Citrus Sinensis ID: 030402

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------18
MGSEAALPKWASNPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKRSNFERMDI
ccccccccccccccEEEEEccccccccccHHEEEEEEEccccccccccccccccccccHHHHHHHHHHHHHcccEEEEEEEEcHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHccccccEEEEcccccHHHHHHHHHcccccccEEEEEccccccHHHHHHHHHHHHHccccccc
ccccccccccccccEEEEEEEEcccccEccEEEEEEEEEHHHHHHHHHccHHHcccccHHHHHHHHHHHHccccccEEEEEEcHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHccccEEEEEEEccccHHHHHHHHHHHccccEEEEEccHHHHcHHHHHHHHHHHHHHHHHccc
mgseaalpkwasnpcimgideagrgpvlgpmvygclycpcsyqqtlatlnfadsktlKEEKREELFEDlkvndsvgwavdiidpRELSAKMLNKNKinlneishdsAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLsqrfpsikfvvskkadslypvvsgASIVAKRSNFERMDI
mgseaalpkwasnpCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELfedlkvndsvgwavDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAklsqrfpsIKFVvskkadslypvvsgasivakrsnfermdi
MGSEAALPKWASNPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKRSNFERMDI
*********WASNPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKT*******ELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIV***********
****AALPKWASNPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKRSNFERMDI
********KWASNPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKRSNFERMDI
**********ASNPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKRSNFERMD*
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
ooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MGSEAALPKWASNPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKRSNFERMDI
no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST ?

Original result of BLAST against SWISS-PROT Database

ID ?Alignment graph ?Length ? Definition ? RBH(Q2H) ? RBH(H2Q) ? Q cover ? H cover ? Identity ? E-value ?
Query178 2.2.26 [Sep-21-2011]
Q9SEZ6 296 Ribonuclease H2 subunit A yes no 0.949 0.570 0.786 5e-77
Q5U209 301 Ribonuclease H2 subunit A yes no 0.876 0.518 0.554 1e-45
O75792 299 Ribonuclease H2 subunit A yes no 0.876 0.521 0.551 2e-45
Q9VPP5 347 Ribonuclease H2 subunit A yes no 0.876 0.449 0.55 3e-45
Q9CWY8 301 Ribonuclease H2 subunit A yes no 0.876 0.518 0.547 3e-44
Q2TBT5 299 Ribonuclease H2 subunit A yes no 0.882 0.525 0.531 7e-44
Q54D13289 Ribonuclease H2 subunit A yes no 0.938 0.577 0.525 6e-43
Q10236326 Ribonuclease H2 subunit A yes no 0.876 0.478 0.518 2e-37
Q9U6P6 297 Ribonuclease H2 subunit A yes no 0.915 0.548 0.461 8e-36
P53942 307 Ribonuclease H2 subunit A yes no 0.865 0.501 0.441 4e-29
>sp|Q9SEZ6|RNH2A_ARATH Ribonuclease H2 subunit A OS=Arabidopsis thaliana GN=At2g25100 PE=2 SV=2 Back     alignment and function desciption
 Score =  286 bits (732), Expect = 5e-77,   Method: Compositional matrix adjust.
 Identities = 133/169 (78%), Positives = 154/169 (91%)

Query: 1   MGSEAALPKWASNPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEE 60
           M SE   P+WAS PC+MGIDEAGRGPVLGPMVYGC+YCP SYQ +LA+L+FADSKTLKEE
Sbjct: 1   MESECLTPEWASQPCLMGIDEAGRGPVLGPMVYGCMYCPISYQSSLASLHFADSKTLKEE 60

Query: 61  KREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGIL 120
           KREEL+E LK++ S+GWAVD+IDPRELSAKML KNK NLNEISH+SA+GLI RVL++G+L
Sbjct: 61  KREELYESLKLDKSLGWAVDVIDPRELSAKMLAKNKTNLNEISHNSAMGLIKRVLDMGVL 120

Query: 121 LTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAK 169
           LTE YLDTVGD +KY+ KLS+RFPSIKFVVSKKADSL+P+VSGASIVAK
Sbjct: 121 LTEAYLDTVGDPDKYRIKLSERFPSIKFVVSKKADSLFPIVSGASIVAK 169
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|Q5U209|RNH2A_RAT Ribonuclease H2 subunit A OS=Rattus norvegicus GN=Rnaseh2a 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|Q9VPP5|RNH2A_DROME Ribonuclease H2 subunit A OS=Drosophila melanogaster GN=CG13690 PE=2 SV=1 Back     alignment and function description
>sp|Q9CWY8|RNH2A_MOUSE Ribonuclease H2 subunit A OS=Mus musculus 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|Q54D13|RNH2A_DICDI Ribonuclease H2 subunit A OS=Dictyostelium discoideum GN=rnaseh2A PE=3 SV=1 Back     alignment and function description
>sp|Q10236|RNH2A_SCHPO Ribonuclease H2 subunit A OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rnh201 PE=3 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|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

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

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query178
225464178 297 PREDICTED: ribonuclease H2 subunit A iso 0.949 0.569 0.852 2e-81
255549406 299 ribonuclease hi large subunit, putative 0.949 0.565 0.847 3e-80
224097610 297 predicted protein [Populus trichocarpa] 0.949 0.569 0.822 3e-77
449468774 297 PREDICTED: ribonuclease H2 subunit A-lik 0.949 0.569 0.798 5e-77
18400719 296 Ribonuclease H2 subunit A [Arabidopsis t 0.949 0.570 0.786 2e-75
356536350 297 PREDICTED: ribonuclease H2 subunit A-lik 0.943 0.565 0.822 2e-75
255640332219 unknown [Glycine max] 0.943 0.767 0.822 2e-75
297825539 296 predicted protein [Arabidopsis lyrata su 0.949 0.570 0.781 3e-75
294464821 293 unknown [Picea sitchensis] 0.943 0.573 0.786 5e-72
21593541 280 putative ribonuclease large subunit [Ara 0.859 0.546 0.803 1e-68
>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 =  306 bits (785), Expect = 2e-81,   Method: Compositional matrix adjust.
 Identities = 144/169 (85%), Positives = 159/169 (94%)

Query: 1   MGSEAALPKWASNPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEE 60
           MGSE ALPKWAS PC+MGIDEAGRGPVLGPMVYGCLYC  SY  TL+TLNFADSKTLKEE
Sbjct: 1   MGSETALPKWASEPCMMGIDEAGRGPVLGPMVYGCLYCARSYHNTLSTLNFADSKTLKEE 60

Query: 61  KREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGIL 120
           KREELFE+LK ++S+GWAVD+IDP ELSAKML KNKINLNEISHDSAIGLITRVLN+G+L
Sbjct: 61  KREELFENLKADESIGWAVDVIDPWELSAKMLKKNKINLNEISHDSAIGLITRVLNMGVL 120

Query: 121 LTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAK 169
           LTEVY+DTVGDAEKY+ KLS+RFP++KFVV+KKADSLYPVVSGASIVAK
Sbjct: 121 LTEVYVDTVGDAEKYRIKLSERFPAVKFVVAKKADSLYPVVSGASIVAK 169

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>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|224097610|ref|XP_002311009.1| predicted protein [Populus trichocarpa] gi|222850829|gb|EEE88376.1| predicted protein [Populus trichocarpa] 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|18400719|ref|NP_565584.1| Ribonuclease H2 subunit A [Arabidopsis thaliana] gi|49066054|sp|Q9SEZ6.2|RNH2A_ARATH RecName: Full=Ribonuclease H2 subunit A; Short=RNase H2 subunit A; AltName: Full=Ribonuclease HI large subunit; Short=RNase HI large subunit; AltName: Full=Ribonuclease HI subunit A gi|26450346|dbj|BAC42289.1| putative ribonuclease large subunit [Arabidopsis thaliana] gi|28973385|gb|AAO64017.1| putative ribonuclease large subunit [Arabidopsis thaliana] gi|330252563|gb|AEC07657.1| Ribonuclease H2 subunit A [Arabidopsis thaliana] 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|255640332|gb|ACU20454.1| unknown [Glycine max] Back     alignment and taxonomy information
>gi|297825539|ref|XP_002880652.1| predicted protein [Arabidopsis lyrata subsp. lyrata] gi|297326491|gb|EFH56911.1| predicted protein [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|294464821|gb|ADE77916.1| unknown [Picea sitchensis] Back     alignment and taxonomy information
>gi|21593541|gb|AAM65508.1| putative ribonuclease large subunit [Arabidopsis thaliana] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query178
TAIR|locus:2040189 296 AT2G25100 [Arabidopsis thalian 0.949 0.570 0.786 5.5e-70
ZFIN|ZDB-GENE-040426-976 307 rnaseh2a "ribonuclease H2, sub 0.870 0.504 0.576 3.5e-43
FB|FBgn0031252 347 CG13690 [Drosophila melanogast 0.876 0.449 0.55 5.7e-43
RGD|1307248 301 Rnaseh2a "ribonuclease H2, sub 0.876 0.518 0.554 1.9e-42
UNIPROTKB|Q5U209 301 Rnaseh2a "Ribonuclease H2 subu 0.876 0.518 0.554 1.9e-42
UNIPROTKB|O75792 299 RNASEH2A "Ribonuclease H2 subu 0.876 0.521 0.551 4e-42
UNIPROTKB|Q2TBT5 299 RNASEH2A "Ribonuclease H2 subu 0.910 0.541 0.521 1.7e-41
MGI|MGI:1916974 301 Rnaseh2a "ribonuclease H2, lar 0.876 0.518 0.547 2.2e-41
UNIPROTKB|E2RQK5 299 RNASEH2A "Ribonuclease" [Canis 0.876 0.521 0.541 2.8e-41
UNIPROTKB|F1SDX8 301 RNASEH2A "Ribonuclease" [Sus s 0.876 0.518 0.535 2.8e-41
TAIR|locus:2040189 AT2G25100 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 709 (254.6 bits), Expect = 5.5e-70, P = 5.5e-70
 Identities = 133/169 (78%), Positives = 154/169 (91%)

Query:     1 MGSEAALPKWASNPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEE 60
             M SE   P+WAS PC+MGIDEAGRGPVLGPMVYGC+YCP SYQ +LA+L+FADSKTLKEE
Sbjct:     1 MESECLTPEWASQPCLMGIDEAGRGPVLGPMVYGCMYCPISYQSSLASLHFADSKTLKEE 60

Query:    61 KREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGIL 120
             KREEL+E LK++ S+GWAVD+IDPRELSAKML KNK NLNEISH+SA+GLI RVL++G+L
Sbjct:    61 KREELYESLKLDKSLGWAVDVIDPRELSAKMLAKNKTNLNEISHNSAMGLIKRVLDMGVL 120

Query:   121 LTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAK 169
             LTE YLDTVGD +KY+ KLS+RFPSIKFVVSKKADSL+P+VSGASIVAK
Sbjct:   121 LTEAYLDTVGDPDKYRIKLSERFPSIKFVVSKKADSLFPIVSGASIVAK 169
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
ZFIN|ZDB-GENE-040426-976 rnaseh2a "ribonuclease H2, subunit A" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
FB|FBgn0031252 CG13690 [Drosophila melanogaster (taxid:7227)] 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|O75792 RNASEH2A "Ribonuclease H2 subunit A" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|Q2TBT5 RNASEH2A "Ribonuclease H2 subunit A" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
MGI|MGI:1916974 Rnaseh2a "ribonuclease H2, large subunit" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
UNIPROTKB|E2RQK5 RNASEH2A "Ribonuclease" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|F1SDX8 RNASEH2A "Ribonuclease" [Sus scrofa (taxid:9823)] 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, ., 40.78690.94940.5709yesno

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 Layer3.1.260.921
3rd Layer3.1.26.40.914

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query178
cd07181221 cd07181, RNase_HII_eukaryota_like, Mammalian RNase 4e-94
cd06266210 cd06266, RNase_HII, Ribonuclease H (RNase H) type 5e-90
pfam01351199 pfam01351, RNase_HII, Ribonuclease HII 2e-42
TIGR00729206 TIGR00729, TIGR00729, ribonuclease H, mammalian HI 5e-36
cd07180204 cd07180, RNase_HII_Archaea_like, Archaeal ribonucl 3e-31
COG0164199 COG0164, RnhB, Ribonuclease HII [DNA replication, 6e-31
PRK00015197 PRK00015, rnhB, ribonuclease HII; Validated 1e-21
cd07182179 cd07182, RNase_HII_bacteria_HII_like, bacterial Ri 2e-16
PRK14551212 PRK14551, rnhB, ribonuclease HII; Provisional 3e-15
cd06590207 cd06590, RNase_HII_bacteria_HIII_like, bacterial R 1e-14
PRK13926207 PRK13926, PRK13926, ribonuclease HII; Provisional 8e-09
TIGR00716284 TIGR00716, rnhC, ribonuclease HIII 8e-09
COG1039297 COG1039, RnhC, Ribonuclease HIII [DNA replication, 9e-09
PRK00996304 PRK00996, PRK00996, ribonuclease HIII; Provisional 1e-05
PRK13925198 PRK13925, rnhB, ribonuclease HII; Provisional 5e-05
PRK14550204 PRK14550, rnhB, ribonuclease HII; Provisional 6e-05
>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 =  272 bits (697), Expect = 4e-94
 Identities = 105/154 (68%), Positives = 124/154 (80%), Gaps = 1/154 (0%)

Query: 17  MGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKV-NDSV 75
           +GIDEAGRGPVLGPMVYG  YCP SY++ L  L FADSKTL EEKREELF+ LK  +D++
Sbjct: 1   LGIDEAGRGPVLGPMVYGAAYCPISYKEELKKLGFADSKTLTEEKREELFKKLKEKDDAL 60

Query: 76  GWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKY 135
           GWA  I+ P+ +S KML + K NLNEISHD+AIGLI  VL+ G+ +TEVY+DTVG  EKY
Sbjct: 61  GWATRILSPQYISTKMLARTKYNLNEISHDAAIGLIREVLDKGVNVTEVYVDTVGPPEKY 120

Query: 136 QAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAK 169
           QAKL ++FP IKF V KKADSLYP+VS ASIVAK
Sbjct: 121 QAKLQKKFPGIKFTVEKKADSLYPIVSAASIVAK 154

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|216451 pfam01351, RNase_HII, Ribonuclease 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|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|187695 cd07182, RNase_HII_bacteria_HII_like, bacterial Ribonuclease HII-like Back     alignment and domain information
>gnl|CDD|237752 PRK14551, rnhB, ribonuclease HII; Provisional Back     alignment and domain information
>gnl|CDD|187692 cd06590, RNase_HII_bacteria_HIII_like, bacterial Ribonuclease HIII-like Back     alignment and domain information
>gnl|CDD|184400 PRK13926, PRK13926, ribonuclease HII; Provisional Back     alignment and domain information
>gnl|CDD|129799 TIGR00716, rnhC, ribonuclease HIII Back     alignment and domain information
>gnl|CDD|223969 COG1039, RnhC, Ribonuclease HIII [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|234886 PRK00996, PRK00996, ribonuclease HIII; Provisional Back     alignment and domain information
>gnl|CDD|184399 PRK13925, rnhB, ribonuclease HII; Provisional Back     alignment and domain information
>gnl|CDD|173015 PRK14550, rnhB, ribonuclease HII; Provisional Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 178
cd07181216 RNaseH_typeII_eukaryota_like Eukaryotic Ribonuclea 100.0
cd07180204 RNaseH_typeII_Archaea_like Archaeal ribonuclease H 100.0
KOG2299 301 consensus Ribonuclease HI [Replication, recombinat 100.0
cd06590208 RNaseH_typeII_bacteria_HIII_like bacterial Ribonuc 100.0
cd06266193 RNaseH_typeII Ribonuclease H type II. Ribonuclease 100.0
TIGR00729206 ribonuclease H, mammalian HI/archaeal HII subfamil 100.0
PRK14551212 rnhB ribonuclease HII; Provisional 100.0
PRK00996304 ribonuclease HIII; Provisional 100.0
PRK13925198 rnhB ribonuclease HII; Provisional 100.0
cd07182179 RNaseH_typeII_bacteria_HII_like bacterial Ribonucl 100.0
PRK14550204 rnhB ribonuclease HII; Provisional 100.0
PRK00015197 rnhB ribonuclease HII; Validated 100.0
PF01351198 RNase_HII: Ribonuclease HII; InterPro: IPR024567 R 100.0
COG0164199 RnhB Ribonuclease HII [DNA replication, recombinat 100.0
TIGR00716284 rnhC ribonuclease HIII. Two types of ribonuclease 100.0
PRK13926207 ribonuclease HII; Provisional 100.0
COG1039297 RnhC Ribonuclease HIII [DNA replication, recombina 100.0
PF12686235 DUF3800: Protein of unknown function (DUF3800); In 82.64
>cd07181 RNaseH_typeII_eukaryota_like Eukaryotic Ribonuclease HII; putative role in Okazaki fragment removal during replication Back     alignment and domain information 
Probab=100.00  E-value=4.7e-50  Score=327.18  Aligned_cols=161  Identities=65%  Similarity=1.022  Sum_probs=144.2

Q ss_pred             eeeccCCCCCcccceeeEEEEecccCchhhhhcCcCCCCCCCHHHHHHHHHHhhhcC-ceeEEEEEEchhchhHHhhhhc
Q 030402           17 MGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVND-SVGWAVDIIDPRELSAKMLNKN   95 (178)
Q Consensus        17 iG~DEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~~-~~~~~i~~i~~~~id~~~~~~~   95 (178)
                      +|||||||||+|||||||||+++++..+.+..+|++|||+||+++|++||++|++.. .+.|.+.+++|++||+.+...+
T Consensus         1 iGiDEaGRG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~L~~~I~~~~~~~~~~i~~i~~~~id~~~~~~~   80 (216)
T cd07181           1 LGIDEAGRGPVLGPMVYGIAYCPISYEEDLKKLGFADSKTLTEEKREELFKKIKEKSEALGWATRILSPQYISAKMLART   80 (216)
T ss_pred             CCCcCCCCCCChhhhEEEEEEEchHhhhhhhhcCCCcCCcCCHHHHHHHHHHHHhccccceEEEEEECHHHHCHHhhhcc
Confidence            699999999999999999999998877778788999999999999999999998732 5689999999999998765444


