Citrus Sinensis ID: 030386

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-------18
MCSLQSQHFLNSPLLIFPKFNDNRKFHLNRTRNFGQRIGALSSVEEFLPNATRRKKDSLWRGGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERSFSDILITAIFSFSCHFAIFFTVLNSTSVGI
ccccccccEEcccEEccccccccHHHHHcccccccccccccccccccccccccccccccccccEEEEEEccccEEEEEEEccEEEEEcEEEEEccccHHHHHHHHHHHccccEEEEEccccccccccHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHcccccEEEEEEEccccccc
cccccccccccccEEEccccccccEEEEcccccccccEEEEccHHHccccHHHccccccccccEEEEEEcccEEEEEEEccccEEcccEHHHcccccHHHHHHHHHHHccccEEEEEccccccccccHHHHHHHHHHHHHHHHHHHccccHEEEEHHHEccccEEEEEEEEccccccc
mcslqsqhflnspllifpkfndnrkfHLNRTRNFGQRIGALSSVEeflpnatrrkkdslwrggfslgvdlglsrtglalskgfcvrpltVLKLRGEKLELQLLEIAQReetdefiiglpkswdgsetpqsnkvrSVAGRLAVRAAERSFSDILITAIFSFSCHFAIFFTVLNSTSVGI
mcslqsqhflnspllifPKFNDNRKFHLNRTRNFgqrigalssveeflpnatrrkkdslwrgGFSLGVDLGLSrtglalskgfcvRPLTVLKLRGEKLELQLLEiaqreetdeFIIGlpkswdgsetpqsnkvrsVAGRLAVRAAERSFSDILITAIFSFSCHFAIFFTVLNSTSVGI
MCSLQSQHFLNSPLLIFPKFNDNRKFHLNRTRNFGQRIGALSSVEEFLPNATRRKKDSLWRGGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERSFSDILITAIFSFSCHFAIFFTVLNSTSVGI
********FLNSPLLIFPKFNDNRKFHLNRTRNFGQRIGALSSVEEFLPNATRRKKDSLWRGGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQREETDEFIIGLPKS**************VAGRLAVRAAERSFSDILITAIFSFSCHFAIFFTVLN******
*********LNSPLLIFPKFNDNRKFHL************************************SLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERSFSDILITAIFSFSCHFAIFFTVLNSTSVG*
MCSLQSQHFLNSPLLIFPKFNDNRKFHLNRTRNFGQRIGALSSVEEFLPNATRRKKDSLWRGGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQREETDEFIIGLPKSWD************VAGRLAVRAAERSFSDILITAIFSFSCHFAIFFTVLNSTSVGI
*C**QSQHFLNSPLLIFPKFNDNRKFHLNRTRNFGQRIGALSSVEEFLPNATRRKKDSLWRGGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERSFSDILITAIFSFSCHFAIFFTVLNS*****
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SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHoooooooo
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SSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MCSLQSQHFLNSPLLIFPKFNDNRKFHLNRTRNFGQRIGALSSVEEFLPNATRRKKDSLWRGGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERSFSDILITAIFSFSCHFAIFFTVLNSTSVGI
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 ?
Query178 2.2.26 [Sep-21-2011]
A1SJC8156 Putative Holliday junctio yes no 0.483 0.551 0.380 4e-07
A5CCV6157 Putative Holliday junctio yes no 0.516 0.585 0.317 3e-05
Q2IQC1137 Putative Holliday junctio yes no 0.426 0.554 0.379 3e-05
A1AZC8158 Putative Holliday junctio yes no 0.455 0.512 0.357 4e-05
A7HDE0137 Putative Holliday junctio yes no 0.426 0.554 0.379 8e-05
Q2RHZ7140 Putative Holliday junctio yes no 0.404 0.514 0.346 9e-05
Q5NPF1163 Putative Holliday junctio yes no 0.483 0.527 0.314 0.0001
B3CU37157 Putative Holliday junctio yes no 0.522 0.592 0.300 0.0001
B1KXB5137 Putative Holliday junctio yes no 0.382 0.496 0.352 0.0001
A7GGE9137 Putative Holliday junctio yes no 0.382 0.496 0.352 0.0001
>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 = 54.3 bits (129), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 35/92 (38%), Positives = 51/92 (55%), Gaps = 6/92 (6%)

