Citrus Sinensis ID: 022217

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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-
Protein Sequence
MEAGTIFYSAIPWKPKQPFPRNPSSFPRFIRASASSQSQGGYRGPKPSQDLVADWVMNNDDAVRSLPIYVGGASLLAVLFNRTVSGIAPVADASSSQSRADLLAISLAVTSILTGLVWLSIRPKSITVNSFSLFQVNPKGVECQMICSYLPDSVVSELLWAWESLSAVTCCRSLVVVYDGIYLLQIGMAAESGNSGEAVIVDASKLKQGSVYLGVMRSKAQRYLANLLLYPGRSELPFLPSNTQAVILQPLGDKGIAIIGGDTIRGFTTSDQSWIAFIGEKLDATLAKYSNIVPSMVQEGI
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccEEEcccccHHHHHHHHHHHHHHHHHccccEEEEEEccEEEEEEEEEccccccccHHHHHHHcccccHHHHHHHHcccccccccccccccccccccccccccEEEEEEccccEEEEEEccccccccHHHHHHHHHHHHHHHHHHHHHcccccccccccc
Secondary Structure Prediction (SSPRO)
cccccHHccccccccccccccccccccccccccccccccccccccccccHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHcccccccccccccEEEEEcccccHHHHHHHHHHHHHHHHccccEEEEEEEcccEEEEEEEcccccccccccccccccccccHHHHHHHHccccEEEEEccccccccccccccccccEEEEEEccccEEEEEEccccccccHHHHHHHHHHHHHHHHHHHHHHcccccHHcccc
Coil and Loop (DISEMBL)
MEAGTIFYsaipwkpkqpfprnpssfprfirasassqsqggyrgpkpsqdlVADWVMnnddavrslpiyvGGASLLAVLFNRtvsgiapvadasssqSRADLLAISLAVTSILTGLVWlsirpksitvnsfslfqvnpkgvecqmicsylpdsVVSELLWAWESLSAVTCCRSLVVVYDGIYLLQIGMaaesgnsgeAVIVDASKLKQGSVYLGVMRSKAQRYLANLLlypgrselpflpsntqavilqplgdkgiaiiggdtirgfttsdQSWIAFIGEKLDATLAKYSNIVPSMVQEGI
Flexible Loop (DISEMBL)
meagtifysaipwkpkqpFPRNPSSFPRFIRASassqsqggyrgpKPSQDLVADWVMNNDDAVRSLPIYVGGASLLAVLFNRTVSGIAPVADASSSQSRADLLAISLAVTSILTGLVWLSIRPKSITVNSFSLFQVNPKGVECQMICSYLPDSVVSELLWAWESLSAVTCCRSLVVVYDGIYLLQIGMAAESGNSGEAVIVDASKLKQGSVYLGVMRSKAQRYLANLLLYPGRSELPFLPSNTQAVILQPLGDKGIAIIGGDTIRGFTTSDQSWIAFIGEKLDATLAKYSNIVPSMVQEGI
Low Complexity Region (SEG)
MEAGTIFYSAIPWKPKQpfprnpssfprfIRASASSQSQGGYRGPKPSQDLVADWVMNNDDAVRSLPIYVGGASLLAVLFNRTVSGIAPVADASSSQSRADLLAISLAVTSILTGLVWLSIRPKSITVNSFSLFQVNPKGVECQMICSYLPDSVVSELLWAWESLSAVTCCRSLVVVYDGIYLLQIGMAAESGNSGEAVIVDASKLKQGSVYLGVMRSKAQRYLANLLLYPGRSELPFLPSNTQAVILQPLGDKGIAIIGGDTIRGFTTSDQSWIAFIGEKLDATLAKYSNIVPSMVQEGI
Disordered region (IsUnstruct)
*****IFYSAIPW*************************************LVADWVMNNDDAVRSLPIYVGGASLLAVLFNRTVSGIAPVA********ADLLAISLAVTSILTGLVWLSIRPKSITVNSFSLFQVNPKGVECQMICSYLPDSVVSELLWAWESLSAVTCCRSLVVVYDGIYLLQIGMAAESGNSGEAVIVDASKLKQGSVYLGVMRSKAQRYLANLLLYPGRSELPFLPSNTQAVILQPLGDKGIAIIGGDTIRGFTTSDQSWIAFIGEKLDATLAKYSNIV********
Disordered Region (DISOPRED)
********SAIPWKPKQPF**********************************DWVMNNDDAVRSLPIYVGGASLLAVLFNRTVSGIAPVA***SSQSRADLLAISLAVTSILTGLVWLSI*******************VECQMICSYLPDSVVSELLWAWESLSAVTCCRSLVVVYDGIYLLQIGMAAESGNSGEAVIVDASKLKQ*S*********AQRYLANLLLYPGRSELPFLPSNTQAVILQPLGDKGIAIIGGDTIRGFTTSDQSWIAFIGEKLDATLAKY************
Disordered Region (DISEMBL)
MEAGTIFYSAIPWKPKQPFPRNPSSFPRFIRA*************KPSQDLVADWVMNNDDAVRSLPIYVGGASLLAVLFNRTVSGIAPVA********ADLLAISLAVTSILTGLVWLSIRPKSITVNSFSLFQVNPKGVECQMICSYLPDSVVSELLWAWESLSAVTCCRSLVVVYDGIYLLQIGMAAESGNSGEAVIVDASKLKQGSVYLGVMRSKAQRYLANLLLYPGRSELPFLPSNTQAVILQPLGDKGIAIIGGDTIRGFTTSDQSWIAFIGEKLDATLAKYSNIVPSMVQEGI
Disordered Region (DISPRO)
****TIFYSAIPWKPKQPFPRNPSSF********************PSQDLVADWVMNNDDAVRSLPIYVGGASLLAVLFNRTVSGIAPVADASSSQSRADLLAISLAVTSILTGLVWLSIRPKSIT*NSFSLFQVNPKGVECQMICSYLPDSVVSELLWAWESLSAVTCCRSLVVVYDGIYLLQIGMAAESGNSGEAVIVDASKLKQGSVYLGVMRSKAQRYLANLLLYPGRSELPFLPSNTQAVILQPLGDKGIAIIGGDTIRGFTTSDQSWIAFIGEKLDATLAKYSNIVP*******
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHoooooooooHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHooooooooooooooooooooHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEAGTIFYSAIPWKPKQPFPRNPSSFPRFIRASASSQSQGGYRGPKPSQDLVADWVMNNDDAVRSLPIYVGGASLLAVLFNRTVSGIAPVADASSSQSRADLLAISLAVTSILTGLVWLSIRPKSITVNSFSLFQVNPKGVECQMICSYLPDSVVSELLWAWESLSAVTCCRSLVVVYDGIYLLQIGMAAESGNSGEAVIVDASKLKQGSVYLGVMRSKAQRYLANLLLYPGRSELPFLPSNTQAVILQPLGDKGIAIIGGDTIRGFTTSDQSWIAFIGEKLDATLAKYSNIVPSMVQEGI
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

No hits with e-value below 0.001 by BLAST

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	301
255558330	336	conserved hypothetical protein [Ricinus	0.976	0.875	0.702	1e-113
42562815	297	cofactor assembly of complex C [Arabidop	0.936	0.949	0.715	1e-110
297840573	298	hypothetical protein ARALYDRAFT_475325 [	0.936	0.946	0.709	1e-110
449434863	300	PREDICTED: uncharacterized protein LOC10	0.933	0.936	0.713	1e-109
449523652	300	PREDICTED: uncharacterized LOC101208049	0.933	0.936	0.713	1e-108
5080827	305	Hypothetical protein [Arabidopsis thalia	0.936	0.924	0.693	1e-108
225424815	291	PREDICTED: uncharacterized protein LOC10	0.963	0.996	0.695	1e-101
356501956	299	PREDICTED: uncharacterized protein LOC10	0.963	0.969	0.623	3e-95
51971242	242	hypothetical protein [Arabidopsis thalia	0.787	0.979	0.696	4e-87
218195714	293	hypothetical protein OsI_17698 [Oryza sa	0.827	0.849	0.636	1e-84

>gi|255558330|ref|XP_002520192.1| conserved hypothetical protein [Ricinus communis] gi|223540684|gb|EEF42247.1| conserved hypothetical protein [Ricinus communis]

 Score =  413 bits (1061), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 213/303 (70%), Positives = 242/303 (79%), Gaps = 9/303 (2%)

Query: 1   MEAGTIFYSAIPWKPKQPFP--RNPSSFPRFIRASASSQSQGGYRGPKPSQDLVADWVMN 58
           MEAGTI  ++I ++    FP  R   +   F+RAS+   SQG YRGPKP +DLVADWV N
Sbjct: 41  MEAGTILPTSILFRSPFHFPISRPLQNLRFFVRASSDLNSQGKYRGPKPKRDLVADWVSN 100

Query: 59  NDDAVRSLPIYVGGASLLAVLFNRTVSGIAPVADASSSQSRADLLAISLAVTSILTGLVW 118
           NDD VRSLPIYVGGASLLAVLFNR  SGIAPVADASSSQSRADLL + LAVT+IL GL+W
Sbjct: 101 NDDTVRSLPIYVGGASLLAVLFNRAASGIAPVADASSSQSRADLLTLGLAVTNILAGLIW 160

Query: 119 LSIRPKSITVNSFSLFQVNPKGVECQMICSYLPDSVVSELLWAWESLSAVTCCRSLVVVY 178
           LSI+PKSI++       VNP+GVECQ+I S+LPD VVSELLWAWESLSA TCCRSLVVVY
Sbjct: 161 LSIKPKSISL-------VNPQGVECQIILSHLPDYVVSELLWAWESLSAATCCRSLVVVY 213

Query: 179 DGIYLLQIGMAAESGNSGEAVIVDASKLKQGSVYLGVMRSKAQRYLANLLLYPGRSELPF 238
           D +  LQIGMAAES N GEA+ VDA+KL QGS+   + +S AQ YLANL LYPGR+ELPF
Sbjct: 214 DCVCFLQIGMAAESPNKGEALSVDAAKLMQGSLVQAIKKSGAQSYLANLSLYPGRTELPF 273

Query: 239 LPSNTQAVILQPLGDKGIAIIGGDTIRGFTTSDQSWIAFIGEKLDATLAKYSNIVPSMVQ 298
           LP NTQAVILQPLGDKG+AIIGGDTIRGFTTSDQ+WI FIGEKLD+TLAK     P  +Q
Sbjct: 274 LPLNTQAVILQPLGDKGVAIIGGDTIRGFTTSDQAWITFIGEKLDSTLAKCVISSPLAMQ 333

Query: 299 EGI 301
           + I
Sbjct: 334 DRI 336

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|42562815|ref|NP_176193.2| cofactor assembly of complex C [Arabidopsis thaliana] gi|42571921|ref|NP_974051.1| cofactor assembly of complex C [Arabidopsis thaliana] gi|34146872|gb|AAQ62444.1| At1g59840 [Arabidopsis thaliana] gi|51968666|dbj|BAD43025.1| hypothetical protein [Arabidopsis thaliana] gi|51968878|dbj|BAD43131.1| hypothetical protein [Arabidopsis thaliana] gi|62320426|dbj|BAD94887.1| hypothetical protein [Arabidopsis thaliana] gi|332195505|gb|AEE33626.1| cofactor assembly of complex C [Arabidopsis thaliana] gi|332195506|gb|AEE33627.1| cofactor assembly of complex C [Arabidopsis thaliana]

 Score =  405 bits (1042), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 209/292 (71%), Positives = 235/292 (80%), Gaps = 10/292 (3%)

Query: 1   MEAGTIFYS-AIPWKPKQPFPRNPSSFPRFIRASASSQSQG--GYRGPKPSQDLVADWVM 57
           MEA  I     IPW   + F   P  FPRFIRAS+SS SQ    Y GPKP ++LVAD++ 
Sbjct: 1   MEARIILLRIQIPWSANRQFSHPPLDFPRFIRASSSSTSQKPKTYEGPKPRKNLVADFIS 60

Query: 58  NNDDAVRSLPIYVGGASLLAVLFNRTVSGIAPVADASSSQSRADLLAISLAVTSILTGLV 117
            NDD VRSLPIYVGGASLLAVLFNRTVSGIAPVADASSSQSRADLLA+ LAVT++LTGLV
Sbjct: 61  KNDDLVRSLPIYVGGASLLAVLFNRTVSGIAPVADASSSQSRADLLALGLAVTNLLTGLV 120

Query: 118 WLSIRPKSITVNSFSLFQVNPKGVECQMICSYLPDSVVSELLWAWESLSAVTCCRSLVVV 177
           WLSIRPKSIT        VNPKGVEC+++ S LP S+VSELLWAWESL   TCC+SLV+V
Sbjct: 121 WLSIRPKSIT-------PVNPKGVECKVVESDLPASMVSELLWAWESLKVATCCKSLVIV 173

Query: 178 YDGIYLLQIGMAAESGNSGEAVIVDASKLKQGSVYLGVMRSKAQRYLANLLLYPGRSELP 237
           Y+GI L+QIGM AES    + VIV   KL QGSVY GVM+SKAQ YLANL LYPGRSELP
Sbjct: 174 YNGICLIQIGMVAESPEDKKTVIVKTDKLMQGSVYRGVMKSKAQSYLANLSLYPGRSELP 233

Query: 238 FLPSNTQAVILQPLGDKGIAIIGGDTIRGFTTSDQSWIAFIGEKLDATLAKY 289
           FLP+NTQAVILQPLGDKGIA+IGG+TIRGFT+SDQ+WI+ IGEKLDATL +Y
Sbjct: 234 FLPANTQAVILQPLGDKGIAVIGGNTIRGFTSSDQAWISSIGEKLDATLGRY 285

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297840573|ref|XP_002888168.1| hypothetical protein ARALYDRAFT_475325 [Arabidopsis lyrata subsp. lyrata] gi|297334009|gb|EFH64427.1| hypothetical protein ARALYDRAFT_475325 [Arabidopsis lyrata subsp. lyrata]

 Score =  403 bits (1036), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 208/293 (70%), Positives = 237/293 (80%), Gaps = 11/293 (3%)

Query: 1   MEAGTIFYSAIPWKPKQPFPRNPSSFPRFIRA----SASSQSQGGYRGPKPSQDLVADWV 56
           MEA  I    IPW P + F R PS FPRFIRA    S++SQ    YRGPKPS++LVAD++
Sbjct: 1   MEARIILQIQIPWNPNRKFSRTPSDFPRFIRAYSSSSSTSQKPRSYRGPKPSKNLVADFI 60

Query: 57  MNNDDAVRSLPIYVGGASLLAVLFNRTVSGIAPVADASSSQSRADLLAISLAVTSILTGL 116
             NDD VRSLPIYVGGASLLAVLFNRTVSGIAPVADASSSQSRADLLA+ LAVT++LTGL
Sbjct: 61  SKNDDLVRSLPIYVGGASLLAVLFNRTVSGIAPVADASSSQSRADLLALGLAVTNLLTGL 120

Query: 117 VWLSIRPKSITVNSFSLFQVNPKGVECQMICSYLPDSVVSELLWAWESLSAVTCCRSLVV 176
           VWLSIRPKSIT        V P GVE +++ S LP SVVSELLWAWES    TCC+SLV+
Sbjct: 121 VWLSIRPKSIT-------PVQPDGVEWKVVESGLPASVVSELLWAWESFKVATCCKSLVI 173

Query: 177 VYDGIYLLQIGMAAESGNSGEAVIVDASKLKQGSVYLGVMRSKAQRYLANLLLYPGRSEL 236
           VY+GI L+QIGM AES    +AV+V+  KL QGSVY GVM+SKAQ YLANL LYPGRSEL
Sbjct: 174 VYNGICLIQIGMVAESPEDKKAVVVNTDKLMQGSVYRGVMKSKAQSYLANLSLYPGRSEL 233

Query: 237 PFLPSNTQAVILQPLGDKGIAIIGGDTIRGFTTSDQSWIAFIGEKLDATLAKY 289
           PFLP+NTQAVILQPLGDKGIA+IGG+TIRGFT++DQ+WI+ IGEKLDATL +Y
Sbjct: 234 PFLPANTQAVILQPLGDKGIAVIGGNTIRGFTSADQAWISSIGEKLDATLGRY 286

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449434863|ref|XP_004135215.1| PREDICTED: uncharacterized protein LOC101208049 [Cucumis sativus]

 Score =  399 bits (1026), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 212/297 (71%), Positives = 236/297 (79%), Gaps = 16/297 (5%)

Query: 1   MEAGTIF-YSAIPWKPKQPFPRNPSS----FPRFIRASASSQSQGGYRGPKPSQDLVADW 55
           MEAG  F  ++IPW     F R  SS    FP  +RAS SS SQ  YRGPKPS +LVADW
Sbjct: 1   MEAGIFFPLTSIPWTFN--FKRTHSSLRPSFPLIVRAS-SSTSQRSYRGPKPSTNLVADW 57

Query: 56  VMNNDDAVRSLPIYVGGASLLAVLFNRTVSGIAPVADASSSQSRADLLAISLAVTSILTG 115
           V NNDD VRSLPIYVGG SLL VLFNR VSGIAPVADASSSQSRADLL + LAVT++L G
Sbjct: 58  VSNNDDTVRSLPIYVGGISLLIVLFNRAVSGIAPVADASSSQSRADLLTLGLAVTNVLAG 117

Query: 116 LVWLSIRPKSITVNSFSLFQVNPKGVECQMICSYLPDSVVSELLWAWESLSAVTCCRSLV 175
           LVWLSIRPKSIT        VNP GVE + ICS LPD V SELLW W+SLS VTCCRSLV
Sbjct: 118 LVWLSIRPKSIT-------PVNPLGVENERICSSLPDRVTSELLWVWKSLSEVTCCRSLV 170

Query: 176 VVYDGIYLLQIGMAAESGN-SGEAVIVDASKLKQGSVYLGVMRSKAQRYLANLLLYPGRS 234
           VVYDG  + Q+G AAES   +GEA  V+A KL QGS+Y GV++S+AQ YLANL LYPG+S
Sbjct: 171 VVYDGTCIFQVGFAAESAEGNGEAEHVEAGKLMQGSLYKGVLKSQAQSYLANLSLYPGKS 230

Query: 235 ELPFLPSNTQAVILQPLGDKGIAIIGGDTIRGFTTSDQSWIAFIGEKLDATLAKYSN 291
           ELPFLPSNTQAVILQPLG+KGIAIIGG+TIRGFTTSDQ+WI+F+GEKLDATL+KYSN
Sbjct: 231 ELPFLPSNTQAVILQPLGEKGIAIIGGNTIRGFTTSDQAWISFVGEKLDATLSKYSN 287

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449523652|ref|XP_004168837.1| PREDICTED: uncharacterized LOC101208049 [Cucumis sativus]

 Score =  399 bits (1024), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 212/297 (71%), Positives = 236/297 (79%), Gaps = 16/297 (5%)

Query: 1   MEAGTIF-YSAIPWKPKQPFPRNPSS----FPRFIRASASSQSQGGYRGPKPSQDLVADW 55
           MEAG  F  ++IPW     F R  SS    FP  +RAS SS SQ  YRGPKPS +LVADW
Sbjct: 1   MEAGIFFPLTSIPWTFN--FKRTHSSLRPSFPLIVRAS-SSTSQRSYRGPKPSTNLVADW 57

Query: 56  VMNNDDAVRSLPIYVGGASLLAVLFNRTVSGIAPVADASSSQSRADLLAISLAVTSILTG 115
           V NNDD VRSLPIYVGG SLL VLFNR VSGIAPVADASSSQSRADLL + LAVT++L G
Sbjct: 58  VSNNDDTVRSLPIYVGGISLLIVLFNRAVSGIAPVADASSSQSRADLLTLGLAVTNVLAG 117

Query: 116 LVWLSIRPKSITVNSFSLFQVNPKGVECQMICSYLPDSVVSELLWAWESLSAVTCCRSLV 175
           LVWLSIRPKSIT        VNP GVE + ICS LPD V SELLW W+SLS VTCCRSLV
Sbjct: 118 LVWLSIRPKSIT-------PVNPLGVENERICSSLPDRVTSELLWVWKSLSEVTCCRSLV 170

Query: 176 VVYDGIYLLQIGMAAESGN-SGEAVIVDASKLKQGSVYLGVMRSKAQRYLANLLLYPGRS 234
           VVYDG  + Q+G AAES   +GEA  V+A KL QGS+Y GV++S+AQ YLANL LYPG+S
Sbjct: 171 VVYDGKCIFQVGFAAESAEGNGEAEHVEAGKLMQGSLYKGVLKSQAQSYLANLSLYPGKS 230

Query: 235 ELPFLPSNTQAVILQPLGDKGIAIIGGDTIRGFTTSDQSWIAFIGEKLDATLAKYSN 291
           ELPFLPSNTQAVILQPLG+KGIAIIGG+TIRGFTTSDQ+WI+F+GEKLDATL+KYSN
Sbjct: 231 ELPFLPSNTQAVILQPLGEKGIAIIGGNTIRGFTTSDQAWISFVGEKLDATLSKYSN 287

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|5080827|gb|AAD39336.1|AC007258_25 Hypothetical protein [Arabidopsis thaliana]

 Score =  398 bits (1022), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 208/300 (69%), Positives = 236/300 (78%), Gaps = 18/300 (6%)

Query: 1   MEAGTIFYS-AIPWKPKQPFPRNPSSFPRFIRASASSQSQG--GYRGPKPSQDLVADWVM 57
           MEA  I     IPW   + F   P  FPRFIRAS+SS SQ    Y GPKP ++LVAD++ 
Sbjct: 1   MEARIILLRIQIPWSANRQFSHPPLDFPRFIRASSSSTSQKPKTYEGPKPRKNLVADFIS 60

Query: 58  NNDDAVRSLPIYVGGASLLAVLFNRTVSGIAPVADASSSQSRADLLAISLAVTSILTGLV 117
            NDD VRSLPIYVGGASLLAVLFNRTVSGIAPVADASSSQSRADLLA+ LAVT++LTGLV
Sbjct: 61  KNDDLVRSLPIYVGGASLLAVLFNRTVSGIAPVADASSSQSRADLLALGLAVTNLLTGLV 120

Query: 118 WLSIRPKSITVNSFSLFQVNPKGVECQMICSYLPDSVVSELLWAWESLSAVTCCRSLVVV 177
           WLSIRPKSIT        VNPKGVEC+++ S LP S+VSELLWAWESL   TCC+SLV+V
Sbjct: 121 WLSIRPKSIT-------PVNPKGVECKVVESDLPASMVSELLWAWESLKVATCCKSLVIV 173

Query: 178 YDGIYLLQIGMAAESGNSGEAVIVDASKLKQGSVYLGVMRSKAQR--------YLANLLL 229
           Y+GI L+QIGM AES    + VIV   KL QGSVY GVM+SKA++        YLANL L
Sbjct: 174 YNGICLIQIGMVAESPEDKKTVIVKTDKLMQGSVYRGVMKSKARKNNDCLSESYLANLSL 233

Query: 230 YPGRSELPFLPSNTQAVILQPLGDKGIAIIGGDTIRGFTTSDQSWIAFIGEKLDATLAKY 289
           YPGRSELPFLP+NTQAVILQPLGDKGIA+IGG+TIRGFT+SDQ+WI+ IGEKLDATL +Y
Sbjct: 234 YPGRSELPFLPANTQAVILQPLGDKGIAVIGGNTIRGFTSSDQAWISSIGEKLDATLGRY 293

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225424815|ref|XP_002267988.1| PREDICTED: uncharacterized protein LOC100255235 [Vitis vinifera] gi|296086476|emb|CBI32065.3| unnamed protein product [Vitis vinifera]

 Score =  373 bits (958), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 210/302 (69%), Positives = 244/302 (80%), Gaps = 12/302 (3%)

Query: 1   MEAGTIFYSAIPWKPKQPFPRNPSSFPRFIRASASSQSQGGYRGPKPSQDLVADWVMNND 60
           MEAG +  + IPW+PK     +P +FPRF+RAS  S+SQG YRGPKP +D +ADWV NND
Sbjct: 1   MEAGRLLRTPIPWRPK--LAPSPPTFPRFVRAS--SKSQGRYRGPKPRRDWLADWVSNND 56

Query: 61  DAVRSLPIYVGGASLLAVLFNRTVSGIAPVADASSSQSRADLLAISLAVTSILTGLVWLS 120
           D VRSLPIYVGG SLL+VLFNRT+SGIAPVADASSSQSRADLL + LAVT+IL GLVWLS
Sbjct: 57  DTVRSLPIYVGGVSLLSVLFNRTISGIAPVADASSSQSRADLLTLGLAVTNILAGLVWLS 116

Query: 121 IRPKSITVNSFSLFQVNPKGVECQMICSYLPDSVVSELLWAWESLSAVTCCRSLVVVYDG 180
           IRPKSI+V       VNP+GVE + I   +  S+VSELLW WESLS VTCCRSLV++YD 
Sbjct: 117 IRPKSISV-------VNPQGVESRRIYPNIAASLVSELLWVWESLSVVTCCRSLVILYDS 169

Query: 181 IYLLQIGMAAES-GNSGEAVIVDASKLKQGSVYLGVMRSKAQRYLANLLLYPGRSELPFL 239
           I +LQIGMAAES    GEA+ VDA+KL QGS+Y GVM+S AQ YLANL LYPG+SELPFL
Sbjct: 170 ICILQIGMAAESSAGDGEAMAVDATKLMQGSLYQGVMKSGAQSYLANLSLYPGKSELPFL 229

Query: 240 PSNTQAVILQPLGDKGIAIIGGDTIRGFTTSDQSWIAFIGEKLDATLAKYSNIVPSMVQE 299
           PSNTQAVILQP+GDKGI IIGGDTIRGFT SDQ+WI  IGEK+DA+L+KY N +P  VQ+
Sbjct: 230 PSNTQAVILQPIGDKGIIIIGGDTIRGFTASDQAWITLIGEKVDASLSKYVNNLPVAVQD 289

Query: 300 GI 301
            +
Sbjct: 290 RV 291

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356501956|ref|XP_003519789.1| PREDICTED: uncharacterized protein LOC100776666 [Glycine max]

 Score =  354 bits (909), Expect = 3e-95,   Method: Compositional matrix adjust.
 Identities = 192/308 (62%), Positives = 224/308 (72%), Gaps = 18/308 (5%)

Query: 1   MEAGTIFYSAIPWKPKQPFPRNPSSF------PRFIRASASSQSQGGY--RGPKPSQDLV 52
           MEAGT    ++    + P P N ++       PRF  +S S  S   Y  RGP P +  +
Sbjct: 1   MEAGTAL--SLRLHTRIPIPINTANSNTLLFQPRFTLSSHSPSSFSAYSYRGPTPKRPFL 58

Query: 53  ADWVMNNDDAVRSLPIYVGGASLLAVLFNRTVSGIAPVADASSSQSRADLLAISLAVTSI 112
           ADWV  NDD VR+LPIYVG ASL A+L NR++SGIAPV DA SSQSRADLL + LAVT+I
Sbjct: 59  ADWVSQNDDVVRTLPIYVGSASLFAILLNRSLSGIAPVVDAGSSQSRADLLTLGLAVTNI 118

Query: 113 LTGLVWLSIRPKSITVNSFSLFQVNPKGVECQMICSYLPDSVVSELLWAWESLSAVTCCR 172
           L GLVWLS++PKSITV       VNP+GVEC+ +C+ LP+   +ELLW WESLS  TCCR
Sbjct: 119 LAGLVWLSVKPKSITV-------VNPRGVECKSLCATLPEVARNELLWVWESLSDATCCR 171

Query: 173 SLVVVYDGIYLLQIGMAAESG-NSGEAVIVDASKLKQGSVYLGVMRSKAQRYLANLLLYP 231
           SLVVVY+   +LQIG AAES    G+AV VDA+KL QGSVY GVM+S AQ YLANL LYP
Sbjct: 172 SLVVVYESSCVLQIGFAAESSPGDGDAVSVDANKLMQGSVYQGVMKSGAQSYLANLSLYP 231

Query: 232 GRSELPFLPSNTQAVILQPLGDKGIAIIGGDTIRGFTTSDQSWIAFIGEKLDATLAKYSN 291
           G+SELPFLPSNTQAVILQPLGDKGIAIIGGDTIRGFT SDQ WI +IG KLD++LAKY  
Sbjct: 232 GKSELPFLPSNTQAVILQPLGDKGIAIIGGDTIRGFTGSDQVWITYIGAKLDSSLAKYLK 291

Query: 292 IVPSMVQE 299
             P   Q+
Sbjct: 292 HHPLTSQD 299

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|51971242|dbj|BAD44313.1| hypothetical protein [Arabidopsis thaliana] gi|51971329|dbj|BAD44329.1| hypothetical protein [Arabidopsis thaliana]

 Score =  327 bits (838), Expect = 4e-87,   Method: Compositional matrix adjust.
 Identities = 172/247 (69%), Positives = 192/247 (77%), Gaps = 10/247 (4%)

Query: 1   MEAGTIFYS-AIPWKPKQPFPRNPSSFPRFIRASASSQSQG--GYRGPKPSQDLVADWVM 57
           MEA  I     IPW   + F   P  FPRFIRAS+SS SQ    Y GPKP ++LVAD++ 
Sbjct: 1   MEARIILLRIQIPWSANRQFSHPPLDFPRFIRASSSSTSQKPKTYEGPKPRKNLVADFIS 60

Query: 58  NNDDAVRSLPIYVGGASLLAVLFNRTVSGIAPVADASSSQSRADLLAISLAVTSILTGLV 117
            NDD VRSLPIYVGGASLLAVLFNRTVSGIAPVADASSSQSRADLLA+ LAVT++LTGLV
Sbjct: 61  KNDDLVRSLPIYVGGASLLAVLFNRTVSGIAPVADASSSQSRADLLALGLAVTNLLTGLV 120

Query: 118 WLSIRPKSITVNSFSLFQVNPKGVECQMICSYLPDSVVSELLWAWESLSAVTCCRSLVVV 177
           WLSIRPKSIT        VNPKGVEC+++ S LP S+VSELLWAWESL   TCC+SLV+V
Sbjct: 121 WLSIRPKSIT-------PVNPKGVECKVVESDLPASMVSELLWAWESLKVATCCKSLVIV 173

Query: 178 YDGIYLLQIGMAAESGNSGEAVIVDASKLKQGSVYLGVMRSKAQRYLANLLLYPGRSELP 237
           Y+GI L+QIGM AES    + VIV   KL QGSVY GVM+SKAQ YLANL LYPGRSELP
Sbjct: 174 YNGICLIQIGMVAESPEDKKTVIVKTDKLMQGSVYRGVMKSKAQSYLANLSLYPGRSELP 233

Query: 238 FLPSNTQ 244
           FLP+NTQ
Sbjct: 234 FLPANTQ 240

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|218195714|gb|EEC78141.1| hypothetical protein OsI_17698 [Oryza sativa Indica Group]

 Score =  319 bits (817), Expect = 1e-84,   Method: Compositional matrix adjust.
 Identities = 163/256 (63%), Positives = 193/256 (75%), Gaps = 7/256 (2%)

Query: 33  SASSQSQGGYRGPKPSQDLVADWVMNNDDAVRSLPIYVGGASLLAVLFNRTVSGIAPVAD 92
           S   Q +   R  +P QD V +WV +ND  VR LPI VGGASLLAVL NR VSGIA VAD
Sbjct: 44  SNQQQQEMHIRALQPRQDWVGEWVRSNDTLVRGLPILVGGASLLAVLLNRAVSGIAAVAD 103

Query: 93  ASSSQSRADLLAISLAVTSILTGLVWLSIRPKSITVNSFSLFQVNPKGVECQMICSYLPD 152
           ASSSQSRAD+L ++L+VT IL GLVWLSIRPKSI+        V P+GVEC+ + + + D
Sbjct: 104 ASSSQSRADILTLALSVTDILAGLVWLSIRPKSIS-------PVVPRGVECKRVGTGVLD 156

Query: 153 SVVSELLWAWESLSAVTCCRSLVVVYDGIYLLQIGMAAESGNSGEAVIVDASKLKQGSVY 212
           S + ELLW W+SL+  TCC+SLVVVY G  +LQIG+AA S   G AV+VDA K  QGS+Y
Sbjct: 157 SALRELLWTWDSLTTATCCKSLVVVYGGNCVLQIGVAAGSPEDGNAVMVDAQKFMQGSLY 216

Query: 213 LGVMRSKAQRYLANLLLYPGRSELPFLPSNTQAVILQPLGDKGIAIIGGDTIRGFTTSDQ 272
              M SK Q YLANL LYPGR+ELPFLP+NTQA+ILQP+GDKGIA+IGGDTIRGFT  DQ
Sbjct: 217 RSAMESKKQSYLANLALYPGRTELPFLPANTQALILQPIGDKGIAVIGGDTIRGFTNLDQ 276

Query: 273 SWIAFIGEKLDATLAK 288
           +WIA I +KLDATL+K
Sbjct: 277 AWIAMIADKLDATLSK 292

Source: Oryza sativa Indica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

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	301
TAIR|locus:2025896	297	CCB4 "AT1G59840" [Arabidopsis	0.936	0.949	0.695	9.4e-98

TAIR|locus:2025896 CCB4 "AT1G59840" [Arabidopsis thaliana (taxid:3702)]

 Score = 971 (346.9 bits), Expect = 9.4e-98, P = 9.4e-98
 Identities = 203/292 (69%), Positives = 229/292 (78%)

Query:     1 MEAGTIFYSA-IPWKPKQXXXXXXXXXXXXIRASASSQSQGG--YRGPKPSQDLVADWVM 57
             MEA  I     IPW   +            IRAS+SS SQ    Y GPKP ++LVAD++ 
Sbjct:     1 MEARIILLRIQIPWSANRQFSHPPLDFPRFIRASSSSTSQKPKTYEGPKPRKNLVADFIS 60

Query:    58 NNDDAVRSLPIYVGGASLLAVLFNRTVSGIAPVADASSSQSRADLLAISLAVTSILTGLV 117
              NDD VRSLPIYVGGASLLAVLFNRTVSGIAPVADASSSQSRADLLA+ LAVT++LTGLV
Sbjct:    61 KNDDLVRSLPIYVGGASLLAVLFNRTVSGIAPVADASSSQSRADLLALGLAVTNLLTGLV 120

Query:   118 WLSIRPKSITVNSFSLFQVNPKGVECQMICSYLPDSVVSELLWAWESLSAVTCCRSLVVV 177
             WLSIRPKSIT        VNPKGVEC+++ S LP S+VSELLWAWESL   TCC+SLV+V
Sbjct:   121 WLSIRPKSIT-------PVNPKGVECKVVESDLPASMVSELLWAWESLKVATCCKSLVIV 173

Query:   178 YDGIYLLQIGMAAESGNSGEAVIVDASKLKQGSVYLGVMRSKAQRYLANLLLYPGRSELP 237
             Y+GI L+QIGM AES    + VIV   KL QGSVY GVM+SKAQ YLANL LYPGRSELP
Sbjct:   174 YNGICLIQIGMVAESPEDKKTVIVKTDKLMQGSVYRGVMKSKAQSYLANLSLYPGRSELP 233

Query:   238 FLPSNTQAVILQPLGDKGIAIIGGDTIRGFTTSDQSWIAFIGEKLDATLAKY 289
             FLP+NTQAVILQPLGDKGIA+IGG+TIRGFT+SDQ+WI+ IGEKLDATL +Y
Sbjct:   234 FLPANTQAVILQPLGDKGIAVIGGNTIRGFTSSDQAWISSIGEKLDATLGRY 285


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.318   0.133   0.388    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      301       289   0.00088  115 3  11 22  0.38    34
                                                     33  0.43    37


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  607 (65 KB)
  Total size of DFA:  196 KB (2110 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  20.56u 0.09s 20.65t   Elapsed:  00:00:01
  Total cpu time:  20.56u 0.09s 20.65t   Elapsed:  00:00:01
  Start:  Sat May 11 10:59:07 2013   End:  Sat May 11 10:59:08 2013

GO:0003674 "molecular_function" evidence=ND

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0010190 "cytochrome b6f complex assembly" evidence=IMP

GO:0010207 "photosystem II assembly" evidence=RCA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

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	301
pfam11152	195	pfam11152, DUF2930, Protein of unknown function (D	8e-66

>gnl|CDD|221004 pfam11152, DUF2930, Protein of unknown function (DUF2930)

 Score =  204 bits (521), Expect = 8e-66
 Identities = 77/218 (35%), Positives = 113/218 (51%), Gaps = 23/218 (10%)

Query: 66  LPIYVGGASLLAVLFNRTVSGIAPVADASSSQSRADLLAISLAVTSILTGLVWLSIRPKS 125
           LP+  G    L +L NR  +     AD + SQSRAD+L + LA   IL GL+W   +P+S
Sbjct: 1   LPLIAGLLGGLLLLLNRLST-----ADITPSQSRADVLGLLLAAGLILVGLLWTRAQPRS 55

Query: 126 ITVNSFSLFQVNPKGVECQMICSYLPDSVVSELLWAWESLSAVTCCRSLVVVYDGIYLLQ 185
                     V+ +G +   +   L +++  EL WA   L   T   S++V +DG  LL+
Sbjct: 56  PE-------AVDLEGEQGFELSPDLSEALKEELAWASHLLLTATPAASVLVYWDGQVLLR 108

Query: 186 IGMAAESGNSGEAVIVDASKLKQGSVYLGVMRSKAQRYLANLLLYPGRSELPFLPSNTQA 245
            G+                K + G +    + ++   YL NL LYPGR E  +LP NTQA
Sbjct: 109 RGILGP-----------PVKFEPGEICKRALETQQLVYLVNLKLYPGRIEFDYLPPNTQA 157

Query: 246 VILQPLGDKGIAIIGGDTIRGFTTSDQSWIAFIGEKLD 283
           VI+QPLG++G+ ++GG + R FT SD+ WI    +KL 
Sbjct: 158 VIVQPLGNRGVLVLGGWSPRCFTRSDERWIEGWADKLR 195

This family of proteins has no known function. Length = 195

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	301
PF11152	195	DUF2930: Protein of unknown function (DUF2930); In	100.0
PF13492	129	GAF_3: GAF domain; PDB: 3EEA_A 4DMZ_A 4DN0_A 1VHM_	96.82
PF13185	148	GAF_2: GAF domain; PDB: 2QYB_A 3KSG_B 3KSF_C 3KSI_	96.81
smart00065	149	GAF Domain present in phytochromes and cGMP-specif	96.8
PF01590	154	GAF: GAF domain; InterPro: IPR003018 This domain i	96.33
PRK11061	748	fused phosphoenolpyruvate-protein phosphotransfera	95.74
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	94.15
TIGR02851	180	spore_V_T stage V sporulation protein T. Members o	92.35
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	91.72
COG1956	163	GAF domain-containing protein [Signal transduction	89.73

>PF11152 DUF2930: Protein of unknown function (DUF2930); InterPro: IPR021325 This family of proteins has no known function

Probab=100.00  E-value=6.1e-80  Score=552.01  Aligned_cols=195  Identities=43%  Similarity=0.677  Sum_probs=190.3

Q ss_pred             hhHHHHHHHHHHHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHhhhhcccCCCccccccccccCCCCcccee
Q 022217           66 LPIYVGGASLLAVLFNRTVSGIAPVADASSSQSRADLLAISLAVTSILTGLVWLSIRPKSITVNSFSLFQVNPKGVECQM  145 (301)
Q Consensus        66 LP~~vG~l~~~llL~Nr~lsgiApv~~~t~aQ~RaevLgl~Lsa~liL~Gllw~~~~P~~~~~~~~s~~~V~L~G~e~f~  145 (301)
                      ||+++|+++++++++||+++     +++||||+|||+||++||++|||+|++|+++||+++++       |+|+|+|+|+
T Consensus         1 LPl~vG~l~~~lll~N~~~~-----~~~t~sq~RaevLg~~ls~~liL~g~lw~~l~p~~~~~-------v~L~G~~~f~   68 (195)
T PF11152_consen    1 LPLIVGLLGGSLLLLNRLSG-----ADATPSQSRAEVLGLILSAVLILTGLLWQRLKPRSPEA-------VDLPGEQGFE   68 (195)
T ss_pred             CceEehHHHHHHHHhhhccc-----CCCCHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCc-------cCCCCccceE
Confidence            69999999999999999665     89999999999999999999999999999999999999       9999999999


Q ss_pred             ecCCCCHHHHHHHHHHHHHHhhhccccEEEEEECCEEEEEEeeccCCCCCccchhhcccccchhhHHHHHhhccCceecc
Q 022217          146 ICSYLPDSVVSELLWAWESLSAVTCCRSLVVVYDGIYLLQIGMAAESGNSGEAVIVDASKLKQGSVYLGVMRSKAQRYLA  225 (301)
Q Consensus       146 l~~~Lsd~~k~ELAWas~~LLtnT~a~svlV~~~G~vll~RG~~~~~~~~g~a~~~d~~~~~pG~I~~r~~~~~~~iyL~  225 (301)
                      |++||||++|+||||+||+|||||+|+||+|||||+++||||+++++           ++|+||+||+++|++++++||+
T Consensus        69 l~~~L~~~~k~ELAWas~~LLt~T~a~svlV~~~g~~llrrG~~~~~-----------~~~~~g~i~~~~~~~~~~~yL~  137 (195)
T PF11152_consen   69 LSPDLSDAAKEELAWASYALLTNTNARSVLVYYDGRVLLRRGILGSP-----------SKFKPGPICQRAMESGKLIYLV  137 (195)
T ss_pred             ECCCCCHHHHHHHHHHHHHHHhhCCceEEEEEECCEEEEEeeccCCC-----------CCcchHHHHHHHHhcCCceecc
Confidence            99999999999999999999999999999999999999999999864           3899999999999999999999


Q ss_pred             ccccCCCCCCCCCCCCCCCeeEEEecCCCeEEEEecCCCcccChhhHHHHHHHHHHHH
Q 022217          226 NLLLYPGRSELPFLPSNTQAVILQPLGDKGIAIIGGDTIRGFTTSDQSWIAFIGEKLD  283 (301)
Q Consensus       226 nl~lyPGr~Ef~~LP~ntqsVlvQPig~~Gvlvlgs~s~R~FT~kDe~WI~~iA~KL~  283 (301)
                      |++|||||+||+|||+|||||||||+|++||+|+|||++||||||||+||++|||||+
T Consensus       138 nl~lyPGr~Ef~~lP~ntq~VlvqP~g~~G~lvlgs~~~R~ft~~D~~Wi~~iA~Kl~  195 (195)
T PF11152_consen  138 NLKLYPGRVEFDYLPENTQSVLVQPLGQNGVLVLGSNSPRAFTKSDEAWIAGIADKLR  195 (195)
T ss_pred             ccccCCCchhhhhcCCCCcEEEEEEcCCCeEEEEeeCCccccCHHHHHHHHHHHHhcC
Confidence            9999999999999999999999999999999999999999999999999999999985

>PF13492 GAF_3: GAF domain; PDB: 3EEA_A 4DMZ_A 4DN0_A 1VHM_A

Probab=96.82  E-value=0.007  Score=46.78  Aligned_cols=111  Identities=10%  Similarity=0.156  Sum_probs=72.0

Q ss_pred             HHHhhhccccEEEEE--ECC--EEEEEEeeccCCCCCccchhhcccccchhhHHHHHhhccCceeccccccCCCCCCCCC
Q 022217          163 ESLSAVTCCRSLVVV--YDG--IYLLQIGMAAESGNSGEAVIVDASKLKQGSVYLGVMRSKAQRYLANLLLYPGRSELPF  238 (301)
Q Consensus       163 ~~LLtnT~a~svlV~--~~G--~vll~RG~~~~~~~~g~a~~~d~~~~~pG~I~~r~~~~~~~iyL~nl~lyPGr~Ef~~  238 (301)
                      +.+...+.+..+.|+  .++  +..+..+. ...... .. .+    ...-+++.++.++++.++..+.   +.+.+   
T Consensus        11 ~~l~~~~~~~~~~l~~~d~~~~~~~~~~~~-~~~~~~-~~-~l----~~~~~~~~~~~~~~~~~~~~~~---~~~~~---   77 (129)
T PF13492_consen   11 ELLRELLGADRAALFLLDEDGNRLRVVAGW-GGDPRL-SE-SL----PEDDPLIGRALETGEPVSVPDI---DERDF---   77 (129)
T ss_dssp             HHHHHHST-SEEEEEEEETTCECEEEEEEE-SS-GCG-HH-CE----ETTSHHHHHHHHHTS-EEESTC---CC-TT---
T ss_pred             HHHHHHhCCCEEEEEEEECCCCEEEEEEEe-CCCccc-cc-cC----CCCccHHHHHHhhCCeEEeccc---ccccC---
Confidence            445566666665544  333  34455665 221100 00 00    1345778999999998777553   22222   


Q ss_pred             CCCCCCeeEEEecCC----CeEEEEecCCCcccChhhHHHHHHHHHHHHHHHhh
Q 022217          239 LPSNTQAVILQPLGD----KGIAIIGGDTIRGFTTSDQSWIAFIGEKLDATLAK  288 (301)
Q Consensus       239 LP~ntqsVlvQPig~----~Gvlvlgs~s~R~FT~kDe~WI~~iA~KL~~tL~~  288 (301)
                        .+.+++++.||..    -|+|.++....+.||++|+..++.+|+-+..++++
T Consensus        78 --~~~~s~~~vPl~~~~~~~Gvl~~~~~~~~~~~~~d~~~l~~~a~~~a~alen  129 (129)
T PF13492_consen   78 --LGIRSLLVVPLRSRDRVIGVLCLDSREPEEFSDEDLQLLESLANQLAIALEN  129 (129)
T ss_dssp             --TTTCEEEEEEEEETTEEEEEEEEEECTTCG-SHHHHHHHHHHHHHHHHHHH-
T ss_pred             --CCCCEEEEEEEeECCEEEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHhCC
Confidence              6679999999954    49999999999999999999999999999988763

>PF13185 GAF_2: GAF domain; PDB: 2QYB_A 3KSG_B 3KSF_C 3KSI_A 3KSH_A 3MMH_A 3RFB_B 1F5M_A 3KO6_B 3HCY_A

Probab=96.81  E-value=0.011  Score=46.83  Aligned_cols=71  Identities=11%  Similarity=0.214  Sum_probs=51.5

Q ss_pred             HhhccCceecc-ccccCCCCCCCCCCCCCCCeeEEEecCCC----eEEEEecCCCcccChhhHHHHHHHHHHHHHHHh
Q 022217          215 VMRSKAQRYLA-NLLLYPGRSELPFLPSNTQAVILQPLGDK----GIAIIGGDTIRGFTTSDQSWIAFIGEKLDATLA  287 (301)
Q Consensus       215 ~~~~~~~iyL~-nl~lyPGr~Ef~~LP~ntqsVlvQPig~~----Gvlvlgs~s~R~FT~kDe~WI~~iA~KL~~tL~  287 (301)
                      ++++++++++. +...++.  .....-.|.+++++.||-.+    |+|.+.+..++.||+.|+.+++.+|+-+...|+
T Consensus        73 ~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~s~l~vPl~~~~~~~Gvl~l~~~~~~~f~~~~~~~l~~la~~~a~aie  148 (148)
T PF13185_consen   73 VLRTGEPIIINDDDSSFPP--WELARHPGIRSILCVPLRSGGEVIGVLSLYSKEPNAFSEEDLELLEALADQIAIAIE  148 (148)
T ss_dssp             HHHHTS-EEESCCCGGGST--THHHCCTT-SEEEEEEEEETTEEEEEEEEEESSTT---HHHHHHHHHHHHHHHHHHH
T ss_pred             HHhcCceEEEeCccccccc--hhhhccccCCEEEEEEEeECCEEEEEEEEeeCCCCCcCHHHHHHHHHHHHHHHHHhC
Confidence            37889999988 2222222  22455678999999999543    999999999999999999999999999887764

...

>smart00065 GAF Domain present in phytochromes and cGMP-specific phosphodiesterases

Probab=96.80  E-value=0.0086  Score=44.54  Aligned_cols=80  Identities=15%  Similarity=0.159  Sum_probs=61.4

Q ss_pred             hHHHHHhhccCceeccccccCCCCCCCCCCC-CCCCeeEEEecCCC----eEEEEecC-CCcccChhhHHHHHHHHHHHH
Q 022217          210 SVYLGVMRSKAQRYLANLLLYPGRSELPFLP-SNTQAVILQPLGDK----GIAIIGGD-TIRGFTTSDQSWIAFIGEKLD  283 (301)
Q Consensus       210 ~I~~r~~~~~~~iyL~nl~lyPGr~Ef~~LP-~ntqsVlvQPig~~----Gvlvlgs~-s~R~FT~kDe~WI~~iA~KL~  283 (301)
                      +++.+++++++.++..+..-.|-..+....+ .+..+.++.||..+    |++.+... .+|.|++.|+..+..+|+.+.
T Consensus        57 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~Pl~~~~~~~G~l~~~~~~~~~~~~~~~~~~l~~~~~~i~  136 (149)
T smart00065       57 GLAGRVAETGRPLNIPDVEADPVFALDLLGRYQGVRSFLAVPLVADGELVGVLALHNKDSPRPFTEEDEELLQALANQLA  136 (149)
T ss_pred             ChHHHHHHcCCeEEeechhhCCccccccccceeceeeEEEeeeeecCEEEEEEEEEecCCCCCCCHHHHHHHHHHHHHHH
Confidence            6688999999999988776444111112222 23799999998543    88888887 799999999999999999999


Q ss_pred             HHHhhc
Q 022217          284 ATLAKY  289 (301)
Q Consensus       284 ~tL~~~  289 (301)
                      ..+++.
T Consensus       137 ~~l~~~  142 (149)
T smart00065      137 IALANA  142 (149)
T ss_pred             HHHHHH
Confidence            988763

Mutations within these domains in PDE6B result in autosomal recessive inheritance of retinitis pigmentosa.

>PF01590 GAF: GAF domain; InterPro: IPR003018 This domain is present in phytochromes and cGMP-specific phosphodiesterases

Probab=96.33  E-value=0.012  Score=46.74  Aligned_cols=78  Identities=15%  Similarity=0.208  Sum_probs=64.2

Q ss_pred             hhHHHHHhhccCceeccccccCCCCCCC----CCC------------CCCCCeeEEEecCCC----eEEEEecCCC-ccc
Q 022217          209 GSVYLGVMRSKAQRYLANLLLYPGRSEL----PFL------------PSNTQAVILQPLGDK----GIAIIGGDTI-RGF  267 (301)
Q Consensus       209 G~I~~r~~~~~~~iyL~nl~lyPGr~Ef----~~L------------P~ntqsVlvQPig~~----Gvlvlgs~s~-R~F  267 (301)
                      .++|..++++++.+.+.|..-.|-..+.    ..+            ..+..++++-|+..+    |+|.+....+ |.|
T Consensus        56 ~~~~~~~~~~~~~~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~l~vPi~~~g~~~G~l~l~~~~~~~~~  135 (154)
T PF01590_consen   56 ESICGQVLQSREPIVISDVAADPRFAPQIAAQSALRALSSAERPFLAEYGVRSYLCVPIISGGRLIGVLSLYRTRPGRPF  135 (154)
T ss_dssp             SSHHHHHHHHTSCEEESSSGGSTTSSCHHHHHHTTBTTTHHHHHHHHTTTESEEEEEEEEETTEEEEEEEEEEESSSSS-
T ss_pred             ccHHHHHHhCCCeEeeccccccccccccccccccccccccccccccccccCceeeEeeeecccCcEEEEEEEECCCCCCc
Confidence            5779999999999999999877765555    223            569999999998543    9999999999 999


Q ss_pred             ChhhHHHHHHHHHHHHHHH
Q 022217          268 TTSDQSWIAFIGEKLDATL  286 (301)
Q Consensus       268 T~kDe~WI~~iA~KL~~tL  286 (301)
                      |+.|...++.+|+.+..++
T Consensus       136 ~~~d~~ll~~~a~~~a~ai  154 (154)
T PF01590_consen  136 TEEDLALLESFAQQLAIAI  154 (154)
T ss_dssp             -HHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHhhC
Confidence            9999999999999988764

cGMP-dependent 3',5'-cyclic phosphodiesterase (3.1.4.17 from EC) catalyses the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. A phytochrome is a regulatory photoreceptor which exists in 2 forms that are reversibly interconvertible by light, the PR form that absorbs maximally in the red region of the spectrum, and the PFR form that absorbs maximally in the far-red region. This domain is also found in NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation. NifA interacts with sigma-54.; GO: 0005515 protein binding; PDB: 2Y8H_A 3DBA_B 3CI6_A 3E0Y_B 2W3G_B 2W3D_A 2W3E_A 2Y79_B 2W3H_A 2W3F_A ....

>PRK11061 fused phosphoenolpyruvate-protein phosphotransferase PtsP/GAF domain; Provisional

Probab=95.74  E-value=0.13  Score=55.00  Aligned_cols=84  Identities=20%  Similarity=0.252  Sum_probs=66.5

Q ss_pred             cchh-hHHHHHhhccCceeccccccCCCCCCCC-CCCCCCCeeEEEecCCC----eEEEEecCCCcccChhhHHHHHHHH
Q 022217          206 LKQG-SVYLGVMRSKAQRYLANLLLYPGRSELP-FLPSNTQAVILQPLGDK----GIAIIGGDTIRGFTTSDQSWIAFIG  279 (301)
Q Consensus       206 ~~pG-~I~~r~~~~~~~iyL~nl~lyPGr~Ef~-~LP~ntqsVlvQPig~~----Gvlvlgs~s~R~FT~kDe~WI~~iA  279 (301)
                      +.+| .+|.++.++++++.+.|..--|....++ ..-+++.|+++.|+-.+    |+|-+....+|.||+.|+.++..+|
T Consensus        68 l~~geGi~G~Va~tg~pV~V~Dv~~dprf~~~~~~~~~~~~S~L~VPL~~~geVIGVL~v~~~~~~~Fs~~d~~lL~~LA  147 (748)
T PRK11061         68 LAFDEGIVGLVGRLAEPINLADAQKHPSFKYIPSVKEERFRAFLGVPIIYRRQLLGVLVVQQRELRQFDESEESFLVTLA  147 (748)
T ss_pred             ccCCcchHHHHhccCceEEECCcccCcccccCccccCccceEEEEEEEeeCCEEEEEEEEeeCCCCCCCHHHHHHHHHHH
Confidence            4443 4689999999999999998655432221 12467899999999543    8888999999999999999999999


Q ss_pred             HHHHHHHhhc
Q 022217          280 EKLDATLAKY  289 (301)
Q Consensus       280 ~KL~~tL~~~  289 (301)
                      .-+..+++.-
T Consensus       148 ~~aAiAL~na  157 (748)
T PRK11061        148 TQLAAILSQS  157 (748)
T ss_pred             HHHHHHHHHH
Confidence            9998888653

>TIGR01817 nifA Nif-specific regulatory protein

Probab=94.15  E-value=0.66  Score=47.04  Aligned_cols=79  Identities=10%  Similarity=0.143  Sum_probs=61.2

Q ss_pred             hhHHHHHhhccCceeccccccCCCCCC-CCCCCCCCCeeEEEecCCC----eEEEEecCC-CcccChhhHHHHHHHHHHH
Q 022217          209 GSVYLGVMRSKAQRYLANLLLYPGRSE-LPFLPSNTQAVILQPLGDK----GIAIIGGDT-IRGFTTSDQSWIAFIGEKL  282 (301)
Q Consensus       209 G~I~~r~~~~~~~iyL~nl~lyPGr~E-f~~LP~ntqsVlvQPig~~----Gvlvlgs~s-~R~FT~kDe~WI~~iA~KL  282 (301)
                      -.+|.++.++++++.+.|...-|-... ......+++++||.||..+    |+|.+.+.. ++.||+.|...+..+|+.+
T Consensus        73 ~gi~g~v~~~~~pvii~Dv~~d~~~~~~~~~~~~~~~S~l~VPL~~~g~viGvL~v~s~~~~~~ft~~d~~lL~~lA~~i  152 (534)
T TIGR01817        73 EGAIGQIVATGNSLVVPDVAAEPLFLDRLSLYDPGPVPFIGVPIKADSETIGVLAADRDFRSRERLEEEVRFLEMVANLI  152 (534)
T ss_pred             ccHHHHHHhcCCeEEecccccCchhhhccccccCCcceEEEEEEcCCCEEEEEEEEEeccccccccHHHHHHHHHHHHHH
Confidence            367899999999999998865443211 1233567899999999543    788888864 5788999999999999998


Q ss_pred             HHHHh
Q 022217          283 DATLA  287 (301)
Q Consensus       283 ~~tL~  287 (301)
                      ...+.
T Consensus       153 a~aI~  157 (534)
T TIGR01817       153 GQTVR  157 (534)
T ss_pred             HHHHH
Confidence            88763

This model represents NifA, a DNA-binding regulatory protein for nitrogen fixation. The model produces scores between the trusted and noise cutoffs for a well-described NifA homolog in Aquifex aeolicus (which lacks nitrogenase), for transcriptional activators of alternative nitrogenases (VFe or FeFe instead of MoFe), and truncated forms.

>TIGR02851 spore_V_T stage V sporulation protein T

Probab=92.35  E-value=1.5  Score=39.40  Aligned_cols=116  Identities=10%  Similarity=0.048  Sum_probs=79.5

Q ss_pred             HHHHHHHHHHHHHhhhccccEEEEEECCEEEEEEeeccCCCCCccchhhcccccchhhHHHHHhhccCceeccccccCCC
Q 022217          153 SVVSELLWAWESLSAVTCCRSLVVVYDGIYLLQIGMAAESGNSGEAVIVDASKLKQGSVYLGVMRSKAQRYLANLLLYPG  232 (301)
Q Consensus       153 ~~k~ELAWas~~LLtnT~a~svlV~~~G~vll~RG~~~~~~~~g~a~~~d~~~~~pG~I~~r~~~~~~~iyL~nl~lyPG  232 (301)
                      ...+...=.-+.|...|.+ +|.|..+.++|...|.-...-..+        .  --+.++++|++++.....+.     
T Consensus        53 ~~~~~A~~~aeII~~~t~~-aVaITDr~~ILA~~G~g~d~~~~~--------~--is~~t~~~i~~gk~~~~~~~-----  116 (180)
T TIGR02851        53 ELGDFAKEYAESLYQSLGH-IVLITDRDTVIAVAGVSKKEYLNK--------P--ISDELEDTMEERKTVILSDT-----  116 (180)
T ss_pred             chHHHHHHHHHHHHHHhCC-EEEEECCCcEEEEECCChhhcCCC--------c--cCHHHHHHHHcCCEEEecCC-----
Confidence            3445555567899999999 999999999999888765311000        1  12345888988887765442     


Q ss_pred             CCC--CCCC-CCC--CCeeEEEecCCC----eEEEEecCCCc--ccChhhHHHHHHHHHHHHHHH
Q 022217          233 RSE--LPFL-PSN--TQAVILQPLGDK----GIAIIGGDTIR--GFTTSDQSWIAFIGEKLDATL  286 (301)
Q Consensus       233 r~E--f~~L-P~n--tqsVlvQPig~~----Gvlvlgs~s~R--~FT~kDe~WI~~iA~KL~~tL  286 (301)
                       .|  .... -++  ..+.++.||-.+    |.|.+- ...+  .||+.++.+..++|+=|..-|
T Consensus       117 -~~~~i~c~~~~~~~l~s~ii~Pl~~~g~viGtLkly-~k~~~~~~~~~e~~la~glA~lLS~QL  179 (180)
T TIGR02851       117 -KDGPIEIIDGQEFEYTSQVIAPIIAEGDPIGAVIIF-SKEPGEKLGEVEQKAAETAAAFLGKQM  179 (180)
T ss_pred             -ccceeccccCCCCCcceEEEEEEEECCeEEEEEEEE-ECCccCCCCHHHHHHHHHHHHHHHHhh
Confidence             22  1111 122  568999999432    666666 6666  999999999999998877654

Members of this protein family are the stage V sporulation protein T (SpoVT), a protein of the sporulation/germination program in Bacillus subtilis and related species. The amino-terminal 50 amino acids are nearly perfectly conserved across all endospore-forming bacteria. SpoVT is a DNA-binding transcriptional regulator related to AbrB (See PFAM model pfam04014).

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional

Probab=91.72  E-value=2.2  Score=44.77  Aligned_cols=81  Identities=21%  Similarity=0.241  Sum_probs=62.6

Q ss_pred             hhhHHHHHhhccCceeccccc---cCC-CCCCCCCCCCCCCeeEEEecCC----CeEEEEecCCCcccChhhHHHHHHHH
Q 022217          208 QGSVYLGVMRSKAQRYLANLL---LYP-GRSELPFLPSNTQAVILQPLGD----KGIAIIGGDTIRGFTTSDQSWIAFIG  279 (301)
Q Consensus       208 pG~I~~r~~~~~~~iyL~nl~---lyP-Gr~Ef~~LP~ntqsVlvQPig~----~Gvlvlgs~s~R~FT~kDe~WI~~iA  279 (301)
                      .|.+...++++++++.+.+..   +.+ ++..++....++.++|+.||..    -|+|.+++...+.||++|..-++.+|
T Consensus       255 ~~~l~g~V~~~~~p~lv~~~~~d~~~~~~~~~~~~~~~~~~s~l~vPL~~~~~v~GvL~l~~~~~~~F~~~dl~lL~~iA  334 (686)
T PRK15429        255 AGTLTERVFKSKEMLLINLHERDDLAPYERMLFDTWGNQIQTLCLLPLMSGDTMLGVLKLAQCEEKVFTTTNLKLLRQIA  334 (686)
T ss_pred             ccchHHHHHhcCceEEEECccCcccchhhhhhhhcccccceEEEEEeEEECCEEEEEEEEeeCCCCcCCHHHHHHHHHHH
Confidence            457889999999988774432   111 2233445567899999999843    39999988888999999999999999


Q ss_pred             HHHHHHHhh
Q 022217          280 EKLDATLAK  288 (301)
Q Consensus       280 ~KL~~tL~~  288 (301)
                      +....+++.
T Consensus       335 ~~~A~Aie~  343 (686)
T PRK15429        335 ERVAIAVDN  343 (686)
T ss_pred             HHHHHHHHH
Confidence            999988854

>COG1956 GAF domain-containing protein [Signal transduction mechanisms]

Probab=89.73  E-value=1.2  Score=40.03  Aligned_cols=74  Identities=16%  Similarity=0.244  Sum_probs=63.5

Q ss_pred             hHHHHHhhccCceeccccccCCCCCCCCCCCCCCCeeEEEecCCC----eEEEEecCCCcccChhhHHHHHHHHHHHHHH
Q 022217          210 SVYLGVMRSKAQRYLANLLLYPGRSELPFLPSNTQAVILQPLGDK----GIAIIGGDTIRGFTTSDQSWIAFIGEKLDAT  285 (301)
Q Consensus       210 ~I~~r~~~~~~~iyL~nl~lyPGr~Ef~~LP~ntqsVlvQPig~~----Gvlvlgs~s~R~FT~kDe~WI~~iA~KL~~t  285 (301)
                      -+|..+-++++.+=.-|..-|||-+.=|   +.++|=||.|+-.+    |+|=+=|.++=.||+.||.||+.+|+-|...
T Consensus        83 GVCg~A~~~~~t~~V~DV~~~~ghiaCD---~as~SEIVvPi~~~g~~iGvlDiDS~~~~~Fd~~D~~~Le~~~~~l~~~  159 (163)
T COG1956          83 GVCGTAAATGETVRVDDVHAFPGHIACD---AASNSEIVVPIFKDGKLIGVLDIDSPTPGRFDEEDEAGLEKLAALLEKS  159 (163)
T ss_pred             chhHHHHhcCCeEEecccccCCCccccc---cccCceEEEEEEECCEEEEEEecCCCCcccCCHHHHHHHHHHHHHHHHH
Confidence            5799999999999999999999987776   46889999999654    6666778999999999999999999888765


Q ss_pred             H
Q 022217          286 L  286 (301)
Q Consensus       286 L  286 (301)
                      +
T Consensus       160 ~  160 (163)
T COG1956         160 L  160 (163)
T ss_pred             h
Confidence            4

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	301
3mmh_A	167	FRMSR, methionine-R-sulfoxide reductase; oxidoredu	97.79
3ksh_A	160	Putative uncharacterized protein; FRMSR, free-Met-	97.59
3rfb_A	171	Putative uncharacterized protein; FRMSR, GAF, oxid	97.59
1vhm_A	195	Protein YEBR; structural genomics, unknown functio	97.56
3e0y_A	181	Conserved domain protein; APC87688.2, geobacter su	97.41
3p01_A	184	Two-component response regulator; PSI-2, midwest c	97.4
2w3g_A	153	DOSS, two component sensor histidine kinase DEVS (	97.36
3trc_A	171	Phosphoenolpyruvate-protein phosphotransferase; si	97.31
3ci6_A	171	Phosphoenolpyruvate-protein phosphotransferase; PE	97.27
2zmf_A	189	CAMP and CAMP-inhibited CGMP 3',5'-cyclic phospho	97.04
3o5y_A	165	Sensor protein; GAF domain, histidine, kinase, PSI	96.95
3k2n_A	177	Sigma-54-dependent transcriptional regulator; PSI-	96.93
3oov_A	169	Methyl-accepting chemotaxis protein, putative; str	96.89
2vjw_A	149	GAF-B, GAF family protein; histidine kinase, hypox	96.83
2qyb_A	181	Membrane protein, putative; GAF domain, domain of	96.81
1f5m_A	180	GAF; CGMP binding, signaling protein; 1.90A {Sacch	96.74
3hcy_A	151	Putative two-component sensor histidine kinase PR;	96.66
2e4s_A	189	CAMP and CAMP-inhibited CGMP 3',5'-cyclic phosphod	96.49
3dba_A	180	CONE CGMP-specific 3',5'-cyclic phosphodiesterase	94.88
3ibj_A	691	CGMP-dependent 3',5'-cyclic phosphodiesterase; PDE	94.81
1mc0_A	368	3',5'-cyclic nucleotide phosphodiesterase 2A; GAF	94.72
2lb5_A	208	Sensor histidine kinase; PCB, transferase, GAF dom	94.22
2k2n_A	172	Sensor protein, SYB-CPH1(GAF); phytochrome, GAF do	94.13
1ykd_A	398	Adenylate cyclase; GAF domain, bound cyclic AMP li	93.03
1ykd_A	398	Adenylate cyclase; GAF domain, bound cyclic AMP li	92.47
4glq_A	171	Methyl-accepting chemotaxis protein; chromophore,	92.01
1mc0_A	368	3',5'-cyclic nucleotide phosphodiesterase 2A; GAF	88.03
2w1r_A	123	Spovt, stage V sporulation protein T; regulatory G	87.6
3cit_A	160	Sensor histidine kinase; MEGA: 3.30.450.40, struct	84.57
3ibj_A	691	CGMP-dependent 3',5'-cyclic phosphodiesterase; PDE	81.12

>3mmh_A FRMSR, methionine-R-sulfoxide reductase; oxidoreductase; HET: SME MRD; 1.25A {Neisseria meningitidis} SCOP: d.110.2.0

Probab=97.79  E-value=0.00033  Score=59.67  Aligned_cols=82  Identities=13%  Similarity=0.211  Sum_probs=69.8

Q ss_pred             ccchh-hHHHHHhhccCceeccccccCCCCCCCCCCCCCCCeeEEEecC--CC--eEEEEecCCCcccChhhHHHHHHHH
Q 022217          205 KLKQG-SVYLGVMRSKAQRYLANLLLYPGRSELPFLPSNTQAVILQPLG--DK--GIAIIGGDTIRGFTTSDQSWIAFIG  279 (301)
Q Consensus       205 ~~~pG-~I~~r~~~~~~~iyL~nl~lyPGr~Ef~~LP~ntqsVlvQPig--~~--Gvlvlgs~s~R~FT~kDe~WI~~iA  279 (301)
                      .+.+| -+|.++.++++++.+.|..-+|+....+   .+++|.+|.||-  ++  |||-+.+..++.||+.|+..++.+|
T Consensus        77 ~i~~geGi~G~v~~~g~~~~v~Dv~~~p~~~~~~---~~~~S~i~vPi~~~g~viGVL~i~s~~~~~F~~~d~~~L~~lA  153 (167)
T 3mmh_A           77 RIPFGRGVCGQAWAKGGTVVVGDVDAHPDHIACS---SLSRSEIVVPLFSDGRCIGVLDADSEHLAQFDETDALYLGELA  153 (167)
T ss_dssp             EEETTSHHHHHHHHHTSCEEESCGGGSTTCCCSS---TTCCEEEEEEEEETTEEEEEEEEEESSTTCCCHHHHHHHHHHH
T ss_pred             EeccCCChHHHHHhCCcEEEECCcccCcchhhcC---ccCCeEEEEEeccCCEEEEEEEEecCCCCCCCHHHHHHHHHHH
Confidence            45665 6899999999999999999999854433   579999999994  32  9999999999999999999999999


Q ss_pred             HHHHHHHhhc
Q 022217          280 EKLDATLAKY  289 (301)
Q Consensus       280 ~KL~~tL~~~  289 (301)
                      +-+..++.-+
T Consensus       154 ~~la~~i~~~  163 (167)
T 3mmh_A          154 KILEKRFEAS  163 (167)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHhh
Confidence            9999887643

>3ksh_A Putative uncharacterized protein; FRMSR, free-Met-R-SO, oxidoreductase; 1.50A {Staphylococcus aureus} SCOP: d.110.2.0 PDB: 3ksf_A 3ksi_A 3ksg_A*

Probab=97.59  E-value=0.0013  Score=56.12  Aligned_cols=105  Identities=15%  Similarity=0.256  Sum_probs=79.6

Q ss_pred             ccccEEEEEECCEEEEEEeeccCCCCCccchhhcccccchh-hHHHHHhhccCceeccccccCCCCCCCCCCCCCCCeeE
Q 022217          169 TCCRSLVVVYDGIYLLQIGMAAESGNSGEAVIVDASKLKQG-SVYLGVMRSKAQRYLANLLLYPGRSELPFLPSNTQAVI  247 (301)
Q Consensus       169 T~a~svlV~~~G~vll~RG~~~~~~~~g~a~~~d~~~~~pG-~I~~r~~~~~~~iyL~nl~lyPGr~Ef~~LP~ntqsVl  247 (301)
                      .+.+++-++.+++..  -|-....+.        ...+..| -+|.++.++++++.+.|..-+|+....+   +.++|.|
T Consensus        50 ~~~~gfYL~~~~~L~--l~~~~G~~a--------~~ri~~GeGv~G~aa~~~~~i~V~Dv~~~p~~i~~~---~~~~Sei  116 (160)
T 3ksh_A           50 INWVGFYLLEQNELI--LGPFQGHPA--------CVHIPIGKGVCGTAVSERRTQVVADVHQFKGHIACD---ANSKSEI  116 (160)
T ss_dssp             CSEEEEEEEETTEEE--EEEEEESCC--------CSEEETTSHHHHHHHHHTSCEEESCGGGSTTCCGGG---TTCSEEE
T ss_pred             CCEEEEEEEECCEEE--EEeccCCcc--------cEEeeCCCCHHHHHHhhCCEEEECCcccCccccccC---cccCceE
Confidence            556777666676533  232221110        1245666 6899999999999999999999854432   4689999


Q ss_pred             EEec--CCC--eEEEEecCCCcccChhhHHHHHHHHHHHHHHH
Q 022217          248 LQPL--GDK--GIAIIGGDTIRGFTTSDQSWIAFIGEKLDATL  286 (301)
Q Consensus       248 vQPi--g~~--Gvlvlgs~s~R~FT~kDe~WI~~iA~KL~~tL  286 (301)
                      |.||  +++  |||-+.+..++.|++.|+.+++.+|+-+...+
T Consensus       117 ~VPI~~~g~viGVL~i~s~~~~~F~e~D~~~L~~lA~~la~~~  159 (160)
T 3ksh_A          117 VVPIFKDDKIIGVLDIDAPITDRFDDNDKEHLEAIVKIIEKQL  159 (160)
T ss_dssp             EEEEEETTEEEEEEEEEESSSSCCCHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEECCEEEEEEEEecCCCCCCCHHHHHHHHHHHHHHHHHh
Confidence            9999  333  99999999999999999999999999988765

>3rfb_A Putative uncharacterized protein; FRMSR, GAF, oxidoreductase, SME; HET: SME; 2.30A {Streptococcus pneumoniae}

Probab=97.59  E-value=0.00046  Score=59.77  Aligned_cols=80  Identities=13%  Similarity=0.204  Sum_probs=69.0

Q ss_pred             ccchh-hHHHHHhhccCceeccccccCCCCCCCCCCCCCCCeeEEEec--CCC--eEEEEecCCCcccChhhHHHHHHHH
Q 022217          205 KLKQG-SVYLGVMRSKAQRYLANLLLYPGRSELPFLPSNTQAVILQPL--GDK--GIAIIGGDTIRGFTTSDQSWIAFIG  279 (301)
Q Consensus       205 ~~~pG-~I~~r~~~~~~~iyL~nl~lyPGr~Ef~~LP~ntqsVlvQPi--g~~--Gvlvlgs~s~R~FT~kDe~WI~~iA  279 (301)
                      .+..| -||.++.++++++.+.|..-+|+....+   +.++|.||.||  +++  |||-+.+..++.||+.|+.+++.+|
T Consensus        77 ri~~GeGv~G~va~tg~~i~V~Dv~~~p~~i~~~---~~~~Sei~VPI~~~g~viGVL~i~s~~~~~F~e~D~~~L~~lA  153 (171)
T 3rfb_A           77 RIALGKGVCGEAAHFQETVIVGDVTTYLNYISCD---SLAKSEIVVPMMKNGQLLGVLDLDSSEIEDYDAMDRDYLEQFV  153 (171)
T ss_dssp             EEETTSHHHHHHHHTTSCEEESCTTSCSSCCCSC---TTCCEEEEEEEEETTEEEEEEEEEESSTTCCCHHHHHHHHHHH
T ss_pred             EeeCCcCHHHHHHhhCCEEEECCcccCccccccC---cccCceEEEEEEECCEEEEEEEEecCCCCCCCHHHHHHHHHHH
Confidence            45666 6899999999999999999999864433   47899999999  343  9999999999999999999999999


Q ss_pred             HHHHHHHh
Q 022217          280 EKLDATLA  287 (301)
Q Consensus       280 ~KL~~tL~  287 (301)
                      +-+..++.
T Consensus       154 ~~la~~~~  161 (171)
T 3rfb_A          154 AILLEKTT  161 (171)
T ss_dssp             HHHHHSCB
T ss_pred             HHHHHHhc
Confidence            99988763

>1vhm_A Protein YEBR; structural genomics, unknown function; HET: MES; 2.10A {Escherichia coli} SCOP: d.110.2.1

Probab=97.56  E-value=0.0025  Score=55.68  Aligned_cols=80  Identities=19%  Similarity=0.296  Sum_probs=69.8

Q ss_pred             ccchh-hHHHHHhhccCceeccccccCCCCCCCCCCCCCCCeeEEEecCCC----eEEEEecCCCcccChhhHHHHHHHH
Q 022217          205 KLKQG-SVYLGVMRSKAQRYLANLLLYPGRSELPFLPSNTQAVILQPLGDK----GIAIIGGDTIRGFTTSDQSWIAFIG  279 (301)
Q Consensus       205 ~~~pG-~I~~r~~~~~~~iyL~nl~lyPGr~Ef~~LP~ntqsVlvQPig~~----Gvlvlgs~s~R~FT~kDe~WI~~iA  279 (301)
                      .+..| -+|.++.++++.+.+.|..-+|+....+   .+++|.||.||-.+    |||-+.+..++.||+.|+..++.+|
T Consensus        88 ~i~~GeGi~G~aa~tg~~i~V~Dv~~~p~~~~~~---~~~~S~l~VPI~~~g~viGVL~i~s~~~~~F~e~d~~~L~~lA  164 (195)
T 1vhm_A           88 RIPVGRGVCGTAVARNQVQRIEDVHVFDGHIACD---AASNSEIVLPLVVKNQIIGVLDIDSTVFGRFTDEDEQGLRQLV  164 (195)
T ss_dssp             EEETTSHHHHHHHHHTSCEEESCTTTCTTCCCSC---CCCSEEEEEEEEETTEEEEEEEEEESSTTCCCHHHHHHHHHHH
T ss_pred             EecCCCChHHHHHhcCCEEEECCcccCcchhhcC---CCccEEEEEeEeECCEEEEEEEecCCCCCCCCHHHHHHHHHHH
Confidence            45566 5799999999999999999889865543   47899999999533    9999999999999999999999999


Q ss_pred             HHHHHHHh
Q 022217          280 EKLDATLA  287 (301)
Q Consensus       280 ~KL~~tL~  287 (301)
                      +-+..+++
T Consensus       165 ~~ia~ale  172 (195)
T 1vhm_A          165 AQLEKVLA  172 (195)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99999987

>3e0y_A Conserved domain protein; APC87688.2, geobacter sulfurreducens PCA, structural genomics, PSI-2, midwest center for structural G MCSG; 3.10A {Geobacter sulfurreducens}

Probab=97.41  E-value=0.0025  Score=49.84  Aligned_cols=79  Identities=16%  Similarity=0.275  Sum_probs=61.5

Q ss_pred             hHHHHHhhccCceeccccccCCCCCCCC-CCCCCCCeeEEEecCC----CeEEEEecCCCcccChhhHHHHHHHHHHHHH
Q 022217          210 SVYLGVMRSKAQRYLANLLLYPGRSELP-FLPSNTQAVILQPLGD----KGIAIIGGDTIRGFTTSDQSWIAFIGEKLDA  284 (301)
Q Consensus       210 ~I~~r~~~~~~~iyL~nl~lyPGr~Ef~-~LP~ntqsVlvQPig~----~Gvlvlgs~s~R~FT~kDe~WI~~iA~KL~~  284 (301)
                      .+|.+++++++++++.|..--|....+. ....+.+++++.||-.    -|+|.+.+..++.||+.|...++.+|+.+..
T Consensus        83 ~~~~~~~~~~~~~~i~d~~~~~~~~~~~~~~~~~~~s~l~vPl~~~~~~iGvl~~~~~~~~~f~~~~~~~l~~la~~~a~  162 (181)
T 3e0y_A           83 GITGSVARDGQYISLSRASQDPRYRYFPELQEEKYNSMLSFPIGDKKEVYGVINLNTTSIRSFHEDEIYFVSIIANLILT  162 (181)
T ss_dssp             SSHHHHHHHCCCEEEEEECCCCCC---------CEEEEEEEEEECSSCEEEEEEEEESSCCCCCHHHHHHHHHHHHHHHH
T ss_pred             CeeeehhhcCCeEEecCcccCccccccccccccCcceEEEEEEEeCCeEEEEEEEeeCCCCCCCHHHHHHHHHHHHHHHH
Confidence            4688999999999998886544432221 2235789999999944    2999999999999999999999999999999


Q ss_pred             HHhh
Q 022217          285 TLAK  288 (301)
Q Consensus       285 tL~~  288 (301)
                      +++.
T Consensus       163 al~~  166 (181)
T 3e0y_A          163 AIKL  166 (181)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            8864

>3p01_A Two-component response regulator; PSI-2, midwest center for structural genomics, protein struc initiative, MCSG, signali protein; 2.65A {Nostoc SP}

Probab=97.40  E-value=0.0011  Score=54.06  Aligned_cols=109  Identities=11%  Similarity=0.139  Sum_probs=75.2

Q ss_pred             EEEEEECCEEEEEEeeccCCCCCccchhhcccccchhhHHHHHhhccCceeccccccCCCCCCCC-CCCCCCCeeEEEec
Q 022217          173 SLVVVYDGIYLLQIGMAAESGNSGEAVIVDASKLKQGSVYLGVMRSKAQRYLANLLLYPGRSELP-FLPSNTQAVILQPL  251 (301)
Q Consensus       173 svlV~~~G~vll~RG~~~~~~~~g~a~~~d~~~~~pG~I~~r~~~~~~~iyL~nl~lyPGr~Ef~-~LP~ntqsVlvQPi  251 (301)
                      ++..+.+|+.....+..... +.+..      .+...+++.+++++++++.+.|..--|.-.+-+ +-..+.+++++.||
T Consensus        66 ~i~l~~~~~~~~~~~~~~~~-~~~~~------~~~~~~~~~~~~~~~~~~~i~d~~~~~~~~~~~~~~~~~~~s~l~vPL  138 (184)
T 3p01_A           66 ILQMLEGQTLSTIQGFYSQQ-GTVNN------WLNQDPLTNEAIATGQIQVAANIAKDPKLASISQYQDNGIQSHVVIPI  138 (184)
T ss_dssp             EEEEEETTEEEEEEEEEESS-SSCCC------CGGGCHHHHHHHHHCSCEEESCGGGCHHHHTCHHHHHHTCCEEEEEEE
T ss_pred             EEEEecCCceeeeeeecccc-CccCc------ccCCCcHHHHHHhhCCeEEEeccccCccccchhHHHHhCccEEEEEEE
Confidence            34444667655555523322 11111      233367889999999999988876444111111 11238899999999


Q ss_pred             C--C--CeEEEEecCCCcccChhhHHHHHHHHHHHHHHHhh
Q 022217          252 G--D--KGIAIIGGDTIRGFTTSDQSWIAFIGEKLDATLAK  288 (301)
Q Consensus       252 g--~--~Gvlvlgs~s~R~FT~kDe~WI~~iA~KL~~tL~~  288 (301)
                      -  +  -|+|.+.+..+|.||+.|...++.+|+.+..+++.
T Consensus       139 ~~~~~~~GvL~l~~~~~~~f~~~d~~ll~~lA~q~aiAi~n  179 (184)
T 3p01_A          139 TYRNEMLGVLSLQWQQPISLREDELTLIHLSAQLVAIALTS  179 (184)
T ss_dssp             EETTEEEEEEEEEESSCCCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             EECCEEEEEEEeCcCCCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            4  2  39999999999999999999999999999998875

>2w3g_A DOSS, two component sensor histidine kinase DEVS (GAF family protein); redox sensor, heme, hypoxia, GAF domain, transferase; HET: HEM; 1.40A {Mycobacterium tuberculosis} PDB: 2w3d_A* 2w3f_A* 2w3e_A* 2w3h_A* 2y79_A* 2y8h_A* 2vzw_A*

Probab=97.36  E-value=0.00095  Score=50.84  Aligned_cols=79  Identities=13%  Similarity=0.144  Sum_probs=65.3

Q ss_pred             hHHHHHhhccCceeccccccCCCCCCCCCCCCCCCeeEEEecCC----CeEEEEecCCC-cccChhhHHHHHHHHHHHHH
Q 022217          210 SVYLGVMRSKAQRYLANLLLYPGRSELPFLPSNTQAVILQPLGD----KGIAIIGGDTI-RGFTTSDQSWIAFIGEKLDA  284 (301)
Q Consensus       210 ~I~~r~~~~~~~iyL~nl~lyPGr~Ef~~LP~ntqsVlvQPig~----~Gvlvlgs~s~-R~FT~kDe~WI~~iA~KL~~  284 (301)
                      .++.+++++++.+++.|..--|....+.....+.+++++.||-.    -|+|.+.+..+ |.||+.|...++.+|+.+..
T Consensus        62 ~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~s~l~vPl~~~~~~~Gvl~l~~~~~~~~f~~~~~~~l~~la~~~a~  141 (153)
T 2w3g_A           62 GVIGLLIEDPKPLRLDDVSAHPASIGFPPYHPPMRTFLGVPVRVRDESFGTLYLTDKTNGQPFSDDDEVLVQALAAAAGI  141 (153)
T ss_dssp             THHHHHHHSCSCEEESSGGGSTTCCCCCTTCCCCCCEEEEEEEETTEEEEEEEEEEETTSCCCCHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHhcCCcEEecCcccCchhcCCCCcCCCCCeEEEeeEEECCEEEEEEEEeeCCCCCCCCHHHHHHHHHHHHHHHH
Confidence            57899999999999988765554433433557889999999943    29999999888 89999999999999999999


Q ss_pred             HHhh
Q 022217          285 TLAK  288 (301)
Q Consensus       285 tL~~  288 (301)
                      .++.
T Consensus       142 ai~~  145 (153)
T 2w3g_A          142 AVAN  145 (153)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            8875

>3trc_A Phosphoenolpyruvate-protein phosphotransferase; signal transduction; HET: MSE; 1.65A {Coxiella burnetii}

Probab=97.31  E-value=0.0054  Score=47.60  Aligned_cols=79  Identities=18%  Similarity=0.196  Sum_probs=64.5

Q ss_pred             hHHHHHhhccCceeccccccCCCCCCCC-CCCCCCCeeEEEecCC----CeEEEEecCCCcccChhhHHHHHHHHHHHHH
Q 022217          210 SVYLGVMRSKAQRYLANLLLYPGRSELP-FLPSNTQAVILQPLGD----KGIAIIGGDTIRGFTTSDQSWIAFIGEKLDA  284 (301)
Q Consensus       210 ~I~~r~~~~~~~iyL~nl~lyPGr~Ef~-~LP~ntqsVlvQPig~----~Gvlvlgs~s~R~FT~kDe~WI~~iA~KL~~  284 (301)
                      .++.++.++++++++.|..--|....+. .-..+..++++.||-.    -|++.+.+..++.||+.|...++.+|+.+..
T Consensus        78 ~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~s~l~vPl~~~~~~~Gvl~~~~~~~~~f~~~d~~~l~~la~~~a~  157 (171)
T 3trc_A           78 GLIGLVGEREEPINLADAPLHPAYKHRPELGEEDYHGFLGIPIIEQGELLGILVIQQLESHHFAEEEEAFCVTLAIHLAA  157 (171)
T ss_dssp             HHHHHHHHHTSCEEESCGGGSTTCCCCGGGCCCCCCEEEEEEEEETTEEEEEEEEEESSSCCCCHHHHHHHHHHHHHHHH
T ss_pred             ChhhHHHhcCCeEEeCCCCCCCcccccccCCcccccEEEEEeEEECCEEEEEEEEeecCCCCCCHHHHHHHHHHHHHHHH
Confidence            6788999999999998876544333332 1236889999999943    3999999999999999999999999999999


Q ss_pred             HHhh
Q 022217          285 TLAK  288 (301)
Q Consensus       285 tL~~  288 (301)
                      +++.
T Consensus       158 ai~~  161 (171)
T 3trc_A          158 EIAH  161 (171)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            8875

>3ci6_A Phosphoenolpyruvate-protein phosphotransferase; PEP-phosphotransferase, GAF domain, structura genomics, PSI-2, protein structure initiative; HET: MSE P4G; 1.55A {Acinetobacter SP}

Probab=97.27  E-value=0.0058  Score=46.62  Aligned_cols=79  Identities=14%  Similarity=0.120  Sum_probs=61.6

Q ss_pred             hHHHHHhhccCceeccccccCCCCCCCC-CCCCCCCeeEEEecCC----CeEEEEecCCCcccChhhHHHHHHHHHHHHH
Q 022217          210 SVYLGVMRSKAQRYLANLLLYPGRSELP-FLPSNTQAVILQPLGD----KGIAIIGGDTIRGFTTSDQSWIAFIGEKLDA  284 (301)
Q Consensus       210 ~I~~r~~~~~~~iyL~nl~lyPGr~Ef~-~LP~ntqsVlvQPig~----~Gvlvlgs~s~R~FT~kDe~WI~~iA~KL~~  284 (301)
                      .++.++++++++++..|..--|....+. +-..+..++++.||-.    -|+|.+++..++.||+.|...++.+|+.+..
T Consensus        80 ~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~s~l~vPl~~~~~~~Gvl~l~~~~~~~f~~~~~~~l~~la~~~a~  159 (171)
T 3ci6_A           80 GLVGLVGQREEIVNLENASKHERFAYLPETGEEIYNSFLGVPVMYRRKVMGVLVVQNKQPQDFSEAAESFLVTLCAQLSG  159 (171)
T ss_dssp             HHHHHHHHHTSCEEESSGGGSTTC---------CCCEEEEEEEEETTEEEEEEEEEESSCCCCCHHHHHHHHHHHHHHHH
T ss_pred             CeehhhhccCceEEecCCCcCcchhccccccccccceEEEEeEEECCEEEEEEEEecCCCCCCCHHHHHHHHHHHHHHHH
Confidence            4789999999999998876555433332 2556789999999843    2999999999999999999999999999999


Q ss_pred             HHhh
Q 022217          285 TLAK  288 (301)
Q Consensus       285 tL~~  288 (301)
                      .++.
T Consensus       160 al~~  163 (171)
T 3ci6_A          160 VIAH  163 (171)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            8875

>2zmf_A CAMP and CAMP-inhibited CGMP 3',5'-cyclic phospho 10A; GAF domain, phosphodiesterase, CGMP-binding, HYD nucleotide-binding, structural genomics; HET: MSE CMP; 2.10A {Homo sapiens}

Probab=97.04  E-value=0.0051  Score=48.53  Aligned_cols=79  Identities=11%  Similarity=0.129  Sum_probs=61.5

Q ss_pred             hHHHHHhhccCceeccccccCCCCCCC--CCCCCCCCeeEEEecCCC----eEEEE-ecCCCcccChhhHHHHHHHHHHH
Q 022217          210 SVYLGVMRSKAQRYLANLLLYPGRSEL--PFLPSNTQAVILQPLGDK----GIAII-GGDTIRGFTTSDQSWIAFIGEKL  282 (301)
Q Consensus       210 ~I~~r~~~~~~~iyL~nl~lyPGr~Ef--~~LP~ntqsVlvQPig~~----Gvlvl-gs~s~R~FT~kDe~WI~~iA~KL  282 (301)
                      .++.++.++++.+.+.|...-|.....  .....++++++|.|+-.+    |++.+ ....+|.||+.|...++.+|+.+
T Consensus        91 ~~~~~v~~~~~~~~i~d~~~~~~~~~~~~~~~~~~~~s~l~vPl~~~~~~~Gvl~l~~~~~~~~f~~~d~~ll~~lA~q~  170 (189)
T 2zmf_A           91 GIAGQVARTGEVLNIPDAYADPRFNREVDLYTGYTTRNILCMPIVSRGSVIGVVQMVNKISGSAFSKTDENNFKMFAVFC  170 (189)
T ss_dssp             HHHHHHHHHCCCEEESCGGGSTTCCTHHHHHHCCCCCCEEEEEEEETTEEEEEEEEEEETTSSSCCHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHhCCeEEEecccccccccccchhhcccccceEEEeeecccCceeeEEEEEEcCCCCCcCHHHHHHHHHHHHHH
Confidence            567889999999999888765554333  223346889999998432    67754 56778999999999999999999


Q ss_pred             HHHHhh
Q 022217          283 DATLAK  288 (301)
Q Consensus       283 ~~tL~~  288 (301)
                      ...++.
T Consensus       171 a~Ai~n  176 (189)
T 2zmf_A          171 ALALHC  176 (189)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            988865

>3o5y_A Sensor protein; GAF domain, histidine, kinase, PSI, MCSG, structural genomics, midwest center for structural genomics, protein S initiative; 2.45A {Bacillus halodurans}

Probab=96.95  E-value=0.024  Score=47.16  Aligned_cols=79  Identities=11%  Similarity=0.234  Sum_probs=61.2

Q ss_pred             hhHHHHHhhccCceeccccccCCCCCCC-C-CCCCCCCeeEEEecCC----CeEEEEecCCCcccChhhHHHHHHHHHHH
Q 022217          209 GSVYLGVMRSKAQRYLANLLLYPGRSEL-P-FLPSNTQAVILQPLGD----KGIAIIGGDTIRGFTTSDQSWIAFIGEKL  282 (301)
Q Consensus       209 G~I~~r~~~~~~~iyL~nl~lyPGr~Ef-~-~LP~ntqsVlvQPig~----~Gvlvlgs~s~R~FT~kDe~WI~~iA~KL  282 (301)
                      +.+|..++++++.+-+ |..--|.+.-. . +...+.+|++|.||-.    -|+|.+++..++.||+.|..+++.+|+.+
T Consensus        59 ~s~~~~v~~~~~~~v~-~~~~~~~~~~~~~~~~~~~~~S~l~vPL~~~~~~iGvl~l~~~~~~~f~~~d~~~l~~la~~~  137 (165)
T 3o5y_A           59 QSLYWSALDQRQTIFR-SLTDTQDNFYEKQYLAILDLKSILVIPIYSKNKRVGVLSIGRKQQIDWSLDDLAFLEQLTDHL  137 (165)
T ss_dssp             TCHHHHHHHHTSCEEE-ESCCTTCCCTTHHHHHTTTCCEEEEEEEECSSCEEEEEEEEESSCCCCCHHHHHHHHHHHHHH
T ss_pred             cCHHHHHHHhCCeEEE-cCcccccccccchHHHhhCCCEEEEeCeeECCEEEEEEEEEeCCCCCCCHHHHHHHHHHHHHH
Confidence            4788999999999863 43222221111 1 2356899999999943    39999999999999999999999999999


Q ss_pred             HHHHhh
Q 022217          283 DATLAK  288 (301)
Q Consensus       283 ~~tL~~  288 (301)
                      ...++.
T Consensus       138 aiai~n  143 (165)
T 3o5y_A          138 AVSIEN  143 (165)
T ss_dssp             HHHHHT
T ss_pred             HHHHHH
Confidence            998875

>3k2n_A Sigma-54-dependent transcriptional regulator; PSI-2, protein structure initiative, structural genomics; 2.50A {Chlorobium tepidum tls}

Probab=96.93  E-value=0.0011  Score=52.50  Aligned_cols=79  Identities=10%  Similarity=0.149  Sum_probs=62.1

Q ss_pred             hhHHHHHhhccCceeccccccCCCCCCCC-------CCCCCCCeeEEEecCC----CeEEEEecCCCcccChhhHHHHHH
Q 022217          209 GSVYLGVMRSKAQRYLANLLLYPGRSELP-------FLPSNTQAVILQPLGD----KGIAIIGGDTIRGFTTSDQSWIAF  277 (301)
Q Consensus       209 G~I~~r~~~~~~~iyL~nl~lyPGr~Ef~-------~LP~ntqsVlvQPig~----~Gvlvlgs~s~R~FT~kDe~WI~~  277 (301)
                      +.++.+++++++.+.. |..-.+.+....       ....|++++++.||-.    -|+|.+.+..++.||+.|...++.
T Consensus        77 ~~~~~~v~~~~~~~~~-d~~~~~~~~~~~~~~~~~~~~~~~~~s~l~vPL~~~~~~iGvL~l~~~~~~~f~~~d~~ll~~  155 (177)
T 3k2n_A           77 GTWLEGHLDDRTVTVA-SIARDIPSFGADGAPLLWTLHELGMRQIVLSPLRSGGRVIGFLSFVSAEEKLWSDGDKSLLSG  155 (177)
T ss_dssp             TSGGGGGTTCCSCEEE-ETTTTCTTTTTTTCHHHHHHHHHTCCEEEEEEEEETTEEEEEEEEEESSCCCCCHHHHHHHHH
T ss_pred             ccHHHHHhccCCceEe-chhhcccccCCcchhHHHHHHHcCceEEEEEEEEECCEEEEEEEEEECCCCCCCHHHHHHHHH
Confidence            4567888998888877 765422222222       3456899999999943    399999999999999999999999


Q ss_pred             HHHHHHHHHhh
Q 022217          278 IGEKLDATLAK  288 (301)
Q Consensus       278 iA~KL~~tL~~  288 (301)
                      +|+.+..+++.
T Consensus       156 lA~~~a~Ai~n  166 (177)
T 3k2n_A          156 VSSSIAIAVSN  166 (177)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            99999988865

>3oov_A Methyl-accepting chemotaxis protein, putative; structural genomics, PSI-2, protein structure initiative; 2.20A {Geobacter sulfurreducens}

Probab=96.89  E-value=0.017  Score=44.65  Aligned_cols=80  Identities=11%  Similarity=0.282  Sum_probs=63.4

Q ss_pred             hhHHHHHhhccCceeccccccCCCCCC----C-CCCCCCCCeeEEEecCC----CeEEEEecCCC-cccChhhHHHHHHH
Q 022217          209 GSVYLGVMRSKAQRYLANLLLYPGRSE----L-PFLPSNTQAVILQPLGD----KGIAIIGGDTI-RGFTTSDQSWIAFI  278 (301)
Q Consensus       209 G~I~~r~~~~~~~iyL~nl~lyPGr~E----f-~~LP~ntqsVlvQPig~----~Gvlvlgs~s~-R~FT~kDe~WI~~i  278 (301)
                      ..++.+++++++++++.|..-.|....    . ..-..+..++++.||-.    -|+|.+++..+ +.||+.|...++.+
T Consensus        73 ~~~~~~~~~~~~~~~i~d~~~~~~~~~~~~~~~~~~~~~~~s~l~vPl~~~~~~iGvl~~~~~~~~~~f~~~d~~~l~~~  152 (169)
T 3oov_A           73 GGVITKCFTDRQVYMIDDVSAYPTDFRLQSPYDAIRALRSKSFVICPIVVKGEAIGVFAVDNRSSRRSLNDTDVDTIKLF  152 (169)
T ss_dssp             GHHHHHHHHHTCCEEESCGGGSCGGGSCCTTGGGCGGGCCSSEEEEEEEETTEEEEEEEEECTTSSSCCCHHHHHHHHHH
T ss_pred             cchHHHHHhcCCCEEeccccchhhhhhccccHHHHHhcCcCcEEEEEEEeCCcEEEEEEEEccccCCCCCHHHHHHHHHH
Confidence            467899999999999998876554321    1 12346889999999943    29999998765 56999999999999


Q ss_pred             HHHHHHHHhh
Q 022217          279 GEKLDATLAK  288 (301)
Q Consensus       279 A~KL~~tL~~  288 (301)
                      |+.+..+++.
T Consensus       153 a~~~a~ai~n  162 (169)
T 3oov_A          153 ADQASSAIVR  162 (169)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9999988865

>2vjw_A GAF-B, GAF family protein; histidine kinase, hypoxia sensing, hydrolase; HET: MSE; 2.0A {Mycobacterium smegmatis} PDB: 2vks_A

Probab=96.83  E-value=0.015  Score=47.18  Aligned_cols=70  Identities=16%  Similarity=0.129  Sum_probs=60.7

Q ss_pred             hhHHHHHhhccCceeccccccCCCCCCCCCCCCCCCeeEEEecCC----CeEEEEecC-CCcccChhhHHHHHHHHHHHH
Q 022217          209 GSVYLGVMRSKAQRYLANLLLYPGRSELPFLPSNTQAVILQPLGD----KGIAIIGGD-TIRGFTTSDQSWIAFIGEKLD  283 (301)
Q Consensus       209 G~I~~r~~~~~~~iyL~nl~lyPGr~Ef~~LP~ntqsVlvQPig~----~Gvlvlgs~-s~R~FT~kDe~WI~~iA~KL~  283 (301)
                      +.++.+++++++++.+.|..--|          ++.+++|.||..    -|+|.+... .++.||+.|..-++.+|+...
T Consensus        60 ~g~~g~v~~~g~~v~v~d~~~d~----------~~~s~l~vPL~~~~~~~GvL~l~~~~~~~~f~~~d~~ll~~lA~~aa  129 (149)
T 2vjw_A           60 DNAIGQAFRDRAPRRLDVLDGPG----------LGGPALVLPLRATDTVAGVLVAVQGSGARPFTAEQLEMMTGFADQAA  129 (149)
T ss_dssp             SSHHHHHHHHCCCEEESCCCTTS----------CEEEEEEEEEEETTEEEEEEEEEEETTCCCCCHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHhhcCceEEecCcccCC----------CCCeEEEEEEccCCeEEEEEEEeeCCCCCCCCHHHHHHHHHHHHHHH
Confidence            37889999999999998876544          789999999953    299999998 889999999999999999988


Q ss_pred             HHHhh
Q 022217          284 ATLAK  288 (301)
Q Consensus       284 ~tL~~  288 (301)
                      ..++.
T Consensus       130 ~al~~  134 (149)
T 2vjw_A          130 VAWQL  134 (149)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            88754

>2qyb_A Membrane protein, putative; GAF domain, domain of putative membrane protein, PSI-2, MCSG structural genomics; 2.40A {Geobacter sulfurreducens pca}

Probab=96.81  E-value=0.0017  Score=51.87  Aligned_cols=79  Identities=8%  Similarity=0.069  Sum_probs=64.9

Q ss_pred             hHHHHHhhccCceeccccccCCCCCCC--CCCCCCCCeeEEEecC--CC---eEEEEec-CCCcccChhhHHHHHHHHHH
Q 022217          210 SVYLGVMRSKAQRYLANLLLYPGRSEL--PFLPSNTQAVILQPLG--DK---GIAIIGG-DTIRGFTTSDQSWIAFIGEK  281 (301)
Q Consensus       210 ~I~~r~~~~~~~iyL~nl~lyPGr~Ef--~~LP~ntqsVlvQPig--~~---Gvlvlgs-~s~R~FT~kDe~WI~~iA~K  281 (301)
                      .+|.++++++++++..|....|. ..+  .+...|..++++.||.  ++   |+|.+.+ ..++.||+.|...++.+|+-
T Consensus        73 ~~~~~~~~~~~~~~v~d~~~~~~-~~~~~~~~~~g~~s~~~vPl~~~~~~~~GvL~l~~~~~~~~f~~~d~~lL~~la~~  151 (181)
T 2qyb_A           73 TYIGEAFLSNRLQFVNDTQYMTK-PLTRELMQKEGIKSFAHIPISRKGEPPFGILSVFSRTIVGLFNEPFLNLLESLAGQ  151 (181)
T ss_dssp             SHHHHHHHHTSCEEESCGGGCSC-HHHHHHHHHTTCCEEEEEEECCTTSCCCEEEEEEESSCSSCCCHHHHHHHHHHHHH
T ss_pred             CchhhhhhcCCCEEecChhcCCc-hhhHHHHHhcCcceEEEEEEEeCCCeEEEEEEEecCCCCCCCCHHHHHHHHHHHHH
Confidence            57899999999999988876663 111  1224579999999983  34   9999999 89999999999999999999


Q ss_pred             HHHHHhhc
Q 022217          282 LDATLAKY  289 (301)
Q Consensus       282 L~~tL~~~  289 (301)
                      +...+++.
T Consensus       152 ~a~al~~a  159 (181)
T 2qyb_A          152 LAQAVKIV  159 (181)
T ss_dssp             HHHHHHHC
T ss_pred             HHHHHHHH
Confidence            99999864

>1f5m_A GAF; CGMP binding, signaling protein; 1.90A {Saccharomyces cerevisiae} SCOP: d.110.2.1 PDB: 3ko6_A*

Probab=96.74  E-value=0.0057  Score=52.07  Aligned_cols=79  Identities=18%  Similarity=0.324  Sum_probs=67.1

Q ss_pred             ccchh-hHHHHHhhccCceeccccccCCCCCCCCCCCCCCCeeEEEecCC-C----eEEEEecCCCcccChhhHHHHHHH
Q 022217          205 KLKQG-SVYLGVMRSKAQRYLANLLLYPGRSELPFLPSNTQAVILQPLGD-K----GIAIIGGDTIRGFTTSDQSWIAFI  278 (301)
Q Consensus       205 ~~~pG-~I~~r~~~~~~~iyL~nl~lyPGr~Ef~~LP~ntqsVlvQPig~-~----Gvlvlgs~s~R~FT~kDe~WI~~i  278 (301)
                      .+.+| -+|.++.++++.+.+.|..-.|+...   ...++.|.+|.||-. +    |||-+.+..++.||+.|+..++.+
T Consensus        93 ~i~~g~Gi~G~aa~~g~~v~v~Dv~~dp~~~~---~~~~~~S~l~vPi~~~~g~viGVL~l~s~~~~~F~~~d~~~L~~l  169 (180)
T 1f5m_A           93 MIQFGKGVCGTAASTKETQIVPDVNKYPGHIA---CDGETKSEIVVPIISNDGKTLGVIDIDCLDYEGFDHVDKEFLEKL  169 (180)
T ss_dssp             EEETTSHHHHHHHHHTSCEEESCGGGSTTCCC---SSTTCCEEEEEEEECTTSCEEEEEEEEESSTTCCCHHHHHHHHHH
T ss_pred             eecCCCcchhhhhhcCCEEEeCCcccCccccc---cCcccceEEEEEEEcCCCeEEEEEEeccCCCCCcCHHHHHHHHHH
Confidence            35555 47999999999999999998887543   346899999999964 2    999999999999999999999999


Q ss_pred             HHHHHHHH
Q 022217          279 GEKLDATL  286 (301)
Q Consensus       279 A~KL~~tL  286 (301)
                      |+-+..++
T Consensus       170 a~~~a~~~  177 (180)
T 1f5m_A          170 AKLINKSC  177 (180)
T ss_dssp             HHHHHHHC
T ss_pred             HHHHHHhc
Confidence            99988765

>3hcy_A Putative two-component sensor histidine kinase PR; two-component sensor histidine kinase protein, structural GE PSI, MCSG; 2.80A {Sinorhizobium meliloti}

Probab=96.66  E-value=0.00076  Score=52.43  Aligned_cols=78  Identities=15%  Similarity=0.128  Sum_probs=61.0

Q ss_pred             HHHHHhhccCceeccccccCCCCCCC--CCCCCCCCeeEEEecCCC----eEEEEecCCCcccChhhHHHHHHHHHHHHH
Q 022217          211 VYLGVMRSKAQRYLANLLLYPGRSEL--PFLPSNTQAVILQPLGDK----GIAIIGGDTIRGFTTSDQSWIAFIGEKLDA  284 (301)
Q Consensus       211 I~~r~~~~~~~iyL~nl~lyPGr~Ef--~~LP~ntqsVlvQPig~~----Gvlvlgs~s~R~FT~kDe~WI~~iA~KL~~  284 (301)
                      +|.+++++++++++.|..--|....+  .....|.+++++.||-.+    |++.+....+|.||+.|...++.+|+.+..
T Consensus        56 ~~~~~~~~~~~~~i~d~~~~~~~~~~~~~~~~~g~~s~~~vPl~~~~~~iGvl~~~~~~~~~f~~~~~~ll~~~a~~~a~  135 (151)
T 3hcy_A           56 PWITGANEPEPIFVENVDDAEFSRELKESIVGEGIAALGFFPLVTEGRLIGKFMTYYDRPHRFADSEIGMALTIARQLGF  135 (151)
T ss_dssp             SCC---CCCCCEEESCGGGSCCCHHHHHHHHHHTCCEEEEEEEESSSSEEEEEEEEESSCCCCCHHHHHHHHHHHHHHHH
T ss_pred             chhhhhhcCCcEEEeChhhCcccchhHHHHHhcCchheEEeceEECCEEEEEEEEecCCCCCCCHHHHHHHHHHHHHHHH
Confidence            47788999999999988765533222  234568899999999432    899999999999999999999999999998


Q ss_pred             HHhh
Q 022217          285 TLAK  288 (301)
Q Consensus       285 tL~~  288 (301)
                      .+++
T Consensus       136 ai~~  139 (151)
T 3hcy_A          136 SIQR  139 (151)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            8865

>3dba_A CONE CGMP-specific 3',5'-cyclic phosphodiesterase alpha'; 3', GAF domain, cyclic nucleotide phosphodiesterase hydrolase, lipoprotein, membrane; HET: 35G; 2.57A {Gallus gallus}

Probab=94.88  E-value=0.039  Score=45.41  Aligned_cols=77  Identities=10%  Similarity=0.010  Sum_probs=58.4

Q ss_pred             hHHHHHhhccCceeccccccCCCCCCC-CC-CCCCCCeeEEEecCCC----eEEEEecCCCc-ccChhhHHHHHHHHHHH
Q 022217          210 SVYLGVMRSKAQRYLANLLLYPGRSEL-PF-LPSNTQAVILQPLGDK----GIAIIGGDTIR-GFTTSDQSWIAFIGEKL  282 (301)
Q Consensus       210 ~I~~r~~~~~~~iyL~nl~lyPGr~Ef-~~-LP~ntqsVlvQPig~~----Gvlvlgs~s~R-~FT~kDe~WI~~iA~KL  282 (301)
                      .|+.++.++++++.+.|..--|..... +. .-..++|+||.||-.+    |||-+...... .||+.|+.-++.+|+-.
T Consensus        88 gi~g~v~~tg~~v~i~d~~~d~~f~~~~~~~~~~~~~S~L~vPl~~~~~viGVL~l~n~~~~~~Ft~~d~~lL~~lA~~a  167 (180)
T 3dba_A           88 GIAGWVAHTKKFFNIPDVKKNNHFSDYLDKKTGYTTVNMMAIPITQGKEVLAVVMALNKLNASEFSKEDEEVFKKYLNFI  167 (180)
T ss_dssp             SHHHHHHHHTCCEEESCGGGCTTCCCHHHHHHCCCCCCEEEEEEEETTEEEEEEEEEEESSSSSCCHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHhCCEEEecCCCCCcccChhhccccCccccEEEEEEeccCCEEEEEEEEEeCCCCCCCCHHHHHHHHHHHHHH
Confidence            678999999999999988754422111 11 1135799999999432    99999888775 99999999999999876


Q ss_pred             HHHH
Q 022217          283 DATL  286 (301)
Q Consensus       283 ~~tL  286 (301)
                      ...+
T Consensus       168 a~~i  171 (180)
T 3dba_A          168 SLVL  171 (180)
T ss_dssp             HHHT
T ss_pred             HHHH
Confidence            6554

>3ibj_A CGMP-dependent 3',5'-cyclic phosphodiesterase; PDE2A, GAF-domains, allosteric regulation hydrolase, membrane; 3.02A {Homo sapiens}

Probab=94.81  E-value=0.45  Score=47.65  Aligned_cols=79  Identities=11%  Similarity=0.068  Sum_probs=60.0

Q ss_pred             hHHHHHhhccCceeccccccCCCCCC-CC-CCCCCCCeeEEEecCCC-----eEEEEecCCCc-ccChhhHHHHHHHHHH
Q 022217          210 SVYLGVMRSKAQRYLANLLLYPGRSE-LP-FLPSNTQAVILQPLGDK-----GIAIIGGDTIR-GFTTSDQSWIAFIGEK  281 (301)
Q Consensus       210 ~I~~r~~~~~~~iyL~nl~lyPGr~E-f~-~LP~ntqsVlvQPig~~-----Gvlvlgs~s~R-~FT~kDe~WI~~iA~K  281 (301)
                      .++.++.++++++.+.|..--|.... .+ ....++++++|.||-.+     |||.+....++ .||+.|+.-++.+|+.
T Consensus       251 gi~g~v~~~g~~v~i~d~~~d~~~~~~~~~~~g~~~rS~L~vPL~~~~g~viGVL~l~~~~~~~~f~~~d~~ll~~lA~~  330 (691)
T 3ibj_A          251 GIAGHVATTGQILNIPDAYAHPLFYRGVDDSTGFRTRNILCFPIKNENQEVIGVAELVNKINGPWFSKFDEDLATAFSIY  330 (691)
T ss_dssp             HHHHHHHHHCSCEEESCSTTSTTC------CCSCCCCCEEEEECCCSSSCCCEEEEEEEESSSSSCCTTTTHHHHHHHHH
T ss_pred             CHHHHHHHhCCEEEecCcccCccccchhhcccCCeeeeEEEEeEECCCCCEEEEEEEEECCCCCCCCHHHHHHHHHHHHH
Confidence            67889999999999988764443211 11 11235789999999543     99999888776 7999999999999999


Q ss_pred             HHHHHhh
Q 022217          282 LDATLAK  288 (301)
Q Consensus       282 L~~tL~~  288 (301)
                      +..+++.
T Consensus       331 ~aiAIen  337 (691)
T 3ibj_A          331 CGISIAH  337 (691)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            8887754

>1mc0_A 3',5'-cyclic nucleotide phosphodiesterase 2A; GAF domain, 3',5' guanosine monophosphate, hydrolase; HET: PCG; 2.86A {Mus musculus} SCOP: d.110.2.1 d.110.2.1

Probab=94.72  E-value=0.058  Score=47.98  Aligned_cols=79  Identities=11%  Similarity=0.035  Sum_probs=59.7

Q ss_pred             hHHHHHhhccCceeccccccCCCCCCC-CC-CCCCCCeeEEEecCCC-----eEEEEecCCCc-ccChhhHHHHHHHHHH
Q 022217          210 SVYLGVMRSKAQRYLANLLLYPGRSEL-PF-LPSNTQAVILQPLGDK-----GIAIIGGDTIR-GFTTSDQSWIAFIGEK  281 (301)
Q Consensus       210 ~I~~r~~~~~~~iyL~nl~lyPGr~Ef-~~-LP~ntqsVlvQPig~~-----Gvlvlgs~s~R-~FT~kDe~WI~~iA~K  281 (301)
                      .++.++.++++++.+.|..--|..... +. ..-.++++++.||-.+     |+|.+....++ .||+.|...++.+|+-
T Consensus       251 ~~~~~~~~~~~~~~i~d~~~~~~~~~~~~~~~~~~~~s~l~vPl~~~~~~~iGvl~l~~~~~~~~f~~~d~~ll~~la~~  330 (368)
T 1mc0_A          251 GIAGHVATTGQILNIPDAYAHPLFYRGVDDSTGFRTRNILCFPIKNENQEVIGVAELVNKINGPWFSKFDEDLATAFSIY  330 (368)
T ss_dssp             HHHHHHHHHCCCEEESCSTTCTTCCCTTHHHHTCCCCCEEEEEEECTTSCEEEEEEEEEETTSSSCCHHHHHHHHHHHHH
T ss_pred             ceeeeehhhCCEEEecCcccCcccchhhhhccCCccceEEEEeeECCCCcEEEEEEEEECCCCCCCCHHHHHHHHHHHHH
Confidence            578899999999998887543321111 00 0113589999999543     99999998886 8999999999999999


Q ss_pred             HHHHHhh
Q 022217          282 LDATLAK  288 (301)
Q Consensus       282 L~~tL~~  288 (301)
                      +..++++
T Consensus       331 ~a~ai~n  337 (368)
T 1mc0_A          331 CGISIAH  337 (368)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9888864

>2lb5_A Sensor histidine kinase; PCB, transferase, GAF domain, phosphoprotein; HET: CYC; NMR {Synechococcus SP} PDB: 2lb9_A*

Probab=94.22  E-value=0.074  Score=43.87  Aligned_cols=49  Identities=10%  Similarity=0.283  Sum_probs=43.8

Q ss_pred             CCCCCeeEEEecC--C--CeEEEEecCCCcccChhhHHHHHHHHHHHHHHHhh
Q 022217          240 PSNTQAVILQPLG--D--KGIAIIGGDTIRGFTTSDQSWIAFIGEKLDATLAK  288 (301)
Q Consensus       240 P~ntqsVlvQPig--~--~Gvlvlgs~s~R~FT~kDe~WI~~iA~KL~~tL~~  288 (301)
                      ..|++|+||.||-  +  -|+|.+-...+|.||+.|...++.+|+-+..++++
T Consensus       145 ~~~~~S~l~vPi~~~~~l~GvL~~~~~~~~~~~~~e~~ll~~la~~~a~ai~~  197 (208)
T 2lb5_A          145 SMGVASSLVVPLMHHQELWGLLVSHHAEPRPYSQEELQVVQLLADQVSIAIAQ  197 (208)
T ss_dssp             HTTCSEEEEEEEEETTEEEEEEEEEESCCCCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             hcCCcEEEEEEEEECCEeEEEEEEeeCCCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            3589999999984  3  29999999999999999999999999999998875

>2k2n_A Sensor protein, SYB-CPH1(GAF); phytochrome, GAF domain, phycocyanobilin, PCB, bacteriophytochrome, cyanobacterial phytochrome, kinase; HET: CYC; NMR {Synechococcus SP} SCOP: d.110.2.1 PDB: 2kli_A* 2koi_A*

Probab=94.13  E-value=0.1  Score=41.90  Aligned_cols=49  Identities=10%  Similarity=0.280  Sum_probs=44.0

Q ss_pred             CCCCCeeEEEecCC----CeEEEEecCCCcccChhhHHHHHHHHHHHHHHHhh
Q 022217          240 PSNTQAVILQPLGD----KGIAIIGGDTIRGFTTSDQSWIAFIGEKLDATLAK  288 (301)
Q Consensus       240 P~ntqsVlvQPig~----~Gvlvlgs~s~R~FT~kDe~WI~~iA~KL~~tL~~  288 (301)
                      ..+++|+|+.||-.    -|+|.+-...+|.||+.|...++.+|+.+..++++
T Consensus       115 ~~~~~s~l~vPi~~~~~l~G~l~~~~~~~~~~~~~e~~~l~~la~~~a~ai~~  167 (172)
T 2k2n_A          115 SMGVASSLVVPLMHHQELWGLLVSHHAEPRPYSQEELQVVQLLADQVSIAIAQ  167 (172)
T ss_dssp             TTTCSEEEECCCSCSSCCCEEEEEEECSCCCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             hcCCeEEEEEEEEECCEEEEEEEEEeCCCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            46899999999943    39999999999999999999999999999988875

>1ykd_A Adenylate cyclase; GAF domain, bound cyclic AMP ligand, lyase; HET: CMP; 1.90A {Anabaena SP}

Probab=93.03  E-value=0.11  Score=47.15  Aligned_cols=79  Identities=13%  Similarity=0.132  Sum_probs=60.8

Q ss_pred             hHHHHHhhccCceecc-ccccCCCCCCC---C-CCCCCCCeeEEEecCC-C----eEEEEecCC----------------
Q 022217          210 SVYLGVMRSKAQRYLA-NLLLYPGRSEL---P-FLPSNTQAVILQPLGD-K----GIAIIGGDT----------------  263 (301)
Q Consensus       210 ~I~~r~~~~~~~iyL~-nl~lyPGr~Ef---~-~LP~ntqsVlvQPig~-~----Gvlvlgs~s----------------  263 (301)
                      .++.++.++++.+.+. |..--|.....   + .....+.+++|.||-. +    |+|.+....                
T Consensus       268 ~~~~~v~~~~~~~~i~~d~~~~~~~~~~~~~~~~~~~~~~s~l~vPl~~~~~~~iGvl~l~~~~~~~~~~~~~~~~~~~~  347 (398)
T 1ykd_A          268 GFAGIVAASGQKLNIPFDLYDHPDSATAKQIDQQNGYRTCSLLCMPVFNGDQELIGVTQLVNKKKTGEFPPYNPETWPIA  347 (398)
T ss_dssp             HHHHHHHHHCCCEEECSCGGGSTTCHHHHHHHHHHTCCCCCEEEEEEECSSSCEEEEEEEEEECCSSCCCCCCGGGTTCC
T ss_pred             chhhHHhccCCeEEeccccccCcccCcccchhhhcCCeeeeEEEEeeecCCCCEEEEEEEEecCCccccccccccccccc
Confidence            5688899999999988 76544432211   0 0122489999999963 3    999999887                


Q ss_pred             ----CcccChhhHHHHHHHHHHHHHHHhh
Q 022217          264 ----IRGFTTSDQSWIAFIGEKLDATLAK  288 (301)
Q Consensus       264 ----~R~FT~kDe~WI~~iA~KL~~tL~~  288 (301)
                          ++.||+.|..-++.+|+.+..++++
T Consensus       348 ~~~~~~~f~~~d~~ll~~la~~~a~al~n  376 (398)
T 1ykd_A          348 PECFQASFDRNDEEFMEAFNIQAGVALQN  376 (398)
T ss_dssp             CGGGCCCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccccCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence                8999999999999999999988865

>1ykd_A Adenylate cyclase; GAF domain, bound cyclic AMP ligand, lyase; HET: CMP; 1.90A {Anabaena SP}

Probab=92.47  E-value=0.26  Score=44.55  Aligned_cols=79  Identities=15%  Similarity=0.099  Sum_probs=59.7

Q ss_pred             hHHHHHhhccCceeccccccCCCCCCCC-C----CCCCCCeeEEEecCC--C---eEEEEecC---------------CC
Q 022217          210 SVYLGVMRSKAQRYLANLLLYPGRSELP-F----LPSNTQAVILQPLGD--K---GIAIIGGD---------------TI  264 (301)
Q Consensus       210 ~I~~r~~~~~~~iyL~nl~lyPGr~Ef~-~----LP~ntqsVlvQPig~--~---Gvlvlgs~---------------s~  264 (301)
                      .+|..+.++++.+.+.|...-..+..|. .    ...+++++++.||-.  +   |+|.+...               .+
T Consensus        81 g~~g~v~~~~~~v~i~d~~~~~~~~~~~~~~~~~~~~~~~s~l~vPl~~~~g~~iGvl~l~~~~~~~~~~~~~l~~~~~~  160 (398)
T 1ykd_A           81 GIAGEVATFKQVVNIPFDFYHDPRSIFAQKQEKITGYRTYTMLALPLLSEQGRLVAVVQLLNKLKPYSPPDALLAERIDN  160 (398)
T ss_dssp             HHHHHHHHHCCCEEECSCGGGSGGGHHHHHHHHHHCCCCSCEEEEEEECSSCCEEEEEEEEEEBCSCCCTTCCHHHHBCT
T ss_pred             chhhhhhccCcEEeccchhcccchhhcccccCcccCcCCceEEEEEEECCCCCEEEEEEEeccCCccccccccccccccc
Confidence            5789999999999998875321123331 1    124688999999842  2   89988887               78


Q ss_pred             cccChhhHHHHHHHHHHHHHHHhh
Q 022217          265 RGFTTSDQSWIAFIGEKLDATLAK  288 (301)
Q Consensus       265 R~FT~kDe~WI~~iA~KL~~tL~~  288 (301)
                      +.||+.|+.-++.+|+.+...++.
T Consensus       161 ~~f~~~d~~~l~~~a~~~~~al~~  184 (398)
T 1ykd_A          161 QGFTSADEQLFQEFAPSIRLILES  184 (398)
T ss_dssp             TCCCHHHHHHGGGTHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999888877763

>4glq_A Methyl-accepting chemotaxis protein; chromophore, phytochrome, cyanobacteriochrome, phycoviolobil bilin, BILI-protein; HET: PVN; 1.77A {Thermosynechococcus elongatus} PDB: 4fof_A*

Probab=92.01  E-value=0.19  Score=41.88  Aligned_cols=128  Identities=13%  Similarity=0.181  Sum_probs=81.0

Q ss_pred             HHHHHHHHHHHhhhccccEEEEEE-C----CEEEEEEeeccC-CCCCccchhhcccccchhhHHHHHhhccCceeccccc
Q 022217          155 VSELLWAWESLSAVTCCRSLVVVY-D----GIYLLQIGMAAE-SGNSGEAVIVDASKLKQGSVYLGVMRSKAQRYLANLL  228 (301)
Q Consensus       155 k~ELAWas~~LLtnT~a~svlV~~-~----G~vll~RG~~~~-~~~~g~a~~~d~~~~~pG~I~~r~~~~~~~iyL~nl~  228 (301)
                      .+=|.-+...+...+.+.-++||. +    |+++.. -.-.. ++-.|..  ...+.| | +-+....++++.+.+.|..
T Consensus        13 ~~il~~~v~~v~~~l~~DRv~Iy~f~~d~~g~vvaE-~~~~~~~s~lg~~--~~~~~~-~-~~~~~~~~~g~~~~I~Dv~   87 (171)
T 4glq_A           13 QAIFETLVAKGRELLACDRVIVYAFDDNYVGTVVAE-SVAEGWPQARDQV--IEDPCF-R-EHWVEAYRQGRIQATTDIF   87 (171)
T ss_dssp             HHHHHHHHHHHHHHHTCSEEEEEEECTTCCEEEEEE-EECTTSCCCTTCE--ECCTHH-H-HHTHHHHHTTCCEEESCGG
T ss_pred             HHHHHHHHHHHHHHHCCCeEEEEEEeCCCCeEEEEE-EcCCCCccccCCc--cCcccc-H-HHHHHHHHcCCEEEEcCcC
Confidence            344556677788888888888873 2    454433 21111 1111100  000011 1 2234567788888887765


Q ss_pred             cCCCCCCC--CC-CCCCCCeeEEEecC--C--CeEEEEec-CCCcccChhhHHHHHHHHHHHHHHHhh
Q 022217          229 LYPGRSEL--PF-LPSNTQAVILQPLG--D--KGIAIIGG-DTIRGFTTSDQSWIAFIGEKLDATLAK  288 (301)
Q Consensus       229 lyPGr~Ef--~~-LP~ntqsVlvQPig--~--~Gvlvlgs-~s~R~FT~kDe~WI~~iA~KL~~tL~~  288 (301)
                      . ++..+-  +| -.-|.+|.|+.||-  +  -|+|.+-. ..+|.||+.|..++..+|+.+..++.+
T Consensus        88 ~-~~~~~~~~~~l~~~~v~S~L~vPi~~~~~l~GlL~~~~~~~~r~w~~~ei~ll~~lA~ql~iAi~q  154 (171)
T 4glq_A           88 K-AGLTECHLNQLRPLKVRANLVVPMVIDDQLFGLLIAHQASEPRQWQEIEIDQFSELASTGSLVLER  154 (171)
T ss_dssp             G-TTCCHHHHHHHGGGTEEEEEEEEEEETTEEEEEEEEEEESSCCCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             c-CCCCHHHHHHHHhcCCcEEEEEEEEECCEEEEEEEEEeCCCCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            3 222211  22 25689999999983  3  39999887 789999999999999999999999876

>1mc0_A 3',5'-cyclic nucleotide phosphodiesterase 2A; GAF domain, 3',5' guanosine monophosphate, hydrolase; HET: PCG; 2.86A {Mus musculus} SCOP: d.110.2.1 d.110.2.1

Probab=88.03  E-value=0.5  Score=41.88  Aligned_cols=77  Identities=19%  Similarity=0.090  Sum_probs=55.9

Q ss_pred             hHHHHHhhccCceeccccccCCCCCCCC-CCCCCCCeeEEEecCCC------eEEEEecCCC-cccChhhHHHHHHHHHH
Q 022217          210 SVYLGVMRSKAQRYLANLLLYPGRSELP-FLPSNTQAVILQPLGDK------GIAIIGGDTI-RGFTTSDQSWIAFIGEK  281 (301)
Q Consensus       210 ~I~~r~~~~~~~iyL~nl~lyPGr~Ef~-~LP~ntqsVlvQPig~~------Gvlvlgs~s~-R~FT~kDe~WI~~iA~K  281 (301)
                      .+|..+.++++++.+.|..--|- .+++ ..-.+++++++.||-.+      |+|.+.+..+ +.||+.|+.-+..+|+-
T Consensus        81 g~~g~~~~~~~~~~i~d~~~~~~-~~~~~~~~~~~~s~l~vPl~~~~~~~~~Gvl~l~~~~~~~~f~~~d~~~l~~la~~  159 (368)
T 1mc0_A           81 GRLGQVVEDKQCIQLKDLTSDDV-QQLQNMLGCELQAMLCVPVISRATDQVVALACAFNKLGGDFFTDEDEHVIQHCFHY  159 (368)
T ss_dssp             SSHHHHHHHCCCEEGGGSCHHHH-HHHHHHHCSCCCCEEEEEEECTTTCSEEEEEEEEEESSCSSCCSHHHHHHHHHHHH
T ss_pred             CHHHHHHhcCCeEEecccccccc-cccccccCcccceEEEEEeecCCCCcEEEEEEeecCCCCCCCCHHHHHHHHHHHHH
Confidence            46888999999999988764331 1111 01123899999999443      8888776555 56999999999999988


Q ss_pred             HHHHHh
Q 022217          282 LDATLA  287 (301)
Q Consensus       282 L~~tL~  287 (301)
                      +...+.
T Consensus       160 ~~~al~  165 (368)
T 1mc0_A          160 TGTVLT  165 (368)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            877765

>2w1r_A Spovt, stage V sporulation protein T; regulatory GAF domain of spovt, transcription, transcription regulation, repressor, activator; 1.50A {Bacillus subtilis}

Probab=87.60  E-value=1.8  Score=34.71  Aligned_cols=110  Identities=8%  Similarity=0.096  Sum_probs=71.4

Q ss_pred             HHHHhhhccccEEEEEECCEEEEEEeeccCCCCCccchhhcccccchhhHHHHHhhccCceeccccccCCCCCCCCCCCC
Q 022217          162 WESLSAVTCCRSLVVVYDGIYLLQIGMAAESGNSGEAVIVDASKLKQGSVYLGVMRSKAQRYLANLLLYPGRSELPFLPS  241 (301)
Q Consensus       162 s~~LLtnT~a~svlV~~~G~vll~RG~~~~~~~~g~a~~~d~~~~~pG~I~~r~~~~~~~iyL~nl~lyPGr~Ef~~LP~  241 (301)
                      .+.|...|.+ .|.|..+.+++..-|.-..       --.+ .+.  +..++++|++++.++..|...++--.+-+   .
T Consensus         8 AeiI~~~~~~-aV~ItD~~~ilA~~G~g~~-------~~~~-~~i--s~~~~~~i~~~k~~~~~~~~~~~~~~~~~---~   73 (123)
T 2w1r_A            8 ADALYDSLGH-SVLICDRDVYIAVSGSSKK-------DYLN-KSI--SEMLERTMDQRSSVLESDAKSVQLVNGID---E   73 (123)
T ss_dssp             HHHHHHHHCS-EEEEECSSBEEEEESSCHH-------HHBT-CBB--CHHHHHHHHHCSCEEESSCEEEESBTTCE---E
T ss_pred             HHHHHHHHCC-eEEEEcCccEEEEEecChh-------hcCC-Ccc--CHHHHHHHHcCCEEEEcCCccccccCCCC---C
Confidence            4678889999 9999999988766674211       0111 122  55579999999999886654433221111   1


Q ss_pred             CCCeeEEEecCC----CeEEEEecCCCcccChhhHHHHHHHHHHHHHHH
Q 022217          242 NTQAVILQPLGD----KGIAIIGGDTIRGFTTSDQSWIAFIGEKLDATL  286 (301)
Q Consensus       242 ntqsVlvQPig~----~Gvlvlgs~s~R~FT~kDe~WI~~iA~KL~~tL  286 (301)
                      ...+.++.||-.    -|.|.+- ...+.|++.++.-.+++|+=|..-+
T Consensus        74 ~~~s~ii~PI~~~g~viG~i~l~-~~~~~~~~~~~~la~gla~lls~Qm  121 (123)
T 2w1r_A           74 DMNSYTVGPIVANGDPIGAVVIF-SKDQTMGEVEHKAVETAAGFLARQM  121 (123)
T ss_dssp             EESEEEEEEEEETTEEEEEEEEE-ESSSCCCHHHHHHHHHHHHHHC---
T ss_pred             CeeEEEEEEEEECCEEEEEEEEE-EcCCCCCHHHHHHHHHHHHHHHHHh
Confidence            246789999832    2888777 4444599999998888887665543

>3cit_A Sensor histidine kinase; MEGA: 3.30.450.40, structural genomics, sensor histidine KIN pseudomonas syringae, PSI-2; HET: MSE; 1.90A {Pseudomonas syringae PV}

Probab=84.57  E-value=2.2  Score=36.81  Aligned_cols=47  Identities=23%  Similarity=0.395  Sum_probs=38.7

Q ss_pred             CCCeeEEEec-CCC----eEEEEecC-CCcccChhhHHHHHHHHHHHHHHHhh
Q 022217          242 NTQAVILQPL-GDK----GIAIIGGD-TIRGFTTSDQSWIAFIGEKLDATLAK  288 (301)
Q Consensus       242 ntqsVlvQPi-g~~----Gvlvlgs~-s~R~FT~kDe~WI~~iA~KL~~tL~~  288 (301)
                      -|++|+|.|+ +.+    |++++... ...+|++.|..=++.+|.-+..+++.
T Consensus        95 ~t~svl~vPL~~~~g~~~Gvlql~N~~~~~~f~~eD~e~l~lLA~~~a~aien  147 (160)
T 3cit_A           95 HLPCVLLLPLRGADEGSFGTLVLANSVAISAPDGEDIESLQLLATLLAAHLEN  147 (160)
T ss_dssp             SSCEEEEEEEECSSSSEEEEEEEEESSCCCCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccceeEEEeeecCCCcEEEEEEEeccCCCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            4899999999 554    78777544 44589999999999999999888765

>3ibj_A CGMP-dependent 3',5'-cyclic phosphodiesterase; PDE2A, GAF-domains, allosteric regulation hydrolase, membrane; 3.02A {Homo sapiens}

Probab=81.12  E-value=0.59  Score=46.74  Aligned_cols=79  Identities=18%  Similarity=0.073  Sum_probs=56.1

Q ss_pred             hhHHHHHhhccCceeccccccCCCCCCCCCCCCCCCeeEEEecCCC------eEEEEecCC-CcccChhhHHHHHHHHHH
Q 022217          209 GSVYLGVMRSKAQRYLANLLLYPGRSELPFLPSNTQAVILQPLGDK------GIAIIGGDT-IRGFTTSDQSWIAFIGEK  281 (301)
Q Consensus       209 G~I~~r~~~~~~~iyL~nl~lyPGr~Ef~~LP~ntqsVlvQPig~~------Gvlvlgs~s-~R~FT~kDe~WI~~iA~K  281 (301)
                      |.|+.+++++++++.+.|..--|-+.........+++++|.||-.+      |+|.+.... ++.||+.|+.-+..+|.-
T Consensus        80 ~Gi~g~v~~~~~pv~i~d~~~~~~~~~~~~~~~~~~S~L~vPI~~~~~g~viGvL~l~~~~~~~~ft~~d~~lL~~la~~  159 (691)
T 3ibj_A           80 TGCLGQVVEDKKSIQLKDLTSEDVQQLQSMLGCELQAMLCVPVISRATDQVVALACAFNKLEGDLFTDEDEHVIQHCFHY  159 (691)
T ss_dssp             CSSSHHHHHHCCCEEGGGSCHHHHHHHHHHHTSCCSCEEEEEEECSSSCSEEEEEEEESBSSSCCCCTTHHHHHHHHHHH
T ss_pred             ccHHHHHHHHCCeEEeccchhccccccccccCCccceEEEEEeEcCCCCcEEEEEEEEcCCCCCCCCHHHHHHHHHHHHH
Confidence            3678999999999999887633311000111223899999999654      888866554 468999999999998877


Q ss_pred             HHHHHh
Q 022217          282 LDATLA  287 (301)
Q Consensus       282 L~~tL~  287 (301)
                      +...+.
T Consensus       160 ~a~al~  165 (691)
T 3ibj_A          160 TSTVLT  165 (691)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            766553

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	301
d1vhma_	159	Hypothetical protein YebR {Escherichia coli [TaxId	97.93
d1f5ma_	176	Hypothetical protein ykl069wp {Baker's yeast (Sacc	97.58
d1mc0a1	187	3',5'-cyclic nucleotide phosphodiesterase 2A, GAF	95.52
d1mc0a2	154	3',5'-cyclic nucleotide phosphodiesterase 2A, GAF	92.22
d2k2na1	170	Sensor protein CYB2465 {Synechococcus sp. [TaxId:	82.37

>d1vhma_ d.110.2.1 (A:) Hypothetical protein YebR {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: GAF domain-like
family: GAF domain
domain: Hypothetical protein YebR
species: Escherichia coli [TaxId: 562]

Probab=97.93  E-value=0.00011  Score=59.32  Aligned_cols=118  Identities=16%  Similarity=0.198  Sum_probs=85.4

Q ss_pred             HHHHHHHHhh---hccccEEEEEECCEEEEEEeeccCCCCCccchhhcccccchh-hHHHHHhhccCceeccccccCCCC
Q 022217          158 LLWAWESLSA---VTCCRSLVVVYDGIYLLQIGMAAESGNSGEAVIVDASKLKQG-SVYLGVMRSKAQRYLANLLLYPGR  233 (301)
Q Consensus       158 LAWas~~LLt---nT~a~svlV~~~G~vll~RG~~~~~~~~g~a~~~d~~~~~pG-~I~~r~~~~~~~iyL~nl~lyPGr  233 (301)
                      |+-.+..|.+   ++...++.+..++...+  +.......        ...+..| .+|.++.++++++.+.|..-.|..
T Consensus        27 L~~i~~~l~~~~~~~~~~~~yl~d~~~~~l--~~~~~~~~--------~~~i~~g~g~~g~v~~~~~~~~v~d~~~d~~~   96 (159)
T d1vhma_          27 LANTSALLYERLTDINWAGFYLLEDDTLVL--GPFQGKIA--------CVRIPVGRGVCGTAVARNQVQRIEDVHVFDGH   96 (159)
T ss_dssp             HHHHHHHHHHHSSSCSEEEEEEEETTEEEE--EEEEESCC--------CSEEETTSHHHHHHHHHTSCEEESCTTTCTTC
T ss_pred             HHHHHHHHHHhhccCceEEEEEEECCEeee--eeecCCcc--------eeEEecCCChHHHHHHcCCcEEecChHHhhhh
Confidence            5666666643   44445565656665443  22222111        0134444 478999999999999999877764


Q ss_pred             CCCCCCCCCCCeeEEEecC--CC--eEEEEecCCCcccChhhHHHHHHHHHHHHHHHhh
Q 022217          234 SELPFLPSNTQAVILQPLG--DK--GIAIIGGDTIRGFTTSDQSWIAFIGEKLDATLAK  288 (301)
Q Consensus       234 ~Ef~~LP~ntqsVlvQPig--~~--Gvlvlgs~s~R~FT~kDe~WI~~iA~KL~~tL~~  288 (301)
                      .   ....+.+|++|.||-  ++  |+|.+++..++.||+.|...++.+|+.+..+++.
T Consensus        97 ~---~~~~~~~S~l~vPl~~~~~viGvl~v~s~~~~~F~~~d~~ll~~la~qia~ai~~  152 (159)
T d1vhma_          97 I---ACDAASNSEIVLPLVVKNQIIGVLDIDSTVFGRFTDEDEQGLRQLVAQLEKVLAT  152 (159)
T ss_dssp             C---CSCCCCSEEEEEEEEETTEEEEEEEEEESSTTCCCHHHHHHHHHHHHHHHHHHHT
T ss_pred             h---hcccccceeEEeCEEECCEEEEEEEecCCCCCCCCHHHHHHHHHHHHHHHHHHHc
Confidence            4   346789999999984  32  9999999999999999999999999999999875

>d1f5ma_ d.110.2.1 (A:) Hypothetical protein ykl069wp {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: GAF domain-like
family: GAF domain
domain: Hypothetical protein ykl069wp
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.58  E-value=0.00016  Score=59.41  Aligned_cols=77  Identities=18%  Similarity=0.349  Sum_probs=65.5

Q ss_pred             cchh-hHHHHHhhccCceeccccccCCCCCCCCCCCCCCCeeEEEec-CCC----eEEEEecCCCcccChhhHHHHHHHH
Q 022217          206 LKQG-SVYLGVMRSKAQRYLANLLLYPGRSELPFLPSNTQAVILQPL-GDK----GIAIIGGDTIRGFTTSDQSWIAFIG  279 (301)
Q Consensus       206 ~~pG-~I~~r~~~~~~~iyL~nl~lyPGr~Ef~~LP~ntqsVlvQPi-g~~----Gvlvlgs~s~R~FT~kDe~WI~~iA  279 (301)
                      +..| .+|.++.++++++++.|..-.|.   |.....++++.+|.|| ..+    |||-+.+..++.||+.|+.+++.+|
T Consensus        91 i~~g~Gi~G~v~~~g~~i~v~D~~~dpr---~~~~~~~~~S~l~vPl~~~~g~~~GVl~v~s~~~~~F~~~d~~~l~~~A  167 (176)
T d1f5ma_          91 IQFGKGVCGTAASTKETQIVPDVNKYPG---HIACDGETKSEIVVPIISNDGKTLGVIDIDCLDYEGFDHVDKEFLEKLA  167 (176)
T ss_dssp             EETTSHHHHHHHHHTSCEEESCGGGSTT---CCCSSTTCCEEEEEEEECTTSCEEEEEEEEESSTTCCCHHHHHHHHHHH
T ss_pred             ecCCCcHHHHHHHhCCeEEecCcccCcc---hhhccccccceEEecccccCCcEEEEEEeccCCCCCcCHHHHHHHHHHH
Confidence            4455 68999999999999999987774   4455678999999999 333    8999999999999999999999999


Q ss_pred             HHHHHH
Q 022217          280 EKLDAT  285 (301)
Q Consensus       280 ~KL~~t  285 (301)
                      +-+..+
T Consensus       168 ~~ia~a  173 (176)
T d1f5ma_         168 KLINKS  173 (176)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            988754

>d1mc0a1 d.110.2.1 (A:215-401) 3',5'-cyclic nucleotide phosphodiesterase 2A, GAF A and GAF B domains {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: GAF domain-like
family: GAF domain
domain: 3',5'-cyclic nucleotide phosphodiesterase 2A, GAF A and GAF B domains
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.52  E-value=0.0035  Score=49.92  Aligned_cols=79  Identities=19%  Similarity=0.056  Sum_probs=57.6

Q ss_pred             hHHHHHhhccCceeccccccCCCCCCCCCCCCCCCeeEEEecC----C--CeEE-EEecCCCcccChhhHHHHHHHHHHH
Q 022217          210 SVYLGVMRSKAQRYLANLLLYPGRSELPFLPSNTQAVILQPLG----D--KGIA-IIGGDTIRGFTTSDQSWIAFIGEKL  282 (301)
Q Consensus       210 ~I~~r~~~~~~~iyL~nl~lyPGr~Ef~~LP~ntqsVlvQPig----~--~Gvl-vlgs~s~R~FT~kDe~WI~~iA~KL  282 (301)
                      .++.++.++++++++.|..-=|-.......-.++.+++|.|+-    +  -||+ +.-....+.||+.|...+..+|+-+
T Consensus        73 g~~~~v~~~~~~~~i~d~~~d~~~~~~~~~~~~~~s~l~vPl~~~~~~~~iGvl~~~~~~~~~~fs~~d~~~l~~~a~~~  152 (187)
T d1mc0a1          73 GRLGQVVEDKQCIQLKDLTSDDVQQLQNMLGCELQAMLCVPVISRATDQVVALACAFNKLGGDFFTDEDEHVIQHCFHYT  152 (187)
T ss_dssp             SSHHHHHHHCCCEEGGGSCHHHHHHHHHHHCSCCCCEEEEEEECTTTCSEEEEEEEEEESSCSSCCSHHHHHHHHHHHHH
T ss_pred             cHHHHHHHhhhhhhhhccccccccccchhhhhhHHHHHhhhhhccccccceEEEEEEcccccchhhhHHHHHHHHHHHHH
Confidence            5678899999999999976211100112334578899999992    2  3777 4445677999999999999999998


Q ss_pred             HHHHhh
Q 022217          283 DATLAK  288 (301)
Q Consensus       283 ~~tL~~  288 (301)
                      ...++.
T Consensus       153 a~ai~n  158 (187)
T d1mc0a1         153 GTVLTS  158 (187)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            887753

>d1mc0a2 d.110.2.1 (A:402-555) 3',5'-cyclic nucleotide phosphodiesterase 2A, GAF A and GAF B domains {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: GAF domain-like
family: GAF domain
domain: 3',5'-cyclic nucleotide phosphodiesterase 2A, GAF A and GAF B domains
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.22  E-value=1.4  Score=31.76  Aligned_cols=80  Identities=11%  Similarity=0.016  Sum_probs=53.3

Q ss_pred             hhHHHHHhhccCceeccccccCCCCCCCC--CCCCCCCeeEEEec-C-C---CeEEE-EecCCCcccChhhHHHHHHHHH
Q 022217          209 GSVYLGVMRSKAQRYLANLLLYPGRSELP--FLPSNTQAVILQPL-G-D---KGIAI-IGGDTIRGFTTSDQSWIAFIGE  280 (301)
Q Consensus       209 G~I~~r~~~~~~~iyL~nl~lyPGr~Ef~--~LP~ntqsVlvQPi-g-~---~Gvlv-lgs~s~R~FT~kDe~WI~~iA~  280 (301)
                      ..++.++..+++.+...|...-+-.....  .......+.+|.|+ . +   -|++. .....+|.||+.|..-++.+|+
T Consensus        55 ~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~f~~~d~~ll~~la~  134 (154)
T d1mc0a2          55 QGIAGHVATTGQILNIPDAYAHPLFYRGVDDSTGFRTRNILCFPIKNENQEVIGVAELVNKINGPWFSKFDEDLATAFSI  134 (154)
T ss_dssp             SHHHHHHHHHCCCEEESCSTTCTTCCCTTHHHHTCCCCCEEEEEEECTTSCEEEEEEEEEETTSSSCCHHHHHHHHHHHH
T ss_pred             ccchhheeccCcEEEEEeccccccccchhhhhhcccceeEEEEecccccceeeEEEEeecccccccccHHHHHHHHHHHH
Confidence            46788899999999887776444333331  11223333344433 2 2   24444 4466899999999999999999


Q ss_pred             HHHHHHhh
Q 022217          281 KLDATLAK  288 (301)
Q Consensus       281 KL~~tL~~  288 (301)
                      .+...+++
T Consensus       135 q~aiAi~n  142 (154)
T d1mc0a2         135 YCGISIAH  142 (154)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99888865

>d2k2na1 d.110.2.1 (A:31-200) Sensor protein CYB2465 {Synechococcus sp. [TaxId: 1131]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: GAF domain-like
family: GAF domain
domain: Sensor protein CYB2465
species: Synechococcus sp. [TaxId: 1131]

Probab=82.37  E-value=1.4  Score=33.78  Aligned_cols=48  Identities=10%  Similarity=0.283  Sum_probs=43.3

Q ss_pred             CCCCeeEEEecCC----CeEEEEecCCCcccChhhHHHHHHHHHHHHHHHhh
Q 022217          241 SNTQAVILQPLGD----KGIAIIGGDTIRGFTTSDQSWIAFIGEKLDATLAK  288 (301)
Q Consensus       241 ~ntqsVlvQPig~----~Gvlvlgs~s~R~FT~kDe~WI~~iA~KL~~tL~~  288 (301)
                      -|.+|.++.|+..    -|+|++=...+|..++.|...++.+|+.+...+++
T Consensus       116 ~~v~s~l~vPi~~~~~lwGlL~~h~~~~r~W~~~Ei~ll~~iA~qlaiAI~q  167 (170)
T d2k2na1         116 MGVASSLVVPLMHHQELWGLLVSHHAEPRPYSQEELQVVQLLADQVSIAIAQ  167 (170)
T ss_dssp             TTCSEEEECCCSCSSCCCEEEEEEECSCCCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccccceEEEeeecCCceEEEEEEecCCCCcCCHHHHHHHHHHHHHHHHHHHH
Confidence            4789999999954    39999999999999999999999999999998865