Citrus Sinensis ID: 023161

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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
MSILPYNSLMQLKIPSHSCAKTTRKSFSICARLDNSQQEEQQLNLSVLRFTFGIPGFDESYLPRWIGYGFGSLIVLNHFAFSNSVTSAQLRSEVLGLSLAAFSVTLPYLGKFLKGASPVSQKSLPESGEQIFVMSQNISDALKENLAWATYVLLRNTNSISVLISIRGELCVRGYWQTPDGASKTQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGKSIWIDLK
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccEEcccccHHHHHHccccEEEEEcccccccccccHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccEEcEEEcccccHHHHHHHHHHHHHHHHcccccEEEEEEccEEEEEEEEcccccccHHHHHHHHHHHHcccccccccccccccccccccccccccccccEEEEEEccccccccccccccccEEEEEEEcccccccHHHHHHHHHHHHHHcccccccccc
Secondary Structure Prediction (SSPRO)
ccccEccccccccccccccccccccEEEEEEEccccccccccccEEEEEEEcccccccHcHccHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccEEEEEcccccHHHHHHHHHHHHHHHHccccEEEEEEEccEEEEEEccccccccccHHHHHHHHHHcccEEEEEccccEEccccccccccccccccccEEEEEEccccccccccccccccEEEEEEccccccccHHHHHHHHHHHHHHcccEEEEEcc
Coil and Loop (DISEMBL)
msilpynslmqlkipshscakttrKSFSICARLDNSQQEEQQLNLSVLRftfgipgfdesylprwigygFGSLIVLNHfafsnsvtsAQLRSEVLGLSLAAFSVTLPYlgkflkgaspvsqkslpesgEQIFVMSQNISDALKENLAWATYVLLRNTNSISVLISIRGELcvrgywqtpdgaskTQLLEWFERQIENIglsdlkdslyfpqsadagqwemlpkgtcsvfvqpviqapnpsavevEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGKSIWIDLK
Flexible Loop (DISEMBL)
msilpynslmqlkipshscaKTTRKSFSICARLDNSQQEEQQLNLSVLRFTFGIPGFDESYLPRWIGYGFGSLIVLNHFAFSNSVTSAQLRSEVLGLSLAAFSVTLPYLGKFLKGASPVSQKSLPESGEQIFVMSQNISDALKENLAWATYVLLRNTNSISVLISIRGELCVRGYWQTPDGASKTQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKavsnkfrgksiwidlk
Low Complexity Region (SEG)
MSILPYNSLMQLKIPSHSCAKTTRKSFSICARLDNSQQEEQQLNLSVLRFTFGIPGFDESYLPRWIGYGFGSLIVLNHFAFSNSVTSAQLRSEVLGLSLAAFSVTLPYLGKFLKGASPVSQKSLPESGEQIFVMSQNISDALKENLAWATYVLLRNTNSISVLISIRGELCVRGYWQTPDGASKTQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGKSIWIDLK
Disordered region (IsUnstruct)
**************************FSICAR*********QLNLSVLRFTFGIPGFDESYLPRWIGYGFGSLIVLNHFAFSNSVTSAQLRSEVLGLSLAAFSVTLPYLGKFLKG***************IFVMSQNISDALKENLAWATYVLLRNTNSISVLISIRGELCVRGYWQTPDGASKTQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGKSIWID**
Disordered Region (DISOPRED)
****PYNSLMQLK*********************************VLRFTFGIPGFDESYLPRWIGYGFGSLIVLNHFAFSNSVTSAQLRSEVLGLSLAAFSVTLPYLGKFL*****************IFVMSQNISDALKENLAWATYVLLRNTNSISVLISIRGELCVRGYWQ*********LLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGKSIWIDL*
Disordered Region (DISEMBL)
MSILPYNSLMQLKIPSHSCAKTTRKSFSICARLDNSQQEEQQLNLSVLRFTFGIPGFDESYLPRWIGYGFGSLIVLNHFAFSNSVTSAQLRSEVLGLSLAAFSVTLPYLGKFLKGASPVSQKSLPESGEQIFVMSQNISDALKENLAWATYVLLRNTNSISVLISIRGELCVRGYWQTPDGASKTQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGKSIWIDLK
Disordered Region (DISPRO)
*SILPYNSLMQLKIPSHSCA*TTRKSFSICARLDNSQQEEQQLNLSVLRFTFGIPGFDESYLPRWIGYGFGSLIVLNHFAFSNSVTSAQLRSEVLGLSLAAFSVTLPYLGKFLKGASPVSQKSLPESGEQIFVMSQNISDALKENLAWATYVLLRNTNSISVLISIRGELCVRGYWQTPDGASKTQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGKSIWIDLK
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHooooooooooooooooHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSILPYNSLMQLKIPSHSCAKTTRKSFSICARLDNSQQEEQQLNLSVLRFTFGIPGFDESYLPRWIGYGFGSLIVLNHFAFSNSVTSAQLRSEVLGLSLAAFSVTLPYLGKFLKGASPVSQKSLPESGEQIFVMSQNISDALKENLAWATYVLLRNTNSISVLISIRGELCVRGYWQTPDGASKTQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGKSIWIDLK
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	286
225455453	311	PREDICTED: uncharacterized protein LOC10	0.895	0.823	0.726	1e-107
297741104	313	unnamed protein product [Vitis vinifera]	0.891	0.814	0.725	1e-106
224136914	265	predicted protein [Populus trichocarpa]	0.905	0.977	0.698	1e-99
255539547	308	conserved hypothetical protein [Ricinus	0.947	0.879	0.647	4e-98
449446061	288	PREDICTED: uncharacterized protein LOC10	0.916	0.909	0.642	1e-94
15242277	275	uncharacterized protein [Arabidopsis tha	0.905	0.941	0.609	5e-90
297796017	272	hypothetical protein ARALYDRAFT_495283 [	0.905	0.952	0.609	8e-90
147816662	349	hypothetical protein VITISV_012455 [Viti	0.895	0.733	0.588	9e-90
356559871	287	PREDICTED: uncharacterized protein LOC10	0.828	0.825	0.640	2e-84
242040471	293	hypothetical protein SORBIDRAFT_01g03118	0.951	0.928	0.537	6e-78

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

 Score =  392 bits (1008), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 191/263 (72%), Positives = 218/263 (82%), Gaps = 7/263 (2%)

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

Query: 78  HFAFS--NSVTSAQLRSEVLGLSLAAFSVTLPYLGKFLKGASPVSQKSLPESGEQIFVMS 135
           HF  S  N++T+AQLR+E LGL LAAFSV LPYLGKFLKGA+PV Q +LPE  EQIFVM+
Sbjct: 109 HFVGSDLNTITAAQLRTEALGLCLAAFSVVLPYLGKFLKGAAPVDQTTLPEGIEQIFVMT 168

Query: 136 QNISDALKENLAWATYVLLRNTNSISVLISIRGELCVRGYWQTPDGASKTQLLEWFERQI 195
           QNISD LKE+LAWATY+LLRNTN+I+VLISIRG LCVRGYW TPD  SK ++L+W E++I
Sbjct: 169 QNISDILKEDLAWATYILLRNTNTIAVLISIRGALCVRGYWNTPDDVSKARVLDWVEKEI 228

Query: 196 ENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLAS 255
           E IGLSDLKD+LYFPQSAD+G WEMLPKGTCS+ VQPV Q P+    E+EKI+GFVLLAS
Sbjct: 229 EKIGLSDLKDTLYFPQSADSGLWEMLPKGTCSLLVQPVSQIPSQGTDEMEKIDGFVLLAS 288

Query: 256 SMTYAYSHKDRAWIKAVSNKFRG 278
           SM YAY+ KDRAWI AV+NKFRG
Sbjct: 289 SMNYAYTDKDRAWIGAVANKFRG 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 =  390 bits (1003), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 190/262 (72%), Positives = 217/262 (82%), Gaps = 7/262 (2%)

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

Query: 78  HFAFS--NSVTSAQLRSEVLGLSLAAFSVTLPYLGKFLKGASPVSQKSLPESGEQIFVMS 135
           HF  S  N++T+AQLR+E LGL LAAFSV LPYLGKFLKGA+PV Q +LPE  EQIFVM+
Sbjct: 109 HFVGSDLNTITAAQLRTEALGLCLAAFSVVLPYLGKFLKGAAPVDQTTLPEGIEQIFVMT 168

Query: 136 QNISDALKENLAWATYVLLRNTNSISVLISIRGELCVRGYWQTPDGASKTQLLEWFERQI 195
           QNISD LKE+LAWATY+LLRNTN+I+VLISIRG LCVRGYW TPD  SK ++L+W E++I
Sbjct: 169 QNISDILKEDLAWATYILLRNTNTIAVLISIRGALCVRGYWNTPDDVSKARVLDWVEKEI 228

Query: 196 ENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLAS 255
           E IGLSDLKD+LYFPQSAD+G WEMLPKGTCS+ VQPV Q P+    E+EKI+GFVLLAS
Sbjct: 229 EKIGLSDLKDTLYFPQSADSGLWEMLPKGTCSLLVQPVSQIPSQGTDEMEKIDGFVLLAS 288

Query: 256 SMTYAYSHKDRAWIKAVSNKFR 277
           SM YAY+ KDRAWI AV+NKFR
Sbjct: 289 SMNYAYTDKDRAWIGAVANKFR 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 =  369 bits (946), Expect = 1e-99,   Method: Compositional matrix adjust.
 Identities = 183/262 (69%), Positives = 217/262 (82%), Gaps = 3/262 (1%)

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

Query: 78  HFAFSN-SVTSAQLRSEVLGLSLAAFSVTLPYLGKFLKGASPVSQKSLPESGEQIFVMSQ 136
           HF  SN   T AQLR+EVLGLSLAAFS  LPY G+FLKGA+PV Q +LP+  EQIF MSQ
Sbjct: 64  HFLGSNPDTTQAQLRTEVLGLSLAAFSAALPYFGRFLKGATPVDQGTLPQDAEQIFAMSQ 123

Query: 137 NISDALKENLAWATYVLLRNTNSISVLISIRGELCVRGYWQTPDGASKTQLLEWFERQIE 196
           NISDA KE+LAWATY+LLRNTN+I+VLISI+GELCVRGYW+T D  SK ++L+WF+ QIE
Sbjct: 124 NISDAQKEDLAWATYILLRNTNTIAVLISIQGELCVRGYWKTSDKMSKDEVLDWFKEQIE 183

Query: 197 NIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASS 256
           NIGLSD+KD+LYFPQ+ ++  WEMLP+GT S+ V+PV+QA   S  + E  EGF+LLASS
Sbjct: 184 NIGLSDVKDTLYFPQTTESEIWEMLPEGTRSLLVEPVLQATVQSGNKTENNEGFILLASS 243

Query: 257 MTYAYSHKDRAWIKAVSNKFRG 278
           + YAYS KDRAWI+A  NKFRG
Sbjct: 244 IGYAYSDKDRAWIRATGNKFRG 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 =  363 bits (933), Expect = 4e-98,   Method: Compositional matrix adjust.
 Identities = 182/281 (64%), Positives = 226/281 (80%), Gaps = 10/281 (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-AQLRSEVLGLSLAAFSVTLPYLGKFLKG 115
            DESYLPRWIGYGFGSL+VLNHF  SNSVTS  Q+R+E LGLSLAAFS+ LPY G+FLKG
Sbjct: 59  LDESYLPRWIGYGFGSLLVLNHFLGSNSVTSLPQMRTEALGLSLAAFSIALPYFGRFLKG 118

Query: 116 ASPVSQKSLPESGEQIFVMSQNISDALKENLAWATYVLLRNTNSISVLISIRGELCVRGY 175
           A+PV Q +LP+  EQIFVMS+N+SD LKE+LAWATYVLLRNTNSI+VLI I+GELCVRGY
Sbjct: 119 ATPVDQTALPQGSEQIFVMSENVSDTLKEDLAWATYVLLRNTNSIAVLIYIQGELCVRGY 178

Query: 176 WQTPDGASKTQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQ 235
           W TPD  SK Q+++WF+ +IE+IGL DLKD+LYFPQ+A++  WEMLP+GT S+ V+PV+ 
Sbjct: 179 WNTPDNISKAQVIDWFKGRIEDIGLFDLKDTLYFPQTAESRLWEMLPRGTRSLLVEPVLL 238

Query: 236 APNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKF 276
               +A E+++ EGFVLLASS+  AY+ KDRAWI AV+NKF
Sbjct: 239 Q---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 =  352 bits (902), Expect = 1e-94,   Method: Compositional matrix adjust.
 Identities = 171/266 (64%), Positives = 210/266 (78%), Gaps = 4/266 (1%)

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

Query: 79  FAFSNS---VTSAQLRSEVLGLSLAAFSVTLPYLGKFLKGASPVSQKSLPESGEQIFVMS 135
           F  SNS    T AQLR+E LG+SLAAFS+ LPYLGKFLKGA P  +  LPE  EQIF++S
Sbjct: 82  FVGSNSAALTTPAQLRTEALGISLAAFSIALPYLGKFLKGALPSGEAILPEGTEQIFLLS 141

Query: 136 QNISDALKENLAWATYVLLRNTNSISVLISIRGELCVRGYWQTPDGASKTQLLEWFERQI 195
           Q +SD LKE++AWATY+LLRNTNSISVLI  +G LCVRGYW +P+  S   LL WFE Q+
Sbjct: 142 QILSDNLKEDIAWATYILLRNTNSISVLIQTQGALCVRGYWNSPNDISSADLLAWFEEQL 201

Query: 196 ENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLAS 255
           ++IGLS LKD++YFPQ +++G W+MLPKGT SV VQPV+Q    S  EV+ + GF+LLAS
Sbjct: 202 QSIGLSALKDAVYFPQISESGLWQMLPKGTRSVLVQPVVQNLKQSGNEVQNMGGFILLAS 261

Query: 256 SMTYAYSHKDRAWIKAVSNKFRGKSI 281
           S++YA+S KDRAWI+AV+NKF  ++I
Sbjct: 262 SLSYAFSDKDRAWIRAVANKFDDRAI 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 =  337 bits (863), Expect = 5e-90,   Method: Compositional matrix adjust.
 Identities = 164/269 (60%), Positives = 212/269 (78%), Gaps = 10/269 (3%)

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

Query: 71  GSLIVLNHFAFSNSVTSAQLRSEVLGLSLAAFSVTLPYLGKFLKGASPVSQKSLPESGEQ 130
           GSL++LNHF+ S  ++ +Q+RSE LGLSLAAFS+ LPY+GKFLKG S V Q+SLPE GEQ
Sbjct: 72  GSLLLLNHFSASAPISESQMRSEALGLSLAAFSIALPYIGKFLKG-SVVEQRSLPEEGEQ 130

Query: 131 IFVMSQNISDALKENLAWATYVLLRNTNSISVLISIRGELCVRGYWQTPDGASKTQLLEW 190
           +FV+S NI D+LKE+LAWATYVLLRNT++I+VLIS++GELCVRGYW  PD  SK QL +W
Sbjct: 131 VFVISSNIGDSLKEDLAWATYVLLRNTSTIAVLISVQGELCVRGYWNCPDQMSKAQLHDW 190

Query: 191 FERQIENIGLSDLKDSLYFPQSADAG-QWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEG 249
           F+++++ IGL+D+K++LYFPQ A +    ++LP GT S+FVQP++Q  N    E +K+ G
Sbjct: 191 FKKKVDEIGLADVKETLYFPQYAGSALSLDILPDGTRSLFVQPLVQNTN----EPQKVNG 246

Query: 250 FVLLASSMTYAYSHKDRAWIKAVSNKFRG 278
           F+L+AS+  YAYS KDRAWI A++ KFRG
Sbjct: 247 FLLVASTAGYAYSDKDRAWIGAMAEKFRG 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 =  336 bits (861), Expect = 8e-90,   Method: Compositional matrix adjust.
 Identities = 162/266 (60%), Positives = 212/266 (79%), Gaps = 7/266 (2%)

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

Query: 74  IVLNHFAFSNSVTSAQLRSEVLGLSLAAFSVTLPYLGKFLKGASPVSQKSLPESGEQIFV 133
           ++LNHF+ S  ++ +Q+RSE LGLSLA+FS+ LPY+GKFLKG S V Q++LPE GEQIFV
Sbjct: 72  LLLNHFSASAPISESQMRSEALGLSLASFSIALPYIGKFLKG-SVVEQRTLPEEGEQIFV 130

Query: 134 MSQNISDALKENLAWATYVLLRNTNSISVLISIRGELCVRGYWQTPDGASKTQLLEWFER 193
           +S NI D+LKE+LAWATYVLLRNT++I+VLI ++GELCVRGYW  PD  SK QL +WF++
Sbjct: 131 ISSNIGDSLKEDLAWATYVLLRNTSTIAVLILVQGELCVRGYWNCPDQMSKAQLHDWFKK 190

Query: 194 QIENIGLSDLKDSLYFPQSADAG-QWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVL 252
           +++ IGL+D+KD+LYFPQ A +   W++LP GT S+F+QP++Q    +  E +K+ GF+L
Sbjct: 191 KVDEIGLADVKDTLYFPQYAGSALSWDILPDGTRSLFMQPLVQ----NISEPQKVNGFLL 246

Query: 253 LASSMTYAYSHKDRAWIKAVSNKFRG 278
           +AS+  YAYS KDRAWI A++ KFRG
Sbjct: 247 VASTAGYAYSDKDRAWIGAMAEKFRG 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 =  335 bits (860), Expect = 9e-90,   Method: Compositional matrix adjust.
 Identities = 177/301 (58%), Positives = 204/301 (67%), Gaps = 45/301 (14%)

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

Query: 78  HFAFS--NSVTSAQLRSEVLGLSLAAFSVTLPYLGKFLKGASPVSQKSLPESGEQIFVMS 135
           HF  S  N++T+AQLR+E LGL LAAFSV LPY GKFLKGA+PV Q +LPE  EQIFVM+
Sbjct: 109 HFVGSDLNTITAAQLRTEALGLCLAAFSVVLPYXGKFLKGAAPVDQTTLPEGIEQIFVMT 168

Query: 136 QNISDALKENLAWAT---------YVLLRNTNSISV------------------------ 162
           QNISD L+  L             +  +   + I V                        
Sbjct: 169 QNISDILERGLGLGNIHFAAEHKHHCCVVKGDIIVVSMRSQLCIYEVCFLFKYQXLLELY 228

Query: 163 -----LISIRGELCVRGYWQTPDGASKTQLLEWFERQIENIGLSDLKDSLYFPQSADAGQ 217
                LISIRG LCVRGYW TPD  SK ++L+W E++IE IGLSDLKD+LYFPQSAD+G 
Sbjct: 229 CLNFQLISIRGALCVRGYWNTPDDVSKARVLDWVEKEIEKIGLSDLKDTLYFPQSADSGL 288

Query: 218 WEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFR 277
           WEMLPKGTCS+ VQPV Q P+    E+EKI+GFVLLASSM YAY+ KDRAWI AV+NKFR
Sbjct: 289 WEMLPKGTCSLLVQPVXQIPSQGTDEMEKIDGFVLLASSMNYAYTDKDRAWIGAVANKFR 348

Query: 278 G 278
           G
Sbjct: 349 G 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 =  318 bits (815), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 153/239 (64%), Positives = 190/239 (79%), Gaps = 2/239 (0%)

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

Query: 101 AFSVTLPYLGKFLKGASPVSQKSLPESGEQIFVMSQNISDALKENLAWATYVLLRNTNSI 160
           +FS+ LPYLGKFLKGA PV +K++P+  EQIFVMS +  D LKE+LAWA+YVLL NTN+I
Sbjct: 108 SFSIVLPYLGKFLKGAQPVDEKTIPDGTEQIFVMSTDRVDGLKEDLAWASYVLLCNTNAI 167

Query: 161 SVLISIRGELCVRGYWQTPDGASKTQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEM 220
           ++LI I+GE+C RGYW  PD  SK  L  WF+++IEN GL DLKD+LYFPQ AD+   ++
Sbjct: 168 AMLIFIQGEICARGYWNIPDDTSKEILPGWFKKKIENAGLYDLKDTLYFPQDADSEFQDL 227

Query: 221 LPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGK 279
           +P GT  + +QPV+Q  N S   ++K  GF+LLAS+  YA+S+KD+AWI AV+NKFRGK
Sbjct: 228 VPIGTRCLLIQPVLQVSNESDTGLQKPGGFILLASTTRYAFSNKDKAWIAAVANKFRGK 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 =  296 bits (759), Expect = 6e-78,   Method: Compositional matrix adjust.
 Identities = 150/279 (53%), Positives = 196/279 (70%), Gaps = 7/279 (2%)

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

Query: 59  ESYLPRWIGYGFGSLIVLNHFAFSNSVTSAQLRSEVLGLSLAAFSVTLPYLGKFLKGASP 118
           ESYLPRWIG GFG+L+VLNH   S S T AQLRSE LGL LAAFS TLP+LG+FL+GA  
Sbjct: 76  ESYLPRWIGLGFGALVVLNHL-ISPSPTPAQLRSEALGLCLAAFSATLPFLGRFLEGADA 134

Query: 119 VSQKSLPESGEQIFVMSQNISDALKENLAWATYVLLRNTNSISVLISIRGELCVRGYWQT 178
            S+  LPE   Q+FVMS+N+S   KE++AWA+YVLLRNTN+ SV+I+I    C+RGYW  
Sbjct: 135 ASRVPLPEGSSQVFVMSENLSAVQKEDMAWASYVLLRNTNTTSVVIAIGDLFCIRGYWNP 194

Query: 179 PDGASKTQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPN 238
           P   SK  ++EWF+ Q++ +GL DLKD+LYFP S+D+   ++LP G  SV  QP++   +
Sbjct: 195 PANTSKYAMIEWFKSQMQQLGLVDLKDALYFPNSSDSQLVKILPDGILSVLAQPILSL-D 253

Query: 239 PSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFR 277
           P+  E  K EG +LLAS+  YAYS KDRAWI+ V+NKF+
Sbjct: 254 PANNET-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	286
TAIR|locus:2173048	275	HCF208 "AT5G52110" [Arabidopsi	0.905	0.941	0.609	1.7e-84

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

 Score = 846 (302.9 bits), Expect = 1.7e-84, P = 1.7e-84
 Identities = 164/269 (60%), Positives = 212/269 (78%)

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

Query:    71 GSLIVLNHFAFSNSVTSAQLRSEVLGLSLAAFSVTLPYLGKFLKGASPVSQKSLPESGEQ 130
             GSL++LNHF+ S  ++ +Q+RSE LGLSLAAFS+ LPY+GKFLKG S V Q+SLPE GEQ
Sbjct:    72 GSLLLLNHFSASAPISESQMRSEALGLSLAAFSIALPYIGKFLKG-SVVEQRSLPEEGEQ 130

Query:   131 IFVMSQNISDALKENLAWATYVLLRNTNSISVLISIRGELCVRGYWQTPDGASKTQLLEW 190
             +FV+S NI D+LKE+LAWATYVLLRNT++I+VLIS++GELCVRGYW  PD  SK QL +W
Sbjct:   131 VFVISSNIGDSLKEDLAWATYVLLRNTSTIAVLISVQGELCVRGYWNCPDQMSKAQLHDW 190

Query:   191 FERQIENIGLSDLKDSLYFPQSADAG-QWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEG 249
             F+++++ IGL+D+K++LYFPQ A +    ++LP GT S+FVQP++Q  N    E +K+ G
Sbjct:   191 FKKKVDEIGLADVKETLYFPQYAGSALSLDILPDGTRSLFVQPLVQNTN----EPQKVNG 246

Query:   250 FVLLASSMTYAYSHKDRAWIKAVSNKFRG 278
             F+L+AS+  YAYS KDRAWI A++ KFRG
Sbjct:   247 FLLVASTAGYAYSDKDRAWIGAMAEKFRG 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      286       286   0.00086  115 3  11 22  0.37    34
                                                     33  0.42    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 (2117 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:  22.33u 0.21s 22.54t   Elapsed:  00:00:01
  Total cpu time:  22.33u 0.21s 22.54t   Elapsed:  00:00:01
  Start:  Sat May 11 13:39:25 2013   End:  Sat May 11 13:39:26 2013

GO:0003674 "molecular_function" evidence=ND

GO:0009507 "chloroplast" evidence=ISM;IDA

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

GO:0010207 "photosystem II assembly" evidence=RCA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	286
pfam11152	195	pfam11152, DUF2930, Protein of unknown function (D	6e-56

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

 Score =  178 bits (454), Expect = 6e-56
 Identities = 66/217 (30%), Positives = 105/217 (48%), Gaps = 23/217 (10%)

Query: 62  LPRWIGYGFGSLIVLNHFAFSNSVTSAQLRSEVLGLSLAAFSVTLPYLGKFLKGASPVSQ 121
           LP   G   G L++LN    +  +T +Q R++VLGL LAA  + +  L    +  SP   
Sbjct: 1   LPLIAGLLGGLLLLLNRL-STADITPSQSRADVLGLLLAAGLILVGLLWTRAQPRSP-EA 58

Query: 122 KSLPESGEQIFVMSQNISDALKENLAWATYVLLRNTNSISVLISIRGELCVR-GYWQTPD 180
             L   GEQ F +S ++S+ALKE LAWA+++LL  T + SVL+   G++ +R G    P 
Sbjct: 59  VDLE--GEQGFELSPDLSEALKEELAWASHLLLTATPAASVLVYWDGQVLLRRGILGPPV 116

Query: 181 GASKTQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPS 240
              K +  E  +R +E   L  L +   +P   +   ++ LP  T +V VQP+       
Sbjct: 117 ---KFEPGEICKRALETQQLVYLVNLKLYPGRIE---FDYLPPNTQAVIVQPLGN----- 165

Query: 241 AVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFR 277
                   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	286
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_	95.25
PF13492	129	GAF_3: GAF domain; PDB: 3EEA_A 4DMZ_A 4DN0_A 1VHM_	94.96
PRK11061	748	fused phosphoenolpyruvate-protein phosphotransfera	92.61
smart00065	149	GAF Domain present in phytochromes and cGMP-specif	91.99
PF01590	154	GAF: GAF domain; InterPro: IPR003018 This domain i	90.33
TIGR02851	180	spore_V_T stage V sporulation protein T. Members o	89.43
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	85.2
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	82.6

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

Probab=100.00  E-value=2e-73  Score=506.90  Aligned_cols=194  Identities=37%  Similarity=0.544  Sum_probs=185.2

Q ss_pred             hhHHHHHHHHHHHHhhhhccCCCCChhhHHHHHHHHHHHHhhhhhhhhhhhhcccCCCCCCCCCCCCeeceEeccCchHH
Q 023161           62 LPRWIGYGFGSLIVLNHFAFSNSVTSAQLRSEVLGLSLAAFSVTLPYLGKFLKGASPVSQKSLPESGEQIFVMSQNISDA  141 (286)
Q Consensus        62 LP~~vG~l~g~Lll~N~~~s~a~~t~aQ~RsevLg~~Laa~~v~L~l~G~~w~~~~P~~~~~v~l~geq~F~l~~~Lsd~  141 (286)
                      ||+++|+++++++++||++++ .+||||+||||||++||+++   +++|++|++++|++++.+++.|+|+|+|++||||+
T Consensus         1 LPl~vG~l~~~lll~N~~~~~-~~t~sq~RaevLg~~ls~~l---iL~g~lw~~l~p~~~~~v~L~G~~~f~l~~~L~~~   76 (195)
T PF11152_consen    1 LPLIVGLLGGSLLLLNRLSGA-DATPSQSRAEVLGLILSAVL---ILTGLLWQRLKPRSPEAVDLPGEQGFELSPDLSDA   76 (195)
T ss_pred             CceEehHHHHHHHHhhhcccC-CCCHHHHHHHHHHHHHHHHH---HHHHHHHhhccCCCCCccCCCCccceEECCCCCHH
Confidence            799999999999999997776 68999999999999999555   89999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhhccccEEEEEECCEEE-EeeeecCCCCCChHHHHHHHHHhhhhcccccCCCcccccCCcccccccc
Q 023161          142 LKENLAWATYVLLRNTNSISVLISIRGELC-VRGYWQTPDGASKTQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEM  220 (286)
Q Consensus       142 ~k~ELAWaS~~LLtnT~a~svlV~~~g~ll-~RG~~~~p~~~~~g~I~~~~~~~~~~~~Lv~L~~t~lyPgr~E~~~~~~  220 (286)
                      +|+|||||||+|||||+|+||+|||||++| +||++++++++++|+||++++++++.+||+|+   .|||||+|   |+|
T Consensus        77 ~k~ELAWas~~LLt~T~a~svlV~~~g~~llrrG~~~~~~~~~~g~i~~~~~~~~~~~yL~nl---~lyPGr~E---f~~  150 (195)
T PF11152_consen   77 AKEELAWASYALLTNTNARSVLVYYDGRVLLRRGILGSPSKFKPGPICQRAMESGKLIYLVNL---KLYPGRVE---FDY  150 (195)
T ss_pred             HHHHHHHHHHHHHhhCCceEEEEEECCEEEEEeeccCCCCCcchHHHHHHHHhcCCceecccc---ccCCCchh---hhh
Confidence            999999999999999999999999999966 58999888999999999999999888888877   89999999   899


Q ss_pred             CCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHHhhhc
Q 023161          221 LPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFR  277 (286)
Q Consensus       221 LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kDe~WI~~iA~KL~  277 (286)
                      ||+|||||||||+|+            +||||+|||++||||+|||+||++|||||+
T Consensus       151 lP~ntq~VlvqP~g~------------~G~lvlgs~~~R~ft~~D~~Wi~~iA~Kl~  195 (195)
T PF11152_consen  151 LPENTQSVLVQPLGQ------------NGVLVLGSNSPRAFTKSDEAWIAGIADKLR  195 (195)
T ss_pred             cCCCCcEEEEEEcCC------------CeEEEEeeCCccccCHHHHHHHHHHHHhcC
Confidence            999999999999999            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=95.25  E-value=0.027  Score=44.32  Aligned_cols=54  Identities=19%  Similarity=0.234  Sum_probs=41.8

Q ss_pred             ccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHHhhhcccc
Q 023161          219 EMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGKS  280 (286)
Q Consensus       219 ~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kDe~WI~~iA~KL~~~~  280 (286)
                      .+.=.|.+++++.||..+        .+.=|+|.+.+..++.||+.|+.+++.+|+-+..++
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=94.96  E-value=0.093  Score=40.28  Aligned_cols=108  Identities=17%  Similarity=0.211  Sum_probs=67.6

Q ss_pred             HHHhhhccccEEEEE--ECC-E-E-EEeeeecCCC---C-CChHHHHHHHHHhhhhcccccCCCcccccCCccccccccC
Q 023161          151 YVLLRNTNSISVLIS--IRG-E-L-CVRGYWQTPD---G-ASKTQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEML  221 (286)
Q Consensus       151 ~~LLtnT~a~svlV~--~~g-~-l-l~RG~~~~p~---~-~~~g~I~~~~~~~~~~~~Lv~L~~t~lyPgr~E~~~~~~L  221 (286)
                      +.+...+.+..+.||  .++ . + +..++-+.+.   . .....++.++.++.+..+         .|+-.+..+    
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            445566666666554  434 2 2 2366511111   1 145567677777665432         233222111    


Q ss_pred             CCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHHhhhcccc
Q 023161          222 PKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGKS  280 (286)
Q Consensus       222 P~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kDe~WI~~iA~KL~~~~  280 (286)
                       .+.+++++.||..+        .+.-|+|.+++..++.||++|+..++.+|+-+..++
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        356899999999999999999999999999876554

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

Probab=92.61  E-value=1.1  Score=47.79  Aligned_cols=128  Identities=11%  Similarity=0.172  Sum_probs=79.7

Q ss_pred             CchHHHHHHHHHHHHHHhhhccccEEEEEECCE--EEEeeeecC------CCCCC-hHHHHHHHHHhhhhcccccCCCcc
Q 023161          137 NISDALKENLAWATYVLLRNTNSISVLISIRGE--LCVRGYWQT------PDGAS-KTQLLEWFERQIENIGLSDLKDSL  207 (286)
Q Consensus       137 ~Lsd~~k~ELAWaS~~LLtnT~a~svlV~~~g~--ll~RG~~~~------p~~~~-~g~I~~~~~~~~~~~~Lv~L~~t~  207 (286)
                      ++.+.+..=+..+...+  +...+++.+++.+.  +..+...+.      +-.+. ..-++.++.++.+.....|.....
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  222322221      11122 233678888888888887775433


Q ss_pred             cccCCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHHhhhccc
Q 023161          208 YFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGK  279 (286)
Q Consensus       208 lyPgr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kDe~WI~~iA~KL~~~  279 (286)
                      .|..+.+     ..-+++.|+++.||-..        .+.=|+|-+....+|.||+.|+.++..+|.-+..+
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            3322222     12467999999999752        24579999999999999999999999999877544

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

Probab=91.99  E-value=0.48  Score=34.94  Aligned_cols=49  Identities=16%  Similarity=0.350  Sum_probs=40.8

Q ss_pred             CCceeEEEeccCCCCCCcccccccceEEEEeeC-CccccchhhHHHHHHHHhhhcccc
Q 023161          224 GTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASS-MTYAYSHKDRAWIKAVSNKFRGKS  280 (286)
Q Consensus       224 ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~-s~RafT~kDe~WI~~iA~KL~~~~  280 (286)
                      +..+.++.||..+        .+.-|++.+... .+|.|+..|+..++.+|+.+..+.
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.

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

Probab=90.33  E-value=0.39  Score=37.91  Aligned_cols=83  Identities=18%  Similarity=0.189  Sum_probs=55.5

Q ss_pred             HHHHHHHHHhhhhcccccCCCcccccCCcccc-ccccC------------CCCCceeEEEeccCCCCCCcccccccceEE
Q 023161          185 TQLLEWFERQIENIGLSDLKDSLYFPQSADAG-QWEML------------PKGTCSVFVQPVIQAPNPSAVEVEKIEGFV  251 (286)
Q Consensus       185 g~I~~~~~~~~~~~~Lv~L~~t~lyPgr~E~~-~~~~L------------P~ntqsVlvQPig~~~~~~~~~~~~~~Gvl  251 (286)
                      ..++..+.+..+...+.+.   .-.|-..+.. .-..+            ..+..++++-||..        ..+.-|+|
T Consensus        56 ~~~~~~~~~~~~~~~i~d~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~l~vPi~~--------~g~~~G~l  124 (154)
T PF01590_consen   56 ESICGQVLQSREPIVISDV---AADPRFAPQIAAQSALRALSSAERPFLAEYGVRSYLCVPIIS--------GGRLIGVL  124 (154)
T ss_dssp             SSHHHHHHHHTSCEEESSS---GGSTTSSCHHHHHHTTBTTTHHHHHHHHTTTESEEEEEEEEE--------TTEEEEEE
T ss_pred             ccHHHHHHhCCCeEeeccc---cccccccccccccccccccccccccccccccCceeeEeeeec--------ccCcEEEE
Confidence            3456666777666665555   3333322100 00112            56999999999865        23457999


Q ss_pred             EEeeCCc-cccchhhHHHHHHHHhhhcc
Q 023161          252 LLASSMT-YAYSHKDRAWIKAVSNKFRG  278 (286)
Q Consensus       252 vlgs~s~-RafT~kDe~WI~~iA~KL~~  278 (286)
                      .+....+ |.||+.|+..++.+|+.+..
T Consensus       125 ~l~~~~~~~~~~~~d~~ll~~~a~~~a~  152 (154)
T PF01590_consen  125 SLYRTRPGRPFTEEDLALLESFAQQLAI  152 (154)
T ss_dssp             EEEEESSSSS--HHHHHHHHHHHHHHHH
T ss_pred             EEEECCCCCCcCHHHHHHHHHHHHHHHh
Confidence            9999999 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=89.43  E-value=4.1  Score=36.38  Aligned_cols=148  Identities=11%  Similarity=0.019  Sum_probs=86.5

Q ss_pred             hcccCCCCCCCCCCCCe-eceEeccCchHHHHHHHHHHHHHHhhhccccEEEEEECCEEEE-eeeecCCCCCChHHHHHH
Q 023161          113 LKGASPVSQKSLPESGE-QIFVMSQNISDALKENLAWATYVLLRNTNSISVLISIRGELCV-RGYWQTPDGASKTQLLEW  190 (286)
Q Consensus       113 w~~~~P~~~~~v~l~ge-q~F~l~~~Lsd~~k~ELAWaS~~LLtnT~a~svlV~~~g~ll~-RG~~~~p~~~~~g~I~~~  190 (286)
                      =.+++++++..+...++ ++..-.-+.-....+...=....|...|.+ +|.|-...++++ -|.-..  ...++++-+.
T Consensus        24 ~l~i~~gd~~~~~~~~~~~iil~k~~~~~~~~~~A~~~aeII~~~t~~-aVaITDr~~ILA~~G~g~d--~~~~~~is~~  100 (180)
T TIGR02851        24 TLRIREGDPLEIFTDREGEVILKKYSPIGELGDFAKEYAESLYQSLGH-IVLITDRDTVIAVAGVSKK--EYLNKPISDE  100 (180)
T ss_pred             HcCCCCCCeEEEEEeCCCEEEEEECCcccchHHHHHHHHHHHHHHhCC-EEEEECCCcEEEEECCChh--hcCCCccCHH
Confidence            34677777766643332 222222222233444555567899999999 999999999887 886631  1111122222


Q ss_pred             HHHhhhhccc--ccCCCcccccCCccccccccCCCC--CceeEEEeccCCCCCCcccccccceEEEEeeCCcc--ccchh
Q 023161          191 FERQIENIGL--SDLKDSLYFPQSADAGQWEMLPKG--TCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTY--AYSHK  264 (286)
Q Consensus       191 ~~~~~~~~~L--v~L~~t~lyPgr~E~~~~~~LP~n--tqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~R--afT~k  264 (286)
                      ..+.++....  ++-.+..+||=..        -++  ..+.+|.||-.+        .++-|.|.+- ...+  .+|+.
T Consensus       101 t~~~i~~gk~~~~~~~~~~~i~c~~--------~~~~~l~s~ii~Pl~~~--------g~viGtLkly-~k~~~~~~~~~  163 (180)
T TIGR02851       101 LEDTMEERKTVILSDTKDGPIEIID--------GQEFEYTSQVIAPIIAE--------GDPIGAVIIF-SKEPGEKLGEV  163 (180)
T ss_pred             HHHHHHcCCEEEecCCccceecccc--------CCCCCcceEEEEEEEEC--------CeEEEEEEEE-ECCccCCCCHH
Confidence            3333333222  1111111122110        122  579999999763        2346877777 6666  99999


Q ss_pred             hHHHHHHHHhhhcccc
Q 023161          265 DRAWIKAVSNKFRGKS  280 (286)
Q Consensus       265 De~WI~~iA~KL~~~~  280 (286)
                      ++.+..++|+=|...+
T Consensus       164 e~~la~glA~lLS~QL  179 (180)
T TIGR02851       164 EQKAAETAAAFLGKQM  179 (180)
T ss_pred             HHHHHHHHHHHHHHhh
Confidence            9999999999876543

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=85.20  E-value=5.4  Score=41.72  Aligned_cols=85  Identities=11%  Similarity=0.198  Sum_probs=60.2

Q ss_pred             hHHHHHHHHHhhhhcccccCCC-ccccc-CCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCcccc
Q 023161          184 KTQLLEWFERQIENIGLSDLKD-SLYFP-QSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAY  261 (286)
Q Consensus       184 ~g~I~~~~~~~~~~~~Lv~L~~-t~lyP-gr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~Raf  261 (286)
                      .+.+..++.+..++..+ +..+ ..+.+ ++..   .+....++.++++.||...        .++-|||.+++...+.|
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 1112   3445678999999999762        34579999998889999


Q ss_pred             chhhHHHHHHHHhhhcccc
Q 023161          262 SHKDRAWIKAVSNKFRGKS  280 (286)
Q Consensus       262 T~kDe~WI~~iA~KL~~~~  280 (286)
                      +++|..-++.+|+....+.
T Consensus       323 ~~~dl~lL~~iA~~~A~Ai  341 (686)
T PRK15429        323 TTTNLKLLRQIAERVAIAV  341 (686)
T ss_pred             CHHHHHHHHHHHHHHHHHH
Confidence            9999999999999877654

>TIGR01817 nifA Nif-specific regulatory protein

Probab=82.60  E-value=12  Score=37.85  Aligned_cols=82  Identities=9%  Similarity=0.129  Sum_probs=56.9

Q ss_pred             HHHHHHHHHhhhhcccccCCCcccccCCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCC-ccccch
Q 023161          185 TQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSM-TYAYSH  263 (286)
Q Consensus       185 g~I~~~~~~~~~~~~Lv~L~~t~lyPgr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s-~RafT~  263 (286)
                      ..++.++.+..++.-+.|..+..-|-.+.     .....+++|++|.||..+        .+.=|+|.+.+.. ++.||+
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             hhHHHHHHHHhhhccc
Q 023161          264 KDRAWIKAVSNKFRGK  279 (286)
Q Consensus       264 kDe~WI~~iA~KL~~~  279 (286)
                      .|...+..+|+.+..+
T Consensus       140 ~d~~lL~~lA~~ia~a  155 (534)
T TIGR01817       140 EEVRFLEMVANLIGQT  155 (534)
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            9999999999987654

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	286
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-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 = 45.2 bits (106), Expect = 2e-05
 Identities = 40/224 (17%), Positives = 77/224 (34%), Gaps = 62/224 (27%)

Query: 28  SICARLDNSQQEEQQLNL--SVLRFTFGIPGFDESYLPRWIGYGFGSLIVLNHF------ 79
           +  +R D+S   + +++   + LR         + Y           L+VL +       
Sbjct: 212 NWTSRSDHSSNIKLRIHSIQAELRRLL----KSKPY-EN-------CLLVLLNVQNAKAW 259

Query: 80  -AFSNS----VTSAQLRSEVLGLSLAAFSVTLPYLGKFLKGASPVSQKSLPESGEQIF-- 132
            AF+ S    +T+   R + +   L+A + T   L       +P       E  + +   
Sbjct: 260 NAFNLSCKILLTT---RFKQVTDFLSAATTTHISLDHHSMTLTP------DEV-KSLLLK 309

Query: 133 VMSQNISDALKENLAWATYVLLRNTNSISVLI--SIRGELCVRGYWQTPDGASKTQLLEW 190
            +     D L         VL  N   +S +I  SIR  L     W+  +    T ++E 
Sbjct: 310 YLDCRPQD-LPRE------VLTTNPRRLS-IIAESIRDGLATWDNWKHVNCDKLTTIIES 361

Query: 191 FERQIENIGLSDLKDSLY-----FPQSADAGQWEMLPKGTCSVF 229
               +  +  ++ +  ++     FP SA       +P    S+ 
Sbjct: 362 S---LNVLEPAEYRK-MFDRLSVFPPSAH------IPTILLSLI 395

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	286
3rfb_A	171	Putative uncharacterized protein; FRMSR, GAF, oxid	97.04
3mmh_A	167	FRMSR, methionine-R-sulfoxide reductase; oxidoredu	97.01
3p01_A	184	Two-component response regulator; PSI-2, midwest c	96.75
3ksh_A	160	Putative uncharacterized protein; FRMSR, free-Met-	96.67
3e0y_A	181	Conserved domain protein; APC87688.2, geobacter su	96.53
1f5m_A	180	GAF; CGMP binding, signaling protein; 1.90A {Sacch	96.36
1vhm_A	195	Protein YEBR; structural genomics, unknown functio	96.31
3trc_A	171	Phosphoenolpyruvate-protein phosphotransferase; si	96.31
3o5y_A	165	Sensor protein; GAF domain, histidine, kinase, PSI	96.04
3ci6_A	171	Phosphoenolpyruvate-protein phosphotransferase; PE	96.02
3oov_A	169	Methyl-accepting chemotaxis protein, putative; str	95.61
2w3g_A	153	DOSS, two component sensor histidine kinase DEVS (	95.4
2e4s_A	189	CAMP and CAMP-inhibited CGMP 3',5'-cyclic phosphod	95.35
3hcy_A	151	Putative two-component sensor histidine kinase PR;	95.3
2zmf_A	189	CAMP and CAMP-inhibited CGMP 3',5'-cyclic phospho	95.2
3dba_A	180	CONE CGMP-specific 3',5'-cyclic phosphodiesterase	95.03
2vjw_A	149	GAF-B, GAF family protein; histidine kinase, hypox	94.58
2qyb_A	181	Membrane protein, putative; GAF domain, domain of	94.41
3k2n_A	177	Sigma-54-dependent transcriptional regulator; PSI-	94.36
2lb5_A	208	Sensor histidine kinase; PCB, transferase, GAF dom	92.64
2k2n_A	172	Sensor protein, SYB-CPH1(GAF); phytochrome, GAF do	92.06
3ibj_A	691	CGMP-dependent 3',5'-cyclic phosphodiesterase; PDE	91.79
1ykd_A	398	Adenylate cyclase; GAF domain, bound cyclic AMP li	91.31
1mc0_A	368	3',5'-cyclic nucleotide phosphodiesterase 2A; GAF	90.38
4glq_A	171	Methyl-accepting chemotaxis protein; chromophore,	90.28
1ykd_A	398	Adenylate cyclase; GAF domain, bound cyclic AMP li	85.93

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

Probab=97.04  E-value=0.0095  Score=51.14  Aligned_cols=110  Identities=16%  Similarity=0.156  Sum_probs=79.6

Q ss_pred             hccccEEEEEECCEEEEeeeecCCCC--CCh-HHHHHHHHHhhhhcccccCCCcccccCCccccccccCCCCCceeEEEe
Q 023161          156 NTNSISVLISIRGELCVRGYWQTPDG--ASK-TQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQP  232 (286)
Q Consensus       156 nT~a~svlV~~~g~ll~RG~~~~p~~--~~~-g~I~~~~~~~~~~~~Lv~L~~t~lyPgr~E~~~~~~LP~ntqsVlvQP  232 (286)
                      ..+.+++-++.++++.+..+-+.++.  +.. .-||-++.++.+..-.-|.   .-+|+...   .+   ..++|.||.|
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 3477888888888877666   55676543   12   4689999999


Q ss_pred             ccCCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHHhhhccccce
Q 023161          233 VIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGKSIW  282 (286)
Q Consensus       233 ig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kDe~WI~~iA~KL~~~~~~  282 (286)
                      |-.+        .+.=|||-+.+..++.|++.|+.+++.+|+-+..+..|
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=97.01  E-value=0.0093  Score=50.37  Aligned_cols=128  Identities=9%  Similarity=0.016  Sum_probs=84.8

Q ss_pred             cCchHHHHHHHHHHHHHHhhhccccEEEEEE--CCEEEEeeeecCCCC--CCh-HHHHHHHHHhhhhcccccCCCccccc
Q 023161          136 QNISDALKENLAWATYVLLRNTNSISVLISI--RGELCVRGYWQTPDG--ASK-TQLLEWFERQIENIGLSDLKDSLYFP  210 (286)
Q Consensus       136 ~~Lsd~~k~ELAWaS~~LLtnT~a~svlV~~--~g~ll~RG~~~~p~~--~~~-g~I~~~~~~~~~~~~Lv~L~~t~lyP  210 (286)
                      .|+.+.+.+=++-..+.+  ..+.+++.++.  ++++..+-+-+.+..  +.. .-+|-++.++.+..-.-|.   .-+|
T Consensus        30 ~dl~~~L~~v~~~l~~~l--~~~~~~iyL~d~~~~~L~l~a~~G~~~~~~i~~geGi~G~v~~~g~~~~v~Dv---~~~p  104 (167)
T 3mmh_A           30 TDWVANLANTAAVLKEAF--GWFWVGFYLVDTRSDELVLAPFQGPLACTRIPFGRGVCGQAWAKGGTVVVGDV---DAHP  104 (167)
T ss_dssp             CCHHHHHHHHHHHHHHHH--CCSEEEEEEEETTTTEEEEEEEESSCCCSEEETTSHHHHHHHHHTSCEEESCG---GGST
T ss_pred             CCHHHHHHHHHHHHHHHc--CCcEEEEEEEECCCCEEEEEEecccccceEeccCCChHHHHHhCCcEEEECCc---ccCc
Confidence            345455554444444444  35566666663  345554433333332  222 2477888888888876666   4556


Q ss_pred             CCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHHhhhccccce
Q 023161          211 QSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGKSIW  282 (286)
Q Consensus       211 gr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kDe~WI~~iA~KL~~~~~~  282 (286)
                      +...   .   -.+++|.+|.||-.+        .+.=|||-+.+..++.||+.|+..++.+|+-+.....|
T Consensus       105 ~~~~---~---~~~~~S~i~vPi~~~--------g~viGVL~i~s~~~~~F~~~d~~~L~~lA~~la~~i~~  162 (167)
T 3mmh_A          105 DHIA---C---SSLSRSEIVVPLFSD--------GRCIGVLDADSEHLAQFDETDALYLGELAKILEKRFEA  162 (167)
T ss_dssp             TCCC---S---STTCCEEEEEEEEET--------TEEEEEEEEEESSTTCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             chhh---c---CccCCeEEEEEeccC--------CEEEEEEEEecCCCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence            5433   1   257999999999652        24579999999999999999999999999988766544

>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=0.0088  Score=48.35  Aligned_cols=109  Identities=9%  Similarity=0.045  Sum_probs=72.0

Q ss_pred             cEEEEEECCEEEE-eeeecCCC----CCChHHHHHHHHHhhhhcccccCCCcccccCCccccccccCCCCCceeEEEecc
Q 023161          160 ISVLISIRGELCV-RGYWQTPD----GASKTQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVI  234 (286)
Q Consensus       160 ~svlV~~~g~ll~-RG~~~~p~----~~~~g~I~~~~~~~~~~~~Lv~L~~t~lyPgr~E~~~~~~LP~ntqsVlvQPig  234 (286)
                      +++..+.+|++.. .+.+..++    .+....++.++.+..+....-|..+..-|+.+.     .+-..+.+|+++.||-
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            3444456776543 44232221    123467888888888877665653333333211     1223488999999996


Q ss_pred             CCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHHhhhccccc
Q 023161          235 QAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGKSI  281 (286)
Q Consensus       235 ~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kDe~WI~~iA~KL~~~~~  281 (286)
                      .+        .+.-|+|.+.+..+|.||+.|...++.+|+.+..+.+
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=96.67  E-value=0.028  Score=47.57  Aligned_cols=125  Identities=14%  Similarity=0.180  Sum_probs=83.9

Q ss_pred             CchHHHHHHHHHHHHHHhhhccccEEEEEECCEEEEeeeecCCCC--CCh-HHHHHHHHHhhhhcccccCCCcccccCCc
Q 023161          137 NISDALKENLAWATYVLLRNTNSISVLISIRGELCVRGYWQTPDG--ASK-TQLLEWFERQIENIGLSDLKDSLYFPQSA  213 (286)
Q Consensus       137 ~Lsd~~k~ELAWaS~~LLtnT~a~svlV~~~g~ll~RG~~~~p~~--~~~-g~I~~~~~~~~~~~~Lv~L~~t~lyPgr~  213 (286)
                      |+.+.+.+=.+-..+.+ ...+.+++-++.++++.+..+-+.++.  +.. .-+|-++.++.+..-.-|.   .-+|+..
T Consensus        31 dl~~~L~~v~~ll~~~l-~~~~~~gfYL~~~~~L~l~~~~G~~a~~ri~~GeGv~G~aa~~~~~i~V~Dv---~~~p~~i  106 (160)
T 3ksh_A           31 HMIAILSNMSALLNDNL-DQINWVGFYLLEQNELILGPFQGHPACVHIPIGKGVCGTAVSERRTQVVADV---HQFKGHI  106 (160)
T ss_dssp             CHHHHHHHHHHHHHHHC-SSCSEEEEEEEETTEEEEEEEEESCCCSEEETTSHHHHHHHHHTSCEEESCG---GGSTTCC
T ss_pred             CHHHHHHHHHHHHHHHc-ccCCEEEEEEEECCEEEEEeccCCcccEEeeCCCCHHHHHHhhCCEEEECCc---ccCcccc
Confidence            44444444333333333 235677877778888554333333332  222 3477888888888877666   5677654


Q ss_pred             cccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHHhhhccc
Q 023161          214 DAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGK  279 (286)
Q Consensus       214 E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kDe~WI~~iA~KL~~~  279 (286)
                      .   .+   ..++|.+|.||-.+        .+.=|||-+.+..++.|++.|+.+++.+|+-+...
T Consensus       107 ~---~~---~~~~Sei~VPI~~~--------g~viGVL~i~s~~~~~F~e~D~~~L~~lA~~la~~  158 (160)
T 3ksh_A          107 A---CD---ANSKSEIVVPIFKD--------DKIIGVLDIDAPITDRFDDNDKEHLEAIVKIIEKQ  158 (160)
T ss_dssp             G---GG---TTCSEEEEEEEEET--------TEEEEEEEEEESSSSCCCHHHHHHHHHHHHHHHHH
T ss_pred             c---cC---cccCceEEEEEEEC--------CEEEEEEEEecCCCCCCCHHHHHHHHHHHHHHHHH
Confidence            3   12   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=96.53  E-value=0.022  Score=44.18  Aligned_cols=82  Identities=11%  Similarity=0.156  Sum_probs=57.0

Q ss_pred             HHHHHHHHhhhhcccccCCCcccccCCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhh
Q 023161          186 QLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKD  265 (286)
Q Consensus       186 ~I~~~~~~~~~~~~Lv~L~~t~lyPgr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kD  265 (286)
                      .++.++.+..+....-+..+...|..+.+     ....+.+++++.||..+        .+.-|+|.+.+..++.||+.|
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            35677888887776655543222222111     12357899999999763        345799999999999999999


Q ss_pred             HHHHHHHHhhhcccc
Q 023161          266 RAWIKAVSNKFRGKS  280 (286)
Q Consensus       266 e~WI~~iA~KL~~~~  280 (286)
                      ...++.+|+.+..+.
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

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

Probab=96.36  E-value=0.055  Score=45.62  Aligned_cols=131  Identities=12%  Similarity=0.084  Sum_probs=82.3

Q ss_pred             CchHHHHHHHHHHHHHHh---hhccccEEEEEEC---CEEEEeeeecCCCCC--Ch-HHHHHHHHHhhhhcccccCCCcc
Q 023161          137 NISDALKENLAWATYVLL---RNTNSISVLISIR---GELCVRGYWQTPDGA--SK-TQLLEWFERQIENIGLSDLKDSL  207 (286)
Q Consensus       137 ~Lsd~~k~ELAWaS~~LL---tnT~a~svlV~~~---g~ll~RG~~~~p~~~--~~-g~I~~~~~~~~~~~~Lv~L~~t~  207 (286)
                      ++.+.+.+-++-..+.+-   ...+..++-++.+   +++....+.+.++..  .. .-+|-++.++.+..-.-|.   .
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             cccCCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHHhhhcccccee
Q 023161          208 YFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGKSIWI  283 (286)
Q Consensus       208 lyPgr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kDe~WI~~iA~KL~~~~~~~  283 (286)
                      -+|+..      -...++.|++|.||-.+       ..+.-|||-+.+..++.|++.|+..++.+|+-+..+..|+
T Consensus       118 ~dp~~~------~~~~~~~S~l~vPi~~~-------~g~viGVL~l~s~~~~~F~~~d~~~L~~la~~~a~~~~~~  180 (180)
T 1f5m_A          118 KYPGHI------ACDGETKSEIVVPIISN-------DGKTLGVIDIDCLDYEGFDHVDKEFLEKLAKLINKSCVFK  180 (180)
T ss_dssp             GSTTCC------CSSTTCCEEEEEEEECT-------TSCEEEEEEEEESSTTCCCHHHHHHHHHHHHHHHHHCBC-
T ss_pred             cCcccc------ccCcccceEEEEEEEcC-------CCeEEEEEEeccCCCCCcCHHHHHHHHHHHHHHHHhcCCC
Confidence            344433      23468999999999751       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=46.62  Aligned_cols=109  Identities=10%  Similarity=0.085  Sum_probs=75.0

Q ss_pred             hccccEEEEEECCEEEEeeeecCCCC--CCh-HHHHHHHHHhhhhcccccCCCcccccCCccccccccCCCCCceeEEEe
Q 023161          156 NTNSISVLISIRGELCVRGYWQTPDG--ASK-TQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQP  232 (286)
Q Consensus       156 nT~a~svlV~~~g~ll~RG~~~~p~~--~~~-g~I~~~~~~~~~~~~Lv~L~~t~lyPgr~E~~~~~~LP~ntqsVlvQP  232 (286)
                      ..+..++-++.++++.....-+.++.  +.. .-+|-++.++.+..-.-|+   .-+|+...   .   ..+++|.||.|
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 2377888888888766666   34565443   2   24789999999


Q ss_pred             ccCCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHHhhhccccc
Q 023161          233 VIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGKSI  281 (286)
Q Consensus       233 ig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kDe~WI~~iA~KL~~~~~  281 (286)
                      |-.+        .+.-|||-+.+..++.|++.|+..++.+|+-+..+.+
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        3457999999999999999999999999998876554

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

Probab=96.31  E-value=0.071  Score=41.01  Aligned_cols=83  Identities=11%  Similarity=0.213  Sum_probs=61.0

Q ss_pred             HHHHHHHHHhhhhcccccCCCcccccCCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccchh
Q 023161          185 TQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHK  264 (286)
Q Consensus       185 g~I~~~~~~~~~~~~Lv~L~~t~lyPgr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~k  264 (286)
                      ..++.++.+..+...+-+..+..-|....+     .-..+..++++.||-.+        .+.-|+|.+.+..++.||+.
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            357788888888776666543222322222     12368899999999762        34579999999999999999


Q ss_pred             hHHHHHHHHhhhcccc
Q 023161          265 DRAWIKAVSNKFRGKS  280 (286)
Q Consensus       265 De~WI~~iA~KL~~~~  280 (286)
                      |...++.+|+.+..+.
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            9999999999876654

>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=96.04  E-value=0.069  Score=44.15  Aligned_cols=110  Identities=16%  Similarity=0.166  Sum_probs=71.1

Q ss_pred             ccccEEEEEECCEEEEeeeecCCC-------CCCh-HHHHHHHHHhhhhcccccCCCcccccCC-ccccccccCCCCCce
Q 023161          157 TNSISVLISIRGELCVRGYWQTPD-------GASK-TQLLEWFERQIENIGLSDLKDSLYFPQS-ADAGQWEMLPKGTCS  227 (286)
Q Consensus       157 T~a~svlV~~~g~ll~RG~~~~p~-------~~~~-g~I~~~~~~~~~~~~Lv~L~~t~lyPgr-~E~~~~~~LP~ntqs  227 (286)
                      ....+++.+.+|++..+-..+...       .+.. +.++.++.++.+..- .+..+.   |.+ .+  -..+...+.+|
T Consensus        23 ~d~~~l~L~~~~~L~l~a~~~~~~~~~~~~~~ip~~~s~~~~v~~~~~~~v-~~~~~~---~~~~~~--~~~~~~~~~~S   96 (165)
T 3o5y_A           23 FDRISFLLLANETLKLSHVYPKGSHSLDIGSTIPKEQSLYWSALDQRQTIF-RSLTDT---QDNFYE--KQYLAILDLKS   96 (165)
T ss_dssp             CSEEEEEEEETTEEEEEEEESTTCCSSCTTCEECSTTCHHHHHHHHTSCEE-EESCCT---TCCCTT--HHHHHTTTCCE
T ss_pred             cceEEEEEEECCEEEEEEEecCCccccccccccCCccCHHHHHHHhCCeEE-EcCccc---cccccc--chHHHhhCCCE
Confidence            344566667788755433232211       1111 467788888887763 343211   111 00  00134578999


Q ss_pred             eEEEeccCCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHHhhhcccc
Q 023161          228 VFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGKS  280 (286)
Q Consensus       228 VlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kDe~WI~~iA~KL~~~~  280 (286)
                      ++|.||-.+        .+.-|+|.+++..++.||+.|..+++.+|+.+..+.
T Consensus        97 ~l~vPL~~~--------~~~iGvl~l~~~~~~~f~~~d~~~l~~la~~~aiai  141 (165)
T 3o5y_A           97 ILVIPIYSK--------NKRVGVLSIGRKQQIDWSLDDLAFLEQLTDHLAVSI  141 (165)
T ss_dssp             EEEEEEECS--------SCEEEEEEEEESSCCCCCHHHHHHHHHHHHHHHHHH
T ss_pred             EEEeCeeEC--------CEEEEEEEEEeCCCCCCCHHHHHHHHHHHHHHHHHH
Confidence            999999763        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=96.02  E-value=0.091  Score=39.71  Aligned_cols=82  Identities=13%  Similarity=0.203  Sum_probs=56.6

Q ss_pred             HHHHHHHHhhhhcccccCCCcccccCCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhh
Q 023161          186 QLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKD  265 (286)
Q Consensus       186 ~I~~~~~~~~~~~~Lv~L~~t~lyPgr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kD  265 (286)
                      .++.++.+..+....-+..+...|....+     +-..+..++++.||-.+        .+.-|+|.+++..++.||+.|
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 023161          266 RAWIKAVSNKFRGKS  280 (286)
Q Consensus       266 e~WI~~iA~KL~~~~  280 (286)
                      ...++.+|+.+..++
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=95.61  E-value=0.21  Score=38.20  Aligned_cols=122  Identities=12%  Similarity=0.045  Sum_probs=75.3

Q ss_pred             HHHHHhhhccccEEEEE-EC-C--EEEEeeeecCCC----C----CC-hHHHHHHHHHhhhhcccccCCCc-ccccCCcc
Q 023161          149 ATYVLLRNTNSISVLIS-IR-G--ELCVRGYWQTPD----G----AS-KTQLLEWFERQIENIGLSDLKDS-LYFPQSAD  214 (286)
Q Consensus       149 aS~~LLtnT~a~svlV~-~~-g--~ll~RG~~~~p~----~----~~-~g~I~~~~~~~~~~~~Lv~L~~t-~lyPgr~E  214 (286)
                      .-+.+...+.+....|+ ++ +  .+..+...+...    .    +. ...++.++.+..+....-+..+. .+++.+.+
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  343333333221    1    11 36788888888887766655321 12322221


Q ss_pred             ccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCc-cccchhhHHHHHHHHhhhcccc
Q 023161          215 AGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMT-YAYSHKDRAWIKAVSNKFRGKS  280 (286)
Q Consensus       215 ~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~-RafT~kDe~WI~~iA~KL~~~~  280 (286)
                        .-..-..+..++++.||-.+        .+.-|+|.+++..+ +.|++.|...++.+|+.+..+.
T Consensus       104 --~~~~~~~~~~s~l~vPl~~~--------~~~iGvl~~~~~~~~~~f~~~d~~~l~~~a~~~a~ai  160 (169)
T 3oov_A          104 --YDAIRALRSKSFVICPIVVK--------GEAIGVFAVDNRSSRRSLNDTDVDTIKLFADQASSAI  160 (169)
T ss_dssp             --GGGCGGGCCSSEEEEEEEET--------TEEEEEEEEECTTSSSCCCHHHHHHHHHHHHHHHHHH
T ss_pred             --HHHHHhcCcCcEEEEEEEeC--------CcEEEEEEEEccccCCCCCHHHHHHHHHHHHHHHHHH
Confidence              00123467899999999752        34579999998765 5699999999999999877654

>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=95.40  E-value=0.033  Score=41.95  Aligned_cols=81  Identities=11%  Similarity=0.072  Sum_probs=57.6

Q ss_pred             HHHHHHHHhhhhcccccCCCcccccCCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCc-cccchh
Q 023161          186 QLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMT-YAYSHK  264 (286)
Q Consensus       186 ~I~~~~~~~~~~~~Lv~L~~t~lyPgr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~-RafT~k  264 (286)
                      .++.++.+..+....-+..+...|.+..      ....+..++++.||-.+        .+.-|+|.+.+..+ |.||+.
T Consensus        62 ~~~~~~~~~~~~~~~~d~~~~~~~~~~~------~~~~~~~s~l~vPl~~~--------~~~~Gvl~l~~~~~~~~f~~~  127 (153)
T 2w3g_A           62 GVIGLLIEDPKPLRLDDVSAHPASIGFP------PYHPPMRTFLGVPVRVR--------DESFGTLYLTDKTNGQPFSDD  127 (153)
T ss_dssp             THHHHHHHSCSCEEESSGGGSTTCCCCC------TTCCCCCCEEEEEEEET--------TEEEEEEEEEEETTSCCCCHH
T ss_pred             CHHHHHHhcCCcEEecCcccCchhcCCC------CcCCCCCeEEEeeEEEC--------CEEEEEEEEeeCCCCCCCCHH
Confidence            4667777777766555543222222211      13468899999999652        23479999999888 899999


Q ss_pred             hHHHHHHHHhhhcccc
Q 023161          265 DRAWIKAVSNKFRGKS  280 (286)
Q Consensus       265 De~WI~~iA~KL~~~~  280 (286)
                      |...++.+|+-+..+.
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            9999999999886654

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

Probab=95.30  E-value=0.0061  Score=47.03  Aligned_cols=53  Identities=6%  Similarity=0.108  Sum_probs=44.2

Q ss_pred             CCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHHhhhccccc
Q 023161          221 LPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGKSI  281 (286)
Q Consensus       221 LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kDe~WI~~iA~KL~~~~~  281 (286)
                      ...|.+++++.||..+        .+.-|+|.+.+..+|.||+.|...++.+|+.+..+.+
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=95.20  E-value=0.018  Score=45.24  Aligned_cols=84  Identities=15%  Similarity=0.129  Sum_probs=56.4

Q ss_pred             HHHHHHHHHhhhhcccccCCCcccccCCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEE-eeCCccccch
Q 023161          185 TQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLL-ASSMTYAYSH  263 (286)
Q Consensus       185 g~I~~~~~~~~~~~~Lv~L~~t~lyPgr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvl-gs~s~RafT~  263 (286)
                      ..++.++.++.+...+-+..+...|+....    .....++++++|.|+..+        .+.-|+|.+ ....+|.||+
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            346778888887776555432222221111    223447889999998763        234688855 5677899999


Q ss_pred             hhHHHHHHHHhhhcccc
Q 023161          264 KDRAWIKAVSNKFRGKS  280 (286)
Q Consensus       264 kDe~WI~~iA~KL~~~~  280 (286)
                      .|...++.+|+.+..+.
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=95.03  E-value=0.024  Score=46.43  Aligned_cols=81  Identities=16%  Similarity=0.269  Sum_probs=57.2

Q ss_pred             HHHHHHHHHhhhhcccccCCCcccccCCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCcc-ccch
Q 023161          185 TQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTY-AYSH  263 (286)
Q Consensus       185 g~I~~~~~~~~~~~~Lv~L~~t~lyPgr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~R-afT~  263 (286)
                      .-|+.++.++++..-+-|..+..-|+...+    ...-..++|+||.||-.+        .+.=|||-+.+..+. .||+
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            357889999998877666643333332211    001135799999999762        345799999988775 9999


Q ss_pred             hhHHHHHHHHhhhc
Q 023161          264 KDRAWIKAVSNKFR  277 (286)
Q Consensus       264 kDe~WI~~iA~KL~  277 (286)
                      .|+..++.+|+-..
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=94.58  E-value=0.28  Score=39.27  Aligned_cols=72  Identities=8%  Similarity=0.068  Sum_probs=55.7

Q ss_pred             HHHHHHHHHhhhhcccccCCCcccccCCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeC-Cccccch
Q 023161          185 TQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASS-MTYAYSH  263 (286)
Q Consensus       185 g~I~~~~~~~~~~~~Lv~L~~t~lyPgr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~-s~RafT~  263 (286)
                      +.++.++.+++++.-+-|..        .+       | +..|+||.||..+        .+.-|+|.+... .++.||+
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            35778888888887665552        12       1 7899999999752        234799999998 8899999


Q ss_pred             hhHHHHHHHHhhhcccc
Q 023161          264 KDRAWIKAVSNKFRGKS  280 (286)
Q Consensus       264 kDe~WI~~iA~KL~~~~  280 (286)
                      .|..-++.+|+....++
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            99999999998765543

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

Probab=94.41  E-value=0.34  Score=38.09  Aligned_cols=82  Identities=10%  Similarity=0.017  Sum_probs=58.5

Q ss_pred             HHHHHHHHhhhhcccccCCCcccccCCcccccc-ccCCCCCceeEEEeccCCCCCCcccccc-cceEEEEee-CCccccc
Q 023161          186 QLLEWFERQIENIGLSDLKDSLYFPQSADAGQW-EMLPKGTCSVFVQPVIQAPNPSAVEVEK-IEGFVLLAS-SMTYAYS  262 (286)
Q Consensus       186 ~I~~~~~~~~~~~~Lv~L~~t~lyPgr~E~~~~-~~LP~ntqsVlvQPig~~~~~~~~~~~~-~~Gvlvlgs-~s~RafT  262 (286)
                      .++.++.++.+....-+.   ...|. ..  +. .+...|..++++.||..+        .+ .-|+|.+.+ ..++.||
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            477788888777665554   22232 11  00 122458999999999762        22 469999999 9999999


Q ss_pred             hhhHHHHHHHHhhhccccc
Q 023161          263 HKDRAWIKAVSNKFRGKSI  281 (286)
Q Consensus       263 ~kDe~WI~~iA~KL~~~~~  281 (286)
                      +.|...++.+|+-+..+++
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=94.36  E-value=0.043  Score=42.89  Aligned_cols=52  Identities=17%  Similarity=0.296  Sum_probs=44.7

Q ss_pred             CCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHHhhhcccc
Q 023161          221 LPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGKS  280 (286)
Q Consensus       221 LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kDe~WI~~iA~KL~~~~  280 (286)
                      ...|++++++.||-.+        .+.-|+|.+.+..++.||+.|...++.+|+.+..+.
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        255899999999999999999999999999877654

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

Probab=92.64  E-value=0.12  Score=42.47  Aligned_cols=51  Identities=14%  Similarity=0.296  Sum_probs=43.7

Q ss_pred             CCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHHhhhcccc
Q 023161          222 PKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGKS  280 (286)
Q Consensus       222 P~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kDe~WI~~iA~KL~~~~  280 (286)
                      ..|++|+|+.||-.+        .+.-|+|.+-...+|.||+.|...++.+|+-+..+.
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        344799999999999999999999999999887554

>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=92.06  E-value=0.17  Score=40.50  Aligned_cols=51  Identities=14%  Similarity=0.296  Sum_probs=43.7

Q ss_pred             CCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHHhhhcccc
Q 023161          222 PKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGKS  280 (286)
Q Consensus       222 P~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kDe~WI~~iA~KL~~~~  280 (286)
                      ..|++|+|+.||-.+        .+.-|+|.+-...+|.||+.|...++.+|+-+..+.
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        234799999999999999999999999999876553

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

Probab=91.79  E-value=1.3  Score=43.95  Aligned_cols=85  Identities=13%  Similarity=0.086  Sum_probs=57.7

Q ss_pred             HHHHHHHHHhhhhcccccCCCcccccCCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCcc-ccch
Q 023161          185 TQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTY-AYSH  263 (286)
Q Consensus       185 g~I~~~~~~~~~~~~Lv~L~~t~lyPgr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~R-afT~  263 (286)
                      ..++.++.++++....-+..+...|+...+    ...-.++++++|.||..+       ..+.-|||.+....++ .||+
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            457788889888876666543322322221    112245789999999762       1234699999988776 7999


Q ss_pred             hhHHHHHHHHhhhcccc
Q 023161          264 KDRAWIKAVSNKFRGKS  280 (286)
Q Consensus       264 kDe~WI~~iA~KL~~~~  280 (286)
                      .|+.-++.+|+.+..+.
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=91.31  E-value=0.35  Score=43.51  Aligned_cols=132  Identities=12%  Similarity=0.052  Sum_probs=75.1