Query: 60  WRGGFSLGVDLGLSRTGLALSK--GFCVRPL-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 FIIGLPKSWDGSETPQSNKVRSVAGRLAVRAA 145
            ++GLP+S  G E P + KVR  AGRLA R A
Sbjct: 61  VVVGLPRSLSGREGPAAAKVREFAGRLAARVA 92
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|A5CCV6|RUVX_ORITB Putative Holliday junction resolvase OS=Orientia tsutsugamushi (strain Boryong) GN=OTBS_0498 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|A1AZC8|RUVX_PARDP Putative Holliday junction resolvase OS=Paracoccus denitrificans (strain Pd 1222) GN=Pden_0510 PE=3 SV=1 Back     alignment and function description
>sp|A7HDE0|RUVX_ANADF Putative Holliday junction resolvase OS=Anaeromyxobacter sp. (strain Fw109-5) GN=Anae109_2535 PE=3 SV=1 Back     alignment and function description
>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|Q5NPF1|RUVX_ZYMMO Putative Holliday junction resolvase OS=Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4) GN=ZMO0785 PE=3 SV=2 Back     alignment and function description
>sp|B3CU37|RUVX_ORITI Putative Holliday junction resolvase OS=Orientia tsutsugamushi (strain Ikeda) GN=OTT_1426 PE=3 SV=1 Back     alignment and function description
>sp|B1KXB5|RUVX_CLOBM Putative Holliday junction resolvase OS=Clostridium botulinum (strain Loch Maree / Type A3) GN=CLK_1947 PE=3 SV=1 Back     alignment and function description
>sp|A7GGE9|RUVX_CLOBL Putative Holliday junction resolvase OS=Clostridium botulinum (strain Langeland / NCTC 10281 / Type F) GN=CLI_2625 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 ?
Query178
224129716254 predicted protein [Populus trichocarpa] 0.752 0.527 0.688 2e-44
297734533 679 unnamed protein product [Vitis vinifera] 0.629 0.164 0.787 5e-42
359489199229 PREDICTED: putative Holliday junction re 0.629 0.489 0.787 2e-40
356506432226 PREDICTED: putative Holliday junction re 0.629 0.495 0.725 1e-39
449431960235 PREDICTED: putative Holliday junction re 0.606 0.459 0.743 1e-38
255573708239 hydrolase, acting on ester bonds, putati 0.825 0.615 0.606 6e-35
297844086238 DNA binding protein [Arabidopsis lyrata 0.792 0.592 0.578 8e-35
242035117214 hypothetical protein SORBIDRAFT_01g02939 0.646 0.537 0.641 8e-32
414867730235 TPA: holliday junction resolvase [Zea ma 0.567 0.429 0.689 1e-31
226500782235 holliday junction resolvase [Zea mays] g 0.567 0.429 0.689 2e-31
>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 =  183 bits (465), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 93/135 (68%), Positives = 107/135 (79%), Gaps = 1/135 (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 SVAGRLAVRAAERSF 149
           SVAGR AV AA R +
Sbjct: 161 SVAGRFAVLAAHRGW 175

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|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|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|242035117|ref|XP_002464953.1| hypothetical protein SORBIDRAFT_01g029390 [Sorghum bicolor] gi|241918807|gb|EER91951.1| hypothetical protein SORBIDRAFT_01g029390 [Sorghum bicolor] Back     alignment and taxonomy information
>gi|414867730|tpg|DAA46287.1| TPA: holliday junction resolvase [Zea mays] Back     alignment and taxonomy information
>gi|226500782|ref|NP_001149481.1| holliday junction resolvase [Zea mays] gi|195627468|gb|ACG35564.1| 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 ?
Query178
TAIR|locus:1009023117254 AT1G12244 [Arabidopsis thalian 0.808 0.566 0.587 8.9e-38
UNIPROTKB|P0A8I1138 yqgF [Escherichia coli K-12 (t 0.438 0.565 0.308 1.8e-05
TAIR|locus:1009023117 AT1G12244 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 405 (147.6 bits), Expect = 8.9e-38, P = 8.9e-38
 Identities = 91/155 (58%), Positives = 111/155 (71%)

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 IIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERSF 149
             IIGLP+S DG ET QSNK+RSVAGRLA++AAER +
Sbjct:   133 IIGLPRSSDGKETIQSNKIRSVAGRLAIQAAERGW 167
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

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 ?
Query178
pfam03652134 pfam03652, UPF0081, Uncharacterized protein family 9e-14
PRK00109138 PRK00109, PRK00109, Holliday junction resolvase-li 8e-12
COG0816141 COG0816, COG0816, Predicted endonuclease involved 4e-10
smart0073299 smart00732, YqgFc, Likely ribonuclease with RNase 4e-09
TIGR00250130 TIGR00250, RNAse_H_YqgF, RNAse H-fold protein YqgF 5e-07
>gnl|CDD|217659 pfam03652, UPF0081, Uncharacterized protein family (UPF0081) Back     alignment and domain information 
 Score = 64.4 bits (158), Expect = 9e-14
 Identities = 27/81 (33%), Positives = 44/81 (54%), Gaps = 3/81 (3%)

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 DGSETPQSNKVRSVAGRLAVR 143
           DGSE   + +VR  A RL  R
Sbjct: 64  DGSEGEMTKRVRKFARRLKKR 84

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|128971 smart00732, YqgFc, Likely ribonuclease with RNase H fold Back     alignment and domain information
>gnl|CDD|129352 TIGR00250, RNAse_H_YqgF, RNAse H-fold protein YqgF Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 178
PF03652135 UPF0081: Uncharacterised protein family (UPF0081); 99.97
COG0816141 Predicted endonuclease involved in recombination ( 99.97
PRK00109138 Holliday junction resolvase-like protein; Reviewed 99.97
TIGR00250130 RNAse_H_YqgF RNAse H-fold protein YqgF. This prote 99.97
smart0073299 YqgFc Likely ribonuclease with RNase H fold. YqgF 99.56
cd00529154 RuvC_resolvase Holliday junction resolvases (HJRs) 97.25
PF02075149 RuvC: Crossover junction endodeoxyribonuclease Ruv 97.19
PRK00039164 ruvC Holliday junction resolvase; Reviewed 97.18
COG1548 330 Predicted transcriptional regulator/sugar kinase [ 96.42
PF14639150 YqgF: Holliday-junction resolvase-like of SPT6 ; P 96.26
TIGR00228156 ruvC crossover junction endodeoxyribonuclease RuvC 96.01
COG2183 780 Tex Transcriptional accessory protein [Transcripti 94.12
TIGR0176682 tspaseT_teng_C transposase, IS605 OrfB family, cen 94.12
COG0817160 RuvC Holliday junction resolvasome, endonuclease s 92.82
COG1940 314 NagC Transcriptional regulator/sugar kinase [Trans 88.8
PRK05082 291 N-acetylmannosamine kinase; Provisional 88.3
PRK09557 301 fructokinase; Reviewed 87.18
PRK13310 303 N-acetyl-D-glucosamine kinase; Provisional 87.07
TIGR00744 318 ROK_glcA_fam ROK family protein (putative glucokin 86.74
PHA02942383 putative transposase; Provisional 86.14
PF0728269 OrfB_Zn_ribbon: Putative transposase DNA-binding d 85.7
PF04312138 DUF460: Protein of unknown function (DUF460); Inte 85.56
PRK09698 302 D-allose kinase; Provisional 83.97
PF07318 343 DUF1464: Protein of unknown function (DUF1464); In 82.03
PRK00292 316 glk glucokinase; Provisional 80.06
>PF03652 UPF0081: Uncharacterised protein family (UPF0081); InterPro: IPR005227 Holliday junction resolvases (HJRs) are key enzymes of DNA recombination Back     alignment and domain information 
Probab=99.97  E-value=2.9e-32  Score=214.26  Aligned_cols=104  Identities=29%  Similarity=0.379  Sum_probs=93.1

Q ss_pred             ceEEEEecCCceEEEEeecC--CcccccEEEEccC-hhHHHHHHHHHHHcCCCEEEEeecCCCCCCCCHHHHHHHHHHHH
Q 030386           63 GFSLGVDLGLSRTGLALSKG--FCVRPLTVLKLRG-EKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGR  139 (178)
Q Consensus        63 ~rILgLD~G~KRIGVAiSD~--~~A~Pl~tI~~~~-~~~~~~L~~iI~e~~v~~IVVGLPl~mdG~e~~~a~~Vr~Fa~~  139 (178)
                      |++||||||+||||||+||+  .+|+|+++|.+.+ ..+++.|.+++++|+++.||||+|++|||+++++++.+++|+++
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            58999999999999999995  4799999999764 57899999999999999999999999999999999999999999


Q ss_pred             HHHHhccCCCcEEEEcCCCchhhhHHHHH
Q 030386          140 LAVRAAERSFSDILITAIFSFSCHFAIFF  168 (178)
Q Consensus       140 L~~~~~~~glpV~lvDERlSTs~~~a~~~  168 (178)
                      |+++++  ++||++|||||||..-...+.
T Consensus        81 L~~~~~--~ipV~~~DEr~TT~~A~~~l~  107 (135)
T PF03652_consen   81 LKKRFP--GIPVILVDERLTTKEAERRLR  107 (135)
T ss_dssp             HHHHH---TSEEEEEECSCSHHCCHCCHH
T ss_pred             HHHhcC--CCcEEEECCChhHHHHHHHHH
Confidence            999984  689999999999987665543

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.
>COG0816 Predicted endonuclease involved in recombination (possible Holliday junction resolvase in Mycoplasmas and B Back     alignment and domain information
>PRK00109 Holliday junction resolvase-like protein; Reviewed 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
>cd00529 RuvC_resolvase Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination 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
>PRK00039 ruvC Holliday junction resolvase; Reviewed Back     alignment and domain information
>COG1548 Predicted transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism] Back     alignment and domain information
>PF14639 YqgF: Holliday-junction resolvase-like of SPT6 ; PDB: 3PSI_A 3PSF_A 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
>TIGR01766 tspaseT_teng_C transposase, IS605 OrfB family, central region Back     alignment and domain information
>COG0817 RuvC Holliday junction resolvasome, endonuclease subunit [DNA replication, recombination, and repair] Back     alignment and domain information
>COG1940 NagC Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism] Back     alignment and domain information
>PRK05082 N-acetylmannosamine kinase; Provisional Back     alignment and domain information
>PRK09557 fructokinase; Reviewed Back     alignment and domain information
>PRK13310 N-acetyl-D-glucosamine kinase; Provisional Back     alignment and domain information
>TIGR00744 ROK_glcA_fam ROK family protein (putative glucokinase) Back     alignment and domain information
>PHA02942 putative transposase; 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
>PF04312 DUF460: Protein of unknown function (DUF460); InterPro: IPR007408 This is an archaeal protein of unknown function Back     alignment and domain information
>PRK09698 D-allose kinase; Provisional Back     alignment and domain information
>PF07318 DUF1464: Protein of unknown function (DUF1464); InterPro: IPR009927 This family consists of several hypothetical archaeal proteins of around 350 residues in length Back     alignment and domain information
>PRK00292 glk glucokinase; 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 ?
Query178
1nmn_A138 Structure Of Yqgf From Escherichia Coli, A Hypothet 3e-04
1ovq_A138 Solution Structure Of The Hypothetical Protein Yqgf 3e-04
1nu0_A138 Structure Of The Double Mutant (L6m; F134m, Semet F 4e-04
>pdb|1NMN|A Chain A, Structure Of Yqgf From Escherichia Coli, A Hypothetical Protein Length = 138 Back     alignment and structure 
Iteration: 1

 Score = 41.2 bits (95), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 28/83 (33%), Positives = 43/83 (51%), Gaps = 8/83 (9%)
Query: 62  GGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQRE-ETDEFIIGLPK 120
           G  S+GV +G   TG A       RPL  +K +    +  ++E   +E + DE I+GLP 
Sbjct: 11  GTKSIGVAVGQRITGTA-------RPLPAIKAQDGTPDWNIIERLLKEWQPDEIIVGLPL 63
Query: 121 SWDGSETPQSNKVRSVAGRLAVR 143
           + DG+E P + + R  A R+  R
Sbjct: 64  NMDGTEQPLTARARKFANRIHGR 86
>pdb|1OVQ|A Chain A, Solution Structure Of The Hypothetical Protein Yqgf From Escherichia Coli 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

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query178
1iv0_A98 Hypothetical protein; rnaseh-like, YQGF, structura 7e-16
1vhx_A150 Putative holliday junction resolvase; structural g 9e-15
1nu0_A138 Hypothetical protein YQGF; structural genomics, st 1e-14
>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
 Score = 68.3 bits (168), Expect = 7e-16
 Identities = 21/81 (25%), Positives = 37/81 (45%), Gaps = 3/81 (3%)

Query: 66  LGVDLGLSRTGLALS--KGFCVRPLTVLKLRGEKLEL-QLLEIAQREETDEFIIGLPKSW 122
             +D+G +R GLA+             L  +  + ++  LL+  +RE   + ++GLP   
Sbjct: 4   GALDVGEARIGLAVGEEGVPLASGRGYLVRKTLEEDVEALLDFVRREGLGKLVVGLPLRT 63

Query: 123 DGSETPQSNKVRSVAGRLAVR 143
           D  E+ Q+ KV  +   L  R
Sbjct: 64  DLKESAQAGKVLPLVEALRAR 84
>1vhx_A Putative holliday junction resolvase; structural genomics, hydrolase; 1.96A {Bacillus subtilis} SCOP: c.55.3.8 Length = 150 Back     alignment and structure
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query178
1iv0_A98 Hypothetical protein; rnaseh-like, YQGF, structura 100.0
1nu0_A138 Hypothetical protein YQGF; structural genomics, st 100.0
1vhx_A150 Putative holliday junction resolvase; structural g 99.94
4ep4_A166 Crossover junction endodeoxyribonuclease RUVC; res 98.2
1hjr_A158 Holliday junction resolvase (RUVC); site-specific 97.39
3bzc_A 785 TEX; helix-turn-helix, helix-hairpin-helix, S1 dom 96.19
3psf_A 1030 Transcription elongation factor SPT6; nucleus; 2.5 95.42
3psi_A 1219 Transcription elongation factor SPT6; nucleus; 3.3 95.19
3vov_A 302 Glucokinase, hexokinase; ROK, sugar kinase, transf 93.83
2ch5_A 347 NAGK protein; transferase, N-acetylglucosamine, gl 93.34
3vgl_A 321 Glucokinase; ROK family, transferase; HET: BGC ANP 91.17
3epq_A 302 Putative fructokinase; SCRK, ADP binding, PSI2, MC 90.73
2ap1_A 327 Putative regulator protein; zinc binding protein, 88.9
1saz_A 381 Probable butyrate kinase 2; askha (acetate and sug 88.54
2gup_A 292 ROK family protein; sugar kinase, streptococcus pn 88.5
3r6m_A213 YEAZ, resuscitation promoting factor; actin/HSP70 87.54
2qm1_A 326 Glucokinase; alpha-beta structure, putative helix- 87.23
2e2o_A 299 Hexokinase; acetate and sugar kinases, HSP70, acti 87.19
1z6r_A 406 MLC protein; transcriptional repressor, ROK family 86.04
2hoe_A 380 N-acetylglucosamine kinase; TM1224, structural gen 85.65
3mcp_A 366 Glucokinase; structural genomics, joint center for 84.22
3htv_A 310 D-allose kinase, allokinase; NP_418508.1, structur 83.42
3lm2_A 226 Putative kinase; structural genomics, joint center 83.36
2ivn_A 330 O-sialoglycoprotein endopeptidase; UP1 keops compl 82.78
4htl_A 297 Beta-glucoside kinase; structural genomics, sugar 82.62
1woq_A 267 Inorganic polyphosphate/ATP-glucomannokinase; tran 81.18
>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
Probab=100.00  E-value=5.2e-34  Score=212.71  Aligned_cols=95  Identities=25%  Similarity=0.260  Sum_probs=88.1

Q ss_pred             ceEEEEecCCceEEEEeecC--CcccccEEEEccC-hhHHHHHHHHHHHcCCCEEEEeecCCCCCCCCHHHHHHHHHHHH
Q 030386           63 GFSLGVDLGLSRTGLALSKG--FCVRPLTVLKLRG-EKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGR  139 (178)
Q Consensus        63 ~rILgLD~G~KRIGVAiSD~--~~A~Pl~tI~~~~-~~~~~~L~~iI~e~~v~~IVVGLPl~mdG~e~~~a~~Vr~Fa~~  139 (178)
                      +++||||||+||||||+||+  .+|+|++||.+++ ..++++|.+++++|+++.||||+|++|||+++++++++++|+++
T Consensus         1 mriLglD~G~kriGvAvsd~~~~~A~pl~ti~~~~~~~~~~~l~~li~e~~v~~iVvGlP~~mdGt~~~~~~~~~~f~~~   80 (98)
T 1iv0_A            1 MRVGALDVGEARIGLAVGEEGVPLASGRGYLVRKTLEEDVEALLDFVRREGLGKLVVGLPLRTDLKESAQAGKVLPLVEA   80 (98)
T ss_dssp             CCEEEEEESSSEEEEEEECSCCSSCCCEEEEECCCHHHHHHHHHHHHHHHTCCEEEEECCCCCCSSSCCCSSTTHHHHHH
T ss_pred             CcEEEEEeCCCEEEEEEEeCCCCeeeeeEEEEccCcHHHHHHHHHHHHHcCCCEEEEeeccCCCCCcCHHHHHHHHHHHH
Confidence            36999999999999999995  5899999998654 56889999999999999999999999999999999999999999


Q ss_pred             HHHHhccCCCcEEEEcCCCchh
Q 030386          140 LAVRAAERSFSDILITAIFSFS  161 (178)
Q Consensus       140 L~~~~~~~glpV~lvDERlSTs  161 (178)
                      |+++    ++||++|||||||.
T Consensus        81 L~~~----~lpV~~~DERlTT~   98 (98)
T 1iv0_A           81 LRAR----GVEVELWDERFTTK   98 (98)
T ss_dssp             HHHT----TCEEEEECCSCCCC
T ss_pred             HhcC----CCCEEEECCCCCCC
Confidence            9985    48999999999984
>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
>1vhx_A Putative holliday junction resolvase; structural genomics, hydrolase; 1.96A {Bacillus subtilis} 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
>1hjr_A Holliday junction resolvase (RUVC); site-specific recombinase; 2.50A {Escherichia coli} SCOP: c.55.3.6 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
>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
>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
>3vgl_A Glucokinase; ROK family, transferase; HET: BGC ANP; 1.55A {Streptomyces griseus} PDB: 3vgk_A* 3vgm_A* 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
>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
>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
>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
>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
>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
>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
>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
>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
>3lm2_A Putative kinase; structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-2, transf; HET: MSE; 1.70A {Agrobacterium tumefaciens} Back     alignment and structure
>2ivn_A O-sialoglycoprotein endopeptidase; UP1 keops complex, Fe/Zn dependent nucleotide phosphatase, metalloprotease, hypothetical protein, zinc; HET: ANP; 1.65A {Pyrococcus abyssi} PDB: 2ivo_A 2ivp_A* 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
>1woq_A Inorganic polyphosphate/ATP-glucomannokinase; transferase; HET: BGC; 1.80A {Arthrobacter SP} 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 178
d1iv0a_98 c.55.3.8 (A:) Hypothetical protein, YqgF homologue 6e-10
d1vhxa_140 c.55.3.8 (A:) Hypothetical protein YrrK (RuvX) {Ba 3e-07
d1nu0a_138 c.55.3.8 (A:) Hypothetical protein YqgF (RuvX) {Es 2e-05
>d1iv0a_ c.55.3.8 (A:) Hypothetical protein, YqgF homologue {Thermus thermophilus [TaxId: 274]} Length = 98 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 homologue
species: Thermus thermophilus [TaxId: 274]

