Citrus Sinensis ID: 030509

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------
MKYVKPLRLFEQMLKRKVSKRGRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDLHPVEYKTILDKFAAVGILQEYLDNANRKVNLKANVLRPIIN
cccccHHHHHHHHHHHHccccccEEEEEccccEEEEEEEccccccccccEEEEcccccHHHHHHHHHHHHHHHcccEEEEEccccccccccHHHHHHHHHHHHHHccccccccEEEEcccHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHcHHccccccccccccccc
cccccHHHHHHHHHHcccccccEEEEEEccccEEEEEEEcccccccccEEEEEccccHHcccHHHHHHHHHHccccEEEEEccccccccccccHHHHHHHHHHHHHHHHccccEEEcccHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHcccccccc
MKYVKPLRLFEQMLKRKVSKrgrflgldvgdkyvglsisdpknkiaspLSVLLRKKNTIDLMAEDFRSLISEFnlegfivgypfnrqqnaaDAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELllnpldlhpvEYKTILDKFAAVGILQEYLDNANRKVNLKANVLRPIIN
mkyvkplrlFEQMLKRKvskrgrflgldvgdkyvglsisdpknkiasplsvLLRKKNTIDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDLHPVEYKTILDKFAAVGILQEYldnanrkvnlkanvlrpiin
MKYVKPLRLFEQMLKRKVSKRGRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDLHPVEYKTILDKFAAVGILQEYLDNANRKVNLKANVLRPIIN
******LRLFEQMLKRKVSKRGRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDLHPVEYKTILDKFAAVGILQEYLDNANRKVNLKANVLR****
****KPLRLFEQMLKRKVSKRGRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVE*****************DKFAAVGILQEYLD******************
MKYVKPLRLFEQMLKRKVSKRGRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDLHPVEYKTILDKFAAVGILQEYLDNANRKVNLKANVLRPIIN
*KYVKPLRLFEQMLKRKVSKRGRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDLHPVEYKTILDKFAAVGILQEYLDNANRKVNLKANVLRPIIN
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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iiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MKYVKPLRLFEQMLKRKVSKRGRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDLHPVEYKTILDKFAAVGILQEYLDNANRKVNLKANVLRPIIN
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 ?
Query176 2.2.26 [Sep-21-2011]
B2IEC1165 Putative Holliday junctio yes no 0.801 0.854 0.346 5e-16
Q5NPF1163 Putative Holliday junctio yes no 0.846 0.914 0.325 9e-15
Q1QL26163 Putative Holliday junctio yes no 0.761 0.822 0.314 4e-14
Q3SR28163 Putative Holliday junctio yes no 0.761 0.822 0.321 7e-14
B8EPC5161 Putative Holliday junctio yes no 0.818 0.894 0.326 2e-13
A4J2L0137 Putative Holliday junctio yes no 0.772 0.992 0.321 3e-13
Q0AZP9141 Putative Holliday junctio yes no 0.761 0.950 0.342 4e-13
B0K0Q3139 Putative Holliday junctio yes no 0.772 0.978 0.349 6e-13
Q2IXC6160 Putative Holliday junctio yes no 0.755 0.831 0.316 6e-13
B6IN25188 Putative Holliday junctio yes no 0.812 0.760 0.310 1e-12
>sp|B2IEC1|RUVX_BEII9 Putative Holliday junction resolvase OS=Beijerinckia indica subsp. indica (strain ATCC 9039 / DSM 1715 / NCIB 8712) GN=Bind_1895 PE=3 SV=1 Back     alignment and function desciption
 Score = 84.0 bits (206), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 51/147 (34%), Positives = 77/147 (52%), Gaps = 6/147 (4%)

Query: 14  LKRKVSKRGRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEF 73
           LK  +  R R +G+D+G K +GLS+SD + +IA+PL  + R K T D  AE   +L  +F
Sbjct: 11  LKPLLGPRQRLIGIDLGTKTIGLSLSDVERRIATPLETIRRTKFTKD--AERLLALADQF 68

Query: 74  NLEGFIVGYPFNRQQNAADAVQ-VKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNP 132
           ++  F++G P N   +A   VQ  + F+  LS    L    + YW+E  ++  V   L  
Sbjct: 69  DVAAFVIGLPLNMDGSAGPRVQATEAFVRSLSG---LTSRPFCYWDERLSTAAVTRDLIA 125

Query: 133 LDLHPVEYKTILDKFAAVGILQEYLDN 159
            D    +   ++DK AA  ILQ  LD 
Sbjct: 126 QDASRAKRAAVVDKLAAAFILQGALDR 152
Could be a nuclease that resolves Holliday junction intermediates in genetic recombination.
Beijerinckia indica subsp. indica (strain ATCC 9039 / DSM 1715 / NCIB 8712) (taxid: 395963)
EC: 3EC: .EC: 1EC: .EC: -EC: .EC: -
>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|Q1QL26|RUVX_NITHX Putative Holliday junction resolvase OS=Nitrobacter hamburgensis (strain X14 / DSM 10229) GN=Nham_2279 PE=3 SV=2 Back     alignment and function description
>sp|Q3SR28|RUVX_NITWN Putative Holliday junction resolvase OS=Nitrobacter winogradskyi (strain Nb-255 / ATCC 25391) GN=Nwi_2004 PE=3 SV=1 Back     alignment and function description
>sp|B8EPC5|RUVX_METSB Putative Holliday junction resolvase OS=Methylocella silvestris (strain BL2 / DSM 15510 / NCIMB 13906) GN=Msil_0742 PE=3 SV=1 Back     alignment and function description
>sp|A4J2L0|RUVX_DESRM Putative Holliday junction resolvase OS=Desulfotomaculum reducens (strain MI-1) GN=Dred_0775 PE=3 SV=1 Back     alignment and function description
>sp|Q0AZP9|RUVX_SYNWW Putative Holliday junction resolvase OS=Syntrophomonas wolfei subsp. wolfei (strain Goettingen) GN=Swol_0470 PE=3 SV=1 Back     alignment and function description
>sp|B0K0Q3|RUVX_THEPX Putative Holliday junction resolvase OS=Thermoanaerobacter sp. (strain X514) GN=Teth514_1491 PE=3 SV=1 Back     alignment and function description
>sp|Q2IXC6|RUVX_RHOP2 Putative Holliday junction resolvase OS=Rhodopseudomonas palustris (strain HaA2) GN=RPB_2429 PE=3 SV=1 Back     alignment and function description
>sp|B6IN25|RUVX_RHOCS Putative Holliday junction resolvase OS=Rhodospirillum centenum (strain ATCC 51521 / SW) GN=RC1_1518 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 ?
Query176
224053911170 predicted protein [Populus trichocarpa] 0.954 0.988 0.690 6e-62
297742527224 unnamed protein product [Vitis vinifera] 0.920 0.723 0.716 7e-62
225426409169 PREDICTED: putative Holliday junction re 0.920 0.958 0.716 2e-61
255537457168 conserved hypothetical protein [Ricinus 0.943 0.988 0.684 8e-59
449452328169 PREDICTED: putative Holliday junction re 0.943 0.982 0.668 1e-57
7529715 548 putative protein [Arabidopsis thaliana] 0.937 0.301 0.654 2e-56
297820018 542 hypothetical protein ARALYDRAFT_323835 [ 0.937 0.304 0.648 6e-56
302398811170 GRF domain class transcription factor [M 0.965 1.0 0.697 7e-56
145332817170 Polynucleotidyl transferase/ ribonucleas 0.937 0.970 0.654 2e-55
449452326177 PREDICTED: putative Holliday junction re 0.886 0.881 0.673 4e-55
>gi|224053911|ref|XP_002298037.1| predicted protein [Populus trichocarpa] gi|222845295|gb|EEE82842.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
 Score =  241 bits (616), Expect = 6e-62,   Method: Compositional matrix adjust.
 Identities = 116/168 (69%), Positives = 140/168 (83%)

Query: 1   MKYVKPLRLFEQMLKRKVSKRGRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTID 60
           MKYV+PL LF ++LK     +GRFLGLDVGDKYVGL++SDP NKIASPLSVLLRKK+ I+
Sbjct: 1   MKYVRPLSLFHELLKTSAINQGRFLGLDVGDKYVGLAVSDPLNKIASPLSVLLRKKSNIE 60

Query: 61  LMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEG 120
           LMA DF+SLISE +L GFIVGYPF+RQ+ A DAV+VKLF+DDL  T KLE +K+ YW+E 
Sbjct: 61  LMATDFQSLISELSLGGFIVGYPFDRQRGAPDAVRVKLFVDDLCKTGKLEGVKFTYWDEC 120

Query: 121 FTSKGVELLLNPLDLHPVEYKTILDKFAAVGILQEYLDNANRKVNLKA 168
           FTSK VELL+ PLDLHPV  K+I+DKFAAVGILQ YLD  N+K+ L++
Sbjct: 121 FTSKNVELLVKPLDLHPVHAKSIMDKFAAVGILQGYLDYVNKKMKLES 168

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|297742527|emb|CBI34676.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|225426409|ref|XP_002269986.1| PREDICTED: putative Holliday junction resolvase [Vitis vinifera] Back     alignment and taxonomy information
>gi|255537457|ref|XP_002509795.1| conserved hypothetical protein [Ricinus communis] gi|223549694|gb|EEF51182.1| conserved hypothetical protein [Ricinus communis] Back     alignment and taxonomy information
>gi|449452328|ref|XP_004143911.1| PREDICTED: putative Holliday junction resolvase-like isoform 2 [Cucumis sativus] gi|449495809|ref|XP_004159951.1| PREDICTED: putative Holliday junction resolvase-like isoform 2 [Cucumis sativus] Back     alignment and taxonomy information
>gi|7529715|emb|CAB86895.1| putative protein [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|297820018|ref|XP_002877892.1| hypothetical protein ARALYDRAFT_323835 [Arabidopsis lyrata subsp. lyrata] gi|297323730|gb|EFH54151.1| hypothetical protein ARALYDRAFT_323835 [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|302398811|gb|ADL36700.1| GRF domain class transcription factor [Malus x domestica] Back     alignment and taxonomy information
>gi|145332817|ref|NP_001078274.1| Polynucleotidyl transferase/ ribonuclease H-like protein [Arabidopsis thaliana] gi|26449955|dbj|BAC42098.1| unknown protein [Arabidopsis thaliana] gi|332645487|gb|AEE79008.1| Polynucleotidyl transferase/ ribonuclease H-like protein [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|449452326|ref|XP_004143910.1| PREDICTED: putative Holliday junction resolvase-like isoform 1 [Cucumis sativus] gi|449495806|ref|XP_004159950.1| PREDICTED: putative Holliday junction resolvase-like isoform 1 [Cucumis sativus] 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 ?
Query176
TAIR|locus:4010713830170 AT3G52905 [Arabidopsis thalian 0.937 0.970 0.654 3e-53
UNIPROTKB|Q71ZG8138 LMOf2365_1521 "Putative Hollid 0.772 0.985 0.321 7.1e-13
UNIPROTKB|Q3AEN4138 CHY_0542 "Putative Holliday ju 0.744 0.949 0.328 3.1e-12
TIGR_CMR|CHY_0542138 CHY_0542 "conserved hypothetic 0.744 0.949 0.328 3.1e-12
UNIPROTKB|Q5LQY2154 SPO2350 "Putative Holliday jun 0.727 0.831 0.291 5.8e-11
TIGR_CMR|SPO_2350154 SPO_2350 "conserved hypothetic 0.727 0.831 0.291 5.8e-11
UNIPROTKB|Q81LK2137 BAS4282 "Putative Holliday jun 0.761 0.978 0.289 1.5e-10
TIGR_CMR|BA_4614137 BA_4614 "conserved hypothetica 0.761 0.978 0.289 1.5e-10
UNIPROTKB|Q2GH06156 ECH_0460 "Putative Holliday ju 0.772 0.871 0.281 5.9e-09
TIGR_CMR|ECH_0460156 ECH_0460 "conserved hypothetic 0.772 0.871 0.281 5.9e-09
TAIR|locus:4010713830 AT3G52905 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 551 (199.0 bits), Expect = 3.0e-53, P = 3.0e-53
 Identities = 108/165 (65%), Positives = 129/165 (78%)

Query:     1 MKYVKPLRLFEQMLKRKVSKRGRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTID 60
             MKYVKPL L    LK KVS  GRFLGLDVGDKYVGL+ISDP N +ASPLSVLLRKK+ ID
Sbjct:     1 MKYVKPLSLLGNALKTKVSVPGRFLGLDVGDKYVGLAISDPSNMVASPLSVLLRKKSNID 60

Query:    61 LMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEG 120
             LMA DF++L+  F++ G +VGYPF +  N  D V V LFI++L  T+KL+D+KY YW+E 
Sbjct:    61 LMATDFQNLVKAFSVSGLVVGYPFGKLNNVEDVVTVNLFIEELRKTEKLKDVKYTYWDER 120

Query:   121 FTSKGVELLLNPLDLHPVEYKTILDKFAAVGILQEYLDNANRKVN 165
              +SK VEL+L PL+LHPV+ KT+LDK AAV ILQEYLD ANR VN
Sbjct:   121 LSSKTVELMLKPLNLHPVQEKTMLDKLAAVVILQEYLDYANRYVN 165
GO:0003676 "nucleic acid binding" evidence=IEA
GO:0005737 "cytoplasm" evidence=ISM;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:0016788 "hydrolase activity, acting on ester bonds" evidence=IEA
UNIPROTKB|Q71ZG8 LMOf2365_1521 "Putative Holliday junction resolvase" [Listeria monocytogenes serotype 4b str. F2365 (taxid:265669)] 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
TIGR_CMR|CHY_0542 CHY_0542 "conserved hypothetical protein TIGR00250" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)] Back     alignment and assigned GO terms
UNIPROTKB|Q5LQY2 SPO2350 "Putative Holliday junction resolvase" [Ruegeria pomeroyi DSS-3 (taxid:246200)] Back     alignment and assigned GO terms
TIGR_CMR|SPO_2350 SPO_2350 "conserved hypothetical protein TIGR00250" [Ruegeria pomeroyi DSS-3 (taxid:246200)] 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|Q2GH06 ECH_0460 "Putative Holliday junction resolvase" [Ehrlichia chaffeensis str. Arkansas (taxid:205920)] Back     alignment and assigned GO terms
TIGR_CMR|ECH_0460 ECH_0460 "conserved hypothetical protein TIGR00250" [Ehrlichia chaffeensis str. Arkansas (taxid:205920)] 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

ID ?Name ?Annotated EC number ?Identity ?Query coverage ?Hit coverage ?RBH(Q2H) ?RBH(H2Q) ?
B2IEC1RUVX_BEII93, ., 1, ., -, ., -0.34690.80110.8545yesno
Q5NPF1RUVX_ZYMMO3, ., 1, ., -, ., -0.3250.84650.9141yesno
B8EPC5RUVX_METSB3, ., 1, ., -, ., -0.32660.81810.8944yesno

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Your Input:
estExt_Genewise1_v1.C_LG_I8952
hypothetical protein (171 aa)
(Populus trichocarpa)
Predicted Functional Partners:
estExt_fgenesh4_pg.C_LG_IX0259
alanyl-tRNA synthetase (EC-6.1.1.7) (994 aa)
•       0.784
eugene3.00050325
alanyl-tRNA synthetase (EC-6.1.1.7) (973 aa)
•       0.643
eugene3.55420001
annotation not avaliable (132 aa)
•       0.569
grail3.8458000201
annotation not avaliable (169 aa)
•       0.513
eugene3.27090001
Predicted protein (198 aa)
•     • 0.453
gw1.II.3029.1
hypothetical protein; Exchanges the guanine residue with 7-aminomethyl-7- deazaguanine in tRNAs [...] (392 aa)
•       0.420
eugene3.182270001
Predicted protein (163 aa)
•       0.409

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 ?
Query176
pfam03652134 pfam03652, UPF0081, Uncharacterized protein family 9e-32
PRK00109138 PRK00109, PRK00109, Holliday junction resolvase-li 1e-20
smart0073299 smart00732, YqgFc, Likely ribonuclease with RNase 1e-18
COG0816141 COG0816, COG0816, Predicted endonuclease involved 2e-17
TIGR00250130 TIGR00250, RNAse_H_YqgF, RNAse H-fold protein YqgF 2e-08
>gnl|CDD|217659 pfam03652, UPF0081, Uncharacterized protein family (UPF0081) Back     alignment and domain information 
 Score =  110 bits (278), Expect = 9e-32
 Identities = 50/139 (35%), Positives = 69/139 (49%), Gaps = 6/139 (4%)

Query: 22  GRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVG 81
           GR LGLDVG K +G++ISDP   +ASPL  + RK    D   E+   LI E+  +G +VG
Sbjct: 1   GRILGLDVGTKRIGVAISDPLGILASPLETIRRKNGNPD--LEELAELIKEWQPDGIVVG 58

Query: 82  YPFNRQQNA-ADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDLHPVEY 140
            P N   +      +V+ F   L     L        +E  T+   E +L    L   + 
Sbjct: 59  LPLNMDGSEGEMTKRVRKFARRLKKRFGLP---VELVDERLTTVEAERILREAGLSRKKR 115

Query: 141 KTILDKFAAVGILQEYLDN 159
           K ++D  AAV ILQ YLD+
Sbjct: 116 KEVVDSIAAVIILQSYLDS 134

Length = 134
>gnl|CDD|234639 PRK00109, PRK00109, Holliday junction resolvase-like protein; Reviewed Back     alignment and domain information
>gnl|CDD|128971 smart00732, YqgFc, Likely ribonuclease with RNase H fold 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

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 176
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 99.62
PRK00039164 ruvC Holliday junction resolvase; Reviewed 98.26
cd00529154 RuvC_resolvase Holliday junction resolvases (HJRs) 97.7
PF02075149 RuvC: Crossover junction endodeoxyribonuclease Ruv 97.68
TIGR00228156 ruvC crossover junction endodeoxyribonuclease RuvC 97.59
COG2183 780 Tex Transcriptional accessory protein [Transcripti 97.39
PF04312138 DUF460: Protein of unknown function (DUF460); Inte 97.21
PF14639150 YqgF: Holliday-junction resolvase-like of SPT6 ; P 97.08
COG0817160 RuvC Holliday junction resolvasome, endonuclease s 96.81
COG2433 652 Uncharacterized conserved protein [Function unknow 96.79
PRK05082 291 N-acetylmannosamine kinase; Provisional 95.45
COG1940 314 NagC Transcriptional regulator/sugar kinase [Trans 95.01
COG1548 330 Predicted transcriptional regulator/sugar kinase [ 94.96
PRK09557 301 fructokinase; Reviewed 94.85
PF04848143 Pox_A22: Poxvirus A22 protein; InterPro: IPR006932 93.58
PRK13310 303 N-acetyl-D-glucosamine kinase; Provisional 93.52
PF07318 343 DUF1464: Protein of unknown function (DUF1464); In 93.04
PRK13311256 N-acetyl-D-glucosamine kinase; Provisional 92.92
PRK13321256 pantothenate kinase; Reviewed 92.22
TIGR00744 318 ROK_glcA_fam ROK family protein (putative glucokin 91.39
PF00480179 ROK: ROK family; InterPro: IPR000600 A family of b 89.95
COG1214220 Inactive homolog of metal-dependent proteases, put 89.91
TIGR0176682 tspaseT_teng_C transposase, IS605 OrfB family, cen 89.7
PRK12408 336 glucokinase; Provisional 89.21
PRK00292 316 glk glucokinase; Provisional 88.65
TIGR03725202 bact_YeaZ universal bacterial protein YeaZ. This f 88.24
PRK13318258 pantothenate kinase; Reviewed 88.03
PF01548144 DEDD_Tnp_IS110: Transposase; InterPro: IPR002525 T 87.97
PF14239176 RRXRR: RRXRR protein 86.46
PRK09698 302 D-allose kinase; Provisional 85.11
PRK14101 638 bifunctional glucokinase/RpiR family transcription 84.87
PRK15080267 ethanolamine utilization protein EutJ; Provisional 82.25
>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-46  Score=287.81  Aligned_cols=134  Identities=34%  Similarity=0.555  Sum_probs=123.2

Q ss_pred             CeEEEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhcCCCEEEEeccCC-CCCCchHHHHHHHHH
Q 030509           22 GRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGYPFN-RQQNAADAVQVKLFI  100 (176)
Q Consensus        22 ~~iLglD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~~~~~iVVGlPl~-dG~~s~~~~~v~~Fa  100 (176)
                      |++||||||++|||||+||+.+.+|+|+.++.+.+..  .++++|.+++++|+|+.||||+|++ ||+++++++.+++|+
T Consensus         1 mriL~lD~G~kriGiAvsd~~~~~a~pl~~i~~~~~~--~~~~~l~~li~~~~i~~iVvGlP~~~~G~~~~~~~~v~~f~   78 (135)
T PF03652_consen    1 MRILGLDYGTKRIGIAVSDPLGIIASPLETIPRRNRE--KDIEELKKLIEEYQIDGIVVGLPLNMDGSESEQARRVRKFA   78 (135)
T ss_dssp             -EEEEEEECSSEEEEEEEETTTSSEEEEEEEEECCCC--CCHHHHHHHHHHCCECEEEEEEEBBCTSSC-CCHHHHHHHH
T ss_pred             CeEEEEEeCCCeEEEEEecCCCCeEeeeEEEECCCCc--hHHHHHHHHHHHhCCCEEEEeCCcccCCCccHHHHHHHHHH
Confidence            6899999999999999999999999999999976554  3489999999999999999999999 999999999999999


Q ss_pred             HHHHhccCCCCCcEEEecCcccHHHHHHHhccCCCCCCCCCCCCcHHHHHHHHHHHHhh
Q 030509          101 DDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDLHPVEYKTILDKFAAVGILQEYLDN  159 (176)
Q Consensus       101 ~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g~~~~~~k~~iD~~AA~iILq~yL~~  159 (176)
                      ++|++.  ++++||++|||||||++|++.|++.|.+++++|+.+|++||++|||+||++
T Consensus        79 ~~L~~~--~~~ipV~~~DEr~TT~~A~~~l~~~g~~~~k~k~~iD~~AA~iILq~yLd~  135 (135)
T PF03652_consen   79 EELKKR--FPGIPVILVDERLTTKEAERRLRESGLSRKKRKKKIDSIAAAIILQSYLDS  135 (135)
T ss_dssp             HHHHHH--H-TSEEEEEECSCSHHCCHCCHHHTT-SHHHHCHHHCCCHHHHHHHHHHCC
T ss_pred             HHHHHh--cCCCcEEEECCChhHHHHHHHHHHcCCChhhcCccccHHHHHHHHHHHHhC
Confidence            999984  579999999999999999999999999999999999999999999999984

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
>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
>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
>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
>COG2433 Uncharacterized conserved protein [Function unknown] Back     alignment and domain information
>PRK05082 N-acetylmannosamine kinase; Provisional Back     alignment and domain information
>COG1940 NagC Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism] Back     alignment and domain information
>COG1548 Predicted transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism] Back     alignment and domain information
>PRK09557 fructokinase; Reviewed Back     alignment and domain information
>PF04848 Pox_A22: Poxvirus A22 protein; InterPro: IPR006932 This family, representing the Poxvirus A22 protein, is a Holliday junction resolvase, it specifically cleaves and resolves four-way DNA Holliday junctions into linear duplex products Back     alignment and domain information
>PRK13310 N-acetyl-D-glucosamine 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
>PRK13311 N-acetyl-D-glucosamine kinase; Provisional Back     alignment and domain information
>PRK13321 pantothenate kinase; Reviewed Back     alignment and domain information
>TIGR00744 ROK_glcA_fam ROK family protein (putative glucokinase) Back     alignment and domain information
>PF00480 ROK: ROK family; InterPro: IPR000600 A family of bacterial proteins has been described which groups transcriptional repressors, sugar kinases and yet uncharacterised open reading frames [] Back     alignment and domain information
>COG1214 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>TIGR01766 tspaseT_teng_C transposase, IS605 OrfB family, central region Back     alignment and domain information
>PRK12408 glucokinase; Provisional Back     alignment and domain information
>PRK00292 glk glucokinase; Provisional Back     alignment and domain information
>TIGR03725 bact_YeaZ universal bacterial protein YeaZ Back     alignment and domain information
>PRK13318 pantothenate kinase; 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
>PF14239 RRXRR: RRXRR protein Back     alignment and domain information
>PRK09698 D-allose kinase; Provisional Back     alignment and domain information
>PRK14101 bifunctional glucokinase/RpiR family transcriptional regulator; Provisional Back     alignment and domain information
>PRK15080 ethanolamine utilization protein EutJ; 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 ?
Query176
1vhx_A150 Crystal Structure Of Putative Holliday Junction Res 8e-09
>pdb|1VHX|A Chain A, Crystal Structure Of Putative Holliday Junction Resolvase Length = 150 Back     alignment and structure 
Iteration: 1

 Score = 56.6 bits (135), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 39/140 (27%), Positives = 65/140 (46%), Gaps = 4/140 (2%)
Query: 23  RFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGY 82
           R LGLD+G K +G+++SD     A  +  +   +   D        LI ++ ++  ++G+
Sbjct: 4   RILGLDLGTKTLGVALSDEXGWTAQGIETIKINEAEGDYGLSRLSELIKDYTIDKIVLGF 63
Query: 83  PFNRQQNAADAVQV-KLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDLHPVEYK 141
           P N         +  + F   L  T    ++    W+E  T+   E  L   D+   + K
Sbjct: 64  PKNXNGTVGPRGEASQTFAKVLETTY---NVPVVLWDERLTTXAAEKXLIAADVSRQKRK 120
Query: 142 TILDKFAAVGILQEYLDNAN 161
            ++DK AAV ILQ YLD+ N
Sbjct: 121 KVIDKXAAVXILQGYLDSLN 140

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query176
1vhx_A150 Putative holliday junction resolvase; structural g 6e-37
1nu0_A138 Hypothetical protein YQGF; structural genomics, st 1e-29
1iv0_A98 Hypothetical protein; rnaseh-like, YQGF, structura 3e-24
>1vhx_A Putative holliday junction resolvase; structural genomics, hydrolase; 1.96A {Bacillus subtilis} SCOP: c.55.3.8 Length = 150 Back     alignment and structure
 Score =  123 bits (312), Expect = 6e-37
 Identities = 38/143 (26%), Positives = 66/143 (46%), Gaps = 4/143 (2%)

Query: 21  RGRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIV 80
             R LGLD+G K +G+++SD     A  +  +   +   D        LI ++ ++  ++
Sbjct: 2   SLRILGLDLGTKTLGVALSDEMGWTAQGIETIKINEAEGDYGLSRLSELIKDYTIDKIVL 61

Query: 81  GYPFNRQQNAADAVQ-VKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDLHPVE 139
           G+P N         +  + F   L   +   ++    W+E  T+   E +L   D+   +
Sbjct: 62  GFPKNMNGTVGPRGEASQTFAKVL---ETTYNVPVVLWDERLTTMAAEKMLIAADVSRQK 118

Query: 140 YKTILDKFAAVGILQEYLDNANR 162
            K ++DK AAV ILQ YLD+ N 
Sbjct: 119 RKKVIDKMAAVMILQGYLDSLNE 141
>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
>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 ?
Query176
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 100.0
4ep4_A166 Crossover junction endodeoxyribonuclease RUVC; res 98.64
1hjr_A158 Holliday junction resolvase (RUVC); site-specific 98.15
3bzc_A 785 TEX; helix-turn-helix, helix-hairpin-helix, S1 dom 97.81
3psf_A 1030 Transcription elongation factor SPT6; nucleus; 2.5 97.47
3psi_A 1219 Transcription elongation factor SPT6; nucleus; 3.3 97.24
2gup_A 292 ROK family protein; sugar kinase, streptococcus pn 95.37
3vov_A 302 Glucokinase, hexokinase; ROK, sugar kinase, transf 95.06
2e2o_A 299 Hexokinase; acetate and sugar kinases, HSP70, acti 94.62
2ch5_A 347 NAGK protein; transferase, N-acetylglucosamine, gl 94.58
3epq_A 302 Putative fructokinase; SCRK, ADP binding, PSI2, MC 94.32
4htl_A 297 Beta-glucoside kinase; structural genomics, sugar 93.9
3vgl_A 321 Glucokinase; ROK family, transferase; HET: BGC ANP 93.84
3mcp_A 366 Glucokinase; structural genomics, joint center for 93.74
1saz_A 381 Probable butyrate kinase 2; askha (acetate and sug 93.63
3djc_A 266 Type III pantothenate kinase; structural genomics, 93.44
2qm1_A 326 Glucokinase; alpha-beta structure, putative helix- 93.3
2aa4_A 289 Mannac kinase, putative N-acetylmannosamine kinase 93.19
3r6m_A213 YEAZ, resuscitation promoting factor; actin/HSP70 93.01
3lm2_A226 Putative kinase; structural genomics, joint center 92.37
2ap1_A 327 Putative regulator protein; zinc binding protein, 92.1
2hoe_A 380 N-acetylglucosamine kinase; TM1224, structural gen 92.1
4db3_A 327 Glcnac kinase, N-acetyl-D-glucosamine kinase; stru 92.0
3r8e_A 321 Hypothetical sugar kinase; ribonuclease H-like mot 91.73
1z6r_A 406 MLC protein; transcriptional repressor, ROK family 91.72
1woq_A267 Inorganic polyphosphate/ATP-glucomannokinase; tran 91.61
1z05_A 429 Transcriptional regulator, ROK family; structural 90.89
3htv_A 310 D-allose kinase, allokinase; NP_418508.1, structur 90.1
1zc6_A 305 Probable N-acetylglucosamine kinase; NESG, Q7NU07_ 89.76
2gel_A231 Putative GRAM negative resuscitation promoting FA; 89.74
2ivn_A 330 O-sialoglycoprotein endopeptidase; UP1 keops compl 89.69
2a6a_A218 Hypothetical protein TM0874; glycoprotein endopept 89.44
2q2r_A 373 Glucokinase 1, putative; ATPase hexose kinase fami 89.15
1sz2_A 332 Glucokinase, glucose kinase; ATP-dependent, glucos 88.9
2yhw_A 343 Bifunctional UDP-N-acetylglucosamine 2-epimerase/N 87.04
1zbs_A 291 Hypothetical protein PG1100; alpha-beta protein., 86.97
3eno_A 334 Putative O-sialoglycoprotein endopeptidase; hydrol 86.48
2ych_A 377 Competence protein PILM; cell cycle, type IV pilus 86.05
4ehu_A 276 Activator of 2-hydroxyisocaproyl-COA dehydratase; 85.81
3en9_A 540 Glycoprotease, O-sialoglycoprotein endopeptidase/p 82.42
2h3g_X 268 Biosynthetic protein; pantothenate kinase, anthrax 81.7
3ll3_A 504 Gluconate kinase; xylulose kinase, nysgx, ATP, ADP 81.6
3bex_A249 Type III pantothenate kinase; actin-like fold, ATP 81.09
>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=3.9e-46  Score=287.47  Aligned_cols=134  Identities=20%  Similarity=0.323  Sum_probs=117.1

Q ss_pred             CCeEEEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhcCCCEEEEeccCC-CCCCchHHHHHHHH
Q 030509           21 RGRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGYPFN-RQQNAADAVQVKLF   99 (176)
Q Consensus        21 ~~~iLglD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~~~~~iVVGlPl~-dG~~s~~~~~v~~F   99 (176)
                      ++++||||||++|||||+||+.+.+|+|++||.+.+.+.+  +++|.+++++|+|+.||||+|+| ||+++++++++++|
T Consensus         2 ~~~iLglD~G~kriGvAvsd~~~~~A~pl~ti~~~~~~~~--~~~l~~li~e~~v~~iVvGlP~~mdGt~~~~~~~~~~f   79 (138)
T 1nu0_A            2 SGTLMAFDFGTKSIGVAVGQRITGTARPLPAIKAQDGTPD--WNIIERLLKEWQPDEIIVGLPLNMDGTEQPLTARARKF   79 (138)
T ss_dssp             CCEEEEEECCSSEEEEEEEETTTTEEEEEEEEEEETTEEC--HHHHHHHHHHHCCSEEEEEEEECTTSCBCHHHHHHHHH
T ss_pred             CCeEEEEEeCCCEEEEEEEcCCCCEEeeEEEEEcCCcchH--HHHHHHHHHHcCCCEEEEecccCCCcCcCHHHHHHHHH
Confidence            4689999999999999999999999999999987544433  79999999999999999999999 99999999999999


Q ss_pred             HHHHHhccCCCCCcEEEecCcccHHHHHHHhccCCCCCCCCCCCCcHHHHHHHHHHHHhh
Q 030509          100 IDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDLHPVEYKTILDKFAAVGILQEYLDN  159 (176)
Q Consensus       100 a~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g~~~~~~k~~iD~~AA~iILq~yL~~  159 (176)
                      +++|++.  + ++||++|||||||++|++.|++.+.+++++|+.+|++||++|||+||++
T Consensus        80 ~~~L~~~--~-~lpV~~~DERlTT~~A~~~l~~~~~~~~~~k~~iD~~AA~iILq~yLd~  136 (138)
T 1nu0_A           80 ANRIHGR--F-GVEVKLHDERLSTVEARSGLFEQGGYRALNKGKVDSASAVIILESYMEQ  136 (138)
T ss_dssp             HHHHHHH--H-CCCEEEEEEECCCCCC-------CCCCCCCHHHHTTHHHHHHHHHHHHT
T ss_pred             HHHHHHH--h-CCCEEEEcCCcCHHHHHHHHHHhcCcccccCcchhHHHHHHHHHHHHhc
Confidence            9999974  5 7999999999999999999998776777788899999999999999986
>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
>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
>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
>3vov_A Glucokinase, hexokinase; ROK, sugar kinase, transferase; 2.02A {Thermus thermophilus} 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
>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
>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
>3vgl_A Glucokinase; ROK family, transferase; HET: BGC ANP; 1.55A {Streptomyces griseus} PDB: 3vgk_A* 3vgm_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
>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
>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
>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
>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
>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
>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
>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
>4db3_A Glcnac kinase, N-acetyl-D-glucosamine kinase; structural genomics, center for structural genomics of infec diseases, csgid, transferase; 1.95A {Vibrio vulnificus} 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
>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
>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
>1z05_A Transcriptional regulator, ROK family; structural genomics, protein structure initiative, midwest center for structural genomics; 2.00A {Vibrio cholerae o1 biovar eltor} SCOP: a.4.5.63 c.55.1.10 c.55.1.10 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
>1zc6_A Probable N-acetylglucosamine kinase; NESG, Q7NU07_chrvo, CVR23, struc genomics, PSI, protein structure initiative; 2.20A {Chromobacterium violaceum} SCOP: c.55.1.5 c.55.1.5 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
>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
>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
>2q2r_A Glucokinase 1, putative; ATPase hexose kinase family, transferase; HET: BGC ADP; 2.10A {Trypanosoma cruzi} Back     alignment and structure
>1sz2_A Glucokinase, glucose kinase; ATP-dependent, glucose binding, transferase; HET: MSE BGC; 2.20A {Escherichia coli} SCOP: c.55.1.7 PDB: 1q18_A* Back     alignment and structure
>2yhw_A Bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase; transferase, sialic acid, mannac, ROK family; HET: BM3 2PE; 1.64A {Homo sapiens} PDB: 2yhy_A* 2yi1_A* 3eo3_A Back     alignment and structure
>1zbs_A Hypothetical protein PG1100; alpha-beta protein., structural genomics, PSI, protein struc initiative; 2.30A {Porphyromonas gingivalis} SCOP: c.55.1.5 c.55.1.5 Back     alignment and structure
>3eno_A Putative O-sialoglycoprotein endopeptidase; hydrolase, metal-binding, metalloprotease, protease, zinc, keops complex, ATPase, metal ION binding; 3.02A {Thermoplasma acidophilum} Back     alignment and structure
>2ych_A Competence protein PILM; cell cycle, type IV pilus actin secretion; HET: ATP; 2.20A {Thermus thermophilus} Back     alignment and structure
>4ehu_A Activator of 2-hydroxyisocaproyl-COA dehydratase; actin fold, ATPase, electron transfer, ATP/ADP binding; HET: ANP; 1.60A {Clostridium difficile} PDB: 4eht_A* 4eia_A Back     alignment and structure
>3en9_A Glycoprotease, O-sialoglycoprotein endopeptidase/protein kinase; endopeptidase activity, protein kinase activity; HET: TBR; 2.67A {Methanocaldococcus jannaschii} PDB: 3enh_A* 2vwb_A* Back     alignment and structure
>2h3g_X Biosynthetic protein; pantothenate kinase, anthrax, type III pantothenate kinase, COAX, COAA, askha; 2.00A {Bacillus anthracis str} Back     alignment and structure
>3ll3_A Gluconate kinase; xylulose kinase, nysgx, ATP, ADP, xylulose, transferase, structural genomics, PSI-2, protein structure initiative; HET: ATP DXP XUL ADP; 2.00A {Lactobacillus acidophilus} PDB: 3gbt_A* Back     alignment and structure
>3bex_A Type III pantothenate kinase; actin-like fold, ATP-binding, coenzyme A biosynthesis, cytoplasm, metal-binding, nucleotide-binding, potassium; HET: PAU; 1.51A {Thermotoga maritima} SCOP: c.55.1.13 c.55.1.13 PDB: 3bf1_A* 3bf3_A* 2gtd_A 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 176
d1vhxa_140 c.55.3.8 (A:) Hypothetical protein YrrK (RuvX) {Ba 5e-26
d1nu0a_138 c.55.3.8 (A:) Hypothetical protein YqgF (RuvX) {Es 5e-22
d1iv0a_98 c.55.3.8 (A:) Hypothetical protein, YqgF homologue 1e-18
>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 = 94.8 bits (235), Expect = 5e-26
 Identities = 36/139 (25%), Positives = 64/139 (46%), Gaps = 2/139 (1%)

Query: 23  RFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGY 82
           R LGLD+G K +G+++SD     A  +  +   +   D        LI ++ ++  ++G+
Sbjct: 3   RILGLDLGTKTLGVALSDEMGWTAQGIETIKINEAEGDYGLSRLSELIKDYTIDKIVLGF 62

Query: 83  PFNRQQNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDLHPVEYKT 142
           P N         + +         +   ++    W+E  T+   E +L   D+   + K 
Sbjct: 63  PKNMNGTVGP--RGEASQTFAKVLETTYNVPVVLWDERLTTMAAEKMLIAADVSRQKRKK 120

Query: 143 ILDKFAAVGILQEYLDNAN 161
           ++DK AAV ILQ YLD+ N
Sbjct: 121 VIDKMAAVMILQGYLDSLN 139
>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 ?
Query176
d1vhxa_140 Hypothetical protein YrrK (RuvX) {Bacillus subtili 100.0
d1nu0a_138 Hypothetical protein YqgF (RuvX) {Escherichia coli 100.0
d1iv0a_98 Hypothetical protein, YqgF homologue {Thermus ther 100.0
d3bzka5149 Transcriptional accessory factor Tex {Pseudomonas 98.9
d1hjra_158 RuvC resolvase {Escherichia coli [TaxId: 562]} 98.14
d2aa4a1119 N-acetylmannosamine kinase NanK {Escherichia coli 97.01
d2gupa1114 Hypothetical protein SP2142 {Streptococcus pneumon 96.93
d1xc3a1118 Putative fructokinase YhdR {Bacillus subtilis [Tax 96.81
d2ap1a2117 Putative regulator protein YcfX {Salmonella typhim 96.62
d1z05a3128 Transcriptional regulator VC2007 {Vibrio cholerae 96.5
d1z6ra2129 Mlc protein {Escherichia coli [TaxId: 562]} 96.26
d2hoea3128 N-acetylglucosamine kinase {Thermotoga maritima [T 95.58
d1okja1106 Hypothetical protein YeaZ {Escherichia coli [TaxId 94.96
d1sz2a1 319 Glucokinase Glk {Escherichia coli [TaxId: 562]} 93.82
d1zc6a1114 Probable N-acetylglucosamine kinase CV2896 {Chromo 93.58
d1huxa_ 259 Hydroxyglutaryl-CoA dehydratase component A {Acida 93.04
d2a6aa1103 Hypothetical protein TM0874 {Thermotoga maritima [ 92.47
d1q18a1110 Glucokinase Glk {Escherichia coli [TaxId: 562]} 92.31
d1woqa1129 Inorganic polyphosphate/ATP-glucomannokinase PPGMK 91.55
d1bupa1185 Heat shock protein 70kDa, ATPase fragment {Cow (Bo 88.8
d1dkgd1183 Heat shock protein 70kDa, ATPase fragment {Escheri 86.92
d2ewsa1 267 Type II pantothenate kinase, CoaW {Staphylococcus 86.51
d2ch5a2117 N-acetylglucosamine kinase, NAGK {Human (Homo sapi 85.66
d2p3ra1252 Glycerol kinase {Escherichia coli [TaxId: 562]} 81.77
>d1vhxa_ c.55.3.8 (A:) Hypothetical protein YrrK (RuvX) {Bacillus subtilis [TaxId: 1423]} 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]

Probab=100.00  E-value=2.8e-45  Score=281.20  Aligned_cols=138  Identities=28%  Similarity=0.453  Sum_probs=128.5

Q ss_pred             CCeEEEEecCCCeEEEEEecCCCceeccceeeeCCCCChhhHHHHHHHHHHhcCCCEEEEeccCC-CCCCchHHHHHHHH
Q 030509           21 RGRFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGYPFN-RQQNAADAVQVKLF   99 (176)
Q Consensus        21 ~~~iLglD~G~kriGvAvsd~~~~~a~Pl~~i~~~~~~~~~~~~~L~~li~e~~~~~iVVGlPl~-dG~~s~~~~~v~~F   99 (176)
                      .||+||||||+||||||+||+.+.+|+|+.++.+++.+.+.++.+|.+++.+|+|++||||+|++ ||+++++++.++.|
T Consensus         1 ~mriLgiD~G~kriGvAisd~~~~~a~pl~~i~~~~~~~~~~~~~l~~ii~e~~i~~iViGlP~~~dg~~~~~~~~~~~f   80 (140)
T d1vhxa_           1 SLRILGLDLGTKTLGVALSDEMGWTAQGIETIKINEAEGDYGLSRLSELIKDYTIDKIVLGFPKNMNGTVGPRGEASQTF   80 (140)
T ss_dssp             CEEEEEEEECSSEEEEEEECTTSSSEEEEEEEECBGGGTBCCHHHHHHHHTTSEEEEEEEECCCCBTTBCCHHHHHHHHH
T ss_pred             CceEEEEEeCCCEEEEEEecCCCCcccceeeEeecccccchHHHHHHHHHHhhccceEEEecccccCCcchhHHHHHHHH
Confidence            37999999999999999999999999999999876655444579999999999999999999999 99999999999999


Q ss_pred             HHHHHhccCCCCCcEEEecCcccHHHHHHHhccCCCCCCCCCCCCcHHHHHHHHHHHHhhhh
Q 030509          100 IDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDLHPVEYKTILDKFAAVGILQEYLDNAN  161 (176)
Q Consensus       100 a~~L~~~~~~~~lpV~~~DEr~TT~~A~~~l~~~g~~~~~~k~~iD~~AA~iILq~yL~~~~  161 (176)
                      ++.|++.  + ++||++|||||||++|+++|++.|.+++++|+.+|++||++|||+||++.+
T Consensus        81 ~~~l~~~--~-~i~V~~~DEr~TS~~A~~~l~~~~~~~~~~k~~iD~~AA~iILe~~L~~~n  139 (140)
T d1vhxa_          81 AKVLETT--Y-NVPVVLWDERLTTMAAEKMLIAADVSRQKRKKVIDKMAAVMILQGYLDSLN  139 (140)
T ss_dssp             HHHHHHH--H-CSCEEEECCSSCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHhccC--C-CccEEEeecccCHHHHHHHHHHcCCCcccccccHHHHHHHHHHHHHHHHhc
Confidence            9999974  3 899999999999999999999999999888999999999999999999864
>d1nu0a_ c.55.3.8 (A:) Hypothetical protein YqgF (RuvX) {Escherichia coli [TaxId: 562]} 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
>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
>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
>d1z05a3 c.55.1.10 (A:81-208) Transcriptional regulator VC2007 {Vibrio cholerae [TaxId: 666]} Back     information, alignment and structure
>d1z6ra2 c.55.1.10 (A:82-210) Mlc protein {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
>d1okja1 c.55.1.9 (A:1-106) Hypothetical protein YeaZ {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1sz2a1 c.55.1.7 (A:3-321) Glucokinase Glk {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1zc6a1 c.55.1.5 (A:8-121) Probable N-acetylglucosamine kinase CV2896 {Chromobacterium violaceum [TaxId: 536]} Back     information, alignment and structure
>d1huxa_ c.55.1.5 (A:) Hydroxyglutaryl-CoA dehydratase component A {Acidaminococcus fermentans [TaxId: 905]} 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
>d1q18a1 c.55.1.7 (A:2-111) 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
>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
>d2ewsa1 c.55.1.14 (A:1-267) Type II pantothenate kinase, CoaW {Staphylococcus aureus [TaxId: 1280]} Back     information, alignment and structure
>d2ch5a2 c.55.1.5 (A:1-117) N-acetylglucosamine kinase, NAGK {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure