Citrus Sinensis ID: 026881

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-
MCSLQSQHFLNSPLLIFPKFNDNRKFHLNRTRNFGQRIGALSSVEEFLPNATRRKKDSLWRGGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKTDAYAAVILLERYFSMSGQGTEIVLPKRVDLQEKLRKGALDNDFFPDKPEG
cccccccccccccccccccccccccEEEcccccccccccccccccccccccccccccccccccEEEEEEccccEEEEEEccccEEEEcEEEEEccccHHHHHHHHHHHccccEEEEEccccccccccHHHHHHHHHHHHHHHHHccccccEEEEccHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHcccccccccccccccHHHHHHccccccccccccccc
cccccccccccccEEEcccccccccEEEEcccccccEEEEEccHcccccccHcccccccccccEEEEEEccccEEEEEEccEEccccccHHHHccccccHHHHHHHHHHcccEEEEEcccccccccHHHHHHHHHHHHHHHHHHHHccccEEEEcccccHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHcccccEEEccccHHHHHHHHccccccccccccccc
mcslqsqhflnspllifpkfndnrkfHLNRTRNFGQRIGALSSVEeflpnatrrkkdslwrggfslgvdlglsrtglalskgfcvrpltVLKLRGEKLELQLLEIAQReetdefiiglpkswdgsetpqsnkvrSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKTDAYAAVILLERYFsmsgqgteivlpkRVDLQEKLrkgaldndffpdkpeg
mcslqsqhflnspllifPKFNDNRKFHLNRTRNFgqrigalssveeflpnatrrkkdslwrgGFSLGVDLGLSrtglalskgfcvRPLTVLKLRGEKLELQLLEiaqreetdeFIIGlpkswdgsetpqsnkvrsvagRLAVRAAERGWRVYLLDEHRTSAEAVDRMINmglsksarqtKTDAYAAVILLERYFSmsgqgteivlpkrVDLQEklrkgaldndffpdkpeg
MCSLQSQHFLNSPLLIFPKFNDNRKFHLNRTRNFGQRIGALSSVEEFLPNATRRKKDSLWRGGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKTDAYAAVILLERYFSMSGQGTEIVLPKRVDLQEKLRKGALDNDFFPDKPEG
********FLNSPLLIFPKFNDNRKFHLNRTRNFGQRIGALSSVEEFLPNATRRKKDSLWRGGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQREETDEFIIGLPKSW*************VAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGL******TKTDAYAAVILLERYFSMSGQGTEIVLPKRVDL********************
*******HFLNSPLLIFPKFNDNRKFHLNR*********************************FSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVD****************DAYAAVILLERYFS************************************
MCSLQSQHFLNSPLLIFPKFNDNRKFHLNRTRNFGQRIGALSSVEEFLPNATRRKKDSLWRGGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQREETDEFIIGLPKSWD************VAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKTDAYAAVILLERYFSMSGQGTEIVLPKRVDLQEKLRKGALDNDFFPDKPEG
*****SQHFLNSPLLIFPKFNDNRKFHLNRTRNFGQRIGALSSVEEFLPNATRRKKDSLWRGGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKTDAYAAVILLERYFSMSGQGTEIVLPKRVDLQEKLRKGALDNDFFP*****
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MCSLQSQHFLNSPLLIFPKFNDNRKFHLNRTRNFGQRIGALSSVEEFLPNATRRKKDSLWRGGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKTDAYAAVILLERYFSMSGQGTEIVLPKRVDLQEKLRKGALDNDFFPDKPEG
no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST ?

Original result of BLAST against SWISS-PROT Database

ID ?Alignment graph ?Length ? Definition ? RBH(Q2H) ? RBH(H2Q) ? Q cover ? H cover ? Identity ? E-value ?
Query231 2.2.26 [Sep-21-2011]
A1SJC8156 Putative Holliday junctio yes no 0.575 0.852 0.340 1e-10
Q2RHZ7140 Putative Holliday junctio yes no 0.567 0.935 0.328 3e-10
Q2IQC1137 Putative Holliday junctio yes no 0.549 0.927 0.353 6e-10
A7MJR8138 Putative Holliday junctio yes no 0.575 0.963 0.316 6e-10
B3EPT4144 Putative Holliday junctio yes no 0.567 0.909 0.318 1e-09
B4UH04137 Putative Holliday junctio yes no 0.549 0.927 0.353 2e-09
B7NI12138 Putative Holliday junctio yes no 0.558 0.934 0.325 2e-09
Q3YXS2138 Putative Holliday junctio yes no 0.558 0.934 0.325 2e-09
Q83JS4138 Putative Holliday junctio yes no 0.558 0.934 0.325 2e-09
Q0T0U3138 Putative Holliday junctio yes no 0.558 0.934 0.325 2e-09
>sp|A1SJC8|RUVX_NOCSJ Putative Holliday junction resolvase OS=Nocardioides sp. (strain BAA-499 / JS614) GN=Noca_2408 PE=3 SV=1 Back     alignment and function desciption
 Score = 67.0 bits (162), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 48/141 (34%), Positives = 73/141 (51%), Gaps = 8/141 (5%)

Query: 60  WRGGFSLGVDLGLSRTGLALS--KGFCVRPL-TVLKLRGEKLELQLLEIAQREETD---E 113
            R G  +G+D G +R G+A S   GF   P+ TV + +G+   +  +  A+ +E     E
Sbjct: 1   MRAGVRIGIDPGDARIGVARSDPSGFLATPVETVRRGKGDLARIGRILAAEEDEGATVLE 60

Query: 114 FIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLS 173
            ++GLP+S  G E P + KVR  AGRLA R A     V L+DE  T+  A   + + G +
Sbjct: 61  VVVGLPRSLSGREGPAAAKVREFAGRLAARVAP--VPVRLVDERMTTVSAEAMLRDQGRT 118

Query: 174 KSARQTKTDAYAAVILLERYF 194
              R+   D  AAV++L+   
Sbjct: 119 GGKRRAVVDQAAAVLILQHAL 139
Could be a nuclease that resolves Holliday junction intermediates in genetic recombination.
Nocardioides sp. (strain BAA-499 / JS614) (taxid: 196162)
EC: 3EC: .EC: 1EC: .EC: -EC: .EC: -
>sp|Q2RHZ7|RUVX_MOOTA Putative Holliday junction resolvase OS=Moorella thermoacetica (strain ATCC 39073) GN=Moth_1640 PE=3 SV=1 Back     alignment and function description
>sp|Q2IQC1|RUVX_ANADE Putative Holliday junction resolvase OS=Anaeromyxobacter dehalogenans (strain 2CP-C) GN=Adeh_1232 PE=3 SV=1 Back     alignment and function description
>sp|A7MJR8|RUVX_CROS8 Putative Holliday junction resolvase OS=Cronobacter sakazakii (strain ATCC BAA-894) GN=ESA_00393 PE=3 SV=1 Back     alignment and function description
>sp|B3EPT4|RUVX_CHLPB Putative Holliday junction resolvase OS=Chlorobium phaeobacteroides (strain BS1) GN=Cphamn1_2429 PE=3 SV=1 Back     alignment and function description
>sp|B4UH04|RUVX_ANASK Putative Holliday junction resolvase OS=Anaeromyxobacter sp. (strain K) GN=AnaeK_2633 PE=3 SV=1 Back     alignment and function description
>sp|B7NI12|RUVX_ECO7I Putative Holliday junction resolvase OS=Escherichia coli O7:K1 (strain IAI39 / ExPEC) GN=yqgF PE=3 SV=1 Back     alignment and function description
>sp|Q3YXS2|RUVX_SHISS Putative Holliday junction resolvase OS=Shigella sonnei (strain Ss046) GN=yqgF PE=3 SV=1 Back     alignment and function description
>sp|Q83JS4|RUVX_SHIFL Putative Holliday junction resolvase OS=Shigella flexneri GN=yqgF PE=3 SV=1 Back     alignment and function description
>sp|Q0T0U3|RUVX_SHIF8 Putative Holliday junction resolvase OS=Shigella flexneri serotype 5b (strain 8401) GN=yqgF PE=3 SV=1 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query231
224129716254 predicted protein [Populus trichocarpa] 0.917 0.834 0.691 1e-77
297734533 679 unnamed protein product [Vitis vinifera] 0.839 0.285 0.744 3e-75
359489199229 PREDICTED: putative Holliday junction re 0.839 0.847 0.744 3e-74
356506432226 PREDICTED: putative Holliday junction re 0.826 0.845 0.709 2e-71
255573708239 hydrolase, acting on ester bonds, putati 0.974 0.941 0.623 2e-67
297844086238 DNA binding protein [Arabidopsis lyrata 0.961 0.932 0.605 6e-67
449431960235 PREDICTED: putative Holliday junction re 0.792 0.778 0.702 2e-66
79317769254 putative holliday junction resolvase [Ar 0.826 0.751 0.692 8e-63
147819080213 hypothetical protein VITISV_000639 [Viti 0.753 0.816 0.653 6e-61
414867730235 TPA: holliday junction resolvase [Zea ma 0.722 0.710 0.662 7e-56
>gi|224129716|ref|XP_002328785.1| predicted protein [Populus trichocarpa] gi|222839083|gb|EEE77434.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
 Score =  295 bits (754), Expect = 1e-77,   Method: Compositional matrix adjust.
 Identities = 148/214 (69%), Positives = 173/214 (80%), Gaps = 2/214 (0%)

Query: 15  LIFPKFNDNRKFHLNRTRNFGQRIGALSSVEEFLPNATRRKKDSLWRGGFSLGVDLGLSR 74
           L+FP F  +    L+  +   +R+ AL S+ E  PNA RRK D LWRGGFSLGVDLGLSR
Sbjct: 42  LLFPNFTTS-SLQLDSDKPCRRRLRALLSIHEIPPNALRRKNDPLWRGGFSLGVDLGLSR 100

Query: 75  TGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVR 134
           +G+ALSKGF VRPLTVL+LRG+KLEL+LLEIA+ EE DEFIIGLPKSWDG ETPQSNKVR
Sbjct: 101 SGVALSKGFTVRPLTVLELRGQKLELRLLEIAENEEVDEFIIGLPKSWDGKETPQSNKVR 160

Query: 135 SVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKTDAYAAVILLERYF 194
           SVAGR AV AA RGWRVYL DEH TS EA +RMI+MGL+KS RQ K DAYAAV++LERYF
Sbjct: 161 SVAGRFAVLAAHRGWRVYLQDEHGTSTEATNRMIDMGLNKSTRQKKVDAYAAVMVLERYF 220

Query: 195 SMSGQGTEIVLPKRVDLQEKLRKG-ALDNDFFPD 227
           S  G+GTE+VLPK+ DLQEKL++G   D DF+P+
Sbjct: 221 STFGEGTELVLPKQSDLQEKLQRGPPADIDFYPE 254

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|297734533|emb|CBI16584.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|359489199|ref|XP_002275849.2| PREDICTED: putative Holliday junction resolvase [Vitis vinifera] Back     alignment and taxonomy information
>gi|356506432|ref|XP_003521987.1| PREDICTED: putative Holliday junction resolvase-like [Glycine max] Back     alignment and taxonomy information
>gi|255573708|ref|XP_002527775.1| hydrolase, acting on ester bonds, putative [Ricinus communis] gi|223532810|gb|EEF34585.1| hydrolase, acting on ester bonds, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|297844086|ref|XP_002889924.1| DNA binding protein [Arabidopsis lyrata subsp. lyrata] gi|297335766|gb|EFH66183.1| DNA binding protein [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|449431960|ref|XP_004133768.1| PREDICTED: putative Holliday junction resolvase-like [Cucumis sativus] gi|449522992|ref|XP_004168509.1| PREDICTED: putative Holliday junction resolvase-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|79317769|ref|NP_001031028.1| putative holliday junction resolvase [Arabidopsis thaliana] gi|332190735|gb|AEE28856.1| putative holliday junction resolvase [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|147819080|emb|CAN65349.1| hypothetical protein VITISV_000639 [Vitis vinifera] Back     alignment and taxonomy information
>gi|414867730|tpg|DAA46287.1| TPA: holliday junction resolvase [Zea mays] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query231
TAIR|locus:1009023117254 AT1G12244 [Arabidopsis thalian 0.974 0.885 0.611 2.2e-66
UNIPROTKB|P0A8I1138 yqgF [Escherichia coli K-12 (t 0.558 0.934 0.318 2.2e-11
UNIPROTKB|Q8EBZ8141 SO_3347 "Putative Holliday jun 0.545 0.893 0.287 1.5e-10
TIGR_CMR|SO_3347141 SO_3347 "conserved hypothetica 0.545 0.893 0.287 1.5e-10
UNIPROTKB|Q0BZU8151 HNE_2300 "Putative Holliday ju 0.549 0.841 0.333 3.9e-09
UNIPROTKB|Q81LK2137 BAS4282 "Putative Holliday jun 0.536 0.905 0.276 7.7e-08
TIGR_CMR|BA_4614137 BA_4614 "conserved hypothetica 0.536 0.905 0.276 7.7e-08
UNIPROTKB|Q83A17141 CBU_2094 "Putative Holliday ju 0.536 0.879 0.272 1.7e-07
TIGR_CMR|CBU_2094141 CBU_2094 "conserved hypothetic 0.536 0.879 0.272 1.7e-07
UNIPROTKB|Q3AEN4138 CHY_0542 "Putative Holliday ju 0.549 0.920 0.278 2.2e-07
TAIR|locus:1009023117 AT1G12244 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 675 (242.7 bits), Expect = 2.2e-66, P = 2.2e-66
 Identities = 145/237 (61%), Positives = 176/237 (74%)

Query:     1 MCSLQSQHFLNSPLLIF--PKFNDNRKFHLNRTRNFGQRI----GALSSVEEFLPNATRR 54
             MCSL   H  +S  + F   K+ +    H  R    G R      A++S++E  PNA RR
Sbjct:    18 MCSL---HSFSSVAISFRTQKYVNTSLVH--RLSPIGYRNYPLPWAVTSIDEIPPNAVRR 72

Query:    55 KKDSLWRGGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQREETDEF 114
             K D  WRGGFSLGVDLGLSRTG+A+SKG+ V+PLTVLK RG+KLE +LLEIA+ EE DEF
Sbjct:    73 KIDRNWRGGFSLGVDLGLSRTGIAISKGYTVKPLTVLKSRGQKLETRLLEIAEEEEADEF 132

Query:   115 IIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSK 174
             IIGLP+S DG ET QSNK+RSVAGRLA++AAERGWRVY+ DEH T++EA DRMI MGLSK
Sbjct:   133 IIGLPRSSDGKETIQSNKIRSVAGRLAIQAAERGWRVYVFDEHGTTSEASDRMIVMGLSK 192

Query:   175 SARQTKTDAYAAVILLERYFSMSGQGTEIVLPKRVDLQEKLRKGA-LDNDFFPDKPE 230
             S RQ ++DAYAAVILLERYFS  G G EI+LPK ++LQ K++ GA +D DF P+  E
Sbjct:   193 SERQNRSDAYAAVILLERYFSTQGLGIEIILPKSLELQAKIKNGAPVDPDFNPENLE 249
GO:0003676 "nucleic acid binding" evidence=IEA
GO:0005737 "cytoplasm" evidence=IEA
GO:0006139 "nucleobase-containing compound metabolic process" evidence=IEA
GO:0006281 "DNA repair" evidence=IEA
GO:0006310 "DNA recombination" evidence=IEA
GO:0006974 "response to DNA damage stimulus" evidence=IEA
GO:0009507 "chloroplast" evidence=ISM
GO:0016788 "hydrolase activity, acting on ester bonds" evidence=IEA
UNIPROTKB|P0A8I1 yqgF [Escherichia coli K-12 (taxid:83333)] Back     alignment and assigned GO terms
UNIPROTKB|Q8EBZ8 SO_3347 "Putative Holliday junction resolvase" [Shewanella oneidensis MR-1 (taxid:211586)] Back     alignment and assigned GO terms
TIGR_CMR|SO_3347 SO_3347 "conserved hypothetical protein TIGR00250" [Shewanella oneidensis MR-1 (taxid:211586)] Back     alignment and assigned GO terms
UNIPROTKB|Q0BZU8 HNE_2300 "Putative Holliday junction resolvase" [Hyphomonas neptunium ATCC 15444 (taxid:228405)] Back     alignment and assigned GO terms
UNIPROTKB|Q81LK2 BAS4282 "Putative Holliday junction resolvase" [Bacillus anthracis (taxid:1392)] Back     alignment and assigned GO terms
TIGR_CMR|BA_4614 BA_4614 "conserved hypothetical protein TIGR00250" [Bacillus anthracis str. Ames (taxid:198094)] Back     alignment and assigned GO terms
UNIPROTKB|Q83A17 CBU_2094 "Putative Holliday junction resolvase" [Coxiella burnetii RSA 493 (taxid:227377)] Back     alignment and assigned GO terms
TIGR_CMR|CBU_2094 CBU_2094 "conserved hypothetical protein TIGR00250" [Coxiella burnetii RSA 493 (taxid:227377)] Back     alignment and assigned GO terms
UNIPROTKB|Q3AEN4 CHY_0542 "Putative Holliday junction resolvase" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)] Back     alignment and assigned GO terms

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 ?Alignment Graph ?Length ? Definition ? E-value ?
Query231
pfam03652134 pfam03652, UPF0081, Uncharacterized protein family 2e-29
PRK00109138 PRK00109, PRK00109, Holliday junction resolvase-li 7e-22
COG0816141 COG0816, COG0816, Predicted endonuclease involved 2e-21
TIGR00250130 TIGR00250, RNAse_H_YqgF, RNAse H-fold protein YqgF 4e-15
smart0073299 smart00732, YqgFc, Likely ribonuclease with RNase 1e-10
>gnl|CDD|217659 pfam03652, UPF0081, Uncharacterized protein family (UPF0081) Back     alignment and domain information 
 Score =  106 bits (267), Expect = 2e-29
 Identities = 46/134 (34%), Positives = 71/134 (52%), Gaps = 6/134 (4%)

Query: 66  LGVDLGLSRTGLALSKGFC--VRPLTVLKLRGEKLEL-QLLEIAQREETDEFIIGLPKSW 122
           LG+D+G  R G+A+S        PL  ++ +    +L +L E+ +  + D  ++GLP + 
Sbjct: 4   LGLDVGTKRIGVAISDPLGILASPLETIRRKNGNPDLEELAELIKEWQPDGIVVGLPLNM 63

Query: 123 DGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKTD 182
           DGSE   + +VR  A RL  R    G  V L+DE  T+ EA   +   GLS+  R+   D
Sbjct: 64  DGSEGEMTKRVRKFARRLKKR---FGLPVELVDERLTTVEAERILREAGLSRKKRKEVVD 120

Query: 183 AYAAVILLERYFSM 196
           + AAVI+L+ Y   
Sbjct: 121 SIAAVIILQSYLDS 134

Length = 134
>gnl|CDD|234639 PRK00109, PRK00109, Holliday junction resolvase-like protein; Reviewed Back     alignment and domain information
>gnl|CDD|223886 COG0816, COG0816, Predicted endonuclease involved in recombination (possible Holliday junction resolvase in Mycoplasmas and B Back     alignment and domain information
>gnl|CDD|129352 TIGR00250, RNAse_H_YqgF, RNAse H-fold protein YqgF Back     alignment and domain information
>gnl|CDD|128971 smart00732, YqgFc, Likely ribonuclease with RNase H fold Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 231
PF03652135 UPF0081: Uncharacterised protein family (UPF0081); 100.0
PRK00109138 Holliday junction resolvase-like protein; Reviewed 100.0
COG0816141 Predicted endonuclease involved in recombination ( 100.0
TIGR00250130 RNAse_H_YqgF RNAse H-fold protein YqgF. This prote 100.0
smart0073299 YqgFc Likely ribonuclease with RNase H fold. YqgF 99.5
PRK00039164 ruvC Holliday junction resolvase; Reviewed 97.6
PF02075149 RuvC: Crossover junction endodeoxyribonuclease Ruv 97.31
cd00529154 RuvC_resolvase Holliday junction resolvases (HJRs) 97.15
TIGR00228156 ruvC crossover junction endodeoxyribonuclease RuvC 96.95
COG2183 780 Tex Transcriptional accessory protein [Transcripti 96.79
PF04312138 DUF460: Protein of unknown function (DUF460); Inte 96.12
COG2433 652 Uncharacterized conserved protein [Function unknow 95.93
PF14639150 YqgF: Holliday-junction resolvase-like of SPT6 ; P 95.82
COG0817160 RuvC Holliday junction resolvasome, endonuclease s 95.42
COG1548 330 Predicted transcriptional regulator/sugar kinase [ 94.35
TIGR0176682 tspaseT_teng_C transposase, IS605 OrfB family, cen 92.85
COG1940 314 NagC Transcriptional regulator/sugar kinase [Trans 90.08
PRK09557 301 fructokinase; Reviewed 89.63
PF01548144 DEDD_Tnp_IS110: Transposase; InterPro: IPR002525 T 89.28
TIGR00744 318 ROK_glcA_fam ROK family protein (putative glucokin 88.26
PRK05082 291 N-acetylmannosamine kinase; Provisional 86.73
PRK13310 303 N-acetyl-D-glucosamine kinase; Provisional 85.42
PRK13321256 pantothenate kinase; Reviewed 83.51
PF14239176 RRXRR: RRXRR protein 83.11
PRK09698 302 D-allose kinase; Provisional 82.79
PF0728269 OrfB_Zn_ribbon: Putative transposase DNA-binding d 81.64
PRK13311256 N-acetyl-D-glucosamine kinase; Provisional 81.07
>PF03652 UPF0081: Uncharacterised protein family (UPF0081); InterPro: IPR005227 Holliday junction resolvases (HJRs) are key enzymes of DNA recombination Back     alignment and domain information 
Probab=100.00  E-value=3.5e-42  Score=281.18  Aligned_cols=132  Identities=36%  Similarity=0.524  Sum_probs=121.1

Q ss_pred             ceEEEEecCCCeEEEEEecC--ceeeeeeeeeccc-hhHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHH
Q 026881           63 GFSLGVDLGLSRTGLALSKG--FCVRPLTVLKLRG-EKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGR  139 (231)
Q Consensus        63 g~iLglD~G~kRIGvAvsD~--~~A~Pl~~i~~~~-~~~~~~L~~li~e~~i~~IVVGLPl~~dGt~s~~~~~v~~Fa~~  139 (231)
                      +++||||||+||||||+||.  .+|+|+.+|.+.+ ..++..|.+++++|+++.||||+|++|||+++++++.+++|+++
T Consensus         1 mriL~lD~G~kriGiAvsd~~~~~a~pl~~i~~~~~~~~~~~l~~li~~~~i~~iVvGlP~~~~G~~~~~~~~v~~f~~~   80 (135)
T PF03652_consen    1 MRILGLDYGTKRIGIAVSDPLGIIASPLETIPRRNREKDIEELKKLIEEYQIDGIVVGLPLNMDGSESEQARRVRKFAEE   80 (135)
T ss_dssp             -EEEEEEECSSEEEEEEEETTTSSEEEEEEEEECCCCCCHHHHHHHHHHCCECEEEEEEEBBCTSSC-CCHHHHHHHHHH
T ss_pred             CeEEEEEeCCCeEEEEEecCCCCeEeeeEEEECCCCchHHHHHHHHHHHhCCCEEEEeCCcccCCCccHHHHHHHHHHHH
Confidence            47999999999999999995  4799999998653 46789999999999999999999999999999999999999999


Q ss_pred             HHHHhccCCCcEEEecCCCcHHHHHHHHHHcCCCccccCCCCcHHHHHHHHHHHHcc
Q 026881          140 LAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKTDAYAAVILLERYFSM  196 (231)
Q Consensus       140 L~~~~~~~~lpV~lvDER~TT~eA~~~l~e~G~~rkkrK~~vD~lAA~IILq~yLd~  196 (231)
                      |+++++  ++||++|||||||.+|++.|++.|++++++|+.+|++||++|||+||++
T Consensus        81 L~~~~~--~ipV~~~DEr~TT~~A~~~l~~~g~~~~k~k~~iD~~AA~iILq~yLd~  135 (135)
T PF03652_consen   81 LKKRFP--GIPVILVDERLTTKEAERRLRESGLSRKKRKKKIDSIAAAIILQSYLDS  135 (135)
T ss_dssp             HHHHH---TSEEEEEECSCSHHCCHCCHHHTT-SHHHHCHHHCCCHHHHHHHHHHCC
T ss_pred             HHHhcC--CCcEEEECCChhHHHHHHHHHHcCCChhhcCccccHHHHHHHHHHHHhC
Confidence            999863  8999999999999999999999999999999999999999999999985

The principal HJRs are now known or confidently predicted for all bacteria and archaea whose genomes have been completely sequenced, with many species encoding multiple potential HJRs. Structural and evolutionary relationships of HJRs and related nucleases suggests that the HJR function has evolved independently from at least four distinct structural folds, namely RNase H, endonuclease, endonuclease VII-colicin E and RusA (IPR008822 from INTERPRO): The endonuclease fold, whose structural prototypes are the phage exonuclease, the very short patch repair nuclease (Vsr) and type II restriction enzymes, is shown to encompass by far a greater diversity of nucleases than previously suspected. This fold unifies archaeal HJRs (IPR002732 from INTERPRO), repair nucleases such as RecB (IPR004586 from INTERPRO) and Vsr (IPR004603 from INTERPRO), restriction enzymes and a variety of predicted nucleases whose specific activities remain to be determined. The RNase H fold characterises the RuvC family (IPR002176 from INTERPRO), which is nearly ubiquitous in bacteria, and in addition the YqgF family (IPR005227 from INTERPRO). The proteins of this family, typified by Escherichia coli YqgF, are likely to function as an alternative to RuvC in most bacteria, but could be the principal HJRs in low-GC Gram-positive bacteria and Aquifex. Endonuclease VII of phage T4 (IPR004211 from INTERPRO) is shown to serve as a structural template for many nucleases, including McrA and other type II restriction enzymes. Together with colicin E7, endonuclease VII defines a distinct metal-dependent nuclease fold. Horizontal gene transfer, lineage-specific gene loss and gene family expansion, and non-orthologous gene displacement seem to have been major forces in the evolution of HJRs and related nucleases. A remarkable case of displacement is seen in the Lyme disease spirochete Borrelia burgdorferi, which does not possess any of the typical HJRs, but instead encodes, in its chromosome and each of the linear plasmids, members of the exonuclease family predicted to function as HJRs. The diversity of HJRs and related nucleases in bacteria and archaea contrasts with their near absence in eukaryotes. The few detected eukaryotic representatives of the endonuclease fold and the RNase H fold have probably been acquired from bacteria via horizontal gene transfer. The identity of the principal HJR(s) involved in recombination in eukaryotes remains uncertain; this function could be performed by topoisomerase IB or by a novel, so far undetected, class of enzymes. Likely HJRs and related nucleases were identified in the genomes of numerous bacterial and eukaryotic DNA viruses. Gene flow between viral and cellular genomes has probably played a major role in the evolution of this class of enzymes. This family represents the YqgF family of putative Holliday junction resolvases. With the exception of the spirochetes, the YqgF family is represented in all bacterial lineages, including the mycoplasmas with their highly degenerate genomes. The RuvC resolvases are conspicuously absent in the low-GC Gram-positive bacterial lineage, with the exception of Ureaplasma parvum (Ureaplasma urealyticum biotype 1) (Q9PQY7 from SWISSPROT, []). Furthermore, loss of function ruvC mutants of E. coli show a residual HJR activity that cannot be ascribed to the prophage-encoded RusA resolvase []. This suggests that the YqgF family proteins could be alternative HJRs whose function partially overlaps with that of RuvC [].; GO: 0016788 hydrolase activity, acting on ester bonds, 0006281 DNA repair, 0006310 DNA recombination, 0006974 response to DNA damage stimulus, 0005737 cytoplasm; PDB: 1NU0_A 1OVQ_A 1NMN_B 1VHX_B 1IV0_A.
>PRK00109 Holliday junction resolvase-like protein; Reviewed Back     alignment and domain information
>COG0816 Predicted endonuclease involved in recombination (possible Holliday junction resolvase in Mycoplasmas and B Back     alignment and domain information
>TIGR00250 RNAse_H_YqgF RNAse H-fold protein YqgF Back     alignment and domain information
>smart00732 YqgFc Likely ribonuclease with RNase H fold Back     alignment and domain information
>PRK00039 ruvC Holliday junction resolvase; Reviewed Back     alignment and domain information
>PF02075 RuvC: Crossover junction endodeoxyribonuclease RuvC; InterPro: IPR002176 The Escherichia coli ruvC gene is involved in DNA repair and in the late step of RecE and RecF pathway recombination [] Back     alignment and domain information
>cd00529 RuvC_resolvase Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination Back     alignment and domain information
>TIGR00228 ruvC crossover junction endodeoxyribonuclease RuvC Back     alignment and domain information
>COG2183 Tex Transcriptional accessory protein [Transcription] Back     alignment and domain information
>PF04312 DUF460: Protein of unknown function (DUF460); InterPro: IPR007408 This is an archaeal protein of unknown function Back     alignment and domain information
>COG2433 Uncharacterized conserved protein [Function unknown] Back     alignment and domain information
>PF14639 YqgF: Holliday-junction resolvase-like of SPT6 ; PDB: 3PSI_A 3PSF_A Back     alignment and domain information
>COG0817 RuvC Holliday junction resolvasome, endonuclease subunit [DNA replication, recombination, and repair] Back     alignment and domain information
>COG1548 Predicted transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism] Back     alignment and domain information
>TIGR01766 tspaseT_teng_C transposase, IS605 OrfB family, central region Back     alignment and domain information
>COG1940 NagC Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism] Back     alignment and domain information
>PRK09557 fructokinase; Reviewed Back     alignment and domain information
>PF01548 DEDD_Tnp_IS110: Transposase; InterPro: IPR002525 Transposase proteins are necessary for efficient DNA transposition Back     alignment and domain information
>TIGR00744 ROK_glcA_fam ROK family protein (putative glucokinase) Back     alignment and domain information
>PRK05082 N-acetylmannosamine kinase; Provisional Back     alignment and domain information
>PRK13310 N-acetyl-D-glucosamine kinase; Provisional Back     alignment and domain information
>PRK13321 pantothenate kinase; Reviewed Back     alignment and domain information
>PF14239 RRXRR: RRXRR protein Back     alignment and domain information
>PRK09698 D-allose kinase; Provisional Back     alignment and domain information
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins Back     alignment and domain information
>PRK13311 N-acetyl-D-glucosamine kinase; Provisional Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query231
1ovq_A138 Solution Structure Of The Hypothetical Protein Yqgf 2e-10
1nmn_A138 Structure Of Yqgf From Escherichia Coli, A Hypothet 2e-10
1nu0_A138 Structure Of The Double Mutant (L6m; F134m, Semet F 2e-09
1vhx_A150 Crystal Structure Of Putative Holliday Junction Res 2e-05
>pdb|1OVQ|A Chain A, Solution Structure Of The Hypothetical Protein Yqgf From Escherichia Coli Length = 138 Back     alignment and structure 
Iteration: 1

 Score = 62.0 bits (149), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 43/135 (31%), Positives = 68/135 (50%), Gaps = 6/135 (4%)
Query: 63  GFSLGVDLGLSRTGLALSKGFC--VRPLTVLKLRGEKLELQLLEIAQRE-ETDEFIIGLP 119
           G  L  D G    G+A+ +      RPL  +K +    +  ++E   +E + DE I+GLP
Sbjct: 3   GTLLAFDFGTKSIGVAVGQRITGTARPLPAIKAQDGTPDWNIIERLLKEWQPDEIIVGLP 62
Query: 120 KSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQT 179
            + DG+E P + + R  A R+  R    G  V L DE  ++ EA   +   G  ++  + 
Sbjct: 63  LNMDGTEQPLTARARKFANRIHGRF---GVEVKLHDERLSTVEARSGLFEQGGYRALNKG 119
Query: 180 KTDAYAAVILLERYF 194
           K D+ +AVI+LE YF
Sbjct: 120 KVDSASAVIILESYF 134
>pdb|1NMN|A Chain A, Structure Of Yqgf From Escherichia Coli, A Hypothetical Protein Length = 138 Back     alignment and structure
>pdb|1NU0|A Chain A, Structure Of The Double Mutant (L6m; F134m, Semet Form) Of Yqgf From Escherichia Coli, A Hypothetical Protein Length = 138 Back     alignment and structure
>pdb|1VHX|A Chain A, Crystal Structure Of Putative Holliday Junction Resolvase Length = 150 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query231
1nu0_A138 Hypothetical protein YQGF; structural genomics, st 1e-26
1vhx_A150 Putative holliday junction resolvase; structural g 5e-26
1iv0_A98 Hypothetical protein; rnaseh-like, YQGF, structura 9e-17
>1nu0_A Hypothetical protein YQGF; structural genomics, structure 2 function project, S2F, unknown function; 1.60A {Escherichia coli} SCOP: c.55.3.8 PDB: 1nmn_A 1ovq_A Length = 138 Back     alignment and structure
 Score = 98.7 bits (247), Expect = 1e-26
 Identities = 38/132 (28%), Positives = 63/132 (47%), Gaps = 6/132 (4%)

Query: 66  LGVDLGLSRTGLALS--KGFCVRPLTVLKLRGEKLEL-QLLEIAQREETDEFIIGLPKSW 122
           +  D G    G+A+        RPL  +K +    +   +  + +  + DE I+GLP + 
Sbjct: 6   MAFDFGTKSIGVAVGQRITGTARPLPAIKAQDGTPDWNIIERLLKEWQPDEIIVGLPLNM 65

Query: 123 DGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKTD 182
           DG+E P + + R  A R+  R    G  V L DE  ++ EA   +   G  ++  + K D
Sbjct: 66  DGTEQPLTARARKFANRIHGR---FGVEVKLHDERLSTVEARSGLFEQGGYRALNKGKVD 122

Query: 183 AYAAVILLERYF 194
           + +AVI+LE Y 
Sbjct: 123 SASAVIILESYM 134
>1vhx_A Putative holliday junction resolvase; structural genomics, hydrolase; 1.96A {Bacillus subtilis} SCOP: c.55.3.8 Length = 150 Back     alignment and structure
>1iv0_A Hypothetical protein; rnaseh-like, YQGF, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Thermus thermophilus} SCOP: c.55.3.8 Length = 98 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query231
1nu0_A138 Hypothetical protein YQGF; structural genomics, st 100.0
1vhx_A150 Putative holliday junction resolvase; structural g 100.0
1iv0_A98 Hypothetical protein; rnaseh-like, YQGF, structura 99.97
4ep4_A166 Crossover junction endodeoxyribonuclease RUVC; res 98.24
3bzc_A 785 TEX; helix-turn-helix, helix-hairpin-helix, S1 dom 97.69
1hjr_A158 Holliday junction resolvase (RUVC); site-specific 97.53
3psf_A 1030 Transcription elongation factor SPT6; nucleus; 2.5 96.85
3psi_A 1219 Transcription elongation factor SPT6; nucleus; 3.3 96.74
3vov_A 302 Glucokinase, hexokinase; ROK, sugar kinase, transf 92.43
3epq_A 302 Putative fructokinase; SCRK, ADP binding, PSI2, MC 92.37
3vgl_A 321 Glucokinase; ROK family, transferase; HET: BGC ANP 92.25
1saz_A 381 Probable butyrate kinase 2; askha (acetate and sug 89.27
2ch5_A 347 NAGK protein; transferase, N-acetylglucosamine, gl 88.31
3djc_A266 Type III pantothenate kinase; structural genomics, 88.21
2qm1_A 326 Glucokinase; alpha-beta structure, putative helix- 87.24
2e2o_A 299 Hexokinase; acetate and sugar kinases, HSP70, acti 86.71
2hoe_A 380 N-acetylglucosamine kinase; TM1224, structural gen 85.86
4htl_A 297 Beta-glucoside kinase; structural genomics, sugar 85.36
3r8e_A 321 Hypothetical sugar kinase; ribonuclease H-like mot 85.22
2gel_A231 Putative GRAM negative resuscitation promoting FA; 84.97
2gup_A 292 ROK family protein; sugar kinase, streptococcus pn 84.39
2ap1_A 327 Putative regulator protein; zinc binding protein, 83.87
3r6m_A213 YEAZ, resuscitation promoting factor; actin/HSP70 83.6
3htv_A 310 D-allose kinase, allokinase; NP_418508.1, structur 82.05
1z6r_A 406 MLC protein; transcriptional repressor, ROK family 81.74
3mcp_A 366 Glucokinase; structural genomics, joint center for 80.51
2a6a_A218 Hypothetical protein TM0874; glycoprotein endopept 80.21
2aa4_A 289 Mannac kinase, putative N-acetylmannosamine kinase 80.16
>1nu0_A Hypothetical protein YQGF; structural genomics, structure 2 function project, S2F, unknown function; 1.60A {Escherichia coli} SCOP: c.55.3.8 PDB: 1nmn_A 1ovq_A Back     alignment and structure
Probab=100.00  E-value=2.1e-42  Score=282.59  Aligned_cols=132  Identities=30%  Similarity=0.438  Sum_probs=114.7

Q ss_pred             CceEEEEecCCCeEEEEEecC--ceeeeeeeeeccc-hhHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHH
Q 026881           62 GGFSLGVDLGLSRTGLALSKG--FCVRPLTVLKLRG-EKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAG  138 (231)
Q Consensus        62 ~g~iLglD~G~kRIGvAvsD~--~~A~Pl~~i~~~~-~~~~~~L~~li~e~~i~~IVVGLPl~~dGt~s~~~~~v~~Fa~  138 (231)
                      ++++||||||+||||||+||.  .+|+|+++|.+++ ...+.+|.+++++|+++.||||+|++|||+++++++++++|++
T Consensus         2 ~~~iLglD~G~kriGvAvsd~~~~~A~pl~ti~~~~~~~~~~~l~~li~e~~v~~iVvGlP~~mdGt~~~~~~~~~~f~~   81 (138)
T 1nu0_A            2 SGTLMAFDFGTKSIGVAVGQRITGTARPLPAIKAQDGTPDWNIIERLLKEWQPDEIIVGLPLNMDGTEQPLTARARKFAN   81 (138)
T ss_dssp             CCEEEEEECCSSEEEEEEEETTTTEEEEEEEEEEETTEECHHHHHHHHHHHCCSEEEEEEEECTTSCBCHHHHHHHHHHH
T ss_pred             CCeEEEEEeCCCEEEEEEEcCCCCEEeeEEEEEcCCcchHHHHHHHHHHHcCCCEEEEecccCCCcCcCHHHHHHHHHHH
Confidence            358999999999999999995  5899999997643 3468999999999999999999999999999999999999999


Q ss_pred             HHHHHhccCCCcEEEecCCCcHHHHHHHHHHcCCCccccCCCCcHHHHHHHHHHHHcc
Q 026881          139 RLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKTDAYAAVILLERYFSM  196 (231)
Q Consensus       139 ~L~~~~~~~~lpV~lvDER~TT~eA~~~l~e~G~~rkkrK~~vD~lAA~IILq~yLd~  196 (231)
                      +|++++   ++||++||||+||.+|++.|++.+.+++++|+.+|++||++|||+||+.
T Consensus        82 ~L~~~~---~lpV~~~DERlTT~~A~~~l~~~~~~~~~~k~~iD~~AA~iILq~yLd~  136 (138)
T 1nu0_A           82 RIHGRF---GVEVKLHDERLSTVEARSGLFEQGGYRALNKGKVDSASAVIILESYMEQ  136 (138)
T ss_dssp             HHHHHH---CCCEEEEEEECCCCCC-------CCCCCCCHHHHTTHHHHHHHHHHHHT
T ss_pred             HHHHHh---CCCEEEEcCCcCHHHHHHHHHHhcCcccccCcchhHHHHHHHHHHHHhc
Confidence            999875   7999999999999999999999777777778889999999999999986
>1vhx_A Putative holliday junction resolvase; structural genomics, hydrolase; 1.96A {Bacillus subtilis} SCOP: c.55.3.8 Back     alignment and structure
>1iv0_A Hypothetical protein; rnaseh-like, YQGF, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Thermus thermophilus} SCOP: c.55.3.8 Back     alignment and structure
>4ep4_A Crossover junction endodeoxyribonuclease RUVC; resolvase, hydrolase; 1.28A {Thermus thermophilus} PDB: 4ep5_A Back     alignment and structure
>3bzc_A TEX; helix-turn-helix, helix-hairpin-helix, S1 domain, YQGF domain, transcription, RNA binding protein; 2.27A {Pseudomonas aeruginosa} SCOP: a.60.2.6 a.60.2.6 a.294.1.1 b.40.4.5 c.55.3.13 PDB: 3bzk_A 2oce_A Back     alignment and structure
>1hjr_A Holliday junction resolvase (RUVC); site-specific recombinase; 2.50A {Escherichia coli} SCOP: c.55.3.6 Back     alignment and structure
>3psf_A Transcription elongation factor SPT6; nucleus; 2.59A {Saccharomyces cerevisiae} Back     alignment and structure
>3psi_A Transcription elongation factor SPT6; nucleus; 3.30A {Saccharomyces cerevisiae} Back     alignment and structure
>3vov_A Glucokinase, hexokinase; ROK, sugar kinase, transferase; 2.02A {Thermus thermophilus} Back     alignment and structure
>3vgl_A Glucokinase; ROK family, transferase; HET: BGC ANP; 1.55A {Streptomyces griseus} PDB: 3vgk_A* 3vgm_A* Back     alignment and structure
>1saz_A Probable butyrate kinase 2; askha (acetate and sugar kinases, HSC70, actin) superfamily, acetate kinase, isobutyrate kinase; HET: ACP; 2.50A {Thermotoga maritima} SCOP: c.55.1.2 c.55.1.2 PDB: 1x9j_A* Back     alignment and structure
>2ch5_A NAGK protein; transferase, N-acetylglucosamine, glcnac, sugar kinase, RIBO H fold, sugar kinase/HSP70/actin superfamily, domain rotati conformation; HET: NAG NDG; 1.9A {Homo sapiens} SCOP: c.55.1.5 c.55.1.5 PDB: 2ch6_A* Back     alignment and structure
>3djc_A Type III pantothenate kinase; structural genomics, putative transfera 2, protein structure initiative; 2.40A {Legionella pneumophila subsp} Back     alignment and structure
>2qm1_A Glucokinase; alpha-beta structure, putative helix-turn-helix, structural PSI-2, protein structure initiative; HET: MSE; 2.02A {Enterococcus faecalis} Back     alignment and structure
>2e2o_A Hexokinase; acetate and sugar kinases, HSP70, actin superfamily, ribonuc fold, sugar kinase, glucose, phosphoryl transfer, transferase; HET: BGC; 1.65A {Sulfolobus tokodaii} PDB: 2e2n_A* 2e2p_A* 2e2q_A* Back     alignment and structure
>2hoe_A N-acetylglucosamine kinase; TM1224, structural genomics, PSI-2, protein structure initiative, joint center structural genomics, JCSG; 2.46A {Thermotoga maritima} SCOP: a.4.5.63 c.55.1.10 c.55.1.10 Back     alignment and structure
>4htl_A Beta-glucoside kinase; structural genomics, sugar kinase, ROK family, PSI-biology, center for structural genomics, MCSG, transferase; HET: MSE; 1.64A {Listeria monocytogenes} Back     alignment and structure
>3r8e_A Hypothetical sugar kinase; ribonuclease H-like motif, structural genomics, joint center structural genomics, JCSG; HET: MSE; 1.65A {Cytophaga hutchinsonii} Back     alignment and structure
>2gel_A Putative GRAM negative resuscitation promoting FA; YEAZ, RPF, actin-like-fold, glycoprotease, chaperone; 2.05A {Salmonella typhimurium} PDB: 2gem_A 1okj_A Back     alignment and structure
>2gup_A ROK family protein; sugar kinase, streptococcus pneumoniae TIGR4, AP sucrose, structural genomics, PSI; HET: SUC; 2.01A {Streptococcus pneumoniae} SCOP: c.55.1.10 c.55.1.10 Back     alignment and structure
>2ap1_A Putative regulator protein; zinc binding protein, structural genomics, PSI, protein STRU initiative; 1.90A {Salmonella typhimurium} SCOP: c.55.1.10 c.55.1.10 Back     alignment and structure
>3r6m_A YEAZ, resuscitation promoting factor; actin/HSP70 nucleotide-binding fold, bacterial resuscitation BUT non-culturable state, Y YJEE; 3.10A {Vibrio parahaemolyticus} Back     alignment and structure
>3htv_A D-allose kinase, allokinase; NP_418508.1, structural genomics, joint CEN structural genomics, JCSG, protein structure initiative; HET: MSE; 1.95A {Escherichia coli k-12} Back     alignment and structure
>1z6r_A MLC protein; transcriptional repressor, ROK family protein, DNA binding P helix-turn-helix, phosphotransferase system; 2.70A {Escherichia coli} SCOP: a.4.5.63 c.55.1.10 c.55.1.10 PDB: 3bp8_A Back     alignment and structure
>3mcp_A Glucokinase; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2, transferase; 3.00A {Parabacteroides distasonis} Back     alignment and structure
>2a6a_A Hypothetical protein TM0874; glycoprotein endopeptidase, structural genomics, JOI for structural genomics, JCSG; 2.50A {Thermotoga maritima} SCOP: c.55.1.9 c.55.1.9 Back     alignment and structure
>2aa4_A Mannac kinase, putative N-acetylmannosamine kinase; sugar methabolism, structural genomics, PSI, protein structure initiative; 2.20A {Escherichia coli} SCOP: c.55.1.10 c.55.1.10 Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

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

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 231
d1vhxa_140 c.55.3.8 (A:) Hypothetical protein YrrK (RuvX) {Ba 7e-21
d1nu0a_138 c.55.3.8 (A:) Hypothetical protein YqgF (RuvX) {Es 4e-19
d1iv0a_98 c.55.3.8 (A:) Hypothetical protein, YqgF homologue 2e-12
>d1vhxa_ c.55.3.8 (A:) Hypothetical protein YrrK (RuvX) {Bacillus subtilis [TaxId: 1423]} Length = 140 Back     information, alignment and structure

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Putative Holliday junction resolvase RuvX
domain: Hypothetical protein YrrK (RuvX)
species: Bacillus subtilis [TaxId: 1423]

 Score = 82.9 bits (204), Expect = 7e-21
 Identities = 37/134 (27%), Positives = 65/134 (48%), Gaps = 8/134 (5%)

Query: 66  LGVDLGLSRTGLALS--KGFCVRPLTVLKLR---GEKLELQLLEIAQREETDEFIIGLPK 120
           LG+DLG    G+ALS   G+  + +  +K+    G+    +L E+ +    D+ ++G PK
Sbjct: 5   LGLDLGTKTLGVALSDEMGWTAQGIETIKINEAEGDYGLSRLSELIKDYTIDKIVLGFPK 64

Query: 121 SWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTK 180
           + +G+  P+    ++ A  L          V L DE  T+  A   +I   +S+  R+  
Sbjct: 65  NMNGTVGPRGEASQTFAKVLETT---YNVPVVLWDERLTTMAAEKMLIAADVSRQKRKKV 121

Query: 181 TDAYAAVILLERYF 194
            D  AAV++L+ Y 
Sbjct: 122 IDKMAAVMILQGYL 135
>d1nu0a_ c.55.3.8 (A:) Hypothetical protein YqgF (RuvX) {Escherichia coli [TaxId: 562]} Length = 138 Back     information, alignment and structure
>d1iv0a_ c.55.3.8 (A:) Hypothetical protein, YqgF homologue {Thermus thermophilus [TaxId: 274]} Length = 98 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query231
d1nu0a_138 Hypothetical protein YqgF (RuvX) {Escherichia coli 100.0
d1vhxa_140 Hypothetical protein YrrK (RuvX) {Bacillus subtili 100.0
d1iv0a_98 Hypothetical protein, YqgF homologue {Thermus ther 99.97
d3bzka5149 Transcriptional accessory factor Tex {Pseudomonas 98.79
d1hjra_158 RuvC resolvase {Escherichia coli [TaxId: 562]} 97.6
d1xc3a1118 Putative fructokinase YhdR {Bacillus subtilis [Tax 96.27
d2ap1a2117 Putative regulator protein YcfX {Salmonella typhim 95.66
d2aa4a1119 N-acetylmannosamine kinase NanK {Escherichia coli 95.36
d2gupa1114 Hypothetical protein SP2142 {Streptococcus pneumon 94.6
d1z6ra2129 Mlc protein {Escherichia coli [TaxId: 562]} 94.59
d1z05a3128 Transcriptional regulator VC2007 {Vibrio cholerae 94.25
d2hoea3128 N-acetylglucosamine kinase {Thermotoga maritima [T 93.64
d1okja1106 Hypothetical protein YeaZ {Escherichia coli [TaxId 90.66
d1woqa1129 Inorganic polyphosphate/ATP-glucomannokinase PPGMK 90.17
d1sz2a1 319 Glucokinase Glk {Escherichia coli [TaxId: 562]} 87.95
d1bupa1185 Heat shock protein 70kDa, ATPase fragment {Cow (Bo 86.58
d1q18a1110 Glucokinase Glk {Escherichia coli [TaxId: 562]} 83.07
d1dkgd1183 Heat shock protein 70kDa, ATPase fragment {Escheri 82.87
d2a6aa1103 Hypothetical protein TM0874 {Thermotoga maritima [ 81.97
>d1nu0a_ c.55.3.8 (A:) Hypothetical protein YqgF (RuvX) {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Putative Holliday junction resolvase RuvX
domain: Hypothetical protein YqgF (RuvX)
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=2e-41  Score=274.23  Aligned_cols=132  Identities=30%  Similarity=0.436  Sum_probs=117.2

Q ss_pred             CceEEEEecCCCeEEEEEecC--ceeeeeeeeeccch-hHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHH
Q 026881           62 GGFSLGVDLGLSRTGLALSKG--FCVRPLTVLKLRGE-KLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAG  138 (231)
Q Consensus        62 ~g~iLglD~G~kRIGvAvsD~--~~A~Pl~~i~~~~~-~~~~~L~~li~e~~i~~IVVGLPl~~dGt~s~~~~~v~~Fa~  138 (231)
                      .|++||||||+||||||+||.  .+|+|+.++.+.+. .++..|.+++.+|+|+.||||+|++|+|+.+++++.+++|++
T Consensus         2 ~griLgiD~G~kriGvAvsd~~~~~a~pl~~i~~~~~~~~~~~l~~i~~e~~~~~iVvG~P~~~~g~~~~~~~~v~~f~~   81 (138)
T d1nu0a_           2 SGTLMAFDFGTKSIGVAVGQRITGTARPLPAIKAQDGTPDWNIIERLLKEWQPDEIIVGLPLNMDGTEQPLTARARKFAN   81 (138)
T ss_dssp             CCEEEEEECCSSEEEEEEEETTTTEEEEEEEEEEETTEECHHHHHHHHHHHCCSEEEEEEEECTTSCBCHHHHHHHHHHH
T ss_pred             CCcEEEEEeCCCEEEEEEeCCCCCccccceeeecccchhhHHHHHHHhhccCccEEEeecccccccchHHHHHHHHHHHH
Confidence            389999999999999999995  48999999987543 478999999999999999999999999999999999999999


Q ss_pred             HHHHHhccCCCcEEEecCCCcHHHHHHHHHHcCCCccccCCCCcHHHHHHHHHHHHcc
Q 026881          139 RLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKTDAYAAVILLERYFSM  196 (231)
Q Consensus       139 ~L~~~~~~~~lpV~lvDER~TT~eA~~~l~e~G~~rkkrK~~vD~lAA~IILq~yLd~  196 (231)
                      .|++.+   ++||++||||+||.+|++.|++.|.+++++|+.+|++||++|||+||++
T Consensus        82 ~L~~~~---~i~V~~~DEr~TS~eA~~~l~~~~~~~~~~k~~iD~~AA~lILq~~L~~  136 (138)
T d1nu0a_          82 RIHGRF---GVEVKLHDERLSTVEARSGLFEQGGYRALNKGKVDSASAVIILESYMEQ  136 (138)
T ss_dssp             HHHHHH---CCCEEEEEEECCCCCC-------CCCCCCCHHHHTTHHHHHHHHHHHHT
T ss_pred             HHhhcc---CCCeEEEeccccHHHHHHHHHHccccccccccchhHHHHHHHHHHHHHc
Confidence            999875   8999999999999999999999999999999999999999999999986
>d1vhxa_ c.55.3.8 (A:) Hypothetical protein YrrK (RuvX) {Bacillus subtilis [TaxId: 1423]} Back     information, alignment and structure
>d1iv0a_ c.55.3.8 (A:) Hypothetical protein, YqgF homologue {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d3bzka5 c.55.3.13 (A:325-473) Transcriptional accessory factor Tex {Pseudomonas aeruginosa [TaxId: 287]} Back     information, alignment and structure
>d1hjra_ c.55.3.6 (A:) RuvC resolvase {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1xc3a1 c.55.1.10 (A:1-118) Putative fructokinase YhdR {Bacillus subtilis [TaxId: 1423]} Back     information, alignment and structure
>d2ap1a2 c.55.1.10 (A:1-117) Putative regulator protein YcfX {Salmonella typhimurium [TaxId: 90371]} Back     information, alignment and structure
>d2aa4a1 c.55.1.10 (A:1-119) N-acetylmannosamine kinase NanK {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2gupa1 c.55.1.10 (A:1-114) Hypothetical protein SP2142 {Streptococcus pneumoniae [TaxId: 1313]} Back     information, alignment and structure
>d1z6ra2 c.55.1.10 (A:82-210) Mlc protein {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1z05a3 c.55.1.10 (A:81-208) Transcriptional regulator VC2007 {Vibrio cholerae [TaxId: 666]} Back     information, alignment and structure
>d2hoea3 c.55.1.10 (A:72-199) N-acetylglucosamine kinase {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d1okja1 c.55.1.9 (A:1-106) Hypothetical protein YeaZ {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1woqa1 c.55.1.10 (A:11-139) Inorganic polyphosphate/ATP-glucomannokinase PPGMK {Arthrobacter sp. KM [TaxId: 184230]} Back     information, alignment and structure
>d1sz2a1 c.55.1.7 (A:3-321) Glucokinase Glk {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1bupa1 c.55.1.1 (A:4-188) Heat shock protein 70kDa, ATPase fragment {Cow (Bos taurus) [TaxId: 9913]} Back     information, alignment and structure
>d1q18a1 c.55.1.7 (A:2-111) Glucokinase Glk {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1dkgd1 c.55.1.1 (D:3-185) Heat shock protein 70kDa, ATPase fragment {Escherichia coli, gene dnaK [TaxId: 562]} Back     information, alignment and structure
>d2a6aa1 c.55.1.9 (A:1-103) Hypothetical protein TM0874 {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure