254781076

254781076

ribonuclease HII

GeneID in NCBI database:8210100Locus tag:CLIBASIA_04890
Protein GI in NCBI database:254781076Protein Accession:YP_003065489.1
Gene range:+(1077775, 1078404)Protein Length:209aa
Gene description:ribonuclease HII
COG prediction:[L] Ribonuclease HII
KEGG prediction:rnhB; ribonuclease HII (EC:3.1.26.4); K03470 ribonuclease HII [EC:3.1.26.4]
SEED prediction:Ribonuclease HII (EC 3.1.26.4)
Pathway involved in KEGG:DNA replication [PATH:las03030]
Subsystem involved in SEED:Conserved gene cluster associated with Met-tRNA formyltransferase;
Ribonuclease H
sequencesequence profile

Prediction of Local Sequence Properties

SourceSummaryResult
scaler
NCBI Databasesequence
PSIPREDsecondary structure
SSPROsecondary structure
DISEMBLcoil and loop
DISEMBLflexible loop
SEGlow complexity
DISOPREDdisordered
DISEMBLmissing residues
DISPROdisordered
TMHMMnone TM-Helix
TOPPRED2 TM-Helix
HMMTOP1 TM-Helix
MEMSATnone TM-Helix
MEMSAT_SVMnone TM-Helix
PHOBIUSnone TM-Helix
SignalP_HMMno
SignalP_NNno
COILScoiled coil
70% MSAconservation map
90% MSAconservation map
  
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------21
MFCNSIPERPHFELEAMVREKNMWPVAGIDEVGRGALAGPVVVAAIILDPNNIPFGINDSKKISHKKREELYEKITSSAIISISSASHQYIDKHNIHKATLDAIYHAVENLQVIPRSALIDGRSIPEDLPCQAFAVIKGDSISLSIAAASIIAKVTRDRLMRIAHKKYPDYGFDSHVGYPTAKHQQVIKEKGPSCIHRLTFRPLRNLSV
cccccccccccHHHHHHHHHccccEEEEEcccccccccccEEEEEEEEccccccccccccccccHHHHHHHHHHHHHHHHHHEEEccHHHHHHccHHHHHHHHHHHHHHcccccccEEEEEccccccccccccEEEEccccccHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccHHHHHHHHHHccccHHHccHHHHHHHcc
cccHHHccccccccHHHHHHcccEEEEEEEEEcccccEccEEEEEEEEEHHHHHccccccccccHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHcccccccEEEEccccccccccccHHHEEccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHccccccHHHHHHHHHcccccHHccccccccEEEc
mfcnsiperphfELEAMVReknmwpvagidevgrgalaGPVVVAAIildpnnipfgindskkisHKKREELYEKITSSAIISISSASHQYIDKHNIHKATLDAIYHAVENLqviprsalidgrsipedlpcqafavikgdsISLSIAAASIIAKVTRDRLMRIahkkypdygfdshvgyptakhQQVIkekgpscihrltfrplrnlsv
mfcnsiperpHFELEAMVREKNMWPVAGIDEVGRGALAGPVVVAAIILdpnnipfgindskkisHKKREELYEKITSSAIISISSASHQYIDKHNIHKATLDAIYHAVENLQVIPRSALIDGRSIPEDLPCQAFAVIKGDSISLSIAAASIIAKVTRDRLMRIAHKKYPDYGFDSHVGYPTAKHQQVIKekgpscihrltfrplrnlsv
MFCNSIPERPHFELEAMVREKNMWPVAGIDEVGRGALAGPVVVAAIILDPNNIPFGINDSKKISHKKREELYEKITssaiisissasHQYIDKHNIHKATLDAIYHAVENLQVIPRSALIDGRSIPEDLPCQAFAVIKGDsislsiaaasiiaKVTRDRLMRIAHKKYPDYGFDSHVGYPTAKHQQVIKEKGPSCIHRLTFRPLRNLSV
******PERPHFELEAMVREKNMWPVAGIDEVGRGALAGPVVVAAIILDPNNIPFGINDSKKISHKKREELYEKITSSAIISISSASHQYIDKHNIHKATLDAIYHAVENLQVIPRSALIDGRSIPEDLPCQAFAVIKGDSISLSIAAASIIAKVTRDRLMRIAHKKYPDYGFDSHVGYPTAKHQQVIKEKGPSCIHRLTFRPLRNLSV
MFCNSIPERPHFELEAMVREKNMWPVAGIDEVGRGALAGPVVVAAIILDPNNIPFGINDSKKISHKKREELYEKITSSAIISISSASHQYIDKHNIHKATLDAIYHAVENLQVIPRSALIDGRSIPEDLPCQAFAVIKGDSISLSIAAASIIAKVTRDRLMRIAHKKYPDYGFDSHVGYPTAKHQQVIKEKGPSCIHRLTFRPLRNLSV
MFCNSIPERPHFELEAMVREKNMWPVAGIDEVGRGALAGPVVVAAIILDPNNIPFGINDSKKISHKKREELYEKITSSAIISISSASHQYIDKHNIHKATLDAIYHAVENLQVIPRSALIDGRSIPEDLPCQAFAVIKGDSISLSIAAASIIAKVTRDRLMRIAHKKYPDYGFDSHVGYPTAKHQQVIKEKGPSCIHRLTFRPLRNLSV
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
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MFCNSIPERPHFELEAMVREKNMWPVAGIDEVGRGALAGPVVVAAIILDPNNIPFGINDSKKISHKKREELYEKITSSAIISISSASHQYIDKHNIHKATLDAIYHAVENLQVIPRSALIDGRSIPEDLPCQAFAVIKGDSISLSIAAASIIAKVTRDRLMRIAHKKYPDYGFDSHVGYPTAKHQQVIKEKGPSCIHRLTFRPLRNLSV
MFCNSIPERPHFELEAMVREKNMWPVAGIDEVGRGALAGPVVVAAIILDPNNIPFGINDSKKISHKKREELYEKITSSAIISISSASHQYIDKHNIHKATLDAIYHAVENLQVIPRSALIDGRSIPEDLPCQAFAVIKGDSISLSIAAASIIAKVTRDRLMRIAHKKYPDYGFDSHVGYPTAKHQQVIKEKGPSCIHRLTFRPLRNLSV
MFCNSIPERPHFELEAMVREKNMWPVAGIDEVGRGALAGPVVVAAIILDPNNIPFGINDSKKISHKKREELYEKITSSAIISISSASHQYIDKHNIHKATLDAIYHAVENLQVIPRSALIDGRSIPEDLPCQAFAVIKGDSISLSIAAASIIAKVTRDRLMRIAHKKYPDYGFDSHVGYPTAKHQQVIKEKGPSCIHRLTFRPLRNLSV

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

No hits with e-value below 0.05

Close Homologs Detected BLAST or PSI-BLAST in the First 2 Iterations

IdentityAlignment graphLength Definition Round E-value
Target209 ribonuclease HII [Candidatus Liberibacter asiaticus str
315122464209 ribonuclease HII [Candidatus Liberibacter solanacearum 1 3e-84
227821031231 ribonuclease HII [Sinorhizobium fredii NGR234] Length = 1 9e-57
241203307229 ribonuclease HII [Rhizobium leguminosarum bv. trifolii 1 1e-56
86356514229 ribonuclease HII [Rhizobium etli CFN 42] Length = 229 1 1e-56
209548122229 ribonuclease HII [Rhizobium leguminosarum bv. trifolii 1 2e-56
116250704229 ribonuclease HII [Rhizobium leguminosarum bv. viciae 38 1 2e-56
190890579229 ribonuclease HII protein [Rhizobium etli CIAT 652] Leng 1 2e-56
327190563229 ribonuclease HII protein [Rhizobium etli CNPAF512] Leng 1 3e-56
222147705279 ribonuclease HII [Agrobacterium vitis S4] Length = 279 1 2e-55
159184435217 ribonuclease HII [Agrobacterium tumefaciens str. C58] L 1 7e-55
>gi|315122464|ref|YP_004062953.1| ribonuclease HII [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 209 Back     alignment and organism information
 Score =  315 bits (807), Expect = 3e-84,   Method: Compositional matrix adjust.
 Identities = 158/200 (79%), Positives = 181/200 (90%)

Query: 8   ERPHFELEAMVREKNMWPVAGIDEVGRGALAGPVVVAAIILDPNNIPFGINDSKKISHKK 67
           E+P+FE E MVR+K MWPVAGIDEVGRGALAG VVVAAIILDPNNIP GINDSKKI  KK
Sbjct: 8   EKPNFEFEIMVRQKKMWPVAGIDEVGRGALAGSVVVAAIILDPNNIPPGINDSKKIPPKK 67

Query: 68  REELYEKITSSAIISISSASHQYIDKHNIHKATLDAIYHAVENLQVIPRSALIDGRSIPE 127
           RE LYEKI +SAI+SI+SA ++YID+HNIHKATLD +Y A+ NL++ PRS LIDGRSIPE
Sbjct: 68  REYLYEKIINSAIVSIASAGNRYIDQHNIHKATLDTMYRAINNLKITPRSVLIDGRSIPE 127

Query: 128 DLPCQAFAVIKGDSISLSIAAASIIAKVTRDRLMRIAHKKYPDYGFDSHVGYPTAKHQQV 187
           +LPCQAFA+IKGDS SLSIAAASI+AKVTRDRLM++AHKKYPDYGFDSHVGYPT KH+Q 
Sbjct: 128 NLPCQAFAIIKGDSSSLSIAAASIVAKVTRDRLMKMAHKKYPDYGFDSHVGYPTVKHRQA 187

Query: 188 IKEKGPSCIHRLTFRPLRNL 207
           IKEKGPS IHR++FRPL++L
Sbjct: 188 IKEKGPSRIHRMSFRPLKDL 207


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|227821031|ref|YP_002825001.1| ribonuclease HII [Sinorhizobium fredii NGR234] Length = 231 Back     alignment and organism information
>gi|241203307|ref|YP_002974403.1| ribonuclease HII [Rhizobium leguminosarum bv. trifolii WSM1325] Length = 229 Back     alignment and organism information
>gi|86356514|ref|YP_468406.1| ribonuclease HII [Rhizobium etli CFN 42] Length = 229 Back     alignment and organism information
>gi|209548122|ref|YP_002280039.1| ribonuclease HII [Rhizobium leguminosarum bv. trifolii WSM2304] Length = 229 Back     alignment and organism information
>gi|116250704|ref|YP_766542.1| ribonuclease HII [Rhizobium leguminosarum bv. viciae 3841] Length = 229 Back     alignment and organism information
>gi|190890579|ref|YP_001977121.1| ribonuclease HII protein [Rhizobium etli CIAT 652] Length = 229 Back     alignment and organism information
>gi|327190563|gb|EGE57656.1| ribonuclease HII protein [Rhizobium etli CNPAF512] Length = 229 Back     alignment and organism information
>gi|222147705|ref|YP_002548662.1| ribonuclease HII [Agrobacterium vitis S4] Length = 279 Back     alignment and organism information
>gi|159184435|ref|NP_353745.2| ribonuclease HII [Agrobacterium tumefaciens str. C58] Length = 217 Back     alignment and organism information

Conserved Domains in CDD Database
Detected by RPS-BLAST and HHsearch

Conserved Domains in CDD Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target209 ribonuclease HII [Candidatus Liberibacter asiaticus str
PRK00015197 PRK00015, rnhB, ribonuclease HII; Validated 7e-72
cd06266193 cd06266, RNaseH_typeII, Ribonuclease H type II 3e-61
COG0164199 COG0164, RnhB, Ribonuclease HII [DNA replication, recom 5e-58
PRK13925198 PRK13925, rnhB, ribonuclease HII; Provisional 1e-46
pfam01351197 pfam01351, RNase_HII, Ribonuclease HII 2e-42
PRK13926207 PRK13926, PRK13926, ribonuclease HII; Provisional 9e-40
cd07180204 cd07180, RNaseH_typeII_Archaea_like, Archaeal ribonucle 2e-25
PRK14550204 PRK14550, rnhB, ribonuclease HII; Provisional 4e-20
TIGR00729206 TIGR00729, TIGR00729, ribonuclease H, mammalian HI/arch 5e-17
PRK14551212 PRK14551, rnhB, ribonuclease HII; Provisional 1e-13
cd07181216 cd07181, RNaseH_typeII_eukaryota_like, Eukaryotic Ribon 3e-13
KOG2299301 KOG2299, KOG2299, KOG2299, Ribonuclease HI [Replication 8e-12
TIGR00716284 TIGR00716, rnhC, ribonuclease HIII 1e-05
cd07182179 cd07182, RNaseH_typeII_bacteria_HII_like, bacterial Rib 3e-76
cd06590208 cd06590, RNaseH_typeII_bacteria_HIII_like, bacterial Ri 7e-14
PRK00996304 PRK00996, PRK00996, ribonuclease HIII; Provisional 2e-12
COG1039297 COG1039, RnhC, Ribonuclease HIII [DNA replication, reco 2e-11
>gnl|CDD|178795 PRK00015, rnhB, ribonuclease HII; Validated Back     alignment and domain information
>gnl|CDD|132875 cd06266, RNaseH_typeII, Ribonuclease H type II Back     alignment and domain information
>gnl|CDD|30513 COG0164, RnhB, Ribonuclease HII [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|184399 PRK13925, rnhB, ribonuclease HII; Provisional Back     alignment and domain information
>gnl|CDD|144809 pfam01351, RNase_HII, Ribonuclease HII Back     alignment and domain information
>gnl|CDD|184400 PRK13926, PRK13926, ribonuclease HII; Provisional Back     alignment and domain information
>gnl|CDD|132877 cd07180, RNaseH_typeII_Archaea_like, Archaeal ribonuclease HII Back     alignment and domain information
>gnl|CDD|173015 PRK14550, rnhB, ribonuclease HII; Provisional Back     alignment and domain information
>gnl|CDD|129812 TIGR00729, TIGR00729, ribonuclease H, mammalian HI/archaeal HII subfamily Back     alignment and domain information
>gnl|CDD|184738 PRK14551, rnhB, ribonuclease HII; Provisional Back     alignment and domain information
>gnl|CDD|132878 cd07181, RNaseH_typeII_eukaryota_like, Eukaryotic Ribonuclease HII; putative role in Okazaki fragment removal during replication Back     alignment and domain information
>gnl|CDD|37510 KOG2299, KOG2299, KOG2299, Ribonuclease HI [Replication, recombination and repair] Back     alignment and domain information
>gnl|CDD|129799 TIGR00716, rnhC, ribonuclease HIII Back     alignment and domain information
>gnl|CDD|132879 cd07182, RNaseH_typeII_bacteria_HII_like, bacterial Ribonuclease HII-like Back     alignment and domain information
>gnl|CDD|132876 cd06590, RNaseH_typeII_bacteria_HIII_like, bacterial Ribonuclease HIII-like Back     alignment and domain information
>gnl|CDD|179201 PRK00996, PRK00996, ribonuclease HIII; Provisional Back     alignment and domain information
>gnl|CDD|31241 COG1039, RnhC, Ribonuclease HIII [DNA replication, recombination, and repair] Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 209 ribonuclease HII [Candidatus Liberibacter asiaticus str
PRK13926212 junction RNase; Provisional 100.0
PRK00015197 rnhB ribonuclease HII; Validated 100.0
PRK13925200 rnhB ribonuclease HII; Provisional 100.0
cd07182179 RNaseH_typeII_bacteria_HII_like bacterial Ribonuclease 100.0
COG0164199 RnhB Ribonuclease HII [DNA replication, recombination, 100.0
cd06266193 RNaseH_typeII Ribonuclease H type II. Ribonuclease H (R 100.0
pfam01351197 RNase_HII Ribonuclease HII. 100.0
cd07180204 RNaseH_typeII_Archaea_like Archaeal ribonuclease HII. R 100.0
cd07181216 RNaseH_typeII_eukaryota_like Eukaryotic Ribonuclease HI 100.0
cd06590208 RNaseH_typeII_bacteria_HIII_like bacterial Ribonuclease 100.0
TIGR00729235 TIGR00729 ribonuclease HII; InterPro: IPR004649 Ribonuc 100.0
KOG2299301 consensus 100.0
PRK00996303 ribonuclease HIII; Provisional 100.0
COG1039297 RnhC Ribonuclease HIII [DNA replication, recombination, 99.96
TIGR00716298 rnhC ribonuclease HIII; InterPro: IPR004641 Ribonucleas 99.93
>PRK13926 junction RNase; Provisional Back     alignment and domain information
>PRK00015 rnhB ribonuclease HII; Validated 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
>COG0164 RnhB Ribonuclease HII [DNA replication, recombination, and repair] Back     alignment and domain information
>cd06266 RNaseH_typeII Ribonuclease H type II Back     alignment and domain information
>pfam01351 RNase_HII Ribonuclease HII Back     alignment and domain information
>cd07180 RNaseH_typeII_Archaea_like Archaeal ribonuclease HII Back     alignment and domain information
>cd07181 RNaseH_typeII_eukaryota_like Eukaryotic Ribonuclease HII; putative role in Okazaki fragment removal during replication Back     alignment and domain information
>cd06590 RNaseH_typeII_bacteria_HIII_like bacterial Ribonuclease HIII-like Back     alignment and domain information
>TIGR00729 TIGR00729 ribonuclease HII; InterPro: IPR004649 Ribonuclease HII 3 Back     alignment and domain information
>KOG2299 consensus Back     alignment and domain information
>PRK00996 ribonuclease HIII; Provisional Back     alignment and domain information
>COG1039 RnhC Ribonuclease HIII [DNA replication, recombination, and repair] Back     alignment and domain information
>TIGR00716 rnhC ribonuclease HIII; InterPro: IPR004641 Ribonuclease HIII 3 Back     alignment and domain information

Homologous Structures in PDB Database
Detected by PSI-BLAST, RPS-BLAST and HHsearch

Homologous Structures Detected by PSI-BLAST against Nonredundant Database

IdentityAlignment graphLength Definition E-value
Target209 ribonuclease HII [Candidatus Liberibacter asiaticus str
3o3f_A222 T. Maritima Rnase H2 D107n In Complex With Nucleic 2e-35
3o3g_A222 T. Maritima Rnase H2 In Complex With Nucleic Acid S 2e-35
2etj_A250 Crystal Structure Of Ribonuclease Hii (Ec 3.1.26.4) 1e-34
2dff_A213 Crystal Structure Of Tk-Rnase Hii(1-204)-C Length = 1e-23
2dfh_A221 Crystal Structure Of Tk-Rnase Hii(1-212)-C Length = 1e-23
1io2_A213 Crystal Structure Of Type 2 Ribonuclease H From Hyp 1e-23
2dfe_A209 Crystal Structure Of Tk-Rnase Hii(1-200)-C Length = 3e-22
1uax_A220 Crystal Structure Of The Ribonuclease H2 From Pyroc 3e-22
1i39_A225 Rnase Hii From Archaeoglobus Fulgidus Length = 225 1e-20
3p83_D217 Structure Of The Pcna:rnase Hii Complex From Archae 2e-20
1x1p_A212 Crystal Structure Of Tk-Rnase Hii(1-197)-A(28-42) L 8e-20
3p5j_A301 The Structure Of The Human Rnase H2 Complex Defines 1e-17
3puf_A302 Crystal Structure Of Human Rnase H2 Complex Length 5e-17
1eke_A230 Crystal Structure Of Class Ii Ribonuclease H (Rnase 4e-16
3kio_A301 Mouse Rnase H2 Complex Length = 301 8e-16
3p56_A299 The Structure Of The Human Rnase H2 Complex Defines 5e-15
2d0a_A310 Crystal Structure Of Bst-Rnase Hiii Length = 310 9e-05
>gi|313754409|pdb|3O3F|A Chain A, T. Maritima Rnase H2 D107n In Complex With Nucleic Acid Substrate And Magnesium Ions Length = 222 Back     alignment and structure
 Score =  152 bits (385), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 84/188 (44%), Positives = 113/188 (60%), Gaps = 4/188 (2%)

Query: 17  MVREKNMWPVAGIDEVGRGALAGPVVVAAIILDPNNIPFGINDSKKISHKKREELYEKIT 76
            + +K    VAG+DE GRG LAGPVV AA++L+      GINDSK++S  KRE L ++I 
Sbjct: 4   ELYKKEFGIVAGVDEAGRGCLAGPVVAAAVVLEKE--IEGINDSKQLSPAKRERLLDEIM 61

Query: 77  SSAIISISSASHQYIDKHNIHKATLDAIYHAVENLQVIPRSALIDGRSIPEDLPCQAFAV 136
             A + I  AS + ID +NI  AT  A+  A+ENL V P   L++G+    +L      +
Sbjct: 62  EKAAVGIGIASPEEIDLYNIFNATKLAMNRALENLSVKPSFVLVNGK--GIELSVPGTCL 119

Query: 137 IKGDSISLSIAAASIIAKVTRDRLMRIAHKKYPDYGFDSHVGYPTAKHQQVIKEKGPSCI 196
           +KGD  S  I AASI+AKV RDRLM   H+ YP + F  H GY T +H   I++ G   I
Sbjct: 120 VKGDQKSKLIGAASIVAKVFRDRLMSEFHRMYPQFSFHKHKGYATKEHLNEIRKNGVLPI 179

Query: 197 HRLTFRPL 204
           HRL+F P+
Sbjct: 180 HRLSFEPV 187


>gi|313754412|pdb|3O3G|A Chain A, T. Maritima Rnase H2 In Complex With Nucleic Acid Substrate And Calcium Ions Length = 222 Back     alignment and structure
>gi|83754963|pdb|2ETJ|A Chain A, Crystal Structure Of Ribonuclease Hii (Ec 3.1.26.4) (Rnase Hii) (Tm0915) From Thermotoga Maritima At 1.74 A Resolution Length = 250 Back     alignment and structure
>gi|134104117|pdb|2DFF|A Chain A, Crystal Structure Of Tk-Rnase Hii(1-204)-C Length = 213 Back     alignment and structure
>gi|134104118|pdb|2DFH|A Chain A, Crystal Structure Of Tk-Rnase Hii(1-212)-C Length = 221 Back     alignment and structure
>gi|14278500|pdb|1IO2|A Chain A, Crystal Structure Of Type 2 Ribonuclease H From Hyperthermophilic Archaeon, Thermococcus Kodakaraensis Kod1 Length = 213 Back     alignment and structure
>gi|134104116|pdb|2DFE|A Chain A, Crystal Structure Of Tk-Rnase Hii(1-200)-C Length = 209 Back     alignment and structure
gi|50513813|pdb|1UAX|A Chain A, Crystal Structure Of The Ribonuclease H2 From Pyrococcus Horikoshii Ot3 Length = 220 Back     alignment and structure
>gi|14278646|pdb|1I39|A Chain A, Rnase Hii From Archaeoglobus Fulgidus Length = 225 Back     alignment and structure
>gi|321159924|pdb|3P83|D Chain D, Structure Of The Pcna:rnase Hii Complex From Archaeoglobus Fulgidus. Length = 217 Back     alignment and structure
>gi|88191784|pdb|1X1P|A Chain A, Crystal Structure Of Tk-Rnase Hii(1-197)-A(28-42) Length = 212 Back     alignment and structure
gi|312208159|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
>gi|315364763|pdb|3PUF|A Chain A, Crystal Structure Of Human Rnase H2 Complex Length = 302 Back     alignment and structure
>gi|10835820|pdb|1EKE|A Chain A, Crystal Structure Of Class Ii Ribonuclease H (Rnase Hii) With Mes Ligand Length = 230 Back     alignment and structure
>gi|268612465|pdb|3KIO|A Chain A, Mouse Rnase H2 Complex Length = 301 Back     alignment and structure
>gi|312208153|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
>gi|112490233|pdb|2D0A|A Chain A, Crystal Structure Of Bst-Rnase Hiii Length = 310 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target209 ribonuclease HII [Candidatus Liberibacter asiaticus str
2etj_A250 Ribonuclease HII, RNAse HII; TM0915, ribonuclease HII ( 9e-50
1eke_A230 Ribonuclease HII; endonuclease, structural genomics, BS 5e-45
1io2_A213 Ribonuclease HII; endonuclease, hydrolase; 2.00A {Therm 3e-40
3kio_A301 Ribonuclease H2 subunit A; aicardi-goutieres syndrome, 9e-39
2d0b_A310 RNAse HIII, ribonuclease HIII; RNA/DNA hybrid, hydrolas 1e-38
1i39_A225 Ribonuclease HII, RNAse HII; mixed beta sheet, helix-lo 9e-38
1uax_A220 Ribonuclease HII, ribonuclease H2; RNA*DNA hybrid ribon 2e-31
>2etj_A Ribonuclease HII, RNAse HII; TM0915, ribonuclease HII (EC 3.1.26.4) (RNAse HII), structural genomics, joint center for structural genomics; 1.74A {Thermotoga maritima} SCOP: c.55.3.1 Length = 250 Back     alignment and structure
 Score =  191 bits (487), Expect = 9e-50
 Identities = 87/188 (46%), Positives = 114/188 (60%), Gaps = 4/188 (2%)

Query: 20  EKNMWPVAGIDEVGRGALAGPVVVAAIILDPNNIPFGINDSKKISHKKREELYEKITSSA 79
           +K    VAG+DE GRG LAGPVV AA++L+      GINDSK++S  KRE L ++I   A
Sbjct: 20  KKEFGIVAGVDEAGRGCLAGPVVAAAVVLEKEIE--GINDSKQLSPAKRERLLDEIMEKA 77

Query: 80  IISISSASHQYIDKHNIHKATLDAIYHAVENLQVIPRSALIDGRSIPEDLPCQAFAVIKG 139
            + I  AS + ID +NI  AT  A+  A+ENL V P   L+DG+ I   +P     ++KG
Sbjct: 78  AVGIGIASPEEIDLYNIFNATKLAMNRALENLSVKPSFVLVDGKGIELSVPGTC--LVKG 135

Query: 140 DSISLSIAAASIIAKVTRDRLMRIAHKKYPDYGFDSHVGYPTAKHQQVIKEKGPSCIHRL 199
           D  S  I AASI+AKV RDRLM   H+ YP + F  H GY T +H   I++ G   IHRL
Sbjct: 136 DQKSKLIGAASIVAKVFRDRLMSEFHRMYPQFSFHKHKGYATKEHLNEIRKNGVLPIHRL 195

Query: 200 TFRPLRNL 207
           +F P+  L
Sbjct: 196 SFEPVLEL 203


>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
>1io2_A Ribonuclease HII; endonuclease, hydrolase; 2.00A {Thermococcus kodakarensis KOD1} SCOP: c.55.3.1 PDB: 2dfh_A 2dff_A 2dfe_A 1x1p_A Length = 213 Back     alignment and structure
>3kio_A Ribonuclease H2 subunit A; aicardi-goutieres syndrome, RNAse H2, protein complex, autoimmune disease, endonuclease, hydrolase, metal-binding; 2.90A {Mus musculus} Length = 301 Back     alignment and structure
>2d0b_A RNAse HIII, ribonuclease HIII; RNA/DNA hybrid, hydrolase; 2.10A {Geobacillus stearothermophilus} PDB: 2d0a_A 2d0c_A Length = 310 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 Length = 225 Back     alignment and structure
>1uax_A Ribonuclease HII, ribonuclease H2; RNA*DNA hybrid ribonucleotidohydrolase; 2.00A {Pyrococcus horikoshii OT3} SCOP: c.55.3.1 Length = 220 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target209 ribonuclease HII [Candidatus Liberibacter asiaticus str
2etj_A250 Ribonuclease HII, RNAse HII; TM0915, ribonuclease HII ( 100.0
1uax_A220 Ribonuclease HII, ribonuclease H2; RNA*DNA hybrid ribon 100.0
3kio_A301 Ribonuclease H2 subunit A; aicardi-goutieres syndrome, 100.0
1io2_A213 Ribonuclease HII; endonuclease, hydrolase; 2.00A {Therm 100.0
1i39_A225 Ribonuclease HII, RNAse HII; mixed beta sheet, helix-lo 100.0
2d0b_A310 RNAse HIII, ribonuclease HIII; RNA/DNA hybrid, hydrolas 100.0
1eke_A230 Ribonuclease HII; endonuclease, structural genomics, BS 100.0
>2etj_A Ribonuclease HII, RNAse HII; TM0915, ribonuclease HII (EC 3.1.26.4) (RNAse HII), structural genomics, joint center for structural genomics; 1.74A {Thermotoga maritima} SCOP: c.55.3.1 Back     alignment and structure
Probab=100.00  E-value=0  Score=433.48  Aligned_cols=187  Identities=47%  Similarity=0.671  Sum_probs=178.2

Q ss_pred             HHHHCCCCEEEEEECCCCCCCCCCEEEEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEEEECCCHHHHHHHCH
Q ss_conf             99977994899984278777522255999998701082331152028999998755211012307885156799852047
Q gi|254781076|r   17 MVREKNMWPVAGIDEVGRGALAGPVVVAAIILDPNNIPFGINDSKKISHKKREELYEKITSSAIISISSASHQYIDKHNI   96 (209)
Q Consensus        17 ~l~~~~~~~IiGvDEaGRG~~~GPlvvaav~~~~~~~~~~i~DSK~Ls~~~R~~l~~~i~~~~~~~i~~~~~~eID~~ni   96 (209)
                      .|++.|+..|+|||||||||++||||+|||+++.+.  .|++|||+||+++|++|+..|++.+.|++++++++|||++||
T Consensus        17 ~l~~~~~~~V~GVDEAGRGpv~GPmVvaaV~l~~~~--~gv~DSKkLs~~kR~~l~~~i~~~~~~~i~~~s~~eId~~ni   94 (250)
T 2etj_A           17 ELYKKEFGIVAGVDEAGRGCLAGPVVAAAVVLEKEI--EGINDSKQLSPAKRERLLDEIMEKAAVGIGIASPEEIDLYNI   94 (250)
T ss_dssp             GGGTTTSSSEEEEEEECTTCSBSCEEEEEEEECSCC--C----------CHHHHHHHHHHHHEEEEEEEECHHHHHHHCH
T ss_pred             HHHHCCCCEEEEECCCCCCCCCCEEEEEEEEECCCC--CCCCCCCCCCHHHHHHHHHHCCCCCCEEEEEEECHHHHHCCH
T ss_conf             999869978997748786774100379999978998--877703589999999998753234635999985117652497


Q ss_pred             HHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf             99988654321002575321101265322466212268711478652002366665477589999999887779881028
Q gi|254781076|r   97 HKATLDAIYHAVENLQVIPRSALIDGRSIPEDLPCQAFAVIKGDSISLSIAAASIIAKVTRDRLMRIAHKKYPDYGFDSH  176 (209)
Q Consensus        97 ~~A~~~a~~~ai~~l~~~~~~ilIDg~~~~~~~~~~~~~i~KgD~~~~~VaaASIiAKv~RD~~m~~l~~~~p~Ygf~~n  176 (209)
                      ++|+..||.+|+.+|...++.+++||+.++  .+.+..+++|||++|++||||||||||+||++|.+|+++||+|||+.|
T Consensus        95 ~~a~~~am~rai~~L~~~~~~~~~D~~~~~--~~~~~~~i~KaD~k~~~VaAASIiAKV~RD~~m~~l~~~yp~yg~~~~  172 (250)
T 2etj_A           95 FNATKLAMNRALENLSVKPSFVLVDGKGIE--LSVPGTCLVKGDQKSKLIGAASIVAKVFRDRLMSEFHRMYPQFSFHKH  172 (250)
T ss_dssp             HHHHHHHHHHHHHHSSSCCSEEEEESSSCC--CSSCEEEETTHHHHCHHHHHHHHHHHHHHHHHHHHHHHHCTTSCHHHH
T ss_pred             HHHHHHHHHHHHHHCCCCCCEEEECCCCCC--CCCCCEEEECCCCCCCCEEECHHHHHHHHHHHHHHHHHHCCCCCCCCC
T ss_conf             899999999999965877550310476677--887744667676665511110034687999999999987889998468


Q ss_pred             CCCCCHHHHHHHHHCCCCCCCCCCHHHHHHH
Q ss_conf             9999989999999828583010784888640
Q gi|254781076|r  177 VGYPTAKHQQVIKEKGPSCIHRLTFRPLRNL  207 (209)
Q Consensus       177 kGYgT~~H~~ai~~~G~~~~HR~Sf~~vk~l  207 (209)
                      +||||++|+++|+++|++|+||+||+|+++|
T Consensus       173 sGY~Tk~hl~ai~~~G~~~~hR~Sw~tik~l  203 (250)
T 2etj_A          173 KGYATKEHLNEIRKNGVLPIHRLSFEPVLEL  203 (250)
T ss_dssp             TTCCCHHHHHHHHHHCCCTTBCTTSHHHHTT
T ss_pred             CCCCCHHHHHHHHHHCCCCCCCCCCHHHHHH
T ss_conf             8879599999999878092123883889999



>1uax_A Ribonuclease HII, ribonuclease H2; RNA*DNA hybrid ribonucleotidohydrolase; 2.00A {Pyrococcus horikoshii OT3} SCOP: c.55.3.1 Back     alignment and structure
>3kio_A Ribonuclease H2 subunit A; aicardi-goutieres syndrome, RNAse H2, protein complex, autoimmune disease, endonuclease, hydrolase, metal-binding; 2.90A {Mus musculus} Back     alignment and structure
>1io2_A Ribonuclease HII; endonuclease, hydrolase; 2.00A {Thermococcus kodakarensis KOD1} 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 Back     alignment and structure
>2d0b_A RNAse HIII, ribonuclease HIII; RNA/DNA hybrid, hydrolase; 2.10A {Geobacillus stearothermophilus} PDB: 2d0a_A 2d0c_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

Homologous Domains in SCOP and MMDB Database
Detected by RPS-BLAST and HHsearch

Homologous Domains in SCOP70 (Version1.75) Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 209 ribonuclease HII [Candidatus Liberibacter asiaticus str
d2etja1221 c.55.3.1 (A:1-221) Class II ribonuclease H (RNase HII) 7e-47
d1io2a_213 c.55.3.1 (A:) Class II ribonuclease H (RNase HII) {Arch 1e-36
d1uaxa_211 c.55.3.1 (A:) Class II ribonuclease H (RNase HII) {Arch 1e-32
d1i39a_200 c.55.3.1 (A:) Class II ribonuclease H (RNase HII) {Arch 4e-29
d1ekea_225 c.55.3.1 (A:) Class II ribonuclease H (RNase HII) {Arch 4e-29
>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

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: Thermotoga maritima [TaxId: 2336]
 Score =  180 bits (458), Expect = 7e-47
 Identities = 87/188 (46%), Positives = 114/188 (60%), Gaps = 4/188 (2%)

Query: 20  EKNMWPVAGIDEVGRGALAGPVVVAAIILDPNNIPFGINDSKKISHKKREELYEKITSSA 79
           +K    VAG+DE GRG LAGPVV AA++L+      GINDSK++S  KRE L ++I   A
Sbjct: 8   KKEFGIVAGVDEAGRGCLAGPVVAAAVVLEKEIE--GINDSKQLSPAKRERLLDEIMEKA 65

Query: 80  IISISSASHQYIDKHNIHKATLDAIYHAVENLQVIPRSALIDGRSIPEDLPCQAFAVIKG 139
            + I  AS + ID +NI  AT  A+  A+ENL V P   L+DG+ I   +P     ++KG
Sbjct: 66  AVGIGIASPEEIDLYNIFNATKLAMNRALENLSVKPSFVLVDGKGIELSVPGTC--LVKG 123

Query: 140 DSISLSIAAASIIAKVTRDRLMRIAHKKYPDYGFDSHVGYPTAKHQQVIKEKGPSCIHRL 199
           D  S  I AASI+AKV RDRLM   H+ YP + F  H GY T +H   I++ G   IHRL
Sbjct: 124 DQKSKLIGAASIVAKVFRDRLMSEFHRMYPQFSFHKHKGYATKEHLNEIRKNGVLPIHRL 183

Query: 200 TFRPLRNL 207
           +F P+  L
Sbjct: 184 SFEPVLEL 191


>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
>d1ekea_ c.55.3.1 (A:) Class II ribonuclease H (RNase HII) {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 225 Back     information, alignment and structure

Homologous Domains in SCOP70 (Version 1.75) Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target209 ribonuclease HII [Candidatus Liberibacter asiaticus str
d2etja1221 Class II ribonuclease H (RNase HII) {Thermotoga maritim 100.0
d1uaxa_211 Class II ribonuclease H (RNase HII) {Archaeon Pyrococcu 100.0
d1io2a_213 Class II ribonuclease H (RNase HII) {Archaeon Thermococ 100.0
d1i39a_200 Class II ribonuclease H (RNase HII) {Archaeon Archaeogl 100.0
d1ekea_225 Class II ribonuclease H (RNase HII) {Archaeon Methanoco 100.0
>d2etja1 c.55.3.1 (A:1-221) Class II ribonuclease H (RNase HII) {Thermotoga maritima [TaxId: 2336]} 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: Thermotoga maritima [TaxId: 2336]
Probab=100.00  E-value=0  Score=430.07  Aligned_cols=188  Identities=46%  Similarity=0.664  Sum_probs=178.9

Q ss_pred             HHHHCCCCEEEEEECCCCCCCCCCEEEEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEEEECCCHHHHHHHCH
Q ss_conf             99977994899984278777522255999998701082331152028999998755211012307885156799852047
Q gi|254781076|r   17 MVREKNMWPVAGIDEVGRGALAGPVVVAAIILDPNNIPFGINDSKKISHKKREELYEKITSSAIISISSASHQYIDKHNI   96 (209)
Q Consensus        17 ~l~~~~~~~IiGvDEaGRG~~~GPlvvaav~~~~~~~~~~i~DSK~Ls~~~R~~l~~~i~~~~~~~i~~~~~~eID~~ni   96 (209)
                      .|+++|+.+|||||||||||++||||+|||+++++.  .|++|||+||+++|++++..|++.+.|++++++++|||++||
T Consensus         5 ~l~~~~~~~iiGiDEAGRGpv~GPmVvaav~~~~~~--~gv~DSK~Lt~~kR~~l~~~i~~~~~~~i~~~~~~eid~~ni   82 (221)
T d2etja1           5 ELYKKEFGIVAGVDEAGRGCLAGPVVAAAVVLEKEI--EGINDSKQLSPAKRERLLDEIMEKAAVGIGIASPEEIDLYNI   82 (221)
T ss_dssp             GGGTTTSSSEEEEEEECTTCSBSCEEEEEEEECSCC--C----------CHHHHHHHHHHHHEEEEEEEECHHHHHHHCH
T ss_pred             HHHHCCCCEEEEECCCCCCCCCCCEEEEEEEECCCC--CHHHHHCCCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHCCH
T ss_conf             998769977998637887874132468999977986--521563039999998875532203415998565548775292


Q ss_pred             HHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf             99988654321002575321101265322466212268711478652002366665477589999999887779881028
Q gi|254781076|r   97 HKATLDAIYHAVENLQVIPRSALIDGRSIPEDLPCQAFAVIKGDSISLSIAAASIIAKVTRDRLMRIAHKKYPDYGFDSH  176 (209)
Q Consensus        97 ~~A~~~a~~~ai~~l~~~~~~ilIDg~~~~~~~~~~~~~i~KgD~~~~~VaaASIiAKv~RD~~m~~l~~~~p~Ygf~~n  176 (209)
                      ++|+.+||.+++.+|...++.+++||+.++  .+.++.+++|||++|++||||||+|||+||++|.+|++.||+|||+.|
T Consensus        83 ~~a~~~a~~~ai~~l~~~~~~~~~D~~~~~--~~~~~~~~~KaD~~~~~VaAASIiAKv~RD~~m~~l~~~~p~yg~~~~  160 (221)
T d2etja1          83 FNATKLAMNRALENLSVKPSFVLVDGKGIE--LSVPGTCLVKGDQKSKLIGAASIVAKVFRDRLMSEFHRMYPQFSFHKH  160 (221)
T ss_dssp             HHHHHHHHHHHHHHSSSCCSEEEEESSSCC--CSSCEEEETTHHHHCHHHHHHHHHHHHHHHHHHHHHHHHCTTSCHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCCCCC--CCCCCEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC
T ss_conf             778999999999975222200003466778--888733577487432110388899999999999999987889987358


Q ss_pred             CCCCCHHHHHHHHHCCCCCCCCCCHHHHHHHC
Q ss_conf             99999899999998285830107848886403
Q gi|254781076|r  177 VGYPTAKHQQVIKEKGPSCIHRLTFRPLRNLS  208 (209)
Q Consensus       177 kGYgT~~H~~ai~~~G~~~~HR~Sf~~vk~l~  208 (209)
                      +||||++|+++|+++|++++||+||+||++|-
T Consensus       161 sGY~T~~h~~ai~~~G~~~~hR~Sw~tvk~~l  192 (221)
T d2etja1         161 KGYATKEHLNEIRKNGVLPIHRLSFEPVLELL  192 (221)
T ss_dssp             TTCCCHHHHHHHHHHCCCTTBCTTSHHHHTTC
T ss_pred             CCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHH
T ss_conf             68796999999998680903328829899986



>d1uaxa_ c.55.3.1 (A:) Class II ribonuclease H (RNase HII) {Archaeon Pyrococcus horikoshii [TaxId: 53953]} Back     information, alignment and structure
>d1io2a_ c.55.3.1 (A:) Class II ribonuclease H (RNase HII) {Archaeon Thermococcus kodakaraensis [TaxId: 311400]} 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

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 209 ribonuclease HII [Candidatus Liberibacter asiaticu
2etj_A_1-171171 (A:1-171) Ribonuclease HII, RNAse HII; TM0915, rib 1e-46
1i39_A_1-182182 (A:1-182) Ribonuclease HII, RNAse HII; mixed beta 5e-45
1io2_A_1-168168 (A:1-168) Ribonuclease HII; endonuclease, hydrolas 1e-41
3kio_A_1-208208 (A:1-208) Ribonuclease H2 subunit A; aicardi-gouti 2e-40
1uax_A_1-168168 (A:1-168) Ribonuclease HII, ribonuclease H2; RNA*D 2e-40
1eke_A_1-180180 (A:1-180) Ribonuclease HII; endonuclease, structur 1e-38
2d0b_A_83-265183 (A:83-265) RNAse HIII, ribonuclease HIII; RNA/DNA 5e-38
2etj_A_172-25079 (A:172-250) Ribonuclease HII, RNAse HII; TM0915, r 1e-07
>2etj_A (A:1-171) Ribonuclease HII, RNAse HII; TM0915, ribonuclease HII (EC 3.1.26.4) (RNAse HII), structural genomics, joint center for structural genomics; 1.74A {Thermotoga maritima}Length = 171 Back     alignment and structure
 Score =  180 bits (459), Expect = 1e-46
 Identities = 73/166 (43%), Positives = 95/166 (57%), Gaps = 4/166 (2%)

Query: 9   RPHFELEAMVREKNMWPVAGIDEVGRGALAGPVVVAAIILDPNNIPFGINDSKKISHKKR 68
             H      + +K    VAG+DE GRG LAGPVV AA++L+      GINDSK++S  KR
Sbjct: 9   HHHHXGIDELYKKEFGIVAGVDEAGRGCLAGPVVAAAVVLEKE--IEGINDSKQLSPAKR 66

Query: 69  EELYEKITSSAIISISSASHQYIDKHNIHKATLDAIYHAVENLQVIPRSALIDGRSIPED 128
           E L ++I   A + I  AS + ID +NI  AT  A   A+ENL V P   L+DG+ I   
Sbjct: 67  ERLLDEIXEKAAVGIGIASPEEIDLYNIFNATKLAXNRALENLSVKPSFVLVDGKGIELS 126

Query: 129 LPCQAFAVIKGDSISLSIAAASIIAKVTRDRLMRIAHKKYPDYGFD 174
           +P     ++KGD  S  I AASI+AKV RDRL    H+ YP + F 
Sbjct: 127 VPGT--CLVKGDQKSKLIGAASIVAKVFRDRLXSEFHRXYPQFSFH 170


>1i39_A (A:1-182) Ribonuclease HII, RNAse HII; mixed beta sheet, helix-loop-helix, hydrolase; 1.95A {Archaeoglobus fulgidus}Length = 182 Back     alignment and structure
>1io2_A (A:1-168) Ribonuclease HII; endonuclease, hydrolase; 2.00A {Thermococcus kodakarensis KOD1}Length = 168 Back     alignment and structure
>3kio_A (A:1-208) Ribonuclease H2 subunit A; aicardi-goutieres syndrome, RNAse H2, protein complex, autoimmune disease, endonuclease, hydrolase, metal-binding; 2.90A {Mus musculus}Length = 208 Back     alignment and structure
>1uax_A (A:1-168) Ribonuclease HII, ribonuclease H2; RNA*DNA hybrid ribonucleotidohydrolase; 2.00A {Pyrococcus horikoshii OT3}Length = 168 Back     alignment and structure
>1eke_A (A:1-180) Ribonuclease HII; endonuclease, structural genomics, BSGC structure funded by NIH, protein structure initiative, PSI; HET: MES; 2.00A {Methanocaldococcus jannaschii}Length = 180 Back     alignment and structure
>2d0b_A (A:83-265) RNAse HIII, ribonuclease HIII; RNA/DNA hybrid, hydrolase; 2.10A {Geobacillus stearothermophilus} PDB: 2d0a_A 2d0c_ALength = 183 Back     alignment and structure
>2etj_A (A:172-250) Ribonuclease HII, RNAse HII; TM0915, ribonuclease HII (EC 3.1.26.4) (RNAse HII), structural genomics, joint center for structural genomics; 1.74A {Thermotoga maritima}Length = 79 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target209 ribonuclease HII [Candidatus Liberibacter asiaticus str
2etj_A_1-171171 Ribonuclease HII, RNAse HII; TM0915, ribonuclease 100.0
1i39_A_1-182182 Ribonuclease HII, RNAse HII; mixed beta sheet, hel 100.0
3kio_A_1-208208 Ribonuclease H2 subunit A; aicardi-goutieres syndr 100.0
1io2_A_1-168168 Ribonuclease HII; endonuclease, hydrolase; 2.00A { 100.0
1uax_A_1-168168 Ribonuclease HII, ribonuclease H2; RNA*DNA hybrid 100.0
1eke_A_1-180180 Ribonuclease HII; endonuclease, structural genomic 100.0
2d0b_A_83-265183 RNAse HIII, ribonuclease HIII; RNA/DNA hybrid, hyd 100.0
2etj_A_172-25079 Ribonuclease HII, RNAse HII; TM0915, ribonuclease 99.09
>2etj_A (A:1-171) Ribonuclease HII, RNAse HII; TM0915, ribonuclease HII (EC 3.1.26.4) (RNAse HII), structural genomics, joint center for structural genomics; 1.74A {Thermotoga maritima} Back     alignment and structure
Probab=100.00  E-value=0  Score=333.37  Aligned_cols=164  Identities=44%  Similarity=0.589  Sum_probs=154.5

Q ss_pred             CCCCHHHHHHHHHCCCCEEEEEECCCCCCCCCCEEEEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             88688899999977994899984278777522255999998701082331152028999998755211012307885156
Q gi|254781076|r    8 ERPHFELEAMVREKNMWPVAGIDEVGRGALAGPVVVAAIILDPNNIPFGINDSKKISHKKREELYEKITSSAIISISSAS   87 (209)
Q Consensus         8 ~~p~~~~E~~l~~~~~~~IiGvDEaGRG~~~GPlvvaav~~~~~~~~~~i~DSK~Ls~~~R~~l~~~i~~~~~~~i~~~~   87 (209)
                      ..|.+.+|+.++..++.+++|+|||||||+|||||+|||+++.+.  .|++|||+||+++|++|++.|++.+.|++.+++
T Consensus         8 ~~~~~~~~~~~~~~~~~~viGiDEaGrG~~~GPlvvaav~~~~~~--~gi~DSK~Ls~~~r~~l~~~I~~~~~~~v~~i~   85 (171)
T 2etj_A            8 HHHHHXGIDELYKKEFGIVAGVDEAGRGCLAGPVVAAAVVLEKEI--EGINDSKQLSPAKRERLLDEIXEKAAVGIGIAS   85 (171)
T ss_dssp             -----CCGGGGGTTTSSSEEEEEEECTTCSBSCEEEEEEEECSCC--C----------CHHHHHHHHHHHHEEEEEEEEC
T ss_pred             HHHCCCCHHHHHHCCCCEEEEECCCCCCCCCCCEEEEEEEECCCC--CCCCCCCCCCHHHHHHHHHHCCCCCCEEEEECC
T ss_conf             110246699999769977998637787885253689999977887--756411029989999876412245416999577


Q ss_pred             HHHHHHHCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             79985204799988654321002575321101265322466212268711478652002366665477589999999887
Q gi|254781076|r   88 HQYIDKHNIHKATLDAIYHAVENLQVIPRSALIDGRSIPEDLPCQAFAVIKGDSISLSIAAASIIAKVTRDRLMRIAHKK  167 (209)
Q Consensus        88 ~~eID~~ni~~A~~~a~~~ai~~l~~~~~~ilIDg~~~~~~~~~~~~~i~KgD~~~~~VaaASIiAKv~RD~~m~~l~~~  167 (209)
                      |++||++||++++..+|.+++.++..+++.++||++..+.  ++++.+++|||+++++||||||||||+||++|..|++.
T Consensus        86 p~~id~~ni~~~~~~~~~~~i~~l~~~~~~v~iD~~~~~~--~~~~~~~~KaD~~~~~VaaASIiAKv~RD~~m~~l~~~  163 (171)
T 2etj_A           86 PEEIDLYNIFNATKLAXNRALENLSVKPSFVLVDGKGIEL--SVPGTCLVKGDQKSKLIGAASIVAKVFRDRLXSEFHRX  163 (171)
T ss_dssp             HHHHHHHCHHHHHHHHHHHHHHHSSSCCSEEEEESSSCCC--SSCEEEETTHHHHCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC--CCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             8999870938899999999999534210100135777789--97856787788665400577778889999999999997


Q ss_pred             CCCCCCCC
Q ss_conf             77988102
Q gi|254781076|r  168 YPDYGFDS  175 (209)
Q Consensus       168 ~p~Ygf~~  175 (209)
                      ||+|||++
T Consensus       164 yp~ygf~k  171 (171)
T 2etj_A          164 YPQFSFHK  171 (171)
T ss_dssp             CTTSCHHH
T ss_pred             CCCCCCCC
T ss_conf             87889846



>1i39_A (A:1-182) Ribonuclease HII, RNAse HII; mixed beta sheet, helix-loop-helix, hydrolase; 1.95A {Archaeoglobus fulgidus} Back     alignment and structure
>3kio_A (A:1-208) Ribonuclease H2 subunit A; aicardi-goutieres syndrome, RNAse H2, protein complex, autoimmune disease, endonuclease, hydrolase, metal-binding; 2.90A {Mus musculus} Back     alignment and structure
>1io2_A (A:1-168) Ribonuclease HII; endonuclease, hydrolase; 2.00A {Thermococcus kodakarensis KOD1} Back     alignment and structure
>1uax_A (A:1-168) Ribonuclease HII, ribonuclease H2; RNA*DNA hybrid ribonucleotidohydrolase; 2.00A {Pyrococcus horikoshii OT3} Back     alignment and structure
>1eke_A (A:1-180) Ribonuclease HII; endonuclease, structural genomics, BSGC structure funded by NIH, protein structure initiative, PSI; HET: MES; 2.00A {Methanocaldococcus jannaschii} Back     alignment and structure
>2d0b_A (A:83-265) RNAse HIII, ribonuclease HIII; RNA/DNA hybrid, hydrolase; 2.10A {Geobacillus stearothermophilus} PDB: 2d0a_A 2d0c_A Back     alignment and structure
>2etj_A (A:172-250) Ribonuclease HII, RNAse HII; TM0915, ribonuclease HII (EC 3.1.26.4) (RNAse HII), structural genomics, joint center for structural genomics; 1.74A {Thermotoga maritima} Back     alignment and structure