Citrus Sinensis ID: 029710

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------19
MHDRSGKNLHFFIFQVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTCTSHFKDIVEVLWESDEMDEDVSSRRSGKRQLKLSDIGFSSSKRRSEEIESSGKGRCKFLEARKLEQLTHF
cccccHHcccccEEEEEEcccccHHHHHHHHHHHccccEEEEEcccccccccHHHHHHHHHHHHHHHHHcHHHHHHHHHHcccccccccccHHHHHHHHHccccccccccccccccHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccHHHccccccccHHHHccccccccc
cccHHHHHccccEEEEEEEccccHHHHHHHHHHHccccEEEEEccHHHHcHHHHHHHHHHHHHHHHHHHHcccHcccccccccccccccccHHHHHHHHHccccccccccEEEEcHHHHHHHHHccccEEcccccccccccHHcccccEEEEcccccccccccccccccccccccHHHHHccccEcccc
mhdrsgknlHFFIFQVYLDTVGDAEKYQAKLsqrfpsikfvvskkadslypvvsgASIVAKVtrdrtlrgwIFEETAENmhrnfgsgypgdpetkawltdhkhiifgfpslvrfswgtctSHFKDIVEVLWesdemdedvssrrsgkrqlklsdigfssskrrseeieSSGKGRCKFLEARKLEQLTHF
mhdrsgknlhFFIFQVYLDTVGDAEKYQAKLSQRFPSIKFVvskkadslypvvsgasivakvtrdrTLRGWIFeetaenmhrnfgsgYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTCTSHFKDIVEVLWESDEMdedvssrrsgkrqlklsdigfssskrrseeiessgkgrckflearkleqlthf
MHDRSGKNLHFFIFQVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTCTSHFKDIVEVLWESDEMDEDVSSRRSGKRQLKLSDIGFssskrrseeiessgkgrCKFLEARKLEQLTHF
*******NLHFFIFQVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTCTSHFKDIVEVLWE*********************************************************
***RSGKNLHFFIFQVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTCTSHFKDIVEVLWESDE*****************************************FLEARKLEQL**F
MHDRSGKNLHFFIFQVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTCTSHFKDIVEVLWESD***************LKLSDIGF***************GRCKFLEARKLEQLTHF
**DRSGKNLHFFIFQVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTCTSHFKDIVEVLWESD*************RQL**********************************Q****
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MHDRSGKNLHFFIFQVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTCTSHFKDIVEVLWESDEMDEDVSSRRSGKRQLKLSDIGFSSSKRRSEEIESSGKGRCKFLEARKLEQLTHF
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 ?
Query189 2.2.26 [Sep-21-2011]
Q9SEZ6296 Ribonuclease H2 subunit A yes no 0.957 0.611 0.692 3e-72
Q9CWY8301 Ribonuclease H2 subunit A yes no 0.703 0.441 0.507 2e-34
Q5U209301 Ribonuclease H2 subunit A yes no 0.671 0.421 0.515 7e-34
Q9VPP5347 Ribonuclease H2 subunit A yes no 0.883 0.481 0.451 2e-33
O75792299 Ribonuclease H2 subunit A yes no 0.634 0.401 0.520 2e-32
Q2TBT5299 Ribonuclease H2 subunit A yes no 0.650 0.411 0.524 5e-32
Q9U6P6297 Ribonuclease H2 subunit A yes no 0.746 0.474 0.454 2e-26
Q54D13289 Ribonuclease H2 subunit A yes no 0.719 0.470 0.406 2e-25
P53942307 Ribonuclease H2 subunit A yes no 0.783 0.482 0.415 2e-21
Q9P5X8317 Ribonuclease H2 subunit A N/A no 0.566 0.337 0.456 6e-21
>sp|Q9SEZ6|RNH2A_ARATH Ribonuclease H2 subunit A OS=Arabidopsis thaliana GN=At2g25100 PE=2 SV=2 Back     alignment and function desciption
 Score =  270 bits (691), Expect = 3e-72,   Method: Compositional matrix adjust.
 Identities = 126/182 (69%), Positives = 152/182 (83%), Gaps = 1/182 (0%)

Query: 8   NLHFFIFQVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRT 67
           ++   + + YLDTVGD +KY+ KLS+RFPSIKFVVSKKADSL+P+VSGASIVAKVTRDR 
Sbjct: 116 DMGVLLTEAYLDTVGDPDKYRIKLSERFPSIKFVVSKKADSLFPIVSGASIVAKVTRDRA 175

Query: 68  LRGWIFEETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTCTSHFKDIV 127
           L+ W+ EET E+++RNFGSGYPGDPETKAWL  HKH +FGFPSLVRFSWGTCT+H K  V
Sbjct: 176 LKEWLVEETGEDINRNFGSGYPGDPETKAWLVQHKHSVFGFPSLVRFSWGTCTTHLKGEV 235

Query: 128 EVLWESDEMDEDVSSRRSGKRQLKLSDIGFSSSKRRSEEIESSGKGRCKFLEARKLEQLT 187
           EV WE+DE +E+  +  S KRQ KLS  GF + ++RSEEIESSGKGRCKFL+ARK++QLT
Sbjct: 236 EVAWEADE-NEESGNGSSSKRQAKLSSFGFKTCEKRSEEIESSGKGRCKFLQARKIQQLT 294

Query: 188 HF 189
            F
Sbjct: 295 QF 296
Catalytic subunit of RNase HII, an endonuclease that specifically degrades the RNA of RNA:DNA hybrids. Participates in DNA replication, possibly by mediating the removal of lagging-strand Okazaki fragment RNA primers during DNA replication. Mediates the excision of single ribonucleotides from DNA:RNA duplexes.
Arabidopsis thaliana (taxid: 3702)
EC: 3EC: .EC: 1EC: .EC: 2EC: 6EC: .EC: 4
>sp|Q9CWY8|RNH2A_MOUSE Ribonuclease H2 subunit A OS=Mus musculus GN=Rnaseh2a PE=1 SV=2 Back     alignment and function description
>sp|Q5U209|RNH2A_RAT Ribonuclease H2 subunit A OS=Rattus norvegicus GN=Rnaseh2a PE=2 SV=1 Back     alignment and function description
>sp|Q9VPP5|RNH2A_DROME Ribonuclease H2 subunit A OS=Drosophila melanogaster GN=CG13690 PE=2 SV=1 Back     alignment and function description
>sp|O75792|RNH2A_HUMAN Ribonuclease H2 subunit A OS=Homo sapiens GN=RNASEH2A PE=1 SV=2 Back     alignment and function description
>sp|Q2TBT5|RNH2A_BOVIN Ribonuclease H2 subunit A OS=Bos taurus GN=RNASEH2A PE=1 SV=1 Back     alignment and function description
>sp|Q9U6P6|RNH2A_CAEEL Ribonuclease H2 subunit A OS=Caenorhabditis elegans GN=rnh-2 PE=2 SV=1 Back     alignment and function description
>sp|Q54D13|RNH2A_DICDI Ribonuclease H2 subunit A OS=Dictyostelium discoideum GN=rnaseh2A PE=3 SV=1 Back     alignment and function description
>sp|P53942|RNH2A_YEAST Ribonuclease H2 subunit A OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RNH201 PE=1 SV=1 Back     alignment and function description
>sp|Q9P5X8|RNH2A_NEUCR Ribonuclease H2 subunit A OS=Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) GN=rnh-201 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 ?
Query189
225464178 297 PREDICTED: ribonuclease H2 subunit A iso 0.962 0.612 0.752 6e-79
225464176278 PREDICTED: ribonuclease H2 subunit A iso 0.962 0.654 0.752 9e-79
449468774 297 PREDICTED: ribonuclease H2 subunit A-lik 0.962 0.612 0.736 9e-78
255549406 299 ribonuclease hi large subunit, putative 0.962 0.608 0.758 1e-77
356536350 297 PREDICTED: ribonuclease H2 subunit A-lik 0.952 0.606 0.743 2e-75
356536352278 PREDICTED: ribonuclease H2 subunit A-lik 0.952 0.647 0.743 4e-75
224097610 297 predicted protein [Populus trichocarpa] 0.962 0.612 0.741 6e-74
125533439 298 hypothetical protein OsI_35154 [Oryza sa 0.962 0.610 0.686 2e-71
115484243 298 Os11g0153900 [Oryza sativa Japonica Grou 0.962 0.610 0.686 2e-71
357160839 299 PREDICTED: ribonuclease H2 subunit A-lik 0.962 0.608 0.686 4e-71
>gi|225464178|ref|XP_002269817.1| PREDICTED: ribonuclease H2 subunit A isoform 1 [Vitis vinifera] gi|296086584|emb|CBI32219.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
 Score =  298 bits (763), Expect = 6e-79,   Method: Compositional matrix adjust.
 Identities = 137/182 (75%), Positives = 161/182 (88%)

Query: 8   NLHFFIFQVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRT 67
           N+   + +VY+DTVGDAEKY+ KLS+RFP++KFVV+KKADSLYPVVSGASIVAKVTRDR 
Sbjct: 116 NMGVLLTEVYVDTVGDAEKYRIKLSERFPAVKFVVAKKADSLYPVVSGASIVAKVTRDRA 175

Query: 68  LRGWIFEETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTCTSHFKDIV 127
           LR W+  ETAENMHRNFGSGYPGDP TK+WL  HKH +FGFP+LVRFSWGTCT++ KDIV
Sbjct: 176 LRDWVLVETAENMHRNFGSGYPGDPVTKSWLQHHKHSVFGFPTLVRFSWGTCTAYSKDIV 235

Query: 128 EVLWESDEMDEDVSSRRSGKRQLKLSDIGFSSSKRRSEEIESSGKGRCKFLEARKLEQLT 187
           EVLWE+D+++ED S+ R+GKRQLKLS +GF  SKR+SEEIESSGKGRCKF +ARKLEQLT
Sbjct: 236 EVLWEADKVEEDGSTNRNGKRQLKLSSVGFIESKRKSEEIESSGKGRCKFFQARKLEQLT 295

Query: 188 HF 189
            F
Sbjct: 296 QF 297

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|225464176|ref|XP_002269852.1| PREDICTED: ribonuclease H2 subunit A isoform 2 [Vitis vinifera] Back     alignment and taxonomy information
>gi|449468774|ref|XP_004152096.1| PREDICTED: ribonuclease H2 subunit A-like [Cucumis sativus] gi|449529756|ref|XP_004171864.1| PREDICTED: ribonuclease H2 subunit A-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|255549406|ref|XP_002515756.1| ribonuclease hi large subunit, putative [Ricinus communis] gi|223545084|gb|EEF46595.1| ribonuclease hi large subunit, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|356536350|ref|XP_003536702.1| PREDICTED: ribonuclease H2 subunit A-like isoform 1 [Glycine max] Back     alignment and taxonomy information
>gi|356536352|ref|XP_003536703.1| PREDICTED: ribonuclease H2 subunit A-like isoform 2 [Glycine max] Back     alignment and taxonomy information
>gi|224097610|ref|XP_002311009.1| predicted protein [Populus trichocarpa] gi|222850829|gb|EEE88376.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|125533439|gb|EAY79987.1| hypothetical protein OsI_35154 [Oryza sativa Indica Group] Back     alignment and taxonomy information
>gi|115484243|ref|NP_001065783.1| Os11g0153900 [Oryza sativa Japonica Group] gi|62701661|gb|AAX92734.1| ribonuclease HII, putative [Oryza sativa Japonica Group] gi|77548724|gb|ABA91521.1| ribonuclease HI large subunit, putative, expressed [Oryza sativa Japonica Group] gi|113644487|dbj|BAF27628.1| Os11g0153900 [Oryza sativa Japonica Group] gi|125576251|gb|EAZ17473.1| hypothetical protein OsJ_33004 [Oryza sativa Japonica Group] Back     alignment and taxonomy information
>gi|357160839|ref|XP_003578893.1| PREDICTED: ribonuclease H2 subunit A-like [Brachypodium distachyon] 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 ?
Query189
TAIR|locus:2040189296 AT2G25100 [Arabidopsis thalian 0.920 0.587 0.651 2.2e-59
MGI|MGI:1916974301 Rnaseh2a "ribonuclease H2, lar 0.703 0.441 0.507 3.2e-33
RGD|1307248301 Rnaseh2a "ribonuclease H2, sub 0.671 0.421 0.515 1.4e-32
UNIPROTKB|Q5U209301 Rnaseh2a "Ribonuclease H2 subu 0.671 0.421 0.515 1.4e-32
UNIPROTKB|F1SDX8301 RNASEH2A "Ribonuclease" [Sus s 0.698 0.438 0.496 1.6e-31
FB|FBgn0031252347 CG13690 [Drosophila melanogast 0.883 0.481 0.435 3.3e-31
UNIPROTKB|O75792299 RNASEH2A "Ribonuclease H2 subu 0.693 0.438 0.496 3.3e-31
ZFIN|ZDB-GENE-040426-976307 rnaseh2a "ribonuclease H2, sub 0.687 0.423 0.488 5.4e-31
UNIPROTKB|E2RQK5299 RNASEH2A "Ribonuclease" [Canis 0.666 0.421 0.515 6.9e-31
UNIPROTKB|Q2TBT5299 RNASEH2A "Ribonuclease H2 subu 0.650 0.411 0.524 8.8e-31
TAIR|locus:2040189 AT2G25100 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 609 (219.4 bits), Expect = 2.2e-59, P = 2.2e-59
 Identities = 114/175 (65%), Positives = 134/175 (76%)

