Citrus Sinensis ID: 020759

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-
Protein Sequence
MVQVLSLSTLTTSGNGGFYGSPALWRRHFKLLEKSRIGIDRPCFCHQFVQGLHLRVTFNLLRQRNLRANAGWLFKGGSDRGLDASSERSESANEDILFFFFQLDLATRVQCALNMEEYDIAQQLRNKLTEVEEEISRQLEAKRGLSSKSEAQDKALSIIRLRADLQKAIDSENYALAADLRDQICKLEAESLAASATALAFENARFAFRLGQKVNHKIFGYRAVICGMDPVCCESSSWMEIAQVEKLQQGPSQPFYQLLRRICWLLTNQTWQGLIIPIFLSCFTGRIQLEISSQSSSCERSTTGLDMKFPQIQKMRSCSNA
Secondary Structure (PSIPRED)
ccccccccccEEccccccccccHHHHHHHHHHHHHcccccccccEEEEcccccccccccHHHHHHHHHHHcccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccEEEcccEEEEEEEcccEEEEcccccccccHHHHHHccccccccccccccEEEEEEccccEEccccccccccccccccccHHHHHHHccccccccccccccccccHHHHHHccccc
Secondary Structure Prediction (SSPRO)
ccEEEEEEEEEEcccccccccHHHHHHHccHEEEcEcccccccEHHHHEccccEcccHHHHcccccEEEEHEEccccccccccccccccccHcHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccEEEEEEEEEEEEEccEEEEEEcccccccccHHHHHHcccccccccccccHHHHHHHHHHHHHHHHccccEEEEEEEccccEEEEEEEcccccccccccccccccHHHHHccccccc
Coil and Loop (DISEMBL)
MVQVLSLStlttsgnggfygspalWRRHFKLLEksrigidrpcfchqfVQGLHLRVTFNLLRQRNLRANAgwlfkggsdrgldassersesanEDILFFFFQLDLATRVQCALNMEEYDIAQQLRNKLTEVEEEISRQLEAkrglsskseAQDKALSIIRLRADLQKAIDSENYALAADLRDQICKLEAESLAASATALAFENARFAFRLGQKVNHKIFGYRAVicgmdpvccessswMEIAQVEklqqgpsqpfYQLLRRICWLLTNQTWQGLIIPIFLSCFTGRIQLeissqssscersttgldmkfpqiqkmrscsna
Flexible Loop (DISEMBL)
MVQVLSLStlttsgnggfygspaLWRRHFKLLEKSRIGIDRPCFCHQFVQGLHLRVTFNLLRQRNLRANAGWLFKGGSDRGLDASSERSESANEDILFFFFQLDLATRVQCALNMEEYDIAQQLRNKLTEVEEEISRQleakrglsskseaqDKALSIIRLRADLQKAIDSENYALAADLRDQICKLEAESLAASATALAFENARFAFRLGQKVNHKIFGYRAVICGMDPVCCESSSWMEIAQVEKLQQGPSQPFYQLLRRICWLLTNQTWQGLIIPIFLSCFTGRIQLEISsqssscersttgldmkfpqiqkmrscsna
Low Complexity Region (SEG)
MVQVLSLSTLTTSGNGGFYGSPALWRRHFKLLEKSRIGIDRPCFCHQFVQGLHLRVTFNLLRQRNLRANAGWLFKGGSDRGLDASSERSESANEDILFFFFQLDLATRVQCALNMEEYDIAQQLRNKLTEVEEEISRQLEAKRGLSSKSEAQDKALSIIRLRADLQKAIDSENYALAADLRDQICKleaeslaasatalafenaRFAFRLGQKVNHKIFGYRAVICGMDPVCCESSSWMEIAQVEKLQQGPSQPFYQLLRRICWLLTNQTWQGLIIPIFLSCFTGriqleissqssscersttGLDMKFPQIQKMRSCSNA
Disordered region (IsUnstruct)
*********LTTSGNGGFYGSPALWRRHFKLLEKSRIGIDRPCFCHQFVQGLHLRVTFNLLRQRNLRANAGWLFKG******************DILFFFFQLDLATRVQCALNMEEYDIAQQLR******************************LSIIRLRADLQKAIDSENYALAADLRDQICKLEAESLAASATALAFENARFAFRLGQKVNHKIFGYRAVICGMDPVCCESSSWMEIAQVEKLQQGPSQPFYQLLRRICWLLTNQTWQGLIIPIFLSCFTGRIQLEI******************************
Disordered Region (DISOPRED)
************SGNGGFYGSPALWRRHFKLLEKSRIGIDRPCFCHQFVQGLHLRV********NLRANAGWL*******************NEDILFFFFQLDLATRVQCALNMEEYDIAQQLR********************************IIRLRADLQKAIDSENYALA*****************************AFRLGQKVNHKIFGYRAVICGMDPVCCESSSWMEIAQVE****GPSQPFYQLLRRICWLLTNQTWQGLIIPIFLSCFTGRIQLEI******************PQI**MR*****
Disordered Region (DISEMBL)
MVQVLSLSTLTTSGNGGFYGSPALWRRHFKLLEKSRIGIDRPCFCHQFVQGLHLRVTFNLLRQRNLRANAGWLFKGGS************SANEDILFFFFQLDLATRVQCALNMEEYDIAQQLRNKLTEVEE*******************DKALSIIRLRADLQKAIDSENYALAADLRDQICKLEAESLAASATALAFENARFAFRLGQKVNHKIFGYRAVICGMDPVCCESSSWMEIAQVEKLQQGPSQPFYQLLRRICWLLTNQTWQGLIIPIFLSCFTGRIQLEI***********TGLDMKFPQIQKMRSCSNA
Disordered Region (DISPRO)
MVQVLSLSTLTTSGNGGFYGSPALWRRHFKLLEKSRIGIDRPCFCHQFVQGLHLRVTFNLLRQRNLRANAGWLFKGG*************SANEDILFFFFQLDLATRVQCALNMEEYDIAQQLRNKLTEVEEEISRQLEAK****SKSEAQDKALSIIRLRADLQKAIDSENYALAADLRDQICKLEAESLAASATALAFENARFAFRLGQKVNHKIFGYRAVICGMDPVCCESSSWMEIAQVEKLQQGPSQPFYQLLRRICWLLTNQTWQGLIIPIFLSCFTGRIQLEISS************DMK*************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MVQVLSLSTLTTSGNGGFYGSPALWRRHFKLLEKSRIGIDRPCFCHQFVQGLHLRVTFNLLRQRNLRANAGWLFKGGSDRGLDASSERSESANEDILFFFFQLDLATRVQCALxxxxxxxxxxxxxxxxxxxxxxxxxxxxKRGLSSKSEAQDKALSIIRLRADLQKAIDSENYALAADLRDQICKLEAESLAASATALAFENARFAFRLGQKVNHKIFGYRAVICGMDPVCCESSSWMEIAQVEKLQQGPSQPFYQLLRRICWLLTNQTWQGLIIPIFLSCFTGRIQLEISSQSSSCERSTTGLDMKFPQIQKMRSCSNA
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	321	2.2.26 [Sep-21-2011]
Q8VDH1	627	F-box only protein 21 OS=	yes	no	0.161	0.082	0.384	5e-05
Q5R5S1	621	F-box only protein 21 OS=	yes	no	0.161	0.083	0.384	5e-05
O94952	628	F-box only protein 21 OS=	yes	no	0.161	0.082	0.384	6e-05

>sp|Q8VDH1|FBX21_MOUSE F-box only protein 21 OS=Mus musculus GN=Fbxo21 PE=2 SV=1

 Score = 48.9 bits (115), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 20/52 (38%), Positives = 26/52 (50%)

Query: 208 FRLGQKVNHKIFGYRAVICGMDPVCCESSSWMEIAQVEKLQQGPSQPFYQLL 259
           + +G  + HK +GY  VI G DP C     W+    V  L  G  QPFY +L
Sbjct: 503 YSIGLVMKHKRYGYNCVIYGWDPTCMMGHEWIRNMNVHSLPHGHHQPFYNVL 554

Substrate-recognition component of the SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex.
Mus musculus (taxid: 10090)

>sp|Q5R5S1|FBX21_PONAB F-box only protein 21 OS=Pongo abelii GN=FBXO21 PE=2 SV=1

 Score = 48.9 bits (115), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 20/52 (38%), Positives = 26/52 (50%)

Query: 208 FRLGQKVNHKIFGYRAVICGMDPVCCESSSWMEIAQVEKLQQGPSQPFYQLL 259
           + +G  + HK +GY  VI G DP C     W+    V  L  G  QPFY +L
Sbjct: 496 YSIGLIMKHKRYGYNCVIYGWDPTCMMGHEWIRNMNVHSLPHGHHQPFYNVL 547

Substrate-recognition component of the SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex.

Pongo abelii (taxid: 9601)

>sp|O94952|FBX21_HUMAN F-box only protein 21 OS=Homo sapiens GN=FBXO21 PE=2 SV=2

 Score = 48.9 bits (115), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 20/52 (38%), Positives = 26/52 (50%)

Query: 208 FRLGQKVNHKIFGYRAVICGMDPVCCESSSWMEIAQVEKLQQGPSQPFYQLL 259
           + +G  + HK +GY  VI G DP C     W+    V  L  G  QPFY +L
Sbjct: 503 YSIGLIMKHKRYGYNCVIYGWDPTCMMGHEWIRNMNVHSLPHGHHQPFYNVL 554

Substrate-recognition component of the SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex.

Homo sapiens (taxid: 9606)

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	321
147818712	1072	hypothetical protein VITISV_009461 [Viti	0.806	0.241	0.716	1e-100
225423547	340	PREDICTED: uncharacterized protein LOC10	0.806	0.761	0.716	1e-100
255542114	336	DNA binding protein, putative [Ricinus c	0.794	0.758	0.709	2e-95
449452875	336	PREDICTED: uncharacterized protein LOC10	0.803	0.767	0.616	6e-85
356499859	327	PREDICTED: uncharacterized protein LOC10	0.785	0.770	0.674	1e-83
42568906	330	uvrB/uvrC motif-containing protein [Arab	0.797	0.775	0.642	3e-83
297817996	331	hypothetical protein ARALYDRAFT_904615 [	0.797	0.773	0.643	7e-83
357487407	300	F-box only protein [Medicago truncatula]	0.853	0.913	0.602	2e-80
356494893	303	PREDICTED: uncharacterized protein LOC10	0.619	0.656	0.751	5e-75
125527819	275	hypothetical protein OsI_03852 [Oryza sa	0.598	0.698	0.712	3e-74

>gi|147818712|emb|CAN65041.1| hypothetical protein VITISV_009461 [Vitis vinifera]

 Score =  371 bits (952), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 187/261 (71%), Positives = 214/261 (81%), Gaps = 2/261 (0%)

Query: 1   MVQVLSLSTLTTSGNGGFYGSPALWRRHFKLLEKSRI--GIDRPCFCHQFVQGLHLRVTF 58
           MVQ +S+STLTTSGNGG YGS ALW RHF+L+ K++I  G +R    H   Q L      
Sbjct: 1   MVQCVSVSTLTTSGNGGVYGSTALWGRHFQLMRKTQIRTGSERNFLWHHCAQRLFFAGQL 60

Query: 59  NLLRQRNLRANAGWLFKGGSDRGLDASSERSESANEDILFFFFQLDLATRVQCALNMEEY 118
            + RQRNLR  AGWLFKGG D+GLDASSE SESANEDIL FFFQLDLATRVQ ALN E+Y
Sbjct: 61  VMQRQRNLRVEAGWLFKGGGDQGLDASSECSESANEDILIFFFQLDLATRVQYALNTEQY 120

Query: 119 DIAQQLRNKLTEVEEEISRQLEAKRGLSSKSEAQDKALSIIRLRADLQKAIDSENYALAA 178
           +IAQQLR+KLTEVE E+ +Q EAKRG +SKSEAQDKALS+IRLRADLQKAI++ENYALAA
Sbjct: 121 EIAQQLRDKLTEVEAEVVKQREAKRGSTSKSEAQDKALSMIRLRADLQKAIEAENYALAA 180

Query: 179 DLRDQICKLEAESLAASATALAFENARFAFRLGQKVNHKIFGYRAVICGMDPVCCESSSW 238
           +LRD+I KLEAESLAASA AL +EN  +AFRLGQKV HK+FGY AVICGMDPVCCESSSW
Sbjct: 181 ELRDEINKLEAESLAASANALVYENTPYAFRLGQKVRHKVFGYSAVICGMDPVCCESSSW 240

Query: 239 MEIAQVEKLQQGPSQPFYQLL 259
            E A V+KL +G +QPFYQ+L
Sbjct: 241 RESAHVDKLTRGSNQPFYQVL 261

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225423547|ref|XP_002274826.1| PREDICTED: uncharacterized protein LOC100266199 [Vitis vinifera] gi|297738051|emb|CBI27252.3| unnamed protein product [Vitis vinifera]

 Score =  370 bits (950), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 187/261 (71%), Positives = 214/261 (81%), Gaps = 2/261 (0%)

Query: 1   MVQVLSLSTLTTSGNGGFYGSPALWRRHFKLLEKSRI--GIDRPCFCHQFVQGLHLRVTF 58
           MVQ +S+STLTTSGNGG YGS ALW RHF+L+ K++I  G +R    H   Q L      
Sbjct: 1   MVQCVSVSTLTTSGNGGVYGSTALWGRHFQLMRKTQIRTGSERNFLWHHCAQRLFFAGQL 60

Query: 59  NLLRQRNLRANAGWLFKGGSDRGLDASSERSESANEDILFFFFQLDLATRVQCALNMEEY 118
            + RQRNLR  AGWLFKGG D+GLDASSE SESANEDIL FFFQLDLATRVQ ALN E+Y
Sbjct: 61  VMQRQRNLRVEAGWLFKGGGDQGLDASSECSESANEDILIFFFQLDLATRVQYALNTEQY 120

Query: 119 DIAQQLRNKLTEVEEEISRQLEAKRGLSSKSEAQDKALSIIRLRADLQKAIDSENYALAA 178
           +IAQQLR+KLTEVE E+ +Q EAKRG +SKSEAQDKALS+IRLRADLQKAI++ENYALAA
Sbjct: 121 EIAQQLRDKLTEVEAEVVKQREAKRGSTSKSEAQDKALSMIRLRADLQKAIEAENYALAA 180

Query: 179 DLRDQICKLEAESLAASATALAFENARFAFRLGQKVNHKIFGYRAVICGMDPVCCESSSW 238
           +LRD+I KLEAESLAASA AL +EN  +AFRLGQKV HK+FGY AVICGMDPVCCESSSW
Sbjct: 181 ELRDEINKLEAESLAASANALVYENTPYAFRLGQKVRHKVFGYSAVICGMDPVCCESSSW 240

Query: 239 MEIAQVEKLQQGPSQPFYQLL 259
            E A V+KL +G +QPFYQ+L
Sbjct: 241 RESAHVDKLTRGSNQPFYQVL 261

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255542114|ref|XP_002512121.1| DNA binding protein, putative [Ricinus communis] gi|223549301|gb|EEF50790.1| DNA binding protein, putative [Ricinus communis]

 Score =  355 bits (910), Expect = 2e-95,   Method: Compositional matrix adjust.
 Identities = 186/262 (70%), Positives = 207/262 (79%), Gaps = 7/262 (2%)

Query: 1   MVQVLSLSTLTTSGNGGFYGSPALWR-RHFKLLEKSR--IGIDRPCFCHQFVQGLHLRVT 57
           MVQ LSL+ LT S N G   S   WR RHFKL+ ++    GIDR    HQ VQ L+    
Sbjct: 1   MVQNLSLNALTVSRNCGICVSLPSWRGRHFKLVRRTHNAFGIDR----HQLVQSLYFMGN 56

Query: 58  FNLLRQRNLRANAGWLFKGGSDRGLDASSERSESANEDILFFFFQLDLATRVQCALNMEE 117
            NL R RNLR  AGWLF  G ++  +AS ERSESANEDIL FFFQLDLATRVQ ALN E+
Sbjct: 57  PNLSRHRNLRVEAGWLFNRGGNQESEASCERSESANEDILIFFFQLDLATRVQYALNTEQ 116

Query: 118 YDIAQQLRNKLTEVEEEISRQLEAKRGLSSKSEAQDKALSIIRLRADLQKAIDSENYALA 177
           YDIAQQLRNKLTEVE E+ RQ EAKRG SSKSEAQDKALSIIRLRADLQ AI++ENYA+A
Sbjct: 117 YDIAQQLRNKLTEVEAEVIRQQEAKRGSSSKSEAQDKALSIIRLRADLQNAIENENYAMA 176

Query: 178 ADLRDQICKLEAESLAASATALAFENARFAFRLGQKVNHKIFGYRAVICGMDPVCCESSS 237
           A LRDQI KLEAESLAAS  ALA+ENA++AFRLGQKV HK FGY+AV+CGMDPVCCESSS
Sbjct: 177 AQLRDQISKLEAESLAASVNALAYENAQYAFRLGQKVTHKTFGYQAVVCGMDPVCCESSS 236

Query: 238 WMEIAQVEKLQQGPSQPFYQLL 259
           WME AQVEKL +G +QPFYQ+L
Sbjct: 237 WMETAQVEKLSRGSNQPFYQVL 258

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449452875|ref|XP_004144184.1| PREDICTED: uncharacterized protein LOC101203572 [Cucumis sativus]

 Score =  320 bits (820), Expect = 6e-85,   Method: Compositional matrix adjust.
 Identities = 161/261 (61%), Positives = 197/261 (75%), Gaps = 3/261 (1%)

Query: 1   MVQVLSLSTLTTSGNGGFYGSPALWRRHFKLLEKSRIG--IDRPCFCHQFVQGLHLRVTF 58
           MVQ LS+  +T  G+   YGS   WRR+FK  +++ +     R CF HQ ++   L    
Sbjct: 1   MVQDLSIHAMTALGDPNVYGSALSWRRNFKYFKQTSLTQLTSRQCFWHQCMRSFSLTSQP 60

Query: 59  NLLRQRNLRANAGWLFKGGSDRGLDASSERSESANEDILFFFFQLDLATRVQCALNMEEY 118
              ++ + +  AGWLFKGG         ERSE+AN DIL FFFQLDLATRVQ ALN+E+Y
Sbjct: 61  RRSKRGSFKIRAGWLFKGGGQES-GGRIERSENANNDILIFFFQLDLATRVQYALNIEQY 119

Query: 119 DIAQQLRNKLTEVEEEISRQLEAKRGLSSKSEAQDKALSIIRLRADLQKAIDSENYALAA 178
           +IAQ+LR KLTEVE E+ +Q E+K+GL+SKSE QDK L+IIRLRADLQKA++SENYALAA
Sbjct: 120 EIAQELRMKLTEVEAEVIKQQESKKGLTSKSEVQDKGLNIIRLRADLQKAVESENYALAA 179

Query: 179 DLRDQICKLEAESLAASATALAFENARFAFRLGQKVNHKIFGYRAVICGMDPVCCESSSW 238
            LRD+I KLE +SLAASA  LA+E+A ++FRLGQKV HKIFGYR VICGMDPVCCESSSW
Sbjct: 180 QLRDEISKLETDSLAASAKVLAYESAEYSFRLGQKVRHKIFGYRGVICGMDPVCCESSSW 239

Query: 239 MEIAQVEKLQQGPSQPFYQLL 259
           MEIAQVEKL +G +QPFYQ+L
Sbjct: 240 MEIAQVEKLSRGSNQPFYQVL 260

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356499859|ref|XP_003518753.1| PREDICTED: uncharacterized protein LOC100794023 [Glycine max]

 Score =  316 bits (809), Expect = 1e-83,   Method: Compositional matrix adjust.
 Identities = 176/261 (67%), Positives = 206/261 (78%), Gaps = 9/261 (3%)

Query: 1   MVQVLSLSTLTTSGNGGFYGSPALWRRHFKLLEKSRIGID--RPCFCHQFVQGLHLRVTF 58
           MVQV+SLSTL T GN    GS   W   F+  ++S+I     R    +  VQ L L    
Sbjct: 1   MVQVVSLSTLATCGNSRLCGSSPSWMAPFEPYKRSQITSSNGRHLVWNNSVQSLFL---- 56

Query: 59  NLLRQRNLRANAGWLFKGGSDRGLDASSERSESANEDILFFFFQLDLATRVQCALNMEEY 118
              R  + RA A W+F+GG ++GLDASSE SESANEDIL FFFQLDLATRVQ ALNME+Y
Sbjct: 57  --TRHSDFRAEAAWMFRGG-EQGLDASSEHSESANEDILMFFFQLDLATRVQYALNMEQY 113

Query: 119 DIAQQLRNKLTEVEEEISRQLEAKRGLSSKSEAQDKALSIIRLRADLQKAIDSENYALAA 178
           DIA+QLRNKL EVEEE+ +Q ++KRGLSSK EAQDKA+SIIRLR+DLQKAI++E+YALAA
Sbjct: 114 DIAKQLRNKLAEVEEEVIKQQQSKRGLSSKGEAQDKAISIIRLRSDLQKAIENEDYALAA 173

Query: 179 DLRDQICKLEAESLAASATALAFENARFAFRLGQKVNHKIFGYRAVICGMDPVCCESSSW 238
           +LRD+I KLEAESLAASATALA ENA++AFRLGQKV HK FGYRAVICGMDPVC ESSSW
Sbjct: 174 ELRDEISKLEAESLAASATALAHENAQYAFRLGQKVRHKKFGYRAVICGMDPVCSESSSW 233

Query: 239 MEIAQVEKLQQGPSQPFYQLL 259
           ME AQV+KL +G +QPFYQ+L
Sbjct: 234 MENAQVKKLSRGSAQPFYQVL 254

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|42568906|ref|NP_178438.2| uvrB/uvrC motif-containing protein [Arabidopsis thaliana] gi|51971212|dbj|BAD44298.1| unknown protein [Arabidopsis thaliana] gi|51971335|dbj|BAD44332.1| unknown protein [Arabidopsis thaliana] gi|330250601|gb|AEC05695.1| uvrB/uvrC motif-containing protein [Arabidopsis thaliana]

 Score =  314 bits (805), Expect = 3e-83,   Method: Compositional matrix adjust.
 Identities = 167/260 (64%), Positives = 193/260 (74%), Gaps = 4/260 (1%)

Query: 1   MVQVLSLSTLTTSGNGGFYGSPALWRRHFKLLEKSRIGIDRPCFCHQFVQGLHLRVTFNL 60
           MVQ  SLSTLT  G+       +L R     ++ S +  DR   C    +    R  +  
Sbjct: 1   MVQSQSLSTLTICGS---VKVSSLLRNRLNSVKASSLIGDRCVSCQFLRKSPSFRSHWKS 57

Query: 61  LRQRNL-RANAGWLFKGGSDRGLDASSERSESANEDILFFFFQLDLATRVQCALNMEEYD 119
           L+QRNL R  A W F+GG ++GLD SSERSESANEDIL FFFQLDLATRVQ A+N+E+YD
Sbjct: 58  LKQRNLLRVEARWPFQGGGEQGLDPSSERSESANEDILIFFFQLDLATRVQYAMNLEQYD 117

Query: 120 IAQQLRNKLTEVEEEISRQLEAKRGLSSKSEAQDKALSIIRLRADLQKAIDSENYALAAD 179
           IAQQLR KLTEVEEE  R  E KRG S+KSEAQDK +SIIRLRADLQ AIDSE+Y LAA 
Sbjct: 118 IAQQLREKLTEVEEESIRLQEGKRGSSAKSEAQDKGISIIRLRADLQNAIDSEDYGLAAK 177

Query: 180 LRDQICKLEAESLAASATALAFENARFAFRLGQKVNHKIFGYRAVICGMDPVCCESSSWM 239
           LRD+I KLEAESLA SA ALAFE A +AFRLGQK+ HK FGYRAV+CGMDP+C ESSSWM
Sbjct: 178 LRDEISKLEAESLAVSAKALAFEKAEYAFRLGQKLRHKTFGYRAVVCGMDPICSESSSWM 237

Query: 240 EIAQVEKLQQGPSQPFYQLL 259
           E A+VEKL +G +QPFYQ+L
Sbjct: 238 EAAEVEKLPRGSNQPFYQVL 257

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297817996|ref|XP_002876881.1| hypothetical protein ARALYDRAFT_904615 [Arabidopsis lyrata subsp. lyrata] gi|297322719|gb|EFH53140.1| hypothetical protein ARALYDRAFT_904615 [Arabidopsis lyrata subsp. lyrata]

 Score =  313 bits (802), Expect = 7e-83,   Method: Compositional matrix adjust.
 Identities = 168/261 (64%), Positives = 194/261 (74%), Gaps = 5/261 (1%)

Query: 1   MVQVLSLSTLTTSGNGGFYGSPALWRRHFKLLEKSRIGIDRPCFCHQFVQGLHLRVTFNL 60
           MVQ  SLSTLT  G+       +L R      + S +  DR   C    +    R  +  
Sbjct: 1   MVQSQSLSTLTICGS---VKVSSLLRNRLNSSKASSLIGDRCVSCQFLRKSPSFRSHWKS 57

Query: 61  LRQRNL-RANAGWLFKGGS-DRGLDASSERSESANEDILFFFFQLDLATRVQCALNMEEY 118
           ++QRNL R  A W F+GG  ++GLD SSERSESANEDIL FFFQLDLATRVQ A+N+E+Y
Sbjct: 58  IKQRNLLRVEARWPFQGGGGEQGLDPSSERSESANEDILIFFFQLDLATRVQYAMNLEQY 117

Query: 119 DIAQQLRNKLTEVEEEISRQLEAKRGLSSKSEAQDKALSIIRLRADLQKAIDSENYALAA 178
           DIAQQLR KLTEVEEE  R  E KRG S+KSEAQDK +SIIRLRADLQ AIDSE+Y LAA
Sbjct: 118 DIAQQLREKLTEVEEESIRLQEGKRGSSAKSEAQDKGISIIRLRADLQNAIDSEDYGLAA 177

Query: 179 DLRDQICKLEAESLAASATALAFENARFAFRLGQKVNHKIFGYRAVICGMDPVCCESSSW 238
            LRD+I KLEAESLA SA ALAFENA +AFRLGQK+ HK FGYRAV+CGMDP+CCESSSW
Sbjct: 178 KLRDEISKLEAESLAVSAKALAFENAEYAFRLGQKLRHKTFGYRAVVCGMDPICCESSSW 237

Query: 239 MEIAQVEKLQQGPSQPFYQLL 259
           ME A+VEKL +G +QPFYQ+L
Sbjct: 238 MEAAEVEKLPRGSNQPFYQVL 258

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357487407|ref|XP_003613991.1| F-box only protein [Medicago truncatula] gi|355515326|gb|AES96949.1| F-box only protein [Medicago truncatula]

 Score =  305 bits (780), Expect = 2e-80,   Method: Compositional matrix adjust.
 Identities = 173/287 (60%), Positives = 215/287 (74%), Gaps = 13/287 (4%)

Query: 1   MVQVLSLSTLTTSGNGGFYGSPALWRRHFKLLEKSRI--GIDRPCFCHQFVQGL-HLRVT 57
           MVQ +SLSTL T G    YGSP      F+  ++S I     +    ++ V+ L  +   
Sbjct: 1   MVQGVSLSTLATCGKSRIYGSP------FEPFKQSHITSSTGKHLVWNKCVKSLVFIGYP 54

Query: 58  FNLLRQRNLRANAGWLFKGGSDRGLDASSERSESANEDILFFFFQLDLATRVQCALNMEE 117
           F   ++   +  AGW+F+GG ++ LDAS E+SESANEDIL FFFQLDLATRVQCALNMEE
Sbjct: 55  FASRQRSGFKVEAGWMFRGG-EQELDASVEQSESANEDILMFFFQLDLATRVQCALNMEE 113

Query: 118 YDIAQQLRNKLTEVEEEISRQLEAKRGLSSKSEAQDKALSIIRLRADLQKAIDSENYALA 177
           YDIA+QLRNKLTEVEEE+ +Q ++KRG+SSKSEAQDKALS+IRLR+DLQ AI++E+YALA
Sbjct: 114 YDIAKQLRNKLTEVEEEVIKQKQSKRGMSSKSEAQDKALSVIRLRSDLQSAIENEDYALA 173

Query: 178 ADLRDQICKLEAESLAASATALAFENARFAFRLGQKVNHKIFGYRAVICGMDPVCCESSS 237
           A LRD+I KLEAESLAASA ALA ENA++ FRLGQKV HK+FGYRA+I GMDPVC ESSS
Sbjct: 174 AKLRDEISKLEAESLAASAKALAHENAQYVFRLGQKVKHKMFGYRAIIVGMDPVCSESSS 233

Query: 238 WMEIAQVEKLQQGPSQPFYQLL---RRICWLLTNQTWQGLIIPIFLS 281
           WME AQV+KL +G +QPFYQ+L   R    LL      GL+ P++++
Sbjct: 234 WMENAQVKKLSRGTAQPFYQVLVDVRAEPDLLVAYGKAGLVGPVWMT 280

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356494893|ref|XP_003516316.1| PREDICTED: uncharacterized protein LOC100783767 [Glycine max]

 Score =  287 bits (734), Expect = 5e-75,   Method: Compositional matrix adjust.
 Identities = 151/201 (75%), Positives = 175/201 (87%), Gaps = 2/201 (0%)

Query: 60  LLRQRNLRANAGWLFKGGSDRGLDASSERSESANEDIL-FFFFQLDLATRVQCALNMEEY 118
           L R    RA A W+F+GG ++GLD SSE SESANEDIL FFFFQLDLATRVQ ALNME+Y
Sbjct: 31  LTRHSGFRAEAAWMFRGG-EQGLDVSSEHSESANEDILMFFFFQLDLATRVQYALNMEQY 89

Query: 119 DIAQQLRNKLTEVEEEISRQLEAKRGLSSKSEAQDKALSIIRLRADLQKAIDSENYALAA 178
           DIA+QLRNKL EVEEE+ +Q ++KRGLSSKSEAQDKA+SIIRL +DLQ AI++E+YALAA
Sbjct: 90  DIAKQLRNKLAEVEEEVIKQQQSKRGLSSKSEAQDKAISIIRLHSDLQNAIENEHYALAA 149

Query: 179 DLRDQICKLEAESLAASATALAFENARFAFRLGQKVNHKIFGYRAVICGMDPVCCESSSW 238
           +LRD+I KLEAESLAASA ALA ENA++AFRLGQKV HK FGY+AVICGMDPVC ESSSW
Sbjct: 150 ELRDEISKLEAESLAASAKALAHENAQYAFRLGQKVRHKKFGYKAVICGMDPVCSESSSW 209

Query: 239 MEIAQVEKLQQGPSQPFYQLL 259
           ME AQV+KL +G +QPFYQ+L
Sbjct: 210 MENAQVKKLSRGSAQPFYQVL 230

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|125527819|gb|EAY75933.1| hypothetical protein OsI_03852 [Oryza sativa Indica Group] gi|125572130|gb|EAZ13645.1| hypothetical protein OsJ_03562 [Oryza sativa Japonica Group]

 Score =  285 bits (728), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 139/195 (71%), Positives = 164/195 (84%), Gaps = 3/195 (1%)

Query: 66  LRANAGWLFKGGSDRGL-DASSERSESANEDILFFFFQLDLATRVQCALNMEEYDIAQQL 124
           +R NA WLF GG DR   +A  ERSESANEDIL F+FQLDL TR+Q ALN+E++D+A+QL
Sbjct: 5   VRTNAKWLF-GGDDRSSSNARLERSESANEDILIFYFQLDLQTRIQYALNIEQFDVAKQL 63

Query: 125 RNKLTEVEEEISRQLEAKRGLSSKSEAQDKALSIIRLRADLQKAIDSENYALAADLRDQI 184
           R KLTE+E EI RQ EAKRG SSK+EAQDKA++++R+RADLQKA+DSENYALAA LRD+I
Sbjct: 64  REKLTEIETEIIRQREAKRG-SSKTEAQDKAINLLRVRADLQKAVDSENYALAAALRDEI 122

Query: 185 CKLEAESLAASATALAFENARFAFRLGQKVNHKIFGYRAVICGMDPVCCESSSWMEIAQV 244
            KLE ESLA SA ALA++N  +AFRLGQKV HK+ GYRAVICGMDPVCCES SWME A V
Sbjct: 123 AKLETESLAVSAKALAYQNVEYAFRLGQKVRHKVHGYRAVICGMDPVCCESKSWMETANV 182

Query: 245 EKLQQGPSQPFYQLL 259
           E L +GP+QPFYQ+L
Sbjct: 183 ENLSKGPNQPFYQVL 197

Source: Oryza sativa Indica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	321
TAIR|locus:2063761	330	AT2G03390 [Arabidopsis thalian	0.794	0.772	0.601	4.3e-70
UNIPROTKB|F1NDZ7	612	FBXO21 "Uncharacterized protei	0.161	0.084	0.423	3.2e-05
UNIPROTKB|H0YHF6	225	FBXO21 "F-box only protein 21"	0.161	0.231	0.384	0.00066
ZFIN|ZDB-GENE-100922-229	611	fbxo21 "F-box protein 21" [Dan	0.161	0.085	0.423	0.00085
UNIPROTKB|H0YIE9	505	FBXO21 "F-box only protein 21"	0.161	0.102	0.384	0.0009
RGD|1307346	572	Fbxo21 "F-box protein 21" [Rat	0.161	0.090	0.384	0.00096

TAIR|locus:2063761 AT2G03390 [Arabidopsis thaliana (taxid:3702)]

 Score = 710 (255.0 bits), Expect = 4.3e-70, P = 4.3e-70
 Identities = 157/261 (60%), Positives = 181/261 (69%)

Query:     1 MVQVLSLSTLTTSGNGGFYGSPALWRRHFKLLEKSRIGIDRPCFCHQFVQ-GLHLRVTFN 59
             MVQ  SLSTLT  G+     S  L  R   +   S IG DR C   QF++     R  + 
Sbjct:     1 MVQSQSLSTLTICGSVKV--SSLLRNRLNSVKASSLIG-DR-CVSCQFLRKSPSFRSHWK 56

Query:    60 LLRQRNL-RANAGWLFKGGSDRGLDASSERSESANEDILFFFFQLDLATRVQCALNMEEY 118
              L+QRNL R  A W F+GG ++GLD SSERSESANEDIL FFFQLDLATRVQ A+N+E+Y
Sbjct:    57 SLKQRNLLRVEARWPFQGGGEQGLDPSSERSESANEDILIFFFQLDLATRVQYAMNLEQY 116

Query:   119 DIAQQLRNKLTEVEEEISRQLEAKRGLSSKSEAQDKALSIIRLRADLQKAIDSENYALAA 178
             DIAQQLR KLTEVEEE  R  E KRG S+KSEAQDK +SIIRLRADLQ AIDSE+Y LAA
Sbjct:   117 DIAQQLREKLTEVEEESIRLQEGKRGSSAKSEAQDKGISIIRLRADLQNAIDSEDYGLAA 176

Query:   179 DLRDQICKXXXXXXXXXXXXXXXXXXRFAFRLGQKVNHKIFGYRAVICGMDPVCCESSSW 238
              LRD+I K                   +AFRLGQK+ HK FGYRAV+CGMDP+C ESSSW
Sbjct:   177 KLRDEISKLEAESLAVSAKALAFEKAEYAFRLGQKLRHKTFGYRAVVCGMDPICSESSSW 236

Query:   239 MEIAQVEKLQQGPSQPFYQLL 259
             ME A+VEKL +G +QPFYQ+L
Sbjct:   237 MEAAEVEKLPRGSNQPFYQVL 257

GO:0003677 "DNA binding" evidence=IEA;ISS

GO:0004518 "nuclease activity" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM

GO:0006289 "nucleotide-excision repair" evidence=IEA;ISS

GO:0009507 "chloroplast" evidence=ISM;IDA

UNIPROTKB|F1NDZ7 FBXO21 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 121 (47.7 bits), Expect = 3.2e-05, Sum P(2) = 3.2e-05
 Identities = 22/52 (42%), Positives = 27/52 (51%)

Query:   208 FRLGQKVNHKIFGYRAVICGMDPVCCESSSWMEIAQVEKLQQGPSQPFYQLL 259
             F +G  + HK +GY  VI G DP C     W+    V  L  GP QPFY +L
Sbjct:   477 FSIGLIMKHKRYGYNCVIYGWDPACMMGHEWIRNMNVHSLPHGPHQPFYNVL 528

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|H0YHF6 FBXO21 "F-box only protein 21" [Homo sapiens (taxid:9606)]

 Score = 109 (43.4 bits), Expect = 0.00066, P = 0.00066
 Identities = 20/52 (38%), Positives = 26/52 (50%)

Query:   208 FRLGQKVNHKIFGYRAVICGMDPVCCESSSWMEIAQVEKLQQGPSQPFYQLL 259
             + +G  + HK +GY  VI G DP C     W+    V  L  G  QPFY +L
Sbjct:   155 YSIGLIMKHKRYGYNCVIYGWDPTCMMGHEWIRNMNVHSLPHGHHQPFYNVL 206

GO:0003677 "DNA binding" evidence=IEA

ZFIN|ZDB-GENE-100922-229 fbxo21 "F-box protein 21" [Danio rerio (taxid:7955)]

 Score = 115 (45.5 bits), Expect = 0.00085, P = 0.00085
 Identities = 22/52 (42%), Positives = 28/52 (53%)

Query:   208 FRLGQKVNHKIFGYRAVICGMDPVCCESSSWMEIAQVEKLQQGPSQPFYQLL 259
             F  G  + HK  GY  VI G DP C  S  W+   +V +L +G  QPFY +L
Sbjct:   496 FSTGLIMKHKRSGYNCVIYGWDPKCTMSQEWINTMRVHQLSKGADQPFYNVL 547

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|H0YIE9 FBXO21 "F-box only protein 21" [Homo sapiens (taxid:9606)]

 Score = 109 (43.4 bits), Expect = 0.00090, Sum P(2) = 0.00090
 Identities = 20/52 (38%), Positives = 26/52 (50%)

Query:   208 FRLGQKVNHKIFGYRAVICGMDPVCCESSSWMEIAQVEKLQQGPSQPFYQLL 259
             + +G  + HK +GY  VI G DP C     W+    V  L  G  QPFY +L
Sbjct:   380 YSIGLIMKHKRYGYNCVIYGWDPTCMMGHEWIRNMNVHSLPHGHHQPFYNVL 431

GO:0003677 "DNA binding" evidence=IEA

RGD|1307346 Fbxo21 "F-box protein 21" [Rattus norvegicus (taxid:10116)]

 Score = 110 (43.8 bits), Expect = 0.00096, Sum P(2) = 0.00096
 Identities = 20/52 (38%), Positives = 26/52 (50%)

Query:   208 FRLGQKVNHKIFGYRAVICGMDPVCCESSSWMEIAQVEKLQQGPSQPFYQLL 259
             + +G  + HK +GY  VI G DP C     W+    V  L  G  QPFY +L
Sbjct:   448 YSIGLVMKHKRYGYNCVIYGWDPTCMMGHEWIRNMNVHSLPHGHHQPFYNVL 499

GO:0003677 "DNA binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00030079001 SubName- Full=Chromosome chr1 scaffold_5, whole genome shotgun sequence; (230 aa) (Vitis vinifera)

Predicted Functional Partners:

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

---

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	321
pfam08755	100	pfam08755, YccV-like, Hemimethylated DNA-binding p	1e-18
TIGR02097	101	TIGR02097, yccV, hemimethylated DNA binding domain	9e-18
smart00992	98	smart00992, YccV-like, Hemimethylated DNA-binding	9e-10
COG3785	116	COG3785, COG3785, Uncharacterized conserved protei	5e-06
pfam02151	36	pfam02151, UVR, UvrB/uvrC motif	7e-05
COG0556	663	COG0556, UvrB, Helicase subunit of the DNA excisio	7e-05
PRK14129	105	PRK14129, PRK14129, heat shock protein HspQ; Provi	0.001
PRK05298	652	PRK05298, PRK05298, excinuclease ABC subunit B; Pr	0.003

>gnl|CDD|220004 pfam08755, YccV-like, Hemimethylated DNA-binding protein YccV like

 Score = 79.2 bits (196), Expect = 1e-18
 Identities = 22/52 (42%), Positives = 29/52 (55%), Gaps = 1/52 (1%)

Query: 208 FRLGQKVNHKIFGYRAVICGMDPVCCESSSWMEIAQVEKLQQGPSQPFYQLL 259
           FR+GQ V H++FGYR VI  +DP    S  W E    ++      QPFY +L
Sbjct: 4   FRIGQVVRHRLFGYRGVIFDVDPEFAASEEWYEAIPEDRR-PARDQPFYHVL 54

YccV is a hemimethylated DNA binding protein which has been shown to regulate dnaA gene expression. The structure of one of the hypothetical proteins in this family has been solved and it forms a beta sheet structure with a terminating alpha helix. Length = 100

>gnl|CDD|131152 TIGR02097, yccV, hemimethylated DNA binding domain

 Score = 77.0 bits (190), Expect = 9e-18
 Identities = 22/53 (41%), Positives = 30/53 (56%), Gaps = 1/53 (1%)

Query: 207 AFRLGQKVNHKIFGYRAVICGMDPVCCESSSWMEIAQVEKLQQGPSQPFYQLL 259
            FR+GQ V HK+FGYR V+  +DP    +  W++   VE       QPFY +L
Sbjct: 3   KFRIGQVVRHKLFGYRGVVIDVDPEYSNTEEWLDAIPVEIRPLR-DQPFYHVL 54

This model describes the small protein from E. coli YccV and its homologs in other Proteobacteria. YccV is now described as a hemimethylated DNA binding protein. The model also describes a domain in longer eukaryotic proteins. Length = 101

>gnl|CDD|214961 smart00992, YccV-like, Hemimethylated DNA-binding protein YccV like

 Score = 54.6 bits (132), Expect = 9e-10
 Identities = 21/54 (38%), Positives = 28/54 (51%), Gaps = 5/54 (9%)

Query: 208 FRLGQKVNHKIFGYRAVICGMDPVCCESSSWMEIAQVEKLQQGP--SQPFYQLL 259
           FR+GQ V HK+FGYR V+   DP    +  W +    +     P   QPFY +L
Sbjct: 4   FRIGQVVRHKLFGYRGVVFDWDPEFANTEEWYDEIPED---SRPPRDQPFYHVL 54

YccV is a hemimethylated DNA binding protein which has been shown to regulate dnaA gene expression. The structure of one of the hypothetical proteins in this family has been solved and it forms a beta sheet structure with a terminating alpha helix. Length = 98

>gnl|CDD|226308 COG3785, COG3785, Uncharacterized conserved protein [Function unknown]

 Score = 44.4 bits (105), Expect = 5e-06
 Identities = 18/52 (34%), Positives = 26/52 (50%), Gaps = 1/52 (1%)

Query: 208 FRLGQKVNHKIFGYRAVICGMDPVCCESSSWMEIAQVEKLQQGPSQPFYQLL 259
           F +GQ V H++F +R V+  +DP    +  W +   V        QPFY LL
Sbjct: 15  FGIGQVVRHRLFPFRGVVFDVDPEYANTEEWPDEIPVNIRPL-RDQPFYHLL 65

Length = 116

>gnl|CDD|145355 pfam02151, UVR, UvrB/uvrC motif

 Score = 39.3 bits (93), Expect = 7e-05
 Identities = 13/33 (39%), Positives = 21/33 (63%)

Query: 158 IIRLRADLQKAIDSENYALAADLRDQICKLEAE 190
           I  L  ++++A + E++  AA LRDQI  LE +
Sbjct: 4   IKELEEEMEEAAEEEDFEKAAKLRDQIKALEKQ 36

Length = 36

>gnl|CDD|223630 COG0556, UvrB, Helicase subunit of the DNA excision repair complex [DNA replication, recombination, and repair]

 Score = 44.1 bits (105), Expect = 7e-05
 Identities = 25/92 (27%), Positives = 42/92 (45%), Gaps = 5/92 (5%)

Query: 108 RVQCALNMEEYDIAQQLRNK----LTEVEEEISRQLEAKRGLSSKSEAQDKALSIIRLRA 163
            +Q A N EE+ I  Q   K    + + E E           +SK   ++    I +L  
Sbjct: 573 EIQMAYN-EEHGITPQTIKKKIRDILDGEYEEDEYKAKIEKKASKMSKKELEKLIKKLEK 631

Query: 164 DLQKAIDSENYALAADLRDQICKLEAESLAAS 195
           ++++A  +  +  AA LRD+I +L+ E L  S
Sbjct: 632 EMKEAAKNLEFEEAARLRDEIKELKEELLGKS 663

Length = 663

>gnl|CDD|184526 PRK14129, PRK14129, heat shock protein HspQ; Provisional

 Score = 37.4 bits (87), Expect = 0.001
 Identities = 16/45 (35%), Positives = 25/45 (55%), Gaps = 1/45 (2%)

Query: 208 FRLGQKVNHKIFGYRAVICGMDPV-CCESSSWMEIAQVEKLQQGP 251
           F +GQ+V H + GY  V+  +DP    E  S  E+A  ++L+  P
Sbjct: 6   FGIGQQVRHSLLGYLGVVVDIDPEYSLEEPSPDELAVNDELRAAP 50

Length = 105

>gnl|CDD|235395 PRK05298, PRK05298, excinuclease ABC subunit B; Provisional

 Score = 38.9 bits (92), Expect = 0.003
 Identities = 17/62 (27%), Positives = 31/62 (50%), Gaps = 1/62 (1%)

Query: 134 EISRQLEAKRGLSSKSEAQDKALSIIRLRADLQKAIDSENYALAADLRDQICKLEAESLA 193
           +I   L++       S+ + + L I  L   +++A  +  +  AA LRD+I +L+ E L 
Sbjct: 592 KIRDILDSVYKKDKLSKKELEKL-IKELEKQMKEAAKNLEFEEAARLRDEIKELKEELLG 650

Query: 194 AS 195
            S
Sbjct: 651 LS 652

Length = 652

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	321
PF08755	100	YccV-like: Hemimethylated DNA-binding protein YccV	99.94
TIGR02097	101	yccV hemimethylated DNA binding domain. This model	99.92
PRK14129	105	heat shock protein HspQ; Provisional	99.73
COG3880	176	Modulator of heat shock repressor CtsR, McsA [Sign	99.71
COG3785	116	Uncharacterized conserved protein [Function unknow	99.6
PF02151	36	UVR: UvrB/uvrC motif; InterPro: IPR001943 During t	97.98
PRK00558	598	uvrC excinuclease ABC subunit C; Validated	94.7
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	94.24
KOG4408	386	consensus Putative Mg2+ and Co2+ transporter CorD	93.66
PRK12306	519	uvrC excinuclease ABC subunit C; Reviewed	93.07
PRK14671	621	uvrC excinuclease ABC subunit C; Provisional	93.03
TIGR00194	574	uvrC excinuclease ABC, C subunit. This family cons	92.84
PRK14667	567	uvrC excinuclease ABC subunit C; Provisional	92.78
PRK14666	694	uvrC excinuclease ABC subunit C; Provisional	92.54
PRK05298	652	excinuclease ABC subunit B; Provisional	92.45
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	92.07
PRK07883	557	hypothetical protein; Validated	91.98
PRK14672	691	uvrC excinuclease ABC subunit C; Provisional	91.54
PRK14669	624	uvrC excinuclease ABC subunit C; Provisional	91.42
PRK14670	574	uvrC excinuclease ABC subunit C; Provisional	90.36
PRK14668	577	uvrC excinuclease ABC subunit C; Provisional	89.84
COG0322	581	UvrC Nuclease subunit of the excinuclease complex	89.63

>PF08755 YccV-like: Hemimethylated DNA-binding protein YccV like; InterPro: IPR011722 This entry describes the small protein from Escherichia coli YccV and its homologs in other Proteobacteria

Probab=99.94  E-value=2.2e-28  Score=199.39  Aligned_cols=83  Identities=33%  Similarity=0.633  Sum_probs=41.4

Q ss_pred             cccccCcEEEeeecCceEEEEcccccccCChhHHHHhhhhccCCCCCCCceEEEEeCC------ccCccccccC-----C
Q 020759          206 FAFRLGQKVNHKIFGYRAVICGMDPVCCESSSWMEIAQVEKLQQGPSQPFYQLLRRIC------WLLTNQTWQG-----L  274 (321)
Q Consensus       206 vkFrVGQVvrHR~ygYrGVIvGWDp~c~a~eeW~~~~~v~~l~~gr~QPFYhVLVD~r------~v~~~ql~~~-----~  274 (321)
                      ++|+|||+|+||+|||+|||+|||+.|.++++|+.+++++.++. ++||||+||||++      |++++++.+.     +
T Consensus         2 ~~f~vGqvv~Hr~~~y~GVIvgwD~~~~~~~~W~~~~~~~~~~~-~~qPfY~vLv~~~~~~~~~YVaEenL~~~~~~~~i   80 (100)
T PF08755_consen    2 VKFRVGQVVRHRRYGYRGVIVGWDPECQAPEEWIEQMGVDNLPR-RNQPFYHVLVDDRDSPPVRYVAEENLEPDSTPEPI   80 (100)
T ss_dssp             -SS-TT-EEEETTT--EEEEEEEE-------------------------EEEEEEE-SS--EEEEEEGGGEEE---S--T
T ss_pred             cccccCCEEEEeeeCccEEEECcccccCCCchHHHhcccccccc-CCCCcEEEEEecCCccceEEecccccccCCCCCCc
Confidence            68999999999999999999999999999999999999887766 9999999999974      4666655331     1


Q ss_pred             ---CccceeeeecceEEE
Q 020759          275 ---IIPIFLSCFTGRIQL  289 (321)
Q Consensus       275 ---~i~~~f~~FdGr~y~  289 (321)
                         .|+.||+.|||.+|+
T Consensus        81 ~hp~i~~yF~~fd~~~y~   98 (100)
T PF08755_consen   81 NHPEIGRYFKRFDGGRYV   98 (100)
T ss_dssp             T-HHHHHHHHHHTT----
T ss_pred             CChHHHHHHHhhCCCcCc
Confidence               667999999999997

YccV is now described as a hemimethylated DNA binding protein []. The model entry describes a domain in longer eukaryotic proteins.; PDB: 1VBV_A.

>TIGR02097 yccV hemimethylated DNA binding domain

Probab=99.92  E-value=4.6e-26  Score=187.81  Aligned_cols=83  Identities=29%  Similarity=0.525  Sum_probs=70.9

Q ss_pred             cccccCcEEEeeecCceEEEEcccccccCChhHHHHhhhhccCCCCCCCceEEEEeCCc-------cCccccccC-----
Q 020759          206 FAFRLGQKVNHKIFGYRAVICGMDPVCCESSSWMEIAQVEKLQQGPSQPFYQLLRRICW-------LLTNQTWQG-----  273 (321)
Q Consensus       206 vkFrVGQVvrHR~ygYrGVIvGWDp~c~a~eeW~~~~~v~~l~~gr~QPFYhVLVD~r~-------v~~~ql~~~-----  273 (321)
                      ++|+|||+|+||+|||+|||+||||.|.++++|+.+|+++.++. ++||||||||++++       |++++|-..     
T Consensus         2 ~kf~IGqvvrHr~~~yrGVI~gwDp~~~~~eeW~~~~~~~~~p~-~~qPfYhvLv~~~~~~~~~aYVaE~nL~~~~~~~~   80 (101)
T TIGR02097         2 AKFRIGQVVRHKLFGYRGVVIDVDPEYSNTEEWLDAIPVEIRPL-RDQPFYHVLAEDDEGLPYVAYVAEQNLLYDDSDEP   80 (101)
T ss_pred             ceecCCCEEEecccCCCEEEEeEChhccCChHHHHhhhcccCcc-cCCCceEEEEeCCCCcceeEEeehhhcccCCCCCC
Confidence            68999999999999999999999999999999999999887655 99999999998643       556555441     


Q ss_pred             C---CccceeeeecceEEE
Q 020759          274 L---IIPIFLSCFTGRIQL  289 (321)
Q Consensus       274 ~---~i~~~f~~FdGr~y~  289 (321)
                      +   .|..+|+.|||.+|.
T Consensus        81 i~hP~~~~~F~~~~~~~y~   99 (101)
T TIGR02097        81 IEHPQVDELFDGFDEGLQK   99 (101)
T ss_pred             CCCCCHHHHHhhhccCccc
Confidence            2   344899999999885

This model describes the small protein from E. coli YccV and its homologs in other Proteobacteria. YccV is now described as a hemimethylated DNA binding protein. The model also describes a domain in longer eukaryotic proteins.

>PRK14129 heat shock protein HspQ; Provisional

Probab=99.73  E-value=3.1e-18  Score=142.06  Aligned_cols=65  Identities=23%  Similarity=0.393  Sum_probs=55.6

Q ss_pred             cccccCcEEEeeecCceEEEEcccccccCChhHHHHhhhhccCCCCCCCceEEEEeCC-------ccCcccccc
Q 020759          206 FAFRLGQKVNHKIFGYRAVICGMDPVCCESSSWMEIAQVEKLQQGPSQPFYQLLRRIC-------WLLTNQTWQ  272 (321)
Q Consensus       206 vkFrVGQVvrHR~ygYrGVIvGWDp~c~a~eeW~~~~~v~~l~~gr~QPFYhVLVD~r-------~v~~~ql~~  272 (321)
                      .+|.|||+||||+|||||||+|.||+|..+++|+..+..+  .+.++||||||||++.       |+++.+|.+
T Consensus         4 akF~IGQ~VrHrl~~yrGVV~DVDP~fs~~e~w~~~ia~~--~p~kdqPwYHvl~en~~~~~v~tYVaE~nL~~   75 (105)
T PRK14129          4 SKFGIGQQVRHSLLGYLGVVVDIDPEYSLEEPSPDELAVN--DELRAAPWYHVVMEDDDGQPVHTYLAEAQLSS   75 (105)
T ss_pred             ccccCCcEEEEeecCCCeEEEeeCCCcCCCchhHHhhccC--CCccCCCceEEEEEcCCCceEEEEeeecccCC
Confidence            4899999999999999999999999999999999999654  6789999999999653       345555554

>COG3880 Modulator of heat shock repressor CtsR, McsA [Signal transduction mechanisms]

Probab=99.71  E-value=5e-18  Score=151.18  Aligned_cols=93  Identities=24%  Similarity=0.258  Sum_probs=81.1

Q ss_pred             Cceeeecccccccc-----cccccccHHhhHHHHHHHHHHHHHHHHHhhhhhcccCC-CcchhHHHHHHHHHHHHHHHHH
Q 020759           94 EDILFFFFQLDLAT-----RVQCALNMEEYDIAQQLRNKLTEVEEEISRQLEAKRGL-SSKSEAQDKALSIIRLRADLQK  167 (321)
Q Consensus        94 ~~i~cf~cqldl~~-----RLgCp~cYe~F~~a~~Lr~~L~~ih~~~~~~h~GK~p~-~~~~~~~d~a~qLlqLr~~L~~  167 (321)
                      +.+.|+.||+++..     |+||+.||.+|..  .|.|.+++||++.. .|+||+|. .++.+.  -..+|+.|+..|++
T Consensus        73 e~l~C~~C~~Tfk~f~~~g~fGCaeCY~tf~~--~i~pi~~rvq~g~~-~H~GK~P~~~~~~i~--~~~~I~~L~e~Lq~  147 (176)
T COG3880          73 ELLGCHNCGMTFKEFIQSGLFGCAECYKTFES--QISPIITRVQGGYV-EHVGKVPKRIGRKIN--PKRKIIALKEALQD  147 (176)
T ss_pred             HHhcCccccccHHHHHHhcccchHHHHHHHHH--HhhHHHHHhhCCce-eecCcCccccccccc--HHHHHHHHHHHHHH
Confidence            36899999998865     9999999999997  99999999999954 38999995 333444  44569999999999


Q ss_pred             hhchhhHHHhhHHHHHHhhHHHhh
Q 020759          168 AIDSENYALAADLRDQICKLEAES  191 (321)
Q Consensus       168 AI~~E~YE~AA~LRD~Ir~Leeq~  191 (321)
                      +|+.||||+||.+||+|+.|+++.
T Consensus       148 ~i~~EefEeAA~iRDqIr~Lk~k~  171 (176)
T COG3880         148 LIEREEFEEAAVIRDQIRALKAKN  171 (176)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhc
Confidence            999999999999999999999773

>COG3785 Uncharacterized conserved protein [Function unknown]

Probab=99.60  E-value=2.9e-16  Score=131.07  Aligned_cols=66  Identities=27%  Similarity=0.509  Sum_probs=57.1

Q ss_pred             cccccCcEEEeeecCceEEEEcccccccCChhHHHHhhhhccCCCCCCCceEEEEeCCc------cCcccccc
Q 020759          206 FAFRLGQKVNHKIFGYRAVICGMDPVCCESSSWMEIAQVEKLQQGPSQPFYQLLRRICW------LLTNQTWQ  272 (321)
Q Consensus       206 vkFrVGQVvrHR~ygYrGVIvGWDp~c~a~eeW~~~~~v~~l~~gr~QPFYhVLVD~r~------v~~~ql~~  272 (321)
                      .||.|||+|||++|+|+|||++.||++..+++|...+.++ .++-++|||||+|+++.+      +.+.+|.+
T Consensus        13 aKF~IGQvVRHrlfpfrGVV~DvDPeyanteew~~~ip~~-~rp~rdqPfYHllaEnde~~yvaYvsEqnL~~   84 (116)
T COG3785          13 AKFGIGQVVRHRLFPFRGVVFDVDPEYANTEEWPDEIPVN-IRPLRDQPFYHLLAENDETEYVAYVSEQNLVS   84 (116)
T ss_pred             hhcchhhhhhhhhcccceEEEecCcccccCccChhhcccc-ccccccCCceeeeeecCCccceeeehhhhccc
Confidence            5899999999999999999999999999999999999654 478999999999997653      44445555

>PF02151 UVR: UvrB/uvrC motif; InterPro: IPR001943 During the process of Escherichia coli nucleotide excision repair, DNA damage recognition and processing are achieved by the action of the uvrA, uvrB, and uvrC gene products []

Probab=97.98  E-value=8.6e-06  Score=55.73  Aligned_cols=34  Identities=35%  Similarity=0.556  Sum_probs=30.5

Q ss_pred             HHHHHHHHHHHhhchhhHHHhhHHHHHHhhHHHh
Q 020759          157 SIIRLRADLQKAIDSENYALAADLRDQICKLEAE  190 (321)
Q Consensus       157 qLlqLr~~L~~AI~~E~YE~AA~LRD~Ir~Leeq  190 (321)
                      .|..|+.+|..|++.++||+||.|||.|..|++|
T Consensus         3 ~i~~l~~~m~~a~~~~dfE~Aa~~Rd~i~~l~~q   36 (36)
T PF02151_consen    3 LIKELEEKMEEAVENEDFEKAARLRDQIKALKKQ   36 (36)
T ss_dssp             HHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHcC
Confidence            3778899999999999999999999999999875

UvrB and UvrC share a common domain of around 35 amino acids, the so called UVR domain. This domain in UvrB can interact with the homologous domain in UvrC throughout a putative coiled coil structure. This interaction is important for the incision of the damaged strand [].; GO: 0003677 DNA binding, 0004518 nuclease activity, 0006289 nucleotide-excision repair; PDB: 3PXG_D 3PXI_C 1E52_B 1QOJ_B 2D7D_B 2NMV_B.

>PRK00558 uvrC excinuclease ABC subunit C; Validated

Probab=94.70  E-value=0.051  Score=57.22  Aligned_cols=35  Identities=26%  Similarity=0.325  Sum_probs=32.1

Q ss_pred             HHHHHHHHHHhhchhhHHHhhHHHHHHhhHHHhhh
Q 020759          158 IIRLRADLQKAIDSENYALAADLRDQICKLEAESL  192 (321)
Q Consensus       158 LlqLr~~L~~AI~~E~YE~AA~LRD~Ir~Leeq~~  192 (321)
                      +.+|+.+|++|.++.+||+||.+||.|..|+.-.+
T Consensus       204 i~~L~~~M~~aa~~l~FE~Aa~~RD~i~aL~~~~~  238 (598)
T PRK00558        204 LKELEEKMEEASENLEFERAARYRDQIQALRRVQE  238 (598)
T ss_pred             HHHHHHHHHHHHHhhCHHHHHHHHHHHHHHHHHHh
Confidence            66888999999999999999999999999997655

>COG0556 UvrB Helicase subunit of the DNA excision repair complex [DNA replication, recombination, and repair]

Probab=94.24  E-value=0.093  Score=55.48  Aligned_cols=40  Identities=30%  Similarity=0.412  Sum_probs=35.4

Q ss_pred             HHHHHHHHHHHHHHHhhchhhHHHhhHHHHHHhhHHHhhh
Q 020759          153 DKALSIIRLRADLQKAIDSENYALAADLRDQICKLEAESL  192 (321)
Q Consensus       153 d~a~qLlqLr~~L~~AI~~E~YE~AA~LRD~Ir~Leeq~~  192 (321)
                      +.+..|..|+.+|++|-++-+||+||.|||.|.+|+++..
T Consensus       621 e~~~~I~~Le~~M~~aA~~l~FE~Aa~lRD~i~~L~~~~~  660 (663)
T COG0556         621 ELEKLIKKLEKEMKEAAKNLEFEEAARLRDEIKELKEELL  660 (663)
T ss_pred             HHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhc
Confidence            4455688999999999999999999999999999998754

>KOG4408 consensus Putative Mg2+ and Co2+ transporter CorD [Inorganic ion transport and metabolism]

Probab=93.66  E-value=0.05  Score=54.41  Aligned_cols=26  Identities=27%  Similarity=0.450  Sum_probs=21.9

Q ss_pred             cccccccCcEEEeeecCceEEEE-ccc
Q 020759          204 ARFAFRLGQKVNHKIFGYRAVIC-GMD  229 (321)
Q Consensus       204 ~~vkFrVGQVvrHR~ygYrGVIv-GWD  229 (321)
                      ..-+|.-||.|+|+.|||+|||+ -|+
T Consensus        63 ~~~~~etgqsF~h~~f~yvgvv~~~w~   89 (386)
T KOG4408|consen   63 KTQKYETGQSFLHDTFGYVGVVLFPWA   89 (386)
T ss_pred             cCCcccccceeeeeecccceEEEEech
Confidence            34589999999999999999988 344

>PRK12306 uvrC excinuclease ABC subunit C; Reviewed

Probab=93.07  E-value=0.16  Score=52.82  Aligned_cols=35  Identities=20%  Similarity=0.336  Sum_probs=30.8

Q ss_pred             HHHHHHHHHHhhchhhHHHhhHHHHHHhhHHHhhh
Q 020759          158 IIRLRADLQKAIDSENYALAADLRDQICKLEAESL  192 (321)
Q Consensus       158 LlqLr~~L~~AI~~E~YE~AA~LRD~Ir~Leeq~~  192 (321)
                      +.+|+.+|++|-+..+||+||.+||.|+.|+.-..
T Consensus       194 ~~~L~~~M~~aa~~l~FE~Aa~~RD~l~~l~~~~~  228 (519)
T PRK12306        194 IEKLEEEMAEKAKNQQFERALVIRDEINAIENLQE  228 (519)
T ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHh
Confidence            56788899999999999999999999999986433

>PRK14671 uvrC excinuclease ABC subunit C; Provisional

Probab=93.03  E-value=0.15  Score=54.07  Aligned_cols=35  Identities=31%  Similarity=0.390  Sum_probs=31.0

Q ss_pred             HHHHHHHHHHhhchhhHHHhhHHHHHHhhHHHhhh
Q 020759          158 IIRLRADLQKAIDSENYALAADLRDQICKLEAESL  192 (321)
Q Consensus       158 LlqLr~~L~~AI~~E~YE~AA~LRD~Ir~Leeq~~  192 (321)
                      +.+|+.+|++|-+..+||+||++||.|+.|+.-..
T Consensus       217 ~~~L~~~M~~as~~l~FE~Aa~~RD~i~~l~~~~~  251 (621)
T PRK14671        217 IRSLTEEMQRAAAELKFEEAAELKDQIESLKRYAE  251 (621)
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHh
Confidence            56788899999999999999999999999986443

>TIGR00194 uvrC excinuclease ABC, C subunit

Probab=92.84  E-value=0.19  Score=52.86  Aligned_cols=72  Identities=22%  Similarity=0.278  Sum_probs=45.2

Q ss_pred             HHHHHHHHHHhhchhhHHHhhHHHHHHhhHHHhhhhhhhhhhhcccccc---ccccCcEEEeeecCce-EEEEcccc
Q 020759          158 IIRLRADLQKAIDSENYALAADLRDQICKLEAESLAASATALAFENARF---AFRLGQKVNHKIFGYR-AVICGMDP  230 (321)
Q Consensus       158 LlqLr~~L~~AI~~E~YE~AA~LRD~Ir~Leeq~~aasa~a~~~~n~~v---kFrVGQVvrHR~ygYr-GVIvGWDp  230 (321)
                      +.+|+.+|++|-++.+||+||.+||.|+.|+.-............+..+   ....|..+.+ +|-+| |.|+|.+.
T Consensus       196 ~~~L~~~M~~aa~~l~FE~Aa~~Rd~i~~l~~~~~~Q~v~~~~~~d~Dvi~~~~~~~~~~v~-v~~vR~G~l~~~~~  271 (574)
T TIGR00194       196 IKELEQKMEKASENLEFEEAARIRDQIAAVRELNEKQHVSLTDLIDLDIIAVAFDGNVAAIQ-VFFIRQGKLIGRDQ  271 (574)
T ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhcCeeecCCCCCceEEEEEEcCCcEEEE-EEEEECCEEeccee
Confidence            5578889999999999999999999999998654421111111122222   2333444333 33344 78887763

This family consists of the DNA repair enzyme UvrC, an ABC excinuclease subunit which interacts with the UvrA/UvrB complex to excise UV-damaged nucleotide segments.

>PRK14667 uvrC excinuclease ABC subunit C; Provisional

Probab=92.78  E-value=0.16  Score=53.45  Aligned_cols=35  Identities=26%  Similarity=0.223  Sum_probs=31.2

Q ss_pred             HHHHHHHHHHhhchhhHHHhhHHHHHHhhHHHhhh
Q 020759          158 IIRLRADLQKAIDSENYALAADLRDQICKLEAESL  192 (321)
Q Consensus       158 LlqLr~~L~~AI~~E~YE~AA~LRD~Ir~Leeq~~  192 (321)
                      +..|+.+|++|-++.+||+||++||.|+.|+.-..
T Consensus       201 ~~~L~~~M~~aa~~l~FE~Aa~~RD~i~~l~~~~~  235 (567)
T PRK14667        201 LPELYDKIEEYSQKLMFEKAAVIRDQILALENLIK  235 (567)
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHh
Confidence            56788899999999999999999999999987544

>PRK14666 uvrC excinuclease ABC subunit C; Provisional

Probab=92.54  E-value=0.2  Score=54.06  Aligned_cols=35  Identities=31%  Similarity=0.387  Sum_probs=31.3

Q ss_pred             HHHHHHHHHHhhchhhHHHhhHHHHHHhhHHHhhh
Q 020759          158 IIRLRADLQKAIDSENYALAADLRDQICKLEAESL  192 (321)
Q Consensus       158 LlqLr~~L~~AI~~E~YE~AA~LRD~Ir~Leeq~~  192 (321)
                      +..|+.+|++|-++.+||+||++||.|+.|+.-..
T Consensus       203 ~~~L~~~M~~AAe~l~FE~AA~lRD~i~aL~~~~~  237 (694)
T PRK14666        203 VDALRTEMEAASEALEFERAAVLRDQIRAVERTVE  237 (694)
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHh
Confidence            56788899999999999999999999999987544

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=92.45  E-value=0.18  Score=53.37  Aligned_cols=36  Identities=33%  Similarity=0.434  Sum_probs=32.5

Q ss_pred             HHHHHHHHHHHhhchhhHHHhhHHHHHHhhHHHhhh
Q 020759          157 SIIRLRADLQKAIDSENYALAADLRDQICKLEAESL  192 (321)
Q Consensus       157 qLlqLr~~L~~AI~~E~YE~AA~LRD~Ir~Leeq~~  192 (321)
                      .+..|+.+|++|.++.+||+||.+||+|+.|+....
T Consensus       614 ~~~~l~~~M~~aa~~l~fE~Aa~~Rd~i~~l~~~~~  649 (652)
T PRK05298        614 LIKELEKQMKEAAKNLEFEEAARLRDEIKELKEELL  649 (652)
T ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHhc
Confidence            477888999999999999999999999999997643

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=92.07  E-value=0.14  Score=54.42  Aligned_cols=32  Identities=31%  Similarity=0.469  Sum_probs=29.3

Q ss_pred             HHHHHHHHHHHhhchhhHHHhhHHHHHHhhHH
Q 020759          157 SIIRLRADLQKAIDSENYALAADLRDQICKLE  188 (321)
Q Consensus       157 qLlqLr~~L~~AI~~E~YE~AA~LRD~Ir~Le  188 (321)
                      .|..|+.+|++|.++.+||+||.+||+|+.|+
T Consensus       624 ~i~~l~~~M~~aa~~l~FE~Aa~~RD~i~~L~  655 (655)
T TIGR00631       624 LIKQLEKEMKQAARNLEFEEAARLRDEILELK  655 (655)
T ss_pred             HHHHHHHHHHHHHHccCHHHHHHHHHHHHhcC
Confidence            47788999999999999999999999999874

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University)

>PRK07883 hypothetical protein; Validated

Probab=91.98  E-value=0.15  Score=53.14  Aligned_cols=35  Identities=29%  Similarity=0.413  Sum_probs=31.1

Q ss_pred             HHHHHHHHHHhhchhhHHHhhHHHHHHhhHHHhhh
Q 020759          158 IIRLRADLQKAIDSENYALAADLRDQICKLEAESL  192 (321)
Q Consensus       158 LlqLr~~L~~AI~~E~YE~AA~LRD~Ir~Leeq~~  192 (321)
                      +.+|+.+|++|-++.+||+||++||+|+.|+.-..
T Consensus       408 ~~~l~~~M~~aa~~l~FE~Aa~~Rd~i~~l~~~~~  442 (557)
T PRK07883        408 LAALRARIDRLAAAERFEEAARLRDRLAALLRALA  442 (557)
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHH
Confidence            56788899999999999999999999999986443

>PRK14672 uvrC excinuclease ABC subunit C; Provisional

Probab=91.54  E-value=0.3  Score=52.62  Aligned_cols=35  Identities=26%  Similarity=0.474  Sum_probs=30.9

Q ss_pred             HHHHHHHHHHhhchhhHHHhhHHHHHHhhHHHhhh
Q 020759          158 IIRLRADLQKAIDSENYALAADLRDQICKLEAESL  192 (321)
Q Consensus       158 LlqLr~~L~~AI~~E~YE~AA~LRD~Ir~Leeq~~  192 (321)
                      +.+|+.+|++|-++.+||+||++||.|+.|+.-..
T Consensus       207 l~~L~~~M~~AA~~l~FE~AA~lRD~i~aL~~~~~  241 (691)
T PRK14672        207 VARLEKRMKRAVRQEAFEAAARIRDDIQAIRCITH  241 (691)
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHh
Confidence            56788899999999999999999999999985433

>PRK14669 uvrC excinuclease ABC subunit C; Provisional

Probab=91.42  E-value=0.34  Score=51.64  Aligned_cols=35  Identities=31%  Similarity=0.323  Sum_probs=31.0

Q ss_pred             HHHHHHHHHHhhchhhHHHhhHHHHHHhhHHHhhh
Q 020759          158 IIRLRADLQKAIDSENYALAADLRDQICKLEAESL  192 (321)
Q Consensus       158 LlqLr~~L~~AI~~E~YE~AA~LRD~Ir~Leeq~~  192 (321)
                      +..|+.+|+.|-++.+||+||++||.|+.|+.-..
T Consensus       205 ~~~L~~~M~~aa~~l~FE~Aa~~RD~i~~l~~~~~  239 (624)
T PRK14669        205 ARSLRARMEAAALEMQFELAAKYRDLITTVEELEE  239 (624)
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHh
Confidence            55788899999999999999999999999986544

>PRK14670 uvrC excinuclease ABC subunit C; Provisional

Probab=90.36  E-value=0.46  Score=50.19  Aligned_cols=35  Identities=20%  Similarity=0.330  Sum_probs=31.3

Q ss_pred             HHHHHHHHHHhhchhhHHHhhHHHHHHhhHHHhhh
Q 020759          158 IIRLRADLQKAIDSENYALAADLRDQICKLEAESL  192 (321)
Q Consensus       158 LlqLr~~L~~AI~~E~YE~AA~LRD~Ir~Leeq~~  192 (321)
                      +.+|+.+|..|-++.+||+||++||.|+.|+.-..
T Consensus       179 ~~~L~~~M~~aa~~l~FE~Aa~~RD~i~al~~~~~  213 (574)
T PRK14670        179 LSQIEIKMKEAIQKEDFEAAIKLKETKRSLIEISQ  213 (574)
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHh
Confidence            56788899999999999999999999999987544

>PRK14668 uvrC excinuclease ABC subunit C; Provisional

Probab=89.84  E-value=0.34  Score=51.08  Aligned_cols=34  Identities=29%  Similarity=0.428  Sum_probs=30.6

Q ss_pred             HHHHHHHHHHhhchhhHHHhhHHHHHHhhHHHhh
Q 020759          158 IIRLRADLQKAIDSENYALAADLRDQICKLEAES  191 (321)
Q Consensus       158 LlqLr~~L~~AI~~E~YE~AA~LRD~Ir~Leeq~  191 (321)
                      +..|+.+|++|-++.+||+||.+||.|+.|+.-.
T Consensus       201 ~~~l~~~m~~aa~~l~FE~Aa~~Rd~i~~l~~~~  234 (577)
T PRK14668        201 ADPLRREMEAAAQAQEFERAANLRDRLEAVEAFH  234 (577)
T ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHH
Confidence            5678899999999999999999999999998644

>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]

Probab=89.63  E-value=0.49  Score=50.15  Aligned_cols=75  Identities=21%  Similarity=0.188  Sum_probs=50.4

Q ss_pred             HHHHHHHHHHhhchhhHHHhhHHHHHHhhHHHhhhhh--h-hhhhhccccccccccCcEEEeeecCceEEEEcccccc
Q 020759          158 IIRLRADLQKAIDSENYALAADLRDQICKLEAESLAA--S-ATALAFENARFAFRLGQKVNHKIFGYRAVICGMDPVC  232 (321)
Q Consensus       158 LlqLr~~L~~AI~~E~YE~AA~LRD~Ir~Leeq~~aa--s-a~a~~~~n~~vkFrVGQVvrHR~ygYrGVIvGWDp~c  232 (321)
                      +..|+.+|++|-+..+||+||.+||.|..|+.-....  . .+....+.-...+.-|....+..+-..|-++|-+..+
T Consensus       204 ~~~L~~~M~~As~~l~FE~Aa~~RD~i~al~~l~~~q~v~~~~~~~~Dv~a~~~~~~~~~v~vf~~R~Gkllg~~~~f  281 (581)
T COG0322         204 LQELEEKMEEASENLDFERAARLRDQIKALEKLQEKQAVSLFKLQDLDVIAGAVDGGEACVQVFFVRGGKLLGRRAYF  281 (581)
T ss_pred             HHHHHHHHHHHHHhhchHHHHHHHHHHHHHHHHHhccccccCCccchhhheeeecCCeEEEEEEEeecchhcCCccee
Confidence            5678889999999999999999999999998655421  1 1112222333355556666665555557777766433

---

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	321
1vbv_A	105	Hypothetical protein B0966; protein degradation, s	1e-13
1qzv_F	154	Plant photosystem I: subunit PSAF; photosynthesis,	6e-04

>1vbv_A Hypothetical protein B0966; protein degradation, structural genomics, unknown function; 2.70A {Escherichia coli} SCOP: b.34.17.1 Length = 105

 Score = 65.3 bits (159), Expect = 1e-13
 Identities = 15/52 (28%), Positives = 25/52 (48%), Gaps = 2/52 (3%)

Query: 208 FRLGQKVNHKIFGYRAVICGMDPVCCESSSWMEIAQVEKLQQGPSQPFYQLL 259
           F +GQ+V H + GY  V+  +DPV   S    +   V       + P+Y ++
Sbjct: 6   FGIGQQVRHSLLGYLGVVVDIDPVYSLSEPSPDELAVNDE--LRAAPWYHVV 55

>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant photosynthetic reaction center, peripheral antenna; HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1 Length = 154

 Score = 38.8 bits (89), Expect = 6e-04
 Identities = 12/28 (42%), Positives = 15/28 (53%), Gaps = 6/28 (21%)

Query: 181 RDQICKLEAESL---AA-SATALAFENA 204
           +  + KL+A SL   A  SA ALA   A
Sbjct: 19  KQALKKLQA-SLKLYADDSAPALAI-KA 44

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	321
1vbv_A	105	Hypothetical protein B0966; protein degradation, s	99.92
1e52_A	63	Excinuclease ABC subunit; DNA excision repair, UVR	97.56
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	95.28
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	93.98

>1vbv_A Hypothetical protein B0966; protein degradation, structural genomics, unknown function; 2.70A {Escherichia coli} SCOP: b.34.17.1

Probab=99.92  E-value=1.8e-26  Score=189.62  Aligned_cols=83  Identities=23%  Similarity=0.361  Sum_probs=52.5

Q ss_pred             ccccccCcEEEeeecCceEEEEcccccccCChhHHHHhhhhccCCCCCCCceEEEEeCC-------ccCccccccCC---
Q 020759          205 RFAFRLGQKVNHKIFGYRAVICGMDPVCCESSSWMEIAQVEKLQQGPSQPFYQLLRRIC-------WLLTNQTWQGL---  274 (321)
Q Consensus       205 ~vkFrVGQVvrHR~ygYrGVIvGWDp~c~a~eeW~~~~~v~~l~~gr~QPFYhVLVD~r-------~v~~~ql~~~~---  274 (321)
                      .++|+|||||+||+|||+|||+||||.|+++++|+..|+.+  .++++|||||||||++       ||++++|.+..   
T Consensus         3 ~~kf~IGqvvrHr~~gyrGVI~d~Dp~~~~~eew~~~~~~~--~~~~~QPfYhVL~e~~~~~~~~~YVaEenL~~~~s~~   80 (105)
T 1vbv_A            3 ASKFGIGQQVRHSLLGYLGVVVDIDPVYSLSEPSPDELAVN--DELRAAPWYHVVMEDDNGLPVHTYLAEAQLSSELQDE   80 (105)
T ss_dssp             CCSSCTTCEEEETTTCCEEEEEEEECC--------------------CCCEEEEEEECSSCCEEEEEEEGGGEEECCCSC
T ss_pred             cceecCCCEEEecccCCCEEEEeECcccCCCHHHHHhcccc--CccCCCCceEEEEeCCCCceeeeEEcHHhccccCCCC
Confidence            47999999999999999999999999999999999999766  4799999999999865       46666655311   


Q ss_pred             -----CccceeeeecceEEE
Q 020759          275 -----IIPIFLSCFTGRIQL  289 (321)
Q Consensus       275 -----~i~~~f~~FdGr~y~  289 (321)
                           .|+.+|+.|+|.+|+
T Consensus        81 ~i~HP~i~~~F~~f~~~~y~  100 (105)
T 1vbv_A           81 HPEQPSMDELAQTIRKQLQA  100 (105)
T ss_dssp             CTTCHHHHHHHHHHTTC---
T ss_pred             CcCCCCHHHHhHhhcCCccc
Confidence                 344899999999996

>2d7d_A Uvrabc system protein B; helicase, protein-DNA-ADP ternary complex, hydrolase/DNA complex; HET: ADP; 2.10A {Bacillus subtilis} PDB: 2nmv_A* 2fdc_A* 1t5l_A 3uwx_B 1d9z_A* 1d9x_A 2d7d_B* 2nmv_B*

Probab=95.28  E-value=0.0091  Score=60.89  Aligned_cols=35  Identities=26%  Similarity=0.457  Sum_probs=26.9

Q ss_pred             HHHHHHHHHHHHhhchhhHHHhhHHHHHHhhHHHh
Q 020759          156 LSIIRLRADLQKAIDSENYALAADLRDQICKLEAE  190 (321)
Q Consensus       156 ~qLlqLr~~L~~AI~~E~YE~AA~LRD~Ir~Leeq  190 (321)
                      ..|.+|+.+|++|.++++||+||+|||+|+.|+++
T Consensus       626 ~~i~~l~~~m~~aa~~~~fe~Aa~~Rd~i~~l~~~  660 (661)
T 2d7d_A          626 KVVEQMEHEMKEAAKALDFERAAELRDLLLELKAE  660 (661)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHC------
T ss_pred             HHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHhc
Confidence            34778899999999999999999999999999865

>1c4o_A DNA nucleotide excision repair enzyme UVRB; uvrabc, helicase, hypertherm protein, replication; HET: DNA BOG; 1.50A {Thermus thermophilus} SCOP: c.37.1.19 c.37.1.19 PDB: 1d2m_A*

Probab=93.98  E-value=0.0098  Score=60.71  Aligned_cols=35  Identities=34%  Similarity=0.429  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHhhchhhHHHhhHHHHHHhhHHHhh
Q 020759          157 SIIRLRADLQKAIDSENYALAADLRDQICKLEAES  191 (321)
Q Consensus       157 qLlqLr~~L~~AI~~E~YE~AA~LRD~Ir~Leeq~  191 (321)
                      .|.+|+.+|++|.+.++||+||.|||+|++|+++.
T Consensus       612 ~i~~l~~~m~~aa~~l~fe~Aa~lRd~i~~l~~~~  646 (664)
T 1c4o_A          612 RIAELELAMWQAAEALDFERAARLRDEIRALEARL  646 (664)
T ss_dssp             -----------------------------------
T ss_pred             HHHHHHHHHHHHHHhcChHHHHHHHHHHHHHHHHH
Confidence            47788899999999999999999999999999874

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	321
d1vbva1	95	b.34.17.1 (A:3-97) Hypothetical protein YccV {Esch	1e-14
d1e52a_	56	a.2.9.1 (A:) C-terminal UvrC-binding domain of Uvr	6e-04

>d1vbva1 b.34.17.1 (A:3-97) Hypothetical protein YccV {Escherichia coli [TaxId: 562]} Length = 95

class: All beta proteins
fold: SH3-like barrel
superfamily: YccV-like
family: YccV-like
domain: Hypothetical protein YccV
species: Escherichia coli [TaxId: 562]

 Score = 66.4 bits (162), Expect = 1e-14
 Identities = 15/52 (28%), Positives = 26/52 (50%), Gaps = 2/52 (3%)

Query: 208 FRLGQKVNHKIFGYRAVICGMDPVCCESSSWMEIAQVEKLQQGPSQPFYQLL 259
           F +GQ+V H + GY  V+  +DPV   S    +   V    +  + P+Y ++
Sbjct: 4   FGIGQQVRHSLLGYLGVVVDIDPVYSLSEPSPDELAVNDELR--AAPWYHVV 53

>d1e52a_ a.2.9.1 (A:) C-terminal UvrC-binding domain of UvrB {Escherichia coli [TaxId: 562]} Length = 56

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: C-terminal UvrC-binding domain of UvrB
family: C-terminal UvrC-binding domain of UvrB
domain: C-terminal UvrC-binding domain of UvrB
species: Escherichia coli [TaxId: 562]

 Score = 35.1 bits (81), Expect = 6e-04
 Identities = 11/38 (28%), Positives = 19/38 (50%)

Query: 158 IIRLRADLQKAIDSENYALAADLRDQICKLEAESLAAS 195
           I  L   + +   +  +  AA +RDQ+ +L    +AAS
Sbjct: 19  IHELEGLMMQHAQNLEFEEAAQIRDQLHQLRELFIAAS 56

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	321
d1vbva1	95	Hypothetical protein YccV {Escherichia coli [TaxId	99.87
d1e52a_	56	C-terminal UvrC-binding domain of UvrB {Escherichi	97.64

>d1vbva1 b.34.17.1 (A:3-97) Hypothetical protein YccV {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: SH3-like barrel
superfamily: YccV-like
family: YccV-like
domain: Hypothetical protein YccV
species: Escherichia coli [TaxId: 562]

Probab=99.87  E-value=1.2e-23  Score=168.85  Aligned_cols=56  Identities=27%  Similarity=0.469  Sum_probs=36.0

Q ss_pred             cccccCcEEEeeecCceEEEEcccccccCChhHHHHhhhhccCCCCCCCceEEEEeCC
Q 020759          206 FAFRLGQKVNHKIFGYRAVICGMDPVCCESSSWMEIAQVEKLQQGPSQPFYQLLRRIC  263 (321)
Q Consensus       206 vkFrVGQVvrHR~ygYrGVIvGWDp~c~a~eeW~~~~~v~~l~~gr~QPFYhVLVD~r  263 (321)
                      .||+|||+|+||+|||||||+||||.|.++++|+.+|+++.  ++++|||||||||++
T Consensus         2 aKF~IGqivrHr~~~yrGVI~~wDp~~~~~~eW~~~~~~~~--~~r~QPfYhvLv~~~   57 (95)
T d1vbva1           2 SKFGIGQQVRHSLLGYLGVVVDIDPVYSLSEPSPDELAVND--ELRAAPWYHVVMEDD   57 (95)
T ss_dssp             CSSCTTCEEEETTTCCEEEEEEEECC--------------------CCCEEEEEEECS
T ss_pred             CccccCcEEEEeecCcCEEEEeeEEEecCCHHHHHhccccC--CCCCCCcEEEEEEcC
Confidence            58999999999999999999999999999999999998774  578999999999854

>d1e52a_ a.2.9.1 (A:) C-terminal UvrC-binding domain of UvrB {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: C-terminal UvrC-binding domain of UvrB
family: C-terminal UvrC-binding domain of UvrB
domain: C-terminal UvrC-binding domain of UvrB
species: Escherichia coli [TaxId: 562]

Probab=97.64  E-value=2.5e-05  Score=56.12  Aligned_cols=37  Identities=24%  Similarity=0.314  Sum_probs=33.9

Q ss_pred             HHHHHHHHHHHhhchhhHHHhhHHHHHHhhHHHhhhh
Q 020759          157 SIIRLRADLQKAIDSENYALAADLRDQICKLEAESLA  193 (321)
Q Consensus       157 qLlqLr~~L~~AI~~E~YE~AA~LRD~Ir~Leeq~~a  193 (321)
                      .|.+|+.+|++|.+..+||+||.+||+|+.|++...+
T Consensus        18 ~i~~Le~~M~~aa~~l~FE~AA~~RD~I~~l~~~l~~   54 (56)
T d1e52a_          18 KIHELEGLMMQHAQNLEFEEAAQIRDQLHQLRELFIA   54 (56)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHh
Confidence            4889999999999999999999999999999987653