Citrus Sinensis ID: 023083

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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-------
Protein Sequence
MSILPYNSLMQLKIPSHSCAKTTRKSFSICARLDNSQQEEQQLNLSVLRFTFGIPGFDESYLPRWIGYGFGSLIVLNHFAFSNSVTSAQLRSEVLGLSLAAFSVTLPYLGKFLKQGASPVSQKSLPESGEQIFVMSQNISDALKENLAWATYVLLRNTNSISVLISIRGELCVRGYWQTPDGASKTQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGKSIWIDLK
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccEEcccccHHHHHHccccEEEEEcccccccccccHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccEEcEEEcccccHHHHHHHHHHHHHHHHcccccEEEEEEccEEEEEEEEcccccccHHHHHHHHHHHHcccccccccccccccccccccccccccccccEEEEEEccccccccccccccccEEEEEEEcccccccHHHHHHHHHHHHHHcccccccccc
Secondary Structure Prediction (SSPRO)
ccccEccccccccccccccccccccEEEEEEEccccccccccccEEEEEEEcccccccHcHccHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccEEEEEcccccHHHHHHHHHHHHHHHHccccEEEEEEEccEEEEEEccccccccccHHHHHHHHHHcccEEEEEccHcEEEcccccccccccccccccEEEEEEccccccccccccccccEEEEEEccccccccHHHHHHHHHHHHHHcccEEEEEcc
Coil and Loop (DISEMBL)
msilpynslmqlkipshscakttrKSFSICARLDNSQQEEQQLNLSVLRftfgipgfdesylprwigygFGSLIVLNHfafsnsvtsAQLRSEVLGLSLAAFSVTLPYLGKflkqgaspvsqkslpesgEQIFVMSQNISDALKENLAWATYVLLRNTNSISVLISIRGELcvrgywqtpdgaskTQLLEWFERQIENIglsdlkdslyfpqsadagqwemlpkgtcsvfvqpviqapnpsavevEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGKSIWIDLK
Flexible Loop (DISEMBL)
msilpynslmqlkipshscaKTTRKSFSICARLDNSQQEEQQLNLSVLRFTFGIPGFDESYLPRWIGYGFGSLIVLNHFAFSNSVTSAQLRSEVLGLSLAAFSVTLPYLGKFLKQGASPVSQKSLPESGEQIFVMSQNISDALKENLAWATYVLLRNTNSISVLISIRGELCVRGYWQTPDGASKTQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKavsnkfrgksiwidlk
Low Complexity Region (SEG)
MSILPYNSLMQLKIPSHSCAKTTRKSFSICARLDNSQQEEQQLNLSVLRFTFGIPGFDESYLPRWIGYGFGSLIVLNHFAFSNSVTSAQLRSEVLGLSLAAFSVTLPYLGKFLKQGASPVSQKSLPESGEQIFVMSQNISDALKENLAWATYVLLRNTNSISVLISIRGELCVRGYWQTPDGASKTQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGKSIWIDLK
Disordered region (IsUnstruct)
**************************FSICAR*********QLNLSVLRFTFGIPGFDESYLPRWIGYGFGSLIVLNHFAFSNSVTSAQLRSEVLGLSLAAFSVTLPYLGKFLK*****************IFVMSQNISDALKENLAWATYVLLRNTNSISVLISIRGELCVRGYWQTPDGASKTQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGKSIWID**
Disordered Region (DISOPRED)
****PYNSLMQLK*********************************VLRFTFGIPGFDESYLPRWIGYGFGSLIVLNHFAFSNSVTSAQLRSEVLGLSLAAFSVTLPYLGKFLK*****************IFVMSQNISDALKENLAWATYVLLRNTNSISVLISIRGELCVRGYWQ*********LLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGKSIWIDL*
Disordered Region (DISEMBL)
MSILPYNSLMQLKIPSHSCAKTTRKSFSICARLDNSQQEEQQLNLSVLRFTFGIPGFDESYLPRWIGYGFGSLIVLNHFAFSNSVTSAQLRSEVLGLSLAAFSVTLPYLGKFLK***********PESGEQIFVMSQNISDALKENLAWATYVLLRNTNSISVLISIRGELCVRGYWQTPDGASKTQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGKSIWIDLK
Disordered Region (DISPRO)
*SILPYNSLMQLKIPSHSCA*TTRKSFSICARLDNSQQEEQQLNLSVLRFTFGIPGFDESYLPRWIGYGFGSLIVLNHFAFSNSVTSAQLRSEVLGLSLAAFSVTLPYLGKFLKQGASPVSQKSLPESGEQIFVMSQNISDALKENLAWATYVLLRNTNSISVLISIRGELCVRGYWQTPDGASKTQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGKSIWIDLK
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHoooooooooooooooHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSILPYNSLMQLKIPSHSCAKTTRKSFSICARLDNSQQEEQQLNLSVLRFTFGIPGFDESYLPRWIGYGFGSLIVLNHFAFSNSVTSAQLRSEVLGLSLAAFSVTLPYLGKFLKQGASPVSQKSLPESGEQIFVMSQNISDALKENLAWATYVLLRNTNSISVLISIRGELCVRGYWQTPDGASKTQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGKSIWIDLK
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	287
225455453	311	PREDICTED: uncharacterized protein LOC10	0.891	0.823	0.723	1e-105
297741104	313	unnamed protein product [Vitis vinifera]	0.888	0.814	0.722	1e-105
224136914	265	predicted protein [Populus trichocarpa]	0.902	0.977	0.695	3e-98
255539547	308	conserved hypothetical protein [Ricinus	0.944	0.879	0.645	1e-96
449446061	288	PREDICTED: uncharacterized protein LOC10	0.912	0.909	0.640	4e-93
15242277	275	uncharacterized protein [Arabidopsis tha	0.902	0.941	0.603	3e-89
297796017	272	hypothetical protein ARALYDRAFT_495283 [	0.902	0.952	0.602	5e-89
147816662	349	hypothetical protein VITISV_012455 [Viti	0.891	0.733	0.586	2e-88
356559871	287	PREDICTED: uncharacterized protein LOC10	0.825	0.825	0.637	5e-83
242040471	293	hypothetical protein SORBIDRAFT_01g03118	0.947	0.928	0.535	1e-76

>gi|225455453|ref|XP_002274647.1| PREDICTED: uncharacterized protein LOC100252183 [Vitis vinifera]

 Score =  388 bits (997), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 191/264 (72%), Positives = 218/264 (82%), Gaps = 8/264 (3%)

Query: 18  SCAKTTRKSFSICARLDNSQQEEQQLNLSVLRFTFGIPGFDESYLPRWIGYGFGSLIVLN 77
           S   TTRK  SI A       ++QQLNLSVLRFT GIPGFDESYLPRWIGYGFGS I+LN
Sbjct: 54  STINTTRKFQSISA-----SNQQQQLNLSVLRFTLGIPGFDESYLPRWIGYGFGSFILLN 108

Query: 78  HFAFS--NSVTSAQLRSEVLGLSLAAFSVTLPYLGKFLKQGASPVSQKSLPESGEQIFVM 135
           HF  S  N++T+AQLR+E LGL LAAFSV LPYLGKFLK GA+PV Q +LPE  EQIFVM
Sbjct: 109 HFVGSDLNTITAAQLRTEALGLCLAAFSVVLPYLGKFLK-GAAPVDQTTLPEGIEQIFVM 167

Query: 136 SQNISDALKENLAWATYVLLRNTNSISVLISIRGELCVRGYWQTPDGASKTQLLEWFERQ 195
           +QNISD LKE+LAWATY+LLRNTN+I+VLISIRG LCVRGYW TPD  SK ++L+W E++
Sbjct: 168 TQNISDILKEDLAWATYILLRNTNTIAVLISIRGALCVRGYWNTPDDVSKARVLDWVEKE 227

Query: 196 IENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLA 255
           IE IGLSDLKD+LYFPQSAD+G WEMLPKGTCS+ VQPV Q P+    E+EKI+GFVLLA
Sbjct: 228 IEKIGLSDLKDTLYFPQSADSGLWEMLPKGTCSLLVQPVSQIPSQGTDEMEKIDGFVLLA 287

Query: 256 SSMTYAYSHKDRAWIKAVSNKFRG 279
           SSM YAY+ KDRAWI AV+NKFRG
Sbjct: 288 SSMNYAYTDKDRAWIGAVANKFRG 311

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297741104|emb|CBI31835.3| unnamed protein product [Vitis vinifera]

 Score =  386 bits (991), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 190/263 (72%), Positives = 217/263 (82%), Gaps = 8/263 (3%)

Query: 18  SCAKTTRKSFSICARLDNSQQEEQQLNLSVLRFTFGIPGFDESYLPRWIGYGFGSLIVLN 77
           S   TTRK  SI A       ++QQLNLSVLRFT GIPGFDESYLPRWIGYGFGS I+LN
Sbjct: 54  STINTTRKFQSISA-----SNQQQQLNLSVLRFTLGIPGFDESYLPRWIGYGFGSFILLN 108

Query: 78  HFAFS--NSVTSAQLRSEVLGLSLAAFSVTLPYLGKFLKQGASPVSQKSLPESGEQIFVM 135
           HF  S  N++T+AQLR+E LGL LAAFSV LPYLGKFLK GA+PV Q +LPE  EQIFVM
Sbjct: 109 HFVGSDLNTITAAQLRTEALGLCLAAFSVVLPYLGKFLK-GAAPVDQTTLPEGIEQIFVM 167

Query: 136 SQNISDALKENLAWATYVLLRNTNSISVLISIRGELCVRGYWQTPDGASKTQLLEWFERQ 195
           +QNISD LKE+LAWATY+LLRNTN+I+VLISIRG LCVRGYW TPD  SK ++L+W E++
Sbjct: 168 TQNISDILKEDLAWATYILLRNTNTIAVLISIRGALCVRGYWNTPDDVSKARVLDWVEKE 227

Query: 196 IENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLA 255
           IE IGLSDLKD+LYFPQSAD+G WEMLPKGTCS+ VQPV Q P+    E+EKI+GFVLLA
Sbjct: 228 IEKIGLSDLKDTLYFPQSADSGLWEMLPKGTCSLLVQPVSQIPSQGTDEMEKIDGFVLLA 287

Query: 256 SSMTYAYSHKDRAWIKAVSNKFR 278
           SSM YAY+ KDRAWI AV+NKFR
Sbjct: 288 SSMNYAYTDKDRAWIGAVANKFR 310

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224136914|ref|XP_002322447.1| predicted protein [Populus trichocarpa] gi|222869443|gb|EEF06574.1| predicted protein [Populus trichocarpa]

 Score =  363 bits (933), Expect = 3e-98,   Method: Compositional matrix adjust.
 Identities = 183/263 (69%), Positives = 217/263 (82%), Gaps = 4/263 (1%)

Query: 20  AKTTRKSFSICARLDN--SQQEEQQLNLSVLRFTFGIPGFDESYLPRWIGYGFGSLIVLN 77
           AK TRKS +I A  DN  SQ+++QQLNLSVLRFTFGIPG DESYLPRWIGYGFGSL++LN
Sbjct: 4   AKKTRKSIAIHASSDNPQSQRQQQQLNLSVLRFTFGIPGLDESYLPRWIGYGFGSLLILN 63

Query: 78  HFAFSN-SVTSAQLRSEVLGLSLAAFSVTLPYLGKFLKQGASPVSQKSLPESGEQIFVMS 136
           HF  SN   T AQLR+EVLGLSLAAFS  LPY G+FLK GA+PV Q +LP+  EQIF MS
Sbjct: 64  HFLGSNPDTTQAQLRTEVLGLSLAAFSAALPYFGRFLK-GATPVDQGTLPQDAEQIFAMS 122

Query: 137 QNISDALKENLAWATYVLLRNTNSISVLISIRGELCVRGYWQTPDGASKTQLLEWFERQI 196
           QNISDA KE+LAWATY+LLRNTN+I+VLISI+GELCVRGYW+T D  SK ++L+WF+ QI
Sbjct: 123 QNISDAQKEDLAWATYILLRNTNTIAVLISIQGELCVRGYWKTSDKMSKDEVLDWFKEQI 182

Query: 197 ENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLAS 256
           ENIGLSD+KD+LYFPQ+ ++  WEMLP+GT S+ V+PV+QA   S  + E  EGF+LLAS
Sbjct: 183 ENIGLSDVKDTLYFPQTTESEIWEMLPEGTRSLLVEPVLQATVQSGNKTENNEGFILLAS 242

Query: 257 SMTYAYSHKDRAWIKAVSNKFRG 279
           S+ YAYS KDRAWI+A  NKFRG
Sbjct: 243 SIGYAYSDKDRAWIRATGNKFRG 265

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255539547|ref|XP_002510838.1| conserved hypothetical protein [Ricinus communis] gi|223549953|gb|EEF51440.1| conserved hypothetical protein [Ricinus communis]

 Score =  358 bits (920), Expect = 1e-96,   Method: Compositional matrix adjust.
 Identities = 182/282 (64%), Positives = 226/282 (80%), Gaps = 11/282 (3%)

Query: 1   MSILPYNSLM-QLKIPSHSCAKTTRKSFSICARLDNSQQ---EEQQLNLSVLRFTFGIPG 56
           MS L  N L+   K  +++  K+  K+ SI  R+DNSQ+   ++Q LNLSVLRFTFGIPG
Sbjct: 1   MSNLSINPLITHPKFRANNSVKS--KNASIIVRIDNSQRKKDQQQDLNLSVLRFTFGIPG 58

Query: 57  FDESYLPRWIGYGFGSLIVLNHFAFSNSVTS-AQLRSEVLGLSLAAFSVTLPYLGKFLKQ 115
            DESYLPRWIGYGFGSL+VLNHF  SNSVTS  Q+R+E LGLSLAAFS+ LPY G+FLK 
Sbjct: 59  LDESYLPRWIGYGFGSLLVLNHFLGSNSVTSLPQMRTEALGLSLAAFSIALPYFGRFLK- 117

Query: 116 GASPVSQKSLPESGEQIFVMSQNISDALKENLAWATYVLLRNTNSISVLISIRGELCVRG 175
           GA+PV Q +LP+  EQIFVMS+N+SD LKE+LAWATYVLLRNTNSI+VLI I+GELCVRG
Sbjct: 118 GATPVDQTALPQGSEQIFVMSENVSDTLKEDLAWATYVLLRNTNSIAVLIYIQGELCVRG 177

Query: 176 YWQTPDGASKTQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVI 235
           YW TPD  SK Q+++WF+ +IE+IGL DLKD+LYFPQ+A++  WEMLP+GT S+ V+PV+
Sbjct: 178 YWNTPDNISKAQVIDWFKGRIEDIGLFDLKDTLYFPQTAESRLWEMLPRGTRSLLVEPVL 237

Query: 236 QAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKF 277
                +A E+++ EGFVLLASS+  AY+ KDRAWI AV+NKF
Sbjct: 238 LQ---NAKEMDRAEGFVLLASSIDTAYTDKDRAWIGAVANKF 276

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449446061|ref|XP_004140790.1| PREDICTED: uncharacterized protein LOC101219803 [Cucumis sativus] gi|449530412|ref|XP_004172189.1| PREDICTED: uncharacterized LOC101219803 [Cucumis sativus]

 Score =  347 bits (890), Expect = 4e-93,   Method: Compositional matrix adjust.
 Identities = 171/267 (64%), Positives = 210/267 (78%), Gaps = 5/267 (1%)

Query: 20  AKTTRKSFSICARLDNSQQE-EQQLNLSVLRFTFGIPGFDESYLPRWIGYGFGSLIVLNH 78
           AK+  K  +I ARLD+S+    QQLNLSVLRFT GIPG DESYLPRWIGYGFGSL++LNH
Sbjct: 22  AKSKTKGPAISARLDDSKNSANQQLNLSVLRFTLGIPGLDESYLPRWIGYGFGSLLLLNH 81

Query: 79  FAFSNS---VTSAQLRSEVLGLSLAAFSVTLPYLGKFLKQGASPVSQKSLPESGEQIFVM 135
           F  SNS    T AQLR+E LG+SLAAFS+ LPYLGKFLK GA P  +  LPE  EQIF++
Sbjct: 82  FVGSNSAALTTPAQLRTEALGISLAAFSIALPYLGKFLK-GALPSGEAILPEGTEQIFLL 140

Query: 136 SQNISDALKENLAWATYVLLRNTNSISVLISIRGELCVRGYWQTPDGASKTQLLEWFERQ 195
           SQ +SD LKE++AWATY+LLRNTNSISVLI  +G LCVRGYW +P+  S   LL WFE Q
Sbjct: 141 SQILSDNLKEDIAWATYILLRNTNSISVLIQTQGALCVRGYWNSPNDISSADLLAWFEEQ 200

Query: 196 IENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLA 255
           +++IGLS LKD++YFPQ +++G W+MLPKGT SV VQPV+Q    S  EV+ + GF+LLA
Sbjct: 201 LQSIGLSALKDAVYFPQISESGLWQMLPKGTRSVLVQPVVQNLKQSGNEVQNMGGFILLA 260

Query: 256 SSMTYAYSHKDRAWIKAVSNKFRGKSI 282
           SS++YA+S KDRAWI+AV+NKF  ++I
Sbjct: 261 SSLSYAFSDKDRAWIRAVANKFDDRAI 287

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15242277|ref|NP_200024.1| uncharacterized protein [Arabidopsis thaliana] gi|79330641|ref|NP_001032060.1| uncharacterized protein [Arabidopsis thaliana] gi|10177746|dbj|BAB11059.1| unnamed protein product [Arabidopsis thaliana] gi|117959001|gb|ABK59697.1| At5g52110 [Arabidopsis thaliana] gi|332008789|gb|AED96172.1| uncharacterized protein [Arabidopsis thaliana] gi|332008790|gb|AED96173.1| uncharacterized protein [Arabidopsis thaliana]

 Score =  334 bits (856), Expect = 3e-89,   Method: Compositional matrix adjust.
 Identities = 163/270 (60%), Positives = 211/270 (78%), Gaps = 11/270 (4%)

Query: 15  PSHSCAKTTRKSFSICARLDN----SQQEEQQLNLSVLRFTFGIPGFDESYLPRWIGYGF 70
           P  +     ++S  I AR +N    S+  +QQLNLSVLRFTFGIPGFDESYLPRWIGYGF
Sbjct: 12  PKFALQPRAQRSTRIFARTENDSPQSKTSDQQLNLSVLRFTFGIPGFDESYLPRWIGYGF 71

Query: 71  GSLIVLNHFAFSNSVTSAQLRSEVLGLSLAAFSVTLPYLGKFLKQGASPVSQKSLPESGE 130
           GSL++LNHF+ S  ++ +Q+RSE LGLSLAAFS+ LPY+GKFLK   S V Q+SLPE GE
Sbjct: 72  GSLLLLNHFSASAPISESQMRSEALGLSLAAFSIALPYIGKFLK--GSVVEQRSLPEEGE 129

Query: 131 QIFVMSQNISDALKENLAWATYVLLRNTNSISVLISIRGELCVRGYWQTPDGASKTQLLE 190
           Q+FV+S NI D+LKE+LAWATYVLLRNT++I+VLIS++GELCVRGYW  PD  SK QL +
Sbjct: 130 QVFVISSNIGDSLKEDLAWATYVLLRNTSTIAVLISVQGELCVRGYWNCPDQMSKAQLHD 189

Query: 191 WFERQIENIGLSDLKDSLYFPQSADAG-QWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIE 249
           WF+++++ IGL+D+K++LYFPQ A +    ++LP GT S+FVQP++Q  N    E +K+ 
Sbjct: 190 WFKKKVDEIGLADVKETLYFPQYAGSALSLDILPDGTRSLFVQPLVQNTN----EPQKVN 245

Query: 250 GFVLLASSMTYAYSHKDRAWIKAVSNKFRG 279
           GF+L+AS+  YAYS KDRAWI A++ KFRG
Sbjct: 246 GFLLVASTAGYAYSDKDRAWIGAMAEKFRG 275

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297796017|ref|XP_002865893.1| hypothetical protein ARALYDRAFT_495283 [Arabidopsis lyrata subsp. lyrata] gi|297311728|gb|EFH42152.1| hypothetical protein ARALYDRAFT_495283 [Arabidopsis lyrata subsp. lyrata]

 Score =  333 bits (854), Expect = 5e-89,   Method: Compositional matrix adjust.
 Identities = 161/267 (60%), Positives = 211/267 (79%), Gaps = 8/267 (2%)

Query: 15  PSHSCAKTTRKSFSICARLDN-SQQEEQQLNLSVLRFTFGIPGFDESYLPRWIGYGFGSL 73
           P  +     ++S  I AR +N S Q++QQLNLSVLRFTFGIPG DESYLPRWIGYGFGSL
Sbjct: 12  PKFALQPRAQRSTRIFARTENDSPQQQQQLNLSVLRFTFGIPGLDESYLPRWIGYGFGSL 71

Query: 74  IVLNHFAFSNSVTSAQLRSEVLGLSLAAFSVTLPYLGKFLKQGASPVSQKSLPESGEQIF 133
           ++LNHF+ S  ++ +Q+RSE LGLSLA+FS+ LPY+GKFLK   S V Q++LPE GEQIF
Sbjct: 72  LLLNHFSASAPISESQMRSEALGLSLASFSIALPYIGKFLK--GSVVEQRTLPEEGEQIF 129

Query: 134 VMSQNISDALKENLAWATYVLLRNTNSISVLISIRGELCVRGYWQTPDGASKTQLLEWFE 193
           V+S NI D+LKE+LAWATYVLLRNT++I+VLI ++GELCVRGYW  PD  SK QL +WF+
Sbjct: 130 VISSNIGDSLKEDLAWATYVLLRNTSTIAVLILVQGELCVRGYWNCPDQMSKAQLHDWFK 189

Query: 194 RQIENIGLSDLKDSLYFPQSADAG-QWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFV 252
           ++++ IGL+D+KD+LYFPQ A +   W++LP GT S+F+QP++Q    +  E +K+ GF+
Sbjct: 190 KKVDEIGLADVKDTLYFPQYAGSALSWDILPDGTRSLFMQPLVQ----NISEPQKVNGFL 245

Query: 253 LLASSMTYAYSHKDRAWIKAVSNKFRG 279
           L+AS+  YAYS KDRAWI A++ KFRG
Sbjct: 246 LVASTAGYAYSDKDRAWIGAMAEKFRG 272

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147816662|emb|CAN68387.1| hypothetical protein VITISV_012455 [Vitis vinifera]

 Score =  331 bits (848), Expect = 2e-88,   Method: Compositional matrix adjust.
 Identities = 177/302 (58%), Positives = 204/302 (67%), Gaps = 46/302 (15%)

Query: 18  SCAKTTRKSFSICARLDNSQQEEQQLNLSVLRFTFGIPGFDESYLPRWIGYGFGSLIVLN 77
           S   TTRK  SI A       ++QQLNLSVLRFT GIPGFDESYLPRWIGYGFGS I+LN
Sbjct: 54  STINTTRKFQSISA-----SNQQQQLNLSVLRFTLGIPGFDESYLPRWIGYGFGSFILLN 108

Query: 78  HFAFS--NSVTSAQLRSEVLGLSLAAFSVTLPYLGKFLKQGASPVSQKSLPESGEQIFVM 135
           HF  S  N++T+AQLR+E LGL LAAFSV LPY GKFLK GA+PV Q +LPE  EQIFVM
Sbjct: 109 HFVGSDLNTITAAQLRTEALGLCLAAFSVVLPYXGKFLK-GAAPVDQTTLPEGIEQIFVM 167

Query: 136 SQNISDALKENLAWAT---------YVLLRNTNSISV----------------------- 163
           +QNISD L+  L             +  +   + I V                       
Sbjct: 168 TQNISDILERGLGLGNIHFAAEHKHHCCVVKGDIIVVSMRSQLCIYEVCFLFKYQXLLEL 227

Query: 164 ------LISIRGELCVRGYWQTPDGASKTQLLEWFERQIENIGLSDLKDSLYFPQSADAG 217
                 LISIRG LCVRGYW TPD  SK ++L+W E++IE IGLSDLKD+LYFPQSAD+G
Sbjct: 228 YCLNFQLISIRGALCVRGYWNTPDDVSKARVLDWVEKEIEKIGLSDLKDTLYFPQSADSG 287

Query: 218 QWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKF 277
            WEMLPKGTCS+ VQPV Q P+    E+EKI+GFVLLASSM YAY+ KDRAWI AV+NKF
Sbjct: 288 LWEMLPKGTCSLLVQPVXQIPSQGTDEMEKIDGFVLLASSMNYAYTDKDRAWIGAVANKF 347

Query: 278 RG 279
           RG
Sbjct: 348 RG 349

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356559871|ref|XP_003548220.1| PREDICTED: uncharacterized protein LOC100817953 [Glycine max]

 Score =  313 bits (803), Expect = 5e-83,   Method: Compositional matrix adjust.
 Identities = 153/240 (63%), Positives = 190/240 (79%), Gaps = 3/240 (1%)

Query: 43  LNLSVLRFTFGIPGFDESYLPRWIGYGFGSLIVLNHFAFSNS--VTSAQLRSEVLGLSLA 100
           LNLSVLRFT GIPG DESYLPRWIGYGFGSL++LNHF  S+S  VT AQL +EVLGLSLA
Sbjct: 48  LNLSVLRFTLGIPGLDESYLPRWIGYGFGSLLLLNHFLGSDSATVTPAQLSTEVLGLSLA 107

Query: 101 AFSVTLPYLGKFLKQGASPVSQKSLPESGEQIFVMSQNISDALKENLAWATYVLLRNTNS 160
           +FS+ LPYLGKFLK GA PV +K++P+  EQIFVMS +  D LKE+LAWA+YVLL NTN+
Sbjct: 108 SFSIVLPYLGKFLK-GAQPVDEKTIPDGTEQIFVMSTDRVDGLKEDLAWASYVLLCNTNA 166

Query: 161 ISVLISIRGELCVRGYWQTPDGASKTQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWE 220
           I++LI I+GE+C RGYW  PD  SK  L  WF+++IEN GL DLKD+LYFPQ AD+   +
Sbjct: 167 IAMLIFIQGEICARGYWNIPDDTSKEILPGWFKKKIENAGLYDLKDTLYFPQDADSEFQD 226

Query: 221 MLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGK 280
           ++P GT  + +QPV+Q  N S   ++K  GF+LLAS+  YA+S+KD+AWI AV+NKFRGK
Sbjct: 227 LVPIGTRCLLIQPVLQVSNESDTGLQKPGGFILLASTTRYAFSNKDKAWIAAVANKFRGK 286

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242040471|ref|XP_002467630.1| hypothetical protein SORBIDRAFT_01g031180 [Sorghum bicolor] gi|241921484|gb|EER94628.1| hypothetical protein SORBIDRAFT_01g031180 [Sorghum bicolor]

 Score =  292 bits (748), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 150/280 (53%), Positives = 196/280 (70%), Gaps = 8/280 (2%)

Query: 3   ILPYNSLMQLKIPSHSCAKTTRKSFSICA--RLDNSQ--QEEQQLNLSVLRFTFGIPGFD 58
           +LP  +    +  +   AK  R++ S  +  R  NS   Q++QQ+NLSVLRFT GIPG D
Sbjct: 16  LLPTATARLRQCSAAPAAKPRRRTLSSSSLVRASNSDPSQQQQQVNLSVLRFTLGIPGLD 75

Query: 59  ESYLPRWIGYGFGSLIVLNHFAFSNSVTSAQLRSEVLGLSLAAFSVTLPYLGKFLKQGAS 118
           ESYLPRWIG GFG+L+VLNH   S S T AQLRSE LGL LAAFS TLP+LG+FL +GA 
Sbjct: 76  ESYLPRWIGLGFGALVVLNHL-ISPSPTPAQLRSEALGLCLAAFSATLPFLGRFL-EGAD 133

Query: 119 PVSQKSLPESGEQIFVMSQNISDALKENLAWATYVLLRNTNSISVLISIRGELCVRGYWQ 178
             S+  LPE   Q+FVMS+N+S   KE++AWA+YVLLRNTN+ SV+I+I    C+RGYW 
Sbjct: 134 AASRVPLPEGSSQVFVMSENLSAVQKEDMAWASYVLLRNTNTTSVVIAIGDLFCIRGYWN 193

Query: 179 TPDGASKTQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAP 238
            P   SK  ++EWF+ Q++ +GL DLKD+LYFP S+D+   ++LP G  SV  QP++   
Sbjct: 194 PPANTSKYAMIEWFKSQMQQLGLVDLKDALYFPNSSDSQLVKILPDGILSVLAQPILSL- 252

Query: 239 NPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFR 278
           +P+  E  K EG +LLAS+  YAYS KDRAWI+ V+NKF+
Sbjct: 253 DPANNET-KTEGVILLASNANYAYSEKDRAWIRTVANKFQ 291

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

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	287
TAIR|locus:2173048	275	HCF208 "AT5G52110" [Arabidopsi	0.902	0.941	0.603	1.2e-83

TAIR|locus:2173048 HCF208 "AT5G52110" [Arabidopsis thaliana (taxid:3702)]

 Score = 838 (300.0 bits), Expect = 1.2e-83, P = 1.2e-83
 Identities = 163/270 (60%), Positives = 211/270 (78%)

Query:    15 PSHSCAKTTRKSFSICARLDN----SQQEEQQLNLSVLRFTFGIPGFDESYLPRWIGYGF 70
             P  +     ++S  I AR +N    S+  +QQLNLSVLRFTFGIPGFDESYLPRWIGYGF
Sbjct:    12 PKFALQPRAQRSTRIFARTENDSPQSKTSDQQLNLSVLRFTFGIPGFDESYLPRWIGYGF 71

Query:    71 GSLIVLNHFAFSNSVTSAQLRSEVLGLSLAAFSVTLPYLGKFLKQGASPVSQKSLPESGE 130
             GSL++LNHF+ S  ++ +Q+RSE LGLSLAAFS+ LPY+GKFLK   S V Q+SLPE GE
Sbjct:    72 GSLLLLNHFSASAPISESQMRSEALGLSLAAFSIALPYIGKFLK--GSVVEQRSLPEEGE 129