Query:    15 QVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFE 74
             + YLDTVGD +KY+ KLS+RFPSIKFVVSKKADSL+P+VSGASIVAKVTRDR L+ W+ E
Sbjct:   123 EAYLDTVGDPDKYRIKLSERFPSIKFVVSKKADSLFPIVSGASIVAKVTRDRALKEWLVE 182

Query:    75 ETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTCTSHFKDIVEVLWESD 134
             ET E+++RNFGSGYPGDPETKAWL  HKH +FGFPSLVRFSWGTCT+H K  VEV WE+D
Sbjct:   183 ETGEDINRNFGSGYPGDPETKAWLVQHKHSVFGFPSLVRFSWGTCTTHLKGEVEVAWEAD 242

Query:   135 EMDEDVSSRRSGKRQLKLSDIGFXXXXXXXXXXXXXXXXXCKFLEARKLEQLTHF 189
             E +E+  +  S KRQ KLS  GF                 CKFL+ARK++QLT F
Sbjct:   243 E-NEESGNGSSSKRQAKLSSFGFKTCEKRSEEIESSGKGRCKFLQARKIQQLTQF 296
GO:0003676 "nucleic acid binding" evidence=IEA
GO:0003723 "RNA binding" evidence=IEA
GO:0003824 "catalytic activity" evidence=ISS
GO:0004523 "ribonuclease H activity" evidence=IEA
GO:0005634 "nucleus" evidence=ISM
GO:0005737 "cytoplasm" evidence=ISM
GO:0016070 "RNA metabolic process" evidence=IEA
MGI|MGI:1916974 Rnaseh2a "ribonuclease H2, large subunit" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
RGD|1307248 Rnaseh2a "ribonuclease H2, subunit A" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
UNIPROTKB|Q5U209 Rnaseh2a "Ribonuclease H2 subunit A" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
UNIPROTKB|F1SDX8 RNASEH2A "Ribonuclease" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
FB|FBgn0031252 CG13690 [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
UNIPROTKB|O75792 RNASEH2A "Ribonuclease H2 subunit A" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-040426-976 rnaseh2a "ribonuclease H2, subunit A" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
UNIPROTKB|E2RQK5 RNASEH2A "Ribonuclease" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|Q2TBT5 RNASEH2A "Ribonuclease H2 subunit A" [Bos taurus (taxid:9913)] 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) ?
Q9SEZ6RNH2A_ARATH3, ., 1, ., 2, 6, ., 40.69230.95760.6114yesno

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

Prediction LevelEC numberConfidence of Prediction
3rd Layer3.1.26.40.914
3rd Layer3.1.260.921

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Your Input:
GSVIVG00001423001
RecName- Full=Ribonuclease; EC=3.1.26.-;; Endonuclease that specifically degrades the RNA of RNA- DNA hybrids (By similarity) (298 aa)
(Vitis vinifera)
Predicted Functional Partners:
GSVIVG00022496001
SubName- Full=Chromosome chr14 scaffold_27, whole genome shotgun sequence; (330 aa)
   •• • 0.922
GSVIVG00024178001
RecName- Full=Proliferating cell nuclear antigen;; This protein is an auxiliary protein of DNA [...] (266 aa)
   •• • 0.769
GSVIVG00022150001
RecName- Full=DNA ligase; EC=6.5.1.1; (783 aa)
•  •  • 0.680
GSVIVG00022048001
RecName- Full=DNA polymerase; EC=2.7.7.7; (2224 aa)
   •• • 0.658
GSVIVG00006013001
RecName- Full=DNA polymerase; EC=2.7.7.7; (1126 aa)
   •  • 0.656
GSVIVG00002439001
RecName- Full=DNA primase; EC=2.7.7.-; (457 aa)
   •  • 0.598
GSVIVG00020561001
SubName- Full=Chromosome chr14 scaffold_21, whole genome shotgun sequence; (220 aa)
   •  • 0.593
MSH2
SubName- Full=Chromosome chr17 scaffold_16, whole genome shotgun sequence; (802 aa)
   •• • 0.581
GSVIVG00006228001
SubName- Full=Chromosome chr1 scaffold_166, whole genome shotgun sequence; (739 aa)
   •  • 0.569
GSVIVG00015413001
SubName- Full=Chromosome chr18 scaffold_1, whole genome shotgun sequence; (360 aa)
   •  • 0.569

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 ?
Query189
cd07181221 cd07181, RNase_HII_eukaryota_like, Mammalian RNase 3e-64
cd06266210 cd06266, RNase_HII, Ribonuclease H (RNase H) type 2e-57
TIGR00729206 TIGR00729, TIGR00729, ribonuclease H, mammalian HI 2e-30
cd07180204 cd07180, RNase_HII_Archaea_like, Archaeal ribonucl 2e-26
pfam01351199 pfam01351, RNase_HII, Ribonuclease HII 1e-18
COG0164199 COG0164, RnhB, Ribonuclease HII [DNA replication, 2e-16
PRK00015197 PRK00015, rnhB, ribonuclease HII; Validated 1e-13
PRK14551212 PRK14551, rnhB, ribonuclease HII; Provisional 6e-12
cd07182179 cd07182, RNase_HII_bacteria_HII_like, bacterial Ri 3e-06
>gnl|CDD|187694 cd07181, RNase_HII_eukaryota_like, Mammalian RNase HII is functional when it forms a complex with two other accessory protein Back     alignment and domain information 
 Score =  196 bits (501), Expect = 3e-64
 Identities = 66/111 (59%), Positives = 80/111 (72%)

Query: 15  QVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFE 74
           +VY+DTVG  EKYQAKL ++FP IKF V KKADSLYP+VS ASIVAKVTRDR L+ W F+
Sbjct: 108 EVYVDTVGPPEKYQAKLQKKFPGIKFTVEKKADSLYPIVSAASIVAKVTRDRALKNWQFD 167

Query: 75  ETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTCTSHFKD 125
           ET      + GSGYP DP+TK WL  +   +FG+P LVRFSW T  +  + 
Sbjct: 168 ETLIKDSGDLGSGYPSDPKTKKWLKKNVDPVFGYPQLVRFSWSTAKTILEK 218

Ribonuclease H (RNase H) is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, and eukaryotic RNase H2/HII). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication and repair. The enzyme can be found in bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite a lack of evidence for homology from sequence comparisons, type I and type II RNase H share a common fold and similar steric configurations of the four acidic active-site residues, suggesting identical or very similar catalytic mechanisms. Eukaryotic RNase HII is active during replication and is believed to play a role in removal of Okazaki fragment primers and single ribonucleotides in DNA-DNA duplexes. Eukaryotic RNase HII is functional when it forms a complex with two other accessory proteins. It is speculated that the two accessory subunits are required for correct folding of the catalytic subunit of RNase HII. Mutations in the three subunits of human RNase HII cause neurological disorder. Length = 221
>gnl|CDD|187691 cd06266, RNase_HII, Ribonuclease H (RNase H) type II family (prokaryotic RNase HII and HIII, and eukaryotic RNase H2/HII) Back     alignment and domain information
>gnl|CDD|129812 TIGR00729, TIGR00729, ribonuclease H, mammalian HI/archaeal HII subfamily Back     alignment and domain information
>gnl|CDD|187693 cd07180, RNase_HII_Archaea_like, Archaeal ribonuclease HII Back     alignment and domain information
>gnl|CDD|216451 pfam01351, RNase_HII, Ribonuclease HII Back     alignment and domain information
>gnl|CDD|223242 COG0164, RnhB, Ribonuclease HII [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|234574 PRK00015, rnhB, ribonuclease HII; Validated Back     alignment and domain information
>gnl|CDD|237752 PRK14551, rnhB, ribonuclease HII; Provisional Back     alignment and domain information
>gnl|CDD|187695 cd07182, RNase_HII_bacteria_HII_like, bacterial Ribonuclease HII-like Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 189
KOG2299301 consensus Ribonuclease HI [Replication, recombinat 100.0
cd07181216 RNaseH_typeII_eukaryota_like Eukaryotic Ribonuclea 100.0
PRK14551212 rnhB ribonuclease HII; Provisional 100.0
TIGR00729206 ribonuclease H, mammalian HI/archaeal HII subfamil 99.97
cd07180204 RNaseH_typeII_Archaea_like Archaeal ribonuclease H 99.97
cd06266193 RNaseH_typeII Ribonuclease H type II. Ribonuclease 99.95
COG0164199 RnhB Ribonuclease HII [DNA replication, recombinat 99.94
PRK00015197 rnhB ribonuclease HII; Validated 99.94
PF01351198 RNase_HII: Ribonuclease HII; InterPro: IPR024567 R 99.94
cd06590208 RNaseH_typeII_bacteria_HIII_like bacterial Ribonuc 99.93
cd07182179 RNaseH_typeII_bacteria_HII_like bacterial Ribonucl 99.92
PRK14550204 rnhB ribonuclease HII; Provisional 99.92
PRK13926207 ribonuclease HII; Provisional 99.91
PRK13925198 rnhB ribonuclease HII; Provisional 99.91
PRK00996304 ribonuclease HIII; Provisional 99.81
TIGR00716284 rnhC ribonuclease HIII. Two types of ribonuclease 99.47
COG1039297 RnhC Ribonuclease HIII [DNA replication, recombina 98.74
>KOG2299 consensus Ribonuclease HI [Replication, recombination and repair] Back     alignment and domain information 
Probab=100.00  E-value=9.6e-55  Score=376.87  Aligned_cols=170  Identities=45%  Similarity=0.767  Sum_probs=147.6

Q ss_pred             hhhhcCCCcccEEEEcCCCChHHHHHHHhhhCCCccEEEEecCCcccchhhhhHHHhHHHHHHHHhccchhhhhhhcCCC
Q 029710            4 RSGKNLHFFIFQVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRN   83 (189)
Q Consensus         4 ~~~l~~gv~~~~V~VDtvG~~~~y~~~L~~~fp~i~~~v~~KADs~yp~VsAASIvAKV~RD~~m~~~~~~e~~~~~~~~   83 (189)
                      +.|+++||++++|||||||+|++||++|+++||+++|+|.+||||+||+||||||||||+||+.++.|+++|.+.....+
T Consensus       130 ~~v~~~gvnvteiyVDTVGpp~~Yq~kLek~FP~~k~tV~kKADSlfpiVS~ASI~AKVtRD~alk~w~~~E~~~~~d~~  209 (301)
T KOG2299|consen  130 DEVLDQGVNVTEIYVDTVGPPAKYQEKLEKRFPGIKFTVTKKADSLFPIVSAASIVAKVTRDRALKEWQFEEKLSDPDED  209 (301)
T ss_pred             HHHHHhCCceEEEEEecCCChHHHHHHHHhhCCCeEEEEeecccccccchhhhhhhhhhhhccccceeeeeeecccCCcc
Confidence            45689999999999999999999999999999999999999999999999999999999999999999999987778889


Q ss_pred             CCccCCCChhHHHHHHhhhccccCCCccccccchhhHHhhcc-cceeeecCcccccccccccCCcccccccccccCCCCC
Q 029710           84 FGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTCTSHFKD-IVEVLWESDEMDEDVSSRRSGKRQLKLSDIGFSSSKR  162 (189)
Q Consensus        84 ~GsGYPsDp~Tk~~L~~~~~~~~G~p~~vR~SW~t~~~~l~~-~~~v~w~~~~~~e~~~~~~~~~~~~~~~s~~~~~~~~  162 (189)
                      |||||||||+|++||+.+++++||||++|||||+|++.+|++ +.++.|+++..+.+..+.      .++++|+.+.+..
T Consensus       210 ~GSGYP~DP~T~~wLk~~v~~VFGfp~lVRfSW~Ta~t~L~~~~~~~~~e~~~~e~~~~~~------~~~T~~~~~~~~s  283 (301)
T KOG2299|consen  210 LGSGYPSDPETKAWLKENVDSVFGFPSLVRFSWKTAKTLLEDRSEPLKWEESGFELDKTPL------LKFTKKFKPNPAS  283 (301)
T ss_pred             ccCCCCCChhHHHHHHhcccccccCccceeeeHHHHHHHHhcccccceeecccccccchHH------HHHHHHhcCCCcc
Confidence            999999999999999999999999999999999999999985 999999988644322111      4688888765433


Q ss_pred             cchhhhccCccccchhhhccccccc
Q 029710          163 RSEEIESSGKGRCKFLEARKLEQLT  187 (189)
Q Consensus       163 ~~~~~~~~~~~r~~ff~~r~l~~~~  187 (189)
                        ..+    . |..+| +|+|+++.
T Consensus       284 --~~~----~-r~~~~-~r~l~~~~  300 (301)
T KOG2299|consen  284 --RSV----P-RSERF-ERHLENWY  300 (301)
T ss_pred             --ccc----c-hhHHH-HHhhhhhc
Confidence              111    2 33356 99999874

>cd07181 RNaseH_typeII_eukaryota_like Eukaryotic Ribonuclease HII; putative role in Okazaki fragment removal during replication Back     alignment and domain information
>PRK14551 rnhB ribonuclease HII; Provisional Back     alignment and domain information
>TIGR00729 ribonuclease H, mammalian HI/archaeal HII subfamily Back     alignment and domain information
>cd07180 RNaseH_typeII_Archaea_like Archaeal ribonuclease HII Back     alignment and domain information
>cd06266 RNaseH_typeII Ribonuclease H type II Back     alignment and domain information
>COG0164 RnhB Ribonuclease HII [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK00015 rnhB ribonuclease HII; Validated Back     alignment and domain information
>PF01351 RNase_HII: Ribonuclease HII; InterPro: IPR024567 Ribonuclease HII and HIII are endonucleases that specifically degrade the RNA of RNA-DNA hybrids Back     alignment and domain information
>cd06590 RNaseH_typeII_bacteria_HIII_like bacterial Ribonuclease HIII-like Back     alignment and domain information
>cd07182 RNaseH_typeII_bacteria_HII_like bacterial Ribonuclease HII-like Back     alignment and domain information
>PRK14550 rnhB ribonuclease HII; Provisional Back     alignment and domain information
>PRK13926 ribonuclease HII; Provisional Back     alignment and domain information
>PRK13925 rnhB ribonuclease HII; Provisional Back     alignment and domain information
>PRK00996 ribonuclease HIII; Provisional Back     alignment and domain information
>TIGR00716 rnhC ribonuclease HIII Back     alignment and domain information
>COG1039 RnhC Ribonuclease HIII [DNA replication, recombination, and repair] 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 ?
Query189
3kio_A301 Mouse Rnase H2 Complex Length = 301 2e-35
3p5j_A301 The Structure Of The Human Rnase H2 Complex Defines 3e-35
3puf_A302 Crystal Structure Of Human Rnase H2 Complex Length 2e-33
3p56_A299 The Structure Of The Human Rnase H2 Complex Defines 1e-32
2dff_A213 Crystal Structure Of Tk-Rnase Hii(1-204)-C Length = 6e-14
1io2_A213 Crystal Structure Of Type 2 Ribonuclease H From Hyp 2e-13
2dfh_A221 Crystal Structure Of Tk-Rnase Hii(1-212)-C Length = 2e-13
2dfe_A209 Crystal Structure Of Tk-Rnase Hii(1-200)-C Length = 3e-13
1uax_A220 Crystal Structure Of The Ribonuclease H2 From Pyroc 3e-13
1x1p_A212 Crystal Structure Of Tk-Rnase Hii(1-197)-A(28-42) L 3e-12
1eke_A230 Crystal Structure Of Class Ii Ribonuclease H (Rnase 5e-12
1i39_A225 Rnase Hii From Archaeoglobus Fulgidus Length = 225 1e-08
3p83_D217 Structure Of The Pcna:rnase Hii Complex From Archae 2e-08
>pdb|3KIO|A Chain A, Mouse Rnase H2 Complex Length = 301 Back     alignment and structure 
Iteration: 1

 Score =  144 bits (364), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 69/136 (50%), Positives = 90/136 (66%), Gaps = 3/136 (2%)
Query: 13  IFQVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWI 72
           + QV++DTVG  E YQA+L Q FP I+  V  KADSL+PVVS ASI AKV RD+ ++ W 
Sbjct: 136 VTQVFVDTVGXPETYQARLQQHFPGIEVTVKAKADSLFPVVSAASIFAKVARDKAVKNWQ 195
Query: 73  FEETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTCTSHF-KDIVEVLW 131
           F E  +++  ++GSGYP DP+TKAWL  H   +FGFP  VRFSW T  +   K+  +V+W
Sbjct: 196 FVENLQDLDSDYGSGYPNDPKTKAWLRKHVDPVFGFPQFVRFSWSTAQAILEKEAEDVIW 255
Query: 132 ESDEMDEDVSSRRSGK 147
           E  E +ED    R GK
Sbjct: 256 EDSEAEED--PERPGK 269
>pdb|3P5J|A Chain A, The Structure Of The Human Rnase H2 Complex Defines Key Interaction Interfaces Relevant To Enzyme Function And Human Disease Length = 301 Back     alignment and structure
>pdb|3PUF|A Chain A, Crystal Structure Of Human Rnase H2 Complex Length = 302 Back     alignment and structure
>pdb|3P56|A Chain A, The Structure Of The Human Rnase H2 Complex Defines Key Interaction Interfaces Relevant To Enzyme Function And Human Disease Length = 299 Back     alignment and structure
>pdb|2DFF|A Chain A, Crystal Structure Of Tk-Rnase Hii(1-204)-C Length = 213 Back     alignment and structure
>pdb|1IO2|A Chain A, Crystal Structure Of Type 2 Ribonuclease H From Hyperthermophilic Archaeon, Thermococcus Kodakaraensis Kod1 Length = 213 Back     alignment and structure
>pdb|2DFH|A Chain A, Crystal Structure Of Tk-Rnase Hii(1-212)-C Length = 221 Back     alignment and structure
>pdb|2DFE|A Chain A, Crystal Structure Of Tk-Rnase Hii(1-200)-C Length = 209 Back     alignment and structure
>pdb|1UAX|A Chain A, Crystal Structure Of The Ribonuclease H2 From Pyrococcus Horikoshii Ot3 Length = 220 Back     alignment and structure
>pdb|1X1P|A Chain A, Crystal Structure Of Tk-Rnase Hii(1-197)-A(28-42) Length = 212 Back     alignment and structure
>pdb|1EKE|A Chain A, Crystal Structure Of Class Ii Ribonuclease H (Rnase Hii) With Mes Ligand Length = 230 Back     alignment and structure
>pdb|1I39|A Chain A, Rnase Hii From Archaeoglobus Fulgidus Length = 225 Back     alignment and structure
>pdb|3P83|D Chain D, Structure Of The Pcna:rnase Hii Complex From Archaeoglobus Fulgidus. Length = 217 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 ?
Query189
3kio_A301 Ribonuclease H2 subunit A; aicardi-goutieres syndr 1e-52
1eke_A230 Ribonuclease HII; endonuclease, structural genomic 9e-37
1i39_A225 Ribonuclease HII, RNAse HII; mixed beta sheet, hel 5e-36
1io2_A213 Ribonuclease HII; endonuclease, hydrolase; 2.00A { 9e-34
1uax_A220 Ribonuclease HII, ribonuclease H2; RNA*DNA hybrid 1e-33
2d0b_A310 RNAse HIII, ribonuclease HIII; RNA/DNA hybrid, hyd 5e-19
2etj_A250 Ribonuclease HII, RNAse HII; TM0915, ribonuclease 5e-05
>3kio_A Ribonuclease H2 subunit A; aicardi-goutieres syndrome, RNAse H2, protein complex, autoimmune disease, endonuclease, hydrolase, metal-binding; 2.90A {Mus musculus} PDB: 3p5j_A 3puf_A 3p56_A Length = 301 Back     alignment and structure
 Score =  169 bits (429), Expect = 1e-52
 Identities = 71/187 (37%), Positives = 104/187 (55%), Gaps = 13/187 (6%)

Query: 4   RSGKNLHFFIFQVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVT 63
           +   + +  + QV++DTVG  E YQA+L Q FP I+  V  KADSL+PVVS ASI AKV 
Sbjct: 127 QYALDQNVNVTQVFVDTVGMPETYQARLQQHFPGIEVTVKAKADSLFPVVSAASIFAKVA 186

Query: 64  RDRTLRGWIFEETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTCTSHF 123
           RD+ ++ W F E  +++  ++GSGYP DP+TKAWL  H   +FGFP  VRFSW T  +  
Sbjct: 187 RDKAVKNWQFVENLQDLDSDYGSGYPNDPKTKAWLRKHVDPVFGFPQFVRFSWSTAQAIL 246

Query: 124 -KDIVEVLWESDEMDEDVSSRRSGKRQLKLSDIGFSSSKRRSEEIESSGKGRCKFLEARK 182
            K+  +V+WE  E +ED       +R  K++       +    +         ++ + R 
Sbjct: 247 EKEAEDVIWEDSEAEED------PERPGKITSYFSQGPQTCRPQA------PHRYFQERG 294

Query: 183 LEQLTHF 189
           LE  +  
Sbjct: 295 LEAASSL 301
>1eke_A Ribonuclease HII; endonuclease, structural genomics, BSGC structure funded by NIH, protein structure initiative, PSI; HET: MES; 2.00A {Methanocaldococcus jannaschii} SCOP: c.55.3.1 Length = 230 Back     alignment and structure
>1i39_A Ribonuclease HII, RNAse HII; mixed beta sheet, helix-loop-helix, hydrolase; 1.95A {Archaeoglobus fulgidus} SCOP: c.55.3.1 PDB: 1i3a_A 3p83_D* Length = 225 Back     alignment and structure
>1io2_A Ribonuclease HII; endonuclease, hydrolase; 2.00A {Thermococcus kodakarensis} SCOP: c.55.3.1 PDB: 2dfh_A 2dff_A 2dfe_A 1x1p_A Length = 213 Back     alignment and structure
>1uax_A Ribonuclease HII, ribonuclease H2; RNA*DNA hybrid ribonucleotidohydrolase, hydrolase; 2.00A {Pyrococcus horikoshii} SCOP: c.55.3.1 Length = 220 Back     alignment and structure
>2d0b_A RNAse HIII, ribonuclease HIII; RNA/DNA hybrid, hydrolase; 2.10A {Geobacillus stearothermophilus} PDB: 2d0a_A 2d0c_A 3asm_A Length = 310 Back     alignment and structure
>2etj_A Ribonuclease HII, RNAse HII; TM0915, ribonuclease HII (EC 3.1.26.4) (RNAse HII), structur genomics, joint center for structural genomics; 1.74A {Thermotoga maritima} SCOP: c.55.3.1 PDB: 3o3g_A* 3o3f_A* 3o3h_A* Length = 250 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query189
3kio_A301 Ribonuclease H2 subunit A; aicardi-goutieres syndr 100.0
1io2_A213 Ribonuclease HII; endonuclease, hydrolase; 2.00A { 100.0
1eke_A230 Ribonuclease HII; endonuclease, structural genomic 100.0
1i39_A225 Ribonuclease HII, RNAse HII; mixed beta sheet, hel 100.0
1uax_A220 Ribonuclease HII, ribonuclease H2; RNA*DNA hybrid 100.0
2etj_A250 Ribonuclease HII, RNAse HII; TM0915, ribonuclease 99.95
2d0b_A310 RNAse HIII, ribonuclease HIII; RNA/DNA hybrid, hyd 99.89
3vn5_A257 RNAse HIII, ribonuclease HIII; hydrolase; 1.98A {A 99.71
>3kio_A Ribonuclease H2 subunit A; aicardi-goutieres syndrome, RNAse H2, protein complex, autoimmune disease, endonuclease, hydrolase, metal-binding; 2.90A {Mus musculus} PDB: 3p5j_A 3puf_A 3p56_A Back     alignment and structure
Probab=100.00  E-value=1.5e-53  Score=375.76  Aligned_cols=174  Identities=40%  Similarity=0.742  Sum_probs=124.6

Q ss_pred             hhhhcCCCcccEEEEcCCCChHHHHHHHhhhCCCccEEEEecCCcccchhhhhHHHhHHHHHHHHhccchhhhhhhcCCC
Q 029710            4 RSGKNLHFFIFQVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRN   83 (189)
Q Consensus         4 ~~~l~~gv~~~~V~VDtvG~~~~y~~~L~~~fp~i~~~v~~KADs~yp~VsAASIvAKV~RD~~m~~~~~~e~~~~~~~~   83 (189)
                      ++++++|++++.||||+++.|++|+++|++.+|++++++++|||++||+||||||||||+||++|+.|.|.|.+...+++
T Consensus       127 ~~~~~l~~~p~~vlVD~~~~p~~y~~~L~~~~p~~~~~~~~KgDs~~~sVAAASIlAKV~RD~~M~~~~f~e~l~~~~~~  206 (301)
T 3kio_A          127 QYALDQNVNVTQVFVDTVGMPETYQARLQQHFPGIEVTVKAKADSLFPVVSAASIFAKVARDKAVKNWQFVENLQDLDSD  206 (301)
T ss_dssp             HHHHHTTCCEEEEEEECSSCCHHHHHHHHHSSTTSEEEEETTGGGTSHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCCC
T ss_pred             HHHHhcCCCCCEEEECCCCChHHHHHHHhhcCCCCceEEEeccchhhhHHHHHHHHHHHHHHHHHHHhhhhhhHHhhCCC
Confidence            34456899999999999999999999999999999999999999999999999999999999999999988888889999


Q ss_pred             CCccCCCChhHHHHHHhhhccccCCCccccccchhhHHhhc-ccceeeecCcccccccccccCCcccccccccccCCCCC
Q 029710           84 FGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTCTSHFK-DIVEVLWESDEMDEDVSSRRSGKRQLKLSDIGFSSSKR  162 (189)
Q Consensus        84 ~GsGYPsDp~Tk~~L~~~~~~~~G~p~~vR~SW~t~~~~l~-~~~~v~w~~~~~~e~~~~~~~~~~~~~~~s~~~~~~~~  162 (189)
                      |||||||||+|++||+++++++||+|++||+||+|++++|+ ++++|.|++|+++++.++.      .+|++||.+....
T Consensus       207 ~GsGYPSDp~T~~~L~~~~~~~~G~p~~vR~SW~tvk~~l~~~~~~v~w~~~~~~~~~~~~------~~~~~~f~~~~~~  280 (301)
T 3kio_A          207 YGSGYPNDPKTKAWLRKHVDPVFGFPQFVRFSWSTAQAILEKEAEDVIWEDSEAEEDPERP------GKITSYFSQGPQT  280 (301)
T ss_dssp             CCSSSTTSHHHHHHHHTTCBTTTBSCTTBCTTSHHHHHHHHHHSCCEECSCC----------------------------
T ss_pred             CCCcCCCCHHHHHHHHHcccccCCCCccccCCcHHHHHHHhcCCceeeecccccccccccc------hhHHHHhcCCCcc
Confidence            99999999999999999999999999999999999999998 5999999988643332111      3799998643211


Q ss_pred             cchhhhccCccccchhhhcccccccCC
Q 029710          163 RSEEIESSGKGRCKFLEARKLEQLTHF  189 (189)
Q Consensus       163 ~~~~~~~~~~~r~~ff~~r~l~~~~~~  189 (189)
                            ..+++||+||++|+|++|+++
T Consensus       281 ------~~~~~~~~~f~~~~l~~~~~~  301 (301)
T 3kio_A          281 ------CRPQAPHRYFQERGLEAASSL  301 (301)
T ss_dssp             ---------------------------
T ss_pred             ------ccccccchhhHhhcccccccC
Confidence                  123679999999999999875
>1io2_A Ribonuclease HII; endonuclease, hydrolase; 2.00A {Thermococcus kodakarensis} SCOP: c.55.3.1 PDB: 2dfh_A 2dff_A 2dfe_A 1x1p_A Back     alignment and structure
>1eke_A Ribonuclease HII; endonuclease, structural genomics, BSGC structure funded by NIH, protein structure initiative, PSI; HET: MES; 2.00A {Methanocaldococcus jannaschii} SCOP: c.55.3.1 Back     alignment and structure
>1i39_A Ribonuclease HII, RNAse HII; mixed beta sheet, helix-loop-helix, hydrolase; 1.95A {Archaeoglobus fulgidus} SCOP: c.55.3.1 PDB: 1i3a_A 3p83_D* Back     alignment and structure
>1uax_A Ribonuclease HII, ribonuclease H2; RNA*DNA hybrid ribonucleotidohydrolase, hydrolase; 2.00A {Pyrococcus horikoshii} SCOP: c.55.3.1 Back     alignment and structure
>2etj_A Ribonuclease HII, RNAse HII; TM0915, ribonuclease HII (EC 3.1.26.4) (RNAse HII), structur genomics, joint center for structural genomics; 1.74A {Thermotoga maritima} SCOP: c.55.3.1 PDB: 3o3g_A* 3o3f_A* 3o3h_A* Back     alignment and structure
>2d0b_A RNAse HIII, ribonuclease HIII; RNA/DNA hybrid, hydrolase; 2.10A {Geobacillus stearothermophilus} PDB: 2d0a_A 2d0c_A 3asm_A Back     alignment and structure
>3vn5_A RNAse HIII, ribonuclease HIII; hydrolase; 1.98A {Aquifex aeolicus} 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 189
d1io2a_213 c.55.3.1 (A:) Class II ribonuclease H (RNase HII) 5e-15
d1ekea_225 c.55.3.1 (A:) Class II ribonuclease H (RNase HII) 4e-14
d1uaxa_211 c.55.3.1 (A:) Class II ribonuclease H (RNase HII) 2e-12
d1i39a_200 c.55.3.1 (A:) Class II ribonuclease H (RNase HII) 4e-11
d2etja1221 c.55.3.1 (A:1-221) Class II ribonuclease H (RNase 1e-09
>d1io2a_ c.55.3.1 (A:) Class II ribonuclease H (RNase HII) {Archaeon Thermococcus kodakaraensis [TaxId: 311400]} Length = 213 Back     information, alignment and structure

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: Class II ribonuclease H (RNase HII)
species: Archaeon Thermococcus kodakaraensis [TaxId: 311400]

 Score = 67.9 bits (165), Expect = 5e-15
 Identities = 44/121 (36%), Positives = 63/121 (52%), Gaps = 8/121 (6%)

Query: 1   MHDRSGKNLHFFIFQVYLDTVG-DAEKYQAKLSQRFPSIKFVVSK-KADSLYPVVSGASI 58
              ++  +L      +Y D    D E++  +L +R      VV+K KAD ++PVVS ASI
Sbjct: 87  NFAKALNSLKVKPDVIYADAADVDEERFARELGERLNFEAEVVAKHKADDIFPVVSAASI 146

Query: 59  VAKVTRDRTLRGWIFEETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGT 118
           +AKVTRDR +     E      +   GSGYP DP T+A+L ++      FP +VR  W T
Sbjct: 147 LAKVTRDRAVEKLKEE------YGEIGSGYPSDPRTRAFLENYYREHGEFPPIVRKGWKT 200

Query: 119 C 119
            
Sbjct: 201 L 201
>d1ekea_ c.55.3.1 (A:) Class II ribonuclease H (RNase HII) {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 225 Back     information, alignment and structure
>d1uaxa_ c.55.3.1 (A:) Class II ribonuclease H (RNase HII) {Archaeon Pyrococcus horikoshii [TaxId: 53953]} Length = 211 Back     information, alignment and structure
>d1i39a_ c.55.3.1 (A:) Class II ribonuclease H (RNase HII) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 200 Back     information, alignment and structure
>d2etja1 c.55.3.1 (A:1-221) Class II ribonuclease H (RNase HII) {Thermotoga maritima [TaxId: 2336]} Length = 221 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 ?
Query189
d1io2a_213 Class II ribonuclease H (RNase HII) {Archaeon Ther 99.97
d1uaxa_211 Class II ribonuclease H (RNase HII) {Archaeon Pyro 99.96
d1ekea_225 Class II ribonuclease H (RNase HII) {Archaeon Meth 99.96
d1i39a_200 Class II ribonuclease H (RNase HII) {Archaeon Arch 99.95
d2etja1221 Class II ribonuclease H (RNase HII) {Thermotoga ma 99.94
>d1io2a_ c.55.3.1 (A:) Class II ribonuclease H (RNase HII) {Archaeon Thermococcus kodakaraensis [TaxId: 311400]} Back     information, alignment and structure
class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: Class II ribonuclease H (RNase HII)
species: Archaeon Thermococcus kodakaraensis [TaxId: 311400]

Probab=99.97  E-value=4e-32  Score=223.47  Aligned_cols=117  Identities=35%  Similarity=0.554  Sum_probs=104.9

Q ss_pred             cchhhhcCCCcccEEEEcCCC-ChHHHHHHHhhhCC-CccEEEEecCCcccchhhhhHHHhHHHHHHHHhccchhhhhhh
Q 029710            2 HDRSGKNLHFFIFQVYLDTVG-DAEKYQAKLSQRFP-SIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAEN   79 (189)
Q Consensus         2 h~~~~l~~gv~~~~V~VDtvG-~~~~y~~~L~~~fp-~i~~~v~~KADs~yp~VsAASIvAKV~RD~~m~~~~~~e~~~~   79 (189)
                      |.+++..++.+++.|++|++. +...|...+.+.++ ...+++.+|||++||+||||||||||+||++|+.|      .+
T Consensus        88 ~~~ai~~l~~~~~~v~~D~~~~~~~~~~~~~~~~~~~~~~~~~~~KgD~~~~~VAAASIlAKv~RD~~m~~l------~~  161 (213)
T d1io2a_          88 FAKALNSLKVKPDVIYADAADVDEERFARELGERLNFEAEVVAKHKADDIFPVVSAASILAKVTRDRAVEKL------KE  161 (213)
T ss_dssp             HHHHHHHCSSCCSEEEEECCSSCHHHHHHHHHHTCSSCCEEEEETTHHHHCHHHHHHHHHHHHHHHHHHHHH------HH
T ss_pred             HHHHHHhcCCCCCEEEECcccccchhhhhhhcccccccceeEEeecccccchhhhHHHHHHHHHHHHHHHHH------HH
Confidence            456677788899999999987 78888888877665 45688889999999999999999999999999986      56


Q ss_pred             cCCCCCccCCCChhHHHHHHhhhccccCCCccccccchhhHHhhc
Q 029710           80 MHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTCTSHFK  124 (189)
Q Consensus        80 ~~~~~GsGYPsDp~Tk~~L~~~~~~~~G~p~~vR~SW~t~~~~l~  124 (189)
                      .||+||+|||+||.|++||+.+.++.+|+|++||+||+|++++++
T Consensus       162 ~y~~~g~GY~s~~h~~a~l~~~~~~~~~~~~~hR~sf~~~k~~l~  206 (213)
T d1io2a_         162 EYGEIGSGYPSDPRTRAFLENYYREHGEFPPIVRKGWKTLKKIAE  206 (213)
T ss_dssp             HHSCCCSSCTTSHHHHHHHHHHHHHHSSCCTTBCTTCHHHHHHHH
T ss_pred             hCCcCCCCCCCHHHHHHHHHhcccccCCCCccccCCcHHHHHHHH
Confidence            788999999999999999999998888999999999999999986
>d1uaxa_ c.55.3.1 (A:) Class II ribonuclease H (RNase HII) {Archaeon Pyrococcus horikoshii [TaxId: 53953]} Back     information, alignment and structure
>d1ekea_ c.55.3.1 (A:) Class II ribonuclease H (RNase HII) {Archaeon Methanococcus jannaschii [TaxId: 2190]} Back     information, alignment and structure
>d1i39a_ c.55.3.1 (A:) Class II ribonuclease H (RNase HII) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Back     information, alignment and structure
>d2etja1 c.55.3.1 (A:1-221) Class II ribonuclease H (RNase HII) {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure