCCEEeeHHHHHHHhCCCHHHHcCcCHHHCcCh
Confidence            3466789999999999998   479999999999999999999999999888433

>2w0n_A Sensor protein DCUS; signal transduction, two-component regulatory system, PAS, kinase, membrane, transferase, solid state cell inner membrane; NMR {Escherichia coli}

Probab=98.43  E-value=1.4e-07  Score=66.34  Aligned_cols=54  Identities=20%  Similarity=0.170  Sum_probs=47.1

Q ss_pred             hhhhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCC---CcccccccccccccCCC
Q 020514          240 SSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGY---DRNEVVGQNCRFLNGVD  296 (325)
Q Consensus       240 ~~~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy---~~~e~iG~~~~~l~~~~  296 (325)
                      ...++.++++++++++++|.   +|+|+++|+++++++||   ++++++|+++..+.++.
T Consensus        14 ~~~~~~il~~~~~~i~~~d~---~g~i~~~N~~~~~~~g~~~~~~~~~~g~~~~~~~~~~   70 (118)
T 2w0n_A           14 FEQRQAMLQSIKEGVVAVDD---RGEVTLINDAAQELLNYRKSQDDEKLSTLSHSWSQVV   70 (118)
T ss_dssp             HHHHHHHHHCCCCCCEEEBT---TTBCCCBCHHHHHHHCSCTTTTTSSCCCTTCCCSCTH
T ss_pred             HHHHHHHHhhccccEEEECC---CCcEeehhHHHHHHhCCCccChhhhhccCcccccCch
Confidence            34577899999999999997   47999999999999998   88999999998887543

>2ykf_A Pdtas, probable sensor histidine kinase pdtas; transferase, two-component system, GAF domain, PAS domain; 2.00A {Mycobacterium tuberculosis} PDB: 2ykh_A

Probab=97.66  E-value=6.9e-08  Score=80.60  Aligned_cols=112  Identities=13%  Similarity=0.090  Sum_probs=75.6

Q ss_pred             HHhhCCCEEEEEcCCCCCCCEEEechHHHHhcC---CChhhhcCCCCCcccCCC---CCh--HHHHHHHHHHHh-CCCeE
Q 020514           23 ALDELPDSFTITDPSISGHPIVFASRGFLKMSG---FSRAEIIGRNGRMFQGPR---TNR--RTIMEIREAIRE-ERPIE   93 (325)
Q Consensus        23 ~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G---~~~~ei~g~~~~~l~~~~---~~~--~~~~~~~~~~~~-~~~~~   93 (325)
                      +++.+++|++++|.+   |+++++|++++++++   ++ ++++|+++..+++..   ...  .+...+..++.+ +....
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 688999887766432   100  111222223333 22222


Q ss_pred             EEEEEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccccchhhhhcccC
Q 020514           94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMS  145 (325)
Q Consensus        94 ~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~~~~~~~  145 (325)
                      .+..   ..  ..++.++..|+.+  +|.+.|.+.+++|||+.++.++++..
T Consensus       251 ~ei~---~~--~~~l~v~~~Pi~~--~g~~~G~Vvv~rDITE~~~lE~eL~~  295 (305)
T 2ykf_A          251 MEVD---AG--GATVLLRTLPLVV--AGRNVGAAILIRDVTEVKRRDRALIS  295 (305)
Confidence            2211   12  2456778889976  57888999999999999998666543

>2jhe_A Transcription regulator TYRR; aromatic hydrocarbons catabolism, TYRR protei nucleotide-binding, transcription regulation, activator; HET: PG4; 2.30A {Escherichia coli}

Probab=98.30  E-value=7.4e-07  Score=68.96  Aligned_cols=53  Identities=15%  Similarity=0.066  Sum_probs=47.9

Q ss_pred             hhhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCC
Q 020514          241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVD  296 (325)
Q Consensus       241 ~~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~  296 (325)
                      ..+..+++++++||+++|.+   |+|+++|+++++++|++.++++|+++..+.++.
T Consensus        80 ~~l~~il~~~~~gvi~~D~~---g~I~~~N~aa~~llg~~~~~~~g~~~~~~~~~~  132 (190)
T 2jhe_A           80 LALSALLEALPEPVLSVDMK---SKVDMANPASCQLFGQKLDRLRNHTAAQLINGF  132 (190)
T ss_dssp             HHHHHHHHHCSSCEEEECTT---CBEEEECHHHHHHHTSCHHHHTTSBGGGTSTTC
T ss_pred             HHHHHHHHhCCCcEEEEcCC---CCEEEEcHHHHHHhCCCHHHhcCccHHHHhCCC
Confidence            45788999999999999984   799999999999999999999999999887654

>2qkp_A Uncharacterized protein; structural genomics, unknown function, PSI-2, protein struct initiative; 1.75A {Streptococcus mutans}

Probab=98.24  E-value=5.6e-07  Score=66.87  Aligned_cols=52  Identities=12%  Similarity=0.151  Sum_probs=45.7

Q ss_pred             hhhHhhhhccCCceEEecCCCCCCCeEEEehh---hHHhhCCCcccccccccccccCCC
Q 020514          241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDA---FLKLTGYDRNEVVGQNCRFLNGVD  296 (325)
Q Consensus       241 ~~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a---~~~~~Gy~~~e~iG~~~~~l~~~~  296 (325)
                      ..|..++++++++|+++|.+   |+|+|+|++   +++++| ..++++|+++.+++++.
T Consensus        19 ~~l~~IL~~~~~gI~~vD~~---g~I~~~N~a~~~~~~i~g-~~~~~iGr~v~~~~~~~   73 (151)
T 2qkp_A           19 EQANLILNHLPLEITFVNKD---DIFQYYNDSVPAAEMVFK-RTPSQVGRNVELCHPPK   73 (151)
T ss_dssp             HHHHHHHHHSSSEEEEEETT---SBEEEECCCSCGGGCSSC-CCGGGTTSBGGGSSCHH
T ss_pred             HHHHHHHHhCCCceEEEcCC---CeEEEEeCCCchhhhhcC-CCHHHcCCCHHHhCCHH
Confidence            45888999999999999985   799999999   999999 66789999999877533

>2ykf_A Pdtas, probable sensor histidine kinase pdtas; transferase, two-component system, GAF domain, PAS domain; 2.00A {Mycobacterium tuberculosis} PDB: 2ykh_A

Probab=97.38  E-value=4e-07  Score=76.01  Aligned_cols=47  Identities=23%  Similarity=0.138  Sum_probs=39.9

Q ss_pred             hhhhccCCceEEecCCCCCCCeEEEehhhHHhhC---CCcccccccccccccCC
Q 020514          245 ISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTG---YDRNEVVGQNCRFLNGV  295 (325)
Q Consensus       245 ~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~G---y~~~e~iG~~~~~l~~~  295 (325)
                      .+++++++||+++|.+   |+|+++|++++++||   ++ ++++|+++.++.++
T Consensus       174 ~~~~~~~dGIivvD~~---G~Ii~~N~aA~~ll~~lG~~-~~~iGk~l~el~~~  223 (305)
T 2ykf_A          174 RSSPRAGDGFIRLDVD---GVVSYASPNALSAYHRMGLT-TELEGVNLIDATRP  223 (305)
Confidence            3677889999999984   799999999999985   54 78999999887754

>3cax_A Uncharacterized protein PF0695; structural genomics, unknown function, PSI-2, protein struct initiative; 2.43A {Pyrococcus furiosus dsm 3638}

Probab=97.76  E-value=2e-05  Score=67.66  Aligned_cols=53  Identities=11%  Similarity=0.116  Sum_probs=47.2

Q ss_pred             chhhhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCC
Q 020514          239 ISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVD  296 (325)
Q Consensus       239 ~~~~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~  296 (325)
                      ....+..+++++++||+++|.+   |+|+++|++ ++++ +++++++|+++.+++++.
T Consensus       237 ~~~~l~~IL~~l~dgIivvD~~---g~I~~~N~a-e~i~-~~~~e~iGr~v~~~~p~~  289 (369)
T 3cax_A          237 NIEELKAIFEALPVDVTFIDKD---DRVRFFSPG-ERIF-TRTPSVLGRPVQLCHPPK  289 (369)
T ss_dssp             CHHHHHHHHHHSSSEEEEECTT---SBEEEECCS-SCSS-CCCGGGTTCBTTTSSCGG
T ss_pred             hHHHHHHHHHhCCCcEEEECCC---CcEEEEcCH-HHcc-CChHHHcCCcHHHHCChh
Confidence            3456889999999999999984   799999999 9999 999999999999887643

>1oj5_A Steroid receptor coactivator 1A; transcriptional coactivator, complex, LXXLL motif, transcriptional regulation; 2.2A {Mus musculus} SCOP: d.110.3.8

Probab=97.70  E-value=0.00012  Score=51.64  Aligned_cols=102  Identities=11%  Similarity=0.106  Sum_probs=77.1

Q ss_pred             EEEEcCCCCCCCEEEechHHHHhcCCCh--hhhcCCCCCcccCCCCCh--HHHHHHHHHHHhCCCeEEEEEEEecCCCeE
Q 020514           31 FTITDPSISGHPIVFASRGFLKMSGFSR--AEIIGRNGRMFQGPRTNR--RTIMEIREAIREERPIEVNLLNYKKDGTPF  106 (325)
Q Consensus        31 i~~~d~~~~~~~~~~~N~~~~~~~G~~~--~ei~g~~~~~l~~~~~~~--~~~~~~~~~~~~~~~~~~e~~~~~~dg~~~  106 (325)
                      +.-.|.+   |+++++.....+ .++..  ++++|+.+.+++++.|..  .+...+.+++..|......+++..++|..+
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---GKIISIDTSSLR-AAGRTGWEDLVRKCIYAFFQPQGREPSYARQLFQEVMTRGTASSPSYRFILNDGTML   85 (132)
T ss_dssp             EEEECTT---CCEEEEECHHHH-TTCCSCHHHHHHHHHHHHTSCBTTBCCHHHHHHHHHHHHSEEECCCEEEECTTSCEE
T ss_pred             EEeecCC---CcEEEEeccccc-ccccccHHHHHHHHHHHHhCcccchHHHHHHHHHHHHHcCCccccceEEEecCCcEE
Confidence            4556788   999999998874 67777  899999999999999855  778888888887776666788889999999


Q ss_pred             EEEEEEEEeecCCCCeeeEEEEEEeccccc
Q 020514          107 WMLFKMSLVFGKEDGRATHFVAVQVPIVSR  136 (325)
Q Consensus       107 ~~~~~~~~~~~~~~g~~~~~~~~~~DITe~  136 (325)
                      |+......++++...++..++++-.=+.+.
T Consensus        86 ~~qT~sk~f~np~t~e~e~Ivs~n~v~r~~  115 (132)
T 1oj5_A           86 SAHTRCKLCYPQSPDMQPFIMGIHIIDREH  115 (132)
T ss_dssp             EEEEEEEEECC----CCCEEEEEEEEECC-
T ss_pred             EEEEEEEEecCCCCCCCCEEEEEEEEEcCC
Confidence            999988888763345555666655444443

>1oj5_A Steroid receptor coactivator 1A; transcriptional coactivator, complex, LXXLL motif, transcriptional regulation; 2.2A {Mus musculus} SCOP: d.110.3.8

Probab=97.41  E-value=8.7e-05  Score=52.28  Aligned_cols=59  Identities=3%  Similarity=-0.093  Sum_probs=47.1

Q ss_pred             CCCeEEEehhhHHhhCCCc--ccccccccccccCCCCCh--HHHHHHHH----------hhccccCCCceeeEE
Q 020514          263 DMPMVYASDAFLKLTGYDR--NEVVGQNCRFLNGVDTDT--TVLYQVSI----------AISPYPKKKSIYMEY  322 (325)
Q Consensus       263 dg~i~~~N~a~~~~~Gy~~--~e~iG~~~~~l~~~~~~~--~~~~~~~~----------e~~~~~kdG~~~~~~  322 (325)
                      ||+|+++..+..+ .+|.+  +|++|+++.+++++++..  ...+...+          -++++.|||+..|+.
T Consensus        16 dGKf~~vDq~~~r-~~~~~g~qdLlGrsiy~f~H~~D~~~s~l~~h~~~vl~~Gq~~S~~YRfr~k~g~~V~~q   88 (132)
T 1oj5_A           16 TGKIISIDTSSLR-AAGRTGWEDLVRKCIYAFFQPQGREPSYARQLFQEVMTRGTASSPSYRFILNDGTMLSAH   88 (132)
T ss_dssp             TCCEEEEECHHHH-TTCCSCHHHHHHHHHHHHTSCBTTBCCHHHHHHHHHHHHSEEECCCEEEECTTSCEEEEE
T ss_pred             CCcEEEEeccccc-ccccccHHHHHHHHHHHHhCcccchHHHHHHHHHHHHHcCCccccceEEEecCCcEEEEE
Confidence            7999999999874 77888  999999999999998854  44443333          667777999988875

>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=96.38  E-value=0.0023  Score=53.65  Aligned_cols=50  Identities=6%  Similarity=0.097  Sum_probs=39.2

Q ss_pred             CceEE-ecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHH
Q 020514          252 QSFVL-IDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLY  303 (325)
Q Consensus       252 ~~i~~-~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~  303 (325)
                      -|+++ ++.  .+++|+.+|..+++++|+++++++|+++.++++|+....+.+
T Consensus        42 ~G~Ll~~~~--~~~~i~~~S~N~~~~lg~~~~~llG~~l~~ll~~~~~~~l~~   92 (337)
T 2ool_A           42 HGYLFVVSE--TDLRIASVSANVEDLLRQPPASLLNVPIAHYLTAASAARLTH   92 (337)
T ss_dssp             TSEEEEECT--TTCBEEEEETTHHHHHSSCGGGGTTCBGGGGBCHHHHHHHHH
T ss_pred             CEEEEEEEC--CCCEEEEEehhHHHHHCcCHHHHcCCCHHHHcCHHHHHHHHH
Confidence            45544 454  368999999999999999999999999999987755444433

>4ew7_A Conjugative transfer: regulation; alpha-beta-alpha structure, structural genomics, midwest CEN structural genomics (MCSG), PSI-biology; 1.67A {Salmonella enterica subsp}

Probab=90.86  E-value=0.6  Score=30.81  Aligned_cols=34  Identities=15%  Similarity=0.198  Sum_probs=28.6

Q ss_pred             hHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCC
Q 020514          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGY  279 (325)
Q Consensus       243 l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy  279 (325)
                      .+.+..++|.++++-+.++   +|+|+|.+|.+||-.
T Consensus        22 iq~iY~nSPVpVCVRNq~R---kilYaN~aF~elF~K   55 (127)
T 4ew7_A           22 IQDIYKNSPVPVCVRNQSR---KIIYANGAFIELFSK   55 (127)
T ss_dssp             HHHHHTTCSSCEEEECTTS---CEEEECHHHHHHTTS
T ss_pred             HHhhhcCCCccEEEecccc---eEEEecchHHHHhhc
Confidence            4557778899999999875   899999999999543

>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=89.64  E-value=0.42  Score=39.95  Aligned_cols=34  Identities=9%  Similarity=-0.032  Sum_probs=30.8

Q ss_pred             CCCEEEechHHHHhcCCChhhhcCCCCCcccCCC
Q 020514           40 GHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPR   73 (325)
Q Consensus        40 ~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~   73 (325)
                      +++++.+|..+..++|+++++++|+++..++++.
T Consensus        52 ~~~i~~~S~N~~~~lg~~~~~llG~~l~~ll~~~   85 (337)
T 2ool_A           52 DLRIASVSANVEDLLRQPPASLLNVPIAHYLTAA   85 (337)
T ss_dssp             TCBEEEEETTHHHHHSSCGGGGTTCBGGGGBCHH
T ss_pred             CCEEEEEehhHHHHHCcCHHHHcCCCHHHHcCHH
Confidence            4889999999999999999999999988888764

>3s7o_A Bacteriophytochrome; biliverdin, PAS, GAF, photoreceptor, fluorescent protein; HET: LBV GOL; 1.24A {Deinococcus radiodurans} PDB: 3s7n_A* 3s7p_A* 3s7q_A* 2o9c_A* 2o9b_A* 1ztu_A*

Probab=85.20  E-value=0.48  Score=39.49  Aligned_cols=42  Identities=17%  Similarity=0.072  Sum_probs=35.4

Q ss_pred             Cce-EEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCC
Q 020514          252 QSF-VLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGV  295 (325)
Q Consensus       252 ~~i-~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~  295 (325)
                      -|+ ++++..  |++|+.++..+.+++|.++++++|+++..++++
T Consensus        52 hG~LL~l~~~--~~~I~~~S~N~~~~lg~~~~~llG~~l~~ll~~   94 (343)
T 3s7o_A           52 HGALLTADGH--SGEVLQMSLNAATFLGQEPTVLRGQTLAALLPE   94 (343)
T ss_dssp             TSEEEEEETT--TCBEEEEETTHHHHHSSCHHHHTTCBHHHHSTT
T ss_pred             CeEEEEEECC--CCEEEEEcccHHHHhCcChHHHcCCCHHHHHhH
Confidence            344 445553  689999999999999999999999999999876

>4e04_A Bacteriophytochrome (light-regulated signal trans histidine kinase), PHYB1; bacteriophytochrome chromophore binding domain; HET: LBV; 1.79A {Rhodopseudomonas palustris}

Probab=81.41  E-value=0.69  Score=38.34  Aligned_cols=44  Identities=23%  Similarity=0.382  Sum_probs=35.7

Q ss_pred             CceE-EecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCC
Q 020514          252 QSFV-LIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTD  298 (325)
Q Consensus       252 ~~i~-~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~  298 (325)
                      -|++ ++| .  |++|+.++..+.+++|.++++++|+++..++++...
T Consensus        29 hG~Ll~~~-~--~~~I~~~S~N~~~~lg~~~~~~lG~~l~~ll~~~~~   73 (327)
T 4e04_A           29 HGLLLALA-A--DMTIVAGSDNLPELTGLAIGALIGRSAADVFDSETH   73 (327)
T ss_dssp             TSEEEEEC-T--TCBEEEEETTHHHHHSCCHHHHTTCBHHHHBCHHHH
T ss_pred             CeEEEEEc-C--CCeEEEEcccHHHHhCCChHhhcCCCHHHHcCHHHH
Confidence            3444 445 2  789999999999999999999999999998865433

---

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	325
d1n9la_	109	d.110.3.6 (A:) Putative blue light receptor, phot-	7e-18
d1n9la_	109	d.110.3.6 (A:) Putative blue light receptor, phot-	2e-10
d1jnua_	104	d.110.3.6 (A:) Photoreceptor phy3 flavin-binding d	1e-15
d1jnua_	104	d.110.3.6 (A:) Photoreceptor phy3 flavin-binding d	5e-10
d1bywa_	110	d.110.3.6 (A:) Erg potassium channel, N-terminal d	8e-10
d1bywa_	110	d.110.3.6 (A:) Erg potassium channel, N-terminal d	9e-09
d1mzua_	110	d.110.3.1 (A:) PYP domain of sensor histidine kina	3e-04
d1p97a_	114	d.110.3.7 (A:) Hypoxia-inducible factor Hif2a, C-t	0.003

>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 = 75.7 bits (185), Expect = 7e-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 = 55.2 bits (132), Expect = 2e-10
 Identities = 26/49 (53%), Positives = 35/49 (71%)

Query: 250 IKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTD 298
           ++ +FV+ D  LPD P+VYAS+ F  +TGY  +EV+G NCRFL G  TD
Sbjct: 2   LRHTFVVADATLPDCPLVYASEGFYAMTGYGPDEVLGHNCRFLQGEGTD 50

>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 = 69.6 bits (169), Expect = 1e-15
 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 = 53.8 bits (128), Expect = 5e-10
 Identities = 25/40 (62%), Positives = 32/40 (80%)

Query: 252 QSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRF 291
           +SFV+ DP LPD P+++ASD FL+LT Y R EV+G NCRF
Sbjct: 1   KSFVITDPRLPDNPIIFASDRFLELTEYTREEVLGNNCRF 40

>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 = 53.5 bits (127), Expect = 8e-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 = 50.5 bits (119), Expect = 9e-09
 Identities = 12/48 (25%), Positives = 24/48 (50%)

Query: 252 QSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDT 299
           + F++ +  + +  ++Y +D F +L GY R EV+ + C         T
Sbjct: 2   RKFIIANARVENCAVIYCNDGFCELCGYSRAEVMQRPCTCDFLHGPCT 49

>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 = 37.4 bits (86), Expect = 3e-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 = 0.003
 Identities = 9/95 (9%), Positives = 32/95 (33%)

Query: 43  IVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKD 102
             +      ++ G+   E++GR+   F     +       +    + + +        K 
Sbjct: 18  FTYCDDRITELIGYHPEELLGRSAYEFYHALDSENMTKSHQNLCTKGQVVSGQYRMLAKH 77

Query: 103 GTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRK 137
           G   W+  + ++++   + +    + V   +   +
Sbjct: 78  GGYVWLETQGTVIYNPRNLQPQCIMCVNYVLSEIE 112

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	325
d1n9la_	109	Putative blue light receptor, phot-lov1 domain {Gr	99.81
d1bywa_	110	Erg potassium channel, N-terminal domain {Human (H	99.75
d1jnua_	104	Photoreceptor phy3 flavin-binding domain, lov2 {Ma	99.75
d1n9la_	109	Putative blue light receptor, phot-lov1 domain {Gr	99.71
d1ew0a_	130	Histidine kinase FixL heme domain {Rhizobium melil	99.71
d1p97a_	114	Hypoxia-inducible factor Hif2a, C-terminal domain	99.65
d1jnua_	104	Photoreceptor phy3 flavin-binding domain, lov2 {Ma	99.6
d1v9ya_	113	Direct oxygen sensor protein, DOS {Escherichia col	99.56
d1ew0a_	130	Histidine kinase FixL heme domain {Rhizobium melil	99.55
d1v9ya_	113	Direct oxygen sensor protein, DOS {Escherichia col	99.53
d1xj3a1	106	Histidine kinase FixL heme domain {Bradyrhizobium	99.53
d1bywa_	110	Erg potassium channel, N-terminal domain {Human (H	99.47
d1nwza_	125	Photoactive yellow protein, PYP {Ectothiorhodospir	99.47
d1mzua_	110	PYP domain of sensor histidine kinase Ppr {Rhodosp	99.46
d1ll8a_	114	N-terminal PAS domain of Pas kinase {Human (Homo s	99.42
d1xj3a1	106	Histidine kinase FixL heme domain {Bradyrhizobium	99.41
d1mzua_	110	PYP domain of sensor histidine kinase Ppr {Rhodosp	99.4
d1nwza_	125	Photoactive yellow protein, PYP {Ectothiorhodospir	99.36
d1ll8a_	114	N-terminal PAS domain of Pas kinase {Human (Homo s	99.27
d1p97a_	114	Hypoxia-inducible factor Hif2a, C-terminal domain	99.25
d1oj5a_	109	PAS domain of steroid receptor coactivator 1A, NCo	99.06
d1oj5a_	109	PAS domain of steroid receptor coactivator 1A, NCo	98.99
d2oola2	114	Sensor protein PhyB2 {Rhodopseudomonas palustris [	97.83
d2oola2	114	Sensor protein PhyB2 {Rhodopseudomonas palustris [	96.99
d2veaa3	127	Phytochrome-like protein Cph1 {Synechocystis sp. p	96.54
d2o9ca2	127	Bacteriophytochrome BphP {Deinococcus radiodurans	96.47
d2veaa3	127	Phytochrome-like protein Cph1 {Synechocystis sp. p	93.44
d2o9ca2	127	Bacteriophytochrome BphP {Deinococcus radiodurans	92.27
d3c2wa3	113	Bacteriophytochrome BphP {Pseudomonas aeruginosa [	81.52

>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=99.81  E-value=7.7e-19  Score=122.88  Aligned_cols=108  Identities=41%  Similarity=0.805  Sum_probs=97.7

Q ss_pred             CCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEEEEEEecCCCeE
Q 020514           27 LPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPF  106 (325)
Q Consensus        27 ~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg~~~  106 (325)
                      +.+++++.|+..++|+++++|++|++++||++++++|+++..+.++.........+...+..+..+..++..+++||..+
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            46789999953333999999999999999999999999988888887777778888899999999999999999999999


Q ss_pred             EEEEEEEEeecCCCCeeeEEEEEEecccc
Q 020514          107 WMLFKMSLVFGKEDGRATHFVAVQVPIVS  135 (325)
Q Consensus       107 ~~~~~~~~~~~~~~g~~~~~~~~~~DITe  135 (325)
                      |+.+++.|+++ ++|.+.+++++.+|||.
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=99.75  E-value=2.2e-17  Score=115.56  Aligned_cols=106  Identities=27%  Similarity=0.498  Sum_probs=92.5

Q ss_pred             EEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcc--cCCCCChHHHHHHHHHHHhCCCeEEEEEEEecCCCeEE
Q 020514           30 SFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMF--QGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFW  107 (325)
Q Consensus        30 ~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l--~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg~~~~  107 (325)
                      .+++.|.+..++.|+|+|++|++++||+.++++|+++...  .+++........+...+..+..+..++...+++|..+|
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            3567786544588999999999999999999999986543  35666677788888889999999999999999999999


Q ss_pred             EEEEEEEeecCCCCeeeEEEEEEeccccc
Q 020514          108 MLFKMSLVFGKEDGRATHFVAVQVPIVSR  136 (325)
Q Consensus       108 ~~~~~~~~~~~~~g~~~~~~~~~~DITe~  136 (325)
                      +.+++.|+++ ++|.+.+++++++|||+|
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 999999999999999986

>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=99.75  E-value=3.2e-17  Score=113.51  Aligned_cols=103  Identities=41%  Similarity=0.824  Sum_probs=94.8

Q ss_pred             EEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEEEEEEecCCCeEEEE
Q 020514           30 SFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWML  109 (325)
Q Consensus        30 ~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg~~~~~~  109 (325)
                      .+++.|+..++++++|+|++|++++||+.++++|+++..+.++.........+...+..+..+..++...+++|+.+|+.
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            46778855445999999999999999999999999998888888888888899999999999999999999999999999


Q ss_pred             EEEEEeecCCCCeeeEEEEEEecc
Q 020514          110 FKMSLVFGKEDGRATHFVAVQVPI  133 (325)
Q Consensus       110 ~~~~~~~~~~~g~~~~~~~~~~DI  133 (325)
                      +++.|+++ ++|++.+++++.+||
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 999999999999997

>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=99.71  E-value=6.5e-18  Score=118.06  Aligned_cols=75  Identities=37%  Similarity=0.757  Sum_probs=67.4

Q ss_pred             cCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH----------hhccccCCCcee
Q 020514          250 IKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI----------AISPYPKKKSIY  319 (325)
Q Consensus       250 ~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~----------e~~~~~kdG~~~  319 (325)
                      ++++|+++|++.|||+|+|||++|++|+||+++|++|+++..+.+|+..+.....+.+          |++.++|||+.+
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            4689999998878999999999999999999999999999999988888877766655          788889999999


Q ss_pred             eEEee
Q 020514          320 MEYVR  324 (325)
Q Consensus       320 ~~~~~  324 (325)
                      |++++
T Consensus        82 w~~~~   86 (109)
T d1n9la_          82 WNLLT   86 (109)
T ss_dssp             EEEEE
T ss_pred             EEEEE
Confidence            99876

>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=99.71  E-value=1.9e-16  Score=114.27  Aligned_cols=123  Identities=17%  Similarity=0.238  Sum_probs=99.8

Q ss_pred             hhhHHhhhhhhHHHHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHH
Q 020514            5 LGLIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIRE   84 (325)
Q Consensus         5 ~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~   84 (325)
                      +...++.+. ..+++++.++++++++++++|.+   |.++++|+++++++||++++++|+++..++++.........+..
T Consensus         4 l~~~e~~l~-~~e~~~~~i~~~~~~~i~~~d~~---g~i~~~N~~~~~l~Gy~~~el~g~~~~~~~~~~~~~~~~~~~~~   79 (130)
T d1ew0a_           4 MLETEDVVR-ARDAHLRSILDTVPDATVVSATD---GTIVSFNAAAVRQFGYAEEEVIGQNLRILMPEPYRHEHDGYLQR   79 (130)
T ss_dssp             HHHHHHHHH-HHTSCHHHHHTTCSSEEEEEETT---SBEEEECHHHHHHHCCCHHHHTTSBGGGGSCTTTGGGHHHHHHH
T ss_pred             HHHHHHHHH-HHHHHHHHHHHcCCCeEEEEeCC---ccEEEEHHHHHHhhcCCHHHhcCCccccccccchhHHHHHHHHH
Confidence            344455555 56668999999999999999999   99999999999999999999999998888777766665555666


Q ss_pred             HHHhCCC----eEEEEEEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccc
Q 020514           85 AIREERP----IEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV  134 (325)
Q Consensus        85 ~~~~~~~----~~~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIT  134 (325)
                      .+..+..    ...++...++||..+|+.+++.|+.. . +. ..++++++|||
T Consensus        80 ~~~~~~~~~~~~~~e~~~~~~dG~~~~v~~~~~~i~~-~-~~-~~~~~i~rDIT  130 (130)
T d1ew0a_          80 YMATGEKRIIGIDRVVSGQRKDGSTFPMKLAVGEMRS-G-GE-RFFTGFIRDLT  130 (130)
T ss_dssp             HHHHCCCSSTTSCEEEEEECTTSCEEEEEEEEEEEEE-T-TE-EEEEEEEEECC
T ss_pred             HHHhCCCccccceeeEEEEcCCCCEEEEEEEEEEEEE-C-Ce-EEEEEEEEECC
Confidence            5654432    46678888999999999999999987 3 43 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=99.65  E-value=1.8e-16  Score=111.56  Aligned_cols=105  Identities=9%  Similarity=0.194  Sum_probs=92.5

Q ss_pred             EEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEEEEEEecCCCeEEEEE
Q 020514           31 FTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLF  110 (325)
Q Consensus        31 i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg~~~~~~~  110 (325)
                      +...+.+   |.++++|+++++++||+.++++|+++..+++|++...+...+...+..+..+..+++..++||..+|+.+
T Consensus         9 i~r~~~d---G~i~~~N~~~~~~~G~~~~el~g~~~~~~~~~ed~~~~~~~~~~~~~~~~~~~~e~~~~~kdG~~~wv~~   85 (114)
T d1p97a_           9 LSRHSMD---MKFTYCDDRITELIGYHPEELLGRSAYEFYHALDSENMTKSHQNLCTKGQVVSGQYRMLAKHGGYVWLET   85 (114)
T ss_dssp             EEEECTT---TSCSEECTTHHHHTSSCHHHHTTSCHHHHSCSSSHHHHHHHHHHHTTTSEEEEEEEEEECTTSCEEEEEE
T ss_pred             EEEECCC---CcEEEECHHHHHHcCCCccccccccccccccccccccceeeeeecccccceeecceeeeeecCcceEEEE
Confidence            4446899   9999999999999999999999999888888888777777777777777777889999999999999999


Q ss_pred             EEEEeecCCCCeeeEEEEEEeccccchh
Q 020514          111 KMSLVFGKEDGRATHFVAVQVPIVSRKH  138 (325)
Q Consensus       111 ~~~~~~~~~~g~~~~~~~~~~DITe~k~  138 (325)
                      +.+|++++.+|.+.+++++.+|||++|+
T Consensus        86 ~~~~~~~~~~~~~~~ii~~~~dite~k~  113 (114)
T d1p97a_          86 QGTVIYNPRNLQPQCIMCVNYVLSEIEK  113 (114)
T ss_dssp             EEEEEECTTTCSEEEEEEEEEEEEEEEC
T ss_pred             EEEEEEeCCCCCEEEEEEEEEECChhhc
Confidence            9999998236899999999999999986

>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=99.60  E-value=7.2e-16  Score=106.51  Aligned_cols=73  Identities=42%  Similarity=0.788  Sum_probs=66.1

Q ss_pred             ceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH----------hhccccCCCceeeEE
Q 020514          253 SFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI----------AISPYPKKKSIYMEY  322 (325)
Q Consensus       253 ~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~----------e~~~~~kdG~~~~~~  322 (325)
                      .++++|+..+||+|+|+|++|++++||+++|++|+++.++.++...+...+.+..          |++.+++||+.+|++
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            5789998888999999999999999999999999999999999988888777766          888899999999998


Q ss_pred             eeC
Q 020514          323 VRV  325 (325)
Q Consensus       323 ~~~  325 (325)
                      +++
T Consensus        82 ~~~   84 (104)
T d1jnua_          82 FHL   84 (104)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            763

>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=99.56  E-value=2.5e-15  Score=105.35  Aligned_cols=80  Identities=23%  Similarity=0.232  Sum_probs=65.9

Q ss_pred             hHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH--------------h
Q 020514          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI--------------A  308 (325)
Q Consensus       243 l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~--------------e  308 (325)
                      |..+++++++||+++|.   ||+|+++|+++++|+||+++|++|+++..+.++.........+..              |
T Consensus         3 ~~~~~e~~~d~i~~~d~---~g~i~~~N~~~~~l~Gy~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e   79 (113)
T d1v9ya_           3 FFPALEQNMMGAVLINE---NDEVMFFNPAAEKLWGYKREEVIGNNIDMLIPRDLRPAHPEYIRHNREGGKARVEGMSRE   79 (113)
T ss_dssp             HHHHHHTCSSEEEEECT---TSBEEEECHHHHHHHSCCGGGTTTSBGGGGSCGGGTTTHHHHHHHHHC----------CE
T ss_pred             HHHHHHcCcCcEEEEeC---CCCEEEEchhHhhhhccchhhhcCcceeccccccccccccccccccccccccccccccee
Confidence            66789999999999998   479999999999999999999999999888765554443333222              6


Q ss_pred             hccccCCCceeeEEeeC
Q 020514          309 ISPYPKKKSIYMEYVRV  325 (325)
Q Consensus       309 ~~~~~kdG~~~~~~~~~  325 (325)
                      ...++|||+.+|+++++
T Consensus        80 ~~~~~~dG~~~~v~~~~   96 (113)
T d1v9ya_          80 LQLEKKDGSKIWTRFAL   96 (113)
T ss_dssp             EEEECTTSCEEEEEEEE
T ss_pred             eeeccccceeEEEEEEE
Confidence            67788999999999863

>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=99.55  E-value=3e-15  Score=107.84  Aligned_cols=82  Identities=22%  Similarity=0.184  Sum_probs=68.7

Q ss_pred             hhhhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH------------
Q 020514          240 SSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI------------  307 (325)
Q Consensus       240 ~~~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~------------  307 (325)
                      ++.|+.++++++++|+++|.   ||+|+++|+++++|+||+++|++|+++..+.++.........+.+            
T Consensus        15 e~~~~~i~~~~~~~i~~~d~---~g~i~~~N~~~~~l~Gy~~~el~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   91 (130)
T d1ew0a_          15 DAHLRSILDTVPDATVVSAT---DGTIVSFNAAAVRQFGYAEEEVIGQNLRILMPEPYRHEHDGYLQRYMATGEKRIIGI   91 (130)
T ss_dssp             TSCHHHHHTTCSSEEEEEET---TSBEEEECHHHHHHHCCCHHHHTTSBGGGGSCTTTGGGHHHHHHHHHHHCCCSSTTS
T ss_pred             HHHHHHHHHcCCCeEEEEeC---CccEEEEHHHHHHhhcCCHHHhcCCccccccccchhHHHHHHHHHHHHhCCCccccc
Confidence            34588899999999999998   579999999999999999999999999888877766554433332            


Q ss_pred             --hhccccCCCceeeEEee
Q 020514          308 --AISPYPKKKSIYMEYVR  324 (325)
Q Consensus       308 --e~~~~~kdG~~~~~~~~  324 (325)
                        ++..++|||+.+|++++
T Consensus        92 ~~e~~~~~~dG~~~~v~~~  110 (130)
T d1ew0a_          92 DRVVSGQRKDGSTFPMKLA  110 (130)
T ss_dssp             CEEEEEECTTSCEEEEEEE
T ss_pred             eeeEEEEcCCCCEEEEEEE
Confidence              66678899999999876

>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=99.53  E-value=6.6e-14  Score=97.86  Aligned_cols=108  Identities=22%  Similarity=0.258  Sum_probs=81.8

Q ss_pred             HHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHh----CCCeEE
Q 020514           19 WVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIRE----ERPIEV   94 (325)
Q Consensus        19 ~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~----~~~~~~   94 (325)
                      .|.+++++++++++++|.+   |.++++|+++++++||+.++++|++...+.++.............+..    ......
T Consensus         2 ~~~~~~e~~~d~i~~~d~~---g~i~~~N~~~~~l~Gy~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (113)
T d1v9ya_           2 IFFPALEQNMMGAVLINEN---DEVMFFNPAAEKLWGYKREEVIGNNIDMLIPRDLRPAHPEYIRHNREGGKARVEGMSR   78 (113)
T ss_dssp             CHHHHHHTCSSEEEEECTT---SBEEEECHHHHHHHSCCGGGTTTSBGGGGSCGGGTTTHHHHHHHHHC----------C
T ss_pred             HHHHHHHcCcCcEEEEeCC---CCEEEEchhHhhhhccchhhhcCcceecccccccccccccccccccccccccccccce
Confidence            3678999999999999999   999999999999999999999999987776655444433333333322    223455


Q ss_pred             EEEEEecCCCeEEEEEEEEEeecCCCCeeeEEEEEEec
Q 020514           95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVP  132 (325)
Q Consensus        95 e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~D  132 (325)
                      +....+++|+.+|+.+++.|+.+ .++.  .++++++|
T Consensus        79 e~~~~~~dG~~~~v~~~~~~i~~-~~~~--~~~~v~rD  113 (113)
T d1v9ya_          79 ELQLEKKDGSKIWTRFALSKVSA-EGKV--YYLALVRD  113 (113)
T ss_dssp             EEEEECTTSCEEEEEEEEEEEEE-TTEE--EEEEEEEC
T ss_pred             eeeeccccceeEEEEEEEEEEEE-CCeE--EEEEEEEC
Confidence            67788999999999999999997 4443  36777776

>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=99.53  E-value=6.1e-14  Score=96.81  Aligned_cols=101  Identities=19%  Similarity=0.193  Sum_probs=81.2

Q ss_pred             CEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCC----CeEEEEEEEecCCC
Q 020514           29 DSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREER----PIEVNLLNYKKDGT  104 (325)
Q Consensus        29 ~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~----~~~~e~~~~~~dg~  104 (325)
                      +||+++|.+   |+++++|+++++++||+.++++|+++..++++.........+........    ....++...++||.
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            579999999   99999999999999999999999998777777655554444444444332    34567888999999


Q ss_pred             eEEEEEEEEEeecCCCCeeeEEEEEEecccc
Q 020514          105 PFWMLFKMSLVFGKEDGRATHFVAVQVPIVS  135 (325)
Q Consensus       105 ~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe  135 (325)
                      .+|+.+++.|+.+ +++  .+++++++||||
T Consensus        78 ~~~v~~~~~~~~~-~~~--~~~~~~~~DITE  105 (106)
T d1xj3a1          78 TFPMHLSIGEMQS-GGE--PYFTGFVRDLTE  105 (106)
T ss_dssp             EEEEEEEEEEEEE-TTE--EEEEEEEEECHH
T ss_pred             EEEEEEEEEEEEE-CCe--EEEEEEEEeCCC
Confidence            9999999999987 443  357899999997

>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=99.47  E-value=3.8e-14  Score=98.69  Aligned_cols=72  Identities=26%  Similarity=0.505  Sum_probs=60.6

Q ss_pred             ceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccc--cCCCCChHHHHHHHH----------hhccccCCCceee
Q 020514          253 SFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFL--NGVDTDTTVLYQVSI----------AISPYPKKKSIYM  320 (325)
Q Consensus       253 ~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l--~~~~~~~~~~~~~~~----------e~~~~~kdG~~~~  320 (325)
                      .++++|++.+|++|+|+|++|++|+||+++|++|+++..+  .+|+........+.+          ++++++++|+.+|
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            4788998878999999999999999999999999988653  356666666666655          8888899999999


Q ss_pred             EEee
Q 020514          321 EYVR  324 (325)
Q Consensus       321 ~~~~  324 (325)
                      ++++
T Consensus        83 ~~~~   86 (110)
T d1bywa_          83 CLVD   86 (110)
T ss_dssp             EEEE
T ss_pred             eeee
Confidence            9876

>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=99.47  E-value=3.1e-13  Score=96.10  Aligned_cols=102  Identities=14%  Similarity=0.042  Sum_probs=84.2

Q ss_pred             hhhHHHHHHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccC-CCCChHHHHHHHHHHHhCCC
Q 020514           13 NNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQG-PRTNRRTIMEIREAIREERP   91 (325)
Q Consensus        13 ~~~~~~~~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~-~~~~~~~~~~~~~~~~~~~~   91 (325)
                      ++++...+..+++++|.|++++|.+   |+++++|+++++++||++++++|+++..++. +.....+...+.+.+..+..
T Consensus        12 e~~~~~~~d~~ld~~p~gi~~lD~~---G~i~~~N~a~~~l~G~~~~e~iG~~~~~~~~p~~~~~~~~~~~~~~~~~g~~   88 (125)
T d1nwza_          12 ENTLAKMDDGQLDGLAFGAIQLDGD---GNILQYNAAEGDITGRDPKQVIGKNFFKDVAPCTDSPEFYGKFKEGVASGNL   88 (125)
T ss_dssp             HHHTTTCCHHHHTTCSSEEEEEETT---CBEEEECHHHHHHHCCCHHHHTTSBCCCCCCGGGCSTTTHHHHHHHHHHTCC
T ss_pred             HHHHHHHHHHHHhCCCccEEEEeCC---CCEEEEcHHHHHhhccchHhhcCCCHHHccCchhhhhheeeeceeeeecCCc
Confidence            3344556788999999999999999   9999999999999999999999999766554 44555566778888888877


Q ss_pred             eEEEEEEEecCCCeEEEEEEEEEeec
Q 020514           92 IEVNLLNYKKDGTPFWMLFKMSLVFG  117 (325)
Q Consensus        92 ~~~e~~~~~~dg~~~~~~~~~~~~~~  117 (325)
                      ...+....+++|..+|+.+++.+..+
T Consensus        89 ~~~~~~~~~~~G~~~~v~v~l~~~~~  114 (125)
T d1nwza_          89 NTMFEYTFDYQMTPTKVKVHMKKALS  114 (125)
T ss_dssp             EEEEEEEECTTSCCEEEEEEEEECSS
T ss_pred             ceEEEEEeccCCcEEEEEEEEEEecC
Confidence            66666667899999999999888754

>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=99.46  E-value=1.6e-14  Score=100.33  Aligned_cols=79  Identities=9%  Similarity=-0.081  Sum_probs=60.4

Q ss_pred             hHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCC-CChHHHHHHHH---------h-hcc
Q 020514          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVD-TDTTVLYQVSI---------A-ISP  311 (325)
Q Consensus       243 l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~-~~~~~~~~~~~---------e-~~~  311 (325)
                      +..+++++|+||+++|.   ||+|+++|+++++|+||+++|++|+++.+++.|. ........+.+         . -..
T Consensus         5 ~~A~ld~~p~gvi~~D~---~G~I~~~N~aa~~~~G~~~eellG~~~~~~~~p~~~~~~~~~~~~~~~~~g~~~~~~~~~   81 (110)
T d1mzua_           5 GTAEFDALPVGAIQVDG---SGVIHRYNRTESRLSGRIPERVIGRNFFTEVAPCTNIPAFSGRFMDGVTSGTLDARFDFV   81 (110)
T ss_dssp             -CTTGGGCSSEEEEEET---TCBEEEECHHHHHHHCCCHHHHTTSBCCCCCCGGGCSTTTHHHHHHHHHTSCCEEEEEEE
T ss_pred             HHHHHhCCCcEEEEEcC---CCCEEEeHHHHHHHHcCCHHHHcCCCHHHhcCChhhhHHHHHHHHHHHhccccCcceEEE
Confidence            45689999999999997   5899999999999999999999999987665543 33333444433         1 112


Q ss_pred             ccCCCceeeEEee
Q 020514          312 YPKKKSIYMEYVR  324 (325)
Q Consensus       312 ~~kdG~~~~~~~~  324 (325)
                      .+++|+.++++++
T Consensus        82 l~~~G~~~~v~v~   94 (110)
T d1mzua_          82 FDFQMAPVRVQIR   94 (110)
T ss_dssp             EECSSCEEEEEEE
T ss_pred             EecCCceEEEEEE
Confidence            4789999998875

>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=99.42  E-value=6.6e-14  Score=98.08  Aligned_cols=76  Identities=13%  Similarity=0.142  Sum_probs=62.1

Q ss_pred             hccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH--------------hhcccc
Q 020514          248 GRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI--------------AISPYP  313 (325)
Q Consensus       248 ~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~--------------e~~~~~  313 (325)
                      +.+.++|+++|..  +|+|+++|++++++|||+++|++|+++.++.++.........+..              ++...+
T Consensus         5 ~~~n~AI~~id~~--~G~I~~~N~a~~~l~Gy~~~el~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~   82 (114)
T d1ll8a_           5 PEFNKAIFTVDAK--TTEILVANDKACGLLGYSSQDLIGQKLTQFFLRSDSDVVEALSEEHMEADGHAAVVFGTVVDIIS   82 (114)
T ss_dssp             TTTTCEEEEEETT--TCBEEEECTTHHHHHTCCTTTTTTSBGGGGSSCTTTHHHHHTTSSTTSSSSCSSCCCSSSEEECC
T ss_pred             hhcCcEEEEEECC--CCEEEEECHHHHHhhcCCHHHHcCCCeeeecCcccHHHHHHHHHHHHhcCCCccceeeEEEEEEc
Confidence            3457899999975  589999999999999999999999999999987776554433322              456678


Q ss_pred             CCCceeeEEeeC
Q 020514          314 KKKSIYMEYVRV  325 (325)
Q Consensus       314 kdG~~~~~~~~~  325 (325)
                      |||+.+|+++++
T Consensus        83 ~~G~~~pvevs~   94 (114)
T d1ll8a_          83 RSGEKIPVSVWM   94 (114)
T ss_dssp             TTCCCEEEECCE
T ss_pred             cCCcEEEEEEEE
Confidence            999999999863

>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=99.41  E-value=9.7e-14  Score=95.77  Aligned_cols=71  Identities=18%  Similarity=0.214  Sum_probs=58.6

Q ss_pred             CceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH--------------hhccccCCCc
Q 020514          252 QSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI--------------AISPYPKKKS  317 (325)
Q Consensus       252 ~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~--------------e~~~~~kdG~  317 (325)
                      +||+++|.+   |+|+++|+++++|+||+++|++|+++..+.++.........+..              ++..++|||+
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            689999984   79999999999999999999999999888877655544433332              5777899999


Q ss_pred             eeeEEeeC
Q 020514          318 IYMEYVRV  325 (325)
Q Consensus       318 ~~~~~~~~  325 (325)
                      .+|+++++
T Consensus        78 ~~~v~~~~   85 (106)
T d1xj3a1          78 TFPMHLSI   85 (106)
T ss_dssp             EEEEEEEE
T ss_pred             EEEEEEEE
Confidence            99998763

>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=99.40  E-value=1.9e-12  Score=89.54  Aligned_cols=95  Identities=16%  Similarity=0.002  Sum_probs=76.4

Q ss_pred             HHHHHhhCCCEEEEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccC-CCCChHHHHHHHHHHHhCCCeEEEEEE
Q 020514           20 VHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQG-PRTNRRTIMEIREAIREERPIEVNLLN   98 (325)
Q Consensus        20 ~~~~~~~~~~~i~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~-~~~~~~~~~~~~~~~~~~~~~~~e~~~   98 (325)
                      +..+++++|++++++|.+   |+++++|+++++++||++++++|+++..++. +.....+...+.+.+..+......-..
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            457899999999999999   9999999999999999999999999765544 444556677788888887654433333


Q ss_pred             EecCCCeEEEEEEEEEeec
Q 020514           99 YKKDGTPFWMLFKMSLVFG  117 (325)
Q Consensus        99 ~~~dg~~~~~~~~~~~~~~  117 (325)
                      .+++|..+++.++..+...
T Consensus        82 l~~~G~~~~v~v~~~~~~~  100 (110)
T d1mzua_          82 FDFQMAPVRVQIRMQNAGV  100 (110)
T ss_dssp             EECSSCEEEEEEEEEECSS
T ss_pred             EecCCceEEEEEEEEEecC
Confidence            5789999999998888754

>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=99.36  E-value=1.9e-13  Score=97.19  Aligned_cols=79  Identities=14%  Similarity=-0.011  Sum_probs=61.7

Q ss_pred             hHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCC-CChHHHHHHHH----------hhcc
Q 020514          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVD-TDTTVLYQVSI----------AISP  311 (325)
Q Consensus       243 l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~-~~~~~~~~~~~----------e~~~  311 (325)
                      +..+++++|+||+++|.   ||+|+++|+++++++||++++++|+++.+++.|+ ..+.....+.+          +...
T Consensus        19 ~d~~ld~~p~gi~~lD~---~G~i~~~N~a~~~l~G~~~~e~iG~~~~~~~~p~~~~~~~~~~~~~~~~~g~~~~~~~~~   95 (125)
T d1nwza_          19 DDGQLDGLAFGAIQLDG---DGNILQYNAAEGDITGRDPKQVIGKNFFKDVAPCTDSPEFYGKFKEGVASGNLNTMFEYT   95 (125)
T ss_dssp             CHHHHTTCSSEEEEEET---TCBEEEECHHHHHHHCCCHHHHTTSBCCCCCCGGGCSTTTHHHHHHHHHHTCCEEEEEEE
T ss_pred             HHHHHhCCCccEEEEeC---CCCEEEEcHHHHHhhccchHhhcCCCHHHccCchhhhhheeeeceeeeecCCcceEEEEE
Confidence            45689999999999998   4799999999999999999999999987766444 33333443333          3334


Q ss_pred             ccCCCceeeEEee
Q 020514          312 YPKKKSIYMEYVR  324 (325)
Q Consensus       312 ~~kdG~~~~~~~~  324 (325)
                      .+++|+.+|++++
T Consensus        96 ~~~~G~~~~v~v~  108 (125)
T d1nwza_          96 FDYQMTPTKVKVH  108 (125)
T ss_dssp             ECTTSCCEEEEEE
T ss_pred             eccCCcEEEEEEE
Confidence            6789999999875

>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=99.27  E-value=2.4e-12  Score=89.90  Aligned_cols=104  Identities=15%  Similarity=0.141  Sum_probs=81.2

Q ss_pred             hhCCCEEEEEcC-CCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCC----CeEEEEEEE
Q 020514           25 DELPDSFTITDP-SISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREER----PIEVNLLNY   99 (325)
Q Consensus        25 ~~~~~~i~~~d~-~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~~~~~~~~~~~~~~----~~~~e~~~~   99 (325)
                      +.+..+|+++|. +   |.|+++|+++++++||++++++|+++.+++++.+.......+...+..+.    .+..++...
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   99999999999999999999999999999888776654443334344332    123356778


Q ss_pred             ecCCCeEEEEEEEEEeecCCCCeeeEEEEEEeccc
Q 020514          100 KKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV  134 (325)
Q Consensus       100 ~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIT  134 (325)
                      +++|..+|+.++++++..  +|.. .++++++||+
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

>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=99.25  E-value=1.7e-12  Score=90.74  Aligned_cols=73  Identities=15%  Similarity=0.153  Sum_probs=59.3

Q ss_pred             CCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH----------hhccccCCCceee
Q 020514          251 KQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI----------AISPYPKKKSIYM  320 (325)
Q Consensus       251 ~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~----------e~~~~~kdG~~~~  320 (325)
                      +...+++-.+ .||+|+|+|+++++++||+++|++|+++..+++|++.....+.+..          +++.++|||+.+|
T Consensus         4 d~~~fi~r~~-~dG~i~~~N~~~~~~~G~~~~el~g~~~~~~~~~ed~~~~~~~~~~~~~~~~~~~~e~~~~~kdG~~~w   82 (114)
T d1p97a_           4 DSKTFLSRHS-MDMKFTYCDDRITELIGYHPEELLGRSAYEFYHALDSENMTKSHQNLCTKGQVVSGQYRMLAKHGGYVW   82 (114)
T ss_dssp             CCEEEEEEEC-TTTSCSEECTTHHHHTSSCHHHHTTSCHHHHSCSSSHHHHHHHHHHHTTTSEEEEEEEEEECTTSCEEE
T ss_pred             CcCEEEEEEC-CCCcEEEECHHHHHHcCCCccccccccccccccccccccceeeeeecccccceeecceeeeeecCcceE
Confidence            3445554322 2789999999999999999999999999999988887766655554          8888999999999


Q ss_pred             EEee
Q 020514          321 EYVR  324 (325)
Q Consensus       321 ~~~~  324 (325)
                      ++++
T Consensus        83 v~~~   86 (114)
T d1p97a_          83 LETQ   86 (114)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            9864

>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=99.06  E-value=1.6e-10  Score=79.34  Aligned_cols=96  Identities=13%  Similarity=0.156  Sum_probs=74.8

Q ss_pred             EEEEcCCCCCCCEEEechHHHHhcCCCh-hhhcCCCCCcccCCCCChH--HHHHHHHHHHhCCCeEEEEEEEecCCCeEE
Q 020514           31 FTITDPSISGHPIVFASRGFLKMSGFSR-AEIIGRNGRMFQGPRTNRR--TIMEIREAIREERPIEVNLLNYKKDGTPFW  107 (325)
Q Consensus        31 i~~~d~~~~~~~~~~~N~~~~~~~G~~~-~ei~g~~~~~l~~~~~~~~--~~~~~~~~~~~~~~~~~e~~~~~~dg~~~~  107 (325)
                      +.-.|.+   |+++++|+++.+++||.+ ++++|+++.++++|+|.+.  ...........+.....++++.++||..+|
T Consensus         5 ~trh~~~---g~~~~vd~~~~~~~gy~~~eelig~s~~~f~HPeD~~~~~~~~~~~~~~~~g~~~~~~yR~~~kdG~~vW   81 (109)
T d1oj5a_           5 MTKQDTT---GKIISIDTSSLRAAGRTGWEDLVRKCIYAFFQPQGREPSYARQLFQEVMTRGTASSPSYRFILNDGTMLS   81 (109)
T ss_dssp             EEEECTT---CCEEEEECHHHHTTCCSCHHHHHHHHHHHHTSCBTTBCCHHHHHHHHHHHHSEEECCCEEEECTTSCEEE
T ss_pred             EEEECCC---ceEEEECHHHhhHhhcCCHHHHcCCcHHHeECcccchHHHhhHHHHHHHhhcccchhhhhhhhccCcEEE
Confidence            3456788   999999999999999985 8999999999999988643  334456667778778888999999999999


Q ss_pred             EEEEEEEeecCCCCeeeEEEEE
Q 020514          108 MLFKMSLVFGKEDGRATHFVAV  129 (325)
Q Consensus       108 ~~~~~~~~~~~~~g~~~~~~~~  129 (325)
                      +..++.++++...+.+..++++
T Consensus        82 v~t~~~~~~~~~~~~~~~Ii~~  103 (109)
T d1oj5a_          82 AHTRCKLCYPQSPDMQPFIMGI  103 (109)
T ss_dssp             EEEEEEEECC----CCCEEEEE
T ss_pred             EEEEEEEEECCCCCcccEEEEE
Confidence            9999999987223444444443

>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=98.99  E-value=4.7e-11  Score=82.11  Aligned_cols=62  Identities=8%  Similarity=0.037  Sum_probs=51.3

Q ss_pred             CCCeEEEehhhHHhhCCCc-ccccccccccccCCCCChHH-----HHHHHH-------hhccccCCCceeeEEee
Q 020514          263 DMPMVYASDAFLKLTGYDR-NEVVGQNCRFLNGVDTDTTV-----LYQVSI-------AISPYPKKKSIYMEYVR  324 (325)
Q Consensus       263 dg~i~~~N~a~~~~~Gy~~-~e~iG~~~~~l~~~~~~~~~-----~~~~~~-------e~~~~~kdG~~~~~~~~  324 (325)
                      ||+|+++|+++++++||.+ +|++|+++.+|++|++.+..     ...+.+       ++++++|||+.+|++.+
T Consensus        11 ~g~~~~vd~~~~~~~gy~~~eelig~s~~~f~HPeD~~~~~~~~~~~~~~~~g~~~~~~yR~~~kdG~~vWv~t~   85 (109)
T d1oj5a_          11 TGKIISIDTSSLRAAGRTGWEDLVRKCIYAFFQPQGREPSYARQLFQEVMTRGTASSPSYRFILNDGTMLSAHTR   85 (109)
T ss_dssp             TCCEEEEECHHHHTTCCSCHHHHHHHHHHHHTSCBTTBCCHHHHHHHHHHHHSEEECCCEEEECTTSCEEEEEEE
T ss_pred             CceEEEECHHHhhHhhcCCHHHHcCCcHHHeECcccchHHHhhHHHHHHHhhcccchhhhhhhhccCcEEEEEEE
Confidence            7899999999999999986 89999999999999886422     122222       88999999999999754

>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=97.83  E-value=5.3e-06  Score=56.62  Aligned_cols=53  Identities=6%  Similarity=0.088  Sum_probs=42.5

Q ss_pred             Cce-EEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHH
Q 020514          252 QSF-VLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVS  306 (325)
Q Consensus       252 ~~i-~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~  306 (325)
                      -|+ +++|.  +||+|++++++..+++|+++++++|+++.++++|+....+.+.+.
T Consensus        17 hG~Llvld~--~d~~I~~vS~N~~~lLG~~~~~llG~~l~dll~~~~~~~i~~~l~   70 (114)
T d2oola2          17 HGYLFVVSE--TDLRIASVSANVEDLLRQPPASLLNVPIAHYLTAASAARLTHALH   70 (114)
T ss_dssp             TSEEEEECT--TTCBEEEEETTHHHHHSSCGGGGTTCBGGGGBCHHHHHHHHHHHC
T ss_pred             CcEEEEEEC--CCCEEEEEcCCHHHHhCCChHHHcCCCHHHhCCHHHHHHHHHHHh
Confidence            344 44565  379999999999999999999999999999998876655555544

>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=96.99  E-value=0.0005  Score=46.35  Aligned_cols=44  Identities=9%  Similarity=0.046  Sum_probs=36.4

Q ss_pred             EEEEc-CCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChH
Q 020514           31 FTITD-PSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRR   77 (325)
Q Consensus        31 i~~~d-~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~   77 (325)
                      ++++| .+   +.+++++++...++|+++++++|+++.+++++.+...
T Consensus        20 Llvld~~d---~~I~~vS~N~~~lLG~~~~~llG~~l~dll~~~~~~~   64 (114)
T d2oola2          20 LFVVSETD---LRIASVSANVEDLLRQPPASLLNVPIAHYLTAASAAR   64 (114)
T ss_dssp             EEEECTTT---CBEEEEETTHHHHHSSCGGGGTTCBGGGGBCHHHHHH
T ss_pred             EEEEECCC---CEEEEEcCCHHHHhCCChHHHcCCCHHHhCCHHHHHH
Confidence            34555 35   9999999999999999999999999998887754433

>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=96.54  E-value=0.00098  Score=45.66  Aligned_cols=50  Identities=10%  Similarity=0.138  Sum_probs=36.5

Q ss_pred             CceE-EecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHH
Q 020514          252 QSFV-LIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLY  303 (325)
Q Consensus       252 ~~i~-~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~  303 (325)
                      -|++ ++|..  |++|+.++....+++|+++++++|+++.+++++.....+..
T Consensus        26 hG~LLald~~--~~~I~~aS~N~~~~lG~~~~~lLG~~l~~ll~~~~~~~l~~   76 (127)
T d2veaa3          26 HGLVVVLQEP--DLTISQISANCTGILGRSPEDLLGRTLGEVFDSFQIDPIQS   76 (127)
T ss_dssp             TSEEEEEETT--TTEEEEEETTHHHHTSCCTTTSSTTTTTTTSBCC-------
T ss_pred             CeEEEEEECC--CCEEEEEcCCHHHHhCcChHHHcCCCHHHHCCHHHHHHHHH
Confidence            4544 44653  78999999999999999999999999999997765544433

>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=96.47  E-value=0.0012  Score=45.28  Aligned_cols=42  Identities=19%  Similarity=0.114  Sum_probs=35.3

Q ss_pred             CceEE-ecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCC
Q 020514          252 QSFVL-IDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGV  295 (325)
Q Consensus       252 ~~i~~-~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~  295 (325)
                      -|+++ +|..  |++|+.++....+++|+++++++|+++.++++.
T Consensus        35 hG~LLald~~--~~~I~~~S~N~~~~lG~~~~~llG~~l~~ll~~   77 (127)
T d2o9ca2          35 HGALLTADGH--SGEVLQMSLNAATFLGQEPTVLRGQTLAALLPE   77 (127)
T ss_dssp             TSEEEEEETT--TCBEEEEETTHHHHHSSCHHHHTTCBHHHHCTT
T ss_pred             CeEEEEEECC--CCEEEEECCCHHHHhCCChHHHcCCCHHHHCCH
Confidence            35544 4653  689999999999999999999999999999843

>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=93.44  E-value=0.052  Score=36.69  Aligned_cols=44  Identities=14%  Similarity=0.062  Sum_probs=34.0

Q ss_pred             EEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCCCCChH
Q 020514           32 TITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRR   77 (325)
Q Consensus        32 ~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~~~~~~   77 (325)
                      +++|..  ++.+..++.....++|+++++++|+++..++++.....
T Consensus        30 Lald~~--~~~I~~aS~N~~~~lG~~~~~lLG~~l~~ll~~~~~~~   73 (127)
T d2veaa3          30 VVLQEP--DLTISQISANCTGILGRSPEDLLGRTLGEVFDSFQIDP   73 (127)
T ss_dssp             EEEETT--TTEEEEEETTHHHHTSCCTTTSSTTTTTTTSBCC----
T ss_pred             EEEECC--CCEEEEEcCCHHHHhCcChHHHcCCCHHHHCCHHHHHH
Confidence            455542  38999999999999999999999999988887654433

>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=92.27  E-value=0.29  Score=32.77  Aligned_cols=39  Identities=10%  Similarity=0.018  Sum_probs=32.6

Q ss_pred             EEEcCCCCCCCEEEechHHHHhcCCChhhhcCCCCCcccCC
Q 020514           32 TITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGP   72 (325)
Q Consensus        32 ~~~d~~~~~~~~~~~N~~~~~~~G~~~~ei~g~~~~~l~~~   72 (325)
                      +++|..  ++.+..++.....++|++.++++|+++..+++.
T Consensus        39 Lald~~--~~~I~~~S~N~~~~lG~~~~~llG~~l~~ll~~   77 (127)
T d2o9ca2          39 LTADGH--SGEVLQMSLNAATFLGQEPTVLRGQTLAALLPE   77 (127)
T ss_dssp             EEEETT--TCBEEEEETTHHHHHSSCHHHHTTCBHHHHCTT
T ss_pred             EEEECC--CCEEEEECCCHHHHhCCChHHHcCCCHHHHCCH
Confidence            455542  399999999999999999999999998887753

>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=81.52  E-value=0.4  Score=31.31  Aligned_cols=39  Identities=15%  Similarity=0.070  Sum_probs=29.8

Q ss_pred             ceE-EecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCC
Q 020514          253 SFV-LIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGV  295 (325)
Q Consensus       253 ~i~-~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~  295 (325)
                      |++ ++|+   |+.|+.++....+++|++++ .+|+...+++.+
T Consensus        23 G~LLald~---~~~I~~~S~N~~~~lg~~~~-~L~~~~~~~~~~   62 (113)
T d3c2wa3          23 GALVTLRA---DGMVLAASENIQALLGFVAS-PGSYLTQEQVGP   62 (113)
T ss_dssp             EEEEEECT---TSBEEEEETTHHHHTSSCCC-TTCBCCHHHHHH
T ss_pred             eEEEEEcC---CCeEEEEcCCHHHHhCCChh-HhcccHHHHhCH
Confidence            444 4554   68999999999999999864 678887776644