Q ss_pred             cchHHHHHHHHHHHHHHHHHhcCCCccEEEEcCCCChHHHHHHhhccCCCcceEEeecCcchhhHHHHHHHHHHHHhhcc
Q 030402           96 KINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKRSNFER  175 (178)
Q Consensus        96 ~~Nin~~~~~~~~~~i~~~~~~~~~~~~i~iD~~~~~~~~~~~L~~~~~~~~~~~~~KgD~~~~sVAAASIiAKv~RD~~  175 (178)
                      ..|+|+++++++.+++++++..+..+..++||+++++++|.++|+..+++.++++++|||++|++||||||||||+||++
T Consensus        81 ~~nln~~~~~~~~~~i~~~~~~~~~~~~vliD~~~~~~~~~~~L~~~~~~~~~~~~~kaD~~~~~VAAASIvAKV~RD~~  160 (216)
T cd07181          81 KYNLNEISHDAAIGLIKSVLDKGVNVTEVYVDTVGPPEKYQAKLKKLFPGIKFTVEKKADSLYPIVSAASIVAKVTRDRA  160 (216)
T ss_pred             cccHHHHHHHHHHHHHHHHHcCCCCCCEEEECCCCChhHHHHhhhhcCCCCceEEeeCcccccHHHHHHHHHHHHHHHHH
Confidence            67999999999999998877666678899999999989999999766666778899999999999999999999999999


Q ss_pred             cc
Q 030402          176 MD  177 (178)
Q Consensus       176 M~  177 (178)
                      |.
T Consensus       161 m~  162 (216)
T cd07181         161 LK  162 (216)
T ss_pred             HH
Confidence            85

Ribonuclease (RNase) HII 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. 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). 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 a type II RNase H that is active during replication and is believed to play a role in removal
>cd07180 RNaseH_typeII_Archaea_like Archaeal ribonuclease HII Back     alignment and domain information
>KOG2299 consensus Ribonuclease HI [Replication, recombination and repair] Back     alignment and domain information
>cd06590 RNaseH_typeII_bacteria_HIII_like bacterial Ribonuclease HIII-like Back     alignment and domain information
>cd06266 RNaseH_typeII Ribonuclease H type II Back     alignment and domain information
>TIGR00729 ribonuclease H, mammalian HI/archaeal HII subfamily Back     alignment and domain information
>PRK14551 rnhB ribonuclease HII; Provisional Back     alignment and domain information
>PRK00996 ribonuclease HIII; Provisional Back     alignment and domain information
>PRK13925 rnhB ribonuclease HII; Provisional 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
>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
>COG0164 RnhB Ribonuclease HII [DNA replication, recombination, and repair] Back     alignment and domain information
>TIGR00716 rnhC ribonuclease HIII Back     alignment and domain information
>PRK13926 ribonuclease HII; Provisional Back     alignment and domain information
>COG1039 RnhC Ribonuclease HIII [DNA replication, recombination, and repair] Back     alignment and domain information
>PF12686 DUF3800: Protein of unknown function (DUF3800); InterPro: IPR024524 This family of proteins is functionally uncharacterised Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query178
3puf_A 302 Crystal Structure Of Human Rnase H2 Complex Length 2e-46
3p5j_A 301 The Structure Of The Human Rnase H2 Complex Defines 3e-45
3p56_A 299 The Structure Of The Human Rnase H2 Complex Defines 1e-44
3kio_A 301 Mouse Rnase H2 Complex Length = 301 1e-43
1eke_A230 Crystal Structure Of Class Ii Ribonuclease H (Rnase 4e-14
1io2_A213 Crystal Structure Of Type 2 Ribonuclease H From Hyp 3e-13
2dfe_A209 Crystal Structure Of Tk-Rnase Hii(1-200)-C Length = 3e-13
2dfh_A221 Crystal Structure Of Tk-Rnase Hii(1-212)-C Length = 3e-13
1x1p_A212 Crystal Structure Of Tk-Rnase Hii(1-197)-A(28-42) L 3e-13
2dff_A213 Crystal Structure Of Tk-Rnase Hii(1-204)-C Length = 3e-13
3p83_D217 Structure Of The Pcna:rnase Hii Complex From Archae 6e-11
1i39_A225 Rnase Hii From Archaeoglobus Fulgidus Length = 225 6e-11
1uax_A220 Crystal Structure Of The Ribonuclease H2 From Pyroc 3e-10
>pdb|3PUF|A Chain A, Crystal Structure Of Human Rnase H2 Complex Length = 302 Back     alignment and structure 
Iteration: 1

 Score =  181 bits (459), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 86/156 (55%), Positives = 108/156 (69%)
Query: 14  PCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVND 73
           PC++G+DEAGRGPVLGPMVY   YCP      L  L  ADSKTL E +RE LF  ++  D
Sbjct: 31  PCVLGVDEAGRGPVLGPMVYAICYCPLPRLADLEALKVADSKTLLESERERLFAKMEDTD 90
Query: 74  SVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAE 133
            VGWA+D++ P  +S  ML + K NLN +SHD+A GLI   L+ G+ +T+V++DTVG  E
Sbjct: 91  FVGWALDVLSPNLISTSMLGRVKYNLNSLSHDTATGLIQYALDQGVNVTQVFVDTVGMPE 150
Query: 134 KYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAK 169
            YQA+L Q FP I+  V  KAD+LYPVVS ASI AK
Sbjct: 151 TYQARLQQSFPGIEVTVKAKADALYPVVSAASICAK 186
>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|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|3KIO|A Chain A, Mouse Rnase H2 Complex Length = 301 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|1IO2|A Chain A, Crystal Structure Of Type 2 Ribonuclease H From Hyperthermophilic Archaeon, Thermococcus Kodakaraensis Kod1 Length = 213 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|2DFH|A Chain A, Crystal Structure Of Tk-Rnase Hii(1-212)-C Length = 221 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|2DFF|A Chain A, Crystal Structure Of Tk-Rnase Hii(1-204)-C Length = 213 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
>pdb|1I39|A Chain A, Rnase Hii From Archaeoglobus Fulgidus Length = 225 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

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query178
3kio_A 301 Ribonuclease H2 subunit A; aicardi-goutieres syndr 3e-72
1eke_A230 Ribonuclease HII; endonuclease, structural genomic 1e-53
1i39_A225 Ribonuclease HII, RNAse HII; mixed beta sheet, hel 6e-52
1uax_A220 Ribonuclease HII, ribonuclease H2; RNA*DNA hybrid 6e-51
1io2_A213 Ribonuclease HII; endonuclease, hydrolase; 2.00A { 6e-51
2d0b_A310 RNAse HIII, ribonuclease HIII; RNA/DNA hybrid, hyd 1e-42
2etj_A250 Ribonuclease HII, RNAse HII; TM0915, ribonuclease 2e-11
>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 =  218 bits (558), Expect = 3e-72
 Identities = 86/163 (52%), Positives = 109/163 (66%), Gaps = 1/163 (0%)

Query: 8   PKWASNPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFE 67
                 PC++G+DEAGRGPVLGPMVY   YCP S    L  L  ADSKTL E +RE LF 
Sbjct: 22  AVCLKEPCVLGVDEAGRGPVLGPMVYAICYCPLSRLADLEALKVADSKTLTENERERLFA 81

Query: 68  DLKVN-DSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYL 126
            ++ + D VGWA+D++ P  +S  ML + K NLN +SHD+A GLI   L+  + +T+V++
Sbjct: 82  KMEEDGDFVGWALDVLSPNLISTSMLGRVKYNLNSLSHDTAAGLIQYALDQNVNVTQVFV 141

Query: 127 DTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAK 169
           DTVG  E YQA+L Q FP I+  V  KADSL+PVVS ASI AK
Sbjct: 142 DTVGMPETYQARLQQHFPGIEVTVKAKADSLFPVVSAASIFAK 184
>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
>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
>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
>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 ?
Query178
3kio_A 301 Ribonuclease H2 subunit A; aicardi-goutieres syndr 100.0
1eke_A230 Ribonuclease HII; endonuclease, structural genomic 100.0
1io2_A213 Ribonuclease HII; endonuclease, hydrolase; 2.00A { 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 100.0
2d0b_A310 RNAse HIII, ribonuclease HIII; RNA/DNA hybrid, hyd 100.0
3vn5_A257 RNAse HIII, ribonuclease HIII; hydrolase; 1.98A {A 100.0
>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=1.7e-50  Score=341.38  Aligned_cols=172  Identities=51%  Similarity=0.849  Sum_probs=154.5

Q ss_pred             CCCCCCC-CCceeeeccCCCCCcccceeeEEEEecccCchhhhhcCcCCCCCCCHHHHHHHHHHhhhc-CceeEEEEEEc
Q 030402            6 ALPKWAS-NPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVN-DSVGWAVDIID   83 (178)
Q Consensus         6 ~~~~~~~-~~~~iG~DEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~-~~~~~~i~~i~   83 (178)
                      ..|.|-. .++++|||||||||+|||||+|||+++.+..+.|..+|++|||+||+++|++||++|++. .++.|.+.+++
T Consensus        19 ~~p~~~~~~~~v~GvDEaGRGplaGPvV~aavil~~~~~~~l~~~gl~DSKkLs~~kRe~L~~~I~~~~~a~~~~v~~~s   98 (301)
T 3kio_A           19 PVPAVCLKEPCVLGVDEAGRGPVLGPMVYAICYCPLSRLADLEALKVADSKTLTENERERLFAKMEEDGDFVGWALDVLS   98 (301)
T ss_dssp             CCCTHHHHSCEEEEEEEECSSCSBSCEEEEEEEEEGGGGGGCCCCCSCC--CCCHHHHHHHHHHHHHTTTTCEEEEEEEC
T ss_pred             CCchhhcCCceEEeeeCCCCCCccccceEEEEEEchhhhhhHhhcCCCccccCCHHHHHHHHHHHHhhcccceEEEEecC
Confidence            3566655 478999999999999999999999999987777888999999999999999999999873 36889999999


Q ss_pred             hhchhHHhhhhccchHHHHHHHHHHHHHHHHHhcCCCccEEEEcCCCChHHHHHHhhccCCCcceEEeecCcchhhHHHH
Q 030402           84 PRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSG  163 (178)
Q Consensus        84 ~~~id~~~~~~~~~Nin~~~~~~~~~~i~~~~~~~~~~~~i~iD~~~~~~~~~~~L~~~~~~~~~~~~~KgD~~~~sVAA  163 (178)
                      |++||+.|+.....|||.++|.+++.++++++..+..++.++||+++.+++|+++|++.+|++++++++|||++|++|||
T Consensus        99 ~~eId~~m~~~~~~nlN~l~~~~~~~~i~~~~~l~~~p~~vlVD~~~~p~~y~~~L~~~~p~~~~~~~~KgDs~~~sVAA  178 (301)
T 3kio_A           99 PNLISTSMLGRVKYNLNSLSHDTAAGLIQYALDQNVNVTQVFVDTVGMPETYQARLQQHFPGIEVTVKAKADSLFPVVSA  178 (301)
T ss_dssp             HHHHHHHHTSSSCCCHHHHHHHHHHHHHHHHHHTTCCEEEEEEECSSCCHHHHHHHHHSSTTSEEEEETTGGGTSHHHHH
T ss_pred             HHHHHHHhhhcccccHHHHHHHHHHHHHHHHHhcCCCCCEEEECCCCChHHHHHHHhhcCCCCceEEEeccchhhhHHHH
Confidence            99999988766678999999988888889888777888999999999999999999888888899999999999999999


Q ss_pred             HHHHHHHHhhcccc
Q 030402          164 ASIVAKRSNFERMD  177 (178)
Q Consensus       164 ASIiAKv~RD~~M~  177 (178)
                      |||||||+||++|.
T Consensus       179 ASIlAKV~RD~~M~  192 (301)
T 3kio_A          179 ASIFAKVARDKAVK  192 (301)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH
Confidence            99999999999985
>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
>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
>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 178
d1ekea_225 c.55.3.1 (A:) Class II ribonuclease H (RNase HII) 5e-20
d1io2a_213 c.55.3.1 (A:) Class II ribonuclease H (RNase HII) 2e-18
d1uaxa_211 c.55.3.1 (A:) Class II ribonuclease H (RNase HII) 2e-15
d1i39a_200 c.55.3.1 (A:) Class II ribonuclease H (RNase HII) 2e-12
d2etja1221 c.55.3.1 (A:1-221) Class II ribonuclease H (RNase 1e-11
>d1ekea_ c.55.3.1 (A:) Class II ribonuclease H (RNase HII) {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 225 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 Methanococcus jannaschii [TaxId: 2190]

 Score = 81.1 bits (199), Expect = 5e-20
 Identities = 56/171 (32%), Positives = 79/171 (46%), Gaps = 11/171 (6%)

Query: 16  IMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSV 75
           I+GIDEAGRGPVLGPMV          ++ L  L   DSK L + KR  L + L+    V
Sbjct: 3   IIGIDEAGRGPVLGPMVVCAFAIEKEREEELKKLGVKDSKELTKNKRAYLKKLLENLGYV 62

Query: 76  GWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGD---- 131
              +   +        +N N I +N  +       +   LNI     E+Y+D        
Sbjct: 63  EKRILEAEEINQLMNSINLNDIEIN--AFSKVAKNLIEKLNIRDDEIEIYIDACSTNTKK 120

Query: 132 -----AEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKRSNFERMD 177
                 +K +  + +R  +IK +   KAD+ YPVVS ASI+AK    E +D
Sbjct: 121 FEDSFKDKIEDIIKERNLNIKIIAEHKADAKYPVVSAASIIAKAERDEIID 171
>d1io2a_ c.55.3.1 (A:) Class II ribonuclease H (RNase HII) {Archaeon Thermococcus kodakaraensis [TaxId: 311400]} Length = 213 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 ?
Query178
d1io2a_213 Class II ribonuclease H (RNase HII) {Archaeon Ther 100.0
d1uaxa_211 Class II ribonuclease H (RNase HII) {Archaeon Pyro 100.0
d1i39a_200 Class II ribonuclease H (RNase HII) {Archaeon Arch 100.0
d1ekea_225 Class II ribonuclease H (RNase HII) {Archaeon Meth 100.0
d2etja1221 Class II ribonuclease H (RNase HII) {Thermotoga ma 100.0
>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=100.00  E-value=1.4e-44  Score=290.51  Aligned_cols=154  Identities=31%  Similarity=0.497  Sum_probs=132.3

Q ss_pred             ceeeeccCCCCCcccceeeEEEEecccCchhhhhcCcCCCCCCCHHHHHHHHHHhhhcCceeEEEEEEchhchhHHhhhh
Q 030402           15 CIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNK   94 (178)
Q Consensus        15 ~~iG~DEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~~~~~~~i~~i~~~~id~~~~~~   94 (178)
                      .++|||||||||+|||||||||+++.+..+.+..+|++|||+||+++|++||++|++. ...|.+..++|++++.     
T Consensus         2 ~i~GvDEaGRG~l~GPvvvaav~~~~~~~~~l~~~gv~DSK~Ls~~kR~~l~~~I~~~-~~~~~i~~~~~~~~~~-----   75 (213)
T d1io2a_           2 KIAGIDEAGRGPVIGPMVIAAVVVDENSLPKLEELKVRDSKKLTPKRREKLFNEILGV-LDDYVILELPPDVIGS-----   75 (213)
T ss_dssp             EEEEEEEECSSCSBSCEEEEEEEEEGGGHHHHHHTTGGGCTTCCHHHHHHHHHHHHTT-CSEEEEEEECHHHHHT-----
T ss_pred             cEEeecCcCccccccceEEEEEEEchhhcchhhhcCcchhhhCcHHHHHHHHHHHHHH-HHHhhhhcccHHHHhh-----
Confidence            3799999999999999999999999998888889999999999999999999999984 6789999999999865     


Q ss_pred             ccchHHHHHHHHHHHHHHHHHhcCCCccEEEEcCCC-ChHHHHHHhhccCC-CcceEEeecCcchhhHHHHHHHHHHHHh
Q 030402           95 NKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVG-DAEKYQAKLSQRFP-SIKFVVSKKADSLYPVVSGASIVAKRSN  172 (178)
Q Consensus        95 ~~~Nin~~~~~~~~~~i~~~~~~~~~~~~i~iD~~~-~~~~~~~~L~~~~~-~~~~~~~~KgD~~~~sVAAASIiAKv~R  172 (178)
                      +..|+|+++..+|.+.+.++   ...++.+++|++. ++..|...+.+..+ ..++++++|||++|++||||||||||+|
T Consensus        76 ~~~~~~~~~~~~~~~ai~~l---~~~~~~v~~D~~~~~~~~~~~~~~~~~~~~~~~~~~~KgD~~~~~VAAASIlAKv~R  152 (213)
T d1io2a_          76 REGTLNEFEVENFAKALNSL---KVKPDVIYADAADVDEERFARELGERLNFEAEVVAKHKADDIFPVVSAASILAKVTR  152 (213)
T ss_dssp             CSSCHHHHHHHHHHHHHHHC---SSCCSEEEEECCSSCHHHHHHHHHHTCSSCCEEEEETTHHHHCHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHhc---CCCCCEEEECcccccchhhhhhhcccccccceeEEeecccccchhhhHHHHHHHHHH
Confidence            45799999888887766654   4457889999997 56667666655443 3457788899999999999999999999


Q ss_pred             hcccc
Q 030402          173 FERMD  177 (178)
Q Consensus       173 D~~M~  177 (178)
                      |++|.
T Consensus       153 D~~m~  157 (213)
T d1io2a_         153 DRAVE  157 (213)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            99985
>d1uaxa_ c.55.3.1 (A:) Class II ribonuclease H (RNase HII) {Archaeon Pyrococcus horikoshii [TaxId: 53953]} 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
>d1ekea_ c.55.3.1 (A:) Class II ribonuclease H (RNase HII) {Archaeon Methanococcus jannaschii [TaxId: 2190]} 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