Citrus Sinensis ID: 027566

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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--
Protein Sequence
MHAFNLSSINVSTEFNATRRRRCLSYNNSLDLEYGRRRRVGRGCKDLTRTYGIVACVGGGGGGSGGGGERLSSSARSFLSRSQAYALLKQQMEVAAKTEDYKEAARIRDSLRSFEEEEPIFRLRRLMKEAVAEERFEDAARYRDKLKEIAPNSLLKCLSDATTLGIRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGKTENIL
Secondary Structure (PSIPRED)
ccccccccccEEEccccccccEEEccccccccccccccccccccccccccccEEEEEccccccccccccccccccccHHcccccHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccEEEEEEEEEccccccccccEEEEEEEEEEEcccccEEEcccEEEEEcccccEEEEc
Secondary Structure Prediction (SSPRO)
cccccHcHcEEEEccccccccEccccccccccccccHHEccccccccEEccEEEEEEcccccccccccccccccccccccHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHccccccccEEEEEEEEEcccccccccccEEEEEEEEEEEcccccEEEEEEEEEEEcccccEEEEc
Coil and Loop (DISEMBL)
mhafnlssinvstefnatRRRRCLSYnnsldleygrrrrvgrgckdlTRTYGIVacvggggggsggggerlsSSARSFLSRSQAYALLKQQMEVAAKTEDYKEAARIRDSLRSFEEEEPIFRLRRLMKEAVAEERFEDAARYRDKLkeiapnsllKCLSDATTLGIRVQVRSVYiedrsqplkgqyFFAYRVRITNNSERPVQLLRRHWiitdangktenil
Flexible Loop (DISEMBL)
mhafnlssinvstefnatrrrrclsynnsldleygrrrrvgrgckdltrTYGIVACVGGGGGGSGGGGERLSSSARSFLSRSQAYALLKQQMEVAAKTEDYKEAARirdslrsfeeeepifrlRRLMKEAVAEERFEDAARYRDKlkeiapnsllkclsdattlgirVQVRsvyiedrsqplkgqyfFAYRVRitnnserpvqllrrhwiitdangktenil
Low Complexity Region (SEG)
MHAFNLSSINVSTEFNATRRRRCLSYNNSLDLEYGRRRRVGRGCKDLTRTYGIVACVggggggsggggErlsssarsflsrsQAYALLKQQMEVAAKTEDYKEAARIRDSLRSFEEEEPIFRLRRLMKEAVAEERFEDAARYRDKLKEIAPNSLLKCLSDATTLGIRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGKTENIL
Disordered region (IsUnstruct)
************TEFNATRRRRCLSYNNSLDLEYGRRRRVGRGCKDLTRTYGIVAC***************************************************************IFRLRRLMKEAVAEERFEDAARYRDKLKEIAPNSLLKCLSDATTLGIRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITD*********
Disordered Region (DISOPRED)
**************FNATRRRRCLSYNNSLDL***************TRTYGIVACV****************SARSFLSRSQAYALLKQQMEVAAKTEDYKEAARIRDSLRSFEEEEPIFRLRRLMKEAVAEERFED*********************DATTLGIRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANG*T**I*
Disordered Region (DISEMBL)
MHAFNLSSINVSTEFNATRRRRCLSYNNSLDLEYGRRRRVGRGCKDLTRTYGIVACVGGG*****************FLSRSQAYALLKQQMEVAAKTEDYKEAARIRDSLRSFEEEEPIFRLRRLMKEAVAEERFEDAARYRDKLKEIAPNSLLKCLSDATTLGIRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGKTENIL
Disordered Region (DISPRO)
****NLSSINVSTEFNATRRRRCLSYNNSLDLEYGRRRRVGRGCKDLTRTYGIVACVG*********************SRSQAYALLKQQMEVAAKTEDYKEAARIRDSLRSFEEEEPIFRLRRLMKEAVAEERFEDAARYRDKLKEIAPNSLLKCLSDATTLGIRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGKTENIL
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MHAFNLSSINVSTEFNATRRRRCLSYNNSLDLEYGRRRRVGRGCKDLTRTYGIVACVGGGGGGSGGGGERLSSSARSFLSRSQAYALLKQQMEVAAKTEDYKEAARIRDSLRSFEEEEPIFRLRRLMKEAVAEERFEDAARYRDKLKEIAPNSLLKCLSDATTLGIRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGKTENIL
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	222	2.2.26 [Sep-21-2011]
Q2IGT4	125	Protein ApaG OS=Anaeromyx	yes	no	0.283	0.504	0.492	6e-12
Q0ASF3	130	Protein ApaG OS=Maricauli	yes	no	0.265	0.453	0.457	2e-11
Q2VZE7	130	Protein ApaG OS=Magnetosp	yes	no	0.270	0.461	0.5	3e-11
B4UHA8	125	Protein ApaG OS=Anaeromyx	yes	no	0.283	0.504	0.492	1e-10
Q6MK56	127	Protein ApaG OS=Bdellovib	no	no	0.252	0.440	0.446	1e-10
A6WVX4	130	Protein ApaG OS=Ochrobact	yes	no	0.274	0.469	0.491	3e-10
B7VIE1	126	Protein ApaG OS=Vibrio sp	yes	no	0.261	0.460	0.517	4e-10
B8JAJ1	125	Protein ApaG OS=Anaeromyx	yes	no	0.283	0.504	0.476	6e-10
Q8EB92	126	Protein ApaG OS=Shewanell	yes	no	0.252	0.444	0.5	7e-10
Q8G2L5	130	Protein ApaG OS=Brucella	yes	no	0.288	0.492	0.453	1e-09

>sp|Q2IGT4|APAG_ANADE Protein ApaG OS=Anaeromyxobacter dehalogenans (strain 2CP-C) GN=apaG PE=3 SV=1

 Score = 70.9 bits (172), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 32/65 (49%), Positives = 44/65 (67%), Gaps = 2/65 (3%)

Query: 158 LSDATTLGIRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGK 217
           +S A T GI V VRS +  +RS+P  G++ F+Y VR+ N  E P QL+ RHWII DANG+
Sbjct: 1   MSTAVTEGIEVTVRSTFRPERSEP--GRFLFSYSVRVVNQGEAPAQLVSRHWIIVDANGE 58

Query: 218 TENIL 222
            E ++
Sbjct: 59  REEVV 63

Anaeromyxobacter dehalogenans (strain 2CP-C) (taxid: 290397)

>sp|Q0ASF3|APAG_MARMM Protein ApaG OS=Maricaulis maris (strain MCS10) GN=apaG PE=3 SV=1

 Score = 69.3 bits (168), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 27/59 (45%), Positives = 43/59 (72%)

Query: 163 TLGIRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGKTENI 221
           + G+R+ V   Y+ED S P +G++ +AY + I N  ++PVQL+ R W+ITDANG+TE++
Sbjct: 6   SCGVRISVSPDYLEDESTPEEGRFVWAYTIEIENTGKQPVQLIARKWMITDANGRTEHV 64

Maricaulis maris (strain MCS10) (taxid: 394221)

>sp|Q2VZE7|APAG_MAGSA Protein ApaG OS=Magnetospirillum magneticum (strain AMB-1 / ATCC 700264) GN=apaG PE=3 SV=1

 Score = 68.9 bits (167), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 30/60 (50%), Positives = 40/60 (66%)

Query: 162 TTLGIRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGKTENI 221
           TT  I V V+  Y++D+S P    + +AYRVRI N   R VQLLRRHW+ITDA G+ + +
Sbjct: 5   TTRDIEVTVKPFYLDDQSSPGDNHFVWAYRVRIVNKGSRTVQLLRRHWVITDAIGRVQEV 64

Magnetospirillum magneticum (strain AMB-1 / ATCC 700264) (taxid: 342108)

>sp|B4UHA8|APAG_ANASK Protein ApaG OS=Anaeromyxobacter sp. (strain K) GN=apaG PE=3 SV=1

 Score = 66.6 bits (161), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 32/65 (49%), Positives = 43/65 (66%), Gaps = 2/65 (3%)

Query: 158 LSDATTLGIRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGK 217
           +S A T GI V VRS +  +RS+P  G++ F+Y VRI N  E P QL+ R WII DANG+
Sbjct: 1   MSTAVTEGIEVTVRSTFRPERSEP--GRFLFSYTVRIANQGEVPAQLVSRRWIILDANGE 58

Query: 218 TENIL 222
            E ++
Sbjct: 59  REEVV 63

Anaeromyxobacter sp. (strain K) (taxid: 447217)

>sp|Q6MK56|APAG_BDEBA Protein ApaG OS=Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIB 9529 / HD100) GN=apaG PE=3 SV=2

 Score = 66.2 bits (160), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 25/56 (44%), Positives = 37/56 (66%)

Query: 166 IRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGKTENI 221
            ++  + VY+   S+P +G +FFAY++ ITN    P QL+ RHW+ITDA GK E +
Sbjct: 9   FQITAKVVYVPSESRPDEGYHFFAYKITITNTGSTPAQLMSRHWVITDALGKKEEV 64

Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIB 9529 / HD100) (taxid: 264462)

>sp|A6WVX4|APAG_OCHA4 Protein ApaG OS=Ochrobactrum anthropi (strain ATCC 49188 / DSM 6882 / NCTC 12168) GN=apaG PE=3 SV=1

 Score = 65.1 bits (157), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 30/61 (49%), Positives = 39/61 (63%)

Query: 161 ATTLGIRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGKTEN 220
           A T GI V V   Y+ED+S+P + +Y + YR+ I NNS   VQL  R+W ITDANG  E 
Sbjct: 4   AVTRGIEVSVEPFYLEDQSEPEENRYVWGYRITIANNSTETVQLRSRYWQITDANGYVEE 63

Query: 221 I 221
           +
Sbjct: 64  V 64

Ochrobactrum anthropi (strain ATCC 49188 / DSM 6882 / NCTC 12168) (taxid: 439375)

>sp|B7VIE1|APAG_VIBSL Protein ApaG OS=Vibrio splendidus (strain LGP32) GN=apaG PE=3 SV=1

 Score = 65.1 bits (157), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 30/58 (51%), Positives = 41/58 (70%)

Query: 160 DATTLGIRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGK 217
           D +T  I+ QV S YIE++S+P K +Y FAY + I N S+  VQL+ R W+ITD+NGK
Sbjct: 2   DISTPCIKCQVHSKYIEEQSEPSKNRYVFAYIITIKNLSKTTVQLMSRSWLITDSNGK 59

Vibrio splendidus (strain LGP32) (taxid: 575788)

>sp|B8JAJ1|APAG_ANAD2 Protein ApaG OS=Anaeromyxobacter dehalogenans (strain 2CP-1 / ATCC BAA-258) GN=apaG PE=3 SV=1

 Score = 64.3 bits (155), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 31/65 (47%), Positives = 43/65 (66%), Gaps = 2/65 (3%)

Query: 158 LSDATTLGIRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGK 217
           +S A T GI V VRS +  +RS+P  G++ F+Y VRI N  E P QL+ R WII DA+G+
Sbjct: 1   MSTAVTEGIEVTVRSTFRPERSEP--GRFLFSYTVRIANQGEVPAQLVSRRWIILDASGE 58

Query: 218 TENIL 222
            E ++
Sbjct: 59  REEVV 63

Anaeromyxobacter dehalogenans (strain 2CP-1 / ATCC BAA-258) (taxid: 455488)

>sp|Q8EB92|APAG_SHEON Protein ApaG OS=Shewanella oneidensis (strain MR-1) GN=apaG PE=1 SV=1

 Score = 64.3 bits (155), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 28/56 (50%), Positives = 38/56 (67%)

Query: 166 IRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGKTENI 221
           IRV+V++ YIE +S P   +Y F+Y + I N  E+  +L  RHWIITDANGKT  +
Sbjct: 8   IRVEVKTEYIEQQSSPEDEKYLFSYTITIINLGEQAAKLETRHWIITDANGKTSEV 63

Shewanella oneidensis (strain MR-1) (taxid: 211586)

>sp|Q8G2L5|APAG_BRUSU Protein ApaG OS=Brucella suis biovar 1 (strain 1330) GN=apaG PE=3 SV=1

 Score = 63.2 bits (152), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 29/64 (45%), Positives = 39/64 (60%)

Query: 158 LSDATTLGIRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGK 217
           +  A T GI V V   Y+E +S+P + +Y + YRV I NNS   VQL  R+W ITDANG 
Sbjct: 1   MYSAVTRGIEVTVEPFYLEVQSEPEENRYVWGYRVTIVNNSSETVQLCSRYWQITDANGH 60

Query: 218 TENI 221
            + +
Sbjct: 61  VQEV 64

Brucella suis biovar 1 (strain 1330) (taxid: 204722)

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	222
297733766	375	unnamed protein product [Vitis vinifera]	0.878	0.52	0.666	7e-72
225457005	277	PREDICTED: uncharacterized protein LOC10	0.855	0.685	0.677	6e-71
224133570	285	predicted protein [Populus trichocarpa]	0.846	0.659	0.718	2e-68
147841526	223	hypothetical protein VITISV_003764 [Viti	0.666	0.663	0.837	2e-67
449469699	261	PREDICTED: F-box protein SKIP16-like [Cu	0.815	0.693	0.691	4e-66
224119374	283	predicted protein [Populus trichocarpa]	0.648	0.508	0.833	3e-65
222630358	300	hypothetical protein OsJ_17287 [Oryza sa	0.662	0.49	0.795	5e-64
115462343	300	Os05g0170800 [Oryza sativa Japonica Grou	0.662	0.49	0.795	5e-64
242089717	290	hypothetical protein SORBIDRAFT_09g00520	0.653	0.5	0.806	6e-64
169730490	300	SKIP interacting protein 10 [Oryza sativ	0.662	0.49	0.795	6e-64

>gi|297733766|emb|CBI15013.3| unnamed protein product [Vitis vinifera]

 Score =  275 bits (704), Expect = 7e-72,   Method: Compositional matrix adjust.
 Identities = 144/216 (66%), Positives = 162/216 (75%), Gaps = 21/216 (9%)

Query: 19  RRRRCLSYNNSLDLEYGRRR-------------RVGRGCKDLTRTYGIVACVGGGGGGSG 65
           R    LS+    DL  GR R             + G  C+D  R   I AC       SG
Sbjct: 97  REMHALSFKGFPDLNVGRERSWPGRLYHCTGTRKDGWNCRDFRRNCRIFAC------SSG 150

Query: 66  GGGERLSSSARSFLSRSQAYALLKQQMEVAAKTEDYKEAARIRDSLRSFEEEEPIFRLRR 125
             GE  S S  SFLSRSQ YALLKQQ++VAAK+EDYKEAAR+RDSLR FEEEEP+ RLRR
Sbjct: 151 ANGENQSPS--SFLSRSQTYALLKQQLQVAAKSEDYKEAARLRDSLRLFEEEEPVLRLRR 208

Query: 126 LMKEAVAEERFEDAARYRDKLKEIAPNSLLKCLSDATTLGIRVQVRSVYIEDRSQPLKGQ 185
           L+KEAVA+ERFEDAARYRD+LKEIAP+SLLKC SDATT+GIRVQVRSVYIE RSQP KGQ
Sbjct: 209 LIKEAVADERFEDAARYRDELKEIAPHSLLKCSSDATTVGIRVQVRSVYIEGRSQPSKGQ 268

Query: 186 YFFAYRVRITNNSERPVQLLRRHWIITDANGKTENI 221
           +FFAYR+RITNNS+RPVQLLRRHWIITDANGK E++
Sbjct: 269 FFFAYRIRITNNSDRPVQLLRRHWIITDANGKIEHV 304

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225457005|ref|XP_002282383.1| PREDICTED: uncharacterized protein LOC100267315 [Vitis vinifera]

 Score =  272 bits (696), Expect = 6e-71,   Method: Compositional matrix adjust.
 Identities = 143/211 (67%), Positives = 161/211 (76%), Gaps = 21/211 (9%)

Query: 24  LSYNNSLDLEYGRRR-------------RVGRGCKDLTRTYGIVACVGGGGGGSGGGGER 70
           LS+    DL  GR R             + G  C+D  R   I AC       SG  GE 
Sbjct: 4   LSFKGFPDLNVGRERSWPGRLYHCTGTRKDGWNCRDFRRNCRIFAC------SSGANGEN 57

Query: 71  LSSSARSFLSRSQAYALLKQQMEVAAKTEDYKEAARIRDSLRSFEEEEPIFRLRRLMKEA 130
            S S  SFLSRSQ YALLKQQ++VAAK+EDYKEAAR+RDSLR FEEEEP+ RLRRL+KEA
Sbjct: 58  QSPS--SFLSRSQTYALLKQQLQVAAKSEDYKEAARLRDSLRLFEEEEPVLRLRRLIKEA 115

Query: 131 VAEERFEDAARYRDKLKEIAPNSLLKCLSDATTLGIRVQVRSVYIEDRSQPLKGQYFFAY 190
           VA+ERFEDAARYRD+LKEIAP+SLLKC SDATT+GIRVQVRSVYIE RSQP KGQ+FFAY
Sbjct: 116 VADERFEDAARYRDELKEIAPHSLLKCSSDATTVGIRVQVRSVYIEGRSQPSKGQFFFAY 175

Query: 191 RVRITNNSERPVQLLRRHWIITDANGKTENI 221
           R+RITNNS+RPVQLLRRHWIITDANGK E++
Sbjct: 176 RIRITNNSDRPVQLLRRHWIITDANGKIEHV 206

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224133570|ref|XP_002321607.1| predicted protein [Populus trichocarpa] gi|222868603|gb|EEF05734.1| predicted protein [Populus trichocarpa]

 Score =  264 bits (675), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 138/192 (71%), Positives = 153/192 (79%), Gaps = 4/192 (2%)

Query: 34  YGRRRRVGRGCKDLTRTYGIVACV----GGGGGGSGGGGERLSSSARSFLSRSQAYALLK 89
           +G   R     ++ +R   IVAC     GGG G S         S  SFLSRSQ YA+LK
Sbjct: 25  FGTEWRQCLNLRNYSRNCRIVACSVERDGGGEGASSSSSSSSDPSPSSFLSRSQTYAMLK 84

Query: 90  QQMEVAAKTEDYKEAARIRDSLRSFEEEEPIFRLRRLMKEAVAEERFEDAARYRDKLKEI 149
           QQMEVAA++EDY+EAAR+RDSLRSFEE EP+ RLRRL+KEAVA+ERFEDA RYRD+LKEI
Sbjct: 85  QQMEVAAQSEDYEEAARLRDSLRSFEEVEPVLRLRRLLKEAVADERFEDATRYRDELKEI 144

Query: 150 APNSLLKCLSDATTLGIRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHW 209
           AP SLLKC SDATTLGIRVQVRSVYIE RSQP KGQYFFAYR+RITNNS+RPVQLLRRHW
Sbjct: 145 APLSLLKCSSDATTLGIRVQVRSVYIEGRSQPSKGQYFFAYRIRITNNSDRPVQLLRRHW 204

Query: 210 IITDANGKTENI 221
           IITDANGKTEN 
Sbjct: 205 IITDANGKTENF 216

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147841526|emb|CAN75322.1| hypothetical protein VITISV_003764 [Vitis vinifera]

 Score =  260 bits (665), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 124/148 (83%), Positives = 139/148 (93%)

Query: 74  SARSFLSRSQAYALLKQQMEVAAKTEDYKEAARIRDSLRSFEEEEPIFRLRRLMKEAVAE 133
           S  SFLSRSQ YALLKQQ++VAAK+EDYKEAAR+RDSLR FEEEEP+ RLRRL+KEAVA+
Sbjct: 5   SPSSFLSRSQTYALLKQQLQVAAKSEDYKEAARLRDSLRLFEEEEPVLRLRRLIKEAVAD 64

Query: 134 ERFEDAARYRDKLKEIAPNSLLKCLSDATTLGIRVQVRSVYIEDRSQPLKGQYFFAYRVR 193
           ERFEDAARYRD+LKEIAP+SLLKC SDATT+GIRVQVRSVYIE RSQP KGQ+FFAYR+R
Sbjct: 65  ERFEDAARYRDELKEIAPHSLLKCSSDATTVGIRVQVRSVYIEGRSQPSKGQFFFAYRIR 124

Query: 194 ITNNSERPVQLLRRHWIITDANGKTENI 221
           ITNNS+RPVQLLRRHWIITDANGK E++
Sbjct: 125 ITNNSDRPVQLLRRHWIITDANGKIEHV 152

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449469699|ref|XP_004152556.1| PREDICTED: F-box protein SKIP16-like [Cucumis sativus] gi|449487861|ref|XP_004157837.1| PREDICTED: F-box protein SKIP16-like [Cucumis sativus]

 Score =  256 bits (654), Expect = 4e-66,   Method: Compositional matrix adjust.
 Identities = 132/191 (69%), Positives = 149/191 (78%), Gaps = 10/191 (5%)

Query: 34  YGRRRRVGRGCKDLTRTYGIVACVGGGGGGSGGGGERLSSSARSFLSRS---QAYALLKQ 90
           +G RR  GR C+       IVAC      G GG G+  S+S     S     + YALLKQ
Sbjct: 9   FGGRRAFGRSCR-------IVACASERNIGDGGEGQSQSASTSRSRSFLSRSETYALLKQ 61

Query: 91  QMEVAAKTEDYKEAARIRDSLRSFEEEEPIFRLRRLMKEAVAEERFEDAARYRDKLKEIA 150
           Q+EVAAK+EDY+EAARIRDSL+ FEEEEP+ RLRRLMKEA++ ERFEDAA+YRD+L EIA
Sbjct: 62  QLEVAAKSEDYEEAARIRDSLKLFEEEEPVLRLRRLMKEAISSERFEDAAKYRDELNEIA 121

Query: 151 PNSLLKCLSDATTLGIRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWI 210
           P+ LLKC SDATTLGIRVQVRSVYIE RSQP K QYFFAYR+RITNNS RPVQLLRRHWI
Sbjct: 122 PHCLLKCASDATTLGIRVQVRSVYIEGRSQPSKNQYFFAYRIRITNNSNRPVQLLRRHWI 181

Query: 211 ITDANGKTENI 221
           ITDANGKTEN+
Sbjct: 182 ITDANGKTENV 192

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224119374|ref|XP_002318056.1| predicted protein [Populus trichocarpa] gi|222858729|gb|EEE96276.1| predicted protein [Populus trichocarpa]

 Score =  254 bits (648), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 120/144 (83%), Positives = 135/144 (93%)

Query: 78  FLSRSQAYALLKQQMEVAAKTEDYKEAARIRDSLRSFEEEEPIFRLRRLMKEAVAEERFE 137
           FLSRSQ YA+LKQQMEVAA++EDY+EAARIRDSL+SFEEEEP+ RL RL+KEAVA+E+FE
Sbjct: 71  FLSRSQTYAMLKQQMEVAAQSEDYEEAARIRDSLKSFEEEEPVLRLHRLLKEAVADEQFE 130

Query: 138 DAARYRDKLKEIAPNSLLKCLSDATTLGIRVQVRSVYIEDRSQPLKGQYFFAYRVRITNN 197
           DAARYRD+LKEI P+SLLKC SDATTLGIR QVRS+YIE RSQP KGQYFFAYR+RITNN
Sbjct: 131 DAARYRDELKEIVPHSLLKCSSDATTLGIRNQVRSLYIEGRSQPSKGQYFFAYRIRITNN 190

Query: 198 SERPVQLLRRHWIITDANGKTENI 221
           S+RPVQLLRRHWIITDA GKTEN+
Sbjct: 191 SDRPVQLLRRHWIITDAKGKTENV 214

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|222630358|gb|EEE62490.1| hypothetical protein OsJ_17287 [Oryza sativa Japonica Group]

 Score =  249 bits (636), Expect = 5e-64,   Method: Compositional matrix adjust.
 Identities = 117/147 (79%), Positives = 136/147 (92%)

Query: 75  ARSFLSRSQAYALLKQQMEVAAKTEDYKEAARIRDSLRSFEEEEPIFRLRRLMKEAVAEE 134
           A +FL RSQ YA+LKQQ+ VAA+ EDYKEAAR+RDSL+SFEEEEP+ RLRR +K+AV EE
Sbjct: 83  AAAFLMRSQKYAMLKQQLAVAAQFEDYKEAARLRDSLKSFEEEEPVLRLRRSLKKAVEEE 142

Query: 135 RFEDAARYRDKLKEIAPNSLLKCLSDATTLGIRVQVRSVYIEDRSQPLKGQYFFAYRVRI 194
           RFEDAA+YRD+LK +AP++LLKC SDATTLGIRVQVRSVYIE RSQPLKGQ+FFAYR+RI
Sbjct: 143 RFEDAAKYRDELKILAPHALLKCSSDATTLGIRVQVRSVYIESRSQPLKGQFFFAYRIRI 202

Query: 195 TNNSERPVQLLRRHWIITDANGKTENI 221
           TNNS+RPVQLLRRHWI+TDANG+TENI
Sbjct: 203 TNNSQRPVQLLRRHWIVTDANGRTENI 229

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|115462343|ref|NP_001054771.1| Os05g0170800 [Oryza sativa Japonica Group] gi|52353765|gb|AAU44331.1| unknown protein [Oryza sativa Japonica Group] gi|113578322|dbj|BAF16685.1| Os05g0170800 [Oryza sativa Japonica Group] gi|125550999|gb|EAY96708.1| hypothetical protein OsI_18629 [Oryza sativa Indica Group]

 Score =  249 bits (636), Expect = 5e-64,   Method: Compositional matrix adjust.
 Identities = 117/147 (79%), Positives = 136/147 (92%)

Query: 75  ARSFLSRSQAYALLKQQMEVAAKTEDYKEAARIRDSLRSFEEEEPIFRLRRLMKEAVAEE 134
           A +FL RSQ YA+LKQQ+ VAA+ EDYKEAAR+RDSL+SFEEEEP+ RLRR +K+AV EE
Sbjct: 83  AAAFLMRSQKYAMLKQQLAVAAQFEDYKEAARLRDSLKSFEEEEPVLRLRRSLKKAVEEE 142

Query: 135 RFEDAARYRDKLKEIAPNSLLKCLSDATTLGIRVQVRSVYIEDRSQPLKGQYFFAYRVRI 194
           RFEDAA+YRD+LK +AP++LLKC SDATTLGIRVQVRSVYIE RSQPLKGQ+FFAYR+RI
Sbjct: 143 RFEDAAKYRDELKILAPHALLKCSSDATTLGIRVQVRSVYIESRSQPLKGQFFFAYRIRI 202

Query: 195 TNNSERPVQLLRRHWIITDANGKTENI 221
           TNNS+RPVQLLRRHWI+TDANG+TENI
Sbjct: 203 TNNSQRPVQLLRRHWIVTDANGRTENI 229

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242089717|ref|XP_002440691.1| hypothetical protein SORBIDRAFT_09g005200 [Sorghum bicolor] gi|241945976|gb|EES19121.1| hypothetical protein SORBIDRAFT_09g005200 [Sorghum bicolor]

 Score =  249 bits (636), Expect = 6e-64,   Method: Compositional matrix adjust.
 Identities = 117/145 (80%), Positives = 133/145 (91%)

Query: 77  SFLSRSQAYALLKQQMEVAAKTEDYKEAARIRDSLRSFEEEEPIFRLRRLMKEAVAEERF 136
           S L RSQ YA+LKQQ+ VAA+ EDYKEAAR+RDSLRSFEEEEP+ RLRRLMK+A+ EERF
Sbjct: 76  SLLMRSQKYAMLKQQLAVAAQFEDYKEAARLRDSLRSFEEEEPVLRLRRLMKKAIDEERF 135

Query: 137 EDAARYRDKLKEIAPNSLLKCLSDATTLGIRVQVRSVYIEDRSQPLKGQYFFAYRVRITN 196
           EDAA+YRD+L  +AP+SLLKC SDATTLGIRVQVRSVYIE RSQPLKGQ+FFAYR+RITN
Sbjct: 136 EDAAKYRDELMILAPHSLLKCSSDATTLGIRVQVRSVYIESRSQPLKGQFFFAYRIRITN 195

Query: 197 NSERPVQLLRRHWIITDANGKTENI 221
           NS+RPVQLLRRHWI+TD NG+TENI
Sbjct: 196 NSQRPVQLLRRHWIVTDGNGRTENI 220

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|169730490|gb|ACA64811.1| SKIP interacting protein 10 [Oryza sativa]

 Score =  249 bits (636), Expect = 6e-64,   Method: Compositional matrix adjust.
 Identities = 117/147 (79%), Positives = 136/147 (92%)

Query: 75  ARSFLSRSQAYALLKQQMEVAAKTEDYKEAARIRDSLRSFEEEEPIFRLRRLMKEAVAEE 134
           A +FL RSQ YA+LKQQ+ VAA+ EDYKEAAR+RDSL+SFEEEEP+ RLRR +K+AV EE
Sbjct: 83  AAAFLMRSQKYAMLKQQLAVAAQFEDYKEAARLRDSLKSFEEEEPVLRLRRSLKKAVEEE 142

Query: 135 RFEDAARYRDKLKEIAPNSLLKCLSDATTLGIRVQVRSVYIEDRSQPLKGQYFFAYRVRI 194
           RFEDAA+YRD+LK +AP++LLKC SDATTLGIRVQVRSVYIE RSQPLKGQ+FFAYR+RI
Sbjct: 143 RFEDAAKYRDELKILAPHALLKCSSDATTLGIRVQVRSVYIESRSQPLKGQFFFAYRIRI 202

Query: 195 TNNSERPVQLLRRHWIITDANGKTENI 221
           TNNS+RPVQLLRRHWI+TDANG+TENI
Sbjct: 203 TNNSQRPVQLLRRHWIVTDANGRTENI 229

Source: Oryza sativa

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	222
UNIPROTKB|Q8EB92	126	apaG "Protein ApaG" [Shewanell	0.252	0.444	0.5	1.2e-10
TIGR_CMR|SO_3640	126	SO_3640 "apaG protein" [Shewan	0.252	0.444	0.5	1.2e-10
UNIPROTKB|Q60C69	126	apaG "Protein ApaG" [Methyloco	0.256	0.452	0.473	3.2e-10
UNIPROTKB|Q9KUS3	126	apaG "Protein ApaG" [Vibrio ch	0.234	0.412	0.480	5.9e-09
TIGR_CMR|VC_0442	126	VC_0442 "apaG protein" [Vibrio	0.234	0.412	0.480	5.9e-09
UNIPROTKB|Q0BYU0	138	apaG "ApaG protein" [Hyphomona	0.279	0.449	0.338	7.6e-09
UNIPROTKB|Q2GIY5	135	apaG "ApaG protein" [Anaplasma	0.301	0.496	0.376	3.4e-07
TIGR_CMR|APH_1120	135	APH_1120 "apaG protein" [Anapl	0.301	0.496	0.376	3.4e-07
UNIPROTKB|Q2GFG4	134	apaG "Protein ApaG" [Ehrlichia	0.229	0.380	0.431	1.8e-06
TIGR_CMR|ECH_1033	134	ECH_1033 "apaG protein" [Ehrli	0.229	0.380	0.431	1.8e-06

UNIPROTKB|Q8EB92 apaG "Protein ApaG" [Shewanella oneidensis MR-1 (taxid:211586)]

 Score = 149 (57.5 bits), Expect = 1.2e-10, P = 1.2e-10
 Identities = 28/56 (50%), Positives = 38/56 (67%)

Query:   166 IRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGKTENI 221
             IRV+V++ YIE +S P   +Y F+Y + I N  E+  +L  RHWIITDANGKT  +
Sbjct:     8 IRVEVKTEYIEQQSSPEDEKYLFSYTITIINLGEQAAKLETRHWIITDANGKTSEV 63

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

TIGR_CMR|SO_3640 SO_3640 "apaG protein" [Shewanella oneidensis MR-1 (taxid:211586)]

 Score = 149 (57.5 bits), Expect = 1.2e-10, P = 1.2e-10
 Identities = 28/56 (50%), Positives = 38/56 (67%)

Query:   166 IRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGKTENI 221
             IRV+V++ YIE +S P   +Y F+Y + I N  E+  +L  RHWIITDANGKT  +
Sbjct:     8 IRVEVKTEYIEQQSSPEDEKYLFSYTITIINLGEQAAKLETRHWIITDANGKTSEV 63

GO:0008150 "biological_process" evidence=ND

GO:0003674 "molecular_function" evidence=ND

UNIPROTKB|Q60C69 apaG "Protein ApaG" [Methylococcus capsulatus str. Bath (taxid:243233)]

 Score = 145 (56.1 bits), Expect = 3.2e-10, P = 3.2e-10
 Identities = 27/57 (47%), Positives = 39/57 (68%)

Query:   166 IRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGKTENIL 222
             ++V+V++VY+ + S+P   QY FAY V + N    P +LL R WIITDANGKT  ++
Sbjct:     8 LKVEVKAVYLREHSRPDAHQYTFAYTVTMENTGTVPAKLLGRRWIITDANGKTVEVV 64

GO:0003674 "molecular_function" evidence=ND

UNIPROTKB|Q9KUS3 apaG "Protein ApaG" [Vibrio cholerae O1 biovar El Tor str. N16961 (taxid:243277)]

 Score = 133 (51.9 bits), Expect = 5.9e-09, P = 5.9e-09
 Identities = 25/52 (48%), Positives = 38/52 (73%)

Query:   166 IRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGK 217
             I++QV++ YIE++S P   ++ FAY + I N S + VQL+ R W+ITDA+GK
Sbjct:     8 IKIQVQTRYIEEQSNPEYQRFVFAYLITIKNLSSQTVQLMSRRWLITDADGK 59

GO:0008150 "biological_process" evidence=ND

TIGR_CMR|VC_0442 VC_0442 "apaG protein" [Vibrio cholerae O1 biovar El Tor (taxid:686)]

 Score = 133 (51.9 bits), Expect = 5.9e-09, P = 5.9e-09
 Identities = 25/52 (48%), Positives = 38/52 (73%)

Query:   166 IRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGK 217
             I++QV++ YIE++S P   ++ FAY + I N S + VQL+ R W+ITDA+GK
Sbjct:     8 IKIQVQTRYIEEQSNPEYQRFVFAYLITIKNLSSQTVQLMSRRWLITDADGK 59

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|Q0BYU0 apaG "ApaG protein" [Hyphomonas neptunium ATCC 15444 (taxid:228405)]

 Score = 132 (51.5 bits), Expect = 7.6e-09, P = 7.6e-09
 Identities = 21/62 (33%), Positives = 40/62 (64%)

Query:   160 DATTLGIRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGKTE 219
             +A T G+R++VR  ++ D S+P + ++ + Y V + N S+R   ++RRHW I D+ G+ +
Sbjct:    11 EAITDGVRIRVRPKFLHDESEPTRAKFMWQYTVEVENESDRTWTIIRRHWRIVDSAGRLQ 70

Query:   220 NI 221
              +
Sbjct:    71 AV 72

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|Q2GIY5 apaG "ApaG protein" [Anaplasma phagocytophilum HZ (taxid:212042)]

 Score = 117 (46.2 bits), Expect = 3.4e-07, P = 3.4e-07
 Identities = 26/69 (37%), Positives = 39/69 (56%)

Query:   153 SLLKCLSDATTLGIRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIIT 212
             ++L+C  +A    I V+V   Y+E+ S P +  Y + Y VRI N S+  VQLL+R W I 
Sbjct:     2 TVLECGKEAGL--IEVEVTPSYLEEHSIPHENCYIWLYSVRINNRSDSTVQLLKRSWKII 59

Query:   213 DANGKTENI 221
             D+ G    +
Sbjct:    60 DSKGVVNEV 68

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

TIGR_CMR|APH_1120 APH_1120 "apaG protein" [Anaplasma phagocytophilum HZ (taxid:212042)]

 Score = 117 (46.2 bits), Expect = 3.4e-07, P = 3.4e-07
 Identities = 26/69 (37%), Positives = 39/69 (56%)

Query:   153 SLLKCLSDATTLGIRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIIT 212
             ++L+C  +A    I V+V   Y+E+ S P +  Y + Y VRI N S+  VQLL+R W I 
Sbjct:     2 TVLECGKEAGL--IEVEVTPSYLEEHSIPHENCYIWLYSVRINNRSDSTVQLLKRSWKII 59

Query:   213 DANGKTENI 221
             D+ G    +
Sbjct:    60 DSKGVVNEV 68

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|Q2GFG4 apaG "Protein ApaG" [Ehrlichia chaffeensis str. Arkansas (taxid:205920)]

 Score = 111 (44.1 bits), Expect = 1.8e-06, P = 1.8e-06
 Identities = 22/51 (43%), Positives = 31/51 (60%)

Query:   166 IRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANG 216
             I V+V   Y+E++S P +  Y + Y +R+ N S   VQLLRR W I D+ G
Sbjct:    12 IEVKVVPSYLEEQSAPHENCYIWLYNIRVKNKSNSTVQLLRRSWKIIDSTG 62

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

TIGR_CMR|ECH_1033 ECH_1033 "apaG protein" [Ehrlichia chaffeensis str. Arkansas (taxid:205920)]

 Score = 111 (44.1 bits), Expect = 1.8e-06, P = 1.8e-06
 Identities = 22/51 (43%), Positives = 31/51 (60%)

Query:   166 IRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANG 216
             I V+V   Y+E++S P +  Y + Y +R+ N S   VQLLRR W I D+ G
Sbjct:    12 IEVKVVPSYLEEQSAPHENCYIWLYNIRVKNKSNSTVQLLRRSWKIIDSTG 62


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        0.321   0.134   0.381    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      222       198   0.00083  111 3  11 22  0.43    32
                                                     31  0.45    35


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:  10
  No. of states in DFA:  578 (61 KB)
  Total size of DFA:  147 KB (2090 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:  18.01u 0.07s 18.08t   Elapsed:  00:00:01
  Total cpu time:  18.01u 0.07s 18.08t   Elapsed:  00:00:01
  Start:  Fri May 10 23:05:33 2013   End:  Fri May 10 23:05:34 2013

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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	222
PRK05461	127	PRK05461, apaG, CO2+/MG2+ efflux protein ApaG; Rev	9e-32
COG2967	126	COG2967, ApaG, Uncharacterized protein affecting M	7e-22
pfam04379	90	pfam04379, DUF525, Protein of unknown function (DU	3e-21
pfam02151	36	pfam02151, UVR, UvrB/uvrC motif	2e-06
TIGR00631	655	TIGR00631, uvrb, excinuclease ABC, B subunit	5e-06
PRK05298	652	PRK05298, PRK05298, excinuclease ABC subunit B; Pr	9e-06
COG0556	663	COG0556, UvrB, Helicase subunit of the DNA excisio	8e-05
PRK00558	598	PRK00558, uvrC, excinuclease ABC subunit C; Valida	1e-04
PRK00558	598	PRK00558, uvrC, excinuclease ABC subunit C; Valida	2e-04
PRK07883	557	PRK07883, PRK07883, hypothetical protein; Validate	2e-04
pfam02151	36	pfam02151, UVR, UvrB/uvrC motif	6e-04
COG0322	581	COG0322, UvrC, Nuclease subunit of the excinucleas	0.001
COG0556	663	COG0556, UvrB, Helicase subunit of the DNA excisio	0.003
PRK05298	652	PRK05298, PRK05298, excinuclease ABC subunit B; Pr	0.004

>gnl|CDD|180098 PRK05461, apaG, CO2+/MG2+ efflux protein ApaG; Reviewed

 Score =  112 bits (282), Expect = 9e-32
 Identities = 31/61 (50%), Positives = 41/61 (67%)

Query: 159 SDATTLGIRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGKT 218
             A T GI V V+  Y+E++S P +G+Y FAY + I N    PVQLL RHW+ITDANG+ 
Sbjct: 2   YSAVTYGIEVSVQPRYLEEQSDPEEGRYVFAYTITIENLGRVPVQLLSRHWLITDANGRV 61

Query: 219 E 219
           +
Sbjct: 62  Q 62

Length = 127

>gnl|CDD|225515 COG2967, ApaG, Uncharacterized protein affecting Mg2+/Co2+ transport [Inorganic ion transport and metabolism]

 Score = 86.6 bits (215), Expect = 7e-22
 Identities = 29/60 (48%), Positives = 40/60 (66%)

Query: 160 DATTLGIRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGKTE 219
            A++  I VQV+  Y+E++S P + +Y FAY V I N  E PVQLL R+W+ITD NG+  
Sbjct: 2   MASSPDIEVQVQPRYLEEQSSPEEERYVFAYTVTIRNLGEVPVQLLSRYWLITDGNGRVT 61

Length = 126

>gnl|CDD|202989 pfam04379, DUF525, Protein of unknown function (DUF525)

 Score = 83.7 bits (208), Expect = 3e-21
 Identities = 25/45 (55%), Positives = 31/45 (68%)

Query: 175 IEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGKTE 219
           + ++S P +G+Y FAY + I N     VQLL RHWIITDANGK E
Sbjct: 1   LPEQSSPEEGRYVFAYTITIENLGPETVQLLSRHWIITDANGKVE 45

Members of this family include the bacterial protein ApaG and the C termini of some F-box proteins (pfam00646). F-box proteins contain a carboxyl-terminal domain that interacts with protein substrates, so this family may be involved in protein-protein interaction. The function of ApaG proteins is unknown, but mutations in the Salmonella typhimurium ApaG homologue corD gives a phenotype of low-level cobalt resistance and decreased magnesium efflux by effects on the CorA magnesium transport system. Length = 90

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

 Score = 42.8 bits (102), Expect = 2e-06
 Identities = 14/33 (42%), Positives = 21/33 (63%)

Query: 117 EEPIFRLRRLMKEAVAEERFEDAARYRDKLKEI 149
           ++ I  L   M+EA  EE FE AA+ RD++K +
Sbjct: 1   KKLIKELEEEMEEAAEEEDFEKAAKLRDQIKAL 33

Length = 36

>gnl|CDD|233063 TIGR00631, uvrb, excinuclease ABC, B subunit

 Score = 46.1 bits (110), Expect = 5e-06
 Identities = 17/64 (26%), Positives = 31/64 (48%)

Query: 86  ALLKQQMEVAAKTEDYKEAARIRDSLRSFEEEEPIFRLRRLMKEAVAEERFEDAARYRDK 145
            +L  +++        K+       L   E ++ I +L + MK+A     FE+AAR RD+
Sbjct: 591 DILDIELKEKEDAAKKKKKGEDLSDLSKKELKKLIKQLEKEMKQAARNLEFEEAARLRDE 650

Query: 146 LKEI 149
           + E+
Sbjct: 651 ILEL 654

All proteins in this family for wich functions are known are DNA helicases that function in the nucleotide excision repair and are endonucleases that make the 3' incision next to DNA damage. They are part of a pathway requiring UvrA, UvrB, UvrC, and UvrD homologs. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 655

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

 Score = 45.4 bits (109), Expect = 9e-06
 Identities = 20/53 (37%), Positives = 29/53 (54%), Gaps = 9/53 (16%)

Query: 106 RIRDSLRSFEEEEP---------IFRLRRLMKEAVAEERFEDAARYRDKLKEI 149
           +IRD L S  +++          I  L + MKEA     FE+AAR RD++KE+
Sbjct: 592 KIRDILDSVYKKDKLSKKELEKLIKELEKQMKEAAKNLEFEEAARLRDEIKEL 644

Length = 652

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

 Score = 42.6 bits (101), Expect = 8e-05
 Identities = 21/52 (40%), Positives = 32/52 (61%), Gaps = 1/52 (1%)

Query: 99  EDYKEAARIRDSLRSFEE-EEPIFRLRRLMKEAVAEERFEDAARYRDKLKEI 149
           ++YK     + S  S +E E+ I +L + MKEA     FE+AAR RD++KE+
Sbjct: 604 DEYKAKIEKKASKMSKKELEKLIKKLEKEMKEAAKNLEFEEAARLRDEIKEL 655

Length = 663

>gnl|CDD|234792 PRK00558, uvrC, excinuclease ABC subunit C; Validated

 Score = 42.4 bits (101), Expect = 1e-04
 Identities = 23/77 (29%), Positives = 41/77 (53%), Gaps = 15/77 (19%)

Query: 75  ARSFLS-RSQAY-ALLKQQMEVAAKTEDYKEAARIRDSLRSFEEEEPIFRLRRLM-KEAV 131
           A+ FLS ++      L+++ME A++  +++ AAR RD +++         LRR+  K+ V
Sbjct: 192 AKLFLSGKTDEVLKELEEKMEEASENLEFERAARYRDQIQA---------LRRVQEKQKV 242

Query: 132 AEERFEDA---ARYRDK 145
           + +  EDA   A   D 
Sbjct: 243 SLKDGEDADVIAIAVDG 259

Length = 598

>gnl|CDD|234792 PRK00558, uvrC, excinuclease ABC subunit C; Validated

 Score = 41.6 bits (99), Expect = 2e-04
 Identities = 17/50 (34%), Positives = 26/50 (52%), Gaps = 2/50 (4%)

Query: 99  EDYKEAAR-IRDSLRSFEEEEPIFRLRRLMKEAVAEERFEDAARYRDKLK 147
           E+Y E     +  L   + +E +  L   M+EA     FE AARYRD+++
Sbjct: 183 EEYAELVDEAKLFLSG-KTDEVLKELEEKMEEASENLEFERAARYRDQIQ 231

Length = 598

>gnl|CDD|236123 PRK07883, PRK07883, hypothetical protein; Validated

 Score = 41.8 bits (99), Expect = 2e-04
 Identities = 18/49 (36%), Positives = 28/49 (57%), Gaps = 2/49 (4%)

Query: 99  EDY-KEAARIRDSLRSFEEEEPIFRLRRLMKEAVAEERFEDAARYRDKL 146
            +Y +  AR R +L   +++  +  LR  +    A ERFE+AAR RD+L
Sbjct: 387 AEYAEAVARARAALTG-DDDAVLAALRARIDRLAAAERFEEAARLRDRL 434

Length = 557

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

 Score = 35.8 bits (84), Expect = 6e-04
 Identities = 12/30 (40%), Positives = 26/30 (86%)

Query: 88  LKQQMEVAAKTEDYKEAARIRDSLRSFEEE 117
           L+++ME AA+ ED+++AA++RD +++ E++
Sbjct: 7   LEEEMEEAAEEEDFEKAAKLRDQIKALEKQ 36

Length = 36

>gnl|CDD|223399 COG0322, UvrC, Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]

 Score = 39.2 bits (92), Expect = 0.001
 Identities = 16/60 (26%), Positives = 29/60 (48%), Gaps = 6/60 (10%)

Query: 93  EVAAKTEDYKEAARIRDSLRSF---EEEEPIFRLRRLMKEAVAEERFEDAARYRDKLKEI 149
                 E+Y+E     + ++ F   +++  +  L   M+EA     FE AAR RD++K +
Sbjct: 177 VGLISEEEYREIV---EEVKGFLKGKDDAVLQELEEKMEEASENLDFERAARLRDQIKAL 233

Length = 581

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

 Score = 38.0 bits (89), Expect = 0.003
 Identities = 13/30 (43%), Positives = 24/30 (80%)

Query: 88  LKQQMEVAAKTEDYKEAARIRDSLRSFEEE 117
           L+++M+ AAK  +++EAAR+RD ++  +EE
Sbjct: 629 LEKEMKEAAKNLEFEEAARLRDEIKELKEE 658

Length = 663

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

 Score = 37.3 bits (88), Expect = 0.004
 Identities = 14/31 (45%), Positives = 24/31 (77%)

Query: 88  LKQQMEVAAKTEDYKEAARIRDSLRSFEEEE 118
           L++QM+ AAK  +++EAAR+RD ++  +EE 
Sbjct: 618 LEKQMKEAAKNLEFEEAARLRDEIKELKEEL 648

Length = 652

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	222
COG2967	126	ApaG Uncharacterized protein affecting Mg2+/Co2+ t	99.89
PRK05461	127	apaG CO2+/MG2+ efflux protein ApaG; Reviewed	99.89
PF04379	90	DUF525: Protein of unknown function (DUF525); Inte	99.71
KOG4408	386	consensus Putative Mg2+ and Co2+ transporter CorD	99.51
COG3880	176	Modulator of heat shock repressor CtsR, McsA [Sign	99.23
PF02151	36	UVR: UvrB/uvrC motif; InterPro: IPR001943 During t	98.17
COG3880	176	Modulator of heat shock repressor CtsR, McsA [Sign	97.93
PF02151	36	UVR: UvrB/uvrC motif; InterPro: IPR001943 During t	97.68
PRK07883	557	hypothetical protein; Validated	95.99
PRK00558	598	uvrC excinuclease ABC subunit C; Validated	95.93
PRK05298	652	excinuclease ABC subunit B; Provisional	95.75
PRK14666	694	uvrC excinuclease ABC subunit C; Provisional	95.69
PRK12306	519	uvrC excinuclease ABC subunit C; Reviewed	95.67
TIGR00194	574	uvrC excinuclease ABC, C subunit. This family cons	95.56
PRK14670	574	uvrC excinuclease ABC subunit C; Provisional	95.54
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	95.53
PRK14669	624	uvrC excinuclease ABC subunit C; Provisional	95.47
PRK14671	621	uvrC excinuclease ABC subunit C; Provisional	95.46
PRK14672	691	uvrC excinuclease ABC subunit C; Provisional	95.42
PRK14667	567	uvrC excinuclease ABC subunit C; Provisional	95.35
PRK14668	577	uvrC excinuclease ABC subunit C; Provisional	95.32
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	94.91
COG0322	581	UvrC Nuclease subunit of the excinuclease complex	94.54
KOG4825	666	consensus Component of synaptic membrane glycine-,	94.03
PF11611	123	DUF4352: Domain of unknown function (DUF4352); Int	93.45
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	92.36
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	92.04
PRK05298	652	excinuclease ABC subunit B; Provisional	90.74
PRK07883	557	hypothetical protein; Validated	90.49
PRK00558	598	uvrC excinuclease ABC subunit C; Validated	90.27
PRK12306	519	uvrC excinuclease ABC subunit C; Reviewed	87.95
PRK14666	694	uvrC excinuclease ABC subunit C; Provisional	87.65
PF15469	182	Sec5: Exocyst complex component Sec5	87.47
PRK14668	577	uvrC excinuclease ABC subunit C; Provisional	86.79
PRK14669	624	uvrC excinuclease ABC subunit C; Provisional	86.5
PRK14672	691	uvrC excinuclease ABC subunit C; Provisional	86.41
PRK14671	621	uvrC excinuclease ABC subunit C; Provisional	86.41
PRK14667	567	uvrC excinuclease ABC subunit C; Provisional	86.27
PRK14670	574	uvrC excinuclease ABC subunit C; Provisional	86.03
TIGR00194	574	uvrC excinuclease ABC, C subunit. This family cons	85.56
PF14263	124	DUF4354: Domain of unknown function (DUF4354); PDB	84.74
PF07743	78	HSCB_C: HSCB C-terminal oligomerisation domain; In	84.11
COG0322	581	UvrC Nuclease subunit of the excinuclease complex	83.58
PF06476	115	DUF1090: Protein of unknown function (DUF1090); In	80.23

>COG2967 ApaG Uncharacterized protein affecting Mg2+/Co2+ transport [Inorganic ion transport and metabolism]

Probab=99.89  E-value=1.1e-23  Score=170.07  Aligned_cols=62  Identities=47%  Similarity=0.784  Sum_probs=60.0

Q ss_pred             eeccCCeEEEEEeEEecCcccCCCCceEEEEEEEEEeCCCCCeEEeeceEEEEcCCCcEEec
Q 027566          160 DATTLGIRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGKTENI  221 (222)
Q Consensus       160 ~a~T~gIkV~V~t~Ylpe~S~P~~~rYvFaY~ItIeN~s~~tVQLlsRhW~ItD~~G~v~eV  221 (222)
                      .+.|..|.|+|.|.|+|+||+|.+++|+|+|+|||.|+|+.+|||++|||+|||+||+++||
T Consensus         2 ~~~~~~I~V~V~~~yleeQS~P~~~RyvfaYtitI~N~g~~~vqLlsR~W~ITd~~g~v~eV   63 (126)
T COG2967           2 MASSPDIEVQVQPRYLEEQSSPEEERYVFAYTVTIRNLGEVPVQLLSRYWLITDGNGRVTEV   63 (126)
T ss_pred             CcccCceEEEEeeEEccccCCcccceEEEEEEEEEecCCCccceeeeeEEEEecCCCcEEEE
Confidence            35788999999999999999999999999999999999999999999999999999999998

>PRK05461 apaG CO2+/MG2+ efflux protein ApaG; Reviewed

Probab=99.89  E-value=1.6e-23  Score=170.08  Aligned_cols=63  Identities=49%  Similarity=0.898  Sum_probs=60.9

Q ss_pred             eeeccCCeEEEEEeEEecCcccCCCCceEEEEEEEEEeCCCCCeEEeeceEEEEcCCCcEEec
Q 027566          159 SDATTLGIRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGKTENI  221 (222)
Q Consensus       159 s~a~T~gIkV~V~t~Ylpe~S~P~~~rYvFaY~ItIeN~s~~tVQLlsRhW~ItD~~G~v~eV  221 (222)
                      +.++|+||+|+|.|.|+|++|+|.+++|+|+|+|||+|.++.+|||++|||+|+|++|++++|
T Consensus         2 ~~~~t~gI~V~V~~~y~~e~S~p~~~~y~f~Y~ItI~N~~~~~vQL~~R~W~I~d~~g~~~~V   64 (127)
T PRK05461          2 YSAVTYGIEVSVQPRYLEEQSDPEEGRYVFAYTITIENLGRVPVQLLSRHWLITDANGRVQEV   64 (127)
T ss_pred             cccccCCEEEEEEEEECcccCCCcCCEEEEEEEEEEEECCCCCEEEEeeeEEEEECCCCEEEE
Confidence            457899999999999999999999999999999999999999999999999999999999987

>PF04379 DUF525: Protein of unknown function (DUF525); InterPro: IPR007474 This domain is found in the bacterial protein ApaG and at the C termini of some F-box proteins (IPR001810 from INTERPRO)

Probab=99.71  E-value=8.1e-18  Score=129.47  Aligned_cols=47  Identities=53%  Similarity=1.023  Sum_probs=41.2

Q ss_pred             ecCcccCCCCceEEEEEEEEEeCCCCCeEEeeceEEEEcCCCcEEec
Q 027566          175 IEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGKTENI  221 (222)
Q Consensus       175 lpe~S~P~~~rYvFaY~ItIeN~s~~tVQLlsRhW~ItD~~G~v~eV  221 (222)
                      +|++|+|.+++|+|+|+|+|+|.++.+|||++|||+|+|++|++++|
T Consensus         1 ~~e~S~p~~~~y~f~Y~I~I~N~~~~~vqL~sR~W~I~d~~g~~~~V   47 (90)
T PF04379_consen    1 VPEQSDPSQNRYVFAYRIRIENHSDESVQLLSRHWIITDADGHVEEV   47 (90)
T ss_dssp             -GGG-BGGGTBEEEEEEEEEEE-SSS-EEEEEEEEEEEETTS-EEEE
T ss_pred             CccccCCCCCeEEEEEEEEEEECCCCCEEEEccEEEEEeCCCCEEEE
Confidence            68999999999999999999999999999999999999999999987

F-box proteins contain a carboxy-terminal domain that interacts with protein substrates []. The ApaG domain is ~125 amino acids in length, and is named after the bacterial ApaG protein, of which it forms the core. The Salmonella typhimurium ApaG domain protein, CorD, is involved in Co(2+) resistance and Mg(2+) efflux. Tertiary structures from different ApaG proteins show a fold of several beta-sheets. The ApaG domain may be involved in protein-protein interactions which could be implicated in substrate-specificity [, , ].; PDB: 2F1E_A 1XVS_A 1TZA_A 1XQ4_D.

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

Probab=99.51  E-value=2.6e-14  Score=132.59  Aligned_cols=65  Identities=38%  Similarity=0.604  Sum_probs=61.2

Q ss_pred             cceeeccCCeEEEEEeEEecCcccCCCCceEEEEEEEEEe-CCCCCeEEeeceEEEEcCCCcEEec
Q 027566          157 CLSDATTLGIRVQVRSVYIEDRSQPLKGQYFFAYRVRITN-NSERPVQLLRRHWIITDANGKTENI  221 (222)
Q Consensus       157 ~~s~a~T~gIkV~V~t~Ylpe~S~P~~~rYvFaY~ItIeN-~s~~tVQLlsRhW~ItD~~G~v~eV  221 (222)
                      ....++|+||+|+|.|+|+|+.|.+..+.|+|+|.|+|+| ....+|||..|||.|+..||.+++|
T Consensus       248 dVh~etTenI~Vtvstfylge~s~~~pp~YwwrY~IRien~l~e~svQLreRhWrI~slng~le~V  313 (386)
T KOG4408|consen  248 DVHRETTENIRVTVSTFYLGERSSVHPPVYWWRYCIRIENALPEKSVQLRERHWRIFSLNGTLETV  313 (386)
T ss_pred             hCChhhcCCeEEEEEEeeecccccCCCCceEEEEEEEeecCCCCcceEEeEeeEEEEecccchhhc
Confidence            3556899999999999999999999999999999999999 7889999999999999999999887

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

Probab=99.23  E-value=1.4e-11  Score=105.03  Aligned_cols=67  Identities=15%  Similarity=0.360  Sum_probs=60.0

Q ss_pred             cccccChHHHHHHHHHHHHHHHhc-------------cchHHHHHHHHHhhhhcccchHHHHHHHHHHHHHhhhHHHHHH
Q 027566           75 ARSFLSRSQAYALLKQQMEVAAKT-------------EDYKEAARIRDSLRSFEEEEPIFRLRRLMKEAVAEERFEDAAR  141 (222)
Q Consensus        75 ~~~~~gc~~cye~Lk~qL~~AIk~-------------EdyE~AA~LRDeI~~l~~~Dpv~~L~~~L~~AV~eErYE~AA~  141 (222)
                      ..++|||+.||.+|..+|.+.|.+             .+-+.+..++.+|         ..|++.|++.|+.|+||+||.
T Consensus        89 ~~g~fGCaeCY~tf~~~i~pi~~rvq~g~~~H~GK~P~~~~~~i~~~~~I---------~~L~e~Lq~~i~~EefEeAA~  159 (176)
T COG3880          89 QSGLFGCAECYKTFESQISPIITRVQGGYVEHVGKVPKRIGRKINPKRKI---------IALKEALQDLIEREEFEEAAV  159 (176)
T ss_pred             HhcccchHHHHHHHHHHhhHHHHHhhCCceeecCcCcccccccccHHHHH---------HHHHHHHHHHHHHHHHHHHHH
Confidence            457899999999999999999988             3355566678888         999999999999999999999


Q ss_pred             HHHHhhhhC
Q 027566          142 YRDKLKEIA  150 (222)
Q Consensus       142 lRD~i~~L~  150 (222)
                      +||+|+.|+
T Consensus       160 iRDqIr~Lk  168 (176)
T COG3880         160 IRDQIRALK  168 (176)
T ss_pred             HHHHHHHHH
Confidence            999999997

>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=98.17  E-value=1.8e-06  Score=56.08  Aligned_cols=31  Identities=48%  Similarity=0.676  Sum_probs=26.1

Q ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHhhhhC
Q 027566          120 IFRLRRLMKEAVAEERFEDAARYRDKLKEIA  150 (222)
Q Consensus       120 v~~L~~~L~~AV~eErYE~AA~lRD~i~~L~  150 (222)
                      +..|..+|..|+++++||+||.|||+|..|+
T Consensus         4 i~~l~~~m~~a~~~~dfE~Aa~~Rd~i~~l~   34 (36)
T PF02151_consen    4 IKELEEKMEEAVENEDFEKAARLRDQIKALK   34 (36)
T ss_dssp             HHHHHHHHHHHHHTT-CHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCHHHHHHHHHHHHHHH
Confidence            3788899999999999999999999998874

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.

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

Probab=97.93  E-value=1e-05  Score=69.47  Aligned_cols=45  Identities=22%  Similarity=0.383  Sum_probs=40.4

Q ss_pred             CcccccChHHHHHHHHHHHHHHHhccchHHHHHHHHHhhhhcccc
Q 027566           74 SARSFLSRSQAYALLKQQMEVAAKTEDYKEAARIRDSLRSFEEEE  118 (222)
Q Consensus        74 ~~~~~~gc~~cye~Lk~qL~~AIk~EdyE~AA~LRDeI~~l~~~D  118 (222)
                      +.+..+.....+..|++.|+++|++|+||+||.+||+|++|+.++
T Consensus       127 ~~~~~i~~~~~I~~L~e~Lq~~i~~EefEeAA~iRDqIr~Lk~k~  171 (176)
T COG3880         127 RIGRKINPKRKIIALKEALQDLIEREEFEEAAVIRDQIRALKAKN  171 (176)
T ss_pred             cccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            366778888999999999999999999999999999998888553

>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=97.68  E-value=5.9e-05  Score=48.94  Aligned_cols=33  Identities=33%  Similarity=0.632  Sum_probs=28.6

Q ss_pred             HHHHHHHHHHHHHHhccchHHHHHHHHHhhhhc
Q 027566           83 QAYALLKQQMEVAAKTEDYKEAARIRDSLRSFE  115 (222)
Q Consensus        83 ~cye~Lk~qL~~AIk~EdyE~AA~LRDeI~~l~  115 (222)
                      .-+..|+.+|..|++.++||+|+.+||+|..|+
T Consensus         2 ~~i~~l~~~m~~a~~~~dfE~Aa~~Rd~i~~l~   34 (36)
T PF02151_consen    2 KLIKELEEKMEEAVENEDFEKAARLRDQIKALK   34 (36)
T ss_dssp             HHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHH
Confidence            457899999999999999999999999996554

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.

>PRK07883 hypothetical protein; Validated

Probab=95.99  E-value=0.0082  Score=59.21  Aligned_cols=44  Identities=30%  Similarity=0.474  Sum_probs=35.9

Q ss_pred             HHHHhhhhccc--chHHHHHHHHHHHHHhhhHHHHHHHHHHhhhhC
Q 027566          107 IRDSLRSFEEE--EPIFRLRRLMKEAVAEERFEDAARYRDKLKEIA  150 (222)
Q Consensus       107 LRDeI~~l~~~--Dpv~~L~~~L~~AV~eErYE~AA~lRD~i~~L~  150 (222)
                      +++-+.-|+++  +.+..|.++|++|-++.+||+||++||+|..|+
T Consensus       393 v~~~~~fL~G~~~~~~~~l~~~M~~aa~~l~FE~Aa~~Rd~i~~l~  438 (557)
T PRK07883        393 VARARAALTGDDDAVLAALRARIDRLAAAERFEEAARLRDRLAALL  438 (557)
T ss_pred             HHHHHHHHCCCcHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHH
Confidence            34444556554  455799999999999999999999999999985

>PRK00558 uvrC excinuclease ABC subunit C; Validated

Probab=95.93  E-value=0.0098  Score=59.28  Aligned_cols=50  Identities=32%  Similarity=0.505  Sum_probs=38.6

Q ss_pred             cchHHHHHHHHHhhhhccc--chHHHHHHHHHHHHHhhhHHHHHHHHHHhhhhC
Q 027566           99 EDYKEAARIRDSLRSFEEE--EPIFRLRRLMKEAVAEERFEDAARYRDKLKEIA  150 (222)
Q Consensus        99 EdyE~AA~LRDeI~~l~~~--Dpv~~L~~~L~~AV~eErYE~AA~lRD~i~~L~  150 (222)
                      |+|.+  .+..-+.-|+++  +.+..|+.+|++|.++.+||+||.+||+|.+|+
T Consensus       183 e~Y~~--~v~~~~~fL~G~~~~~i~~L~~~M~~aa~~l~FE~Aa~~RD~i~aL~  234 (598)
T PRK00558        183 EEYAE--LVDEAKLFLSGKTDEVLKELEEKMEEASENLEFERAARYRDQIQALR  234 (598)
T ss_pred             HHHHH--HHHHHHHHhcCChHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHHHH
Confidence            44533  334444455554  556899999999999999999999999999985

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=95.75  E-value=0.023  Score=56.87  Aligned_cols=33  Identities=45%  Similarity=0.633  Sum_probs=30.2

Q ss_pred             chHHHHHHHHHHHHHhhhHHHHHHHHHHhhhhC
Q 027566          118 EPIFRLRRLMKEAVAEERFEDAARYRDKLKEIA  150 (222)
Q Consensus       118 Dpv~~L~~~L~~AV~eErYE~AA~lRD~i~~L~  150 (222)
                      +-+..|+.+|++|.++.+||+||++||+|.+|+
T Consensus       613 ~~~~~l~~~M~~aa~~l~fE~Aa~~Rd~i~~l~  645 (652)
T PRK05298        613 KLIKELEKQMKEAAKNLEFEEAARLRDEIKELK  645 (652)
T ss_pred             HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHH
Confidence            345799999999999999999999999999985

>PRK14666 uvrC excinuclease ABC subunit C; Provisional

Probab=95.69  E-value=0.014  Score=59.38  Aligned_cols=50  Identities=28%  Similarity=0.344  Sum_probs=38.2

Q ss_pred             cchHHHHHHHHHhhhhccc--chHHHHHHHHHHHHHhhhHHHHHHHHHHhhhhC
Q 027566           99 EDYKEAARIRDSLRSFEEE--EPIFRLRRLMKEAVAEERFEDAARYRDKLKEIA  150 (222)
Q Consensus        99 EdyE~AA~LRDeI~~l~~~--Dpv~~L~~~L~~AV~eErYE~AA~lRD~i~~L~  150 (222)
                      |+|.+...  .-+.-|+++  +.+..|+++|++|.++.+||+||+|||+|..|+
T Consensus       182 e~Y~~~V~--~v~~fL~G~~~~l~~~L~~~M~~AAe~l~FE~AA~lRD~i~aL~  233 (694)
T PRK14666        182 ETYAALVR--KVEMLLSGRSGELVDALRTEMEAASEALEFERAAVLRDQIRAVE  233 (694)
T ss_pred             HHHHHHHH--HHHHHHcCCCHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHH
Confidence            55544443  333345554  556899999999999999999999999999985

>PRK12306 uvrC excinuclease ABC subunit C; Reviewed

Probab=95.67  E-value=0.016  Score=57.20  Aligned_cols=50  Identities=26%  Similarity=0.453  Sum_probs=38.7

Q ss_pred             cchHHHHHHHHHhhhhccc--chHHHHHHHHHHHHHhhhHHHHHHHHHHhhhhC
Q 027566           99 EDYKEAARIRDSLRSFEEE--EPIFRLRRLMKEAVAEERFEDAARYRDKLKEIA  150 (222)
Q Consensus        99 EdyE~AA~LRDeI~~l~~~--Dpv~~L~~~L~~AV~eErYE~AA~lRD~i~~L~  150 (222)
                      |+|.+  .+..-+.-|+++  +.+..|..+|+.|-++.+||+||++||.|..|+
T Consensus       173 e~Y~~--~v~~~~~fL~G~~~~~~~~L~~~M~~aa~~l~FE~Aa~~RD~l~~l~  224 (519)
T PRK12306        173 DEYLE--QVKKAEEVLKGKIDELIEKLEEEMAEKAKNQQFERALVIRDEINAIE  224 (519)
T ss_pred             HHHHH--HHHHHHHHHcCCcHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHH
Confidence            44533  334444556654  556799999999999999999999999999985

>TIGR00194 uvrC excinuclease ABC, C subunit

Probab=95.56  E-value=0.017  Score=57.42  Aligned_cols=43  Identities=30%  Similarity=0.389  Sum_probs=35.5

Q ss_pred             HHHhhhhccc--chHHHHHHHHHHHHHhhhHHHHHHHHHHhhhhC
Q 027566          108 RDSLRSFEEE--EPIFRLRRLMKEAVAEERFEDAARYRDKLKEIA  150 (222)
Q Consensus       108 RDeI~~l~~~--Dpv~~L~~~L~~AV~eErYE~AA~lRD~i~~L~  150 (222)
                      ..-+.-|+++  +.+..|..+|++|-++.+||+||++||.|..|+
T Consensus       182 ~~~~~fL~g~~~~~~~~L~~~M~~aa~~l~FE~Aa~~Rd~i~~l~  226 (574)
T TIGR00194       182 EKIELFFNGRPQEVIKELEQKMEKASENLEFEEAARIRDQIAAVR  226 (574)
T ss_pred             HHHHHHHCCCcHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHH
Confidence            3444445554  556799999999999999999999999999985

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.

>PRK14670 uvrC excinuclease ABC subunit C; Provisional

Probab=95.54  E-value=0.015  Score=57.95  Aligned_cols=50  Identities=18%  Similarity=0.367  Sum_probs=38.1

Q ss_pred             cchHHHHHHHHHhhhhcc--cchHHHHHHHHHHHHHhhhHHHHHHHHHHhhhhC
Q 027566           99 EDYKEAARIRDSLRSFEE--EEPIFRLRRLMKEAVAEERFEDAARYRDKLKEIA  150 (222)
Q Consensus        99 EdyE~AA~LRDeI~~l~~--~Dpv~~L~~~L~~AV~eErYE~AA~lRD~i~~L~  150 (222)
                      |+|.+...  .-+.-|++  .+.+..|..+|++|-++.+||+||++||+|..|+
T Consensus       158 e~Y~~~v~--~~~~fL~G~~~~~~~~L~~~M~~aa~~l~FE~Aa~~RD~i~al~  209 (574)
T PRK14670        158 KEYQKEVD--KIKHILNGNISKLLSQIEIKMKEAIQKEDFEAAIKLKETKRSLI  209 (574)
T ss_pred             HHHHHHHH--HHHHHHcCCcHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHH
Confidence            44444332  33334554  3667899999999999999999999999999985

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=95.53  E-value=0.018  Score=57.94  Aligned_cols=32  Identities=41%  Similarity=0.562  Sum_probs=29.3

Q ss_pred             hHHHHHHHHHHHHHhhhHHHHHHHHHHhhhhC
Q 027566          119 PIFRLRRLMKEAVAEERFEDAARYRDKLKEIA  150 (222)
Q Consensus       119 pv~~L~~~L~~AV~eErYE~AA~lRD~i~~L~  150 (222)
                      -+..|+.+|++|.++.+||+||.+||+|++|+
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            34699999999999999999999999999884

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

>PRK14669 uvrC excinuclease ABC subunit C; Provisional

Probab=95.47  E-value=0.017  Score=58.18  Aligned_cols=50  Identities=38%  Similarity=0.470  Sum_probs=38.2

Q ss_pred             cchHHHHHHHHHhhhhccc--chHHHHHHHHHHHHHhhhHHHHHHHHHHhhhhC
Q 027566           99 EDYKEAARIRDSLRSFEEE--EPIFRLRRLMKEAVAEERFEDAARYRDKLKEIA  150 (222)
Q Consensus        99 EdyE~AA~LRDeI~~l~~~--Dpv~~L~~~L~~AV~eErYE~AA~lRD~i~~L~  150 (222)
                      |+|.+...  +-+.-|+++  +.+..|..+|+.|-++.+||+||++||+|..|+
T Consensus       184 e~Y~~~v~--~v~~fL~G~~~~l~~~L~~~M~~aa~~l~FE~Aa~~RD~i~~l~  235 (624)
T PRK14669        184 EAYAEAVR--DVRLFLEGRHSDLARSLRARMEAAALEMQFELAAKYRDLITTVE  235 (624)
T ss_pred             HHHHHHHH--HHHHHHCCCCHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHH
Confidence            45544443  333445543  556799999999999999999999999999985

>PRK14671 uvrC excinuclease ABC subunit C; Provisional

Probab=95.46  E-value=0.019  Score=57.60  Aligned_cols=50  Identities=32%  Similarity=0.492  Sum_probs=38.4

Q ss_pred             cchHHHHHHHHHhhhhccc--chHHHHHHHHHHHHHhhhHHHHHHHHHHhhhhC
Q 027566           99 EDYKEAARIRDSLRSFEEE--EPIFRLRRLMKEAVAEERFEDAARYRDKLKEIA  150 (222)
Q Consensus        99 EdyE~AA~LRDeI~~l~~~--Dpv~~L~~~L~~AV~eErYE~AA~lRD~i~~L~  150 (222)
                      |+|.+..  ..-+.-|+++  +.+..|..+|++|-++.+||+||++||+|..|+
T Consensus       196 e~Y~~~v--~~~~~fL~G~~~~l~~~L~~~M~~as~~l~FE~Aa~~RD~i~~l~  247 (621)
T PRK14671        196 EDYLEMI--EEIVRLLKGKTSALIRSLTEEMQRAAAELKFEEAAELKDQIESLK  247 (621)
T ss_pred             HHHHHHH--HHHHHHHcCCcHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHH
Confidence            4554333  3333445554  566899999999999999999999999999985

>PRK14672 uvrC excinuclease ABC subunit C; Provisional

Probab=95.42  E-value=0.02  Score=58.34  Aligned_cols=39  Identities=41%  Similarity=0.568  Sum_probs=33.5

Q ss_pred             hhhccc--chHHHHHHHHHHHHHhhhHHHHHHHHHHhhhhC
Q 027566          112 RSFEEE--EPIFRLRRLMKEAVAEERFEDAARYRDKLKEIA  150 (222)
Q Consensus       112 ~~l~~~--Dpv~~L~~~L~~AV~eErYE~AA~lRD~i~~L~  150 (222)
                      .-|+++  +.+..|..+|++|-++.+||+||+|||+|..|+
T Consensus       197 ~fL~G~~~~ll~~L~~~M~~AA~~l~FE~AA~lRD~i~aL~  237 (691)
T PRK14672        197 LLLEGNIDATVARLEKRMKRAVRQEAFEAAARIRDDIQAIR  237 (691)
T ss_pred             HHHcCCcHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHH
Confidence            345543  556899999999999999999999999999985

>PRK14667 uvrC excinuclease ABC subunit C; Provisional

Probab=95.35  E-value=0.022  Score=56.65  Aligned_cols=43  Identities=21%  Similarity=0.237  Sum_probs=35.1

Q ss_pred             HHHhhhhccc--chHHHHHHHHHHHHHhhhHHHHHHHHHHhhhhC
Q 027566          108 RDSLRSFEEE--EPIFRLRRLMKEAVAEERFEDAARYRDKLKEIA  150 (222)
Q Consensus       108 RDeI~~l~~~--Dpv~~L~~~L~~AV~eErYE~AA~lRD~i~~L~  150 (222)
                      ..-+.-|+++  +.+..|..+|++|-++.+||+||+|||.|..|+
T Consensus       187 ~~~~~fL~G~~~~l~~~L~~~M~~aa~~l~FE~Aa~~RD~i~~l~  231 (567)
T PRK14667        187 KSAKAFLSGNVKEVLPELYDKIEEYSQKLMFEKAAVIRDQILALE  231 (567)
T ss_pred             HHHHHHHcCCcHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHH
Confidence            3444445554  455799999999999999999999999999985

>PRK14668 uvrC excinuclease ABC subunit C; Provisional

Probab=95.32  E-value=0.024  Score=56.53  Aligned_cols=37  Identities=41%  Similarity=0.535  Sum_probs=32.5

Q ss_pred             hccc--chHHHHHHHHHHHHHhhhHHHHHHHHHHhhhhC
Q 027566          114 FEEE--EPIFRLRRLMKEAVAEERFEDAARYRDKLKEIA  150 (222)
Q Consensus       114 l~~~--Dpv~~L~~~L~~AV~eErYE~AA~lRD~i~~L~  150 (222)
                      |+++  +.+..|+.+|++|-++.+||+||++||+|.+|+
T Consensus       193 L~G~~~~~~~~l~~~m~~aa~~l~FE~Aa~~Rd~i~~l~  231 (577)
T PRK14668        193 FEGETGVLADPLRREMEAAAQAQEFERAANLRDRLEAVE  231 (577)
T ss_pred             HcCCcHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHH
Confidence            5554  455799999999999999999999999999985

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

Probab=94.91  E-value=0.034  Score=55.77  Aligned_cols=32  Identities=47%  Similarity=0.670  Sum_probs=29.0

Q ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHhhhhCC
Q 027566          120 IFRLRRLMKEAVAEERFEDAARYRDKLKEIAP  151 (222)
Q Consensus       120 v~~L~~~L~~AV~eErYE~AA~lRD~i~~L~p  151 (222)
                      +..|..+|++|.++-+||+||+|||+|.+|+.
T Consensus       626 I~~Le~~M~~aA~~l~FE~Aa~lRD~i~~L~~  657 (663)
T COG0556         626 IKKLEKEMKEAAKNLEFEEAARLRDEIKELKE  657 (663)
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHH
Confidence            46899999999999999999999999999864

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

Probab=94.54  E-value=0.042  Score=54.98  Aligned_cols=49  Identities=31%  Similarity=0.532  Sum_probs=36.7

Q ss_pred             cchHHHHHHHHHhhh-hccc--chHHHHHHHHHHHHHhhhHHHHHHHHHHhhhhC
Q 027566           99 EDYKEAARIRDSLRS-FEEE--EPIFRLRRLMKEAVAEERFEDAARYRDKLKEIA  150 (222)
Q Consensus        99 EdyE~AA~LRDeI~~-l~~~--Dpv~~L~~~L~~AV~eErYE~AA~lRD~i~~L~  150 (222)
                      |+|.+...   +++. |.++  .-+..|+++|++|-++.+||.||+|||.|.+|.
T Consensus       183 e~Y~e~v~---~~~~fL~G~~~~v~~~L~~~M~~As~~l~FE~Aa~~RD~i~al~  234 (581)
T COG0322         183 EEYREIVE---EVKGFLKGKDDAVLQELEEKMEEASENLDFERAARLRDQIKALE  234 (581)
T ss_pred             HHHHHHHH---HHHHHHcCCHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHHHH
Confidence            55554443   3333 4444  233699999999999999999999999999986

>KOG4825 consensus Component of synaptic membrane glycine-, glutamate- and thienylcyclohexylpiperidine-binding glycoprotein (43kDa) [Signal transduction mechanisms]

Probab=94.03  E-value=0.067  Score=52.89  Aligned_cols=68  Identities=19%  Similarity=0.285  Sum_probs=59.8

Q ss_pred             HHHHHHHHHHHHHHhccchHHHHHHHHHhhhhccc-chHHHHHHHHHHHHHhhhHHHHHHHHHHhhhhC
Q 027566           83 QAYALLKQQMEVAAKTEDYKEAARIRDSLRSFEEE-EPIFRLRRLMKEAVAEERFEDAARYRDKLKEIA  150 (222)
Q Consensus        83 ~cye~Lk~qL~~AIk~EdyE~AA~LRDeI~~l~~~-Dpv~~L~~~L~~AV~eErYE~AA~lRD~i~~L~  150 (222)
                      .-+-.+.+.=+.||.+|+|.-|.+++..|++|+.. ..+++|...=..||++|+|..|-.+.|+|.+|+
T Consensus       171 aiIgaidenKqeAVakEdfdlAKkaklAiaDLkKsgeeleelEndKgcAVadEDfdlAkdkkdeiealR  239 (666)
T KOG4825|consen  171 AIIGAIDENKQEAVAKEDFDLAKKAKLAIADLKKSGEELEELENDKGCAVADEDFDLAKDKKDEIEALR  239 (666)
T ss_pred             HHHHHHHhhHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHhhcccccccchhhhHHHHHHHHHHHHH
Confidence            44556777778899999999999999999999865 778899999999999999999999999999864

>PF11611 DUF4352: Domain of unknown function (DUF4352); InterPro: IPR021652 This entry is represented by Bacteriophage A118, Gp32

Probab=93.45  E-value=0.54  Score=35.79  Aligned_cols=59  Identities=27%  Similarity=0.483  Sum_probs=40.2

Q ss_pred             eccCCeEEEEEeE-Eec---CcccCCCCceEEEEEEEEEeCCCCCeEEeeceEEEEcCCCcEE
Q 027566          161 ATTLGIRVQVRSV-YIE---DRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGKTE  219 (222)
Q Consensus       161 a~T~gIkV~V~t~-Ylp---e~S~P~~~rYvFaY~ItIeN~s~~tVQLlsRhW~ItD~~G~v~  219 (222)
                      ..+.+++|+|... +..   +...|.++..+..=.++|+|.+++++.+-.-++.+.|.+|...
T Consensus         7 ~~~~~~~vtV~~v~~~~~~~~~~~~~~g~~fv~v~v~v~N~~~~~~~~~~~~f~l~d~~g~~~   69 (123)
T PF11611_consen    7 VSVGGIEVTVNSVEKTDGSNEYSKPKEGNKFVVVDVTVKNNGDEPLDFSPSDFKLYDSDGNKY   69 (123)
T ss_dssp             EEETTEEEEEEEE-EEE-SS-BEES---SEEEEEEEEEEE-SSS-EEEEGGGEEEE-TT--B-
T ss_pred             EEECCEEEEEEEEEeecCCccccccCCCCEEEEEEEEEEECCCCcEEecccceEEEeCCCCEE
Confidence            3468999999887 332   3345666677788999999999999999889999999988754

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a group of putative lipoproteins of unknown function.; PDB: 3CFU_A.

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

Probab=92.36  E-value=0.15  Score=51.32  Aligned_cols=39  Identities=31%  Similarity=0.456  Sum_probs=33.9

Q ss_pred             cccChHHHHHHHHHHHHHHHhccchHHHHHHHHHhhhhc
Q 027566           77 SFLSRSQAYALLKQQMEVAAKTEDYKEAARIRDSLRSFE  115 (222)
Q Consensus        77 ~~~gc~~cye~Lk~qL~~AIk~EdyE~AA~LRDeI~~l~  115 (222)
                      +.-..+..++.|+.+|.+|.+.-+||+||+|||+|.+|+
T Consensus       618 ~~~e~~~~I~~Le~~M~~aA~~l~FE~Aa~lRD~i~~L~  656 (663)
T COG0556         618 SKKELEKLIKKLEKEMKEAAKNLEFEEAARLRDEIKELK  656 (663)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHH
Confidence            445567889999999999999999999999999995554

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=92.04  E-value=0.19  Score=50.74  Aligned_cols=34  Identities=29%  Similarity=0.528  Sum_probs=30.4

Q ss_pred             HHHHHHHHHHHHHHHhccchHHHHHHHHHhhhhc
Q 027566           82 SQAYALLKQQMEVAAKTEDYKEAARIRDSLRSFE  115 (222)
Q Consensus        82 ~~cye~Lk~qL~~AIk~EdyE~AA~LRDeI~~l~  115 (222)
                      ..-++.|+++|..|.+..+||+||++||+|++|+
T Consensus       622 ~~~i~~l~~~M~~aa~~l~FE~Aa~~RD~i~~L~  655 (655)
T TIGR00631       622 KKLIKQLEKEMKQAARNLEFEEAARLRDEILELK  655 (655)
T ss_pred             HHHHHHHHHHHHHHHHccCHHHHHHHHHHHHhcC
Confidence            4677899999999999999999999999997663

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

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=90.74  E-value=0.28  Score=49.23  Aligned_cols=33  Identities=36%  Similarity=0.591  Sum_probs=29.7

Q ss_pred             HHHHHHHHHHHHHHhccchHHHHHHHHHhhhhc
Q 027566           83 QAYALLKQQMEVAAKTEDYKEAARIRDSLRSFE  115 (222)
Q Consensus        83 ~cye~Lk~qL~~AIk~EdyE~AA~LRDeI~~l~  115 (222)
                      .-++.|+.+|..|.+..+||+|+++||+|++|+
T Consensus       613 ~~~~~l~~~M~~aa~~l~fE~Aa~~Rd~i~~l~  645 (652)
T PRK05298        613 KLIKELEKQMKEAAKNLEFEEAARLRDEIKELK  645 (652)
T ss_pred             HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHH
Confidence            578889999999999999999999999995554

>PRK07883 hypothetical protein; Validated

Probab=90.49  E-value=0.33  Score=48.08  Aligned_cols=30  Identities=37%  Similarity=0.588  Sum_probs=28.6

Q ss_pred             HHHHHHHHHHHHHHHhccchHHHHHHHHHh
Q 027566           82 SQAYALLKQQMEVAAKTEDYKEAARIRDSL  111 (222)
Q Consensus        82 ~~cye~Lk~qL~~AIk~EdyE~AA~LRDeI  111 (222)
                      ..-++.|+.+|+.|.++.+||+||++||+|
T Consensus       405 ~~~~~~l~~~M~~aa~~l~FE~Aa~~Rd~i  434 (557)
T PRK07883        405 DAVLAALRARIDRLAAAERFEEAARLRDRL  434 (557)
T ss_pred             HHHHHHHHHHHHHHHHhcCHHHHHHHHHHH
Confidence            468899999999999999999999999999

>PRK00558 uvrC excinuclease ABC subunit C; Validated

Probab=90.27  E-value=0.35  Score=48.41  Aligned_cols=34  Identities=26%  Similarity=0.506  Sum_probs=30.7

Q ss_pred             HHHHHHHHHHHHHHHhccchHHHHHHHHHhhhhc
Q 027566           82 SQAYALLKQQMEVAAKTEDYKEAARIRDSLRSFE  115 (222)
Q Consensus        82 ~~cye~Lk~qL~~AIk~EdyE~AA~LRDeI~~l~  115 (222)
                      ..-++.|+++|+.|.++.+||+||.+||+|..|+
T Consensus       201 ~~~i~~L~~~M~~aa~~l~FE~Aa~~RD~i~aL~  234 (598)
T PRK00558        201 DEVLKELEEKMEEASENLEFERAARYRDQIQALR  234 (598)
T ss_pred             HHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHHHH
Confidence            4678999999999999999999999999996554

>PRK12306 uvrC excinuclease ABC subunit C; Reviewed

Probab=87.95  E-value=0.55  Score=46.53  Aligned_cols=34  Identities=26%  Similarity=0.450  Sum_probs=31.1

Q ss_pred             HHHHHHHHHHHHHHHhccchHHHHHHHHHhhhhc
Q 027566           82 SQAYALLKQQMEVAAKTEDYKEAARIRDSLRSFE  115 (222)
Q Consensus        82 ~~cye~Lk~qL~~AIk~EdyE~AA~LRDeI~~l~  115 (222)
                      ..-++.|+.+|+.|.++.+||+||++||.|..|+
T Consensus       191 ~~~~~~L~~~M~~aa~~l~FE~Aa~~RD~l~~l~  224 (519)
T PRK12306        191 DELIEKLEEEMAEKAKNQQFERALVIRDEINAIE  224 (519)
T ss_pred             HHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHH
Confidence            4678889999999999999999999999998876

>PRK14666 uvrC excinuclease ABC subunit C; Provisional

Probab=87.65  E-value=0.59  Score=48.00  Aligned_cols=33  Identities=27%  Similarity=0.511  Sum_probs=29.6

Q ss_pred             HHHHHHHHHHHHHHHhccchHHHHHHHHHhhhh
Q 027566           82 SQAYALLKQQMEVAAKTEDYKEAARIRDSLRSF  114 (222)
Q Consensus        82 ~~cye~Lk~qL~~AIk~EdyE~AA~LRDeI~~l  114 (222)
                      ..=++.|+.+|+.|.++.+||+||++||+|+.|
T Consensus       200 ~~l~~~L~~~M~~AAe~l~FE~AA~lRD~i~aL  232 (694)
T PRK14666        200 GELVDALRTEMEAASEALEFERAAVLRDQIRAV  232 (694)
T ss_pred             HHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHH
Confidence            467889999999999999999999999999444

>PF15469 Sec5: Exocyst complex component Sec5

Probab=87.47  E-value=2.5  Score=35.23  Aligned_cols=51  Identities=20%  Similarity=0.392  Sum_probs=46.6

Q ss_pred             cchHHHHHHHHHhhhhcccchHHHHHHHHHHHHHhhhHHHHHHHHHHhhhh
Q 027566           99 EDYKEAARIRDSLRSFEEEEPIFRLRRLMKEAVAEERFEDAARYRDKLKEI  149 (222)
Q Consensus        99 EdyE~AA~LRDeI~~l~~~Dpv~~L~~~L~~AV~eErYE~AA~lRD~i~~L  149 (222)
                      +.-+++.+++..+.-|+....+..|=..|+++|+.++|+.|...-...+.+
T Consensus        65 ~~~~k~~~l~~~l~~l~r~~flF~LP~~L~~~i~~~dy~~~i~dY~kak~l  115 (182)
T PF15469_consen   65 ERREKADKLRNALEFLQRNRFLFNLPSNLRECIKKGDYDQAINDYKKAKSL  115 (182)
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHcCcHHHHHHHHHHHHHH
Confidence            888899999999999999999999999999999999999998877777766

>PRK14668 uvrC excinuclease ABC subunit C; Provisional

Probab=86.79  E-value=0.68  Score=46.36  Aligned_cols=34  Identities=32%  Similarity=0.541  Sum_probs=30.3

Q ss_pred             HHHHHHHHHHHHHHHhccchHHHHHHHHHhhhhc
Q 027566           82 SQAYALLKQQMEVAAKTEDYKEAARIRDSLRSFE  115 (222)
Q Consensus        82 ~~cye~Lk~qL~~AIk~EdyE~AA~LRDeI~~l~  115 (222)
                      ..-++.|+.+|+.|.++.+||+||++||+|+.|+
T Consensus       198 ~~~~~~l~~~m~~aa~~l~FE~Aa~~Rd~i~~l~  231 (577)
T PRK14668        198 GVLADPLRREMEAAAQAQEFERAANLRDRLEAVE  231 (577)
T ss_pred             HHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHH
Confidence            4678899999999999999999999999995544

>PRK14669 uvrC excinuclease ABC subunit C; Provisional

Probab=86.50  E-value=0.75  Score=46.57  Aligned_cols=34  Identities=32%  Similarity=0.392  Sum_probs=30.8

Q ss_pred             HHHHHHHHHHHHHHHhccchHHHHHHHHHhhhhc
Q 027566           82 SQAYALLKQQMEVAAKTEDYKEAARIRDSLRSFE  115 (222)
Q Consensus        82 ~~cye~Lk~qL~~AIk~EdyE~AA~LRDeI~~l~  115 (222)
                      ..-++.|+.+|+.|.+..+||+||++||+|+.|+
T Consensus       202 ~~l~~~L~~~M~~aa~~l~FE~Aa~~RD~i~~l~  235 (624)
T PRK14669        202 SDLARSLRARMEAAALEMQFELAAKYRDLITTVE  235 (624)
T ss_pred             HHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHH
Confidence            4678899999999999999999999999997665

>PRK14672 uvrC excinuclease ABC subunit C; Provisional

Probab=86.41  E-value=0.89  Score=46.72  Aligned_cols=34  Identities=32%  Similarity=0.557  Sum_probs=30.9

Q ss_pred             HHHHHHHHHHHHHHHhccchHHHHHHHHHhhhhc
Q 027566           82 SQAYALLKQQMEVAAKTEDYKEAARIRDSLRSFE  115 (222)
Q Consensus        82 ~~cye~Lk~qL~~AIk~EdyE~AA~LRDeI~~l~  115 (222)
                      ..-++.|+.+|+.|.++.+||+||++||+|+.|+
T Consensus       204 ~~ll~~L~~~M~~AA~~l~FE~AA~lRD~i~aL~  237 (691)
T PRK14672        204 DATVARLEKRMKRAVRQEAFEAAARIRDDIQAIR  237 (691)
T ss_pred             HHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHH
Confidence            4678999999999999999999999999997665

>PRK14671 uvrC excinuclease ABC subunit C; Provisional

Probab=86.41  E-value=0.89  Score=45.91  Aligned_cols=34  Identities=29%  Similarity=0.442  Sum_probs=30.9

Q ss_pred             HHHHHHHHHHHHHHHhccchHHHHHHHHHhhhhc
Q 027566           82 SQAYALLKQQMEVAAKTEDYKEAARIRDSLRSFE  115 (222)
Q Consensus        82 ~~cye~Lk~qL~~AIk~EdyE~AA~LRDeI~~l~  115 (222)
                      ..-++.|+.+|+.|.+..+||+||++||.|..|+
T Consensus       214 ~~l~~~L~~~M~~as~~l~FE~Aa~~RD~i~~l~  247 (621)
T PRK14671        214 SALIRSLTEEMQRAAAELKFEEAAELKDQIESLK  247 (621)
T ss_pred             HHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHH
Confidence            4788999999999999999999999999996664

>PRK14667 uvrC excinuclease ABC subunit C; Provisional

Probab=86.27  E-value=0.79  Score=45.90  Aligned_cols=34  Identities=24%  Similarity=0.333  Sum_probs=30.7

Q ss_pred             HHHHHHHHHHHHHHHhccchHHHHHHHHHhhhhc
Q 027566           82 SQAYALLKQQMEVAAKTEDYKEAARIRDSLRSFE  115 (222)
Q Consensus        82 ~~cye~Lk~qL~~AIk~EdyE~AA~LRDeI~~l~  115 (222)
                      ..-++.|+.+|..|.+..+||+||++||.|..|+
T Consensus       198 ~~l~~~L~~~M~~aa~~l~FE~Aa~~RD~i~~l~  231 (567)
T PRK14667        198 KEVLPELYDKIEEYSQKLMFEKAAVIRDQILALE  231 (567)
T ss_pred             HHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHH
Confidence            3678899999999999999999999999997665

>PRK14670 uvrC excinuclease ABC subunit C; Provisional

Probab=86.03  E-value=0.83  Score=45.84  Aligned_cols=34  Identities=24%  Similarity=0.443  Sum_probs=30.9

Q ss_pred             HHHHHHHHHHHHHHHhccchHHHHHHHHHhhhhc
Q 027566           82 SQAYALLKQQMEVAAKTEDYKEAARIRDSLRSFE  115 (222)
Q Consensus        82 ~~cye~Lk~qL~~AIk~EdyE~AA~LRDeI~~l~  115 (222)
                      ..=++.|+.+|..|.+..+||+||++||+|..|+
T Consensus       176 ~~~~~~L~~~M~~aa~~l~FE~Aa~~RD~i~al~  209 (574)
T PRK14670        176 SKLLSQIEIKMKEAIQKEDFEAAIKLKETKRSLI  209 (574)
T ss_pred             HHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHH
Confidence            4678899999999999999999999999997665

>TIGR00194 uvrC excinuclease ABC, C subunit

Probab=85.56  E-value=0.87  Score=45.61  Aligned_cols=34  Identities=35%  Similarity=0.546  Sum_probs=30.0

Q ss_pred             HHHHHHHHHHHHHHHhccchHHHHHHHHHhhhhc
Q 027566           82 SQAYALLKQQMEVAAKTEDYKEAARIRDSLRSFE  115 (222)
Q Consensus        82 ~~cye~Lk~qL~~AIk~EdyE~AA~LRDeI~~l~  115 (222)
                      ..=+..|+.+|+.|.++.+||+||++||+|+.|+
T Consensus       193 ~~~~~~L~~~M~~aa~~l~FE~Aa~~Rd~i~~l~  226 (574)
T TIGR00194       193 QEVIKELEQKMEKASENLEFEEAARIRDQIAAVR  226 (574)
T ss_pred             HHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHH
Confidence            4667889999999999999999999999995554

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.

>PF14263 DUF4354: Domain of unknown function (DUF4354); PDB: 3NRF_B 3SB3_A

Probab=84.74  E-value=3  Score=34.42  Aligned_cols=60  Identities=18%  Similarity=0.176  Sum_probs=46.0

Q ss_pred             eeeccCCeEEEEEeEEecCcccCCCCceEEEEEEEEEeCCCCCeEEeeceEEEEcCCCcE
Q 027566          159 SDATTLGIRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGKT  218 (222)
Q Consensus       159 s~a~T~gIkV~V~t~Ylpe~S~P~~~rYvFaY~ItIeN~s~~tVQLlsRhW~ItD~~G~v  218 (222)
                      +..++++|.|-....=.+.-|...+..|-=+|.|++.|.++.++.|-.=...-.+.+|+.
T Consensus        20 ~a~~~d~i~V~At~~~~Gs~sv~~k~~ytktF~V~vaN~s~~~idLsk~Cf~a~~~~gk~   79 (124)
T PF14263_consen   20 NASAPDNIAVYATEKSQGSVSVGGKSFYTKTFDVTVANLSDKDIDLSKMCFKAYSPDGKE   79 (124)
T ss_dssp             -----SSEEEEEEEEEEEEEEETTEEEEEEEEEEEEEE-SSS-EE-TT-EEEEEETTS-E
T ss_pred             hhccCCCeEEEEEecCCccEeecCccceEEEEEEEEecCCCCccccccchhhhccccCCE
Confidence            344578999999999888889888889999999999999999999998899988888864

>PF07743 HSCB_C: HSCB C-terminal oligomerisation domain; InterPro: IPR009073 This entry represents the C-terminal oligomerisation domain found in HscB (heat shock cognate protein B), which is also known as HSC20 (20K heat shock cognate protein)

Probab=84.11  E-value=6.5  Score=28.51  Aligned_cols=59  Identities=27%  Similarity=0.374  Sum_probs=42.5

Q ss_pred             HHHHHHHHHHHHHhccchHHHHHHHHHhhhhcccchHHHHHHHHHHHHHhhhHHHHHHHHHHhh
Q 027566           84 AYALLKQQMEVAAKTEDYKEAARIRDSLRSFEEEEPIFRLRRLMKEAVAEERFEDAARYRDKLK  147 (222)
Q Consensus        84 cye~Lk~qL~~AIk~EdyE~AA~LRDeI~~l~~~Dpv~~L~~~L~~AV~eErYE~AA~lRD~i~  147 (222)
                      ....++++|+.+...++-..-..+..++     +..+..+...|..++..++|+.|+.+=.+++
T Consensus         9 e~mE~rE~le~~~~~~~~~~L~~l~~~~-----~~~~~~~~~~l~~~f~~~d~~~A~~~~~kLk   67 (78)
T PF07743_consen    9 EQMELREELEEAQNSDDEAELEELKKEI-----EERIKELIKELAEAFDAKDWEEAKEALRKLK   67 (78)
T ss_dssp             HHHHHHHHHHHHCCCTSHHHHHHHHHHH-----HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhcCCCHHHHHHHHHHH-----HHHHHHHHHHHHHHHccCcHHHHHHHHHHHH
Confidence            4567778888777655555556666665     3445788999999999999999998766665

HscB acts as a co-chaperone to regulate the ATPase activity and peptide-binding specificity of the molecular chaperone HscA, also known as HSC66 (HSP70 class). HscB proteins contain two domains, an N-terminal J-domain, which is involved in interactions with HscA, connected by a short loop to the C-terminal oligomerisation domain; the two domains make contact through a hydrophobic interface. The core of the oligomerisation domain is thought to bind and target proteins to HscA and consists of an open, three-helical bundle []. HscB, along with HscA, has been shown to play a role in the biogenesis of iron-sulphur proteins.; GO: 0006457 protein folding; PDB: 1FPO_C 3BVO_B 3HHO_A 3UO2_B 3UO3_B.

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

Probab=83.58  E-value=1.2  Score=44.82  Aligned_cols=32  Identities=31%  Similarity=0.580  Sum_probs=28.9

Q ss_pred             HHHHHHHHHHHHHHhccchHHHHHHHHHhhhh
Q 027566           83 QAYALLKQQMEVAAKTEDYKEAARIRDSLRSF  114 (222)
Q Consensus        83 ~cye~Lk~qL~~AIk~EdyE~AA~LRDeI~~l  114 (222)
                      .-+..|+++|+.|-+..+||.||++||+|.+|
T Consensus       202 ~v~~~L~~~M~~As~~l~FE~Aa~~RD~i~al  233 (581)
T COG0322         202 AVLQELEEKMEEASENLDFERAARLRDQIKAL  233 (581)
T ss_pred             HHHHHHHHHHHHHHHhhchHHHHHHHHHHHHH
Confidence            67889999999999999999999999999443

>PF06476 DUF1090: Protein of unknown function (DUF1090); InterPro: IPR009468 This family consists of several bacterial proteins of unknown function and is known as YqjC in Escherichia coli

Probab=80.23  E-value=8  Score=31.21  Aligned_cols=74  Identities=19%  Similarity=0.235  Sum_probs=61.6

Q ss_pred             cccccChHHHHHHHHHHHHHHHhccchHHHHHHHHHhhhhcc------------------cchHHHHHHHHHHHHHhhhH
Q 027566           75 ARSFLSRSQAYALLKQQMEVAAKTEDYKEAARIRDSLRSFEE------------------EEPIFRLRRLMKEAVAEERF  136 (222)
Q Consensus        75 ~~~~~gc~~cye~Lk~qL~~AIk~EdyE~AA~LRDeI~~l~~------------------~Dpv~~L~~~L~~AV~eErY  136 (222)
                      ....-||......+..||+-|=...+-...+-|...+.+++.                  +..|..-+.+|++|.+..+.
T Consensus        16 ~~~~~gC~~K~~~Ie~qI~~Ak~~gN~~rv~GLe~AL~~v~~~Ctd~~l~~e~q~ki~~~~~kV~ere~eL~eA~~~G~~   95 (115)
T PF06476_consen   16 AAALTGCEAKEQAIEKQIEYAKAHGNQHRVAGLEKALEEVKAHCTDEGLKAERQQKIAEKQQKVAEREAELKEAQAKGDS   95 (115)
T ss_pred             ccccCcHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhcCCchhhHHHHHHHHHHHHHHHHHHHHHHHHHHhCCH
Confidence            345789999999999999999999998888888777776652                  34556788899999999999


Q ss_pred             HHHHHHHHHhhh
Q 027566          137 EDAARYRDKLKE  148 (222)
Q Consensus       137 E~AA~lRD~i~~  148 (222)
                      ++.+..+..|.+
T Consensus        96 ~KI~K~~~KL~e  107 (115)
T PF06476_consen   96 DKIAKRQKKLAE  107 (115)
T ss_pred             HHHHHHHHHHHH
Confidence            999988888765

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	222
1tza_A	134	X-Ray Structure Of Northeast Structural Genomics Co		9e-11
1xq4_A	139	Crystal Structure Of The Putative Apaa Protein From		2e-09
2f1e_A	127	Solution Structure Of Apag Protein Length = 127		4e-09
1xvs_A	126	Crystal Structure Of Apag Protein From Vibrio Chole		3e-08

>pdb|1TZA|A Chain A, X-Ray Structure Of Northeast Structural Genomics Consortium Target Sor45 Length = 134

Iteration: 1
 Score = 63.5 bits (153), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 28/56 (50%), Positives = 38/56 (67%)
Query: 166 IRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGKTENI 221
           IRV+V++ YIE +S P   +Y F+Y + I N  E+  +L  RHWIITDANGKT  +
Sbjct: 8   IRVEVKTEYIEQQSSPEDEKYLFSYTITIINLGEQAAKLETRHWIITDANGKTSEV 63

>pdb|1XQ4|A Chain A, Crystal Structure Of The Putative Apaa Protein From Bordetella Pertussis, Northeast Structural Genomics Target Ber40 Length = 139

Iteration: 1
 Score = 58.9 bits (141), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 24/56 (42%), Positives = 34/56 (60%)
Query: 166 IRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGKTENI 221
           + V V   Y+ ++S P + QY FAY VRITN    P Q++ RHWIITD   + + +
Sbjct: 13  LTVSVTPRYVPEQSDPSQQQYVFAYTVRITNTGSHPAQVISRHWIITDGEERVQEV 68

>pdb|2F1E|A Chain A, Solution Structure Of Apag Protein Length = 127

Iteration: 1
 Score = 57.8 bits (138), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 24/56 (42%), Positives = 36/56 (64%)
Query: 166 IRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGKTENI 221
           + V+V   ++  +S P +G+Y FAY +RI N    P +L+ RHW ITD NG+TE +
Sbjct: 9   VEVEVSPRFLAHQSTPDEGRYAFAYSIRIQNAGAVPARLVARHWQITDGNGRTEQV 64

>pdb|1XVS|A Chain A, Crystal Structure Of Apag Protein From Vibrio Cholerae Length = 126

Iteration: 1
 Score = 55.1 bits (131), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 26/58 (44%), Positives = 39/58 (67%)
Query: 160 DATTLGIRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGK 217
           D +   I++QV++ YIE++S P   ++ FAY + I N S + VQL  R W+ITDA+GK
Sbjct: 2   DVSLPCIKIQVQTRYIEEQSNPEYQRFVFAYLITIKNLSSQTVQLXSRRWLITDADGK 59

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	222
1xvs_A	126	Protein APAG; MCSG APC26324, midwest center for st	4e-27
1xq4_A	139	Protein APAG; all beta protein, structural genomic	8e-27
2f1e_A	127	Protein APAG; APAG protein, xanthomonas axonopodis	1e-26
1tza_A	134	APAG protein, SOR45; structural genomics, PSI, pro	2e-26
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-07
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	7e-06
1e52_A	63	Excinuclease ABC subunit; DNA excision repair, UVR	4e-05
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	2e-04

>1xvs_A Protein APAG; MCSG APC26324, midwest center for structural genomics, structure initiative, PSI, structural genomics, unknown FUN; 2.01A {Vibrio cholerae} SCOP: b.1.23.1 Length = 126

 Score = 99.5 bits (248), Expect = 4e-27
 Identities = 26/62 (41%), Positives = 41/62 (66%)

Query: 160 DATTLGIRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGKTE 219
           D +   I++QV++ YIE++S P   ++ FAY + I N S + VQL+ R W+ITDA+GK  
Sbjct: 2   DVSLPCIKIQVQTRYIEEQSNPEYQRFVFAYLITIKNLSSQTVQLMSRRWLITDADGKQT 61

Query: 220 NI 221
            +
Sbjct: 62  VV 63

>1xq4_A Protein APAG; all beta protein, structural genomics, protein structure initiative, PSI, northeast structural genomics consortium, NESG; 2.70A {Bordetella pertussis} SCOP: b.1.23.1 Length = 139

 Score = 99.2 bits (247), Expect = 8e-27
 Identities = 24/63 (38%), Positives = 34/63 (53%)

Query: 159 SDATTLGIRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGKT 218
                  + V V   Y+ ++S P + QY FAY VRITN    P Q++ RHWIITD   + 
Sbjct: 6   RPVKPYDLTVSVTPRYVPEQSDPSQQQYVFAYTVRITNTGSHPAQVISRHWIITDGEERV 65

Query: 219 ENI 221
           + +
Sbjct: 66  QEV 68

>2f1e_A Protein APAG; APAG protein, xanthomonas axonopodis PV.citri, structural genomics, unknown function; NMR {Xanthomonas axonopodis PV} Length = 127

 Score = 98.4 bits (245), Expect = 1e-26
 Identities = 25/63 (39%), Positives = 37/63 (58%)

Query: 159 SDATTLGIRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGKT 218
            D     + V+V   ++  +S P +G+Y FAY +RI N    P +L+ RHW ITD NG+T
Sbjct: 2   QDDPRYRVEVEVSPRFLAHQSTPDEGRYAFAYSIRIQNAGAVPARLVARHWQITDGNGRT 61

Query: 219 ENI 221
           E +
Sbjct: 62  EQV 64

>1tza_A APAG protein, SOR45; structural genomics, PSI, protein structure initiative, NORT structural genomics consortium, NESG, unknown function; 2.40A {Shewanella oneidensis} SCOP: b.1.23.1 Length = 134

 Score = 98.4 bits (245), Expect = 2e-26
 Identities = 29/61 (47%), Positives = 39/61 (63%)

Query: 161 ATTLGIRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGKTEN 220
           A    IRV+V++ YIE +S P   +Y F+Y + I N  E+  +L  RHWIITDANGKT  
Sbjct: 3   ALDNSIRVEVKTEYIEQQSSPEDEKYLFSYTITIINLGEQAAKLETRHWIITDANGKTSE 62

Query: 221 I 221
           +
Sbjct: 63  V 63

>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 = 48.3 bits (114), Expect = 8e-07
 Identities = 42/303 (13%), Positives = 83/303 (27%), Gaps = 115/303 (37%)

Query: 5   NLSSINVSTEFNATRRRRCLS---YNNSL----DLEYGRRRRVGR----GCKDL--TRTY 51
           + S+I +         RR L    Y N L    ++   +  +        CK L  TR  
Sbjct: 219 HSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNV---QNAKAWNAFNLSCKILLTTRFK 275

Query: 52  GIVACVGGGGGGSGGGGERLSSSARSFLSRSQAYALLKQQMEVAAKTEDYKE-------- 103
            +   +                     L+  +  +LL + ++   + +D           
Sbjct: 276 QVTDFLSAATTT-----HISLDHHSMTLTPDEVKSLLLKYLDC--RPQDLPREVLTTNPR 328

Query: 104 -----AARIRD----------------------SLRSFEEEEP--------IFR------ 122
                A  IRD                      SL   E  E         +F       
Sbjct: 329 RLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIP 388

Query: 123 ---LRRLMKEAVAEERFEDAARYRDKLKEIAPNSLLKCLSDATTLGI-------RVQVRS 172
              L  +  + +  +      +           SL++     +T+ I       +V++ +
Sbjct: 389 TILLSLIWFDVIKSDVMVVVNKLHKY-------SLVEKQPKESTISIPSIYLELKVKLEN 441

Query: 173 VY------IE-----------DRSQPLKGQYFF---AYRVRITNNSERPVQLLRR----- 207
            Y      ++           D   P   QYF+    + ++   + ER + L R      
Sbjct: 442 EYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPER-MTLFRMVFLDF 500

Query: 208 HWI 210
            ++
Sbjct: 501 RFL 503

>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* Length = 661

 Score = 45.2 bits (108), Expect = 7e-06
 Identities = 17/63 (26%), Positives = 29/63 (46%)

Query: 87  LLKQQMEVAAKTEDYKEAARIRDSLRSFEEEEPIFRLRRLMKEAVAEERFEDAARYRDKL 146
           +++  +    K E   +AA     +   E ++ + ++   MKEA     FE AA  RD L
Sbjct: 595 VIRATVAAEDKAEYKTKAAPKLSKMTKKERQKVVEQMEHEMKEAAKALDFERAAELRDLL 654

Query: 147 KEI 149
            E+
Sbjct: 655 LEL 657

>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* Length = 664

 Score = 40.6 bits (96), Expect = 2e-04
 Identities = 15/49 (30%), Positives = 22/49 (44%)

Query: 101 YKEAARIRDSLRSFEEEEPIFRLRRLMKEAVAEERFEDAARYRDKLKEI 149
             E A +   L   +  E I  L   M +A     FE AAR RD+++ +
Sbjct: 594 GYEEAPLEADLSGEDLRERIAELELAMWQAAEALDFERAARLRDEIRAL 642

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	222
2f1e_A	127	Protein APAG; APAG protein, xanthomonas axonopodis	99.91
1xvs_A	126	Protein APAG; MCSG APC26324, midwest center for st	99.9
1tza_A	134	APAG protein, SOR45; structural genomics, PSI, pro	99.89
1xq4_A	139	Protein APAG; all beta protein, structural genomic	99.89
1e52_A	63	Excinuclease ABC subunit; DNA excision repair, UVR	97.88
1e52_A	63	Excinuclease ABC subunit; DNA excision repair, UVR	97.21
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	96.59
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	95.74
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	94.86
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	92.97
3cfu_A	159	Uncharacterized lipoprotein YJHA; YJHA_bacsu, SR56	88.48
3nrf_A	106	APAG protein; structural genomics, joint center fo	87.37

>2f1e_A Protein APAG; APAG protein, xanthomonas axonopodis PV.citri, structural genomics, unknown function; NMR {Xanthomonas axonopodis PV}

Probab=99.91  E-value=1.7e-24  Score=174.49  Aligned_cols=63  Identities=40%  Similarity=0.777  Sum_probs=58.4

Q ss_pred             eeeccCCeEEEEEeEEecCcccCCCCceEEEEEEEEEeCCCCCeEEeeceEEEEcCCCcEEec
Q 027566          159 SDATTLGIRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGKTENI  221 (222)
Q Consensus       159 s~a~T~gIkV~V~t~Ylpe~S~P~~~rYvFaY~ItIeN~s~~tVQLlsRhW~ItD~~G~v~eV  221 (222)
                      ++++|+||+|+|.|.|+|++|+|.+++|+|+|+|||+|.++.+|||++|||+|+|++|+++||
T Consensus         2 ~~~~t~~I~V~V~~~y~~e~S~p~~~~y~faY~I~I~N~~~~~vQL~sRhW~Itd~~g~~~eV   64 (127)
T 2f1e_A            2 QDDPRYRVEVEVSPRFLAHQSTPDEGRYAFAYSIRIQNAGAVPARLVARHWQITDGNGRTEQV   64 (127)
T ss_dssp             ----CCCEEEEEEEEECSTTCBGGGTBEEEEEEEEEEECSSSCEEEEEEEEEEEETTSCEEEE
T ss_pred             ccceECCEEEEEEEEEchhhCCCcCCEEEEEEEEEEEeCCCCCEEEEeceEEEEeCCCCEEEE
Confidence            468899999999999999999999999999999999999999999999999999999999997

>1xvs_A Protein APAG; MCSG APC26324, midwest center for structural genomics, structure initiative, PSI, structural genomics, unknown FUN; 2.01A {Vibrio cholerae} SCOP: b.1.23.1

Probab=99.90  E-value=3.5e-24  Score=172.59  Aligned_cols=62  Identities=42%  Similarity=0.735  Sum_probs=60.2

Q ss_pred             eeccCCeEEEEEeEEecCcccCCCCceEEEEEEEEEeCCCCCeEEeeceEEEEcCCCcEEec
Q 027566          160 DATTLGIRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGKTENI  221 (222)
Q Consensus       160 ~a~T~gIkV~V~t~Ylpe~S~P~~~rYvFaY~ItIeN~s~~tVQLlsRhW~ItD~~G~v~eV  221 (222)
                      +.+|+||+|+|.|.|+|++|+|.+++|+|+|+|||+|.++.+|||++|||+|+|++|+++||
T Consensus         2 ~~~t~~I~V~V~~~y~~e~S~p~~~~y~faY~I~I~N~~~~~vQL~sRhW~Itd~~g~~~eV   63 (126)
T 1xvs_A            2 DVSLPCIKIQVQTRYIEEQSNPEYQRFVFAYLITIKNLSSQTVQLMSRRWLITDADGKQTVV   63 (126)
T ss_dssp             BCSCCCEEEEEEEEECGGGCBGGGTBEEEEEEEEEEECSSSCEEEEEEEEEEEETTCCEEEE
T ss_pred             CcccCCEEEEEEEEEchhcCCCcCCEEEEEEEEEEEECCCCCEEEEecEEEEEeCCCCEEEE
Confidence            46899999999999999999999999999999999999999999999999999999999997

>1tza_A APAG protein, SOR45; structural genomics, PSI, protein structure initiative, NORT structural genomics consortium, NESG, unknown function; 2.40A {Shewanella oneidensis} SCOP: b.1.23.1

Probab=99.89  E-value=9.3e-24  Score=171.79  Aligned_cols=61  Identities=48%  Similarity=0.809  Sum_probs=59.6

Q ss_pred             eccCCeEEEEEeEEecCcccCCCCceEEEEEEEEEeCCCCCeEEeeceEEEEcCCCcEEec
Q 027566          161 ATTLGIRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGKTENI  221 (222)
Q Consensus       161 a~T~gIkV~V~t~Ylpe~S~P~~~rYvFaY~ItIeN~s~~tVQLlsRhW~ItD~~G~v~eV  221 (222)
                      ++|+||+|+|.|.|+|++|+|.+.+|+|+|+|||+|.++.+|||++|||+|+|++|+++||
T Consensus         3 ~~t~~I~V~V~~~y~~e~S~p~~~~y~faY~ItI~N~~~~~vQL~sRhW~Itd~~g~~~eV   63 (134)
T 1tza_A            3 ALDNSIRVEVKTEYIEQQSSPEDEKYLFSYTITIINLGEQAAKLETRHWIITDANGKTSEV   63 (134)
T ss_dssp             CGGGTEEEEEEEEEEEECCBTTBCCEEEEEEEEEEECSSSCEEEEEEEEEEEETTSCEEEE
T ss_pred             CccCCEEEEEEEEEchhhCCCCCCEEEEEEEEEEEeCCCCCEEEEecEEEEEeCCCCEEEE
Confidence            5799999999999999999999999999999999999999999999999999999999997

>1xq4_A Protein APAG; all beta protein, structural genomics, protein structure initiative, PSI, northeast structural genomics consortium, NESG; 2.70A {Bordetella pertussis} SCOP: b.1.23.1

Probab=99.89  E-value=1.1e-23  Score=172.38  Aligned_cols=65  Identities=37%  Similarity=0.706  Sum_probs=60.5

Q ss_pred             cceeeccCCeEEEEEeEEecCcccCCCCceEEEEEEEEEeCCCCCeEEeeceEEEEcCCCcEEec
Q 027566          157 CLSDATTLGIRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGKTENI  221 (222)
Q Consensus       157 ~~s~a~T~gIkV~V~t~Ylpe~S~P~~~rYvFaY~ItIeN~s~~tVQLlsRhW~ItD~~G~v~eV  221 (222)
                      .....+|+||+|+|.|.|+|++|+|.+.+|+|+|+|||+|.++.+|||++|||+|+|++|+++||
T Consensus         4 ~~~~~tT~gI~V~V~~~y~~e~S~p~~~~y~FaY~ItI~N~~~~~vQL~sRhW~ItD~~G~~~eV   68 (139)
T 1xq4_A            4 RERPVKPYDLTVSVTPRYVPEQSDPSQQQYVFAYTVRITNTGSHPAQVISRHWIITDGEERVQEV   68 (139)
T ss_dssp             ---CCCSSCEEEEEEEEECGGGCBGGGTBEEEEEEEEEEECSSSCEEEEEEEEEEECTTSCEEEE
T ss_pred             cccccccCCEEEEEEEEEchhhCCCCCCEEEEEEEEEEEeCCCCCEEEEecEEEEEeCCCCEEEE
Confidence            34567899999999999999999999999999999999999999999999999999999999997

>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=96.59  E-value=0.0015  Score=63.16  Aligned_cols=31  Identities=39%  Similarity=0.458  Sum_probs=25.9

Q ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHhhhhC
Q 027566          120 IFRLRRLMKEAVAEERFEDAARYRDKLKEIA  150 (222)
Q Consensus       120 v~~L~~~L~~AV~eErYE~AA~lRD~i~~L~  150 (222)
                      +..|+++|++|.++++||+||+|||+|++|+
T Consensus       628 i~~l~~~m~~aa~~~~fe~Aa~~Rd~i~~l~  658 (661)
T 2d7d_A          628 VEQMEHEMKEAAKALDFERAAELRDLLLELK  658 (661)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHC----
T ss_pred             HHHHHHHHHHHHHccCHHHHHHHHHHHHHHH
Confidence            4799999999999999999999999999996

>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=95.74  E-value=0.0017  Score=62.96  Aligned_cols=34  Identities=32%  Similarity=0.427  Sum_probs=0.0

Q ss_pred             hHHHHHHHHHHHHHhhhHHHHHHHHHHhhhhCCC
Q 027566          119 PIFRLRRLMKEAVAEERFEDAARYRDKLKEIAPN  152 (222)
Q Consensus       119 pv~~L~~~L~~AV~eErYE~AA~lRD~i~~L~p~  152 (222)
                      -+..|+++|++|.++++||+||+|||+|++|+..
T Consensus       612 ~i~~l~~~m~~aa~~l~fe~Aa~lRd~i~~l~~~  645 (664)
T 1c4o_A          612 RIAELELAMWQAAEALDFERAARLRDEIRALEAR  645 (664)
T ss_dssp             ----------------------------------
T ss_pred             HHHHHHHHHHHHHHhcChHHHHHHHHHHHHHHHH
Confidence            4578999999999999999999999999999754

>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=94.86  E-value=0.019  Score=55.61  Aligned_cols=36  Identities=31%  Similarity=0.482  Sum_probs=28.7

Q ss_pred             hHHHHHHHHHHHHHHHhccchHHHHHHHHHhhhhcc
Q 027566           81 RSQAYALLKQQMEVAAKTEDYKEAARIRDSLRSFEE  116 (222)
Q Consensus        81 c~~cye~Lk~qL~~AIk~EdyE~AA~LRDeI~~l~~  116 (222)
                      ..+-+..|+.+|..|.+..+||+||++||+|++|+.
T Consensus       624 ~~~~i~~l~~~m~~aa~~~~fe~Aa~~Rd~i~~l~~  659 (661)
T 2d7d_A          624 RQKVVEQMEHEMKEAAKALDFERAAELRDLLLELKA  659 (661)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHC-----
T ss_pred             HHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHh
Confidence            446788999999999999999999999999987764

>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=92.97  E-value=0.018  Score=55.76  Aligned_cols=36  Identities=36%  Similarity=0.471  Sum_probs=0.0

Q ss_pred             hHHHHHHHHHHHHHHHhccchHHHHHHHHHhhhhcc
Q 027566           81 RSQAYALLKQQMEVAAKTEDYKEAARIRDSLRSFEE  116 (222)
Q Consensus        81 c~~cye~Lk~qL~~AIk~EdyE~AA~LRDeI~~l~~  116 (222)
                      ....++.|+.+|.+|++..+||+||+|||+|++|+.
T Consensus       609 ~~~~i~~l~~~m~~aa~~l~fe~Aa~lRd~i~~l~~  644 (664)
T 1c4o_A          609 LRERIAELELAMWQAAEALDFERAARLRDEIRALEA  644 (664)
T ss_dssp             ------------------------------------
T ss_pred             HHHHHHHHHHHHHHHHHhcChHHHHHHHHHHHHHHH
Confidence            446788999999999999999999999999966654

>3cfu_A Uncharacterized lipoprotein YJHA; YJHA_bacsu, SR562, NESG, structural genomics, PSI-2, protein structure initiative; 2.40A {Bacillus subtilis}

Probab=88.48  E-value=2.5  Score=34.20  Aligned_cols=59  Identities=12%  Similarity=0.028  Sum_probs=42.8

Q ss_pred             eccCCeEEEEEeEEecC---c--------ccC---CCCceEEEEEEEEEeCCCCCeEEeeceEEEEcCCCcEE
Q 027566          161 ATTLGIRVQVRSVYIED---R--------SQP---LKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGKTE  219 (222)
Q Consensus       161 a~T~gIkV~V~t~Ylpe---~--------S~P---~~~rYvFaY~ItIeN~s~~tVQLlsRhW~ItD~~G~v~  219 (222)
                      ....+++|+|...-...   .        ..|   .++.-+..-.|||+|.|+.+...-.=.|.+.|++|+..
T Consensus         8 v~~~~~evTVnsv~~~~~~e~~~~~~~~~~~p~~~~~G~~fviV~VTIeN~g~e~~~~s~~~F~L~d~dG~~~   80 (159)
T 3cfu_A            8 FKAGHTNFTVNKVDRVQKGEYMNVGGAVNEETKTIKDDEERLIIEVTMENIGEDSISYNFIGFDLRDKNDQSV   80 (159)
T ss_dssp             EEETTEEEEEEEEEEECSSCBEESSCC------CBCCCSEEEEEEEEEEECSSSCEEEEGGGEEEECTTCCBC
T ss_pred             EEECCEEEEEEEEEEcCCCceeecccccccCccccCCCCEEEEEEEEEEECCCCceeeCcccEEEEeCCCCEE
Confidence            33467899987753321   2        345   56655678999999999999998878899999999753

>3nrf_A APAG protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2, unknown function; 1.50A {Pseudomonas aeruginosa} PDB: 3sb3_A

Probab=87.37  E-value=1.2  Score=34.84  Aligned_cols=58  Identities=21%  Similarity=0.163  Sum_probs=50.4

Q ss_pred             eccCCeEEEEEeEEecCcccCCCCceEEEEEEEEEeCCCCCeEEeeceEEEEcCCCcE
Q 027566          161 ATTLGIRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGKT  218 (222)
Q Consensus       161 a~T~gIkV~V~t~Ylpe~S~P~~~rYvFaY~ItIeN~s~~tVQLlsRhW~ItD~~G~v  218 (222)
                      +++++|.|-..+.=.+.-|.+.+..|-=+|.|.|.|.++.++.|-.=...-++.+|+.
T Consensus         2 ~~~d~v~V~At~k~~GS~s~~~k~~ytktFdV~vaNl~~~~idLsk~C~~a~~~~gke   59 (106)
T 3nrf_A            2 AAPDAVMVFARQGDKGSVSVGDKHFRTQAFKVRLVNAAKSEISLKNSCLVAQSAAGQS   59 (106)
T ss_dssp             ---CCCEEEEEEEEEEEEEETTEEEEEEEEEEEEECCSSSCEECTTCEEEEEETTSCE
T ss_pred             CCcCcEEEEeeccccccEEeCCeeEEEEEEEEEEecCCCCccccchhhheeeCcCCCE
Confidence            4688999999999899889888888999999999999999999999999999888864

---

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	222
d1xvsa_	124	b.1.23.1 (A:) ApaG {Vibrio cholerae [TaxId: 666]}	2e-28
d1tzaa_	132	b.1.23.1 (A:) ApaG {Shewanella oneidensis [TaxId:	2e-27
d1xq4a_	123	b.1.23.1 (A:) ApaG {Bordetella pertussis [TaxId: 5	7e-26
d1e52a_	56	a.2.9.1 (A:) C-terminal UvrC-binding domain of Uvr	2e-05
d1e52a_	56	a.2.9.1 (A:) C-terminal UvrC-binding domain of Uvr	8e-05

>d1xvsa_ b.1.23.1 (A:) ApaG {Vibrio cholerae [TaxId: 666]} Length = 124

class: All beta proteins
fold: Immunoglobulin-like beta-sandwich
superfamily: ApaG-like
family: ApaG-like
domain: ApaG
species: Vibrio cholerae [TaxId: 666]

 Score =  101 bits (254), Expect = 2e-28
 Identities = 26/62 (41%), Positives = 41/62 (66%)

Query: 160 DATTLGIRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGKTE 219
           D +   I++QV++ YIE++S P   ++ FAY + I N S + VQL+ R W+ITDA+GK  
Sbjct: 2   DVSLPCIKIQVQTRYIEEQSNPEYQRFVFAYLITIKNLSSQTVQLMSRRWLITDADGKQT 61

Query: 220 NI 221
            +
Sbjct: 62  VV 63

>d1tzaa_ b.1.23.1 (A:) ApaG {Shewanella oneidensis [TaxId: 70863]} Length = 132

class: All beta proteins
fold: Immunoglobulin-like beta-sandwich
superfamily: ApaG-like
family: ApaG-like
domain: ApaG
species: Shewanella oneidensis [TaxId: 70863]

 Score = 99.5 bits (248), Expect = 2e-27
 Identities = 29/61 (47%), Positives = 39/61 (63%)

Query: 161 ATTLGIRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGKTEN 220
           A    IRV+V++ YIE +S P   +Y F+Y + I N  E+  +L  RHWIITDANGKT  
Sbjct: 1   ALDNSIRVEVKTEYIEQQSSPEDEKYLFSYTITIINLGEQAAKLETRHWIITDANGKTSE 60

Query: 221 I 221
           +
Sbjct: 61  V 61

>d1xq4a_ b.1.23.1 (A:) ApaG {Bordetella pertussis [TaxId: 520]} Length = 123

class: All beta proteins
fold: Immunoglobulin-like beta-sandwich
superfamily: ApaG-like
family: ApaG-like
domain: ApaG
species: Bordetella pertussis [TaxId: 520]

 Score = 95.2 bits (237), Expect = 7e-26
 Identities = 24/56 (42%), Positives = 34/56 (60%)

Query: 166 IRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGKTENI 221
           + V V   Y+ ++S P + QY FAY VRITN    P Q++ RHWIITD   + + +
Sbjct: 7   LTVSVTPRYVPEQSDPSQQQYVFAYTVRITNTGSHPAQVISRHWIITDGEERVQEV 62

>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 = 38.6 bits (90), Expect = 2e-05
 Identities = 12/47 (25%), Positives = 22/47 (46%)

Query: 103 EAARIRDSLRSFEEEEPIFRLRRLMKEAVAEERFEDAARYRDKLKEI 149
           E   +   +     ++ I  L  LM +      FE+AA+ RD+L ++
Sbjct: 2   EPDNVPMDMSPKALQQKIHELEGLMMQHAQNLEFEEAAQIRDQLHQL 48

>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 = 37.0 bits (86), Expect = 8e-05
 Identities = 11/30 (36%), Positives = 17/30 (56%)

Query: 88  LKQQMEVAAKTEDYKEAARIRDSLRSFEEE 117
           L+  M   A+  +++EAA+IRD L    E 
Sbjct: 22  LEGLMMQHAQNLEFEEAAQIRDQLHQLREL 51

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	222
d1tzaa_	132	ApaG {Shewanella oneidensis [TaxId: 70863]}	99.89
d1xvsa_	124	ApaG {Vibrio cholerae [TaxId: 666]}	99.88
d1xq4a_	123	ApaG {Bordetella pertussis [TaxId: 520]}	99.85
d1e52a_	56	C-terminal UvrC-binding domain of UvrB {Escherichi	97.82
d1e52a_	56	C-terminal UvrC-binding domain of UvrB {Escherichi	97.32
d1fpoa2	95	HSC20 (HSCB), C-terminal oligomerisation domain {E	86.04
d2fzta1	78	Hypothetical protein TM0693 {Thermotoga maritima [	82.21

>d1tzaa_ b.1.23.1 (A:) ApaG {Shewanella oneidensis [TaxId: 70863]}

class: All beta proteins
fold: Immunoglobulin-like beta-sandwich
superfamily: ApaG-like
family: ApaG-like
domain: ApaG
species: Shewanella oneidensis [TaxId: 70863]

Probab=99.89  E-value=9.3e-24  Score=169.48  Aligned_cols=61  Identities=48%  Similarity=0.809  Sum_probs=59.6

Q ss_pred             eccCCeEEEEEeEEecCcccCCCCceEEEEEEEEEeCCCCCeEEeeceEEEEcCCCcEEec
Q 027566          161 ATTLGIRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGKTENI  221 (222)
Q Consensus       161 a~T~gIkV~V~t~Ylpe~S~P~~~rYvFaY~ItIeN~s~~tVQLlsRhW~ItD~~G~v~eV  221 (222)
                      |+|+||+|+|.|.|+|++|+|.+.+|+|+|+|||+|.++.+|||++|||+|+|++|++++|
T Consensus         1 a~t~gI~V~V~t~y~~e~S~p~~~~y~F~Y~ItI~N~~~~~vQLlsR~W~I~d~~G~~~eV   61 (132)
T d1tzaa_           1 ALDNSIRVEVKTEYIEQQSSPEDEKYLFSYTITIINLGEQAAKLETRHWIITDANGKTSEV   61 (132)
T ss_dssp             CGGGTEEEEEEEEEEEECCBTTBCCEEEEEEEEEEECSSSCEEEEEEEEEEEETTSCEEEE
T ss_pred             CccCCEEEEEEEEEchhcCCCCCCeEEEEEEEEEEeCCCCCEEEEeeEEEEECCCCCEEEE
Confidence            5799999999999999999999999999999999999999999999999999999999987

>d1xvsa_ b.1.23.1 (A:) ApaG {Vibrio cholerae [TaxId: 666]}

class: All beta proteins
fold: Immunoglobulin-like beta-sandwich
superfamily: ApaG-like
family: ApaG-like
domain: ApaG
species: Vibrio cholerae [TaxId: 666]

Probab=99.88  E-value=3.3e-23  Score=164.60  Aligned_cols=62  Identities=42%  Similarity=0.735  Sum_probs=59.8

Q ss_pred             eeccCCeEEEEEeEEecCcccCCCCceEEEEEEEEEeCCCCCeEEeeceEEEEcCCCcEEec
Q 027566          160 DATTLGIRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGKTENI  221 (222)
Q Consensus       160 ~a~T~gIkV~V~t~Ylpe~S~P~~~rYvFaY~ItIeN~s~~tVQLlsRhW~ItD~~G~v~eV  221 (222)
                      +.+|.||+|+|.|.|+|++|+|.+.+|+|+|+|+|+|.++++|||++|||+|+|++|++++|
T Consensus         2 d~~~~~I~V~V~~~y~~e~S~p~~~~y~f~Y~I~I~N~~~~~vQLlsR~W~I~d~~g~~~~V   63 (124)
T d1xvsa_           2 DVSLPCIKIQVQTRYIEEQSNPEYQRFVFAYLITIKNLSSQTVQLMSRRWLITDADGKQTVV   63 (124)
T ss_dssp             BCSCCCEEEEEEEEECGGGCBGGGTBEEEEEEEEEEECSSSCEEEEEEEEEEEETTCCEEEE
T ss_pred             CcccCCEEEEEEEEEchhhCCCCCCEEEEEEEEEEEeCCCCCEEEEeeEEEEEeCCCCEEEe
Confidence            35789999999999999999999999999999999999999999999999999999999987

>d1xq4a_ b.1.23.1 (A:) ApaG {Bordetella pertussis [TaxId: 520]}

class: All beta proteins
fold: Immunoglobulin-like beta-sandwich
superfamily: ApaG-like
family: ApaG-like
domain: ApaG
species: Bordetella pertussis [TaxId: 520]

Probab=99.85  E-value=3.8e-22  Score=158.20  Aligned_cols=60  Identities=40%  Similarity=0.797  Sum_probs=58.1

Q ss_pred             ccCCeEEEEEeEEecCcccCCCCceEEEEEEEEEeCCCCCeEEeeceEEEEcCCCcEEec
Q 027566          162 TTLGIRVQVRSVYIEDRSQPLKGQYFFAYRVRITNNSERPVQLLRRHWIITDANGKTENI  221 (222)
Q Consensus       162 ~T~gIkV~V~t~Ylpe~S~P~~~rYvFaY~ItIeN~s~~tVQLlsRhW~ItD~~G~v~eV  221 (222)
                      .++.|+|+|.|.|+|++|+|.+++|+|+|+|+|+|.++.+|||++|||+|+|++|.+++|
T Consensus         3 ~~~~I~V~V~~~y~~e~S~~~~~~y~F~Y~I~I~N~~~~~vQL~sR~W~I~d~~g~~~eV   62 (123)
T d1xq4a_           3 KPYDLTVSVTPRYVPEQSDPSQQQYVFAYTVRITNTGSHPAQVISRHWIITDGEERVQEV   62 (123)
T ss_dssp             CSSCEEEEEEEEECGGGCBGGGTBEEEEEEEEEEECSSSCEEEEEEEEEEECTTSCEEEE
T ss_pred             CCCcEEEEEEEEEchhcCCCCCCeEEEEEEEEEEECCCCcEEEEeeeEEEEeCCCCEEEc
Confidence            367999999999999999999999999999999999999999999999999999999987

>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=97.82  E-value=5.5e-06  Score=56.59  Aligned_cols=29  Identities=34%  Similarity=0.562  Sum_probs=16.8

Q ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHhhhh
Q 027566          121 FRLRRLMKEAVAEERFEDAARYRDKLKEI  149 (222)
Q Consensus       121 ~~L~~~L~~AV~eErYE~AA~lRD~i~~L  149 (222)
                      ..|+.+|..|.++.+||+||+|||+|..|
T Consensus        20 ~~Le~~M~~aa~~l~FE~AA~~RD~I~~l   48 (56)
T d1e52a_          20 HELEGLMMQHAQNLEFEEAAQIRDQLHQL   48 (56)
T ss_dssp             HHHHHHHHHHHHTTCHHHHTTHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCHHHHHHHHHHHHHH
Confidence            45555555555555555555555555555

>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=97.32  E-value=0.00016  Score=49.15  Aligned_cols=31  Identities=35%  Similarity=0.426  Sum_probs=29.3

Q ss_pred             HHHHHHHHHHHHHHHhccchHHHHHHHHHhh
Q 027566           82 SQAYALLKQQMEVAAKTEDYKEAARIRDSLR  112 (222)
Q Consensus        82 ~~cye~Lk~qL~~AIk~EdyE~AA~LRDeI~  112 (222)
                      ...++.|+.+|..+.++.+||+||.+||+|.
T Consensus        16 ~k~i~~Le~~M~~aa~~l~FE~AA~~RD~I~   46 (56)
T d1e52a_          16 QQKIHELEGLMMQHAQNLEFEEAAQIRDQLH   46 (56)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHTTHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHH
Confidence            5789999999999999999999999999993

>d1fpoa2 a.23.1.1 (A:77-171) HSC20 (HSCB), C-terminal oligomerisation domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: Open three-helical up-and-down bundle
superfamily: HSC20 (HSCB), C-terminal oligomerisation domain
family: HSC20 (HSCB), C-terminal oligomerisation domain
domain: HSC20 (HSCB), C-terminal oligomerisation domain
species: Escherichia coli [TaxId: 562]

Probab=86.04  E-value=1.5  Score=30.64  Aligned_cols=60  Identities=17%  Similarity=0.217  Sum_probs=45.9

Q ss_pred             HHHHHHHHHHHHHHhccchHHHHHHHHHhhhhcccchHHHHHHHHHHHHHhhhHHHHHHHHHHhh
Q 027566           83 QAYALLKQQMEVAAKTEDYKEAARIRDSLRSFEEEEPIFRLRRLMKEAVAEERFEDAARYRDKLK  147 (222)
Q Consensus        83 ~cye~Lk~qL~~AIk~EdyE~AA~LRDeI~~l~~~Dpv~~L~~~L~~AV~eErYE~AA~lRD~i~  147 (222)
                      -....++++|+.+-..++.+.-..+..+|     ...+..+...|+.++...+|+.|+..=.+++
T Consensus        17 MeqME~RE~lee~~~~~d~~~l~~l~~ei-----~~~~~~~~~~l~~~~~~~d~~~A~~~~~kLk   76 (95)
T d1fpoa2          17 MEQLELREELDEIEQAKDEARLESFIKRV-----KKMFDTRHQLMVEQLDNETWDAAADTCRKLR   76 (95)
T ss_dssp             HHHHHHHHHHHHHHHHTCHHHHHHHHHHH-----HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhcCCCHHHHHHHHHHH-----HHHHHHHHHHHHHHHhhccHHHHHHHHHHhH
Confidence            45678899999987778877666666666     3344788899999999999999987655544

>d2fzta1 a.46.3.1 (A:1-78) Hypothetical protein TM0693 {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: Methionine synthase domain-like
superfamily: TM0693-like
family: TM0693-like
domain: Hypothetical protein TM0693
species: Thermotoga maritima [TaxId: 2336]

Probab=82.21  E-value=4.6  Score=28.03  Aligned_cols=65  Identities=14%  Similarity=0.279  Sum_probs=45.4

Q ss_pred             HHHHHHHHHHHHhccchHHHHHHHHHhhhhcccchHHHHHHHHHHHHH---------hhhHHHHHHHHHHhhhh
Q 027566           85 YALLKQQMEVAAKTEDYKEAARIRDSLRSFEEEEPIFRLRRLMKEAVA---------EERFEDAARYRDKLKEI  149 (222)
Q Consensus        85 ye~Lk~qL~~AIk~EdyE~AA~LRDeI~~l~~~Dpv~~L~~~L~~AV~---------eErYE~AA~lRD~i~~L  149 (222)
                      +..+..+++.||++||||.--.|-++-++|-..-|-..|..-++.--+         .+=|.++..+|+--+.|
T Consensus         3 I~EiErkIDeaIE~EDyE~L~~LL~kReell~~Lp~~~L~ei~EkD~kR~e~i~k~~~~L~q~~~~ir~~~~~l   76 (78)
T d2fzta1           3 IDEIERKIDEAIEKEDYETLLSLLNKRKELMEGLPKDKLSEILEKDRKRLEIIEKRKTALFQEINVIREARSSL   76 (78)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHCcHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            567889999999999999999998888777777776666655543221         22255666666554433