Citrus Sinensis ID: 021027

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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-------32
Protein Sequence
MDSQLGLIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQACTEG
Secondary Structure (PSIPRED)
ccccccHHHHHHccHHHHHHHHHHHHcccEEEEEccccccccEEEEcHHHHHHHcccccccccccccccccccccHHHHHHHHHHHHccccEEEEEEccccccccEEEEEEEEEEEccccccEEEEEEEEEcccccccccccccccccccccccccHHHcccccccccccccHHHHHHHccccccccccccccccHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccHHHHHHHccccccEEEEccccccccEEEEcHHHHHHHccccHHHccccccccccccccHHHHHHHHHHHHcccccccc
Secondary Structure Prediction (SSPRO)
ccccccccHHHHHHHHHHHHHHHHHHcccEEEEEEcccccccEEEEcHHHHHHHcccHHHHccccHHHHccccccHHHHHHHHHHHHHcccEEEEEEEEcccccEEEEEEEEEEEcccccccEEEEEEEEEcccHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccHHHHHHHHHcccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHcccEEEEEEcccccccEEEEcHHHHHHHcccHHHHccccHHHHccccccHHHHHHHHHHHHHcccEEcc
Coil and Loop (DISEMBL)
MDSQLGLIEQSFNNRYTLWVHEALdelpdsftitdpsisghpivfasrgflkmsgfsraeiigrngrmfqgprtnrRTIMEIREAIREErpievnllnykkdgtpfWMLFKMSLVfgkedgratHFVAVQVPIvsrkhmrnsgmsysedgggsrlREIVFGScrrevcsdsLLDLDRVlaldsddtgleiedsceaSDLEKRKAATAIDNILSVLTHYSQLtgrlvcgkrcslpgmgfiSSSLYISLGRikqsfvlidphlpdmpmvyASDAFLKltgydrnevvgqncrflngvdtdTTVLYQIKESIQteqacteg
Flexible Loop (DISEMBL)
MDSQLGLIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEiigrngrmfqgprtnrrTIMEIReaireerpievnllnykkdgtpFWMLFKMSLVFGKEDGRATHFVAVqvpivsrkhmrnsgmsysedgggsrLREIVFGSCRREVCSDSLLDLDRVlaldsddtgleiedsceasdlEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKesiqteqacteg
Low Complexity Region (SEG)
MDSQLGLIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNrrtimeireaireerpieVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQACTEG
Disordered region (IsUnstruct)
******LIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSR******************LREIVFGSCRREVCSDSLLDLDRVLALDSDDTGLEI************KAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKE***********
Disordered Region (DISOPRED)
***QLGL***********WVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTE******
Disordered Region (DISEMBL)
MDSQLGLIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNS*********GSRLREIVFGSCRREVCSDSLLDLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESI*********
Disordered Region (DISPRO)
*****GLIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDRVLALD**DTGLE****C***D**K****************************RCSLPGMGFISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQAC***
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MDSQLGLIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQACTEG
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	318	2.2.26 [Sep-21-2011]
O64511	399	Protein TWIN LOV 1 OS=Ara	yes	no	0.952	0.759	0.646	1e-113
P93025	915	Phototropin-2 OS=Arabidop	no	no	0.899	0.312	0.322	2e-36
Q9ST27	907	Phototropin-2 OS=Oryza sa	no	no	0.336	0.117	0.444	4e-21
Q2RBR1	921	Phototropin-1B OS=Oryza s	no	no	0.336	0.116	0.407	3e-19
Q2QYY8	921	Phototropin-1A OS=Oryza s	no	no	0.336	0.116	0.407	3e-19
Q48IV1	534	Blue-light-activated prot	yes	no	0.342	0.204	0.418	4e-19
O48963	996	Phototropin-1 OS=Arabidop	no	no	0.336	0.107	0.398	2e-18
Q4ZSY3	534	Blue-light-activated prot	yes	no	0.327	0.194	0.419	5e-18
Q9HPU8	674	Bacterioopsin transcripti	yes	no	0.361	0.170	0.362	1e-17
O34627	261	Blue-light photoreceptor	yes	no	0.364	0.444	0.361	1e-17

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

 Score =  408 bits (1049), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 199/308 (64%), Positives = 242/308 (78%), Gaps = 5/308 (1%)

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

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

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

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

Query: 249 RIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKES 308
           RIKQSFVL +P LPDMP++YASDAFL LTGY R EV+GQNCRFL+GVDTD++VLY++KE 
Sbjct: 256 RIKQSFVLTNPCLPDMPIIYASDAFLTLTGYKRQEVLGQNCRFLSGVDTDSSVLYEMKEC 315

Query: 309 IQTEQACT 316
           I   Q+CT
Sbjct: 316 ILKGQSCT 323

Arabidopsis thaliana (taxid: 3702)

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

 Score =  153 bits (387), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 108/335 (32%), Positives = 172/335 (51%), Gaps = 49/335 (14%)

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

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

Query: 136 RKHMRNSGMSYSEDGGGSRLREIVFGSC---------RREVCSDSLLDLDRVLALDSDDT 186
            K +R +G+S S     +R +E    S          R+    +S+ + D ++  DS  T
Sbjct: 245 DKALRPNGLSKSLIRYDARQKEKALDSITEVVQTIRHRKSQVQESVSN-DTMVKPDSSTT 303

Query: 187 ---GLEIEDSCEASDL------------EKRKAATAIDNILSVLTHYSQLTGRLVCGKRC 231
              G +   S EAS               K K++      L  +     +    V G+R 
Sbjct: 304 PTPGRQTRQSDEASKSFRTPGRVSTPTGSKLKSSNNRHEDLLRMEPEELMLSTEVIGQRD 363

Query: 232 SL----------PGMGFISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDR 281
           S            G+      L  +L RI+++FV+ DP LPD P+++ASD+FL+LT Y R
Sbjct: 364 SWDLSDRERDIRQGI-----DLATTLERIEKNFVISDPRLPDNPIIFASDSFLELTEYSR 418

Query: 282 NEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQACT 316
            E++G+NCRFL G +TD   + +I+++I+ ++  T
Sbjct: 419 EEILGRNCRFLQGPETDQATVQKIRDAIRDQREIT 453

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 (254), Expect = 4e-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 = 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|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 = 43/108 (39%), Positives = 68/108 (62%), Gaps = 1/108 (0%)

Query: 24  LDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIR 83
           L+ +  +F ITDP +  +PI+FAS  FL+++ +SR EI+GRN R  QGP T+  T+ +IR
Sbjct: 470 LERIEKNFVITDPRLPDNPIIFASDSFLELTEYSREEILGRNCRFLQGPETDLTTVKKIR 529

Query: 84  EAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQV 131
            AI  +  + V L+NY K G  FW +F +  +  ++ G   +F+ VQ+
Sbjct: 530 NAIDNQTEVTVQLINYTKSGKKFWNIFHLQPMRDQK-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|Q9HPU8|BAT_HALSA Bacterioopsin transcriptional activator OS=Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) GN=bat PE=1 SV=1

 Score = 90.9 bits (224), 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)

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

 Score = 90.9 bits (224), Expect = 1e-17,   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)

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	318
224110804	396	predicted protein [Populus trichocarpa]	0.971	0.780	0.701	1e-128
224102353	396	predicted protein [Populus trichocarpa]	0.971	0.780	0.688	1e-126
225424899	397	PREDICTED: protein TWIN LOV 1 [Vitis vin	0.987	0.790	0.700	1e-124
255558228	375	twin lov protein, putative [Ricinus comm	0.955	0.810	0.696	1e-123
297817884	386	pac motif-containing protein [Arabidopsi	0.946	0.779	0.647	1e-112
18395411	399	protein TWIN LOV 1 [Arabidopsis thaliana	0.952	0.759	0.646	1e-111
30678020	397	protein TWIN LOV 1 [Arabidopsis thaliana	0.952	0.763	0.646	1e-111
42570655	358	protein TWIN LOV 1 [Arabidopsis thaliana	0.952	0.846	0.646	1e-111
350537683	398	LOV/LOV protein [Solanum lycopersicum] g	0.987	0.788	0.598	1e-110
449434827	385	PREDICTED: protein TWIN LOV 1-like [Cucu	0.959	0.792	0.606	1e-110

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

 Score =  463 bits (1192), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 223/318 (70%), Positives = 264/318 (83%), Gaps = 9/318 (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 GRVIHFIGVQVPILRNKRS-------TDDGADAAWNEIVFGSCRREVCSDSLVELGRVLA 173

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

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

Query: 299 TTVLYQIKESIQTEQACT 316
           ++VL QI+ES+Q EQACT
Sbjct: 294 SSVLNQIQESMQVEQACT 311

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 =  458 bits (1178), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 219/318 (68%), Positives = 265/318 (83%), Gaps = 9/318 (2%)

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 TTVLYQIKESIQTEQACT 316
           +++L+Q++ESIQ EQ CT
Sbjct: 294 SSILHQVQESIQVEQPCT 311

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  451 bits (1159), Expect = e-124,   Method: Compositional matrix adjust.
 Identities = 225/321 (70%), Positives = 264/321 (82%), Gaps = 7/321 (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 DTDTTVLYQIKESIQTEQACT 316
           DTD + L Q+KESIQTEQACT
Sbjct: 299 DTDPSTLLQVKESIQTEQACT 319

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  449 bits (1154), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 216/310 (69%), Positives = 258/310 (83%), Gaps = 6/310 (1%)

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 LGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIK 306
           LGRI+QSFVL DPHLPDMP+VYASDAFLKLTGY R+EV+ +NCRFL G+DTD +V+ QIK
Sbjct: 246 LGRIRQSFVLTDPHLPDMPIVYASDAFLKLTGYARHEVLWRNCRFLGGIDTDRSVIEQIK 305

Query: 307 ESIQTEQACT 316
           ++IQ EQACT
Sbjct: 306 KNIQAEQACT 315

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

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 =  410 bits (1053), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 200/309 (64%), Positives = 245/309 (79%), Gaps = 8/309 (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 GRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKE 307
           GRIKQSFVL +P LPDMP++YASDAFL LTGY R EV+GQNCRFL+GVDTD++VLY+IKE
Sbjct: 242 GRIKQSFVLTNPCLPDMPIIYASDAFLTLTGYKRQEVLGQNCRFLSGVDTDSSVLYEIKE 301

Query: 308 SIQTEQACT 316
            I   Q+CT
Sbjct: 302 CILKGQSCT 310

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 =  408 bits (1049), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 199/308 (64%), Positives = 242/308 (78%), Gaps = 5/308 (1%)

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

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

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

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

Query: 249 RIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKES 308
           RIKQSFVL +P LPDMP++YASDAFL LTGY R EV+GQNCRFL+GVDTD++VLY++KE 
Sbjct: 256 RIKQSFVLTNPCLPDMPIIYASDAFLTLTGYKRQEVLGQNCRFLSGVDTDSSVLYEMKEC 315

Query: 309 IQTEQACT 316
           I   Q+CT
Sbjct: 316 ILKGQSCT 323

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 =  408 bits (1049), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 199/308 (64%), Positives = 242/308 (78%), Gaps = 5/308 (1%)

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

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

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

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

Query: 249 RIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKES 308
           RIKQSFVL +P LPDMP++YASDAFL LTGY R EV+GQNCRFL+GVDTD++VLY++KE 
Sbjct: 256 RIKQSFVLTNPCLPDMPIIYASDAFLTLTGYKRQEVLGQNCRFLSGVDTDSSVLYEMKEC 315

Query: 309 IQTEQACT 316
           I   Q+CT
Sbjct: 316 ILKGQSCT 323

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 =  407 bits (1046), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 199/308 (64%), Positives = 242/308 (78%), Gaps = 5/308 (1%)

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

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

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

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

Query: 249 RIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKES 308
           RIKQSFVL +P LPDMP++YASDAFL LTGY R EV+GQNCRFL+GVDTD++VLY++KE 
Sbjct: 256 RIKQSFVLTNPCLPDMPIIYASDAFLTLTGYKRQEVLGQNCRFLSGVDTDSSVLYEMKEC 315

Query: 309 IQTEQACT 316
           I   Q+CT
Sbjct: 316 ILKGQSCT 323

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 =  403 bits (1035), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 194/324 (59%), Positives = 249/324 (76%), Gaps = 10/324 (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 NGVDTDTTVLYQIKESIQTEQACT 316
           +G DT+    +QIK+ IQ EQ CT
Sbjct: 299 SGEDTERGTQFQIKQCIQNEQPCT 322

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 =  402 bits (1034), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 193/318 (60%), Positives = 245/318 (77%), Gaps = 13/318 (4%)

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

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

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

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

Query: 239 ISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTD 298
           + SSL  SL RIKQSFVL DP+LPDMP+VYASD FLKLTGY R EV+G+NCRFL+G+DTD
Sbjct: 230 LCSSLNTSLNRIKQSFVLTDPNLPDMPIVYASDEFLKLTGYTRCEVLGRNCRFLSGIDTD 289

Query: 299 TTVLYQIKESIQTEQACT 316
           ++ L++IKES+Q+EQACT
Sbjct: 290 SSTLFKIKESLQSEQACT 307

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	318
TAIR|locus:2058852	399	PLPB "PAS/LOV PROTEIN C" [Arab	0.959	0.764	0.6	1e-93
TAIR|locus:2155821	915	PHOT2 "phototropin 2" [Arabido	0.386	0.134	0.378	4.5e-30
UNIPROTKB|Q2QYY8	921	PHOT1A "Phototropin-1A" [Oryza	0.345	0.119	0.360	1.6e-29
UNIPROTKB|Q2RBR1	921	PHOT1B "Phototropin-1B" [Oryza	0.345	0.119	0.360	2.4e-29
UNIPROTKB|Q9ST27	907	PHOT2 "Phototropin-2" [Oryza s	0.415	0.145	0.308	1e-28
UNIPROTKB|Q8H935	963	Vfphot1a "Phototropin" [Vicia	0.336	0.111	0.361	2.1e-12
TAIR|locus:2102674	996	PHOT1 "phototropin 1" [Arabido	0.845	0.270	0.267	5.2e-13
UNIPROTKB|G4NFS7	961	MGG_08735 "Uncharacterized pro	0.327	0.108	0.371	1.4e-11
UNIPROTKB|Q887F0	425	PSPTO_1346 "Sensory box/GGDEF	0.349	0.261	0.278	0.00033
UNIPROTKB|G4ND74	816	MGG_00295 "Uncharacterized pro	0.207	0.080	0.484	5.9e-08

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

 Score = 933 (333.5 bits), Expect = 1.0e-93, P = 1.0e-93
 Identities = 186/310 (60%), Positives = 227/310 (73%)

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

Query:   307 ESIQTEQACT 316
             E I   Q+CT
Sbjct:   314 ECILKGQSCT 323

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 = 4.5e-30, Sum P(2) = 4.5e-30
 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 = 1.6e-29, Sum P(2) = 1.6e-29
 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 = 2.4e-29, Sum P(2) = 2.4e-29
 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 = 1.0e-28, Sum P(2) = 1.0e-28
 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 = 2.1e-12, P = 2.1e-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 = 5.2e-13, P = 5.2e-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 = 1.4e-11, P = 1.4e-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 = 0.00033, P = 0.00033
 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|G4ND74 MGG_00295 "Uncharacterized protein" [Magnaporthe oryzae 70-15 (taxid:242507)]

 Score = 154 (59.3 bits), Expect = 5.9e-08, P = 5.9e-08
 Identities = 32/66 (48%), Positives = 41/66 (62%)

Query:   253 SFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTE 312
             SF L DP LPD P+ +ASD FL L+G  R EVVGQNCRFL G       + +IK ++ + 
Sbjct:   342 SFCLTDPLLPDNPIAFASDGFLGLSGCPREEVVGQNCRFLQGGGLQNLGVTRIKSAVSSA 401

Query:   313 QACTEG 318
              A + G
Sbjct:   402 SAGSAG 407

GO:0005575 "cellular_component" evidence=ND

---

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	0.6461	0.9528	0.7593	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

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

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	318
PRK13558	665	PRK13558, PRK13558, bacterio-opsin activator; Prov	4e-30
PRK13557	540	PRK13557, PRK13557, histidine kinase; Provisional	3e-27
PRK13559	361	PRK13559, PRK13559, hypothetical protein; Provisio	4e-27
pfam13426	101	pfam13426, PAS_9, PAS domain	2e-21
PRK13559	361	PRK13559, PRK13559, hypothetical protein; Provisio	7e-18
PRK13557	540	PRK13557, PRK13557, histidine kinase; Provisional	4e-15
PRK13558	665	PRK13558, PRK13558, bacterio-opsin activator; Prov	1e-13
pfam13426	101	pfam13426, PAS_9, PAS domain	8e-09
TIGR02938	494	TIGR02938, nifL_nitrog, nitrogen fixation negative	6e-08
TIGR00229	124	TIGR00229, sensory_box, PAS domain S-box	4e-07
COG2202	232	COG2202, AtoS, FOG: PAS/PAC domain [Signal transdu	3e-04
cd00130	103	cd00130, PAS, PAS domain; PAS motifs appear in arc	8e-04
pfam00989	113	pfam00989, PAS, PAS fold	0.004

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

 Score =  119 bits (301), Expect = 4e-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 = 3e-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 =  108 bits (272), Expect = 4e-27
 Identities = 45/98 (45%), Positives = 60/98 (61%), Gaps = 1/98 (1%)

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

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

Length = 361

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

 Score = 87.0 bits (216), Expect = 2e-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 = 82.6 bits (204), Expect = 7e-18
 Identities = 30/67 (44%), Positives = 43/67 (64%)

Query: 249 RIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKES 308
           + + +  + DPH PD+P+V A+ AFL LTGY   EVVG+NCRFL G  TD   + +I+ +
Sbjct: 51  QTRMAMCITDPHQPDLPIVLANQAFLDLTGYAAEEVVGRNCRFLQGAATDPIAVAKIRAA 110

Query: 309 IQTEQAC 315
           I  E+  
Sbjct: 111 IAAEREI 117

Length = 361

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

 Score = 75.5 bits (186), Expect = 4e-15
 Identities = 24/55 (43%), Positives = 41/55 (74%)

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

Length = 540

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

 Score = 71.0 bits (174), Expect = 1e-13
 Identities = 26/59 (44%), Positives = 42/59 (71%)

Query: 258 DPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQACT 316
           D  LPD P++Y +DAF ++TGY  +EV+G+NCRFL G DT+   + +++E+I  E+  +
Sbjct: 165 DATLPDEPLIYINDAFERITGYSPDEVLGRNCRFLQGEDTNEERVAELREAIDEERPTS 223

Length = 665

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

 Score = 52.0 bits (125), Expect = 8e-09
 Identities = 20/64 (31%), Positives = 37/64 (57%), Gaps = 3/64 (4%)

Query: 254 FVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQ 313
            +++DP   D  +VYA+DA L+L GY R E++G++ R L G   D   + +++E+++   
Sbjct: 1   ILVLDP---DGRIVYANDAALRLLGYTREELLGKSIRDLFGPGDDEEAVARLREALRNGG 57

Query: 314 ACTE 317
               
Sbjct: 58  EVEV 61

Length = 101

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

 Score = 53.4 bits (128), 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 = 4e-07
 Identities = 29/117 (24%), Positives = 51/117 (43%), Gaps = 8/117 (6%)

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

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

The PAS domain was previously described. This sensory box, or S-box domain occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include heme in the oxygen sensor FixL, FAD in the redox potential sensor NifL, and a 4-hydroxycinnamyl chromophore in photoactive yellow protein. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator [Regulatory functions, Small molecule interactions]. Length = 124

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

 Score = 41.0 bits (94), Expect = 3e-04
 Identities = 26/124 (20%), Positives = 45/124 (36%), Gaps = 6/124 (4%)

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

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

Query: 137 KHMR 140
           K   
Sbjct: 229 KQAE 232

Length = 232

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

 Score = 38.0 bits (88), Expect = 8e-04
 Identities = 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 = 36.2 bits (84), Expect = 0.004
 Identities = 19/90 (21%), Positives = 33/90 (36%), Gaps = 6/90 (6%)

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

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

The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya. Length = 113

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	318
PRK13560	807	hypothetical protein; Provisional	99.82
TIGR02040	442	PpsR-CrtJ transcriptional regulator PpsR. This mod	99.82
TIGR02040	442	PpsR-CrtJ transcriptional regulator PpsR. This mod	99.79
TIGR02938	494	nifL_nitrog nitrogen fixation negative regulator N	99.77
PRK09776	1092	putative diguanylate cyclase; Provisional	99.77
PRK09776	1092	putative diguanylate cyclase; Provisional	99.76
PRK13560	807	hypothetical protein; Provisional	99.73
PF13426	104	PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_	99.72
PRK11359	799	cyclic-di-GMP phosphodiesterase; Provisional	99.69
PF08448	110	PAS_4: PAS fold; InterPro: IPR013656 The PAS fold	99.66
PF00989	113	PAS: PAS fold; InterPro: IPR013767 PAS domains are	99.64
PRK11091	779	aerobic respiration control sensor protein ArcB; P	99.44
PRK13559	361	hypothetical protein; Provisional	99.43
PRK13557	540	histidine kinase; Provisional	99.4
PRK13558	665	bacterio-opsin activator; Provisional	99.29
PRK10060	663	RNase II stability modulator; Provisional	99.22
PF00989	113	PAS: PAS fold; InterPro: IPR013767 PAS domains are	99.22
TIGR00229	124	sensory_box PAS domain S-box. The PAS domain was p	99.18
PF08447	91	PAS_3: PAS fold; InterPro: IPR013655 The PAS fold	99.17
PF13426	104	PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_	99.13
PRK11359	799	cyclic-di-GMP phosphodiesterase; Provisional	99.03
PF13596	106	PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.	98.99
cd00130	103	PAS PAS domain; PAS motifs appear in archaea, euba	98.98
PF12860	115	PAS_7: PAS fold	98.93
PF08448	110	PAS_4: PAS fold; InterPro: IPR013656 The PAS fold	98.86
COG3829	560	RocR Transcriptional regulator containing PAS, AAA	98.82
COG3829	560	RocR Transcriptional regulator containing PAS, AAA	98.81
PRK11360	607	sensory histidine kinase AtoS; Provisional	98.79
PF14598	111	PAS_11: PAS domain; PDB: 1P97_A 3F1O_A 2A24_A 3H7W	98.77
KOG0501	971	consensus K+-channel KCNQ [Inorganic ion transport	98.76
TIGR02966	333	phoR_proteo phosphate regulon sensor kinase PhoR.	98.75
PRK13557	540	histidine kinase; Provisional	98.7
PRK11073	348	glnL nitrogen regulation protein NR(II); Provision	98.7
KOG3558	768	consensus Hypoxia-inducible factor 1/Neuronal PAS	98.62
PRK10060	663	RNase II stability modulator; Provisional	98.62
PRK13559	361	hypothetical protein; Provisional	98.6
PF13188	64	PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.	98.58
COG5002	459	VicK Signal transduction histidine kinase [Signal	98.57
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	98.42
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	98.36
PRK11006	430	phoR phosphate regulon sensor protein; Provisional	98.27
PF13188	64	PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.	98.23
PRK11091	779	aerobic respiration control sensor protein ArcB; P	98.2
TIGR00229	124	sensory_box PAS domain S-box. The PAS domain was p	98.2
TIGR02938	494	nifL_nitrog nitrogen fixation negative regulator N	98.13
TIGR02966	333	phoR_proteo phosphate regulon sensor kinase PhoR.	98.04
PRK11073	348	glnL nitrogen regulation protein NR(II); Provision	98.03
COG2202	232	AtoS FOG: PAS/PAC domain [Signal transduction mech	98.01
cd00130	103	PAS PAS domain; PAS motifs appear in archaea, euba	98.0
PRK13558	665	bacterio-opsin activator; Provisional	97.98
PRK11086	542	sensory histidine kinase DcuS; Provisional	97.94
PF08447	91	PAS_3: PAS fold; InterPro: IPR013655 The PAS fold	97.9
smart00091	67	PAS PAS domain. PAS motifs appear in archaea, euba	97.9
COG5000	712	NtrY Signal transduction histidine kinase involved	97.89
PRK11006	430	phoR phosphate regulon sensor protein; Provisional	97.78
KOG1229	775	consensus 3'5'-cyclic nucleotide phosphodiesterase	97.78
PF14598	111	PAS_11: PAS domain; PDB: 1P97_A 3F1O_A 2A24_A 3H7W	97.77
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	97.76
KOG1229	775	consensus 3'5'-cyclic nucleotide phosphodiesterase	97.74
PF12860	115	PAS_7: PAS fold	97.73
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	97.61
PF13596	106	PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.	97.6
KOG3559	598	consensus Transcriptional regulator SIM1 [Transcri	97.48
KOG3558	768	consensus Hypoxia-inducible factor 1/Neuronal PAS	97.4
PF08670	148	MEKHLA: MEKHLA domain; InterPro: IPR013978 The MEK	97.4
PRK09959	1197	hybrid sensory histidine kinase in two-component r	97.39
COG3290	537	CitA Signal transduction histidine kinase regulati	97.39
PRK15053	545	dpiB sensor histidine kinase DpiB; Provisional	97.37
COG2461	409	Uncharacterized conserved protein [Function unknow	97.27
COG3852	363	NtrB Signal transduction histidine kinase, nitroge	97.27
smart00091	67	PAS PAS domain. PAS motifs appear in archaea, euba	97.27
PRK11360	607	sensory histidine kinase AtoS; Provisional	97.24
COG2202	232	AtoS FOG: PAS/PAC domain [Signal transduction mech	97.08
PF08670	148	MEKHLA: MEKHLA domain; InterPro: IPR013978 The MEK	97.05
TIGR02373	124	photo_yellow photoactive yellow protein. Members o	97.02
TIGR02373	124	photo_yellow photoactive yellow protein. Members o	96.83
COG3283	511	TyrR Transcriptional regulator of aromatic amino a	96.68
KOG0501	971	consensus K+-channel KCNQ [Inorganic ion transport	96.43
PRK15053	545	dpiB sensor histidine kinase DpiB; Provisional	96.4
COG3852	363	NtrB Signal transduction histidine kinase, nitroge	96.4
COG3283	511	TyrR Transcriptional regulator of aromatic amino a	96.14
KOG3753	1114	consensus Circadian clock protein period [Signal t	96.1
PRK11086	542	sensory histidine kinase DcuS; Provisional	96.05
COG5002	459	VicK Signal transduction histidine kinase [Signal	95.94
smart00086	43	PAC Motif C-terminal to PAS motifs (likely to cont	95.75
COG3290	537	CitA Signal transduction histidine kinase regulati	95.7
KOG3561	803	consensus Aryl-hydrocarbon receptor nuclear transl	95.65
KOG3560	712	consensus Aryl-hydrocarbon receptor [Transcription	95.49
PF07310	137	PAS_5: PAS domain; InterPro: IPR009922 This family	95.29
COG5000	712	NtrY Signal transduction histidine kinase involved	94.42
KOG3561	803	consensus Aryl-hydrocarbon receptor nuclear transl	93.7
PF08446	110	PAS_2: PAS fold; InterPro: IPR013654 The PAS fold	92.62
PRK09959	1197	hybrid sensory histidine kinase in two-component r	91.0
KOG3559	598	consensus Transcriptional regulator SIM1 [Transcri	90.63
KOG3560	712	consensus Aryl-hydrocarbon receptor [Transcription	89.76
COG3284	606	AcoR Transcriptional activator of acetoin/glycerol	88.33
PF08446	110	PAS_2: PAS fold; InterPro: IPR013654 The PAS fold	87.77
PRK10841	924	hybrid sensory kinase in two-component regulatory	87.67
KOG3753	1114	consensus Circadian clock protein period [Signal t	87.08

>PRK13560 hypothetical protein; Provisional

Probab=99.82  E-value=1.2e-18  Score=166.69  Aligned_cols=179  Identities=15%  Similarity=0.145  Sum_probs=144.0

Q ss_pred             hhHHHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEE
Q 021027           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV   94 (318)
Q Consensus        15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   94 (318)
                      +..++++.++++++++++++|.+   |+++++|++++.++||+.++++|+++..+.++.............+..+.....
T Consensus       201 ~~~~~l~~l~e~~~~~i~~~d~~---g~i~~~N~~~~~~~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  277 (807)
T PRK13560        201 EALHFLQQLLDNIADPAFWKDED---AKVFGCNDAACLACGFRREEIIGMSIHDFAPAQPADDYQEADAAKFDADGSQII  277 (807)
T ss_pred             HHHHHHHHHHhhCCCeEEEEcCC---CCEEEEhHHHHHHhCCCHHHHcCCcchhcCCcchhHHHHHHHHHHhccCCceEE
Confidence            56678999999999999999999   999999999999999999999999988887665544443444445555666777


Q ss_pred             EEEEEecCCcEEEEEEEE--EeeccCCCCceeEEEEEEeccccccccccccccccccCCCCchhhHhhhccccccccccc
Q 021027           95 NLLNYKKDGTPFWMLFKM--SLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSL  172 (318)
Q Consensus        95 ~~~~~~~~g~~~~~~~~~--~~i~~~~~g~~~~~i~~~~DIte~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  172 (318)
                      +..+.+++|..+|+.+..  .|+.+ .+|.+.+++++++|||++|++                                 
T Consensus       278 e~~~~~~dG~~~~~~~~~~~~~~~~-~~g~~~g~~~~~~DITerk~~---------------------------------  323 (807)
T PRK13560        278 EAEFQNKDGRTRPVDVIFNHAEFDD-KENHCAGLVGAITDISGRRAA---------------------------------  323 (807)
T ss_pred             EEEEEcCCCCEEEEEEEecceEEEc-CCCCEEEEEEEEEechHHHHH---------------------------------
Confidence            888889999999766654  45567 788999999999999999997                                 


Q ss_pred             hhccccccccCCCCCcCcccchhhhhHHHHHHHhhhhhhhhhccccccccceeeeeeecCCCCccccchhHHHHHhccCC
Q 021027          173 LDLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQ  252 (318)
Q Consensus       173 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  252 (318)
                                               +...+..                                   +..++.+++++++
T Consensus       324 -------------------------e~~L~~s-----------------------------------e~~l~~l~~~~~~  343 (807)
T PRK13560        324 -------------------------ERELLEK-----------------------------------EDMLRAIIEAAPI  343 (807)
T ss_pred             -------------------------HHHHHHH-----------------------------------HHHHHHHHHhCcc
Confidence                                     1111111                                   1226668888999


Q ss_pred             cEEEecCCCCCCCeeEe-cHHHHHHhCCCcccccCCCccccc
Q 021027          253 SFVLIDPHLPDMPMVYA-SDAFLKLTGYDRNEVVGQNCRFLN  293 (318)
Q Consensus       253 ~i~i~d~~~~~~~i~~~-N~a~~~~~Gy~~~el~G~~~~~l~  293 (318)
                      +|+++|.++   .++++ |+++++++||+.++++|+++..+.
T Consensus       344 ~i~~~d~~g---~i~~~nn~~~~~~~G~~~~e~~g~~~~~~~  382 (807)
T PRK13560        344 AAIGLDADG---NICFVNNNAAERMLGWSAAEVMGKPLPGMD  382 (807)
T ss_pred             cEEEEcCCC---CEEEecCHHHHHHhCCCHHHHcCCCccccC
Confidence            999999997   89887 678888999999999999876654

>TIGR02040 PpsR-CrtJ transcriptional regulator PpsR

Probab=99.82  E-value=1.2e-19  Score=161.36  Aligned_cols=201  Identities=14%  Similarity=0.084  Sum_probs=145.2

Q ss_pred             HhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcC-CeEEEEEEEecC
Q 021027           24 LDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREER-PIEVNLLNYKKD  102 (318)
Q Consensus        24 ~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~  102 (318)
                      ++.++++++++|.+   |+++++|++++.++||+.++++|+++..+++++........+......+. .+..+.....++
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            56789999999999   99999999999999999999999998888887765554555545555443 345554444556


Q ss_pred             CcEEEEEEEEEeeccCCCCceeEEEEEEeccccccccccccccccccCCCCchhhHhhhccccccccccchhcccccccc
Q 021027          103 GTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDRVLALD  182 (318)
Q Consensus       103 g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  182 (318)
                      |...|+.++..++.+   +  .+++++.+|||+.+..++++..                                     
T Consensus        79 g~~~~~~~~~~~~~~---~--~~~~~i~rDi~~~~~~~~~l~~-------------------------------------  116 (442)
T TIGR02040        79 SFELPMRFILVRLGA---D--RGVLALGRDLRAVAELQQQLVA-------------------------------------  116 (442)
T ss_pred             CCccCeEEEEEEeCC---C--CeEEEEecccHHHHHHHHHHHH-------------------------------------
Confidence            667777776666543   2  2668899999998775111100                                     


Q ss_pred             CCCCCcCcccchhhhhHHHHHHHhhhhhhhhhccccccccceeeeeeecCCCCccccchhHHHHHhccCCcEEEecC-CC
Q 021027          183 SDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQSFVLIDP-HL  261 (318)
Q Consensus       183 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~i~i~d~-~~  261 (318)
                                       ......+....                         ++..+.+++.++++++++|+++|. +|
T Consensus       117 -----------------~~~~~e~~~~~-------------------------l~~~e~r~~~l~e~~~~~i~~~d~~~g  154 (442)
T TIGR02040       117 -----------------AQQAMERDYWT-------------------------LREMETRYRVVLEVSSDAVLLVDMSTG  154 (442)
T ss_pred             -----------------HHHHHHHHHHH-------------------------HHHHHHHHHHHHhhCCceEEEEECCCC
Confidence                             00000000000                         011233477889999999999997 56


Q ss_pred             CCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhcccc
Q 021027          262 PDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQA  314 (318)
Q Consensus       262 ~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~~~  314 (318)
                         +|+++|+++++|+||+.++++|+++..+++|.+...+...+......+..
T Consensus       155 ---~i~~~N~a~~~l~G~~~~el~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~  204 (442)
T TIGR02040       155 ---RIVEANSAAAALLGGVGQSLVGRAFPQEFEGRRREELMLTLRNVRATGSA  204 (442)
T ss_pred             ---EEEEEcHHHHHHhCcCHHHHcCCCHHHhCCHHHHHHHHHHHHHHHhcCCC
Confidence               99999999999999999999999999998888877778888877766544

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).

>TIGR02040 PpsR-CrtJ transcriptional regulator PpsR

Probab=99.79  E-value=8e-18  Score=149.63  Aligned_cols=173  Identities=18%  Similarity=0.167  Sum_probs=130.1

Q ss_pred             hhHHHHHHHHhcCCCeEEEEcC-CCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeE
Q 021027           15 RYTLWVHEALDELPDSFTITDP-SISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIE   93 (318)
Q Consensus        15 ~~~~~~~~~~~~~~~~i~~~d~-~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~   93 (318)
                      ..+++++.+++.++++++++|. +   |+++++|++++.++||++++++|+++..+++++........+......+....
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            3457899999999999999997 7   99999999999999999999999988777777665555666666665555544


Q ss_pred             EEEEEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEeccccccccccccccccccCCCCchhhHhhhccccccccccch
Q 021027           94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLL  173 (318)
Q Consensus        94 ~~~~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  173 (318)
                      .+..  .++|...| .+...++..  .+. ..+++...|||+++++                                  
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  23333333 345556544  333 3567788899998875                                  


Q ss_pred             hccccccccCCCCCcCcccchhhhhHHHHHHHhhhhhhhhhccccccccceeeeeeecCCCCccccchhHHHHHhccCCc
Q 021027          174 DLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQS  253 (318)
Q Consensus       174 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  253 (318)
                                              +....                                      ..++.++++++++
T Consensus       247 ------------------------e~~~~--------------------------------------~~~~~l~e~~~d~  264 (442)
T TIGR02040       247 ------------------------GDELS--------------------------------------ENLARLYHEAPDA  264 (442)
T ss_pred             ------------------------hHHHH--------------------------------------HHHHHHHHhCCce
Confidence                                    11000                                      0156688899999


Q ss_pred             EEEecCCCCCCCeeEecHHHHHHhCCC-cccccCCCcccccCC
Q 021027          254 FVLIDPHLPDMPMVYASDAFLKLTGYD-RNEVVGQNCRFLNGV  295 (318)
Q Consensus       254 i~i~d~~~~~~~i~~~N~a~~~~~Gy~-~~el~G~~~~~l~~~  295 (318)
                      |+++|.+|   +|++||++|++++||+ .++++|+++..+..+
T Consensus       265 I~v~D~~G---~I~~~N~a~~~l~G~~~~~~l~G~~~~~~~~~  304 (442)
T TIGR02040       265 IVFSDADG---TIRGANEAFLELTDSSSLEAVRGRTLDRWLGR  304 (442)
T ss_pred             EEEEcCCC---cEEehhHHHHHHhCCCChHHHcCCCHHHHhCC
Confidence            99999987   9999999999999997 578999999877653

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=99.77  E-value=3.2e-18  Score=154.53  Aligned_cols=180  Identities=22%  Similarity=0.338  Sum_probs=147.0

Q ss_pred             HHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEEEEE
Q 021027           18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLL   97 (318)
Q Consensus        18 ~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~   97 (318)
                      ..++.+++.++.+++++|.+   ++++++|++++.++|+++++++|+....+.++.........+...+..+.++..+..
T Consensus         4 ~~~~~i~~~~~~~i~~~d~~---g~~~~~N~~~~~~~G~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (494)
T TIGR02938         4 EAYRQTVDQAPLAISITDLK---ANILYANDAFTRITGYTKEEIIGKNESVLSNHTTPPEVYQALWGSLAEQKPWAGKLL   80 (494)
T ss_pred             HHHHHHHHhCCceEEEECCC---CcEEEEchhheeecCCCHHHHhCCCchhhcCCCCCHHHHHHHHHHHHhCCcccceee
Confidence            46889999999999999999   999999999999999999999998866665555555556666677777777777777


Q ss_pred             EEecCCcEEEEEEEEEeeccCCCCceeEEEEEEeccccccccccccccccccCCCCchhhHhhhccccccccccchhccc
Q 021027           98 NYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDR  177 (318)
Q Consensus        98 ~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  177 (318)
                      ..+++|..+|+.....|+.+ .+|.+.+++++++|||++|++                                      
T Consensus        81 ~~~~~g~~~~~~~~~~~~~~-~~g~~~~~~~~~~DIt~~k~~--------------------------------------  121 (494)
T TIGR02938        81 NRRKDGELYLAELTVAPVLN-EAGETTHFLGMHRDITELHRL--------------------------------------  121 (494)
T ss_pred             ccCCCccchhhheeeEEEEC-CCCCEEEEEEehhhhhHHHHH--------------------------------------
Confidence            77889999999999999998 889999999999999999987                                      


Q ss_pred             cccccCCCCCcCcccchhhhhHHHHHHHhhhhhhhhhccccccccceeeeeeecCCCCccccchhHHHHHhccCCcEEEe
Q 021027          178 VLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQSFVLI  257 (318)
Q Consensus       178 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~i~i~  257 (318)
                                          +...+...                                   ..+..++++++++++++
T Consensus       122 --------------------e~~l~~~~-----------------------------------~~~~~~~~~~~~~i~~~  146 (494)
T TIGR02938       122 --------------------EQVVANQK-----------------------------------LLIESVVDAAPVAFVLL  146 (494)
T ss_pred             --------------------HHHHHHHH-----------------------------------HHHHHHHhcccceEEEE
Confidence                                11111111                                   12556778889999999


Q ss_pred             cCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCC
Q 021027          258 DPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDT  297 (318)
Q Consensus       258 d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~  297 (318)
                      |.++   .++++|++|++++|+...+..+..+..+.++..
T Consensus       147 d~~~---~i~~~N~~~~~~~g~~~~~~~~~~~~~~~~~~~  183 (494)
T TIGR02938       147 DPTG---RVILDNQEYKKLATDLRVKEPAHTVLDLLREAW  183 (494)
T ss_pred             cCCC---CEEEechhHHHhhchhhhhHHHHHHHHHhhHHh
Confidence            9887   999999999999999998888776655554443

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

>PRK09776 putative diguanylate cyclase; Provisional

Probab=99.77  E-value=9.2e-18  Score=165.35  Aligned_cols=201  Identities=13%  Similarity=0.160  Sum_probs=162.4

Q ss_pred             hhHHHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhc-CCeE
Q 021027           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREE-RPIE   93 (318)
Q Consensus        15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~-~~~~   93 (318)
                      ..+++++.++++++++++++|.+   |+++++|+++++++||+.++++|+++..+.+|++.......+....... ..+.
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   9999999999999999999999999888877776655554444444333 3356


Q ss_pred             EEEEEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEeccccccccccccccccccCCCCchhhHhhhccccccccccch
Q 021027           94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLL  173 (318)
Q Consensus        94 ~~~~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  173 (318)
                      .+.+..+++|..+|+.....|+.+ .+|.+.+++++.+|||++|++|+                                
T Consensus       357 ~e~~~~~~dG~~~~~~~~~~~~~~-~~g~~~~~i~~~~DITerk~~e~--------------------------------  403 (1092)
T PRK09776        357 MEKRYYRRDGEVVWALLAVSLVRD-TDGTPLYFIAQIEDINELKRTEQ--------------------------------  403 (1092)
T ss_pred             eeeEEEcCCCCEEEEEEEEEEEEC-CCCCEeeehhhHHhhHHHHHHHH--------------------------------
Confidence            777888999999999999999998 88999999999999999999722                                


Q ss_pred             hccccccccCCCCCcCcccchhhhhHHHHHHHhhhhhhhhhccccccccceeeeeeecCCCCccccchhHHHHHhccCCc
Q 021027          174 DLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQS  253 (318)
Q Consensus       174 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  253 (318)
                                                +.+...                                   ..++.+++..+.+
T Consensus       404 --------------------------~l~~~~-----------------------------------~~~~~~~~~~~~~  422 (1092)
T PRK09776        404 --------------------------VNERLM-----------------------------------ERITLANEAGGIG  422 (1092)
T ss_pred             --------------------------HHHHHH-----------------------------------HHHHHHHHhcCce
Confidence                                      112111                                   1144566778999


Q ss_pred             EEEecCCCCCCCeeEecHHHHHHhCCCcccccCCC-cccccCCCCCHHHHHHHHHHHhcccce
Q 021027          254 FVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQN-CRFLNGVDTDTTVLYQIKESIQTEQAC  315 (318)
Q Consensus       254 i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~-~~~l~~~~~~~~~~~~~~~~l~~~~~~  315 (318)
                      ++.+|.++   .++++|+++++++||+.++..+.. +...++|++.......+.+++..+.++
T Consensus       423 i~~~d~~~---~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~~p~d~~~~~~~~~~~~~~~~~~  482 (1092)
T PRK09776        423 IWEWDLKP---NIISWDKRMFELYEIPPHIKPTWQVWYACLHPEDRQRVEKEIRDALQGRSPF  482 (1092)
T ss_pred             EEEEecCC---CeEeeCHHHHHHhCCCcccCCCHHHHHHhcCHhHHHHHHHHHHHHHhcCCCe
Confidence            99999997   999999999999999999855432 345677888888888888888887765

>PRK09776 putative diguanylate cyclase; Provisional

Probab=99.76  E-value=3.5e-17  Score=161.26  Aligned_cols=179  Identities=16%  Similarity=0.165  Sum_probs=148.1

Q ss_pred             hhHHHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCC-CCcccCCCCChHHHHHHHHHHHhcCCeE
Q 021027           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRN-GRMFQGPRTNRRTIMEIREAIREERPIE   93 (318)
Q Consensus        15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~-~~~l~~~~~~~~~~~~~~~~~~~~~~~~   93 (318)
                      +..++++.+++..+.+++.+|.+   +.++++|+++++++|++.++..+.. +....+|++.......+...+..+.++.
T Consensus       407 ~~~~~~~~~~~~~~~~i~~~d~~---~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~~p~d~~~~~~~~~~~~~~~~~~~  483 (1092)
T PRK09776        407 RLMERITLANEAGGIGIWEWDLK---PNIISWDKRMFELYEIPPHIKPTWQVWYACLHPEDRQRVEKEIRDALQGRSPFK  483 (1092)
T ss_pred             HHHHHHHHHHHhcCceEEEEecC---CCeEeeCHHHHHHhCCCcccCCCHHHHHHhcCHhHHHHHHHHHHHHHhcCCCee
Confidence            45677888999999999999999   9999999999999999988744322 3334566666666667777778888889


Q ss_pred             EEEEEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEeccccccccccccccccccCCCCchhhHhhhccccccccccch
Q 021027           94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLL  173 (318)
Q Consensus        94 ~~~~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  173 (318)
                      .+++..+++| .+|+.....|+.+ ++|.+.+++++.+|||++|+++                                 
T Consensus       484 ~e~r~~~~dG-~~w~~~~~~~~~d-~~G~~~~~ig~~~DITerk~~e---------------------------------  528 (1092)
T PRK09776        484 LEFRIVVKDG-VRHIRALANRVLN-KDGEVERLLGINMDMTEVRQLN---------------------------------  528 (1092)
T ss_pred             EEEEEEcCCc-eEEEEEeeEEEEC-CCCCEEEEEeeeeehhHHHHHH---------------------------------
Confidence            9999999999 9999999999998 8999999999999999999971                                 


Q ss_pred             hccccccccCCCCCcCcccchhhhhHHHHHHHhhhhhhhhhccccccccceeeeeeecCCCCccccchhHHHHHhccCCc
Q 021027          174 DLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQS  253 (318)
Q Consensus       174 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  253 (318)
                                               +..+...                                   ++++.++++++++
T Consensus       529 -------------------------~~L~~~~-----------------------------------~~l~~~l~~~~~~  548 (1092)
T PRK09776        529 -------------------------EALFQEK-----------------------------------ERLHITLDSIGEA  548 (1092)
T ss_pred             -------------------------HHHHHHH-----------------------------------HHHHHHHhccccE
Confidence                                     1111111                                   1255678888999


Q ss_pred             EEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccC
Q 021027          254 FVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNG  294 (318)
Q Consensus       254 i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~  294 (318)
                      |+++|.++   +++++|+++++++||+.+|++|+++..+.+
T Consensus       549 i~~~D~~g---~i~~~N~a~~~l~G~~~~e~iG~~~~~~~~  586 (1092)
T PRK09776        549 VVCTDMAM---KVTFMNPVAEKMTGWTQEEALGVPLLTVLH  586 (1092)
T ss_pred             EEEECCCC---eEEEEcHHHHHHhCCCHHHHcCCCHHHHcc
Confidence            99999997   999999999999999999999999877764

>PRK13560 hypothetical protein; Provisional

Probab=99.73  E-value=2.3e-16  Score=150.95  Aligned_cols=194  Identities=11%  Similarity=0.070  Sum_probs=137.4

Q ss_pred             HHHHHHHhcCCCeEEEEcCCCCCCc--EEEecHhHHHhcCCChhhhcCCC--CCcccCCCCChHHHH-------HHHHHH
Q 021027           18 LWVHEALDELPDSFTITDPSISGHP--IVFASRGFLKMSGFSRAEIIGRN--GRMFQGPRTNRRTIM-------EIREAI   86 (318)
Q Consensus        18 ~~~~~~~~~~~~~i~~~d~~~~~~~--i~~~N~~~~~~~G~~~~e~~g~~--~~~l~~~~~~~~~~~-------~~~~~~   86 (318)
                      ..++.+++++|.++++++.+ +++.  +.+++++...++|+.+.++++..  +..+.+|++......       .+..++
T Consensus        68 ~~~r~l~~~~p~~i~~~~~~-~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~p~d~~~~~~~~~~~~~~~~~~~  146 (807)
T PRK13560         68 QCERNLKANIPGGMFLFALD-GDGTFSFPSLLDANGELAAIAKHDLMADKGLLAMLIGGDDGDFFFANPFRSAETIAMAL  146 (807)
T ss_pred             HHHHHHHhcCCceEEEEEEc-CccccccceeeccchhHHHhcCcccCCccchhhhhcCCCcchhhhhChhhHHHHHHHHh
Confidence            34489999999999998876 2233  33478888888888887766543  344566665544332       222333


Q ss_pred             HhcCCeEEEEEEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEeccccccccccccccccccCCCCchhhHhhhccccc
Q 021027           87 REERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRRE  166 (318)
Q Consensus        87 ~~~~~~~~~~~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  166 (318)
                      ..+.....++++.+++|.  |+.+...|.++ .+|.+ .+.++..|||++|++                           
T Consensus       147 ~~~~~~~~e~r~~~~dg~--~~~~~~~~~~~-~~g~~-~~~g~~~DIT~rk~a---------------------------  195 (807)
T PRK13560        147 QSDDWQEEEGHFRCGDGR--FIDCCLRFERH-AHADD-QVDGFAEDITERKRA---------------------------  195 (807)
T ss_pred             ccCcccceEEEEEeCCcc--EEEEEeeeeec-CCCce-EEEEEEEccchHHHH---------------------------
Confidence            344556778888888986  66777788877 66665 689999999999997                           


Q ss_pred             cccccchhccccccccCCCCCcCcccchhhhhHHHHHHHhhhhhhhhhccccccccceeeeeeecCCCCccccchhHHHH
Q 021027          167 VCSDSLLDLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYIS  246 (318)
Q Consensus       167 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  246 (318)
                                                     +...+...                                   ..++.+
T Consensus       196 -------------------------------e~~l~~~~-----------------------------------~~l~~l  209 (807)
T PRK13560        196 -------------------------------EERIDEAL-----------------------------------HFLQQL  209 (807)
T ss_pred             -------------------------------HHHHHHHH-----------------------------------HHHHHH
Confidence                                           21111111                                   226668


Q ss_pred             HhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhcc
Q 021027          247 LGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTE  312 (318)
Q Consensus       247 ~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~  312 (318)
                      ++++|++++++|.+|   +|+++|+++++++||+.+|++|+++.++.++.............+..+
T Consensus       210 ~e~~~~~i~~~d~~g---~i~~~N~~~~~~~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~  272 (807)
T PRK13560        210 LDNIADPAFWKDEDA---KVFGCNDAACLACGFRREEIIGMSIHDFAPAQPADDYQEADAAKFDAD  272 (807)
T ss_pred             HhhCCCeEEEEcCCC---CEEEEhHHHHHHhCCCHHHHcCCcchhcCCcchhHHHHHHHHHHhccC
Confidence            899999999999987   999999999999999999999999999885554444334444444443

>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=99.72  E-value=2.5e-16  Score=110.99  Aligned_cols=104  Identities=27%  Similarity=0.431  Sum_probs=95.0

Q ss_pred             CCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEEEEEEEecCCcEEE
Q 021027           28 PDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFW  107 (318)
Q Consensus        28 ~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~  107 (318)
                      |++++++|.+   |+++++|+++++++|+++++++|+++..++++.........+.+.+..+..+..+....+++|..+|
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   9999999999999999999999999988888877788888899999988889999999999999999


Q ss_pred             EEEEEEeeccCCCCceeEEEEEEecccc
Q 021027          108 MLFKMSLVFGKEDGRATHFVAVQVPIVS  135 (318)
Q Consensus       108 ~~~~~~~i~~~~~g~~~~~i~~~~DIte  135 (318)
                      +.+++.|+.+ ++|.+.+++++++|||+
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

...

>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional

Probab=99.69  E-value=1.2e-15  Score=145.73  Aligned_cols=193  Identities=19%  Similarity=0.262  Sum_probs=144.8

Q ss_pred             HHHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcC----Ce
Q 021027           17 TLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREER----PI   92 (318)
Q Consensus        17 ~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~----~~   92 (318)
                      ...+...++.++.+++++|.+   ++++++|+++++++||++++++|++...+.+++........+......+.    .+
T Consensus        11 ~~~~~~~le~~~~~i~~~d~~---g~i~~~N~~~~~l~G~s~eeliG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   87 (799)
T PRK11359         11 DGIFFPALEQNMMGAVLINEN---DEVLFFNPAAEKLWGYKREEVIGNNIDMLIPRDLRPAHPEYIRHNREGGKARVEGM   87 (799)
T ss_pred             hhhHHHHHHhhcCcEEEEcCC---CeEEEEcHHHHHHhCCCHHHHcCCCHHHhcCccccccchHHHhhhhccCCcccccc
Confidence            345567889999999999999   99999999999999999999999988877776654433333333333322    23


Q ss_pred             EEEEEEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEeccccccccccccccccccCCCCchhhHhhhccccccccccc
Q 021027           93 EVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSL  172 (318)
Q Consensus        93 ~~~~~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  172 (318)
                      ..++...+++|..+|+.+...|+..  +|. .+++++..|||++++.                                 
T Consensus        88 ~~e~~~~~~dG~~~~v~~~~~~~~~--~g~-~~~~~~~~DiT~~~~~---------------------------------  131 (799)
T PRK11359         88 SRELQLEKKDGSKIWTRFALSKVSA--EGK-VYYLALVRDASVEMAQ---------------------------------  131 (799)
T ss_pred             ceeeEEecCCcCEEEEEEEeeeecc--CCc-eEEEEEEeeccchhhh---------------------------------
Confidence            4467778899999999999888743  444 4578889999998775                                 


Q ss_pred             hhccccccccCCCCCcCcccchhhhhHHHHHHHhhhhhhhhhccccccccceeeeeeecCCCCccccchhHHHHHhccCC
Q 021027          173 LDLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQ  252 (318)
Q Consensus       173 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  252 (318)
                                               ....+                                       .+..+++++++
T Consensus       132 -------------------------~~~~~---------------------------------------~~~~~~~~~~~  147 (799)
T PRK11359        132 -------------------------KEQTR---------------------------------------QLIIAVDHLDR  147 (799)
T ss_pred             -------------------------HHHHH---------------------------------------HHHHHHhcCCC
Confidence                                     11110                                       02235667899


Q ss_pred             cEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccC-CCCCHHHHHHHHHHHhcccce
Q 021027          253 SFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNG-VDTDTTVLYQIKESIQTEQAC  315 (318)
Q Consensus       253 ~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~-~~~~~~~~~~~~~~l~~~~~~  315 (318)
                      +++++|.++   +++++|+++++++||+.++++|+++..+.+ +.+.......+...+..+..+
T Consensus       148 ~i~~~d~~g---~i~~~N~~~~~l~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  208 (799)
T PRK11359        148 PVIVLDPER---RIVQCNRAFTEMFGYCISEASGMQPDTLLNIPEFPADNRIRLQQLLWKTARD  208 (799)
T ss_pred             cEEEEcCCC---cEEEEChhhHhhhCCCHHHHCCCChHHhcCCCCCcHHHHHHHHHhhccCCCC
Confidence            999999987   999999999999999999999999887754 445555566666666655443

>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=99.66  E-value=1.8e-15  Score=107.78  Aligned_cols=110  Identities=26%  Similarity=0.452  Sum_probs=97.6

Q ss_pred             HhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEEEEEEEecCC
Q 021027           24 LDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDG  103 (318)
Q Consensus        24 ~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g  103 (318)
                      |++++++++++|.+   ++++++|+++.+++|++.++++|+++..++++.........+.+++..+.....+..... +|
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            57899999999999   999999999999999999999999988888887777788888888888877666655443 89


Q ss_pred             cEEEEEEEEEeeccCCCCceeEEEEEEeccccccc
Q 021027          104 TPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKH  138 (318)
Q Consensus       104 ~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~  138 (318)
                      ...|+.++..|+.+ .+|.+.+++.+++|||++|+
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 89999999999999999985

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

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

Probab=99.64  E-value=6.4e-15  Score=105.45  Aligned_cols=112  Identities=23%  Similarity=0.363  Sum_probs=93.8

Q ss_pred             HHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEE-EE
Q 021027           18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV-NL   96 (318)
Q Consensus        18 ~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~-~~   96 (318)
                      +++++++++++++++++|.+   |+|+++|+++++++|++.++++|+++..+.++++.......+...+..+..... ..
T Consensus         1 e~~~~i~~~~~~~i~~~d~~---g~I~~~N~a~~~l~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   77 (113)
T PF00989_consen    1 ERYRAILENSPDGIFVIDED---GRILYVNQAAEELLGYSREELIGKSLFDLIHPEDRRELRERLRQALSQGESGESFEV   77 (113)
T ss_dssp             HHHHHHHHCSSSEEEEEETT---SBEEEECHHHHHHHSS-HHHHTTSBGGGGCSGGGHHHHHHHHHHHHHHCCHECEEEE
T ss_pred             CHHHHHHhcCCceEEEEeCc---CeEEEECHHHHHHHccCHHHHcCCcHHHhcCchhhHHHHHHHHHHHHcCCCceeEEE
Confidence            46889999999999999999   999999999999999999999999988888776655566777777776665443 33


Q ss_pred             EEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEecc
Q 021027           97 LNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPI  133 (318)
Q Consensus        97 ~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DI  133 (318)
                      ....++|..+|+.+...|+.+ .++.+.+++++++||
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            333459999999999999999 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=2.9e-12  Score=122.17  Aligned_cols=122  Identities=15%  Similarity=0.193  Sum_probs=106.7

Q ss_pred             hhHHHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEE
Q 021027           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV   94 (318)
Q Consensus        15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   94 (318)
                      +..++++.++++++++++++|.+   |+++++|+++++++|++.++++|+++..++++.............+..+.....
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            35567889999999999999999   999999999999999999999999988887766555555555666677777788


Q ss_pred             EEEEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEeccccccccc
Q 021027           95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMR  140 (318)
Q Consensus        95 ~~~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~~~  140 (318)
                      +.....++|..+|+.++..|+.+ .+|.+.+++++++|||++|+++
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 8899999999999999999983

>PRK13559 hypothetical protein; Provisional

Probab=99.43  E-value=8.1e-12  Score=108.42  Aligned_cols=124  Identities=37%  Similarity=0.669  Sum_probs=105.6

Q ss_pred             hhHHHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEE
Q 021027           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV   94 (318)
Q Consensus        15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   94 (318)
                      .....+..+++.++++++++|.+..++.++++|+++++++||+.++++|+++..+.++.........+...+..+..+..
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            35567888999999999999974223789999999999999999999999877776666555666667777777777778


Q ss_pred             EEEEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEecccccccc
Q 021027           95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM  139 (318)
Q Consensus        95 ~~~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~~  139 (318)
                      +....+++|..+|+.+...|+++ .+|.+.+++++.+|||++|++
T Consensus       120 e~~~~~~dG~~~~~~~~~~~i~d-~~G~~~~~v~~~~DITerk~~  163 (361)
T PRK13559        120 ELLNYRKDGEPFWNALHLGPVYG-EDGRLLYFFGSQWDVTDIRAV  163 (361)
T ss_pred             EEEEEcCCCCEEEEEEEEEEEEc-CCCCEEEeeeeeeehhcchhh
Confidence            88888899999999999999998 889999999999999999986

>PRK13557 histidine kinase; Provisional

Probab=99.40  E-value=4.9e-12  Score=115.73  Aligned_cols=127  Identities=37%  Similarity=0.688  Sum_probs=109.9

Q ss_pred             hhHHHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEE
Q 021027           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV   94 (318)
Q Consensus        15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   94 (318)
                      .....|..+++.++.+++++|.+..+++++|+|++|++++||+.++++|+++..+.+++........+...+..+..+..
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            34678999999999999999963233899999999999999999999999988888777766667777777777777777


Q ss_pred             EEEEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEeccccccccccc
Q 021027           95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNS  142 (318)
Q Consensus        95 ~~~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~~~~~  142 (318)
                      +....+++|..+|+.++..|+.+ .+|.+.+++++..|||+++++++.
T Consensus       107 ~~~~~~~~G~~~~~~~~~~~i~~-~~g~~~~~~~~~~dit~~~~~e~~  153 (540)
T PRK13557        107 EILNYRKDGSSFWNALFVSPVYN-DAGDLVYFFGSQLDVSRRRDAEDA  153 (540)
T ss_pred             EEEEEeCCCCEEEEEEEEEEeEC-CCCCEEEEEEEecChHHHHHHHHH
Confidence            77778899999999999999998 889999999999999999987543

>PRK13558 bacterio-opsin activator; Provisional

Probab=99.29  E-value=6.2e-11  Score=111.13  Aligned_cols=125  Identities=38%  Similarity=0.695  Sum_probs=106.5

Q ss_pred             HHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEEEEEE
Q 021027           19 WVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLN   98 (318)
Q Consensus        19 ~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   98 (318)
                      .+..+++.++.+++++|...+++.++++|+++++++||++++++|+++..+.++.........+...+..+.++..+...
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            45678999999999998532348999999999999999999999998877777666656666677777777888888888


Q ss_pred             EecCCcEEEEEEEEEeeccCCCCceeEEEEEEeccccccccccccc
Q 021027           99 YKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGM  144 (318)
Q Consensus        99 ~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~~~~~~~  144 (318)
                      ++++|..+|+.+...|+.+ .+|.+.+++++..|||++|++|+++.
T Consensus       229 ~~~dG~~~~~~~~~~pi~d-~~G~~~~~vgi~~DITerk~~E~~L~  273 (665)
T PRK13558        229 YRKDGSTFWNQVDIAPIRD-EDGTVTHYVGFQTDVTERKEAELALQ  273 (665)
T ss_pred             ECCCCCEEEEEEEEEEEEC-CCCCEEEEEEEEEeCcHHHHHHHHHH
Confidence            8999999999999999998 89999999999999999999865543

>PRK10060 RNase II stability modulator; Provisional

Probab=99.22  E-value=4.2e-10  Score=104.93  Aligned_cols=120  Identities=14%  Similarity=0.190  Sum_probs=93.8

Q ss_pred             hHHHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCccc-CCCCChHHHHHHHHHHHhcCCeEE
Q 021027           16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQ-GPRTNRRTIMEIREAIREERPIEV   94 (318)
Q Consensus        16 ~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~-~~~~~~~~~~~~~~~~~~~~~~~~   94 (318)
                      ...++..+++.++++++++|.+   |+++++|+++++++||+.++++|+++..++ ++.........+...+..+..+..
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            3456778999999999999999   999999999999999999999999865544 444444445556666777888888


Q ss_pred             EEEEEecCCcEEEEEEEEEeeccCCCC-ceeEEEEEEeccccccccc
Q 021027           95 NLLNYKKDGTPFWMLFKMSLVFGKEDG-RATHFVAVQVPIVSRKHMR  140 (318)
Q Consensus        95 ~~~~~~~~g~~~~~~~~~~~i~~~~~g-~~~~~i~~~~DIte~k~~~  140 (318)
                      +....+++|..+|+.....+ .. ..| ....++++.+|||++|+++
T Consensus       186 e~~~~~~~G~~~~~~~~~~~-~~-~~g~~~~~~i~~~~DITe~k~~e  230 (663)
T PRK10060        186 ERWIKTRKGQRLFLFRNKFV-HS-GSGKNEIFLICSGTDITEERRAQ  230 (663)
T ss_pred             EEEEEeCCCCEEEEEeeeEE-Ec-CCCCceEEEEEEEEechHHHHHH
Confidence            88888999988887655443 33 344 3456788899999999873

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

Probab=99.22  E-value=2.1e-11  Score=87.07  Aligned_cols=72  Identities=17%  Similarity=0.270  Sum_probs=63.2

Q ss_pred             hhHHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhcccce
Q 021027          241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQAC  315 (318)
Q Consensus       241 ~~l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~~~~  315 (318)
                      ++++.++++++++++++|.+|   .|+++|+++++++||+.++++|+++.+++++++.....+.+.+.+..+++.
T Consensus         1 e~~~~i~~~~~~~i~~~d~~g---~I~~~N~a~~~l~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   72 (113)
T PF00989_consen    1 ERYRAILENSPDGIFVIDEDG---RILYVNQAAEELLGYSREELIGKSLFDLIHPEDRRELRERLRQALSQGESG   72 (113)
T ss_dssp             HHHHHHHHCSSSEEEEEETTS---BEEEECHHHHHHHSS-HHHHTTSBGGGGCSGGGHHHHHHHHHHHHHHCCHE
T ss_pred             CHHHHHHhcCCceEEEEeCcC---eEEEECHHHHHHHccCHHHHcCCcHHHhcCchhhHHHHHHHHHHHHcCCCc
Confidence            357889999999999999887   999999999999999999999999999998887667888888888776654

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 ....

>TIGR00229 sensory_box PAS domain S-box

Probab=99.18  E-value=6.6e-10  Score=78.43  Aligned_cols=117  Identities=21%  Similarity=0.349  Sum_probs=90.4

Q ss_pred             HHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhc-CCeEEEE
Q 021027           18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREE-RPIEVNL   96 (318)
Q Consensus        18 ~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~-~~~~~~~   96 (318)
                      ..+..+++.++.+++++|.+   +.++++|+++..++|++..+++|.....+.++.........+...+... .......
T Consensus         3 ~~~~~~~~~~~~~~~~~d~~---~~i~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   79 (124)
T TIGR00229         3 ERYRAIFESSPDAIIVIDLE---GNILYVNPAFEEIFGYSAEELIGRNVLELIPEEDREEVRERIERLLEGEREPVSEER   79 (124)
T ss_pred             hHHHHHHhhCCceEEEEcCC---CcEEEEchHHHHHhCCChHHhcCcchhhhcChhhhHHHHHHHHHHHcCCCCCcceEe
Confidence            45678999999999999999   9999999999999999999999988766666555444444444544422 2233344


Q ss_pred             EEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEecccccccc
Q 021027           97 LNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM  139 (318)
Q Consensus        97 ~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~~  139 (318)
                      .....+|...|+.....|+..  +|...+++++..|||+++++
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~dit~~~~~  120 (124)
T TIGR00229        80 RVRRKDGSEIWVEVSVSPIRT--NGGELGVVGIVRDITERKQA  120 (124)
T ss_pred             eeEcCCCCEEEEEEEEeehhh--CCCeeEEEEEeeehhHHHHH
Confidence            445778899999988888863  67788899999999999886

The PAS domain was previously described. This sensory box, or S-box domain occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include heme in the oxygen sensor FixL, FAD in the redox potential sensor NifL, and a 4-hydroxycinnamyl chromophore in photoactive yellow protein. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator.

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

Probab=99.17  E-value=3.1e-10  Score=77.70  Aligned_cols=86  Identities=26%  Similarity=0.464  Sum_probs=71.7

Q ss_pred             EEEecHhHHHhcCCChhhhcCCC----CCcccCCCCChHHHHHHHH-HHHhcCCeEEEEEEEecCCcEEEEEEEEEeecc
Q 021027           43 IVFASRGFLKMSGFSRAEIIGRN----GRMFQGPRTNRRTIMEIRE-AIREERPIEVNLLNYKKDGTPFWMLFKMSLVFG  117 (318)
Q Consensus        43 i~~~N~~~~~~~G~~~~e~~g~~----~~~l~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~i~~  117 (318)
                      ++++|+.+++++||+++++ +..    +..+.+|++...+...+.. ....+..+..++++++++|..+|+...+.++++
T Consensus         1 ~i~~s~~~~~i~G~~~~~~-~~~~~~~~~~~ihpdD~~~~~~~~~~~~~~~~~~~~~e~R~~~~~G~~~wi~~~~~~~~d   79 (91)
T PF08447_consen    1 IIYWSDNFYEIFGYSPEEI-GKPDFEEWLERIHPDDRERVRQAIQQAALQNGEPFEIEYRIRRKDGEYRWIEVRGRPIFD   79 (91)
T ss_dssp             -EEE-THHHHHHTS-HHHH-TCBEHHHHHHHB-TTTHHHHHHHHHHHHHHTT-EEEEEEEEEGTTSTEEEEEEEEEEEET
T ss_pred             CEEEeHHHHHHhCCCHHHh-ccCCHHHHHhhcCHHHHHHHHHHHHHHhhccCcceEEEEEEECCCCCEEEEEEEEEEEEC
Confidence            5899999999999999999 655    6667899998888888888 677777899999999999999999999999998


Q ss_pred             CCCCceeEEEEEE
Q 021027          118 KEDGRATHFVAVQ  130 (318)
Q Consensus       118 ~~~g~~~~~i~~~  130 (318)
                       .+|.+..++|+.
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.

>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=99.13  E-value=1.3e-10  Score=81.44  Aligned_cols=63  Identities=21%  Similarity=0.406  Sum_probs=56.5

Q ss_pred             CCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhccccee
Q 021027          251 KQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQACT  316 (318)
Q Consensus       251 ~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~~~~~  316 (318)
                      |++++++|.+|   +|++||++|++++||++++++|+++.++.++.........+.++++.+.+|.
T Consensus         1 p~~i~i~d~~g---~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   63 (104)
T PF13426_consen    1 PDGIFILDPDG---RILYVNPAFERLFGYSREELIGKSISDFFPEEDRPEFEEQIERALEEGGSWS   63 (104)
T ss_dssp             -SEEEEEETTS---BEEEE-HHHHHHHTS-HHHHTTSBGGGGCSTTSCHHHHHHHHHHHHHTSSEE
T ss_pred             CEEEEEECCcC---cEEehhHHHHHHHCcCHHHHcCCCcccccCcccchhhHHHHHHHHhcCCcee
Confidence            68999999987   9999999999999999999999999999998889999999999999888764

...

>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional

Probab=99.03  E-value=2.7e-09  Score=102.41  Aligned_cols=121  Identities=19%  Similarity=0.299  Sum_probs=99.6

Q ss_pred             hHHHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccC-CCCChHHHHHHHHHHHhcCCeEE
Q 021027           16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQG-PRTNRRTIMEIREAIREERPIEV   94 (318)
Q Consensus        16 ~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~-~~~~~~~~~~~~~~~~~~~~~~~   94 (318)
                      ..+.+..+++.++.+++++|.+   ++++++|+++++++|++.++++|+.+..+.+ +.........+...+..+..+..
T Consensus       134 ~~~~~~~~~~~~~~~i~~~d~~---g~i~~~N~~~~~l~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  210 (799)
T PRK11359        134 QTRQLIIAVDHLDRPVIVLDPE---RRIVQCNRAFTEMFGYCISEASGMQPDTLLNIPEFPADNRIRLQQLLWKTARDQD  210 (799)
T ss_pred             HHHHHHHHHhcCCCcEEEEcCC---CcEEEEChhhHhhhCCCHHHHCCCChHHhcCCCCCcHHHHHHHHHhhccCCCCcc
Confidence            3455667899999999999999   9999999999999999999999998665543 34444444455555666666667


Q ss_pred             EEEEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEeccccccccc
Q 021027           95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMR  140 (318)
Q Consensus        95 ~~~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~~~  140 (318)
                      +....+++|..+|+.+...|+.+ .+|.+.+++++.+|||++|+++
T Consensus       211 e~~~~~~dG~~~~~~~~~~~v~d-~~g~~~~~~~~~~DITerk~~e  255 (799)
T PRK11359        211 EFLLLTRTGEKIWIKASISPVYD-VLAHLQNLVMTFSDITEERQIR  255 (799)
T ss_pred             eeEEeCCCCCEEEEEeeeeeeec-CCCceeEEEEEeehhhhHHHHH
Confidence            77778899999999999999998 7899999999999999999873

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

Probab=98.99  E-value=4.7e-09  Score=73.99  Aligned_cols=106  Identities=21%  Similarity=0.282  Sum_probs=72.4

Q ss_pred             HHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEEEEEEE
Q 021027           20 VHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNY   99 (318)
Q Consensus        20 ~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   99 (318)
                      ++.++++++.++.++|.+   +++.++|+++.++++..+.+ +|+++..+.++...+.+.. +...+..+.....+... 
T Consensus         1 L~~il~s~~~~i~~vD~~---~~I~~~n~~a~~~f~~~~~~-iGr~l~~~~~~~~~~~l~~-~i~~~~~~~~~~~~~~~-   74 (106)
T PF13596_consen    1 LNNILDSMPIGIIFVDRN---LRIRYFNPAAARLFNLSPSD-IGRPLFDIHPPLSYPNLKK-IIEQVRSGKEEEFEIVI-   74 (106)
T ss_dssp             HHHHHHHSSSEEEEEETT---SBEEEE-SCGC-SS---GGG-TTSBCCCSS-HHHHHHHHH-HHHHHHTTSBSEEEEEE-
T ss_pred             ChHHHhcCCCCEEEEcCC---CeEEEeChhHhhhcCCChHH-CCCCHHHcCCccchHHHHH-HHHHHHcCCCceEEEEe-
Confidence            457899999999999999   99999999999999987654 6999888765533333333 33444455543333332 


Q ss_pred             ecCCcEEEEEEEEEeeccCCCCceeEEEEEEeccc
Q 021027          100 KKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV  134 (318)
Q Consensus       100 ~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIt  134 (318)
                      ..+|.  |+.+...|+++ ++|...|++.++.|||
T Consensus        75 ~~~~~--~~~~~~~P~~~-~~g~~~G~v~~~~DIT  106 (106)
T PF13596_consen   75 PNGGR--WYLVRYRPYRD-EDGEYAGAVITFQDIT  106 (106)
T ss_dssp             EETTE--EEEEEEEEEE--TTS-EEEEEEEEEE-G
T ss_pred             cCCCE--EEEEEEEEEEC-CCCCEEEEEEEEEecC
Confidence            34454  77889999999 8999999999999997

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

Probab=98.98  E-value=3.8e-08  Score=66.08  Aligned_cols=102  Identities=21%  Similarity=0.395  Sum_probs=81.9

Q ss_pred             CCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEEEEEEEecCCcEEE
Q 021027           28 PDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFW  107 (318)
Q Consensus        28 ~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~  107 (318)
                      +.+++++|.+   +.++++|+.+..++|++..+++|.....+.++.........+......+.....+......+|...|
T Consensus         2 ~~~i~~~d~~---~~~~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (103)
T cd00130           2 PDGVIVLDLD---GRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDGSVIW   78 (103)
T ss_pred             CceEEEECCC---CcEEEECHHHHHHhCCCHHHHcCccHHHhcCCccchHHHHHHHHHHhcCcCeEEEEEEEccCCCEEE
Confidence            5788999999   9999999999999999999999988766666666555555555555555556666666777899999


Q ss_pred             EEEEEEeeccCCCCceeEEEEEEecc
Q 021027          108 MLFKMSLVFGKEDGRATHFVAVQVPI  133 (318)
Q Consensus       108 ~~~~~~~i~~~~~g~~~~~i~~~~DI  133 (318)
                      +.+...++.+ ..+...+++++..||
T Consensus        79 ~~~~~~~~~~-~~~~~~~~~~~~~di  103 (103)
T cd00130          79 VLVSLTPIRD-EGGEVIGLLGVVRDI  103 (103)
T ss_pred             EEEEEEEEec-CCCCEEEEEEEEecC
Confidence            9999999887 677888888888876

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.

>PF12860 PAS_7: PAS fold

Probab=98.93  E-value=1e-08  Score=73.48  Aligned_cols=104  Identities=20%  Similarity=0.342  Sum_probs=72.0

Q ss_pred             HhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhh-cCCCCCccc---------CCCCChHHHHHHHHHHHhcCCeE
Q 021027           24 LDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEI-IGRNGRMFQ---------GPRTNRRTIMEIREAIREERPIE   93 (318)
Q Consensus        24 ~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~-~g~~~~~l~---------~~~~~~~~~~~~~~~~~~~~~~~   93 (318)
                      +++++.|++++|.+   ++++++|+.|..++|++.+.+ .|.++..+.         .+.....................
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            47889999999999   999999999999999999887 677654432         11222222223332333333333


Q ss_pred             EEEEEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEeccccccccc
Q 021027           94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMR  140 (318)
Q Consensus        94 ~~~~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~~~  140 (318)
                      .+  ....+|.  |+.+...|..+   |   |++.++.|||+++++|
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  2356676  77888888854   4   6788999999999873

>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=98.86  E-value=3.2e-09  Score=75.20  Aligned_cols=67  Identities=19%  Similarity=0.273  Sum_probs=61.1

Q ss_pred             HhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhccccee
Q 021027          247 LGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQACT  316 (318)
Q Consensus       247 ~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~~~~~  316 (318)
                      |+++|++++++|.++   +|+++|+++++++|++.++++|+++.++.++...+.+...+.++++.+.++.
T Consensus         1 l~~~p~~i~v~D~~~---~i~~~N~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   67 (110)
T PF08448_consen    1 LDSSPDGIFVIDPDG---RIVYANQAAAELFGVSPEELIGRSLFDLLPPEDREEFQAALRRALAGGEPVF   67 (110)
T ss_dssp             HHHCSSEEEEEETTS---BEEEE-HHHHHHHTSTHHHHTTSBHHHHSCCGCHHHHHHHHHHHHHHTSEEE
T ss_pred             CCCCCceeEEECCCC---EEEEEHHHHHHHhCCCHHHHhhccchhccccchhhhhHHHHHHhhccCceEE
Confidence            578899999999998   9999999999999999999999999999988889999999999999987653

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=98.82  E-value=1.5e-08  Score=88.00  Aligned_cols=162  Identities=20%  Similarity=0.177  Sum_probs=116.7

Q ss_pred             HHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEEEEEEEec
Q 021027           22 EALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKK  101 (318)
Q Consensus        22 ~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  101 (318)
                      .+++...+++++++..   ..+..+|..+..+++.....++|.+...+.++...+...        .+...........+
T Consensus         5 ~~l~~~~~~~~vi~~~---~~~~~~~~~a~~~~~~~~~~~i~~~~~~i~~~~~~~~v~--------~~~~~~~~~~~~~~   73 (560)
T COG3829           5 GILKSILDGPVVIDKN---TGIDVANALALAKRQKNAEAVIGRPLREILETLGMERVE--------QSRDKELTERLKLK   73 (560)
T ss_pred             hhhhhcccceEEEEcC---CceeeechHHHHhhhcceEEEecccceeeccccCcceee--------ccCccceeeeeecc
Confidence            4888899999999998   999999999999999998999998877766554332211        11222222222222


Q ss_pred             CCcEEEEEEEEEeeccCCCCceeEEEEEEeccccccccccccccccccCCCCchhhHhhhccccccccccchhccccccc
Q 021027          102 DGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDRVLAL  181 (318)
Q Consensus       102 ~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  181 (318)
                       + ...+.+...|+ + +.+.+.|++.++.|+++....                                          
T Consensus        74 -~-~~~~~~~~~~~-~-~~~~~~g~~~~~~~~~e~~~~------------------------------------------  107 (560)
T COG3829          74 -V-KRIVVVGKTPV-D-EQGRVVGVLEVFLDISEALEL------------------------------------------  107 (560)
T ss_pred             -c-eeEEEcCCcee-e-cCCceeeeehhhhhhHHHHHH------------------------------------------
Confidence             2 33333444455 4 588999999999999995543                                          


Q ss_pred             cCCCCCcCcccchhhhhHHHHHHHhhhhhhhhhccccccccceeeeeeecCCCCccccchhHHHHHhccCCcEEEecCCC
Q 021027          182 DSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQSFVLIDPHL  261 (318)
Q Consensus       182 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~i~i~d~~~  261 (318)
                                      .++.  ....                                ...|..+++.+.++++++|.+|
T Consensus       108 ----------------~~~~--l~~~--------------------------------~~~l~~il~~~~~~l~vvD~~G  137 (560)
T COG3829         108 ----------------IEEN--LRQL--------------------------------RQRLEAILDSIDDGLLVVDEDG  137 (560)
T ss_pred             ----------------HHHH--HHHH--------------------------------HHHHHHHHhhccCceEEEcCCC
Confidence                            1111  1111                                1226678888999999999998


Q ss_pred             CCCCeeEecHHHHHHhCCCcccccCCCccccc
Q 021027          262 PDMPMVYASDAFLKLTGYDRNEVVGQNCRFLN  293 (318)
Q Consensus       262 ~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~  293 (318)
                         .++++|+++..++|++.++++|+++.++.
T Consensus       138 ---~~i~~N~~~~~~~gl~~e~~~gk~~~~v~  166 (560)
T COG3829         138 ---IIIYYNKAYAKLLGLSPEEVLGKHLLDVV  166 (560)
T ss_pred             ---cEEEEcHHHHHHhCCCHHHHcCCcHHHHH
Confidence               99999999999999999999999998886

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

Probab=98.81  E-value=2.1e-07  Score=81.16  Aligned_cols=112  Identities=18%  Similarity=0.377  Sum_probs=83.5

Q ss_pred             hhHHHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEE
Q 021027           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV   94 (318)
Q Consensus        15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   94 (318)
                      ...+.|+.+++.+.+++.++|.+   |.++++|+++..++|++.++++|++..++.....    ......++..+.+...
T Consensus       114 ~~~~~l~~il~~~~~~l~vvD~~---G~~i~~N~~~~~~~gl~~e~~~gk~~~~v~~~~~----~s~~l~vl~~~kp~~~  186 (560)
T COG3829         114 QLRQRLEAILDSIDDGLLVVDED---GIIIYYNKAYAKLLGLSPEEVLGKHLLDVVSAGE----DSTLLEVLRTGKPIRD  186 (560)
T ss_pred             HHHHHHHHHHhhccCceEEEcCC---CcEEEEcHHHHHHhCCCHHHHcCCcHHHHHhccC----CceehhhhhcCCccee
Confidence            45678899999999999999999   9999999999999999999999998666541111    1223445666666554


Q ss_pred             EEEEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEecccccccc
Q 021027           95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM  139 (318)
Q Consensus        95 ~~~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~~  139 (318)
                      ....+  .|...  .....|+..  +|.+.|.+++..|++..+..
T Consensus       187 ~~~~~--~~~~~--i~~~~pv~~--~g~l~G~v~~~~~~~~l~~l  225 (560)
T COG3829         187 VVQTY--NGNKI--IVNVAPVYA--DGQLIGVVGISKDVSELERL  225 (560)
T ss_pred             eeeee--cCCce--eEeeccEec--CCcEEEEEEeecchHHHHHH
Confidence            44333  22222  355667765  77999999999999998876

>PRK11360 sensory histidine kinase AtoS; Provisional

Probab=98.79  E-value=7.1e-08  Score=89.49  Aligned_cols=121  Identities=14%  Similarity=0.181  Sum_probs=94.7

Q ss_pred             hHHHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCC-eEE
Q 021027           16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERP-IEV   94 (318)
Q Consensus        16 ~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~-~~~   94 (318)
                      ....+..+++.++++++++|.+   +.++++|+++++++|+++++++|+++..++++..  .....+...+..+.. ...
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            3456778999999999999999   9999999999999999999999998777766442  223344444544433 334


Q ss_pred             EEEEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEecccccccccccc
Q 021027           95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG  143 (318)
Q Consensus        95 ~~~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~~~~~~  143 (318)
                      +......+|... +.++..|+.+ .+|.+.++++++.|||+++++++++
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 8999999999999999999985443

>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=98.77  E-value=3.9e-07  Score=64.37  Aligned_cols=101  Identities=17%  Similarity=0.262  Sum_probs=82.2

Q ss_pred             EEEcCCCCCCcEEEecHh-HHHhcCCChhhhcCCCCCcccCCCCChH-HHHHHHHHHHhcCCeEEEEEEEecCCcEEEEE
Q 021027           32 TITDPSISGHPIVFASRG-FLKMSGFSRAEIIGRNGRMFQGPRTNRR-TIMEIREAIREERPIEVNLLNYKKDGTPFWML  109 (318)
Q Consensus        32 ~~~d~~~~~~~i~~~N~~-~~~~~G~~~~e~~g~~~~~l~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~  109 (318)
                      ...+.+   |+++++.+. ...++||.+++++|+.+..+++|++... +.......+..|.....-+++..++|...|+.
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            456777   999999999 6999999999999999999999998886 67778888888887777788899999999999


Q ss_pred             EEEEeeccCCCCceeEEEEEEecccc
Q 021027          110 FKMSLVFGKEDGRATHFVAVQVPIVS  135 (318)
Q Consensus       110 ~~~~~i~~~~~g~~~~~i~~~~DIte  135 (318)
                      ....++.++.++++..++++-.=|++
T Consensus        83 t~~~~~~n~~~~~~~~Iv~~n~vlse  108 (111)
T PF14598_consen   83 TKATLFYNPWTSKPEFIVCTNTVLSE  108 (111)
T ss_dssp             EEEEEEEETTTTCEEEEEEEEEEESC
T ss_pred             EEEEEEECCCCCCccEEEEEEEEecc
Confidence            99999886345677777776655554

...

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

Probab=98.76  E-value=7e-08  Score=83.79  Aligned_cols=121  Identities=26%  Similarity=0.531  Sum_probs=99.6

Q ss_pred             HHHHHHHhcCC--C-eEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCC--CCcccCCCCChHHHHHHHHHHHhcCCe
Q 021027           18 LWVHEALDELP--D-SFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRN--GRMFQGPRTNRRTIMEIREAIREERPI   92 (318)
Q Consensus        18 ~~~~~~~~~~~--~-~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~--~~~l~~~~~~~~~~~~~~~~~~~~~~~   92 (318)
                      .+++.++..+.  + .+++-+.+..|..|+|+|++||.+.||.+.+++.++  +.++++..........+.+.+...+.-
T Consensus        14 TFLENiiRRsn~~dtsFlL~NAQiVD~PiVY~NdgFcKlsGY~RAevMQKs~tc~FMyGEltdk~ti~k~~~t~eN~~~~   93 (971)
T KOG0501|consen   14 TFLENIIRRSNNADTSFLLANAQIVDWPIVYCNDGFCKLSGYHRAEVMQKSCTCSFMYGELTDKGTIEKVRQTLENYETN   93 (971)
T ss_pred             hHHHHHHhhccCCCcceeeccceeeccceEEecCcchhccCccHHHHhcccceeeeeeccccchhhHHHHHHHHHhhhhc
Confidence            34555554433  3 344455555668899999999999999999999987  566777777777788888888888778


Q ss_pred             EEEEEEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEecccccccc
Q 021027           93 EVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM  139 (318)
Q Consensus        93 ~~~~~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~~  139 (318)
                      .++...+.++..+.|+.+.+.|+++ +.+.++.+++.+.|||..|+-
T Consensus        94 qfEillyKKN~TPvW~~vqiAPIrN-e~d~VVLfLctFkDIT~~KQP  139 (971)
T KOG0501|consen   94 QFEILLYKKNRTPVWLLVQIAPIRN-EKDKVVLFLCTFKDITALKQP  139 (971)
T ss_pred             ceeeEeeecCCCceEEEEEeecccC-CCceEEEEEeecccchhhcCC
Confidence            8898899999999999999999999 899999999999999999875

>TIGR02966 phoR_proteo phosphate regulon sensor kinase PhoR

Probab=98.75  E-value=8.1e-08  Score=82.19  Aligned_cols=108  Identities=12%  Similarity=0.075  Sum_probs=82.1

Q ss_pred             hhHHHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEE
Q 021027           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV   94 (318)
Q Consensus        15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   94 (318)
                      +..+.++.++++++++++++|.+   |+++++|+++++++|+++++.+|+++..+..+.   .    +...+..+.. ..
T Consensus         3 ~~~~~l~~~~~~~~~~i~~~d~~---g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~---~----~~~~l~~~~~-~~   71 (333)
T TIGR02966         3 ALLSRFRAAAQALPDAVVVLDEE---GQIEWCNPAAERLLGLRWPDDLGQRITNLIRHP---E----FVEYLAAGRF-SE   71 (333)
T ss_pred             hHHHHHHHHHHhCcCcEEEECCC---CcEEEEcHHHHHHhCCChHHHcCCcHHHHccCH---H----HHHHHHhccc-CC
Confidence            44567899999999999999999   999999999999999999999998876665432   2    2223333222 22


Q ss_pred             EEEEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEecccccccc
Q 021027           95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM  139 (318)
Q Consensus        95 ~~~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~~  139 (318)
                      ......+.|..+|+.+...|+.+ . +    ++.+..|||++++.
T Consensus        72 ~~~~~~~~~~~~~~~~~~~p~~~-~-~----~~~~~~dit~~~~~  110 (333)
T TIGR02966        72 PLELPSPINSERVLEIRIAPYGE-E-Q----KLLVARDVTRLRRL  110 (333)
T ss_pred             CeEeecCCCCceEEEEEEEEcCC-C-c----eEEEEeCchHHHHH
Confidence            23344577888899999999876 2 2    67888999998886

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).

>PRK13557 histidine kinase; Provisional

Probab=98.70  E-value=3.4e-08  Score=90.43  Aligned_cols=75  Identities=32%  Similarity=0.762  Sum_probs=67.2

Q ss_pred             hhHHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhcccce
Q 021027          241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQAC  315 (318)
Q Consensus       241 ~~l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~~~~  315 (318)
                      ..|+.++++++++|+++|.++.|++|+|+|++|++++||+.+|++|+++..+.+|.+.......++..+..+.++
T Consensus        30 ~~~~~~~~~~~~~i~v~d~~~~~g~i~~~N~a~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~  104 (540)
T PRK13557         30 DIFFAAVETTRMPMIVTDPNQPDNPIVFANRAFLEMTGYAAEEIIGNNCRFLQGPETDRATVAEVRDAIAERREI  104 (540)
T ss_pred             HHHHHHHHhCcCcEEEEcCCCCCCCEEEEcHHHHHHhCCCHHHhcCCChHhhcCCCCCHHHHHHHHHHHHcCCCc
Confidence            347889999999999999876677999999999999999999999999999998888888888999888877665

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

Probab=98.70  E-value=1.6e-07  Score=81.18  Aligned_cols=111  Identities=14%  Similarity=0.136  Sum_probs=84.2

Q ss_pred             HHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEEEEE
Q 021027           18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLL   97 (318)
Q Consensus        18 ~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~   97 (318)
                      ..+.+++++++++++++|.+   ++++++|+++++++|++..+++|.++..+.++..  .....+...+..+..+.....
T Consensus         7 ~~~~~il~~~~~gi~~~d~~---~~i~~~N~a~~~~~g~~~~~~~g~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~   81 (348)
T PRK11073          7 PDAGQILNSLINSILLLDDD---LAIHYANPAAQQLLAQSSRKLFGTPLPELLSYFS--LNIELMRESLQAGQGFTDNEV   81 (348)
T ss_pred             chHHHHHhcCcCeEEEECCC---CeEeeEcHHHHHHhCCCHHHHcCCCHHHHcCcch--hhHHHHHHHHHcCCcccccce
Confidence            35678999999999999999   9999999999999999999999998777765432  112333444555444433333


Q ss_pred             EEecCCcEEEEEEEEEeeccCCCCceeEEEEEEecccccccc
Q 021027           98 NYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM  139 (318)
Q Consensus        98 ~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~~  139 (318)
                      ....+|..+|+.++..|+..      .+++..++|+|++++.
T Consensus        82 ~~~~~g~~~~~~~~~~~~~~------~~~~~~~~dit~~~~~  117 (348)
T PRK11073         82 TLVIDGRSHILSLTAQRLPE------GMILLEMAPMDNQRRL  117 (348)
T ss_pred             EEEECCceEEEEEEEEEccC------ceeEEEEechhHHHHH
Confidence            44569999999999999853      2467778999998876

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

Probab=98.62  E-value=4.7e-07  Score=80.23  Aligned_cols=61  Identities=20%  Similarity=0.316  Sum_probs=53.2

Q ss_pred             EEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhcccce
Q 021027          254 FVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQAC  315 (318)
Q Consensus       254 i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~~~~  315 (318)
                      ++++-.+ .|.+|+||.+.+..++||+++||+|+++.+|+|+.|...+.+-+.+.+.+|+-+
T Consensus       275 ~FvtRhs-~DmkityCedRisdlm~y~PeeLvGrS~Ye~~Ha~Ds~~v~KSh~dL~~KGQv~  335 (768)
T KOG3558|consen  275 MFVTRHS-LDMKITYCEDRISDLMDYEPEELVGRSCYEFVHALDSDRVRKSHHDLLTKGQVV  335 (768)
T ss_pred             eeEEeee-cceeEEEEchhHHHHhcCCHHHhhchhHHHhhhHhhhhHHHHHHHHHHhcCccc
Confidence            5555444 467999999999999999999999999999999999999999999998888654

>PRK10060 RNase II stability modulator; Provisional

Probab=98.62  E-value=9.1e-08  Score=89.50  Aligned_cols=71  Identities=14%  Similarity=0.132  Sum_probs=58.6

Q ss_pred             HHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCccccc-CCCCCHHHHHHHHHHHhccccee
Q 021027          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLN-GVDTDTTVLYQIKESIQTEQACT  316 (318)
Q Consensus       243 l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~-~~~~~~~~~~~~~~~l~~~~~~~  316 (318)
                      +..+++.++++|+++|.+|   +|+++|+++++++||+.+|++|+++.+++ +|.+.......+...+..+.+|.
T Consensus       113 ~~~v~~~~~~gI~i~D~~g---~I~~~N~a~~~l~Gy~~~eliG~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~  184 (663)
T PRK10060        113 AEQVVSEANSVIVILDSRG---NIQRFNRLCEEYTGLKEHDVIGQSVFKLFMSRREAAASRRNIRGFFRSGNAYE  184 (663)
T ss_pred             HHHHHhhCCceEEEEeCCC---CEEEEcHHHHHHHCcCHHHHcCCCHHHHhCChhhHHHHHHHHHHHHhcCCceE
Confidence            4457788899999999998   99999999999999999999999986655 45555666777777787777664

>PRK13559 hypothetical protein; Provisional

Probab=98.60  E-value=1.2e-07  Score=82.25  Aligned_cols=75  Identities=40%  Similarity=0.759  Sum_probs=65.6

Q ss_pred             hhHHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhcccce
Q 021027          241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQAC  315 (318)
Q Consensus       241 ~~l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~~~~  315 (318)
                      ..+..++++++++|+++|.++.++.|+++|++|++++||+.++++|+++..+.++...+.....+..++..+.++
T Consensus        43 ~~~~~~~e~~~~~i~i~D~~~~~g~i~~~N~a~~~l~G~~~~e~iG~~~~~l~~~~~~~~~~~~~~~~~~~~~~~  117 (361)
T PRK13559         43 RLFEQAMEQTRMAMCITDPHQPDLPIVLANQAFLDLTGYAAEEVVGRNCRFLQGAATDPIAVAKIRAAIAAEREI  117 (361)
T ss_pred             hHHHHHHHhCCCcEEEecCCCCCCcEEEEchHHHHHhCCCHHHHcCCChhhhcCCCCCHHHHHHHHHHhccCCce
Confidence            347778999999999999876667999999999999999999999999998887777888888888888877655

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

Probab=98.58  E-value=9.1e-08  Score=60.52  Aligned_cols=45  Identities=22%  Similarity=0.355  Sum_probs=37.0

Q ss_pred             hHHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCccccc
Q 021027          242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLN  293 (318)
Q Consensus       242 ~l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~  293 (318)
                      +++.+++++|++|+++| ++   +|+++|+++++|+||+   ..|+.+..+.
T Consensus         2 ~~~~l~~~~~~~i~i~d-~~---~i~~~N~~~~~l~g~~---~~~~~~~~~~   46 (64)
T PF13188_consen    2 RYRSLFDNSPDGILIID-GG---RIIYVNPAFEELFGYS---LEGEDIGQLF   46 (64)
T ss_dssp             HHHHHHCCSSSEEEEEE-TS---BEEEE-HHHHHHHCS----HTCCCHHCTS
T ss_pred             HHHHHHHcCccceEEEE-CC---ChHHhhHHHHHHhCCC---CCCCCHHHhC
Confidence            57889999999999999 75   9999999999999999   6677665444

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

Probab=98.57  E-value=9.5e-07  Score=72.53  Aligned_cols=115  Identities=15%  Similarity=0.232  Sum_probs=87.6

Q ss_pred             hhHHHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEE
Q 021027           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV   94 (318)
Q Consensus        15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   94 (318)
                      ...+++..++..+.+|++.+|..   |+++.+|..+.+++|.+.++++|++...+..-.+.-.+    ...+........
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---GKIILINKPALKMLGVSKEDALGRSILELLKIEDTYTF----EDLVEKNDSLLL  180 (459)
T ss_pred             HHHHHHHHHHHHHcCceEeecCC---CcEEEeccHHHHHhCcCHHHHhcccHHHHhCCccceeH----HHHHhcCCcEEE
Confidence            45578899999999999999999   99999999999999999999999986655443332222    222222222222


Q ss_pred             EEEEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEeccccccccc
Q 021027           95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMR  140 (318)
Q Consensus        95 ~~~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~~~  140 (318)
                      +   .+.+++....++..+.+.. +.|-+.|++.+.+|+|++.+.|
T Consensus       181 d---~~~~~E~~~lrv~Fs~i~r-EsGfisGlIaVlhDvTEqek~e  222 (459)
T COG5002         181 D---SSDEEEGYVLRVNFSVIQR-ESGFISGLIAVLHDVTEQEKVE  222 (459)
T ss_pred             e---ecCCCccEEEEEEEEEEee-cccccceeEEEEecccHHHHHH
Confidence            2   2236777777888888888 8999999999999999998873

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=98.42  E-value=3e-06  Score=79.02  Aligned_cols=49  Identities=14%  Similarity=0.127  Sum_probs=44.2

Q ss_pred             HHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccC
Q 021027          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNG  294 (318)
Q Consensus       243 l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~  294 (318)
                      +..++++++++|+++|.+|   +|+++|+++++++|++.++++|+++.+++.
T Consensus       205 ~~~il~~~~~gVl~vD~~G---~I~~~N~aa~~llg~s~~~l~G~~i~~l~~  253 (638)
T PRK11388        205 LNALLESMDDGVIAWDEQG---NLQFLNAQAARLLRLDATASQGRAITELLT  253 (638)
T ss_pred             HHHHHhccCCcEEEECCCC---eEehhhHHHHHHhCcCHHHHCCCcHHHHhc
Confidence            4457788899999999998   999999999999999999999999988873

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=98.36  E-value=3.1e-06  Score=76.62  Aligned_cols=108  Identities=13%  Similarity=0.124  Sum_probs=77.8

Q ss_pred             hHHHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEEE
Q 021027           16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVN   95 (318)
Q Consensus        16 ~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~   95 (318)
                      ....+.++++++++|++++|.+   |+|+++|+++++++|++.++++|+++..+.++..       +...+..+......
T Consensus        78 e~~~L~aIL~sm~eGVi~vD~~---G~I~~iN~aA~~Llg~~~eel~Gk~i~eli~~~~-------l~~~le~~~~~~~~  147 (520)
T PRK10820         78 EHRALSALLEALPEPVLSIDMK---GKVELANPASCQLFGQSEEKLRNHTAAQLINGFN-------FLRWLESEPQDSHN  147 (520)
T ss_pred             HHHHHHHHHHhCCCcEEEECCC---CeeeHhHHHHHHHHCcCHHHHCCCcHHHHcCcch-------HHHHHHcCCCccce
Confidence            4567889999999999999999   9999999999999999999999999877765432       22334444331111


Q ss_pred             EEEEecCCcEEEEEEEEEeec--cCCCCc--eeEEEEEEecccccc
Q 021027           96 LLNYKKDGTPFWMLFKMSLVF--GKEDGR--ATHFVAVQVPIVSRK  137 (318)
Q Consensus        96 ~~~~~~~g~~~~~~~~~~~i~--~~~~g~--~~~~i~~~~DIte~k  137 (318)
                       .....+|..++  +...|+.  + ++|.  ..|.+.+++|+++..
T Consensus       148 -~~v~~~g~~~~--v~~~PI~~~d-~~g~~~~~GaVivlrd~~~l~  189 (520)
T PRK10820        148 -EHVVINGQDFL--MEITPVYLQD-ENDQHVLVGAVVMLRSTARMG  189 (520)
T ss_pred             -EEEEECCEEEE--EEEEeeeecC-CCCceeEEEEEEEeccHHHHH
Confidence             12234566544  5667776  4 4554  379999999998753

>PRK11006 phoR phosphate regulon sensor protein; Provisional

Probab=98.27  E-value=2.6e-06  Score=75.86  Aligned_cols=106  Identities=13%  Similarity=0.149  Sum_probs=73.2

Q ss_pred             hhHHHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEE
Q 021027           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV   94 (318)
Q Consensus        15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   94 (318)
                      ...++++.++++++++++++|.+   |+++++|+++++++|++.++..|+++..+..+.   ....    .+... ....
T Consensus        95 ~~~~~~~~~~~~~~~~i~~~d~~---g~i~~~N~~a~~l~g~~~~~~~g~~~~~~~~~~---~~~~----~~~~~-~~~~  163 (430)
T PRK11006         95 NLIKRFRSGAESLPDAVVLTTEE---GNIFWCNGLAQQLLGFRWPEDNGQNILNLLRYP---EFTQ----YLKTR-DFSR  163 (430)
T ss_pred             HHHHHHHHHHHhCCCeEEEEcCC---CceeHHHHHHHHHhCCCChHhCCCcHHHHhcCH---HHHH----HHHhc-ccCC
Confidence            45678999999999999999999   999999999999999999999999866554322   1111    11111 1111


Q ss_pred             EEEEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEecccccccc
Q 021027           95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM  139 (318)
Q Consensus        95 ~~~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~~  139 (318)
                      .......+|.  ++.+...|..+   +   +.+.+.+|||++++.
T Consensus       164 ~~~~~~~~~~--~~~~~~~~~~~---~---~~~~~~~dit~~~~~  200 (430)
T PRK11006        164 PLTLVLNNGR--HLEIRVMPYTE---G---QLLMVARDVTQMHQL  200 (430)
T ss_pred             CeEEEcCCCC--EEEEEEEEcCC---C---cEEEEEehhhHHHHH
Confidence            2222234444  45566666643   2   356788999998887

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

Probab=98.23  E-value=3e-06  Score=53.43  Aligned_cols=42  Identities=24%  Similarity=0.438  Sum_probs=35.5

Q ss_pred             HHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCC
Q 021027           18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNG   66 (318)
Q Consensus        18 ~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~   66 (318)
                      ++++.++++++.+++++| +   ++++++|+++++++||+   ..|...
T Consensus         1 e~~~~l~~~~~~~i~i~d-~---~~i~~~N~~~~~l~g~~---~~~~~~   42 (64)
T PF13188_consen    1 ERYRSLFDNSPDGILIID-G---GRIIYVNPAFEELFGYS---LEGEDI   42 (64)
T ss_dssp             HHHHHHHCCSSSEEEEEE-T---SBEEEE-HHHHHHHCS----HTCCCH
T ss_pred             CHHHHHHHcCccceEEEE-C---CChHHhhHHHHHHhCCC---CCCCCH
Confidence            468899999999999999 9   89999999999999998   555554

>PRK11091 aerobic respiration control sensor protein ArcB; Provisional

Probab=98.20  E-value=1.8e-06  Score=82.71  Aligned_cols=74  Identities=14%  Similarity=0.060  Sum_probs=63.4

Q ss_pred             cchhHHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhcccce
Q 021027          239 ISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQAC  315 (318)
Q Consensus       239 ~~~~l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~~~~  315 (318)
                      ....++.++++++++|+++|.+|   +|+++|+++++++||+.++++|+++.+++++.............+..+.++
T Consensus       153 ~~~~l~~il~~~~~~i~~~D~~g---~i~~~N~a~~~l~G~~~~eliG~~~~~l~~~~~~~~~~~~~~~~~~~~~~~  226 (779)
T PRK11091        153 QSSLLRSFLDASPDLVYYRNEDG---EFSGCNRAMELLTGKSEKQLIGLTPKDVYSPEAAEKVIETDEKVFRHNVSL  226 (779)
T ss_pred             HHHHHHHHHhcCcceEEEECCCC---cEEeEcHHHHHHhCcCHHHHcCCChHHhCCHHHHHHHHHHHHHHHhcCCCe
Confidence            34558889999999999999997   999999999999999999999999999998877777777777777665544

>TIGR00229 sensory_box PAS domain S-box

Probab=98.20  E-value=4.6e-06  Score=58.21  Aligned_cols=66  Identities=20%  Similarity=0.313  Sum_probs=57.0

Q ss_pred             hHHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHh
Q 021027          242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQ  310 (318)
Q Consensus       242 ~l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~  310 (318)
                      .+..+++.++.+++++|.++   .++++|+++++++|++..+++|+++..+.++.........+..++.
T Consensus         4 ~~~~~~~~~~~~~~~~d~~~---~i~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   69 (124)
T TIGR00229         4 RYRAIFESSPDAIIVIDLEG---NILYVNPAFEEIFGYSAEELIGRNVLELIPEEDREEVRERIERLLE   69 (124)
T ss_pred             HHHHHHhhCCceEEEEcCCC---cEEEEchHHHHHhCCChHHhcCcchhhhcChhhhHHHHHHHHHHHc
Confidence            46778899999999999987   9999999999999999999999999888877777666666666665

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.

>TIGR02938 nifL_nitrog nitrogen fixation negative regulator NifL

Probab=98.13  E-value=3.7e-06  Score=76.08  Aligned_cols=72  Identities=22%  Similarity=0.412  Sum_probs=62.9

Q ss_pred             hhHHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhcccce
Q 021027          241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQAC  315 (318)
Q Consensus       241 ~~l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~~~~  315 (318)
                      ..++.+++.++++++++|.++   +++++|+++++++||++++++|++...+.++.........+.+.+..+.++
T Consensus         4 ~~~~~i~~~~~~~i~~~d~~g---~~~~~N~~~~~~~G~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   75 (494)
T TIGR02938         4 EAYRQTVDQAPLAISITDLKA---NILYANDAFTRITGYTKEEIIGKNESVLSNHTTPPEVYQALWGSLAEQKPW   75 (494)
T ss_pred             HHHHHHHHhCCceEEEECCCC---cEEEEchhheeecCCCHHHHhCCCchhhcCCCCCHHHHHHHHHHHHhCCcc
Confidence            357889999999999999997   999999999999999999999999888877777777788888877766665

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=98.04  E-value=4.3e-06  Score=71.47  Aligned_cols=53  Identities=17%  Similarity=0.171  Sum_probs=48.6

Q ss_pred             chhHHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCC
Q 021027          240 SSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGV  295 (318)
Q Consensus       240 ~~~l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~  295 (318)
                      ...++.++++++++|+++|.+|   .|+++|++|++++||++++++|+++..+..+
T Consensus         5 ~~~l~~~~~~~~~~i~~~d~~g---~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~   57 (333)
T TIGR02966         5 LSRFRAAAQALPDAVVVLDEEG---QIEWCNPAAERLLGLRWPDDLGQRITNLIRH   57 (333)
T ss_pred             HHHHHHHHHhCcCcEEEECCCC---cEEEEcHHHHHHhCCChHHHcCCcHHHHccC
Confidence            4568889999999999999998   9999999999999999999999999888754

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=98.03  E-value=9.1e-06  Score=70.20  Aligned_cols=67  Identities=22%  Similarity=0.223  Sum_probs=54.2

Q ss_pred             hHHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhccc
Q 021027          242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQ  313 (318)
Q Consensus       242 ~l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~~  313 (318)
                      .+..++++++++++++|.++   +|+++|+++++++||+.++++|+++.++.++..  .....+..++..+.
T Consensus         8 ~~~~il~~~~~gi~~~d~~~---~i~~~N~a~~~~~g~~~~~~~g~~~~~~~~~~~--~~~~~~~~~~~~~~   74 (348)
T PRK11073          8 DAGQILNSLINSILLLDDDL---AIHYANPAAQQLLAQSSRKLFGTPLPELLSYFS--LNIELMRESLQAGQ   74 (348)
T ss_pred             hHHHHHhcCcCeEEEECCCC---eEeeEcHHHHHHhCCCHHHHcCCCHHHHcCcch--hhHHHHHHHHHcCC
Confidence            47789999999999999987   999999999999999999999999998875432  22344455555444

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

Probab=98.01  E-value=0.00033  Score=54.07  Aligned_cols=118  Identities=25%  Similarity=0.378  Sum_probs=83.7

Q ss_pred             HHHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChH-HHHHHHH-HHHhcCCeEE
Q 021027           17 TLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRR-TIMEIRE-AIREERPIEV   94 (318)
Q Consensus        17 ~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~-~~~~~~~-~~~~~~~~~~   94 (318)
                      ..++..+++..+.+++.+|.+   +.+.++|+.+..++|++..+..+.....+........ ....... ..........
T Consensus       111 ~~~~~~~~~~~~~~~~~~d~~---~~~~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  187 (232)
T COG2202         111 EERLRALLEASPDGIWVLDED---GRILYANPAAEELLGYSPEEELGRGLSDLIHPEDEERRELELARALAEGRGGPLEI  187 (232)
T ss_pred             HHHHHHHHhhCCceEEEEeCC---CCEEEeCHHHHHHhCCChHHhcCCChhheEecCCCchhhHHHHHHhhccCCCCcce
Confidence            344788999999999999999   9999999999999999988777766544433322211 1111111 1222334566


Q ss_pred             EEEEEecCCcE-EEEEEEEEeeccCCCCceeEEEEEEecccccccc
Q 021027           95 NLLNYKKDGTP-FWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM  139 (318)
Q Consensus        95 ~~~~~~~~g~~-~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~~  139 (318)
                      +......+|.. .+......+...  .|.+..+.....|+++++..
T Consensus       188 ~~~~~~~~g~~~~~~~~~~~~~~~--~~~~~~~~~~~~d~~~~~~~  231 (232)
T COG2202         188 EYRVRRKDGERVRWILSRISPVRD--DGEIVGVVGIARDITERKQA  231 (232)
T ss_pred             EEEEEecCCCEEEEEEeeeeEecC--CCceEEEEEEEechHHHhhc
Confidence            77777889985 777776666643  58888888999999988764

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

Probab=98.00  E-value=1.9e-05  Score=52.45  Aligned_cols=59  Identities=17%  Similarity=0.278  Sum_probs=50.7

Q ss_pred             CCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhcc
Q 021027          251 KQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTE  312 (318)
Q Consensus       251 ~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~  312 (318)
                      +++++++|.++   .++++|+++++++|++..+++|+++..+.++.+.......+...+..+
T Consensus         2 ~~~i~~~d~~~---~~~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   60 (103)
T cd00130           2 PDGVIVLDLDG---RILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGG   60 (103)
T ss_pred             CceEEEECCCC---cEEEECHHHHHHhCCCHHHHcCccHHHhcCCccchHHHHHHHHHHhcC
Confidence            67889999887   999999999999999999999999988888888777777777766543

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.

>PRK13558 bacterio-opsin activator; Provisional

Probab=97.98  E-value=1.8e-05  Score=74.65  Aligned_cols=73  Identities=37%  Similarity=0.715  Sum_probs=63.0

Q ss_pred             HHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhcccce
Q 021027          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQAC  315 (318)
Q Consensus       243 l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~~~~  315 (318)
                      +..+++.++.+++++|..++++.++|+|+++++++||+.++++|+++..+.++.........+..++..+.++
T Consensus       150 ~~~~~~~~~~gi~~~d~~~~dg~i~~~N~~~~~l~G~~~eel~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~  222 (665)
T PRK13558        150 KERALDEAPVGITIADATLPDEPLIYINDAFERITGYSPDEVLGRNCRFLQGEDTNEERVAELREAIDEERPT  222 (665)
T ss_pred             HHHHHhcCCccEEEEcCCCCCCcEEEEcHHHHHHhCcCHHHHcCCCHHHhcCCCccHHHHHHHHHHHhcCCCe
Confidence            3568889999999998765667999999999999999999999999999988887777788888888777654

>PRK11086 sensory histidine kinase DcuS; Provisional

Probab=97.94  E-value=5.7e-05  Score=69.38  Aligned_cols=109  Identities=10%  Similarity=0.139  Sum_probs=75.6

Q ss_pred             hHHHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCCh---hhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCe
Q 021027           16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSR---AEIIGRNGRMFQGPRTNRRTIMEIREAIREERPI   92 (318)
Q Consensus        16 ~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~---~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~   92 (318)
                      ..+.+++++++++++++++|.+   |+++++|+++++++|++.   .+.+|.....+.++       ..+...+..+.+.
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            4456688999999999999999   999999999999998753   34555554433322       1223344444443


Q ss_pred             EEEEEEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEeccccccccc
Q 021027           93 EVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMR  140 (318)
Q Consensus        93 ~~~~~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~~~  140 (318)
                      ....  ...+|.  ++.+...|+.+  +|.+.|++.+++|+|+.++.+
T Consensus       289 ~~~~--~~~~g~--~~~~~~~pi~~--~g~~~g~v~~~rDite~~~l~  330 (542)
T PRK11086        289 RDEE--ININGR--LLLTNTVPVRV--NGEIIGAIATFRDKTEVRQLA  330 (542)
T ss_pred             cceE--EEECCE--EEEEEEEEEeE--CCEEEEEEEEEEEchHHHHHH
Confidence            3221  122444  44566778876  788999999999999988763

>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=97.90  E-value=8.5e-06  Score=55.38  Aligned_cols=50  Identities=24%  Similarity=0.379  Sum_probs=40.3

Q ss_pred             eeEecHHHHHHhCCCcccccCCC----cccccCCCCCHHHHHHHHH-HHhccccee
Q 021027          266 MVYASDAFLKLTGYDRNEVVGQN----CRFLNGVDTDTTVLYQIKE-SIQTEQACT  316 (318)
Q Consensus       266 i~~~N~a~~~~~Gy~~~el~G~~----~~~l~~~~~~~~~~~~~~~-~l~~~~~~~  316 (318)
                      |+|||+++++|+||+++++ |..    +..+++|++...+.+.+.+ ++..+.++.
T Consensus         1 ~i~~s~~~~~i~G~~~~~~-~~~~~~~~~~~ihpdD~~~~~~~~~~~~~~~~~~~~   55 (91)
T PF08447_consen    1 IIYWSDNFYEIFGYSPEEI-GKPDFEEWLERIHPDDRERVRQAIQQAALQNGEPFE   55 (91)
T ss_dssp             -EEE-THHHHHHTS-HHHH-TCBEHHHHHHHB-TTTHHHHHHHHHHHHHHTT-EEE
T ss_pred             CEEEeHHHHHHhCCCHHHh-ccCCHHHHHhhcCHHHHHHHHHHHHHHhhccCcceE
Confidence            6899999999999999999 777    7889999999999999999 677776664

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.

>smart00091 PAS PAS domain

Probab=97.90  E-value=3.5e-05  Score=46.81  Aligned_cols=63  Identities=21%  Similarity=0.275  Sum_probs=51.6

Q ss_pred             HHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHH
Q 021027          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKES  308 (318)
Q Consensus       243 l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~  308 (318)
                      +..+++.+++++++++..+   .+.++|+.+..++|++..++.|+.+..+.++.+.+.....+..+
T Consensus         3 ~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   65 (67)
T smart00091        3 LRAILESLPDGIFVLDLDG---RILYANPAAEELLGYSPEELIGKSLLELIHPEDREEVQEALQRL   65 (67)
T ss_pred             HHHHHhhCCceEEEEcCCC---eEEEECHHHHHHhCCCHHHHcCCcHHHhcCcccHHHHHHHHHHH
Confidence            4567788899999999876   99999999999999999999999888888777765555555443

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).

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

Probab=97.89  E-value=0.0001  Score=65.41  Aligned_cols=112  Identities=12%  Similarity=0.037  Sum_probs=79.1

Q ss_pred             hHHHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCC-eEE
Q 021027           16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERP-IEV   94 (318)
Q Consensus        16 ~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~-~~~   94 (318)
                      ..++++.+++....|++..|.+   |.+..+|+++++|+|.+..+++|.+++.+.+.     +...+...-..+.+ ...
T Consensus       368 rr~f~E~VLsgvtaGVi~~d~~---g~i~t~N~~ae~~l~~~~~~~~G~~lsa~ap~-----~~~vf~~~~a~~~~~~~~  439 (712)
T COG5000         368 RRRFLEAVLSGLTAGVIGFDNR---GCITTVNPSAEQILGKPFDQLLGQSLSAIAPE-----LEEVFAEAGAAARTDKRV  439 (712)
T ss_pred             HHHHHHHHHhcCceeEEEEcCC---CeeEeecchHHHHhcCChhHhhcchhhhhhhH-----HHHHHHHhhhhcCCCccc
Confidence            4467788999999999999999   99999999999999999999999886654321     22222222222222 223


Q ss_pred             EEEEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEecccccccc
Q 021027           95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM  139 (318)
Q Consensus        95 ~~~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~~  139 (318)
                      +.. ....|+.+.+.+..+.... +  .--|++.++.|||....+
T Consensus       440 ev~-~~r~g~~rtl~Vq~t~~~~-d--~~~gyVvt~DDITdLV~A  480 (712)
T COG5000         440 EVK-LAREGEERTLNVQATREPE-D--NGNGYVVTFDDITDLVIA  480 (712)
T ss_pred             eee-cccCCCceeeeeeeeeccc-c--cCCceEEEecchHHHHHH
Confidence            332 3456677777777766544 3  234789999999998887

>PRK11006 phoR phosphate regulon sensor protein; Provisional

Probab=97.78  E-value=1.7e-05  Score=70.69  Aligned_cols=52  Identities=17%  Similarity=0.146  Sum_probs=46.8

Q ss_pred             hhHHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCC
Q 021027          241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGV  295 (318)
Q Consensus       241 ~~l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~  295 (318)
                      ..++.++++++++|+++|.+|   +|+++|+++++++||+.++++|+++..+..+
T Consensus        98 ~~~~~~~~~~~~~i~~~d~~g---~i~~~N~~a~~l~g~~~~~~~g~~~~~~~~~  149 (430)
T PRK11006         98 KRFRSGAESLPDAVVLTTEEG---NIFWCNGLAQQLLGFRWPEDNGQNILNLLRY  149 (430)
T ss_pred             HHHHHHHHhCCCeEEEEcCCC---ceeHHHHHHHHHhCCCChHhCCCcHHHHhcC
Confidence            347788999999999999987   9999999999999999999999999877643

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

Probab=97.78  E-value=1.4e-05  Score=67.64  Aligned_cols=72  Identities=19%  Similarity=0.348  Sum_probs=62.3

Q ss_pred             HHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCC-CCHHHHHHHHHHHhcccceec
Q 021027          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVD-TDTTVLYQIKESIQTEQACTE  317 (318)
Q Consensus       243 l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~-~~~~~~~~~~~~l~~~~~~~~  317 (318)
                      +..+++....+|-|+|.+.   .|.||||+|+.|+||-..|++|+...++...+ ......+.+...+++|..|+-
T Consensus       159 lFaaLD~c~eAiEI~~ddh---ViQYVNpAfE~mmG~hkgEliGke~adlpkkdknradlldtintcikkgke~qG  231 (775)
T KOG1229|consen  159 LFAALDECDEAIEICDDDH---VIQYVNPAFENMMGCHKGELIGKEEADLPKKDKNRADLLDTINTCIKKGKEAQG  231 (775)
T ss_pred             HHHHHhhhhhhheeccchh---HHHHhcHHHHhhhcchhhhhcCCchhhccccccchhhhhhhhhHhhhcCccccc
Confidence            6677888889999999886   99999999999999999999999999986544 466778889999999988863

>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=97.77  E-value=3.2e-05  Score=54.58  Aligned_cols=53  Identities=23%  Similarity=0.259  Sum_probs=46.5

Q ss_pred             CCCeeEecHH-HHHHhCCCcccccCCCcccccCCCCCHH-HHHHHHHHHhcccce
Q 021027          263 DMPMVYASDA-FLKLTGYDRNEVVGQNCRFLNGVDTDTT-VLYQIKESIQTEQAC  315 (318)
Q Consensus       263 ~~~i~~~N~a-~~~~~Gy~~~el~G~~~~~l~~~~~~~~-~~~~~~~~l~~~~~~  315 (318)
                      ||+|+++.+. ...++||.++||+|+++.+++||++... ..+..+..+.+|+..
T Consensus        11 dgki~~~d~~~v~~~lgy~~~eLvG~s~y~~~H~~D~~~~~~~~~~~~~~~g~~~   65 (111)
T PF14598_consen   11 DGKITYVDSRAVSSLLGYLPEELVGRSIYDFVHPDDLQRVLKQHHREVLQKGQSV   65 (111)
T ss_dssp             TSBEEEEETTHHHHHHSS-HHHHTTSBGGGGBSCCTHHHHHHHHHHHHHHHSSEE
T ss_pred             CcEEEEEcCccChhhcCCCcHHHcCCchHHhCCHhhhhhHHHHHHHHHhhCCCcC
Confidence            4599999999 5999999999999999999999999997 778899988888754

...

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=97.76  E-value=2.1e-05  Score=71.24  Aligned_cols=54  Identities=17%  Similarity=0.087  Sum_probs=49.0

Q ss_pred             hhHHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCC
Q 021027          241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDT  297 (318)
Q Consensus       241 ~~l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~  297 (318)
                      ..+..+++++++||+++|.+|   +|+++|+++++++|++.++++|+++.+++++..
T Consensus        80 ~~L~aIL~sm~eGVi~vD~~G---~I~~iN~aA~~Llg~~~eel~Gk~i~eli~~~~  133 (520)
T PRK10820         80 RALSALLEALPEPVLSIDMKG---KVELANPASCQLFGQSEEKLRNHTAAQLINGFN  133 (520)
T ss_pred             HHHHHHHHhCCCcEEEECCCC---eeeHhHHHHHHHHCcCHHHHCCCcHHHHcCcch
Confidence            447889999999999999998   999999999999999999999999999886533

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

Probab=97.74  E-value=1.5e-05  Score=67.46  Aligned_cols=105  Identities=23%  Similarity=0.375  Sum_probs=85.9

Q ss_pred             HHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCC-ChHHHHHHHHHHHhcCCeEEEEEE
Q 021027           20 VHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRT-NRRTIMEIREAIREERPIEVNLLN   98 (318)
Q Consensus        20 ~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~   98 (318)
                      +.+.++....++-++|.+   ..+.|+|++|+.++|+-..+++|+...++...+. ...+...+..+++.|..+.++...
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            345778888899999998   9999999999999999999999999888765443 445677888899999999888777


Q ss_pred             EecCCcEEEEEEEEEeeccCCCCceeEEEE
Q 021027           99 YKKDGTPFWMLFKMSLVFGKEDGRATHFVA  128 (318)
Q Consensus        99 ~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~  128 (318)
                      +++.|...-..+..+|+.+ ..|.+..++.
T Consensus       236 RRksgdS~dqh~~itP~~g-qggkirhfvs  264 (775)
T KOG1229|consen  236 RRKSGDSCDQHFIITPFAG-QGGKIRHFVS  264 (775)
T ss_pred             hhccCCcccceEEEeeecC-CCCceeeehh
Confidence            7788877777788899988 6777766643

>PF12860 PAS_7: PAS fold

Probab=97.73  E-value=2e-05  Score=56.27  Aligned_cols=44  Identities=23%  Similarity=0.310  Sum_probs=39.5

Q ss_pred             HhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccc-cCCCccccc
Q 021027          247 LGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEV-VGQNCRFLN  293 (318)
Q Consensus       247 ~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el-~G~~~~~l~  293 (318)
                      +++++.||+++|.++   ++++||++|.+|+|++.+.+ .|.++..+.
T Consensus         1 Ld~l~~Gv~v~D~~~---rl~~~N~~~~~l~~~~~~~~~~G~~~~~l~   45 (115)
T PF12860_consen    1 LDSLPQGVAVFDSDG---RLVFWNQRFRELFGLPPEMLRPGASFRDLL   45 (115)
T ss_pred             CCCcCceEEEEcCCC---eEEeEcHHHHHHhCCCHHHhcCCCCHHHHH
Confidence            467899999999998   99999999999999999998 899876654

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=97.61  E-value=0.00055  Score=64.14  Aligned_cols=108  Identities=12%  Similarity=0.228  Sum_probs=75.4

Q ss_pred             HHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEEEEEE
Q 021027           19 WVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLN   98 (318)
Q Consensus        19 ~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   98 (318)
                      .+..+++..+++++++|.+   |+|+++|+++++++|++..+++|++...+++..      ..+..++..+.........
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            3456889999999999999   999999999999999999999999877665321      1123344555544332222


Q ss_pred             EecCCcEEEEEEEEEeeccCCCCceeEEEEEEeccccccc
Q 021027           99 YKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKH  138 (318)
Q Consensus        99 ~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~  138 (318)
                      ...+|..+++.+...|+.+ ..|.  +++.+..+++..+.
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 3442  35566678776443

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

Probab=97.60  E-value=3.6e-05  Score=54.04  Aligned_cols=66  Identities=14%  Similarity=0.118  Sum_probs=46.7

Q ss_pred             HHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhcc
Q 021027          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTE  312 (318)
Q Consensus       243 l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~  312 (318)
                      |..++++++.+++++|.++   +|.+.|+++.++++... ..+|+++..+.++...+.+.+.+......+
T Consensus         1 L~~il~s~~~~i~~vD~~~---~I~~~n~~a~~~f~~~~-~~iGr~l~~~~~~~~~~~l~~~i~~~~~~~   66 (106)
T PF13596_consen    1 LNNILDSMPIGIIFVDRNL---RIRYFNPAAARLFNLSP-SDIGRPLFDIHPPLSYPNLKKIIEQVRSGK   66 (106)
T ss_dssp             HHHHHHHSSSEEEEEETTS---BEEEE-SCGC-SS---G-GGTTSBCCCSS-HHHHHHHHHHHHHHHTTS
T ss_pred             ChHHHhcCCCCEEEEcCCC---eEEEeChhHhhhcCCCh-HHCCCCHHHcCCccchHHHHHHHHHHHcCC
Confidence            4568999999999999998   99999999999999764 558999999986645555555554444433

>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]

Probab=97.48  E-value=0.0013  Score=55.16  Aligned_cols=55  Identities=18%  Similarity=0.248  Sum_probs=46.5

Q ss_pred             HHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChH
Q 021027           20 VHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRR   77 (318)
Q Consensus        20 ~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~   77 (318)
                      -..+++.....+++++++   |.|.|++..+.-.+|++.-|+.|....+.+++.+...
T Consensus        81 gshlLqtLDGF~fvva~d---GkimYISETaSvhLGLSQVElTGNsi~eYIH~~D~de  135 (598)
T KOG3559|consen   81 GSHLLQTLDGFIFVVAPD---GKIMYISETASVHLGLSQVELTGNSIYEYIHPQDHDE  135 (598)
T ss_pred             HHhHHHhhcceEEEEeCC---CCEEEEecceeeeecceeeEeecchhhhhhcccchHH
Confidence            345677777788999999   9999999999999999999999998777777766544

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

Probab=97.40  E-value=0.0004  Score=62.30  Aligned_cols=95  Identities=11%  Similarity=0.252  Sum_probs=78.9

Q ss_pred             EcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEEEEEEEecCCcEEEEEEEEE
Q 021027           34 TDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMS  113 (318)
Q Consensus        34 ~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~  113 (318)
                      .+.+   .+|.||.+.+..++||.+++++|+.+..++|..+...+.......+..|.....-+++..++|.+.|+...++
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            4455   8999999999999999999999999999999998888888888888899888888888999999999999988


Q ss_pred             eeccCCCCceeEEEEEEe
Q 021027          114 LVFGKEDGRATHFVAVQV  131 (318)
Q Consensus       114 ~i~~~~~g~~~~~i~~~~  131 (318)
                      .+.+..++....++++-.
T Consensus       357 Vi~~tkn~q~q~IicVnY  374 (768)
T KOG3558|consen  357 VIYNTKNPQEQNIICVNY  374 (768)
T ss_pred             EEecCCCCCcceEEEEEe
Confidence            887612333344444443

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

Probab=97.40  E-value=0.0072  Score=44.51  Aligned_cols=112  Identities=11%  Similarity=0.102  Sum_probs=78.3

Q ss_pred             HHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEEEEE
Q 021027           18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLL   97 (318)
Q Consensus        18 ~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~   97 (318)
                      ..++.+++ .|.+|+-.+.. +|-.++|.|.++..+++++-+++++.+......+.........+.++...|-.....-.
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 88888877654 44789999999999999999999999866665565556666666677766654444444


Q ss_pred             EEecCCcEEEEEE-EEEeeccCCCCceeEEEEEEec
Q 021027           98 NYKKDGTPFWMLF-KMSLVFGKEDGRATHFVAVQVP  132 (318)
Q Consensus        98 ~~~~~g~~~~~~~-~~~~i~~~~~g~~~~~i~~~~D  132 (318)
                      .+.+.|+.+++.- .+--+.+ ++|...|.-..+.+
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            5678888887753 2334456 67887776655554

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

Probab=97.39  E-value=0.0016  Score=65.86  Aligned_cols=42  Identities=10%  Similarity=0.055  Sum_probs=37.1

Q ss_pred             hhHHHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChh
Q 021027           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRA   59 (318)
Q Consensus        15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~   59 (318)
                      ....+++.++++++.+++++|.+   |+++++|++++.++|.+..
T Consensus       573 ~~~~~~~~i~~~~~~~i~~~d~~---g~i~~~N~~~~~~~g~~~~  614 (1197)
T PRK09959        573 NQISFRKALSDSLPNPTYVVNWQ---GNVISHNSAFEHYFTADYY  614 (1197)
T ss_pred             HHHHHHHHHHhhCCCcEEEEcCC---CcEEEehHHHHHHhCcccc
Confidence            34567788999999999999999   9999999999999998643

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

Probab=97.39  E-value=0.0011  Score=58.45  Aligned_cols=109  Identities=13%  Similarity=0.167  Sum_probs=81.1

Q ss_pred             hHHHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChh--hhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeE
Q 021027           16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRA--EIIGRNGRMFQGPRTNRRTIMEIREAIREERPIE   93 (318)
Q Consensus        16 ~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~--e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~   93 (318)
                      ..+...++++++..|++.+|..   |.+..+|.++++++|+...  +.+|++...+++|+..-      ...++.+++..
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---GVITLINQAAQKLLGLRQPSGDPIGRSIVEVLPPDSDL------PEVLETGKPQH  283 (537)
T ss_pred             HHHHHHHHHHHhhceEEEECCC---CeEeehhHHHHHHhcccCcCcccccccceEeeccccCc------HHHHhcCCccc
Confidence            3445678899999999999999   9999999999999999765  68899888877763211      22234444433


Q ss_pred             EEEEEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEecccccccc
Q 021027           94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM  139 (318)
Q Consensus        94 ~~~~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~~  139 (318)
                      .+..  +-+|.  ++.....|+..  ++++.|++..++|-|+-+..
T Consensus       284 ~~e~--~~ng~--~~i~nr~pI~~--~~~~~GaI~tFRdktei~~L  323 (537)
T COG3290         284 DEEI--RINGR--LLVANRVPIRS--GGQIVGAIITFRDKTEIKKL  323 (537)
T ss_pred             chhh--hcCCe--EEEEEeccEEE--CCEEeEEEEEEecHHHHHHH
Confidence            3221  23444  55577788876  89999999999999998876

>PRK15053 dpiB sensor histidine kinase DpiB; Provisional

Probab=97.37  E-value=0.00087  Score=61.70  Aligned_cols=106  Identities=14%  Similarity=0.096  Sum_probs=72.6

Q ss_pred             HHHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCCh--hhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEE
Q 021027           17 TLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSR--AEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV   94 (318)
Q Consensus        17 ~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~--~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   94 (318)
                      ...++.+++...++++++|.+   |+++++|+++++++|++.  .+++|++...+.++...   ..   .... ......
T Consensus       221 ~~~~~~il~~~~egii~~D~~---g~I~~~N~~a~~ll~~~~~~~~~~g~~~~~~~~~~~~---~~---~~~~-~~~~~~  290 (545)
T PRK15053        221 VRQQEALFSSVYEGLIAVDPH---GYITAINRNARKMLGLSSPGRQWLGKPIAEVVRPADF---FT---EQID-EKRQDV  290 (545)
T ss_pred             HHHHHHHHHHhCceEEEECCC---CeEEeecHHHHHHhCCCCcchhhcCCcHHHhCCCchh---hh---hhcC-Ccccce
Confidence            345678999999999999999   999999999999999965  46889886665543211   10   1111 111111


Q ss_pred             EEEEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEecccccccc
Q 021027           95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM  139 (318)
Q Consensus        95 ~~~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~~  139 (318)
                      .   ...+|.  .+.+...|+..  .+.+.|.+.+++|+|+.+..
T Consensus       291 ~---~~~~~~--~~~~~~~~i~~--~~~~~G~v~~~~d~te~~~l  328 (545)
T PRK15053        291 V---ANFNGL--SVIANREAIRS--GDDLLGAIISFRSKDEISTL  328 (545)
T ss_pred             E---EEECCE--EEEEEeeeEEE--CCeEEEEEEEEEchHHHHHH
Confidence            1   122443  34466777765  56778999999999998776

>COG2461 Uncharacterized conserved protein [Function unknown]

Probab=97.27  E-value=0.0011  Score=55.79  Aligned_cols=114  Identities=16%  Similarity=0.162  Sum_probs=89.2

Q ss_pred             hHHHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEEE
Q 021027           16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVN   95 (318)
Q Consensus        16 ~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~   95 (318)
                      ....+++++++.|.-+..+|.+   +++.+.|+. .++|..++.. +|+... +.||..+......+.+.+++|..-..+
T Consensus       288 ~~~e~naif~~lP~Ditfvdk~---diV~ffs~~-~rif~rt~sv-iGr~v~-~chpPksv~iv~ki~~~fksG~kd~~e  361 (409)
T COG2461         288 SLEELNAIFKHLPVDITFVDKN---DIVRFFSGG-ERIFPRTPSV-IGRRVQ-LCHPPKSVHIVEKILKDFKSGEKDFAE  361 (409)
T ss_pred             eHHHHHHHHhhCCCceEEeccc---ceEEecCCc-ceecccChHh-hCCccc-CCCCCchHHHHHHHHHHhhcCCcchHH
Confidence            3457889999999888889999   999999998 8888877664 577644 456667777788888888888765555


Q ss_pred             EEEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEecccccccc
Q 021027           96 LLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM  139 (318)
Q Consensus        96 ~~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~~  139 (318)
                      +. .+..+  .++.++..++++ ++|+..|.+-+.+|||.-+..
T Consensus       362 fw-~~~~~--~~i~i~Y~av~d-e~ge~~g~le~~qdi~~i~~l  401 (409)
T COG2461         362 FW-INMGD--KFIHIRYFAVKD-EEGEYLGTLEVVQDITRIKEL  401 (409)
T ss_pred             Hh-ccCCC--ceEEEEEEEEEc-CCCceeeeehhhhhhHHHHhc
Confidence            54 22223  356688889999 899999999999999998886

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

Probab=97.27  E-value=0.0029  Score=51.78  Aligned_cols=109  Identities=12%  Similarity=0.106  Sum_probs=79.5

Q ss_pred             HHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEEEEEEEe
Q 021027           21 HEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYK  100 (318)
Q Consensus        21 ~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  100 (318)
                      ..++++...++.++|.+   +.+.|+|++++.+||.+...+.|..+..+++..  ......+.+....+.++...-....
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            46899999999999999   999999999999999999999998877776443  2345556666666655442222233


Q ss_pred             cCCcEEEEEEEEEeeccCCCCceeEEEEEEeccccccc
Q 021027          101 KDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKH  138 (318)
Q Consensus       101 ~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~  138 (318)
                      .+|....+...+.|+.. ..|.   ++..++-+..+.+
T Consensus        85 ~~g~~~~v~~~v~~v~~-~~G~---vlle~~~~~~~~r  118 (363)
T COG3852          85 ILGRSHIVDLTVAPVPE-EPGS---VLLEFHPRDMQRR  118 (363)
T ss_pred             ecCccceEEEEEeeccC-CCCe---EEEEechhHHHhH
Confidence            68888899999999976 5564   3444554444443

>smart00091 PAS PAS domain

Probab=97.27  E-value=0.0014  Score=39.29  Aligned_cols=54  Identities=24%  Similarity=0.417  Sum_probs=44.5

Q ss_pred             HHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCC
Q 021027           19 WVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTN   75 (318)
Q Consensus        19 ~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~   75 (318)
                      +++.+++..+.++++++..   +.+.++|+.+..++|++..++.+.....+.++...
T Consensus         2 ~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   55 (67)
T smart00091        2 RLRAILESLPDGIFVLDLD---GRILYANPAAEELLGYSPEELIGKSLLELIHPEDR   55 (67)
T ss_pred             hHHHHHhhCCceEEEEcCC---CeEEEECHHHHHHhCCCHHHHcCCcHHHhcCcccH
Confidence            3566888899999999999   99999999999999999988888765555555443

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).

>PRK11360 sensory histidine kinase AtoS; Provisional

Probab=97.24  E-value=0.00064  Score=63.16  Aligned_cols=67  Identities=19%  Similarity=0.202  Sum_probs=54.6

Q ss_pred             hHHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhccc
Q 021027          242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQ  313 (318)
Q Consensus       242 ~l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~~  313 (318)
                      .+..++++++++++++|.++   .++++|+++++++||++++++|+++.++.++..  .....+.+.+..+.
T Consensus       263 ~~~~i~~~~~~~i~~~d~~g---~i~~~N~~~~~l~g~~~~~~~g~~~~~~~~~~~--~~~~~~~~~~~~~~  329 (607)
T PRK11360        263 LNELILESIADGVIAIDRQG---KITTMNPAAEVITGLQRHELVGKPYSELFPPNT--PFASPLLDTLEHGT  329 (607)
T ss_pred             HHHHHHHhccCeEEEEcCCC---CEEEECHHHHHHhCCChHHhcCCcHHHHcCCch--hHHHHHHHHHhcCC
Confidence            46678899999999999987   999999999999999999999999998886542  33445555655544

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

Probab=97.08  E-value=0.029  Score=42.87  Aligned_cols=52  Identities=23%  Similarity=0.261  Sum_probs=42.9

Q ss_pred             HHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCC
Q 021027          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDT  297 (318)
Q Consensus       243 l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~  297 (318)
                      +..++++++++++++|.++   .++++|+++++++||+..+..++....+.....
T Consensus       114 ~~~~~~~~~~~~~~~d~~~---~~~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~  165 (232)
T COG2202         114 LRALLEASPDGIWVLDEDG---RILYANPAAEELLGYSPEEELGRGLSDLIHPED  165 (232)
T ss_pred             HHHHHhhCCceEEEEeCCC---CEEEeCHHHHHHhCCChHHhcCCChhheEecCC
Confidence            4557777899999999876   999999999999999988888888766654433

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

Probab=97.05  E-value=0.0016  Score=47.93  Aligned_cols=69  Identities=19%  Similarity=0.160  Sum_probs=53.8

Q ss_pred             HHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhcc
Q 021027          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTE  312 (318)
Q Consensus       243 l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~  312 (318)
                      +...+=..|.+|+-.+.. +|..++|.|.++.+|++|+.+|++|.+.+.-..+.....-...+.++.+.|
T Consensus        33 ~~~~L~~ap~ailsh~~~-~dP~f~yaN~aaL~l~e~~w~el~~lPsr~sae~~~r~er~~lL~~v~~qG  101 (148)
T PF08670_consen   33 LAKALWHAPFAILSHGTK-ADPIFIYANQAALDLFETTWDELVGLPSRLSAEEPERKERQSLLAQVMQQG  101 (148)
T ss_pred             HHHHHHcCCCEEEEcCCC-CCCEEEehhHHHHHHhcCCHHHHhcCcHhhccChhhHHHHHHHHHHHHHhC
Confidence            333444489999988887 788999999999999999999999998876666666666666666666554

>TIGR02373 photo_yellow photoactive yellow protein

Probab=97.02  E-value=0.0094  Score=42.03  Aligned_cols=67  Identities=18%  Similarity=0.076  Sum_probs=55.0

Q ss_pred             HHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCC-cccCCCCChHHHHHHHHHHHhcC
Q 021027           21 HEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGR-MFQGPRTNRRTIMEIREAIREER   90 (318)
Q Consensus        21 ~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~-~l~~~~~~~~~~~~~~~~~~~~~   90 (318)
                      ..-++..|-|++-+|.+   |.++..|.+=..+.|++++.++|+++. ++-|....+.+...+......+.
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            35689999999999999   999999999999999999999999844 45444556667777777666554

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.

>TIGR02373 photo_yellow photoactive yellow protein

Probab=96.83  E-value=0.0025  Score=44.85  Aligned_cols=65  Identities=14%  Similarity=0.118  Sum_probs=53.1

Q ss_pred             HHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcc-cccCCCCCHHHHHHHHHHHhccc
Q 021027          246 SLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCR-FLNGVDTDTTVLYQIKESIQTEQ  313 (318)
Q Consensus       246 ~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~-~l~~~~~~~~~~~~~~~~l~~~~  313 (318)
                      -++.+|-|++-.|.+|   +|+..|.+-.++.|++++.++|+++- ++.+=...+.+..+..+..++|.
T Consensus        21 elD~lpFGvI~lD~~G---~V~~YN~aE~~~sg~~p~~vlGr~FF~eVAPC~~~~~f~gRF~~g~~~g~   86 (124)
T TIGR02373        21 QFDALPFGAIQLDGSG---VILRYNAAEGRITGRDPERVIGRNFFKEVAPCTDIPEFSGRFMEGVASGT   86 (124)
T ss_pred             HhhcCCcceEEECCCC---EEEEEecchhhhcCCChhhhhchhhhhhcccccCCHHHHHHHHhhhhcCC
Confidence            3566799999999998   99999999999999999999999974 44433456668888877766653

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.

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

Probab=96.68  E-value=0.0028  Score=53.16  Aligned_cols=59  Identities=17%  Similarity=0.072  Sum_probs=52.2

Q ss_pred             hhHHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHH
Q 021027          241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVL  302 (318)
Q Consensus       241 ~~l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~  302 (318)
                      ..+...++++|++|+-+|..|   .+..+|||++.++|.+.+++.|++...++..-+.+.+.
T Consensus        80 l~L~aLL~al~~pVlsvd~kg---~v~~aNpAa~~l~~~~~~~~~g~~~~~l~~~~nf~~~l  138 (511)
T COG3283          80 LALSALLEALPEPVLSVDMKG---KVDMANPAACQLFGRKEDRLRGHTAAQLINGFNFLRWL  138 (511)
T ss_pred             HHHHHHHHhCCCceEEecccC---ceeecCHHHHHHhCCChhhhcCccHHHhcCcCCHHHHH
Confidence            347889999999999999998   99999999999999999999999999998776655444

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

Probab=96.43  E-value=0.0024  Score=56.54  Aligned_cols=63  Identities=33%  Similarity=0.718  Sum_probs=50.9

Q ss_pred             CCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCc--ccccCCCCCHHHHHHHHHHHhccc
Q 021027          251 KQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNC--RFLNGVDTDTTVLYQIKESIQTEQ  313 (318)
Q Consensus       251 ~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~--~~l~~~~~~~~~~~~~~~~l~~~~  313 (318)
                      ...+++.++.--|+.|+|+|+.||++.||.+.|+..++|  .+......+....+++++++++.+
T Consensus        27 dtsFlL~NAQiVD~PiVY~NdgFcKlsGY~RAevMQKs~tc~FMyGEltdk~ti~k~~~t~eN~~   91 (971)
T KOG0501|consen   27 DTSFLLANAQIVDWPIVYCNDGFCKLSGYHRAEVMQKSCTCSFMYGELTDKGTIEKVRQTLENYE   91 (971)
T ss_pred             CcceeeccceeeccceEEecCcchhccCccHHHHhcccceeeeeeccccchhhHHHHHHHHHhhh
Confidence            445566666667899999999999999999999999876  455555678888999999988654

>PRK15053 dpiB sensor histidine kinase DpiB; Provisional

Probab=96.40  E-value=0.0038  Score=57.48  Aligned_cols=52  Identities=12%  Similarity=0.145  Sum_probs=45.2

Q ss_pred             hHHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCc--ccccCCCcccccCCC
Q 021027          242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDR--NEVVGQNCRFLNGVD  296 (318)
Q Consensus       242 ~l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~--~el~G~~~~~l~~~~  296 (318)
                      .+..+++++++||+++|.+|   +|+++|+++++++|++.  ++++|+++.++.++.
T Consensus       223 ~~~~il~~~~egii~~D~~g---~I~~~N~~a~~ll~~~~~~~~~~g~~~~~~~~~~  276 (545)
T PRK15053        223 QQEALFSSVYEGLIAVDPHG---YITAINRNARKMLGLSSPGRQWLGKPIAEVVRPA  276 (545)
T ss_pred             HHHHHHHHhCceEEEECCCC---eEEeecHHHHHHhCCCCcchhhcCCcHHHhCCCc
Confidence            36678899999999999998   99999999999999976  479999998877543

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

Probab=96.40  E-value=0.0052  Score=50.33  Aligned_cols=67  Identities=19%  Similarity=0.262  Sum_probs=56.6

Q ss_pred             HHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhccccee
Q 021027          245 ISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQACT  316 (318)
Q Consensus       245 ~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~~~~~  316 (318)
                      .+++++..+|++.|.++   .|.|+|++++.+||-|..-+.|.+++.|+...  .....-+.++..++.++.
T Consensus        11 ~~Ln~~~~pVl~vd~~~---~i~yaN~aAe~~~~~Sa~~L~~~~l~~l~~~g--s~ll~ll~q~~~~~~~~~   77 (363)
T COG3852          11 AILNNLINPVLLVDDEL---AIHYANPAAEQLLAVSARRLAGTRLSELLPFG--SLLLSLLDQVLERGQPVT   77 (363)
T ss_pred             hHHhccCCceEEEcCCC---cEEecCHHHHHHHHHHHHHHhcCChHHHcCCC--cHHHHHHHHHHHhcCCcc
Confidence            57888999999999987   99999999999999999999999999887543  345677777777777653

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

Probab=96.14  E-value=0.017  Score=48.67  Aligned_cols=56  Identities=14%  Similarity=0.158  Sum_probs=48.9

Q ss_pred             hHHHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCC
Q 021027           16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRT   74 (318)
Q Consensus        16 ~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~   74 (318)
                      ..-.+.+++++.++++..+|..   |.+..+|++++++||.+++.+.|.+...++....
T Consensus        78 ~hl~L~aLL~al~~pVlsvd~k---g~v~~aNpAa~~l~~~~~~~~~g~~~~~l~~~~n  133 (511)
T COG3283          78 EHLALSALLEALPEPVLSVDMK---GKVDMANPAACQLFGRKEDRLRGHTAAQLINGFN  133 (511)
T ss_pred             HhHHHHHHHHhCCCceEEeccc---CceeecCHHHHHHhCCChhhhcCccHHHhcCcCC
Confidence            3446788999999999999999   9999999999999999999999998776665543

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

Probab=96.10  E-value=0.019  Score=53.26  Aligned_cols=58  Identities=12%  Similarity=0.182  Sum_probs=48.3

Q ss_pred             EEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhcc
Q 021027          254 FVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTE  312 (318)
Q Consensus       254 i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~  312 (318)
                      |+++-.. +.+.|..|..++..++||-+.+|||+.+..++|+.+.....+.-.+.++.+
T Consensus       332 iFtT~HT-ptClf~hVDeaAVp~LGyLPqDLIG~sil~f~H~eDr~vm~q~H~~v~q~~  389 (1114)
T KOG3753|consen  332 IFTTTHT-PTCLFQHVDEAAVPLLGYLPQDLIGTSILAFVHPEDRHVMVQIHQKVLQSG  389 (1114)
T ss_pred             eeEeccC-CcceeeecchhhhhhhccCchhhhccchhhhhcCCchHHHHHHHHHHHHhC
Confidence            4544433 567899999999999999999999999999999999887777777777755

>PRK11086 sensory histidine kinase DcuS; Provisional

Probab=96.05  E-value=0.0092  Score=54.86  Aligned_cols=51  Identities=16%  Similarity=0.221  Sum_probs=43.1

Q ss_pred             hhHHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCC---cccccCCCcccccC
Q 021027          241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYD---RNEVVGQNCRFLNG  294 (318)
Q Consensus       241 ~~l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~---~~el~G~~~~~l~~  294 (318)
                      ..+..++++++++|+++|.+|   +|+++|+++++++|++   ..+.+|+.+..+.+
T Consensus       221 ~~~~~il~~~~~gIi~~D~~g---~I~~~N~~a~~llg~~~~~~~~~~~~~~~~~~~  274 (542)
T PRK11086        221 EQRQAMLQSIKEGVIAVDDRG---EVTLINDEAKRLFNYKKGLEDDPLGTDVESWMP  274 (542)
T ss_pred             HHHHHHHHHhcCcEEEECCCC---eEEEEhHHHHHHhCCCcCCcccccCCcHHHhCC
Confidence            446789999999999999998   9999999999999876   35778888776654

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

Probab=95.94  E-value=0.0096  Score=49.70  Aligned_cols=56  Identities=16%  Similarity=0.246  Sum_probs=48.5

Q ss_pred             hHHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHH
Q 021027          242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTT  300 (318)
Q Consensus       242 ~l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~  300 (318)
                      +|..++.-+.|||+.+|..|   .|+.+|+.+.+|+|.+.++++|+++.++..-.+.-.
T Consensus       112 kL~SvlayMtDGViATdRrG---~iI~iN~~A~k~L~~~~E~~~~~~i~elL~i~d~y~  167 (459)
T COG5002         112 KLDSVLAYMTDGVIATDRRG---KIILINKPALKMLGVSKEDALGRSILELLKIEDTYT  167 (459)
T ss_pred             HHHHHHHHHcCceEeecCCC---cEEEeccHHHHHhCcCHHHHhcccHHHHhCCcccee
Confidence            46667777899999999998   999999999999999999999999988876555433

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

Probab=95.75  E-value=0.1  Score=27.15  Aligned_cols=39  Identities=31%  Similarity=0.463  Sum_probs=31.7

Q ss_pred             EEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEeccccc
Q 021027           97 LNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSR  136 (318)
Q Consensus        97 ~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~  136 (318)
                      .....+|...|+.....++.+ ..+.+.+++++..|||++
T Consensus         5 ~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~di~~~   43 (43)
T smart00086        5 RLRRKDGSYIWVLVSASPIRD-EDGEVEGILGVVRDITER   43 (43)
T ss_pred             EEEecCCCEEEEEEEeEEEEC-CCCCEEEEEEEEEeccCC
Confidence            445678888898888888887 678888999999999863

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

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

Probab=95.70  E-value=0.016  Score=51.46  Aligned_cols=51  Identities=20%  Similarity=0.201  Sum_probs=45.9

Q ss_pred             HHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcc--cccCCCcccccCCC
Q 021027          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRN--EVVGQNCRFLNGVD  296 (318)
Q Consensus       243 l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~--el~G~~~~~l~~~~  296 (318)
                      ...+|.++..||+.+|..|   .|+.+|.++++|+|+...  +.+|+++.++..|+
T Consensus       217 r~A~l~si~EGviAvd~~G---~It~~N~~A~~ll~~~~~~~~~ig~~i~~v~~p~  269 (537)
T COG3290         217 RQAMLQSIKEGVIAVDKKG---VITLINQAAQKLLGLRQPSGDPIGRSIVEVLPPD  269 (537)
T ss_pred             HHHHHHHhhceEEEECCCC---eEeehhHHHHHHhcccCcCcccccccceEeeccc
Confidence            5568899999999999998   999999999999999875  79999999998763

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

Probab=95.65  E-value=0.0053  Score=57.30  Aligned_cols=63  Identities=16%  Similarity=0.198  Sum_probs=48.8

Q ss_pred             chhHHHHHhccCCcE-EEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHH
Q 021027          240 SSSLYISLGRIKQSF-VLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQI  305 (318)
Q Consensus       240 ~~~l~~~~~~~~~~i-~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~  305 (318)
                      ...|.-++-.+-||+ +++..+|   +|+||.++...++||..+|++|+++.++++|.+....++.+
T Consensus        93 ~~eL~~LmLeAlDGF~fvV~cdG---~IvyVSeSVT~~L~y~QsDL~~qSly~ilhp~d~~~~~~ql  156 (803)
T KOG3561|consen   93 NDELTHLILEALDGFLFVVNCDG---RIVYVSESVTSVLGYLQSDLMGQSLYDILHPLDNDKPREQL  156 (803)
T ss_pred             hHHHHHHHHHHhcCeEEEEecCc---eEEEEecchHHhhCcCHHHHhcchHHHhcCccccCcccccc
Confidence            445665444444554 6666666   99999999999999999999999999999998766655543

>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]

Probab=95.49  E-value=0.065  Score=47.25  Aligned_cols=93  Identities=14%  Similarity=0.162  Sum_probs=75.1

Q ss_pred             CcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEEEEEEEecCCcEEEEEEEEEeeccCCC
Q 021027           41 HPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKED  120 (318)
Q Consensus        41 ~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~i~~~~~  120 (318)
                      +..+.+......++||...|+.|.....+++-++..-......+.++.|+..-.-++..+++|+..|+..++..++.  +
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            66778888899999999999999888888877766555667778888888888888888999999999888877775  7


Q ss_pred             CceeEEEEEEecccc
Q 021027          121 GRATHFVAVQVPIVS  135 (318)
Q Consensus       121 g~~~~~i~~~~DIte  135 (318)
                      |.+..++...+-.++
T Consensus       371 gkPD~vi~thr~l~D  385 (712)
T KOG3560|consen  371 GKPDLVIDTHRGLGD  385 (712)
T ss_pred             CCCCEEEecCCCccc
Confidence            888777766554444

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

Probab=95.29  E-value=0.39  Score=35.27  Aligned_cols=87  Identities=13%  Similarity=0.155  Sum_probs=70.6

Q ss_pred             CCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEEEEEEEecCCcEEEEEEEEEeeccCC
Q 021027           40 GHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKE  119 (318)
Q Consensus        40 ~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~i~~~~  119 (318)
                      +.++..+-...+.++|+   ++.|+++..++.+.........+..++....+..........+|....++...-|+.+ +
T Consensus        50 ~~r~RLaGt~i~~~~G~---d~tG~~~~el~~~~~~~~~~~~~~~v~~~~~p~~~~~~~~~~~g~~~~~e~l~LPL~~-~  125 (137)
T PF07310_consen   50 DFRYRLAGTRIVELFGR---DLTGRRLSELFPPEDRERVRRAYRAVVERPAPVRARGRAEDADGRYLEYERLLLPLRS-D  125 (137)
T ss_pred             ceEEEEecHHHHHHhCC---CCCCCCHHHhcChHhHHHHHHHHHHHHcCCceEEEEEEEecCCCCeeEEEEEEcccCC-C
Confidence            46677888999999998   5679988888888777777778888888888877777777778888888888999998 7


Q ss_pred             CCceeEEEEEE
Q 021027          120 DGRATHFVAVQ  130 (318)
Q Consensus       120 ~g~~~~~i~~~  130 (318)
                      +|.+..++|..
T Consensus       126 ~~~v~rilG~~  136 (137)
T PF07310_consen  126 GGTVDRILGAL  136 (137)
T ss_pred             CCCccEEEEec
Confidence            78888887764

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

Probab=94.42  E-value=0.057  Score=48.68  Aligned_cols=48  Identities=13%  Similarity=0.137  Sum_probs=43.4

Q ss_pred             HHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCccccc
Q 021027          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLN  293 (318)
Q Consensus       243 l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~  293 (318)
                      +...++.++-||+..|.+|   +|.-+||++++|+|.+.++++|++.+.+.
T Consensus       372 ~E~VLsgvtaGVi~~d~~g---~i~t~N~~ae~~l~~~~~~~~G~~lsa~a  419 (712)
T COG5000         372 LEAVLSGLTAGVIGFDNRG---CITTVNPSAEQILGKPFDQLLGQSLSAIA  419 (712)
T ss_pred             HHHHHhcCceeEEEEcCCC---eeEeecchHHHHhcCChhHhhcchhhhhh
Confidence            5568888999999999998   99999999999999999999999977664

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

Probab=93.70  E-value=0.061  Score=50.54  Aligned_cols=58  Identities=17%  Similarity=0.292  Sum_probs=48.7

Q ss_pred             HHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHH
Q 021027           19 WVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTI   79 (318)
Q Consensus        19 ~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~   79 (318)
                      +-..+++++...++++.-+   |+|+||++....++||..+|++|.++..+.++.+.....
T Consensus        96 L~~LmLeAlDGF~fvV~cd---G~IvyVSeSVT~~L~y~QsDL~~qSly~ilhp~d~~~~~  153 (803)
T KOG3561|consen   96 LTHLILEALDGFLFVVNCD---GRIVYVSESVTSVLGYLQSDLMGQSLYDILHPLDNDKPR  153 (803)
T ss_pred             HHHHHHHHhcCeEEEEecC---ceEEEEecchHHhhCcCHHHHhcchHHHhcCccccCccc
Confidence            3345778887778899999   999999999999999999999999988888877654433

>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=92.62  E-value=0.15  Score=35.87  Aligned_cols=42  Identities=29%  Similarity=0.521  Sum_probs=33.9

Q ss_pred             EEEecCCCCCCCeeEecHHHHHHhCCC---cccccCCCcccccCCCC
Q 021027          254 FVLIDPHLPDMPMVYASDAFLKLTGYD---RNEVVGQNCRFLNGVDT  297 (318)
Q Consensus       254 i~i~d~~~~~~~i~~~N~a~~~~~Gy~---~~el~G~~~~~l~~~~~  297 (318)
                      ++..|..  +++|+.++.....++|.+   .++++|+++..++.+..
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            3445554  369999999999999999   99999999999986544

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

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

Probab=91.00  E-value=0.36  Score=49.24  Aligned_cols=42  Identities=10%  Similarity=-0.047  Sum_probs=35.7

Q ss_pred             hhHHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCccccc
Q 021027          241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVV  285 (318)
Q Consensus       241 ~~l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~  285 (318)
                      ..++.++++++++|+++|.+|   +|+++|+++++++|++.....
T Consensus       576 ~~~~~i~~~~~~~i~~~d~~g---~i~~~N~~~~~~~g~~~~~~~  617 (1197)
T PRK09959        576 SFRKALSDSLPNPTYVVNWQG---NVISHNSAFEHYFTADYYKNA  617 (1197)
T ss_pred             HHHHHHHhhCCCcEEEEcCCC---cEEEehHHHHHHhCccccccc
Confidence            346678999999999999987   999999999999998754433

>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]

Probab=90.63  E-value=0.54  Score=40.16  Aligned_cols=85  Identities=8%  Similarity=0.051  Sum_probs=58.0

Q ss_pred             eEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEEEEEEEecCCcEEEEE
Q 021027           30 SFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWML  109 (318)
Q Consensus        30 ~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~  109 (318)
                      .+++...+   ..+++......+++||.+.+++++.+...++..+...+.......+..|....--+++..+.|...|+.
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            45566777   899999999999999999999999877666666555554444444444443333334456777777776


Q ss_pred             EEEEeecc
Q 021027          110 FKMSLVFG  117 (318)
Q Consensus       110 ~~~~~i~~  117 (318)
                      -....+.+
T Consensus       304 syat~vHn  311 (598)
T KOG3559|consen  304 SYATFVHN  311 (598)
T ss_pred             EeeEEEec
Confidence            65555443

>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]

Probab=89.76  E-value=0.36  Score=42.83  Aligned_cols=63  Identities=14%  Similarity=0.187  Sum_probs=54.6

Q ss_pred             HHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHH
Q 021027          244 YISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESI  309 (318)
Q Consensus       244 ~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l  309 (318)
                      ...+.+++.-++++..+|   .|.|+....+..+|+-..+++-+++.+|+|.++...+.+.+.-++
T Consensus       114 e~lLqsLnGF~lVvt~eg---~ifyAS~tIedYLGFhQSDV~HQsVYdlIHseDR~dfqrQLhwa~  176 (712)
T KOG3560|consen  114 ELLLQSLNGFALVVTAEG---EIFYASATIEDYLGFHQSDVMHQSVYDLIHSEDRQDFQRQLHWAM  176 (712)
T ss_pred             HHHHHhcCCeEEEEecCc---eEEEehhhHHhhhcccccchhhhhHHHHhhhhhHHHHHHHHhhcc
Confidence            345666777778888887   999999999999999999999999999999999999888876554

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

Probab=88.33  E-value=13  Score=34.43  Aligned_cols=41  Identities=17%  Similarity=0.212  Sum_probs=33.5

Q ss_pred             cCCcEEEecCCCCCCCeeEecHHHHHHhCCC-cccccCCCccccc
Q 021027          250 IKQSFVLIDPHLPDMPMVYASDAFLKLTGYD-RNEVVGQNCRFLN  293 (318)
Q Consensus       250 ~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~-~~el~G~~~~~l~  293 (318)
                      .+.+.+++|.++   +|...|+++..+++.+ ..-++|.....+.
T Consensus       231 ~~~~~lavd~~g---rvl~at~aA~~~La~~~~~~l~g~p~~~~~  272 (606)
T COG3284         231 QSEALLAVDQDG---RVLGATRAARQLLALTDRQRLIGQPVEDFL  272 (606)
T ss_pred             ccceeeeecCcc---hhhhccHHHHHhhccchhhHhhcCCccccc
Confidence            467888999887   9999999999999988 5566777766554

>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=87.77  E-value=0.82  Score=32.09  Aligned_cols=43  Identities=26%  Similarity=0.397  Sum_probs=34.4

Q ss_pred             eEEEEcCCCCCCcEEEecHhHHHhcCCC---hhhhcCCCCCcccCCCC
Q 021027           30 SFTITDPSISGHPIVFASRGFLKMSGFS---RAEIIGRNGRMFQGPRT   74 (318)
Q Consensus        30 ~i~~~d~~~~~~~i~~~N~~~~~~~G~~---~~e~~g~~~~~l~~~~~   74 (318)
                      .++++|.+  +++|+.++.....++|.+   .++++|+++..++.+..
T Consensus        17 ~LLa~d~~--~~~I~~~S~N~~~~lg~~~~~~~~llG~~l~~ll~~~~   62 (110)
T PF08446_consen   17 ALLALDPD--DLRIVQASENIAELLGIPPELPEELLGRPLSELLGAES   62 (110)
T ss_dssp             EEEEEETT--TTBEEEEETTHHHHHSS----HHHHTTCBHHHHSCCCC
T ss_pred             EEEEEECC--CCEEEEEcCCHHHHhCCccccchhhcccCHHHHhCHHH
Confidence            34566654  499999999999999999   99999999888876543

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 ....

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

Probab=87.67  E-value=6.5  Score=39.05  Aligned_cols=42  Identities=7%  Similarity=0.025  Sum_probs=34.6

Q ss_pred             hhHHHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCCh
Q 021027           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSR   58 (318)
Q Consensus        15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~   58 (318)
                      ..++.++.+++..|.++++++..  ++.++++|+.+..++|+..
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  3999999999999888743

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

Probab=87.08  E-value=1.9  Score=40.85  Aligned_cols=90  Identities=9%  Similarity=0.092  Sum_probs=64.1

Q ss_pred             CCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCe---EEEEEEEecCCcEEEEEEEEEee
Q 021027           39 SGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPI---EVNLLNYKKDGTPFWMLFKMSLV  115 (318)
Q Consensus        39 ~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~g~~~~~~~~~~~i  115 (318)
                      ++..+..+..++..++||-+.++||+.+..++++.+...+.....+.++.+...   .-.+++..++|.++.+......+
T Consensus       339 ptClf~hVDeaAVp~LGyLPqDLIG~sil~f~H~eDr~vm~q~H~~v~q~~G~p~F~~sp~Rf~aqNG~yv~ldTeWSsF  418 (1114)
T KOG3753|consen  339 PTCLFQHVDEAAVPLLGYLPQDLIGTSILAFVHPEDRHVMVQIHQKVLQSGGKPVFSHSPIRFCAQNGSYVRLDTEWSSF  418 (1114)
T ss_pred             CcceeeecchhhhhhhccCchhhhccchhhhhcCCchHHHHHHHHHHHHhCCCCcccccceeeeecCCcEEEEechhhhc
Confidence            347788899999999999999999999888888888887777777777755332   23456677899877665554444


Q ss_pred             ccCCCCceeEEEE
Q 021027          116 FGKEDGRATHFVA  128 (318)
Q Consensus       116 ~~~~~g~~~~~i~  128 (318)
                      .++...++..+++
T Consensus       419 VNPWSRKieFVvG  431 (1114)
T KOG3753|consen  419 VNPWSRKIEFVVG  431 (1114)
T ss_pred             cChhhhheeeeee
Confidence            4423344444444

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	318
3ue6_A	166	The Dark Structure Of The Blue-light Photoreceptor		1e-16
3ue6_A	166	The Dark Structure Of The Blue-light Photoreceptor		2e-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		2e-12
2z6d_A	130	Crystal Structure Of Lov1 Domain Of Phototropin2 Fr		2e-16
2z6d_A	130	Crystal Structure Of Lov1 Domain Of Phototropin2 Fr		2e-12
2wkq_A	332	Structure Of A Photoactivatable Rac1 Containing The		2e-16
2wkq_A	332	Structure Of A Photoactivatable Rac1 Containing The		3e-15
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-16
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-16
2wkp_A	332	Structure Of A Photoactivatable Rac1 Containing Lov		2e-16
4eeu_A	118	Crystal Structure Of Philov2.1 Length = 118		3e-16
4eeu_A	118	Crystal Structure Of Philov2.1 Length = 118		2e-14
4ees_A	115	Crystal Structure Of Ilov Length = 115		4e-16
4ees_A	115	Crystal Structure Of Ilov Length = 115		5e-14
2wkr_A	332	Structure Of A Photoactivatable Rac1 Containing The		5e-16
2wkr_A	332	Structure Of A Photoactivatable Rac1 Containing The		4e-15
4eer_A	115	Crystal Structure Of Lov2 Domain Of Arabidopsis Tha		3e-15
4eer_A	115	Crystal Structure Of Lov2 Domain Of Arabidopsis Tha		7e-14
1n9l_A	109	Crystal Structure Of The Phot-lov1 Domain From Chla		4e-15
1n9l_A	109	Crystal Structure Of The Phot-lov1 Domain From Chla		3e-13
4eep_A	115	Crystal Structure Of Lov2 Domain Of Arabidopsis Tha		7e-15
4eep_A	115	Crystal Structure Of Lov2 Domain Of Arabidopsis Tha		9e-15
2z6c_A	129	Crystal Structure Of Lov1 Domain Of Phototropin1 Fr		3e-14
2z6c_A	129	Crystal Structure Of Lov1 Domain Of Phototropin1 Fr		1e-12
2pr5_A	132	Structural Basis For Light-dependent Signaling In T		9e-14
2pr5_A	132	Structural Basis For Light-dependent Signaling In T		2e-10
1g28_A	104	Structure Of A Flavin-Binding Domain, Lov2, From Th		2e-13
3t50_A	128	X-Ray Structure Of The Lov Domain From The Lov-Hk S		3e-13
3p7n_A	258	Crystal Structure Of Light Activated Transcription		4e-10
3p7n_A	258	Crystal Structure Of Light Activated Transcription		3e-07
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		9e-07
4hj6_A	178	Crystal Structure Of Rhodobacter Sphaeroides Lov Pr		9e-07
4hj3_A	176	Crystal Structure Of Rhodobacter Sphaeroides Lov Pr		1e-06
4hia_A	176	Crystal Structure Of Rhodobacter Sphaeroides Lov Pr		1e-06
3sw1_A	162	Structure Of A Full-Length Bacterial Lov Protein Le		1e-05
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
1byw_A	110	Structure Of The N-Terminal Domain Of The Human-Erg		5e-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 = 69.7 bits (169), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 32/68 (47%), Positives = 47/68 (69%)
Query: 242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTV 301
           SL  +L   +Q+FV+ D  LPD P+VYAS  FL LTGY  ++++G+NCRFL G +TD   
Sbjct: 36  SLVKALQMAQQNFVITDASLPDNPIVYASRGFLTLTGYSLDQILGRNCRFLQGPETDPRA 95
Query: 302 LYQIKESI 309
           + +I+ +I
Sbjct: 96  VDKIRNAI 103

>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 = 69.7 bits (169), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 32/68 (47%), Positives = 47/68 (69%)
Query: 242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTV 301
           SL  +L   +Q+FV+ D  LPD P+VYAS  FL LTGY  ++++G+NCRFL G +TD   
Sbjct: 40  SLVKALQMAQQNFVITDASLPDNPIVYASRGFLTLTGYSLDQILGRNCRFLQGPETDPRA 99
Query: 302 LYQIKESI 309
           + +I+ +I
Sbjct: 100 VDKIRNAI 107

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

Iteration: 1
 Score = 83.2 bits (204), Expect = 2e-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 = 70.1 bits (170), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 30/72 (41%), Positives = 46/72 (63%)
Query: 239 ISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTD 298
           +S  L  +L  ++Q+FV+ D   P  P+VYAS  F  +TGY   E+VG+NCRFL G DTD
Sbjct: 4   VSQELKTALSTLQQTFVVSDATQPHCPIVYASSGFFTMTGYSSKEIVGRNCRFLQGPDTD 63
Query: 299 TTVLYQIKESIQ 310
              + +I++ ++
Sbjct: 64  KNEVAKIRDCVK 75

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

Iteration: 1
 Score = 82.8 bits (203), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 41/120 (34%), Positives = 65/120 (54%), Gaps = 3/120 (2%)
Query: 24  LDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNXXXXXXXX 83
           L+ +  +F ITDP +  +PI+FAS  FL+++ +SR EI+GRN R  QGP T+        
Sbjct: 17  LERIEKNFVITDPRLPDNPIIFASDSFLQLTEYSREEILGRNARFLQGPETDRATVRKIR 76
Query: 84  XXXXXXXXXXVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG 143
                     V L+NY K G  FW LF +  +  ++ G   +F+ VQ+     +H+R++ 
Sbjct: 77  DAIDNQTEVTVQLINYTKSGKKFWNLFHLQPMRDQK-GDVQYFIGVQLD--GTEHVRDAA 133

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

Iteration: 1
 Score = 79.3 bits (194), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 34/75 (45%), Positives = 54/75 (72%)
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 LYQIKESIQTEQACT 316
           + +I+++I  +   T
Sbjct: 72  VRKIRDAIDNQTEVT 86

>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 = 82.4 bits (202), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 34/74 (45%), Positives = 54/74 (72%)
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 YQIKESIQTEQACT 316
            +I+++I  +   T
Sbjct: 62  RKIRDAIDNQTEVT 75

>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 = 82.8 bits (203), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 34/74 (45%), Positives = 54/74 (72%)
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 YQIKESIQTEQACT 316
            +I+++I  +   T
Sbjct: 64  RKIRDAIDNQTEVT 77

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

Iteration: 1
 Score = 82.8 bits (203), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 35/75 (46%), Positives = 55/75 (73%)
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 LYQIKESIQTEQACT 316
           + +I+++I  +   T
Sbjct: 72  VRKIRDAIDNQTEVT 86

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

Iteration: 1
 Score = 82.0 bits (201), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 40/102 (39%), Positives = 56/102 (54%), Gaps = 1/102 (0%)
Query: 30  SFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNXXXXXXXXXXXXXX 89
           SF ITDP +  +PI+FAS GFL+++ +SR EI+GRN R  QGP T+              
Sbjct: 12  SFVITDPRLPDYPIIFASDGFLELTEYSREEIMGRNARFLQGPETDQATVQKIRDAIRDQ 71
Query: 90  XXXXVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQV 131
               V L+NY K G  FW L  +  V  ++ G   +F+ VQ+
Sbjct: 72  RETTVQLINYTKSGKKFWNLLHLQPVRDRKGG-LQYFIGVQL 112

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

Iteration: 1
 Score = 76.6 bits (187), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 31/67 (46%), Positives = 50/67 (74%)
Query: 250 IKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESI 309
           I++SFV+ DP LPD P+++ASD FL+LT Y R E++G+N RFL G +TD   + +I+++I
Sbjct: 9   IEKSFVITDPRLPDYPIIFASDGFLELTEYSREEIMGRNARFLQGPETDQATVQKIRDAI 68
Query: 310 QTEQACT 316
           + ++  T
Sbjct: 69  RDQRETT 75

>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 = 75.1 bits (183), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 30/67 (44%), Positives = 50/67 (74%)
Query: 250 IKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESI 309
           I+++FV+ DP LPD P+++ASD FL+LT Y R E++G+N RFL G +TD   + +I+++I
Sbjct: 6   IEKNFVITDPRLPDNPIIFASDGFLELTEYSREEILGRNARFLQGPETDQATVQKIRDAI 65
Query: 310 QTEQACT 316
           + ++  T
Sbjct: 66  RDQRETT 72

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

Iteration: 1
 Score = 81.6 bits (200), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 41/120 (34%), Positives = 65/120 (54%), Gaps = 3/120 (2%)
Query: 24  LDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNXXXXXXXX 83
           L+ +  +F ITDP +  +PI+FAS  FL+++ +SR EI+GRN R  QGP T+        
Sbjct: 17  LERIEKNFVITDPRLPDNPIIFASDSFLQLTEYSREEILGRNMRFLQGPETDRATVRKIR 76
Query: 84  XXXXXXXXXXVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG 143
                     V L+NY K G  FW LF +  +  ++ G   +F+ VQ+     +H+R++ 
Sbjct: 77  DAIDNQTEVTVQLINYTKSGKKFWNLFHLQPMRDQK-GDVQYFIGVQLD--GTEHVRDAA 133

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

Iteration: 1
 Score = 78.6 bits (192), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 34/75 (45%), Positives = 54/75 (72%)
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 LYQIKESIQTEQACT 316
           + +I+++I  +   T
Sbjct: 72  VRKIRDAIDNQTEVT 86

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

Iteration: 1
 Score = 79.0 bits (193), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 37/102 (36%), Positives = 55/102 (53%), 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  REITVQLINYTKSGKKFWNLFHLQPM-RDQKGELQYFIGVQL 109

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

Iteration: 1
 Score = 74.7 bits (182), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 30/67 (44%), Positives = 51/67 (76%)
Query: 250 IKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESI 309
           I+++FV+ DP LPD P+++ASD+FL+LT Y R E++G+N RFL G +TD   + +I+++I
Sbjct: 6   IEKNFVISDPRLPDNPIIFASDSFLELTEYSREEILGRNARFLQGPETDQATVQKIRDAI 65
Query: 310 QTEQACT 316
           + ++  T
Sbjct: 66  RDQREIT 72

>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 = 4e-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 = 72.4 bits (176), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 30/67 (44%), Positives = 47/67 (70%)
Query: 250 IKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESI 309
           ++ +FV+ D  LPD P+VYAS+ F  +TGY  +EV+G NCRFL G  TD   + +I+++I
Sbjct: 2   LRHTFVVADATLPDCPLVYASEGFYAMTGYGPDEVLGHNCRFLQGEGTDPKEVQKIRDAI 61
Query: 310 QTEQACT 316
           +  +AC+
Sbjct: 62  KKGEACS 68

>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 = 7e-15,   Method: Compositional matrix adjust.
 Identities = 37/102 (36%), Positives = 55/102 (53%), 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  REITVQLINYTKSGKKFWNLFHLQPM-RDQKGELQYFIGVQL 109

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

Iteration: 1
 Score = 77.4 bits (189), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 31/67 (46%), Positives = 52/67 (77%)
Query: 250 IKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESI 309
           I+++FV+ DP LPD P+++ASD+FL+LT Y R E++G+NCRFL G +TD   + +I+++I
Sbjct: 6   IEKNFVISDPRLPDNPIIFASDSFLELTEYSREEILGRNCRFLQGPETDQATVQKIRDAI 65
Query: 310 QTEQACT 316
           + ++  T
Sbjct: 66  RDQREIT 72

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

Iteration: 1
 Score = 75.9 bits (185), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 36/114 (31%), Positives = 59/114 (51%), Gaps = 1/114 (0%)
Query: 20  VHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNXXXX 79
           + +AL     +F ++D +   +PI++AS GF  M+G++  E++GRN R  QG  T+    
Sbjct: 9   LKDALSTFQQTFVVSDATKPDYPIMYASAGFFNMTGYTSKEVVGRNCRFLQGSGTDADEL 68
Query: 80  XXXXXXXXXXXXXXVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPI 133
                           +LNYKKDGT FW L  ++ +   E G+   F+ +QV +
Sbjct: 69  AKIRETLAAGNNYCGRILNYKKDGTSFWNLLTIAPI-KDESGKVLKFIGMQVEV 121

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

Iteration: 1
 Score = 70.5 bits (171), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 33/75 (44%), Positives = 47/75 (62%)
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 VDTDTTVLYQIKESI 309
             TD   L +I+E++
Sbjct: 61  SGTDADELAKIRETL 75

>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 = 38/114 (33%), Positives = 58/114 (50%), Gaps = 3/114 (2%)
Query: 24  LDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNXXXXXXXX 83
           LD +     ITDP++  +PIV+ ++GF++M+G+   EI+G+N R  QG  T+        
Sbjct: 5   LDHVRVGVVITDPALEDNPIVYVNQGFVQMTGYETEEILGKNCRFLQGKHTDPAEVDNIR 64
Query: 84  XXXXXXXXXXVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRK 137
                     V + NYKKDGT FW    +  +   E    T+FV +Q  I  +K
Sbjct: 65  TALQNKEPVTVQIQNYKKDGTMFWNELNIDPM---EIEDKTYFVGIQNDITKQK 115

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

Iteration: 1
 Score = 63.2 bits (152), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 26/70 (37%), Positives = 44/70 (62%)
Query: 247 LGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIK 306
           L  ++   V+ DP L D P+VY +  F+++TGY+  E++G+NCRFL G  TD   +  I+
Sbjct: 5   LDHVRVGVVITDPALEDNPIVYVNQGFVQMTGYETEEILGKNCRFLQGKHTDPAEVDNIR 64
Query: 307 ESIQTEQACT 316
            ++Q ++  T
Sbjct: 65  TALQNKEPVT 74

>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 = 31/65 (47%), Positives = 46/65 (70%)
Query: 252 QSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQT 311
           +SFV+ DP LPD P+++ASD FL+LT Y R EV+G NCRFL G  TD   +  I+++++ 
Sbjct: 1   KSFVITDPRLPDNPIIFASDRFLELTEYTREEVLGNNCRFLQGRGTDRKAVQLIRDAVKE 60
Query: 312 EQACT 316
           ++  T
Sbjct: 61  QRDVT 65

>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 = 72.4 bits (176), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 31/59 (52%), Positives = 44/59 (74%)
Query: 255 VLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQ 313
           ++ +PHLPD P+V+A+ AFLKLTGY+ +EV+G+NCRFL G  TD   +  IK +I  E+
Sbjct: 11  LITNPHLPDNPIVFANPAFLKLTGYEADEVMGRNCRFLQGHGTDPAHVRAIKSAIAAEK 69

>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 = 52.4 bits (124), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 23/59 (38%), Positives = 36/59 (61%)
Query: 255 VLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQ 313
           V+ DP L D P++  + AF  LTGY   E VG+NCRFL G  T+  +  +I++ ++  +
Sbjct: 77  VVSDPRLADNPLIAINQAFTDLTGYSEEECVGRNCRFLAGSGTEPWLTDKIRQGVREHK 135

>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 = 52.4 bits (124), 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 = 52.4 bits (124), 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 = 52.4 bits (124), 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 = 50.8 bits (120), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 20/58 (34%), Positives = 36/58 (62%)
Query: 253 SFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQ 310
           +  L+D  LP+ P+V A+  FL++TGY   +++G NCRFL   D +      I+++++
Sbjct: 20  ALTLVDMSLPEQPLVLANPPFLRMTGYTEGQILGFNCRFLQRGDENAQARADIRDALK 77

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

Iteration: 1
 Score = 50.8 bits (120), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 20/58 (34%), Positives = 36/58 (62%)
Query: 253 SFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQ 310
           +  L+D  LP+ P+V A+  FL++TGY   +++G NCRFL   D +      I+++++
Sbjct: 21  ALTLVDMSLPEQPLVLANPPFLRMTGYTEGQILGFNCRFLQRGDENAQARADIRDALK 78

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

Iteration: 1
 Score = 50.8 bits (120), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 20/58 (34%), Positives = 36/58 (62%)
Query: 253 SFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQ 310
           +  L+D  LP+ P+V A+  FL++TGY   +++G NCRFL   D +      I+++++
Sbjct: 19  ALTLVDMSLPEQPLVLANPPFLRMTGYTEGQILGFNCRFLQRGDENAQARADIRDALK 76

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

Iteration: 1
 Score = 50.4 bits (119), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 20/58 (34%), Positives = 36/58 (62%)
Query: 253 SFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQ 310
           +  L+D  LP+ P+V A+  FL++TGY   +++G NCRFL   D +      I+++++
Sbjct: 19  ALTLVDMSLPEQPVVLANPPFLRMTGYTEGQILGFNCRFLQRGDENAQARADIRDALK 76

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

Iteration: 1
 Score = 47.4 bits (111), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 22/64 (34%), Positives = 37/64 (57%)
Query: 254 FVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQ 313
            V+ +    D  ++Y + AF  LTGY R+E++ Q+CRFL G D D     +I++++   +
Sbjct: 38  IVVAEKEGDDTILIYVNAAFEYLTGYSRDEILYQDCRFLQGDDRDQLGRARIRKAMAEGR 97
Query: 314 ACTE 317
            C E
Sbjct: 98  PCRE 101

>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 = 43.5 bits (101), 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 = 43.1 bits (100), 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|1BYW|A Chain A, Structure Of The N-Terminal Domain Of The Human-Erg Potassium Channel Length = 110

Iteration: 1
 Score = 42.0 bits (97), Expect = 5e-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	318
2z6d_A	130	Phototropin-2; PAS-fold, LOV-fold, alternative spl	2e-50
2z6d_A	130	Phototropin-2; PAS-fold, LOV-fold, alternative spl	2e-25
4eet_B	115	Phototropin-2; LOV, blue light photoreceptor, sign	2e-49
4eet_B	115	Phototropin-2; LOV, blue light photoreceptor, sign	2e-27
2v0u_A	146	NPH1-1, LOV2; kinase, transferase, ATP-binding, se	7e-49
2v0u_A	146	NPH1-1, LOV2; kinase, transferase, ATP-binding, se	2e-26
3t50_A	128	Blue-light-activated histidine kinase; PAS superfa	3e-48
3t50_A	128	Blue-light-activated histidine kinase; PAS superfa	9e-25
3ue6_A	166	Aureochrome1; PAS/LOV domain, FMN-binding blue-lig	1e-47
3ue6_A	166	Aureochrome1; PAS/LOV domain, FMN-binding blue-lig	8e-25
2pr5_A	132	Blue-light photoreceptor; light-oxygen-voltage, LO	4e-47
2pr5_A	132	Blue-light photoreceptor; light-oxygen-voltage, LO	8e-24
1n9l_A	109	PHOT-LOV1, putative blue light receptor; phototrop	5e-47
1n9l_A	109	PHOT-LOV1, putative blue light receptor; phototrop	4e-27
3p7n_A	258	Sensor histidine kinase; LOV domain, light-activat	7e-47
3p7n_A	258	Sensor histidine kinase; LOV domain, light-activat	4e-22
2l0w_A	138	Potassium voltage-gated channel, subfamily H (EAG	1e-45
2l0w_A	138	Potassium voltage-gated channel, subfamily H (EAG	5e-23
3sw1_A	162	Sensory box protein; light-oxygen-voltage, LOV, PA	5e-45
3sw1_A	162	Sensory box protein; light-oxygen-voltage, LOV, PA	4e-22
1byw_A	110	Protein (human ERG potassium channel); PAS domain,	7e-43
1byw_A	110	Protein (human ERG potassium channel); PAS domain,	1e-24
3d72_A	149	Vivid PAS protein VVD; circadian, photoreceptor, b	2e-42
3d72_A	149	Vivid PAS protein VVD; circadian, photoreceptor, b	1e-22
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	5e-26
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	4e-06
3ewk_A	227	Sensor protein; PAS domain, alpha/beta fold, kinas	6e-06
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	3e-07
3bwl_A	126	Sensor protein; structural genomics, APC87707.1, P	3e-07
2r78_A	117	Sensor protein; sensory box sensor histidine kinas	3e-06
3olo_A	118	Two-component sensor histidine kinase; structural	1e-04
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-04
3mfx_A	129	Sensory BOX/ggdef family protein; alpha-beta prote	5e-04
3fc7_A	125	HTR-like protein, sensor protein; APC87712.1, HTR-	5e-04
3luq_A	114	Sensor protein; PAS, histidine, kinase, PSI, MCSG,	8e-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 =  162 bits (413), 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 = 97.6 bits (244), Expect = 2e-25
 Identities = 29/75 (38%), Positives = 46/75 (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 YQIKESIQTEQACTE 317
            +I++ ++  ++   
Sbjct: 68  AKIRDCVKNGKSYCG 82

>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 (405), 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 =  102 bits (257), Expect = 2e-27
 Identities = 30/69 (43%), Positives = 50/69 (72%)

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

Query: 309 IQTEQACTE 317
           I+ ++  T 
Sbjct: 65  IRDQRETTV 73

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

 Score =  159 bits (404), Expect = 7e-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 =  100 bits (252), Expect = 2e-26
 Identities = 34/75 (45%), Positives = 54/75 (72%)

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 YQIKESIQTEQACTE 317
            +I+++I  +   T 
Sbjct: 64  RKIRDAIDNQTEVTV 78

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

 Score =  156 bits (398), 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 = 95.7 bits (239), Expect = 9e-25
 Identities = 31/66 (46%), Positives = 44/66 (66%)

Query: 252 QSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQT 311
              ++ +PHLPD P+V+A+ AFLKLTGY+ +EV+G+NCRFL G  TD   +  IK +I  
Sbjct: 8   MPMLITNPHLPDNPIVFANPAFLKLTGYEADEVMGRNCRFLQGHGTDPAHVRAIKSAIAA 67

Query: 312 EQACTE 317
           E+    
Sbjct: 68  EKPIDI 73

>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 =  156 bits (397), Expect = 1e-47
 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 = 97.4 bits (243), Expect = 8e-25
 Identities = 31/75 (41%), Positives = 47/75 (62%)

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

Query: 303 YQIKESIQTEQACTE 317
            +I+ +I      + 
Sbjct: 97  DKIRNAITKGVDTSV 111

>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 (391), Expect = 4e-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 = 93.4 bits (233), Expect = 8e-24
 Identities = 25/66 (37%), Positives = 41/66 (62%)

Query: 252 QSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQT 311
              V+ DP L D P+VY +  F+++TGY+  E++G+NCRFL G  TD   +  I+ ++Q 
Sbjct: 10  VGVVITDPALEDNPIVYVNQGFVQMTGYETEEILGKNCRFLQGKHTDPAEVDNIRTALQN 69

Query: 312 EQACTE 317
           ++  T 
Sbjct: 70  KEPVTV 75

>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 (388), 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 =  101 bits (254), Expect = 4e-27
 Identities = 30/68 (44%), Positives = 47/68 (69%)

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

Query: 310 QTEQACTE 317
           +  +AC+ 
Sbjct: 62  KKGEACSV 69

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

 Score =  157 bits (399), Expect = 7e-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 = 92.4 bits (229), Expect = 4e-22
 Identities = 23/66 (34%), Positives = 37/66 (56%)

Query: 252 QSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQT 311
            + V+ DP L D P++  + AF  LTGY   E VG+NCRFL G  T+  +  +I++ ++ 
Sbjct: 74  IASVVSDPRLADNPLIAINQAFTDLTGYSEEECVGRNCRFLAGSGTEPWLTDKIRQGVRE 133

Query: 312 EQACTE 317
            +    
Sbjct: 134 HKPVLV 139

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

 Score =  150 bits (382), Expect = 1e-45
 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 = 91.5 bits (228), Expect = 5e-23
 Identities = 17/68 (25%), Positives = 34/68 (50%), Gaps = 2/68 (2%)

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

Query: 310 QTEQACTE 317
              +    
Sbjct: 90  LGAEERKV 97

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

 Score =  149 bits (379), Expect = 5e-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 = 90.0 bits (224), Expect = 4e-22
 Identities = 22/66 (33%), Positives = 37/66 (56%)

Query: 252 QSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQT 311
              V+ +    D  ++Y + AF  LTGY R+E++ Q+CRFL G D D     +I++++  
Sbjct: 36  DGIVVAEKEGDDTILIYVNAAFEYLTGYSRDEILYQDCRFLQGDDRDQLGRARIRKAMAE 95

Query: 312 EQACTE 317
            + C E
Sbjct: 96  GRPCRE 101

>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 = 7e-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 = 94.9 bits (237), Expect = 1e-24
 Identities = 17/68 (25%), Positives = 34/68 (50%), Gaps = 2/68 (2%)

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

Query: 310 QTEQACTE 317
              +    
Sbjct: 62  LGAEERKV 69

>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 = 90.5 bits (225), Expect = 1e-22
 Identities = 25/76 (32%), Positives = 38/76 (50%), Gaps = 11/76 (14%)

Query: 253 SFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVD-----------TDTTV 301
           + +L D    D P+VYAS+AFL +TGY   EV+G+NCRFL   D            D+  
Sbjct: 37  ALILCDLKQKDTPIVYASEAFLYMTGYSNAEVLGRNCRFLQSPDGMVKPKSTRKYVDSNT 96

Query: 302 LYQIKESIQTEQACTE 317
           +  ++++I        
Sbjct: 97  INTMRKAIDRNAEVQV 112

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

 Score =  130 bits (327), 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 =  104 bits (260), Expect = 5e-26
 Identities = 34/77 (44%), Positives = 54/77 (70%)

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 TVLYQIKESIQTEQACT 316
             + +I+++I  +   T
Sbjct: 70  ATVRKIRDAIDNQTEVT 86

>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 = 79.1 bits (196), 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 = 46.3 bits (110), Expect = 4e-06
 Identities = 13/47 (27%), Positives = 25/47 (53%)

Query: 267 VYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQ 313
           +YA+ A  + +G    E++GQ+   L+    D   L  ++E++Q  Q
Sbjct: 134 IYANPALCRFSGMAEGELLGQSPSILDSPLADQETLAAMQEALQAGQ 180

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

 Score = 45.5 bits (108), Expect = 6e-06
 Identities = 13/44 (29%), Positives = 23/44 (52%)

Query: 267 VYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQ 310
           +YA+D F  ++ Y R E+VGQ+ R +N        +  +  +I 
Sbjct: 12  LYANDNFCAVSRYGREELVGQDHRIVNSGYHGKAYIRDMWRTIS 55

>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 = 56.0 bits (136), 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 = 48.0 bits (115), Expect = 3e-07
 Identities = 18/106 (16%), Positives = 37/106 (34%), Gaps = 7/106 (6%)

Query: 24  LDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIR 83
           L+ + D   I +    G  +++A+    K  G++  E++  +               +I 
Sbjct: 5   LETIEDMILIINRE--GR-LLYANTAVPKKLGYTHEELMSMHILTIT-SAGKMAEGEKIL 60

Query: 84  EAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAV 129
             +   +   + L   KK+GT      K  +  GK         A+
Sbjct: 61  AELFAGKKESLPLSLEKKEGTSIPA--KARIWQGKWHNE-PCLFAI 103

>3bwl_A Sensor protein; structural genomics, APC87707.1, PAS domain, HTR-like protei protein structure initiative; HET: MSE I3A; 1.73A {Haloarcula marismortui atcc 43049} Length = 126

 Score = 47.9 bits (115), Expect = 3e-07
 Identities = 17/102 (16%), Positives = 37/102 (36%), Gaps = 7/102 (6%)

Query: 28  PDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIR 87
           PD   + D    G  I   ++ F    G+  +E++GR+   F     +   +        
Sbjct: 27  PDMIDVLDAD--GT-ICEVNQRFCAELGYDESEVLGRSIWEF-DLMFDAEDVQTQLSGFS 82

Query: 88  EERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAV 129
            +   +   L  ++DG+   +   +       +G    F+A+
Sbjct: 83  VDERRKFEGLYERRDGSTMSVEVHLLRF--NLEGE-DRFLAI 121

>2r78_A Sensor protein; sensory box sensor histidine kinase/response regulator, structural genomics, PSI, MCSG; 1.60A {Geobacter sulfurreducens pca} Length = 117

 Score = 44.5 bits (106), Expect = 3e-06
 Identities = 14/102 (13%), Positives = 31/102 (30%), Gaps = 10/102 (9%)

Query: 28  PDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIR 87
            D   I D    GH  +  +       G++R E +  +  +      +          I 
Sbjct: 21  IDGIFIMDAE--GH-YLDVNPAICSAIGYTRDEFLALDWGVLSRG-VDSGWAAASLARIV 76

Query: 88  EERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAV 129
              P+      + ++G    +     L+    DG+    + +
Sbjct: 77  GGEPLREERTVWTRNGDQLTVELSAHLL---PDGK---ILGI 112

>3olo_A Two-component sensor histidine kinase; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG, TRA; 2.09A {Nostoc SP} Length = 118

 Score = 39.9 bits (94), Expect = 1e-04
 Identities = 12/109 (11%), Positives = 36/109 (33%), Gaps = 11/109 (10%)

Query: 21  HEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIM 80
           H  ++   ++      +      ++ +    +M+ +SR +++  N +       +    +
Sbjct: 16  HYLINNAVEASFCLGDN--WQ-FLYVNDATCRMTEYSREQLLSMNLQDI-----DVDFAL 67

Query: 81  EIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAV 129
              E IR++           + G  F +   ++ +   ED         
Sbjct: 68  HDWEEIRQKNNYTFKTRYRSQSGRIFLVEMSLTFL---EDQERRFSCVF 113

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 41.8 bits (97), Expect = 3e-04
 Identities = 43/346 (12%), Positives = 90/346 (26%), Gaps = 96/346 (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 -------HLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTD 298
                   + D    +  D +  +       ++      LN ++  
Sbjct: 329 RLSIIAESIRDGLATW--DNWKHVNCDKLTTIIE---SSLNVLEPA 369

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

 Score = 38.6 bits (90), Expect = 5e-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 = 38.5 bits (90), Expect = 5e-04
 Identities = 7/70 (10%), Positives = 19/70 (27%), Gaps = 3/70 (4%)

Query: 24 LDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIR 83
          + + PD       +  G  I+  +       G     ++G+            + +   +
Sbjct: 25 VSDSPDGIVHLTTN--GT-ILSVNPSMAGRLGADPDTLVGQQLSAVMDSEAANQRLEAGK 81

Query: 84 EAIREERPIE 93
           A+       
Sbjct: 82 SAVENGTATR 91

>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 = 8e-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	318
3ewk_A	227	Sensor protein; PAS domain, alpha/beta fold, kinas	99.97
2gj3_A	120	Nitrogen fixation regulatory protein; PAS domain,	99.82
4hia_A	176	LOV protein; PAS, HTH, signaling protein; HET: FMN	99.78
3f1p_B	121	ARYL hydrocarbon receptor nuclear translocator; PA	99.76
1n9l_A	109	PHOT-LOV1, putative blue light receptor; phototrop	99.75
2pr5_A	132	Blue-light photoreceptor; light-oxygen-voltage, LO	99.75
3p7n_A	258	Sensor histidine kinase; LOV domain, light-activat	99.74
3ue6_A	166	Aureochrome1; PAS/LOV domain, FMN-binding blue-lig	99.73
3mr0_A	142	Sensory box histidine kinase/response regulator; P	99.72
3t50_A	128	Blue-light-activated histidine kinase; PAS superfa	99.72
3f1p_A	117	Endothelial PAS domain-containing protein 1; PAS d	99.72
4eet_B	115	Phototropin-2; LOV, blue light photoreceptor, sign	99.71
3mqq_A	120	Transcriptional regulator, LUXR family; PAS domain	99.69
3lyx_A	124	Sensory BOX/ggdef domain protein; structural genom	99.69
3nja_A	125	Probable ggdef family protein; structural genomics	99.69
2z6d_A	130	Phototropin-2; PAS-fold, LOV-fold, alternative spl	99.67
1d06_A	130	Nitrogen fixation regulatory protein FIXL; oxygen	99.66
4f3l_A	361	Mclock, circadian locomoter output cycles protein	99.65
3sw1_A	162	Sensory box protein; light-oxygen-voltage, LOV, PA	99.65
3h9w_A	115	Diguanylate cyclase with PAS/PAC sensor; alpha-bet	99.64
2vv6_A	119	FIXL, sensor protein FIXL; signaling protein, tran	99.64
2r78_A	117	Sensor protein; sensory box sensor histidine kinas	99.64
3mxq_A	152	Sensor protein; PSI2, MCSG, structural genomics, p	99.64
3luq_A	114	Sensor protein; PAS, histidine, kinase, PSI, MCSG,	99.62
3k3c_A	158	Protein RV1364C/MT1410; sensor, PAS, signal transd	99.62
2wkq_A	332	NPH1-1, RAS-related C3 botulinum toxin substrate 1	99.62
3kx0_X	185	Uncharacterized protein RV1364C/MT1410; PAS domain	99.61
3ewk_A	227	Sensor protein; PAS domain, alpha/beta fold, kinas	99.59
3rty_A	339	Period circadian protein; PAS domain, signalling,	99.59
3icy_A	118	Sensor protein; sensory box histidine kinase/respo	99.58
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	99.58
2v0u_A	146	NPH1-1, LOV2; kinase, transferase, ATP-binding, se	99.57
2kdk_A	121	ARYL hydrocarbon receptor nuclear translocator-LI	99.56
3mjq_A	126	Uncharacterized protein; NESG, structural genomics	99.53
3olo_A	118	Two-component sensor histidine kinase; structural	99.53
2l0w_A	138	Potassium voltage-gated channel, subfamily H (EAG	99.52
1byw_A	110	Protein (human ERG potassium channel); PAS domain,	99.51
3eeh_A	125	Putative light and redox sensing histidine kinase;	99.5
3bwl_A	126	Sensor protein; structural genomics, APC87707.1, P	99.5
4eho_A	635	Bacteriophytochrome, PAS/PAC sensor; photoreceptor	99.48
1v9y_A	167	Heme PAS sensor protein; signaling protein; HET: H	99.48
3d72_A	149	Vivid PAS protein VVD; circadian, photoreceptor, b	99.45
3mfx_A	129	Sensory BOX/ggdef family protein; alpha-beta prote	99.43
3fc7_A	125	HTR-like protein, sensor protein; APC87712.1, HTR-	99.43
3vol_A	233	Aerotaxis transducer AER2; heme, oxygen sensor pro	99.43
3fg8_A	118	Uncharacterized protein RHA05790; PAS domain, stru	99.37
2qkp_A	151	Uncharacterized protein; structural genomics, unkn	99.36
4hi4_A	121	Aerotaxis transducer AER2; PAS domain, diatomic GA	99.36
2gj3_A	120	Nitrogen fixation regulatory protein; PAS domain,	99.36
1n9l_A	109	PHOT-LOV1, putative blue light receptor; phototrop	99.34
4dj3_A	317	Period circadian protein homolog 3; PAS domain, ci	99.34
4f3l_A	361	Mclock, circadian locomoter output cycles protein	99.34
2vlg_A	111	Sporulation kinase A; histidine kinase, two-compon	99.33
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	99.31
3gdi_A	309	Period circadian protein homolog 2; tandem PAS dom	99.31
4dj2_A	320	Period circadian protein homolog 1; PAS domains, c	99.3
2pr5_A	132	Blue-light photoreceptor; light-oxygen-voltage, LO	99.29
3b33_A	115	Sensor protein; structural genomics, PAS domain, n	99.23
2r78_A	117	Sensor protein; sensory box sensor histidine kinas	99.2
1d06_A	130	Nitrogen fixation regulatory protein FIXL; oxygen	99.17
3cax_A	369	Uncharacterized protein PF0695; structural genomic	99.15
3f1p_B	121	ARYL hydrocarbon receptor nuclear translocator; PA	99.12
4hia_A	176	LOV protein; PAS, HTH, signaling protein; HET: FMN	99.11
3p7n_A	258	Sensor histidine kinase; LOV domain, light-activat	99.1
3mxq_A	152	Sensor protein; PSI2, MCSG, structural genomics, p	99.08
3fg8_A	118	Uncharacterized protein RHA05790; PAS domain, stru	99.07
4eet_B	115	Phototropin-2; LOV, blue light photoreceptor, sign	99.06
3rty_A	339	Period circadian protein; PAS domain, signalling,	99.05
3ue6_A	166	Aureochrome1; PAS/LOV domain, FMN-binding blue-lig	99.05
3a0r_A	349	Sensor protein; four helix bundle, PAS fold, kinas	99.03
3mfx_A	129	Sensory BOX/ggdef family protein; alpha-beta prote	99.02
3f1p_A	117	Endothelial PAS domain-containing protein 1; PAS d	99.01
2w0n_A	118	Sensor protein DCUS; signal transduction, two-comp	99.01
1ll8_A	114	PAS kinase; PAS domain, ligand binding, ligand scr	99.01
2kdk_A	121	ARYL hydrocarbon receptor nuclear translocator-LI	99.01
2vlg_A	111	Sporulation kinase A; histidine kinase, two-compon	99.01
3a0s_A	96	Sensor protein; PAS-fold, kinase, phosphoprotein,	99.01
1mzu_A	129	PPR; photoactive yellow protein, PAS, PYP, signali	99.0
2jhe_A	190	Transcription regulator TYRR; aromatic hydrocarbon	98.99
1nwz_A	125	PYP, photoactive yellow protein; PAS, LOV, GAF, do	98.99
3luq_A	114	Sensor protein; PAS, histidine, kinase, PSI, MCSG,	98.98
3t50_A	128	Blue-light-activated histidine kinase; PAS superfa	98.98
2vv6_A	119	FIXL, sensor protein FIXL; signaling protein, tran	98.96
3mqq_A	120	Transcriptional regulator, LUXR family; PAS domain	98.95
3bwl_A	126	Sensor protein; structural genomics, APC87707.1, P	98.91
4dj3_A	317	Period circadian protein homolog 3; PAS domain, ci	98.9
3fc7_A	125	HTR-like protein, sensor protein; APC87712.1, HTR-	98.89
1nwz_A	125	PYP, photoactive yellow protein; PAS, LOV, GAF, do	98.88
1mzu_A	129	PPR; photoactive yellow protein, PAS, PYP, signali	98.86
2wkq_A	332	NPH1-1, RAS-related C3 botulinum toxin substrate 1	98.86
3olo_A	118	Two-component sensor histidine kinase; structural	98.85
3lyx_A	124	Sensory BOX/ggdef domain protein; structural genom	98.85
2z6d_A	130	Phototropin-2; PAS-fold, LOV-fold, alternative spl	98.84
3k3c_A	158	Protein RV1364C/MT1410; sensor, PAS, signal transd	98.81
3gdi_A	309	Period circadian protein homolog 2; tandem PAS dom	98.8
3nja_A	125	Probable ggdef family protein; structural genomics	98.79
3mr0_A	142	Sensory box histidine kinase/response regulator; P	98.79
4dj2_A	320	Period circadian protein homolog 1; PAS domains, c	98.78
2v0u_A	146	NPH1-1, LOV2; kinase, transferase, ATP-binding, se	98.78
1ll8_A	114	PAS kinase; PAS domain, ligand binding, ligand scr	98.77
3d72_A	149	Vivid PAS protein VVD; circadian, photoreceptor, b	98.76
3mjq_A	126	Uncharacterized protein; NESG, structural genomics	98.75
3kx0_X	185	Uncharacterized protein RV1364C/MT1410; PAS domain	98.75
3sw1_A	162	Sensory box protein; light-oxygen-voltage, LOV, PA	98.7
3b33_A	115	Sensor protein; structural genomics, PAS domain, n	98.69
4hi4_A	121	Aerotaxis transducer AER2; PAS domain, diatomic GA	98.68
3icy_A	118	Sensor protein; sensory box histidine kinase/respo	98.67
1byw_A	110	Protein (human ERG potassium channel); PAS domain,	98.67
3a0s_A	96	Sensor protein; PAS-fold, kinase, phosphoprotein,	98.63
2l0w_A	138	Potassium voltage-gated channel, subfamily H (EAG	98.63
3eeh_A	125	Putative light and redox sensing histidine kinase;	98.63
2w0n_A	118	Sensor protein DCUS; signal transduction, two-comp	98.59
3vol_A	233	Aerotaxis transducer AER2; heme, oxygen sensor pro	98.53
1v9y_A	167	Heme PAS sensor protein; signaling protein; HET: H	98.52
2qkp_A	151	Uncharacterized protein; structural genomics, unkn	98.5
3a0r_A	349	Sensor protein; four helix bundle, PAS fold, kinas	98.45
2ykf_A	305	Pdtas, probable sensor histidine kinase pdtas; tra	97.78
2jhe_A	190	Transcription regulator TYRR; aromatic hydrocarbon	98.37
3h9w_A	115	Diguanylate cyclase with PAS/PAC sensor; alpha-bet	98.36
2ykf_A	305	Pdtas, probable sensor histidine kinase pdtas; tra	97.52
4eho_A	635	Bacteriophytochrome, PAS/PAC sensor; photoreceptor	98.13
3cax_A	369	Uncharacterized protein PF0695; structural genomic	98.02
1oj5_A	132	Steroid receptor coactivator 1A; transcriptional c	97.74
1oj5_A	132	Steroid receptor coactivator 1A; transcriptional c	95.27
2ool_A	337	Sensor protein; bacteriophytochrome, photoconversi	94.53
2ool_A	337	Sensor protein; bacteriophytochrome, photoconversi	90.68
4ew7_A	127	Conjugative transfer: regulation; alpha-beta-alpha	89.33
4ew7_A	127	Conjugative transfer: regulation; alpha-beta-alpha	85.77
4e04_A	327	Bacteriophytochrome (light-regulated signal trans	81.45
3s7o_A	343	Bacteriophytochrome; biliverdin, PAS, GAF, photore	80.06

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

Probab=99.97  E-value=2.7e-28  Score=196.58  Aligned_cols=182  Identities=21%  Similarity=0.405  Sum_probs=162.1

Q ss_pred             EEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEEEEEEEecCCcEEEEEE
Q 021027           31 FTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLF  110 (318)
Q Consensus        31 i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~  110 (318)
                      |+++|.+   |+++++|+++++++||++++++|++...+.++.........++..+..+..+..+....+++|..+|+.+
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            6789999   9999999999999999999999999887777666667777778888888899999999999999999999


Q ss_pred             EEEeeccCCCCceeEEEEEEeccccccccccccccccccCCCCchhhHhhhccccccccccchhccccccccCCCCCcCc
Q 021027          111 KMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDRVLALDSDDTGLEI  190 (318)
Q Consensus       111 ~~~~i~~~~~g~~~~~i~~~~DIte~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  190 (318)
                      +..|+++ .+|.+.+++++.+|||++|++                                                   
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            9999999 899999999999999999997                                                   


Q ss_pred             ccchhhhhHHHHHHHhhhhhhhhhccccccccceeeeeeecCCCCccccchhHHHHHhccCCcEEEecCCCCCCCeeEec
Q 021027          191 EDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQSFVLIDPHLPDMPMVYAS  270 (318)
Q Consensus       191 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~i~i~d~~~~~~~i~~~N  270 (318)
                             +.+.+.                                       +..++++++++|+++|.+|   +|+++|
T Consensus       107 -------e~~l~~---------------------------------------~~~~~~~~~~~i~~~d~~g---~i~~~N  137 (227)
T 3ewk_A          107 -------EAQLAR---------------------------------------LKQAMDANSEMILLTDRAG---RIIYAN  137 (227)
T ss_dssp             -------HHHHHH---------------------------------------HHHHHHTCCSEEEEECTTS---CEEEEC
T ss_pred             -------HHHHHH---------------------------------------HHHHHhcCcCeEEEEcCCC---cEEEEc
Confidence                   211111                                       3345677899999999887   999999


Q ss_pred             HHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhccccee
Q 021027          271 DAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQACT  316 (318)
Q Consensus       271 ~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~~~~~  316 (318)
                      ++|++++||+++|++|+++..+.+|.+.+.....+++++..+++|.
T Consensus       138 ~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  183 (227)
T 3ewk_A          138 PALCRFSGMAEGELLGQSPSILDSPLADQETLAAMQEALQAGQPWS  183 (227)
T ss_dssp             HHHHHHHTCCTHHHHSSCGGGGBCTTSCHHHHHHHHHHHHHTCCEE
T ss_pred             hHHHHHhCCCHHHHcCCChhhccCCCCCHHHHHHHHHHHHcCCcee
Confidence            9999999999999999999999999999999999999999998875

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

Probab=99.82  E-value=6.9e-19  Score=126.63  Aligned_cols=118  Identities=19%  Similarity=0.374  Sum_probs=105.6

Q ss_pred             hHHHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEEE
Q 021027           16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVN   95 (318)
Q Consensus        16 ~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~   95 (318)
                      ..++++.++++++++++++|.+   |+++++|++|++++||+.++++|++...+.++.........+...+..+..+..+
T Consensus         3 ~~~~~~~~~~~~~~~i~~~d~~---g~i~~~N~a~~~~~G~~~~elig~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e   79 (120)
T 2gj3_A            3 LPEIFRQTVEHAPIAISITDLK---ANILYANRAFRTITGYGSEEVLGKNESILSNGTTPRLVYQALWGRLAQKKPWSGV   79 (120)
T ss_dssp             CHHHHHHHHHHCSSEEEEECTT---CBEEEECHHHHHHHCCCTTGGGGCBGGGGCCTTSCHHHHHHHHHHHHTTCCEEEE
T ss_pred             hHHHHHHHHHhCCCeEEEECCC---CCEEeehHHHHHHHCcCHHHHcCCCHHHcCCCCCCHHHHHHHHHHHHcCCCEEEE
Confidence            3457889999999999999999   9999999999999999999999998887777666665666777778888888888


Q ss_pred             EEEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEecccccc
Q 021027           96 LLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRK  137 (318)
Q Consensus        96 ~~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k  137 (318)
                      ...++++|..+|+.++..|+++ .+|.+.+++++++|||++|
T Consensus        80 ~~~~~~dG~~~~~~~~~~pi~~-~~g~~~~~v~~~~DITe~k  120 (120)
T 2gj3_A           80 LVNRRKDKTLYLAELTVAPVLN-EAGETIYYLGMHRDTSELH  120 (120)
T ss_dssp             EEEECTTSCEEEEEEEEEEEEC-TTSCEEEEEEEEEECCSCC
T ss_pred             EEEEcCCCCEEEEEEEEEEEEC-CCCCEEEEEEEeccCcccC
Confidence            8889999999999999999998 8999999999999999986

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

Probab=99.78  E-value=9e-18  Score=129.11  Aligned_cols=127  Identities=25%  Similarity=0.413  Sum_probs=114.3

Q ss_pred             hhHHHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEE
Q 021027           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV   94 (318)
Q Consensus        15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   94 (318)
                      +..++++.++++++++++++|.+.++|+++++|+++++++||++++++|+++..+.++.........+...+..+.++..
T Consensus         4 ~~~~~~~~~~~~~~~~i~~~d~~~~~g~i~~~N~a~~~~~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   83 (176)
T 4hia_A            4 KQFEKIRAVFDRSGVALTLVDMSLPEQPVVLANPPFLRMTGYTEGQILGFNCRFLQRGDENAQARADIRDALKLGRELQV   83 (176)
T ss_dssp             HHHHHHHHHHHHCSSCCEEEETTSTTCCEEEECHHHHHHHTCCHHHHTTSCGGGGCCTTCCHHHHHHHHHHHHHTCCEEE
T ss_pred             HHHHHHHHHHhcCCCcEEEEecCCCCCcEEEECHHHHHHHCcCHHHHcCCCcceeeCCCCCHHHHHHHHHHHHcCCceEE
Confidence            34467889999999999999986666999999999999999999999999988888888877778888888888888888


Q ss_pred             EEEEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEeccccccccccc
Q 021027           95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNS  142 (318)
Q Consensus        95 ~~~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~~~~~  142 (318)
                      +....+++|..+|+.++..|+.+ .+|.+.+++++++|||++|++|++
T Consensus        84 e~~~~~~dG~~~~~~~~~~pi~~-~~g~~~~~~~~~~DITe~k~~e~~  130 (176)
T 4hia_A           84 VLRNYRANDEPFDNLLFLHPVGG-RPDAPDYFLGSQFELGRSGNSEEA  130 (176)
T ss_dssp             EEEEECTTCCEEEEEEEEEEESS-BTTBCSEEEEEEEEESSSGGGHHH
T ss_pred             EEEEEcCCCCEEEEEEEEEEeeC-CCCCeEEEEEEEEECcHhhHHHHH
Confidence            88888999999999999999998 899999999999999999998544

>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=99.76  E-value=8.5e-18  Score=120.95  Aligned_cols=115  Identities=10%  Similarity=0.128  Sum_probs=98.5

Q ss_pred             HHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHH-hcCCeEEEEEE
Q 021027           20 VHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIR-EERPIEVNLLN   98 (318)
Q Consensus        20 ~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~   98 (318)
                      ...+++++++.++++|.+   |+++|+|+++++++||++++++|+++..+++|++.......+...+. .+..+..++++
T Consensus         4 ~~ll~e~~~d~i~~~d~~---g~i~~~n~~~~~~~G~~~~el~g~~~~~~i~p~d~~~~~~~~~~~~~~~~~~~~~e~r~   80 (121)
T 3f1p_B            4 KGLNVCQPTRFISRHNIE---GIFTFVDHRCVATVGYQPQELLGKNIVEFCHPEDQQLLRDSFQQVVKLKGQVLSVMFRF   80 (121)
T ss_dssp             ----CCCCCEEEEEECTT---SBEEEECTTHHHHHSCCGGGTTTSBGGGGBCTTTHHHHHHHHHHHTTSTTCCEEEEEEE
T ss_pred             ccceecCCCceEEEECCC---ceEEEECcchhhhhCCChHHHcCCCHHHeECHHHHHHHHHHHHHHHhcCCCcccEEEEE
Confidence            446889999999999999   99999999999999999999999998888898887777777777664 45568889999


Q ss_pred             EecCCcEEEEEEEEEeeccCC-CCceeEEEEEEeccccccc
Q 021027           99 YKKDGTPFWMLFKMSLVFGKE-DGRATHFVAVQVPIVSRKH  138 (318)
Q Consensus        99 ~~~~g~~~~~~~~~~~i~~~~-~g~~~~~i~~~~DIte~k~  138 (318)
                      ++++|..+|+..+..|+.+ . +|.+.+++++.+|||++|+
T Consensus        81 ~~~dG~~~w~~~~~~~~~~-~~~g~~~~iv~~~~DIT~~kq  120 (121)
T 3f1p_B           81 RSKNQEWLWMRTSSFTFQN-PYSDEIEYIICTNTNVKNSSQ  120 (121)
T ss_dssp             ECTTSCEEEEEEEEEEECC-TTCCCCCEEEEEEEECCCC--
T ss_pred             EecCCCEEEEEEEEEEEEC-CCCCceeEEEEEeEEcccccC
Confidence            9999999999999999987 5 7889999999999999986

>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=99.75  E-value=5.2e-17  Score=114.66  Aligned_cols=108  Identities=41%  Similarity=0.805  Sum_probs=96.1

Q ss_pred             CCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEEEEEEEecCCcEE
Q 021027           27 LPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPF  106 (318)
Q Consensus        27 ~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~  106 (318)
                      ++++++++|...++++++++|++|++++||+.++++|++...+.++.........++..+..+.++..++..++++|..+
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            57899999953333999999999999999999999999987777777666667788888889999999999999999999


Q ss_pred             EEEEEEEeeccCCCCceeEEEEEEecccc
Q 021027          107 WMLFKMSLVFGKEDGRATHFVAVQVPIVS  135 (318)
Q Consensus       107 ~~~~~~~~i~~~~~g~~~~~i~~~~DIte  135 (318)
                      |+.+++.|+++ ++|.+.+++++.+|||+
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            99999999999 89999999999999996

>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=6e-17  Score=118.44  Aligned_cols=116  Identities=37%  Similarity=0.687  Sum_probs=97.4

Q ss_pred             HHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEEEEEEEec
Q 021027           22 EALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKK  101 (318)
Q Consensus        22 ~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  101 (318)
                      .++++++++++++|.+.++++++++|+++++++||+.++++|+++..+.++.........+...+..+.++..+...+++
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            57899999999999871123999999999999999999999998877777766666666777778888888888888899


Q ss_pred             CCcEEEEEEEEEeeccCCCCceeEEEEEEeccccccccc
Q 021027          102 DGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMR  140 (318)
Q Consensus       102 ~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~~~  140 (318)
                      +|..+|+.++..|+.+ .+  +.+++++++|||++|++|
T Consensus        83 dG~~~~~~~~~~~~~~-~~--~~~~~~~~~DITe~k~~e  118 (132)
T 2pr5_A           83 DGTMFWNELNIDPMEI-ED--KTYFVGIQNDITKQKEYE  118 (132)
T ss_dssp             TSCEEEEEEEEEEEEE-TT--EEEEEEEEEECHHHHHHH
T ss_pred             CCCeeeeEEEEEeccC-CC--eeEEEEEEEeCcHHHHHH
Confidence            9999999999999987 43  788999999999999983

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

Probab=99.74  E-value=1.8e-16  Score=129.77  Aligned_cols=121  Identities=30%  Similarity=0.586  Sum_probs=106.3

Q ss_pred             hhHHHHHHHHhcCCCeEEEEcC---CCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCC
Q 021027           15 RYTLWVHEALDELPDSFTITDP---SISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERP   91 (318)
Q Consensus        15 ~~~~~~~~~~~~~~~~i~~~d~---~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~   91 (318)
                      ...++++.++++++++++++|.   +   |+++++|+++++++||++++++|+++..+.++.........+...+..+.+
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            3456889999999999999999   7   899999999999999999999999988888888888888888888888999


Q ss_pred             eEEEEEEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEecccccccc
Q 021027           92 IEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM  139 (318)
Q Consensus        92 ~~~~~~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~~  139 (318)
                      +..+....+++|..+|+.+...|+.+ .+|.+.+++++++|||++|..
T Consensus       137 ~~~e~~~~~~dG~~~~~~~~~~pi~d-~~g~~~~~v~~~~DITerk~~  183 (258)
T 3p7n_A          137 VLVEILNYKKDGTPFRNAVLVAPIYD-DDDELLYFLGSQVEVDDDQPN  183 (258)
T ss_dssp             EEEEEEEECTTSCEEEEEEEEEEEEC-TTSCSEEEEEEEEEC------
T ss_pred             eEEEEEEEcCCCCEEEEeeEEEEEEc-CCCCEEEEEEEeeecchhhhh
Confidence            99999889999999999999999998 899999999999999999543

>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=6.1e-17  Score=122.91  Aligned_cols=120  Identities=39%  Similarity=0.656  Sum_probs=109.7

Q ss_pred             hHHHHHHHHhcCCCeEEEEcC---CCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCe
Q 021027           16 YTLWVHEALDELPDSFTITDP---SISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPI   92 (318)
Q Consensus        16 ~~~~~~~~~~~~~~~i~~~d~---~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~   92 (318)
                      ....+..++++++++++++|.   +   ++++++|+++++++|++.++++|+++..+.++.........+...+..+..+
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            446788999999999999999   7   9999999999999999999999999888888877777777888888888888


Q ss_pred             EEEEEEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEecccccccc
Q 021027           93 EVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM  139 (318)
Q Consensus        93 ~~~~~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~~  139 (318)
                      ..+....+++|..+|+.+...|+.+ .+|.+.+++++++|||++|++
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            8888888999999999999999998 889999999999999999986

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

Probab=99.72  E-value=1.5e-16  Score=117.98  Aligned_cols=122  Identities=14%  Similarity=0.213  Sum_probs=105.9

Q ss_pred             hhHHHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCC--CCCcccCCCCChHHHHHHHHHHHhcCCe
Q 021027           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGR--NGRMFQGPRTNRRTIMEIREAIREERPI   92 (318)
Q Consensus        15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~--~~~~l~~~~~~~~~~~~~~~~~~~~~~~   92 (318)
                      ..+++|+.+++.++.++|.+|..   +..+++|+++..++||+++++.+.  .+..+++|++...+...+...+..+.++
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  3556778888888888888888888889


Q ss_pred             EEEEEEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEeccccccccc
Q 021027           93 EVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMR  140 (318)
Q Consensus        93 ~~~~~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~~~  140 (318)
                      ..++++.+++|..+|+.....|+.+ .+|.+.+++|++.|||++|++|
T Consensus        83 ~~e~r~~~~~G~~~w~~~~~~~~~d-~~g~~~~~~G~~~DITerk~~E  129 (142)
T 3mr0_A           83 DVEYRVRTRSGDFRWIQSRGQALWN-SAGEPYRMVGWIMDVTDRKRDE  129 (142)
T ss_dssp             EEEEEEECTTSCEEEEEEEEEEEEC-TTSCEEEEEEEEEECHHHHHHH
T ss_pred             EEEEEEECCCCCEEEEEEEEEEEEC-CCCCEEEEEEEEEcCchHHHHH
Confidence            9999999999999999999999998 8999999999999999999983

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

Probab=99.72  E-value=1.1e-16  Score=116.05  Aligned_cols=117  Identities=38%  Similarity=0.664  Sum_probs=102.8

Q ss_pred             HHhcCCCeEEEEcC---CCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEEEEEEE
Q 021027           23 ALDELPDSFTITDP---SISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNY   99 (318)
Q Consensus        23 ~~~~~~~~i~~~d~---~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   99 (318)
                      ++++++++++++|.   +   ++++++|++++.++|++.++++|+++..+.++.........+...+..+..+..+....
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            46789999999999   7   99999999999999999999999998888877777777778888888888888888888


Q ss_pred             ecCCcEEEEEEEEEeeccCCCCceeEEEEEEecccccccccccc
Q 021027          100 KKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG  143 (318)
Q Consensus       100 ~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~~~~~~  143 (318)
                      .++|..+|+.++..|+.+ .+|.+.+++++++|||++|+++++.
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=99.72  E-value=4.3e-17  Score=116.45  Aligned_cols=108  Identities=8%  Similarity=0.170  Sum_probs=97.4

Q ss_pred             CCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEEEEEEEecCCcEE
Q 021027           27 LPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPF  106 (318)
Q Consensus        27 ~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~  106 (318)
                      +++.++++|.+   |+++++|+++++++||++++++|+++..+++|++.......+...+..+..+..++++++++|..+
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            45778899999   999999999999999999999999988888888877777778888887777777888899999999


Q ss_pred             EEEEEEEeeccCC-CCceeEEEEEEeccccccc
Q 021027          107 WMLFKMSLVFGKE-DGRATHFVAVQVPIVSRKH  138 (318)
Q Consensus       107 ~~~~~~~~i~~~~-~g~~~~~i~~~~DIte~k~  138 (318)
                      |+.++..|+.+ + +|.+.+++++.+|||++|+
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 7889999999999999987

>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=99.71  E-value=5.9e-16  Score=109.45  Aligned_cols=111  Identities=41%  Similarity=0.778  Sum_probs=99.1

Q ss_pred             HHhcCCCeEEEEcC---CCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEEEEEEE
Q 021027           23 ALDELPDSFTITDP---SISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNY   99 (318)
Q Consensus        23 ~~~~~~~~i~~~d~---~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   99 (318)
                      .+++++++++++|.   +   ++++++|+++++++|++.++++|+++..+.++.........+...+..+..+..+....
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            47889999999999   8   99999999999999999999999998888877777777777888888888888888888


Q ss_pred             ecCCcEEEEEEEEEeeccCCCCceeEEEEEEecccccc
Q 021027          100 KKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRK  137 (318)
Q Consensus       100 ~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k  137 (318)
                      +++|..+|+.++..|+.+ .+|.+.+++++++|||+++
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 8899999999999999975

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

Probab=99.69  E-value=1.8e-16  Score=113.72  Aligned_cols=114  Identities=12%  Similarity=0.109  Sum_probs=91.4

Q ss_pred             HHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCC-hHHHHHHHHHHHhcCCeEEEEEE
Q 021027           20 VHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTN-RRTIMEIREAIREERPIEVNLLN   98 (318)
Q Consensus        20 ~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~   98 (318)
                      |+.++++++++++ ++.+   ++++++|+++++++||++++++|+++..+++++.. ......+...+..+..+..+...
T Consensus         5 ~~~~~~~~~~~i~-~~~~---g~i~~~N~a~~~l~G~~~~el~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~   80 (120)
T 3mqq_A            5 YKTAFHLAPIGLV-LSRD---RVIEDCNDELAAIFRCARADLIGRSFEVLYPSSDEFERIGERISPVMIAHGSYADDRIM   80 (120)
T ss_dssp             HHHHHHHCSSEEE-EEET---TEEEEECHHHHHHTTSCHHHHTTCBGGGGSSSHHHHHHHHHHHHHHHHHHSCEEEEEEE
T ss_pred             HHHHHhcCCceEE-EecC---CEEHHHHHHHHHHhCcCHHHhCCCchhhccCChhhHHHHHHHHHHHHhcCCcceEEEEE
Confidence            6789999999996 4778   99999999999999999999999987777655322 33444555666777788888888


Q ss_pred             EecCCcEEEEEEEEEeeccCCCCceeEEEEEEecccccccc
Q 021027           99 YKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM  139 (318)
Q Consensus        99 ~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~~  139 (318)
                      .+++|..+|+.++..|+.  .++...+++++++|||++|++
T Consensus        81 ~~~dG~~~~~~~~~~~~~--~~~~~~~~v~~~~DITerk~~  119 (120)
T 3mqq_A           81 KRAGGELFWCHVTGRALD--RTAPLAAGVWTFEDLSATRRV  119 (120)
T ss_dssp             ECTTSCEEEEEEEEEESS--TTSTTSSEEEEEEESCC----
T ss_pred             EeCCCCEEEEEEEEEECC--CCCCceeEEEEEEcccHhhcc
Confidence            999999999999999994  466677889999999999985

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

Probab=99.69  E-value=1.4e-15  Score=108.39  Aligned_cols=120  Identities=20%  Similarity=0.261  Sum_probs=104.6

Q ss_pred             hhHHHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEE
Q 021027           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV   94 (318)
Q Consensus        15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   94 (318)
                      .....++.++++++++++++|.+   +.++++|++++.++|++.++++|.+...+.++.........+...+..+..+..
T Consensus         4 ~~~~~~~~~~~~~~~~i~~~d~~---~~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (124)
T 3lyx_A            4 DILKQRAKAFDYVFDAIVVTDLQ---GFIIDWNKGSETLYGYSKEQAIGQPVNMLHVPGDTEHITSEVISAVENQGKWTG   80 (124)
T ss_dssp             CHHHHHHHGGGTCSSEEEEEETT---CBEEEECHHHHHHHCCCHHHHTTSBGGGGSCTTTHHHHHHHHHHHHHHTSCEEE
T ss_pred             hHHHHHHHHHhhcCceEEEECCC---CcEeehhhHHHHHhCCCHHHHcCCCHHHhcCcchhhHHHHHHHHHHHcCCcccc
Confidence            34567889999999999999999   999999999999999999999999877666666555566667778888888888


Q ss_pred             EEEEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEeccccccc
Q 021027           95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKH  138 (318)
Q Consensus        95 ~~~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~  138 (318)
                      +......+|..+|+.+...|+.+ .+|.+.+++++++|||++|+
T Consensus        81 ~~~~~~~~g~~~~~~~~~~~~~~-~~g~~~~~~~~~~Dit~~~~  123 (124)
T 3lyx_A           81 EIRMLHKDGHIGWIESMCVPIYG-ENYQMVGALGINRDITKRKK  123 (124)
T ss_dssp             EEEEECTTSCEEEEEEEEEEEEC-STTCEEEEEEEEEECSCC--
T ss_pred             eEEEEccCCCEEEEEEEEEEEEC-CCCCEEEEEEEEecchhhhc
Confidence            88888999999999999999998 78999999999999999986

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

Probab=99.69  E-value=2.8e-16  Score=112.93  Aligned_cols=120  Identities=14%  Similarity=0.090  Sum_probs=92.8

Q ss_pred             hhHHHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcC--CCCCcccCCCCChHHHHHHHHHHHhcCCe
Q 021027           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIG--RNGRMFQGPRTNRRTIMEIREAIREERPI   92 (318)
Q Consensus        15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g--~~~~~l~~~~~~~~~~~~~~~~~~~~~~~   92 (318)
                      ..+++++.+++.++.+++++|.+   +.++++|++++.++|++++++.|  ..+..+.+|++...+...+...+..+.++
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            34567888999999999999999   99999999999999999999988  33445667777777777777888888888


Q ss_pred             EEEEEEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEeccccccc
Q 021027           93 EVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKH  138 (318)
Q Consensus        93 ~~~~~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~  138 (318)
                      ..+++..+++|..+|+.+...|+.+ .+|.+.+++++++|||++|+
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            8888888999999999999999998 89999999999999999985

>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=99.67  E-value=3.4e-15  Score=107.24  Aligned_cols=121  Identities=37%  Similarity=0.725  Sum_probs=103.9

Q ss_pred             hHHHHHHHHhcCCCeEEEEc---CCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCe
Q 021027           16 YTLWVHEALDELPDSFTITD---PSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPI   92 (318)
Q Consensus        16 ~~~~~~~~~~~~~~~i~~~d---~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~   92 (318)
                      ....++.++++++++++++|   .+   +.++++|++++.++|++.++++|+++..+.++.........+...+..+..+
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            44567889999999999999   88   9999999999999999999999999888877777777677777778888888


Q ss_pred             EEEEEEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEeccccccccc
Q 021027           93 EVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMR  140 (318)
Q Consensus        93 ~~~~~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~~~  140 (318)
                      ..+......+|..+|+.+...|+.+ .+|.+.+++++++|||++++++
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 7899999999999999999873

>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=99.66  E-value=2.1e-15  Score=109.85  Aligned_cols=124  Identities=16%  Similarity=0.218  Sum_probs=93.8

Q ss_pred             hhhhHHHhhhhhhHHHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHH
Q 021027            4 QLGLIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIR   83 (318)
Q Consensus         4 ~l~~~~~~~~~~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~   83 (318)
                      ++...++.+. +.+.+++.++++++++++++|.+   |+++++|+++++++||++++++|+++..+.++.........+.
T Consensus         3 ~~~~~e~~l~-~~~~~~~~l~~~~~d~i~~~d~~---g~i~~~N~a~~~l~Gy~~~eliG~~~~~l~~~~~~~~~~~~~~   78 (130)
T 1d06_A            3 HMLETEDVVR-ARDAHLRSILDTVPDATVVSATD---GTIVSFNAAAVRQFGYAEEEVIGQNLRILMPEPYRHEHDGYLQ   78 (130)
T ss_dssp             HHHHHHHHHH-HHTSCHHHHHTTCSSEEEEEETT---SBEEEECHHHHHHHCCCHHHHTTSBGGGGSCTTHHHHHHHHHH
T ss_pred             hHHHHHHHHH-HHHHHHHHHHhhCcCeEEEECCC---CeEEEEcHHHHHHHCCCHHHHcCCcHHHHCCchhHHHHHHHHH
Confidence            3445555555 45567889999999999999999   9999999999999999999999998877776654333333333


Q ss_pred             HHHHhcCC----eEEEEEEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEeccc
Q 021027           84 EAIREERP----IEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV  134 (318)
Q Consensus        84 ~~~~~~~~----~~~~~~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIt  134 (318)
                      .....+..    ...+...+++||..+|+.++..|+.+ .  ...+++++++|||
T Consensus        79 ~~~~~~~~~~~~~~~e~~~~~kdG~~~~~~~~~~~~~~-~--~~~~~~~~~~DIT  130 (130)
T 1d06_A           79 RYMATGEKRIIGIDRVVSGQRKDGSTFPMKLAVGEMRS-G--GERFFTGFIRDLT  130 (130)
T ss_dssp             HHHHHCCCSSTTSCEEEEEECTTSCEEEEEEEEEEEEE-T--TEEEEEEEEEECC
T ss_pred             HHHhcCCccccCCeeEEEEEeCCCCEEEEEEEEEEEEE-C--CeEEEEEEEEECc
Confidence            33333332    23456678999999999999999975 2  3346889999997

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

Probab=99.65  E-value=2.1e-15  Score=129.17  Aligned_cols=65  Identities=9%  Similarity=0.109  Sum_probs=56.0

Q ss_pred             HHHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHH
Q 021027           17 TLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIRE   84 (318)
Q Consensus        17 ~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~   84 (318)
                      .++...++++++..+++++.+   |+++|+|+++..++||++++++|+++.++.+|++...+...+..
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            345566789999999999999   99999999999999999999999999999999887766655543

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

Probab=99.65  E-value=2.5e-15  Score=113.48  Aligned_cols=125  Identities=23%  Similarity=0.427  Sum_probs=111.4

Q ss_pred             hhHHHHHHHHhcCCCeEEEEcCCCCCC---cEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCC
Q 021027           15 RYTLWVHEALDELPDSFTITDPSISGH---PIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERP   91 (318)
Q Consensus        15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~---~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~   91 (318)
                      ...++++.+++.++++++++|.+   +   +++++|++++.++|++.++++|+.+..+.++.........+...+..+..
T Consensus        22 ~~~~~~~~i~~~~~~~i~~~d~~---~~~~~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~   98 (162)
T 3sw1_A           22 INAQLLQSMVDASNDGIVVAEKE---GDDTILIYVNAAFEYLTGYSRDEILYQDCRFLQGDDRDQLGRARIRKAMAEGRP   98 (162)
T ss_dssp             CCHHHHHHHHHTCSSEEEEEEEE---TTEEEEEEECHHHHHHHTCCHHHHTTSBGGGGTTTCCCCHHHHHHHHHHHHTCC
T ss_pred             chHHHHHHHHhhccCcEEEEeCC---CCccEEEEECHHHHHHHCCCHHHHcCCCcceecCCCcCHHHHHHHHHHHhcCCC
Confidence            35568899999999999999999   9   99999999999999999999999988887777777777778888888888


Q ss_pred             eEEEEEEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEecccccccccccc
Q 021027           92 IEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG  143 (318)
Q Consensus        92 ~~~~~~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~~~~~~  143 (318)
                      +..+......+|..+|+.+...|+.+ .+|.+.+++++++|||+++++++++
T Consensus        99 ~~~~~~~~~~~g~~~~~~~~~~~i~~-~~g~~~~~~~~~~DiTe~k~~e~~l  149 (162)
T 3sw1_A           99 CREVLRNYRKDGSAFWNELSITPVKS-DFDQRTYFIGIQKDVSRQVELEREL  149 (162)
T ss_dssp             EEEEEEEECTTCCEEEEEEEEEEEEC-SSSSCEEEEEEEEECHHHHHHHHHH
T ss_pred             CcceEEEECCCCCEEEEEEEEEEeec-CCCCEEEEEEEEEeCcHHHHHHHHH
Confidence            88888888899999999999999998 7899999999999999999984443

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

Probab=99.64  E-value=9.1e-16  Score=109.16  Aligned_cols=110  Identities=9%  Similarity=0.080  Sum_probs=94.3

Q ss_pred             CCCeEEEEc-CCCCCCcEEEecHhHHHhcCCChhhhcCCC-CCcccCCCCChHHHHHHHHHHHhcCCeEEEEEEEecCCc
Q 021027           27 LPDSFTITD-PSISGHPIVFASRGFLKMSGFSRAEIIGRN-GRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGT  104 (318)
Q Consensus        27 ~~~~i~~~d-~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~-~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~  104 (318)
                      +++++|.+| ..   +++.|+|+++++++||+++++.+.. +..+++|++.......+...+..+.++..++++++++|.
T Consensus         2 a~~giw~~d~~~---~~~~~~n~~~~~l~G~~~~e~~~~~~~~~~ihpdd~~~~~~~~~~~~~~~~~~~~e~r~~~~dG~   78 (115)
T 3h9w_A            2 TKAIPWKINWQT---MAFEYIGPQIEALLGWPQGSWKSVEDWATRMHPEDQEWVVNFCVKQSECGVDHEADYRALHRDGH   78 (115)
T ss_dssp             -CCEEEEEETTT---TEEEEECTHHHHHHCSCGGGCCBHHHHHHSBCHHHHHHHHHHHHHHHHTTCCEEEEEEEECTTSC
T ss_pred             cceEEEEEEcCC---CcEEEEChhHHHHhCCChHHccCHHHHHHhcCHHHHHHHHHHHHHHHhcCCcccEEEEEEcCCCC
Confidence            468899999 45   8899999999999999999998832 345677877777777788888888888999999999999


Q ss_pred             EEEEEEEEEeeccCCCCceeEEEEEEeccccccccc
Q 021027          105 PFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMR  140 (318)
Q Consensus       105 ~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~~~  140 (318)
                      .+|+.....|+++ ++|.+.+++++..|||++|.+|
T Consensus        79 ~~w~~~~~~~~~d-~~G~~~~~~G~~~Dit~~k~~~  113 (115)
T 3h9w_A           79 YVWIRDVVHVVRD-DSGEVEALIGFMFDISLEHHHH  113 (115)
T ss_dssp             EEEEEEEEEEEEC-TTSCEEEEEEEEEECGGGGC--
T ss_pred             EEEEEEEEEEEEC-CCCCEEEEEEEEeccCcccccc
Confidence            9999999999998 8999999999999999999973

>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=99.64  E-value=4e-15  Score=106.49  Aligned_cols=111  Identities=19%  Similarity=0.231  Sum_probs=78.0

Q ss_pred             CCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCC----eEEEEEEEecC
Q 021027           27 LPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERP----IEVNLLNYKKD  102 (318)
Q Consensus        27 ~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~  102 (318)
                      ++++++++|.+   |+++++|+++++++||++++++|+++..+.++.........+......+..    ...+....++|
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    23456678999


Q ss_pred             CcEEEEEEEEEeeccCCCCceeEEEEEEecccccccccccc
Q 021027          103 GTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG  143 (318)
Q Consensus       103 g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~~~~~~  143 (318)
                      |..+|+.++..|+.+ .  ...+++++++|||++|++|+++
T Consensus        79 G~~~~~~~~~~~~~~-~--~~~~~~~~~~DITerk~~e~~l  116 (119)
T 2vv6_A           79 GTTFPMHLSIGEMQS-G--GEPYFTGFVRDLTEHQQTQARL  116 (119)
T ss_dssp             SCEEEEEEEEEEEEE-T--TEEEEEEEEEECC---------
T ss_pred             CCEEEEEEEEEEEEE-C--CeEEEEEEEEEcHHHHHHHHHH
Confidence            999999999999976 3  3346889999999999985544

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

Probab=99.64  E-value=1.4e-14  Score=103.43  Aligned_cols=110  Identities=10%  Similarity=0.123  Sum_probs=86.5

Q ss_pred             hhHHHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEE
Q 021027           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV   94 (318)
Q Consensus        15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   94 (318)
                      ..+++|+.++++++++++++|.+   |+++++|+++++++||++++++|+++..+.++... .........+..+..+..
T Consensus         8 ~se~~~~~l~e~~~d~i~~~d~~---g~i~~vN~a~~~l~Gy~~~el~g~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~   83 (117)
T 2r78_A            8 FQSNAYRALFEHAIDGIFIMDAE---GHYLDVNPAICSAIGYTRDEFLALDWGVLSRGVDS-GWAAASLARIVGGEPLRE   83 (117)
T ss_dssp             HHHHHHHHHHHHCSSEEEEECTT---SBEEEECHHHHHHHCCCHHHHTTCBTTTTTTCSTT-SHHHHHHHHHHTTCCEEE
T ss_pred             HhHHHHHHHHhcCCceEEEECCC---CCEEEecHHHHHHHCcCHHHHcCCCHHHhCCccch-hHHHHHHHHHHcCCcEEE
Confidence            45668899999999999999999   99999999999999999999999986665443322 222334445566667778


Q ss_pred             EEEEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEeccc
Q 021027           95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV  134 (318)
Q Consensus        95 ~~~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIt  134 (318)
                      +....+++|..+|+.++..|+.+   |.   ++++++|||
T Consensus        84 e~~~~~kdG~~~~v~~~~~~~~~---g~---~~~i~~DIT  117 (117)
T 2r78_A           84 ERTVWTRNGDQLTVELSAHLLPD---GK---ILGIARDVS  117 (117)
T ss_dssp             EEEEECTTSCEEEEEEEEEECTT---SC---EEEEEEC--
T ss_pred             EEEEEecCCCEEEEEEEEEEecC---Ce---EEEEEEeCC
Confidence            88888999999999999999853   44   678889997

>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=1.2e-15  Score=113.63  Aligned_cols=120  Identities=16%  Similarity=0.121  Sum_probs=94.0

Q ss_pred             hhHHHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEE
Q 021027           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV   94 (318)
Q Consensus        15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   94 (318)
                      .....+..++++++++++++|.+   |+|+++|+++++++|+++++++|+++.+++++ ....+...+..++..|.+...
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            45557789999999999999999   99999999999999999999999998888776 445555667788877765332


Q ss_pred             EE---------E---EEecCCcEEEEEEEEEeeccCCCCceeEEEEEEecccccccc
Q 021027           95 NL---------L---NYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM  139 (318)
Q Consensus        95 ~~---------~---~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~~  139 (318)
                      .+         .   ...++|...|..++..|+.+ ++|.+.+++.++.|||+++++
T Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ti~Pl~d-~~G~v~gv~~ii~DVTe~~~a  150 (152)
T 3mxq_A           95 SWEQKPHLLPFKSSRPVSGEEEQMYQNLEVIPIHS-EDGTIEHVCLCVYDVTIQASQ  150 (152)
T ss_dssp             ECCSSSCSSCC----------CCEEEEEEEEEEEC-TTSCEEEEEEEEEEEECC---
T ss_pred             ecccccccccccccCCCCCCCcEEEEEEEEEEEEC-CCCCEEEEEEEEEECCHHHhc
Confidence            11         1   12245677888999999999 899999999999999999876

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

Probab=99.62  E-value=7e-15  Score=103.72  Aligned_cols=111  Identities=16%  Similarity=0.225  Sum_probs=90.0

Q ss_pred             HHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEE-EE
Q 021027           18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV-NL   96 (318)
Q Consensus        18 ~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~-~~   96 (318)
                      ++++.++++++++++++|.+   ++++++|+++++++|+++++++|+++..++ |+........+...+. +..... ..
T Consensus         3 ~~~~~~~~~~~~~i~~~d~~---g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~-~~~~~~~~~~~~~~~~-~~~~~~~~~   77 (114)
T 3luq_A            3 ERLRLFTEHAPAALAMFDRE---MRYLAVSRRWREDYGLGDGDILGMSHYDIF-PEIGEEWKSVHRRGLA-GEVIRVEED   77 (114)
T ss_dssp             HHHHHHHHTCSSEEEEEETT---CBEEEECHHHHHHTTCCSSCCTTCBHHHHC-TTCCHHHHHHHHHHHT-TCCEEEEEE
T ss_pred             HHHHHHHhcCCceEEEEcCC---cEEEEECHHHHHHHCCCHHHHcCCcHHHHC-CccHHHHHHHHHHHhc-CCcceeeee
Confidence            46788999999999999999   999999999999999999999999877776 4444544444445444 444443 33


Q ss_pred             EEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEeccc
Q 021027           97 LNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV  134 (318)
Q Consensus        97 ~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIt  134 (318)
                      ....++|..+|+.+...|+.+ .+|.+.+++++++|||
T Consensus        78 ~~~~~~g~~~~~~~~~~p~~~-~~g~~~~~~~~~~DIT  114 (114)
T 3luq_A           78 CFVRADGRTQWLRWEVRPWYE-GEGRVGGVVIFTEDIT  114 (114)
T ss_dssp             EEEC--CCEEEEEEEEEEEEC-TTSCEEEEEEEEEECC
T ss_pred             EEEcCCCcEEEEEEEEEEeEC-CCCCEEEEEEEEeeCC
Confidence            667889999999999999998 8999999999999997

>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=99.62  E-value=2e-15  Score=113.70  Aligned_cols=123  Identities=12%  Similarity=0.115  Sum_probs=100.9

Q ss_pred             hhHHHHHHHHhcCCCeEEEEc-CCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeE
Q 021027           15 RYTLWVHEALDELPDSFTITD-PSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIE   93 (318)
Q Consensus        15 ~~~~~~~~~~~~~~~~i~~~d-~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~   93 (318)
                      +..++|+.++++++.+++++| .+   ++++++|++++.++|++  +++|+++..++++.........+..++..+.+..
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            456789999999999999999 99   99999999999999999  8999988877777655556677777887777755


Q ss_pred             EEEE-E--Ee-cC-CcEEEEEEEEEeeccCCCCceeEEEEEEecccccccccccc
Q 021027           94 VNLL-N--YK-KD-GTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG  143 (318)
Q Consensus        94 ~~~~-~--~~-~~-g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~~~~~~  143 (318)
                      .... .  .. .+ |..+|+.++..|+++ .+|.+.+++++++|||++|++++++
T Consensus        89 ~~~~~~~~~~~~~~g~~~~~~~~~~pi~~-~~g~~~g~~~~~~DITe~k~~e~~l  142 (158)
T 3k3c_A           89 GSEWRLQTDYDGSGVEERYFDFVVTPRRR-ADGSIEGVQLIVDDVTSRVRARQAA  142 (158)
T ss_dssp             EEEEEEEEESSSSCEEEEEEEEEEEEEEC-TTSCEEEEEEEEEECHHHHHHHHHH
T ss_pred             ccceeEEeccCCCCcceEEEEEEEEEeEC-CCCCEEEEEEEEEehhHHHHHHHHH
Confidence            4322 2  22 22 677899999999998 8999999999999999999984443

>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=99.62  E-value=8.4e-15  Score=124.33  Aligned_cols=116  Identities=39%  Similarity=0.744  Sum_probs=106.3

Q ss_pred             HHHhcCCCeEEEEcC---CCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEEEEEE
Q 021027           22 EALDELPDSFTITDP---SISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLN   98 (318)
Q Consensus        22 ~~~~~~~~~i~~~d~---~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   98 (318)
                      .+++.++++++++|.   +   |+++++|+++++++||++++++|+++..+.+++........+...+..+..+..+...
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   9999999999999999999999999888888777777778888888888889999989


Q ss_pred             EecCCcEEEEEEEEEeeccCCCCceeEEEEEEecccccccccc
Q 021027           99 YKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRN  141 (318)
Q Consensus        99 ~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~~~~  141 (318)
                      .+++|..+|+.++..|+++ .+|.+.+++++.+|||++++.++
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

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

Probab=99.61  E-value=4.8e-15  Score=114.91  Aligned_cols=122  Identities=12%  Similarity=0.136  Sum_probs=99.5

Q ss_pred             hhHHHHHHHHhcCCCeEEEEc-CCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeE
Q 021027           15 RYTLWVHEALDELPDSFTITD-PSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIE   93 (318)
Q Consensus        15 ~~~~~~~~~~~~~~~~i~~~d-~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~   93 (318)
                      +..++|+.++++++++++++| .+   ++++++|++++.++|++  +++|+++..++++.........+..++..+.+..
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            456789999999999999999 99   99999999999999999  8999998887777665555666777777777765


Q ss_pred             EEEEEE---ec-C-CcEEEEEEEEEeeccCCCCceeEEEEEEeccccccccccc
Q 021027           94 VNLLNY---KK-D-GTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNS  142 (318)
Q Consensus        94 ~~~~~~---~~-~-g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~~~~~  142 (318)
                      ......   .. + |...|+.+...|+.+ .+|.+.+++++++|||++|++|++
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            442222   11 2 777899999999998 899999999999999999999666

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

Probab=99.59  E-value=3e-14  Score=114.20  Aligned_cols=112  Identities=20%  Similarity=0.457  Sum_probs=103.0

Q ss_pred             HHHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEEEE
Q 021027           17 TLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNL   96 (318)
Q Consensus        17 ~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~   96 (318)
                      .+.+..++++++++++++|.+   |+++++|+++++++||++++++|+++..+.++.........++..+..+.++..+.
T Consensus       110 l~~~~~~~~~~~~~i~~~d~~---g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~  186 (227)
T 3ewk_A          110 LARLKQAMDANSEMILLTDRA---GRIIYANPALCRFSGMAEGELLGQSPSILDSPLADQETLAAMQEALQAGQPWSGRL  186 (227)
T ss_dssp             HHHHHHHHHTCCSEEEEECTT---SCEEEECHHHHHHHTCCTHHHHSSCGGGGBCTTSCHHHHHHHHHHHHHTCCEECCE
T ss_pred             HHHHHHHHhcCcCeEEEEcCC---CcEEEEchHHHHHhCCCHHHHcCCChhhccCCCCCHHHHHHHHHHHHcCCceeEEE
Confidence            356778999999999999999   99999999999999999999999998888888888888888999999999999998


Q ss_pred             EEEecCCc------EEEEEEEEEeeccCCCCceeEEEEEEec
Q 021027           97 LNYKKDGT------PFWMLFKMSLVFGKEDGRATHFVAVQVP  132 (318)
Q Consensus        97 ~~~~~~g~------~~~~~~~~~~i~~~~~g~~~~~i~~~~D  132 (318)
                      ..++++|.      .+|+.++..|+++ .+|.+.+++++.+|
T Consensus       187 ~~~~k~G~~~~dg~~~~~~~~~~pi~d-~~g~~~~~v~i~~D  227 (227)
T 3ewk_A          187 LNRRRTGPAPHDAEDYWAEISTTPIHT-DGNGLVGYVQIQHD  227 (227)
T ss_dssp             EEEEECCSSSSCEEEEEEEEEEEEEEC-SSSCEEEEEEEEEC
T ss_pred             EEECCCCCcCcccceEEEEEEEEEEEC-CCCCEEEEEEEecC
Confidence            88888886      8999999999999 89999999999987

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

Probab=99.59  E-value=2.1e-14  Score=120.77  Aligned_cols=61  Identities=8%  Similarity=0.041  Sum_probs=53.9

Q ss_pred             CCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhcccc
Q 021027          251 KQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQA  314 (318)
Q Consensus       251 ~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~~~  314 (318)
                      .+.++..+.+|   .++|||+++..++||+++|++|+++.+++||++.+...+.+++.++.|+.
T Consensus       154 ~~fi~r~~~dG---~~~yvn~~~~~lLGY~peELiG~s~~~~vHPdD~~~~~~~~~~~l~~G~~  214 (339)
T 3rty_A          154 PKFAIRHTATG---IISHVDSAAVSALGYLPQDLIGRSIMDFYHHEDLSVMKETYETVMKKGQT  214 (339)
T ss_dssp             CEEEEEEETTC---BEEEECTTHHHHHCCCHHHHTTSBGGGGBCGGGHHHHHHHHHHHHHHTTS
T ss_pred             ceEEEEECCCC---eEEEcChhhhcccCCCHHHHcCCcHHHEECHHHHHHHHHHHHHHHHcCCc
Confidence            35566677776   99999999999999999999999999999999999988888888887664

>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=6.2e-15  Score=104.86  Aligned_cols=114  Identities=10%  Similarity=0.061  Sum_probs=101.1

Q ss_pred             HHHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCC--CCcccCCCCChHHHHHHHHHHHhcCCeEE
Q 021027           17 TLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRN--GRMFQGPRTNRRTIMEIREAIREERPIEV   94 (318)
Q Consensus        17 ~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~--~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   94 (318)
                      +++++.++++++++++.+|.+   +.++++|+++.+++|++++++.+..  +..+.+|++.......+...+..+..+..
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            467889999999999999999   9999999999999999999987764  34567787777777777777788888888


Q ss_pred             EEEEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEeccc
Q 021027           95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV  134 (318)
Q Consensus        95 ~~~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIt  134 (318)
                      ++++.+++|..+|+.....|+.+ ++|.+.+++++++|||
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 8899999999999998

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

Probab=99.58  E-value=3.4e-14  Score=122.53  Aligned_cols=61  Identities=13%  Similarity=0.104  Sum_probs=53.7

Q ss_pred             CCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhcccc
Q 021027          251 KQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQA  314 (318)
Q Consensus       251 ~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~~~  314 (318)
                      .+.++..+.+|   .++|||++++.++||+++|++|+++.+++||++.+.+.+.+.+.++.+++
T Consensus       278 ~~fi~~~~~dg---~~~~vn~~~~~ilGY~~eEl~g~~~~~~iHpdD~~~~~~~~~~~l~~~~~  338 (387)
T 4f3l_B          278 MEYVSRHAIDG---KFVFVDQRATAILAYLPQELLGTSCYEYFHQDDIGHLAECHRQVLQTREK  338 (387)
T ss_dssp             CEEEEEECTTS---BEEEECTHHHHHHCCCHHHHTTSBGGGTBCHHHHHHHHHHHHHHTTCSSC
T ss_pred             ceEEEEECCCC---EEEEECCCcccccCCCHHHHcCCcHHHeeCHHHHHHHHHHHHHHHhcCCC
Confidence            45566677776   99999999999999999999999999999999999999999888876654

>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=99.57  E-value=4.5e-14  Score=103.65  Aligned_cols=116  Identities=39%  Similarity=0.742  Sum_probs=104.2

Q ss_pred             HHHHHhcCCCeEEEEcC---CCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEEEE
Q 021027           20 VHEALDELPDSFTITDP---SISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNL   96 (318)
Q Consensus        20 ~~~~~~~~~~~i~~~d~---~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~   96 (318)
                      ++.+++.++++++++|.   +   +.++++|++++.++|++.++++|+++..+.++.........+...+..+.++..+.
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             EEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEecccccccc
Q 021027           97 LNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM  139 (318)
Q Consensus        97 ~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~~  139 (318)
                      ....++|..+|+.+...|+.+ .+|.+.++++++.|||++++.
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            888899999999999999998 889999999999999999985

>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=5.7e-14  Score=100.55  Aligned_cols=112  Identities=11%  Similarity=0.085  Sum_probs=93.5

Q ss_pred             HHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcC-CeEEEEEEEe
Q 021027           22 EALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREER-PIEVNLLNYK  100 (318)
Q Consensus        22 ~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~  100 (318)
                      .++++++++++++|.+   ++++++|+++++++||++++++|+++..+.+|++.......+...+..+. ....+++..+
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            3677889999999999   99999999999999999999999988888888776666666666665433 3567888889


Q ss_pred             cCCcEEEEEEEEEeeccCCC-CceeEEEEEEecccccc
Q 021027          101 KDGTPFWMLFKMSLVFGKED-GRATHFVAVQVPIVSRK  137 (318)
Q Consensus       101 ~~g~~~~~~~~~~~i~~~~~-g~~~~~i~~~~DIte~k  137 (318)
                      ++|..+|+.++..|+++ .. +.+.+++++..||++.+
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 56677899999999865

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

Probab=99.53  E-value=4.9e-14  Score=101.28  Aligned_cols=116  Identities=12%  Similarity=0.112  Sum_probs=87.3

Q ss_pred             HHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEEEEEEEe
Q 021027           21 HEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYK  100 (318)
Q Consensus        21 ~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  100 (318)
                      +.++++++++++++|.+   |+++++|+++++++|++.++++|+++..+.++.........+......+.. ..+.....
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   999999999999999999999999877777766655555555555554444 66777778


Q ss_pred             cCCcEEEEEEEEEeeccCCCCceeEEEEEEecccccccccccc
Q 021027          101 KDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG  143 (318)
Q Consensus       101 ~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~~~~~~  143 (318)
                      ++|..+|+.+...|...   +...+++++++|||++|++++..
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            99999999999887654   34568899999999999985444

>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=99.53  E-value=2.8e-13  Score=96.15  Aligned_cols=108  Identities=10%  Similarity=0.117  Sum_probs=86.1

Q ss_pred             hHHHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEEE
Q 021027           16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVN   95 (318)
Q Consensus        16 ~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~   95 (318)
                      ..+.++.++++++++++++|.+   |+++++|+++++++||++++++|+++..+.++.....     ...+..+..+..+
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            4456788999999999999999   9999999999999999999999998777765433222     2233445567778


Q ss_pred             EEEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEeccc
Q 021027           96 LLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV  134 (318)
Q Consensus        96 ~~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIt  134 (318)
                      ....+++|..+|+.++..|+..  .+. .+++++++|||
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            8888999999999999999876  333 46778999997

>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=99.52  E-value=5.5e-13  Score=96.83  Aligned_cols=115  Identities=26%  Similarity=0.486  Sum_probs=97.2

Q ss_pred             HHHHHHHhcCCCeEEEEcC---CCCCCcEEEecHhHHHhcCCChhhhcCCC--CCcccCCCCChHHHHHHHHHHHhcCCe
Q 021027           18 LWVHEALDELPDSFTITDP---SISGHPIVFASRGFLKMSGFSRAEIIGRN--GRMFQGPRTNRRTIMEIREAIREERPI   92 (318)
Q Consensus        18 ~~~~~~~~~~~~~i~~~d~---~~~~~~i~~~N~~~~~~~G~~~~e~~g~~--~~~l~~~~~~~~~~~~~~~~~~~~~~~   92 (318)
                      +.+...++.++.+++++|.   +   ++++++|++++.++|++.++++|++  ...+.++.........+...+..+..+
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            4455667889999999999   8   9999999999999999999999998  455666665555566666777777777


Q ss_pred             EEEEEEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEeccccc
Q 021027           93 EVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSR  136 (318)
Q Consensus        93 ~~~~~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~  136 (318)
                      ..+.....++|..+|+.+...|+.+ .+|.+.+++++++|||++
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            7788788899999999999999998 789999999999999975

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

Probab=99.51  E-value=9.5e-13  Score=91.33  Aligned_cols=107  Identities=27%  Similarity=0.520  Sum_probs=89.1

Q ss_pred             CeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCC--CCcccCCCCChHHHHHHHHHHHhcCCeEEEEEEEecCCcEE
Q 021027           29 DSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRN--GRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPF  106 (318)
Q Consensus        29 ~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~--~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~  106 (318)
                      .+++++|...++++++++|+++++++|++.++++|++  ...+.++.........+...+..+..+..+.....++|..+
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            5788888743349999999999999999999999997  45555555555556667777777788888888888999999


Q ss_pred             EEEEEEEeeccCCCCceeEEEEEEeccccc
Q 021027          107 WMLFKMSLVFGKEDGRATHFVAVQVPIVSR  136 (318)
Q Consensus       107 ~~~~~~~~i~~~~~g~~~~~i~~~~DIte~  136 (318)
                      |+.+...|+.+ .+|.+.+++++++|||++
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

>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=1.5e-13  Score=98.04  Aligned_cols=116  Identities=9%  Similarity=0.060  Sum_probs=94.6

Q ss_pred             hhHHHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCC--CCcccCCCCChHHHHHHHHHHHhcCCe
Q 021027           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRN--GRMFQGPRTNRRTIMEIREAIREERPI   92 (318)
Q Consensus        15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~--~~~l~~~~~~~~~~~~~~~~~~~~~~~   92 (318)
                      +..++++.++++++++++++|.+  ++.++++|+++++++|+++++++|..  +..+.++++...+...+.. +..+..+
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            45567889999999999999975  47999999999999999999999876  4445555544444444444 5567777


Q ss_pred             EEEEEEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEeccc
Q 021027           93 EVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV  134 (318)
Q Consensus        93 ~~~~~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIt  134 (318)
                      ..++....++|...|+.+...|+.+ .+|.+.+++++++|||
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

>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=99.50  E-value=8.2e-13  Score=95.11  Aligned_cols=118  Identities=13%  Similarity=0.175  Sum_probs=83.2

Q ss_pred             hHHHhhhhhhHHHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhc--CCCCCcccCCCCChHHHHHHHH
Q 021027            7 LIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEII--GRNGRMFQGPRTNRRTIMEIRE   84 (318)
Q Consensus         7 ~~~~~~~~~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~--g~~~~~l~~~~~~~~~~~~~~~   84 (318)
                      ..++.+. +.+++++.++++++++++++|.+   |+++++|+++++++||++++++  |++...+.+  +.......+..
T Consensus         7 ~~e~~L~-~~~~~~~~l~e~~~~~i~~~d~~---g~i~~~N~a~~~~~G~~~~el~g~g~~~~~~~~--~~~~~~~~~~~   80 (126)
T 3bwl_A            7 RREKRLE-ETSSRLEALFENSPDMIDVLDAD---GTICEVNQRFCAELGYDESEVLGRSIWEFDLMF--DAEDVQTQLSG   80 (126)
T ss_dssp             HHHHHHH-HHHHHHHHHHHHCSSEEEEECTT---CBEEEECHHHHHHHTCCGGGTTTSBGGGTBTTC--CHHHHHHHHHT
T ss_pred             HHHHHHH-HHHHHHHHHHhhCCcEEEEEcCC---CCEEEEcHHHHHHhCCCHHHHhhCCCchhhccC--CHHHHHHHHHH
Confidence            3444454 56678999999999999999999   9999999999999999999994  565555544  21221111111


Q ss_pred             HHHhcCCeEEEEEEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEeccc
Q 021027           85 AIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV  134 (318)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIt  134 (318)
                       ...+.....+..+.+++|..+|+.++..|+..  +|.. .++++++|||
T Consensus        81 -~~~~~~~~~e~~~~~~dG~~~~~~~~~~~~~~--~~~~-~~~~~~~DIT  126 (126)
T 3bwl_A           81 -FSVDERRKFEGLYERRDGSTMSVEVHLLRFNL--EGED-RFLAISRDIT  126 (126)
T ss_dssp             -CCTTCEEEEEEEEECTTSCEEEEEEEEEEEEE--TTEE-EEEEEEEEC-
T ss_pred             -HhcCCCcceEEEEEeCCCCEEEEEEEeEEEec--CCcE-EEEEEEEeCC
Confidence             11223344556667899999999988888754  4443 5788899997

>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=99.48  E-value=2.8e-13  Score=102.30  Aligned_cols=122  Identities=20%  Similarity=0.247  Sum_probs=84.3

Q ss_pred             hHHHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCC----
Q 021027           16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERP----   91 (318)
Q Consensus        16 ~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~----   91 (318)
                      ....+..+++.++++++++|.+   +.++++|++++.++|++.++++|+++..++++.........+......+..    
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   999999999999999999999999877777665544444444444433322    


Q ss_pred             eEEEEEEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEecccccccccccc
Q 021027           92 IEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG  143 (318)
Q Consensus        92 ~~~~~~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~~~~~~  143 (318)
                      +..+......+|..+|+.+...|+.  .+|.+ +++++++|||+++++++++
T Consensus       115 ~~~~~~~~~~~g~~~~~~~~~~~~~--~~g~~-~~~~~~~DiT~~~~~e~~l  163 (167)
T 1v9y_A          115 MSRELQLEKKDGSKIWTRFALSKVS--AEGKV-YYLALVRDASVEMAQKEQT  163 (167)
T ss_dssp             --CEEEEECTTSCEEEEEEEEEEEE--ETTEE-EEEEEEEC-----------
T ss_pred             cceEEEEEcCCCcEEEEEEEEEEEe--cCCCE-EEEEEEecCcHHHHHHHHH
Confidence            3446667788999999999999994  46665 4899999999999985443

>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=99.45  E-value=1.6e-12  Score=96.52  Aligned_cols=106  Identities=34%  Similarity=0.562  Sum_probs=91.4

Q ss_pred             HHHhcCCCeEEEEc---CCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCC-----------ChHHHHHHHHHHH
Q 021027           22 EALDELPDSFTITD---PSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRT-----------NRRTIMEIREAIR   87 (318)
Q Consensus        22 ~~~~~~~~~i~~~d---~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~-----------~~~~~~~~~~~~~   87 (318)
                      .+++.. ++++++|   .+   |+++++|+++++++||+.++++|+++..+.+++.           .......+...+.
T Consensus        30 ~~~~~~-~~i~~~d~~d~~---g~i~~~N~a~~~l~G~~~~el~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  105 (149)
T 3d72_A           30 GPVDTS-VALILCDLKQKD---TPIVYASEAFLYMTGYSNAEVLGRNCRFLQSPDGMVKPKSTRKYVDSNTINTMRKAID  105 (149)
T ss_dssp             CSCCTT-SCEEEEETTSTT---CCEEEECHHHHHHHCCCHHHHTTSCGGGGGSTTSCCCTTCCCSSSCHHHHHHHHHHHH
T ss_pred             HhhcCC-ccEEEEeccCCC---CcEEEECHHHHHHHCcCHHHHcCCChhHhCCccccccccccccccChHHHHHHHHHHH
Confidence            456664 8999999   67   9999999999999999999999999887777663           5566667777888


Q ss_pred             hcCCeEEEEEEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEec
Q 021027           88 EERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVP  132 (318)
Q Consensus        88 ~~~~~~~~~~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~D  132 (318)
                      .+..+..+....+++|..+|+.++..|+.+ .+|.+.+++++++|
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=99.43  E-value=1.8e-12  Score=93.96  Aligned_cols=112  Identities=11%  Similarity=0.072  Sum_probs=82.2

Q ss_pred             HHHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcC------
Q 021027           17 TLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREER------   90 (318)
Q Consensus        17 ~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~------   90 (318)
                      ...+..++++++++++++|.+   |+|+++|+++++++||++++++|+++..++++.........+......+.      
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            346788999999999999999   99999999999999999999999998888776654332221111111111      


Q ss_pred             -CeEEEEEEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEecccc
Q 021027           91 -PIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVS  135 (318)
Q Consensus        91 -~~~~~~~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte  135 (318)
                       ....+....++||..+|+.++++|+.+ +..   .++++++|...
T Consensus        83 ~~~~~E~~~~rkdG~~~~velsis~i~~-~~~---~~v~~~~~~~~  124 (129)
T 3mfx_A           83 QHPAQETTLICASGKAKDVELSISYIPG-HEP---MFVMVMHDLEH  124 (129)
T ss_dssp             CEEEEEEEEECTTSCEEEEEEEEEEECS-SSC---EEEEEEEEC--
T ss_pred             CCCceEEEEEcCCCCEEEEEEEEEEecC-CCc---EEEEEEechhh
Confidence             234677788999999999999999965 222   36777888654

>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=99.43  E-value=3.8e-13  Score=96.53  Aligned_cols=108  Identities=10%  Similarity=0.081  Sum_probs=74.7

Q ss_pred             hHHHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEEE
Q 021027           16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVN   95 (318)
Q Consensus        16 ~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~   95 (318)
                      .+++++.++++++++++++|.+   |+++++|+++++++|+++++++|+++..+++++...............+...   
T Consensus        17 ~~~~~~~i~~~~~~~i~~~d~~---g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---   90 (125)
T 3fc7_A           17 TRKKFESLVSDSPDGIVHLTTN---GTILSVNPSMAGRLGADPDTLVGQQLSAVMDSEAANQRLEAGKSAVENGTAT---   90 (125)
T ss_dssp             ---------CCSCCEEEEEETT---SBEEEECHHHHHHHTSCHHHHTTSBGGGSSCHHHHHHHHHHHHHHHHHTSCE---
T ss_pred             HHHHHHHHHhcCCCeEEEEcCC---CeEEEECHHHHHHhCCCHHHHcCccHHHhCCHHHHHHHHHHHHHHhcCCCeE---
Confidence            5678899999999999999999   9999999999999999999999999887763322222222223444444433   


Q ss_pred             EEEEecCCc-EEEEEEEEEeeccCCCCceeEEEEEEeccc
Q 021027           96 LLNYKKDGT-PFWMLFKMSLVFGKEDGRATHFVAVQVPIV  134 (318)
Q Consensus        96 ~~~~~~~g~-~~~~~~~~~~i~~~~~g~~~~~i~~~~DIt  134 (318)
                         ...+|. ..|+.+...|+.+  +|...+++++++|||
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               122344 6789999999876  577789999999997

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

Probab=99.43  E-value=2.1e-12  Score=103.71  Aligned_cols=110  Identities=15%  Similarity=0.206  Sum_probs=85.4

Q ss_pred             hHHHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhc------------CCChhhhcCCCCCcccCCCCChHHHHHHH
Q 021027           16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMS------------GFSRAEIIGRNGRMFQGPRTNRRTIMEIR   83 (318)
Q Consensus        16 ~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~------------G~~~~e~~g~~~~~l~~~~~~~~~~~~~~   83 (318)
                      ...++..++++++.+++++|.+   |+|+|+|+++++++            ||++++++|+++..+.+.   +.....++
T Consensus        20 e~~~l~~iLd~~~~~vii~D~~---g~I~~~N~a~~~ll~~~~~~~~~~l~G~~~~eliG~~~~~~~~~---~~~~~~~~   93 (233)
T 3vol_A           20 HMARIKSALDNVSANVMIADND---LNIIYMNRTVSEMLGRAEADIRKQLPNFDAGRLMGANIDVFHKN---PAHQRHLL   93 (233)
T ss_dssp             HHHHHHHHHTTSSSEEEEEETT---SBEEEECHHHHHHHHHTHHHHHTTCTTCCTTSCTTCBGGGGSSS---HHHHHHHH
T ss_pred             HHHHHHHHHhcCCCcEEEECCC---CcEEEecHHHHHHHHHHHHHHHhhcCCCCHHHHcCCCHHHHcCC---HHHHHHHH
Confidence            4467889999999999999999   99999999999998            899999999998777643   22222222


Q ss_pred             HHHHhcCCeEEEEEEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEecccccccc
Q 021027           84 EAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM  139 (318)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~~  139 (318)
                      ..+.  ..+..++   ..+|.  |+.++..|+.+ ++|.+.|++.+++|||+++++
T Consensus        94 ~~~~--~~~~~~~---~~~g~--~~~~~~~Pi~d-~~G~~~g~v~~~~DITe~~~~  141 (233)
T 3vol_A           94 ANLT--GVHKAEL---NLGGR--RFSLDVVPVFN-DANERLGSAVQWTDRTEEHRA  141 (233)
T ss_dssp             HTCC--SCEEEEE---EETTE--EEEEEEEEEEC-TTCCEEEEEEEEEECHHHHHH
T ss_pred             Hhcc--cceeEEE---EECCE--EEEEEEEEEEC-CCCCEEEEEEEEehhhHHHHH
Confidence            2211  2333333   23553  77899999998 899999999999999999997

>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=99.37  E-value=2.5e-12  Score=91.68  Aligned_cols=107  Identities=14%  Similarity=0.072  Sum_probs=85.2

Q ss_pred             HHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEEEEE
Q 021027           18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLL   97 (318)
Q Consensus        18 ~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~   97 (318)
                      ..+++++++++++++++|.+   ++++++|+++++++|+++++++|+++..++++.........+..++..+.+...++.
T Consensus        12 ~~~~~il~~~~~~i~~~D~~---g~i~~~N~a~~~l~g~~~~e~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   88 (118)
T 3fg8_A           12 SGRENLYFQGGLGFMALDED---LRIIYVNSGCLRHVRRSRDELLGRVVTEVLPETQGSYFDALCRKVLATGREQQTRVD   88 (118)
T ss_dssp             -CCCCSSSCTTCEEEEECTT---CBEEEECHHHHHHHTCCHHHHTTSBHHHHCGGGTTSHHHHHHHHHHHHCCCEEEEEE
T ss_pred             chHHHHHhhCCceEEEECCC---CeEEEECHHHHHHhCCCHHHHcCCcHHHHcCccchHHHHHHHHHHHHcCCceEEEEE
Confidence            34567899999999999999   999999999999999999999999987777666555666777788888887776432


Q ss_pred             EEecCCcEEEEEEEEEeeccCCCCceeEEEEEEeccccc
Q 021027           98 NYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSR  136 (318)
Q Consensus        98 ~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~  136 (318)
                      ....+|  .|+.+...|+.+       +++++++|||++
T Consensus        89 ~~~~~g--~~~~~~~~p~~~-------g~v~~~~DITer  118 (118)
T 3fg8_A           89 SLYSPG--MTIEVTAAADSG-------ALVVHFRDVTAE  118 (118)
T ss_dssp             CSSSTT--CEEEEEEEEETT-------EEEEEEEECSCC
T ss_pred             EEcCCC--eEEEEEEEEcCC-------cEEEEEEeccCC
Confidence            223355  478888888754       378889999985

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

Probab=99.36  E-value=9.5e-12  Score=92.55  Aligned_cols=118  Identities=13%  Similarity=0.126  Sum_probs=90.6

Q ss_pred             HHHHHHHHhcCCCeEEEEcCCCCCCcEEEecHh---HHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeE
Q 021027           17 TLWVHEALDELPDSFTITDPSISGHPIVFASRG---FLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIE   93 (318)
Q Consensus        17 ~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~---~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~   93 (318)
                      ...+..++++++.+++++|.+   ++++|+|++   +++++| ..++++|+++..+.++. .......+...++.+....
T Consensus        18 ~~~l~~IL~~~~~gI~~vD~~---g~I~~~N~a~~~~~~i~g-~~~~~iGr~v~~~~~~~-~~~~v~~i~~~l~~g~~~~   92 (151)
T 2qkp_A           18 VEQANLILNHLPLEITFVNKD---DIFQYYNDSVPAAEMVFK-RTPSQVGRNVELCHPPK-VLDKVKKVFELLRNGQRDK   92 (151)
T ss_dssp             HHHHHHHHHHSSSEEEEEETT---SBEEEECCCSCGGGCSSC-CCGGGTTSBGGGSSCHH-HHHHHHHHHHHHHTTSBSE
T ss_pred             HHHHHHHHHhCCCceEEEcCC---CeEEEEeCCCchhhhhcC-CCHHHcCCCHHHhCCHH-HHHHHHHHHHHHHcCCccE
Confidence            356889999999999999999   999999999   999999 55789999987765422 2233445566677677665


Q ss_pred             EEEEEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEecccccccccc
Q 021027           94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRN  141 (318)
Q Consensus        94 ~~~~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~~~~  141 (318)
                      .+.... .++...++.++..|+++ ++|.+.|++.+++|||+.++.++
T Consensus        93 ~~~~~~-~~~~~~~v~v~~~Pi~d-~~G~~~G~vev~~Dit~l~~le~  138 (151)
T 2qkp_A           93 VNMWFQ-SERLGKFVYVTYAAVRD-QAGDFQGVLEYVQDIKPFFELDS  138 (151)
T ss_dssp             EEEEEE-ETTTTEEEEEEEEEEEC-TTCCEEEEEEEEEECGGGGGGGG
T ss_pred             EEEEEe-cCCCCeEEEEEEEEEEC-CCCCEEEEEEEEEECHHHHhhhh
Confidence            554432 23212467888999998 78999999999999999988733

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

Probab=99.36  E-value=1.8e-11  Score=87.60  Aligned_cols=106  Identities=16%  Similarity=0.219  Sum_probs=78.2

Q ss_pred             HHHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcC------------CChhhhcCCCCCcccCCCCChHHHHHHHH
Q 021027           17 TLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSG------------FSRAEIIGRNGRMFQGPRTNRRTIMEIRE   84 (318)
Q Consensus        17 ~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G------------~~~~e~~g~~~~~l~~~~~~~~~~~~~~~   84 (318)
                      ..++++++++++++++++|.+   |+++++|+++++++|            +++++++|++...+.+.   +.....+..
T Consensus         4 ~~rl~~il~~~~~gviv~D~~---g~I~~~N~a~~~llg~~~~~i~~~~~g~~~~~~~G~~~~~~~~~---~~~~~~~~~   77 (121)
T 4hi4_A            4 MARIASALDNVSANVMIADND---LNIIYMNRTVSEMLGRAEADIRKQLPNFDAGRLMGANIDVFHKN---PAHQRHLLA   77 (121)
T ss_dssp             HHHHHHHHTTSSSEEEEEETT---CBEEEECHHHHHHHHHTHHHHHHHCTTCCGGGCTTCBGGGGCSS---HHHHHHHHH
T ss_pred             HHHHHHHHhcCCccEEEEcCC---CeEEEecHHHHHHHHHHHHHHHHhcCCCChHHhcCCCHHHhcCC---HHHHHHHHh
Confidence            357889999999999999999   999999999999996            88899999987776543   122222222


Q ss_pred             HHHhcCCeEEEEEEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEeccccc
Q 021027           85 AIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSR  136 (318)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~  136 (318)
                      ...  ..+..+..   .+|.  ++.++..|+.+ .+|.+.|++.+++|||++
T Consensus        78 ~~~--~~~~~~~~---~~~~--~~~~~~~pi~~-~~g~~~g~v~~~~DiTee  121 (121)
T 4hi4_A           78 NLT--GVHKAELN---LGGR--RFSLDVVPVFN-DANARLGSAVQWTDRTEE  121 (121)
T ss_dssp             HCS--SCEEEEEE---ETTE--EEEEEEEEEEC-TTSCEEEEEEEEEECC--
T ss_pred             CcC--CCcEEEEE---ECCE--EEEEEEEEEEC-CCCCEEEEEEEEEEecCC
Confidence            111  23333322   2454  55788999998 789999999999999974

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

Probab=99.36  E-value=2.7e-12  Score=91.74  Aligned_cols=74  Identities=20%  Similarity=0.320  Sum_probs=66.1

Q ss_pred             chhHHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhccccee
Q 021027          240 SSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQACT  316 (318)
Q Consensus       240 ~~~l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~~~~~  316 (318)
                      ...++.++++++++|+++|.+|   +|+|+|++|++++||+++|++|+++..+.++.........++.++..+.+|.
T Consensus         4 ~~~~~~~~~~~~~~i~~~d~~g---~i~~~N~a~~~~~G~~~~elig~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~   77 (120)
T 2gj3_A            4 PEIFRQTVEHAPIAISITDLKA---NILYANRAFRTITGYGSEEVLGKNESILSNGTTPRLVYQALWGRLAQKKPWS   77 (120)
T ss_dssp             HHHHHHHHHHCSSEEEEECTTC---BEEEECHHHHHHHCCCTTGGGGCBGGGGCCTTSCHHHHHHHHHHHHTTCCEE
T ss_pred             HHHHHHHHHhCCCeEEEECCCC---CEEeehHHHHHHHCcCHHHHcCCCHHHcCCCCCCHHHHHHHHHHHHcCCCEE
Confidence            3457889999999999999997   9999999999999999999999999999888887778888888888887763

>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=99.34  E-value=2.2e-12  Score=90.63  Aligned_cols=67  Identities=45%  Similarity=0.942  Sum_probs=60.4

Q ss_pred             cCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhccccee
Q 021027          250 IKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQACT  316 (318)
Q Consensus       250 ~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~~~~~  316 (318)
                      ++++|+++|.+.++++|+|+|++|++++||+++|++|+++..+.+|...+...+.+++++..+++|.
T Consensus         2 ~~~~i~i~d~~~~~g~i~~~N~a~~~l~Gy~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~   68 (109)
T 1n9l_A            2 LRHTFVVADATLPDCPLVYASEGFYAMTGYGPDEVLGHNCRFLQGEGTDPKEVQKIRDAIKKGEACS   68 (109)
T ss_dssp             CSCEEEEEETTSTTCCEEEECHHHHHHHCCCHHHHTTSCGGGGCCTTCCHHHHHHHHHHHHHTCCEE
T ss_pred             CccEEEEEcCCCCCCeEEEEchHHHHHHCcCHHHHcCCCchhcCCCCCCHHHHHHHHHHHHcCCcEE
Confidence            5899999997655679999999999999999999999999999888888888999999999988874

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

Probab=99.34  E-value=4.5e-11  Score=99.44  Aligned_cols=58  Identities=9%  Similarity=0.085  Sum_probs=50.6

Q ss_pred             cEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhccc
Q 021027          253 SFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQ  313 (318)
Q Consensus       253 ~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~~  313 (318)
                      .+...+.+|   .++|||+++..++||+++|++|+++.+++||++.+.+.+...+.++.+.
T Consensus       176 Fitrh~~dG---~~~yvs~~~~~lLGY~peELig~s~~~~vHPdD~~~~~~~~~~~l~~~~  233 (317)
T 4dj3_A          176 FTTTHTPGC---VFLEVDERAVPLLGYLPQDLIGTSILTYLHPEDRPLMVAIHQKVLKYAG  233 (317)
T ss_dssp             EEEEECTTS---BEEEECTTHHHHHSCCHHHHTTSBGGGGBCTTTTTHHHHHHHHHHHTTT
T ss_pred             eEEEecCCC---eEEEEChHHhhhcCcChHHHcCCCHHHeECHHHHHHHHHHHHHHHHcCC
Confidence            344455555   9999999999999999999999999999999999999988888888654

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

Probab=99.34  E-value=2.2e-12  Score=110.38  Aligned_cols=108  Identities=8%  Similarity=0.097  Sum_probs=95.4

Q ss_pred             CCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEEEEEEEecCCcEEE
Q 021027           28 PDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFW  107 (318)
Q Consensus        28 ~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~  107 (318)
                      ...++..+.+   |.++|+|+++..++||++++++|+++..+++|++.......+...+..+.....++++++++|..+|
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            3455667778   9999999999999999999999999999999988877777788888877777778889999999999


Q ss_pred             EEEEEEeeccCC-CCceeEEEEEEecccccccc
Q 021027          108 MLFKMSLVFGKE-DGRATHFVAVQVPIVSRKHM  139 (318)
Q Consensus       108 ~~~~~~~i~~~~-~g~~~~~i~~~~DIte~k~~  139 (318)
                      +.....|+.+ . +|.+.+++++.+|||+++..
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 6 79999999999999998864

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

Probab=99.33  E-value=6.6e-12  Score=88.34  Aligned_cols=90  Identities=18%  Similarity=0.173  Sum_probs=68.5

Q ss_pred             HHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEEEEEEEec
Q 021027           22 EALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKK  101 (318)
Q Consensus        22 ~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  101 (318)
                      .+++++++.++++|.+   |+++|+|+++++++||++++++|+++.++.+|++.......+.   ..+.....+++++++
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   223334567788899


Q ss_pred             CCcEEEEEEEEEeecc
Q 021027          102 DGTPFWMLFKMSLVFG  117 (318)
Q Consensus       102 ~g~~~~~~~~~~~i~~  117 (318)
                      ||..+|+..++.++.+
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

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

Probab=99.31  E-value=6.6e-12  Score=108.29  Aligned_cols=108  Identities=8%  Similarity=0.019  Sum_probs=88.8

Q ss_pred             CCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCC-eEEEEEEEecCCcEE
Q 021027           28 PDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERP-IEVNLLNYKKDGTPF  106 (318)
Q Consensus        28 ~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~g~~~  106 (318)
                      ...++..+.+   |.++|+|+++..++||++++++|+++..++||++.......+...+..+.. ...++++++++|..+
T Consensus       278 ~~fi~~~~~d---g~~~~vn~~~~~ilGY~~eEl~g~~~~~~iHpdD~~~~~~~~~~~l~~~~~~~~~eyR~~~kdG~~v  354 (387)
T 4f3l_B          278 MEYVSRHAID---GKFVFVDQRATAILAYLPQELLGTSCYEYFHQDDIGHLAECHRQVLQTREKITTNCYKFKIKDGSFI  354 (387)
T ss_dssp             CEEEEEECTT---SBEEEECTHHHHHHCCCHHHHTTSBGGGTBCHHHHHHHHHHHHHHTTCSSCEECCCEEEECTTSCEE
T ss_pred             ceEEEEECCC---CEEEEECCCcccccCCCHHHHcCCcHHHeeCHHHHHHHHHHHHHHHhcCCCeeeEEEEEEccCCCEE
Confidence            3456667888   999999999999999999999999988899998877777777676655544 456888999999999


Q ss_pred             EEEEEEEeeccCCCCceeEEEEEEeccccccc
Q 021027          107 WMLFKMSLVFGKEDGRATHFVAVQVPIVSRKH  138 (318)
Q Consensus       107 ~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~  138 (318)
                      |+.....++.++.+|.+.+++++.+|||++|+
T Consensus       355 Wv~~~~~~~~~~~~g~~~~ivg~~~dIT~Rk~  386 (387)
T 4f3l_B          355 TLRSRWFSFMNPWTKEVEYIVSTNTVVLANVL  386 (387)
T ss_dssp             EEEEEEEEEEETTTTEEEEEEEEEEECC----
T ss_pred             EEEEEEEEEECCCCCCEEEEEEEEEEcchhhc
Confidence            99999999998237899999999999999985

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

Probab=99.31  E-value=3.1e-11  Score=100.17  Aligned_cols=58  Identities=12%  Similarity=0.060  Sum_probs=49.8

Q ss_pred             cEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhccc
Q 021027          253 SFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQ  313 (318)
Q Consensus       253 ~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~~  313 (318)
                      .+...+.+|   .++|+|+++..++||+++|++|+++.+++||++.....+...+.++.+.
T Consensus       167 Fitrh~~dG---~~~yvd~~~~~lLGY~peELig~s~~~~iHpdD~~~~~~~~~~~l~~~g  224 (309)
T 3gdi_A          167 FTTTHTPNC---LFQAVDERAVPLLGYLPQDLIETPVLVQLHPSDRPLMLAIHKKILQAGG  224 (309)
T ss_dssp             EEEEECTTC---BEEEECTTHHHHHSCCHHHHTTSBHHHHBCTTSHHHHHHHHHHHHHTTT
T ss_pred             EEEEecCCC---eEEEECcccccccCcCHHHHcCCCHHHhCCHHHHHHHHHHHHHHHhcCC
Confidence            344455555   9999999999999999999999999999999999888888888887543

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

Probab=99.30  E-value=1.7e-11  Score=102.08  Aligned_cols=57  Identities=14%  Similarity=0.095  Sum_probs=49.7

Q ss_pred             CcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhc
Q 021027          252 QSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQT  311 (318)
Q Consensus       252 ~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~  311 (318)
                      ..+...+.+|   .++|||+++..++||+++|++|+++.+++||++.+.+.+...+.++.
T Consensus       177 ~Fitrh~~dG---~~~yvd~~~~~lLGY~peELig~s~~~~vHPdD~~~~~~~~~~~l~~  233 (320)
T 4dj2_A          177 IFTTRHTPSC---LFQDVDERAAPLLGYLPQDLLGAPVLLFLHPEDRPLMLAIHKKILQL  233 (320)
T ss_dssp             EEEEEECTTC---BEEEECTTHHHHHSCCHHHHTTSBGGGGBCGGGHHHHHHHHHHHTTS
T ss_pred             eEEEEecCCc---eEEEcCcceeccCCcChHHHcCCcHHHhCCHHHHHHHHHHHHHHHhc
Confidence            3445556565   99999999999999999999999999999999999888888888874

>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=99.29  E-value=6e-12  Score=91.49  Aligned_cols=72  Identities=36%  Similarity=0.763  Sum_probs=61.4

Q ss_pred             HHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhccccee
Q 021027          245 ISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQACT  316 (318)
Q Consensus       245 ~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~~~~~  316 (318)
                      .++++++++|+++|.+|++++|+|||++|++++||+++|++|+++..+.++.........+..++..+.++.
T Consensus         3 ~~~~~~~~~i~~~d~~g~~~~i~~~N~a~~~~~G~~~~el~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~   74 (132)
T 2pr5_A            3 HMLDHVRVGVVITDPALEDNPIVYVNQGFVQMTGYETEEILGKNCRFLQGKHTDPAEVDNIRTALQNKEPVT   74 (132)
T ss_dssp             ---CCCCCEEEEECTTSTTCCEEEECHHHHHHHSCCHHHHTTSCGGGGCCTTCCHHHHHHHHHHHHHTCCEE
T ss_pred             hHHhcCCCcEEEEeCCCCCCcEEEECHHHHHHhCcCHHHHcCCChhhhCCCCCCHHHHHHHHHHHHcCCCeE
Confidence            467889999999999866679999999999999999999999999988888888888888888888777653

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

Probab=99.23  E-value=1.2e-10  Score=82.13  Aligned_cols=106  Identities=12%  Similarity=0.122  Sum_probs=80.5

Q ss_pred             HHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCe-EEEEEE
Q 021027           20 VHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPI-EVNLLN   98 (318)
Q Consensus        20 ~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~   98 (318)
                      ...++++++++++++|.+   |+++++|+++++++|++.++++|+++..++++...  ....+...+..+... ..+...
T Consensus         9 ~~~il~~~~~~i~~~D~~---g~I~~~N~aa~~l~g~~~~~~~g~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~   83 (115)
T 3b33_A            9 PSAILNNMVTATLILDDG---LAIRYANPAAELLFSQSAKRIVEQSLSQLIQHASL--DLALLTQPLQSGQSITDSDVTF   83 (115)
T ss_dssp             HHHHHHHCSSEEEEECTT---CBEEEECHHHHHHTTSCHHHHTTCBHHHHCSEEEC--CTHHHHHHHHHCCCEEEEEEEE
T ss_pred             HHHHHhhcCceEEEECCC---CcEEEECHHHHHHhCCCHHHHhCCCHHHHhCccch--hhHHHHHHHHcCCcccCCceEE
Confidence            456999999999999999   99999999999999999999999987666543221  123344455556553 345544


Q ss_pred             EecCCcEEEEEEEEEeeccCCCCceeEEEEEEeccc
Q 021027           99 YKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV  134 (318)
Q Consensus        99 ~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIt  134 (318)
                      . ++|..+|+.++..|+.+  +|. .+++.+++||+
T Consensus        84 ~-~~g~~~~~~~~~~pi~~--~g~-~~~l~~~~Di~  115 (115)
T 3b33_A           84 V-VDGRPLMLEVTVSPITW--QRQ-LMLLVEMRKID  115 (115)
T ss_dssp             E-ETTEEEEEEEEEEEEEE--TTE-EEEEEEEEEC-
T ss_pred             e-cCCCEEEEEEEEEEeec--CCc-eEEEEEEEeCC
Confidence            4 68988999999999975  454 58889999985

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

Probab=99.20  E-value=2.6e-11  Score=86.19  Aligned_cols=74  Identities=14%  Similarity=0.112  Sum_probs=57.2

Q ss_pred             ccchhHHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhcccce
Q 021027          238 FISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQAC  315 (318)
Q Consensus       238 ~~~~~l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~~~~  315 (318)
                      ..+..++.++++++++|+++|.+|   +|++||+++++|+||+++|++|+++..+.++... .........+..+.++
T Consensus         8 ~se~~~~~l~e~~~d~i~~~d~~g---~i~~vN~a~~~l~Gy~~~el~g~~~~~~~~~~~~-~~~~~~~~~~~~~~~~   81 (117)
T 2r78_A            8 FQSNAYRALFEHAIDGIFIMDAEG---HYLDVNPAICSAIGYTRDEFLALDWGVLSRGVDS-GWAAASLARIVGGEPL   81 (117)
T ss_dssp             HHHHHHHHHHHHCSSEEEEECTTS---BEEEECHHHHHHHCCCHHHHTTCBTTTTTTCSTT-SHHHHHHHHHHTTCCE
T ss_pred             HhHHHHHHHHhcCCceEEEECCCC---CEEEecHHHHHHHCcCHHHHcCCCHHHhCCccch-hHHHHHHHHHHcCCcE
Confidence            345668899999999999999987   9999999999999999999999998877544332 2333444555555443

>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=99.17  E-value=2.3e-11  Score=88.08  Aligned_cols=68  Identities=22%  Similarity=0.207  Sum_probs=55.4

Q ss_pred             hhHHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhc
Q 021027          241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQT  311 (318)
Q Consensus       241 ~~l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~  311 (318)
                      ..++.++++++++|+++|.+|   +|++||+++++|+||+++|++|+++..+.++.........+...+..
T Consensus        16 ~~~~~l~~~~~d~i~~~d~~g---~i~~~N~a~~~l~Gy~~~eliG~~~~~l~~~~~~~~~~~~~~~~~~~   83 (130)
T 1d06_A           16 AHLRSILDTVPDATVVSATDG---TIVSFNAAAVRQFGYAEEEVIGQNLRILMPEPYRHEHDGYLQRYMAT   83 (130)
T ss_dssp             SCHHHHHTTCSSEEEEEETTS---BEEEECHHHHHHHCCCHHHHTTSBGGGGSCTTHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhCcCeEEEECCCC---eEEEEcHHHHHHHCCCHHHHcCCcHHHHCCchhHHHHHHHHHHHHhc
Confidence            347789999999999999987   99999999999999999999999999988666544444444444433

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

Probab=99.15  E-value=3.6e-10  Score=96.79  Aligned_cols=115  Identities=18%  Similarity=0.282  Sum_probs=92.2

Q ss_pred             hHHHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEEE
Q 021027           16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVN   95 (318)
Q Consensus        16 ~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~   95 (318)
                      ....+.+++++++++|+++|.+   |+|+++|++ ++++ ++.++++|+++..++++. .......+...+..+.....+
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            4467889999999999999999   999999999 9999 889999999988776543 233344556667777665544


Q ss_pred             EEEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEeccccccccc
Q 021027           96 LLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMR  140 (318)
Q Consensus        96 ~~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~~~  140 (318)
                      ... ..+|  .++.++..|+++ .+|.+.|++.+++|||+.++.+
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            433 3455  478899999998 8999999999999999998873

>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=99.12  E-value=6.8e-11  Score=84.36  Aligned_cols=65  Identities=8%  Similarity=0.116  Sum_probs=58.1

Q ss_pred             HHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhc
Q 021027          244 YISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQT  311 (318)
Q Consensus       244 ~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~  311 (318)
                      ..+++++++.|++.|.+|   +|+|+|+++++++||+++|++|+++.++++|++.+.+.+.+.++++.
T Consensus         5 ~ll~e~~~d~i~~~d~~g---~i~~~n~~~~~~~G~~~~el~g~~~~~~i~p~d~~~~~~~~~~~~~~   69 (121)
T 3f1p_B            5 GLNVCQPTRFISRHNIEG---IFTFVDHRCVATVGYQPQELLGKNIVEFCHPEDQQLLRDSFQQVVKL   69 (121)
T ss_dssp             ---CCCCCEEEEEECTTS---BEEEECTTHHHHHSCCGGGTTTSBGGGGBCTTTHHHHHHHHHHHTTS
T ss_pred             cceecCCCceEEEECCCc---eEEEECcchhhhhCCChHHHcCCCHHHeECHHHHHHHHHHHHHHHhc
Confidence            357788999999999997   99999999999999999999999999999999999999999888853

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

Probab=99.11  E-value=1.4e-10  Score=88.60  Aligned_cols=76  Identities=28%  Similarity=0.579  Sum_probs=67.8

Q ss_pred             hhHHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhccccee
Q 021027          241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQACT  316 (318)
Q Consensus       241 ~~l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~~~~~  316 (318)
                      ..++.++++++++|+++|.+.++++|+++|++|++++||++++++|+++..+.++.+.+.....+..++..+.++.
T Consensus         7 ~~~~~~~~~~~~~i~~~d~~~~~g~i~~~N~a~~~~~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (176)
T 4hia_A            7 EKIRAVFDRSGVALTLVDMSLPEQPVVLANPPFLRMTGYTEGQILGFNCRFLQRGDENAQARADIRDALKLGRELQ   82 (176)
T ss_dssp             HHHHHHHHHCSSCCEEEETTSTTCCEEEECHHHHHHHTCCHHHHTTSCGGGGCCTTCCHHHHHHHHHHHHHTCCEE
T ss_pred             HHHHHHHhcCCCcEEEEecCCCCCcEEEECHHHHHHHCcCHHHHcCCCcceeeCCCCCHHHHHHHHHHHHcCCceE
Confidence            3477899999999999999833349999999999999999999999999999999999999999999999888764

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

Probab=99.10  E-value=2.6e-10  Score=92.96  Aligned_cols=78  Identities=29%  Similarity=0.514  Sum_probs=69.0

Q ss_pred             cchhHHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhccccee
Q 021027          239 ISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQACT  316 (318)
Q Consensus       239 ~~~~l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~~~~~  316 (318)
                      ....++.++++++++|+++|..+.+++|++||++|++++||+++|++|+++.++.+|.+.+.....+..++..+.+|.
T Consensus        61 ~~~~~~~i~~~~~~~i~~~d~~~~~g~i~~~N~a~~~l~G~~~~el~g~~~~~l~~~~~~~~~~~~~~~~l~~~~~~~  138 (258)
T 3p7n_A           61 PAQWVLDLIEASPIASVVSDPRLADNPLIAINQAFTDLTGYSEEECVGRNCRFLAGSGTEPWLTDKIRQGVREHKPVL  138 (258)
T ss_dssp             CCHHHHHHHHTCSSEEEEECTTSTTCCEEEECHHHHHHHCCCGGGTTTSCGGGGCCTTCCHHHHHHHHHHHHHTCCEE
T ss_pred             HHHHHHHHHhcCCccEEEEcCCCCCCcEEEEhHHHHHHcCCCHHHHCCCChhhccCCCCchhHHHHHHHHHHcCCCeE
Confidence            345588899999999999999332349999999999999999999999999999999999999999999999888764

>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=99.08  E-value=6e-11  Score=88.17  Aligned_cols=68  Identities=15%  Similarity=0.169  Sum_probs=61.1

Q ss_pred             HHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhcccc
Q 021027          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQA  314 (318)
Q Consensus       243 l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~~~  314 (318)
                      +..+++++++||+++|.+|   +|++||+++++++|+++++++|+++.+++++ ....+...++.++..|.+
T Consensus        24 l~~il~~~~~gi~v~D~~g---~I~~~N~a~~~~~G~~~~eviG~~~~~~~p~-~~~~~~~~l~~vl~~G~~   91 (152)
T 3mxq_A           24 LSELLDQLSFALCIVRNDY---VIVKVNEYFESRVIFDGETMQGKNILELFPE-SADYLKRKIDTALVIESS   91 (152)
T ss_dssp             HHHHHHHHCCEEEEEETTS---BEEEECHHHHHTSSSCHHHHTTSBHHHHSGG-GHHHHHHHHHHHHHHTSC
T ss_pred             HHHHHhcCCCCEEEEcCCC---EEEEECHHHHHHHCcCHHHHCCCCHHHhcCC-hHHHHHHHHHHHHhcCCc
Confidence            5678999999999999998   9999999999999999999999999999876 666667779999998775

>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=99.07  E-value=5.2e-11  Score=84.75  Aligned_cols=72  Identities=13%  Similarity=0.111  Sum_probs=63.6

Q ss_pred             hHHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhccccee
Q 021027          242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQACT  316 (318)
Q Consensus       242 ~l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~~~~~  316 (318)
                      ..+.++++++++|+++|.++   +|+++|+++++++||++++++|+++.+++++.....+...+.++++.++++.
T Consensus        13 ~~~~il~~~~~~i~~~D~~g---~i~~~N~a~~~l~g~~~~e~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   84 (118)
T 3fg8_A           13 GRENLYFQGGLGFMALDEDL---RIIYVNSGCLRHVRRSRDELLGRVVTEVLPETQGSYFDALCRKVLATGREQQ   84 (118)
T ss_dssp             CCCCSSSCTTCEEEEECTTC---BEEEECHHHHHHHTCCHHHHTTSBHHHHCGGGTTSHHHHHHHHHHHHCCCEE
T ss_pred             hHHHHHhhCCceEEEECCCC---eEEEECHHHHHHhCCCHHHHcCCcHHHHcCccchHHHHHHHHHHHHcCCceE
Confidence            35568899999999999987   9999999999999999999999999999877777777888889998887754

>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=99.06  E-value=4.1e-10  Score=78.84  Aligned_cols=71  Identities=44%  Similarity=0.837  Sum_probs=59.8

Q ss_pred             HHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhccccee
Q 021027          246 SLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQACT  316 (318)
Q Consensus       246 ~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~~~~~  316 (318)
                      ++++++++|+++|...++++|+++|+++++++||++++++|+++..+.++.........+..++..+.++.
T Consensus         2 ~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   72 (115)
T 4eet_B            2 SPEFIEKNFVITDPRLPDNPIIFASDGFLELTEYSREEILGRNARFLQGPETDQATVQKIRDAIRDQRETT   72 (115)
T ss_dssp             ---CCCCSEEEECTTSTTCCEEEECHHHHHHHCCCHHHHTTSCGGGGCCTTSCHHHHHHHHHHHHTTCCEE
T ss_pred             ccccCCCcEEEEcCCCCCCcEEEEcHHHHHHHCcCHHHHhCCCHHHhcCCCCChHHHHHHHHHHHcCCCcc
Confidence            46788999999999211239999999999999999999999999999988888888999999998887763

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

Probab=99.05  E-value=1.4e-09  Score=91.40  Aligned_cols=108  Identities=9%  Similarity=0.037  Sum_probs=91.3

Q ss_pred             CCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCC-----eEEEEEEEecC
Q 021027           28 PDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERP-----IEVNLLNYKKD  102 (318)
Q Consensus        28 ~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~  102 (318)
                      .+.++..+.+   |.++|+|+++..++||++++++|+++..++||++.......+...+..|..     ...++++++++
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            4567778888   999999999999999999999999999999999888777777777776654     34678889999


Q ss_pred             CcEEEEEEEEEeeccCCCCceeEEEEEEeccccccc
Q 021027          103 GTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKH  138 (318)
Q Consensus       103 g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~  138 (318)
                      |..+|+..+..+++++.++.+..+++..+.|+....
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            999999999999998345677788888888887654

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

Probab=99.05  E-value=4.8e-10  Score=84.38  Aligned_cols=81  Identities=40%  Similarity=0.684  Sum_probs=69.2

Q ss_pred             ccccchhHHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhcccce
Q 021027          236 MGFISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQAC  315 (318)
Q Consensus       236 ~~~~~~~l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~~~~  315 (318)
                      +......+..++++++++|+++|...++++|+++|++|++++||++++++|+++..+.++.........+..++..+.++
T Consensus        30 l~~~~~~~~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~  109 (166)
T 3ue6_A           30 LEDPDYSLVKALQMAQQNFVITDASLPDNPIVYASRGFLTLTGYSLDQILGRNCRFLQGPETDPRAVDKIRNAITKGVDT  109 (166)
T ss_dssp             -CCCCCHHHHHHHHTTSCEEEEETTSTTCCEEEECHHHHHHHCCCHHHHTTSCGGGGCCTTSCHHHHHHHHHHHHHTCCE
T ss_pred             HHHHHHHHHHHHhcCCceEEEEEccCCCCcEEEECHHHHHHhCcCHHHHcCCCHhheeCCCCCHHHHHHHHHHHhcCCce
Confidence            33445668899999999999999831224999999999999999999999999999998988899999999999888776


Q ss_pred             e
Q 021027          316 T  316 (318)
Q Consensus       316 ~  316 (318)
                      .
T Consensus       110 ~  110 (166)
T 3ue6_A          110 S  110 (166)
T ss_dssp             E
T ss_pred             E
Confidence            4

>3a0r_A Sensor protein; four helix bundle, PAS fold, kinase, phosphoprotein, transfe two-component regulatory system; 3.80A {Thermotoga maritima}

Probab=99.03  E-value=2.6e-10  Score=97.19  Aligned_cols=117  Identities=8%  Similarity=0.074  Sum_probs=86.0

Q ss_pred             hHHHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEEE
Q 021027           16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVN   95 (318)
Q Consensus        16 ~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~   95 (318)
                      ..++++.++++++++++++|.+   |+++++|+++++++||++++++|+++..+.++.   .........+..+.+....
T Consensus         6 ~~~~~~~i~~~~~~~i~~~d~~---g~i~~~N~a~~~l~G~~~~e~~G~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~   79 (349)
T 3a0r_A            6 LRNFSESILESLETAIITLSKD---GRITEWNKKAEQLFGLKKENVLGRRLKDLPDFE---EIGSVAESVFENKEPVFLN   79 (349)
T ss_dssp             ---CCCSSGGGSSSEEEEEESS---SBCSCBCHHHHHHHSCCSTTTTTCBSTTSTTTT---HHHHHHHHHHHHCCCCEEE
T ss_pred             HHHHHHHHHhhhcCeEEEECCC---CCEEeeHHHHHHHhCCCHHHHcCcCHHHCcChh---HHHHHHHHHHhcCCceeec
Confidence            3445678999999999999999   999999999999999999999999877763322   2333344455555554332


Q ss_pred             EEEEecCCcEEEEEEEEEeeccCCCCce-eEEEEEEecccccccccccc
Q 021027           96 LLNYKKDGTPFWMLFKMSLVFGKEDGRA-THFVAVQVPIVSRKHMRNSG  143 (318)
Q Consensus        96 ~~~~~~~g~~~~~~~~~~~i~~~~~g~~-~~~i~~~~DIte~k~~~~~~  143 (318)
                      .    ..+...|+.+...|+.+ ..+.. .+++++++|||++++++++.
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    12233478888999987 66654 68999999999999985544

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

Probab=99.02  E-value=1.1e-10  Score=84.51  Aligned_cols=57  Identities=9%  Similarity=0.151  Sum_probs=51.4

Q ss_pred             hhHHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHH
Q 021027          241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTT  300 (318)
Q Consensus       241 ~~l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~  300 (318)
                      ..+..++++++++|+++|.+|   +|+++|+++++|+||++++++|+++.+++++.....
T Consensus         7 ~~l~~i~~~~~d~i~~~D~~g---~I~~~N~aa~~l~G~~~~el~G~~~~~l~~~~~~~~   63 (129)
T 3mfx_A            7 ETIELFIQHLTEAMILVNANG---FIRSCNQRSAELLDCPQVSLKGQDWRNFLTEHHQAR   63 (129)
T ss_dssp             HHHHHHHTTCSSEEEEEETTS---BEEEECHHHHHHTTSCHHHHTTSBGGGGBCTTCCGG
T ss_pred             HHHHHHHhcCCceEEEECCCC---EEEeEhHHHHHHHCcCHHHHcCCcHHHHcChHhHHH
Confidence            347789999999999999997   999999999999999999999999999987776543

>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=99.01  E-value=2.2e-10  Score=81.12  Aligned_cols=63  Identities=14%  Similarity=0.180  Sum_probs=57.4

Q ss_pred             cCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhcccce
Q 021027          250 IKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQAC  315 (318)
Q Consensus       250 ~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~~~~  315 (318)
                      .++.|++.|.+|   +++|+|+++++++||+++|++|+++..+++|++.+.+.+.+.+++..+.++
T Consensus         8 ~~~~i~~~d~~g---~i~~~n~~~~~~~Gy~~~el~g~~~~~~~~p~d~~~~~~~~~~~~~~~~~~   70 (117)
T 3f1p_A            8 SKTFLSEHSMDM---KFTYCDDRITELIGYHPEELLGRSAYEFYHALDSENMTKSHQNLCTKGQVV   70 (117)
T ss_dssp             GGEEEEEECTTC---BEEEECTHHHHHHCCCHHHHTTSBGGGGBCGGGHHHHHHHHHHHHHHSEEE
T ss_pred             CccEEEEECCCc---eEEEECcChhhhhCCCHHHHcCCchhheECHHHHHHHHHHHHHHHhCCCee
Confidence            367888899887   999999999999999999999999999999999999999999998877765

>2w0n_A Sensor protein DCUS; signal transduction, two-component regulatory system, PAS, kinase, membrane, transferase, solid state cell inner membrane; NMR {Escherichia coli}

Probab=99.01  E-value=1.8e-10  Score=81.25  Aligned_cols=104  Identities=9%  Similarity=0.083  Sum_probs=78.7

Q ss_pred             hhHHHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCC---ChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCC
Q 021027           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGF---SRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERP   91 (318)
Q Consensus        15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~---~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~   91 (318)
                      .....++.++++++++++++|.+   |+++++|+++++++|+   +.++++|+++..+.++..       +...+..+..
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            45667889999999999999999   9999999999999997   788999998777665431       3344444443


Q ss_pred             eEEEEEEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEeccc
Q 021027           92 IEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV  134 (318)
Q Consensus        92 ~~~~~~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIt  134 (318)
                      .....  ...+|  .|+.+...|+.+  +|.+.+++++++|||
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            32111  12345  367788889876  677888999999997

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

Probab=99.01  E-value=4.2e-10  Score=79.28  Aligned_cols=103  Identities=16%  Similarity=0.154  Sum_probs=72.7

Q ss_pred             cCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHH-HHHh-cCCe---EEEEEEEe
Q 021027           26 ELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIRE-AIRE-ERPI---EVNLLNYK  100 (318)
Q Consensus        26 ~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~-~~~~-~~~~---~~~~~~~~  100 (318)
                      +.+++++++|.+  +|+|+++|+++++++||++++++|+++..++++..... ...+.. .... +...   ..+....+
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  38999999999999999999999999888877654332 222111 1111 1111   22455678


Q ss_pred             cCCcEEEEEEEEEeeccCCCCceeEEEEEEeccc
Q 021027          101 KDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV  134 (318)
Q Consensus       101 ~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIt  134 (318)
                      ++|..+|+.++..|+.+ ..+  .+++++++|++
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

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

Probab=99.01  E-value=3e-10  Score=80.83  Aligned_cols=67  Identities=15%  Similarity=0.148  Sum_probs=59.1

Q ss_pred             HHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhccc
Q 021027          244 YISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQ  313 (318)
Q Consensus       244 ~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~~  313 (318)
                      ..++++++++|+++|.+|   +|+|+|+++++++||+++|++|+++.++++|++.....+.+.+++..+.
T Consensus         6 ~~~~~~~~~~i~~~d~~g---~i~~~N~~~~~~~G~~~~el~g~~~~~~~~p~d~~~~~~~~~~~~~~~~   72 (121)
T 2kdk_A            6 GEINVKPTEFITRFAVNG---KFVYVDQRATAILGYLPQELLGTSCYEYFHQDDHNNLTDKHKAVLQSKE   72 (121)
T ss_dssp             TCCCCCSSEEEEEECTTS---BEEEECTHHHHHTCCCTTTSBTSBTTTTBCSSSHHHHHHHHHHHHTSSS
T ss_pred             cccccCCccEEEEECCCe---eEEEEChhHHHHHCCCHHHHcCCcHHHeeCHHHHHHHHHHHHHHHhCCC
Confidence            346778899999999987   9999999999999999999999999999999988888888888777544

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

Probab=99.01  E-value=1.7e-10  Score=81.06  Aligned_cols=58  Identities=14%  Similarity=0.134  Sum_probs=47.6

Q ss_pred             HHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHH
Q 021027          245 ISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQI  305 (318)
Q Consensus       245 ~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~  305 (318)
                      .++++++++|+++|.+|   +|+|+|+++++++||+++|++|+++.++++|++.+.+.+.+
T Consensus         3 ~lle~~~d~i~v~d~~G---~i~yvn~~~~~~lGy~~~el~G~~~~~~ihp~D~~~~~~~~   60 (111)
T 2vlg_A            3 FPLQTKTDIHAVLASNG---RIIYISANSKLHLGYLQGEMIGSFLKTFLHEEDQFLVESYF   60 (111)
T ss_dssp             ------CCEEEEECTTS---BEEEECTTHHHHHSCCHHHHTTSBGGGGBCGGGHHHHHHHH
T ss_pred             chhhcCCCEEEEEcCCC---eEEEEChHHHHHhCCCHHHHcCCcHHHeECHhHHHHHHHHH
Confidence            36788899999999887   99999999999999999999999999999999877765544

>3a0s_A Sensor protein; PAS-fold, kinase, phosphoprotein, transferase, two-component regulatory system; HET: PG4 PGE; 1.47A {Thermotoga maritima} PDB: 3a0v_A*

Probab=99.01  E-value=8.7e-09  Score=69.01  Aligned_cols=95  Identities=9%  Similarity=0.110  Sum_probs=70.0

Q ss_pred             CCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEEEEEEEecCCcEE
Q 021027           27 LPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPF  106 (318)
Q Consensus        27 ~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~  106 (318)
                      ++++++++|.+   ++++++|+++++++|++.++++|+++..+  +. .......+...+..+......  ..  ++...
T Consensus         1 ~~~~i~~~d~~---g~i~~~N~~~~~l~g~~~~~~~g~~~~~~--~~-~~~~~~~~~~~~~~~~~~~~~--~~--~~~~~   70 (96)
T 3a0s_A            1 METAIITLSKD---GRITEWNKKAEQLFGLKKENVLGRRLKDL--PD-FEEIGSVAESVFENKEPVFLN--FY--KFGER   70 (96)
T ss_dssp             CCCEEEEEETT---SBEEEECHHHHHHHCCCHHHHTTSBGGGS--TT-CHHHHHHHHHHHHHTCCEEEE--EE--EETTE
T ss_pred             CCceEEEEcCC---CCEeehhHHHHHHhCCCHHHhcCCCHHHC--cc-hHHHHHHHHHHhccCCeEEEE--EE--cCCcE
Confidence            46899999999   99999999999999999999999987766  22 233344455556666555332  22  33446


Q ss_pred             EEEEEEEeeccCCCCc-eeEEEEEEec
Q 021027          107 WMLFKMSLVFGKEDGR-ATHFVAVQVP  132 (318)
Q Consensus       107 ~~~~~~~~i~~~~~g~-~~~~i~~~~D  132 (318)
                      |+.++..|+.+ .+|. +.+++++++|
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

>1mzu_A PPR; photoactive yellow protein, PAS, PYP, signaling protein; HET: HC4; 2.00A {Rhodospirillum centenum} SCOP: d.110.3.1

Probab=99.00  E-value=7.9e-09  Score=73.01  Aligned_cols=100  Identities=15%  Similarity=0.081  Sum_probs=75.4

Q ss_pred             HHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCc-ccCCCCChHHHHHHHHHHHhcCCeEEEEEE-
Q 021027           21 HEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRM-FQGPRTNRRTIMEIREAIREERPIEVNLLN-   98 (318)
Q Consensus        21 ~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~-l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-   98 (318)
                      ..++++++.|++++|.+   ++|++||.+++++.|+++++++|+++.. +.+......+...+...+..+. ......+ 
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   9999999999999999999999999765 4444566667778888888666 4444433 


Q ss_pred             EecCCcEEEEEEEEEeeccCCCCceeEEE
Q 021027           99 YKKDGTPFWMLFKMSLVFGKEDGRATHFV  127 (318)
Q Consensus        99 ~~~~g~~~~~~~~~~~i~~~~~g~~~~~i  127 (318)
                      .+.+|.+..+.++..  .. .++...+++
T Consensus       101 ~~~~~~p~~v~i~l~--~~-~~~~~~~i~  126 (129)
T 1mzu_A          101 FDFQMAPVRVQIRMQ--NA-GVPDRYWIF  126 (129)
T ss_dssp             EECSSCEEEEEEEEE--EC-SSTTEEEEE
T ss_pred             EcCCCCEEEEEEEEE--Ec-CCCCEEEEE
Confidence            478888666555544  44 566655543

>2jhe_A Transcription regulator TYRR; aromatic hydrocarbons catabolism, TYRR protei nucleotide-binding, transcription regulation, activator; HET: PG4; 2.30A {Escherichia coli}

Probab=98.99  E-value=1.1e-09  Score=84.74  Aligned_cols=108  Identities=14%  Similarity=0.140  Sum_probs=79.7

Q ss_pred             hhHHHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcC-C-e
Q 021027           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREER-P-I   92 (318)
Q Consensus        15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~-~-~   92 (318)
                      +....++.++++++++++++|.+   |+++++|+++++++|++.++++|+++..+.++...       ...+..+. . .
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   99999999999999999999999988777655321       12333333 2 2


Q ss_pred             EEEEEEEecCCcEEEEEEEEEeeccCCCCc----eeEEEEEEeccccccc
Q 021027           93 EVNLLNYKKDGTPFWMLFKMSLVFGKEDGR----ATHFVAVQVPIVSRKH  138 (318)
Q Consensus        93 ~~~~~~~~~~g~~~~~~~~~~~i~~~~~g~----~~~~i~~~~DIte~k~  138 (318)
                      ..+..   .+|.  ++.+...|+.+ .++.    +.|++.+++|||++++
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  45677889876 4555    6788888999999864

>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=98.99  E-value=1.4e-08  Score=71.59  Aligned_cols=100  Identities=14%  Similarity=0.084  Sum_probs=76.1

Q ss_pred             HHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCc-ccCCCCChHHHHHHHHHHHhcCCeEEEEEE-
Q 021027           21 HEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRM-FQGPRTNRRTIMEIREAIREERPIEVNLLN-   98 (318)
Q Consensus        21 ~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~-l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-   98 (318)
                      ..++++++.|++++|.+   ++|+++|.+++++.|+++++++|+++.. +.+......+...+...+..+. ......+ 
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   9999999999999999999999999765 4444566677777888888666 4444433 


Q ss_pred             EecCCcEEEEEEEEEeeccCCCCceeEEE
Q 021027           99 YKKDGTPFWMLFKMSLVFGKEDGRATHFV  127 (318)
Q Consensus        99 ~~~~g~~~~~~~~~~~i~~~~~g~~~~~i  127 (318)
                      .+.+|.+..+.++..  .. .+|...+++
T Consensus        96 ~~~~~~p~~v~i~l~--~~-~~~~~~~i~  121 (125)
T 1nwz_A           96 FDYQMTPTKVKVHMK--KA-LSGDSYWVF  121 (125)
T ss_dssp             ECTTSCCEEEEEEEE--EC-SSSSEEEEE
T ss_pred             EcCCCCEEEEEEEEE--Ec-CCCCEEEEE
Confidence            488888666555554  44 566655543

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

Probab=98.98  E-value=1.3e-09  Score=76.13  Aligned_cols=68  Identities=7%  Similarity=0.091  Sum_probs=58.7

Q ss_pred             chhHHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhc
Q 021027          240 SSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQT  311 (318)
Q Consensus       240 ~~~l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~  311 (318)
                      +..++.++++++++|+++|.++   +|+++|+++++++||++++++|+++.+++ |++.......+..++..
T Consensus         2 e~~~~~~~~~~~~~i~~~d~~g---~i~~~N~~~~~~~g~~~~~~~g~~~~~~~-~~~~~~~~~~~~~~~~~   69 (114)
T 3luq_A            2 DERLRLFTEHAPAALAMFDREM---RYLAVSRRWREDYGLGDGDILGMSHYDIF-PEIGEEWKSVHRRGLAG   69 (114)
T ss_dssp             CHHHHHHHHTCSSEEEEEETTC---BEEEECHHHHHHTTCCSSCCTTCBHHHHC-TTCCHHHHHHHHHHHTT
T ss_pred             hHHHHHHHhcCCceEEEEcCCc---EEEEECHHHHHHHCCCHHHHcCCcHHHHC-CccHHHHHHHHHHHhcC
Confidence            3468889999999999999887   99999999999999999999999999987 77777666666666653

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

Probab=98.98  E-value=9.7e-10  Score=78.80  Aligned_cols=71  Identities=44%  Similarity=0.780  Sum_probs=62.1

Q ss_pred             HHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhccccee
Q 021027          246 SLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQACT  316 (318)
Q Consensus       246 ~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~~~~~  316 (318)
                      ++++++++|+++|..+++++|+++|+++++++||+.++++|+++..+.++.........+..++..+.++.
T Consensus         2 ~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~g~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   72 (128)
T 3t50_A            2 ASEFTLMPMLITNPHLPDNPIVFANPAFLKLTGYEADEVMGRNCRFLQGHGTDPAHVRAIKSAIAAEKPID   72 (128)
T ss_dssp             CCCCCSSCEEEECTTSTTCCEEEECHHHHHHHCCCHHHHTTSCGGGGCCTTSCHHHHHHHHHHHHTTCCEE
T ss_pred             ccccCcccEEEecCCCCCCcEEEEcHHHHHHhCcCHHHHcCCCHhhhcCCccCHHHHHHHHHHHHcCCCce
Confidence            46788999999999322349999999999999999999999999999988888999999999998887663

>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=98.96  E-value=6.3e-10  Score=79.01  Aligned_cols=58  Identities=24%  Similarity=0.230  Sum_probs=46.6

Q ss_pred             cCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHh
Q 021027          250 IKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQ  310 (318)
Q Consensus       250 ~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~  310 (318)
                      ++++|+++|.+|   +|++||+++++|+||+++|++|+++..+.++.........+.....
T Consensus         2 ~~d~i~~~d~~g---~i~~~N~a~~~l~G~~~~el~G~~~~~l~~~~~~~~~~~~~~~~~~   59 (119)
T 2vv6_A            2 IPDAMIVIDGHG---IIQLFSTAAERLFGWSELEAIGQNVNILMPEPDRSRHDSYISRYRT   59 (119)
T ss_dssp             CCCEEEEEETTS---BEEEECHHHHHHHCCCHHHHTTSBGGGGSCTTHHHHHHHHHHHHHH
T ss_pred             CcceEEEECCCC---eEEEEhHHHHHHhCCCHHHHcCCCHHHhCCchHHHHHHHHHHHHhc
Confidence            589999999997   9999999999999999999999999988766554433334444433

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

Probab=98.95  E-value=4.7e-10  Score=79.79  Aligned_cols=70  Identities=10%  Similarity=0.134  Sum_probs=55.7

Q ss_pred             hHHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCC-HHHHHHHHHHHhcccce
Q 021027          242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTD-TTVLYQIKESIQTEQAC  315 (318)
Q Consensus       242 ~l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~-~~~~~~~~~~l~~~~~~  315 (318)
                      .++.++++++++|++ +.++   +|++||++|++|+||++++++|+++..+.++... ......+...+..+.++
T Consensus         4 ~~~~~~~~~~~~i~~-~~~g---~i~~~N~a~~~l~G~~~~el~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   74 (120)
T 3mqq_A            4 DYKTAFHLAPIGLVL-SRDR---VIEDCNDELAAIFRCARADLIGRSFEVLYPSSDEFERIGERISPVMIAHGSY   74 (120)
T ss_dssp             CHHHHHHHCSSEEEE-EETT---EEEEECHHHHHHTTSCHHHHTTCBGGGGSSSHHHHHHHHHHHHHHHHHHSCE
T ss_pred             hHHHHHhcCCceEEE-ecCC---EEHHHHHHHHHHhCcCHHHhCCCchhhccCChhhHHHHHHHHHHHHhcCCcc
Confidence            377899999999975 5565   9999999999999999999999999888754332 45556666777766655

>3bwl_A Sensor protein; structural genomics, APC87707.1, PAS domain, HTR-like protei protein structure initiative; HET: MSE I3A; 1.73A {Haloarcula marismortui atcc 43049}

Probab=98.91  E-value=1.4e-09  Score=77.83  Aligned_cols=50  Identities=18%  Similarity=0.062  Sum_probs=44.2

Q ss_pred             hHHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccc--cCCCcccccC
Q 021027          242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEV--VGQNCRFLNG  294 (318)
Q Consensus       242 ~l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el--~G~~~~~l~~  294 (318)
                      .++.++++++++|+++|.+|   +|++||+++++++||+++|+  +|+++..+.+
T Consensus        18 ~~~~l~e~~~~~i~~~d~~g---~i~~~N~a~~~~~G~~~~el~g~g~~~~~~~~   69 (126)
T 3bwl_A           18 RLEALFENSPDMIDVLDADG---TICEVNQRFCAELGYDESEVLGRSIWEFDLMF   69 (126)
T ss_dssp             HHHHHHHHCSSEEEEECTTC---BEEEECHHHHHHHTCCGGGTTTSBGGGTBTTC
T ss_pred             HHHHHHhhCCcEEEEEcCCC---CEEEEcHHHHHHhCCCHHHHhhCCCchhhccC
Confidence            36778999999999999987   99999999999999999999  5677777764

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

Probab=98.90  E-value=2.1e-08  Score=83.43  Aligned_cols=106  Identities=8%  Similarity=0.037  Sum_probs=86.4

Q ss_pred             CeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCC---eEEEEEEEecCCcE
Q 021027           29 DSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERP---IEVNLLNYKKDGTP  105 (318)
Q Consensus        29 ~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~g~~  105 (318)
                      ..+...+.+   |+++|+|+++..++||.+++++|+++..++||++.......+...+..+..   ...+++++++||..
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            455667778   999999999999999999999999999999999988887777787776554   34678889999999


Q ss_pred             EEEEEEEEeeccCCCCceeEEEEEEecccccc
Q 021027          106 FWMLFKMSLVFGKEDGRATHFVAVQVPIVSRK  137 (318)
Q Consensus       106 ~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k  137 (318)
                      +|+.....++.++.++.+..+++...-++...
T Consensus       252 vwvet~~~~~~np~s~~~e~II~~h~v~~~p~  283 (317)
T 4dj3_A          252 VILDSSWSSFVNPWSRKVSFIIGRHKVRTSPL  283 (317)
T ss_dssp             EEEEEEEEEEECSSSCCEEEEEEEEEECCCCS
T ss_pred             EEEEEEEEEEECCCCCcccEEEEEEEeccCCC
Confidence            99999999998734566667777666555443

>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=98.89  E-value=8.6e-10  Score=78.65  Aligned_cols=71  Identities=11%  Similarity=0.121  Sum_probs=49.1

Q ss_pred             chhHHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhccc
Q 021027          240 SSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQ  313 (318)
Q Consensus       240 ~~~l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~~  313 (318)
                      +..++.++++++++|+++|.+|   +|+++|+++++++||++++++|+++.++.++................+.
T Consensus        18 ~~~~~~i~~~~~~~i~~~d~~g---~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~   88 (125)
T 3fc7_A           18 RKKFESLVSDSPDGIVHLTTNG---TILSVNPSMAGRLGADPDTLVGQQLSAVMDSEAANQRLEAGKSAVENGT   88 (125)
T ss_dssp             --------CCSCCEEEEEETTS---BEEEECHHHHHHHTSCHHHHTTSBGGGSSCHHHHHHHHHHHHHHHHHTS
T ss_pred             HHHHHHHHhcCCCeEEEEcCCC---eEEEECHHHHHHhCCCHHHHcCccHHHhCCHHHHHHHHHHHHHHhcCCC
Confidence            4457889999999999999997   9999999999999999999999999998833222222222344554443

>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=98.88  E-value=2.2e-09  Score=75.79  Aligned_cols=66  Identities=17%  Similarity=0.138  Sum_probs=57.4

Q ss_pred             HHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccc-cCCCCCHHHHHHHHHHHhccc
Q 021027          245 ISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFL-NGVDTDTTVLYQIKESIQTEQ  313 (318)
Q Consensus       245 ~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l-~~~~~~~~~~~~~~~~l~~~~  313 (318)
                      .++++++.|+++.|.++   +|++||+++++++||++++++|+++.+. .+....+.+...+.+.+++|.
T Consensus        21 ~~ld~l~~Gii~lD~~g---~I~~~N~~~e~~sG~~~~eviGk~~f~~~~~~~~~~~f~~rf~~~~~~g~   87 (125)
T 1nwz_A           21 GQLDGLAFGAIQLDGDG---NILQYNAAEGDITGRDPKQVIGKNFFKDVAPCTDSPEFYGKFKEGVASGN   87 (125)
T ss_dssp             HHHTTCSSEEEEEETTC---BEEEECHHHHHHHCCCHHHHTTSBCCCCCCGGGCSTTTHHHHHHHHHHTC
T ss_pred             HHHhccCceEEEECCCC---EEEEEHHHHHHHhCCCHHHHcCCchhhhccchhcccHHHHHHHHHHhcCc
Confidence            46899999999999997   9999999999999999999999999764 444577788888888888665

>1mzu_A PPR; photoactive yellow protein, PAS, PYP, signaling protein; HET: HC4; 2.00A {Rhodospirillum centenum} SCOP: d.110.3.1

Probab=98.86  E-value=2.4e-09  Score=75.67  Aligned_cols=65  Identities=9%  Similarity=0.054  Sum_probs=57.1

Q ss_pred             HHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccc-cCCCCCHHHHHHHHHHHhccc
Q 021027          246 SLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFL-NGVDTDTTVLYQIKESIQTEQ  313 (318)
Q Consensus       246 ~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l-~~~~~~~~~~~~~~~~l~~~~  313 (318)
                      ++++++.||++.|.++   +|++||+++++++||++++++|+++... .+....+.+...+.+.+++|.
T Consensus        27 ~ld~l~~GiivlD~dg---~I~~~N~~~e~isG~s~eeviGk~~f~~~~p~~~~~~f~grf~~~~~~G~   92 (129)
T 1mzu_A           27 EFDALPVGAIQVDGSG---VIHRYNRTESRLSGRIPERVIGRNFFTEVAPCTNIPAFSGRFMDGVTSGT   92 (129)
T ss_dssp             TGGGCSSEEEEEETTC---BEEEECHHHHHHHCCCHHHHTTSBCCCCCCGGGCSTTTHHHHHHHHHTSC
T ss_pred             HHhccCceEEEECCCC---eEEEEHHHHHHHhCCCHHHHcCCchhhhccchhcccHHHHHHHHHHhcCc
Confidence            6889999999999997   9999999999999999999999999764 444577888888888888665

>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=98.86  E-value=4.1e-09  Score=89.11  Aligned_cols=73  Identities=44%  Similarity=0.861  Sum_probs=63.8

Q ss_pred             HHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhccccee
Q 021027          244 YISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQACT  316 (318)
Q Consensus       244 ~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~~~~~  316 (318)
                      ..++++++++|+++|...++|+|++||++|++++||+++|++|+++.++.+|.+.....+.+.+++..+.++.
T Consensus        14 ~~~~~~~~~~i~~~D~~~~~g~i~~~N~a~~~l~G~~~~el~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~   86 (332)
T 2wkq_A           14 ATTLERIEKNFVITDPRLPDNPIIFASDSFLQLTEYSREEILGRNARFLQGPETDRATVRKIRDAIDNQTEVT   86 (332)
T ss_dssp             CCCGGGCCSEEEEECTTSTTCCEEEECHHHHHHHCCCHHHHTTSCGGGGCCTTCCHHHHHHHHHHHHTTCCEE
T ss_pred             HhHhhcCCCcEEEecCCCCCCCEEEeehHHHHHhCCCHHHHcCCCchhhcCCCCCHHHHHHHHHHHHcCCeeE
Confidence            3467889999999999222349999999999999999999999999999998999999999999999888764

>3olo_A Two-component sensor histidine kinase; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG, TRA; 2.09A {Nostoc SP}

Probab=98.85  E-value=2.3e-09  Score=75.48  Aligned_cols=50  Identities=14%  Similarity=0.238  Sum_probs=45.8

Q ss_pred             HHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCC
Q 021027          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGV  295 (318)
Q Consensus       243 l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~  295 (318)
                      ++.++++++++|+++|.+|   +|+++|+++++++||++++++|+++.++.++
T Consensus        15 ~~~~~~~~~~~i~~~d~~g---~i~~~N~~~~~l~G~~~~el~g~~~~~~~~~   64 (118)
T 3olo_A           15 AHYLINNAVEASFCLGDNW---QFLYVNDATCRMTEYSREQLLSMNLQDIDVD   64 (118)
T ss_dssp             HHHHHHHCSSEEEEECTTS---BEEEECHHHHHHHCCCHHHHTTCBGGGTBTT
T ss_pred             HHHHHhcCCceEEEECCCC---cEEEEHHHHHHHHCCCHHHHhCCChhhcccc
Confidence            5668899999999999887   9999999999999999999999999988744

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

Probab=98.85  E-value=5.9e-09  Score=73.37  Aligned_cols=73  Identities=12%  Similarity=0.185  Sum_probs=63.8

Q ss_pred             hhHHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhccccee
Q 021027          241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQACT  316 (318)
Q Consensus       241 ~~l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~~~~~  316 (318)
                      ..+..++++++++++++|.++   .|+++|+++++++|++.++++|+++..+.++.........+..++..+.++.
T Consensus         7 ~~~~~~~~~~~~~i~~~d~~~---~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   79 (124)
T 3lyx_A            7 KQRAKAFDYVFDAIVVTDLQG---FIIDWNKGSETLYGYSKEQAIGQPVNMLHVPGDTEHITSEVISAVENQGKWT   79 (124)
T ss_dssp             HHHHHGGGTCSSEEEEEETTC---BEEEECHHHHHHHCCCHHHHTTSBGGGGSCTTTHHHHHHHHHHHHHHTSCEE
T ss_pred             HHHHHHHhhcCceEEEECCCC---cEeehhhHHHHHhCCCHHHHcCCCHHHhcCcchhhHHHHHHHHHHHcCCccc
Confidence            457889999999999999987   9999999999999999999999999977777777777778888888877653

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

Probab=98.84  E-value=8.6e-09  Score=73.09  Aligned_cols=73  Identities=42%  Similarity=0.840  Sum_probs=64.3

Q ss_pred             chhHHHHHhccCCcEEEec---CCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhcccce
Q 021027          240 SSSLYISLGRIKQSFVLID---PHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQAC  315 (318)
Q Consensus       240 ~~~l~~~~~~~~~~i~i~d---~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~~~~  315 (318)
                      +..+..++++++++++++|   .++   .|+++|+++++++||+.++++|+++..+.++.........+..++..+.++
T Consensus         5 ~~~~~~~~~~~~~~i~~~d~~d~~~---~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (130)
T 2z6d_A            5 SQELKTALSTLQQTFVVSDATQPHC---PIVYASSGFFTMTGYSSKEIVGRNCRFLQGPDTDKNEVAKIRDCVKNGKSY   80 (130)
T ss_dssp             --CHHHHHHHTTCEEEEEETTSTTC---CEEEECHHHHHHHCCCHHHHTTSCGGGGCCTTSCHHHHHHHHHHHHTTCCE
T ss_pred             HHHHHHHHHhcccceeeeeccCCCC---cEEEecHHHHHHhCcCHHHHcCCChhhccCCCCCchHHHHHHHHHHcCCcc
Confidence            4457889999999999999   666   999999999999999999999999999998888888888888888877665

>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=98.81  E-value=3.6e-09  Score=79.01  Aligned_cols=70  Identities=16%  Similarity=0.150  Sum_probs=62.1

Q ss_pred             hhHHHHHhccCCcEEEec-CCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhcccce
Q 021027          241 SSLYISLGRIKQSFVLID-PHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQAC  315 (318)
Q Consensus       241 ~~l~~~~~~~~~~i~i~d-~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~~~~  315 (318)
                      ..++.++++++++|+++| .++   +|+++|+++++++||+  +++|+++.+++++.........+.+++++|+++
T Consensus        17 ~~~~~~~~~~~~~i~~~d~~~~---~i~~~N~~~~~~~g~~--~~~G~~~~~~~~~~~~~~~~~~~~~~~~~g~~~   87 (158)
T 3k3c_A           17 EDVRRIFEHIPAILVGLEGPDH---RFVAVNAAYRGFSPLL--DTVGQPAREVYPELEGQQIYEMLDRVYQTGEPQ   87 (158)
T ss_dssp             HHHHHHHHHCSSEEEEEETTTT---EEEEECHHHHHHCTTC--CSTTSBHHHHSGGGGGTTHHHHHHHHHHHCCCE
T ss_pred             HHHHHHHhcCCceEEEEECCCc---EeHHHHHHHHHHcCCc--hhcCCcHHHhCCchhHHHHHHHHHHHHHhCCcc
Confidence            458889999999999999 886   9999999999999999  999999999988777667788888898888764

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

Probab=98.80  E-value=4.8e-08  Score=81.01  Aligned_cols=105  Identities=8%  Similarity=0.030  Sum_probs=86.8

Q ss_pred             eEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCC-eE-EEEEEEecCCcEEE
Q 021027           30 SFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERP-IE-VNLLNYKKDGTPFW  107 (318)
Q Consensus        30 ~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~-~~-~~~~~~~~~g~~~~  107 (318)
                      .+...+.+   |+++|+|+++..++||.+++++|+++..++||++.......+.+.+..+.. .. ..+++++++|..+|
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            55667788   999999999999999999999999988899999887777777777775443 44 58899999999999


Q ss_pred             EEEEEEeeccCCCCceeEEEEEEecccccc
Q 021027          108 MLFKMSLVFGKEDGRATHFVAVQVPIVSRK  137 (318)
Q Consensus       108 ~~~~~~~i~~~~~g~~~~~i~~~~DIte~k  137 (318)
                      +.....++.++.++++..+++...-++...
T Consensus       244 vet~~~~~~np~s~~~e~ii~~h~v~~gp~  273 (309)
T 3gdi_A          244 LDTSWSSFINPWSRKISFIIGRHKVRVGPL  273 (309)
T ss_dssp             EEEEEEEEECTTTCCEEEEEEEEEEEECCS
T ss_pred             EEEEEEEEECCCCCcccEEEEEEEEccCCC
Confidence            999998888734677878888877776643

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

Probab=98.79  E-value=4.7e-09  Score=74.45  Aligned_cols=74  Identities=9%  Similarity=-0.030  Sum_probs=56.1

Q ss_pred             cchhHHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccC--CCcccccCCCCCHHHHHHHHHHHhcccce
Q 021027          239 ISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVG--QNCRFLNGVDTDTTVLYQIKESIQTEQAC  315 (318)
Q Consensus       239 ~~~~l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G--~~~~~l~~~~~~~~~~~~~~~~l~~~~~~  315 (318)
                      .+..++.++++++++++++|.++   .++++|+++++++||++++++|  ..+..+++|++.+.+...+..+++.+.++
T Consensus         5 ~~~~l~~~~~~~~~~i~~~d~~~---~~~~~n~~~~~~~G~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~   80 (125)
T 3nja_A            5 AEKLLHTAESDAGIGSWVLHMES---GRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDRPF   80 (125)
T ss_dssp             ------------CCEEEEEETTT---TEEEECHHHHHHHTCCTTTCCCBHHHHHHHBCTTTHHHHHHHHHHHHHSCCCE
T ss_pred             HHHHHHHHHHhCCeeEEEEEcCC---CcEEECHHHHHHhCCCcccccccHHHHHhhcChhHHHHHHHHHHHHHhcCCCc
Confidence            34567889999999999999997   9999999999999999999999  56677888999998889999998888765

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

Probab=98.79  E-value=1.3e-08  Score=74.62  Aligned_cols=77  Identities=17%  Similarity=0.250  Sum_probs=63.5

Q ss_pred             cccchhHHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCC--CcccccCCCCCHHHHHHHHHHHhcccc
Q 021027          237 GFISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQ--NCRFLNGVDTDTTVLYQIKESIQTEQA  314 (318)
Q Consensus       237 ~~~~~~l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~--~~~~l~~~~~~~~~~~~~~~~l~~~~~  314 (318)
                      ...+.+++.+++.++++++.+|..+   .++++|+++++++||+++++.+.  .+..+++|++.+.+...+..++..+.+
T Consensus         5 ~~se~rl~~~~~~~~~g~w~~d~~~---~~~~~s~~~~~~~G~~~~~~~~~~~~~~~~ihpdD~~~~~~~~~~~~~~~~~   81 (142)
T 3mr0_A            5 SASEERFQLAVSGASAGLWDWNPKT---GAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAALKAHLEHRDT   81 (142)
T ss_dssp             ----CCHHHHHHHTTCEEEEECTTT---CCEEECHHHHHHTTCCGGGSCSEEC---CCBCTTTHHHHHHHHHHHHHHCCC
T ss_pred             HHHHHHHHHHHHhCCcEEEEEEcCC---CeEEECHHHHHHhCCCccccCCCHHHHHhhcCHHHHHHHHHHHHHHHhCCCc
Confidence            4456679999999999999999987   89999999999999999999873  567789999999999999999988876


Q ss_pred             ee
Q 021027          315 CT  316 (318)
Q Consensus       315 ~~  316 (318)
                      +.
T Consensus        82 ~~   83 (142)
T 3mr0_A           82 YD   83 (142)
T ss_dssp             EE
T ss_pred             eE
Confidence            54

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

Probab=98.78  E-value=3.5e-08  Score=82.21  Aligned_cols=107  Identities=9%  Similarity=0.044  Sum_probs=86.9

Q ss_pred             CeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHh-cCCe-EEEEEEEecCCcEE
Q 021027           29 DSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIRE-ERPI-EVNLLNYKKDGTPF  106 (318)
Q Consensus        29 ~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~-~~~~-~~~~~~~~~~g~~~  106 (318)
                      ..+...+.+   |+++|+|+++..++||.++|++|+++..+++|++.......+...+.. +... ..++++++++|..+
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            345667788   999999999999999999999999999999999877766666666664 3344 35788899999999


Q ss_pred             EEEEEEEeeccCCCCceeEEEEEEeccccccc
Q 021027          107 WMLFKMSLVFGKEDGRATHFVAVQVPIVSRKH  138 (318)
Q Consensus       107 ~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~  138 (318)
                      |+.....++.++.++++..+++...-++....
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            99999988887346788888888877776543

>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=98.78  E-value=1.2e-08  Score=74.15  Aligned_cols=70  Identities=43%  Similarity=0.875  Sum_probs=63.4

Q ss_pred             HHHHHhccCCcEEEecC---CCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhcccce
Q 021027          243 LYISLGRIKQSFVLIDP---HLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQAC  315 (318)
Q Consensus       243 l~~~~~~~~~~i~i~d~---~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~~~~  315 (318)
                      +..++++++++++++|.   ++   .|+++|+++++++||+.++++|+++..+.++.........+..++..+.++
T Consensus         4 l~~~~~~~~~~i~~~d~~~~~~---~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   76 (146)
T 2v0u_A            4 LATTLERIEKNFVITDPRLPDN---PIIFASDSFLQLTEYSREEILGRNCRFLQGPETDRATVRKIRDAIDNQTEV   76 (146)
T ss_dssp             CCCTGGGSSSCEEEECTTSTTC---CEEEECHHHHHHHCCCHHHHTTSCGGGGCCTTSCHHHHHHHHHHHHTTCCE
T ss_pred             HHHHHhcCCCcEEEEcCCCCCc---eEEEEcHHHHHHHCcCHHHHcCCCHHHhcCCcCChHHHHHHHHHHhcCCCc
Confidence            55678999999999998   66   999999999999999999999999999998988888889999988887765

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

Probab=98.77  E-value=8.8e-09  Score=72.36  Aligned_cols=46  Identities=17%  Similarity=0.306  Sum_probs=41.6

Q ss_pred             cCCcEEEecCC-CCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCC
Q 021027          250 IKQSFVLIDPH-LPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTD  298 (318)
Q Consensus       250 ~~~~i~i~d~~-~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~  298 (318)
                      .+++|+++|.+ |   +|+++|+++++|+||+++|++|+++.+++++...
T Consensus         7 ~~~~i~~~d~~~g---~I~~~N~aa~~l~G~~~~el~g~~~~~l~~~~~~   53 (114)
T 1ll8_A            7 FNKAIFTVDAKTT---EILVANDKACGLLGYSSQDLIGQKLTQFFLRSDS   53 (114)
T ss_dssp             TTCEEEEEETTTC---BEEEECTTHHHHHTCCTTTTTTSBGGGGSSCTTT
T ss_pred             CCceEEEEECCCC---eEEEehHHHHHHhCCCHHHHcCCCHHHhcCcchh
Confidence            46799999988 7   9999999999999999999999999999877644

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

Probab=98.76  E-value=1.2e-08  Score=75.13  Aligned_cols=70  Identities=36%  Similarity=0.698  Sum_probs=56.1

Q ss_pred             HHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCC-----------CHHHHHHHHHHHhcccc
Q 021027          246 SLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDT-----------DTTVLYQIKESIQTEQA  314 (318)
Q Consensus       246 ~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~-----------~~~~~~~~~~~l~~~~~  314 (318)
                      ++++ +++|+++|...++++|+++|+++++++||+++|++|+++..+.++..           .......+..++..+.+
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            3444 48999998322224999999999999999999999999999887764           77778888888887776


Q ss_pred             ee
Q 021027          315 CT  316 (318)
Q Consensus       315 ~~  316 (318)
                      +.
T Consensus       110 ~~  111 (149)
T 3d72_A          110 VQ  111 (149)
T ss_dssp             EE
T ss_pred             eE
Confidence            53

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

Probab=98.75  E-value=3.9e-09  Score=75.17  Aligned_cols=67  Identities=16%  Similarity=0.188  Sum_probs=57.7

Q ss_pred             HHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhccc
Q 021027          244 YISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQ  313 (318)
Q Consensus       244 ~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~~  313 (318)
                      +.++++++++|+++|.+|   +|+++|+++++++||+.++++|+++.++.++.+.......+...+..+.
T Consensus         2 ~~l~~~~~~~i~~~d~~g---~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~   68 (126)
T 3mjq_A            2 KNFLETIEDMILIINREG---RLLYANTAVPKKLGYTHEELMSMHILTITSAGKMAEGEKILAELFAGKK   68 (126)
T ss_dssp             CTTGGGCSSEEEEEETTS---BEEEECTHHHHHHSCCHHHHHHSBHHHHHCTTCHHHHHHHHHHHHHTCC
T ss_pred             hhHHhhCCceEEEEeCCC---cEEEEcHHHHHHHCCCHHHHcCCCHHHHcCchhHHHHHHHHHHHHhCCC
Confidence            457888999999999987   9999999999999999999999999999988777777777776665443

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

Probab=98.75  E-value=7.5e-09  Score=79.72  Aligned_cols=71  Identities=15%  Similarity=0.153  Sum_probs=62.0

Q ss_pred             chhHHHHHhccCCcEEEec-CCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhcccce
Q 021027          240 SSSLYISLGRIKQSFVLID-PHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQAC  315 (318)
Q Consensus       240 ~~~l~~~~~~~~~~i~i~d-~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~~~~  315 (318)
                      ...++.++++++++|+++| .++   +|+++|+++++++||+  +++|+++.+++++.........+..++++|+++
T Consensus        36 ~~~l~~l~~~~~~~i~~~d~~~g---~i~~~N~a~~~l~G~~--~~~G~~~~~~~~~~~~~~~~~~~~~~~~~g~~~  107 (185)
T 3kx0_X           36 AEDVRRIFEHIPAILVGLEGPDH---RFVAVNAAYRGFSPLL--DTVGQPAREVYPELEGQQIYEMLDRVYQTGEPQ  107 (185)
T ss_dssp             HHHHHHHHHHCSSEEEEEETTTT---EEEEECHHHHHHCCCC--SCTTSBHHHHCTTSCSSSSHHHHHHHHHHCCCE
T ss_pred             HHHHHHHHhcCCceEEEEECCCc---EEEEEcHHHHHHcCCc--cccCCcHHHHCCchhhhhHHHHHHHHHHcCCcc
Confidence            3458889999999999999 887   9999999999999999  999999999987777666777888888777764

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

Probab=98.70  E-value=1.5e-08  Score=75.77  Aligned_cols=77  Identities=29%  Similarity=0.510  Sum_probs=66.8

Q ss_pred             chhHHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhccccee
Q 021027          240 SSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQACT  316 (318)
Q Consensus       240 ~~~l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~~~~~  316 (318)
                      ...+..++++++++|+++|.++.+++|+++|+++++++||+.++++|+++..+.++.........+..++..+.++.
T Consensus        24 ~~~~~~i~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  100 (162)
T 3sw1_A           24 AQLLQSMVDASNDGIVVAEKEGDDTILIYVNAAFEYLTGYSRDEILYQDCRFLQGDDRDQLGRARIRKAMAEGRPCR  100 (162)
T ss_dssp             HHHHHHHHHTCSSEEEEEEEETTEEEEEEECHHHHHHHTCCHHHHTTSBGGGGTTTCCCCHHHHHHHHHHHHTCCEE
T ss_pred             HHHHHHHHhhccCcEEEEeCCCCccEEEEECHHHHHHHCCCHHHHcCCCcceecCCCcCHHHHHHHHHHHhcCCCCc
Confidence            45588899999999999998742238999999999999999999999999999988888888888999888887653

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

Probab=98.69  E-value=8.8e-09  Score=72.36  Aligned_cols=66  Identities=20%  Similarity=0.177  Sum_probs=52.1

Q ss_pred             HHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhcccc
Q 021027          244 YISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQA  314 (318)
Q Consensus       244 ~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~~~  314 (318)
                      ..++++++++|+++|.+|   +|+++|+++++++||+.++++|+++.++.++...  ....+.++++.+.+
T Consensus        10 ~~il~~~~~~i~~~D~~g---~I~~~N~aa~~l~g~~~~~~~g~~~~~~~~~~~~--~~~~~~~~~~~~~~   75 (115)
T 3b33_A           10 SAILNNMVTATLILDDGL---AIRYANPAAELLFSQSAKRIVEQSLSQLIQHASL--DLALLTQPLQSGQS   75 (115)
T ss_dssp             HHHHHHCSSEEEEECTTC---BEEEECHHHHHHTTSCHHHHTTCBHHHHCSEEEC--CTHHHHHHHHHCCC
T ss_pred             HHHHhhcCceEEEECCCC---cEEEECHHHHHHhCCCHHHHhCCCHHHHhCccch--hhHHHHHHHHcCCc
Confidence            458999999999999998   9999999999999999999999999887654321  12344555555544

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

Probab=98.68  E-value=2.2e-08  Score=71.23  Aligned_cols=51  Identities=16%  Similarity=0.430  Sum_probs=46.8

Q ss_pred             hhHHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhC------------CCcccccCCCcccccC
Q 021027          241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTG------------YDRNEVVGQNCRFLNG  294 (318)
Q Consensus       241 ~~l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~G------------y~~~el~G~~~~~l~~  294 (318)
                      .+++.++++++++|+++|.+|   +|+++|++|++++|            |++++++|+++..+.+
T Consensus         5 ~rl~~il~~~~~gviv~D~~g---~I~~~N~a~~~llg~~~~~i~~~~~g~~~~~~~G~~~~~~~~   67 (121)
T 4hi4_A            5 ARIASALDNVSANVMIADNDL---NIIYMNRTVSEMLGRAEADIRKQLPNFDAGRLMGANIDVFHK   67 (121)
T ss_dssp             HHHHHHHTTSSSEEEEEETTC---BEEEECHHHHHHHHHTHHHHHHHCTTCCGGGCTTCBGGGGCS
T ss_pred             HHHHHHHhcCCccEEEEcCCC---eEEEecHHHHHHHHHHHHHHHHhcCCCChHHhcCCCHHHhcC
Confidence            458889999999999999998   99999999999995            9999999999988874

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

Probab=98.67  E-value=4.1e-09  Score=74.16  Aligned_cols=74  Identities=8%  Similarity=-0.065  Sum_probs=65.0

Q ss_pred             chhHHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCc--ccccCCCCCHHHHHHHHHHHhccccee
Q 021027          240 SSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNC--RFLNGVDTDTTVLYQIKESIQTEQACT  316 (318)
Q Consensus       240 ~~~l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~--~~l~~~~~~~~~~~~~~~~l~~~~~~~  316 (318)
                      +++++.++++++++++.+|.++   .++++|+++++++||++++++|+..  ..+++|++.+.+.+.+..+++.+.++.
T Consensus         3 ~~~~~~l~~~~~~~i~~~d~~~---~~~~~n~~~~~~~G~~~~~~~~~~~~~~~~i~p~d~~~~~~~~~~~~~~~~~~~   78 (118)
T 3icy_A            3 AEELQALVDNIPAAIYHLDVSG---QATIRFRPPAFLKTLVSEHAGTTRLNTLSMIHHDDRHMLSNAYSKLREAKHSLT   78 (118)
T ss_dssp             HHHHHHHHTTCCCCCEEECTTS---CEEECCCCCGGGGGGEEEETTEEEEGGGGGBCGGGHHHHHHHHHHHHHSCCEEE
T ss_pred             HHHHHHHHhcCCceEEEEEcCC---CceEEechhHhhcCCCHHHccCChhHHHHHcCHHHHHHHHHHHHHHHhcCCCce
Confidence            3568889999999999999987   9999999999999999999988754  678899999999999999888877653

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

Probab=98.67  E-value=5.8e-08  Score=66.52  Aligned_cols=64  Identities=27%  Similarity=0.573  Sum_probs=52.7

Q ss_pred             CcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCC--cccccCCCCCHHHHHHHHHHHhcccce
Q 021027          252 QSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQN--CRFLNGVDTDTTVLYQIKESIQTEQAC  315 (318)
Q Consensus       252 ~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~--~~~l~~~~~~~~~~~~~~~~l~~~~~~  315 (318)
                      .+|+++|...++++|+++|+++++++||+.++++|++  ...+.++.........+..++..+.++
T Consensus         2 ~~i~i~d~~~~~g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   67 (110)
T 1byw_A            2 RKFIIANARVENCAVIYCNDGFCELCGYSRAEVMQRPCTCDFLHGPCTQRRAAAQIAQALLGAEER   67 (110)
T ss_dssp             CEEEEEETTSSSCBEEEECHHHHHHHTCCHHHHTTSBTTCGGGCCTTCCHHHHHHHHHHHHTTCCE
T ss_pred             CCEEEEeccCCCCcEEEECHHHHHHhCCCHHHHccCCCccccccCCcCCHHHHHHHHHHHhcCCCc
Confidence            5788999864456999999999999999999999998  566666667777778888888777655

>3a0s_A Sensor protein; PAS-fold, kinase, phosphoprotein, transferase, two-component regulatory system; HET: PG4 PGE; 1.47A {Thermotoga maritima} PDB: 3a0v_A*

Probab=98.63  E-value=6.1e-08  Score=64.71  Aligned_cols=60  Identities=8%  Similarity=0.122  Sum_probs=48.8

Q ss_pred             cCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhcccce
Q 021027          250 IKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQAC  315 (318)
Q Consensus       250 ~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~~~~  315 (318)
                      ++++|+++|.++   +|+++|+++++++||+.++++|+++..+  + ........+.+++..+.++
T Consensus         1 ~~~~i~~~d~~g---~i~~~N~~~~~l~g~~~~~~~g~~~~~~--~-~~~~~~~~~~~~~~~~~~~   60 (96)
T 3a0s_A            1 METAIITLSKDG---RITEWNKKAEQLFGLKKENVLGRRLKDL--P-DFEEIGSVAESVFENKEPV   60 (96)
T ss_dssp             CCCEEEEEETTS---BEEEECHHHHHHHCCCHHHHTTSBGGGS--T-TCHHHHHHHHHHHHHTCCE
T ss_pred             CCceEEEEcCCC---CEeehhHHHHHHhCCCHHHhcCCCHHHC--c-chHHHHHHHHHHhccCCeE
Confidence            478999999987   9999999999999999999999999888  3 2344556666776666554

>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=98.63  E-value=1e-07  Score=68.39  Aligned_cols=71  Identities=24%  Similarity=0.513  Sum_probs=59.8

Q ss_pred             hHHHHHhccCCcEEEecC---CCCCCCeeEecHHHHHHhCCCcccccCCC--cccccCCCCCHHHHHHHHHHHhcccce
Q 021027          242 SLYISLGRIKQSFVLIDP---HLPDMPMVYASDAFLKLTGYDRNEVVGQN--CRFLNGVDTDTTVLYQIKESIQTEQAC  315 (318)
Q Consensus       242 ~l~~~~~~~~~~i~i~d~---~~~~~~i~~~N~a~~~~~Gy~~~el~G~~--~~~l~~~~~~~~~~~~~~~~l~~~~~~  315 (318)
                      .+...+++++++|+++|.   ++   +|+++|+++++++||+.++++|++  +..+.++.........+..++..+.++
T Consensus        20 ~~~~~~~~~~~~i~~~d~~~~~g---~i~~~N~~~~~l~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   95 (138)
T 2l0w_A           20 TIIRKFEGQSRKFIIANARVENC---AVIYCNDGFCELCGYSRAEVMQRPCTCDFLHGPRTQRRAAAQIAQALLGAEER   95 (138)
T ss_dssp             HHHHHHTTTTSEEEEEESSSTTC---BEEEECSHHHHHHSCCHHHHTTSBTTCGGGCCTTCCHHHHHHHHHHTTCSSCE
T ss_pred             HHHHHHhcCCCCEEEEecCCCCC---EEEEeCHHHHHHhCCCHHHHcCCCCcccccCCcccchhHHHHHHHHHhhcCCc
Confidence            355667779999999998   65   999999999999999999999999  566777777777788888888777654

>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=98.63  E-value=1.6e-08  Score=71.29  Aligned_cols=75  Identities=3%  Similarity=-0.074  Sum_probs=59.0

Q ss_pred             cccchhHHHHHhccCCcEEEecCC-CCCCCeeEecHHHHHHhCCCcccccCCC--cccccCCCCCHHHHHHHHHHHhccc
Q 021027          237 GFISSSLYISLGRIKQSFVLIDPH-LPDMPMVYASDAFLKLTGYDRNEVVGQN--CRFLNGVDTDTTVLYQIKESIQTEQ  313 (318)
Q Consensus       237 ~~~~~~l~~~~~~~~~~i~i~d~~-~~~~~i~~~N~a~~~~~Gy~~~el~G~~--~~~l~~~~~~~~~~~~~~~~l~~~~  313 (318)
                      ......++.++++++++++++|.+ +   .++++|+++++++||++++++|+.  +..+++|++...+...+.. +..+.
T Consensus         7 ~~~~~~~~~~~~~~~~~i~~~d~~~~---~i~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~   82 (125)
T 3eeh_A            7 AKSERRVRELTEATNDILWEFTADLS---EVLVINSAYEDIWGRSVAKLRENPHDFLNGIHPEDRELMKDTMQS-LMDGE   82 (125)
T ss_dssp             ---CHHHHHHHSCCCCEEEEEETTSS---CEEEECTHHHHHHSSCHHHHHHCGGGGGGGBCHHHHHHHHHHHHH-HHTTC
T ss_pred             HHHHHHHHHHHhcCCceEEEEEcCCC---cEEEecHHHHHHHCCCHHHHccCcHHHHHhcCHHHHHHHHHHHHH-HHcCC
Confidence            344567889999999999999998 7   999999999999999999999987  5667777766666666655 45554


Q ss_pred             ce
Q 021027          314 AC  315 (318)
Q Consensus       314 ~~  315 (318)
                      ++
T Consensus        83 ~~   84 (125)
T 3eeh_A           83 SA   84 (125)
T ss_dssp             CE
T ss_pred             Cc
Confidence            43

>2w0n_A Sensor protein DCUS; signal transduction, two-component regulatory system, PAS, kinase, membrane, transferase, solid state cell inner membrane; NMR {Escherichia coli}

Probab=98.59  E-value=4.6e-08  Score=68.54  Aligned_cols=52  Identities=21%  Similarity=0.213  Sum_probs=47.0

Q ss_pred             hhHHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCC---CcccccCCCcccccCC
Q 021027          241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGY---DRNEVVGQNCRFLNGV  295 (318)
Q Consensus       241 ~~l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy---~~~el~G~~~~~l~~~  295 (318)
                      ..++.++++++++|+++|.+|   +|+++|+++++++||   +.++++|+++..+.++
T Consensus        15 ~~~~~il~~~~~~i~~~d~~g---~i~~~N~~~~~~~g~~~~~~~~~~g~~~~~~~~~   69 (118)
T 2w0n_A           15 EQRQAMLQSIKEGVVAVDDRG---EVTLINDAAQELLNYRKSQDDEKLSTLSHSWSQV   69 (118)
T ss_dssp             HHHHHHHHCCCCCCEEEBTTT---BCCCBCHHHHHHHCSCTTTTTSSCCCTTCCCSCT
T ss_pred             HHHHHHHhhccccEEEECCCC---cEeehhHHHHHHhCCCccChhhhhccCcccccCc
Confidence            447789999999999999987   999999999999998   8899999999888754

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

Probab=98.53  E-value=1.6e-07  Score=75.12  Aligned_cols=63  Identities=11%  Similarity=0.310  Sum_probs=52.5

Q ss_pred             hhHHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHh------------CCCcccccCCCcccccCCCCCHHHHHHHHHH
Q 021027          241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLT------------GYDRNEVVGQNCRFLNGVDTDTTVLYQIKES  308 (318)
Q Consensus       241 ~~l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~------------Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~  308 (318)
                      .++..++++++++|+++|++|   +|+|+|++|++++            ||++++++|+++..+...   +.....+.+.
T Consensus        22 ~~l~~iLd~~~~~vii~D~~g---~I~~~N~a~~~ll~~~~~~~~~~l~G~~~~eliG~~~~~~~~~---~~~~~~~~~~   95 (233)
T 3vol_A           22 ARIKSALDNVSANVMIADNDL---NIIYMNRTVSEMLGRAEADIRKQLPNFDAGRLMGANIDVFHKN---PAHQRHLLAN   95 (233)
T ss_dssp             HHHHHHHTTSSSEEEEEETTS---BEEEECHHHHHHHHHTHHHHHTTCTTCCTTSCTTCBGGGGSSS---HHHHHHHHHT
T ss_pred             HHHHHHHhcCCCcEEEECCCC---cEEEecHHHHHHHHHHHHHHHhhcCCCCHHHHcCCCHHHHcCC---HHHHHHHHHh
Confidence            557889999999999999998   9999999999998            899999999999988742   4444455444


Q ss_pred             H
Q 021027          309 I  309 (318)
Q Consensus       309 l  309 (318)
                      +
T Consensus        96 ~   96 (233)
T 3vol_A           96 L   96 (233)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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=98.52  E-value=1.5e-07  Score=70.40  Aligned_cols=70  Identities=24%  Similarity=0.284  Sum_probs=57.5

Q ss_pred             chhHHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhcc
Q 021027          240 SSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTE  312 (318)
Q Consensus       240 ~~~l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~  312 (318)
                      ...+..++++++++|+++|.++   .|+++|+++++++||+.++++|+++..+.++.........+......+
T Consensus        39 ~~~~~~~l~~~~~~i~~~d~~g---~i~~~N~~~~~l~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~  108 (167)
T 1v9y_A           39 DGIFFPALEQNMMGAVLINEND---EVMFFNPAAEKLWGYKREEVIGNNIDMLIPRDLRPAHPEYIRHNREGG  108 (167)
T ss_dssp             -CCHHHHHHTCSSEEEEECTTS---BEEEECHHHHHHHSCCGGGTTTSBGGGGSCGGGTTTHHHHHHHHHC--
T ss_pred             hHHHHHHHHhCCCCEEEECCCC---cEEEECHHHHHHhCCCHHHHcCCChhhccCccccchHHHHHHHHhhcC
Confidence            4458889999999999999887   999999999999999999999999999887766655556665555544

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

Probab=98.50  E-value=5.6e-08  Score=72.05  Aligned_cols=70  Identities=11%  Similarity=0.109  Sum_probs=57.1

Q ss_pred             hhHHHHHhccCCcEEEecCCCCCCCeeEecHH---HHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhcccce
Q 021027          241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDA---FLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQAC  315 (318)
Q Consensus       241 ~~l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a---~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~~~~  315 (318)
                      ..+..+|++++++|+++|.++   +|+|+|++   +++++| ..++++|+++.++.+ .........+.+++++|++.
T Consensus        19 ~~l~~IL~~~~~gI~~vD~~g---~I~~~N~a~~~~~~i~g-~~~~~iGr~v~~~~~-~~~~~~v~~i~~~l~~g~~~   91 (151)
T 2qkp_A           19 EQANLILNHLPLEITFVNKDD---IFQYYNDSVPAAEMVFK-RTPSQVGRNVELCHP-PKVLDKVKKVFELLRNGQRD   91 (151)
T ss_dssp             HHHHHHHHHSSSEEEEEETTS---BEEEECCCSCGGGCSSC-CCGGGTTSBGGGSSC-HHHHHHHHHHHHHHHTTSBS
T ss_pred             HHHHHHHHhCCCceEEEcCCC---eEEEEeCCCchhhhhcC-CCHHHcCCCHHHhCC-HHHHHHHHHHHHHHHcCCcc
Confidence            458889999999999999998   99999999   999999 568899999998764 33344456677777777653

>3a0r_A Sensor protein; four helix bundle, PAS fold, kinase, phosphoprotein, transfe two-component regulatory system; 3.80A {Thermotoga maritima}

Probab=98.45  E-value=1.4e-07  Score=80.22  Aligned_cols=69  Identities=9%  Similarity=0.099  Sum_probs=54.3

Q ss_pred             hhHHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhcccce
Q 021027          241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQAC  315 (318)
Q Consensus       241 ~~l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~~~~  315 (318)
                      ..++.++++++++|+++|.+|   +|++||+++++++||++++++|+++.++.++   ......+...+..+.++
T Consensus         8 ~~~~~i~~~~~~~i~~~d~~g---~i~~~N~a~~~l~G~~~~e~~G~~~~~~~~~---~~~~~~~~~~~~~~~~~   76 (349)
T 3a0r_A            8 NFSESILESLETAIITLSKDG---RITEWNKKAEQLFGLKKENVLGRRLKDLPDF---EEIGSVAESVFENKEPV   76 (349)
T ss_dssp             -CCCSSGGGSSSEEEEEESSS---BCSCBCHHHHHHHSCCSTTTTTCBSTTSTTT---THHHHHHHHHHHHCCCC
T ss_pred             HHHHHHHhhhcCeEEEECCCC---CEEeeHHHHHHHhCCCHHHHcCcCHHHCcCh---hHHHHHHHHHHhcCCce
Confidence            346678999999999999987   9999999999999999999999999988433   23344455555555543

>2ykf_A Pdtas, probable sensor histidine kinase pdtas; transferase, two-component system, GAF domain, PAS domain; 2.00A {Mycobacterium tuberculosis} PDB: 2ykh_A

Probab=97.78  E-value=3.1e-08  Score=82.35  Aligned_cols=113  Identities=13%  Similarity=0.096  Sum_probs=76.3

Q ss_pred             HHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcC---CChhhhcCCCCCcccCCC---CCh--HHHHHHHHHHHh-cCCeE
Q 021027           23 ALDELPDSFTITDPSISGHPIVFASRGFLKMSG---FSRAEIIGRNGRMFQGPR---TNR--RTIMEIREAIRE-ERPIE   93 (318)
Q Consensus        23 ~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G---~~~~e~~g~~~~~l~~~~---~~~--~~~~~~~~~~~~-~~~~~   93 (318)
                      +++++++|++++|.+   |+|+++|++++++++   ++ ++++|+++..+.++.   ...  .+...+...+.. +....
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 688999877765432   100  111212223332 22222


Q ss_pred             EEEEEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEeccccccccccccccc
Q 021027           94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSY  146 (318)
Q Consensus        94 ~~~~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte~k~~~~~~~~~  146 (318)
                      .+.   ..+  ..++.++..|+.+  +|.+.|++.+++|||+.++.++++..+
T Consensus       251 ~ei---~~~--~~~l~v~~~Pi~~--~g~~~G~Vvv~rDITE~~~lE~eL~~K  296 (305)
T 2ykf_A          251 MEV---DAG--GATVLLRTLPLVV--AGRNVGAAILIRDVTEVKRRDRALISK  296 (305)
Confidence            221   112  2466788889876  578889999999999999997666544

>2jhe_A Transcription regulator TYRR; aromatic hydrocarbons catabolism, TYRR protei nucleotide-binding, transcription regulation, activator; HET: PG4; 2.30A {Escherichia coli}

Probab=98.37  E-value=4.8e-07  Score=69.68  Aligned_cols=54  Identities=15%  Similarity=0.064  Sum_probs=49.0

Q ss_pred             hhHHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCC
Q 021027          241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDT  297 (318)
Q Consensus       241 ~~l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~  297 (318)
                      ..+..+++++++||+++|.+|   +|+++|+++++++|++.++++|+++..+.++..
T Consensus        80 ~~l~~il~~~~~gvi~~D~~g---~I~~~N~aa~~llg~~~~~~~g~~~~~~~~~~~  133 (190)
T 2jhe_A           80 LALSALLEALPEPVLSVDMKS---KVDMANPASCQLFGQKLDRLRNHTAAQLINGFN  133 (190)
T ss_dssp             HHHHHHHHHCSSCEEEECTTC---BEEEECHHHHHHHTSCHHHHTTSBGGGTSTTCC
T ss_pred             HHHHHHHHhCCCcEEEEcCCC---CEEEEcHHHHHHhCCCHHHhcCccHHHHhCCCC
Confidence            457889999999999999998   999999999999999999999999999876543

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

Probab=98.36  E-value=1.1e-07  Score=66.60  Aligned_cols=65  Identities=11%  Similarity=-0.018  Sum_probs=53.6

Q ss_pred             cCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCC-cccccCCCCCHHHHHHHHHHHhccccee
Q 021027          250 IKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQN-CRFLNGVDTDTTVLYQIKESIQTEQACT  316 (318)
Q Consensus       250 ~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~-~~~l~~~~~~~~~~~~~~~~l~~~~~~~  316 (318)
                      ++++++.+|...  ++++|+|+++++++||++++++|.. +..+++|++.+.+.+.+.+++..+.++.
T Consensus         2 a~~giw~~d~~~--~~~~~~n~~~~~l~G~~~~e~~~~~~~~~~ihpdd~~~~~~~~~~~~~~~~~~~   67 (115)
T 3h9w_A            2 TKAIPWKINWQT--MAFEYIGPQIEALLGWPQGSWKSVEDWATRMHPEDQEWVVNFCVKQSECGVDHE   67 (115)
T ss_dssp             -CCEEEEEETTT--TEEEEECTHHHHHHCSCGGGCCBHHHHHHSBCHHHHHHHHHHHHHHHHTTCCEE
T ss_pred             cceEEEEEEcCC--CcEEEEChhHHHHhCCChHHccCHHHHHHhcCHHHHHHHHHHHHHHHhcCCccc
Confidence            468899999543  4899999999999999999999942 3568899999999999999998887653

>2ykf_A Pdtas, probable sensor histidine kinase pdtas; transferase, two-component system, GAF domain, PAS domain; 2.00A {Mycobacterium tuberculosis} PDB: 2ykh_A

Probab=97.52  E-value=1.7e-07  Score=77.85  Aligned_cols=46  Identities=24%  Similarity=0.152  Sum_probs=40.1

Q ss_pred             HHhccCCcEEEecCCCCCCCeeEecHHHHHHhC---CCcccccCCCcccccCC
Q 021027          246 SLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTG---YDRNEVVGQNCRFLNGV  295 (318)
Q Consensus       246 ~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~G---y~~~el~G~~~~~l~~~  295 (318)
                      .++++++||+++|.+|   +|+++|+++++++|   ++ ++++|+++.++...
T Consensus       175 ~~~~~~dGIivvD~~G---~Ii~~N~aA~~ll~~lG~~-~~~iGk~l~el~~~  223 (305)
T 2ykf_A          175 SSPRAGDGFIRLDVDG---VVSYASPNALSAYHRMGLT-TELEGVNLIDATRP  223 (305)
Confidence            5677899999999998   99999999999985   55 78999999888754

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

Probab=98.02  E-value=3.3e-06  Score=72.16  Aligned_cols=72  Identities=11%  Similarity=0.131  Sum_probs=59.3

Q ss_pred             ccchhHHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhcccce
Q 021027          238 FISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQAC  315 (318)
Q Consensus       238 ~~~~~l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~~~~  315 (318)
                      .....+..+++++++||+++|.+|   +|+++|++ ++++ ++.++++|+++..+++ .........+..++++|++.
T Consensus       236 ~~~~~l~~IL~~l~dgIivvD~~g---~I~~~N~a-e~i~-~~~~e~iGr~v~~~~p-~~~~~~~~~l~~~l~~g~~~  307 (369)
T 3cax_A          236 LNIEELKAIFEALPVDVTFIDKDD---RVRFFSPG-ERIF-TRTPSVLGRPVQLCHP-PKSVYVVNKILKAFKEGRKK  307 (369)
T ss_dssp             ECHHHHHHHHHHSSSEEEEECTTS---BEEEECCS-SCSS-CCCGGGTTCBTTTSSC-GGGHHHHHHHHHHHHHTSCS
T ss_pred             hhHHHHHHHHHhCCCcEEEECCCC---cEEEEcCH-HHcc-CChHHHcCCcHHHHCC-hhhHHHHHHHHHHHHcCCce
Confidence            334568899999999999999998   99999999 9999 9999999999998874 34445566677777777653

>1oj5_A Steroid receptor coactivator 1A; transcriptional coactivator, complex, LXXLL motif, transcriptional regulation; 2.2A {Mus musculus} SCOP: d.110.3.8

Probab=97.74  E-value=9.5e-05  Score=51.90  Aligned_cols=102  Identities=11%  Similarity=0.095  Sum_probs=77.0

Q ss_pred             eEEEEcCCCCCCcEEEecHhHHHhcCCCh--hhhcCCCCCcccCCCCCh--HHHHHHHHHHHhcCCeEEEEEEEecCCcE
Q 021027           30 SFTITDPSISGHPIVFASRGFLKMSGFSR--AEIIGRNGRMFQGPRTNR--RTIMEIREAIREERPIEVNLLNYKKDGTP  105 (318)
Q Consensus        30 ~i~~~d~~~~~~~i~~~N~~~~~~~G~~~--~e~~g~~~~~l~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~g~~  105 (318)
                      -+.-.|.+   |+++++.....+ .++.+  +|++|+.+.+++++++..  .+......++..|......++.+.++|..
T Consensus         9 F~sRh~~d---GKf~~vDq~~~r-~~~~~g~qdLlGrsiy~f~H~~D~~~s~l~~h~~~vl~~Gq~~S~~YRfr~k~g~~   84 (132)
T 1oj5_A            9 FMTKQDTT---GKIISIDTSSLR-AAGRTGWEDLVRKCIYAFFQPQGREPSYARQLFQEVMTRGTASSPSYRFILNDGTM   84 (132)
T ss_dssp             EEEEECTT---CCEEEEECHHHH-TTCCSCHHHHHHHHHHHHTSCBTTBCCHHHHHHHHHHHHSEEECCCEEEECTTSCE
T ss_pred             eEEeecCC---CcEEEEeccccc-ccccccHHHHHHHHHHHHhCcccchHHHHHHHHHHHHHcCCccccceEEEecCCcE
Confidence            34456778   999999998874 67777  899999999999998855  77777888887777677778888999999


Q ss_pred             EEEEEEEEeeccCCCCceeEEEEEEecccc
Q 021027          106 FWMLFKMSLVFGKEDGRATHFVAVQVPIVS  135 (318)
Q Consensus       106 ~~~~~~~~~i~~~~~g~~~~~i~~~~DIte  135 (318)
                      +|+......++++..+++..++++-.=+.+
T Consensus        85 V~~qT~sk~f~np~t~e~e~Ivs~n~v~r~  114 (132)
T 1oj5_A           85 LSAHTRCKLCYPQSPDMQPFIMGIHIIDRE  114 (132)
T ss_dssp             EEEEEEEEEECC----CCCEEEEEEEEECC
T ss_pred             EEEEEEEEEecCCCCCCCCEEEEEEEEEcC
Confidence            999988888887334566666665544443

>1oj5_A Steroid receptor coactivator 1A; transcriptional coactivator, complex, LXXLL motif, transcriptional regulation; 2.2A {Mus musculus} SCOP: d.110.3.8

Probab=95.27  E-value=0.0081  Score=42.15  Aligned_cols=56  Identities=9%  Similarity=0.003  Sum_probs=45.9

Q ss_pred             EecCCCCCCCeeEecHHHHHHhCCCc--ccccCCCcccccCCCCCH--HHHHHHHHHHhcccce
Q 021027          256 LIDPHLPDMPMVYASDAFLKLTGYDR--NEVVGQNCRFLNGVDTDT--TVLYQIKESIQTEQAC  315 (318)
Q Consensus       256 i~d~~~~~~~i~~~N~a~~~~~Gy~~--~el~G~~~~~l~~~~~~~--~~~~~~~~~l~~~~~~  315 (318)
                      -.|.+|   .|++|..+..+ .+|..  +||+|+++.+++++.+..  ...+...+++..|...
T Consensus        12 Rh~~dG---Kf~~vDq~~~r-~~~~~g~qdLlGrsiy~f~H~~D~~~s~l~~h~~~vl~~Gq~~   71 (132)
T 1oj5_A           12 KQDTTG---KIISIDTSSLR-AAGRTGWEDLVRKCIYAFFQPQGREPSYARQLFQEVMTRGTAS   71 (132)
T ss_dssp             EECTTC---CEEEEECHHHH-TTCCSCHHHHHHHHHHHHTSCBTTBCCHHHHHHHHHHHHSEEE
T ss_pred             eecCCC---cEEEEeccccc-ccccccHHHHHHHHHHHHhCcccchHHHHHHHHHHHHHcCCcc
Confidence            345555   99999999874 78888  899999999999999965  7788888888877644

>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=94.53  E-value=0.025  Score=47.12  Aligned_cols=55  Identities=5%  Similarity=0.108  Sum_probs=40.8

Q ss_pred             CCcEE-EecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhc
Q 021027          251 KQSFV-LIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQT  311 (318)
Q Consensus       251 ~~~i~-i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~  311 (318)
                      |-|++ +.+..  +++|+.+|..+++++|+++++++|+++.+++++.    ....+++.+..
T Consensus        41 p~G~Ll~~~~~--~~~i~~~S~N~~~~lg~~~~~llG~~l~~ll~~~----~~~~l~~~l~~   96 (337)
T 2ool_A           41 PHGYLFVVSET--DLRIASVSANVEDLLRQPPASLLNVPIAHYLTAA----SAARLTHALHG   96 (337)
T ss_dssp             TTSEEEEECTT--TCBEEEEETTHHHHHSSCGGGGTTCBGGGGBCHH----HHHHHHHHHCC
T ss_pred             CCEEEEEEECC--CCEEEEEehhHHHHHCcCHHHHcCCCHHHHcCHH----HHHHHHHHHhc
Confidence            34544 34433  4699999999999999999999999999998653    34455555544

>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=90.68  E-value=0.41  Score=39.85  Aligned_cols=40  Identities=8%  Similarity=-0.007  Sum_probs=33.3

Q ss_pred             EEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCC
Q 021027           32 TITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPR   73 (318)
Q Consensus        32 ~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~   73 (318)
                      ++++.+  +++++.+|..+..++|+++++++|+++..++++.
T Consensus        46 l~~~~~--~~~i~~~S~N~~~~lg~~~~~llG~~l~~ll~~~   85 (337)
T 2ool_A           46 FVVSET--DLRIASVSANVEDLLRQPPASLLNVPIAHYLTAA   85 (337)
T ss_dssp             EEECTT--TCBEEEEETTHHHHHSSCGGGGTTCBGGGGBCHH
T ss_pred             EEEECC--CCEEEEEehhHHHHHCcCHHHHcCCCHHHHcCHH
Confidence            345532  4899999999999999999999999988887654

>4ew7_A Conjugative transfer: regulation; alpha-beta-alpha structure, structural genomics, midwest CEN structural genomics (MCSG), PSI-biology; 1.67A {Salmonella enterica subsp}

Probab=89.33  E-value=1.2  Score=29.29  Aligned_cols=34  Identities=15%  Similarity=0.198  Sum_probs=29.3

Q ss_pred             HHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCC
Q 021027          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGY  279 (318)
Q Consensus       243 l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy  279 (318)
                      .+.+..+.|.++++-+...   .|+|.|.+|.+|+--
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            5567788899999999987   899999999999643

>4ew7_A Conjugative transfer: regulation; alpha-beta-alpha structure, structural genomics, midwest CEN structural genomics (MCSG), PSI-biology; 1.67A {Salmonella enterica subsp}

Probab=85.77  E-value=5.7  Score=26.14  Aligned_cols=91  Identities=9%  Similarity=0.139  Sum_probs=54.5

Q ss_pred             HHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHH-HHHHhcCCeEEEEE
Q 021027           19 WVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIR-EAIREERPIEVNLL   97 (318)
Q Consensus        19 ~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~-~~~~~~~~~~~~~~   97 (318)
                      ..+.+..++|.++.+-+..   ..++|.|.+|.++|-.....+-|.+....    ..+.+...+. .+..-|....+ .+
T Consensus        21 ~iq~iY~nSPVpVCVRNq~---RkilYaN~aF~elF~Ked~~~sg~S~~~~----~vE~~LS~LELeCqsLGhG~af-~r   92 (127)
T 4ew7_A           21 SIQDIYKNSPVPVCVRNQS---RKIIYANGAFIELFSKEDQPLSGDSYNRY----GVEVFLSSLELECQSLGHGAAF-CR   92 (127)
T ss_dssp             HHHHHHTTCSSCEEEECTT---SCEEEECHHHHHHTTSCCCGGGCTTSSHH----HHHHHHHHHHHHHHHHCTTCEE-EE
T ss_pred             hHHhhhcCCCccEEEeccc---ceEEEecchHHHHhhcccCcccCccccee----eehhhHHHHHHHHHhhcCCceE-EE
Confidence            4567899999999999999   99999999999997665544444432211    0011111111 22222332222 22


Q ss_pred             EEecCCcEEEEEEEEEeecc
Q 021027           98 NYKKDGTPFWMLFKMSLVFG  117 (318)
Q Consensus        98 ~~~~~g~~~~~~~~~~~i~~  117 (318)
                      ...-.|+.+.+++....+.+
T Consensus        93 ~Fn~~~e~yQIRmE~iSf~~  112 (127)
T 4ew7_A           93 RFNFHGEIYQIRMENISFDN  112 (127)
T ss_dssp             EEEETTEEEEEEEEEEECTT
T ss_pred             EeecCCceEEEEEEEeeecC
Confidence            34456777777776666644

>4e04_A Bacteriophytochrome (light-regulated signal trans histidine kinase), PHYB1; bacteriophytochrome chromophore binding domain; HET: LBV; 1.79A {Rhodopseudomonas palustris}

Probab=81.45  E-value=1.8  Score=35.72  Aligned_cols=53  Identities=17%  Similarity=0.301  Sum_probs=39.9

Q ss_pred             CcE-EEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhc
Q 021027          252 QSF-VLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQT  311 (318)
Q Consensus       252 ~~i-~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~  311 (318)
                      -|+ +..|.   +++|+.++..+..++|.++++++|+++..++.+    .....++.++..
T Consensus        29 hG~Ll~~~~---~~~I~~~S~N~~~~lg~~~~~~lG~~l~~ll~~----~~~~~l~~~l~~   82 (327)
T 4e04_A           29 HGLLLALAA---DMTIVAGSDNLPELTGLAIGALIGRSAADVFDS----ETHNRLTIALAE   82 (327)
T ss_dssp             TSEEEEECT---TCBEEEEETTHHHHHSCCHHHHTTCBHHHHBCH----HHHHHHHHHHHS
T ss_pred             CeEEEEEcC---CCeEEEEcccHHHHhCCChHhhcCCCHHHHcCH----HHHHHHHHHhhc
Confidence            344 44553   459999999999999999999999999998843    445556666543

>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=80.06  E-value=0.89  Score=37.77  Aligned_cols=42  Identities=17%  Similarity=0.072  Sum_probs=34.2

Q ss_pred             CcE-EEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCC
Q 021027          252 QSF-VLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGV  295 (318)
Q Consensus       252 ~~i-~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~  295 (318)
                      -|+ +..|..  +++|+.++..+..++|.++++++|+++..++.+
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 444542  469999999999999999999999999998855

---

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	318
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	1e-10
d1bywa_	110	d.110.3.6 (A:) Erg potassium channel, N-terminal d	7e-10
d1bywa_	110	d.110.3.6 (A:) Erg potassium channel, N-terminal d	7e-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 = 55.3 bits (132), Expect = 1e-10
 Identities = 31/65 (47%), Positives = 46/65 (70%)

Query: 252 QSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQT 311
           +SFV+ DP LPD P+++ASD FL+LT Y R EV+G NCRFL G  TD   +  I+++++ 
Sbjct: 1   KSFVITDPRLPDNPIIFASDRFLELTEYTREEVLGNNCRFLQGRGTDRKAVQLIRDAVKE 60

Query: 312 EQACT 316
           ++  T
Sbjct: 61  QRDVT 65

>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 = 7e-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 = 50.8 bits (120), Expect = 7e-09
 Identities = 13/64 (20%), Positives = 27/64 (42%)

Query: 252 QSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQT 311
           + F++ +  + +  ++Y +D F +L GY R EV+ + C         T      + +   
Sbjct: 2   RKFIIANARVENCAVIYCNDGFCELCGYSRAEVMQRPCTCDFLHGPCTQRRAAAQIAQAL 61

Query: 312 EQAC 315
             A 
Sbjct: 62  LGAE 65

>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	318
d1n9la_	109	Putative blue light receptor, phot-lov1 domain {Gr	99.84
d1bywa_	110	Erg potassium channel, N-terminal domain {Human (H	99.78
d1jnua_	104	Photoreceptor phy3 flavin-binding domain, lov2 {Ma	99.77
d1ew0a_	130	Histidine kinase FixL heme domain {Rhizobium melil	99.71
d1p97a_	114	Hypoxia-inducible factor Hif2a, C-terminal domain	99.65
d1xj3a1	106	Histidine kinase FixL heme domain {Bradyrhizobium	99.55
d1v9ya_	113	Direct oxygen sensor protein, DOS {Escherichia col	99.54
d1n9la_	109	Putative blue light receptor, phot-lov1 domain {Gr	99.51
d1nwza_	125	Photoactive yellow protein, PYP {Ectothiorhodospir	99.46
d1mzua_	110	PYP domain of sensor histidine kinase Ppr {Rhodosp	99.4
d1jnua_	104	Photoreceptor phy3 flavin-binding domain, lov2 {Ma	99.37
d1mzua_	110	PYP domain of sensor histidine kinase Ppr {Rhodosp	99.31
d1ll8a_	114	N-terminal PAS domain of Pas kinase {Human (Homo s	99.26
d1ew0a_	130	Histidine kinase FixL heme domain {Rhizobium melil	99.25
d1bywa_	110	Erg potassium channel, N-terminal domain {Human (H	99.23
d1v9ya_	113	Direct oxygen sensor protein, DOS {Escherichia col	99.2
d1nwza_	125	Photoactive yellow protein, PYP {Ectothiorhodospir	99.13
d1oj5a_	109	PAS domain of steroid receptor coactivator 1A, NCo	99.05
d1xj3a1	106	Histidine kinase FixL heme domain {Bradyrhizobium	98.99
d1ll8a_	114	N-terminal PAS domain of Pas kinase {Human (Homo s	98.89
d1p97a_	114	Hypoxia-inducible factor Hif2a, C-terminal domain	98.71
d1oj5a_	109	PAS domain of steroid receptor coactivator 1A, NCo	98.09
d2oola2	114	Sensor protein PhyB2 {Rhodopseudomonas palustris [	97.48
d2oola2	114	Sensor protein PhyB2 {Rhodopseudomonas palustris [	97.28
d2veaa3	127	Phytochrome-like protein Cph1 {Synechocystis sp. p	95.05
d2veaa3	127	Phytochrome-like protein Cph1 {Synechocystis sp. p	94.78
d2o9ca2	127	Bacteriophytochrome BphP {Deinococcus radiodurans	93.81
d2o9ca2	127	Bacteriophytochrome BphP {Deinococcus radiodurans	93.25

>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=99.84  E-value=5.9e-20  Score=128.12  Aligned_cols=108  Identities=41%  Similarity=0.805  Sum_probs=99.3

Q ss_pred             CCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEEEEEEEecCCcEE
Q 021027           27 LPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPF  106 (318)
Q Consensus        27 ~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~  106 (318)
                      ..++++++|...||++|+|+|++|++++||++++++|+++..+.+++..+.....+...+..+.++..++..+++||..+
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            46789999965556999999999999999999999999988888888778888888999999999999999999999999


Q ss_pred             EEEEEEEeeccCCCCceeEEEEEEecccc
Q 021027          107 WMLFKMSLVFGKEDGRATHFVAVQVPIVS  135 (318)
Q Consensus       107 ~~~~~~~~i~~~~~g~~~~~i~~~~DIte  135 (318)
                      |+.+++.|+++ ++|.+.+++++.+|||.
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=99.78  E-value=5e-18  Score=118.44  Aligned_cols=106  Identities=27%  Similarity=0.519  Sum_probs=93.9

Q ss_pred             eEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCc--ccCCCCChHHHHHHHHHHHhcCCeEEEEEEEecCCcEEE
Q 021027           30 SFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRM--FQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFW  107 (318)
Q Consensus        30 ~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~--l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~  107 (318)
                      .++++|.+.+|..|+|+|+++++++||+.++++|+++..  +.+++........+...+..+.++..+...++++|..+|
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            467788766669999999999999999999999998654  345666677788888899999999999999999999999


Q ss_pred             EEEEEEeeccCCCCceeEEEEEEeccccc
Q 021027          108 MLFKMSLVFGKEDGRATHFVAVQVPIVSR  136 (318)
Q Consensus       108 ~~~~~~~i~~~~~g~~~~~i~~~~DIte~  136 (318)
                      +.+++.|+++ ++|.+.+++++++|||+|
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=99.77  E-value=5.8e-18  Score=116.84  Aligned_cols=103  Identities=41%  Similarity=0.824  Sum_probs=96.0

Q ss_pred             eEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEEEEEEEecCCcEEEEE
Q 021027           30 SFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWML  109 (318)
Q Consensus        30 ~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~  109 (318)
                      .++++|+..||++|+|+|++|++++||+.++++|+++..+.+++..+.....+...+..+..+..+...++++|+.+|+.
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            36788866566999999999999999999999999998888888888889999999999999999999999999999999


Q ss_pred             EEEEeeccCCCCceeEEEEEEecc
Q 021027          110 FKMSLVFGKEDGRATHFVAVQVPI  133 (318)
Q Consensus       110 ~~~~~i~~~~~g~~~~~i~~~~DI  133 (318)
                      +++.|+++ ++|.+.+++++.+||
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

>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=1.3e-16  Score=114.66  Aligned_cols=124  Identities=17%  Similarity=0.239  Sum_probs=100.5

Q ss_pred             hhhhHHHhhhhhhHHHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHH
Q 021027            4 QLGLIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIR   83 (318)
Q Consensus         4 ~l~~~~~~~~~~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~   83 (318)
                      ++...++.+. ..+++++.++++++++++++|.+   |+|+++|+++++++||++++++|+++..+.++.........+.
T Consensus         3 ~l~~~e~~l~-~~e~~~~~i~~~~~~~i~~~d~~---g~i~~~N~~~~~l~Gy~~~el~g~~~~~~~~~~~~~~~~~~~~   78 (130)
T d1ew0a_           3 HMLETEDVVR-ARDAHLRSILDTVPDATVVSATD---GTIVSFNAAAVRQFGYAEEEVIGQNLRILMPEPYRHEHDGYLQ   78 (130)
T ss_dssp             HHHHHHHHHH-HHTSCHHHHHTTCSSEEEEEETT---SBEEEECHHHHHHHCCCHHHHTTSBGGGGSCTTTGGGHHHHHH
T ss_pred             hHHHHHHHHH-HHHHHHHHHHHcCCCeEEEEeCC---ccEEEEHHHHHHhhcCCHHHhcCCccccccccchhHHHHHHHH
Confidence            3445555555 56678999999999999999999   9999999999999999999999999888877776666566666


Q ss_pred             HHHHhcCC----eEEEEEEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEeccc
Q 021027           84 EAIREERP----IEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV  134 (318)
Q Consensus        84 ~~~~~~~~----~~~~~~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIt  134 (318)
                      ..+..+..    ...++...++||..+|+.++..|+.. . +. ..++++++|||
T Consensus        79 ~~~~~~~~~~~~~~~e~~~~~~dG~~~~v~~~~~~i~~-~-~~-~~~~~i~rDIT  130 (130)
T d1ew0a_          79 RYMATGEKRIIGIDRVVSGQRKDGSTFPMKLAVGEMRS-G-GE-RFFTGFIRDLT  130 (130)
T ss_dssp             HHHHHCCCSSTTSCEEEEEECTTSCEEEEEEEEEEEEE-T-TE-EEEEEEEEECC
T ss_pred             HHHHhCCCccccceeeEEEEcCCCCEEEEEEEEEEEEE-C-Ce-EEEEEEEEECC
Confidence            65654433    45677778999999999999999986 3 33 35788999998

>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=2e-16  Score=110.94  Aligned_cols=106  Identities=8%  Similarity=0.184  Sum_probs=92.2

Q ss_pred             eEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcCCeEEEEEEEecCCcEEEEE
Q 021027           30 SFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWML  109 (318)
Q Consensus        30 ~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~  109 (318)
                      .+...+++   |+++|+|++++.++||+.++++|+++..+.+|++.......+...+..+..+..+++..+++|..+|+.
T Consensus         8 fi~r~~~d---G~i~~~N~~~~~~~G~~~~el~g~~~~~~~~~ed~~~~~~~~~~~~~~~~~~~~e~~~~~kdG~~~wv~   84 (114)
T d1p97a_           8 FLSRHSMD---MKFTYCDDRITELIGYHPEELLGRSAYEFYHALDSENMTKSHQNLCTKGQVVSGQYRMLAKHGGYVWLE   84 (114)
T ss_dssp             EEEEECTT---TSCSEECTTHHHHTSSCHHHHTTSCHHHHSCSSSHHHHHHHHHHHTTTSEEEEEEEEEECTTSCEEEEE
T ss_pred             EEEEECCC---CcEEEECHHHHHHcCCCccccccccccccccccccccceeeeeecccccceeecceeeeeecCcceEEE
Confidence            34446888   999999999999999999999999988888888877777777777666667788889999999999999


Q ss_pred             EEEEeeccCCCCceeEEEEEEeccccccc
Q 021027          110 FKMSLVFGKEDGRATHFVAVQVPIVSRKH  138 (318)
Q Consensus       110 ~~~~~i~~~~~g~~~~~i~~~~DIte~k~  138 (318)
                      ++..|++++.+|.+.+++++.+|||++|+
T Consensus        85 ~~~~~~~~~~~~~~~~ii~~~~dite~k~  113 (114)
T d1p97a_          85 TQGTVIYNPRNLQPQCIMCVNYVLSEIEK  113 (114)
T ss_dssp             EEEEEEECTTTCSEEEEEEEEEEEEEEEC
T ss_pred             EEEEEEEeCCCCCEEEEEEEEEECChhhc
Confidence            99999998236899999999999999987

>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=99.55  E-value=3.2e-14  Score=97.85  Aligned_cols=101  Identities=19%  Similarity=0.193  Sum_probs=81.3

Q ss_pred             CeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcC----CeEEEEEEEecCCc
Q 021027           29 DSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREER----PIEVNLLNYKKDGT  104 (318)
Q Consensus        29 ~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~g~  104 (318)
                      ++|+++|.+   |+|+++|+++++++||+.++++|+++..++++.........+...+....    ....+....+++|.
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    24567788899999


Q ss_pred             EEEEEEEEEeeccCCCCceeEEEEEEecccc
Q 021027          105 PFWMLFKMSLVFGKEDGRATHFVAVQVPIVS  135 (318)
Q Consensus       105 ~~~~~~~~~~i~~~~~g~~~~~i~~~~DIte  135 (318)
                      .+|+.+++.|+.+ +++  .+++++++||||
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 433  468899999997

>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=99.54  E-value=4.9e-14  Score=98.11  Aligned_cols=108  Identities=22%  Similarity=0.264  Sum_probs=81.8

Q ss_pred             HHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHh----cCCeEE
Q 021027           19 WVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIRE----ERPIEV   94 (318)
Q Consensus        19 ~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~----~~~~~~   94 (318)
                      .|.+++++++++++++|.+   |+++++|+++++++||+.++++|++...+.++.........+...+..    ......
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   999999999999999999999999977776655444444433333322    223445


Q ss_pred             EEEEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEec
Q 021027           95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVP  132 (318)
Q Consensus        95 ~~~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~D  132 (318)
                      +....+++|+.+|+.++..|+.+ +++  ..++++++|
T Consensus        79 e~~~~~~dG~~~~v~~~~~~i~~-~~~--~~~~~v~rD  113 (113)
T d1v9ya_          79 ELQLEKKDGSKIWTRFALSKVSA-EGK--VYYLALVRD  113 (113)
T ss_dssp             EEEEECTTSCEEEEEEEEEEEEE-TTE--EEEEEEEEC
T ss_pred             eeeeccccceeEEEEEEEEEEEE-CCe--EEEEEEEEC
Confidence            66778999999999999999987 444  346777776

>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=99.51  E-value=1.4e-14  Score=100.30  Aligned_cols=67  Identities=45%  Similarity=0.942  Sum_probs=62.5

Q ss_pred             cCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhccccee
Q 021027          250 IKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQACT  316 (318)
Q Consensus       250 ~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~~~~~  316 (318)
                      +.++++++|+..||++|+|||++|++|+||+++|++|+++..+.+|+..+...+.++++++.+++|+
T Consensus         2 i~~~~vi~Da~~pdg~Ii~vN~a~~~~~Gy~~~El~G~~~~~l~~~~~~~~~~~~~~~~l~~~~~~~   68 (109)
T d1n9la_           2 LRHTFVVADATLPDCPLVYASEGFYAMTGYGPDEVLGHNCRFLQGEGTDPKEVQKIRDAIKKGEACS   68 (109)
T ss_dssp             CSCEEEEEETTSTTCCEEEECHHHHHHHCCCHHHHTTSCGGGGCCTTCCHHHHHHHHHHHHHTCCEE
T ss_pred             ccceEEEEeCCCCCCeEEEEcHHHHHHHCcCHHHHcCCcceeeecccCCHHHhhhhhhHhhcCCcee
Confidence            4789999998777889999999999999999999999999999999999999999999999999885

>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=99.46  E-value=3.8e-13  Score=95.24  Aligned_cols=111  Identities=13%  Similarity=0.042  Sum_probs=88.0

Q ss_pred             hhHHHHHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCccc-CCCCChHHHHHHHHHHHhcCCeE
Q 021027           15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQ-GPRTNRRTIMEIREAIREERPIE   93 (318)
Q Consensus        15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~-~~~~~~~~~~~~~~~~~~~~~~~   93 (318)
                      +..+.+..+++++|.|++++|.+   |+++++|+++++++|+++++++|+++..++ ++.....+...+.+++..+....
T Consensus        14 ~~~~~~d~~ld~~p~gi~~lD~~---G~i~~~N~a~~~l~G~~~~e~iG~~~~~~~~p~~~~~~~~~~~~~~~~~g~~~~   90 (125)
T d1nwza_          14 TLAKMDDGQLDGLAFGAIQLDGD---GNILQYNAAEGDITGRDPKQVIGKNFFKDVAPCTDSPEFYGKFKEGVASGNLNT   90 (125)
T ss_dssp             HTTTCCHHHHTTCSSEEEEEETT---CBEEEECHHHHHHHCCCHHHHTTSBCCCCCCGGGCSTTTHHHHHHHHHHTCCEE
T ss_pred             HHHHHHHHHHhCCCccEEEEeCC---CCEEEEcHHHHHhhccchHhhcCCCHHHccCchhhhhheeeeceeeeecCCcce
Confidence            44456678999999999999999   999999999999999999999999976555 44455566777888888887766


Q ss_pred             EEEEEEecCCcEEEEEEEEEeeccCCCCceeEEEEEEecc
Q 021027           94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPI  133 (318)
Q Consensus        94 ~~~~~~~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DI  133 (318)
                      ......+++|..+|+.++..+..+   |.  .+..+.+||
T Consensus        91 ~~~~~~~~~G~~~~v~v~l~~~~~---g~--~~~v~V~di  125 (125)
T d1nwza_          91 MFEYTFDYQMTPTKVKVHMKKALS---GD--SYWVFVKRV  125 (125)
T ss_dssp             EEEEEECTTSCCEEEEEEEEECSS---SS--EEEEEEEEC
T ss_pred             EEEEEeccCCcEEEEEEEEEEecC---CC--EEEEEEEEC
Confidence            666667899999999999888755   33  233455654

>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=2.2e-12  Score=88.85  Aligned_cols=95  Identities=16%  Similarity=-0.005  Sum_probs=76.4

Q ss_pred             HHHHHhcCCCeEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCccc-CCCCChHHHHHHHHHHHhcCCeEEEEEE
Q 021027           20 VHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQ-GPRTNRRTIMEIREAIREERPIEVNLLN   98 (318)
Q Consensus        20 ~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~   98 (318)
                      +.++++++|++++++|.+   |+|+++|+++++++||++++++|+++..++ ++...+.+...+.+.+..+.........
T Consensus         5 ~~A~ld~~p~gvi~~D~~---G~I~~~N~aa~~~~G~~~eellG~~~~~~~~p~~~~~~~~~~~~~~~~~g~~~~~~~~~   81 (110)
T d1mzua_           5 GTAEFDALPVGAIQVDGS---GVIHRYNRTESRLSGRIPERVIGRNFFTEVAPCTNIPAFSGRFMDGVTSGTLDARFDFV   81 (110)
T ss_dssp             -CTTGGGCSSEEEEEETT---CBEEEECHHHHHHHCCCHHHHTTSBCCCCCCGGGCSTTTHHHHHHHHHTSCCEEEEEEE
T ss_pred             HHHHHhCCCcEEEEEcCC---CCEEEeHHHHHHHHcCCHHHHcCCCHHHhcCChhhhHHHHHHHHHHHhccccCcceEEE
Confidence            456899999999999999   999999999999999999999999975544 4455566677788888887764432233


Q ss_pred             EecCCcEEEEEEEEEeecc
Q 021027           99 YKKDGTPFWMLFKMSLVFG  117 (318)
Q Consensus        99 ~~~~g~~~~~~~~~~~i~~  117 (318)
                      .+++|..+++.++..+...
T Consensus        82 l~~~G~~~~v~v~~~~~~~  100 (110)
T d1mzua_          82 FDFQMAPVRVQIRMQNAGV  100 (110)
T ss_dssp             EECSSCEEEEEEEEEECSS
T ss_pred             EecCCceEEEEEEEEEecC
Confidence            5789999999999888754

>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=99.37  E-value=5.5e-13  Score=91.23  Aligned_cols=64  Identities=48%  Similarity=0.930  Sum_probs=60.3

Q ss_pred             cEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhccccee
Q 021027          253 SFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQACT  316 (318)
Q Consensus       253 ~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~~~~~  316 (318)
                      .++++|+..||++|+|||++|++++||+.+|++|+++.++.++.+.+...+.+..+++.+++|+
T Consensus         2 ~fvi~d~~~pd~~I~y~N~a~~~~~G~s~~e~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   65 (104)
T d1jnua_           2 SFVITDPRLPDNPIIFASDRFLELTEYTREEVLGNNCRFLQGRGTDRKAVQLIRDAVKEQRDVT   65 (104)
T ss_dssp             EEEEECTTSTTCCEEEECHHHHHHHTCCHHHHTTSCGGGGCCTTSCHHHHHHHHHHHHHTCCEE
T ss_pred             eEEEEcCCCCCCEEEEEcHHHHHHHCcCHHHHCCccceeccccccchHHHhhhhhhhhcCceeE
Confidence            5789998878889999999999999999999999999999999999999999999999999885

>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=99.31  E-value=6.8e-13  Score=91.53  Aligned_cols=69  Identities=9%  Similarity=0.003  Sum_probs=59.3

Q ss_pred             HHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCC-CCCHHHHHHHHHHHhcccc
Q 021027          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGV-DTDTTVLYQIKESIQTEQA  314 (318)
Q Consensus       243 l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~-~~~~~~~~~~~~~l~~~~~  314 (318)
                      +..+++++|++|+++|.+|   +|++||+++++|+||+++|++|+++.+++.| ...+.+...+.+++++|+.
T Consensus         5 ~~A~ld~~p~gvi~~D~~G---~I~~~N~aa~~~~G~~~eellG~~~~~~~~p~~~~~~~~~~~~~~~~~g~~   74 (110)
T d1mzua_           5 GTAEFDALPVGAIQVDGSG---VIHRYNRTESRLSGRIPERVIGRNFFTEVAPCTNIPAFSGRFMDGVTSGTL   74 (110)
T ss_dssp             -CTTGGGCSSEEEEEETTC---BEEEECHHHHHHHCCCHHHHTTSBCCCCCCGGGCSTTTHHHHHHHHHTSCC
T ss_pred             HHHHHhCCCcEEEEEcCCC---CEEEeHHHHHHHHcCCHHHHcCCCHHHhcCChhhhHHHHHHHHHHHhcccc
Confidence            4467899999999999997   9999999999999999999999998765554 4567778889899888864

>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=99.26  E-value=3e-12  Score=89.03  Aligned_cols=104  Identities=15%  Similarity=0.141  Sum_probs=80.2

Q ss_pred             hcCCCeEEEEcC-CCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhcC----CeEEEEEEE
Q 021027           25 DELPDSFTITDP-SISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREER----PIEVNLLNY   99 (318)
Q Consensus        25 ~~~~~~i~~~d~-~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~   99 (318)
                      +.+.++|+++|. +   |.|+++|++++++|||+.++++|+++.++.++.........+...+..+.    .+..++...
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            456788999994 6   99999999999999999999999999998887766554443333333332    122356678


Q ss_pred             ecCCcEEEEEEEEEeeccCCCCceeEEEEEEeccc
Q 021027          100 KKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV  134 (318)
Q Consensus       100 ~~~g~~~~~~~~~~~i~~~~~g~~~~~i~~~~DIt  134 (318)
                      +++|..+|+.++..++..  +|.. .++++++||+
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            899999999999999976  4544 4789999994

>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=99.25  E-value=3.7e-12  Score=90.76  Aligned_cols=71  Identities=21%  Similarity=0.205  Sum_probs=62.4

Q ss_pred             chhHHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhccc
Q 021027          240 SSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQ  313 (318)
Q Consensus       240 ~~~l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~~  313 (318)
                      +.+++.++++++++|+++|.+|   +|++||+++++|+||+++|++|+++..+.++.........+...+..+.
T Consensus        15 e~~~~~i~~~~~~~i~~~d~~g---~i~~~N~~~~~l~Gy~~~el~g~~~~~~~~~~~~~~~~~~~~~~~~~~~   85 (130)
T d1ew0a_          15 DAHLRSILDTVPDATVVSATDG---TIVSFNAAAVRQFGYAEEEVIGQNLRILMPEPYRHEHDGYLQRYMATGE   85 (130)
T ss_dssp             TSCHHHHHTTCSSEEEEEETTS---BEEEECHHHHHHHCCCHHHHTTSBGGGGSCTTTGGGHHHHHHHHHHHCC
T ss_pred             HHHHHHHHHcCCCeEEEEeCCc---cEEEEHHHHHHhhcCCHHHhcCCccccccccchhHHHHHHHHHHHHhCC
Confidence            4458899999999999999997   9999999999999999999999999999888887777777777776554

>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=99.23  E-value=8.2e-12  Score=86.15  Aligned_cols=64  Identities=25%  Similarity=0.526  Sum_probs=57.0

Q ss_pred             cEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCccc--ccCCCCCHHHHHHHHHHHhccccee
Q 021027          253 SFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRF--LNGVDTDTTVLYQIKESIQTEQACT  316 (318)
Q Consensus       253 ~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~--l~~~~~~~~~~~~~~~~l~~~~~~~  316 (318)
                      .++|+|+.++|++|+|||++|++|+||+++|++|+++..  +.+|+..+.....+..+++++++++
T Consensus         3 ~f~i~~~~~~d~~I~~~N~a~~~l~G~~~~eiiG~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~   68 (110)
T d1bywa_           3 KFIIANARVENCAVIYCNDGFCELCGYSRAEVMQRPCTCDFLHGPCTQRRAAAQIAQALLGAEERK   68 (110)
T ss_dssp             EEEEEETTSSSCBEEEECHHHHHHHTCCHHHHTTSBTTCGGGCCTTCCHHHHHHHHHHHHTTCCEE
T ss_pred             eEEEEcCCCCCCEEEEEcHHHHHHhCCCHHHhcccCcccccceeeheecccccccchhhccccccc
Confidence            478899988899999999999999999999999998865  4467788899999999999998875

>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=99.20  E-value=1.2e-11  Score=85.65  Aligned_cols=67  Identities=25%  Similarity=0.301  Sum_probs=55.6

Q ss_pred             HHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhcc
Q 021027          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTE  312 (318)
Q Consensus       243 l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~  312 (318)
                      |..++++++++|+++|.+|   +|+++|+++++|+||+++|++|+++..+.++.........+...+..+
T Consensus         3 ~~~~~e~~~d~i~~~d~~g---~i~~~N~~~~~l~Gy~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~   69 (113)
T d1v9ya_           3 FFPALEQNMMGAVLINEND---EVMFFNPAAEKLWGYKREEVIGNNIDMLIPRDLRPAHPEYIRHNREGG   69 (113)
T ss_dssp             HHHHHHTCSSEEEEECTTS---BEEEECHHHHHHHSCCGGGTTTSBGGGGSCGGGTTTHHHHHHHHHC--
T ss_pred             HHHHHHcCcCcEEEEeCCC---CEEEEchhHhhhhccchhhhcCcceecccccccccccccccccccccc
Confidence            6789999999999999987   999999999999999999999999998887666655555555555433

>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=99.13  E-value=2.2e-11  Score=85.91  Aligned_cols=70  Identities=16%  Similarity=0.077  Sum_probs=59.7

Q ss_pred             HHHHHhccCCcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCC-CCCHHHHHHHHHHHhcccce
Q 021027          243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGV-DTDTTVLYQIKESIQTEQAC  315 (318)
Q Consensus       243 l~~~~~~~~~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~-~~~~~~~~~~~~~l~~~~~~  315 (318)
                      +..+++++|+||+++|.+|   +|+++|+++++++||++++++|+++.+++.| ...+.+...+.+++.+|...
T Consensus        19 ~d~~ld~~p~gi~~lD~~G---~i~~~N~a~~~l~G~~~~e~iG~~~~~~~~p~~~~~~~~~~~~~~~~~g~~~   89 (125)
T d1nwza_          19 DDGQLDGLAFGAIQLDGDG---NILQYNAAEGDITGRDPKQVIGKNFFKDVAPCTDSPEFYGKFKEGVASGNLN   89 (125)
T ss_dssp             CHHHHTTCSSEEEEEETTC---BEEEECHHHHHHHCCCHHHHTTSBCCCCCCGGGCSTTTHHHHHHHHHHTCCE
T ss_pred             HHHHHhCCCccEEEEeCCC---CEEEEcHHHHHhhccchHhhcCCCHHHccCchhhhhheeeeceeeeecCCcc
Confidence            4468899999999999998   9999999999999999999999998776655 45566778888888877653

>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=99.05  E-value=1.4e-10  Score=79.31  Aligned_cols=95  Identities=13%  Similarity=0.162  Sum_probs=74.1

Q ss_pred             EEEEcCCCCCCcEEEecHhHHHhcCCCh-hhhcCCCCCcccCCCCChH--HHHHHHHHHHhcCCeEEEEEEEecCCcEEE
Q 021027           31 FTITDPSISGHPIVFASRGFLKMSGFSR-AEIIGRNGRMFQGPRTNRR--TIMEIREAIREERPIEVNLLNYKKDGTPFW  107 (318)
Q Consensus        31 i~~~d~~~~~~~i~~~N~~~~~~~G~~~-~e~~g~~~~~l~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~  107 (318)
                      +.-.|.+   |+++++|+++.+++||.+ ++++|+++.++++|++.+.  ........+..+.....+++++++||..+|
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            3456778   999999999999999975 8999999999999987643  223345666778778888999999999999


Q ss_pred             EEEEEEeeccCCC-CceeEEEEE
Q 021027          108 MLFKMSLVFGKED-GRATHFVAV  129 (318)
Q Consensus       108 ~~~~~~~i~~~~~-g~~~~~i~~  129 (318)
                      +..++.++++ +. +.+..++++
T Consensus        82 v~t~~~~~~~-~~~~~~~~Ii~~  103 (109)
T d1oj5a_          82 AHTRCKLCYP-QSPDMQPFIMGI  103 (109)
T ss_dssp             EEEEEEEECC-----CCCEEEEE
T ss_pred             EEEEEEEEEC-CCCCcccEEEEE
Confidence            9999999997 44 444444443

>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=98.99  E-value=2.1e-10  Score=78.08  Aligned_cols=60  Identities=23%  Similarity=0.225  Sum_probs=51.1

Q ss_pred             CcEEEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhcccc
Q 021027          252 QSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQA  314 (318)
Q Consensus       252 ~~i~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~~~  314 (318)
                      +||+++|.+|   +|+++|+++++|+||+++|++|+++..+.++.........+...+..+..
T Consensus         1 dgi~~~D~~G---~I~~~N~a~~~l~Gy~~~el~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~   60 (106)
T d1xj3a1           1 DAMIVIDGHG---IIQLFSTAAERLFGWSELEAIGQNVNILMPEPDRSRHDSYISRYRTTSDP   60 (106)
T ss_dssp             CCEEEEETTS---BEEEECHHHHHHHCCCHHHHTTSBGGGGSCTTHHHHHHHHHHHHHHHCCC
T ss_pred             CEEEEECCCC---cEEEEcHHHHHHhhhchHhhcCCCcccccccccccchhhhhhhhhhhccc
Confidence            6899999998   99999999999999999999999999998887777766666666655543

>d1ll8a_ d.110.3.5 (A:) N-terminal PAS domain of Pas kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: N-terminal PAS domain of Pas kinase
domain: N-terminal PAS domain of Pas kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.89  E-value=4.2e-10  Score=77.82  Aligned_cols=62  Identities=16%  Similarity=0.254  Sum_probs=51.5

Q ss_pred             hccCCcEEEecC-CCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhcc
Q 021027          248 GRIKQSFVLIDP-HLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTE  312 (318)
Q Consensus       248 ~~~~~~i~i~d~-~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~  312 (318)
                      ..+.++|+++|. +|   .|++||+++++++||+++|++|+++.+|.++.+.......+...++++
T Consensus         5 ~~~n~AI~~id~~~G---~I~~~N~a~~~l~Gy~~~el~g~~~~~l~~~~~~~~~~~~~~~~~~~~   67 (114)
T d1ll8a_           5 PEFNKAIFTVDAKTT---EILVANDKACGLLGYSSQDLIGQKLTQFFLRSDSDVVEALSEEHMEAD   67 (114)
T ss_dssp             TTTTCEEEEEETTTC---BEEEECTTHHHHHTCCTTTTTTSBGGGGSSCTTTHHHHHTTSSTTSSS
T ss_pred             hhcCcEEEEEECCCC---EEEEECHHHHHhhcCCHHHHcCCCeeeecCcccHHHHHHHHHHHHhcC
Confidence            346889999996 45   999999999999999999999999999998887776666555555544

>d1p97a_ d.110.3.7 (A:) Hypoxia-inducible factor Hif2a, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Hypoxia-inducible factor Hif2a, C-terminal domain
domain: Hypoxia-inducible factor Hif2a, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.71  E-value=2.8e-09  Score=73.51  Aligned_cols=62  Identities=15%  Similarity=0.214  Sum_probs=52.2

Q ss_pred             CCcEEE--ecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhcccce
Q 021027          251 KQSFVL--IDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTEQAC  315 (318)
Q Consensus       251 ~~~i~i--~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~~~~  315 (318)
                      +...++  .|.+|   +|+|||+++++++||+++|++|+++.++++|++.+.+.+.+...+..+..+
T Consensus         4 d~~~fi~r~~~dG---~i~~~N~~~~~~~G~~~~el~g~~~~~~~~~ed~~~~~~~~~~~~~~~~~~   67 (114)
T d1p97a_           4 DSKTFLSRHSMDM---KFTYCDDRITELIGYHPEELLGRSAYEFYHALDSENMTKSHQNLCTKGQVV   67 (114)
T ss_dssp             CCEEEEEEECTTT---SCSEECTTHHHHTSSCHHHHTTSCHHHHSCSSSHHHHHHHHHHHTTTSEEE
T ss_pred             CcCEEEEEECCCC---cEEEECHHHHHHcCCCccccccccccccccccccccceeeeeeccccccee
Confidence            344444  57666   999999999999999999999999999999999888888888887766554

>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=98.09  E-value=4.7e-07  Score=61.28  Aligned_cols=57  Identities=11%  Similarity=0.053  Sum_probs=44.9

Q ss_pred             EecCCCCCCCeeEecHHHHHHhCCCc-ccccCCCcccccCCCCCHH--HHHHHHHHHhcccce
Q 021027          256 LIDPHLPDMPMVYASDAFLKLTGYDR-NEVVGQNCRFLNGVDTDTT--VLYQIKESIQTEQAC  315 (318)
Q Consensus       256 i~d~~~~~~~i~~~N~a~~~~~Gy~~-~el~G~~~~~l~~~~~~~~--~~~~~~~~l~~~~~~  315 (318)
                      -.|.+|   +|+++|+++++++||.+ +||+|+++.+|+||+|.+.  .......++..|.++
T Consensus         7 rh~~~g---~~~~vd~~~~~~~gy~~~eelig~s~~~f~HPeD~~~~~~~~~~~~~~~~g~~~   66 (109)
T d1oj5a_           7 KQDTTG---KIISIDTSSLRAAGRTGWEDLVRKCIYAFFQPQGREPSYARQLFQEVMTRGTAS   66 (109)
T ss_dssp             EECTTC---CEEEEECHHHHTTCCSCHHHHHHHHHHHHTSCBTTBCCHHHHHHHHHHHHSEEE
T ss_pred             EECCCc---eEEEECHHHhhHhhcCCHHHHcCCcHHHeECcccchHHHhhHHHHHHHhhcccc
Confidence            346665   99999999999999986 8999999999999998653  233456666666654

>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=97.48  E-value=3.6e-05  Score=52.08  Aligned_cols=52  Identities=6%  Similarity=0.075  Sum_probs=39.5

Q ss_pred             EEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHHHHHHHHHHHhcc
Q 021027          255 VLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQIKESIQTE  312 (318)
Q Consensus       255 ~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~~~~~~~~~l~~~  312 (318)
                      +++|..  |++|+||+++...++|+++++++|+++.+++++.+    ...+++.++..
T Consensus        21 lvld~~--d~~I~~vS~N~~~lLG~~~~~llG~~l~dll~~~~----~~~i~~~l~~~   72 (114)
T d2oola2          21 FVVSET--DLRIASVSANVEDLLRQPPASLLNVPIAHYLTAAS----AARLTHALHGG   72 (114)
T ss_dssp             EEECTT--TCBEEEEETTHHHHHSSCGGGGTTCBGGGGBCHHH----HHHHHHHHCC-
T ss_pred             EEEECC--CCEEEEEcCCHHHHhCCChHHHcCCCHHHhCCHHH----HHHHHHHHhcC
Confidence            445532  35999999999999999999999999999996644    44555555433

>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=97.28  E-value=0.00023  Score=47.96  Aligned_cols=46  Identities=9%  Similarity=0.034  Sum_probs=37.0

Q ss_pred             eEEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChH
Q 021027           30 SFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRR   77 (318)
Q Consensus        30 ~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~   77 (318)
                      .++++|..  +++|++++++...++|+++++++|+++.+++++++...
T Consensus        19 ~Llvld~~--d~~I~~vS~N~~~lLG~~~~~llG~~l~dll~~~~~~~   64 (114)
T d2oola2          19 YLFVVSET--DLRIASVSANVEDLLRQPPASLLNVPIAHYLTAASAAR   64 (114)
T ss_dssp             EEEEECTT--TCBEEEEETTHHHHHSSCGGGGTTCBGGGGBCHHHHHH
T ss_pred             EEEEEECC--CCEEEEEcCCHHHHhCCChHHHcCCCHHHhCCHHHHHH
Confidence            34556642  39999999999999999999999999988887754333

>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=95.05  E-value=0.0078  Score=40.80  Aligned_cols=47  Identities=11%  Similarity=0.150  Sum_probs=35.1

Q ss_pred             CcE-EEecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccCCCCCHH
Q 021027          252 QSF-VLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTT  300 (318)
Q Consensus       252 ~~i-~i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~~~~~~~  300 (318)
                      -|+ +..|..  +++|+.++.....++|+++++++|+++.+++.+.....
T Consensus        26 hG~LLald~~--~~~I~~aS~N~~~~lG~~~~~lLG~~l~~ll~~~~~~~   73 (127)
T d2veaa3          26 HGLVVVLQEP--DLTISQISANCTGILGRSPEDLLGRTLGEVFDSFQIDP   73 (127)
T ss_dssp             TSEEEEEETT--TTEEEEEETTHHHHTSCCTTTSSTTTTTTTSBCC----
T ss_pred             CeEEEEEECC--CCEEEEEcCCHHHHhCcChHHHcCCCHHHHCCHHHHHH
Confidence            344 344532  35999999999999999999999999999986655443

>d2veaa3 d.110.3.9 (A:4-130) Phytochrome-like protein Cph1 {Synechocystis sp. pcc 6803 [TaxId: 1148]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: BphP N-terminal domain-like
domain: Phytochrome-like protein Cph1
species: Synechocystis sp. pcc 6803 [TaxId: 1148]

Probab=94.78  E-value=0.022  Score=38.50  Aligned_cols=45  Identities=13%  Similarity=0.062  Sum_probs=34.6

Q ss_pred             EEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCCCCChH
Q 021027           31 FTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRR   77 (318)
Q Consensus        31 i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~   77 (318)
                      ++++|..  ++++..++.....++|.++++++|+++..++.+.....
T Consensus        29 LLald~~--~~~I~~aS~N~~~~lG~~~~~lLG~~l~~ll~~~~~~~   73 (127)
T d2veaa3          29 VVVLQEP--DLTISQISANCTGILGRSPEDLLGRTLGEVFDSFQIDP   73 (127)
T ss_dssp             EEEEETT--TTEEEEEETTHHHHTSCCTTTSSTTTTTTTSBCC----
T ss_pred             EEEEECC--CCEEEEEcCCHHHHhCcChHHHcCCCHHHHCCHHHHHH
Confidence            4556642  38999999999999999999999999988886654333

>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=93.81  E-value=0.13  Score=34.48  Aligned_cols=40  Identities=10%  Similarity=0.034  Sum_probs=33.4

Q ss_pred             EEEEcCCCCCCcEEEecHhHHHhcCCChhhhcCCCCCcccCC
Q 021027           31 FTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGP   72 (318)
Q Consensus        31 i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~   72 (318)
                      ++++|..  ++.|..++.....++|++.++++|+++..+++.
T Consensus        38 LLald~~--~~~I~~~S~N~~~~lG~~~~~llG~~l~~ll~~   77 (127)
T d2o9ca2          38 LLTADGH--SGEVLQMSLNAATFLGQEPTVLRGQTLAALLPE   77 (127)
T ss_dssp             EEEEETT--TCBEEEEETTHHHHHSSCHHHHTTCBHHHHCTT
T ss_pred             EEEEECC--CCEEEEECCCHHHHhCCChHHHcCCCHHHHCCH
Confidence            4556642  399999999999999999999999998887743

>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=93.25  E-value=0.021  Score=38.60  Aligned_cols=41  Identities=17%  Similarity=0.089  Sum_probs=33.7

Q ss_pred             CcEE-EecCCCCCCCeeEecHHHHHHhCCCcccccCCCcccccC
Q 021027          252 QSFV-LIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNG  294 (318)
Q Consensus       252 ~~i~-i~d~~~~~~~i~~~N~a~~~~~Gy~~~el~G~~~~~l~~  294 (318)
                      -|++ ..|..  ++.|++++.....++|++.++++|+++.+++.
T Consensus        35 hG~LLald~~--~~~I~~~S~N~~~~lG~~~~~llG~~l~~ll~   76 (127)
T d2o9ca2          35 HGALLTADGH--SGEVLQMSLNAATFLGQEPTVLRGQTLAALLP   76 (127)
T ss_dssp             TSEEEEEETT--TCBEEEEETTHHHHHSSCHHHHTTCBHHHHCT
T ss_pred             CeEEEEEECC--CCEEEEECCCHHHHhCCChHHHcCCCHHHHCC
Confidence            4444 44542  35999999999999999999999999999984