 Score = 51.8 bits (124), Expect = 6e-10
 Identities = 21/81 (25%), Positives = 38/81 (46%), Gaps = 3/81 (3%)

Query: 66  LGVDLGLSRTGLALS--KGFCVRPLTVLKLRGEKLELQ-LLEIAQREETDEFIIGLPKSW 122
             +D+G +R GLA+             L  +  + +++ LL+  +RE   + ++GLP   
Sbjct: 4   GALDVGEARIGLAVGEEGVPLASGRGYLVRKTLEEDVEALLDFVRREGLGKLVVGLPLRT 63

Query: 123 DGSETPQSNKVRSVAGRLAVR 143
           D  E+ Q+ KV  +   L  R
Sbjct: 64  DLKESAQAGKVLPLVEALRAR 84
>d1vhxa_ c.55.3.8 (A:) Hypothetical protein YrrK (RuvX) {Bacillus subtilis [TaxId: 1423]} Length = 140 Back     information, alignment and structure
>d1nu0a_ c.55.3.8 (A:) Hypothetical protein YqgF (RuvX) {Escherichia coli [TaxId: 562]} Length = 138 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 ?
Query178
d1iv0a_98 Hypothetical protein, YqgF homologue {Thermus ther 100.0
d1nu0a_138 Hypothetical protein YqgF (RuvX) {Escherichia coli 99.97
d1vhxa_140 Hypothetical protein YrrK (RuvX) {Bacillus subtili 99.97
d3bzka5149 Transcriptional accessory factor Tex {Pseudomonas 98.24
d1hjra_158 RuvC resolvase {Escherichia coli [TaxId: 562]} 97.49
d2aa4a1119 N-acetylmannosamine kinase NanK {Escherichia coli 96.18
d1xc3a1118 Putative fructokinase YhdR {Bacillus subtilis [Tax 96.16
d2gupa1114 Hypothetical protein SP2142 {Streptococcus pneumon 95.79
d2ap1a2117 Putative regulator protein YcfX {Salmonella typhim 95.28
d1z05a3128 Transcriptional regulator VC2007 {Vibrio cholerae 93.75
d1sz2a1 319 Glucokinase Glk {Escherichia coli [TaxId: 562]} 92.4
d1woqa1129 Inorganic polyphosphate/ATP-glucomannokinase PPGMK 91.56
d1okja1106 Hypothetical protein YeaZ {Escherichia coli [TaxId 90.97
d2hoea3128 N-acetylglucosamine kinase {Thermotoga maritima [T 89.16
d1q18a1110 Glucokinase Glk {Escherichia coli [TaxId: 562]} 88.16
d1z6ra2129 Mlc protein {Escherichia coli [TaxId: 562]} 87.99
d1bupa1185 Heat shock protein 70kDa, ATPase fragment {Cow (Bo 87.98
d1dkgd1183 Heat shock protein 70kDa, ATPase fragment {Escheri 85.55
d1uf3a_ 228 Hypothetical protein TT1561 {Thermus thermophilus 84.54
>d1iv0a_ c.55.3.8 (A:) Hypothetical protein, YqgF homologue {Thermus thermophilus [TaxId: 274]} 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 homologue
species: Thermus thermophilus [TaxId: 274]

Probab=100.00  E-value=1.4e-34  Score=213.83  Aligned_cols=95  Identities=25%  Similarity=0.260  Sum_probs=88.2

Q ss_pred             ceEEEEecCCceEEEEeecC--CcccccEEEEccC-hhHHHHHHHHHHHcCCCEEEEeecCCCCCCCCHHHHHHHHHHHH
Q 030386           63 GFSLGVDLGLSRTGLALSKG--FCVRPLTVLKLRG-EKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGR  139 (178)
Q Consensus        63 ~rILgLD~G~KRIGVAiSD~--~~A~Pl~tI~~~~-~~~~~~L~~iI~e~~v~~IVVGLPl~mdG~e~~~a~~Vr~Fa~~  139 (178)
                      +|+||||||+||||||+||.  .+|+|++++.+++ .+++++|.+++++|+|+.||||+|++|||+++++++++++|+++
T Consensus         1 MriLglD~G~kriGiAisd~~~~~a~pl~~i~~~~~~~~~~~l~~ii~e~~i~~iVvGlP~~~dG~~~~~~~~v~~f~~~   80 (98)
T d1iv0a_           1 MRVGALDVGEARIGLAVGEEGVPLASGRGYLVRKTLEEDVEALLDFVRREGLGKLVVGLPLRTDLKESAQAGKVLPLVEA   80 (98)
T ss_dssp             CCEEEEEESSSEEEEEEECSCCSSCCCEEEEECCCHHHHHHHHHHHHHHHTCCEEEEECCCCCCSSSCCCSSTTHHHHHH
T ss_pred             CcEEEEEcCCCEEEEEEecCCCCeEcceEEEECCCchHHHHHHHHHHHhhccceeEcccccccCCCcCHHHHHHHHHHHH
Confidence            58999999999999999995  5899999998766 56889999999999999999999999999999999999999999


Q ss_pred             HHHHhccCCCcEEEEcCCCchh
Q 030386          140 LAVRAAERSFSDILITAIFSFS  161 (178)
Q Consensus       140 L~~~~~~~glpV~lvDERlSTs  161 (178)
                      |+++    ++||++|||||||.
T Consensus        81 L~~~----~lpv~~~DErlTSk   98 (98)
T d1iv0a_          81 LRAR----GVEVELWDERFTTK   98 (98)
T ss_dssp             HHHT----TCEEEEECCSCCCC
T ss_pred             HhhC----CCCEEEEcCCCCCC
Confidence            9743    69999999999984
>d1nu0a_ c.55.3.8 (A:) Hypothetical protein YqgF (RuvX) {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1vhxa_ c.55.3.8 (A:) Hypothetical protein YrrK (RuvX) {Bacillus subtilis [TaxId: 1423]} 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
>d2aa4a1 c.55.1.10 (A:1-119) N-acetylmannosamine kinase NanK {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
>d2gupa1 c.55.1.10 (A:1-114) Hypothetical protein SP2142 {Streptococcus pneumoniae [TaxId: 1313]} 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
>d1z05a3 c.55.1.10 (A:81-208) Transcriptional regulator VC2007 {Vibrio cholerae [TaxId: 666]} Back     information, alignment and structure
>d1sz2a1 c.55.1.7 (A:3-321) Glucokinase Glk {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
>d1okja1 c.55.1.9 (A:1-106) Hypothetical protein YeaZ {Escherichia coli [TaxId: 562]} 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
>d1q18a1 c.55.1.7 (A:2-111) Glucokinase Glk {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1z6ra2 c.55.1.10 (A:82-210) Mlc protein {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
>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
>d1uf3a_ d.159.1.6 (A:) Hypothetical protein TT1561 {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure