Psyllid ID: psy15839

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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---
Protein Sequence
MHKILFGNVDSFNITPNKPLPLKIRFNCIREVSAVLKNTKVVPYSQGFPPWYSDFPVVDLSLYGSKTIQNTSCAVYAGGSAKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNTSIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGAEFVNLSSPADLISVGKKYIHEKWQKSWSDLTNNKLKCVKPTIGPWNVSDCNNRYEEVVLTRVRIGHTRLTHSYLFTRSDPPSCQSSQLSSQSSEDKSKSPEQRSEVVLVLY
Secondary Structure (PSIPRED)
cccEEEcccccccccccccccccccccHHHHHHHHccccccccccccccccccccccEEEEEccccccccEEEEEEEccccEEEEccccccHHHHHHHHHHHHHHHccccccccEEEEccHHHHHHHHHHHcccHHHHHHHHHHHHHHHccccEEEEEEccccccccHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccHHHHHHHHHHHHccccccHHHHcccccccccccccccccccccccccHHHHHHHHHHHc
Secondary Structure Prediction (SSPRO)
ccEEEEEcccccccccccccccccccccccccccccccccccHHHHHHHHHHcccccEEEEEccccccccEEEEEEEcccEEEEcccccccHHHHHHHHHHHHHHHHHHcccccEEEEEccHHHHHHHHccccccHHHHHHHHHHHHHHHcccEEEEEEEcccccccccHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccHHHHHHHHHHHccccccHHHHHcccccccccHHccccccccccccccHHHHHHHHEHcc
Coil and Loop (DISEMBL)
mhkilfgnvdsfnitpnkplplkirFNCIREVSAVLKntkvvpysqgfppwysdfpvvdlslygsktiqntscavyaggsAKSYILNNINSIFTAELLALVFCLdsvknrpdvntlIVCDSMSALTSIANKNTSIPLIAHILNTWHTLKscgkkvaflwcpshtgisgneIVDRAtrqldgaefvnlsspadlISVGKKYIHEKWQKSWSDLtnnklkcvkptigpwnvsdcnnryeEVVLTRVRIghtrlthsylftrsdppscqssqlssqssedkskspeqrsEVVLVLY
Flexible Loop (DISEMBL)
mhkilfgnvdsfnitpnkplplKIRFNCIREVSAVLKNTKvvpysqgfppwysDFPVVDLSLYGSKTIQNTSCAVYAGGSAKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNTSIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGAEFVNLSSPADLISVGKKYIHEKWQKSWSDLTNNKLKCVkptigpwnvsdcnnRYEEVVLTRVRIGHTRLTHsylftrsdppscqSSQLssqssedkskspeqrsevvlvly
Low Complexity Region (SEG)
MHKILFGNVDSFNITPNKPLPLKIRFNCIREVSAVLKNTKVVPYSQGFPPWYSDFPVVDLSLYGSKTIQNTSCAVYAGGSAKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNTSIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGAEFVNLSSPADLISVGKKYIHEKWQKSWSDLTNNKLKCVKPTIGPWNVSDCNNRYEEVVLTRVRIGHTRLTHSYLFTRsdppscqssqlssqssedkskspeqRSEVVLVLY
Disordered region (IsUnstruct)
***ILFGNVDSFNITPNKPLPLKIRFNCIREVSAVLKNTKVVPYSQGFPPWYSDFPVVDLSLYGSKTIQNTSCAVYAGGSAKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNTSIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGAEFVNLSSPADLISVGKKYIHEKWQKSWSDLTNNKLKCVKPTIGPWNVSDCNNRYEEVVLTRVRIGHTRLTHSYLFT***********************************
Disordered Region (DISOPRED)
*HKILFGNVDSFNITPNKPLPLKIRFNCIREVS***********SQGFPPWYSDFPVVDLSLYGSKTIQNTSCAVYAGGSAKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNTSIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGAEFVNLSSPADLISVGKKYIHEKWQKSWSDLTNNKLKCVKPTIGPWNVSDCNNRYEEVVLTRVRIGHTRLTHSYLFTRSDPPSCQSSQLSSQSSEDKSKSPEQRSEVVLVLY
Disordered Region (DISEMBL)
MHKILFGNVDSFNITPNKPLPLKIRFNCIREVSAVLKNTKVVPYSQGFPPWYSDFPVVDLSLYGSKTIQNTSCAVYAGGSAKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNTSIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGAEFVNLSSPADLISVGKKYIHEKWQKSWSDLTNNKLKCVKPTIGPWNVSDCNNRYEEVVLTRVRIGHTRLTHSYLFTR********************************LY
Disordered Region (DISPRO)
MHKILFGNVDSFNITPNKPLPLKIRFNCIREVSAVLKNTKVVPYSQGFPPWYSDFPVVDLSLYGSKTIQNTSCAVYAGGSAKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNTSIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGAEFVNLSSPADLISVGKKYIHEKWQKSWSDLTNNKLKCVKPTIGPWNVSDCNNRYEEVVLTRVRIGHTRLTHSYLFTRSDPPSCQSSQLSSQSSEDKSKSPEQRSEVVLVLY
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MHKILFGNVDSFNITPNKPLPLKIRFNCIREVSAVLKNTKVVPYSQGFPPWYSDFPVVDLSLYGSKTIQNTSCAVYAGGSAKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNTSIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGAEFVNLSSPADLISVGKKYIHEKWQKSWSDLTNNKLKCVKPTIGPWNVSDCNNRYEEVVLTRVRIGHTRLTHSYLFTRSDPPSCQSSQLSSQSSEDKSKSPEQRSEVVLVLY
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	293
443721618	471	hypothetical protein CAPTEDRAFT_200496,	0.689	0.428	0.356	2e-30
443693558	502	hypothetical protein CAPTEDRAFT_189741,	0.750	0.438	0.351	4e-30
443712830	397	hypothetical protein CAPTEDRAFT_202466 [	0.836	0.617	0.319	6e-30
443695973	261	hypothetical protein CAPTEDRAFT_23017, p	0.764	0.858	0.349	1e-29
443724607	397	hypothetical protein CAPTEDRAFT_208903 [	0.836	0.617	0.307	1e-26
427778603	1397	Putative tick transposon [Rhipicephalus	0.675	0.141	0.336	5e-26
427791321	1210	Putative tick transposon, partial [Rhipi	0.699	0.169	0.357	2e-25
427791807	1212	Putative tick transposon, partial [Rhipi	0.699	0.169	0.357	2e-25
443713753	266	hypothetical protein CAPTEDRAFT_215116 [	0.761	0.838	0.312	8e-25
443682433	619	hypothetical protein CAPTEDRAFT_222606 [	0.689	0.326	0.330	3e-24

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

 Score =  138 bits (348), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 73/205 (35%), Positives = 108/205 (52%), Gaps = 3/205 (1%)

Query: 64  GSKTIQNTSCAVYAGGSAKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVC-DSM 122
           GSK+  + +C+ ++        L    S+FT+E++A++  L  V+   + +  ++C DS+
Sbjct: 27  GSKSEDSVACSFFSSRLKLKMKLPVQMSVFTSEIIAILSALRCVEADNEQHQFVICSDSL 86

Query: 123 SALTSIANKNTSIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDR-ATRQLDG 181
           SA+ +I   +   P +  +L    ++    K V F+WCPSH GI GNE+ D  A   L  
Sbjct: 87  SAIMAIHGMDVRHPYVLQVLYAIKSISQQEKIVVFMWCPSHVGIPGNEMADTLAKEALSS 146

Query: 182 AEFVNLSSPA-DLISVGKKYIHEKWQKSWSDLTNNKLKCVKPTIGPWNVSDCNNRYEEVV 240
                L  PA DL  + KKYI  +WQ  W +  +NKL  + PTIGPW       R EE+V
Sbjct: 147 TNLAELPVPASDLRCLIKKYIRSRWQHEWDEQHSNKLHSIHPTIGPWPPCQREKRREEIV 206

Query: 241 LTRVRIGHTRLTHSYLFTRSDPPSC 265
           L R+RIGHT  TH Y+    D   C
Sbjct: 207 LARIRIGHTHYTHDYIPRGDDQTEC 231

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score =  138 bits (347), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 78/222 (35%), Positives = 113/222 (50%), Gaps = 2/222 (0%)

Query: 46  QGFPPWYSDFPVVDLSLYGSKTIQNTSCAVYAGGSAKSYILNNINSIFTAELLALVFCLD 105
           Q F      +P +++   GSK+    +CA         + L    SI+TAEL+A+   L 
Sbjct: 70  QEFYNLIDKYPGINIYTDGSKSNNAVACAFTCSTYQIQFGLPTQMSIYTAELIAIEQALI 129

Query: 106 SVKNRPDVNTLIVC-DSMSALTSIANKNTSIPLIAHILNTWHTLKSCGKKVAFLWCPSHT 164
            ++   D +   +C DS+S+LT+++N + + P +  IL   + L   GK V F+WCPSH 
Sbjct: 130 FIETVKDEDQFNICSDSLSSLTALSNCDITHPYLLSILTKQNNLVRKGKLVVFIWCPSHV 189

Query: 165 GISGNEIVDRATRQLDGAEFVNLSSP-ADLISVGKKYIHEKWQKSWSDLTNNKLKCVKPT 223
           GI GNE+ DR  +Q        L  P  D  S  + Y+   WQ  W + T+NKL  ++P 
Sbjct: 190 GILGNEVADRLAKQALVMPVTKLPLPHTDYKSPIRSYVKSLWQNEWDEETDNKLHSIQPV 249

Query: 224 IGPWNVSDCNNRYEEVVLTRVRIGHTRLTHSYLFTRSDPPSC 265
           I  W      +R  E+VL R RIGH+ LTH YL  R   P C
Sbjct: 250 ISEWKQGPQIDRRGEIVLARARIGHSHLTHGYLLRREVAPFC 291

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 =  137 bits (344), Expect = 6e-30,   Method: Compositional matrix adjust.
 Identities = 79/247 (31%), Positives = 122/247 (49%), Gaps = 2/247 (0%)

Query: 21  PLKIRFNCIREVSAVLKNTKVVPYSQGFPPWYSDFPVVDLSLYGSKTIQNTSCAVYAGGS 80
           P  + ++ ++ +    +   V  ++  F      +P +++   GSK+    +CA      
Sbjct: 94  PDMVHYSFLKHLPCTAQQIVVDAFNHEFYNLIDKYPGINIYTDGSKSNDTVACAFTCSTY 153

Query: 81  AKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVC-DSMSALTSIANKNTSIPLIA 139
              + L    SI+TAEL+A+   L  ++   D +   +C DS+S+LT+++N + + P + 
Sbjct: 154 QIQFGLPAQMSIYTAELIAIEQALIFIETVKDEDQFNICSDSLSSLTALSNCDITHPYLL 213

Query: 140 HILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGAEFVNLSSP-ADLISVGK 198
            IL   + L   GKKV F+WCPSH GI GNE+ DR  +Q        L  P  D  S  +
Sbjct: 214 SILTKQNNLVRKGKKVVFIWCPSHVGILGNEVADRQAKQALVMPVTKLPLPHTDYKSPIR 273

Query: 199 KYIHEKWQKSWSDLTNNKLKCVKPTIGPWNVSDCNNRYEEVVLTRVRIGHTRLTHSYLFT 258
            Y+   WQ  W   T+NKL  ++P I  W      +R  E+VL   RIGH+ LTH YL  
Sbjct: 274 SYVKSLWQNEWDGETDNKLHIIQPVISEWKQGPQIDRRGEIVLACARIGHSHLTHGYLLR 333

Query: 259 RSDPPSC 265
           R   P C
Sbjct: 334 REVAPFC 340

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 =  136 bits (342), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 79/226 (34%), Positives = 114/226 (50%), Gaps = 2/226 (0%)

Query: 46  QGFPPWYSDFPVVDLSLYGSKTIQNTSCAVYAGGSAKSYILNNINSIFTAELLALVFCLD 105
           Q F      +P +++   GSK+    +CA         + L    SI+TAEL+A+   L 
Sbjct: 24  QEFYNLIDKYPGINIYTDGSKSNDAVACAFTCSTYQIQFGLPAQMSIYTAELIAIEQALI 83

Query: 106 SVKNRPDVNTLIVC-DSMSALTSIANKNTSIPLIAHILNTWHTLKSCGKKVAFLWCPSHT 164
            ++   D +   +C DS+S+LT+++N + + P +  IL   + L   GK V F+WCPSH 
Sbjct: 84  FIETVKDEDQFNICSDSLSSLTALSNCDITHPYLLSILTKQNNLVRKGKLVVFIWCPSHV 143

Query: 165 GISGNEIVDRATRQLDGAEFVNLSSP-ADLISVGKKYIHEKWQKSWSDLTNNKLKCVKPT 223
           GI GNE+ DR  +Q        L  P  D  S  + Y+   WQ  W + T+NKL  ++P 
Sbjct: 144 GILGNEVADRLAKQALVMPVTKLPLPHTDYKSPIRSYVKSLWQNEWDEETDNKLHSIQPV 203

Query: 224 IGPWNVSDCNNRYEEVVLTRVRIGHTRLTHSYLFTRSDPPSCQSSQ 269
           I  W      +R  E+VL R RIGH+ LTH YL  R   P C   Q
Sbjct: 204 ISEWKQGPQIDRRGEIVLARARIGHSHLTHGYLLRREVAPFCIPCQ 249

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 =  126 bits (316), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 76/247 (30%), Positives = 120/247 (48%), Gaps = 2/247 (0%)

Query: 21  PLKIRFNCIREVSAVLKNTKVVPYSQGFPPWYSDFPVVDLSLYGSKTIQNTSCAVYAGGS 80
           P  + ++ ++ +    +   V  ++  F      +P +++   GSK+    +CA      
Sbjct: 94  PDMVHYSFLKHLPCTAQQIVVDAFNHEFYNLIDKYPGINIYTDGSKSNDAVACAFTCSTY 153

Query: 81  AKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVC-DSMSALTSIANKNTSIPLIA 139
              + L    SI+TAEL+A+   L  ++   D +   +C DS+S+LT+++N + + P + 
Sbjct: 154 QIQFGLPAQMSIYTAELIAIEQALIFIETMKDEDQFNICSDSLSSLTALSNCDITHPYLL 213

Query: 140 HILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGAEFVNLSSP-ADLISVGK 198
            IL   + L   GK V F+WCPSH GI GNE+ DR  +Q        L  P  D  S  +
Sbjct: 214 SILTKQNNLVRKGKLVVFIWCPSHVGILGNEVADRLAKQALVMPVTKLPLPHTDYKSPIR 273

Query: 199 KYIHEKWQKSWSDLTNNKLKCVKPTIGPWNVSDCNNRYEEVVLTRVRIGHTRLTHSYLFT 258
            Y+    Q  W + T+NKL  ++P I  W      +R  E+VL    IGH+ LTH YL  
Sbjct: 274 SYVKSLRQNEWDEETDNKLHTIQPVISEWKQGPQIDRRGEIVLACACIGHSHLTHGYLLR 333

Query: 259 RSDPPSC 265
           R   P C
Sbjct: 334 REVAPFC 340

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score =  124 bits (311), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 70/208 (33%), Positives = 110/208 (52%), Gaps = 10/208 (4%)

Query: 64   GSKTIQNTSCAVYAGGSAKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMS 123
            GSK+  + SCA Y    + +  L+   SIFTAE   ++  ++ +K      ++I  DS+S
Sbjct: 1115 GSKSQTSVSCAAYGESFSDAKTLHAHTSIFTAEAYGILLIVEHIKQHMIRRSIIYTDSLS 1174

Query: 124  ALTSIA-NKNTSIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGA 182
             +T+++  K +  P+   +LN  H   +    +   W P H GI+GNE+VD+  R+    
Sbjct: 1175 VVTALSCGKCSKNPVFNKLLNNMHEAYNQNLSIVLCWVPGHAGITGNEMVDKNAREAASR 1234

Query: 183  EFVNLSS--PADLISVGKKYIHEKWQKSWSDLTNNKLKCVKPTIG---PWNVSDCNNRYE 237
              +++SS    DL  V ++ +   WQ  W    +NKL  VKP +    P  +    NR+ 
Sbjct: 1235 HTIDISSVPGVDLNPVVRRGLRSHWQVEWDKQVDNKLHLVKPHLSKVLPQKL----NRFT 1290

Query: 238  EVVLTRVRIGHTRLTHSYLFTRSDPPSC 265
            EV L R+RIGHT  TH +L T +DPP+C
Sbjct: 1291 EVTLARLRIGHTYATHKHLLTGTDPPTC 1318

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|427791321|gb|JAA61112.1| Putative tick transposon, partial [Rhipicephalus pulchellus]

 Score =  122 bits (306), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 74/207 (35%), Positives = 102/207 (49%), Gaps = 2/207 (0%)

Query: 64   GSKTIQNTSCAVYAGGSAKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMS 123
            GSKT  +    +  G SA S  +    SIFTAE+ AL      +        +I  DS+S
Sbjct: 943  GSKTRDHVGIGIVTGESAFSVRVPQCISIFTAEVYALYEAARKIIAGKHKKAIIYTDSLS 1002

Query: 124  ALTSIANKNTSIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGAE 183
            AL ++  K+   PL+  ILN    + S    + F W PSH GI GNE  D+         
Sbjct: 1003 ALKALHIKSECEPLVGDILNMV-LINSKVISMRFCWVPSHVGIPGNEKADKCASLAAHKT 1061

Query: 184  FVNLSSP-ADLISVGKKYIHEKWQKSWSDLTNNKLKCVKPTIGPWNVSDCNNRYEEVVLT 242
               +  P  D     +  +  KWQ+ W   T+NKL  VKPT+G W       R+ EV+L 
Sbjct: 1062 LTKIRIPLKDSQRTIRLALLAKWQQQWDSCTSNKLHLVKPTLGEWKNCRHQERFIEVILC 1121

Query: 243  RVRIGHTRLTHSYLFTRSDPPSCQSSQ 269
            R+RIGHT LTH++L T+ + P C+  Q
Sbjct: 1122 RLRIGHTHLTHNFLLTKEEQPMCEKCQ 1148

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 =  122 bits (305), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 74/207 (35%), Positives = 102/207 (49%), Gaps = 2/207 (0%)

Query: 64   GSKTIQNTSCAVYAGGSAKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMS 123
            GSKT  +    +  G SA S  +    SIFTAE+ AL      +        +I  DS+S
Sbjct: 946  GSKTRDHVGIGIVTGESAFSVRVPQCISIFTAEVYALYEAARKIIAGKHKKAIIYTDSLS 1005

Query: 124  ALTSIANKNTSIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGAE 183
            AL ++  K+   PL+  ILN    + S    + F W PSH GI GNE  D+         
Sbjct: 1006 ALKALHIKSECEPLVGDILNMV-LINSKVISMRFCWVPSHVGIPGNEKADKCASLAAHKT 1064

Query: 184  FVNLSSP-ADLISVGKKYIHEKWQKSWSDLTNNKLKCVKPTIGPWNVSDCNNRYEEVVLT 242
               +  P  D     +  +  KWQ+ W   T+NKL  VKPT+G W       R+ EV+L 
Sbjct: 1065 LTKIRIPLKDSQRTIRLALLAKWQQQWDSCTSNKLHLVKPTLGEWKNCRHQERFIEVILC 1124

Query: 243  RVRIGHTRLTHSYLFTRSDPPSCQSSQ 269
            R+RIGHT LTH++L T+ + P C+  Q
Sbjct: 1125 RLRIGHTHLTHNFLLTKEEQPMCEKCQ 1151

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|443713753|gb|ELU06453.1| hypothetical protein CAPTEDRAFT_215116 [Capitella teleta]

 Score =  120 bits (301), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 82/262 (31%), Positives = 125/262 (47%), Gaps = 39/262 (14%)

Query: 18  KPLPLKIRFNCIREVSAVLKNTKVVPYSQGFPPWYSDFPVVDLSLYGSK-------TIQN 70
           +P P +I  + +  V +      V+P +   PPW+   P VDLSL  SK       TI++
Sbjct: 8   QPFPYRIE-DHMDTVGSSPVTHHVIPET---PPWHLVQPEVDLSLTFSKKDSMSALTIRS 63

Query: 71  ----------TSCAVYAGGS------AKSYILNNIN---------SIFTAELLALVFCLD 105
                      S   Y  GS      A+S+  + +          S+FT+E++A++  L 
Sbjct: 64  EFEDALDSYPVSTVFYTDGSKSEDSVARSFFSSRLKLKMKLPVQMSVFTSEIIAILSALK 123

Query: 106 SVKNRPDVNTLIVC-DSMSALTSIANKNTSIPLIAHILNTWHTLKSCGKKVAFLWCPSHT 164
            ++   + +  ++C DS+SA+ +I   +   P +  +L    ++    K V F+WCPSH 
Sbjct: 124 CLEADNEQHQFVICSDSLSAIMAIHGMDVHHPYVLQVLYAIKSISQQEKIVVFMWCPSHV 183

Query: 165 GISGNEIVDR-ATRQLDGAEFVNLSSPA-DLISVGKKYIHEKWQKSWSDLTNNKLKCVKP 222
           GI GNE+    A + L       L  PA DL  + KKYI  +WQ  W +  NNKL  + P
Sbjct: 184 GIPGNEMAHTLAEKALSSTNLAELPVPASDLRGLIKKYIRSQWQHEWEEQHNNKLHSIHP 243

Query: 223 TIGPWNVSDCNNRYEEVVLTRV 244
           TIGPW       R EE+VL R+
Sbjct: 244 TIGPWPPCQREKRREEIVLVRI 265

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|443682433|gb|ELT87030.1| hypothetical protein CAPTEDRAFT_222606 [Capitella teleta]

 Score =  118 bits (295), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 67/203 (33%), Positives = 104/203 (51%), Gaps = 1/203 (0%)

Query: 64  GSKTIQNTSCAVYAGGSAKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMS 123
           GSK+     CA ++     +  L    S++TAEL+A+   L S+   P    +I  DS S
Sbjct: 3   GSKSEDAVGCAFHSRDFNLALGLPCQMSVYTAELIAINETLTSIALLPYDEFVICTDSFS 62

Query: 124 ALTSIANKNTSIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGAE 183
           ++ +I++ +     +  IL     L    K++ F+WCPSH GI GNE  D   +Q  G  
Sbjct: 63  SILAISSIDLIHSYVQSILQKCTNLAGRDKRIIFIWCPSHVGIPGNETADTLAQQASGMN 122

Query: 184 FVNLSSP-ADLISVGKKYIHEKWQKSWSDLTNNKLKCVKPTIGPWNVSDCNNRYEEVVLT 242
            +N   P  D   + + ++  +WQ      T NKL  ++P IG W       R +E+V+ 
Sbjct: 123 ILNCPIPHTDFKPITRSFVETQWQSESDQETGNKLHDIEPDIGSWPPCQREKRRDEIVIA 182

Query: 243 RVRIGHTRLTHSYLFTRSDPPSC 265
           R+RIGHT LT+S+L + +D P C
Sbjct: 183 RLRIGHTFLTYSHLLSGNDAPMC 205

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	293
ASPGD|ASPL0000075333	486	AN10625 [Emericella nidulans (	0.610	0.368	0.235	1.8e-05

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

 Score = 128 (50.1 bits), Expect = 1.8e-05, P = 1.8e-05
 Identities = 45/191 (23%), Positives = 79/191 (41%)

Query:    80 SAKSYILNNINS-IFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNTSIP-- 136
             S  SY+     S ++ AEL  ++  L  +  R   + +I  D+ + L ++ N  +     
Sbjct:   208 SRSSYMGQQSESTVYVAELQGILLALVIILQRQMQHAVIFTDNQATLQALRNPGSQSGQY 267

Query:   137 LIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGAEFVNLSSPADLI-S 195
             ++  I+   +  +  G  V F W P+H G+ GNE  DR  ++  G   +        I S
Sbjct:   268 ILEAIIMALNKGRKAGLNVHFRWIPAHRGVEGNEQADRRAKEATGWRRIRGHRGRMTIRS 327

Query:   196 VGKKYIHE----KWQKSWSDLTNNKLK---CVKPTIGPWNVSDCNNRYEEVVLTRVRIGH 248
               K+  HE    +W+  W    + +        PT     V    +R    ++ ++R G 
Sbjct:   328 AVKRRAHEVVNARWENDWKSCHHGRELYELTPTPTRKVLRVHQDLHRALSTIIVQMRTGK 387

Query:   249 TRLTHSYLFTR 259
               L H YL+ R
Sbjct:   388 IGLRH-YLYQR 397


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        0.320   0.134   0.417    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      293       268   0.00096  114 3  11 22  0.46    33
                                                     32  0.39    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:  616 (65 KB)
  Total size of DFA:  219 KB (2120 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:  22.90u 0.16s 23.06t   Elapsed:  00:00:01
  Total cpu time:  22.90u 0.16s 23.06t   Elapsed:  00:00:01
  Start:  Thu Aug 15 14:12:05 2013   End:  Thu Aug 15 14:12:06 2013

GO:0008150 "biological_process" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	293
cd09276	128	cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom	1e-24
pfam00075	126	pfam00075, RNase_H, RNase H	6e-11
cd06222	123	cd06222, RNase_H, RNase H is an endonuclease that	5e-05
cd09273	135	cd09273, RNase_HI_RT_Bel, Bel/Pao family of RNase	0.003

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

 Score = 95.8 bits (239), Expect = 1e-24
 Identities = 40/133 (30%), Positives = 58/133 (43%), Gaps = 14/133 (10%)

Query: 51  WYSDFPVVDLSLYGSKTIQNTSCAVYA--GGSA-KSYILNNINSIFTAELLALVFCLDSV 107
            Y+D         GSK    T         G+  +SY L    S+F AELLA++  L   
Sbjct: 2   IYTD---------GSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLA 52

Query: 108 KNRPD-VNTLIVC-DSMSALTSIANKNTSIPLIAHILNTWHTLKSCGKKVAFLWCPSHTG 165
                    + +  DS +AL ++ +  +S PL+  I      L + G KV   W P H+G
Sbjct: 53  LREGRRARKITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSG 112

Query: 166 ISGNEIVDRATRQ 178
           I GNE  DR  ++
Sbjct: 113 IEGNERADRLAKE 125

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 = 58.4 bits (142), Expect = 6e-11
 Identities = 30/93 (32%), Positives = 43/93 (46%), Gaps = 11/93 (11%)

Query: 90  NSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSI----ANKNTSIPLIAHILNTW 145
            +   AELLAL+  L+++  +  VN  I  DS   +  I      K+ S P+   I    
Sbjct: 38  TTNQRAELLALIEALEALSGQK-VN--IYTDSQYVIGGITNGWPTKSESKPIKNEIWE-- 92

Query: 146 HTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQ 178
             L     KV   W P H+GI GNE+ D+  +Q
Sbjct: 93  --LLQKKHKVYIQWVPGHSGIPGNELADKLAKQ 123

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

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

 Score = 41.6 bits (98), Expect = 5e-05
 Identities = 21/92 (22%), Positives = 34/92 (36%), Gaps = 4/92 (4%)

Query: 87  NNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNTSIPLIAHILNTWH 146
               +   AELLAL+  L+   +      +I  DS   +  I + +        +L    
Sbjct: 34  IPAATNNEAELLALLEALELALDLGLKKLIIETDSKYVVDLINSWSKGWKKNNLLLWDIL 93

Query: 147 TLKSCGKKVAFLWCPSHTGISGNEIVDRATRQ 178
            L S    + F   P      GNE+ DR  ++
Sbjct: 94  LLLSKFIDIRFEHVPR----EGNEVADRLAKE 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

>gnl|CDD|187697 cd09273, RNase_HI_RT_Bel, Bel/Pao family of RNase HI in long-term repeat retroelements

 Score = 36.9 bits (86), Expect = 0.003
 Identities = 31/102 (30%), Positives = 42/102 (41%), Gaps = 22/102 (21%)

Query: 94  TAELLALVFCLDSVKNRPDVNTLIVCDS---MSALTSIA------NKNTSIPLIAH---I 141
            AEL+AL+  L+  K +P VN  I  DS      L ++          T  P IA    I
Sbjct: 37  RAELIALIRALELAKGKP-VN--IYTDSAYAFGILHALETIWKERGFLTGKP-IALASLI 92

Query: 142 LNTWHTLKSCGKKVAFLWCPSHTG-----ISGNEIVDRATRQ 178
           L     +    K VA +   +H+G       GN   D+A RQ
Sbjct: 93  LQLQKAI-QRPKPVAVIHIRAHSGLPGPLALGNARADQAARQ 133

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 eukaryote. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in 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. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. Bel/Pao family has been described only in metazoan genomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription. Length = 135

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	293
PRK06548	161	ribonuclease H; Provisional	99.91
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	99.9
PRK08719	147	ribonuclease H; Reviewed	99.89
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	99.89
PRK00203	150	rnhA ribonuclease H; Reviewed	99.88
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	99.79
KOG3752|consensus	371		99.78
PRK13907	128	rnhA ribonuclease H; Provisional	99.76
PRK07708	219	hypothetical protein; Validated	99.64
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	99.57
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	99.34

>PRK06548 ribonuclease H; Provisional

Probab=99.91  E-value=1.5e-23  Score=174.97  Aligned_cols=123  Identities=24%  Similarity=0.215  Sum_probs=93.7

Q ss_pred             eEEEEEecCCC-CCC-eeEEEEECCeeEEeecCCCCchhHHHHHHHHHHHHHhhcCCCccEEEEeCcHHHHHHhhcC---
Q psy15839         57 VVDLSLYGSKT-IQN-TSCAVYAGGSAKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANK---  131 (293)
Q Consensus        57 ~~~iytDGS~~-~~~-~G~~v~~~~~~~~~~~~~~~~~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~~~---  131 (293)
                      .+.||||||+. +++ .|+|++..+.....+....+||+.|||.||+.||+.+.. ....|.|+|||++|+++|++|   
T Consensus         5 ~~~IytDGa~~gnpg~~G~g~~~~~~~~~~g~~~~~TNnraEl~Aii~aL~~~~~-~~~~v~I~TDS~yvi~~i~~W~~~   83 (161)
T PRK06548          5 EIIAATDGSSLANPGPSGWAWYVDENTWDSGGWDIATNNIAELTAVRELLIATRH-TDRPILILSDSKYVINSLTKWVYS   83 (161)
T ss_pred             EEEEEEeeccCCCCCceEEEEEEeCCcEEccCCCCCCHHHHHHHHHHHHHHhhhc-CCceEEEEeChHHHHHHHHHHHHH
Confidence            57899999988 444 677766443222223334679999999999999987653 345799999999999999952   


Q ss_pred             -----C-C-Ch-h-HHHHHHHHHHHHhhCCceEEEEEeCCCCCChhhHHHHHHHhhccC
Q psy15839        132 -----N-T-SI-P-LIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDG  181 (293)
Q Consensus       132 -----~-~-~~-~-~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~  181 (293)
                           + + ++ + ..+++++.+..+... ..|+|.|||||+|++|||.||+||++|+.
T Consensus        84 Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~-~~v~~~wVkgHsg~~gNe~aD~LA~~aa~  141 (161)
T PRK06548         84 WKMRKWRKADGKPVLNQEIIQEIDSLMEN-RNIRMSWVNAHTGHPLNEAADSLARQAAN  141 (161)
T ss_pred             HHHCCCcccCCCccccHHHHHHHHHHHhc-CceEEEEEecCCCCHHHHHHHHHHHHHHH
Confidence                 2 2 23 3 357777777776654 47999999999999999999999999874

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

Probab=99.90  E-value=3.3e-23  Score=170.38  Aligned_cols=126  Identities=20%  Similarity=0.177  Sum_probs=100.8

Q ss_pred             eEEEEEecCCC-CCC-eeEEEE--ECCeeEEe--ecCCCCchhHHHHHHHHHHHHHhhcCCCccEEEEeCcHHHHHHhhc
Q psy15839         57 VVDLSLYGSKT-IQN-TSCAVY--AGGSAKSY--ILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIAN  130 (293)
Q Consensus        57 ~~~iytDGS~~-~~~-~G~~v~--~~~~~~~~--~~~~~~~~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~~  130 (293)
                      .+.||||||+. |+| .|+|++  .++..+.+  +.. .+||++||+.|++.||+.+.+.+...|.|+|||++|+++|..
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 KVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEG-RTTNNRAELRALIEALEALKELGACEVTLYTDSKYVVEGITR   81 (154)
T ss_pred             ceEEEecCccCCCCCCceEEEEEEcCCceEEEeeeee-cccChHHHHHHHHHHHHHHHhcCCceEEEEecHHHHHHHHHH
Confidence            57899999998 555 455644  34433323  333 789999999999999999998888999999999999999995


Q ss_pred             C---CCC--------hh-HHHHHHHHHHHHhhCCceEEEEEeCCCCCChhhHHHHHHHhhccCCc
Q psy15839        131 K---NTS--------IP-LIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGAE  183 (293)
Q Consensus       131 ~---~~~--------~~-~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~~  183 (293)
                      +   ++.        .| ...++++.+.++......|.+.|||||+|.++||.||+||++|+..+
T Consensus        82 w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~~~~~~  146 (154)
T COG0328          82 WIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAREAARAA  146 (154)
T ss_pred             HHhhccccCccccccCccccHHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHHHHHhh
Confidence            4   111        13 35677888888877788999999999999999999999999997654

>PRK08719 ribonuclease H; Reviewed

Probab=99.89  E-value=1.1e-22  Score=168.05  Aligned_cols=120  Identities=21%  Similarity=0.238  Sum_probs=90.8

Q ss_pred             eEEEEEecCCC-CCC----eeEEEE--ECCe----eEEeecCCCCchhHHHHHHHHHHHHHhhcCCCccEEEEeCcHHHH
Q psy15839         57 VVDLSLYGSKT-IQN----TSCAVY--AGGS----AKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSAL  125 (293)
Q Consensus        57 ~~~iytDGS~~-~~~----~G~~v~--~~~~----~~~~~~~~~~~~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai  125 (293)
                      .+.||||||+. +++    .|+|++  .++.    ....++....|+++|||.|++.||+.+.+.    ..|+|||++|+
T Consensus         4 ~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~----~~i~tDS~yvi   79 (147)
T PRK08719          4 SYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARDG----DVIYSDSDYCV   79 (147)
T ss_pred             eEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCC----CEEEechHHHH
Confidence            46799999997 332    477754  3321    223345556799999999999999999753    37999999999


Q ss_pred             HHhh--------cCCC-C-h-h-HHHHHHHHHHHHhhCCceEEEEEeCCCCCChhhHHHHHHHhhccC
Q psy15839        126 TSIA--------NKNT-S-I-P-LIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDG  181 (293)
Q Consensus       126 ~~l~--------~~~~-~-~-~-~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~  181 (293)
                      ++|+        +.+. + + + ...++++.+..+.. ...|+|.|||||+|++|||.||+||++|+.
T Consensus        80 ~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~-~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~  146 (147)
T PRK08719         80 RGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRA-RKYVEVEKVTAHSGIEGNEAADMLAQAAAE  146 (147)
T ss_pred             HHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhC-CCcEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence            9994        3443 3 2 2 24567777777665 567999999999999999999999999863

>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=8e-23  Score=165.00  Aligned_cols=116  Identities=28%  Similarity=0.348  Sum_probs=86.9

Q ss_pred             eEEEEEecCCC-C-CCeeEEE-EECCeeEEeecCCCCchhHHHHHHHHHHHHHhhcCCCccEEEEeCcHHHHHHhhc---
Q psy15839         57 VVDLSLYGSKT-I-QNTSCAV-YAGGSAKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIAN---  130 (293)
Q Consensus        57 ~~~iytDGS~~-~-~~~G~~v-~~~~~~~~~~~~~~~~~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~~---  130 (293)
                      .+.||||||+. + +..|+|+ +..+......++ ..+++.|||.||..||+.+ .  ...+.|+|||+++++.|..   
T Consensus         3 ~~~iytDgS~~~~~~~~~~g~v~~~~~~~~~~~~-~~s~~~aEl~Ai~~AL~~~-~--~~~v~I~tDS~~v~~~l~~~~~   78 (132)
T PF00075_consen    3 AIIIYTDGSCRPNPGKGGAGYVVWGGRNFSFRLG-GQSNNRAELQAIIEALKAL-E--HRKVTIYTDSQYVLNALNKWLH   78 (132)
T ss_dssp             SEEEEEEEEECTTTTEEEEEEEEETTEEEEEEEE-SECHHHHHHHHHHHHHHTH-S--TSEEEEEES-HHHHHHHHTHHH
T ss_pred             cEEEEEeCCccCCCCceEEEEEEECCeEEEeccc-ccchhhhheehHHHHHHHh-h--cccccccccHHHHHHHHHHhcc
Confidence            46799999977 3 3345554 454543344455 8899999999999999944 3  3899999999999998887   


Q ss_pred             --CCC-C--h-hHHHHHHHHHHHHhhCCceEEEEEeCCCCCC-hhhHHHHHHHhhcc
Q psy15839        131 --KNT-S--I-PLIAHILNTWHTLKSCGKKVAFLWCPSHTGI-SGNEIVDRATRQLD  180 (293)
Q Consensus       131 --~~~-~--~-~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi-~gNe~AD~lAk~a~  180 (293)
                        .+. .  + ++..+|++.+    ..+..|.|.|||||+|+ .||+.||+|||+|+
T Consensus        79 ~~~~~~~~~~~~i~~~i~~~~----~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~  131 (132)
T PF00075_consen   79 GNGWKKTSNGRPIKNEIWELL----SRGIKVRFRWVPGHSGVPQGNERADRLAKEAA  131 (132)
T ss_dssp             HTTSBSCTSSSBHTHHHHHHH----HHSSEEEEEESSSSSSSHHHHHHHHHHHHHHH
T ss_pred             ccccccccccccchhheeecc----ccceEEeeeeccCcCCCchhHHHHHHHHHHhc
Confidence              332 1  2 3555555443    45899999999999999 69999999999985

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 ....

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=99.88  E-value=3.4e-22  Score=165.91  Aligned_cols=125  Identities=16%  Similarity=0.173  Sum_probs=91.7

Q ss_pred             eEEEEEecCCC-CCC-eeEEEE--ECCeeEEe-ecCCCCchhHHHHHHHHHHHHHhhcCCCccEEEEeCcHHHHHHhhcC
Q psy15839         57 VVDLSLYGSKT-IQN-TSCAVY--AGGSAKSY-ILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANK  131 (293)
Q Consensus        57 ~~~iytDGS~~-~~~-~G~~v~--~~~~~~~~-~~~~~~~~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~~~  131 (293)
                      .+.||||||+. +++ .|+|++  .++....+ +.....|++.|||.|++.||+.+.+  ...+.|+|||++++++|..+
T Consensus         3 ~v~iytDGs~~~n~~~~g~g~v~~~~~~~~~~~~~~~~~TN~~aEL~Ai~~AL~~~~~--~~~v~I~tDS~yvi~~i~~w   80 (150)
T PRK00203          3 QVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGEALTTNNRMELMAAIEALEALKE--PCEVTLYTDSQYVRQGITEW   80 (150)
T ss_pred             eEEEEEEecccCCCCceEEEEEEEECCeeEEEecCCCCCcHHHHHHHHHHHHHHHcCC--CCeEEEEECHHHHHHHHHHH
Confidence            47899999998 444 566654  33433222 2334678999999999999998865  35799999999999999963


Q ss_pred             --------CC--Ch-hH-HHHHHHHHHHHhhCCceEEEEEeCCCCCChhhHHHHHHHhhccCCcc
Q psy15839        132 --------NT--SI-PL-IAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGAEF  184 (293)
Q Consensus       132 --------~~--~~-~~-~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~~~  184 (293)
                              +.  .+ ++ ..++++.+..+.. ...|.|.|||||+|++||+.||+|||+|...+.
T Consensus        81 ~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~-~~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~~~  144 (150)
T PRK00203         81 IHGWKKNGWKTADKKPVKNVDLWQRLDAALK-RHQIKWHWVKGHAGHPENERCDELARAGAEEAT  144 (150)
T ss_pred             HHHHHHcCCcccCCCccccHHHHHHHHHHhc-cCceEEEEecCCCCCHHHHHHHHHHHHHHHHhh
Confidence                    22  22 22 2345555555443 378999999999999999999999999976543

>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=99.79  E-value=2e-18  Score=135.72  Aligned_cols=121  Identities=23%  Similarity=0.231  Sum_probs=92.8

Q ss_pred             EEEecCCCC--CCeeEEEEE--CCeeEEe---ecCCCCchhHHHHHHHHHHHHHhhcCCCccEEEEeCcHHHHHHhhcCC
Q psy15839         60 LSLYGSKTI--QNTSCAVYA--GGSAKSY---ILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKN  132 (293)
Q Consensus        60 iytDGS~~~--~~~G~~v~~--~~~~~~~---~~~~~~~~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~~~~  132 (293)
                      +|||||...  ++.|+|++.  .+....+   ......+++.||+.|++.||+.+.......+.|++||+.++..+.+..
T Consensus         2 ~~~Dgs~~~~~~~~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~~~~~~~i~i~~Ds~~~~~~~~~~~   81 (130)
T cd06222           2 IYTDGSCRGNPGPAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALELGGKKVNIYTDSQYVINALTGWY   81 (130)
T ss_pred             EEecccCCCCCCceEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHHhCCCceEEEEECHHHHHHHhhccc
Confidence            799999984  467887653  2222222   222577899999999999999998878899999999999999999876


Q ss_pred             C-ChhHHHHHHHHHHHHhhCCceEEEEEeCCCCCChhhHHHHHHHhhcc
Q psy15839        133 T-SIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLD  180 (293)
Q Consensus       133 ~-~~~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~  180 (293)
                      . ..+....++..+..+...+..++|.|||+|+|+.+|+.||.|||+|.
T Consensus        82 ~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~~  130 (130)
T cd06222          82 EGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKEAA  130 (130)
T ss_pred             cCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence            4 22223333334444445788999999999999999999999999873

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=1.6e-18  Score=158.76  Aligned_cols=132  Identities=22%  Similarity=0.180  Sum_probs=99.9

Q ss_pred             CCCCCCC--CeEEEEEecCCC-CC----CeeEEEEECCe---eEEeecC-CCCchhHHHHHHHHHHHHHhhcCCCccEEE
Q psy15839         49 PPWYSDF--PVVDLSLYGSKT-IQ----NTSCAVYAGGS---AKSYILN-NINSIFTAELLALVFCLDSVKNRPDVNTLI  117 (293)
Q Consensus        49 ~~W~~~~--~~~~iytDGS~~-~~----~~G~~v~~~~~---~~~~~~~-~~~~~~~AEl~Ai~~AL~~~~~~~~~~i~I  117 (293)
                      ..|..+.  ....||||||+. +|    .+|+||+.++.   .+...+. ..+++|.|||.||..||+.+.+....++.|
T Consensus       202 k~~~d~e~~~~~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~~~~kv~I  281 (371)
T KOG3752|consen  202 KLENDREEIEIQVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSKNINKVVI  281 (371)
T ss_pred             hcccccccccceEEEecCccccCCCCCCcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHhcCCCcEEE
Confidence            3444443  347799999988 33    48999987653   4566666 789999999999999999999888889999


Q ss_pred             EeCcHHHHHHhhcCC--------C--Ch-h-H-----HHHHHHHHHHHhh--CCceEEEEEeCCCCCChhhHHHHHHHhh
Q psy15839        118 VCDSMSALTSIANKN--------T--SI-P-L-----IAHILNTWHTLKS--CGKKVAFLWCPSHTGISGNEIVDRATRQ  178 (293)
Q Consensus       118 ~tDS~~ai~~l~~~~--------~--~~-~-~-----~~~i~~~~~~l~~--~~~~v~~~WVpgH~gi~gNe~AD~lAk~  178 (293)
                      .|||++++++|+.|-        .  .+ + +     .......+..|.+  .+..|++.|||||.|+.|||+||.||++
T Consensus       282 ~TDS~~~i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~Ad~lARk  361 (371)
T KOG3752|consen  282 RTDSEYFINSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEMADALARK  361 (371)
T ss_pred             EechHHHHHHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHHHHHHHhh
Confidence            999999999999762        1  11 1 0     1122223333333  3689999999999999999999999999


Q ss_pred             cc
Q psy15839        179 LD  180 (293)
Q Consensus       179 a~  180 (293)
                      ++
T Consensus       362 gs  363 (371)
T KOG3752|consen  362 GS  363 (371)
T ss_pred             hh
Confidence            85

>PRK13907 rnhA ribonuclease H; Provisional

Probab=99.76  E-value=1.2e-17  Score=134.84  Aligned_cols=120  Identities=17%  Similarity=0.120  Sum_probs=91.4

Q ss_pred             EEEEEecCCC-C-CCeeEEEEEC--CeeEEee-cCCCCchhHHHHHHHHHHHHHhhcCCCccEEEEeCcHHHHHHhhcCC
Q psy15839         58 VDLSLYGSKT-I-QNTSCAVYAG--GSAKSYI-LNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKN  132 (293)
Q Consensus        58 ~~iytDGS~~-~-~~~G~~v~~~--~~~~~~~-~~~~~~~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~~~~  132 (293)
                      +.||||||+. + +..|+|++..  +....++ .....+++.||+.|++.||+.+.+.+...+.|+|||+.+++.+++.+
T Consensus         2 ~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~~~~~~~tn~~AE~~All~aL~~a~~~g~~~v~i~sDS~~vi~~~~~~~   81 (128)
T PRK13907          2 IEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLPLGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEKEY   81 (128)
T ss_pred             EEEEEeeCCCCCCCccEEEEEEEECCeeEEEEecccccCCcHHHHHHHHHHHHHHHhCCCCEEEEEechHHHHHHHhHHH
Confidence            5799999988 3 4477776532  2222222 23456889999999999999999988889999999999999999976


Q ss_pred             CChhHHHHHHHHHHHHhhCCceEEEEEeCCCCCChhhHHHHHHHhhccC
Q psy15839        133 TSIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDG  181 (293)
Q Consensus       133 ~~~~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~  181 (293)
                      ...+-...+++.+..+......+.|.|||.    ++|+.||.||++|..
T Consensus        82 ~~~~~~~~l~~~~~~l~~~f~~~~~~~v~r----~~N~~Ad~LA~~a~~  126 (128)
T PRK13907         82 AKNKMFAPLLEEALQYIKSFDLFFIKWIPS----SQNKVADELARKAIL  126 (128)
T ss_pred             hcChhHHHHHHHHHHHHhcCCceEEEEcCc----hhchhHHHHHHHHHh
Confidence            533333444445555566778888999996    599999999999864

>PRK07708 hypothetical protein; Validated

Probab=99.64  E-value=6.2e-15  Score=129.31  Aligned_cols=124  Identities=12%  Similarity=0.010  Sum_probs=89.5

Q ss_pred             CCeEEEEEecCCC--CCCeeEEEE--ECCe--eEE----eecCCCCchhHHHHHHHHHHHHHhhcCCCcc--EEEEeCcH
Q psy15839         55 FPVVDLSLYGSKT--IQNTSCAVY--AGGS--AKS----YILNNINSIFTAELLALVFCLDSVKNRPDVN--TLIVCDSM  122 (293)
Q Consensus        55 ~~~~~iytDGS~~--~~~~G~~v~--~~~~--~~~----~~~~~~~~~~~AEl~Ai~~AL~~~~~~~~~~--i~I~tDS~  122 (293)
                      ++.+.+|+|||+.  .+..|+|++  .++.  ...    ..+....+++.||+.|++.||+.+.+.+.+.  |.|++||+
T Consensus        71 p~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~DSq  150 (219)
T PRK07708         71 PHEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFRGDSQ  150 (219)
T ss_pred             CCcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHcCCCcceEEEEeccH
Confidence            4467899999986  345777753  3322  211    2355557899999999999999999887654  89999999


Q ss_pred             HHHHHhhcCCC-ChhHHHHHHHHHHHHh-hCCceEEEEEeCCCCCChhhHHHHHHHhhccCC
Q psy15839        123 SALTSIANKNT-SIPLIAHILNTWHTLK-SCGKKVAFLWCPSHTGISGNEIVDRATRQLDGA  182 (293)
Q Consensus       123 ~ai~~l~~~~~-~~~~~~~i~~~~~~l~-~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~  182 (293)
                      .+++.+.+.+. .++....+++.+..+. .....+.|.|||    .+.|+.||+||++|...
T Consensus       151 lVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~Vp----R~~N~~AD~LAk~Al~~  208 (219)
T PRK07708        151 VVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPIS----RKQNKEADQLATQALEG  208 (219)
T ss_pred             HHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECC----chhhhHHHHHHHHHHhc
Confidence            99999999875 4443333444443333 334457889998    57899999999999864

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=99.57  E-value=3.9e-14  Score=134.09  Aligned_cols=120  Identities=14%  Similarity=0.113  Sum_probs=91.6

Q ss_pred             eEEEEEecCCC-C-CCeeEEEE--ECC-e-e-EEe-ecCCCCchhHHHHHHHHHHHHHhhcCCCccEEEEeCcHHHHHHh
Q psy15839         57 VVDLSLYGSKT-I-QNTSCAVY--AGG-S-A-KSY-ILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSI  128 (293)
Q Consensus        57 ~~~iytDGS~~-~-~~~G~~v~--~~~-~-~-~~~-~~~~~~~~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l  128 (293)
                      .+.||||||+. + +..|+|++  ..+ . . ..+ ..-...+++.||+.|++.||+.+.+.+...|.|++||+.+++.+
T Consensus         2 ~~~i~~DGa~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~~~tnn~AE~~All~gL~~a~~~g~~~v~i~~DS~lvi~~i   81 (372)
T PRK07238          2 KVVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIGRATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQM   81 (372)
T ss_pred             eEEEEecCCCCCCCCceEEEEEEEeCCCCcEEEEeecccCCCCchHHHHHHHHHHHHHHHhCCCCeEEEEeCcHHHHHHh
Confidence            46799999988 4 34677754  332 2 1 122 22236778899999999999999998888999999999999999


Q ss_pred             hcCCC-ChhHHHHHHHHHHHHhhCCceEEEEEeCCCCCChhhHHHHHHHhhcc
Q psy15839        129 ANKNT-SIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLD  180 (293)
Q Consensus       129 ~~~~~-~~~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~  180 (293)
                      .+.+. +++-...+...+..+..+...++|.|||.    .+|+.||.||++|.
T Consensus        82 ~~~~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~r----~~N~~AD~LA~~a~  130 (372)
T PRK07238         82 SGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPR----ARNAHADRLANEAM  130 (372)
T ss_pred             CCCCccCChHHHHHHHHHHHHHhcCCceEEEECCc----hhhhHHHHHHHHHH
Confidence            98775 44433334444555667778999999995    79999999999985

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

Probab=99.34  E-value=6.8e-12  Score=93.38  Aligned_cols=85  Identities=18%  Similarity=0.131  Sum_probs=65.4

Q ss_pred             hhHHHHHHHHHHHHHhhcCCCccEEEEeCcHHHHHHhhcCCCChhHHHHHHHHHHHHhhCCceEEEEEeCCCCCChhhHH
Q psy15839         92 IFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNTSIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEI  171 (293)
Q Consensus        92 ~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~~~~~~~~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~  171 (293)
                      +..||+.|+..||+.+.+.+..+|.|.|||+.+++.|++..........+...+..+......+.|.|||    .++|..
T Consensus         1 ~~~aE~~al~~al~~a~~~g~~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~----r~~N~~   76 (87)
T PF13456_consen    1 PLEAEALALLEALQLAWELGIRKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDRFWNVSVSHIP----REQNKV   76 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHCCT-SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCCCSCEEEEE------GGGSHH
T ss_pred             CcHHHHHHHHHHHHHHHHCCCCEEEEEecCccccccccccccccccccccchhhhhhhccccceEEEEEC----hHHhHH
Confidence            4689999999999999999999999999999999999998642112223444445556678999999999    799999


Q ss_pred             HHHHHhhcc
Q psy15839        172 VDRATRQLD  180 (293)
Q Consensus       172 AD~lAk~a~  180 (293)
                      ||.|||.|.
T Consensus        77 A~~LA~~a~   85 (87)
T PF13456_consen   77 ADALAKFAL   85 (87)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHh
Confidence            999999874

---

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	293
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	8e-06
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	7e-05
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	3e-04

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

 Score = 43.9 bits (104), Expect = 8e-06
 Identities = 12/90 (13%), Positives = 24/90 (26%), Gaps = 7/90 (7%)

Query: 87  NNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKN--TSIPLIAHILNT 144
                    E+ A ++ +        V   I+ D    +   A                 
Sbjct: 45  AATMRNVAGEIAAALYAVKKASQLG-VKIRILHDYAG-IAFWATGEWKAKNEFTQAYAKL 102

Query: 145 WHTLKSCGKKVAFLWCPSHTGISGNEIVDR 174
            +  +      +F    +H+G   N+ VD 
Sbjct: 103 MNQYR---GIYSFEKVKAHSGNEFNDYVDM 129

>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 = 41.4 bits (97), Expect = 7e-05
 Identities = 22/91 (24%), Positives = 38/91 (41%), Gaps = 11/91 (12%)

Query: 95  AELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNTSIPLIAHILNTWHTLKSCGKK 154
           AEL+AL   L   +    +N  +  DS  A  + A+ ++    I +       LK+    
Sbjct: 66  AELIALTQALKMAE-GKKLN--VYTDSRYAF-ATAHVHSEGREIKNKNEILALLKALFLP 121

Query: 155 --VAFLWCPSHTG-----ISGNEIVDRATRQ 178
             ++ + CP H         GN + D+A R+
Sbjct: 122 KRLSIIHCPGHQKGNSAEARGNRMADQAARE 152

>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 = 41.3 bits (97), Expect = 3e-04
 Identities = 29/84 (34%), Positives = 40/84 (47%), Gaps = 14/84 (16%)

Query: 95  AELLALVFCL-DSVKNRPDVNTLIVCDSMSALTSIANK--NTSIPLIAHILNTWHTLKSC 151
            EL A+   L DS     +VN  IV DS  AL  I  +   +   L+  I+      +  
Sbjct: 479 TELQAIYLALQDS---GLEVN--IVTDSQYALGIIQAQPDKSESELVNQIIE-----QLI 528

Query: 152 GKKVAFL-WCPSHTGISGNEIVDR 174
            K+  +L W P+H GI GNE VD+
Sbjct: 529 KKEKVYLAWVPAHKGIGGNEQVDK 552

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	293
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.92
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.91
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	99.9
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.9
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	99.9
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.89
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	99.89
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.88
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	99.87
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	99.84
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	99.84
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	99.81
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	99.81
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	99.79
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	99.41
4htu_A	134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	99.23
1rw3_A	455	POL polyprotein; RNA and DNA dependent DNA polymer	81.07

>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=3.2e-24  Score=176.86  Aligned_cols=121  Identities=24%  Similarity=0.254  Sum_probs=89.9

Q ss_pred             eEEEEEecCCC-CCC-eeEEEEEC-CeeEEeecCCCCchhHHHHHHHHHHHHHhhcCCCccEEEEeCcHHHHHHhhcCC-
Q psy15839         57 VVDLSLYGSKT-IQN-TSCAVYAG-GSAKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKN-  132 (293)
Q Consensus        57 ~~~iytDGS~~-~~~-~G~~v~~~-~~~~~~~~~~~~~~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~~~~-  132 (293)
                      .+.||||||+. +++ .|+|++.. +....+++ ..+|++.||+.|++.||+.+    ..+|.|+|||++++++|+++. 
T Consensus        12 ~~~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~-~~~Tnn~aEl~A~i~AL~~~----~~~v~i~tDS~~v~~~i~~w~~   86 (150)
T 3qio_A           12 AETFYVDGAANRETKLGKAGYVTNRGRQKVVTL-TDTTNQKTELQAIYLALQDS----GLEVNIVTDSQYALGIITQWIH   86 (150)
T ss_dssp             CEEEEEEEEECTTTCCEEEEEEETTSCEEEEEE-SSCCHHHHHHHHHHHHHHHS----CSEEEEEESCHHHHHHHHHHHH
T ss_pred             CEEEEEccCCCCCCCCeEEEEEEEcCCEEEEeC-CCCCHHHHHHHHHHHHHHhC----CCcEEEEeCcHHHHHHHHHHHH
Confidence            68899999997 544 56676543 33333444 46789999999999999986    378999999999999999861 


Q ss_pred             -------C--Ch-h-HHHHHHHHHHHHhhCCceEEEEEeCCCCCChhhHHHHHHHhhccCC
Q psy15839        133 -------T--SI-P-LIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGA  182 (293)
Q Consensus       133 -------~--~~-~-~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~  182 (293)
                             .  .+ + ...++++.+..+..++..|.|.|||||+|++|||.||+||++|+..
T Consensus        87 ~W~~~gw~~~~g~~v~n~~l~~~l~~~l~~~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~  147 (150)
T 3qio_A           87 NWKKRGWKTADKKPVKNVDLVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRK  147 (150)
T ss_dssp             HHCC------------CHHHHHHHHHHHTTCSEEEEEECCTTSCCHHHHHHHHHHHTTTSC
T ss_pred             HHhhcCcCcCcCcccccHHHHHHHHHHHhhcCceEEEEccCcCCChhHHHHHHHHHHHHHH
Confidence                   1  12 2 2234444433333467899999999999999999999999999754

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

Probab=99.91  E-value=3.1e-24  Score=177.58  Aligned_cols=126  Identities=20%  Similarity=0.210  Sum_probs=96.9

Q ss_pred             eEEEEEecCCC-CCC----eeEEEEECC---eeEEeecCCCCchhHHHHHHHHHHHHHhhcCCCccEEEEeCcHHHHHHh
Q psy15839         57 VVDLSLYGSKT-IQN----TSCAVYAGG---SAKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSI  128 (293)
Q Consensus        57 ~~~iytDGS~~-~~~----~G~~v~~~~---~~~~~~~~~~~~~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l  128 (293)
                      .+.||||||+. +++    .|+|++..+   ......+...++++.||+.|++.||+.+.+.+..+|.|+|||+++++.|
T Consensus         7 ~~~iytDGs~~~n~~~~~~aG~Gvv~~~~~~~~~~~~l~~~~tn~~aEl~A~~~aL~~~~~~~~~~v~i~tDS~~vi~~i   86 (154)
T 2qkb_A            7 FVVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQAKTQNINKLVLYTNSMFTINGI   86 (154)
T ss_dssp             EEEEEEEEEEETTTSSSCEEEEEEECSTTCTTCEEEECCSSCCHHHHHHHHHHHHHHHHHHTTCCEEEEEESCHHHHHHH
T ss_pred             eEEEEEccCcCCCCCCCCcEEEEEEEECCCceeEEeecCCCCchHHHHHHHHHHHHHHHHhCCCceEEEEECcHHHHhhh
Confidence            67899999997 443    688877533   1234455557899999999999999999887778999999999999999


Q ss_pred             hcC--------CC--Ch-h-HHHHHHHHHHHHhhCCceEEEEEeCCCCCChhhHHHHHHHhhccCCc
Q psy15839        129 ANK--------NT--SI-P-LIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGAE  183 (293)
Q Consensus       129 ~~~--------~~--~~-~-~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~~  183 (293)
                      .++        +.  .+ + ....+++.+..+.. +..|.|.|||||+|++|||.||+|||+|+..+
T Consensus        87 ~~~~~~w~~~~w~~~~~~~~~n~~l~~~i~~l~~-~~~v~~~~V~~H~g~~~N~~AD~LA~~a~~~~  152 (154)
T 2qkb_A           87 TNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQ-GMDIQWMHVPGHSGFIGNEEADRLAREGAKQS  152 (154)
T ss_dssp             HTHHHHHHTTTSBCTTSSBCTTHHHHHHHHHHHT-TCEEEEEECCTTSSCHHHHHHHHHHHHHHTCC
T ss_pred             hhhHHHHHhccccccCCCccccHHHHHHHHHHHc-CCceEEEEccCCCCCHhHHHHHHHHHHHHHhc
Confidence            974        21  12 2 22344444444443 45799999999999999999999999998653

>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=99.90  E-value=9.5e-25  Score=179.47  Aligned_cols=125  Identities=13%  Similarity=0.050  Sum_probs=94.4

Q ss_pred             CeEEEEEecCCCCCCeeEEEE--ECCeeE--Ee-ec--CC--CCchhHHHHHHHHHHHHHhhcCCCccEEEEeCcHHHHH
Q psy15839         56 PVVDLSLYGSKTIQNTSCAVY--AGGSAK--SY-IL--NN--INSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALT  126 (293)
Q Consensus        56 ~~~~iytDGS~~~~~~G~~v~--~~~~~~--~~-~~--~~--~~~~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~  126 (293)
                      ..+.||||||+..+..|+|++  ..+...  .. +.  +.  .++|+.||+.|++.||+.+.+.+. +|.|+|||+.+.+
T Consensus         5 ~~i~iytDGs~~~g~~G~G~vi~~~g~~~~~~~~~~~~~~~~~~tNn~aEl~A~~~AL~~a~~~~~-~v~I~tDS~~i~~   83 (147)
T 2kq2_A            5 TEYDVYTDGSYVNGQYAWAYAFVKDGKVHYEDADVGKNPAAATMRNVAGEIAAALYAVKKASQLGV-KIRILHDYAGIAF   83 (147)
T ss_dssp             SCCEEECCCCCBTTBCEEEEEEEETTEEEEEEEEECCCGGGGGTCTTHHHHHHHHHHHHHHHHHTC-CCCBSSCCSTHHH
T ss_pred             CeEEEEECCCCCCCCcEEEEEEEECCEEEEEEeccccccccccccHHHHHHHHHHHHHHHHHHCCC-eEEEEECcHHHHH
Confidence            357899999999866888865  344322  22 22  22  368999999999999999877666 9999999999888


Q ss_pred             HhhcCCC-ChhHHHHHHHHHHHHhhCCceEEEEEeCCCCCChhhHHHHHHHhhccCCcc
Q psy15839        127 SIANKNT-SIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGAEF  184 (293)
Q Consensus       127 ~l~~~~~-~~~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~~~  184 (293)
                      .+.+.++ +.+....+.+++..+..   .|.|.|||||+|++|||.||+|||+|+..+.
T Consensus        84 w~~~~w~~~~~~~~~~~~l~~~l~~---~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~~~  139 (147)
T 2kq2_A           84 WATGEWKAKNEFTQAYAKLMNQYRG---IYSFEKVKAHSGNEFNDYVDMKAKSALGIRD  139 (147)
T ss_dssp             HTTSSSSCCHHHHHHHHCGGGGGST---TCCBCCCCCCCCCHHHHHHHHHHHHHHTCCC
T ss_pred             HHhCCCccCCcchHHHHHHHHHhcC---CeeEEEecCcCCCcchHHHHHHHHHHHhccc
Confidence            8887765 44433344444444432   8999999999999999999999999986543

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

Probab=99.90  E-value=1.2e-23  Score=172.37  Aligned_cols=122  Identities=16%  Similarity=0.133  Sum_probs=87.4

Q ss_pred             eEEEEEecCCC-CCC-eeEEEE--ECCeeEEe-ecCCCCchhHHHHHHHHHHHHHhhcCCCccEEEEeCcHHHHHHhhc-
Q psy15839         57 VVDLSLYGSKT-IQN-TSCAVY--AGGSAKSY-ILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIAN-  130 (293)
Q Consensus        57 ~~~iytDGS~~-~~~-~G~~v~--~~~~~~~~-~~~~~~~~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~~-  130 (293)
                      .+.||||||+. +++ .|+|++  .++....+ +....+|++.||+.|++.||+.+.+  ..+|.|+|||++|++.|.+ 
T Consensus         4 ~i~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~AL~~~~~--~~~v~I~tDS~~vi~~i~~~   81 (146)
T 3h08_A            4 TITIYTDGAASGNPGKGGWGALLMYGSSRKEISGYDPATTNNRMELMAAIKGLEALKE--PARVQLYSDSAYLVNAMNEG   81 (146)
T ss_dssp             EEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEEEEECHHHHHHHHHHHHHHTCSS--CCEEEEEESCHHHHHHHHSS
T ss_pred             eEEEEEecCCCCCCCceEEEEEEEECCeeEEeecCCCCCcHHHHHHHHHHHHHHhcCc--cCcEEEEeChHHHHHHHHHH
Confidence            57899999998 443 677765  34422222 2223578999999999999999976  5799999999999999988 


Q ss_pred             C--------CC--Ch-h-HHHHHHHHHHHHhhCCceEEEEEeCCCCCChhhHHHHHHHhhccC
Q psy15839        131 K--------NT--SI-P-LIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDG  181 (293)
Q Consensus       131 ~--------~~--~~-~-~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~  181 (293)
                      +        +.  .+ + ....+++.+..+... ..|.|.|||||+|++|||.||+|||+|+.
T Consensus        82 w~~~W~~~~w~~~~~~~v~n~~l~~~~~~~~~~-~~v~~~~V~gH~g~~~N~~AD~LA~~a~~  143 (146)
T 3h08_A           82 WLKRWVKNGWKTAAKKPVENIDLWQEILKLTTL-HRVTFHKVKGHSDNPYNSRADELARLAIK  143 (146)
T ss_dssp             HHHHHHHTTCC----CCCTTHHHHHHHHHHHHH-SEEEEEECCC-CCSHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCccCCCCCcCCHHHHHHHHHHHhh-CceEEEEcCCcCCcHhHHHHHHHHHHHHH
Confidence            2        11  11 1 123334434333332 46999999999999999999999999974

>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=99.90  E-value=2.7e-23  Score=172.20  Aligned_cols=125  Identities=18%  Similarity=0.225  Sum_probs=93.0

Q ss_pred             eEEEEEecCCC-CCC-eeEEEEE--CCeeEEe--ecCCCCchhHHHHHHHHHHHHHhhcCCCccEEEEeCcHHHHHHhhc
Q psy15839         57 VVDLSLYGSKT-IQN-TSCAVYA--GGSAKSY--ILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIAN  130 (293)
Q Consensus        57 ~~~iytDGS~~-~~~-~G~~v~~--~~~~~~~--~~~~~~~~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~~  130 (293)
                      .+.||||||+. +++ .|+|++.  .+....+  ++ ..+|++.||+.|++.||+.+.+.  .+|.|+|||+++++.|.+
T Consensus         4 ~~~iytDGs~~~n~~~~G~G~v~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~~~~~--~~v~I~tDS~~vi~~i~~   80 (155)
T 1jl1_A            4 QVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGY-TRTTNNRMELMAAIVALEALKEH--AEVILSTDSQYVRQGITQ   80 (155)
T ss_dssp             CEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCCSC--CEEEEEECCHHHHHHHHT
T ss_pred             eEEEEEccccCCCCCceEEEEEEEECCeEEEEecCC-CCCcHHHHHHHHHHHHHHHhCcC--CcEEEEeCHHHHHHHHHH
Confidence            57899999998 444 6777653  3432222  23 35689999999999999999763  789999999999999997


Q ss_pred             C--------C-C-Ch-h-HHHHHHHHHHHHhhCCceEEEEEeCCCCCChhhHHHHHHHhhccCCccc
Q psy15839        131 K--------N-T-SI-P-LIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGAEFV  185 (293)
Q Consensus       131 ~--------~-~-~~-~-~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~~~~  185 (293)
                      |        + . ++ + ....+++.+..+.. ...|.|.|||||+|++|||.||+|||+|+..+..
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 WIHNWKKRGWKTADKKPVKNVDLWQRLDAALG-QHQIKWEWVKGHAGHPENERADELARAAAMNPTL  146 (155)
T ss_dssp             THHHHHHTTTBCTTSCBCTTHHHHHHHHHHTT-TCEEEEEECCSSTTCHHHHHHHHHHHHHHHSCCB
T ss_pred             HHHHHhhcccccccCCccCCHHHHHHHHHHHc-cCceEEEEcCCCCCCHHHHHHHHHHHHHHhccch
Confidence            3        2 1 12 2 12344455555443 4689999999999999999999999999866544

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

Probab=99.89  E-value=4.1e-23  Score=171.65  Aligned_cols=123  Identities=18%  Similarity=0.241  Sum_probs=91.6

Q ss_pred             CeEEEEEecCCC-CCC-eeEEEEE--CCeeEEe--ecCCCCchhHHHHHHHHHHHHHhhcCCCccEEEEeCcHHHHHHhh
Q psy15839         56 PVVDLSLYGSKT-IQN-TSCAVYA--GGSAKSY--ILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIA  129 (293)
Q Consensus        56 ~~~~iytDGS~~-~~~-~G~~v~~--~~~~~~~--~~~~~~~~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~  129 (293)
                      ..+.||||||+. +++ .|+|++.  .+....+  ++ ..+|++.||+.|++.||+.+.+.  ..|.|+|||++|++.|.
T Consensus         5 ~~i~iytDGs~~~n~g~~G~G~v~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~AL~~~~~~--~~v~I~tDS~~vi~~i~   81 (158)
T 2e4l_A            5 KLIHIFTDGSCLGNPGPGGYGIVMNYKGHTKEMSDGF-SLTTNNRMELLAPIVALEALKEP--CKIILTSDSQYMRQGIM   81 (158)
T ss_dssp             CEEEEEEEEEESSSSEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCSSC--CEEEEEECCHHHHHHHH
T ss_pred             CeEEEEEcccccCCCCcEEEEEEEEECCEEEEEecCc-CCCccHHHHHHHHHHHHHHhccC--CeEEEEeCHHHHHHHHH
Confidence            467899999998 444 6777653  4432222  23 35789999999999999998653  78999999999999999


Q ss_pred             c--------CCC--Ch-h-HHHHHHHHHHHHhhCCceEEEEEeCCCCCChhhHHHHHHHhhccCC
Q psy15839        130 N--------KNT--SI-P-LIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGA  182 (293)
Q Consensus       130 ~--------~~~--~~-~-~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~  182 (293)
                      +        .+.  .+ + ....+++.+..+.. ...|.|.|||||+|++|||.||+|||+|+..
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 TWIHGWKKKGWMTSNRTPVKNVDLWKRLDKAAQ-LHQIDWRWVKGHAGHAENERCDQLARAAAEA  145 (158)
T ss_dssp             THHHHHHHTTTBCTTSSBCTTHHHHHHHHHHHT-TSEEEEEECCTTCCCHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHccccccCCCcccCHHHHHHHHHHHc-cCcEEEEEccCCCCchhHHHHHHHHHHHHHh
Confidence            8        331  12 2 12344444444443 4689999999999999999999999999865

>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=99.89  E-value=3e-23  Score=173.57  Aligned_cols=125  Identities=18%  Similarity=0.186  Sum_probs=90.2

Q ss_pred             eEEEEEecCCC-CCC-eeEEE--EECCeeE-EeecCCCCchhHHHHHHHHHHHHHhhcCCCccEEEEeCcHHHHHHhhcC
Q psy15839         57 VVDLSLYGSKT-IQN-TSCAV--YAGGSAK-SYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANK  131 (293)
Q Consensus        57 ~~~iytDGS~~-~~~-~G~~v--~~~~~~~-~~~~~~~~~~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~~~  131 (293)
                      .+.||||||+. +++ .|+|+  +.++... ..+....++|+.||+.|++.||+.+.   ...|.|+|||++++++|-..
T Consensus        23 ~i~iytDGs~~~npG~~g~G~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~~---~~~v~I~tDS~~vi~~iw~~   99 (165)
T 3p1g_A           23 DYTWYTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMAE---GKKLNVYTDSRYAFATAHVH   99 (165)
T ss_dssp             SEEEEEEEEEEEETTEEEEEEEEECSSCEEEEEEECTTCCHHHHHHHHHHHHHHHTB---TSEEEEEECCHHHHHHHHSC
T ss_pred             CEEEEEEcccCCCCCceEEEEEEEECCEEEEEecCCCCCcHHHHHHHHHHHHHHHcc---CceEEEEEchHHHHhhhhcc
Confidence            37899999998 444 56664  3333322 22456678999999999999999992   57899999999999999211


Q ss_pred             CCChhH-HHHHH-HHHHHHhhCCceEEEEEeCCCCC-----ChhhHHHHHHHhhccCCccc
Q psy15839        132 NTSIPL-IAHIL-NTWHTLKSCGKKVAFLWCPSHTG-----ISGNEIVDRATRQLDGAEFV  185 (293)
Q Consensus       132 ~~~~~~-~~~i~-~~~~~l~~~~~~v~~~WVpgH~g-----i~gNe~AD~lAk~a~~~~~~  185 (293)
                      ....++ ..+++ +++..+ ..+..|.|.|||||+|     ++|||.||+|||+|+..+..
T Consensus       100 ~~g~~v~n~dl~~~l~~~l-~~~~~v~~~wVkgH~g~~~~~~~gNe~AD~LA~~aa~~~~~  159 (165)
T 3p1g_A          100 SEGREIKNKNEILALLKAL-FLPKRLSIIHCPGHQKGNSAEARGNRMADQAAREAAMKAVL  159 (165)
T ss_dssp             CCSCCCSSHHHHHHHHHHT-TSBSEEEEEECCSSCCSCSHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             cCCCcccCHHHHHHHHHHH-hcCCceEEEEecCCCCCCcCcchHHHHHHHHHHHHHhcCCC
Confidence            111121 22322 233333 3578999999999999     99999999999999865433

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

Probab=99.88  E-value=4e-23  Score=173.14  Aligned_cols=125  Identities=20%  Similarity=0.118  Sum_probs=91.6

Q ss_pred             eEEEEEecCCC-CCC-eeEEEEE--CCeeEEee-cCCCCchhHHHHHHHHHHHHHhhcCCCccEEEEeCcHHHHHHhhc-
Q psy15839         57 VVDLSLYGSKT-IQN-TSCAVYA--GGSAKSYI-LNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIAN-  130 (293)
Q Consensus        57 ~~~iytDGS~~-~~~-~G~~v~~--~~~~~~~~-~~~~~~~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~~-  130 (293)
                      .+.||||||+. +++ .|+|++.  .+....+. ....+|++.||+.|++.||+.+...  .+|.|+|||+++++.|.+ 
T Consensus         8 ~i~iytDGs~~~n~g~~G~G~v~~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~~~~--~~v~I~tDS~~vi~~i~~~   85 (166)
T 1ril_A            8 RVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKEP--CEVDLYTDSHYLKKAFTEG   85 (166)
T ss_dssp             CCCEEEEEEESSTTEEEEEEEEECBTTBCCEECCEEEEECHHHHHHHHHHHHHHSCCSC--CEEEEECCCHHHHHHHHSS
T ss_pred             cEEEEECccccCCCCCEEEEEEEEECCEEEEEecCCCCCcHHHHHHHHHHHHHHHhccC--CeEEEEeChHHHHHHHhhh
Confidence            56799999998 444 6778664  33222221 1135789999999999999998764  589999999999999998 


Q ss_pred             C--------C-C-Ch-h-HHHHHHHHHHHHhhCCceEEEEEeCCCCCChhhHHHHHHHhhccCCcc
Q psy15839        131 K--------N-T-SI-P-LIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGAEF  184 (293)
Q Consensus       131 ~--------~-~-~~-~-~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~~~  184 (293)
                      |        + . ++ + ....+++.+..+.. ...|.|.|||||+|++||+.||+|||+|+....
T Consensus        86 w~~~W~~~~w~~~~g~~v~n~~l~~~i~~l~~-~~~v~~~wV~gH~g~~~Ne~AD~LAk~a~~~~~  150 (166)
T 1ril_A           86 WLEGWRKRGWRTAEGKPVKNRDLWEALLLAMA-PHRVRFHFVKGHTGHPENERVDREARRQAQSQA  150 (166)
T ss_dssp             HHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHT-TSEEECCCCCGGGSCTHHHHHHHHHHHHHTSSC
T ss_pred             HHHHHHhcccccccCCccCcHHHHHHHHHHHh-cCeEEEEEeeCCCCchhHHHHHHHHHHHHHHhh
Confidence            2        2 2 22 2 12344444444444 358999999999999999999999999986543

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

Probab=99.87  E-value=9.4e-22  Score=164.39  Aligned_cols=123  Identities=15%  Similarity=0.107  Sum_probs=88.5

Q ss_pred             eEEEEEecCCC-CCC------eeEEEEE--CC----eeEEeecC-CCCchhHHHHHHHHHHHHHhhcCCCccEEEEeCcH
Q psy15839         57 VVDLSLYGSKT-IQN------TSCAVYA--GG----SAKSYILN-NINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSM  122 (293)
Q Consensus        57 ~~~iytDGS~~-~~~------~G~~v~~--~~----~~~~~~~~-~~~~~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~  122 (293)
                      .+.|||||||. |++      .|+||+.  .+    ....+... ...+++.||+.|+..||+.+.+.+ .+|.|+|||+
T Consensus         7 evviYTDGsc~gNpgp~~~~~aG~Gv~~~~~~~~~~~~~~~~~~tnn~te~~Aei~Al~~al~~al~~~-~~v~I~TDS~   85 (165)
T 2lsn_A            7 EGVFYTDGSAIKSPDPTKSNNAGMGIVHATYKPEYQVLNQWSIPLGNHTAQMAEIAAVEFACKKALKIP-GPVLVITDSF   85 (165)
T ss_dssp             SEEEEEEEEEEECSSCTTCEEEEEEEEEECCSSSCCEEEEEEEEESSCCHHHHHHHHHHHHHHHHHHSS-SCEEEEESCH
T ss_pred             eEEEEEcCCCCCCCCCCCCCcEEEEEEEEECCCccEEeccccCCchHHHHHHHHHHHHHHHHHHHhcCC-CeEEEEeChH
Confidence            36799999998 544      6788763  22    12233332 456788999999999999887643 5799999999


Q ss_pred             HHHHHhhcC--------CC--Ch-h-HHHHHHHHHHHHhhCCceEEEEEeCCCCCC------hhhHHHHHHHhhcc
Q psy15839        123 SALTSIANK--------NT--SI-P-LIAHILNTWHTLKSCGKKVAFLWCPSHTGI------SGNEIVDRATRQLD  180 (293)
Q Consensus       123 ~ai~~l~~~--------~~--~~-~-~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi------~gNe~AD~lAk~a~  180 (293)
                      +|+++|..|        +.  .+ + ...++++.+..+......|.|.|||||+|+      +|||.||+||++|+
T Consensus        86 Yvi~~it~w~~~Wk~ngw~~~~~~pVkN~dL~~~l~~~~~~~~~v~~~~VkgH~g~~~~~~~~gNe~AD~LA~~gA  161 (165)
T 2lsn_A           86 YVAESANKELPYWKSNGFVNNKKKPLKHISKWKSIAECLSMKPDITIQHEKGHQPTNTSIHTEGNALADKLATQGS  161 (165)
T ss_dssp             HHHHHHHTHHHHHHHTTSCSCSSSCCSSHHHHHHHHHHHHHCTTCEEEECCSSSCSSSCHHHHHHHHHHHHHHHHH
T ss_pred             HHHhhhhhhhhhheeccccccCCCcccCHHHHHHHHHHHhCCCCEEEEEEeCCCCccCCCCChHHHHHHHHHHHhh
Confidence            999999863        21  12 2 233444444444445568999999999994      68999999999986

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

Probab=99.84  E-value=8.2e-21  Score=153.33  Aligned_cols=121  Identities=12%  Similarity=0.063  Sum_probs=89.8

Q ss_pred             eEEEEEecCCC-CC-CeeEEEEE-C-C-ee-EEe-ecCCCCchhHHHHHHHHHHHHHhhcCCCc----cEEEEeCcHHHH
Q psy15839         57 VVDLSLYGSKT-IQ-NTSCAVYA-G-G-SA-KSY-ILNNINSIFTAELLALVFCLDSVKNRPDV----NTLIVCDSMSAL  125 (293)
Q Consensus        57 ~~~iytDGS~~-~~-~~G~~v~~-~-~-~~-~~~-~~~~~~~~~~AEl~Ai~~AL~~~~~~~~~----~i~I~tDS~~ai  125 (293)
                      .+.||||||+. ++ ..|+|++. . + .. ..+ +....+|++.||+.|++.||+.+.+.+..    +|.|+|||++++
T Consensus         3 ~~~iy~DGs~~~n~g~~G~G~v~~~~~g~~~~~~~~~~~~~tn~~aEl~A~~~aL~~a~~~~~~~~~~~v~i~tDS~~vi   82 (140)
T 3u3g_D            3 KIIIYTDGGARGNPGPAGIGVVITDEKGNTLHESSAYIGETTNNVAEYEALIRALEDLQMFGDKLVDMEVEVRMDSELIV   82 (140)
T ss_dssp             EEEEEEEEEESSTTEEEEEEEEEECTTSCEEEEEEEEEEEECHHHHHHHHHHHHHHHHGGGGGGGTTCEEEEEESCHHHH
T ss_pred             eEEEEEecCCCCCCCCcEEEEEEEeCCCCEEEEEEeeCCCCchHHHHHHHHHHHHHHHHHcCCCCCCceEEEEeChHHHH
Confidence            57899999998 43 36777653 2 2 11 122 22234689999999999999999887666    999999999999


Q ss_pred             HHhhcCCC-ChhHHHHHHHHHHHH-hhCCceEEEEEeCCCCCChhhHHHHHHHhhccC
Q psy15839        126 TSIANKNT-SIPLIAHILNTWHTL-KSCGKKVAFLWCPSHTGISGNEIVDRATRQLDG  181 (293)
Q Consensus       126 ~~l~~~~~-~~~~~~~i~~~~~~l-~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~  181 (293)
                      +.+++++. .++-...++..+..+ ......|.|.|||    .++||.||+|||+|..
T Consensus        83 ~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~~v~~~~V~----~~~N~~AD~LA~~a~~  136 (140)
T 3u3g_D           83 RQMQGVYKVKEPTLKEKFAKIAHIKMERVPNLVFVHIP----REKNARADELVNEAID  136 (140)
T ss_dssp             HHHTTSSCCCCGGGHHHHHHHHHHHHHHCTTCEEEECC----GGGGHHHHHHHHHHHH
T ss_pred             HHhCCCcccCCHHHHHHHHHHHHHhhcCCCcEEEEEcC----chhhHHHHHHHHHHHH
Confidence            99999875 443222334444444 4556789999999    4899999999999864

>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=99.84  E-value=7.8e-21  Score=153.99  Aligned_cols=121  Identities=14%  Similarity=0.150  Sum_probs=93.0

Q ss_pred             eEEEEEecCCC-CC-CeeEEEE--ECC--e-eEEe-ecCCCCchhHHHHHHHHHHHHHhhcCCCccEEEEeCcHHHHHHh
Q psy15839         57 VVDLSLYGSKT-IQ-NTSCAVY--AGG--S-AKSY-ILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSI  128 (293)
Q Consensus        57 ~~~iytDGS~~-~~-~~G~~v~--~~~--~-~~~~-~~~~~~~~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l  128 (293)
                      .+.||||||+. ++ ..|+|++  ..+  . ...+ +....++++.||+.|++.||+.+.+.+..+|.|+|||+++++.+
T Consensus         3 ~~~iy~DGs~~~~~g~~g~G~v~~~~~~~~~~~~~~~~~~~~tn~~aEl~A~~~aL~~a~~~~~~~v~i~tDS~~vv~~i   82 (141)
T 3hst_B            3 KVVIEADGGSRGNPGPAGYGAVVWTADHSTVLAESKQAIGRATNNVAEYRGLIAGLDDAVKLGATEAAVLMDSKLVVEQM   82 (141)
T ss_dssp             EEEEEEEEEESSSSEEEEEEEEEEETTSCSEEEEEEEEEEEECHHHHHHHHHHHHHHHHHHHTCSEEEEEESCHHHHHHH
T ss_pred             EEEEEEecCCCCCCCCcEEEEEEEeCCCCcEEEeeeccCCCCchHHHHHHHHHHHHHHHHHCCCceEEEEeChHHHHHHH
Confidence            47899999988 33 3677754  332  1 1122 22236789999999999999999987788999999999999999


Q ss_pred             hcCCC-ChhHHHHHHHHHHHHhhCCceEEEEEeCCCCCChhhHHHHHHHhhccC
Q psy15839        129 ANKNT-SIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDG  181 (293)
Q Consensus       129 ~~~~~-~~~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~  181 (293)
                      ++.++ .++....+++.+..+...+..|.|.|||+    ++|+.||+|||+|..
T Consensus        83 ~~~~~~~~~~l~~~~~~i~~l~~~~~~v~~~~V~~----~~N~~AD~LA~~a~~  132 (141)
T 3hst_B           83 SGRWKVKHPDLLKLYVQAQALASQFRRINYEWVPR----ARNTYADRLANDAMD  132 (141)
T ss_dssp             TTSSCCCSHHHHHHHHHHHHHHTTSSEEEEEECCG----GGCHHHHHHHHHHHH
T ss_pred             hCCcccCCHHHHHHHHHHHHHHhcCCeEEEEEcCC----cccHHHHHHHHHHHH
Confidence            99765 44434445555566666778999999994    899999999999964

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

Probab=99.81  E-value=9.6e-20  Score=149.46  Aligned_cols=119  Identities=14%  Similarity=0.108  Sum_probs=87.8

Q ss_pred             EEEEEecCCC--C-CCeeE-EEE--ECCee-EEee--cC---CCCchhHHHHHHHHHHHHHhhcCCCccEEEEeCcHHHH
Q psy15839         58 VDLSLYGSKT--I-QNTSC-AVY--AGGSA-KSYI--LN---NINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSAL  125 (293)
Q Consensus        58 ~~iytDGS~~--~-~~~G~-~v~--~~~~~-~~~~--~~---~~~~~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai  125 (293)
                      +.||||||+.  + +..|+ |++  ..+.. ..++  .+   ..++++.||+.|++.||+.+.+.+..+|.|+|||++++
T Consensus         2 ~~iy~DGs~~~~n~g~~G~~G~vi~~~g~~~~~~~~~~~~~~~~~tnn~aEl~A~~~aL~~a~~~g~~~v~i~tDS~~vi   81 (149)
T 2ehg_A            2 IIGYFDGLCEPKNPGGIATFGFVIYLDNRKIEGYGLAEKPFSINSTNNVAEYSGLICLMETMLRLGISSPIIKGDSQLVI   81 (149)
T ss_dssp             CEEEEEEEEESSSSSSEEEEEEEEECSSCEEEEEEECSCTTCTTCCHHHHHHHHHHHHHHHHHHHTCCSCEEEESCHHHH
T ss_pred             EEEEEeeccCCCCCChheEEEEEEEECCEEEEEeccccCCCCCCccHHHHHHHHHHHHHHHHHHcCCCEEEEEeChHHHH
Confidence            5799999987  3 44675 754  32322 2222  22   36889999999999999999987788999999999999


Q ss_pred             HHhhcCCC-ChhHHHHHHHHHHHHhhCCceEEEEEeCCCCCChhhHHHHHHHhhccC
Q psy15839        126 TSIANKNT-SIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDG  181 (293)
Q Consensus       126 ~~l~~~~~-~~~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~  181 (293)
                      +.+++++. +++....+++.+..+.... .|.|.|||+    ++|+.||+||++|..
T Consensus        82 ~~i~~~w~~~~~~~~~l~~~i~~l~~~~-~v~~~~V~~----~~N~~AD~LA~~a~~  133 (149)
T 2ehg_A           82 KQMNGEYKVKAKRIIPLYEKAIELKKKL-NATLIWVPR----EENKEADRLSRVAYE  133 (149)
T ss_dssp             HHHTTSSCCCCTTHHHHHHHHHHHHHHH-TCEEEECCG----GGCHHHHHHHHHHHH
T ss_pred             HHHhCccccCCHHHHHHHHHHHHHHhcC-CEEEEEcCC----cccHHHHHHHHHHHH
Confidence            99999875 3333333444444433333 499999998    599999999999974

>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=99.81  E-value=2.6e-19  Score=176.18  Aligned_cols=115  Identities=23%  Similarity=0.291  Sum_probs=87.7

Q ss_pred             eEEEEEecCCC-CCC-eeEEEEEC-CeeEEeecCCCCchhHHHHHHHHHHHHHhhcCCCccEEEEeCcHHHHHHhhcCCC
Q psy15839         57 VVDLSLYGSKT-IQN-TSCAVYAG-GSAKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNT  133 (293)
Q Consensus        57 ~~~iytDGS~~-~~~-~G~~v~~~-~~~~~~~~~~~~~~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~~~~~  133 (293)
                      .+.||||||+. +++ .|+|++.. +....... ..+||+.||+.|++.||+.    ...++.|+|||++|+++|+++..
T Consensus       436 ~~~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~-~~~TNn~aEl~A~i~aL~~----~~~~v~I~tDS~~v~~~i~~~~~  510 (555)
T 1mu2_A          436 AETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKL-EQTTNQQAELEAFAMALTD----SGPKVNIIVDSQYVMGIVASQPT  510 (555)
T ss_dssp             CEEEEEEEEECTTTCCEEEEEEETTSCEEEEEE-SSCCHHHHHHHHHHHHHHT----SCSEEEEEESCHHHHHHHHTCCS
T ss_pred             ceEEEEcccccCCCCCceEEEEEEeCCEeeccC-CCCCHHHHHHHHHHHHHHc----CCCeEEEEEehHHHHHHHhcccc
Confidence            47899999998 444 56676532 22223333 3678999999999999998    45799999999999999999764


Q ss_pred             -Ch-hHHHHHHHHHHHHhhCCceEEEEEeCCCCCChhhHHHHHHHhhcc
Q psy15839        134 -SI-PLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLD  180 (293)
Q Consensus       134 -~~-~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~  180 (293)
                       ++ ++...+.+.   + ..+..|.|.|||||+|++|||.||+||++|+
T Consensus       511 ~~~~~l~~~~~~~---~-~~~~~v~~~wV~~H~g~~~Ne~AD~LA~~a~  555 (555)
T 1mu2_A          511 ESESKIVNQIIEE---M-IKKEAIYVAWVPAHKGIGGNQEVDHLVSQGI  555 (555)
T ss_dssp             EESCHHHHHHHHH---H-HHCSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             cccHHHHHHHHHH---h-ccCCcEEEEEEECCCCChhHHHHHHHHHhhC
Confidence             33 344443332   2 2367899999999999999999999999884

>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=99.79  E-value=1.9e-19  Score=177.32  Aligned_cols=114  Identities=26%  Similarity=0.341  Sum_probs=85.8

Q ss_pred             eEEEEEecCCC-CCC-eeEEEEE-CCeeEEeecCCCCchhHHHHHHHHHHHHHhhcCCCccEEEEeCcHHHHHHhhcCCC
Q psy15839         57 VVDLSLYGSKT-IQN-TSCAVYA-GGSAKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNT  133 (293)
Q Consensus        57 ~~~iytDGS~~-~~~-~G~~v~~-~~~~~~~~~~~~~~~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~~~~~  133 (293)
                      .+.||||||+. +++ .|+|++. .+....++. ..+||+.||+.|++.||+.+    ..++.|+|||++|++.|+++..
T Consensus       439 ~~~iytDGs~~~n~g~~g~g~v~~~~~~~~~~~-~~~TNn~aEl~Ai~~aL~~~----~~~v~I~tDS~~vi~~i~~~~~  513 (557)
T 2zd1_A          439 AETFYVDGAANRETKLGKAGYVTNKGRQKVVPL-TNTTNQKTELQAIYLALQDS----GLEVNIVTDSQYALGIIQAQPD  513 (557)
T ss_dssp             SCEEEEEEEECTTTCCEEEEEEETTSCEEEEEE-CSCCHHHHHHHHHHHHHHHS----CSEEEEEECCHHHHHHHTTCCS
T ss_pred             CEEEEEccCCCCCCCceEEEEEEECCcEEEecC-CCCCHHHHHHHHHHHHHHhC----CCcEEEEeChHHHHHHHhcCCc
Confidence            47899999987 544 5666553 333333443 46789999999999999998    4789999999999999999865


Q ss_pred             C-h-hHHHHHHHHHHHHhhCCceEEEEEeCCCCCChhhHHHHHHHhhc
Q psy15839        134 S-I-PLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQL  179 (293)
Q Consensus       134 ~-~-~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a  179 (293)
                      . + ++..++.+   .+.. ...|.|.|||||+|++|||.||+||++|
T Consensus       514 ~~~~~l~~~~~~---~l~~-~~~v~~~wV~~H~g~~~Ne~AD~LA~~a  557 (557)
T 2zd1_A          514 KSESELVNQIIE---QLIK-KEKVYLAWVPAHKGIGGNEQVDKLVSAG  557 (557)
T ss_dssp             EESSHHHHHHHH---HHHH-CSEEEEEECCSSSCCTTCCGGGGCC---
T ss_pred             cCCHHHHHHHHH---HHhc-CCCEEEEEcCCCCCChhHHHHHHHHhcC
Confidence            3 3 35444433   3333 4689999999999999999999999986

>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=99.41  E-value=4.1e-14  Score=115.06  Aligned_cols=114  Identities=19%  Similarity=0.072  Sum_probs=78.5

Q ss_pred             eEEEEEecCCC-CCC-eeEEEEEC--CeeEEeec-CCCCchhHHHHHHHHHHHHHhhcCCCccEEEEeCcHHHHHHhhcC
Q psy15839         57 VVDLSLYGSKT-IQN-TSCAVYAG--GSAKSYIL-NNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANK  131 (293)
Q Consensus        57 ~~~iytDGS~~-~~~-~G~~v~~~--~~~~~~~~-~~~~~~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~~~  131 (293)
                      .+.||||||+. +++ .|+|++..  +.....+. -..+||+.||+.|++.||+.+.+.+. .|.|+|||++|++.+.+.
T Consensus        11 ~~~iy~DGa~~gNpG~~G~G~vl~~~g~~~~~~~~~~~~TNN~aEl~A~i~aL~~~~~~~~-~v~i~tDS~~vi~w~~~~   89 (142)
T 1zbf_A           11 WESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERNS-RKPIYSNSQTAIKWVKDK   89 (142)
T ss_dssp             SSSEEEEEEECSSSEEEEEEEEETTTCCEEEECCCEEEECHHHHHHHHHHHHHHHHHHTTC-CCCEEESCHHHHHHHHHT
T ss_pred             eEEEEEeeccCCCCCCeEEEEEEEeCCEEEEEecccCCcCcHHHHHHHHHHHHHHHHhCCC-eEEEEEehHHHHHHHHcC
Confidence            56799999988 544 67786643  22222211 12568999999999999999998766 899999999999999987


Q ss_pred             CC-C--h-h-HHHHHHHHH----HHHhhCCceEEEEEeCCCCCChhhHHHH
Q psy15839        132 NT-S--I-P-LIAHILNTW----HTLKSCGKKVAFLWCPSHTGISGNEIVD  173 (293)
Q Consensus       132 ~~-~--~-~-~~~~i~~~~----~~l~~~~~~v~~~WVpgH~gi~gNe~AD  173 (293)
                      +. .  + + ...++++.+    .-+..  ..++...|.-|++.-||.-||
T Consensus        90 ~~k~~~~~~v~n~dLw~~l~~~~~w~~~--~~~~~~~~kw~~~~~ge~pad  138 (142)
T 1zbf_A           90 KAKSTLVRNEETALIWKLVDEAEEWLNT--HTYETPILKWQTDKWGEIKAD  138 (142)
T ss_dssp             CCCCCCCCSTTTHHHHHHHHHHHHHHHH--CCCCCCEEECCHHHHCSCTTC
T ss_pred             CccCCCCCCcccHHHHHHHHHHHHHHhh--CCCceeEEEeccCccCcCccc
Confidence            62 1  1 1 233344433    33333  334445566688888998887

>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=99.23  E-value=1e-11  Score=99.44  Aligned_cols=74  Identities=20%  Similarity=0.113  Sum_probs=54.9

Q ss_pred             eEEEEEecCCC-CCC-eeE-EEEECC-eeE-EeecCCCCchhHHHHHHHHHHHHHhhcCCCccEEEEeCcHHHHHHhhcC
Q psy15839         57 VVDLSLYGSKT-IQN-TSC-AVYAGG-SAK-SYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANK  131 (293)
Q Consensus        57 ~~~iytDGS~~-~~~-~G~-~v~~~~-~~~-~~~~~~~~~~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~~~  131 (293)
                      ...||||||++ |++ .|+ ||+..+ ... ..+.-..+||+.||+.|++.||+.+.+.+.. +.|+|||++|++.|.++
T Consensus         5 ~~~iytDGac~GNPGp~G~ggV~~~~g~~~~~~g~~~~tTNN~aEl~A~i~aL~~l~~~~~~-v~i~tDSqyVi~wi~~~   83 (134)
T 4htu_A            5 WESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERNSR-KPIYSNSQTAIKWVKDK   83 (134)
T ss_dssp             SSSEEEEEEEETTTEEEEEEEEETTTCCEEEEEEEEEEECHHHHHHHHHHHHHHHHHHTTCC-CCEEESCHHHHHHHHHT
T ss_pred             ceEEEEeeccCCCCCCeEEEEEEEECCEEEEEecCCCCCchHHHHHHHHHHHHHHHHhCCCC-EEEEcchHHHHHHHHcC
Confidence            45699999998 655 666 454332 222 1221236789999999999999999876543 89999999999999975

>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=81.07  E-value=0.44  Score=44.92  Aligned_cols=42  Identities=5%  Similarity=-0.137  Sum_probs=32.1

Q ss_pred             CCchhHHHHHHHHHHHHHhhcC-CCccEEEEeCcHHHHHHhhcC
Q psy15839         89 INSIFTAELLALVFCLDSVKNR-PDVNTLIVCDSMSALTSIANK  131 (293)
Q Consensus        89 ~~~~~~AEl~Ai~~AL~~~~~~-~~~~i~I~tDS~~ai~~l~~~  131 (293)
                      .-+++..|++||..|++..... ....+.|+||+. ++..+.+.
T Consensus       386 ~ys~~ekEllAi~~a~~~~~~yl~g~~~~v~tDh~-~~~~l~~~  428 (455)
T 1rw3_A          386 GWPPCLRMVAAIAVLTKDAGKLTMGQPLVIKAPHA-VEALVKQP  428 (455)
T ss_dssp             SSCCSSHHHHHHHHHHHHHHGGGCSSCEEEECSSC-TTTTSSST
T ss_pred             ccchHHHHHHHHHHHHHHHHHHcCCCcEEEEecCh-HHHHhCCC
Confidence            3456789999999999988654 457899999996 55555543

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	293
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.92
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	99.9
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.88
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	99.77
d1zbfa1	132	BH0863-like Ribonuclease H {Bacillus halodurans [T	99.58

>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=99.92  E-value=5e-25  Score=174.52  Aligned_cols=115  Identities=21%  Similarity=0.232  Sum_probs=86.1

Q ss_pred             eEEEEEecCCC-CCC-eeEEEEECC-eeEEeecCCCCchhHHHHHHHHHHHHHhhcCCCccEEEEeCcHHHHHHhhcCCC
Q psy15839         57 VVDLSLYGSKT-IQN-TSCAVYAGG-SAKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNT  133 (293)
Q Consensus        57 ~~~iytDGS~~-~~~-~G~~v~~~~-~~~~~~~~~~~~~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~~~~~  133 (293)
                      ...||||||+. +++ .|+|++... ......+. ..|++.|||.||++||+..    ...+.|+|||++|++.+.++++
T Consensus         7 ~~t~YTDGS~~~n~~~~~~g~~~~~~~~~~~~~~-~~tnn~AEl~Ai~~al~~~----~~~i~I~tDS~~v~~~~~~~~~   81 (126)
T d1mu2a1           7 AETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKLE-QTTNQQAELEAFAMALTDS----GPKVNIIVDSQYVMGIVASQPT   81 (126)
T ss_dssp             CEEEEEEEEECTTTCCEEEEEEETTSCEEEEEES-SCCHHHHHHHHHHHHHHTS----CSEEEEEESCHHHHHHHHTCCS
T ss_pred             CcEEEEcCCCCCCCCcEEEEEEecCCCEEEEecC-CCcchHHHHHHHHHHhccC----CcceEEEechHHHHHHHhcCCc
Confidence            46799999987 555 455665444 33333443 5689999999999999864    4689999999999999999875


Q ss_pred             C--hhHHHHHHHHHHHHhhCCceEEEEEeCCCCCChhhHHHHHHHhhcc
Q psy15839        134 S--IPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLD  180 (293)
Q Consensus       134 ~--~~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~  180 (293)
                      .  .+..   ...+..+.. ...|.|.|||||+|++|||+||+||++|.
T Consensus        82 ~~~~~~~---~~~~~~~~~-~~~v~~~wV~gH~g~~gNe~AD~LA~~ai  126 (126)
T d1mu2a1          82 ESESKIV---NQIIEEMIK-KEAIYVAWVPAHKGIGGNQEVDHLVSQGI  126 (126)
T ss_dssp             EESCHHH---HHHHHHHHH-CSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             cccchHH---HHHHHHhhh-cceeEEEEEeCCCCCcchHHHHHHHHhhC
Confidence            2  2322   222333333 46899999999999999999999999973

>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=99.90  E-value=8.7e-24  Score=171.78  Aligned_cols=131  Identities=17%  Similarity=0.188  Sum_probs=95.1

Q ss_pred             eEEEEEecCCC-CCC-eeEEEE--ECCeeEEee-cCCCCchhHHHHHHHHHHHHHhhcCCCccEEEEeCcHHHHHHhhcC
Q psy15839         57 VVDLSLYGSKT-IQN-TSCAVY--AGGSAKSYI-LNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANK  131 (293)
Q Consensus        57 ~~~iytDGS~~-~~~-~G~~v~--~~~~~~~~~-~~~~~~~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~~~  131 (293)
                      .+.||||||+. |++ .|+|++  ..+....+. .....+++.||+.|++.||+.+..  ...+.|++||++++..+..+
T Consensus         2 ~I~IYtDGS~~~N~g~aG~G~vi~~~~~~~~~~~~~~~~tnn~aE~~Ai~~Al~~~~~--~~~i~i~tds~~~i~~~~~~   79 (152)
T d1jl1a_           2 QVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKE--HAEVILSTDSQYVRQGITQW   79 (152)
T ss_dssp             CEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEEEEECHHHHHHHHHHHHHHTCCS--CCEEEEEECCHHHHHHHHTT
T ss_pred             EEEEEEeCCCCCCCCcEEEEEEEEECCeEEEeccccCcccHHHHHHhhhhhhhhhhcc--cceEEEeecceeeEEcccch
Confidence            47899999988 444 677754  455433332 224567899999999999998754  46789999999999998765


Q ss_pred             C---------C-Ch-h-HHHHHHHHHHHHhhCCceEEEEEeCCCCCChhhHHHHHHHhhccCCcccCCCCh
Q psy15839        132 N---------T-SI-P-LIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGAEFVNLSSP  190 (293)
Q Consensus       132 ~---------~-~~-~-~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~~~~~~~~~  190 (293)
                      .         . .+ + ....++..+..+. ....|+|+|||||+|++|||.||+|||+|+..|.....+|
T Consensus        80 ~~~~~~~~~~~~~~~~~~n~~~~~~i~~~~-~~~~V~~~wV~gH~g~~gNe~AD~LAk~aa~~~~~~d~~~  149 (152)
T d1jl1a_          80 IHNWKKRGWKTADKKPVKNVDLWQRLDAAL-GQHQIKWEWVKGHAGHPENERADELARAAAMNPTLEDTGY  149 (152)
T ss_dssp             HHHHHHTTTBCTTSCBCTTHHHHHHHHHHT-TTCEEEEEECCSSTTCHHHHHHHHHHHHHHHSCCBCCTTC
T ss_pred             hhHhHhccchhcccCeeecHHHHHHHHHHh-hcceeEEEEecccCCCccHHHHHHHHHHHHhCCCCCccCC
Confidence            2         1 11 1 1222333333433 3568999999999999999999999999998877766554

>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=99.88  E-value=8.3e-24  Score=171.53  Aligned_cols=124  Identities=19%  Similarity=0.113  Sum_probs=88.8

Q ss_pred             eEEEEEecCCC-CCC-eeEEEEE--CCe-eEEeecCCCCchhHHHHHHHHHHHHHhhcCCCccEEEEeCcHHHHHHhhcC
Q psy15839         57 VVDLSLYGSKT-IQN-TSCAVYA--GGS-AKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANK  131 (293)
Q Consensus        57 ~~~iytDGS~~-~~~-~G~~v~~--~~~-~~~~~~~~~~~~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~~~  131 (293)
                      .+.||||||+. |++ .|+|++.  .+. ....+....+|+++||+.|++.||+++..  ...+.|++||+++++.+...
T Consensus         3 ~i~iytDGs~~~N~g~~G~g~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~~~--~~~i~i~tds~~~~~~~~~~   80 (147)
T d1rila_           3 RVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKE--PCEVDLYTDSHYLKKAFTEG   80 (147)
T ss_dssp             CCCEEEEEEESSTTEEEEEEEEECBTTBCCEECCEEEEECHHHHHHHHHHHHHHSCCS--CCEEEEECCCHHHHHHHHSS
T ss_pred             EEEEEEccCCCCCCCccEEEEEEEECCcceEEecccccccHHHHHHHHHHHHhhhccC--CceEEEecchhhhhcccccc
Confidence            36799999998 554 5667553  332 22222233568899999999999998754  46799999999999988764


Q ss_pred             C----------C-Ch-hH-HHHHHHHHHHHhhCCceEEEEEeCCCCCChhhHHHHHHHhhccCCc
Q psy15839        132 N----------T-SI-PL-IAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGAE  183 (293)
Q Consensus       132 ~----------~-~~-~~-~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~~  183 (293)
                      +          . .+ ++ ..++++.+..+. ....|+|.|||||+|++|||.||+|||+|+...
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            2          1 11 21 233344444433 457899999999999999999999999998653

>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=99.77  E-value=1.8e-18  Score=133.11  Aligned_cols=98  Identities=22%  Similarity=0.278  Sum_probs=70.8

Q ss_pred             eEEEEEecCCC-CCCee-EEEEECC-eeEEeecCCCCchhHHHHHHHHHHHHHhhcCCCccEEEEeCcHHHHHHhhcCCC
Q psy15839         57 VVDLSLYGSKT-IQNTS-CAVYAGG-SAKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNT  133 (293)
Q Consensus        57 ~~~iytDGS~~-~~~~G-~~v~~~~-~~~~~~~~~~~~~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~~~~~  133 (293)
                      ...+|||||+. +++.| +|++..+ ......+ ..+||+.|||.||+.||+..    ...+.|+|||++|++++.++..
T Consensus         8 ~~t~ytDGs~~~n~~~g~~g~~~~~~~~~~~~~-~~~TNn~aEl~Avi~aL~~~----~~~v~I~TDS~yvi~~i~~~~~   82 (110)
T d1s1ta1           8 AETFYVDGAANRETKLGKAGYVTNRGRQKVVTL-TDTTNQKTELQAIYLALQDS----GLEVNIVTDSQYALGIIQAQPD   82 (110)
T ss_dssp             SEEEEEEEEEETTTTEEEEEEEETTSCEEEEEE-SSCCHHHHHHHHHHHHHHHS----CSEEEEEECCHHHHHHHHHCCS
T ss_pred             CcEEEEeCCCCCCCCCcEEEEEEecCCeEEEec-ccCcHHHHHHHHHHHHHHhC----CCeEEEEEehHHHHHHHhcCcc
Confidence            46799999987 65554 4554433 3333334 35689999999999999854    4579999999999999999875


Q ss_pred             C--hhHHHHHHHHHHHHhhCCceEEEEEeCCC
Q psy15839        134 S--IPLIAHILNTWHTLKSCGKKVAFLWCPSH  163 (293)
Q Consensus       134 ~--~~~~~~i~~~~~~l~~~~~~v~~~WVpgH  163 (293)
                      .  .++..+|.+   .+. ....|.|.|||||
T Consensus        83 ~~~~~l~~~il~---~l~-~~~~v~i~WVpgH  110 (110)
T d1s1ta1          83 QSESELVNQIIE---QLI-KKEKVYLAWVPAH  110 (110)
T ss_dssp             EESCHHHHHHHH---HHH-HCSEEEEEECCSS
T ss_pred             ccchHHHHHHHH---HHh-cCCceEEEEeCCC
Confidence            2  234444433   333 3578999999999

>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=99.58  E-value=1.7e-16  Score=124.71  Aligned_cols=112  Identities=19%  Similarity=0.063  Sum_probs=78.7

Q ss_pred             EEEEecCCC-CCC-eeEEEEEC--CeeEEeec-CCCCchhHHHHHHHHHHHHHhhcCCCccEEEEeCcHHHHHHhhcCCC
Q psy15839         59 DLSLYGSKT-IQN-TSCAVYAG--GSAKSYIL-NNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNT  133 (293)
Q Consensus        59 ~iytDGS~~-~~~-~G~~v~~~--~~~~~~~~-~~~~~~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~~~~~  133 (293)
                      .||||||++ |+| .|+|++..  +....++. -..+||++||+.|++.||+.+.+.+ .++.|+|||++|++.+.++.-
T Consensus         6 sIy~DGa~~GNPGp~g~g~v~~~~~~~~~~sg~~~~~TNN~aEl~A~i~aL~~~~~~~-~~i~I~tDS~yvi~wv~~~~~   84 (132)
T d1zbfa1           6 SLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERN-SRKPIYSNSQTAIKWVKDKKA   84 (132)
T ss_dssp             SEEEEEEECSSSEEEEEEEEETTTCCEEEECCCEEEECHHHHHHHHHHHHHHHHHHTT-CCCCEEESCHHHHHHHHHTCC
T ss_pred             eEEEeecCCCCCchheEEEEEEcCCEEEEEEcCcCccchHHHHHHHHHHHHHHhhcCC-ceEEEEeccHHHHHHHHhCce
Confidence            489999998 666 66676542  22222221 2456899999999999999998754 579999999999999988641


Q ss_pred             ---Ch--hHHHHHHHHHH----HHhhCCceEEEEEeCCCCCChhhHHHH
Q psy15839        134 ---SI--PLIAHILNTWH----TLKSCGKKVAFLWCPSHTGISGNEIVD  173 (293)
Q Consensus       134 ---~~--~~~~~i~~~~~----~l~~~~~~v~~~WVpgH~gi~gNe~AD  173 (293)
                         .+  ....++++.+.    .+.  ...+.+.|++.|+..-||..||
T Consensus        85 kt~~~~~vkN~~l~~~i~~a~~~lk--~h~~~~~~~KW~~~~wG~i~AD  131 (132)
T d1zbfa1          85 KSTLVRNEETALIWKLVDEAEEWLN--THTYETPILKWQTDKWGEIKAD  131 (132)
T ss_dssp             CCCCCCSTTTHHHHHHHHHHHHHHH--HCCCCCCEEECCHHHHCSCTTC
T ss_pred             ecCcCCCcccHHHHHHHHHHHHHHH--hCCcCceeEEecCcccccCCCC
Confidence               11  12333333333    333  3557788999999989998887