Query:   131 QIFVMSQNISDALKENLAWATYVLLRNTNSISVLISIRGELCVRGYWQTPDGASKTQLLE 190
             Q+FV+S NI D+LKE+LAWATYVLLRNT++I+VLIS++GELCVRGYW  PD  SK QL +
Sbjct:   130 QVFVISSNIGDSLKEDLAWATYVLLRNTSTIAVLISVQGELCVRGYWNCPDQMSKAQLHD 189

Query:   191 WFERQIENIGLSDLKDSLYFPQSADAG-QWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIE 249
             WF+++++ IGL+D+K++LYFPQ A +    ++LP GT S+FVQP++Q  N    E +K+ 
Sbjct:   190 WFKKKVDEIGLADVKETLYFPQYAGSALSLDILPDGTRSLFVQPLVQNTN----EPQKVN 245

Query:   250 GFVLLASSMTYAYSHKDRAWIKAVSNKFRG 279
             GF+L+AS+  YAYS KDRAWI A++ KFRG
Sbjct:   246 GFLLVASTAGYAYSDKDRAWIGAMAEKFRG 275


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        0.319   0.133   0.395    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      287       287   0.00087  115 3  11 22  0.37    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:  612 (65 KB)
  Total size of DFA:  213 KB (2118 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:  22.58u 0.10s 22.68t   Elapsed:  00:00:01
  Total cpu time:  22.58u 0.10s 22.68t   Elapsed:  00:00:01
  Start:  Sat May 11 09:57:15 2013   End:  Sat May 11 09:57:16 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

Your Input:
	gw1.XV.3200.1	hypothetical protein (265 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	gw1.I.6006.1	hypothetical protein (200 aa)			•				•		0.647
	gw1.I.3658.1	hypothetical protein (201 aa)			•	•					0.512
	gw1.XIII.568.1	SubName- Full=Putative uncharacterized protein; (212 aa)			•						0.506
	gw1.II.1221.1	hypothetical protein (155 aa)			•						0.506
	gw1.II.1028.1	hypothetical protein (152 aa)			•						0.506
	gw1.29.56.1	hypothetical protein (278 aa)			•						0.506
	gw1.131.248.1	hypothetical protein (212 aa)			•						0.506
	grail3.0063005001	hypothetical protein (186 aa)			•						0.506
	grail3.0037013703	hypothetical protein (146 aa)			•						0.506
	eugene3.121720001	hypothetical protein (63 aa)			•						0.506

---

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	287
pfam11152	195	pfam11152, DUF2930, Protein of unknown function (D	5e-55

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

 Score =  176 bits (448), Expect = 5e-55
 Identities = 65/218 (29%), Positives = 107/218 (49%), Gaps = 24/218 (11%)

Query: 62  LPRWIGYGFGSLIVLNHFAFSNSVTSAQLRSEVLGLSLAAFSVTLPYLGKFLKQGASPVS 121
           LP   G   G L++LN    +  +T +Q R++VLGL LAA  + +  L    +    P S
Sbjct: 1   LPLIAGLLGGLLLLLNRL-STADITPSQSRADVLGLLLAAGLILVGLLWTRAQ----PRS 55

Query: 122 QKSLPESGEQIFVMSQNISDALKENLAWATYVLLRNTNSISVLISIRGELCVR-GYWQTP 180
            +++   GEQ F +S ++S+ALKE LAWA+++LL  T + SVL+   G++ +R G    P
Sbjct: 56  PEAVDLEGEQGFELSPDLSEALKEELAWASHLLLTATPAASVLVYWDGQVLLRRGILGPP 115

Query: 181 DGASKTQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNP 240
               K +  E  +R +E   L  L +   +P   +   ++ LP  T +V VQP+      
Sbjct: 116 V---KFEPGEICKRALETQQLVYLVNLKLYPGRIE---FDYLPPNTQAVIVQPLGN---- 165

Query: 241 SAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFR 278
                    G ++L       ++  D  WI+  ++K R
Sbjct: 166 --------RGVLVLGGWSPRCFTRSDERWIEGWADKLR 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	287
PF11152	195	DUF2930: Protein of unknown function (DUF2930); In	100.0
PF13185	148	GAF_2: GAF domain; PDB: 2QYB_A 3KSG_B 3KSF_C 3KSI_	95.28
PF13492	129	GAF_3: GAF domain; PDB: 3EEA_A 4DMZ_A 4DN0_A 1VHM_	94.91
smart00065	149	GAF Domain present in phytochromes and cGMP-specif	91.86
PRK11061	748	fused phosphoenolpyruvate-protein phosphotransfera	91.82
PF01590	154	GAF: GAF domain; InterPro: IPR003018 This domain i	90.55
TIGR02851	180	spore_V_T stage V sporulation protein T. Members o	89.49
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	85.24
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	83.01

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

Probab=100.00  E-value=3.5e-73  Score=505.57  Aligned_cols=194  Identities=38%  Similarity=0.552  Sum_probs=185.3

Q ss_pred             hhHHHHHHHHHHHHhhhhccCCCCChhhHHHHHHHHHHHHHHhhhhhhhhhhhccccCCCCCCCCCCCeeceEeccCchH
Q 023083           62 LPRWIGYGFGSLIVLNHFAFSNSVTSAQLRSEVLGLSLAAFSVTLPYLGKFLKQGASPVSQKSLPESGEQIFVMSQNISD  141 (287)
Q Consensus        62 LP~~vG~l~g~Lll~N~~~s~a~~t~aQ~RsevLg~~Laa~lillP~~G~~Lw~~~~P~~~~~v~l~geq~F~l~~~Lsd  141 (287)
                      ||+++|+++++++++||++++ .+||||+||||||++||+++||   +|. +|++++|++++.+++.|+|+|+|++||||
T Consensus         1 LPl~vG~l~~~lll~N~~~~~-~~t~sq~RaevLg~~ls~~liL---~g~-lw~~l~p~~~~~v~L~G~~~f~l~~~L~~   75 (195)
T PF11152_consen    1 LPLIVGLLGGSLLLLNRLSGA-DATPSQSRAEVLGLILSAVLIL---TGL-LWQRLKPRSPEAVDLPGEQGFELSPDLSD   75 (195)
T ss_pred             CceEehHHHHHHHHhhhcccC-CCCHHHHHHHHHHHHHHHHHHH---HHH-HHhhccCCCCCccCCCCccceEECCCCCH
Confidence            799999999999999997776 6899999999999999999999   994 99999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhhhccccEEEEEECCEEE-EeeeecCCCCCChHHHHHHHHHhhhhcccccCCCcccccCCccccccc
Q 023083          142 ALKENLAWATYVLLRNTNSISVLISIRGELC-VRGYWQTPDGASKTQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWE  220 (287)
Q Consensus       142 ~~k~ELAWaS~~LLtnT~a~svlV~~~g~ll-~RG~~~~p~~~~~g~i~~~~~~~~~~~~Lv~L~~t~lyPgr~E~~~~~  220 (287)
                      ++|+|||||||+|||||+|+||+|||||++| +||++++++++++|+||++++++++.+||+|+   .|||||+|   |+
T Consensus        76 ~~k~ELAWas~~LLt~T~a~svlV~~~g~~llrrG~~~~~~~~~~g~i~~~~~~~~~~~yL~nl---~lyPGr~E---f~  149 (195)
T PF11152_consen   76 AAKEELAWASYALLTNTNARSVLVYYDGRVLLRRGILGSPSKFKPGPICQRAMESGKLIYLVNL---KLYPGRVE---FD  149 (195)
T ss_pred             HHHHHHHHHHHHHHhhCCceEEEEEECCEEEEEeeccCCCCCcchHHHHHHHHhcCCceecccc---ccCCCchh---hh
Confidence            9999999999999999999999999999966 58999888999999999999998888888777   89999999   89


Q ss_pred             cCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHHhhhc
Q 023083          221 MLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFR  278 (287)
Q Consensus       221 ~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kDe~WI~~iA~KL~  278 (287)
                      |||+|||||||||+|+            +||||+|||++||||+|||+||++|||||+
T Consensus       150 ~lP~ntq~VlvqP~g~------------~G~lvlgs~~~R~ft~~D~~Wi~~iA~Kl~  195 (195)
T PF11152_consen  150 YLPENTQSVLVQPLGQ------------NGVLVLGSNSPRAFTKSDEAWIAGIADKLR  195 (195)
T ss_pred             hcCCCCcEEEEEEcCC------------CeEEEEeeCCccccCHHHHHHHHHHHHhcC
Confidence            9999999999999999            599999999999999999999999999996

>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=95.28  E-value=0.026  Score=44.41  Aligned_cols=54  Identities=19%  Similarity=0.234  Sum_probs=41.8

Q ss_pred             ccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHHhhhcccc
Q 023083          220 EMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGKS  281 (287)
Q Consensus       220 ~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kDe~WI~~iA~KL~~~~  281 (287)
                      .+.=.|.+++++.||..+        .+.=|+|.+.+..++.||+.|+.+++.+|+-+..++
T Consensus        94 ~~~~~~~~s~l~vPl~~~--------~~~~Gvl~l~~~~~~~f~~~~~~~l~~la~~~a~ai  147 (148)
T PF13185_consen   94 LARHPGIRSILCVPLRSG--------GEVIGVLSLYSKEPNAFSEEDLELLEALADQIAIAI  147 (148)
T ss_dssp             HHCCTT-SEEEEEEEEET--------TEEEEEEEEEESSTT---HHHHHHHHHHHHHHHHHH
T ss_pred             hhccccCCEEEEEEEeEC--------CEEEEEEEEeeCCCCCcCHHHHHHHHHHHHHHHHHh
Confidence            345678999999999873        245799999999999999999999999999876554

...

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

Probab=94.91  E-value=0.097  Score=40.17  Aligned_cols=108  Identities=17%  Similarity=0.211  Sum_probs=67.3

Q ss_pred             HHHhhhccccEEEEE--ECC-E-E-EEeeeecCCC---C-CChHHHHHHHHHhhhhcccccCCCcccccCCccccccccC
Q 023083          152 YVLLRNTNSISVLIS--IRG-E-L-CVRGYWQTPD---G-ASKTQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEML  222 (287)
Q Consensus       152 ~~LLtnT~a~svlV~--~~g-~-l-l~RG~~~~p~---~-~~~g~i~~~~~~~~~~~~Lv~L~~t~lyPgr~E~~~~~~L  222 (287)
                      +.+...+.+..+.||  .++ . + +..++-+.+.   . .....++.++.++.+..+         .|+-.+..+    
T Consensus        11 ~~l~~~~~~~~~~l~~~d~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~---------~~~~~~~~~----   77 (129)
T PF13492_consen   11 ELLRELLGADRAALFLLDEDGNRLRVVAGWGGDPRLSESLPEDDPLIGRALETGEPVS---------VPDIDERDF----   77 (129)
T ss_dssp             HHHHHHST-SEEEEEEEETTCECEEEEEEESS-GCGHHCEETTSHHHHHHHHHTS-EE---------ESTCCC-TT----
T ss_pred             HHHHHHhCCCEEEEEEEECCCCEEEEEEEeCCCccccccCCCCccHHHHHHhhCCeEE---------ecccccccC----
Confidence            445566666665554  434 2 2 2366511111   1 144567667777665432         233222111    


Q ss_pred             CCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHHhhhcccc
Q 023083          223 PKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGKS  281 (287)
Q Consensus       223 P~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kDe~WI~~iA~KL~~~~  281 (287)
                       .+.+++++.||..+        .+.-|+|.+++..++.||++|+..++.+|+-+..+.
T Consensus        78 -~~~~s~~~vPl~~~--------~~~~Gvl~~~~~~~~~~~~~d~~~l~~~a~~~a~al  127 (129)
T PF13492_consen   78 -LGIRSLLVVPLRSR--------DRVIGVLCLDSREPEEFSDEDLQLLESLANQLAIAL  127 (129)
T ss_dssp             -TTTCEEEEEEEEET--------TEEEEEEEEEECTTCG-SHHHHHHHHHHHHHHHHHH
T ss_pred             -CCCCEEEEEEEeEC--------CEEEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHh
Confidence             66799999999873        366899999999999999999999999999876554

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

Probab=91.86  E-value=0.5  Score=34.82  Aligned_cols=49  Identities=16%  Similarity=0.350  Sum_probs=40.9

Q ss_pred             CCceeEEEeccCCCCCCcccccccceEEEEeeC-CccccchhhHHHHHHHHhhhcccc
Q 023083          225 GTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASS-MTYAYSHKDRAWIKAVSNKFRGKS  281 (287)
Q Consensus       225 ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~-s~RafT~kDe~WI~~iA~KL~~~~  281 (287)
                      +..+.++.||..+        .+.-|++.+... .+|.|+..|+..++.+|+.+..+.
T Consensus        90 ~~~s~~~~Pl~~~--------~~~~G~l~~~~~~~~~~~~~~~~~~l~~~~~~i~~~l  139 (149)
T smart00065       90 GVRSFLAVPLVAD--------GELVGVLALHNKDSPRPFTEEDEELLQALANQLAIAL  139 (149)
T ss_pred             ceeeEEEeeeeec--------CEEEEEEEEEecCCCCCCCHHHHHHHHHHHHHHHHHH
Confidence            3899999998763        234699999988 899999999999999999886554

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

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

Probab=91.82  E-value=1.6  Score=46.58  Aligned_cols=128  Identities=11%  Similarity=0.170  Sum_probs=80.2

Q ss_pred             CchHHHHHHHHHHHHHHhhhccccEEEEEECCE--EEEeeeecCC------CCCC-hHHHHHHHHHhhhhcccccCCCcc
Q 023083          138 NISDALKENLAWATYVLLRNTNSISVLISIRGE--LCVRGYWQTP------DGAS-KTQLLEWFERQIENIGLSDLKDSL  208 (287)
Q Consensus       138 ~Lsd~~k~ELAWaS~~LLtnT~a~svlV~~~g~--ll~RG~~~~p------~~~~-~g~i~~~~~~~~~~~~Lv~L~~t~  208 (287)
                      ++.+.+..=+..+...+  +...+++.+++.+.  +..+...+.+      -.+. ..-++.++.++.+.....|.....
T Consensus        17 dL~e~L~~Iv~~~~~~l--~~d~~sI~L~D~~~~~L~~~as~Gl~~~~~~~~~l~~geGi~G~Va~tg~pV~V~Dv~~dp   94 (748)
T PRK11061         17 RLNEALDILVTETCLAM--DTEVCSVYLADHDRRCYYLMATRGLKKPRGRTVTLAFDEGIVGLVGRLAEPINLADAQKHP   94 (748)
T ss_pred             CHHHHHHHHHHHHHHHh--CCCEEEEEEEECCCCEEEEEEeeCCChHhccceeccCCcchHHHHhccCceEEECCcccCc
Confidence            44444444444444444  55556666665443  2223222211      1122 233678888888888887775433


Q ss_pred             cccCCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHHhhhccc
Q 023083          209 YFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGK  280 (287)
Q Consensus       209 lyPgr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kDe~WI~~iA~KL~~~  280 (287)
                      .|..+.+     ..-+++.|+++.||-..        .+.=|+|-+....+|.||+.|+.++..+|.-+..+
T Consensus        95 rf~~~~~-----~~~~~~~S~L~VPL~~~--------geVIGVL~v~~~~~~~Fs~~d~~lL~~LA~~aAiA  153 (748)
T PRK11061         95 SFKYIPS-----VKEERFRAFLGVPIIYR--------RQLLGVLVVQQRELRQFDESEESFLVTLATQLAAI  153 (748)
T ss_pred             ccccCcc-----ccCccceEEEEEEEeeC--------CEEEEEEEEeeCCCCCCCHHHHHHHHHHHHHHHHH
Confidence            3432222     12467999999999752        24579999999999999999999999999877544

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

Probab=90.55  E-value=0.33  Score=38.33  Aligned_cols=84  Identities=18%  Similarity=0.223  Sum_probs=55.4

Q ss_pred             HHHHHHHHHhhhhcccccCCCcccccCCccccccccC------------CCCCceeEEEeccCCCCCCcccccccceEEE
Q 023083          186 TQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEML------------PKGTCSVFVQPVIQAPNPSAVEVEKIEGFVL  253 (287)
Q Consensus       186 g~i~~~~~~~~~~~~Lv~L~~t~lyPgr~E~~~~~~L------------P~ntqsVlvQPig~~~~~~~~~~~~~~Gvlv  253 (287)
                      ..++..+.+..+...+.+......+......  -..+            ..+..++++-||..        ..+.-|+|.
T Consensus        56 ~~~~~~~~~~~~~~~i~d~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~s~l~vPi~~--------~g~~~G~l~  125 (154)
T PF01590_consen   56 ESICGQVLQSREPIVISDVAADPRFAPQIAA--QSALRALSSAERPFLAEYGVRSYLCVPIIS--------GGRLIGVLS  125 (154)
T ss_dssp             SSHHHHHHHHTSCEEESSSGGSTTSSCHHHH--HHTTBTTTHHHHHHHHTTTESEEEEEEEEE--------TTEEEEEEE
T ss_pred             ccHHHHHHhCCCeEeeccccccccccccccc--cccccccccccccccccccCceeeEeeeec--------ccCcEEEEE
Confidence            3456666676666665555322222221110  0112            56999999999865        234579999


Q ss_pred             EeeCCc-cccchhhHHHHHHHHhhhcc
Q 023083          254 LASSMT-YAYSHKDRAWIKAVSNKFRG  279 (287)
Q Consensus       254 lgs~s~-RafT~kDe~WI~~iA~KL~~  279 (287)
                      +....+ |.||+.|+..++.+|+.+..
T Consensus       126 l~~~~~~~~~~~~d~~ll~~~a~~~a~  152 (154)
T PF01590_consen  126 LYRTRPGRPFTEEDLALLESFAQQLAI  152 (154)
T ss_dssp             EEEESSSSS--HHHHHHHHHHHHHHHH
T ss_pred             EEECCCCCCcCHHHHHHHHHHHHHHHh
Confidence            999999 99999999999999998764

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 ....

>TIGR02851 spore_V_T stage V sporulation protein T

Probab=89.49  E-value=3.9  Score=36.49  Aligned_cols=146  Identities=11%  Similarity=0.026  Sum_probs=85.5

Q ss_pred             cccCCCCCCCCCCCe-eceEeccCchHHHHHHHHHHHHHHhhhccccEEEEEECCEEEE-eeeecCCCCCChHHHHHHHH
Q 023083          116 GASPVSQKSLPESGE-QIFVMSQNISDALKENLAWATYVLLRNTNSISVLISIRGELCV-RGYWQTPDGASKTQLLEWFE  193 (287)
Q Consensus       116 ~~~P~~~~~v~l~ge-q~F~l~~~Lsd~~k~ELAWaS~~LLtnT~a~svlV~~~g~ll~-RG~~~~p~~~~~g~i~~~~~  193 (287)
                      +++++++..+...++ ++..-.-+.-....+...=....|...|.+ +|.|-...++++ -|.-..  ...++++-+...
T Consensus        26 ~i~~gd~~~~~~~~~~~iil~k~~~~~~~~~~A~~~aeII~~~t~~-aVaITDr~~ILA~~G~g~d--~~~~~~is~~t~  102 (180)
T TIGR02851        26 RIREGDPLEIFTDREGEVILKKYSPIGELGDFAKEYAESLYQSLGH-IVLITDRDTVIAVAGVSKK--EYLNKPISDELE  102 (180)
T ss_pred             CCCCCCeEEEEEeCCCEEEEEECCcccchHHHHHHHHHHHHHHhCC-EEEEECCCcEEEEECCChh--hcCCCccCHHHH
Confidence            667777766643332 222222222233444555567899999999 999999999887 786631  111112222233


Q ss_pred             Hhhhhccc--ccCCCcccccCCccccccccCCCC--CceeEEEeccCCCCCCcccccccceEEEEeeCCcc--ccchhhH
Q 023083          194 RQIENIGL--SDLKDSLYFPQSADAGQWEMLPKG--TCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTY--AYSHKDR  267 (287)
Q Consensus       194 ~~~~~~~L--v~L~~t~lyPgr~E~~~~~~LP~n--tqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~R--afT~kDe  267 (287)
                      +.++....  ++-.+..+||=..        -++  ..+.+|.||-.+        .++-|.|.+- ...+  .+|+.++
T Consensus       103 ~~i~~gk~~~~~~~~~~~i~c~~--------~~~~~l~s~ii~Pl~~~--------g~viGtLkly-~k~~~~~~~~~e~  165 (180)
T TIGR02851       103 DTMEERKTVILSDTKDGPIEIID--------GQEFEYTSQVIAPIIAE--------GDPIGAVIIF-SKEPGEKLGEVEQ  165 (180)
T ss_pred             HHHHcCCEEEecCCccceecccc--------CCCCCcceEEEEEEEEC--------CeEEEEEEEE-ECCccCCCCHHHH
Confidence            33333222  1111111122110        122  579999999763        2346877777 6666  9999999


Q ss_pred             HHHHHHHhhhcccc
Q 023083          268 AWIKAVSNKFRGKS  281 (287)
Q Consensus       268 ~WI~~iA~KL~~~~  281 (287)
                      .+..++|+=|...+
T Consensus       166 ~la~glA~lLS~QL  179 (180)
T TIGR02851       166 KAAETAAAFLGKQM  179 (180)
T ss_pred             HHHHHHHHHHHHhh
Confidence            99999999876543

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=85.24  E-value=5.3  Score=41.75  Aligned_cols=85  Identities=11%  Similarity=0.198  Sum_probs=60.2

Q ss_pred             hHHHHHHHHHhhhhcccccCCC-ccccc-CCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCcccc
Q 023083          185 KTQLLEWFERQIENIGLSDLKD-SLYFP-QSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAY  262 (287)
Q Consensus       185 ~g~i~~~~~~~~~~~~Lv~L~~-t~lyP-gr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~Raf  262 (287)
                      .+.+..++.+..+...+ +..+ ..+.+ ++..   .+....++.++++.||...        .++-|||.+++...+.|
T Consensus       255 ~~~l~g~V~~~~~p~lv-~~~~~d~~~~~~~~~---~~~~~~~~~s~l~vPL~~~--------~~v~GvL~l~~~~~~~F  322 (686)
T PRK15429        255 AGTLTERVFKSKEMLLI-NLHERDDLAPYERML---FDTWGNQIQTLCLLPLMSG--------DTMLGVLKLAQCEEKVF  322 (686)
T ss_pred             ccchHHHHHhcCceEEE-ECccCcccchhhhhh---hhcccccceEEEEEeEEEC--------CEEEEEEEEeeCCCCcC
Confidence            34677888888876644 4432 11111 1122   3445678999999999762        34579999998889999


Q ss_pred             chhhHHHHHHHHhhhcccc
Q 023083          263 SHKDRAWIKAVSNKFRGKS  281 (287)
Q Consensus       263 T~kDe~WI~~iA~KL~~~~  281 (287)
                      +++|..-++.+|+....+.
T Consensus       323 ~~~dl~lL~~iA~~~A~Ai  341 (686)
T PRK15429        323 TTTNLKLLRQIAERVAIAV  341 (686)
T ss_pred             CHHHHHHHHHHHHHHHHHH
Confidence            9999999999999887654

>TIGR01817 nifA Nif-specific regulatory protein

Probab=83.01  E-value=12  Score=37.96  Aligned_cols=83  Identities=8%  Similarity=0.123  Sum_probs=57.3

Q ss_pred             HHHHHHHHHhhhhcccccCCCcccccCCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCC-ccccch
Q 023083          186 TQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSM-TYAYSH  264 (287)
Q Consensus       186 g~i~~~~~~~~~~~~Lv~L~~t~lyPgr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s-~RafT~  264 (287)
                      ..++.++.+..++.-+.|..+..-|-.+.     .....+++|++|.||..+        .+.=|+|.+.+.. ++.||+
T Consensus        73 ~gi~g~v~~~~~pvii~Dv~~d~~~~~~~-----~~~~~~~~S~l~VPL~~~--------g~viGvL~v~s~~~~~~ft~  139 (534)
T TIGR01817        73 EGAIGQIVATGNSLVVPDVAAEPLFLDRL-----SLYDPGPVPFIGVPIKAD--------SETIGVLAADRDFRSRERLE  139 (534)
T ss_pred             ccHHHHHHhcCCeEEecccccCchhhhcc-----ccccCCcceEEEEEEcCC--------CEEEEEEEEEeccccccccH
Confidence            45777888887777666653221111111     123457899999999752        2347999999875 577899


Q ss_pred             hhHHHHHHHHhhhcccc
Q 023083          265 KDRAWIKAVSNKFRGKS  281 (287)
Q Consensus       265 kDe~WI~~iA~KL~~~~  281 (287)
                      .|...+..+|+.+..+.
T Consensus       140 ~d~~lL~~lA~~ia~aI  156 (534)
T TIGR01817       140 EEVRFLEMVANLIGQTV  156 (534)
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            99999999999877543

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.

---

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

ID	Length	Definition	E-value
Query	287
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-05

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

 Score = 44.1 bits (103), Expect = 4e-05
 Identities = 36/236 (15%), Positives = 66/236 (27%), Gaps = 85/236 (36%)

Query: 28  SICARLDNSQQEEQQLNL--SVLRFTFGIPGFDESYLPRWIGYGFGSLIVL--------- 76
           +  +R D+S   + +++   + LR         + Y           L+VL         
Sbjct: 212 NWTSRSDHSSNIKLRIHSIQAELRRLL----KSKPY-EN-------CLLVLLNVQNAKAW 259

Query: 77  NHFAFS---------NSVT---SAQLRSEV-LGLSLAAFSV--TLPYLGKFLKQGASPVS 121
           N F  S           VT   SA   + + L       +       L K+L        
Sbjct: 260 NAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLD-----CR 314

Query: 122 QKSLPESGEQI--FVMSQNISDALKENLAWATYVLLRNTNSISVLISIRGELCVRGYWQT 179
            + LP          +S          +                  SIR  L     W+ 
Sbjct: 315 PQDLPREVLTTNPRRLS----------IIAE---------------SIRDGLATWDNWKH 349

Query: 180 PDGASKTQLLEWFERQIENIGLSDLKDSLY-----FPQSADAGQWEMLPKGTCSVF 230
            +    T ++E     +  +  ++ +  ++     FP SA       +P    S+ 
Sbjct: 350 VNCDKLTTIIESS---LNVLEPAEYRK-MFDRLSVFPPSAH------IPTILLSLI 395

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	287
3rfb_A	171	Putative uncharacterized protein; FRMSR, GAF, oxid	97.05
3mmh_A	167	FRMSR, methionine-R-sulfoxide reductase; oxidoredu	97.04
3p01_A	184	Two-component response regulator; PSI-2, midwest c	96.75
3ksh_A	160	Putative uncharacterized protein; FRMSR, free-Met-	96.68
3e0y_A	181	Conserved domain protein; APC87688.2, geobacter su	96.55
3trc_A	171	Phosphoenolpyruvate-protein phosphotransferase; si	96.5
1f5m_A	180	GAF; CGMP binding, signaling protein; 1.90A {Sacch	96.37
1vhm_A	195	Protein YEBR; structural genomics, unknown functio	96.31
3o5y_A	165	Sensor protein; GAF domain, histidine, kinase, PSI	96.08
3ci6_A	171	Phosphoenolpyruvate-protein phosphotransferase; PE	96.03
3oov_A	169	Methyl-accepting chemotaxis protein, putative; str	95.6
2e4s_A	189	CAMP and CAMP-inhibited CGMP 3',5'-cyclic phosphod	95.4
2w3g_A	153	DOSS, two component sensor histidine kinase DEVS (	95.37
3hcy_A	151	Putative two-component sensor histidine kinase PR;	95.35
2zmf_A	189	CAMP and CAMP-inhibited CGMP 3',5'-cyclic phospho	95.24
3dba_A	180	CONE CGMP-specific 3',5'-cyclic phosphodiesterase	95.08
2vjw_A	149	GAF-B, GAF family protein; histidine kinase, hypox	94.59
2qyb_A	181	Membrane protein, putative; GAF domain, domain of	94.46
3k2n_A	177	Sigma-54-dependent transcriptional regulator; PSI-	94.42
2k2n_A	172	Sensor protein, SYB-CPH1(GAF); phytochrome, GAF do	92.84
2lb5_A	208	Sensor histidine kinase; PCB, transferase, GAF dom	92.72
3ibj_A	691	CGMP-dependent 3',5'-cyclic phosphodiesterase; PDE	91.84
1ykd_A	398	Adenylate cyclase; GAF domain, bound cyclic AMP li	91.52
1mc0_A	368	3',5'-cyclic nucleotide phosphodiesterase 2A; GAF	90.38
4glq_A	171	Methyl-accepting chemotaxis protein; chromophore,	90.36
1ykd_A	398	Adenylate cyclase; GAF domain, bound cyclic AMP li	86.18

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

Probab=97.05  E-value=0.0096  Score=51.16  Aligned_cols=110  Identities=16%  Similarity=0.156  Sum_probs=79.6

Q ss_pred             hccccEEEEEECCEEEEeeeecCCCC--CCh-HHHHHHHHHhhhhcccccCCCcccccCCccccccccCCCCCceeEEEe
Q 023083          157 NTNSISVLISIRGELCVRGYWQTPDG--ASK-TQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQP  233 (287)
Q Consensus       157 nT~a~svlV~~~g~ll~RG~~~~p~~--~~~-g~i~~~~~~~~~~~~Lv~L~~t~lyPgr~E~~~~~~LP~ntqsVlvQP  233 (287)
                      ..+.+++-++.++++.+..+-+.++.  +.. .-||-++.++.+..-.-|.   .-+|+...   .+   ..++|.||.|
T Consensus        50 ~~~~~gfYL~~~~~L~l~a~~G~~a~~ri~~GeGv~G~va~tg~~i~V~Dv---~~~p~~i~---~~---~~~~Sei~VP  120 (171)
T 3rfb_A           50 NTVFAGFYLFDGKELVLGPFQGGVSCIRIALGKGVCGEAAHFQETVIVGDV---TTYLNYIS---CD---SLAKSEIVVP  120 (171)
T ss_dssp             TEEEEEEEEECSSEEEEEEEESSSCCCEEETTSHHHHHHHHTTSCEEESCT---TSCSSCCC---SC---TTCCEEEEEE
T ss_pred             CCCEEEEEEEECCEEEEEeccCCccceEeeCCcCHHHHHHhhCCEEEECCc---ccCccccc---cC---cccCceEEEE
Confidence            35566766667777554333333332  222 3477888888888776666   56676543   12   4689999999


