Psyllid ID: psy3058

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240----
Protein Sequence
MSTYRLNSLSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLFCKNILIHDIQVACHKLILKGNNVKIIWIPSHCGIAGNEEVDKAAQSFINAQNYSLITHVDLKAFLKNEFKKKWQIWWDNIQPPNKIKDTVKEWQTSNRNSRKEEIILSRLRIGHTRLTHGFLMERTDPPQCEVCNVTITVKHILCHCTKYTQIRLKYNLNNLQIKDILGDNPRTIDLLFRFLKDSNLLPKL
Secondary Structure (PSIPRED)
ccEEcccccccHHHHHHHHHHHHHHHHHHccccccEEEEEccHHHHHHHHHHccccHHHHHHHHHHHHHHHcccEEEEEEEEccccccccHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccHHHHHHHHHHHHccccccccccccccccccccccccccccHHHHccccccHHHHHHcccccHHHHHHccccHHHHHHHHHHHHHccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccHHHHHHHHHHHHHHHHHHccccccEEEEEccHHHHHHHHccccccHHHHHHHHHHHHHHHcccEEEEEEEcccccccccHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccHHHHHHHHHHHHccccccHHHHcccccccccHcccccccEEEEEEccHHHHHHHHHHccccccHHHHHcccHHHHHHHHHHHHHcccHccc
Coil and Loop (DISEMBL)
mstyrlnslsssFTAEAFAMEMCLDnlinrpipdniliFTDSKSLISSMQQLFCKNILIHDIQVACHKLILkgnnvkiiwipshcgiagneEVDKAAQSFINAQNYSLITHVDLKAFLKNEFKKKWQIWwdniqppnkikDTVKEWQTSNRNSRKEEIILSRLRIGhtrlthgflmertdppqcevcnvtITVKHILCHCTKYTQIRLKYNLnnlqikdilgdnprTIDLLFRFLkdsnllpkl
Flexible Loop (DISEMBL)
mstyrlnslssSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLFCKNILIHDIQVACHKLILKGNNVKIIWIPSHCGIAGNEEVDKAAQSFINAQNYSLITHVDLKAFLKNEFKKKWQiwwdniqppnkikdtvkewqtsnrnsrkeeiilsrlriGHTRLThgflmertdppqCEVCNVTITVKHILCHCTKYTQIRLKYNLNNLQIKDILGDNPRTIDLLFrflkdsnllpkl
Low Complexity Region (SEG)
MSTYRLNSLSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLFCKNILIHDIQVACHKLILKGNNVKIIWIPSHCGIAGNEEVDKAAQSFINAQNYSLITHVDLKAFLKNEFKKKWQIWWDNIQPPNKIKDTVKEWQTSNRNSRKEEIILSRLRIGHTRLTHGFLMERTDPPQCEVCNVTITVKHILCHCTKYTQIRLKYNLNNLQIKDILGDNPRTIDLLFRFLKDSNLLPKL
Disordered region (IsUnstruct)
************FTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLFCKNILIHDIQVACHKLILKGNNVKIIWIPSHCGIAGNEEVDKAAQSFINAQNYSLITHVDLKAFLKNEFKKKWQIWWDNIQPPNKIKDTVK************EIILSRLRIGHTRLTHGFLMERTDPPQCEVCNVTITVKHILCHCTKYTQIRLKYNLNNLQIKDILGDNPRTIDLLFRFLKD*******
Disordered Region (DISOPRED)
*STYRLNSLSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLFCKNILIHDIQVACHKLILKGNNVKIIWIPSHCGIAGNEEVDKAAQSFINAQNYSLITHVDLKAFLKNEFKKKWQIWWDNIQPPNKIKDTVKEWQTSNRNSRKEEIILSRLRIGHTRLTHGFLMERTDPPQCEVCNVTITVKHILCHCTKYTQIRLKYNLNNLQIKDILGDNPRTIDLLFRFLKDSNLLPKL
Disordered Region (DISEMBL)
********LSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLFCKNILIHDIQVACHKLILKGNNVKIIWIPSHCGIAGNEEVDKAAQSFINAQNYSLITHVDLKAFLKNEFKKKWQIWWDNIQPPNKIKDTVKEWQTSNRNSRKEEIILSRLRIGHTRLTHGFLMERTDPPQCEVCNVTITVKHILCHCTKYTQIRLKYNLNNLQIKDILGDNPRTIDLLFRFLKDSNLLPKL
Disordered Region (DISPRO)
**TYRLNSLSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLFCKNILIHDIQVACHKLILKGNNVKIIWIPSHCGIAGNEEVDKAAQSFINAQNYSLITHVDLKAFLKNEFKKKWQIWWDNIQPPNKIKDTVKEWQTSNRNSRKEEIILSRLRIGHTRLTHGFLMERTDPPQCEVCNVTITVKHILCHCTKYTQIRLKYNLNNLQIKDILGDNPRTIDLLFRFLKDSNLLPKL
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSTYRLNSLSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLFCKNILIHDIQVACHKLILKGNNVKIIWIPSHCGIAGNEEVDKAAQSFINAQNYSLITHVDLKAFLKNEFKKKWQIWWDNIQPPNKIKDTVKEWQTSNRNSRKEEIILSRLRIGHTRLTHGFLMERTDPPQCEVCNVTITVKHILCHCTKYTQIRLKYNLNNLQIKDILGDNPRTIDLLFRFLKDSNLLPKL
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

No hits with e-value below 0.001 by BLAST

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	244
328720146	164	PREDICTED: hypothetical protein LOC10056	0.631	0.939	0.431	8e-27
125901787	1222	pol-like protein [Biomphalaria glabrata]	0.885	0.176	0.313	4e-24
6635955	1208	pol-like protein [Aedes aegypti]	0.934	0.188	0.299	5e-24
427791063	1035	Putative tick transposon, partial [Rhipi	0.831	0.196	0.355	8e-24
443712830	397	hypothetical protein CAPTEDRAFT_202466 [	0.946	0.581	0.325	9e-23
443693558	502	hypothetical protein CAPTEDRAFT_189741,	0.856	0.416	0.345	3e-22
443695973	261	hypothetical protein CAPTEDRAFT_23017, p	0.811	0.758	0.342	2e-21
427778603	1397	Putative tick transposon [Rhipicephalus	0.827	0.144	0.331	6e-21
443730613	233	hypothetical protein CAPTEDRAFT_206814 [	0.614	0.643	0.352	4e-20
443733872	400	hypothetical protein CAPTEDRAFT_197082 [	0.561	0.342	0.380	6e-20

>gi|328720146|ref|XP_003246964.1| PREDICTED: hypothetical protein LOC100568990, partial [Acyrthosiphon pisum]

 Score =  126 bits (316), Expect = 8e-27,   Method: Compositional matrix adjust.
 Identities = 69/160 (43%), Positives = 98/160 (61%), Gaps = 6/160 (3%)

Query: 73  GNNVKIIWIPSHCGIAGNEEVDKAAQSFINAQNYSLI---THVDLKAFLKNEFKKKWQIW 129
           G ++  +W P HCGI GNE+ D  A    ++ +  L+   T+ D K  +K    +KW I 
Sbjct: 2   GMDICYMWAPGHCGIQGNEKADLEASKAASSPDTPLLNIYTYEDKKKQIKQVLDQKWLIQ 61

Query: 130 WDNIQPP-NKIKDTVKEWQTSNRNSRKEEIILSRLRIGHTRLTHGFLMERTDPPQCEVCN 188
           W N     N+IK+ ++ W+    N RKEE IL+RLRIGHT +TH  LME+ DPP CE+C 
Sbjct: 62  WINQHTKLNQIKNNIQTWKNPGLN-RKEETILNRLRIGHTFITHRHLMEKNDPPICEMCG 120

Query: 189 VTITVKHILCHCTKYTQIRLKYNLNNLQIKDILGDNPRTI 228
           V +TVKHI+  C KY  +R KYN++  QI + LG + ++I
Sbjct: 121 VDLTVKHIITECRKYDDMRKKYNISQ-QIGEALGPDTQSI 159

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|125901787|gb|ABN58714.1| pol-like protein [Biomphalaria glabrata]

 Score =  117 bits (293), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 72/230 (31%), Positives = 122/230 (53%), Gaps = 14/230 (6%)

Query: 5    RLNSLSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLFCKNILIHDIQV 64
            RL    S FTAE  A+ + L   +        +I +DSKS + ++ ++     L+H    
Sbjct: 984  RLPDGCSIFTAELHAILLAL-MAVKASERSKFIICSDSKSALQALGRMKTDIPLVHKSLK 1042

Query: 65   ACHKLILKGNNVKIIWIPSHCGIAGNEEVDKAAQSFIN-AQNYSLITHVDLKAFLKNEFK 123
                +     +V  IW+PSH GI GNE  D+ A+  +N A + + I + DL+  + +   
Sbjct: 1043 LLDLITADRRDVTFIWVPSHVGIEGNEAADREAKRALNHAVSGTQIPYSDLRQSIASATY 1102

Query: 124  KKWQIWWDNIQPPNKIKDTVKE--WQTSNRN-SRKEEIILSRLRIGHTRLTHGFLMERTD 180
            ++WQ  W+  +  +K++  V +  W+ +++  +R+    +SRLRIGHT +TH F+++R +
Sbjct: 1103 REWQNRWE-AETHSKLRQIVADVRWRPTSKGLTRRGSTTMSRLRIGHTYITHSFVLKREE 1161

Query: 181  PPQCEVCNVTITVKHILCHCTKYTQIR--------LKYNLNNLQIKDILG 222
            PP CE C+  +TV+HIL  C +Y  +R        LK   NN+    +LG
Sbjct: 1162 PPLCEYCDSRLTVEHILVDCPRYQDVRAKHFRATNLKTLFNNVDPGKVLG 1211

Source: Biomphalaria glabrata

Species: Biomphalaria glabrata

Genus: Biomphalaria

Family: Planorbidae

Class: Gastropoda

Phylum: Mollusca

Superkingdom: Eukaryota

>gi|6635955|gb|AAF20019.1|AF134900_2 pol-like protein [Aedes aegypti]

 Score =  117 bits (292), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 73/244 (29%), Positives = 126/244 (51%), Gaps = 16/244 (6%)

Query: 4    YRLNSLSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLFCKNILIHDIQ 63
            YRL    S F+AEA A+ +        P P  I + +DS S+++++     ++  I  +Q
Sbjct: 978  YRLPDQCSVFSAEAAAILLASTT----PAPKPICVISDSASVLATINSSSTRHPWIQAVQ 1033

Query: 64   VACHKLILKGNNVKIIWIPSHCGIAGNEEVDKAAQSFINAQNYSLIT-HVDLKAFLKNEF 122
                      +    +W+P HCGI GN E D  A    + + ++ +T  +DLK + K++ 
Sbjct: 1034 KNS------PSQTVFLWVPGHCGIRGNVEADHLASKGRSGRLFTRLTPGMDLKNWTKSQI 1087

Query: 123  KKKWQIWWDNIQPP--NKIKDTVKEWQTSNRNSRKEEIILSRLRIGHTRLTHGFLMERTD 180
            +  W + W N++     KIK   K W  +N  +R+++ +LSRLR GHT  TH    ER  
Sbjct: 1088 RSSWALEWVNLRDKFIRKIKGETKRWIDTN--NRRDQQVLSRLRTGHTHATHNMGNERPF 1145

Query: 181  PPQCEVCNVTITVKHILCHCTKYTQIRLKYNLNNLQIKDILGDNPRTIDLLFRFLKDSNL 240
              +C VCN T++V+H++ +C  +   R ++N+ +  I+D L +   +   +  F KD+ L
Sbjct: 1146 RKKCIVCNTTMSVEHMIINCPCFQAPRERHNIPD-SIRDALSNEASSEAAIISFFKDAGL 1204

Query: 241  LPKL 244
              K+
Sbjct: 1205 YNKI 1208

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|427791063|gb|JAA60983.1| Putative tick transposon, partial [Rhipicephalus pulchellus]

 Score =  116 bits (291), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 76/214 (35%), Positives = 115/214 (53%), Gaps = 11/214 (5%)

Query: 6    LNSLSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQL--FCKNILIHDIQ 63
            L+  +S FTAEA+A+ + + ++    +P  + I+TDS S++ +++ L      +L     
Sbjct: 824  LHQNTSIFTAEAYAIFVAVKHIEQLKLPSAV-IYTDSLSVVKALKTLKKHKNPVLASLYS 882

Query: 64   VACHKLILKGNNVKIIWIPSHCGIAGNEEVDKAAQSFIN--AQNYSLITHVDLKAFLKNE 121
            + C    LK  +V + W+P H  I GN   D+ A S     A  +  I  +DLK  LK +
Sbjct: 883  LLCTVYALK-QHVVVCWVPGHREIQGNVLADQLAASAHENAAHTFLAIPALDLKPLLKRK 941

Query: 122  FKKKWQIWWDNIQPPNK---IKDTVKEWQTSNRNSRKEEIILSRLRIGHTRLTHGFLMER 178
             +  WQ  WD  Q  NK   IK  + EW  +++ SR+ EI L+RLR GHT  TH +L+  
Sbjct: 942  LRAYWQSIWDT-QTQNKLHAIKPQLGEWPPASK-SRRTEITLTRLRTGHTHTTHAYLLSG 999

Query: 179  TDPPQCEVCNVTITVKHILCHCTKYTQIRLKYNL 212
             DPP+CE C   +TV HIL  C +   +R K+ L
Sbjct: 1000 NDPPRCERCGEPLTVLHILIQCNELDAMRRKHFL 1033

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|443712830|gb|ELU05953.1| hypothetical protein CAPTEDRAFT_202466 [Capitella teleta]

 Score =  113 bits (282), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 81/249 (32%), Positives = 122/249 (48%), Gaps = 18/249 (7%)

Query: 2   STYR----LNSLSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLFCKNI 57
           STY+    L +  S +TAE  A+E  L  +      D   I +DS S ++++      + 
Sbjct: 151 STYQIQFGLPAQMSIYTAELIAIEQALIFIETVKDEDQFNICSDSLSSLTALSNCDITHP 210

Query: 58  LIHDIQVACHKLILKGNNVKIIWIPSHCGIAGNEEVDKAA-QSFINAQNYSLITHVDLKA 116
            +  I    + L+ KG  V  IW PSH GI GNE  D+ A Q+ +       + H D K+
Sbjct: 211 YLLSILTKQNNLVRKGKKVVFIWCPSHVGILGNEVADRQAKQALVMPVTKLPLPHTDYKS 270

