Psyllid ID: psy11794

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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-------250-------260-------270-------280-------290-------300-------310-------320-----
Protein Sequence
MCSTLLYLLDVEGALRYSNFYFGSNGMSYEYCWWSNKTYLHHENFSVMLLLGTLRKLINYTLHLQSVMQLFIFHIDTDTAYRLQENRYSCCYLGTLVGPGPRYFNLTTIYLAELLALYLCLKEISEFHSSSRIAIISDSLSVLSALGNICFSHPFISKIYQLWKLIVTRGTDVVFLWCPSHCGIDGNEAVDSAANHHTHPRHVNLCSTDDLKPWIKAIVKKDIVDMWNSIPPSNKLKRIKPTVDSWTSSFRNNRYEEVVLTRLRIGHTRVTHNHLFKKLPPPICQCGSVLTVVHILECPTLTPARISLSPQPNLGALHETKSTTG
Secondary Structure (PSIPRED)
cccccHHHHHcccccEEccccccccccccccccccccccccccccccHHcccHHHHHHccHHHHHHHHccccEEEEEcccccccccEEEEEEEEEcccccccccccccHHHHHHHHHHHHHHHHHHHccccEEEEEcccHHHHHHHcccccccHHHHHHHHHHHHHHHcccEEEEEEEccccccccHHHHHHHHccccccccccccccccHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccHHHHHcccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccHHHHHHHHHHHHEEccEEEcccccEEEEEEEccccEEcccccHHHHHHHHHHHHHHHHHHHHHHHHccEEEEEcccccccccccEEEEEEccccccccccccccHHHHHHHHHHHHHHHHHHHccccccEEEEEccHHHHHHHHccccccHHHHHHHHHHHHHHHcccEEEEEEEcccccccccHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccHHHHHHHHHHHccccHHHHHHccccccccccccccccHHHEEccHHHHHHHHHHHcccccccHcccHHHcc
Coil and Loop (DISEMBL)
MCSTLLYLLDVEGalrysnfyfgsngmsyEYCWwsnktylhheNFSVMLLLGTLRKLINYTLHLQSVMQLFIFHIDTDTayrlqenrysccylgtlvgpgpryfNLTTIYLAELLALYLCLKEISEFHSSSRIAIISDSLSVLSALGnicfshpfISKIYQLWKLIVTRGTDVVflwcpshcgidgneavdsaanhhthprhvnlcstddlKPWIKAIVKKDIVdmwnsippsnklkrikptvdswtssfrnnryeEVVLTRLRIGhtrvthnhlfkklpppicqcgsvltvvhilecptltparislspqpnlgalhetksttg
Flexible Loop (DISEMBL)
MCSTLLYLLDVEGALRYSNFYFGSNGMSYEYCWWSNKTYLHHENFSVMLLLGTLRKLINYTLHLQSVMQLFIFHIDTDTAYRLQENRYSCCYLGTLVGPGPRYFNLTTIYLAELLALYLCLKEISEFHSSSRIAIISDSLSVLSALGNICFSHPFISKIYQLWKLIVTRGTDVVFLWCPSHCGIDGNEAVDSAANHHTHPrhvnlcstddlKPWIKAIVKKDIVDmwnsippsnklkrikptvdswtssfrnnryeeVVLTRLRIGHTRVTHNHLFKKLPPPICQCGSVLTVVHILECPTLTparislspqpnlgalhetksttg
Low Complexity Region (SEG)
MCSTLLYLLDVEGALRYSNFYFGSNGMSYEYCWWSNKTYLHHENFSVMLLLGTLRKLINYTLHLQSVMQLFIFHIDTDTAYRLQENRYSCCYLGTLVGPGPRYFNlttiylaellalylclkeiSEFHSSSRIAIISDSLSVLSALGNICFSHPFISKIYQLWKLIVTRGTDVVFLWCPSHCGIDGNEAVDSAANHHTHPRHVNLCSTDDLKPWIKAIVKKDIVDMWNSIPPSNKLKRIKPTVDSWTSSFRNNRYEEVVLTRLRIGHTRVTHNHLFKKLPPPICQCGSVLTVVHILECPTLTPARISLSPQPNLGALHETKSTTG
Disordered region (IsUnstruct)
***TLLYLLDVEGALRYSNFYFGSNGMSYEYCWWSNKTYLHHENFSVMLLLGTLRKLINYTLHLQSVMQLFIFHIDTDTAYRLQENRYSCCYLGTLVGPGPRYFNLTTIYLAELLALYLCLK**********IAIISDSLSVLSALGNICFSHPFISKIYQLWKLIVTRGTDVVFLWCPSHCGIDGNEAVDSAANHHTHPRHVNLCSTDDLKPWIKAIVKKDIVDMWNSIPPSNKLKRIKPTVDSWTSSFRNNRYEEVVLTRLRIGHTRVTHNHLFKKLPPPICQCGSVLTVVHILECPTLTPARI*******************
Disordered Region (DISOPRED)
**STLLYLLDVEGALRYSNFYFGSNGMSYEYCWWSNKTYLHHENFSVMLLLG*L****NYTLHLQSVMQLFIFHIDTDTAYRLQENRYSCCYLGTLVGPGPRYFNLTTIYLAELLALYLCLKEISEFHSSSRIAIISDSLSVLSALGNICFSHPFISKIYQLWKLIVTRGTDVVFLWCPSHCGIDGNEAVDSAANHHTHPRHVNLCSTDDLKPWIKAIVKKDIVDMWNSIPPSNKLKRIKPTVDSWTSSFRNNRYEEVVLTRLRIGHTRVTHNHLFKKLPPPICQCGSVLTVVHILECPTLTPARISLSP***************
Disordered Region (DISEMBL)
MCSTLLYLLDVEGALRYSNFYFGSNGMSYEYCWWSNKTYLHHENFSVMLLLGTLRKLINYTLHLQSVMQLFIFHIDTDTAYRLQENRYSCCYLGTLVGPGPRYFNLTTIYLAELLALYLCLKEISEFHSSSRIAIISDSLSVLSALGNICFSHPFISKIYQLWKLIVTRGTDVVFLWCPSHCGIDGNEAVDSAANHHTHPRHVNLCSTDDLKPWIKAIVKKDIVDMWNSIPPSNKLKRIKPTVDSWTSSFRNNRYEEVVLTRLRIGHTRVTHNHLFKKLPPPICQCGSVLTVVHILECPTLTPARISLSPQPNLGA*********
Disordered Region (DISPRO)
MCSTLLYLLDVEGALRYSNFYFGSNGMSYEYCWWSNKTYLHHENFSVMLLLGTLRKLINYTLHLQSVMQLFIFHIDTDTAYRLQENRYSCCYLGTLVGPGPRYFNLTTIYLAELLALYLCLKEISEFHSSSRIAIISDSLSVLSALGNICFSHPFISKIYQLWKLIVTRGTDVVFLWCPSHCGIDGNEAVDSAANHHTHPRHVNLCSTDDLKPWIKAIVKKDIVDMWNSIPPSNKLKRIKPTVDSWTSSFRNNRYEEVVLTRLRIGHTRVTHNHLFKKLPPPICQCGSVLTVVHILECPTLTPARISLSPQPNLGALHE******
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MCSTLLYLLDVEGALRYSNFYFGSNGMSYEYCWWSNKTYLHHENFSVMLLLGTLRKLINYTLHLQSVMQLFIFHIDTDTAYRLQENRYSCCYLGTLVGPGPRYFNLTTIYLAELLALYLCLKEISEFHSSSRIAIISDSLSVLSALGNICFSHPFISKIYQLWKLIVTRGTDVVFLWCPSHCGIDGNEAVDSAANHHTHPRHVNLCSTDDLKPWIKAIVKKDIVDMWNSIPPSNKLKRIKPTVDSWTSSFRNNRYEEVVLTRLRIGHTRVTHNHLFKKLPPPICQCGSVLTVVHILECPTLTPARISLSPQPNLGALHETKSTTG
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	325
443693558	502	hypothetical protein CAPTEDRAFT_189741,	0.578	0.374	0.382	1e-23
443695973	261	hypothetical protein CAPTEDRAFT_23017, p	0.578	0.720	0.376	4e-23
443712830	397	hypothetical protein CAPTEDRAFT_202466 [	0.578	0.473	0.376	7e-23
443733872	400	hypothetical protein CAPTEDRAFT_197082 [	0.584	0.475	0.359	6e-22
443724607	397	hypothetical protein CAPTEDRAFT_208903 [	0.578	0.473	0.371	2e-21
125901787	1222	pol-like protein [Biomphalaria glabrata]	0.64	0.170	0.356	6e-21
427778603	1397	Putative tick transposon [Rhipicephalus	0.664	0.154	0.334	8e-21
443721618	471	hypothetical protein CAPTEDRAFT_200496,	0.649	0.447	0.313	6e-20
427791063	1035	Putative tick transposon, partial [Rhipi	0.603	0.189	0.357	9e-20
427791807	1212	Putative tick transposon, partial [Rhipi	0.6	0.160	0.358	2e-19

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

 Score =  117 bits (292), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 73/191 (38%), Positives = 99/191 (51%), Gaps = 3/191 (1%)

Query: 108 TIYLAELLALYLCLKEISEFHSSSRIAIISDSLSVLSALGNICFSHPFISKIYQLWKLIV 167
           +IY AEL+A+   L  I       +  I SDSLS L+AL N   +HP++  I      +V
Sbjct: 115 SIYTAELIAIEQALIFIETVKDEDQFNICSDSLSSLTALSNCDITHPYLLSILTKQNNLV 174

Query: 168 TRGTDVVFLWCPSHCGIDGNEAVDSAANHH-THPRHVNLCSTDDLKPWIKAIVKKDIVDM 226
            +G  VVF+WCPSH GI GNE  D  A      P         D K  I++ VK    + 
Sbjct: 175 RKGKLVVFIWCPSHVGILGNEVADRLAKQALVMPVTKLPLPHTDYKSPIRSYVKSLWQNE 234

Query: 227 WNSIPPSNKLKRIKPTVDSWTSSFRNNRYEEVVLTRLRIGHTRVTHNHLFKKLPPPIC-Q 285
           W+     NKL  I+P +  W    + +R  E+VL R RIGH+ +TH +L ++   P C  
Sbjct: 235 WDE-ETDNKLHSIQPVISEWKQGPQIDRRGEIVLARARIGHSHLTHGYLLRREVAPFCIP 293

Query: 286 CGSVLTVVHIL 296
           C S+LTV HIL
Sbjct: 294 CQSLLTVKHIL 304

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 =  115 bits (287), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 72/191 (37%), Positives = 99/191 (51%), Gaps = 3/191 (1%)

Query: 108 TIYLAELLALYLCLKEISEFHSSSRIAIISDSLSVLSALGNICFSHPFISKIYQLWKLIV 167
           +IY AEL+A+   L  I       +  I SDSLS L+AL N   +HP++  I      +V
Sbjct: 69  SIYTAELIAIEQALIFIETVKDEDQFNICSDSLSSLTALSNCDITHPYLLSILTKQNNLV 128

Query: 168 TRGTDVVFLWCPSHCGIDGNEAVDSAANHH-THPRHVNLCSTDDLKPWIKAIVKKDIVDM 226
            +G  VVF+WCPSH GI GNE  D  A      P         D K  I++ VK    + 
Sbjct: 129 RKGKLVVFIWCPSHVGILGNEVADRLAKQALVMPVTKLPLPHTDYKSPIRSYVKSLWQNE 188

Query: 227 WNSIPPSNKLKRIKPTVDSWTSSFRNNRYEEVVLTRLRIGHTRVTHNHLFKKLPPPIC-Q 285
           W+     NKL  I+P +  W    + +R  E+VL R RIGH+ +TH +L ++   P C  
Sbjct: 189 WDE-ETDNKLHSIQPVISEWKQGPQIDRRGEIVLARARIGHSHLTHGYLLRREVAPFCIP 247

Query: 286 CGSVLTVVHIL 296
           C S+L+V HIL
Sbjct: 248 CQSLLSVKHIL 258

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score =  114 bits (284), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 72/191 (37%), Positives = 98/191 (51%), Gaps = 3/191 (1%)

Query: 108 TIYLAELLALYLCLKEISEFHSSSRIAIISDSLSVLSALGNICFSHPFISKIYQLWKLIV 167
           +IY AEL+A+   L  I       +  I SDSLS L+AL N   +HP++  I      +V
Sbjct: 164 SIYTAELIAIEQALIFIETVKDEDQFNICSDSLSSLTALSNCDITHPYLLSILTKQNNLV 223

Query: 168 TRGTDVVFLWCPSHCGIDGNEAVDSAANHH-THPRHVNLCSTDDLKPWIKAIVKKDIVDM 226
            +G  VVF+WCPSH GI GNE  D  A      P         D K  I++ VK    + 
Sbjct: 224 RKGKKVVFIWCPSHVGILGNEVADRQAKQALVMPVTKLPLPHTDYKSPIRSYVKSLWQNE 283

Query: 227 WNSIPPSNKLKRIKPTVDSWTSSFRNNRYEEVVLTRLRIGHTRVTHNHLFKKLPPPIC-Q 285
           W+     NKL  I+P +  W    + +R  E+VL   RIGH+ +TH +L ++   P C  
Sbjct: 284 WDG-ETDNKLHIIQPVISEWKQGPQIDRRGEIVLACARIGHSHLTHGYLLRREVAPFCIP 342

Query: 286 CGSVLTVVHIL 296
           C S+LTV HIL
Sbjct: 343 CQSLLTVKHIL 353

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 =  110 bits (276), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 73/203 (35%), Positives = 109/203 (53%), Gaps = 13/203 (6%)

Query: 102 RYFNLTTIYLAELLALYLCLKEISEFHSSSRIAIISDSLSVLSALGNICFSHPFISKIYQ 161
           R  +  +I+ AELLA+Y   K ++    S+  +  +DSL  L  +GN    HP++ KI +
Sbjct: 33  RLPDSASIFSAELLAIY---KVLTLLECSASSSSSTDSLLSLQGIGNFNIKHPYVVKILE 89

Query: 162 LWKLIVTRGTDVVFLWCPSHCGIDGNEAVDSAANHHTHPRHVNLCS----TDDLKPWIKA 217
              L+  +G D+V  WCPSH G+ GNE  D  A           C+    + D KP    
Sbjct: 90  KCTLLHKKGIDLVMTWCPSHVGVMGNERADLLAKEALS---FTTCTIRIPSSDFKPITHE 146

Query: 218 IVKKDIVDMWNSIPPSNKLKRIKPTVDSWTSSFRNNRYEEVVLTRLRIGHTRVTHNHLFK 277
             K+   + W+S    NKL  I+PT+  W  S R  R EE+VL R RIGH+ +TH +L +
Sbjct: 147 FYKEKWQEQWSS-EQENKLYCIQPTLGKWAKSSREIRREEIVLARARIGHSHLTHGYLLR 205

Query: 278 KLPPPIC-QCGSVLTVVHI-LEC 298
           +  PP+C  C ++L++ HI +EC
Sbjct: 206 REMPPVCIPCQNILSIKHIFIEC 228

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|443724607|gb|ELU12531.1| hypothetical protein CAPTEDRAFT_208903 [Capitella teleta]

 Score =  109 bits (273), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 71/191 (37%), Positives = 97/191 (50%), Gaps = 3/191 (1%)

Query: 108 TIYLAELLALYLCLKEISEFHSSSRIAIISDSLSVLSALGNICFSHPFISKIYQLWKLIV 167
           +IY AEL+A+   L  I       +  I SDSLS L+AL N   +HP++  I      +V
Sbjct: 164 SIYTAELIAIEQALIFIETMKDEDQFNICSDSLSSLTALSNCDITHPYLLSILTKQNNLV 223

Query: 168 TRGTDVVFLWCPSHCGIDGNEAVDSAANHH-THPRHVNLCSTDDLKPWIKAIVKKDIVDM 226
            +G  VVF+WCPSH GI GNE  D  A      P         D K  I++ VK    + 
Sbjct: 224 RKGKLVVFIWCPSHVGILGNEVADRLAKQALVMPVTKLPLPHTDYKSPIRSYVKSLRQNE 283

Query: 227 WNSIPPSNKLKRIKPTVDSWTSSFRNNRYEEVVLTRLRIGHTRVTHNHLFKKLPPPIC-Q 285
           W+     NKL  I+P +  W    + +R  E+VL    IGH+ +TH +L ++   P C  
Sbjct: 284 WDE-ETDNKLHTIQPVISEWKQGPQIDRRGEIVLACACIGHSHLTHGYLLRREVAPFCIP 342

Query: 286 CGSVLTVVHIL 296
           C S+LTV HIL
Sbjct: 343 CQSLLTVKHIL 353

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score =  107 bits (268), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 76/213 (35%), Positives = 105/213 (49%), Gaps = 5/213 (2%)

Query: 108  TIYLAELLALYLCLKEISEFHSSSRIAIISDSLSVLSALGNICFSHPFISKIYQLWKLIV 167
            +I+ AEL A+ L L  + +    S+  I SDS S L ALG +    P + K  +L  LI 
Sbjct: 990  SIFTAELHAILLALMAV-KASERSKFIICSDSKSALQALGRMKTDIPLVHKSLKLLDLIT 1048

Query: 168  TRGTDVVFLWCPSHCGIDGNEAVDSAANHH-THPRHVNLCSTDDLKPWIKAIVKKDIVDM 226
                DV F+W PSH GI+GNEA D  A     H          DL+  I +   ++  + 
Sbjct: 1049 ADRRDVTFIWVPSHVGIEGNEAADREAKRALNHAVSGTQIPYSDLRQSIASATYREWQNR 1108

Query: 227  WNSIPPSNKLKRIKPTVDSWTSSFRNNRYEEVVLTRLRIGHTRVTHNHLFKKLPPPICQ- 285
            W +   S KL++I   V    +S    R     ++RLRIGHT +TH+ + K+  PP+C+ 
Sbjct: 1109 WEAETHS-KLRQIVADVRWRPTSKGLTRRGSTTMSRLRIGHTYITHSFVLKREEPPLCEY 1167

Query: 286  CGSVLTVVHIL-ECPTLTPARISLSPQPNLGAL 317
            C S LTV HIL +CP     R       NL  L
Sbjct: 1168 CDSRLTVEHILVDCPRYQDVRAKHFRATNLKTL 1200

Source: Biomphalaria glabrata

Species: Biomphalaria glabrata

Genus: Biomphalaria

Family: Planorbidae

Class: Gastropoda

Phylum: Mollusca

Superkingdom: Eukaryota

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

 Score =  107 bits (267), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 75/224 (33%), Positives = 106/224 (47%), Gaps = 8/224 (3%)

Query: 89   SCCYLGTLVGPGPRYFNLTTIYLAELLALYLCLKEISEFHSSSRIAIISDSLSVLSALG- 147
            SC   G            T+I+ AE   + L ++ I + H   R  I +DSLSV++AL  
Sbjct: 1123 SCAAYGESFSDAKTLHAHTSIFTAEAYGILLIVEHIKQ-HMIRRSIIYTDSLSVVTALSC 1181

Query: 148  NICFSHPFISKIYQLWKLIVTRGTDVVFLWCPSHCGIDGNEAVDSAANHHTHPRHVNLCS 207
              C  +P  +K+         +   +V  W P H GI GNE VD  A        +++ S
Sbjct: 1182 GKCSKNPVFNKLLNNMHEAYNQNLSIVLCWVPGHAGITGNEMVDKNAREAASRHTIDISS 1241

Query: 208  TD--DLKPWIKAIVKKDIVDMWNSIPPSNKLKRIKPTVDSWTSSFRNNRYEEVVLTRLRI 265
                DL P ++  ++      W+     NKL  +KP + S     + NR+ EV L RLRI
Sbjct: 1242 VPGVDLNPVVRRGLRSHWQVEWDK-QVDNKLHLVKPHL-SKVLPQKLNRFTEVTLARLRI 1299

Query: 266  GHTRVTHNHLFKKLPPPIC-QCGSVLTVVHIL-ECPTLTPARIS 307
            GHT  TH HL     PP C  CG  LT++H+L ECP L   R++
Sbjct: 1300 GHTYATHKHLLTGTDPPTCIHCGETLTILHVLIECPGLHQERLT 1343

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|443721618|gb|ELU10867.1| hypothetical protein CAPTEDRAFT_200496, partial [Capitella teleta]

 Score =  104 bits (259), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 69/220 (31%), Positives = 108/220 (49%), Gaps = 9/220 (4%)

Query: 85  ENRYSCCYLGTLVGPGPRYFNLTTIYLAELLALYLCLKEISEFHSSSRIAIISDSLSVLS 144
           E+  +C +  + +    +     +++ +E++A+   L+ +   +   +  I SDSLS + 
Sbjct: 31  EDSVACSFFSSRLKLKMKLPVQMSVFTSEIIAILSALRCVEADNEQHQFVICSDSLSAIM 90

Query: 145 ALGNICFSHPFISKIYQLWKLIVTRGTDVVFLWCPSHCGIDGNEAVDSAANHHTHPRHVN 204
           A+  +   HP++ ++    K I  +   VVF+WCPSH GI GNE  D+ A         N
Sbjct: 91  AIHGMDVRHPYVLQVLYAIKSISQQEKIVVFMWCPSHVGIPGNEMADTLAKEALS--STN 148

Query: 205 LCS----TDDLKPWIKAIVKKDIVDMWNSIPPSNKLKRIKPTVDSWTSSFRNNRYEEVVL 260
           L        DL+  IK  ++      W+    SNKL  I PT+  W    R  R EE+VL
Sbjct: 149 LAELPVPASDLRCLIKKYIRSRWQHEWDE-QHSNKLHSIHPTIGPWPPCQREKRREEIVL 207

Query: 261 TRLRIGHTRVTHNHLFKKLPPPIC-QCGSVLTVVH-ILEC 298
            R+RIGHT  TH+++ +      C  C   LTV H I+EC
Sbjct: 208 ARIRIGHTHYTHDYIPRGDDQTECVACVCPLTVQHIIIEC 247

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score =  103 bits (258), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 73/204 (35%), Positives = 106/204 (51%), Gaps = 8/204 (3%)

Query: 107  TTIYLAELLALYLCLKEISEFHSSSRIAIISDSLSVLSALGNIC-FSHPFISKIYQLWKL 165
            T+I+ AE  A+++ +K I +    S + I +DSLSV+ AL  +    +P ++ +Y L   
Sbjct: 828  TSIFTAEAYAIFVAVKHIEQLKLPSAV-IYTDSLSVVKALKTLKKHKNPVLASLYSLLCT 886

Query: 166  IVTRGTDVVFLWCPSHCGIDGNEAVDS-AANHHTHPRHVNLC-STDDLKPWIKAIVKKDI 223
            +      VV  W P H  I GN   D  AA+ H +  H  L     DLKP +K  ++   
Sbjct: 887  VYALKQHVVVCWVPGHREIQGNVLADQLAASAHENAAHTFLAIPALDLKPLLKRKLRAYW 946

Query: 224  VDMWNSIPPSNKLKRIKPTVDSWTSSFRNNRYEEVVLTRLRIGHTRVTHNHLFKKLPPPI 283
              +W++    NKL  IKP +  W  + ++ R  E+ LTRLR GHT  TH +L     PP 
Sbjct: 947  QSIWDT-QTQNKLHAIKPQLGEWPPASKSRR-TEITLTRLRTGHTHTTHAYLLSGNDPPR 1004

Query: 284  CQ-CGSVLTVVHIL-ECPTLTPAR 305
            C+ CG  LTV+HIL +C  L   R
Sbjct: 1005 CERCGEPLTVLHILIQCNELDAMR 1028

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|427791807|gb|JAA61355.1| Putative tick transposon, partial [Rhipicephalus pulchellus]

 Score =  102 bits (255), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 72/201 (35%), Positives = 100/201 (49%), Gaps = 6/201 (2%)

Query: 108  TIYLAELLALYLCLKEISEFHSSSRIAIISDSLSVLSALGNICFSHPFISKIYQLWKLIV 167
            +I+ AE+ ALY   ++I        I I +DSLS L AL       P +  I  +  LI 
Sbjct: 973  SIFTAEVYALYEAARKIIAGKHKKAI-IYTDSLSALKALHIKSECEPLVGDILNM-VLIN 1030

Query: 168  TRGTDVVFLWCPSHCGIDGNEAVDSAANHHTHPRHVNL-CSTDDLKPWIKAIVKKDIVDM 226
            ++   + F W PSH GI GNE  D  A+   H     +     D +  I+  +       
Sbjct: 1031 SKVISMRFCWVPSHVGIPGNEKADKCASLAAHKTLTKIRIPLKDSQRTIRLALLAKWQQQ 1090

Query: 227  WNSIPPSNKLKRIKPTVDSWTSSFRNNRYEEVVLTRLRIGHTRVTHNHLFKKLPPPICQ- 285
            W+S   SNKL  +KPT+  W +     R+ EV+L RLRIGHT +THN L  K   P+C+ 
Sbjct: 1091 WDSCT-SNKLHLVKPTLGEWKNCRHQERFIEVILCRLRIGHTHLTHNFLLTKEEQPMCEK 1149

Query: 286  CGSVLTVVHIL-ECPTLTPAR 305
            C   LT++HIL  CP +   R
Sbjct: 1150 CQEPLTLIHILILCPNIETQR 1170

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

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	325
ASPGD|ASPL0000075333	486	AN10625 [Emericella nidulans (	0.415	0.277	0.255	0.00043

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

 Score = 117 (46.2 bits), Expect = 0.00043, P = 0.00043
 Identities = 38/149 (25%), Positives = 65/149 (43%)

Query:   170 GTDVVFLWCPSHCGIDGNEAVDSAANHHTHPRHVN-----LCSTDDLKPWIKAIVKKDIV 224
             G +V F W P+H G++GNE  D  A   T  R +      +     +K     +V     
Sbjct:   283 GLNVHFRWIPAHRGVEGNEQADRRAKEATGWRRIRGHRGRMTIRSAVKRRAHEVVNARWE 342

Query:   225 DMWNSIPPSNKLKRIKPTVDSWTSSFRNNRYEEV--VLTRLRIGHTRVTHNHLFKKLPPP 282
             + W S     +L  + PT          + +  +  ++ ++R G   + H +L+++  P 
Sbjct:   343 NDWKSCHHGRELYELTPTPTRKVLRVHQDLHRALSTIIVQMRTGKIGLRH-YLYQRGVPD 401

Query:   283 I----CQCG-SVLTVVHIL-ECPTLTPAR 305
             +    CQCG +  +V HIL  CPT +  R
Sbjct:   402 VPNSDCQCGRATQSVRHILLACPTFSGLR 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   0.137   0.444    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      325       306   0.00099  115 3  11 22  0.49    33
                                                     33  0.45    37


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:  618 (66 KB)
  Total size of DFA:  251 KB (2134 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:  25.27u 0.10s 25.37t   Elapsed:  00:00:04
  Total cpu time:  25.27u 0.10s 25.37t   Elapsed:  00:00:04
  Start:  Thu Aug 15 16:23:38 2013   End:  Thu Aug 15 16:23:42 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	3.1.26.4	LOW CONFIDENCE prediction!
3rd Layer	3.1.26	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	325
cd09276	128	cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom	1e-23
pfam00075	126	pfam00075, RNase_H, RNase H	4e-13
cd06222	123	cd06222, RNase_H, RNase H is an endonuclease that	3e-08

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

 Score = 93.5 bits (233), Expect = 1e-23
 Identities = 29/89 (32%), Positives = 43/89 (48%), Gaps = 1/89 (1%)

Query: 107 TTIYLAELLALYLCLKEISEFHSS-SRIAIISDSLSVLSALGNICFSHPFISKIYQLWKL 165
            +++ AELLA+   L+          +I I SDS + L AL +   S P + +I +  + 
Sbjct: 35  CSVFDAELLAILEALQLALREGRRARKITIFSDSQAALKALRSPRSSSPLVLRIRKAIRE 94

Query: 166 IVTRGTDVVFLWCPSHCGIDGNEAVDSAA 194
           +   G  V   W P H GI+GNE  D  A
Sbjct: 95  LANHGVKVRLHWVPGHSGIEGNERADRLA 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 = 65.0 bits (159), Expect = 4e-13
 Identities = 29/92 (31%), Positives = 41/92 (44%), Gaps = 12/92 (13%)

Query: 107 TTIYLAELLALYLCLKEISEFHSSSRIAIISDSLSV----LSALGNICFSHPFISKIYQL 162
           TT   AELLAL   L+ +S      ++ I +DS  V     +       S P  ++I++L
Sbjct: 38  TTNQRAELLALIEALEALS----GQKVNIYTDSQYVIGGITNGWPTKSESKPIKNEIWEL 93

Query: 163 WKLIVTRGTDVVFLWCPSHCGIDGNEAVDSAA 194
               + +   V   W P H GI GNE  D  A
Sbjct: 94  ----LQKKHKVYIQWVPGHSGIPGNELADKLA 121

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 = 51.2 bits (123), Expect = 3e-08
 Identities = 23/108 (21%), Positives = 39/108 (36%), Gaps = 9/108 (8%)

Query: 89  SCCYLGTLVGPGPRYFNLTTIYLAELLALYLCLKEISEFHSSSRIAIISDSLSVLSALGN 148
              +L       P      T   AELLAL   L+   +     ++ I +DS  V+  + +
Sbjct: 23  EGAWLFAGSLSIPAA----TNNEAELLALLEALELALD-LGLKKLIIETDSKYVVDLINS 77

Query: 149 ICFSHPFISKIYQLWKLIVTRGTDVVFLWCPSHCGIDGNEAVDSAANH 196
                   + +     L++++  D+ F   P      GNE  D  A  
Sbjct: 78  WSKGWKKNNLLLWDILLLLSKFIDIRFEHVPRE----GNEVADRLAKE 121

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	325
PRK06548	161	ribonuclease H; Provisional	99.93
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	99.92
PRK08719	147	ribonuclease H; Reviewed	99.9
PRK00203	150	rnhA ribonuclease H; Reviewed	99.89
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	99.89
PRK13907	128	rnhA ribonuclease H; Provisional	99.81
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	99.81
KOG3752|consensus	371		99.78
PRK07708	219	hypothetical protein; Validated	99.7
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	99.65
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	99.31
PF13966	86	zf-RVT: zinc-binding in reverse transcriptase	93.8
PF05380	159	Peptidase_A17: Pao retrotransposon peptidase ; Int	85.31

>PRK06548 ribonuclease H; Provisional

Probab=99.93  E-value=3.2e-25  Score=190.24  Aligned_cols=128  Identities=21%  Similarity=0.200  Sum_probs=96.6

Q ss_pred             cEEEEEcCCccCCCCceeEEEEEeecCCCCccCCCCchHHHHHHHHHHHHHHhHhhcCCceEEEEeccHHHHHHhcCC--
Q psy11794         72 IFHIDTDTAYRLQENRYSCCYLGTLVGPGPRYFNLTTIYLAELLALYLCLKEISEFHSSSRIAIISDSLSVLSALGNI--  149 (325)
Q Consensus        72 ~~~IytDGS~~~~~~~~g~a~i~~~~g~~~~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~~i~I~tDS~~ai~~l~~~--  149 (325)
                      .+.||||||+.+++++.|+|++....+....-...+||++|||+|++.||+.+..  ....|.|+|||++|+++++.|  
T Consensus         5 ~~~IytDGa~~gnpg~~G~g~~~~~~~~~~g~~~~~TNnraEl~Aii~aL~~~~~--~~~~v~I~TDS~yvi~~i~~W~~   82 (161)
T PRK06548          5 EIIAATDGSSLANPGPSGWAWYVDENTWDSGGWDIATNNIAELTAVRELLIATRH--TDRPILILSDSKYVINSLTKWVY   82 (161)
T ss_pred             EEEEEEeeccCCCCCceEEEEEEeCCcEEccCCCCCCHHHHHHHHHHHHHHhhhc--CCceEEEEeChHHHHHHHHHHHH
Confidence            3689999999999999999977653211111113589999999999999986643  446799999999999999952  


Q ss_pred             ------CC-C--hHHH-HHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHHHHHhcccCCCC
Q psy11794        150 ------CF-S--HPFI-SKIYQLWKLIVTRGTDVVFLWCPSHCGIDGNEAVDSAANHHTHPRH  202 (325)
Q Consensus       150 ------~~-~--~~~~-~~i~~~~~~l~~~~~~i~~~WVpgH~gi~gNe~AD~LAk~aa~~~~  202 (325)
                            |. +  +++. .++++.+..+... ..|+|.|||||+|++|||.||+||++|+....
T Consensus        83 ~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~-~~v~~~wVkgHsg~~gNe~aD~LA~~aa~~~~  144 (161)
T PRK06548         83 SWKMRKWRKADGKPVLNQEIIQEIDSLMEN-RNIRMSWVNAHTGHPLNEAADSLARQAANNFS  144 (161)
T ss_pred             HHHHCCCcccCCCccccHHHHHHHHHHHhc-CceEEEEEecCCCCHHHHHHHHHHHHHHHHhc
Confidence                  22 2  3443 3455544445433 47999999999999999999999999986544

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

Probab=99.92  E-value=4.2e-25  Score=186.84  Aligned_cols=130  Identities=20%  Similarity=0.167  Sum_probs=102.6

Q ss_pred             cEEEEEcCCccCCCCceeEEEEEeecCCCCcc---CCCCchHHHHHHHHHHHHHHhHhhcCCceEEEEeccHHHHHHhcC
Q psy11794         72 IFHIDTDTAYRLQENRYSCCYLGTLVGPGPRY---FNLTTIYLAELLALYLCLKEISEFHSSSRIAIISDSLSVLSALGN  148 (325)
Q Consensus        72 ~~~IytDGS~~~~~~~~g~a~i~~~~g~~~~l---~~~~s~~~AEl~Ai~~AL~~a~~~~~~~~i~I~tDS~~ai~~l~~  148 (325)
                      .++||||||+.+++|++|+|++..+-.....+   -..+||++||++|++.||+.+.+ .+...|.|+|||++|++.|+.
T Consensus         3 ~v~if~DGa~~gNpG~gG~g~vl~~~~~~~~~s~~~~~tTNNraEl~A~i~AL~~l~~-~~~~~v~l~tDS~yv~~~i~~   81 (154)
T COG0328           3 KVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEGRTTNNRAELRALIEALEALKE-LGACEVTLYTDSKYVVEGITR   81 (154)
T ss_pred             ceEEEecCccCCCCCCceEEEEEEcCCceEEEeeeeecccChHHHHHHHHHHHHHHHh-cCCceEEEEecHHHHHHHHHH
Confidence            35899999999999999999777632111111   12789999999999999999997 678999999999999999995


Q ss_pred             C---CCC--------hHH-HHHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHHHHHhcccCCCC
Q psy11794        149 I---CFS--------HPF-ISKIYQLWKLIVTRGTDVVFLWCPSHCGIDGNEAVDSAANHHTHPRH  202 (325)
Q Consensus       149 ~---~~~--------~~~-~~~i~~~~~~l~~~~~~i~~~WVpgH~gi~gNe~AD~LAk~aa~~~~  202 (325)
                      |   |..        .|+ ...+++.+.++......|.+.|||||+|.++||+||+||+.|++...
T Consensus        82 w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~~~~~~~  147 (154)
T COG0328          82 WIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAREAARAAK  147 (154)
T ss_pred             HHhhccccCccccccCccccHHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHHHHHhhh
Confidence            4   111        122 12455555556667779999999999999999999999999987653

>PRK08719 ribonuclease H; Reviewed

Probab=99.90  E-value=2.4e-23  Score=176.77  Aligned_cols=122  Identities=23%  Similarity=0.145  Sum_probs=90.4

Q ss_pred             cEEEEEcCCccCCCC---ceeEEEEEeec-C-----CCCccCCCCchHHHHHHHHHHHHHHhHhhcCCceEEEEeccHHH
Q psy11794         72 IFHIDTDTAYRLQEN---RYSCCYLGTLV-G-----PGPRYFNLTTIYLAELLALYLCLKEISEFHSSSRIAIISDSLSV  142 (325)
Q Consensus        72 ~~~IytDGS~~~~~~---~~g~a~i~~~~-g-----~~~~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~~i~I~tDS~~a  142 (325)
                      .+.||||||+.++++   ++|+|++...- +     ....+...+||++|||.|++.||+.+.+ .    ..|+|||++|
T Consensus         4 ~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~-~----~~i~tDS~yv   78 (147)
T PRK08719          4 SYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARD-G----DVIYSDSDYC   78 (147)
T ss_pred             eEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCC-C----CEEEechHHH
Confidence            468999999988876   46777654321 1     1112334579999999999999999865 2    3799999999


Q ss_pred             HHHhc--------CCCCC---hHHH-HHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHHHHHhcccC
Q psy11794        143 LSALG--------NICFS---HPFI-SKIYQLWKLIVTRGTDVVFLWCPSHCGIDGNEAVDSAANHHTH  199 (325)
Q Consensus       143 i~~l~--------~~~~~---~~~~-~~i~~~~~~l~~~~~~i~~~WVpgH~gi~gNe~AD~LAk~aa~  199 (325)
                      ++.++        ++|..   .++. .++++.+..+.. ...|.|.|||||+|++|||.||+||++|++
T Consensus        79 i~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~-~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~  146 (147)
T PRK08719         79 VRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRA-RKYVEVEKVTAHSGIEGNEAADMLAQAAAE  146 (147)
T ss_pred             HHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhC-CCcEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence            99994        33432   2221 345555555554 577999999999999999999999999875

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=99.89  E-value=2.7e-23  Score=177.09  Aligned_cols=126  Identities=20%  Similarity=0.194  Sum_probs=93.3

Q ss_pred             EEEEEcCCccCCCCceeEEEEEeecCCCCc---cCCCCchHHHHHHHHHHHHHHhHhhcCCceEEEEeccHHHHHHhcCC
Q psy11794         73 FHIDTDTAYRLQENRYSCCYLGTLVGPGPR---YFNLTTIYLAELLALYLCLKEISEFHSSSRIAIISDSLSVLSALGNI  149 (325)
Q Consensus        73 ~~IytDGS~~~~~~~~g~a~i~~~~g~~~~---l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~~i~I~tDS~~ai~~l~~~  149 (325)
                      +.||||||+.++++.+|+|++....+....   .....||++|||.|++.||+.+.+   ...|.|+|||+++++.|+.|
T Consensus         4 v~iytDGs~~~n~~~~g~g~v~~~~~~~~~~~~~~~~~TN~~aEL~Ai~~AL~~~~~---~~~v~I~tDS~yvi~~i~~w   80 (150)
T PRK00203          4 VEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGEALTTNNRMELMAAIEALEALKE---PCEVTLYTDSQYVRQGITEW   80 (150)
T ss_pred             EEEEEEecccCCCCceEEEEEEEECCeeEEEecCCCCCcHHHHHHHHHHHHHHHcCC---CCeEEEEECHHHHHHHHHHH
Confidence            689999999999888888876643111100   123679999999999999998855   56899999999999999863


Q ss_pred             --------CCC---hHHH-HHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHHHHHhcccCCCC
Q psy11794        150 --------CFS---HPFI-SKIYQLWKLIVTRGTDVVFLWCPSHCGIDGNEAVDSAANHHTHPRH  202 (325)
Q Consensus       150 --------~~~---~~~~-~~i~~~~~~l~~~~~~i~~~WVpgH~gi~gNe~AD~LAk~aa~~~~  202 (325)
                              +..   .++. ..+++.+..+. ....|.|.|||||+|++||+.||+|||+|+....
T Consensus        81 ~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~-~~~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~~~  144 (150)
T PRK00203         81 IHGWKKNGWKTADKKPVKNVDLWQRLDAAL-KRHQIKWHWVKGHAGHPENERCDELARAGAEEAT  144 (150)
T ss_pred             HHHHHHcCCcccCCCccccHHHHHHHHHHh-ccCceEEEEecCCCCCHHHHHHHHHHHHHHHHhh
Confidence                    211   2221 12333333333 3378999999999999999999999999986543

>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=99.89  E-value=2.8e-23  Score=171.85  Aligned_cols=116  Identities=32%  Similarity=0.431  Sum_probs=90.9

Q ss_pred             EEEEEcCCccCCCCceeEEEEEeecCC--CCccCCCCchHHHHHHHHHHHHHHhHhhcCCceEEEEeccHHHHHHhcC--
Q psy11794         73 FHIDTDTAYRLQENRYSCCYLGTLVGP--GPRYFNLTTIYLAELLALYLCLKEISEFHSSSRIAIISDSLSVLSALGN--  148 (325)
Q Consensus        73 ~~IytDGS~~~~~~~~g~a~i~~~~g~--~~~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~~i~I~tDS~~ai~~l~~--  148 (325)
                      +.||||||+.++++..|+|++. ..+.  ...++ ..|+++|||.||..||+.+ .   .+.|+|+|||+++++.+..  
T Consensus         4 ~~iytDgS~~~~~~~~~~g~v~-~~~~~~~~~~~-~~s~~~aEl~Ai~~AL~~~-~---~~~v~I~tDS~~v~~~l~~~~   77 (132)
T PF00075_consen    4 IIIYTDGSCRPNPGKGGAGYVV-WGGRNFSFRLG-GQSNNRAELQAIIEALKAL-E---HRKVTIYTDSQYVLNALNKWL   77 (132)
T ss_dssp             EEEEEEEEECTTTTEEEEEEEE-ETTEEEEEEEE-SECHHHHHHHHHHHHHHTH-S---TSEEEEEES-HHHHHHHHTHH
T ss_pred             EEEEEeCCccCCCCceEEEEEE-ECCeEEEeccc-ccchhhhheehHHHHHHHh-h---cccccccccHHHHHHHHHHhc
Confidence            5899999999888877878744 3322  12233 7899999999999999944 5   4999999999999998887  


Q ss_pred             ---CCCC---h-HHHHHHHHHHHHHHhcCCeEEEEEecCCCCC-ccchHHHHHHhccc
Q psy11794        149 ---ICFS---H-PFISKIYQLWKLIVTRGTDVVFLWCPSHCGI-DGNEAVDSAANHHT  198 (325)
Q Consensus       149 ---~~~~---~-~~~~~i~~~~~~l~~~~~~i~~~WVpgH~gi-~gNe~AD~LAk~aa  198 (325)
                         .+..   . ++..+|.+.   + ..+..|.|.|||||+|+ .|||.||+|||+|+
T Consensus        78 ~~~~~~~~~~~~~i~~~i~~~---~-~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~  131 (132)
T PF00075_consen   78 HGNGWKKTSNGRPIKNEIWEL---L-SRGIKVRFRWVPGHSGVPQGNERADRLAKEAA  131 (132)
T ss_dssp             HHTTSBSCTSSSBHTHHHHHH---H-HHSSEEEEEESSSSSSSHHHHHHHHHHHHHHH
T ss_pred             cccccccccccccchhheeec---c-ccceEEeeeeccCcCCCchhHHHHHHHHHHhc
Confidence               3432   2 566655553   3 56899999999999999 69999999999986

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 ....

>PRK13907 rnhA ribonuclease H; Provisional

Probab=99.81  E-value=2.1e-19  Score=148.79  Aligned_cols=124  Identities=18%  Similarity=0.126  Sum_probs=96.1

Q ss_pred             cEEEEEcCCccCCCCceeEEEEEeecCCCCc---cCCCCchHHHHHHHHHHHHHHhHhhcCCceEEEEeccHHHHHHhcC
Q psy11794         72 IFHIDTDTAYRLQENRYSCCYLGTLVGPGPR---YFNLTTIYLAELLALYLCLKEISEFHSSSRIAIISDSLSVLSALGN  148 (325)
Q Consensus        72 ~~~IytDGS~~~~~~~~g~a~i~~~~g~~~~---l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~~i~I~tDS~~ai~~l~~  148 (325)
                      +++||||||+.++++.+|+|++.........   .....|++.||+.|++.||+.+.+ .+.++|.|+|||+.+++.+++
T Consensus         1 ~~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~~~~~~~tn~~AE~~All~aL~~a~~-~g~~~v~i~sDS~~vi~~~~~   79 (128)
T PRK13907          1 MIEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLPLGTMSNHEAEYHALLAALKYCTE-HNYNIVSFRTDSQLVERAVEK   79 (128)
T ss_pred             CEEEEEeeCCCCCCCccEEEEEEEECCeeEEEEecccccCCcHHHHHHHHHHHHHHHh-CCCCEEEEEechHHHHHHHhH
Confidence            3689999999999999999987764221100   124579999999999999999998 677899999999999999999


Q ss_pred             CCCChHHHHHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHHHHHhcccCC
Q psy11794        149 ICFSHPFISKIYQLWKLIVTRGTDVVFLWCPSHCGIDGNEAVDSAANHHTHP  200 (325)
Q Consensus       149 ~~~~~~~~~~i~~~~~~l~~~~~~i~~~WVpgH~gi~gNe~AD~LAk~aa~~  200 (325)
                      .+...+-...+.+.+..+...+..+.|.|||.    +.|+.||.||+.|...
T Consensus        80 ~~~~~~~~~~l~~~~~~l~~~f~~~~~~~v~r----~~N~~Ad~LA~~a~~~  127 (128)
T PRK13907         80 EYAKNKMFAPLLEEALQYIKSFDLFFIKWIPS----SQNKVADELARKAILQ  127 (128)
T ss_pred             HHhcChhHHHHHHHHHHHHhcCCceEEEEcCc----hhchhHHHHHHHHHhc
Confidence            76542222333443444556777888999996    5999999999998743

>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=99.81  E-value=9e-19  Score=140.75  Aligned_cols=124  Identities=29%  Similarity=0.267  Sum_probs=95.4

Q ss_pred             EEEEcCCccCCCCceeEEEEEeecCC-----CCccCCCCchHHHHHHHHHHHHHHhHhhcCCceEEEEeccHHHHHHhcC
Q psy11794         74 HIDTDTAYRLQENRYSCCYLGTLVGP-----GPRYFNLTTIYLAELLALYLCLKEISEFHSSSRIAIISDSLSVLSALGN  148 (325)
Q Consensus        74 ~IytDGS~~~~~~~~g~a~i~~~~g~-----~~~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~~i~I~tDS~~ai~~l~~  148 (325)
                      .+|||||+..+.+.+|+|++....+.     ........+++.||+.|++.||+.+.. .+.+++.|++||+.+++.+++
T Consensus         1 ~~~~Dgs~~~~~~~~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~~-~~~~~i~i~~Ds~~~~~~~~~   79 (130)
T cd06222           1 VIYTDGSCRGNPGPAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALE-LGGKKVNIYTDSQYVINALTG   79 (130)
T ss_pred             CEEecccCCCCCCceEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHHh-CCCceEEEEECHHHHHHHhhc
Confidence            37999999877778888876653211     111114679999999999999999987 788999999999999999998


Q ss_pred             CCCC-hHHHHHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHHHHHhccc
Q psy11794        149 ICFS-HPFISKIYQLWKLIVTRGTDVVFLWCPSHCGIDGNEAVDSAANHHT  198 (325)
Q Consensus       149 ~~~~-~~~~~~i~~~~~~l~~~~~~i~~~WVpgH~gi~gNe~AD~LAk~aa  198 (325)
                      .... .+....+...+..+...+..+.|.|||+|+|+++|+.||.|||.|.
T Consensus        80 ~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~~  130 (130)
T cd06222          80 WYEGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKEAA  130 (130)
T ss_pred             cccCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence            7642 2222222233333446788999999999999999999999999874

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.

>KOG3752|consensus

Probab=99.78  E-value=8e-19  Score=165.28  Aligned_cols=124  Identities=24%  Similarity=0.239  Sum_probs=94.4

Q ss_pred             EEEEEcCCccCCCCceeEEEEEeecCCCC------ccC-CCCchHHHHHHHHHHHHHHhHhhcCCceEEEEeccHHHHHH
Q psy11794         73 FHIDTDTAYRLQENRYSCCYLGTLVGPGP------RYF-NLTTIYLAELLALYLCLKEISEFHSSSRIAIISDSLSVLSA  145 (325)
Q Consensus        73 ~~IytDGS~~~~~~~~g~a~i~~~~g~~~------~l~-~~~s~~~AEl~Ai~~AL~~a~~~~~~~~i~I~tDS~~ai~~  145 (325)
                      ..||||||+.++......|+++.++|.+.      ++. ..+++|+|||.||..||+-|++ .+..+|+|.|||+++++.
T Consensus       213 ~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~-~~~~kv~I~TDS~~~i~~  291 (371)
T KOG3752|consen  213 QVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARS-KNINKVVIRTDSEYFINS  291 (371)
T ss_pred             eEEEecCccccCCCCCCcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHh-cCCCcEEEEechHHHHHH
Confidence            67999999998754434444555555544      444 7899999999999999999988 677899999999999999


Q ss_pred             hcCCCC--------C---hH----------HHHHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHHHHHhcccC
Q psy11794        146 LGNICF--------S---HP----------FISKIYQLWKLIVTRGTDVVFLWCPSHCGIDGNEAVDSAANHHTH  199 (325)
Q Consensus       146 l~~~~~--------~---~~----------~~~~i~~~~~~l~~~~~~i~~~WVpgH~gi~gNe~AD~LAk~aa~  199 (325)
                      |+.|-.        .   ++          .+.++.++.+++  .+.+|.+.|||||.|+.|||.||.||++++.
T Consensus       292 l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~--~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs~  364 (371)
T KOG3752|consen  292 LTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEI--SNKKVQQEYVGGHSGILGNEMADALARKGST  364 (371)
T ss_pred             HHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhh--ccCceEEEEecCcCCcchHHHHHHHHhhhhh
Confidence            987521        1   22          222333322221  4689999999999999999999999999854

>PRK07708 hypothetical protein; Validated

Probab=99.70  E-value=3e-16  Score=141.48  Aligned_cols=127  Identities=14%  Similarity=0.072  Sum_probs=95.9

Q ss_pred             cEEEEEcCCccCCCCceeEEEEEeec-C-------CCCccCCCCchHHHHHHHHHHHHHHhHhhcCCc--eEEEEeccHH
Q psy11794         72 IFHIDTDTAYRLQENRYSCCYLGTLV-G-------PGPRYFNLTTIYLAELLALYLCLKEISEFHSSS--RIAIISDSLS  141 (325)
Q Consensus        72 ~~~IytDGS~~~~~~~~g~a~i~~~~-g-------~~~~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~--~i~I~tDS~~  141 (325)
                      .+.||+|||+.++++.+|+|++...- +       ....+...+||+.||+.|++.||+.|.+ .+.+  .|.|++||+.
T Consensus        73 ~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e-~g~~~~~V~I~~DSql  151 (219)
T PRK07708         73 EILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEE-LGVKHEPVTFRGDSQV  151 (219)
T ss_pred             cEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHH-cCCCcceEEEEeccHH
Confidence            46899999999999999988776531 1       1123445689999999999999999988 5554  4899999999


Q ss_pred             HHHHhcCCCCC-hHHHHHHHHHHHHHH-hcCCeEEEEEecCCCCCccchHHHHHHhcccCCCCC
Q psy11794        142 VLSALGNICFS-HPFISKIYQLWKLIV-TRGTDVVFLWCPSHCGIDGNEAVDSAANHHTHPRHV  203 (325)
Q Consensus       142 ai~~l~~~~~~-~~~~~~i~~~~~~l~-~~~~~i~~~WVpgH~gi~gNe~AD~LAk~aa~~~~~  203 (325)
                      +++.+++.|.. ++....+.+.+..+. +....+.|.|||    ++.|+.||+||++|.+...+
T Consensus       152 Vi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~Vp----R~~N~~AD~LAk~Al~~~~~  211 (219)
T PRK07708        152 VLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPIS----RKQNKEADQLATQALEGTVI  211 (219)
T ss_pred             HHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECC----chhhhHHHHHHHHHHhcCCC
Confidence            99999998765 444444444333333 334467889997    67899999999999986553

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=99.65  E-value=2e-15  Score=146.60  Aligned_cols=124  Identities=16%  Similarity=0.142  Sum_probs=98.8

Q ss_pred             EEEEEcCCccCCCCceeEEEEEeecCC-------CCccCCCCchHHHHHHHHHHHHHHhHhhcCCceEEEEeccHHHHHH
Q psy11794         73 FHIDTDTAYRLQENRYSCCYLGTLVGP-------GPRYFNLTTIYLAELLALYLCLKEISEFHSSSRIAIISDSLSVLSA  145 (325)
Q Consensus        73 ~~IytDGS~~~~~~~~g~a~i~~~~g~-------~~~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~~i~I~tDS~~ai~~  145 (325)
                      ++||||||+.++++.+|+|++...-..       ...+ ..+||+.||+.|++.||+.+.+ .+.++|.|++||+.+++.
T Consensus         3 ~~i~~DGa~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~-~~~tnn~AE~~All~gL~~a~~-~g~~~v~i~~DS~lvi~~   80 (372)
T PRK07238          3 VVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAI-GRATNNVAEYRGLIAGLEAAAE-LGATEVEVRMDSKLVVEQ   80 (372)
T ss_pred             EEEEecCCCCCCCCceEEEEEEEeCCCCcEEEEeeccc-CCCCchHHHHHHHHHHHHHHHh-CCCCeEEEEeCcHHHHHH
Confidence            589999999999999999987764211       1222 3678999999999999999998 678899999999999999


Q ss_pred             hcCCCCC-hHHHHHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHHHHHhcccCCCC
Q psy11794        146 LGNICFS-HPFISKIYQLWKLIVTRGTDVVFLWCPSHCGIDGNEAVDSAANHHTHPRH  202 (325)
Q Consensus       146 l~~~~~~-~~~~~~i~~~~~~l~~~~~~i~~~WVpgH~gi~gNe~AD~LAk~aa~~~~  202 (325)
                      +++.+.. ++-...+.+.+..+.+++..+.|.|||.    ++|+.||.||+.|.....
T Consensus        81 i~~~~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~r----~~N~~AD~LA~~a~~~~~  134 (372)
T PRK07238         81 MSGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPR----ARNAHADRLANEAMDAAA  134 (372)
T ss_pred             hCCCCccCChHHHHHHHHHHHHHhcCCceEEEECCc----hhhhHHHHHHHHHHHhhc
Confidence            9987754 3333334444445667888999999995    699999999999975544

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

Probab=99.31  E-value=7.9e-12  Score=95.37  Aligned_cols=85  Identities=25%  Similarity=0.176  Sum_probs=64.7

Q ss_pred             hHHHHHHHHHHHHHHhHhhcCCceEEEEeccHHHHHHhcCCCCChHHHHHHHHHHHHHHhcCCeEEEEEecCCCCCccch
Q psy11794        109 IYLAELLALYLCLKEISEFHSSSRIAIISDSLSVLSALGNICFSHPFISKIYQLWKLIVTRGTDVVFLWCPSHCGIDGNE  188 (325)
Q Consensus       109 ~~~AEl~Ai~~AL~~a~~~~~~~~i~I~tDS~~ai~~l~~~~~~~~~~~~i~~~~~~l~~~~~~i~~~WVpgH~gi~gNe  188 (325)
                      +..||+.|++.||+.+.+ .+.++|.|+|||+.+++.|++..........+.+.+..+.+....+.|.|||    .++|.
T Consensus         1 ~~~aE~~al~~al~~a~~-~g~~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~----r~~N~   75 (87)
T PF13456_consen    1 PLEAEALALLEALQLAWE-LGIRKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDRFWNVSVSHIP----REQNK   75 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHC-CT-SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCCCSCEEEEE------GGGSH
T ss_pred             CcHHHHHHHHHHHHHHHH-CCCCEEEEEecCccccccccccccccccccccchhhhhhhccccceEEEEEC----hHHhH
Confidence            468999999999999998 7899999999999999999987543112223333333466788999999999    88999


Q ss_pred             HHHHHHhccc
Q psy11794        189 AVDSAANHHT  198 (325)
Q Consensus       189 ~AD~LAk~aa  198 (325)
                      .||.|||.|.
T Consensus        76 ~A~~LA~~a~   85 (87)
T PF13456_consen   76 VADALAKFAL   85 (87)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHh
Confidence            9999999885

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

Probab=93.80  E-value=0.037  Score=42.30  Aligned_cols=30  Identities=30%  Similarity=0.575  Sum_probs=24.5

Q ss_pred             ccccCCCCCCCc-ccCC-CCCcccc-ccCCCch
Q psy11794        273 NHLFKKLPPPIC-QCGS-VLTVVHI-LECPTLT  302 (325)
Q Consensus       273 ~~r~~~~~sp~C-~Cg~-~et~~H~-~~Cp~~~  302 (325)
                      +.+.+...++.| .|+. .||++|+ +.||...
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            344566678999 9997 9999999 9999753

>PF05380 Peptidase_A17: Pao retrotransposon peptidase ; InterPro: IPR008042 This signature identifies members of the Pao retrotransposon family

Probab=85.31  E-value=4.2  Score=34.63  Aligned_cols=51  Identities=22%  Similarity=0.135  Sum_probs=32.6

Q ss_pred             cEEEEEcCCccCCCCceeEEEEEee----------cCCCCcc-C-CCCchHHHHHHHHHHHHHHhHh
Q psy11794         72 IFHIDTDTAYRLQENRYSCCYLGTL----------VGPGPRY-F-NLTTIYLAELLALYLCLKEISE  126 (325)
Q Consensus        72 ~~~IytDGS~~~~~~~~g~a~i~~~----------~g~~~~l-~-~~~s~~~AEl~Ai~~AL~~a~~  126 (325)
                      .+++|+|+|.    ...|++++...          +....++ | ...|+-+-||+|+..|.+.+..
T Consensus        81 ~L~~F~DAS~----~aygavvYlr~~~~~~~~~~ll~aKsrv~P~k~~tIPRlEL~a~~l~~~l~~~  143 (159)
T PF05380_consen   81 ELHVFCDASE----SAYGAVVYLRSYSDGSVQVRLLFAKSRVAPLKTVTIPRLELLAALLGVRLANT  143 (159)
T ss_pred             eeeEeecccc----cceeeEeEeeeccCCceeeeeeeecccccCCCCCcHHHHHHHHHHHHHHHHHH
Confidence            4689999994    33444433322          1111222 1 2459999999999999998764

---

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	325
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	4e-06
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	1e-05
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	5e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-04

>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 Length = 555

 Score = 47.0 bits (112), Expect = 4e-06
 Identities = 27/88 (30%), Positives = 41/88 (46%), Gaps = 13/88 (14%)

Query: 107 TTIYLAELLALYLCLKEISEFHSSSRIAIISDSLSVLSALGNICFSHPFISKIYQLWKLI 166
           TT   AEL A  + L +     S  ++ II DS  V+     I  S P  S   ++   I
Sbjct: 471 TTNQQAELEAFAMALTD-----SGPKVNIIVDSQYVM----GIVASQPTES-ESKIVNQI 520

Query: 167 V--TRGTDVVFL-WCPSHCGIDGNEAVD 191
           +      + +++ W P+H GI GN+ VD
Sbjct: 521 IEEMIKKEAIYVAWVPAHKGIGGNQEVD 548

>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* ... Length = 557

 Score = 45.5 bits (108), Expect = 1e-05
 Identities = 29/89 (32%), Positives = 46/89 (51%), Gaps = 15/89 (16%)

Query: 107 TTIYLAELLALYLCLKEISEFHSSSRIAIISDSLSVLSALGNICFSHPFISK---IYQLW 163
           TT    EL A+YL L++     S   + I++DS   L     I  + P  S+   + Q+ 
Sbjct: 474 TTNQKTELQAIYLALQD-----SGLEVNIVTDSQYAL----GIIQAQPDKSESELVNQII 524

Query: 164 KLIVTRGTDVVFL-WCPSHCGIDGNEAVD 191
           + ++ +  + V+L W P+H GI GNE VD
Sbjct: 525 EQLIKK--EKVYLAWVPAHKGIGGNEQVD 551

>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 = 42.1 bits (99), Expect = 5e-05
 Identities = 18/92 (19%), Positives = 29/92 (31%), Gaps = 14/92 (15%)

Query: 112 AELLALYLCLKEISEFHSSSRIAIISDSLSVLSALGNICFSHPFISKIYQLWKLI---VT 168
           AEL+AL   LK         ++ + +DS    +             K       +   + 
Sbjct: 66  AELIALTQALKMAEG----KKLNVYTDSRYAFATAHVHSEGRE--IKNKNEILALLKALF 119

Query: 169 RGTDVVFLWCPSHCGID-----GNEAVDSAAN 195
               +  + CP H   +     GN   D AA 
Sbjct: 120 LPKRLSIIHCPGHQKGNSAEARGNRMADQAAR 151

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 42.5 bits (99), Expect = 2e-04
 Identities = 32/168 (19%), Positives = 59/168 (35%), Gaps = 43/168 (25%)

Query: 32  CWWSNKTY-LHHENFSVMLLLGTLRKLIN-YTLHLQSVMQLFIFH--IDTDTAYRLQENR 87
                 T  +        + L    KL N Y LH +S++  +      D+D       ++
Sbjct: 419 KQPKESTISIPS------IYLELKVKLENEYALH-RSIVDHYNIPKTFDSDDLIPPYLDQ 471

Query: 88  YSCCYLGTLVGPGPRYFNLTTIYLAELLA----LYLCLKEISE--FHSSSRIAIISDSLS 141
           Y   ++G          +L  I   E +     ++L  + + +   H S+        L+
Sbjct: 472 YFYSHIG---------HHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILN 522

Query: 142 VLSALGN----ICFSHP-----------FISKIYQLWKLIVTRGTDVV 174
            L  L      IC + P           F+ KI +   LI ++ TD++
Sbjct: 523 TLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEE--NLICSKYTDLL 568

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	325
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.92
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.92
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.92
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	99.91
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	99.91
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	99.91
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.9
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	99.9
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.9
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	99.88
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	99.87
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	99.85
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	99.83
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	99.82
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	99.56
4htu_A	134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	99.42
1rw3_A	455	POL polyprotein; RNA and DNA dependent DNA polymer	86.7

>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=99.92  E-value=4.4e-25  Score=186.98  Aligned_cols=123  Identities=23%  Similarity=0.273  Sum_probs=92.1

Q ss_pred             cEEEEEcCCccCCCCceeEEEEEeecCCCCcc-CCCCchHHHHHHHHHHHHHHhHhhcCCceEEEEeccHHHHHHhcCCC
Q psy11794         72 IFHIDTDTAYRLQENRYSCCYLGTLVGPGPRY-FNLTTIYLAELLALYLCLKEISEFHSSSRIAIISDSLSVLSALGNIC  150 (325)
Q Consensus        72 ~~~IytDGS~~~~~~~~g~a~i~~~~g~~~~l-~~~~s~~~AEl~Ai~~AL~~a~~~~~~~~i~I~tDS~~ai~~l~~~~  150 (325)
                      .+.||||||+.++++.+|+|++... +....+ ...+||++||+.|++.||+.+     ..+|.|+|||++|++.|++|.
T Consensus        12 ~~~iytDGs~~~n~g~~g~G~v~~~-~~~~~~~~~~~Tnn~aEl~A~i~AL~~~-----~~~v~i~tDS~~v~~~i~~w~   85 (150)
T 3qio_A           12 AETFYVDGAANRETKLGKAGYVTNR-GRQKVVTLTDTTNQKTELQAIYLALQDS-----GLEVNIVTDSQYALGIITQWI   85 (150)
T ss_dssp             CEEEEEEEEECTTTCCEEEEEEETT-SCEEEEEESSCCHHHHHHHHHHHHHHHS-----CSEEEEEESCHHHHHHHHHHH
T ss_pred             CEEEEEccCCCCCCCCeEEEEEEEc-CCEEEEeCCCCCHHHHHHHHHHHHHHhC-----CCcEEEEeCcHHHHHHHHHHH
Confidence            4689999999999998888876542 111111 147899999999999999985     479999999999999998751


Q ss_pred             --------CC---hHHH-HHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHHHHHhcccCC
Q psy11794        151 --------FS---HPFI-SKIYQLWKLIVTRGTDVVFLWCPSHCGIDGNEAVDSAANHHTHP  200 (325)
Q Consensus       151 --------~~---~~~~-~~i~~~~~~l~~~~~~i~~~WVpgH~gi~gNe~AD~LAk~aa~~  200 (325)
                              ..   .++. ..+++.+..+...+..|.|.|||||+|++|||.||+||++|++.
T Consensus        86 ~~W~~~gw~~~~g~~v~n~~l~~~l~~~l~~~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~  147 (150)
T 3qio_A           86 HNWKKRGWKTADKKPVKNVDLVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRK  147 (150)
T ss_dssp             HHHCC------------CHHHHHHHHHHHTTCSEEEEEECCTTSCCHHHHHHHHHHHTTTSC
T ss_pred             HHHhhcCcCcCcCcccccHHHHHHHHHHHhhcCceEEEEccCcCCChhHHHHHHHHHHHHHH
Confidence                    11   1111 12222222233468899999999999999999999999999875

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

Probab=99.92  E-value=4.3e-25  Score=185.72  Aligned_cols=120  Identities=21%  Similarity=0.108  Sum_probs=92.4

Q ss_pred             cEEEEEcCCccCCCCceeEEEEEeecCC----CCccCCCCchHHHHHHHHHHHHHHhHhhcCCceEEEEeccHHHHHHhc
Q psy11794         72 IFHIDTDTAYRLQENRYSCCYLGTLVGP----GPRYFNLTTIYLAELLALYLCLKEISEFHSSSRIAIISDSLSVLSALG  147 (325)
Q Consensus        72 ~~~IytDGS~~~~~~~~g~a~i~~~~g~----~~~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~~i~I~tDS~~ai~~l~  147 (325)
                      .+.||||||+.++++.+|+|++....+.    ...+ ..+||++||+.|++.||+.+.+   ..+|.|+|||++|++.|+
T Consensus         4 ~i~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~~~~-~~~Tnn~aEl~A~~~AL~~~~~---~~~v~I~tDS~~vi~~i~   79 (146)
T 3h08_A            4 TITIYTDGAASGNPGKGGWGALLMYGSSRKEISGYD-PATTNNRMELMAAIKGLEALKE---PARVQLYSDSAYLVNAMN   79 (146)
T ss_dssp             EEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCSS---CCEEEEEESCHHHHHHHH
T ss_pred             eEEEEEecCCCCCCCceEEEEEEEECCeeEEeecCC-CCCcHHHHHHHHHHHHHHhcCc---cCcEEEEeChHHHHHHHH
Confidence            3689999999999888898877654221    1112 3579999999999999999965   689999999999999998


Q ss_pred             CCC---------CC--------hHHHHHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHHHHHhcccCC
Q psy11794        148 NIC---------FS--------HPFISKIYQLWKLIVTRGTDVVFLWCPSHCGIDGNEAVDSAANHHTHP  200 (325)
Q Consensus       148 ~~~---------~~--------~~~~~~i~~~~~~l~~~~~~i~~~WVpgH~gi~gNe~AD~LAk~aa~~  200 (325)
                      +.|         ..        .++...|.+    +.. ...|.|.|||||+|+++||.||+|||+|+..
T Consensus        80 ~~w~~~W~~~~w~~~~~~~v~n~~l~~~~~~----~~~-~~~v~~~~V~gH~g~~~N~~AD~LA~~a~~~  144 (146)
T 3h08_A           80 EGWLKRWVKNGWKTAAKKPVENIDLWQEILK----LTT-LHRVTFHKVKGHSDNPYNSRADELARLAIKE  144 (146)
T ss_dssp             SSHHHHHHHTTCC----CCCTTHHHHHHHHH----HHH-HSEEEEEECCC-CCSHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCccCCCCCcCCHHHHHHHHH----HHh-hCceEEEEcCCcCCcHhHHHHHHHHHHHHHh
Confidence            821         11        345444444    322 2479999999999999999999999999854

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

Probab=99.92  E-value=2.9e-24  Score=182.35  Aligned_cols=125  Identities=17%  Similarity=0.189  Sum_probs=95.2

Q ss_pred             ccEEEEEcCCccCCCCc---eeEEEEEeecC---CCCccCCCCchHHHHHHHHHHHHHHhHhhcCCceEEEEeccHHHHH
Q psy11794         71 FIFHIDTDTAYRLQENR---YSCCYLGTLVG---PGPRYFNLTTIYLAELLALYLCLKEISEFHSSSRIAIISDSLSVLS  144 (325)
Q Consensus        71 ~~~~IytDGS~~~~~~~---~g~a~i~~~~g---~~~~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~~i~I~tDS~~ai~  144 (325)
                      ..+.||||||+.++++.   +|+|++...-.   ....+++.+||++||+.|++.||+.+.+ .+.++|.|+|||++|++
T Consensus         6 ~~~~iytDGs~~~n~~~~~~aG~Gvv~~~~~~~~~~~~l~~~~tn~~aEl~A~~~aL~~~~~-~~~~~v~i~tDS~~vi~   84 (154)
T 2qkb_A            6 DFVVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQAKT-QNINKLVLYTNSMFTIN   84 (154)
T ss_dssp             TEEEEEEEEEEETTTSSSCEEEEEEECSTTCTTCEEEECCSSCCHHHHHHHHHHHHHHHHHH-TTCCEEEEEESCHHHHH
T ss_pred             CeEEEEEccCcCCCCCCCCcEEEEEEEECCCceeEEeecCCCCchHHHHHHHHHHHHHHHHh-CCCceEEEEECcHHHHh
Confidence            35689999999988754   56665543210   1123445689999999999999999987 67789999999999999


Q ss_pred             HhcCC--------CCC--------hHHHHHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHHHHHhcccCCC
Q psy11794        145 ALGNI--------CFS--------HPFISKIYQLWKLIVTRGTDVVFLWCPSHCGIDGNEAVDSAANHHTHPR  201 (325)
Q Consensus       145 ~l~~~--------~~~--------~~~~~~i~~~~~~l~~~~~~i~~~WVpgH~gi~gNe~AD~LAk~aa~~~  201 (325)
                      .|+++        |..        .+++.+|.+    +. .+..|.|.|||||+|++|||.||+|||+|+..+
T Consensus        85 ~i~~~~~~w~~~~w~~~~~~~~~n~~l~~~i~~----l~-~~~~v~~~~V~~H~g~~~N~~AD~LA~~a~~~~  152 (154)
T 2qkb_A           85 GITNWVQGWKKNGWKTSAGKEVINKEDFVALER----LT-QGMDIQWMHVPGHSGFIGNEEADRLAREGAKQS  152 (154)
T ss_dssp             HHHTHHHHHHTTTSBCTTSSBCTTHHHHHHHHH----HH-TTCEEEEEECCTTSSCHHHHHHHHHHHHHHTCC
T ss_pred             hhhhhHHHHHhccccccCCCccccHHHHHHHHH----HH-cCCceEEEEccCCCCCHhHHHHHHHHHHHHHhc
Confidence            99874        211        234444433    33 256799999999999999999999999998764

>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=99.91  E-value=1.4e-24  Score=184.80  Aligned_cols=122  Identities=17%  Similarity=0.162  Sum_probs=95.4

Q ss_pred             EEEEEcCCccCCCCceeEEEEEeecCCC----CccCCCCchHHHHHHHHHHHHHHhHhhcCCceEEEEeccHHHHHHhcC
Q psy11794         73 FHIDTDTAYRLQENRYSCCYLGTLVGPG----PRYFNLTTIYLAELLALYLCLKEISEFHSSSRIAIISDSLSVLSALGN  148 (325)
Q Consensus        73 ~~IytDGS~~~~~~~~g~a~i~~~~g~~----~~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~~i~I~tDS~~ai~~l~~  148 (325)
                      +.||||||+.++++.+|+|++....+..    ..+ +.+||++||+.|++.||+.+.+   ..+|.|+|||++|++.|++
T Consensus         5 ~~iytDGs~~~n~~~~G~G~v~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~~~~---~~~v~I~tDS~~vi~~i~~   80 (155)
T 1jl1_A            5 VEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGY-TRTTNNRMELMAAIVALEALKE---HAEVILSTDSQYVRQGITQ   80 (155)
T ss_dssp             EEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCCS---CCEEEEEECCHHHHHHHHT
T ss_pred             EEEEEccccCCCCCceEEEEEEEECCeEEEEecCC-CCCcHHHHHHHHHHHHHHHhCc---CCcEEEEeCHHHHHHHHHH
Confidence            5899999999998888888776542211    112 3578999999999999999975   4899999999999999997


Q ss_pred             C--------CCC--------hHHHHHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHHHHHhcccCCCCC
Q psy11794        149 I--------CFS--------HPFISKIYQLWKLIVTRGTDVVFLWCPSHCGIDGNEAVDSAANHHTHPRHV  203 (325)
Q Consensus       149 ~--------~~~--------~~~~~~i~~~~~~l~~~~~~i~~~WVpgH~gi~gNe~AD~LAk~aa~~~~~  203 (325)
                      |        +..        .++...|.    .+. ....|.|.|||||+|++|||.||+|||+|+..+.+
T Consensus        81 w~~~W~~n~~~~~~g~~v~n~~l~~~i~----~l~-~~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~~~~  146 (155)
T 1jl1_A           81 WIHNWKKRGWKTADKKPVKNVDLWQRLD----AAL-GQHQIKWEWVKGHAGHPENERADELARAAAMNPTL  146 (155)
T ss_dssp             THHHHHHTTTBCTTSCBCTTHHHHHHHH----HHT-TTCEEEEEECCSSTTCHHHHHHHHHHHHHHHSCCB
T ss_pred             HHHHHhhcccccccCCccCCHHHHHHHH----HHH-ccCceEEEEcCCCCCCHHHHHHHHHHHHHHhccch
Confidence            3        211        23333333    343 34699999999999999999999999999987664

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

Probab=99.91  E-value=3.6e-24  Score=184.01  Aligned_cols=131  Identities=15%  Similarity=0.127  Sum_probs=93.6

Q ss_pred             hcccccEEEEEcCCccCCCCc-----eeEEEEEeecCCCCc------c-CCCCchHHHHHHHHHHHHHHhHhhcCCceEE
Q psy11794         67 VMQLFIFHIDTDTAYRLQENR-----YSCCYLGTLVGPGPR------Y-FNLTTIYLAELLALYLCLKEISEFHSSSRIA  134 (325)
Q Consensus        67 ~~~~~~~~IytDGS~~~~~~~-----~g~a~i~~~~g~~~~------l-~~~~s~~~AEl~Ai~~AL~~a~~~~~~~~i~  134 (325)
                      .|.++.+.|||||||.+|+|+     +|+|++....+....      . .+..+++.||+.|+..||+.+.+  ...+|.
T Consensus         2 ~m~~~evviYTDGsc~gNpgp~~~~~aG~Gv~~~~~~~~~~~~~~~~~~tnn~te~~Aei~Al~~al~~al~--~~~~v~   79 (165)
T 2lsn_A            2 AMGQYEGVFYTDGSAIKSPDPTKSNNAGMGIVHATYKPEYQVLNQWSIPLGNHTAQMAEIAAVEFACKKALK--IPGPVL   79 (165)
T ss_dssp             TTCCCSEEEEEEEEEEECSSCTTCEEEEEEEEEECCSSSCCEEEEEEEEESSCCHHHHHHHHHHHHHHHHHH--SSSCEE
T ss_pred             CCCCceEEEEEcCCCCCCCCCCCCCcEEEEEEEEECCCccEEeccccCCchHHHHHHHHHHHHHHHHHHHhc--CCCeEE
Confidence            355677899999999999886     777776654333221      1 24567888888888888888766  346899


Q ss_pred             EEeccHHHHHHhcCC--------CCC---hHHH-HHHHHHHHHHHhcCCeEEEEEecCCCCC------ccchHHHHHHhc
Q psy11794        135 IISDSLSVLSALGNI--------CFS---HPFI-SKIYQLWKLIVTRGTDVVFLWCPSHCGI------DGNEAVDSAANH  196 (325)
Q Consensus       135 I~tDS~~ai~~l~~~--------~~~---~~~~-~~i~~~~~~l~~~~~~i~~~WVpgH~gi------~gNe~AD~LAk~  196 (325)
                      |+|||++|++.|+.|        |..   .++. ..+++.+.++......|.|.|||||+|+      +|||+||+||++
T Consensus        80 I~TDS~Yvi~~it~w~~~Wk~ngw~~~~~~pVkN~dL~~~l~~~~~~~~~v~~~~VkgH~g~~~~~~~~gNe~AD~LA~~  159 (165)
T 2lsn_A           80 VITDSFYVAESANKELPYWKSNGFVNNKKKPLKHISKWKSIAECLSMKPDITIQHEKGHQPTNTSIHTEGNALADKLATQ  159 (165)
T ss_dssp             EEESCHHHHHHHHTHHHHHHHTTSCSCSSSCCSSHHHHHHHHHHHHHCTTCEEEECCSSSCSSSCHHHHHHHHHHHHHHH
T ss_pred             EEeChHHHHhhhhhhhhhheeccccccCCCcccCHHHHHHHHHHHhCCCCEEEEEEeCCCCccCCCCChHHHHHHHHHHH
Confidence            999999999999763        211   1111 1222323334445678999999999995      689999999999


Q ss_pred             ccC
Q psy11794        197 HTH  199 (325)
Q Consensus       197 aa~  199 (325)
                      |+.
T Consensus       160 gA~  162 (165)
T 2lsn_A          160 GSY  162 (165)
T ss_dssp             HHH
T ss_pred             hhh
Confidence            984

>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=99.91  E-value=1.6e-25  Score=188.96  Aligned_cols=125  Identities=18%  Similarity=0.131  Sum_probs=97.1

Q ss_pred             cEEEEEcCCccCCCCceeEEEEEeecCC-------CCccCC--CCchHHHHHHHHHHHHHHhHhhcCCceEEEEeccHHH
Q psy11794         72 IFHIDTDTAYRLQENRYSCCYLGTLVGP-------GPRYFN--LTTIYLAELLALYLCLKEISEFHSSSRIAIISDSLSV  142 (325)
Q Consensus        72 ~~~IytDGS~~~~~~~~g~a~i~~~~g~-------~~~l~~--~~s~~~AEl~Ai~~AL~~a~~~~~~~~i~I~tDS~~a  142 (325)
                      .+.||||||+.+  +++|+|++....+.       +...+.  .+||++||+.|++.||+.+.+ .+. +|.|+|||+.+
T Consensus         6 ~i~iytDGs~~~--g~~G~G~vi~~~g~~~~~~~~~~~~~~~~~~tNn~aEl~A~~~AL~~a~~-~~~-~v~I~tDS~~i   81 (147)
T 2kq2_A            6 EYDVYTDGSYVN--GQYAWAYAFVKDGKVHYEDADVGKNPAAATMRNVAGEIAAALYAVKKASQ-LGV-KIRILHDYAGI   81 (147)
T ss_dssp             CCEEECCCCCBT--TBCEEEEEEEETTEEEEEEEEECCCGGGGGTCTTHHHHHHHHHHHHHHHH-HTC-CCCBSSCCSTH
T ss_pred             eEEEEECCCCCC--CCcEEEEEEEECCEEEEEEeccccccccccccHHHHHHHHHHHHHHHHHH-CCC-eEEEEECcHHH
Confidence            458999999987  88888877653221       111122  369999999999999999877 455 99999999999


Q ss_pred             HHHhcCCCCC-hHHHHHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHHHHHhcccCCCCC
Q psy11794        143 LSALGNICFS-HPFISKIYQLWKLIVTRGTDVVFLWCPSHCGIDGNEAVDSAANHHTHPRHV  203 (325)
Q Consensus       143 i~~l~~~~~~-~~~~~~i~~~~~~l~~~~~~i~~~WVpgH~gi~gNe~AD~LAk~aa~~~~~  203 (325)
                      .+.+.+.|.. .+....+.++++++..   .|.|.|||||+|++|||.||+|||+|+....+
T Consensus        82 ~~w~~~~w~~~~~~~~~~~~l~~~l~~---~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~~~~  140 (147)
T 2kq2_A           82 AFWATGEWKAKNEFTQAYAKLMNQYRG---IYSFEKVKAHSGNEFNDYVDMKAKSALGIRDL  140 (147)
T ss_dssp             HHHTTSSSSCCHHHHHHHHCGGGGGST---TCCBCCCCCCCCCHHHHHHHHHHHHHHTCCCT
T ss_pred             HHHHhCCCccCCcchHHHHHHHHHhcC---CeeEEEecCcCCCcchHHHHHHHHHHHhcccc
Confidence            9888887765 4444455555555433   89999999999999999999999999987653

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

Probab=99.90  E-value=2.4e-24  Score=183.82  Aligned_cols=120  Identities=21%  Similarity=0.234  Sum_probs=93.9

Q ss_pred             cEEEEEcCCccCCCCceeEEEEEeecCC----CCccCCCCchHHHHHHHHHHHHHHhHhhcCCceEEEEeccHHHHHHhc
Q psy11794         72 IFHIDTDTAYRLQENRYSCCYLGTLVGP----GPRYFNLTTIYLAELLALYLCLKEISEFHSSSRIAIISDSLSVLSALG  147 (325)
Q Consensus        72 ~~~IytDGS~~~~~~~~g~a~i~~~~g~----~~~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~~i~I~tDS~~ai~~l~  147 (325)
                      .+.||||||+.++++.+|+|++...-+.    ...+ ..+||++||+.|++.||+.+.+   ..+|.|+|||++|++.|+
T Consensus         6 ~i~iytDGs~~~n~g~~G~G~v~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~AL~~~~~---~~~v~I~tDS~~vi~~i~   81 (158)
T 2e4l_A            6 LIHIFTDGSCLGNPGPGGYGIVMNYKGHTKEMSDGF-SLTTNNRMELLAPIVALEALKE---PCKIILTSDSQYMRQGIM   81 (158)
T ss_dssp             EEEEEEEEEESSSSEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCSS---CCEEEEEECCHHHHHHHH
T ss_pred             eEEEEEcccccCCCCcEEEEEEEEECCEEEEEecCc-CCCccHHHHHHHHHHHHHHhcc---CCeEEEEeCHHHHHHHHH
Confidence            3689999999998888888877654221    1112 3579999999999999999865   389999999999999998


Q ss_pred             C--------CCCC--------hHHHHHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHHHHHhcccCC
Q psy11794        148 N--------ICFS--------HPFISKIYQLWKLIVTRGTDVVFLWCPSHCGIDGNEAVDSAANHHTHP  200 (325)
Q Consensus       148 ~--------~~~~--------~~~~~~i~~~~~~l~~~~~~i~~~WVpgH~gi~gNe~AD~LAk~aa~~  200 (325)
                      +        .+..        .++...|.+    +.. ...|.|.|||||+|+++||.||+|||+|+..
T Consensus        82 ~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~----l~~-~~~v~~~wV~gH~g~~~Ne~AD~LAk~a~~~  145 (158)
T 2e4l_A           82 TWIHGWKKKGWMTSNRTPVKNVDLWKRLDK----AAQ-LHQIDWRWVKGHAGHAENERCDQLARAAAEA  145 (158)
T ss_dssp             THHHHHHHTTTBCTTSSBCTTHHHHHHHHH----HHT-TSEEEEEECCTTCCCHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHccccccCCCcccCHHHHHHHHH----HHc-cCcEEEEEccCCCCchhHHHHHHHHHHHHHh
Confidence            8        3321        234333333    333 4699999999999999999999999999976

>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=99.90  E-value=7.6e-24  Score=182.05  Aligned_cols=123  Identities=21%  Similarity=0.142  Sum_probs=94.6

Q ss_pred             cEEEEEcCCccCCCCceeEEEEEeecCCC---CccCCCCchHHHHHHHHHHHHHHhHhhcCCceEEEEeccHHHHHHhcC
Q psy11794         72 IFHIDTDTAYRLQENRYSCCYLGTLVGPG---PRYFNLTTIYLAELLALYLCLKEISEFHSSSRIAIISDSLSVLSALGN  148 (325)
Q Consensus        72 ~~~IytDGS~~~~~~~~g~a~i~~~~g~~---~~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~~i~I~tDS~~ai~~l~~  148 (325)
                      .+.||||||+.+++|.+|+|++...-+..   ..++..+||++||+.|++.||+.+ .   ..+|.|+|||+++++.+-.
T Consensus        23 ~i~iytDGs~~~npG~~g~G~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~-~---~~~v~I~tDS~~vi~~iw~   98 (165)
T 3p1g_A           23 DYTWYTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMA-E---GKKLNVYTDSRYAFATAHV   98 (165)
T ss_dssp             SEEEEEEEEEEEETTEEEEEEEEECSSCEEEEEEECTTCCHHHHHHHHHHHHHHHT-B---TSEEEEEECCHHHHHHHHS
T ss_pred             CEEEEEEcccCCCCCceEEEEEEEECCEEEEEecCCCCCcHHHHHHHHHHHHHHHc-c---CceEEEEEchHHHHhhhhc
Confidence            57999999999998988888766542221   123457899999999999999998 3   6899999999999999821


Q ss_pred             CCCC-----hHHHHHHHHHHHHHHhcCCeEEEEEecCCCC-----CccchHHHHHHhcccCCCC
Q psy11794        149 ICFS-----HPFISKIYQLWKLIVTRGTDVVFLWCPSHCG-----IDGNEAVDSAANHHTHPRH  202 (325)
Q Consensus       149 ~~~~-----~~~~~~i~~~~~~l~~~~~~i~~~WVpgH~g-----i~gNe~AD~LAk~aa~~~~  202 (325)
                      ....     .+++.++.+   ++ ..+..|.|.|||||+|     ++|||.||+|||+|+....
T Consensus        99 ~~~g~~v~n~dl~~~l~~---~l-~~~~~v~~~wVkgH~g~~~~~~~gNe~AD~LA~~aa~~~~  158 (165)
T 3p1g_A           99 HSEGREIKNKNEILALLK---AL-FLPKRLSIIHCPGHQKGNSAEARGNRMADQAAREAAMKAV  158 (165)
T ss_dssp             CCCSCCCSSHHHHHHHHH---HT-TSBSEEEEEECCSSCCSCSHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCCCcccCHHHHHHHHH---HH-hcCCceEEEEecCCCCCCcCcchHHHHHHHHHHHHHhcCC
Confidence            1111     333333322   22 3678999999999999     9999999999999997654

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

Probab=99.90  E-value=5.4e-24  Score=183.15  Aligned_cols=123  Identities=20%  Similarity=0.118  Sum_probs=94.9

Q ss_pred             cEEEEEcCCccCCCCceeEEEEEeecCCCCcc---CCCCchHHHHHHHHHHHHHHhHhhcCCceEEEEeccHHHHHHhcC
Q psy11794         72 IFHIDTDTAYRLQENRYSCCYLGTLVGPGPRY---FNLTTIYLAELLALYLCLKEISEFHSSSRIAIISDSLSVLSALGN  148 (325)
Q Consensus        72 ~~~IytDGS~~~~~~~~g~a~i~~~~g~~~~l---~~~~s~~~AEl~Ai~~AL~~a~~~~~~~~i~I~tDS~~ai~~l~~  148 (325)
                      .+.||||||+.++++.+|+|++...-+....+   ...+||++||+.|++.||+.+.+   ..+|.|+|||++|++.|++
T Consensus         8 ~i~iytDGs~~~n~g~~G~G~v~~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~~~---~~~v~I~tDS~~vi~~i~~   84 (166)
T 1ril_A            8 RVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKE---PCEVDLYTDSHYLKKAFTE   84 (166)
T ss_dssp             CCCEEEEEEESSTTEEEEEEEEECBTTBCCEECCEEEEECHHHHHHHHHHHHHHSCCS---CCEEEEECCCHHHHHHHHS
T ss_pred             cEEEEECccccCCCCCEEEEEEEEECCEEEEEecCCCCCcHHHHHHHHHHHHHHHhcc---CCeEEEEeChHHHHHHHhh
Confidence            35899999999988888888776542211111   13579999999999999999865   4699999999999999998


Q ss_pred             -C--------CCC--------hHHHHHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHHHHHhcccCCCC
Q psy11794        149 -I--------CFS--------HPFISKIYQLWKLIVTRGTDVVFLWCPSHCGIDGNEAVDSAANHHTHPRH  202 (325)
Q Consensus       149 -~--------~~~--------~~~~~~i~~~~~~l~~~~~~i~~~WVpgH~gi~gNe~AD~LAk~aa~~~~  202 (325)
                       |        |..        .+++..|.+    +.. ...|.|.|||||+|+++||.||+|||+|+....
T Consensus        85 ~w~~~W~~~~w~~~~g~~v~n~~l~~~i~~----l~~-~~~v~~~wV~gH~g~~~Ne~AD~LAk~a~~~~~  150 (166)
T 1ril_A           85 GWLEGWRKRGWRTAEGKPVKNRDLWEALLL----AMA-PHRVRFHFVKGHTGHPENERVDREARRQAQSQA  150 (166)
T ss_dssp             SHHHHHHHTTSBCTTSSBCTTHHHHHHHHH----HHT-TSEEECCCCCGGGSCTHHHHHHHHHHHHHTSSC
T ss_pred             hHHHHHHhcccccccCCccCcHHHHHHHHH----HHh-cCeEEEEEeeCCCCchhHHHHHHHHHHHHHHhh
Confidence             2        221        234444433    333 369999999999999999999999999998765

>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=99.88  E-value=3.3e-22  Score=166.16  Aligned_cols=123  Identities=18%  Similarity=0.185  Sum_probs=98.4

Q ss_pred             EEEEEcCCccCCCCceeEEEEEeecCCCC------ccCCCCchHHHHHHHHHHHHHHhHhhcCCceEEEEeccHHHHHHh
Q psy11794         73 FHIDTDTAYRLQENRYSCCYLGTLVGPGP------RYFNLTTIYLAELLALYLCLKEISEFHSSSRIAIISDSLSVLSAL  146 (325)
Q Consensus        73 ~~IytDGS~~~~~~~~g~a~i~~~~g~~~------~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~~i~I~tDS~~ai~~l  146 (325)
                      +.||||||+.++++.+|+|++......+.      ...+.+||++||+.|++.||+.+.+ .+.++|.|+|||+++++.+
T Consensus         4 ~~iy~DGs~~~~~g~~g~G~v~~~~~~~~~~~~~~~~~~~~tn~~aEl~A~~~aL~~a~~-~~~~~v~i~tDS~~vv~~i   82 (141)
T 3hst_B            4 VVIEADGGSRGNPGPAGYGAVVWTADHSTVLAESKQAIGRATNNVAEYRGLIAGLDDAVK-LGATEAAVLMDSKLVVEQM   82 (141)
T ss_dssp             EEEEEEEEESSSSEEEEEEEEEEETTSCSEEEEEEEEEEEECHHHHHHHHHHHHHHHHHH-HTCSEEEEEESCHHHHHHH
T ss_pred             EEEEEecCCCCCCCCcEEEEEEEeCCCCcEEEeeeccCCCCchHHHHHHHHHHHHHHHHH-CCCceEEEEeChHHHHHHH
Confidence            58999999999988899887776432111      1113679999999999999999988 6788999999999999999


Q ss_pred             cCCCCC-hHHHHHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHHHHHhcccCC
Q psy11794        147 GNICFS-HPFISKIYQLWKLIVTRGTDVVFLWCPSHCGIDGNEAVDSAANHHTHP  200 (325)
Q Consensus       147 ~~~~~~-~~~~~~i~~~~~~l~~~~~~i~~~WVpgH~gi~gNe~AD~LAk~aa~~  200 (325)
                      ++.|.. .+.+..+.+.+..+...+..|.|.|||+    ++|+.||+|||+|+..
T Consensus        83 ~~~~~~~~~~l~~~~~~i~~l~~~~~~v~~~~V~~----~~N~~AD~LA~~a~~~  133 (141)
T 3hst_B           83 SGRWKVKHPDLLKLYVQAQALASQFRRINYEWVPR----ARNTYADRLANDAMDA  133 (141)
T ss_dssp             TTSSCCCSHHHHHHHHHHHHHHTTSSEEEEEECCG----GGCHHHHHHHHHHHHH
T ss_pred             hCCcccCCHHHHHHHHHHHHHHhcCCeEEEEEcCC----cccHHHHHHHHHHHHH
Confidence            997654 4444445555555666789999999994    7999999999998754

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

Probab=99.87  E-value=3.2e-22  Score=165.63  Aligned_cols=121  Identities=20%  Similarity=0.190  Sum_probs=93.3

Q ss_pred             EEEEEcCCccCCCCceeEEEEEee-cCC-----CCccCCCCchHHHHHHHHHHHHHHhHhhcCCc----eEEEEeccHHH
Q psy11794         73 FHIDTDTAYRLQENRYSCCYLGTL-VGP-----GPRYFNLTTIYLAELLALYLCLKEISEFHSSS----RIAIISDSLSV  142 (325)
Q Consensus        73 ~~IytDGS~~~~~~~~g~a~i~~~-~g~-----~~~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~----~i~I~tDS~~a  142 (325)
                      +.||||||+.++++++|+|++... .|.     ...+ +.+||++||+.|++.||+.+.+ .+.+    +|.|+|||+++
T Consensus         4 ~~iy~DGs~~~n~g~~G~G~v~~~~~g~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~a~~-~~~~~~~~~v~i~tDS~~v   81 (140)
T 3u3g_D            4 IIIYTDGGARGNPGPAGIGVVITDEKGNTLHESSAYI-GETTNNVAEYEALIRALEDLQM-FGDKLVDMEVEVRMDSELI   81 (140)
T ss_dssp             EEEEEEEEESSTTEEEEEEEEEECTTSCEEEEEEEEE-EEECHHHHHHHHHHHHHHHHGG-GGGGGTTCEEEEEESCHHH
T ss_pred             EEEEEecCCCCCCCCcEEEEEEEeCCCCEEEEEEeeC-CCCchHHHHHHHHHHHHHHHHH-cCCCCCCceEEEEeChHHH
Confidence            689999999999888898877654 111     1112 3579999999999999999987 5566    99999999999


Q ss_pred             HHHhcCCCCC-hHHHHHHHHHHHHH-HhcCCeEEEEEecCCCCCccchHHHHHHhcccC
Q psy11794        143 LSALGNICFS-HPFISKIYQLWKLI-VTRGTDVVFLWCPSHCGIDGNEAVDSAANHHTH  199 (325)
Q Consensus       143 i~~l~~~~~~-~~~~~~i~~~~~~l-~~~~~~i~~~WVpgH~gi~gNe~AD~LAk~aa~  199 (325)
                      ++.+++++.. .+-+..+.+.+..+ ..+...|.|.|||    .++||.||+|||+|+.
T Consensus        82 i~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~~v~~~~V~----~~~N~~AD~LA~~a~~  136 (140)
T 3u3g_D           82 VRQMQGVYKVKEPTLKEKFAKIAHIKMERVPNLVFVHIP----REKNARADELVNEAID  136 (140)
T ss_dssp             HHHHTTSSCCCCGGGHHHHHHHHHHHHHHCTTCEEEECC----GGGGHHHHHHHHHHHH
T ss_pred             HHHhCCCcccCCHHHHHHHHHHHHHhhcCCCcEEEEEcC----chhhHHHHHHHHHHHH
Confidence            9999998754 22222233333345 5566799999999    4899999999999874

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

Probab=99.85  E-value=3.7e-21  Score=161.99  Aligned_cols=122  Identities=14%  Similarity=0.069  Sum_probs=91.7

Q ss_pred             EEEEEcCCcc-CCCCceeE-EEEEeecCCC-----Cc---cCCCCchHHHHHHHHHHHHHHhHhhcCCceEEEEeccHHH
Q psy11794         73 FHIDTDTAYR-LQENRYSC-CYLGTLVGPG-----PR---YFNLTTIYLAELLALYLCLKEISEFHSSSRIAIISDSLSV  142 (325)
Q Consensus        73 ~~IytDGS~~-~~~~~~g~-a~i~~~~g~~-----~~---l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~~i~I~tDS~~a  142 (325)
                      +.||||||+. ++++++|+ |++...-|..     ..   ....+||++||+.|++.||+.+.+ .+.++|.|+|||+++
T Consensus         2 ~~iy~DGs~~~~n~g~~G~~G~vi~~~g~~~~~~~~~~~~~~~~~tnn~aEl~A~~~aL~~a~~-~g~~~v~i~tDS~~v   80 (149)
T 2ehg_A            2 IIGYFDGLCEPKNPGGIATFGFVIYLDNRKIEGYGLAEKPFSINSTNNVAEYSGLICLMETMLR-LGISSPIIKGDSQLV   80 (149)
T ss_dssp             CEEEEEEEEESSSSSSEEEEEEEEECSSCEEEEEEECSCTTCTTCCHHHHHHHHHHHHHHHHHH-HTCCSCEEEESCHHH
T ss_pred             EEEEEeeccCCCCCChheEEEEEEEECCEEEEEeccccCCCCCCccHHHHHHHHHHHHHHHHHH-cCCCEEEEEeChHHH
Confidence            5799999999 78888885 8766542211     01   113789999999999999999988 677899999999999


Q ss_pred             HHHhcCCCCC-hHHHHHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHHHHHhcccCC
Q psy11794        143 LSALGNICFS-HPFISKIYQLWKLIVTRGTDVVFLWCPSHCGIDGNEAVDSAANHHTHP  200 (325)
Q Consensus       143 i~~l~~~~~~-~~~~~~i~~~~~~l~~~~~~i~~~WVpgH~gi~gNe~AD~LAk~aa~~  200 (325)
                      ++.++++|.. .+....+.+.+..+.+.. +|.|.|||+|    +|+.||+|||+|+..
T Consensus        81 i~~i~~~w~~~~~~~~~l~~~i~~l~~~~-~v~~~~V~~~----~N~~AD~LA~~a~~~  134 (149)
T 2ehg_A           81 IKQMNGEYKVKAKRIIPLYEKAIELKKKL-NATLIWVPRE----ENKEADRLSRVAYEL  134 (149)
T ss_dssp             HHHHTTSSCCCCTTHHHHHHHHHHHHHHH-TCEEEECCGG----GCHHHHHHHHHHHHH
T ss_pred             HHHHhCccccCCHHHHHHHHHHHHHHhcC-CEEEEEcCCc----ccHHHHHHHHHHHHh
Confidence            9999998754 222223333333333333 5999999984    999999999999854

>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=99.83  E-value=1.1e-20  Score=190.87  Aligned_cols=117  Identities=24%  Similarity=0.320  Sum_probs=93.3

Q ss_pred             cEEEEEcCCccCCCCceeEEEEEeecCCCCc-cCCCCchHHHHHHHHHHHHHHhHhhcCCceEEEEeccHHHHHHhcCCC
Q psy11794         72 IFHIDTDTAYRLQENRYSCCYLGTLVGPGPR-YFNLTTIYLAELLALYLCLKEISEFHSSSRIAIISDSLSVLSALGNIC  150 (325)
Q Consensus        72 ~~~IytDGS~~~~~~~~g~a~i~~~~g~~~~-l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~~i~I~tDS~~ai~~l~~~~  150 (325)
                      .+.||||||+.+++|.+|+|++... +.+.. -...+||++||+.|++.||+.     ...+|.|+|||++|++.+++|.
T Consensus       436 ~~~iytDGs~~~n~g~~g~G~v~~~-~~~~~~~~~~~TNn~aEl~A~i~aL~~-----~~~~v~I~tDS~~v~~~i~~~~  509 (555)
T 1mu2_A          436 AETFYTDGSCNRQSKEGKAGYVTDR-GKDKVKKLEQTTNQQAELEAFAMALTD-----SGPKVNIIVDSQYVMGIVASQP  509 (555)
T ss_dssp             CEEEEEEEEECTTTCCEEEEEEETT-SCEEEEEESSCCHHHHHHHHHHHHHHT-----SCSEEEEEESCHHHHHHHHTCC
T ss_pred             ceEEEEcccccCCCCCceEEEEEEe-CCEeeccCCCCCHHHHHHHHHHHHHHc-----CCCeEEEEEehHHHHHHHhccc
Confidence            3689999999999888888876643 21111 114689999999999999997     3679999999999999999975


Q ss_pred             CC--hHHHHHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHHHHHhccc
Q psy11794        151 FS--HPFISKIYQLWKLIVTRGTDVVFLWCPSHCGIDGNEAVDSAANHHT  198 (325)
Q Consensus       151 ~~--~~~~~~i~~~~~~l~~~~~~i~~~WVpgH~gi~gNe~AD~LAk~aa  198 (325)
                      ..  .++..++.+.    ...+..|.|.|||||+|++|||.||+|||+|+
T Consensus       510 ~~~~~~l~~~~~~~----~~~~~~v~~~wV~~H~g~~~Ne~AD~LA~~a~  555 (555)
T 1mu2_A          510 TESESKIVNQIIEE----MIKKEAIYVAWVPAHKGIGGNQEVDHLVSQGI  555 (555)
T ss_dssp             SEESCHHHHHHHHH----HHHCSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             ccccHHHHHHHHHH----hccCCcEEEEEEECCCCChhHHHHHHHHHhhC
Confidence            43  6666655442    23468899999999999999999999999985

>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=99.82  E-value=1.5e-20  Score=189.99  Aligned_cols=115  Identities=24%  Similarity=0.333  Sum_probs=90.3

Q ss_pred             EEEEEcCCccCCCCceeEEEEEeecCCCCcc-CCCCchHHHHHHHHHHHHHHhHhhcCCceEEEEeccHHHHHHhcCCCC
Q psy11794         73 FHIDTDTAYRLQENRYSCCYLGTLVGPGPRY-FNLTTIYLAELLALYLCLKEISEFHSSSRIAIISDSLSVLSALGNICF  151 (325)
Q Consensus        73 ~~IytDGS~~~~~~~~g~a~i~~~~g~~~~l-~~~~s~~~AEl~Ai~~AL~~a~~~~~~~~i~I~tDS~~ai~~l~~~~~  151 (325)
                      +.||||||+.+++|.+|+|++.. .+....+ ...+||++||+.|++.||+.+     ..+|.|+|||++|++.++++..
T Consensus       440 ~~iytDGs~~~n~g~~g~g~v~~-~~~~~~~~~~~~TNn~aEl~Ai~~aL~~~-----~~~v~I~tDS~~vi~~i~~~~~  513 (557)
T 2zd1_A          440 ETFYVDGAANRETKLGKAGYVTN-KGRQKVVPLTNTTNQKTELQAIYLALQDS-----GLEVNIVTDSQYALGIIQAQPD  513 (557)
T ss_dssp             CEEEEEEEECTTTCCEEEEEEET-TSCEEEEEECSCCHHHHHHHHHHHHHHHS-----CSEEEEEECCHHHHHHHTTCCS
T ss_pred             EEEEEccCCCCCCCceEEEEEEE-CCcEEEecCCCCCHHHHHHHHHHHHHHhC-----CCcEEEEeChHHHHHHHhcCCc
Confidence            58999999999988888887664 2221111 146899999999999999998     4799999999999999999765


Q ss_pred             C--hHHHHHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHHHHHhcc
Q psy11794        152 S--HPFISKIYQLWKLIVTRGTDVVFLWCPSHCGIDGNEAVDSAANHH  197 (325)
Q Consensus       152 ~--~~~~~~i~~~~~~l~~~~~~i~~~WVpgH~gi~gNe~AD~LAk~a  197 (325)
                      .  .++..++.+   .+. ....|.|.|||||+|++|||.||+|||+|
T Consensus       514 ~~~~~l~~~~~~---~l~-~~~~v~~~wV~~H~g~~~Ne~AD~LA~~a  557 (557)
T 2zd1_A          514 KSESELVNQIIE---QLI-KKEKVYLAWVPAHKGIGGNEQVDKLVSAG  557 (557)
T ss_dssp             EESSHHHHHHHH---HHH-HCSEEEEEECCSSSCCTTCCGGGGCC---
T ss_pred             cCCHHHHHHHHH---HHh-cCCCEEEEEcCCCCCChhHHHHHHHHhcC
Confidence            5  566655544   233 35689999999999999999999999986

>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=99.56  E-value=1.6e-15  Score=126.78  Aligned_cols=117  Identities=15%  Similarity=0.029  Sum_probs=86.9

Q ss_pred             ccEEEEEcCCccCCCCceeEEEEEeecCC----CCccCCCCchHHHHHHHHHHHHHHhHhhcCCceEEEEeccHHHHHHh
Q psy11794         71 FIFHIDTDTAYRLQENRYSCCYLGTLVGP----GPRYFNLTTIYLAELLALYLCLKEISEFHSSSRIAIISDSLSVLSAL  146 (325)
Q Consensus        71 ~~~~IytDGS~~~~~~~~g~a~i~~~~g~----~~~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~~i~I~tDS~~ai~~l  146 (325)
                      ..+.||||||+.+++|++|+|++...-|.    +..+ ..+||++||++|++.||+.+.+ .+. +|.|+|||++|++.+
T Consensus        10 ~~~~iy~DGa~~gNpG~~G~G~vl~~~g~~~~~~~~~-~~~TNN~aEl~A~i~aL~~~~~-~~~-~v~i~tDS~~vi~w~   86 (142)
T 1zbf_A           10 IWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPI-PIGTNNMGEFLAIVHGLRYLKE-RNS-RKPIYSNSQTAIKWV   86 (142)
T ss_dssp             CSSSEEEEEEECSSSEEEEEEEEETTTCCEEEECCCE-EEECHHHHHHHHHHHHHHHHHH-TTC-CCCEEESCHHHHHHH
T ss_pred             CeEEEEEeeccCCCCCCeEEEEEEEeCCEEEEEeccc-CCcCcHHHHHHHHHHHHHHHHh-CCC-eEEEEEehHHHHHHH
Confidence            45689999999999999999877652211    1122 2579999999999999999988 455 999999999999999


Q ss_pred             cCCCCC---------hHHHHHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHHH
Q psy11794        147 GNICFS---------HPFISKIYQLWKLIVTRGTDVVFLWCPSHCGIDGNEAVDS  192 (325)
Q Consensus       147 ~~~~~~---------~~~~~~i~~~~~~l~~~~~~i~~~WVpgH~gi~gNe~AD~  192 (325)
                      ++.+.+         .++...|.++...+...  .+....|+-|++.-||.-||.
T Consensus        87 ~~~~~k~~~~~~v~n~dLw~~l~~~~~w~~~~--~~~~~~~kw~~~~~ge~pad~  139 (142)
T 1zbf_A           87 KDKKAKSTLVRNEETALIWKLVDEAEEWLNTH--TYETPILKWQTDKWGEIKADY  139 (142)
T ss_dssp             HHTCCCCCCCCSTTTHHHHHHHHHHHHHHHHC--CCCCCEEECCHHHHCSCTTCC
T ss_pred             HcCCccCCCCCCcccHHHHHHHHHHHHHHhhC--CCceeEEEeccCccCcCcccc
Confidence            987621         34555554444444443  445556888998889998884

>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=99.42  E-value=2e-13  Score=112.51  Aligned_cols=94  Identities=16%  Similarity=0.079  Sum_probs=66.9

Q ss_pred             EEEEEcCCccCCCCceeEEEEEeecCCC----CccCCCCchHHHHHHHHHHHHHHhHhhcCCceEEEEeccHHHHHHhcC
Q psy11794         73 FHIDTDTAYRLQENRYSCCYLGTLVGPG----PRYFNLTTIYLAELLALYLCLKEISEFHSSSRIAIISDSLSVLSALGN  148 (325)
Q Consensus        73 ~~IytDGS~~~~~~~~g~a~i~~~~g~~----~~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~~i~I~tDS~~ai~~l~~  148 (325)
                      ..||||||+.+|+|++|+|++....+..    ..+ +.+||++||++|++.||+.+.+ .+. ++.|+|||++|++.|.+
T Consensus         6 ~~iytDGac~GNPGp~G~ggV~~~~g~~~~~~g~~-~~tTNN~aEl~A~i~aL~~l~~-~~~-~v~i~tDSqyVi~wi~~   82 (134)
T 4htu_A            6 ESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPI-PIGTNNMGEFLAIVHGLRYLKE-RNS-RKPIYSNSQTAIKWVKD   82 (134)
T ss_dssp             SSEEEEEEEETTTEEEEEEEEETTTCCEEEEEEEE-EEECHHHHHHHHHHHHHHHHHH-TTC-CCCEEESCHHHHHHHHH
T ss_pred             eEEEEeeccCCCCCCeEEEEEEEECCEEEEEecCC-CCCchHHHHHHHHHHHHHHHHh-CCC-CEEEEcchHHHHHHHHc
Confidence            3789999999999999986554321110    112 3689999999999999999987 443 48999999999999987


Q ss_pred             CCCC---------hHHHHHHHHHHHHHHhc
Q psy11794        149 ICFS---------HPFISKIYQLWKLIVTR  169 (325)
Q Consensus       149 ~~~~---------~~~~~~i~~~~~~l~~~  169 (325)
                      +.-+         .++...+.++...|...
T Consensus        83 ~~~kt~~~~~vkN~dLw~~ld~~~~~l~~~  112 (134)
T 4htu_A           83 KKAKSTLVRNEETALIWKLVDEAEEWLNTH  112 (134)
T ss_dssp             TCCCCCCCCSSTTHHHHHHHHHHHHHHHHC
T ss_pred             CCcccCCCCCccCHHHHHHHHHHHHHHHhC
Confidence            5211         34555555544445433

>1rw3_A POL polyprotein; RNA and DNA dependent DNA polymerase, reverse transcriptase, transferase, replication; 3.00A {Moloney murine leukemia virus} SCOP: e.8.1.2

Probab=86.70  E-value=0.17  Score=49.03  Aligned_cols=42  Identities=12%  Similarity=0.046  Sum_probs=33.5

Q ss_pred             CCchHHHHHHHHHHHHHHhHhhcCCceEEEEeccHHHHHHhcC
Q psy11794        106 LTTIYLAELLALYLCLKEISEFHSSSRIAIISDSLSVLSALGN  148 (325)
Q Consensus       106 ~~s~~~AEl~Ai~~AL~~a~~~~~~~~i~I~tDS~~ai~~l~~  148 (325)
                      ..+.++.|++||..|++.........+++|+||+. ++..+.+
T Consensus       386 ~ys~~ekEllAi~~a~~~~~~yl~g~~~~v~tDh~-~~~~l~~  427 (455)
T 1rw3_A          386 GWPPCLRMVAAIAVLTKDAGKLTMGQPLVIKAPHA-VEALVKQ  427 (455)
T ss_dssp             SSCCSSHHHHHHHHHHHHHHGGGCSSCEEEECSSC-TTTTSSS
T ss_pred             ccchHHHHHHHHHHHHHHHHHHcCCCcEEEEecCh-HHHHhCC
Confidence            35678999999999999887655567999999997 6655554

---

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	325
d1mu2a1	126	c.55.3.1 (A:430-555) HIV RNase H (Domain of revers	0.001

>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 = 36.0 bits (82), Expect = 0.001
 Identities = 26/119 (21%), Positives = 42/119 (35%), Gaps = 7/119 (5%)

Query: 77  TDTAYRLQENRYSCCYLGTLVGPGPRYFNLTTIYLAELLALYLCLKEISEFHSSSRIAII 136
           TD +   Q       Y+        +    TT   AEL A  + L +     +     II
Sbjct: 12  TDGSCNRQSKEGKAGYVTDRGKDKVKKLEQTTNQQAELEAFAMALTDSGPKVN-----II 66

Query: 137 SDSLSVLSALGNICFSHPFISKIYQLWKLIVTRGTDVVFLWCPSHCGIDGNEAVDSAAN 195
            DS  V+  + +             + ++I      +   W P+H GI GN+ VD   +
Sbjct: 67  VDSQYVMGIVASQPTESESKIVNQIIEEMIKKE--AIYVAWVPAHKGIGGNQEVDHLVS 123

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	325
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.93
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.92
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	99.92
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	99.81
d1zbfa1	132	BH0863-like Ribonuclease H {Bacillus halodurans [T	99.71

>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=99.93  E-value=2.8e-26  Score=186.60  Aligned_cols=117  Identities=22%  Similarity=0.294  Sum_probs=88.8

Q ss_pred             EEEEEcCCccCCCCceeEEEEEeecCCCCccCCCCchHHHHHHHHHHHHHHhHhhcCCceEEEEeccHHHHHHhcCCCCC
Q psy11794         73 FHIDTDTAYRLQENRYSCCYLGTLVGPGPRYFNLTTIYLAELLALYLCLKEISEFHSSSRIAIISDSLSVLSALGNICFS  152 (325)
Q Consensus        73 ~~IytDGS~~~~~~~~g~a~i~~~~g~~~~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~~i~I~tDS~~ai~~l~~~~~~  152 (325)
                      ..||||||+.++++.+|+|++...........+.+||++|||.||+.||+..     ..++.|+|||++|++.+++++..
T Consensus         8 ~t~YTDGS~~~n~~~~~~g~~~~~~~~~~~~~~~~tnn~AEl~Ai~~al~~~-----~~~i~I~tDS~~v~~~~~~~~~~   82 (126)
T d1mu2a1           8 ETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKLEQTTNQQAELEAFAMALTDS-----GPKVNIIVDSQYVMGIVASQPTE   82 (126)
T ss_dssp             EEEEEEEEECTTTCCEEEEEEETTSCEEEEEESSCCHHHHHHHHHHHHHHTS-----CSEEEEEESCHHHHHHHHTCCSE
T ss_pred             cEEEEcCCCCCCCCcEEEEEEecCCCEEEEecCCCcchHHHHHHHHHHhccC-----CcceEEEechHHHHHHHhcCCcc
Confidence            4799999999887777777655421111111235799999999999999853     57899999999999999998765


Q ss_pred             --hHHHHHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHHHHHhccc
Q psy11794        153 --HPFISKIYQLWKLIVTRGTDVVFLWCPSHCGIDGNEAVDSAANHHT  198 (325)
Q Consensus       153 --~~~~~~i~~~~~~l~~~~~~i~~~WVpgH~gi~gNe~AD~LAk~aa  198 (325)
                        .+....+   +..+. +...|.|.|||||+|++|||.||+||++|.
T Consensus        83 ~~~~~~~~~---~~~~~-~~~~v~~~wV~gH~g~~gNe~AD~LA~~ai  126 (126)
T d1mu2a1          83 SESKIVNQI---IEEMI-KKEAIYVAWVPAHKGIGGNQEVDHLVSQGI  126 (126)
T ss_dssp             ESCHHHHHH---HHHHH-HCSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             ccchHHHHH---HHHhh-hcceeEEEEEeCCCCCcchHHHHHHHHhhC
Confidence              3333322   22333 456899999999999999999999999984

>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=99.92  E-value=4.3e-26  Score=189.94  Aligned_cols=125  Identities=21%  Similarity=0.162  Sum_probs=93.7

Q ss_pred             EEEEEcCCccCCCCceeEEEEEeecCCCCcc---CCCCchHHHHHHHHHHHHHHhHhhcCCceEEEEeccHHHHHHhcCC
Q psy11794         73 FHIDTDTAYRLQENRYSCCYLGTLVGPGPRY---FNLTTIYLAELLALYLCLKEISEFHSSSRIAIISDSLSVLSALGNI  149 (325)
Q Consensus        73 ~~IytDGS~~~~~~~~g~a~i~~~~g~~~~l---~~~~s~~~AEl~Ai~~AL~~a~~~~~~~~i~I~tDS~~ai~~l~~~  149 (325)
                      +.||||||+.+|+|++|+|+++...+....+   ...+||++||+.|++.||+++..   ...+.|++||+++++.+..+
T Consensus         4 i~iytDGs~~~N~g~~G~g~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~~~---~~~i~i~tds~~~~~~~~~~   80 (147)
T d1rila_           4 VALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKE---PCEVDLYTDSHYLKKAFTEG   80 (147)
T ss_dssp             CCEEEEEEESSTTEEEEEEEEECBTTBCCEECCEEEEECHHHHHHHHHHHHHHSCCS---CCEEEEECCCHHHHHHHHSS
T ss_pred             EEEEEccCCCCCCCccEEEEEEEECCcceEEecccccccHHHHHHHHHHHHhhhccC---CceEEEecchhhhhcccccc
Confidence            5899999999998888888877654432221   23579999999999999998743   67899999999999988764


Q ss_pred             CCC------------hHHH-HHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHHHHHhcccCCC
Q psy11794        150 CFS------------HPFI-SKIYQLWKLIVTRGTDVVFLWCPSHCGIDGNEAVDSAANHHTHPR  201 (325)
Q Consensus       150 ~~~------------~~~~-~~i~~~~~~l~~~~~~i~~~WVpgH~gi~gNe~AD~LAk~aa~~~  201 (325)
                      +..            .++. .++++.+..+. ....|.|+|||||+|++|||.||+|||+|++..
T Consensus        81 ~~~~~~~~~~~~~~~~~v~n~dL~~~l~~~~-~~~~v~~~wVkgHsg~~gNe~AD~LAk~aa~~~  144 (147)
T d1rila_          81 WLEGWRKRGWRTAEGKPVKNRDLWEALLLAM-APHRVRFHFVKGHTGHPENERVDREARRQAQSQ  144 (147)
T ss_dssp             HHHHHHHTTSBCTTSSBCTTHHHHHHHHHHH-TTSEEECCCCCGGGSCTHHHHHHHHHHHHHTSS
T ss_pred             chhhhhhccccccccccchhHHHHHHHHHHh-hhcccceEEccCCCCCcchHHHHHHHHHHHHHh
Confidence            210            1111 11222222233 467899999999999999999999999998764

>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=99.92  E-value=1.2e-25  Score=187.54  Aligned_cols=133  Identities=16%  Similarity=0.159  Sum_probs=97.8

Q ss_pred             cEEEEEcCCccCCCCceeEEEEEeecCCCCcc---CCCCchHHHHHHHHHHHHHHhHhhcCCceEEEEeccHHHHHHhcC
Q psy11794         72 IFHIDTDTAYRLQENRYSCCYLGTLVGPGPRY---FNLTTIYLAELLALYLCLKEISEFHSSSRIAIISDSLSVLSALGN  148 (325)
Q Consensus        72 ~~~IytDGS~~~~~~~~g~a~i~~~~g~~~~l---~~~~s~~~AEl~Ai~~AL~~a~~~~~~~~i~I~tDS~~ai~~l~~  148 (325)
                      .+.||||||+.+|++++|+|+++...+....+   .+.+|+++||++|++.||+++.   ....+.|++||++++..+..
T Consensus         2 ~I~IYtDGS~~~N~g~aG~G~vi~~~~~~~~~~~~~~~~tnn~aE~~Ai~~Al~~~~---~~~~i~i~tds~~~i~~~~~   78 (152)
T d1jl1a_           2 QVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALK---EHAEVILSTDSQYVRQGITQ   78 (152)
T ss_dssp             CEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEEEEECHHHHHHHHHHHHHHTCC---SCCEEEEEECCHHHHHHHHT
T ss_pred             EEEEEEeCCCCCCCCcEEEEEEEEECCeEEEeccccCcccHHHHHHhhhhhhhhhhc---ccceEEEeecceeeEEcccc
Confidence            35899999999999999998776532211110   1357899999999999999874   47889999999999998876


Q ss_pred             CCC--------C---hHHH-HHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHHHHHhcccCCCCCCCCCc
Q psy11794        149 ICF--------S---HPFI-SKIYQLWKLIVTRGTDVVFLWCPSHCGIDGNEAVDSAANHHTHPRHVNLCST  208 (325)
Q Consensus       149 ~~~--------~---~~~~-~~i~~~~~~l~~~~~~i~~~WVpgH~gi~gNe~AD~LAk~aa~~~~~~~~~~  208 (325)
                      +..        .   .++. ..+...+..+ .....|.|+|||||+|++|||.||+|||+|+..+.++..++
T Consensus        79 ~~~~~~~~~~~~~~~~~~~n~~~~~~i~~~-~~~~~V~~~wV~gH~g~~gNe~AD~LAk~aa~~~~~~d~~~  149 (152)
T d1jl1a_          79 WIHNWKKRGWKTADKKPVKNVDLWQRLDAA-LGQHQIKWEWVKGHAGHPENERADELARAAAMNPTLEDTGY  149 (152)
T ss_dssp             THHHHHHTTTBCTTSCBCTTHHHHHHHHHH-TTTCEEEEEECCSSTTCHHHHHHHHHHHHHHHSCCBCCTTC
T ss_pred             hhhHhHhccchhcccCeeecHHHHHHHHHH-hhcceeEEEEecccCCCccHHHHHHHHHHHHhCCCCCccCC
Confidence            521        1   1110 1122222223 24568999999999999999999999999999887665544

>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=99.81  E-value=4.6e-20  Score=146.15  Aligned_cols=98  Identities=21%  Similarity=0.290  Sum_probs=74.9

Q ss_pred             EEEEcCCccCCCCceeEEEEEeecCCCC-ccCCCCchHHHHHHHHHHHHHHhHhhcCCceEEEEeccHHHHHHhcCCCCC
Q psy11794         74 HIDTDTAYRLQENRYSCCYLGTLVGPGP-RYFNLTTIYLAELLALYLCLKEISEFHSSSRIAIISDSLSVLSALGNICFS  152 (325)
Q Consensus        74 ~IytDGS~~~~~~~~g~a~i~~~~g~~~-~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~~i~I~tDS~~ai~~l~~~~~~  152 (325)
                      .+|||||+.++++.+|+|++... +... .....+||++|||.||+.||+..     ..+|.|+|||++|++++++++..
T Consensus        10 t~ytDGs~~~n~~~g~~g~~~~~-~~~~~~~~~~~TNn~aEl~Avi~aL~~~-----~~~v~I~TDS~yvi~~i~~~~~~   83 (110)
T d1s1ta1          10 TFYVDGAANRETKLGKAGYVTNR-GRQKVVTLTDTTNQKTELQAIYLALQDS-----GLEVNIVTDSQYALGIIQAQPDQ   83 (110)
T ss_dssp             EEEEEEEEETTTTEEEEEEEETT-SCEEEEEESSCCHHHHHHHHHHHHHHHS-----CSEEEEEECCHHHHHHHHHCCSE
T ss_pred             EEEEeCCCCCCCCCcEEEEEEec-CCeEEEecccCcHHHHHHHHHHHHHHhC-----CCeEEEEEehHHHHHHHhcCccc
Confidence            68999999998877777665432 2111 11246799999999999999853     56899999999999999998776


Q ss_pred             --hHHHHHHHHHHHHHHhcCCeEEEEEecCC
Q psy11794        153 --HPFISKIYQLWKLIVTRGTDVVFLWCPSH  181 (325)
Q Consensus       153 --~~~~~~i~~~~~~l~~~~~~i~~~WVpgH  181 (325)
                        +++..+|.+.   + .....|.|.|||||
T Consensus        84 ~~~~l~~~il~~---l-~~~~~v~i~WVpgH  110 (110)
T d1s1ta1          84 SESELVNQIIEQ---L-IKKEKVYLAWVPAH  110 (110)
T ss_dssp             ESCHHHHHHHHH---H-HHCSEEEEEECCSS
T ss_pred             cchHHHHHHHHH---H-hcCCceEEEEeCCC
Confidence              6666665542   3 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=99.71  E-value=1.9e-18  Score=139.95  Aligned_cols=113  Identities=14%  Similarity=0.036  Sum_probs=85.8

Q ss_pred             EEEEcCCccCCCCceeEEEEEeecCC----CCccCCCCchHHHHHHHHHHHHHHhHhhcCCceEEEEeccHHHHHHhcCC
Q psy11794         74 HIDTDTAYRLQENRYSCCYLGTLVGP----GPRYFNLTTIYLAELLALYLCLKEISEFHSSSRIAIISDSLSVLSALGNI  149 (325)
Q Consensus        74 ~IytDGS~~~~~~~~g~a~i~~~~g~----~~~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~~i~I~tDS~~ai~~l~~~  149 (325)
                      .||||||+.+|||++|+|++....+.    +..+ +.+||++||++|++.||+.+.+ . ..++.|+|||++|++.+.++
T Consensus         6 sIy~DGa~~GNPGp~g~g~v~~~~~~~~~~sg~~-~~~TNN~aEl~A~i~aL~~~~~-~-~~~i~I~tDS~yvi~wv~~~   82 (132)
T d1zbfa1           6 SLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPI-PIGTNNMGEFLAIVHGLRYLKE-R-NSRKPIYSNSQTAIKWVKDK   82 (132)
T ss_dssp             SEEEEEEECSSSEEEEEEEEETTTCCEEEECCCE-EEECHHHHHHHHHHHHHHHHHH-T-TCCCCEEESCHHHHHHHHHT
T ss_pred             eEEEeecCCCCCchheEEEEEEcCCEEEEEEcCc-CccchHHHHHHHHHHHHHHhhc-C-CceEEEEeccHHHHHHHHhC
Confidence            48999999999999999877643221    1122 4689999999999999999987 3 36799999999999999876


Q ss_pred             CCC---------hHHHHHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHH
Q psy11794        150 CFS---------HPFISKIYQLWKLIVTRGTDVVFLWCPSHCGIDGNEAVD  191 (325)
Q Consensus       150 ~~~---------~~~~~~i~~~~~~l~~~~~~i~~~WVpgH~gi~gNe~AD  191 (325)
                      .-+         .++.+.+.++...+.  ...+.+.||+.|+..-||..||
T Consensus        83 ~~kt~~~~~vkN~~l~~~i~~a~~~lk--~h~~~~~~~KW~~~~wG~i~AD  131 (132)
T d1zbfa1          83 KAKSTLVRNEETALIWKLVDEAEEWLN--THTYETPILKWQTDKWGEIKAD  131 (132)
T ss_dssp             CCCCCCCCSTTTHHHHHHHHHHHHHHH--HCCCCCCEEECCHHHHCSCTTC
T ss_pred             ceecCcCCCcccHHHHHHHHHHHHHHH--hCCcCceeEEecCcccccCCCC
Confidence            411         445554544443343  3457788999999999999988