Q ss_pred             CchHHHHHHHHHHHHHHhhhccccEEEEE--EC--CEEEE---eeeecCCCCC---ChHHHHHHHHHhhhhcccccCCCc
Q 023161          137 NISDALKENLAWATYVLLRNTNSISVLIS--IR--GELCV---RGYWQTPDGA---SKTQLLEWFERQIENIGLSDLKDS  206 (286)
Q Consensus       137 ~Lsd~~k~ELAWaS~~LLtnT~a~svlV~--~~--g~ll~---RG~~~~p~~~---~~g~I~~~~~~~~~~~~Lv~L~~t  206 (286)
                      ++.....+=|.-....+...+.+....||  ..  +++..   .|.-.....+   ....++.++.+..+...+-|....
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   113467788888777665554221


Q ss_pred             ---ccccCCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeC---------------CccccchhhHHH
Q 023161          207 ---LYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASS---------------MTYAYSHKDRAW  268 (286)
Q Consensus       207 ---~lyPgr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~---------------s~RafT~kDe~W  268 (286)
                         ..|+...+    .....+++++++.||-..       ..+.-|+|.+...               .++.||+.|+.-
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               11111111    011246899999999641       1234799999887               789999999999


Q ss_pred             HHHHHhhhccc
Q 023161          269 IKAVSNKFRGK  279 (286)
Q Consensus       269 I~~iA~KL~~~  279 (286)
                      ++.+|+.+..+
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=42.63  Aligned_cols=85  Identities=13%  Similarity=0.086  Sum_probs=57.5

Q ss_pred             HHHHHHHHHhhhhcccccCCCcccccCCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCcc-ccch
Q 023161          185 TQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTY-AYSH  263 (286)
Q Consensus       185 g~I~~~~~~~~~~~~Lv~L~~t~lyPgr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~R-afT~  263 (286)
                      ..++.++.++.+....-+..+...|+...+    ....-.++++++.||...       ..+.-|+|.+.+..++ .||+
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            347788888887766655533333332211    001113699999999751       1344799999998886 8999


Q ss_pred             hhHHHHHHHHhhhcccc
Q 023161          264 KDRAWIKAVSNKFRGKS  280 (286)
Q Consensus       264 kDe~WI~~iA~KL~~~~  280 (286)
                      .|...++.+|+-+..++
T Consensus       319 ~d~~ll~~la~~~a~ai  335 (368)
T 1mc0_A          319 FDEDLATAFSIYCGISI  335 (368)
T ss_dssp             HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            99999999998876554

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

Probab=90.28  E-value=1.2  Score=36.81  Aligned_cols=125  Identities=9%  Similarity=0.018  Sum_probs=75.1

Q ss_pred             HHHHHHHHHHHhhhccccEEEEE-----ECCEEEEeeeec-CCC----CCChHHH---HHHHHHhhhhcccccCCCcccc
Q 023161          143 KENLAWATYVLLRNTNSISVLIS-----IRGELCVRGYWQ-TPD----GASKTQL---LEWFERQIENIGLSDLKDSLYF  209 (286)
Q Consensus       143 k~ELAWaS~~LLtnT~a~svlV~-----~~g~ll~RG~~~-~p~----~~~~g~I---~~~~~~~~~~~~Lv~L~~t~ly  209 (286)
                      .+=|.-+...+...+.+.-++||     +.|++++-..-. -++    .+....+   .....++.+.....|.    +.
T Consensus        13 ~~il~~~v~~v~~~l~~DRv~Iy~f~~d~~g~vvaE~~~~~~~s~lg~~~~~~~~~~~~~~~~~~g~~~~I~Dv----~~   88 (171)
T 4glq_A           13 QAIFETLVAKGRELLACDRVIVYAFDDNYVGTVVAESVAEGWPQARDQVIEDPCFREHWVEAYRQGRIQATTDI----FK   88 (171)
T ss_dssp             HHHHHHHHHHHHHHHTCSEEEEEEECTTCCEEEEEEEECTTSCCCTTCEECCTHHHHHTHHHHHTTCCEEESCG----GG
T ss_pred             HHHHHHHHHHHHHHHCCCeEEEEEEeCCCCeEEEEEEcCCCCccccCCccCccccHHHHHHHHHcCCEEEEcCc----Cc
Confidence            33445567778888888888887     235666532211 011    1111111   1223333333333333    33


Q ss_pred             cCCccccccc-cCCCCCceeEEEeccCCCCCCcccccccceEEEEee-CCccccchhhHHHHHHHHhhhcccc
Q 023161          210 PQSADAGQWE-MLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLAS-SMTYAYSHKDRAWIKAVSNKFRGKS  280 (286)
Q Consensus       210 Pgr~E~~~~~-~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs-~s~RafT~kDe~WI~~iA~KL~~~~  280 (286)
                      ++..+.. -+ +-.-|.+|.|+.||..+        .+.-|+|.+-. ..+|.|++.|..+++.+|+.+..+.
T Consensus        89 ~~~~~~~-~~~l~~~~v~S~L~vPi~~~--------~~l~GlL~~~~~~~~r~w~~~ei~ll~~lA~ql~iAi  152 (171)
T 4glq_A           89 AGLTECH-LNQLRPLKVRANLVVPMVID--------DQLFGLLIAHQASEPRQWQEIEIDQFSELASTGSLVL  152 (171)
T ss_dssp             TTCCHHH-HHHHGGGTEEEEEEEEEEET--------TEEEEEEEEEEESSCCCCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCHHH-HHHHHhcCCcEEEEEEEEEC--------CEEEEEEEEEeCCCCCCCCHHHHHHHHHHHHHHHHHH
Confidence            3322210 12 23679999999999763        23479999988 6899999999999999999887654

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

Probab=85.93  E-value=0.52  Score=42.39  Aligned_cols=86  Identities=14%  Similarity=0.175  Sum_probs=55.0

Q ss_pred             HHHHHHHHhhhhcccc-cCCCcccccCCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCC-------
Q 023161          186 QLLEWFERQIENIGLS-DLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSM-------  257 (286)
Q Consensus       186 ~I~~~~~~~~~~~~Lv-~L~~t~lyPgr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s-------  257 (286)
                      .++.++.++++....- |..+...|....+  +-......+++++|.||-..       ..+.-|+|.+....       
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            4677788877766544 4422111111100  00001224899999999731       12346999999888       


Q ss_pred             -------------ccccchhhHHHHHHHHhhhcccc
Q 023161          258 -------------TYAYSHKDRAWIKAVSNKFRGKS  280 (286)
Q Consensus       258 -------------~RafT~kDe~WI~~iA~KL~~~~  280 (286)
                                   ++.||+.|..-++.+|+.+..++
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                         89999999999999999876543

---

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	286
d1vhma_	159	Hypothetical protein YebR {Escherichia coli [TaxId	97.57
d1f5ma_	176	Hypothetical protein ykl069wp {Baker's yeast (Sacc	96.51
d1mc0a2	154	3',5'-cyclic nucleotide phosphodiesterase 2A, GAF	89.82
d1mc0a1	187	3',5'-cyclic nucleotide phosphodiesterase 2A, GAF	89.8

>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=97.57  E-value=0.00038  Score=55.60  Aligned_cols=124  Identities=13%  Similarity=0.106  Sum_probs=85.6

Q ss_pred             HHHHHHHHhh---hccccEEEEEECCEEEEeeeecCCC--CCCh-HHHHHHHHHhhhhcccccCCCcccccCCccccccc
Q 023161          146 LAWATYVLLR---NTNSISVLISIRGELCVRGYWQTPD--GASK-TQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWE  219 (286)
Q Consensus       146 LAWaS~~LLt---nT~a~svlV~~~g~ll~RG~~~~p~--~~~~-g~I~~~~~~~~~~~~Lv~L~~t~lyPgr~E~~~~~  219 (286)
                      |+-.+..|.+   ++...++.+..++.....-+.+...  .+.. .-++-++.++.++...-|..+   .|..      -
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            5566655533   4455566666666644332222222  2222 337788888888887766632   2332      3


Q ss_pred             cCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHHhhhccccceeecC
Q 023161          220 MLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGKSIWIDLK  286 (286)
Q Consensus       220 ~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kDe~WI~~iA~KL~~~~~~~~~~  286 (286)
                      ....+.+|++|.||..+        .+.-|+|.+++..++.||+.|...++.+|+.+..+++..|++
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=96.51  E-value=0.0032  Score=51.01  Aligned_cols=78  Identities=15%  Similarity=0.165  Sum_probs=60.4

Q ss_pred             HHHHHHHHhhhhcccccCCCcccccCCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhh
Q 023161          186 QLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKD  265 (286)
Q Consensus       186 ~I~~~~~~~~~~~~Lv~L~~t~lyPgr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kD  265 (286)
                      -++.++.++++....-|..   -.|.      |.....+++|.+|.||...       ..+.=|||-+.+..++.||+.|
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   2332      2445678999999999542       1234699999999999999999


Q ss_pred             HHHHHHHHhhhccc
Q 023161          266 RAWIKAVSNKFRGK  279 (286)
Q Consensus       266 e~WI~~iA~KL~~~  279 (286)
                      +.+++.+|+-+..+
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

>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=89.82  E-value=1.7  Score=31.18  Aligned_cols=85  Identities=13%  Similarity=0.062  Sum_probs=49.2

Q ss_pred             hHHHHHHHHHhhhhcccccCCCcccccCCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEE-eeCCccccc
Q 023161          184 KTQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLL-ASSMTYAYS  262 (286)
Q Consensus       184 ~g~I~~~~~~~~~~~~Lv~L~~t~lyPgr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvl-gs~s~RafT  262 (286)
                      ...++.++.+..+.....+-.....++...+    ........+.++.|+-..       ..+.-|++.+ ....+|.||
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            3457778888777765544432233333322    112223334455554221       1223455544 467999999


Q ss_pred             hhhHHHHHHHHhhhccc
Q 023161          263 HKDRAWIKAVSNKFRGK  279 (286)
Q Consensus       263 ~kDe~WI~~iA~KL~~~  279 (286)
                      +.|..-++.+|+-...+
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            99999999999877544

>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=89.80  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 023161          186 QLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLL-ASSMTYAYSHK  264 (286)
Q Consensus       186 ~I~~~~~~~~~~~~Lv~L~~t~lyPgr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvl-gs~s~RafT~k  264 (286)
                      .++.+|.+..+...+.|..+...|..      ....-.++.+++|.||-..      ...+.-||+.+ -....+.||+.
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      1234467889999999531      11233688844 56777999999


Q ss_pred             hHHHHHHHHhhhccc
Q 023161          265 DRAWIKAVSNKFRGK  279 (286)
Q Consensus       265 De~WI~~iA~KL~~~  279 (286)
                      |...+.++|+-+..+
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