Query: 117 FLKNEFKKKWQIWWDNIQPPNK---IKDTVKEWQTSNRNSRKEEIILSRLRIGHTRLTHG 173
            +++  K  WQ  WD  +  NK   I+  + EW+   +  R+ EI+L+  RIGH+ LTHG
Sbjct: 271 PIRSYVKSLWQNEWDG-ETDNKLHIIQPVISEWKQGPQIDRRGEIVLACARIGHSHLTHG 329

Query: 174 FLMERTDPPQCEVCNVTITVKHILCHCTKYTQIRLKYNLNNLQIKDILGD-NP------- 225
           +L+ R   P C  C   +TVKHIL  C  +   R KY  N   ++ +  D +P       
Sbjct: 330 YLLRREVAPFCIPCQSLLTVKHILIDCIDFEISRRKY-FNVFSMRQLFEDTHPSKILLYL 388

Query: 226 RTIDLLFRF 234
           + I L +RF
Sbjct: 389 KEIGLFYRF 397

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|443693558|gb|ELT94903.1| hypothetical protein CAPTEDRAFT_189741, partial [Capitella teleta]

 Score =  110 bits (276), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 77/223 (34%), Positives = 112/223 (50%), Gaps = 14/223 (6%)

Query: 2   STYR----LNSLSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLFCKNI 57
           STY+    L +  S +TAE  A+E  L  +      D   I +DS S ++++      + 
Sbjct: 102 STYQIQFGLPTQMSIYTAELIAIEQALIFIETVKDEDQFNICSDSLSSLTALSNCDITHP 161

Query: 58  LIHDIQVACHKLILKGNNVKIIWIPSHCGIAGNEEVDK-AAQSFINAQNYSLITHVDLKA 116
            +  I    + L+ KG  V  IW PSH GI GNE  D+ A Q+ +       + H D K+
Sbjct: 162 YLLSILTKQNNLVRKGKLVVFIWCPSHVGILGNEVADRLAKQALVMPVTKLPLPHTDYKS 221

Query: 117 FLKNEFKKKWQIWWDNIQPPNK---IKDTVKEWQTSNRNSRKEEIILSRLRIGHTRLTHG 173
            +++  K  WQ  WD  +  NK   I+  + EW+   +  R+ EI+L+R RIGH+ LTHG
Sbjct: 222 PIRSYVKSLWQNEWDE-ETDNKLHSIQPVISEWKQGPQIDRRGEIVLARARIGHSHLTHG 280

Query: 174 FLMERTDPPQCEVCNVTITVKHILCHCTKYTQIRLKYNLNNLQ 216
           +L+ R   P C  C   +TVKHIL  C     I  K +L  LQ
Sbjct: 281 YLLRREVAPFCIPCQSLLTVKHILIDC-----IDFKMSLTYLQ 318

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|443695973|gb|ELT96755.1| hypothetical protein CAPTEDRAFT_23017, partial [Capitella teleta]

 Score =  108 bits (270), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 71/207 (34%), Positives = 106/207 (51%), Gaps = 9/207 (4%)

Query: 2   STYR----LNSLSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLFCKNI 57
           STY+    L +  S +TAE  A+E  L  +      D   I +DS S ++++      + 
Sbjct: 56  STYQIQFGLPAQMSIYTAELIAIEQALIFIETVKDEDQFNICSDSLSSLTALSNCDITHP 115

Query: 58  LIHDIQVACHKLILKGNNVKIIWIPSHCGIAGNEEVDK-AAQSFINAQNYSLITHVDLKA 116
            +  I    + L+ KG  V  IW PSH GI GNE  D+ A Q+ +       + H D K+
Sbjct: 116 YLLSILTKQNNLVRKGKLVVFIWCPSHVGILGNEVADRLAKQALVMPVTKLPLPHTDYKS 175

Query: 117 FLKNEFKKKWQIWWDNIQPPNK---IKDTVKEWQTSNRNSRKEEIILSRLRIGHTRLTHG 173
            +++  K  WQ  WD  +  NK   I+  + EW+   +  R+ EI+L+R RIGH+ LTHG
Sbjct: 176 PIRSYVKSLWQNEWDE-ETDNKLHSIQPVISEWKQGPQIDRRGEIVLARARIGHSHLTHG 234

Query: 174 FLMERTDPPQCEVCNVTITVKHILCHC 200
           +L+ R   P C  C   ++VKHIL  C
Sbjct: 235 YLLRREVAPFCIPCQSLLSVKHILIDC 261

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|427778603|gb|JAA54753.1| Putative tick transposon [Rhipicephalus pulchellus]

 Score =  107 bits (266), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 70/211 (33%), Positives = 114/211 (54%), Gaps = 9/211 (4%)

Query: 6    LNSLSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLFC-KNILIHDIQV 64
            L++ +S FTAEA+ + + ++++    I  +I I+TDS S+++++    C KN + + +  
Sbjct: 1137 LHAHTSIFTAEAYGILLIVEHIKQHMIRRSI-IYTDSLSVVTALSCGKCSKNPVFNKLLN 1195

Query: 65   ACHKLILKGNNVKIIWIPSHCGIAGNEEVDKAAQSFINAQ--NYSLITHVDLKAFLKNEF 122
              H+   +  ++ + W+P H GI GNE VDK A+   +    + S +  VDL   ++   
Sbjct: 1196 NMHEAYNQNLSIVLCWVPGHAGITGNEMVDKNAREAASRHTIDISSVPGVDLNPVVRRGL 1255

Query: 123  KKKWQIWWDNIQPPNK---IKDTVKEWQTSNRNSRKEEIILSRLRIGHTRLTHGFLMERT 179
            +  WQ+ WD  Q  NK   +K  + +      N R  E+ L+RLRIGHT  TH  L+  T
Sbjct: 1256 RSHWQVEWDK-QVDNKLHLVKPHLSKVLPQKLN-RFTEVTLARLRIGHTYATHKHLLTGT 1313

Query: 180  DPPQCEVCNVTITVKHILCHCTKYTQIRLKY 210
            DPP C  C  T+T+ H+L  C    Q RL +
Sbjct: 1314 DPPTCIHCGETLTILHVLIECPGLHQERLTH 1344

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|443730613|gb|ELU16038.1| hypothetical protein CAPTEDRAFT_206814 [Capitella teleta]

 Score =  103 bits (258), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 55/156 (35%), Positives = 88/156 (56%), Gaps = 6/156 (3%)

Query: 72  KGNNVKIIWIPSHCGIAGNEEVDKAAQSFINAQNYSL-ITHVDLKAFLKNEFKKKWQIWW 130
           +G ++ I+W PSH G+ GNE  D  A+  ++     + I   D  +   + ++ KWQ  W
Sbjct: 77  RGFDLVILWCPSHIGVVGNERADLLAKEALSFTACDVRIPAFDFNSVAYSFYRDKWQALW 136

Query: 131 DNIQPPNK---IKDTVKEWQTSNRNSRKEEIILSRLRIGHTRLTHGFLMERTDPPQCEVC 187
            +++  NK   ++  +K+   S+R  R++EI+L+R RIGHT LTHG+L+ R  PP C  C
Sbjct: 137 -SLEQNNKLHSVQPIIKKLTNSSREDRRKEIVLARARIGHTHLTHGYLLRRELPPFCVHC 195

Query: 188 NVTITVKHILCHCTKYTQIRLKYNLNNLQIKDILGD 223
              +TVKHIL  C  +   R +Y  + L IK +  +
Sbjct: 196 QCPLTVKHILIECVDFYLHRQRY-FDVLSIKRLFEE 230

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|443733872|gb|ELU18078.1| hypothetical protein CAPTEDRAFT_197082 [Capitella teleta]

 Score =  103 bits (257), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 54/142 (38%), Positives = 80/142 (56%), Gaps = 5/142 (3%)

Query: 66  CHKLILKGNNVKIIWIPSHCGIAGNEEVDKAAQSFINAQNYSL-ITHVDLKAFLKNEFKK 124
           C  L  KG ++ + W PSH G+ GNE  D  A+  ++    ++ I   D K      +K+
Sbjct: 91  CTLLHKKGIDLVMTWCPSHVGVMGNERADLLAKEALSFTTCTIRIPSSDFKPITHEFYKE 150

Query: 125 KWQIWWDNIQPPNK---IKDTVKEWQTSNRNSRKEEIILSRLRIGHTRLTHGFLMERTDP 181
           KWQ  W + Q  NK   I+ T+ +W  S+R  R+EEI+L+R RIGH+ LTHG+L+ R  P
Sbjct: 151 KWQEQWSSEQE-NKLYCIQPTLGKWAKSSREIRREEIVLARARIGHSHLTHGYLLRREMP 209

Query: 182 PQCEVCNVTITVKHILCHCTKY 203
           P C  C   +++KHI   C  +
Sbjct: 210 PVCIPCQNILSIKHIFIECVDF 231

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	244
ASPGD|ASPL0000075333	486	AN10625 [Emericella nidulans (	0.811	0.407	0.231	3.4e-06

ASPGD|ASPL0000075333 AN10625 [Emericella nidulans (taxid:162425)]

 Score = 133 (51.9 bits), Expect = 3.4e-06, P = 3.4e-06
 Identities = 50/216 (23%), Positives = 97/216 (44%)

Query:     8 SLSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLFCKN--ILIHDIQVA 65
             S S+ + AE   + + L  ++ R +  + +IFTD+++ + +++    ++   ++  I +A
Sbjct:   217 SESTVYVAELQGILLALVIILQRQM-QHAVIFTDNQATLQALRNPGSQSGQYILEAIIMA 275

Query:    66 CHKLILKGNNVKIIWIPSHCGIAGNEEVDKAAQSF-----INAQNYSLITHVDLKAFLKN 120
              +K    G NV   WIP+H G+ GNE+ D+ A+       I      +     +K     
Sbjct:   276 LNKGRKAGLNVHFRWIPAHRGVEGNEQADRRAKEATGWRRIRGHRGRMTIRSAVKRRAHE 335

Query:   121 EFKKKWQIWWDNIQPPNKIKD-----TVKEWQTSNRNSRKEEIILSRLRIGHTRLTHGFL 175
                 +W+  W +     ++ +     T K  +      R    I+ ++R G   L H +L
Sbjct:   336 VVNARWENDWKSCHHGRELYELTPTPTRKVLRVHQDLHRALSTIIVQMRTGKIGLRH-YL 394

Query:   176 MER--TDPPQ--CEVCNVTITVKHILCHCTKYTQIR 207
              +R   D P   C+    T +V+HIL  C  ++ +R
Sbjct:   395 YQRGVPDVPNSDCQCGRATQSVRHILLACPTFSGLR 430


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.323   0.136   0.421    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      244       244   0.00098  113 3  11 22  0.39    33
                                                     32  0.45    36


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  605 (64 KB)
  Total size of DFA:  211 KB (2117 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  21.64u 0.09s 21.73t   Elapsed:  00:00:12
  Total cpu time:  21.64u 0.09s 21.73t   Elapsed:  00:00:13
  Start:  Thu Aug 15 14:35:16 2013   End:  Thu Aug 15 14:35:29 2013

GO:0008150 "biological_process" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.1.26	LOW CONFIDENCE prediction!
3rd Layer	3.1.26.4	LOW CONFIDENCE prediction!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	244
cd09276	128	cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom	9e-22
pfam00075	126	pfam00075, RNase_H, RNase H	5e-13
cd06222	123	cd06222, RNase_H, RNase H is an endonuclease that	7e-07
cd09280	150	cd09280, RNase_HI_eukaryote_like, Eukaryotic RNase	7e-06

>gnl|CDD|187700 cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI domain of reverse transcriptases

 Score = 86.9 bits (216), Expect = 9e-22
 Identities = 29/96 (30%), Positives = 48/96 (50%), Gaps = 1/96 (1%)

Query: 3   TYRLNSLSSSFTAEAFAMEMCLDNLINRPI-PDNILIFTDSKSLISSMQQLFCKNILIHD 61
           +Y+L    S F AE  A+   L   +        I IF+DS++ + +++     + L+  
Sbjct: 28  SYKLGPYCSVFDAELLAILEALQLALREGRRARKITIFSDSQAALKALRSPRSSSPLVLR 87

Query: 62  IQVACHKLILKGNNVKIIWIPSHCGIAGNEEVDKAA 97
           I+ A  +L   G  V++ W+P H GI GNE  D+ A
Sbjct: 88  IRKAIRELANHGVKVRLHWVPGHSGIEGNERADRLA 123

Ribonuclease H (RNase H) is classified into two families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). Ribonuclease HI (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as an adjunct domain to the reverse transcriptase gene in retroviruses, long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamatic acid residue (DEDD), are unvaried across all RNase H domains. The position of the RNase domain of non-LTR and LTR transposons is at the carboxyl terminal of the reverse transcriptase (RT) domain and their RNase domains group together, indicating a common evolutionary origin. Many non-LTR transposons have lost the RNase domain because their activity is at the nucleus and cellular RNase may suffice; however LTR retotransposons always encode their own RNase domain because it requires RNase activity in RNA-protein particles in the cytoplasm. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription. Length = 128

>gnl|CDD|215695 pfam00075, RNase_H, RNase H

 Score = 63.4 bits (155), Expect = 5e-13
 Identities = 26/90 (28%), Positives = 44/90 (48%), Gaps = 4/90 (4%)

Query: 10  SSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLFCKNILIHDIQVACHKL 69
           +++  AE  A+   L+ L  + +     I+TDS+ +I  +   +        I+    +L
Sbjct: 38  TTNQRAELLALIEALEALSGQKV----NIYTDSQYVIGGITNGWPTKSESKPIKNEIWEL 93

Query: 70  ILKGNNVKIIWIPSHCGIAGNEEVDKAAQS 99
           + K + V I W+P H GI GNE  DK A+ 
Sbjct: 94  LQKKHKVYIQWVPGHSGIPGNELADKLAKQ 123

RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral replication cycle, and often found as a domain associated with reverse transcriptases. Structure is a mixed alpha+beta fold with three a/b/a layers. Length = 126

>gnl|CDD|187690 cd06222, RNase_H, RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner

 Score = 46.6 bits (111), Expect = 7e-07
 Identities = 19/95 (20%), Positives = 39/95 (41%), Gaps = 13/95 (13%)

Query: 7   NSLSSSFTAEA----FAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLFCKNILIHDI 62
              +++  AE      A+E+ LD  + +     ++I TDSK ++  +          + +
Sbjct: 34  IPAATNNEAELLALLEALELALDLGLKK-----LIIETDSKYVVDLINSWSKGWKKNNLL 88

Query: 63  QVACHKLILKGNNVKIIWIPSHCGIAGNEEVDKAA 97
                 L+ K  +++   +P      GNE  D+ A
Sbjct: 89  LWDILLLLSKFIDIRFEHVPRE----GNEVADRLA 119

Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, Type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site residues and have the same catalytic mechanism and functions in cells. RNase H is involved in DNA replication, repair and transcription. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription. Length = 123

>gnl|CDD|187704 cd09280, RNase_HI_eukaryote_like, Eukaryotic RNase H is longer and more complex than their prokaryotic counterparts and unlike prokaryote, RNase H are essential in higher eukaryote

 Score = 44.5 bits (106), Expect = 7e-06
 Identities = 25/100 (25%), Positives = 41/100 (41%), Gaps = 17/100 (17%)

Query: 15  AEAFAMEMCLDNLINRPIP-DNILIFTDSKSLISSMQQLF---------------CKNI- 57
           AE  A+   L  +         ++I TDS+ +++ + +                   N  
Sbjct: 46  AELRAVIHALRLIKEVGEGLTKLVIATDSEYVVNGVTEWIPKWKKNGWKTSKGKPVANKD 105

Query: 58  LIHDIQVACHKLILKGNNVKIIWIPSHCGIAGNEEVDKAA 97
           LI ++     +L  +G  VK   +P H GI GNEE D+ A
Sbjct: 106 LIKELDKLLEELEERGIRVKFWHVPGHSGIYGNEEADRLA 145

Ribonuclease H (RNase H) is classified into two families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H is widely present in various organisms, including bacteria, archaea and eukaryote and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, Type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD) residues and have the same catalytic mechanism and functions in cells. Eukaryotic RNase H is longer and more complex than in prokaryotes. Almost all eukaryotic RNase HI have highly conserved regions at the N-terminal called hybrid binding domain (HBD). It is speculated that the HBD contributes to binding the RNA/DNA hybrid. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability, but RNase H is essential in higher eukaryotes. RNase H knockout mice lack mitochondrial DNA replication and die as embryos. Length = 150

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	244
PRK06548	161	ribonuclease H; Provisional	99.79
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	99.79
PRK08719	147	ribonuclease H; Reviewed	99.78
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	99.77
PRK00203	150	rnhA ribonuclease H; Reviewed	99.76
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	99.61
PRK13907	128	rnhA ribonuclease H; Provisional	99.46
KOG3752|consensus	371		99.45
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	99.42
PRK07708	219	hypothetical protein; Validated	99.29
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	99.13
PF13966	86	zf-RVT: zinc-binding in reverse transcriptase	97.03

>PRK06548 ribonuclease H; Provisional

Probab=99.79  E-value=5.8e-19  Score=139.40  Aligned_cols=93  Identities=25%  Similarity=0.340  Sum_probs=76.3

Q ss_pred             CCChHHHHHHHHHHHHHHhhcCCCCCcEEEEeccHHHHHHHhcc--------c---cccHHH-HHHHHHHHHHHhcCCeE
Q psy3058           9 LSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQL--------F---CKNILI-HDIQVACHKLILKGNNV   76 (244)
Q Consensus         9 ~~t~~~AEl~Ai~~al~~~~~~~~~~~i~i~tDs~~al~~l~~~--------~---~~~~~~-~~i~~~~~~l~~~~~~v   76 (244)
                      .+|++.|||.|++.||+.+..  ....|.|+|||++|+++++.+        +   +++++. +++++.+..+... ..|
T Consensus        39 ~~TNnraEl~Aii~aL~~~~~--~~~~v~I~TDS~yvi~~i~~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~-~~v  115 (161)
T PRK06548         39 IATNNIAELTAVRELLIATRH--TDRPILILSDSKYVINSLTKWVYSWKMRKWRKADGKPVLNQEIIQEIDSLMEN-RNI  115 (161)
T ss_pred             CCCHHHHHHHHHHHHHHhhhc--CCceEEEEeChHHHHHHHHHHHHHHHHCCCcccCCCccccHHHHHHHHHHHhc-Cce
Confidence            579999999999999986643  234699999999999999952        1   245665 6777888777654 479


Q ss_pred             EEEeecCCCCCccchhhchHHHHHhhhc
Q psy3058          77 KIIWIPSHCGIAGNEEVDKAAQSFINAQ  104 (244)
Q Consensus        77 ~~~Wvp~H~gi~gNe~AD~lAk~a~~~~  104 (244)
                      +|.|||||+|++|||.||+||++++...
T Consensus       116 ~~~wVkgHsg~~gNe~aD~LA~~aa~~~  143 (161)
T PRK06548        116 RMSWVNAHTGHPLNEAADSLARQAANNF  143 (161)
T ss_pred             EEEEEecCCCCHHHHHHHHHHHHHHHHh
Confidence            9999999999999999999999988653

>PF00075 RNase_H: RNase H; InterPro: IPR002156 The RNase H domain is responsible for hydrolysis of the RNA portion of RNA x DNA hybrids, and this activity requires the presence of divalent cations (Mg2+ or Mn2+) that bind its active site

Probab=99.79  E-value=1.4e-19  Score=138.77  Aligned_cols=90  Identities=27%  Similarity=0.455  Sum_probs=71.0

Q ss_pred             ecCCCCCChHHHHHHHHHHHHHHhhcCCCCCcEEEEeccHHHHHHHhc-----ccccc----HHHHHHHHHHHHHHhcCC
Q psy3058           4 YRLNSLSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQ-----LFCKN----ILIHDIQVACHKLILKGN   74 (244)
Q Consensus         4 ~~l~~~~t~~~AEl~Ai~~al~~~~~~~~~~~i~i~tDs~~al~~l~~-----~~~~~----~~~~~i~~~~~~l~~~~~   74 (244)
                      +.++ ..|++.||+.||..||+ +..   ...++|+|||+++++.+..     .....    ++...|.+.+    ..+.
T Consensus        33 ~~~~-~~s~~~aEl~Ai~~AL~-~~~---~~~v~I~tDS~~v~~~l~~~~~~~~~~~~~~~~~i~~~i~~~~----~~~~  103 (132)
T PF00075_consen   33 FRLG-GQSNNRAELQAIIEALK-ALE---HRKVTIYTDSQYVLNALNKWLHGNGWKKTSNGRPIKNEIWELL----SRGI  103 (132)
T ss_dssp             EEEE-SECHHHHHHHHHHHHHH-THS---TSEEEEEES-HHHHHHHHTHHHHTTSBSCTSSSBHTHHHHHHH----HHSS
T ss_pred             eccc-ccchhhhheehHHHHHH-Hhh---cccccccccHHHHHHHHHHhccccccccccccccchhheeecc----ccce
Confidence            3455 88999999999999999 543   2789999999999998888     32222    3444444433    5689


Q ss_pred             eEEEEeecCCCCC-ccchhhchHHHHHhh
Q psy3058          75 NVKIIWIPSHCGI-AGNEEVDKAAQSFIN  102 (244)
Q Consensus        75 ~v~~~Wvp~H~gi-~gNe~AD~lAk~a~~  102 (244)
                      .|.|+|||||+|+ .||+.||+|||+|+.
T Consensus       104 ~v~~~~V~~H~~~~~~N~~aD~lAk~a~~  132 (132)
T PF00075_consen  104 KVRFRWVPGHSGVPQGNERADRLAKEAAQ  132 (132)
T ss_dssp             EEEEEESSSSSSSHHHHHHHHHHHHHHHH
T ss_pred             EEeeeeccCcCCCchhHHHHHHHHHHhcC
Confidence            9999999999999 699999999999873

This domain is a part of a large family of homologous RNase H enzymes of which the RNase HI protein from Escherichia coli is the best characterised []. Secondary structure predictions for the enzymes from E. coli, yeast, human liver and diverse retroviruses (such as Rous sarcoma virus and the Foamy viruses) supported, in every case, the five beta-strands (1 to 5) and four or five alpha-helices (A, B/C, D, E) that have been identified by crystallography in the RNase H domain of Human immunodeficiency virus 1 (HIV-1) reverse transcriptase and in E. coli RNase H []. Reverse transcriptase (RT) is a modular enzyme carrying polymerase and ribonuclease H (RNase H) activities in separable domains. Reverse transcriptase (RT) converts the single-stranded RNA genome of a retrovirus into a double-stranded DNA copy for integration into the host genome. This process requires ribonuclease H as well as RNA- and DNA-directed DNA polymerase activities. Retroviral RNase H is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. Bacterial RNase H 3.1.26.4 from EC catalyses endonucleolytic cleavage to 5'-phosphomonoester acting on RNA-DNA hybrids. The 3D structure of the RNase H domain from diverse bacteria and retroviruses has been solved [, , ]. All have four beta strands and four to five alpha helices. The E. coli RNase H1 protein binds a single Mg2+ ion cofactor in the active site of the enzyme. The divalent cation is bound by the carboxyl groups of four acidic residues, Asp-10, Glu-48, Asp-70, and Asp-134 []. The first three acidic residues are highly conserved in all bacterial and retroviral RNase H sequences. ; GO: 0003676 nucleic acid binding, 0004523 ribonuclease H activity; PDB: 3LP3_B 2KW4_A 3P1G_A 1RIL_A 2RPI_A 4EQJ_G 4EP2_B 3OTY_P 3U3G_D 2ZQB_D ....

>PRK08719 ribonuclease H; Reviewed

Probab=99.78  E-value=1.2e-18  Score=136.28  Aligned_cols=91  Identities=22%  Similarity=0.284  Sum_probs=73.9

Q ss_pred             CCCCCChHHHHHHHHHHHHHHhhcCCCCCcEEEEeccHHHHHHHhc--------ccc---ccHH-HHHHHHHHHHHHhcC
Q psy3058           6 LNSLSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQ--------LFC---KNIL-IHDIQVACHKLILKG   73 (244)
Q Consensus         6 l~~~~t~~~AEl~Ai~~al~~~~~~~~~~~i~i~tDs~~al~~l~~--------~~~---~~~~-~~~i~~~~~~l~~~~   73 (244)
                      +....|++.||+.|+..||+.+.+.     .+|+|||++|+++++.        .+.   +.++ ..++++.+..+.. .
T Consensus        44 ~~~~~Tnn~aEl~A~~~aL~~~~~~-----~~i~tDS~yvi~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~-~  117 (147)
T PRK08719         44 VNRYTDNAELELLALIEALEYARDG-----DVIYSDSDYCVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRA-R  117 (147)
T ss_pred             CCCCccHHHHHHHHHHHHHHHcCCC-----CEEEechHHHHHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhC-C
Confidence            5556899999999999999998542     3899999999999953        332   2233 2577777777755 5


Q ss_pred             CeEEEEeecCCCCCccchhhchHHHHHhh
Q psy3058          74 NNVKIIWIPSHCGIAGNEEVDKAAQSFIN  102 (244)
Q Consensus        74 ~~v~~~Wvp~H~gi~gNe~AD~lAk~a~~  102 (244)
                      ..|+|.|||||+|++|||.||+||++|+.
T Consensus       118 ~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~  146 (147)
T PRK08719        118 KYVEVEKVTAHSGIEGNEAADMLAQAAAE  146 (147)
T ss_pred             CcEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence            67999999999999999999999999875

>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]

Probab=99.77  E-value=1.2e-18  Score=135.57  Aligned_cols=95  Identities=22%  Similarity=0.269  Sum_probs=80.8

Q ss_pred             CCChHHHHHHHHHHHHHHhhcCCCCCcEEEEeccHHHHHHHhccc---c--------ccHH-HHHHHHHHHHHHhcCCeE
Q psy3058           9 LSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLF---C--------KNIL-IHDIQVACHKLILKGNNV   76 (244)
Q Consensus         9 ~~t~~~AEl~Ai~~al~~~~~~~~~~~i~i~tDs~~al~~l~~~~---~--------~~~~-~~~i~~~~~~l~~~~~~v   76 (244)
                      .+||+.||++|++.||+.+.+. ....|.|+|||++|+++|+.+.   .        +.|+ -+++++.+.++..+...|
T Consensus        40 ~tTNNraEl~A~i~AL~~l~~~-~~~~v~l~tDS~yv~~~i~~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~~v  118 (154)
T COG0328          40 RTTNNRAELRALIEALEALKEL-GACEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELV  118 (154)
T ss_pred             cccChHHHHHHHHHHHHHHHhc-CCceEEEEecHHHHHHHHHHHHhhccccCccccccCccccHHHHHHHHHHHhhCCeE
Confidence            6899999999999999999863 3578999999999999999431   1        1233 257788888888877799


Q ss_pred             EEEeecCCCCCccchhhchHHHHHhhhc
Q psy3058          77 KIIWIPSHCGIAGNEEVDKAAQSFINAQ  104 (244)
Q Consensus        77 ~~~Wvp~H~gi~gNe~AD~lAk~a~~~~  104 (244)
                      .+.|||||+|.++||.||+||+.+++..
T Consensus       119 ~~~WVkgH~g~~~NeraD~LA~~~~~~~  146 (154)
T COG0328         119 FWEWVKGHAGHPENERADQLAREAARAA  146 (154)
T ss_pred             EEEEeeCCCCChHHHHHHHHHHHHHHhh
Confidence            9999999999999999999999998765

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=99.76  E-value=3.9e-18  Score=134.09  Aligned_cols=95  Identities=20%  Similarity=0.306  Sum_probs=75.4

Q ss_pred             CCCChHHHHHHHHHHHHHHhhcCCCCCcEEEEeccHHHHHHHhcc--------c---cccHHH-HHHHHHHHHHHhcCCe
Q psy3058           8 SLSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQL--------F---CKNILI-HDIQVACHKLILKGNN   75 (244)
Q Consensus         8 ~~~t~~~AEl~Ai~~al~~~~~~~~~~~i~i~tDs~~al~~l~~~--------~---~~~~~~-~~i~~~~~~l~~~~~~   75 (244)
                      ...|++.|||.|+..||+.+.+   ...|.|+|||++|++.|..+        +   .++++. .++++.+.++.. ...
T Consensus        39 ~~~TN~~aEL~Ai~~AL~~~~~---~~~v~I~tDS~yvi~~i~~w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~-~~~  114 (150)
T PRK00203         39 ALTTNNRMELMAAIEALEALKE---PCEVTLYTDSQYVRQGITEWIHGWKKNGWKTADKKPVKNVDLWQRLDAALK-RHQ  114 (150)
T ss_pred             CCCcHHHHHHHHHHHHHHHcCC---CCeEEEEECHHHHHHHHHHHHHHHHHcCCcccCCCccccHHHHHHHHHHhc-cCc
Confidence            4678999999999999998854   35799999999999999963        1   123332 345566666543 478


Q ss_pred             EEEEeecCCCCCccchhhchHHHHHhhhcCC
Q psy3058          76 VKIIWIPSHCGIAGNEEVDKAAQSFINAQNY  106 (244)
Q Consensus        76 v~~~Wvp~H~gi~gNe~AD~lAk~a~~~~~~  106 (244)
                      |.|.|||||+|++||+.||+|||+|......
T Consensus       115 v~~~wV~~H~~~~~N~~AD~lA~~a~~~~~~  145 (150)
T PRK00203        115 IKWHWVKGHAGHPENERCDELARAGAEEATL  145 (150)
T ss_pred             eEEEEecCCCCCHHHHHHHHHHHHHHHHhhh
Confidence            9999999999999999999999999876543

>cd06222 RnaseH RNase H (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a not sequence-specific manner

Probab=99.61  E-value=7.5e-15  Score=109.89  Aligned_cols=93  Identities=25%  Similarity=0.363  Sum_probs=77.0

Q ss_pred             CCCChHHHHHHHHHHHHHHhhcCCCCCcEEEEeccHHHHHHHhcccc-ccHHHHHHHHHHHHHHhcCCeEEEEeecCCCC
Q psy3058           8 SLSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLFC-KNILIHDIQVACHKLILKGNNVKIIWIPSHCG   86 (244)
Q Consensus         8 ~~~t~~~AEl~Ai~~al~~~~~~~~~~~i~i~tDs~~al~~l~~~~~-~~~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~g   86 (244)
                      ...+++.||+.|+..||+.+... ....+.|++||+.+++.+.+... .......+...+..+...+..+.|.|||+|+|
T Consensus        37 ~~~s~~~aEl~al~~al~~~~~~-~~~~i~i~~Ds~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~  115 (130)
T cd06222          37 GNTTNNRAELLALIEALELALEL-GGKKVNIYTDSQYVINALTGWYEGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHSG  115 (130)
T ss_pred             CCCcHHHHHHHHHHHHHHHHHhC-CCceEEEEECHHHHHHHhhccccCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCCC
Confidence            57899999999999999999754 35789999999999999998754 22344455555555556788999999999999


Q ss_pred             CccchhhchHHHHHh
Q psy3058          87 IAGNEEVDKAAQSFI  101 (244)
Q Consensus        87 i~gNe~AD~lAk~a~  101 (244)
                      +++|+.||.|||++.
T Consensus       116 ~~~n~~ad~la~~~~  130 (130)
T cd06222         116 IEGNERADALAKEAA  130 (130)
T ss_pred             CcchHHHHHHHHhhC
Confidence            999999999999873

One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H knockout mice lack mitochondrial DNA replication and die as embryos. The retroviral reverse transcriptase contains an RNase H domain that plays an important role in converting a single stranded retroviral genomic RNA into a dsDNA for integration into host chromosomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.

>PRK13907 rnhA ribonuclease H; Provisional

Probab=99.46  E-value=5.1e-13  Score=102.12  Aligned_cols=91  Identities=22%  Similarity=0.228  Sum_probs=76.4

Q ss_pred             CCCChHHHHHHHHHHHHHHhhcCCCCCcEEEEeccHHHHHHHhccccccHHHHHHHHHHHHHHhcCCeEEEEeecCCCCC
Q psy3058           8 SLSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLFCKNILIHDIQVACHKLILKGNNVKIIWIPSHCGI   87 (244)
Q Consensus         8 ~~~t~~~AEl~Ai~~al~~~~~~~~~~~i~i~tDs~~al~~l~~~~~~~~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi   87 (244)
                      ...|++.||+.|++.||+.+...+. ..|.|+|||+.+++.+++.+...+....+++.+..+..++..+.|.|||.    
T Consensus        37 ~~~tn~~AE~~All~aL~~a~~~g~-~~v~i~sDS~~vi~~~~~~~~~~~~~~~l~~~~~~l~~~f~~~~~~~v~r----  111 (128)
T PRK13907         37 GTMSNHEAEYHALLAALKYCTEHNY-NIVSFRTDSQLVERAVEKEYAKNKMFAPLLEEALQYIKSFDLFFIKWIPS----  111 (128)
T ss_pred             cccCCcHHHHHHHHHHHHHHHhCCC-CEEEEEechHHHHHHHhHHHhcChhHHHHHHHHHHHHhcCCceEEEEcCc----
Confidence            3579999999999999999987643 57999999999999999976544455677777777777788888999995    


Q ss_pred             ccchhhchHHHHHhhh
Q psy3058          88 AGNEEVDKAAQSFINA  103 (244)
Q Consensus        88 ~gNe~AD~lAk~a~~~  103 (244)
                      ++|+.||.||+.|...
T Consensus       112 ~~N~~Ad~LA~~a~~~  127 (128)
T PRK13907        112 SQNKVADELARKAILQ  127 (128)
T ss_pred             hhchhHHHHHHHHHhc
Confidence            6999999999998753

>KOG3752|consensus

Probab=99.45  E-value=3.1e-13  Score=117.44  Aligned_cols=99  Identities=23%  Similarity=0.221  Sum_probs=77.2

Q ss_pred             ecCC-CCCChHHHHHHHHHHHHHHhhcCCCCCcEEEEeccHHHHHHHhcccc-----------ccH-----H-HHHHHHH
Q psy3058           4 YRLN-SLSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLFC-----------KNI-----L-IHDIQVA   65 (244)
Q Consensus         4 ~~l~-~~~t~~~AEl~Ai~~al~~~~~~~~~~~i~i~tDs~~al~~l~~~~~-----------~~~-----~-~~~i~~~   65 (244)
                      ++|. ..+|+|.|||.||..||+.+.+... .+++|.|||+.++++|+.+..           .++     + -......
T Consensus       247 ~pv~~g~qtNnrAEl~Av~~ALkka~~~~~-~kv~I~TDS~~~i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e  325 (371)
T KOG3752|consen  247 GPLAGGRQTNNRAELIAAIEALKKARSKNI-NKVVIRTDSEYFINSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNE  325 (371)
T ss_pred             ccCCCCcccccHHHHHHHHHHHHHHHhcCC-CcEEEEechHHHHHHHHHHHhhhccCccccccCCCccceeeecchHHHH
Confidence            4555 7889999999999999999987543 489999999999999997531           122     1 1233444


Q ss_pred             HHHHHh--cCCeEEEEeecCCCCCccchhhchHHHHHhhh
Q psy3058          66 CHKLIL--KGNNVKIIWIPSHCGIAGNEEVDKAAQSFINA  103 (244)
Q Consensus        66 ~~~l~~--~~~~v~~~Wvp~H~gi~gNe~AD~lAk~a~~~  103 (244)
                      +.+|.+  ++..|.+.|||||.|+.|||.||.||++++..
T Consensus       326 ~~~l~q~~~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs~~  365 (371)
T KOG3752|consen  326 LDELEQEISNKKVQQEYVGGHSGILGNEMADALARKGSTL  365 (371)
T ss_pred             HHHHHhhhccCceEEEEecCcCCcchHHHHHHHHhhhhhh
Confidence            444443  36899999999999999999999999998644

>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B

Probab=99.42  E-value=1.1e-12  Score=92.94  Aligned_cols=86  Identities=20%  Similarity=0.197  Sum_probs=68.8

Q ss_pred             hHHHHHHHHHHHHHHhhcCCCCCcEEEEeccHHHHHHHhccccccHHHHHHHHHHHHHHhcCCeEEEEeecCCCCCccch
Q psy3058          12 SFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLFCKNILIHDIQVACHKLILKGNNVKIIWIPSHCGIAGNE   91 (244)
Q Consensus        12 ~~~AEl~Ai~~al~~~~~~~~~~~i~i~tDs~~al~~l~~~~~~~~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe   91 (244)
                      +..||+.|+..||+.+.+.+. ++|+|.|||+.+++.|++..........+...+..+...+..+.|.|||    .++|.
T Consensus         1 ~~~aE~~al~~al~~a~~~g~-~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~----r~~N~   75 (87)
T PF13456_consen    1 PLEAEALALLEALQLAWELGI-RKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDRFWNVSVSHIP----REQNK   75 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHCCT--SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCCCSCEEEEE------GGGSH
T ss_pred             CcHHHHHHHHHHHHHHHHCCC-CEEEEEecCccccccccccccccccccccchhhhhhhccccceEEEEEC----hHHhH
Confidence            468999999999999988654 6899999999999999998543335566777777777888999999999    89999


Q ss_pred             hhchHHHHHhh
Q psy3058          92 EVDKAAQSFIN  102 (244)
Q Consensus        92 ~AD~lAk~a~~  102 (244)
                      .||.|||.|..
T Consensus        76 ~A~~LA~~a~~   86 (87)
T PF13456_consen   76 VADALAKFALS   86 (87)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHhh
Confidence            99999999863

>PRK07708 hypothetical protein; Validated

Probab=99.29  E-value=2.7e-11  Score=100.66  Aligned_cols=98  Identities=11%  Similarity=0.053  Sum_probs=76.4

Q ss_pred             cCCCCCChHHHHHHHHHHHHHHhhcCCCC-CcEEEEeccHHHHHHHhcccc-ccHHHHHHHHHHHHHHhcC-CeEEEEee
Q psy3058           5 RLNSLSSSFTAEAFAMEMCLDNLINRPIP-DNILIFTDSKSLISSMQQLFC-KNILIHDIQVACHKLILKG-NNVKIIWI   81 (244)
Q Consensus         5 ~l~~~~t~~~AEl~Ai~~al~~~~~~~~~-~~i~i~tDs~~al~~l~~~~~-~~~~~~~i~~~~~~l~~~~-~~v~~~Wv   81 (244)
                      .|+...|++.||+.|++.||+.+.+.+.. ..|.|++||+.+++.+++.++ .++....+.+.+..+..+. ..+.|.||
T Consensus       111 ~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~DSqlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~V  190 (219)
T PRK07708        111 YIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFRGDSQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPI  190 (219)
T ss_pred             cccccccCcHHHHHHHHHHHHHHHHcCCCcceEEEEeccHHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEEC
Confidence            45556899999999999999999886543 248999999999999999874 3445555556665554443 35788999


Q ss_pred             cCCCCCccchhhchHHHHHhhhcCC
Q psy3058          82 PSHCGIAGNEEVDKAAQSFINAQNY  106 (244)
Q Consensus        82 p~H~gi~gNe~AD~lAk~a~~~~~~  106 (244)
                      |    ...|+.||+||++|.+....
T Consensus       191 p----R~~N~~AD~LAk~Al~~~~~  211 (219)
T PRK07708        191 S----RKQNKEADQLATQALEGTVI  211 (219)
T ss_pred             C----chhhhHHHHHHHHHHhcCCC
Confidence            8    67899999999999986443

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=99.13  E-value=3.6e-10  Score=101.48  Aligned_cols=92  Identities=20%  Similarity=0.233  Sum_probs=77.2

Q ss_pred             CCChHHHHHHHHHHHHHHhhcCCCCCcEEEEeccHHHHHHHhcccc-ccHHHHHHHHHHHHHHhcCCeEEEEeecCCCCC
Q psy3058           9 LSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLFC-KNILIHDIQVACHKLILKGNNVKIIWIPSHCGI   87 (244)
Q Consensus         9 ~~t~~~AEl~Ai~~al~~~~~~~~~~~i~i~tDs~~al~~l~~~~~-~~~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi   87 (244)
                      ..|++.||+.|++.||+.+.+.+. +.|.|++||+.+++.+++.+. .++-...+...+..+..++..++|.|||.    
T Consensus        42 ~~tnn~AE~~All~gL~~a~~~g~-~~v~i~~DS~lvi~~i~~~~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~r----  116 (372)
T PRK07238         42 RATNNVAEYRGLIAGLEAAAELGA-TEVEVRMDSKLVVEQMSGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPR----  116 (372)
T ss_pred             CCCchHHHHHHHHHHHHHHHhCCC-CeEEEEeCcHHHHHHhCCCCccCChHHHHHHHHHHHHHhcCCceEEEECCc----
Confidence            678999999999999999987643 589999999999999998764 44445566667777778888999999994    


Q ss_pred             ccchhhchHHHHHhhhcC
Q psy3058          88 AGNEEVDKAAQSFINAQN  105 (244)
Q Consensus        88 ~gNe~AD~lAk~a~~~~~  105 (244)
                      .+|+.||.||+.|.....
T Consensus       117 ~~N~~AD~LA~~a~~~~~  134 (372)
T PRK07238        117 ARNAHADRLANEAMDAAA  134 (372)
T ss_pred             hhhhHHHHHHHHHHHhhc
Confidence            799999999999976643

>PF13966 zf-RVT: zinc-binding in reverse transcriptase

Probab=97.03  E-value=0.00034  Score=49.47  Aligned_cols=32  Identities=22%  Similarity=0.380  Sum_probs=26.5

Q ss_pred             ccccCCCCCCCCCCCCC-ccccccccccccCcH
Q psy3058         173 GFLMERTDPPQCEVCNV-TITVKHILCHCTKYT  204 (244)
Q Consensus       173 ~~~~~~~~~p~C~~Cg~-~et~~H~l~~Cp~~~  204 (244)
                      +.+.+...++.|..|+. .||++|++++||...
T Consensus        51 l~~r~~~~~~~C~~C~~~~Et~~Hlf~~C~~a~   83 (86)
T PF13966_consen   51 LQRRGIQVDPICPLCGNEEETIEHLFFHCPFAR   83 (86)
T ss_pred             hhccCCccCCccccCCCccccccceeccCcCcc
Confidence            34456677899999997 899999999999754

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	244
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	3e-04
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	3e-04

>3p1g_A Xenotropic murine leukemia virus-related virus (X H domain; XMRV, RNAse H, reverse transcriptase, transcription; 1.50A {Xenotropic mulv-related virus} PDB: 3v1q_A 3v1o_A 3v1r_A* 2hb5_A Length = 165

 Score = 39.4 bits (92), Expect = 3e-04
 Identities = 15/69 (21%), Positives = 27/69 (39%), Gaps = 6/69 (8%)

Query: 35  NILIFTDSKSLISSMQQLF-CKNILIHDIQVACHKLILKGNNVKIIWIPSHCG-----IA 88
            + ++TDS+   ++       + I   +  +A  K +     + II  P H         
Sbjct: 82  KLNVYTDSRYAFATAHVHSEGREIKNKNEILALLKALFLPKRLSIIHCPGHQKGNSAEAR 141

Query: 89  GNEEVDKAA 97
           GN   D+AA
Sbjct: 142 GNRMADQAA 150

>2kq2_A Ribonuclease H-related protein; PSI, NESG, protein structure, APO enzyme, structural genomics, protein structure initiative; NMR {Desulfitobacterium hafniense dcb-2} PDB: 2kw4_A Length = 147

 Score = 39.3 bits (92), Expect = 3e-04
 Identities = 13/81 (16%), Positives = 25/81 (30%), Gaps = 10/81 (12%)

Query: 19  AMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLFCKNILIHDIQVACHKLILK-GNNVK 77
           A++              I I  D   +       +      ++   A  KL+ +      
Sbjct: 61  AVKKASQL------GVKIRILHDYAGIAFWATGEWKAK---NEFTQAYAKLMNQYRGIYS 111

Query: 78  IIWIPSHCGIAGNEEVDKAAQ 98
              + +H G   N+ VD  A+
Sbjct: 112 FEKVKAHSGNEFNDYVDMKAK 132

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	244
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.82
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.81
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.8
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	99.79
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	99.78
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.77
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	99.75
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.74
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	99.71
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	99.65
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	99.64
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	99.62
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	99.61
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	99.61
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	98.75
4htu_A	134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	98.33

>3qio_A GAG-POL polyprotein; RNAse H, inhibitor, nuclease, transferase, hydrolase- complex; HET: QID; 1.40A {Hiv-1 M} SCOP: c.55.3.1 PDB: 3qin_A* 3hyf_A* 1o1w_A 3lp3_A* 1hrh_A 3k2p_A* 1rdh_A

Probab=99.82  E-value=4.2e-20  Score=144.14  Aligned_cols=91  Identities=26%  Similarity=0.363  Sum_probs=72.4

Q ss_pred             CCCChHHHHHHHHHHHHHHhhcCCCCCcEEEEeccHHHHHHHhccc-----------cccHHH-HHHHHHHHHHHhcCCe
Q psy3058           8 SLSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLF-----------CKNILI-HDIQVACHKLILKGNN   75 (244)
Q Consensus         8 ~~~t~~~AEl~Ai~~al~~~~~~~~~~~i~i~tDs~~al~~l~~~~-----------~~~~~~-~~i~~~~~~l~~~~~~   75 (244)
                      ..+|++.||+.|++.||+.+     +..|.|+|||++|++.|+++.           .+.++. .++++.+..+..++..
T Consensus        45 ~~~Tnn~aEl~A~i~AL~~~-----~~~v~i~tDS~~v~~~i~~w~~~W~~~gw~~~~g~~v~n~~l~~~l~~~l~~~~~  119 (150)
T 3qio_A           45 TDTTNQKTELQAIYLALQDS-----GLEVNIVTDSQYALGIITQWIHNWKKRGWKTADKKPVKNVDLVNQIIEQLIKKEK  119 (150)
T ss_dssp             SSCCHHHHHHHHHHHHHHHS-----CSEEEEEESCHHHHHHHHHHHHHHCC------------CHHHHHHHHHHHTTCSE
T ss_pred             CCCCHHHHHHHHHHHHHHhC-----CCcEEEEeCcHHHHHHHHHHHHHHhhcCcCcCcCcccccHHHHHHHHHHHhhcCc
Confidence            36899999999999999985     368999999999999999862           122222 3455555444457889


Q ss_pred             EEEEeecCCCCCccchhhchHHHHHhhh
Q psy3058          76 VKIIWIPSHCGIAGNEEVDKAAQSFINA  103 (244)
Q Consensus        76 v~~~Wvp~H~gi~gNe~AD~lAk~a~~~  103 (244)
                      |.|.|||||+|++|||.||+||++|+..
T Consensus       120 v~~~wV~gH~g~~~Ne~AD~LA~~a~~~  147 (150)
T 3qio_A          120 VYLAWVPAHKGIGGNEQVDKLVSAGIRK  147 (150)
T ss_dssp             EEEEECCTTSCCHHHHHHHHHHHTTTSC
T ss_pred             eEEEEccCcCCChhHHHHHHHHHHHHHH
Confidence            9999999999999999999999999864

>2qkb_A Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hybrid; 2.40A {Homo sapiens} PDB: 2qk9_A 2qkk_A*

Probab=99.81  E-value=9.5e-20  Score=142.73  Aligned_cols=98  Identities=21%  Similarity=0.315  Sum_probs=78.5

Q ss_pred             cCCCCCChHHHHHHHHHHHHHHhhcCCCCCcEEEEeccHHHHHHHhccc--------c---ccHH-HHHHHHHHHHHHhc
Q psy3058           5 RLNSLSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLF--------C---KNIL-IHDIQVACHKLILK   72 (244)
Q Consensus         5 ~l~~~~t~~~AEl~Ai~~al~~~~~~~~~~~i~i~tDs~~al~~l~~~~--------~---~~~~-~~~i~~~~~~l~~~   72 (244)
                      .|+..+|++.||+.|++.||+.+.+.+ ..+|.|+|||++|++.|.++.        .   +.++ ...+++.+..+.. 
T Consensus        43 ~l~~~~tn~~aEl~A~~~aL~~~~~~~-~~~v~i~tDS~~vi~~i~~~~~~w~~~~w~~~~~~~~~n~~l~~~i~~l~~-  120 (154)
T 2qkb_A           43 RLPGRQTNQRAEIHAACKAIEQAKTQN-INKLVLYTNSMFTINGITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQ-  120 (154)
T ss_dssp             ECCSSCCHHHHHHHHHHHHHHHHHHTT-CCEEEEEESCHHHHHHHHTHHHHHHTTTSBCTTSSBCTTHHHHHHHHHHHT-
T ss_pred             ecCCCCchHHHHHHHHHHHHHHHHhCC-CceEEEEECcHHHHhhhhhhHHHHHhccccccCCCccccHHHHHHHHHHHc-
Confidence            466678999999999999999997643 468999999999999999842        1   1122 2455555655544 


Q ss_pred             CCeEEEEeecCCCCCccchhhchHHHHHhhhc
Q psy3058          73 GNNVKIIWIPSHCGIAGNEEVDKAAQSFINAQ  104 (244)
Q Consensus        73 ~~~v~~~Wvp~H~gi~gNe~AD~lAk~a~~~~  104 (244)
                      +..|.|.|||||+|++|||.||+|||+|+..+
T Consensus       121 ~~~v~~~~V~~H~g~~~N~~AD~LA~~a~~~~  152 (154)
T 2qkb_A          121 GMDIQWMHVPGHSGFIGNEEADRLAREGAKQS  152 (154)
T ss_dssp             TCEEEEEECCTTSSCHHHHHHHHHHHHHHTCC
T ss_pred             CCceEEEEccCCCCCHhHHHHHHHHHHHHHhc
Confidence            56799999999999999999999999998764

>3h08_A RNH (ribonuclease H); RNAse H, 3D-structure, endonuclease, hydrolase, magnesium, metal-binding; 1.60A {Chlorobaculum tepidum}

Probab=99.80  E-value=1.3e-19  Score=140.66  Aligned_cols=92  Identities=21%  Similarity=0.237  Sum_probs=71.1

Q ss_pred             CCChHHHHHHHHHHHHHHhhcCCCCCcEEEEeccHHHHHHHhccc------------cccHH-HHHHHHHHHHHHhcCCe
Q psy3058           9 LSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLF------------CKNIL-IHDIQVACHKLILKGNN   75 (244)
Q Consensus         9 ~~t~~~AEl~Ai~~al~~~~~~~~~~~i~i~tDs~~al~~l~~~~------------~~~~~-~~~i~~~~~~l~~~~~~   75 (244)
                      .+|++.||+.|++.||+.+.+   ...|.|+|||++|++.|++.+            .+.++ .+.+++.+..+... ..
T Consensus        41 ~~Tnn~aEl~A~~~AL~~~~~---~~~v~I~tDS~~vi~~i~~~w~~~W~~~~w~~~~~~~v~n~~l~~~~~~~~~~-~~  116 (146)
T 3h08_A           41 ATTNNRMELMAAIKGLEALKE---PARVQLYSDSAYLVNAMNEGWLKRWVKNGWKTAAKKPVENIDLWQEILKLTTL-HR  116 (146)
T ss_dssp             EECHHHHHHHHHHHHHHTCSS---CCEEEEEESCHHHHHHHHSSHHHHHHHTTCC----CCCTTHHHHHHHHHHHHH-SE
T ss_pred             CCcHHHHHHHHHHHHHHhcCc---cCcEEEEeChHHHHHHHHHHHHHHHHHCCCccCCCCCcCCHHHHHHHHHHHhh-Cc
Confidence            578999999999999999865   478999999999999999821            11121 13444444444433 47


Q ss_pred             EEEEeecCCCCCccchhhchHHHHHhhhc
Q psy3058          76 VKIIWIPSHCGIAGNEEVDKAAQSFINAQ  104 (244)
Q Consensus        76 v~~~Wvp~H~gi~gNe~AD~lAk~a~~~~  104 (244)
                      |.|.|||||+|++|||.||+|||+|+...
T Consensus       117 v~~~~V~gH~g~~~N~~AD~LA~~a~~~~  145 (146)
T 3h08_A          117 VTFHKVKGHSDNPYNSRADELARLAIKEN  145 (146)
T ss_dssp             EEEEECCC-CCSHHHHHHHHHHHHHHHHC
T ss_pred             eEEEEcCCcCCcHhHHHHHHHHHHHHHhC
Confidence            99999999999999999999999998764

>3p1g_A Xenotropic murine leukemia virus-related virus (X H domain; XMRV, RNAse H, reverse transcriptase, transcription; 1.50A {Xenotropic mulv-related virus} PDB: 3v1q_A 3v1o_A 3v1r_A* 2hb5_A 4e89_A

Probab=99.79  E-value=2e-19  Score=142.34  Aligned_cols=99  Identities=20%  Similarity=0.192  Sum_probs=75.6

Q ss_pred             cCCCCCChHHHHHHHHHHHHHHhhcCCCCCcEEEEeccHHHHHHHhccccccHHH-HHHHHHHHHHHhcCCeEEEEeecC
Q psy3058           5 RLNSLSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLFCKNILI-HDIQVACHKLILKGNNVKIIWIPS   83 (244)
Q Consensus         5 ~l~~~~t~~~AEl~Ai~~al~~~~~~~~~~~i~i~tDs~~al~~l~~~~~~~~~~-~~i~~~~~~l~~~~~~v~~~Wvp~   83 (244)
                      .++..+|++.||+.|+..||+.+ +   ...|.|+|||++|++.+-....++++. .+++..+......+..|.|.||||
T Consensus        56 ~~~~~~Tnn~aEl~Ai~~AL~~~-~---~~~v~I~tDS~~vi~~iw~~~~g~~v~n~dl~~~l~~~l~~~~~v~~~wVkg  131 (165)
T 3p1g_A           56 ALPAGTSAQRAELIALTQALKMA-E---GKKLNVYTDSRYAFATAHVHSEGREIKNKNEILALLKALFLPKRLSIIHCPG  131 (165)
T ss_dssp             EECTTCCHHHHHHHHHHHHHHHT-B---TSEEEEEECCHHHHHHHHSCCCSCCCSSHHHHHHHHHHTTSBSEEEEEECCS
T ss_pred             cCCCCCcHHHHHHHHHHHHHHHc-c---CceEEEEEchHHHHhhhhcccCCCcccCHHHHHHHHHHHhcCCceEEEEecC
Confidence            35567899999999999999998 2   478999999999999993222233321 233333322224678999999999


Q ss_pred             CCC-----CccchhhchHHHHHhhhcCCC
Q psy3058          84 HCG-----IAGNEEVDKAAQSFINAQNYS  107 (244)
Q Consensus        84 H~g-----i~gNe~AD~lAk~a~~~~~~~  107 (244)
                      |+|     ++|||.||+|||+|+..+..+
T Consensus       132 H~g~~~~~~~gNe~AD~LA~~aa~~~~~~  160 (165)
T 3p1g_A          132 HQKGNSAEARGNRMADQAAREAAMKAVLE  160 (165)
T ss_dssp             SCCSCSHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCcCcchHHHHHHHHHHHHHhcCCCc
Confidence            999     999999999999999876543

>1jl1_A Ribonuclease HI; RNAse HI, protein stability, thermostability, hydrogen exchange, cooperativity, hydrolase; 1.30A {Escherichia coli} SCOP: c.55.3.1 PDB: 1f21_A 1jxb_A 1g15_A 1rch_A 1rdd_A 1rnh_A* 2rn2_A 1rda_A 1law_A 1rdb_A 1lav_A 3aa4_A 1rbu_A 1gob_A 1rdc_A 1kvc_A 3aa3_A 3aa2_A 3aa5_X 1rbv_A ...

Probab=99.78  E-value=4.7e-19  Score=138.98  Aligned_cols=94  Identities=19%  Similarity=0.256  Sum_probs=75.6

Q ss_pred             CCChHHHHHHHHHHHHHHhhcCCCCCcEEEEeccHHHHHHHhcc--------cc---ccHHH-HHHHHHHHHHHhcCCeE
Q psy3058           9 LSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQL--------FC---KNILI-HDIQVACHKLILKGNNV   76 (244)
Q Consensus         9 ~~t~~~AEl~Ai~~al~~~~~~~~~~~i~i~tDs~~al~~l~~~--------~~---~~~~~-~~i~~~~~~l~~~~~~v   76 (244)
                      .+|++.||+.|+..||+.+.+   ..+|.|+|||++|++.|.++        +.   +.++. ..+++.+..+.. ...|
T Consensus        41 ~~tn~~aEl~A~~~aL~~~~~---~~~v~I~tDS~~vi~~i~~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~-~~~v  116 (155)
T 1jl1_A           41 RTTNNRMELMAAIVALEALKE---HAEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALG-QHQI  116 (155)
T ss_dssp             EECHHHHHHHHHHHHHHTCCS---CCEEEEEECCHHHHHHHHTTHHHHHHTTTBCTTSCBCTTHHHHHHHHHHTT-TCEE
T ss_pred             CCcHHHHHHHHHHHHHHHhCc---CCcEEEEeCHHHHHHHHHHHHHHHhhcccccccCCccCCHHHHHHHHHHHc-cCce
Confidence            578999999999999999865   36899999999999999972        11   22221 345555555544 4689


Q ss_pred             EEEeecCCCCCccchhhchHHHHHhhhcCC
Q psy3058          77 KIIWIPSHCGIAGNEEVDKAAQSFINAQNY  106 (244)
Q Consensus        77 ~~~Wvp~H~gi~gNe~AD~lAk~a~~~~~~  106 (244)
                      .|.|||||+|++||+.||+|||+|+..+..
T Consensus       117 ~~~wV~gH~g~~~Ne~AD~LA~~a~~~~~~  146 (155)
T 1jl1_A          117 KWEWVKGHAGHPENERADELARAAAMNPTL  146 (155)
T ss_dssp             EEEECCSSTTCHHHHHHHHHHHHHHHSCCB
T ss_pred             EEEEcCCCCCCHHHHHHHHHHHHHHhccch
Confidence            999999999999999999999999987654

>2e4l_A Ribonuclease HI, RNAse HI; hydrolase, endoribonuclease; 2.00A {Shewanella oneidensis} PDB: 2zqb_A

Probab=99.77  E-value=9.3e-19  Score=137.70  Aligned_cols=91  Identities=22%  Similarity=0.300  Sum_probs=73.3

Q ss_pred             CCChHHHHHHHHHHHHHHhhcCCCCCcEEEEeccHHHHHHHhc--------ccc---ccHH-HHHHHHHHHHHHhcCCeE
Q psy3058           9 LSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQ--------LFC---KNIL-IHDIQVACHKLILKGNNV   76 (244)
Q Consensus         9 ~~t~~~AEl~Ai~~al~~~~~~~~~~~i~i~tDs~~al~~l~~--------~~~---~~~~-~~~i~~~~~~l~~~~~~v   76 (244)
                      .+|++.||+.|+..||+.+.+   +..|.|+|||++|++.|.+        .+.   +.++ -..++..+..+.. +..|
T Consensus        43 ~~tn~~aEl~A~~~AL~~~~~---~~~v~I~tDS~~vi~~i~~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~-~~~v  118 (158)
T 2e4l_A           43 LTTNNRMELLAPIVALEALKE---PCKIILTSDSQYMRQGIMTWIHGWKKKGWMTSNRTPVKNVDLWKRLDKAAQ-LHQI  118 (158)
T ss_dssp             EECHHHHHHHHHHHHHHTCSS---CCEEEEEECCHHHHHHHHTHHHHHHHTTTBCTTSSBCTTHHHHHHHHHHHT-TSEE
T ss_pred             CCccHHHHHHHHHHHHHHhcc---CCeEEEEeCHHHHHHHHHHHHHHHHHccccccCCCcccCHHHHHHHHHHHc-cCcE
Confidence            478999999999999998854   2789999999999999998        221   1222 1344555555544 4699


Q ss_pred             EEEeecCCCCCccchhhchHHHHHhhh
Q psy3058          77 KIIWIPSHCGIAGNEEVDKAAQSFINA  103 (244)
Q Consensus        77 ~~~Wvp~H~gi~gNe~AD~lAk~a~~~  103 (244)
                      .|.|||||+|++||+.||+|||+|+..
T Consensus       119 ~~~wV~gH~g~~~Ne~AD~LAk~a~~~  145 (158)
T 2e4l_A          119 DWRWVKGHAGHAENERCDQLARAAAEA  145 (158)
T ss_dssp             EEEECCTTCCCHHHHHHHHHHHHHHHS
T ss_pred             EEEEccCCCCchhHHHHHHHHHHHHHh
Confidence            999999999999999999999999987

>2kq2_A Ribonuclease H-related protein; PSI, NESG, protein structure, APO enzyme, structural genomics, protein structure initiative; NMR {Desulfitobacterium hafniense dcb-2} PDB: 2kw4_A

Probab=99.75  E-value=8.3e-20  Score=142.03  Aligned_cols=93  Identities=14%  Similarity=0.059  Sum_probs=74.2

Q ss_pred             CCChHHHHHHHHHHHHHHhhcCCCCCcEEEEeccHHHHHHHhccccc-cHHHHHHHHHHHHHHhcCCeEEEEeecCCCCC
Q psy3058           9 LSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLFCK-NILIHDIQVACHKLILKGNNVKIIWIPSHCGI   87 (244)
Q Consensus         9 ~~t~~~AEl~Ai~~al~~~~~~~~~~~i~i~tDs~~al~~l~~~~~~-~~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi   87 (244)
                      .+||+.||+.|+..||+.+.+.+.  +|.|+|||+.+.+.+.+.+.. ........+.+.+|..   .|.|.|||||+|+
T Consensus        47 ~~tNn~aEl~A~~~AL~~a~~~~~--~v~I~tDS~~i~~w~~~~w~~~~~~~~~~~~l~~~l~~---~v~~~wV~gH~g~  121 (147)
T 2kq2_A           47 TMRNVAGEIAAALYAVKKASQLGV--KIRILHDYAGIAFWATGEWKAKNEFTQAYAKLMNQYRG---IYSFEKVKAHSGN  121 (147)
T ss_dssp             GTCTTHHHHHHHHHHHHHHHHHTC--CCCBSSCCSTHHHHTTSSSSCCHHHHHHHHCGGGGGST---TCCBCCCCCCCCC
T ss_pred             cccHHHHHHHHHHHHHHHHHHCCC--eEEEEECcHHHHHHHhCCCccCCcchHHHHHHHHHhcC---CeeEEEecCcCCC
Confidence            369999999999999998876543  799999999998888776543 2333444455554432   8999999999999


Q ss_pred             ccchhhchHHHHHhhhcCC
Q psy3058          88 AGNEEVDKAAQSFINAQNY  106 (244)
Q Consensus        88 ~gNe~AD~lAk~a~~~~~~  106 (244)
                      +|||.||+|||+|+.....
T Consensus       122 ~~Ne~AD~LA~~a~~~~~~  140 (147)
T 2kq2_A          122 EFNDYVDMKAKSALGIRDL  140 (147)
T ss_dssp             HHHHHHHHHHHHHHTCCCT
T ss_pred             cchHHHHHHHHHHHhcccc
Confidence            9999999999999987653

>1ril_A Ribonuclease H; hydrolase(endoribonuclease); 2.80A {Thermus thermophilus} SCOP: c.55.3.1 PDB: 2rpi_A

Probab=99.74  E-value=1.3e-18  Score=138.00  Aligned_cols=94  Identities=21%  Similarity=0.236  Sum_probs=74.6

Q ss_pred             CCChHHHHHHHHHHHHHHhhcCCCCCcEEEEeccHHHHHHHhc-c--------cc---ccHHH-HHHHHHHHHHHhcCCe
Q psy3058           9 LSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQ-L--------FC---KNILI-HDIQVACHKLILKGNN   75 (244)
Q Consensus         9 ~~t~~~AEl~Ai~~al~~~~~~~~~~~i~i~tDs~~al~~l~~-~--------~~---~~~~~-~~i~~~~~~l~~~~~~   75 (244)
                      .+|++.||+.|++.||+.+.+   ...|.|+|||++|++.|.+ +        +.   +.++. ..++..+..+.. ...
T Consensus        45 ~~Tnn~aEl~Ai~~AL~~~~~---~~~v~I~tDS~~vi~~i~~~w~~~W~~~~w~~~~g~~v~n~~l~~~i~~l~~-~~~  120 (166)
T 1ril_A           45 CTTNNRMELKAAIEGLKALKE---PCEVDLYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMA-PHR  120 (166)
T ss_dssp             EECHHHHHHHHHHHHHHSCCS---CCEEEEECCCHHHHHHHHSSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHT-TSE
T ss_pred             CCcHHHHHHHHHHHHHHHhcc---CCeEEEEeChHHHHHHHhhhHHHHHHhcccccccCCccCcHHHHHHHHHHHh-cCe
Confidence            568999999999999998854   2589999999999999998 2        21   12221 345555555544 359


Q ss_pred             EEEEeecCCCCCccchhhchHHHHHhhhcCC
Q psy3058          76 VKIIWIPSHCGIAGNEEVDKAAQSFINAQNY  106 (244)
Q Consensus        76 v~~~Wvp~H~gi~gNe~AD~lAk~a~~~~~~  106 (244)
                      |.|.|||||+|++||+.||+|||+|+.....
T Consensus       121 v~~~wV~gH~g~~~Ne~AD~LAk~a~~~~~~  151 (166)
T 1ril_A          121 VRFHFVKGHTGHPENERVDREARRQAQSQAK  151 (166)
T ss_dssp             EECCCCCGGGSCTHHHHHHHHHHHHHTSSCC
T ss_pred             EEEEEeeCCCCchhHHHHHHHHHHHHHHhhc
Confidence            9999999999999999999999999987653

>2lsn_A Reverse transcriptase; RNAse H, viral protein; NMR {Simian foamy virus}

Probab=99.71  E-value=1.9e-17  Score=130.76  Aligned_cols=94  Identities=20%  Similarity=0.136  Sum_probs=72.7

Q ss_pred             CCCChHHHHHHHHHHHHHHhhcCCCCCcEEEEeccHHHHHHHhccc-----------cccHHH-HHHHHHHHHHHhcCCe
Q psy3058           8 SLSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLF-----------CKNILI-HDIQVACHKLILKGNN   75 (244)
Q Consensus         8 ~~~t~~~AEl~Ai~~al~~~~~~~~~~~i~i~tDs~~al~~l~~~~-----------~~~~~~-~~i~~~~~~l~~~~~~   75 (244)
                      ...+++.||+.|+..||+.+++.  +..|.|+|||++|++.|+.+.           .+.++. .++++.+.++......
T Consensus        52 nn~te~~Aei~Al~~al~~al~~--~~~v~I~TDS~Yvi~~it~w~~~Wk~ngw~~~~~~pVkN~dL~~~l~~~~~~~~~  129 (165)
T 2lsn_A           52 GNHTAQMAEIAAVEFACKKALKI--PGPVLVITDSFYVAESANKELPYWKSNGFVNNKKKPLKHISKWKSIAECLSMKPD  129 (165)
T ss_dssp             SSCCHHHHHHHHHHHHHHHHHHS--SSCEEEEESCHHHHHHHHTHHHHHHHTTSCSCSSSCCSSHHHHHHHHHHHHHCTT
T ss_pred             hHHHHHHHHHHHHHHHHHHHhcC--CCeEEEEeChHHHHhhhhhhhhhheeccccccCCCcccCHHHHHHHHHHHhCCCC
Confidence            45788899999999999988764  357999999999999998631           122322 3455555555555678


Q ss_pred             EEEEeecCCCCC------ccchhhchHHHHHhhh
Q psy3058          76 VKIIWIPSHCGI------AGNEEVDKAAQSFINA  103 (244)
Q Consensus        76 v~~~Wvp~H~gi------~gNe~AD~lAk~a~~~  103 (244)
                      |.|.|||||+|+      +|||.||+||++|+..
T Consensus       130 v~~~~VkgH~g~~~~~~~~gNe~AD~LA~~gA~~  163 (165)
T 2lsn_A          130 ITIQHEKGHQPTNTSIHTEGNALADKLATQGSYV  163 (165)
T ss_dssp             CEEEECCSSSCSSSCHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEeCCCCccCCCCChHHHHHHHHHHHhhhh
Confidence            999999999995      5899999999999854

>3hst_B Protein RV2228C/MT2287; ribonuclease H1, RV2228C N-terminal domain, fusion protein, maltose binding protein, HYDR; HET: MLR TAR; 2.25A {Mycobacterium tuberculosis}

Probab=99.65  E-value=5.6e-16  Score=118.93  Aligned_cols=91  Identities=20%  Similarity=0.260  Sum_probs=77.6

Q ss_pred             CCChHHHHHHHHHHHHHHhhcCCCCCcEEEEeccHHHHHHHhcccc-ccHHHHHHHHHHHHHHhcCCeEEEEeecCCCCC
Q psy3058           9 LSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLFC-KNILIHDIQVACHKLILKGNNVKIIWIPSHCGI   87 (244)
Q Consensus         9 ~~t~~~AEl~Ai~~al~~~~~~~~~~~i~i~tDs~~al~~l~~~~~-~~~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi   87 (244)
                      .+|++.||+.|++.||+.+.+.+ .++|.|+|||+++++.+++.+. ..+.+..++..+..+..++..|.|.|||+    
T Consensus        43 ~~tn~~aEl~A~~~aL~~a~~~~-~~~v~i~tDS~~vv~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~v~~~~V~~----  117 (141)
T 3hst_B           43 RATNNVAEYRGLIAGLDDAVKLG-ATEAAVLMDSKLVVEQMSGRWKVKHPDLLKLYVQAQALASQFRRINYEWVPR----  117 (141)
T ss_dssp             EECHHHHHHHHHHHHHHHHHHHT-CSEEEEEESCHHHHHHHTTSSCCCSHHHHHHHHHHHHHHTTSSEEEEEECCG----
T ss_pred             CCchHHHHHHHHHHHHHHHHHCC-CceEEEEeChHHHHHHHhCCcccCCHHHHHHHHHHHHHHhcCCeEEEEEcCC----
Confidence            67999999999999999998754 3689999999999999999753 44556667777777877789999999994    


Q ss_pred             ccchhhchHHHHHhhhc
Q psy3058          88 AGNEEVDKAAQSFINAQ  104 (244)
Q Consensus        88 ~gNe~AD~lAk~a~~~~  104 (244)
                      ++|+.||+|||+|....
T Consensus       118 ~~N~~AD~LA~~a~~~~  134 (141)
T 3hst_B          118 ARNTYADRLANDAMDAA  134 (141)
T ss_dssp             GGCHHHHHHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHh
Confidence            89999999999998764

>3u3g_D Ribonuclease H, RNAse H1; hydrolase, cleave the RNA strand of RNA/DNA hybrid; 1.40A {Uncultured organism}

Probab=99.64  E-value=5.5e-16  Score=118.63  Aligned_cols=91  Identities=18%  Similarity=0.204  Sum_probs=74.1

Q ss_pred             CCChHHHHHHHHHHHHHHhhcCCCCC----cEEEEeccHHHHHHHhcccc-ccHHHHHHHHHHHHH-HhcCCeEEEEeec
Q psy3058           9 LSSSFTAEAFAMEMCLDNLINRPIPD----NILIFTDSKSLISSMQQLFC-KNILIHDIQVACHKL-ILKGNNVKIIWIP   82 (244)
Q Consensus         9 ~~t~~~AEl~Ai~~al~~~~~~~~~~----~i~i~tDs~~al~~l~~~~~-~~~~~~~i~~~~~~l-~~~~~~v~~~Wvp   82 (244)
                      .+|++.||+.|+..||+.+.+.+ .+    +|.|+|||++|++.+++.+. ..+.+..++..+..+ ..+...|.|.|||
T Consensus        42 ~~tn~~aEl~A~~~aL~~a~~~~-~~~~~~~v~i~tDS~~vi~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~~v~~~~V~  120 (140)
T 3u3g_D           42 ETTNNVAEYEALIRALEDLQMFG-DKLVDMEVEVRMDSELIVRQMQGVYKVKEPTLKEKFAKIAHIKMERVPNLVFVHIP  120 (140)
T ss_dssp             EECHHHHHHHHHHHHHHHHGGGG-GGGTTCEEEEEESCHHHHHHHTTSSCCCCGGGHHHHHHHHHHHHHHCTTCEEEECC
T ss_pred             CCchHHHHHHHHHHHHHHHHHcC-CCCCCceEEEEeChHHHHHHhCCCcccCCHHHHHHHHHHHHHhhcCCCcEEEEEcC
Confidence            46999999999999999997643 23    89999999999999999764 334344555666666 6666799999999


Q ss_pred             CCCCCccchhhchHHHHHhhhc
Q psy3058          83 SHCGIAGNEEVDKAAQSFINAQ  104 (244)
Q Consensus        83 ~H~gi~gNe~AD~lAk~a~~~~  104 (244)
                          .++|+.||+|||+|+...
T Consensus       121 ----~~~N~~AD~LA~~a~~~~  138 (140)
T 3u3g_D          121 ----REKNARADELVNEAIDKA  138 (140)
T ss_dssp             ----GGGGHHHHHHHHHHHHHH
T ss_pred             ----chhhHHHHHHHHHHHHhc
Confidence                589999999999998753

>2zd1_A Reverse transcriptase/ribonuclease H; P51/P66, hetero dimer, NNRTI, nonnucleoside inhibitor, AIDS, HIV, rilpivirine, diarylpyrimidine, DAPY, DNA recombination; HET: T27; 1.80A {Human immunodeficiency virus 1} PDB: 3is9_A* 3irx_A* 2ze2_A* 3bgr_A* 3qlh_A* 3klf_A* 3qo9_A* 1dlo_A 1bqm_A 2be2_A* 1s6q_A* 1s6p_A* 1s9g_A* 1suq_A* 2b5j_A* 2b6a_A* 2ban_A* 1s9e_A* 1hni_A* 1hnv_A* ...

Probab=99.62  E-value=7.7e-16  Score=143.52  Aligned_cols=84  Identities=27%  Similarity=0.379  Sum_probs=68.6

Q ss_pred             CCCChHHHHHHHHHHHHHHhhcCCCCCcEEEEeccHHHHHHHhcccc--ccHHHHHHHHHHHHHHhcCCeEEEEeecCCC
Q psy3058           8 SLSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLFC--KNILIHDIQVACHKLILKGNNVKIIWIPSHC   85 (244)
Q Consensus         8 ~~~t~~~AEl~Ai~~al~~~~~~~~~~~i~i~tDs~~al~~l~~~~~--~~~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~   85 (244)
                      ..+||+.||+.|++.||+.+     ...|.|+|||++|++.|+++..  .+++..++.+.+    .....|.|.|||||+
T Consensus       472 ~~~TNn~aEl~Ai~~aL~~~-----~~~v~I~tDS~~vi~~i~~~~~~~~~~l~~~~~~~l----~~~~~v~~~wV~~H~  542 (557)
T 2zd1_A          472 TNTTNQKTELQAIYLALQDS-----GLEVNIVTDSQYALGIIQAQPDKSESELVNQIIEQL----IKKEKVYLAWVPAHK  542 (557)
T ss_dssp             CSCCHHHHHHHHHHHHHHHS-----CSEEEEEECCHHHHHHHTTCCSEESSHHHHHHHHHH----HHCSEEEEEECCSSS
T ss_pred             CCCCHHHHHHHHHHHHHHhC-----CCcEEEEeChHHHHHHHhcCCccCCHHHHHHHHHHH----hcCCCEEEEEcCCCC
Confidence            36899999999999999998     3689999999999999999753  356666555433    235689999999999


Q ss_pred             CCccchhhchHHHHH
Q psy3058          86 GIAGNEEVDKAAQSF  100 (244)
Q Consensus        86 gi~gNe~AD~lAk~a  100 (244)
                      |++|||.||+|||+|
T Consensus       543 g~~~Ne~AD~LA~~a  557 (557)
T 2zd1_A          543 GIGGNEQVDKLVSAG  557 (557)
T ss_dssp             CCTTCCGGGGCC---
T ss_pred             CChhHHHHHHHHhcC
Confidence            999999999999986

>2ehg_A Ribonuclease HI; RNAse HI, hyperthermophilic archaeon, D stranded RNA-dependent RNAse, hydrolase; 1.60A {Sulfolobus tokodaii} PDB: 3aly_A

Probab=99.61  E-value=1.3e-15  Score=118.31  Aligned_cols=91  Identities=21%  Similarity=0.227  Sum_probs=73.2

Q ss_pred             CCCChHHHHHHHHHHHHHHhhcCCCCCcEEEEeccHHHHHHHhcccc-ccHHHHHHHHHHHHHHhcCCeEEEEeecCCCC
Q psy3058           8 SLSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLFC-KNILIHDIQVACHKLILKGNNVKIIWIPSHCG   86 (244)
Q Consensus         8 ~~~t~~~AEl~Ai~~al~~~~~~~~~~~i~i~tDs~~al~~l~~~~~-~~~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~g   86 (244)
                      ..+|++.||+.|+..||+.+.+.+ .++|.|+|||++|++.+++++. ..+....+++.+..+..+. .|.|.|||+   
T Consensus        44 ~~~tnn~aEl~A~~~aL~~a~~~g-~~~v~i~tDS~~vi~~i~~~w~~~~~~~~~l~~~i~~l~~~~-~v~~~~V~~---  118 (149)
T 2ehg_A           44 INSTNNVAEYSGLICLMETMLRLG-ISSPIIKGDSQLVIKQMNGEYKVKAKRIIPLYEKAIELKKKL-NATLIWVPR---  118 (149)
T ss_dssp             TTCCHHHHHHHHHHHHHHHHHHHT-CCSCEEEESCHHHHHHHTTSSCCCCTTHHHHHHHHHHHHHHH-TCEEEECCG---
T ss_pred             CCccHHHHHHHHHHHHHHHHHHcC-CCEEEEEeChHHHHHHHhCccccCCHHHHHHHHHHHHHHhcC-CEEEEEcCC---
Confidence            478999999999999999998754 3679999999999999999764 2233455555555555544 599999998   


Q ss_pred             CccchhhchHHHHHhhhc
Q psy3058          87 IAGNEEVDKAAQSFINAQ  104 (244)
Q Consensus        87 i~gNe~AD~lAk~a~~~~  104 (244)
                       ++|+.||+|||+|+...
T Consensus       119 -~~N~~AD~LA~~a~~~~  135 (149)
T 2ehg_A          119 -EENKEADRLSRVAYELV  135 (149)
T ss_dssp             -GGCHHHHHHHHHHHHHH
T ss_pred             -cccHHHHHHHHHHHHhh
Confidence             59999999999998764

>1mu2_A HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polymerase, drug design, transferase; 2.35A {Human immunodeficiency virus 2} SCOP: c.55.3.1 e.8.1.2 PDB: 1mu2_B

Probab=99.61  E-value=1.6e-15  Score=141.33  Aligned_cols=84  Identities=25%  Similarity=0.406  Sum_probs=70.5

Q ss_pred             CCChHHHHHHHHHHHHHHhhcCCCCCcEEEEeccHHHHHHHhccc--cccHHHHHHHHHHHHHHhcCCeEEEEeecCCCC
Q psy3058           9 LSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLF--CKNILIHDIQVACHKLILKGNNVKIIWIPSHCG   86 (244)
Q Consensus         9 ~~t~~~AEl~Ai~~al~~~~~~~~~~~i~i~tDs~~al~~l~~~~--~~~~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~g   86 (244)
                      .+||+.||+.|++.||+.     ....+.|+|||++|++.++++.  +..++.+.+.+.+    ..+..|.|.|||||+|
T Consensus       470 ~~TNn~aEl~A~i~aL~~-----~~~~v~I~tDS~~v~~~i~~~~~~~~~~l~~~~~~~~----~~~~~v~~~wV~~H~g  540 (555)
T 1mu2_A          470 QTTNQQAELEAFAMALTD-----SGPKVNIIVDSQYVMGIVASQPTESESKIVNQIIEEM----IKKEAIYVAWVPAHKG  540 (555)
T ss_dssp             SCCHHHHHHHHHHHHHHT-----SCSEEEEEESCHHHHHHHHTCCSEESCHHHHHHHHHH----HHCSEEEEEECCSSSC
T ss_pred             CCCHHHHHHHHHHHHHHc-----CCCeEEEEEehHHHHHHHhcccccccHHHHHHHHHHh----ccCCcEEEEEEECCCC
Confidence            679999999999999997     2468999999999999999864  3456666554433    3467899999999999


Q ss_pred             CccchhhchHHHHHh
Q psy3058          87 IAGNEEVDKAAQSFI  101 (244)
Q Consensus        87 i~gNe~AD~lAk~a~  101 (244)
                      ++|||.||+|||+|+
T Consensus       541 ~~~Ne~AD~LA~~a~  555 (555)
T 1mu2_A          541 IGGNQEVDHLVSQGI  555 (555)
T ss_dssp             CTTHHHHHHHHHTTC
T ss_pred             ChhHHHHHHHHHhhC
Confidence            999999999999874

>1zbf_A Ribonuclease H-related protein; RNAse H, RNA/DNA hybrid, DDE motif, hydrolase; 1.50A {Bacillus halodurans} SCOP: c.55.3.1 PDB: 1zbi_A 2g8u_A 2g8i_A 2g8h_A 2g8k_A 2g8f_A 2g8v_A 2g8w_A 3ey1_A* 1zbl_A 3d0p_A* 3i8d_A* 2r7y_A*

Probab=98.75  E-value=8.8e-09  Score=78.97  Aligned_cols=83  Identities=14%  Similarity=0.088  Sum_probs=61.6

Q ss_pred             CCChHHHHHHHHHHHHHHhhcCCCCCcEEEEeccHHHHHHHhcccc----c-----cHHHHHHHHHHHHHHhcCCeEEEE
Q psy3058           9 LSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLFC----K-----NILIHDIQVACHKLILKGNNVKII   79 (244)
Q Consensus         9 ~~t~~~AEl~Ai~~al~~~~~~~~~~~i~i~tDs~~al~~l~~~~~----~-----~~~~~~i~~~~~~l~~~~~~v~~~   79 (244)
                      .+|++.||+.|++.||+.+.+...  .|.|+|||++|++.+.+.+.    +     .++.+.+.....-+..  ..++..
T Consensus        48 ~~TNN~aEl~A~i~aL~~~~~~~~--~v~i~tDS~~vi~w~~~~~~k~~~~~~v~n~dLw~~l~~~~~w~~~--~~~~~~  123 (142)
T 1zbf_A           48 IGTNNMGEFLAIVHGLRYLKERNS--RKPIYSNSQTAIKWVKDKKAKSTLVRNEETALIWKLVDEAEEWLNT--HTYETP  123 (142)
T ss_dssp             EECHHHHHHHHHHHHHHHHHHTTC--CCCEEESCHHHHHHHHHTCCCCCCCCSTTTHHHHHHHHHHHHHHHH--CCCCCC
T ss_pred             CcCcHHHHHHHHHHHHHHHHhCCC--eEEEEEehHHHHHHHHcCCccCCCCCCcccHHHHHHHHHHHHHHhh--CCCcee
Confidence            578999999999999999987543  79999999999999998762    1     1344444333333333  345556


Q ss_pred             eecCCCCCccchhhch
Q psy3058          80 WIPSHCGIAGNEEVDK   95 (244)
Q Consensus        80 Wvp~H~gi~gNe~AD~   95 (244)
                      .|.-|++.-||..||.
T Consensus       124 ~~kw~~~~~ge~pad~  139 (142)
T 1zbf_A          124 ILKWQTDKWGEIKADY  139 (142)
T ss_dssp             EEECCHHHHCSCTTCC
T ss_pred             EEEeccCccCcCcccc
Confidence            6777999999999995

>4htu_A Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine, W-C base PAIR, wobble base PAIR, D helix; HET: DNA UCL; 1.49A {Bacillus halodurans} PDB: 3d0p_A* 4hue_A* 4huf_A* 4hug_A* 1zbf_A 1zbi_A 2g8u_A 3uld_A* 3ey1_A* 3twh_A* 2g8f_A 2g8v_A 2g8w_A 2g8i_A 2g8h_A 2g8k_A 3i8d_A* 2r7y_A* 1zbl_A

Probab=98.33  E-value=1.6e-06  Score=65.38  Aligned_cols=42  Identities=19%  Similarity=0.241  Sum_probs=37.0

Q ss_pred             CCChHHHHHHHHHHHHHHhhcCCCCCcEEEEeccHHHHHHHhcc
Q psy3058           9 LSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQL   52 (244)
Q Consensus         9 ~~t~~~AEl~Ai~~al~~~~~~~~~~~i~i~tDs~~al~~l~~~   52 (244)
                      .+||+.||++|++.||+.+.+..  ..+.|+||||+|++.|.+.
T Consensus        42 ~tTNN~aEl~A~i~aL~~l~~~~--~~v~i~tDSqyVi~wi~~~   83 (134)
T 4htu_A           42 IGTNNMGEFLAIVHGLRYLKERN--SRKPIYSNSQTAIKWVKDK   83 (134)
T ss_dssp             EECHHHHHHHHHHHHHHHHHHTT--CCCCEEESCHHHHHHHHHT
T ss_pred             CCchHHHHHHHHHHHHHHHHhCC--CCEEEEcchHHHHHHHHcC
Confidence            57999999999999999998743  2489999999999999875

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	244
d1mu2a1	126	c.55.3.1 (A:430-555) HIV RNase H (Domain of revers	6e-07
d1rila_	147	c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermoph	6e-05

>d1mu2a1 c.55.3.1 (A:430-555) HIV RNase H (Domain of reverse transcriptase) {Human immunodeficiency virus type 2 [TaxId: 11709]} Length = 126

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: HIV RNase H (Domain of reverse transcriptase)
species: Human immunodeficiency virus type 2 [TaxId: 11709]

 Score = 45.3 bits (106), Expect = 6e-07
 Identities = 16/85 (18%), Positives = 33/85 (38%), Gaps = 2/85 (2%)

Query: 17  AFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLFCKNILIHDIQVACHKLILKGNNV 76
               E+    +        + I  DS+ ++  +     ++      Q+    +  +   +
Sbjct: 44  NQQAELEAFAMALTDSGPKVNIIVDSQYVMGIVASQPTESESKIVNQIIEEMIKKE--AI 101

Query: 77  KIIWIPSHCGIAGNEEVDKAAQSFI 101
            + W+P+H GI GN+EVD      I
Sbjct: 102 YVAWVPAHKGIGGNQEVDHLVSQGI 126

>d1rila_ c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermophilus [TaxId: 274]} Length = 147

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: RNase H (RNase HI)
species: Thermus thermophilus [TaxId: 274]

 Score = 39.9 bits (92), Expect = 6e-05
 Identities = 17/104 (16%), Positives = 38/104 (36%), Gaps = 12/104 (11%)

Query: 13  FTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLFCKN------------ILIH 60
            T     ++  ++ L     P  + ++TDS  L  +  + + +              + +
Sbjct: 41  TTNNRMELKAAIEGLKALKEPCEVDLYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKN 100

Query: 61  DIQVACHKLILKGNNVKIIWIPSHCGIAGNEEVDKAAQSFINAQ 104
                   L +  + V+  ++  H G   NE VD+ A+    +Q
Sbjct: 101 RDLWEALLLAMAPHRVRFHFVKGHTGHPENERVDREARRQAQSQ 144

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	244
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.81
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.73
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	99.73
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	99.46
d1zbfa1	132	BH0863-like Ribonuclease H {Bacillus halodurans [T	99.01

>d1mu2a1 c.55.3.1 (A:430-555) HIV RNase H (Domain of reverse transcriptase) {Human immunodeficiency virus type 2 [TaxId: 11709]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: HIV RNase H (Domain of reverse transcriptase)
species: Human immunodeficiency virus type 2 [TaxId: 11709]

Probab=99.81  E-value=1.9e-20  Score=140.10  Aligned_cols=83  Identities=24%  Similarity=0.423  Sum_probs=67.2

Q ss_pred             CCChHHHHHHHHHHHHHHhhcCCCCCcEEEEeccHHHHHHHhccccc--cHHHHHHHHHHHHHHhcCCeEEEEeecCCCC
Q psy3058           9 LSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLFCK--NILIHDIQVACHKLILKGNNVKIIWIPSHCG   86 (244)
Q Consensus         9 ~~t~~~AEl~Ai~~al~~~~~~~~~~~i~i~tDs~~al~~l~~~~~~--~~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~g   86 (244)
                      ..|++.||+.||++||+..     ...+.|+|||++|++.+.+....  ......+   +..+ .....|.|.|||||+|
T Consensus        41 ~~tnn~AEl~Ai~~al~~~-----~~~i~I~tDS~~v~~~~~~~~~~~~~~~~~~~---~~~~-~~~~~v~~~wV~gH~g  111 (126)
T d1mu2a1          41 QTTNQQAELEAFAMALTDS-----GPKVNIIVDSQYVMGIVASQPTESESKIVNQI---IEEM-IKKEAIYVAWVPAHKG  111 (126)
T ss_dssp             SCCHHHHHHHHHHHHHHTS-----CSEEEEEESCHHHHHHHHTCCSEESCHHHHHH---HHHH-HHCSEEEEEECCSSSC
T ss_pred             CCcchHHHHHHHHHHhccC-----CcceEEEechHHHHHHHhcCCccccchHHHHH---HHHh-hhcceeEEEEEeCCCC
Confidence            5799999999999999853     46799999999999999997542  2333322   3333 3456899999999999


Q ss_pred             CccchhhchHHHHH
Q psy3058          87 IAGNEEVDKAAQSF  100 (244)
Q Consensus        87 i~gNe~AD~lAk~a  100 (244)
                      ++|||.||+||++|
T Consensus       112 ~~gNe~AD~LA~~a  125 (126)
T d1mu2a1         112 IGGNQEVDHLVSQG  125 (126)
T ss_dssp             CTTHHHHHHHHHTT
T ss_pred             CcchHHHHHHHHhh
Confidence            99999999999987

>d1rila_ c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: RNase H (RNase HI)
species: Thermus thermophilus [TaxId: 274]

Probab=99.73  E-value=1.7e-18  Score=132.60  Aligned_cols=93  Identities=22%  Similarity=0.233  Sum_probs=72.2

Q ss_pred             CCChHHHHHHHHHHHHHHhhcCCCCCcEEEEeccHHHHHHHhccc------------cccHHH-HHHHHHHHHHHhcCCe
Q psy3058           9 LSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLF------------CKNILI-HDIQVACHKLILKGNN   75 (244)
Q Consensus         9 ~~t~~~AEl~Ai~~al~~~~~~~~~~~i~i~tDs~~al~~l~~~~------------~~~~~~-~~i~~~~~~l~~~~~~   75 (244)
                      .+|+++||+.|+..||+.+..   ...+.|+|||+++++.+....            .+.++. .+++..+..+. ....
T Consensus        40 ~~Tnn~aEl~Ai~~AL~~~~~---~~~i~i~tds~~~~~~~~~~~~~~~~~~~~~~~~~~~v~n~dL~~~l~~~~-~~~~  115 (147)
T d1rila_          40 CTTNNRMELKAAIEGLKALKE---PCEVDLYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAM-APHR  115 (147)
T ss_dssp             EECHHHHHHHHHHHHHHSCCS---CCEEEEECCCHHHHHHHHSSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHH-TTSE
T ss_pred             cccHHHHHHHHHHHHhhhccC---CceEEEecchhhhhccccccchhhhhhccccccccccchhHHHHHHHHHHh-hhcc
Confidence            458999999999999987643   457999999999999987632            112221 33444554543 4678


Q ss_pred             EEEEeecCCCCCccchhhchHHHHHhhhcC
Q psy3058          76 VKIIWIPSHCGIAGNEEVDKAAQSFINAQN  105 (244)
Q Consensus        76 v~~~Wvp~H~gi~gNe~AD~lAk~a~~~~~  105 (244)
                      |.|.|||||+|++|||.||+|||+|+....
T Consensus       116 v~~~wVkgHsg~~gNe~AD~LAk~aa~~~~  145 (147)
T d1rila_         116 VRFHFVKGHTGHPENERVDREARRQAQSQA  145 (147)
T ss_dssp             EECCCCCGGGSCTHHHHHHHHHHHHHTSSC
T ss_pred             cceEEccCCCCCcchHHHHHHHHHHHHHhc
Confidence            999999999999999999999999988754

>d1jl1a_ c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: RNase H (RNase HI)
species: Escherichia coli [TaxId: 562]

Probab=99.73  E-value=3.2e-18  Score=131.42  Aligned_cols=98  Identities=19%  Similarity=0.245  Sum_probs=75.7

Q ss_pred             CCCChHHHHHHHHHHHHHHhhcCCCCCcEEEEeccHHHHHHHhcccc-----------ccHH-HHHHHHHHHHHHhcCCe
Q psy3058           8 SLSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLFC-----------KNIL-IHDIQVACHKLILKGNN   75 (244)
Q Consensus         8 ~~~t~~~AEl~Ai~~al~~~~~~~~~~~i~i~tDs~~al~~l~~~~~-----------~~~~-~~~i~~~~~~l~~~~~~   75 (244)
                      ..+|++.||++|+..||+.+..   ...+.|+|||++++..+.....           +.++ ....+..+..+ .....
T Consensus        38 ~~~tnn~aE~~Ai~~Al~~~~~---~~~i~i~tds~~~i~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~i~~~-~~~~~  113 (152)
T d1jl1a_          38 TRTTNNRMELMAAIVALEALKE---HAEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAA-LGQHQ  113 (152)
T ss_dssp             EEECHHHHHHHHHHHHHHTCCS---CCEEEEEECCHHHHHHHHTTHHHHHHTTTBCTTSCBCTTHHHHHHHHHH-TTTCE
T ss_pred             CcccHHHHHHhhhhhhhhhhcc---cceEEEeecceeeEEcccchhhHhHhccchhcccCeeecHHHHHHHHHH-hhcce
Confidence            3568999999999999998743   3578999999999999876421           1121 12344445554 34568


Q ss_pred             EEEEeecCCCCCccchhhchHHHHHhhhcCCCcc
Q psy3058          76 VKIIWIPSHCGIAGNEEVDKAAQSFINAQNYSLI  109 (244)
Q Consensus        76 v~~~Wvp~H~gi~gNe~AD~lAk~a~~~~~~~~~  109 (244)
                      |+|+|||||+|++|||.||+|||+|+..+...+.
T Consensus       114 V~~~wV~gH~g~~gNe~AD~LAk~aa~~~~~~d~  147 (152)
T d1jl1a_         114 IKWEWVKGHAGHPENERADELARAAAMNPTLEDT  147 (152)
T ss_dssp             EEEEECCSSTTCHHHHHHHHHHHHHHHSCCBCCT
T ss_pred             eEEEEecccCCCccHHHHHHHHHHHHhCCCCCcc
Confidence            9999999999999999999999999998876644

>d1s1ta1 c.55.3.1 (A:430-539) HIV RNase H (Domain of reverse transcriptase) {Human immunodeficiency virus type 1 [TaxId: 11676]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: HIV RNase H (Domain of reverse transcriptase)
species: Human immunodeficiency virus type 1 [TaxId: 11676]

Probab=99.46  E-value=1.2e-13  Score=100.02  Aligned_cols=67  Identities=22%  Similarity=0.312  Sum_probs=54.6

Q ss_pred             CCChHHHHHHHHHHHHHHhhcCCCCCcEEEEeccHHHHHHHhcccc--ccHHHHHHHHHHHHHHhcCCeEEEEeecCC
Q psy3058           9 LSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLFC--KNILIHDIQVACHKLILKGNNVKIIWIPSH   84 (244)
Q Consensus         9 ~~t~~~AEl~Ai~~al~~~~~~~~~~~i~i~tDs~~al~~l~~~~~--~~~~~~~i~~~~~~l~~~~~~v~~~Wvp~H   84 (244)
                      .+||+.|||.||+.||+..     ...|.|+|||++|++++++...  .+++.++|.+.+    .....|.|.|||||
T Consensus        42 ~~TNn~aEl~Avi~aL~~~-----~~~v~I~TDS~yvi~~i~~~~~~~~~~l~~~il~~l----~~~~~v~i~WVpgH  110 (110)
T d1s1ta1          42 DTTNQKTELQAIYLALQDS-----GLEVNIVTDSQYALGIIQAQPDQSESELVNQIIEQL----IKKEKVYLAWVPAH  110 (110)
T ss_dssp             SCCHHHHHHHHHHHHHHHS-----CSEEEEEECCHHHHHHHHHCCSEESCHHHHHHHHHH----HHCSEEEEEECCSS
T ss_pred             cCcHHHHHHHHHHHHHHhC-----CCeEEEEEehHHHHHHHhcCccccchHHHHHHHHHH----hcCCceEEEEeCCC
Confidence            6799999999999999853     3579999999999999999764  445666665443    34678999999999

>d1zbfa1 c.55.3.1 (A:62-193) BH0863-like Ribonuclease H {Bacillus halodurans [TaxId: 86665]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: BH0863-like Ribonuclease H
species: Bacillus halodurans [TaxId: 86665]

Probab=99.01  E-value=9.4e-11  Score=86.49  Aligned_cols=83  Identities=14%  Similarity=0.112  Sum_probs=62.3

Q ss_pred             CCChHHHHHHHHHHHHHHhhcCCCCCcEEEEeccHHHHHHHhcccc----c-----cHHHHHHHHHHHHHHhcCCeEEEE
Q psy3058           9 LSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLFC----K-----NILIHDIQVACHKLILKGNNVKII   79 (244)
Q Consensus         9 ~~t~~~AEl~Ai~~al~~~~~~~~~~~i~i~tDs~~al~~l~~~~~----~-----~~~~~~i~~~~~~l~~~~~~v~~~   79 (244)
                      .+|++.||++|++.||+.+.+..  .++.|+|||++|++.+.+..-    +     ..+.+.+.+...-+  ....+.+.
T Consensus        41 ~~TNN~aEl~A~i~aL~~~~~~~--~~i~I~tDS~yvi~wv~~~~~kt~~~~~vkN~~l~~~i~~a~~~l--k~h~~~~~  116 (132)
T d1zbfa1          41 IGTNNMGEFLAIVHGLRYLKERN--SRKPIYSNSQTAIKWVKDKKAKSTLVRNEETALIWKLVDEAEEWL--NTHTYETP  116 (132)
T ss_dssp             EECHHHHHHHHHHHHHHHHHHTT--CCCCEEESCHHHHHHHHHTCCCCCCCCSTTTHHHHHHHHHHHHHH--HHCCCCCC
T ss_pred             ccchHHHHHHHHHHHHHHhhcCC--ceEEEEeccHHHHHHHHhCceecCcCCCcccHHHHHHHHHHHHHH--HhCCcCce
Confidence            57999999999999999997642  568999999999999987541    1     23333333222223  24568899


Q ss_pred             eecCCCCCccchhhch
Q psy3058          80 WIPSHCGIAGNEEVDK   95 (244)
Q Consensus        80 Wvp~H~gi~gNe~AD~   95 (244)
                      |++.|+..-||..||.
T Consensus       117 ~~KW~~~~wG~i~AD~  132 (132)
T d1zbfa1         117 ILKWQTDKWGEIKADY  132 (132)
T ss_dssp             EEECCHHHHCSCTTCC
T ss_pred             eEEecCcccccCCCCC
Confidence            9999999999999983