Q ss_pred             ccCCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHHhhhcccccc
Q 023083          234 VIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGKSIW  283 (287)
Q Consensus       234 ig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kDe~WI~~iA~KL~~~~~~  283 (287)
                      |-.+        .+.=|||-+.+..++.|++.|+.+++.+|+-+..+..|
T Consensus       121 I~~~--------g~viGVL~i~s~~~~~F~e~D~~~L~~lA~~la~~~~~  162 (171)
T 3rfb_A          121 MMKN--------GQLLGVLDLDSSEIEDYDAMDRDYLEQFVAILLEKTTW  162 (171)
T ss_dssp             EEET--------TEEEEEEEEEESSTTCCCHHHHHHHHHHHHHHHHSCBC
T ss_pred             EEEC--------CEEEEEEEEecCCCCCCCHHHHHHHHHHHHHHHHHhcc
Confidence            9652        24479999999999999999999999999999999888

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

Probab=97.04  E-value=0.0093  Score=50.40  Aligned_cols=127  Identities=9%  Similarity=0.016  Sum_probs=84.5

Q ss_pred             CchHHHHHHHHHHHHHHhhhccccEEEEEE--CCEEEEeeeecCCCC--CCh-HHHHHHHHHhhhhcccccCCCcccccC
Q 023083          138 NISDALKENLAWATYVLLRNTNSISVLISI--RGELCVRGYWQTPDG--ASK-TQLLEWFERQIENIGLSDLKDSLYFPQ  212 (287)
Q Consensus       138 ~Lsd~~k~ELAWaS~~LLtnT~a~svlV~~--~g~ll~RG~~~~p~~--~~~-g~i~~~~~~~~~~~~Lv~L~~t~lyPg  212 (287)
                      |+.+.+.+=++-..+.+  ..+.+++.++.  ++++..+-+-+.+..  +.. .-+|-++.++.+..-.-|.   .-+|+
T Consensus        31 dl~~~L~~v~~~l~~~l--~~~~~~iyL~d~~~~~L~l~a~~G~~~~~~i~~geGi~G~v~~~g~~~~v~Dv---~~~p~  105 (167)
T 3mmh_A           31 DWVANLANTAAVLKEAF--GWFWVGFYLVDTRSDELVLAPFQGPLACTRIPFGRGVCGQAWAKGGTVVVGDV---DAHPD  105 (167)
T ss_dssp             CHHHHHHHHHHHHHHHH--CCSEEEEEEEETTTTEEEEEEEESSCCCSEEETTSHHHHHHHHHTSCEEESCG---GGSTT
T ss_pred             CHHHHHHHHHHHHHHHc--CCcEEEEEEEECCCCEEEEEEecccccceEeccCCChHHHHHhCCcEEEECCc---ccCcc
Confidence            44445544444444444  35666666663  345554433333332  222 2477888888888766666   45665


Q ss_pred             CccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHHhhhcccccc
Q 023083          213 SADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGKSIW  283 (287)
Q Consensus       213 r~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kDe~WI~~iA~KL~~~~~~  283 (287)
                      ...   .   -.+++|.+|.||-.+        .+.=|||-+.+..++.||+.|+.+++.+|+-+.....|
T Consensus       106 ~~~---~---~~~~~S~i~vPi~~~--------g~viGVL~i~s~~~~~F~~~d~~~L~~lA~~la~~i~~  162 (167)
T 3mmh_A          106 HIA---C---SSLSRSEIVVPLFSD--------GRCIGVLDADSEHLAQFDETDALYLGELAKILEKRFEA  162 (167)
T ss_dssp             CCC---S---STTCCEEEEEEEEET--------TEEEEEEEEEESSTTCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhh---c---CccCCeEEEEEeccC--------CEEEEEEEEecCCCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence            433   1   257999999999652        24579999999999999999999999999998776544

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

Probab=96.75  E-value=0.0087  Score=48.37  Aligned_cols=109  Identities=9%  Similarity=0.045  Sum_probs=72.0

Q ss_pred             cEEEEEECCEEEE-eeeecCCC----CCChHHHHHHHHHhhhhcccccCCCcccccCCccccccccCCCCCceeEEEecc
Q 023083          161 ISVLISIRGELCV-RGYWQTPD----GASKTQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVI  235 (287)
Q Consensus       161 ~svlV~~~g~ll~-RG~~~~p~----~~~~g~i~~~~~~~~~~~~Lv~L~~t~lyPgr~E~~~~~~LP~ntqsVlvQPig  235 (287)
                      +++..+.+|++.. .+.+..++    .+....++.++.+..+....-|..+..-|+.+.     .+-..|.+|+++.||-
T Consensus        65 ~~i~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~d~~~~~~~~~~~-----~~~~~~~~s~l~vPL~  139 (184)
T 3p01_A           65 CILQMLEGQTLSTIQGFYSQQGTVNNWLNQDPLTNEAIATGQIQVAANIAKDPKLASIS-----QYQDNGIQSHVVIPIT  139 (184)
T ss_dssp             EEEEEEETTEEEEEEEEEESSSSCCCCGGGCHHHHHHHHHCSCEEESCGGGCHHHHTCH-----HHHHHTCCEEEEEEEE
T ss_pred             EEEEEecCCceeeeeeeccccCccCcccCCCcHHHHHHhhCCeEEEeccccCccccchh-----HHHHhCccEEEEEEEE
Confidence            3444456777543 44232221    123467888888888877665553333333211     1223488999999996


Q ss_pred             CCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHHhhhccccc
Q 023083          236 QAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGKSI  282 (287)
Q Consensus       236 ~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kDe~WI~~iA~KL~~~~~  282 (287)
                      .+        .+.-|+|.+.+..+|.||+.|...++.+|+.+..+.+
T Consensus       140 ~~--------~~~~GvL~l~~~~~~~f~~~d~~ll~~lA~q~aiAi~  178 (184)
T 3p01_A          140 YR--------NEMLGVLSLQWQQPISLREDELTLIHLSAQLVAIALT  178 (184)
T ss_dssp             ET--------TEEEEEEEEEESSCCCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             EC--------CEEEEEEEeCcCCCCCCCHHHHHHHHHHHHHHHHHHH
Confidence            52        3457999999999999999999999999998876543

>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=96.68  E-value=0.028  Score=47.60  Aligned_cols=126  Identities=14%  Similarity=0.182  Sum_probs=84.5

Q ss_pred             cCchHHHHHHHHHHHHHHhhhccccEEEEEECCEEEEeeeecCCCC--CCh-HHHHHHHHHhhhhcccccCCCcccccCC
Q 023083          137 QNISDALKENLAWATYVLLRNTNSISVLISIRGELCVRGYWQTPDG--ASK-TQLLEWFERQIENIGLSDLKDSLYFPQS  213 (287)
Q Consensus       137 ~~Lsd~~k~ELAWaS~~LLtnT~a~svlV~~~g~ll~RG~~~~p~~--~~~-g~i~~~~~~~~~~~~Lv~L~~t~lyPgr  213 (287)
                      .|+.+.+.+=.+-..+.+ ...+.+++-++.++++.+..+-+.++.  +.. .-+|-++.++.+..-.-|.   .-+|+.
T Consensus        30 ~dl~~~L~~v~~ll~~~l-~~~~~~gfYL~~~~~L~l~~~~G~~a~~ri~~GeGv~G~aa~~~~~i~V~Dv---~~~p~~  105 (160)
T 3ksh_A           30 HHMIAILSNMSALLNDNL-DQINWVGFYLLEQNELILGPFQGHPACVHIPIGKGVCGTAVSERRTQVVADV---HQFKGH  105 (160)
T ss_dssp             CCHHHHHHHHHHHHHHHC-SSCSEEEEEEEETTEEEEEEEEESCCCSEEETTSHHHHHHHHHTSCEEESCG---GGSTTC
T ss_pred             CCHHHHHHHHHHHHHHHc-ccCCEEEEEEEECCEEEEEeccCCcccEEeeCCCCHHHHHHhhCCEEEECCc---ccCccc
Confidence            344444444333333333 235677877778888554333333332  222 3477888888888776666   567775


Q ss_pred             ccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHHhhhccc
Q 023083          214 ADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGK  280 (287)
Q Consensus       214 ~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kDe~WI~~iA~KL~~~  280 (287)
                      ..   .+   ..++|.+|.||-.+        .+.=|||-+.+..++.|++.|+.+++.+|+-+...
T Consensus       106 i~---~~---~~~~Sei~VPI~~~--------g~viGVL~i~s~~~~~F~e~D~~~L~~lA~~la~~  158 (160)
T 3ksh_A          106 IA---CD---ANSKSEIVVPIFKD--------DKIIGVLDIDAPITDRFDDNDKEHLEAIVKIIEKQ  158 (160)
T ss_dssp             CG---GG---TTCSEEEEEEEEET--------TEEEEEEEEEESSSSCCCHHHHHHHHHHHHHHHHH
T ss_pred             cc---cC---cccCceEEEEEEEC--------CEEEEEEEEecCCCCCCCHHHHHHHHHHHHHHHHH
Confidence            44   22   46899999999652        24579999999999999999999999999987643

>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=96.55  E-value=0.022  Score=44.25  Aligned_cols=82  Identities=11%  Similarity=0.156  Sum_probs=56.9

Q ss_pred             HHHHHHHHhhhhcccccCCCcccccCCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhh
Q 023083          187 QLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKD  266 (287)
Q Consensus       187 ~i~~~~~~~~~~~~Lv~L~~t~lyPgr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kD  266 (287)
                      .++.++.+..+....-+..+...|..+.+     ....+.+++++.||..+        .+.-|+|.+.+..++.||+.|
T Consensus        83 ~~~~~~~~~~~~~~i~d~~~~~~~~~~~~-----~~~~~~~s~l~vPl~~~--------~~~iGvl~~~~~~~~~f~~~~  149 (181)
T 3e0y_A           83 GITGSVARDGQYISLSRASQDPRYRYFPE-----LQEEKYNSMLSFPIGDK--------KEVYGVINLNTTSIRSFHEDE  149 (181)
T ss_dssp             SSHHHHHHHCCCEEEEEECCCCCC--------------CEEEEEEEEEECS--------SCEEEEEEEEESSCCCCCHHH
T ss_pred             CeeeehhhcCCeEEecCcccCcccccccc-----ccccCcceEEEEEEEeC--------CeEEEEEEEeeCCCCCCCHHH
Confidence            35677888877776655543222222111     12357899999999763        345799999999999999999


Q ss_pred             HHHHHHHHhhhcccc
Q 023083          267 RAWIKAVSNKFRGKS  281 (287)
Q Consensus       267 e~WI~~iA~KL~~~~  281 (287)
                      ...++.+|+.+..+.
T Consensus       150 ~~~l~~la~~~a~al  164 (181)
T 3e0y_A          150 IYFVSIIANLILTAI  164 (181)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHH
Confidence            999999999876554

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

Probab=96.50  E-value=0.067  Score=41.14  Aligned_cols=83  Identities=11%  Similarity=0.213  Sum_probs=61.0

Q ss_pred             HHHHHHHHHhhhhcccccCCCcccccCCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccchh
Q 023083          186 TQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHK  265 (287)
Q Consensus       186 g~i~~~~~~~~~~~~Lv~L~~t~lyPgr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~k  265 (287)
                      ..++.++.+..+...+-+..+..-|....+     .--.+..++++.||-.+        .+.-|+|.+.+..++.||+.
T Consensus        77 ~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~-----~~~~~~~s~l~vPl~~~--------~~~~Gvl~~~~~~~~~f~~~  143 (171)
T 3trc_A           77 EGLIGLVGEREEPINLADAPLHPAYKHRPE-----LGEEDYHGFLGIPIIEQ--------GELLGILVIQQLESHHFAEE  143 (171)
T ss_dssp             CHHHHHHHHHTSCEEESCGGGSTTCCCCGG-----GCCCCCCEEEEEEEEET--------TEEEEEEEEEESSSCCCCHH
T ss_pred             CChhhHHHhcCCeEEeCCCCCCCccccccc-----CCcccccEEEEEeEEEC--------CEEEEEEEEeecCCCCCCHH
Confidence            356778888888776665543222322222     12368899999999762        34579999999999999999


Q ss_pred             hHHHHHHHHhhhcccc
Q 023083          266 DRAWIKAVSNKFRGKS  281 (287)
Q Consensus       266 De~WI~~iA~KL~~~~  281 (287)
                      |...++.+|+.+..+.
T Consensus       144 d~~~l~~la~~~a~ai  159 (171)
T 3trc_A          144 EEAFCVTLAIHLAAEI  159 (171)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            9999999999877654

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

Probab=96.37  E-value=0.055  Score=45.63  Aligned_cols=131  Identities=12%  Similarity=0.085  Sum_probs=81.9

Q ss_pred             CchHHHHHHHHHHHHHHh---hhccccEEEEEEC---CEEEEeeeecCCCCC--Ch-HHHHHHHHHhhhhcccccCCCcc
Q 023083          138 NISDALKENLAWATYVLL---RNTNSISVLISIR---GELCVRGYWQTPDGA--SK-TQLLEWFERQIENIGLSDLKDSL  208 (287)
Q Consensus       138 ~Lsd~~k~ELAWaS~~LL---tnT~a~svlV~~~---g~ll~RG~~~~p~~~--~~-g~i~~~~~~~~~~~~Lv~L~~t~  208 (287)
                      ++.+.+.+-++-..+.+-   ...+..++-++.+   +++....+.+.++..  .. .-+|-++.++.+..-.-|.   .
T Consensus        41 dl~~~L~~v~~~l~~~l~~~~~~~~~~~~yl~d~~~~~~L~l~~~~g~~~~~~i~~g~Gi~G~aa~~g~~v~v~Dv---~  117 (180)
T 1f5m_A           41 NWVCNLSNASSLIWHAYKSLAVDINWAGFYVTQASEENTLILGPFQGKVACQMIQFGKGVCGTAASTKETQIVPDV---N  117 (180)
T ss_dssp             BHHHHHHHHHHHHHHHHHHTTCCEEEEEEEEECSSSSCEEEEEEEEESCCCSEEETTSHHHHHHHHHTSCEEESCG---G
T ss_pred             cHHHHHHHHHHHHHHHHhhccCCccEEEEEEEecCCCCeEEEeecCCCccceeecCCCcchhhhhhcCCEEEeCCc---c
Confidence            344444444444444441   2334455555543   454433222222221  11 2267788888887766665   3


Q ss_pred             cccCCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHHhhhcccccce
Q 023083          209 YFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGKSIWI  284 (287)
Q Consensus       209 lyPgr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kDe~WI~~iA~KL~~~~~~~  284 (287)
                      -+|+...      ...++.|++|.||-.+       ..+.-|||-+.+..++.|++.|+..++.+|+-+..+..|+
T Consensus       118 ~dp~~~~------~~~~~~S~l~vPi~~~-------~g~viGVL~l~s~~~~~F~~~d~~~L~~la~~~a~~~~~~  180 (180)
T 1f5m_A          118 KYPGHIA------CDGETKSEIVVPIISN-------DGKTLGVIDIDCLDYEGFDHVDKEFLEKLAKLINKSCVFK  180 (180)
T ss_dssp             GSTTCCC------SSTTCCEEEEEEEECT-------TSCEEEEEEEEESSTTCCCHHHHHHHHHHHHHHHHHCBC-
T ss_pred             cCccccc------cCcccceEEEEEEEcC-------CCeEEEEEEeccCCCCCcCHHHHHHHHHHHHHHHHhcCCC
Confidence            4444332      2468999999999751       1234799999999999999999999999999999888774

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

Probab=96.31  E-value=0.059  Score=46.65  Aligned_cols=109  Identities=10%  Similarity=0.085  Sum_probs=75.1

Q ss_pred             hccccEEEEEECCEEEEeeeecCCCC--CCh-HHHHHHHHHhhhhcccccCCCcccccCCccccccccCCCCCceeEEEe
Q 023083          157 NTNSISVLISIRGELCVRGYWQTPDG--ASK-TQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQP  233 (287)
Q Consensus       157 nT~a~svlV~~~g~ll~RG~~~~p~~--~~~-g~i~~~~~~~~~~~~Lv~L~~t~lyPgr~E~~~~~~LP~ntqsVlvQP  233 (287)
                      ..+..++-++.++++.....-+.++.  +.. .-+|-++.++.+..-.-|+   .-+|+...   .   ..+++|.||.|
T Consensus        61 ~~~~~~iyL~d~~~L~l~~~~G~~~~~~i~~GeGi~G~aa~tg~~i~V~Dv---~~~p~~~~---~---~~~~~S~l~VP  131 (195)
T 1vhm_A           61 DINWAGFYLLEDDTLVLGPFQGKIACVRIPVGRGVCGTAVARNQVQRIEDV---HVFDGHIA---C---DAASNSEIVLP  131 (195)
T ss_dssp             SCSEEEEEEEETTEEEEEEEEESCCCSEEETTSHHHHHHHHHTSCEEESCT---TTCTTCCC---S---CCCCSEEEEEE
T ss_pred             CCCEEEEEEEECCEEEEEEecCcccceEecCCCChHHHHHhcCCEEEECCc---ccCcchhh---c---CCCccEEEEEe
Confidence            44556666677777544322222222  222 2377888888887766666   34566544   2   24789999999


Q ss_pred             ccCCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHHhhhccccc
Q 023083          234 VIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGKSI  282 (287)
Q Consensus       234 ig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kDe~WI~~iA~KL~~~~~  282 (287)
                      |-.+        .+.-|||-+.+..++.|++.|+..++.+|+-+..+.+
T Consensus       132 I~~~--------g~viGVL~i~s~~~~~F~e~d~~~L~~lA~~ia~ale  172 (195)
T 1vhm_A          132 LVVK--------NQIIGVLDIDSTVFGRFTDEDEQGLRQLVAQLEKVLA  172 (195)
T ss_dssp             EEET--------TEEEEEEEEEESSTTCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             EeEC--------CEEEEEEEecCCCCCCCCHHHHHHHHHHHHHHHHHHH
Confidence            9752        3457999999999999999999999999998876654

>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=96.08  E-value=0.069  Score=44.17  Aligned_cols=109  Identities=17%  Similarity=0.182  Sum_probs=71.2

Q ss_pred             ccccEEEEEECCEEEEeeeecCCC-------CCCh-HHHHHHHHHhhhhcccccCCCc--ccccCCccccccccCCCCCc
Q 023083          158 TNSISVLISIRGELCVRGYWQTPD-------GASK-TQLLEWFERQIENIGLSDLKDS--LYFPQSADAGQWEMLPKGTC  227 (287)
Q Consensus       158 T~a~svlV~~~g~ll~RG~~~~p~-------~~~~-g~i~~~~~~~~~~~~Lv~L~~t--~lyPgr~E~~~~~~LP~ntq  227 (287)
                      ....+++.+.+|++..+-..+...       .+.. +.++.++.++.+..- .+..+.  .+.++      ..+...+.+
T Consensus        23 ~d~~~l~L~~~~~L~l~a~~~~~~~~~~~~~~ip~~~s~~~~v~~~~~~~v-~~~~~~~~~~~~~------~~~~~~~~~   95 (165)
T 3o5y_A           23 FDRISFLLLANETLKLSHVYPKGSHSLDIGSTIPKEQSLYWSALDQRQTIF-RSLTDTQDNFYEK------QYLAILDLK   95 (165)
T ss_dssp             CSEEEEEEEETTEEEEEEEESTTCCSSCTTCEECSTTCHHHHHHHHTSCEE-EESCCTTCCCTTH------HHHHTTTCC
T ss_pred             cceEEEEEEECCEEEEEEEecCCccccccccccCCccCHHHHHHHhCCeEE-EcCcccccccccc------hHHHhhCCC
Confidence            344566667788855433332211       1111 467788888887763 343211  11111      013457899


Q ss_pred             eeEEEeccCCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHHhhhcccc
Q 023083          228 SVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGKS  281 (287)
Q Consensus       228 sVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kDe~WI~~iA~KL~~~~  281 (287)
                      |++|.||-.+        .+.-|+|.+++..++.||+.|..+++.+|+.+..+.
T Consensus        96 S~l~vPL~~~--------~~~iGvl~l~~~~~~~f~~~d~~~l~~la~~~aiai  141 (165)
T 3o5y_A           96 SILVIPIYSK--------NKRVGVLSIGRKQQIDWSLDDLAFLEQLTDHLAVSI  141 (165)
T ss_dssp             EEEEEEEECS--------SCEEEEEEEEESSCCCCCHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEeCeeEC--------CEEEEEEEEEeCCCCCCCHHHHHHHHHHHHHHHHHH
Confidence            9999999763        344799999999999999999999999999876543

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

Probab=96.03  E-value=0.09  Score=39.73  Aligned_cols=82  Identities=13%  Similarity=0.203  Sum_probs=56.6

Q ss_pred             HHHHHHHHhhhhcccccCCCcccccCCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhh
Q 023083          187 QLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKD  266 (287)
Q Consensus       187 ~i~~~~~~~~~~~~Lv~L~~t~lyPgr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kD  266 (287)
                      .++.++.+..+....-+..+...|....+     +-..+..++++.||-.+        .+.-|+|.+++..++.||+.|
T Consensus        80 ~~~~~~~~~~~~~~~~d~~~~~~~~~~~~-----~~~~~~~s~l~vPl~~~--------~~~~Gvl~l~~~~~~~f~~~~  146 (171)
T 3ci6_A           80 GLVGLVGQREEIVNLENASKHERFAYLPE-----TGEEIYNSFLGVPVMYR--------RKVMGVLVVQNKQPQDFSEAA  146 (171)
T ss_dssp             HHHHHHHHHTSCEEESSGGGSTTC--------------CCCEEEEEEEEET--------TEEEEEEEEEESSCCCCCHHH
T ss_pred             CeehhhhccCceEEecCCCcCcchhcccc-----ccccccceEEEEeEEEC--------CEEEEEEEEecCCCCCCCHHH
Confidence            47788888877766655532222222211     14457899999999752        234799999999999999999


Q ss_pred             HHHHHHHHhhhcccc
Q 023083          267 RAWIKAVSNKFRGKS  281 (287)
Q Consensus       267 e~WI~~iA~KL~~~~  281 (287)
                      ...++.+|+.+..+.
T Consensus       147 ~~~l~~la~~~a~al  161 (171)
T 3ci6_A          147 ESFLVTLCAQLSGVI  161 (171)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHH
Confidence            999999999887654

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

Probab=95.60  E-value=0.21  Score=38.18  Aligned_cols=123  Identities=12%  Similarity=0.053  Sum_probs=75.5

Q ss_pred             HHHHHhhhccccEEEEE-EC-C--EEEEeeeecCCC----C----CC-hHHHHHHHHHhhhhcccccCCCc-ccccCCcc
Q 023083          150 ATYVLLRNTNSISVLIS-IR-G--ELCVRGYWQTPD----G----AS-KTQLLEWFERQIENIGLSDLKDS-LYFPQSAD  215 (287)
Q Consensus       150 aS~~LLtnT~a~svlV~-~~-g--~ll~RG~~~~p~----~----~~-~g~i~~~~~~~~~~~~Lv~L~~t-~lyPgr~E  215 (287)
                      .-+.+...+.+....|+ ++ +  .+..+...+...    .    +. ...++.++.+..+....-+..+. .+++.+.+
T Consensus        24 ~~~~~~~~~~~~~~~i~l~d~~~~~l~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~d~~~~~~~~~~~~~  103 (169)
T 3oov_A           24 CAEGLHDVLGYERVNILMADTARTSLSFVAAVGTADFNPAGVVLPLDQRGGVITKCFTDRQVYMIDDVSAYPTDFRLQSP  103 (169)
T ss_dssp             HHHHHHHTTCCSEEEEEEECTTSSEEEEEEEESCSSCCCTTCEEESSGGGHHHHHHHHHTCCEEESCGGGSCGGGSCCTT
T ss_pred             HHHHHHHhhCCceEEEEEEeCCCCeEEEEEEeCchhhhhhcccCCcccccchHHHHHhcCCCEEeccccchhhhhhcccc
Confidence            44555666666655444 33 2  343343333221    1    11 36778888888887766555321 22322221


Q ss_pred             ccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCc-cccchhhHHHHHHHHhhhccccc
Q 023083          216 AGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMT-YAYSHKDRAWIKAVSNKFRGKSI  282 (287)
Q Consensus       216 ~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~-RafT~kDe~WI~~iA~KL~~~~~  282 (287)
                        .-..-..+..++++.||-.+        .+.-|+|.+++..+ +.|++.|...++.+|+.+..+.+
T Consensus       104 --~~~~~~~~~~s~l~vPl~~~--------~~~iGvl~~~~~~~~~~f~~~d~~~l~~~a~~~a~ai~  161 (169)
T 3oov_A          104 --YDAIRALRSKSFVICPIVVK--------GEAIGVFAVDNRSSRRSLNDTDVDTIKLFADQASSAIV  161 (169)
T ss_dssp             --GGGCGGGCCSSEEEEEEEET--------TEEEEEEEEECTTSSSCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             --HHHHHhcCcCcEEEEEEEeC--------CcEEEEEEEEccccCCCCCHHHHHHHHHHHHHHHHHHH
Confidence              00123467899999999752        34579999998765 56999999999999998876543

>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=95.37  E-value=0.034  Score=41.87  Aligned_cols=81  Identities=11%  Similarity=0.069  Sum_probs=57.5

Q ss_pred             HHHHHHHHhhhhcccccCCCcccccCCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCc-cccchh
Q 023083          187 QLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMT-YAYSHK  265 (287)
Q Consensus       187 ~i~~~~~~~~~~~~Lv~L~~t~lyPgr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~-RafT~k  265 (287)
                      .++.++.+..+....-+..+...|.+.      .....+..++++.||-.+        .+.-|+|.+.+..+ |.||+.
T Consensus        62 ~~~~~~~~~~~~~~~~d~~~~~~~~~~------~~~~~~~~s~l~vPl~~~--------~~~~Gvl~l~~~~~~~~f~~~  127 (153)
T 2w3g_A           62 GVIGLLIEDPKPLRLDDVSAHPASIGF------PPYHPPMRTFLGVPVRVR--------DESFGTLYLTDKTNGQPFSDD  127 (153)
T ss_dssp             THHHHHHHSCSCEEESSGGGSTTCCCC------CTTCCCCCCEEEEEEEET--------TEEEEEEEEEEETTSCCCCHH
T ss_pred             CHHHHHHhcCCcEEecCcccCchhcCC------CCcCCCCCeEEEeeEEEC--------CEEEEEEEEeeCCCCCCCCHH
Confidence            466777777776655554322222221      113468899999999652        23479999999888 899999


Q ss_pred             hHHHHHHHHhhhcccc
Q 023083          266 DRAWIKAVSNKFRGKS  281 (287)
Q Consensus       266 De~WI~~iA~KL~~~~  281 (287)
                      |...++.+|+-+..+.
T Consensus       128 ~~~~l~~la~~~a~ai  143 (153)
T 2w3g_A          128 DEVLVQALAAAAGIAV  143 (153)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            9999999999887654

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

Probab=95.35  E-value=0.0061  Score=47.02  Aligned_cols=53  Identities=6%  Similarity=0.108  Sum_probs=44.2

Q ss_pred             CCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHHhhhccccc
Q 023083          222 LPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGKSI  282 (287)
Q Consensus       222 LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kDe~WI~~iA~KL~~~~~  282 (287)
                      ...|.+++++.||..+        .+.-|+|.+.+..+|.||+.|...++.+|+.+..+.+
T Consensus        86 ~~~g~~s~~~vPl~~~--------~~~iGvl~~~~~~~~~f~~~~~~ll~~~a~~~a~ai~  138 (151)
T 3hcy_A           86 VGEGIAALGFFPLVTE--------GRLIGKFMTYYDRPHRFADSEIGMALTIARQLGFSIQ  138 (151)
T ss_dssp             HHHTCCEEEEEEEESS--------SSEEEEEEEEESSCCCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             HhcCchheEEeceEEC--------CEEEEEEEEecCCCCCCCHHHHHHHHHHHHHHHHHHH
Confidence            4568899999999762        2347999999999999999999999999998766543

>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=95.24  E-value=0.018  Score=45.22  Aligned_cols=84  Identities=15%  Similarity=0.129  Sum_probs=56.5

Q ss_pred             HHHHHHHHHhhhhcccccCCCcccccCCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEE-eeCCccccch
Q 023083          186 TQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLL-ASSMTYAYSH  264 (287)
Q Consensus       186 g~i~~~~~~~~~~~~Lv~L~~t~lyPgr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvl-gs~s~RafT~  264 (287)
                      ..++.++.++.+...+-+..+...|+....    .....++++++|.|+..+        .+.-|+|.+ ....+|.||+
T Consensus        90 ~~~~~~v~~~~~~~~i~d~~~~~~~~~~~~----~~~~~~~~s~l~vPl~~~--------~~~~Gvl~l~~~~~~~~f~~  157 (189)
T 2zmf_A           90 KGIAGQVARTGEVLNIPDAYADPRFNREVD----LYTGYTTRNILCMPIVSR--------GSVIGVVQMVNKISGSAFSK  157 (189)
T ss_dssp             SHHHHHHHHHCCCEEESCGGGSTTCCTHHH----HHHCCCCCCEEEEEEEET--------TEEEEEEEEEEETTSSSCCH
T ss_pred             ccHHHHHHHhCCeEEEecccccccccccch----hhcccccceEEEeeeccc--------CceeeEEEEEEcCCCCCcCH
Confidence            346778888887776555432222222111    223446889999998762        234688855 5677899999


Q ss_pred             hhHHHHHHHHhhhcccc
Q 023083          265 KDRAWIKAVSNKFRGKS  281 (287)
Q Consensus       265 kDe~WI~~iA~KL~~~~  281 (287)
                      .|...++.+|+.+..+.
T Consensus       158 ~d~~ll~~lA~q~a~Ai  174 (189)
T 2zmf_A          158 TDENNFKMFAVFCALAL  174 (189)
T ss_dssp             HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            99999999999876554

>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=95.08  E-value=0.024  Score=46.41  Aligned_cols=81  Identities=16%  Similarity=0.269  Sum_probs=57.3

Q ss_pred             HHHHHHHHHhhhhcccccCCCcccccCCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCcc-ccch
Q 023083          186 TQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTY-AYSH  264 (287)
Q Consensus       186 g~i~~~~~~~~~~~~Lv~L~~t~lyPgr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~R-afT~  264 (287)
                      .-|+.++.++++..-+-|..+..-|+...+    ...-..++|+||.||-.+        .+.=|||.+.+..+. .||+
T Consensus        87 ~gi~g~v~~tg~~v~i~d~~~d~~f~~~~~----~~~~~~~~S~L~vPl~~~--------~~viGVL~l~n~~~~~~Ft~  154 (180)
T 3dba_A           87 IGIAGWVAHTKKFFNIPDVKKNNHFSDYLD----KKTGYTTVNMMAIPITQG--------KEVLAVVMALNKLNASEFSK  154 (180)
T ss_dssp             SSHHHHHHHHTCCEEESCGGGCTTCCCHHH----HHHCCCCCCEEEEEEEET--------TEEEEEEEEEEESSSSSCCH
T ss_pred             CCHHHHHHHhCCEEEecCCCCCcccChhhc----cccCccccEEEEEEeccC--------CEEEEEEEEEeCCCCCCCCH
Confidence            357889999988877666643333332221    001135799999999762        345799999988775 9999


Q ss_pred             hhHHHHHHHHhhhc
Q 023083          265 KDRAWIKAVSNKFR  278 (287)
Q Consensus       265 kDe~WI~~iA~KL~  278 (287)
                      .|+..++.+|+-..
T Consensus       155 ~d~~lL~~lA~~aa  168 (180)
T 3dba_A          155 EDEEVFKKYLNFIS  168 (180)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH
Confidence            99999999997543

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

Probab=94.59  E-value=0.29  Score=39.27  Aligned_cols=72  Identities=8%  Similarity=0.068  Sum_probs=55.6

Q ss_pred             HHHHHHHHHhhhhcccccCCCcccccCCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeC-Cccccch
Q 023083          186 TQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASS-MTYAYSH  264 (287)
Q Consensus       186 g~i~~~~~~~~~~~~Lv~L~~t~lyPgr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~-s~RafT~  264 (287)
                      +.++.++.++.++.-.-|..        .+       | +..|+||.||..+        .+.-|+|.+... .++.||+
T Consensus        60 ~g~~g~v~~~g~~v~v~d~~--------~d-------~-~~~s~l~vPL~~~--------~~~~GvL~l~~~~~~~~f~~  115 (149)
T 2vjw_A           60 DNAIGQAFRDRAPRRLDVLD--------GP-------G-LGGPALVLPLRAT--------DTVAGVLVAVQGSGARPFTA  115 (149)
T ss_dssp             SSHHHHHHHHCCCEEESCCC--------TT-------S-CEEEEEEEEEEET--------TEEEEEEEEEEETTCCCCCH
T ss_pred             CCHHHHHhhcCceEEecCcc--------cC-------C-CCCeEEEEEEccC--------CeEEEEEEEeeCCCCCCCCH
Confidence            35778888888877665542        11       1 7899999999752        234799999998 8999999


Q ss_pred             hhHHHHHHHHhhhcccc
Q 023083          265 KDRAWIKAVSNKFRGKS  281 (287)
Q Consensus       265 kDe~WI~~iA~KL~~~~  281 (287)
                      .|..-++.+|+....++
T Consensus       116 ~d~~ll~~lA~~aa~al  132 (149)
T 2vjw_A          116 EQLEMMTGFADQAAVAW  132 (149)
T ss_dssp             HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            99999999998766543

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

Probab=94.46  E-value=0.34  Score=38.04  Aligned_cols=82  Identities=10%  Similarity=0.017  Sum_probs=58.4

Q ss_pred             HHHHHHHHhhhhcccccCCCcccccCCcccccc-ccCCCCCceeEEEeccCCCCCCcccccc-cceEEEEee-CCccccc
Q 023083          187 QLLEWFERQIENIGLSDLKDSLYFPQSADAGQW-EMLPKGTCSVFVQPVIQAPNPSAVEVEK-IEGFVLLAS-SMTYAYS  263 (287)
Q Consensus       187 ~i~~~~~~~~~~~~Lv~L~~t~lyPgr~E~~~~-~~LP~ntqsVlvQPig~~~~~~~~~~~~-~~Gvlvlgs-~s~RafT  263 (287)
                      .++.++.+..+....-+.   ...|. ..  +. .+...|..++++.||..+        .+ .-|+|.+.+ ..++.||
T Consensus        73 ~~~~~~~~~~~~~~v~d~---~~~~~-~~--~~~~~~~~g~~s~~~vPl~~~--------~~~~~GvL~l~~~~~~~~f~  138 (181)
T 2qyb_A           73 TYIGEAFLSNRLQFVNDT---QYMTK-PL--TRELMQKEGIKSFAHIPISRK--------GEPPFGILSVFSRTIVGLFN  138 (181)
T ss_dssp             SHHHHHHHHTSCEEESCG---GGCSC-HH--HHHHHHHTTCCEEEEEEECCT--------TSCCCEEEEEEESSCSSCCC
T ss_pred             CchhhhhhcCCCEEecCh---hcCCc-hh--hHHHHHhcCcceEEEEEEEeC--------CCeEEEEEEEecCCCCCCCC
Confidence            477778887777655554   22232 11  00 122458999999999762        22 469999999 9999999


Q ss_pred             hhhHHHHHHHHhhhccccc
Q 023083          264 HKDRAWIKAVSNKFRGKSI  282 (287)
Q Consensus       264 ~kDe~WI~~iA~KL~~~~~  282 (287)
                      +.|...++.+|+-+..+++
T Consensus       139 ~~d~~lL~~la~~~a~al~  157 (181)
T 2qyb_A          139 EPFLNLLESLAGQLAQAVK  157 (181)
T ss_dssp             HHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHH
Confidence            9999999999998876554

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

Probab=94.42  E-value=0.042  Score=43.00  Aligned_cols=52  Identities=17%  Similarity=0.296  Sum_probs=44.7

Q ss_pred             CCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHHhhhcccc
Q 023083          222 LPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGKS  281 (287)
Q Consensus       222 LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kDe~WI~~iA~KL~~~~  281 (287)
                      ...|++++++.||-.+        .+.-|+|.+.+..++.||+.|...++.+|+.+..+.
T Consensus       113 ~~~~~~s~l~vPL~~~--------~~~iGvL~l~~~~~~~f~~~d~~ll~~lA~~~a~Ai  164 (177)
T 3k2n_A          113 HELGMRQIVLSPLRSG--------GRVIGFLSFVSAEEKLWSDGDKSLLSGVSSSIAIAV  164 (177)
T ss_dssp             HHHTCCEEEEEEEEET--------TEEEEEEEEEESSCCCCCHHHHHHHHHHHHHHHHHH
T ss_pred             HHcCceEEEEEEEEEC--------CEEEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHH
Confidence            4568999999999763        256899999999999999999999999999877654

>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=92.84  E-value=0.054  Score=43.41  Aligned_cols=51  Identities=14%  Similarity=0.296  Sum_probs=43.8

Q ss_pred             CCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHHhhhcccc
Q 023083          223 PKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGKS  281 (287)
Q Consensus       223 P~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kDe~WI~~iA~KL~~~~  281 (287)
                      ..|++|+|+.||-.+        .+.-|+|.+-...+|.||+.|...++.+|+-+..+.
T Consensus       115 ~~~~~s~l~vPi~~~--------~~l~G~l~~~~~~~~~~~~~e~~~l~~la~~~a~ai  165 (172)
T 2k2n_A          115 SMGVASSLVVPLMHH--------QELWGLLVSHHAEPRPYSQEELQVVQLLADQVSIAI  165 (172)
T ss_dssp             TTTCSEEEECCCSCS--------SCCCEEEEEEECSCCCCCHHHHHHHHHHHHHHHHHH
T ss_pred             hcCCeEEEEEEEEEC--------CEEEEEEEEEeCCCCCCCHHHHHHHHHHHHHHHHHH
Confidence            568999999999763        234799999999999999999999999999876554

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

Probab=92.72  E-value=0.11  Score=42.58  Aligned_cols=51  Identities=14%  Similarity=0.296  Sum_probs=43.8

Q ss_pred             CCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHHhhhcccc
Q 023083          223 PKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGKS  281 (287)
Q Consensus       223 P~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kDe~WI~~iA~KL~~~~  281 (287)
                      ..|++|+|+.||-.+        .+.-|+|.+-...+|.||+.|...++.+|+-+..+.
T Consensus       145 ~~~~~S~l~vPi~~~--------~~l~GvL~~~~~~~~~~~~~e~~ll~~la~~~a~ai  195 (208)
T 2lb5_A          145 SMGVASSLVVPLMHH--------QELWGLLVSHHAEPRPYSQEELQVVQLLADQVSIAI  195 (208)
T ss_dssp             HTTCSEEEEEEEEET--------TEEEEEEEEEESCCCCCCHHHHHHHHHHHHHHHHHH
T ss_pred             hcCCcEEEEEEEEEC--------CEeEEEEEEeeCCCCCCCHHHHHHHHHHHHHHHHHH
Confidence            458999999999763        344799999999999999999999999999887654

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

Probab=91.84  E-value=1.3  Score=44.05  Aligned_cols=85  Identities=13%  Similarity=0.086  Sum_probs=57.8

Q ss_pred             HHHHHHHHHhhhhcccccCCCcccccCCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCcc-ccch
Q 023083          186 TQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTY-AYSH  264 (287)
Q Consensus       186 g~i~~~~~~~~~~~~Lv~L~~t~lyPgr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~R-afT~  264 (287)
                      ..++.++.++++....-+..+...|+...+    ...-.++++++|.||..+       ..+.-|||.+....++ .||+
T Consensus       250 ~gi~g~v~~~g~~v~i~d~~~d~~~~~~~~----~~~g~~~rS~L~vPL~~~-------~g~viGVL~l~~~~~~~~f~~  318 (691)
T 3ibj_A          250 QGIAGHVATTGQILNIPDAYAHPLFYRGVD----DSTGFRTRNILCFPIKNE-------NQEVIGVAELVNKINGPWFSK  318 (691)
T ss_dssp             SHHHHHHHHHCSCEEESCSTTSTTC----------CCSCCCCCEEEEECCCS-------SSCCCEEEEEEEESSSSSCCT
T ss_pred             CCHHHHHHHhCCEEEecCcccCccccchhh----cccCCeeeeEEEEeEECC-------CCCEEEEEEEEECCCCCCCCH
Confidence            457788889888876666543332322222    112245789999999762       1234699999988776 7999


Q ss_pred             hhHHHHHHHHhhhcccc
Q 023083          265 KDRAWIKAVSNKFRGKS  281 (287)
Q Consensus       265 kDe~WI~~iA~KL~~~~  281 (287)
                      .|+.-++.+|+.+..+.
T Consensus       319 ~d~~ll~~lA~~~aiAI  335 (691)
T 3ibj_A          319 FDEDLATAFSIYCGISI  335 (691)
T ss_dssp             TTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            99999999999876554

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

Probab=91.52  E-value=0.35  Score=43.51  Aligned_cols=132  Identities=12%  Similarity=0.052  Sum_probs=75.2

Q ss_pred             CchHHHHHHHHHHHHHHhhhccccEEEEE--EC--CEEEE---eeeecCCCCC---ChHHHHHHHHHhhhhcccccCCCc
Q 023083          138 NISDALKENLAWATYVLLRNTNSISVLIS--IR--GELCV---RGYWQTPDGA---SKTQLLEWFERQIENIGLSDLKDS  207 (287)
Q Consensus       138 ~Lsd~~k~ELAWaS~~LLtnT~a~svlV~--~~--g~ll~---RG~~~~p~~~---~~g~i~~~~~~~~~~~~Lv~L~~t  207 (287)
                      ++.....+=|.-....+...+.+....||  ..  +++..   .|.-.....+   ....++.++.+..+...+-|....
T Consensus        22 ~l~~~l~~~l~~i~~~~~~~~~a~~~~i~l~d~~~~~l~~~~~~g~~~~~~~~~~~~~~g~~g~v~~~~~~v~i~d~~~~  101 (398)
T 1ykd_A           22 GFENILQEMLQSITLKTGELLGADRTTIFLLDEEKQELWSIVAAGEGDRSLEIRIPADKGIAGEVATFKQVVNIPFDFYH  101 (398)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHTEEEEEEEEEETTTTEEEEEEECCGGGCCCCCEEETTSHHHHHHHHHCCCEEECSCGGG
T ss_pred             cHHHHHHHHHHHHHHHHHHHhCCceEEEEEEECCCCeEEEEeecCCCCccceeecCCCCchhhhhhccCcEEeccchhcc
Confidence            44444444455555555555666555554  32  23332   3322111111   113467788888777665554321


Q ss_pred             ---ccccCCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeC---------------CccccchhhHHH
Q 023083          208 ---LYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASS---------------MTYAYSHKDRAW  269 (287)
Q Consensus       208 ---~lyPgr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~---------------s~RafT~kDe~W  269 (287)
                         ..|+...+    .....+++++++.||-..       ..+.-|+|.+...               .++.||+.|+.-
T Consensus       102 ~~~~~~~~~~~----~~~~~~~~s~l~vPl~~~-------~g~~iGvl~l~~~~~~~~~~~~~l~~~~~~~~f~~~d~~~  170 (398)
T 1ykd_A          102 DPRSIFAQKQE----KITGYRTYTMLALPLLSE-------QGRLVAVVQLLNKLKPYSPPDALLAERIDNQGFTSADEQL  170 (398)
T ss_dssp             SGGGHHHHHHH----HHHCCCCSCEEEEEEECS-------SCCEEEEEEEEEEBCSCCCTTCCHHHHBCTTCCCHHHHHH
T ss_pred             cchhhcccccC----cccCcCCceEEEEEEECC-------CCCEEEEEEEeccCCcccccccccccccccCCCCHHHHHH
Confidence               11211111    011246889999999641       1234799999887               789999999999


Q ss_pred             HHHHHhhhccc
Q 023083          270 IKAVSNKFRGK  280 (287)
Q Consensus       270 I~~iA~KL~~~  280 (287)
                      ++.+|+.+..+
T Consensus       171 l~~~a~~~~~a  181 (398)
T 1ykd_A          171 FQEFAPSIRLI  181 (398)
T ss_dssp             GGGTHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            99888776544

>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=90.38  E-value=0.36  Score=42.61  Aligned_cols=86  Identities=13%  Similarity=0.082  Sum_probs=58.0

Q ss_pred             HHHHHHHHHhhhhcccccCCCcccccCCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCcc-ccch
Q 023083          186 TQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTY-AYSH  264 (287)
Q Consensus       186 g~i~~~~~~~~~~~~Lv~L~~t~lyPgr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~R-afT~  264 (287)
                      ..++.++.++.+....-+..+...|+...+    ....-.++++++.||...       ..+.-|+|.+.+..++ .||+
T Consensus       250 ~~~~~~~~~~~~~~~i~d~~~~~~~~~~~~----~~~~~~~~s~l~vPl~~~-------~~~~iGvl~l~~~~~~~~f~~  318 (368)
T 1mc0_A          250 QGIAGHVATTGQILNIPDAYAHPLFYRGVD----DSTGFRTRNILCFPIKNE-------NQEVIGVAELVNKINGPWFSK  318 (368)
T ss_dssp             SHHHHHHHHHCCCEEESCSTTCTTCCCTTH----HHHTCCCCCEEEEEEECT-------TSCEEEEEEEEEETTSSSCCH
T ss_pred             CceeeeehhhCCEEEecCcccCcccchhhh----hccCCccceEEEEeeECC-------CCcEEEEEEEEECCCCCCCCH
Confidence            347788888887766655533333332221    001113699999999751       1344799999998886 8999


Q ss_pred             hhHHHHHHHHhhhccccc
Q 023083          265 KDRAWIKAVSNKFRGKSI  282 (287)
Q Consensus       265 kDe~WI~~iA~KL~~~~~  282 (287)
                      .|...++.+|+-+..+.+
T Consensus       319 ~d~~ll~~la~~~a~ai~  336 (368)
T 1mc0_A          319 FDEDLATAFSIYCGISIA  336 (368)
T ss_dssp             HHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHH
Confidence            999999999988766543

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

Probab=90.36  E-value=1.2  Score=36.75  Aligned_cols=124  Identities=9%  Similarity=0.014  Sum_probs=74.5

Q ss_pred             HHHHHHHHHHhhhccccEEEEE-----ECCEEEEeeeec-CCC----CCChHHH---HHHHHHhhhhcccccCCCccccc
Q 023083          145 ENLAWATYVLLRNTNSISVLIS-----IRGELCVRGYWQ-TPD----GASKTQL---LEWFERQIENIGLSDLKDSLYFP  211 (287)
Q Consensus       145 ~ELAWaS~~LLtnT~a~svlV~-----~~g~ll~RG~~~-~p~----~~~~g~i---~~~~~~~~~~~~Lv~L~~t~lyP  211 (287)
                      +=|.-+...+...+.+.-++||     +.|++++-..-. -++    .+....+   .....++.+.....|.    +.+
T Consensus        14 ~il~~~v~~v~~~l~~DRv~Iy~f~~d~~g~vvaE~~~~~~~s~lg~~~~~~~~~~~~~~~~~~g~~~~I~Dv----~~~   89 (171)
T 4glq_A           14 AIFETLVAKGRELLACDRVIVYAFDDNYVGTVVAESVAEGWPQARDQVIEDPCFREHWVEAYRQGRIQATTDI----FKA   89 (171)
T ss_dssp             HHHHHHHHHHHHHHTCSEEEEEEECTTCCEEEEEEEECTTSCCCTTCEECCTHHHHHTHHHHHTTCCEEESCG----GGT
T ss_pred             HHHHHHHHHHHHHHCCCeEEEEEEeCCCCeEEEEEEcCCCCccccCCccCccccHHHHHHHHHcCCEEEEcCc----CcC
Confidence            3445567778888888888887     235666532211 011    1111111   1222333333333333    333


Q ss_pred             CCccccccc-cCCCCCceeEEEeccCCCCCCcccccccceEEEEee-CCccccchhhHHHHHHHHhhhcccc
Q 023083          212 QSADAGQWE-MLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLAS-SMTYAYSHKDRAWIKAVSNKFRGKS  281 (287)
Q Consensus       212 gr~E~~~~~-~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs-~s~RafT~kDe~WI~~iA~KL~~~~  281 (287)
                      +..+.. -+ +-.-|.+|.|+.||..+        .+.-|+|.+-. ..+|.|++.|..+++.+|+.+..+.
T Consensus        90 ~~~~~~-~~~l~~~~v~S~L~vPi~~~--------~~l~GlL~~~~~~~~r~w~~~ei~ll~~lA~ql~iAi  152 (171)
T 4glq_A           90 GLTECH-LNQLRPLKVRANLVVPMVID--------DQLFGLLIAHQASEPRQWQEIEIDQFSELASTGSLVL  152 (171)
T ss_dssp             TCCHHH-HHHHGGGTEEEEEEEEEEET--------TEEEEEEEEEEESSCCCCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHH-HHHHHhcCCcEEEEEEEEEC--------CEEEEEEEEEeCCCCCCCCHHHHHHHHHHHHHHHHHH
Confidence            322210 12 23579999999999763        23479999988 6899999999999999999887654

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

Probab=86.18  E-value=0.53  Score=42.37  Aligned_cols=86  Identities=14%  Similarity=0.175  Sum_probs=55.1

Q ss_pred             HHHHHHHHhhhhcccc-cCCCcccccCCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCC-------
Q 023083          187 QLLEWFERQIENIGLS-DLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSM-------  258 (287)
Q Consensus       187 ~i~~~~~~~~~~~~Lv-~L~~t~lyPgr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s-------  258 (287)
                      .++.++.++++....- |..+...|....+  +-......++|++|.||-..       ..+.-|+|.+....       
T Consensus       268 ~~~~~v~~~~~~~~i~~d~~~~~~~~~~~~--~~~~~~~~~~s~l~vPl~~~-------~~~~iGvl~l~~~~~~~~~~~  338 (398)
T 1ykd_A          268 GFAGIVAASGQKLNIPFDLYDHPDSATAKQ--IDQQNGYRTCSLLCMPVFNG-------DQELIGVTQLVNKKKTGEFPP  338 (398)
T ss_dssp             HHHHHHHHHCCCEEECSCGGGSTTCHHHHH--HHHHHTCCCCCEEEEEEECS-------SSCEEEEEEEEEECCSSCCCC
T ss_pred             chhhHHhccCCeEEeccccccCcccCcccc--hhhhcCCeeeeEEEEeeecC-------CCCEEEEEEEEecCCcccccc
Confidence            4667788877766544 4422111211100  00001224899999999731       12346999999888       


Q ss_pred             -------------ccccchhhHHHHHHHHhhhcccc
Q 023083          259 -------------TYAYSHKDRAWIKAVSNKFRGKS  281 (287)
Q Consensus       259 -------------~RafT~kDe~WI~~iA~KL~~~~  281 (287)
                                   ++.||+.|..-++.+|+.+..++
T Consensus       339 ~~~~~~~~~~~~~~~~f~~~d~~ll~~la~~~a~al  374 (398)
T 1ykd_A          339 YNPETWPIAPECFQASFDRNDEEFMEAFNIQAGVAL  374 (398)
T ss_dssp             CCGGGTTCCCGGGCCCCCHHHHHHHHHHHHHHHHHH
T ss_pred             cccccccccccccCCCCCHHHHHHHHHHHHHHHHHH
Confidence                         89999999999999999876554

---

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	287
d1vhma_	159	Hypothetical protein YebR {Escherichia coli [TaxId	97.52
d1f5ma_	176	Hypothetical protein ykl069wp {Baker's yeast (Sacc	96.3
d1mc0a1	187	3',5'-cyclic nucleotide phosphodiesterase 2A, GAF	89.99
d1mc0a2	154	3',5'-cyclic nucleotide phosphodiesterase 2A, GAF	89.96

>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=97.52  E-value=0.00048  Score=55.04  Aligned_cols=124  Identities=13%  Similarity=0.106  Sum_probs=85.7

Q ss_pred             HHHHHHHHhh---hccccEEEEEECCEEEEeeeecCCC--CCCh-HHHHHHHHHhhhhcccccCCCcccccCCccccccc
Q 023083          147 LAWATYVLLR---NTNSISVLISIRGELCVRGYWQTPD--GASK-TQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWE  220 (287)
Q Consensus       147 LAWaS~~LLt---nT~a~svlV~~~g~ll~RG~~~~p~--~~~~-g~i~~~~~~~~~~~~Lv~L~~t~lyPgr~E~~~~~  220 (287)
                      |+-.+..|.+   ++...++.+..++.....-+.+...  .+.. .-++-++.++.+....-|..+   .|..      -
T Consensus        27 L~~i~~~l~~~~~~~~~~~~yl~d~~~~~l~~~~~~~~~~~i~~g~g~~g~v~~~~~~~~v~d~~~---d~~~------~   97 (159)
T d1vhma_          27 LANTSALLYERLTDINWAGFYLLEDDTLVLGPFQGKIACVRIPVGRGVCGTAVARNQVQRIEDVHV---FDGH------I   97 (159)
T ss_dssp             HHHHHHHHHHHSSSCSEEEEEEEETTEEEEEEEEESCCCSEEETTSHHHHHHHHHTSCEEESCTTT---CTTC------C
T ss_pred             HHHHHHHHHHhhccCceEEEEEEECCEeeeeeecCCcceeEEecCCChHHHHHHcCCcEEecChHH---hhhh------h
Confidence            5556655533   4455566666766644332322222  2222 337788888888877766632   2332      2


Q ss_pred             cCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHHhhhcccccceecC
Q 023083          221 MLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGKSIWIDLK  287 (287)
Q Consensus       221 ~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kDe~WI~~iA~KL~~~~~~~~~~  287 (287)
                      ....+.+|++|.||..+        .+.-|+|.+++..++.||+.|...++.+|+.+..+++..|++
T Consensus        98 ~~~~~~~S~l~vPl~~~--------~~viGvl~v~s~~~~~F~~~d~~ll~~la~qia~ai~~~~~~  156 (159)
T d1vhma_          98 ACDAASNSEIVLPLVVK--------NQIIGVLDIDSTVFGRFTDEDEQGLRQLVAQLEKVLATTDYK  156 (159)
T ss_dssp             CSCCCCSEEEEEEEEET--------TEEEEEEEEEESSTTCCCHHHHHHHHHHHHHHHHHHHTSSGG
T ss_pred             hcccccceeEEeCEEEC--------CEEEEEEEecCCCCCCCCHHHHHHHHHHHHHHHHHHHccchh
Confidence            34678999999999652        244799999999999999999999999999999999888764

>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=96.30  E-value=0.0052  Score=49.70  Aligned_cols=78  Identities=15%  Similarity=0.165  Sum_probs=60.4

Q ss_pred             HHHHHHHHhhhhcccccCCCcccccCCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhh
Q 023083          187 QLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKD  266 (287)
Q Consensus       187 ~i~~~~~~~~~~~~Lv~L~~t~lyPgr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kD  266 (287)
                      -++.++.++++....-|..   -.|.      |.....+++|.+|.||...       ..+.=|||-+.+..++.||+.|
T Consensus        96 Gi~G~v~~~g~~i~v~D~~---~dpr------~~~~~~~~~S~l~vPl~~~-------~g~~~GVl~v~s~~~~~F~~~d  159 (176)
T d1f5ma_          96 GVCGTAASTKETQIVPDVN---KYPG------HIACDGETKSEIVVPIISN-------DGKTLGVIDIDCLDYEGFDHVD  159 (176)
T ss_dssp             HHHHHHHHHTSCEEESCGG---GSTT------CCCSSTTCCEEEEEEEECT-------TSCEEEEEEEEESSTTCCCHHH
T ss_pred             cHHHHHHHhCCeEEecCcc---cCcc------hhhccccccceEEeccccc-------CCcEEEEEEeccCCCCCcCHHH
Confidence            4788999999988776652   2342      2345678999999999542       1234699999999999999999


Q ss_pred             HHHHHHHHhhhccc
Q 023083          267 RAWIKAVSNKFRGK  280 (287)
Q Consensus       267 e~WI~~iA~KL~~~  280 (287)
                      +.+++.+|+-+..+
T Consensus       160 ~~~l~~~A~~ia~a  173 (176)
T d1f5ma_         160 KEFLEKLAKLINKS  173 (176)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH
Confidence            99999999987654

>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=89.99  E-value=0.099  Score=40.86  Aligned_cols=82  Identities=15%  Similarity=0.066  Sum_probs=55.9

Q ss_pred             HHHHHHHHhhhhcccccCCCcccccCCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEE-eeCCccccchh
Q 023083          187 QLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLL-ASSMTYAYSHK  265 (287)
Q Consensus       187 ~i~~~~~~~~~~~~Lv~L~~t~lyPgr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvl-gs~s~RafT~k  265 (287)
                      .++.+|.+..+...+.|..+...|..      ....-.++.+++|.||-..      ...+.-||+.+ -....+.||+.
T Consensus        73 g~~~~v~~~~~~~~i~d~~~d~~~~~------~~~~~~~~~s~l~vPl~~~------~~~~~iGvl~~~~~~~~~~fs~~  140 (187)
T d1mc0a1          73 GRLGQVVEDKQCIQLKDLTSDDVQQL------QNMLGCELQAMLCVPVISR------ATDQVVALACAFNKLGGDFFTDE  140 (187)
T ss_dssp             SSHHHHHHHCCCEEGGGSCHHHHHHH------HHHHCSCCCCEEEEEEECT------TTCSEEEEEEEEEESSCSSCCSH
T ss_pred             cHHHHHHHhhhhhhhhcccccccccc------chhhhhhHHHHHhhhhhcc------ccccceEEEEEEcccccchhhhH
Confidence            35678888888887777643322221      2234467889999999531      11233688844 56777999999


Q ss_pred             hHHHHHHHHhhhccc
Q 023083          266 DRAWIKAVSNKFRGK  280 (287)
Q Consensus       266 De~WI~~iA~KL~~~  280 (287)
                      |...+.++|+-...+
T Consensus       141 d~~~l~~~a~~~a~a  155 (187)
T d1mc0a1         141 DEHVIQHCFHYTGTV  155 (187)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHH
Confidence            999999999876544

>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=89.96  E-value=1.7  Score=31.18  Aligned_cols=85  Identities=13%  Similarity=0.062  Sum_probs=49.1

Q ss_pred             hHHHHHHHHHhhhhcccccCCCcccccCCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEE-eeCCccccc
Q 023083          185 KTQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLL-ASSMTYAYS  263 (287)
Q Consensus       185 ~g~i~~~~~~~~~~~~Lv~L~~t~lyPgr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvl-gs~s~RafT  263 (287)
                      ...++.++.+..+.....+-.....++...+    ........+.++.|+-..       ..+.-|++.+ ....+|.||
T Consensus        54 ~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~-------~~~~~g~~~~~~~~~~~~f~  122 (154)
T d1mc0a2          54 DQGIAGHVATTGQILNIPDAYAHPLFYRGVD----DSTGFRTRNILCFPIKNE-------NQEVIGVAELVNKINGPWFS  122 (154)
T ss_dssp             TSHHHHHHHHHCCCEEESCSTTCTTCCCTTH----HHHTCCCCCEEEEEEECT-------TSCEEEEEEEEEETTSSSCC
T ss_pred             CccchhheeccCcEEEEEeccccccccchhh----hhhcccceeEEEEecccc-------cceeeEEEEeeccccccccc
Confidence            3457777888777665544432233333322    112223334455554221       1223455544 467999999


Q ss_pred             hhhHHHHHHHHhhhccc
Q 023083          264 HKDRAWIKAVSNKFRGK  280 (287)
Q Consensus       264 ~kDe~WI~~iA~KL~~~  280 (287)
                      +.|..-++.+|+-...+
T Consensus       123 ~~d~~ll~~la~q~aiA  139 (154)
T d1mc0a2         123 KFDEDLATAFSIYCGIS  139 (154)
T ss_dssp             HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            99999999999877654