Psyllid ID: psy8412

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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-
Protein Sequence
MFCETINNKYANHTICFTDGSKTPDSTSCAFSIGDVVHSTLLNPVNSIFSAELMAIFLCLEAILESPDHHFLIVSDSKSSLTALFNIRFTNPLISKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNEIVDEAARNAASIDPYKLCTPEDLKPFISFLIKSEWQNQWNHIPNTNKLKAIKPTIEHWATSNQNKRLQEVILTRLRIGHTRITHNHLFTKTDPPFCQCGAALSVILNYIVDNFILVHKHDIGVLFLACRMWNTSSLNVPFGQLKE
Secondary Structure (PSIPRED)
cHHHHHHHHccccEEEEEcccccccccEEEEEEccccEEEEcccccHHHHHHHHHHHHHHHHHHcccccEEEEEcccHHHHHHHHHHccccHHHHHHHHHHHHHHHccccEEEEEEcccccccccHHHHHHHHHHccccccccccccccHHHHHHHHHHHHHHHcccccccccHHcccccccccccccccccHHHHHHHHHHHcccccccccccccccccccccccccccccEEEEccccccHHHHHHHHHHHHHcccccccccccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHccccEEEEEccccccccEEEEEEEEccccEEccccccHHHHHHHHHHHHHHHHHHHcccccEEEEEccHHHHHHHHccccccHHHHHHHHHHHHHHHcccEEEEEEEcccccccccHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHcccccccEEEccccccccccccccccHHHHHHHHHHccccHHHHHHHcccccccccccccccccEEEEEEccHHHHHHHHHHHHHHEcccccccccEEEHHcccc
Coil and Loop (DISEMBL)
mfcetinnkyanhticftdgsktpdstscafsigdvvhstllnpvnsIFSAELMAIFLCLEAIlespdhhflivsdSKSSLTALFNIRFTNPLISKVYSTWSFlklnnknvsfmwcpshcgirgneIVDEAArnaasidpyklctpedlKPFISFLIKSEWqnqwnhipntnklkaikptIEHWATSNQNKRLQEVILTRLRIghtrithnhlftktdppfcqcgAALSVILNYIVDNFILVHKHDIGVLFLACRMwntsslnvpfgqlke
Flexible Loop (DISEMBL)
MFCETINNKYANHTICFTDGSKTPDSTSCAFSIGDVVHSTLLNPVNSIFSAELMAIFLCLEAILESPDHHFLIVSDSKSSLTALFNIRFTNPLISKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNEIVDEAARNAASIDPYKLCTPEDLKPFISFLIKSEWQNQWNHIPNTNKLKAIKPTIEHWatsnqnkrlQEVILTRLRIGHTRIThnhlftktdppFCQCGAALSVILNYIVDNFILVHKHDIGVLFLACRMWNTSslnvpfgqlke
Low Complexity Region (SEG)
MFCETINNKYANHTICFTDGSKTPDSTSCAFSIGDVVHSTLLNPVNSIFSAELMAIFLCLEAILESPDHHFLIVSDSKSSLTALFNIRFTNPLISKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNEIVDEAARNAASIDPYKLCTPEDLKPFISFLIKSEWQNQWNHIPNTNKLKAIKPTIEHWATSNQNKRLQEVILTRLRIGHTRITHNHLFTKTDPPFCQCGAALSVILNYIVDNFILVHKHDIGVLFLACRMWNTSSLNVPFGQLKE
Disordered region (IsUnstruct)
**CETINNKYANHTICFTDGSKTPDSTSCAFSIGDVVHSTLLNPVNSIFSAELMAIFLCLEAILESPDHHFLIVSDSKSSLTALFNIRFTNPLISKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNEIVDEAARNAASIDPYKLCTPEDLKPFISFLIKSEWQNQWNHIPNTNKLKAIKPTIEHWATSNQNKRLQEVILTRLRIGHTRITHNHLFTKTDPPFCQCGAALSVILNYIVDNFILVHKHDIGVLFLACRMWNTSSLNVP******
Disordered Region (DISOPRED)
MFCETINNKYANHTICFTDGSKTPDSTSCAFSIGDVVHSTLLNPVNSIFSAELMAIFLCLEAILESPDHHFLIVSDSKSSLTALFNIRFTNPLISKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNEIVDEAARNAASIDPYKLCTPEDLKPFISFLIKSEWQNQWNHIPNTNKLKAIKPTIEHWATSNQNKRLQEVILTRLRIGHTRITHNHLFTKTDPPFCQCGAALSVILNYIVDNFILVHKHDIGVLFLACRMWNTSSLNVPFG****
Disordered Region (DISEMBL)
MFCETINNKYANHTICFTDGSKTPDSTSCAFSIGDVVHSTLLNPVNSIFSAELMAIFLCLEAILESPDHHFLIVSDSKSSLTALFNIRFTNPLISKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNEIVDEAARNAASIDPYKLCTPEDLKPFISFLIKSEWQNQWNHIPNTNKLKAIKPTIEHWATSNQNKRLQEVILTRLRIGHTRITHNHLFTKTDPPFCQCGAALSVILNYIVDNFILVHKHDIGVLFLACRMWNTSSLNVPFGQLKE
Disordered Region (DISPRO)
MFCETINNKYANHTICFTDGSKTPDSTSCAFSIGDVVHSTLLNPVNSIFSAELMAIFLCLEAILESPDHHFLIVSDSKSSLTALFNIRFTNPLISKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNEIVDEAARNAASIDPYKLCTPEDLKPFISFLIKSEWQNQWNHIPNTNKLKAIKPTIEHWATSNQNKRLQEVILTRLRIGHTRITHNHLFTKTDPPFCQCGAALSVILNYIVDNFILVHKHDIGVLFLACRMWNTSSLNVPFGQLKE
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MFCETINNKYANHTICFTDGSKTPDSTSCAFSIGDVVHSTLLNPVNSIFSAELMAIFLCLEAILESPDHHFLIVSDSKSSLTALFNIRFTNPLISKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNEIVDEAARNAASIDPYKLCTPEDLKPFISFLIKSEWQNQWNHIPNTNKLKAIKPTIEHWATSNQNKRLQEVILTRLRIGHTRITHNHLFTKTDPPFCQCGAALSVILNYIVDNFILVHKHDIGVLFLACRMWNTSSLNVPFGQLKE
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	271
443695973	261	hypothetical protein CAPTEDRAFT_23017, p	0.815	0.846	0.407	2e-32
443721618	471	hypothetical protein CAPTEDRAFT_200496,	0.878	0.505	0.338	8e-32
443693558	502	hypothetical protein CAPTEDRAFT_189741,	0.815	0.440	0.398	4e-31
443712830	397	hypothetical protein CAPTEDRAFT_202466 [	0.815	0.556	0.398	1e-30
125901787	1222	pol-like protein [Biomphalaria glabrata]	0.808	0.179	0.353	3e-29
443682433	619	hypothetical protein CAPTEDRAFT_222606 [	0.749	0.327	0.351	1e-28
427791807	1212	Putative tick transposon, partial [Rhipi	0.826	0.184	0.353	1e-28
427791321	1210	Putative tick transposon, partial [Rhipi	0.826	0.185	0.353	1e-28
443724607	397	hypothetical protein CAPTEDRAFT_208903 [	0.815	0.556	0.389	5e-28
427778603	1397	Putative tick transposon [Rhipicephalus	0.785	0.152	0.374	2e-26

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

 Score =  145 bits (365), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 92/226 (40%), Positives = 122/226 (53%), Gaps = 5/226 (2%)

Query: 8   NKYANHTICFTDGSKTPDSTSCAFSIGDVVHSTLLNPVNSIFSAELMAIFLCLEAILESP 67
           +KY    I +TDGSK+ D+ +CAF+         L    SI++AEL+AI   L  I    
Sbjct: 31  DKYPGINI-YTDGSKSNDAVACAFTCSTYQIQFGLPAQMSIYTAELIAIEQALIFIETVK 89

Query: 68  DH-HFLIVSDSKSSLTALFNIRFTNPLISKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNE 126
           D   F I SDS SSLTAL N   T+P +  + +  + L    K V F+WCPSH GI GNE
Sbjct: 90  DEDQFNICSDSLSSLTALSNCDITHPYLLSILTKQNNLVRKGKLVVFIWCPSHVGILGNE 149

Query: 127 IVDEAARNAASIDPYKLCTPE-DLKPFISFLIKSEWQNQWNHIPNTNKLKAIKPTIEHWA 185
           + D  A+ A  +   KL  P  D K  I   +KS WQN+W+     NKL +I+P I  W 
Sbjct: 150 VADRLAKQALVMPVTKLPLPHTDYKSPIRSYVKSLWQNEWDE-ETDNKLHSIQPVISEWK 208

Query: 186 TSNQNKRLQEVILTRLRIGHTRITHNHLFTKTDPPFC-QCGAALSV 230
              Q  R  E++L R RIGH+ +TH +L  +   PFC  C + LSV
Sbjct: 209 QGPQIDRRGEIVLARARIGHSHLTHGYLLRREVAPFCIPCQSLLSV 254

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score =  143 bits (360), Expect = 8e-32,   Method: Compositional matrix adjust.
 Identities = 84/248 (33%), Positives = 138/248 (55%), Gaps = 10/248 (4%)

Query: 8   NKYANHTICFTDGSKTPDSTSCAFSIGDVVHSTLLNPVNSIFSAELMAIF---LCLEAIL 64
           ++Y + T+ +TDGSK+ DS +C+F    +     L    S+F++E++AI     C+EA  
Sbjct: 15  DRYPDSTVFYTDGSKSEDSVACSFFSSRLKLKMKLPVQMSVFTSEIIAILSALRCVEA-- 72

Query: 65  ESPDHHFLIVSDSKSSLTALFNIRFTNPLISKVYSTWSFLKLNNKNVSFMWCPSHCGIRG 124
           ++  H F+I SDS S++ A+  +   +P + +V      +    K V FMWCPSH GI G
Sbjct: 73  DNEQHQFVICSDSLSAIMAIHGMDVRHPYVLQVLYAIKSISQQEKIVVFMWCPSHVGIPG 132

Query: 125 NEIVDEAARNA-ASIDPYKLCTP-EDLKPFISFLIKSEWQNQWNHIPNTNKLKAIKPTIE 182
           NE+ D  A+ A +S +  +L  P  DL+  I   I+S WQ++W+   ++NKL +I PTI 
Sbjct: 133 NEMADTLAKEALSSTNLAELPVPASDLRCLIKKYIRSRWQHEWDE-QHSNKLHSIHPTIG 191

Query: 183 HWATSNQNKRLQEVILTRLRIGHTRITHNHLFTKTDPPFCQCGAALSVILNYIVD--NFI 240
            W    + KR +E++L R+RIGHT  TH+++    D   C        + + I++  +F+
Sbjct: 192 PWPPCQREKRREEIVLARIRIGHTHYTHDYIPRGDDQTECVACVCPLTVQHIIIECADFL 251

Query: 241 LVHKHDIG 248
            +   D G
Sbjct: 252 HIRYRDKG 259

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 =  140 bits (354), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 90/226 (39%), Positives = 122/226 (53%), Gaps = 5/226 (2%)

Query: 8   NKYANHTICFTDGSKTPDSTSCAFSIGDVVHSTLLNPVNSIFSAELMAIFLCLEAILESP 67
           +KY    I +TDGSK+ ++ +CAF+         L    SI++AEL+AI   L  I    
Sbjct: 77  DKYPGINI-YTDGSKSNNAVACAFTCSTYQIQFGLPTQMSIYTAELIAIEQALIFIETVK 135

Query: 68  DH-HFLIVSDSKSSLTALFNIRFTNPLISKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNE 126
           D   F I SDS SSLTAL N   T+P +  + +  + L    K V F+WCPSH GI GNE
Sbjct: 136 DEDQFNICSDSLSSLTALSNCDITHPYLLSILTKQNNLVRKGKLVVFIWCPSHVGILGNE 195

Query: 127 IVDEAARNAASIDPYKLCTPE-DLKPFISFLIKSEWQNQWNHIPNTNKLKAIKPTIEHWA 185
           + D  A+ A  +   KL  P  D K  I   +KS WQN+W+     NKL +I+P I  W 
Sbjct: 196 VADRLAKQALVMPVTKLPLPHTDYKSPIRSYVKSLWQNEWDE-ETDNKLHSIQPVISEWK 254

Query: 186 TSNQNKRLQEVILTRLRIGHTRITHNHLFTKTDPPFC-QCGAALSV 230
              Q  R  E++L R RIGH+ +TH +L  +   PFC  C + L+V
Sbjct: 255 QGPQIDRRGEIVLARARIGHSHLTHGYLLRREVAPFCIPCQSLLTV 300

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 =  139 bits (351), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 90/226 (39%), Positives = 120/226 (53%), Gaps = 5/226 (2%)

Query: 8   NKYANHTICFTDGSKTPDSTSCAFSIGDVVHSTLLNPVNSIFSAELMAIFLCLEAILESP 67
           +KY    I +TDGSK+ D+ +CAF+         L    SI++AEL+AI   L  I    
Sbjct: 126 DKYPGINI-YTDGSKSNDTVACAFTCSTYQIQFGLPAQMSIYTAELIAIEQALIFIETVK 184

Query: 68  DH-HFLIVSDSKSSLTALFNIRFTNPLISKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNE 126
           D   F I SDS SSLTAL N   T+P +  + +  + L    K V F+WCPSH GI GNE
Sbjct: 185 DEDQFNICSDSLSSLTALSNCDITHPYLLSILTKQNNLVRKGKKVVFIWCPSHVGILGNE 244

Query: 127 IVDEAARNAASIDPYKLCTPE-DLKPFISFLIKSEWQNQWNHIPNTNKLKAIKPTIEHWA 185
           + D  A+ A  +   KL  P  D K  I   +KS WQN+W+     NKL  I+P I  W 
Sbjct: 245 VADRQAKQALVMPVTKLPLPHTDYKSPIRSYVKSLWQNEWDG-ETDNKLHIIQPVISEWK 303

Query: 186 TSNQNKRLQEVILTRLRIGHTRITHNHLFTKTDPPFC-QCGAALSV 230
              Q  R  E++L   RIGH+ +TH +L  +   PFC  C + L+V
Sbjct: 304 QGPQIDRRGEIVLACARIGHSHLTHGYLLRREVAPFCIPCQSLLTV 349

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score =  135 bits (339), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 82/232 (35%), Positives = 117/232 (50%), Gaps = 13/232 (5%)

Query: 6    INNKYANHTICFTDGSKTPDSTSCAFSIGDVVHSTLLNPVNSIFSAELMAIFLCLEAILE 65
            +   Y +    +TDGSK     +CA S  +   S  L    SIF+AEL AI L L A+  
Sbjct: 949  LQESYGDCGTIYTDGSKMEGKVACACSFRNKTISRRLPDGCSIFTAELHAILLALMAVKA 1008

Query: 66   SPDHHFLIVSDSKSSLTALFNIRFTNPLISKVYSTWSFLKLNNKNVSFMWCPSHCGIRGN 125
            S    F+I SDSKS+L AL  ++   PL+ K       +  + ++V+F+W PSH GI GN
Sbjct: 1009 SERSKFIICSDSKSALQALGRMKTDIPLVHKSLKLLDLITADRRDVTFIWVPSHVGIEGN 1068

Query: 126  EIVDEAARNA------ASIDPYKLCTPEDLKPFISFLIKSEWQNQWNHIPNTNKLKAIKP 179
            E  D  A+ A       +  PY      DL+  I+     EWQN+W      +KL+ I  
Sbjct: 1069 EAADREAKRALNHAVSGTQIPY-----SDLRQSIASATYREWQNRW-EAETHSKLRQIVA 1122

Query: 180  TIEHWATSNQNKRLQEVILTRLRIGHTRITHNHLFTKTDPPFCQ-CGAALSV 230
             +    TS    R     ++RLRIGHT ITH+ +  + +PP C+ C + L+V
Sbjct: 1123 DVRWRPTSKGLTRRGSTTMSRLRIGHTYITHSFVLKREEPPLCEYCDSRLTV 1174

Source: Biomphalaria glabrata

Species: Biomphalaria glabrata

Genus: Biomphalaria

Family: Planorbidae

Class: Gastropoda

Phylum: Mollusca

Superkingdom: Eukaryota

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

 Score =  132 bits (333), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 72/205 (35%), Positives = 112/205 (54%), Gaps = 2/205 (0%)

Query: 19  DGSKTPDSTSCAFSIGDVVHSTLLNPVNSIFSAELMAIFLCLEAILESPDHHFLIVSDSK 78
           DGSK+ D+  CAF   D   +  L    S+++AEL+AI   L +I   P   F+I +DS 
Sbjct: 2   DGSKSEDAVGCAFHSRDFNLALGLPCQMSVYTAELIAINETLTSIALLPYDEFVICTDSF 61

Query: 79  SSLTALFNIRFTNPLISKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNEIVDEAARNAASI 138
           SS+ A+ +I   +  +  +    + L   +K + F+WCPSH GI GNE  D  A+ A+ +
Sbjct: 62  SSILAISSIDLIHSYVQSILQKCTNLAGRDKRIIFIWCPSHVGIPGNETADTLAQQASGM 121

Query: 139 DPYKLCTPE-DLKPFISFLIKSEWQNQWNHIPNTNKLKAIKPTIEHWATSNQNKRLQEVI 197
           +      P  D KP     ++++WQ++ +     NKL  I+P I  W    + KR  E++
Sbjct: 122 NILNCPIPHTDFKPITRSFVETQWQSESDQ-ETGNKLHDIEPDIGSWPPCQREKRRDEIV 180

Query: 198 LTRLRIGHTRITHNHLFTKTDPPFC 222
           + RLRIGHT +T++HL +  D P C
Sbjct: 181 IARLRIGHTFLTYSHLLSGNDAPMC 205

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score =  132 bits (333), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 82/232 (35%), Positives = 120/232 (51%), Gaps = 8/232 (3%)

Query: 4    ETINNKYANHTICFTDGSKTPDSTSCAFSIGDVVHSTLLNPVNSIFSAELMAIFLCLEAI 63
              +  KY ++   +TDGSKT D        G+   S  +    SIF+AE+ A++     I
Sbjct: 930  RALQEKYRDYAEFYTDGSKTRDHVGIGIVTGESAFSVRVPQCISIFTAEVYALYEAARKI 989

Query: 64   LESPDHHFLIVSDSKSSLTALFNIRFTNPLISKVYSTWSFLKLNNKNVS--FMWCPSHCG 121
            +       +I +DS S+L AL       PL+  + +    + +N+K +S  F W PSH G
Sbjct: 990  IAGKHKKAIIYTDSLSALKALHIKSECEPLVGDILN---MVLINSKVISMRFCWVPSHVG 1046

Query: 122  IRGNEIVDEAARNAASIDPYKLCTP-EDLKPFISFLIKSEWQNQWNHIPNTNKLKAIKPT 180
            I GNE  D+ A  AA     K+  P +D +  I   + ++WQ QW+    +NKL  +KPT
Sbjct: 1047 IPGNEKADKCASLAAHKTLTKIRIPLKDSQRTIRLALLAKWQQQWDSC-TSNKLHLVKPT 1105

Query: 181  IEHWATSNQNKRLQEVILTRLRIGHTRITHNHLFTKTDPPFCQ-CGAALSVI 231
            +  W      +R  EVIL RLRIGHT +THN L TK + P C+ C   L++I
Sbjct: 1106 LGEWKNCRHQERFIEVILCRLRIGHTHLTHNFLLTKEEQPMCEKCQEPLTLI 1157

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 =  132 bits (333), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 82/232 (35%), Positives = 120/232 (51%), Gaps = 8/232 (3%)

Query: 4    ETINNKYANHTICFTDGSKTPDSTSCAFSIGDVVHSTLLNPVNSIFSAELMAIFLCLEAI 63
              +  KY ++   +TDGSKT D        G+   S  +    SIF+AE+ A++     I
Sbjct: 927  RALQEKYRDYAEFYTDGSKTRDHVGIGIVTGESAFSVRVPQCISIFTAEVYALYEAARKI 986

Query: 64   LESPDHHFLIVSDSKSSLTALFNIRFTNPLISKVYSTWSFLKLNNKNVS--FMWCPSHCG 121
            +       +I +DS S+L AL       PL+  + +    + +N+K +S  F W PSH G
Sbjct: 987  IAGKHKKAIIYTDSLSALKALHIKSECEPLVGDILN---MVLINSKVISMRFCWVPSHVG 1043

Query: 122  IRGNEIVDEAARNAASIDPYKLCTP-EDLKPFISFLIKSEWQNQWNHIPNTNKLKAIKPT 180
            I GNE  D+ A  AA     K+  P +D +  I   + ++WQ QW+    +NKL  +KPT
Sbjct: 1044 IPGNEKADKCASLAAHKTLTKIRIPLKDSQRTIRLALLAKWQQQWDSC-TSNKLHLVKPT 1102

Query: 181  IEHWATSNQNKRLQEVILTRLRIGHTRITHNHLFTKTDPPFCQ-CGAALSVI 231
            +  W      +R  EVIL RLRIGHT +THN L TK + P C+ C   L++I
Sbjct: 1103 LGEWKNCRHQERFIEVILCRLRIGHTHLTHNFLLTKEEQPMCEKCQEPLTLI 1154

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  130 bits (328), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 88/226 (38%), Positives = 118/226 (52%), Gaps = 5/226 (2%)

Query: 8   NKYANHTICFTDGSKTPDSTSCAFSIGDVVHSTLLNPVNSIFSAELMAIFLCLEAILESP 67
           +KY    I +TDGSK+ D+ +CAF+         L    SI++AEL+AI   L  I    
Sbjct: 126 DKYPGINI-YTDGSKSNDAVACAFTCSTYQIQFGLPAQMSIYTAELIAIEQALIFIETMK 184

Query: 68  DH-HFLIVSDSKSSLTALFNIRFTNPLISKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNE 126
           D   F I SDS SSLTAL N   T+P +  + +  + L    K V F+WCPSH GI GNE
Sbjct: 185 DEDQFNICSDSLSSLTALSNCDITHPYLLSILTKQNNLVRKGKLVVFIWCPSHVGILGNE 244

Query: 127 IVDEAARNAASIDPYKLCTPE-DLKPFISFLIKSEWQNQWNHIPNTNKLKAIKPTIEHWA 185
           + D  A+ A  +   KL  P  D K  I   +KS  QN+W+     NKL  I+P I  W 
Sbjct: 245 VADRLAKQALVMPVTKLPLPHTDYKSPIRSYVKSLRQNEWDE-ETDNKLHTIQPVISEWK 303

Query: 186 TSNQNKRLQEVILTRLRIGHTRITHNHLFTKTDPPFC-QCGAALSV 230
              Q  R  E++L    IGH+ +TH +L  +   PFC  C + L+V
Sbjct: 304 QGPQIDRRGEIVLACACIGHSHLTHGYLLRREVAPFCIPCQSLLTV 349

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 =  125 bits (314), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 82/219 (37%), Positives = 115/219 (52%), Gaps = 6/219 (2%)

Query: 17   FTDGSKTPDSTSCAFSIGDVVHSTLLNPVNSIFSAELMAIFLCLEAILESPDHHFLIVSD 76
            F+DGSK+  S SCA        +  L+   SIF+AE   I L +E I +      +I +D
Sbjct: 1112 FSDGSKSQTSVSCAAYGESFSDAKTLHAHTSIFTAEAYGILLIVEHIKQHMIRRSIIYTD 1171

Query: 77   SKSSLTALFNIRFT-NPLISKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNEIVDEAARNA 135
            S S +TAL   + + NP+ +K+ +        N ++   W P H GI GNE+VD+ AR A
Sbjct: 1172 SLSVVTALSCGKCSKNPVFNKLLNNMHEAYNQNLSIVLCWVPGHAGITGNEMVDKNAREA 1231

Query: 136  ASIDPYKLCTPE--DLKPFISFLIKSEWQNQWNHIPNTNKLKAIKPTIEHWATSNQNKRL 193
            AS     + +    DL P +   ++S WQ +W+   + NKL  +KP +        N R 
Sbjct: 1232 ASRHTIDISSVPGVDLNPVVRRGLRSHWQVEWDKQVD-NKLHLVKPHLSKVLPQKLN-RF 1289

Query: 194  QEVILTRLRIGHTRITHNHLFTKTDPPFC-QCGAALSVI 231
             EV L RLRIGHT  TH HL T TDPP C  CG  L+++
Sbjct: 1290 TEVTLARLRIGHTYATHKHLLTGTDPPTCIHCGETLTIL 1328

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	271
ASPGD|ASPL0000075333	486	AN10625 [Emericella nidulans (	0.701	0.390	0.240	8.1e-09
ASPGD|ASPL0000077547	1581	AN8648 [Emericella nidulans (t	0.671	0.115	0.282	6.1e-06
ASPGD|ASPL0000055652	1054	AN0368 [Emericella nidulans (t	0.671	0.172	0.278	2.4e-05

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

 Score = 157 (60.3 bits), Expect = 8.1e-09, P = 8.1e-09
 Identities = 49/204 (24%), Positives = 93/204 (45%)

Query:    46 NSIFSAELMAIFLCLEAILESPDHHFLIVSDSKSSLTALFN--IRFTNPLISKVYSTWSF 103
             ++++ AEL  I L L  IL+    H +I +D++++L AL N   +    ++  +    + 
Sbjct:   219 STVYVAELQGILLALVIILQRQMQHAVIFTDNQATLQALRNPGSQSGQYILEAIIMALNK 278

Query:   104 LKLNNKNVSFMWCPSHCGIRGNEIVDEAARNAAS---IDPYK--LCTPEDLKPFISFLIK 158
              +    NV F W P+H G+ GNE  D  A+ A     I  ++  +     +K     ++ 
Sbjct:   279 GRKAGLNVHFRWIPAHRGVEGNEQADRRAKEATGWRRIRGHRGRMTIRSAVKRRAHEVVN 338

Query:   159 SEWQNQWNHIPNTNKLKAIKPTIEHWATS-NQN-KRLQEVILTRLRIGHTRITHNHLFTK 216
             + W+N W    +  +L  + PT        +Q+  R    I+ ++R G   + H +L+ +
Sbjct:   339 ARWENDWKSCHHGRELYELTPTPTRKVLRVHQDLHRALSTIIVQMRTGKIGLRH-YLYQR 397

Query:   217 TDPPF----CQCGAALSVILNYIV 236
               P      CQCG A   + + ++
Sbjct:   398 GVPDVPNSDCQCGRATQSVRHILL 421

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

ASPGD|ASPL0000077547 AN8648 [Emericella nidulans (taxid:162425)]

 Score = 138 (53.6 bits), Expect = 6.1e-06, P = 6.1e-06
 Identities = 58/205 (28%), Positives = 90/205 (43%)

Query:    44 PVNSIFSAELMAIFLCLEAILESP----DHHFLIVSDSKSSLTALFNIRFT------NPL 93
             P   ++ AE+M     L A L  P        +I+ D+ ++ + L + R T      +  
Sbjct:  1313 PRTEVYDAEIMGAVEGLRAALGQPCVGYSTQLVILLDNLAAASLLASYRPTPHRHGLSET 1372

Query:    94 ISKVYSTW----SFLKLNNKNVSFMWCPSHCGIRGNEIVDEAARNAASI-DPYKLCTPED 148
              S++ + W    S L +  K +   W P H GI GNE+ D+ A+  +SI  P    +P  
Sbjct:  1373 FSQLAAQWMESPSILTMQRKPLQVRWIPGHSGIAGNELADKLAKLGSSIYSPDIPPSPAY 1432

Query:   149 LKPFISFLIKSEWQNQW-NHIPNTNKLKAIKPTIEHWATSNQNKRLQEVILTRL---RIG 204
             L+      +++E    + N  P T K   I+P  +  + S ++K L   +L RL   R G
Sbjct:  1433 LRREAKQWLRTETYTAYANKAPETYKALNIRPHTKE-SRSREHK-LPRWVLGRLVAARTG 1490

Query:   205 HTRITHNHL-FTKTDP-PFCQCGAA 227
             H   T  H  F  TD    C CG A
Sbjct:  1491 HGDFTAYHQRFDHTDYLESCTCGKA 1515

GO:0006278 "RNA-dependent DNA replication" evidence=IEA

GO:0003964 "RNA-directed DNA polymerase activity" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

ASPGD|ASPL0000055652 AN0368 [Emericella nidulans (taxid:162425)]

 Score = 131 (51.2 bits), Expect = 2.4e-05, P = 2.4e-05
 Identities = 57/205 (27%), Positives = 89/205 (43%)

Query:    44 PVNSIFSAELMAIFLCLEAILESP----DHHFLIVSDSKSSLTALFNIRFT------NPL 93
             P   ++ AE+M     L   L  P        +I+ D+ ++ + L + R T      +  
Sbjct:   786 PRTEVYDAEIMGAVEGLRTALGQPCVGYSTQLVILLDNLAAASLLASYRPTPHRHGLSET 845

Query:    94 ISKVYSTW----SFLKLNNKNVSFMWCPSHCGIRGNEIVDEAARNAASI-DPYKLCTPED 148
              S++ + W    S L +  K +   W P H GI GNE+ D+ A+  +SI  P    +P  
Sbjct:   846 FSQLAAQWMESPSILTMQWKPLQVRWIPGHSGIAGNELADKLAKLGSSIYSPDIPPSPAY 905

Query:   149 LKPFISFLIKSEWQNQW-NHIPNTNKLKAIKPTIEHWATSNQNKRLQEVILTRL---RIG 204
             L+      +++E    + N  P T K   I+P  +  + S ++K L   +L RL   R G
Sbjct:   906 LRQEAKQWLRTETYTAYANKAPETYKALNIRPHTKE-SRSREHK-LPRWVLGRLVAARTG 963

Query:   205 HTRITHNHL-FTKTDP-PFCQCGAA 227
             H   T  H  F  TD    C CG A
Sbjct:   964 HGDFTAYHQRFDHTDYLESCTCGKA 988


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.323   0.135   0.430    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      271       271   0.00098  114 3  11 22  0.43    33
                                                     32  0.40    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:  3
  No. of states in DFA:  621 (66 KB)
  Total size of DFA:  239 KB (2128 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:  23.34u 0.11s 23.45t   Elapsed:  00:00:01
  Total cpu time:  23.34u 0.11s 23.45t   Elapsed:  00:00:01
  Start:  Thu Aug 15 12:38:40 2013   End:  Thu Aug 15 12:38:41 2013

GO:0005575 "cellular_component" evidence=ND

GO:0006278 "RNA-dependent DNA replication" evidence=IEA

GO:0003964 "RNA-directed DNA polymerase activity" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

---

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	271
cd09276	128	cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom	5e-35
pfam00075	126	pfam00075, RNase_H, RNase H	4e-14
cd06222	123	cd06222, RNase_H, RNase H is an endonuclease that	8e-12
cd09273	135	cd09273, RNase_HI_RT_Bel, Bel/Pao family of RNase	3e-08
cd09280	150	cd09280, RNase_HI_eukaryote_like, Eukaryotic RNase	1e-04
COG0328	154	COG0328, RnhA, Ribonuclease HI [DNA replication, r	2e-04
cd09278	139	cd09278, RNase_HI_prokaryote_like, RNase HI family	5e-04

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

 Score =  121 bits (307), Expect = 5e-35
 Identities = 45/128 (35%), Positives = 63/128 (49%), Gaps = 5/128 (3%)

Query: 15  ICFTDGSKTPDSTSCAFSI---GDVVHSTLLNPVNSIFSAELMAIFLCLEAILE--SPDH 69
           + +TDGSK    T   F+I   G +  S  L P  S+F AEL+AI   L+  L       
Sbjct: 1   VIYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRRAR 60

Query: 70  HFLIVSDSKSSLTALFNIRFTNPLISKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNEIVD 129
              I SDS+++L AL + R ++PL+ ++      L  +   V   W P H GI GNE  D
Sbjct: 61  KITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGNERAD 120

Query: 130 EAARNAAS 137
             A+ AA 
Sbjct: 121 RLAKEAAK 128

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 = 67.3 bits (165), Expect = 4e-14
 Identities = 31/132 (23%), Positives = 49/132 (37%), Gaps = 13/132 (9%)

Query: 12  NHTICFTDGS--KTPDSTSCAFSIGDVVHSTLLNPVNSIFSAELMAIFLCLEAILESPDH 69
                +TDGS    P      +        +   P  +   AEL+A+   LEA+      
Sbjct: 2   EAVTVYTDGSCNGNPGPGGAGYVTDGGKQRSKPLPGTTNQRAELLALIEALEALSGQK-- 59

Query: 70  HFLIVSDSKSS----LTALFNIRFTNPLISKVYSTWSFLKLNNKNVSFMWCPSHCGIRGN 125
              I +DS+               + P+ ++++     L      V   W P H GI GN
Sbjct: 60  -VNIYTDSQYVIGGITNGWPTKSESKPIKNEIW----ELLQKKHKVYIQWVPGHSGIPGN 114

Query: 126 EIVDEAARNAAS 137
           E+ D+ A+  AS
Sbjct: 115 ELADKLAKQGAS 126

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 = 60.8 bits (148), Expect = 8e-12
 Identities = 27/127 (21%), Positives = 45/127 (35%), Gaps = 11/127 (8%)

Query: 17  FTDGSKTPDSTSCAF-------SIGDVVHSTLLNPVNSIFSAELMAIFLCLEAILESPDH 69
            TDGS   +                 +   +L  P  +   AEL+A+   LE  L+    
Sbjct: 1   NTDGSCKGNPGPAGAGGVLRDHEGAWLFAGSLSIPAATNNEAELLALLEALELALDLGLK 60

Query: 70  HFLIVSDSKSSLTALFNIRFTNPLISKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNEIVD 129
             +I +DSK  +  + +        + +      L     ++ F   P      GNE+ D
Sbjct: 61  KLIIETDSKYVVDLINSWSKGWKKNNLLLWDILLLLSKFIDIRFEHVPRE----GNEVAD 116

Query: 130 EAARNAA 136
             A+ AA
Sbjct: 117 RLAKEAA 123

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 = 50.7 bits (122), Expect = 3e-08
 Identities = 32/138 (23%), Positives = 48/138 (34%), Gaps = 21/138 (15%)

Query: 16  CFTDGSKTPDSTSCA-FSIGDVVHSTLLNPVNSIFSAELMAIFLCLEAILESPDHHFLIV 74
            FTDGS        A  +  DV+    L    S   AEL+A+   + A+  +      I 
Sbjct: 2   VFTDGSSFVRKAGYAVVTGPDVLEIATLPYGTSAQRAELIAL---IRALELAKGKPVNIY 58

Query: 75  SDSK-------SSLTALFNIRFTNPLISKVYS----TWSFLKLNNKNVSFMWCPSHCG-- 121
           +DS        +  T      F       + S        ++     V+ +   +H G  
Sbjct: 59  TDSAYAFGILHALETIWKERGFLTGKPIALASLILQLQKAIQRPKP-VAVIHIRAHSGLP 117

Query: 122 ---IRGNEIVDEAARNAA 136
                GN   D+AAR AA
Sbjct: 118 GPLALGNARADQAARQAA 135

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

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

 Score = 41.0 bits (97), Expect = 1e-04
 Identities = 26/111 (23%), Positives = 36/111 (32%), Gaps = 30/111 (27%)

Query: 51  AELMAIFLCLEAILES--PDHHFLIVSDSK---SSLTALFNIR------FTN-------- 91
           AEL A+   L  I E        +I +DS+   + +T    I       +          
Sbjct: 46  AELRAVIHALRLIKEVGEGLTKLVIATDSEYVVNGVT--EWIPKWKKNGWKTSKGKPVAN 103

Query: 92  -----PLISKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNEIVDEAARNAAS 137
                 L   +      L+     V F   P H GI GNE  D  A+  A 
Sbjct: 104 KDLIKELDKLLEE----LEERGIRVKFWHVPGHSGIYGNEEADRLAKKGAD 150

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

>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and repair]

 Score = 40.4 bits (95), Expect = 2e-04
 Identities = 23/99 (23%), Positives = 35/99 (35%), Gaps = 12/99 (12%)

Query: 51  AELMAIFLCLEAILESPDHHFLIVSDSKSSLTALFNIRFTNPLISKVYSTWSFLKL---- 106
           AEL A+   LEA+ E       + +DSK  +  +              +    +K     
Sbjct: 46  AELRALIEALEALKELGACEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPVKNKDLW 105

Query: 107 --------NNKNVSFMWCPSHCGIRGNEIVDEAARNAAS 137
                    ++ V + W   H G   NE  D+ AR AA 
Sbjct: 106 EELDELLKRHELVFWEWVKGHAGHPENERADQLAREAAR 144

Length = 154

>gnl|CDD|187702 cd09278, RNase_HI_prokaryote_like, RNase HI family found mainly in prokaryotes

 Score = 39.0 bits (92), Expect = 5e-04
 Identities = 13/31 (41%), Positives = 15/31 (48%)

Query: 106 LNNKNVSFMWCPSHCGIRGNEIVDEAARNAA 136
           L    V++ W   H G  GNE  DE A  AA
Sbjct: 108 LAKHQVTWHWVKGHAGHPGNERADELANAAA 138

Ribonuclease H (RNase H) is classified into two evolutionarily unrelated families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, Type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD), residues and have the same catalytic mechanism and functions in cells. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. Prokaryotic RNase H varies greatly in domain structures and substrate specificities. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability. Length = 139

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	271
PRK06548	161	ribonuclease H; Provisional	99.91
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	99.91
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	99.91
PRK08719	147	ribonuclease H; Reviewed	99.9
PRK00203	150	rnhA ribonuclease H; Reviewed	99.89
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	99.82
KOG3752|consensus	371		99.8
PRK13907	128	rnhA ribonuclease H; Provisional	99.78
PRK07708	219	hypothetical protein; Validated	99.68
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	99.6
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	99.44
PF13966	86	zf-RVT: zinc-binding in reverse transcriptase	95.47
PF05380	159	Peptidase_A17: Pao retrotransposon peptidase ; Int	89.15
.; GO: 0004523 ribonuclease H activity" target="_blank" href="http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PF00336">PF00336	245	DNA_pol_viral_C: DNA polymerase (viral) C-terminal	83.14

>PRK06548 ribonuclease H; Provisional

Probab=99.91  E-value=8.1e-24  Score=172.67  Aligned_cols=128  Identities=27%  Similarity=0.267  Sum_probs=94.1

Q ss_pred             CCcEEEEEcCCCCCC--CeeEEEEECCeEEEEecCCCCchHHHHHHHHHHHHHHHHcCCCceEEEEeCCHHHHHHHhcc-
Q psy8412          11 ANHTICFTDGSKTPD--STSCAFSIGDVVHSTLLNPVNSIFSAELMAIFLCLEAILESPDHHFLIVSDSKSSLTALFNI-   87 (271)
Q Consensus        11 ~~~~~iytDGS~~~~--~~G~a~~~~~~~~~~~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~v~I~tDS~~al~~l~~~-   87 (271)
                      +..+.||||||+.++  ..|+|++..+...........|++.|||.||+.||+.+.. +...|.|+|||++|++.++.+ 
T Consensus         3 ~~~~~IytDGa~~gnpg~~G~g~~~~~~~~~~g~~~~~TNnraEl~Aii~aL~~~~~-~~~~v~I~TDS~yvi~~i~~W~   81 (161)
T PRK06548          3 NNEIIAATDGSSLANPGPSGWAWYVDENTWDSGGWDIATNNIAELTAVRELLIATRH-TDRPILILSDSKYVINSLTKWV   81 (161)
T ss_pred             CCEEEEEEeeccCCCCCceEEEEEEeCCcEEccCCCCCCHHHHHHHHHHHHHHhhhc-CCceEEEEeChHHHHHHHHHHH
Confidence            356999999998864  4788877543222222234689999999999999986643 446799999999999999942 


Q ss_pred             --------ccCCccH---HHHHHHHHHHHhCCCceEEEEecCCCCCccchHHHHHHHHhhcCCC
Q psy8412          88 --------RFTNPLI---SKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNEIVDEAARNAASIDP  140 (271)
Q Consensus        88 --------~~~~~~~---~~~~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~~~  140 (271)
                              ...++.+   ++++.++..+... ..|+|.|||||+|++|||.||+||++|+....
T Consensus        82 ~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~-~~v~~~wVkgHsg~~gNe~aD~LA~~aa~~~~  144 (161)
T PRK06548         82 YSWKMRKWRKADGKPVLNQEIIQEIDSLMEN-RNIRMSWVNAHTGHPLNEAADSLARQAANNFS  144 (161)
T ss_pred             HHHHHCCCcccCCCccccHHHHHHHHHHHhc-CceEEEEEecCCCCHHHHHHHHHHHHHHHHhc
Confidence                    2233322   3444444444443 47999999999999999999999999997653

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

Probab=99.91  E-value=8.4e-24  Score=169.96  Aligned_cols=127  Identities=24%  Similarity=0.225  Sum_probs=98.9

Q ss_pred             CcEEEEEcCCCCCC--CeeEEEEE--CCeE--EEEecCCCCchHHHHHHHHHHHHHHHHcCCCceEEEEeCCHHHHHHHh
Q psy8412          12 NHTICFTDGSKTPD--STSCAFSI--GDVV--HSTLLNPVNSIFSAELMAIFLCLEAILESPDHHFLIVSDSKSSLTALF   85 (271)
Q Consensus        12 ~~~~iytDGS~~~~--~~G~a~~~--~~~~--~~~~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~v~I~tDS~~al~~l~   85 (271)
                      ..+.||||||+..+  ..|+|+|.  ++..  .+.... .+||+.||+.|++.||+.+...+...|.|+|||++|++.|+
T Consensus         2 ~~v~if~DGa~~gNpG~gG~g~vl~~~~~~~~~s~~~~-~tTNNraEl~A~i~AL~~l~~~~~~~v~l~tDS~yv~~~i~   80 (154)
T COG0328           2 KKVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEG-RTTNNRAELRALIEALEALKELGACEVTLYTDSKYVVEGIT   80 (154)
T ss_pred             CceEEEecCccCCCCCCceEEEEEEcCCceEEEeeeee-cccChHHHHHHHHHHHHHHHhcCCceEEEEecHHHHHHHHH
Confidence            46899999999864  36777664  2222  233333 89999999999999999999888999999999999999999


Q ss_pred             cccc---CCcc---------HHHHHHHHHHHHhCCCceEEEEecCCCCCccchHHHHHHHHhhcCC
Q psy8412          86 NIRF---TNPL---------ISKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNEIVDEAARNAASID  139 (271)
Q Consensus        86 ~~~~---~~~~---------~~~~~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~~  139 (271)
                      .+..   ..++         ..+++..+..+..+...|.+.|||||+|.++||+||+||+.|++..
T Consensus        81 ~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~~~~~~  146 (154)
T COG0328          81 RWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAREAARAA  146 (154)
T ss_pred             HHHhhccccCccccccCccccHHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHHHHHhh
Confidence            5422   1111         1234444445666777999999999999999999999999998875

>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=99.91  E-value=8.9e-24  Score=167.16  Aligned_cols=122  Identities=31%  Similarity=0.345  Sum_probs=89.0

Q ss_pred             CcEEEEEcCCCCCC--CeeEEEE-ECCeEEEEecCCCCchHHHHHHHHHHHHHHHHcCCCceEEEEeCCHHHHHHHhc--
Q psy8412          12 NHTICFTDGSKTPD--STSCAFS-IGDVVHSTLLNPVNSIFSAELMAIFLCLEAILESPDHHFLIVSDSKSSLTALFN--   86 (271)
Q Consensus        12 ~~~~iytDGS~~~~--~~G~a~~-~~~~~~~~~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~v~I~tDS~~al~~l~~--   86 (271)
                      +.+.||||||+.++  ..|+|++ ..+......++ ..|++.|||.||..||+ +..  ...++|+|||+++++.+..  
T Consensus         2 ~~~~iytDgS~~~~~~~~~~g~v~~~~~~~~~~~~-~~s~~~aEl~Ai~~AL~-~~~--~~~v~I~tDS~~v~~~l~~~~   77 (132)
T PF00075_consen    2 KAIIIYTDGSCRPNPGKGGAGYVVWGGRNFSFRLG-GQSNNRAELQAIIEALK-ALE--HRKVTIYTDSQYVLNALNKWL   77 (132)
T ss_dssp             TSEEEEEEEEECTTTTEEEEEEEEETTEEEEEEEE-SECHHHHHHHHHHHHHH-THS--TSEEEEEES-HHHHHHHHTHH
T ss_pred             CcEEEEEeCCccCCCCceEEEEEEECCeEEEeccc-ccchhhhheehHHHHHH-Hhh--cccccccccHHHHHHHHHHhc
Confidence            57899999997643  2455554 44444444455 88999999999999999 543  4999999999999998877  


Q ss_pred             ---cccCCccHHHHHHHHHHHHhCCCceEEEEecCCCCC-ccchHHHHHHHHhhc
Q psy8412          87 ---IRFTNPLISKVYSTWSFLKLNNKNVSFMWCPSHCGI-RGNEIVDEAARNAAS  137 (271)
Q Consensus        87 ---~~~~~~~~~~~~~~~~~l~~~~~~v~~~WVpgH~gi-~gNe~AD~lAk~a~~  137 (271)
                         ..........+...+.++...+..|.|+|||||+|+ .||+.||+|||+|+.
T Consensus        78 ~~~~~~~~~~~~~i~~~i~~~~~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~~  132 (132)
T PF00075_consen   78 HGNGWKKTSNGRPIKNEIWELLSRGIKVRFRWVPGHSGVPQGNERADRLAKEAAQ  132 (132)
T ss_dssp             HHTTSBSCTSSSBHTHHHHHHHHHSSEEEEEESSSSSSSHHHHHHHHHHHHHHHH
T ss_pred             cccccccccccccchhheeeccccceEEeeeeccCcCCCchhHHHHHHHHHHhcC
Confidence               332221111233333333356899999999999999 699999999999973

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

>PRK08719 ribonuclease H; Reviewed

Probab=99.90  E-value=3.4e-23  Score=167.29  Aligned_cols=122  Identities=22%  Similarity=0.232  Sum_probs=89.5

Q ss_pred             CCcEEEEEcCCCCCCC-----eeEEEEE--CC--eE--EEEecCCCCchHHHHHHHHHHHHHHHHcCCCceEEEEeCCHH
Q psy8412          11 ANHTICFTDGSKTPDS-----TSCAFSI--GD--VV--HSTLLNPVNSIFSAELMAIFLCLEAILESPDHHFLIVSDSKS   79 (271)
Q Consensus        11 ~~~~~iytDGS~~~~~-----~G~a~~~--~~--~~--~~~~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~v~I~tDS~~   79 (271)
                      .+.++||||||+..++     .|+|++.  .+  ..  ....+....|++.|||.|++.||+.+.+.    ..|+|||++
T Consensus         2 ~~~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~----~~i~tDS~y   77 (147)
T PRK08719          2 RASYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARDG----DVIYSDSDY   77 (147)
T ss_pred             CceEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCC----CEEEechHH
Confidence            4678999999997543     4788653  22  22  33445566899999999999999998652    479999999


Q ss_pred             HHHHHhc--------cccCC-ccH---HHHHHHHHHHHhCCCceEEEEecCCCCCccchHHHHHHHHhhc
Q psy8412          80 SLTALFN--------IRFTN-PLI---SKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNEIVDEAARNAAS  137 (271)
Q Consensus        80 al~~l~~--------~~~~~-~~~---~~~~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~  137 (271)
                      |++.++.        .+..+ +.+   .+++..+..+.. ...|+|.|||||+|++|||.||+||++|++
T Consensus        78 vi~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~-~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~  146 (147)
T PRK08719         78 CVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRA-RKYVEVEKVTAHSGIEGNEAADMLAQAAAE  146 (147)
T ss_pred             HHHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhC-CCcEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence            9999943        33322 221   233333333444 577999999999999999999999999975

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=99.89  E-value=1.1e-22  Score=165.16  Aligned_cols=124  Identities=19%  Similarity=0.194  Sum_probs=90.9

Q ss_pred             cEEEEEcCCCCCC--CeeEEEEE--CCeEE-EEecCCCCchHHHHHHHHHHHHHHHHcCCCceEEEEeCCHHHHHHHhcc
Q psy8412          13 HTICFTDGSKTPD--STSCAFSI--GDVVH-STLLNPVNSIFSAELMAIFLCLEAILESPDHHFLIVSDSKSSLTALFNI   87 (271)
Q Consensus        13 ~~~iytDGS~~~~--~~G~a~~~--~~~~~-~~~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~v~I~tDS~~al~~l~~~   87 (271)
                      .+.||||||+..+  ..|+|++.  .+... ........|++.|||.|++.||+.+..  ...+.|+|||+++++.|+.+
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            4899999998753  46777653  33322 222235788999999999999998865  46899999999999999863


Q ss_pred             cc---------CCccH---HHHHHHHHHHHhCCCceEEEEecCCCCCccchHHHHHHHHhhcCC
Q psy8412          88 RF---------TNPLI---SKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNEIVDEAARNAASID  139 (271)
Q Consensus        88 ~~---------~~~~~---~~~~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~~  139 (271)
                      ..         ..+..   .+++..+.++. ....|.|.|||||+|++||+.||+|||+|+...
T Consensus        81 ~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~-~~~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~~  143 (150)
T PRK00203         81 IHGWKKNGWKTADKKPVKNVDLWQRLDAAL-KRHQIKWHWVKGHAGHPENERCDELARAGAEEA  143 (150)
T ss_pred             HHHHHHcCCcccCCCccccHHHHHHHHHHh-ccCceEEEEecCCCCCHHHHHHHHHHHHHHHHh
Confidence            21         11111   22333333343 347899999999999999999999999998764

>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=99.82  E-value=4.4e-19  Score=136.90  Aligned_cols=122  Identities=29%  Similarity=0.338  Sum_probs=94.6

Q ss_pred             EEEEcCCCCCC--CeeEEEEECC--eE---EEEecCCCCchHHHHHHHHHHHHHHHHcCCCceEEEEeCCHHHHHHHhcc
Q psy8412          15 ICFTDGSKTPD--STSCAFSIGD--VV---HSTLLNPVNSIFSAELMAIFLCLEAILESPDHHFLIVSDSKSSLTALFNI   87 (271)
Q Consensus        15 ~iytDGS~~~~--~~G~a~~~~~--~~---~~~~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~v~I~tDS~~al~~l~~~   87 (271)
                      ++|||||...+  ++|+|++..+  ..   .........+++.+|+.|+..||+++...+..++.|++||+.+++.+++.
T Consensus         1 ~~~~Dgs~~~~~~~~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~~~~~~~i~i~~Ds~~~~~~~~~~   80 (130)
T cd06222           1 VIYTDGSCRGNPGPAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALELGGKKVNIYTDSQYVINALTGW   80 (130)
T ss_pred             CEEecccCCCCCCceEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHHhCCCceEEEEECHHHHHHHhhcc
Confidence            48999998865  5788876432  11   11122257899999999999999999988899999999999999999987


Q ss_pred             ccCC-ccHHHHHHHHHHHHhCCCceEEEEecCCCCCccchHHHHHHHHhh
Q psy8412          88 RFTN-PLISKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNEIVDEAARNAA  136 (271)
Q Consensus        88 ~~~~-~~~~~~~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~  136 (271)
                      .... .........+..+...+..+.|.|||+|++.++|+.||.|||.|.
T Consensus        81 ~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~~  130 (130)
T cd06222          81 YEGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKEAA  130 (130)
T ss_pred             ccCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence            6522 222333334444446788999999999999999999999999874

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=99.80  E-value=4.6e-19  Score=158.64  Aligned_cols=136  Identities=21%  Similarity=0.208  Sum_probs=104.1

Q ss_pred             hhhHhhccCCcEEEEEcCCCCCC-----CeeEEEEECCe---EEEEecC-CCCchHHHHHHHHHHHHHHHHcCCCceEEE
Q psy8412           3 CETINNKYANHTICFTDGSKTPD-----STSCAFSIGDV---VHSTLLN-PVNSIFSAELMAIFLCLEAILESPDHHFLI   73 (271)
Q Consensus         3 ~~~~~~~~~~~~~iytDGS~~~~-----~~G~a~~~~~~---~~~~~l~-~~~s~~~AEl~Ai~~AL~~a~~~~~~~v~I   73 (271)
                      +.+++..+.+..++|||||+..+     .+|+||+.++.   ..+..+. +..|+|.|||.||..||+-|.+.+..+|+|
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            34445555566999999998874     37999997643   3456664 899999999999999999999988889999


Q ss_pred             EeCCHHHHHHHhccccC-----------Ccc------HHHHHHHHHHHHh--CCCceEEEEecCCCCCccchHHHHHHHH
Q psy8412          74 VSDSKSSLTALFNIRFT-----------NPL------ISKVYSTWSFLKL--NNKNVSFMWCPSHCGIRGNEIVDEAARN  134 (271)
Q Consensus        74 ~tDS~~al~~l~~~~~~-----------~~~------~~~~~~~~~~l~~--~~~~v~~~WVpgH~gi~gNe~AD~lAk~  134 (271)
                      .|||+++++.|+.|...           ++.      .+..+..+..|.+  .+..|.+.|||||.|+.||++||.||++
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            99999999999866321           110      1122222233433  4789999999999999999999999999


Q ss_pred             hhcC
Q psy8412         135 AASI  138 (271)
Q Consensus       135 a~~~  138 (271)
                      ++..
T Consensus       362 gs~~  365 (371)
T KOG3752|consen  362 GSTL  365 (371)
T ss_pred             hhhh
Confidence            8654

>PRK13907 rnhA ribonuclease H; Provisional

Probab=99.78  E-value=2.3e-18  Score=136.02  Aligned_cols=121  Identities=19%  Similarity=0.126  Sum_probs=93.9

Q ss_pred             EEEEEcCCCCCC--CeeEEEEECC--eEEEE-ecCCCCchHHHHHHHHHHHHHHHHcCCCceEEEEeCCHHHHHHHhccc
Q psy8412          14 TICFTDGSKTPD--STSCAFSIGD--VVHST-LLNPVNSIFSAELMAIFLCLEAILESPDHHFLIVSDSKSSLTALFNIR   88 (271)
Q Consensus        14 ~~iytDGS~~~~--~~G~a~~~~~--~~~~~-~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~v~I~tDS~~al~~l~~~~   88 (271)
                      +.||||||+..+  ..|+|++..+  ..... ......|++.||+.|++.||+.+...+..++.|+|||+.+++.+++.+
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            689999998764  5788877532  21111 223567999999999999999999988889999999999999999876


Q ss_pred             cCCccHHHHHHHHHHHHhCCCceEEEEecCCCCCccchHHHHHHHHhhcC
Q psy8412          89 FTNPLISKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNEIVDEAARNAASI  138 (271)
Q Consensus        89 ~~~~~~~~~~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~  138 (271)
                      ...+....++..+..+......+.|.|||+    +.|+.||.||+.|...
T Consensus        82 ~~~~~~~~l~~~~~~l~~~f~~~~~~~v~r----~~N~~Ad~LA~~a~~~  127 (128)
T PRK13907         82 AKNKMFAPLLEEALQYIKSFDLFFIKWIPS----SQNKVADELARKAILQ  127 (128)
T ss_pred             hcChhHHHHHHHHHHHHhcCCceEEEEcCc----hhchhHHHHHHHHHhc
Confidence            543333445555555667778889999996    5999999999999753

>PRK07708 hypothetical protein; Validated

Probab=99.68  E-value=1.3e-15  Score=130.67  Aligned_cols=126  Identities=13%  Similarity=0.067  Sum_probs=93.8

Q ss_pred             CCcEEEEEcCCCCC--CCeeEEEEE--C-C-eEE----EEecCCCCchHHHHHHHHHHHHHHHHcCCCce--EEEEeCCH
Q psy8412          11 ANHTICFTDGSKTP--DSTSCAFSI--G-D-VVH----STLLNPVNSIFSAELMAIFLCLEAILESPDHH--FLIVSDSK   78 (271)
Q Consensus        11 ~~~~~iytDGS~~~--~~~G~a~~~--~-~-~~~----~~~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~--v~I~tDS~   78 (271)
                      ++.+++|+|||...  +++|+|++.  . + ...    ...++...|++.||+.|++.||+.+...+.+.  |.|++||+
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            34799999999864  457777653  2 2 221    22455668999999999999999999887654  89999999


Q ss_pred             HHHHHHhccccC-CccHHHHHHHHHHHH-hCCCceEEEEecCCCCCccchHHHHHHHHhhcCCC
Q psy8412          79 SSLTALFNIRFT-NPLISKVYSTWSFLK-LNNKNVSFMWCPSHCGIRGNEIVDEAARNAASIDP  140 (271)
Q Consensus        79 ~al~~l~~~~~~-~~~~~~~~~~~~~l~-~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~~~  140 (271)
                      .+++.+++.+.. .+....+...+..+. +....+.+.|||    ++.|+.||+||+.|.+..+
T Consensus       151 lVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~Vp----R~~N~~AD~LAk~Al~~~~  210 (219)
T PRK07708        151 VVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPIS----RKQNKEADQLATQALEGTV  210 (219)
T ss_pred             HHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECC----chhhhHHHHHHHHHHhcCC
Confidence            999999987653 333444444444333 344568889998    5789999999999998654

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=99.60  E-value=1.9e-14  Score=133.38  Aligned_cols=124  Identities=17%  Similarity=0.127  Sum_probs=96.1

Q ss_pred             cEEEEEcCCCCCC--CeeEEEEEC--C-e--E-EEEecCCCCchHHHHHHHHHHHHHHHHcCCCceEEEEeCCHHHHHHH
Q psy8412          13 HTICFTDGSKTPD--STSCAFSIG--D-V--V-HSTLLNPVNSIFSAELMAIFLCLEAILESPDHHFLIVSDSKSSLTAL   84 (271)
Q Consensus        13 ~~~iytDGS~~~~--~~G~a~~~~--~-~--~-~~~~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~v~I~tDS~~al~~l   84 (271)
                      .+.||||||+..+  .+|+|++..  + .  . .........|++.||+.|++.||+.+.+.+.+.|.|++||+.+++.+
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            4789999998865  478887642  1 1  1 22222347889999999999999999999899999999999999999


Q ss_pred             hcccc-CCccHHHHHHHHHHHHhCCCceEEEEecCCCCCccchHHHHHHHHhhcCCC
Q psy8412          85 FNIRF-TNPLISKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNEIVDEAARNAASIDP  140 (271)
Q Consensus        85 ~~~~~-~~~~~~~~~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~~~  140 (271)
                      ++.+. .++....+...+..+.+....++|.|||.    ++|+.||.||+.|.....
T Consensus        82 ~~~~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~r----~~N~~AD~LA~~a~~~~~  134 (372)
T PRK07238         82 SGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPR----ARNAHADRLANEAMDAAA  134 (372)
T ss_pred             CCCCccCChHHHHHHHHHHHHHhcCCceEEEECCc----hhhhHHHHHHHHHHHhhc
Confidence            98764 23333444445555677888999999995    699999999999987653

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

Probab=99.44  E-value=1.1e-12  Score=95.73  Aligned_cols=86  Identities=22%  Similarity=0.162  Sum_probs=69.0

Q ss_pred             hHHHHHHHHHHHHHHHHcCCCceEEEEeCCHHHHHHHhccccCCccHHHHHHHHHHHHhCCCceEEEEecCCCCCccchH
Q psy8412          48 IFSAELMAIFLCLEAILESPDHHFLIVSDSKSSLTALFNIRFTNPLISKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNEI  127 (271)
Q Consensus        48 ~~~AEl~Ai~~AL~~a~~~~~~~v~I~tDS~~al~~l~~~~~~~~~~~~~~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~  127 (271)
                      +..||+.|+..||+++...+.++|.|+|||+.+++.|++..........+...+..+......+.|.|||    .++|..
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            4689999999999999999999999999999999999988544334456666666677789999999999    789999


Q ss_pred             HHHHHHHhhc
Q psy8412         128 VDEAARNAAS  137 (271)
Q Consensus       128 AD~lAk~a~~  137 (271)
                      ||.|||.|.+
T Consensus        77 A~~LA~~a~~   86 (87)
T PF13456_consen   77 ADALAKFALS   86 (87)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHhh
Confidence            9999999874

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

Probab=95.47  E-value=0.008  Score=43.76  Aligned_cols=32  Identities=22%  Similarity=0.358  Sum_probs=22.0

Q ss_pred             eeeeccccc--cc-ccccCCCCCCCcc-cC-Ccccce
Q psy8412         200 RLRIGHTRI--TH-NHLFTKTDPPFCQ-CG-AALSVI  231 (271)
Q Consensus       200 qlrtGH~~~--~h-~~r~~~~~sp~C~-Cg-~~et~~  231 (271)
                      --+.-|..+  +. +.+.+...++.|. |+ +.||++
T Consensus        37 ~W~~~~~rL~t~~~l~~r~~~~~~~C~~C~~~~Et~~   73 (86)
T PF13966_consen   37 LWRALHNRLPTKDNLQRRGIQVDPICPLCGNEEETIE   73 (86)
T ss_pred             eeeeccccchhhhhhhccCCccCCccccCCCcccccc
Confidence            344555565  23 3466677889999 99 489998

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

Probab=89.15  E-value=1.1  Score=36.46  Aligned_cols=51  Identities=18%  Similarity=0.172  Sum_probs=33.2

Q ss_pred             cEEEEEcCCCCCCCeeEEEEEC---C-e-E-----EEEec-C-CCCchHHHHHHHHHHHHHHHHc
Q psy8412          13 HTICFTDGSKTPDSTSCAFSIG---D-V-V-----HSTLL-N-PVNSIFSAELMAIFLCLEAILE   65 (271)
Q Consensus        13 ~~~iytDGS~~~~~~G~a~~~~---~-~-~-----~~~~l-~-~~~s~~~AEl~Ai~~AL~~a~~   65 (271)
                      .+.+|+|+|..  +.|+.+|.+   + . .     ...++ | ...|+-+-||.|+..|.+++..
T Consensus        81 ~L~~F~DAS~~--aygavvYlr~~~~~~~~~~ll~aKsrv~P~k~~tIPRlEL~a~~l~~~l~~~  143 (159)
T PF05380_consen   81 ELHVFCDASES--AYGAVVYLRSYSDGSVQVRLLFAKSRVAPLKTVTIPRLELLAALLGVRLANT  143 (159)
T ss_pred             eeeEeeccccc--ceeeEeEeeeccCCceeeeeeeecccccCCCCCcHHHHHHHHHHHHHHHHHH
Confidence            58899999954  455555432   1 1 1     11112 1 3459999999999999998853

>PF00336 DNA_pol_viral_C: DNA polymerase (viral) C-terminal domain; InterPro: IPR001462 This domain is at the C terminus of hepatitis B-type viruses P proteins and represents a functional domain that controls the RNase H activities of the protein

Probab=83.14  E-value=1.6  Score=36.87  Aligned_cols=89  Identities=21%  Similarity=0.259  Sum_probs=52.3

Q ss_pred             cEEEEEcCCCCCCCeeEEEEECCeEEEEecCCCCchHHHHHHHHHHHHHHHHcCCCceEEEEeCCHHHHHHHhccccCCc
Q psy8412          13 HTICFTDGSKTPDSTSCAFSIGDVVHSTLLNPVNSIFSAELMAIFLCLEAILESPDHHFLIVSDSKSSLTALFNIRFTNP   92 (271)
Q Consensus        13 ~~~iytDGS~~~~~~G~a~~~~~~~~~~~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~v~I~tDS~~al~~l~~~~~~~~   92 (271)
                      --.||+|+.-.    |+|+...+....+.....-.+..|||.|...|.-+.    ..++ |.|||..|+   .+....-|
T Consensus        94 lc~VfaDATpT----gwgi~i~~~~~~~Tfs~~l~IhtaELlaaClAr~~~----~~r~-l~tDnt~Vl---srkyts~P  161 (245)
T PF00336_consen   94 LCQVFADATPT----GWGISITGQRMRGTFSKPLPIHTAELLAACLARLMS----GARC-LGTDNTVVL---SRKYTSFP  161 (245)
T ss_pred             CCceeccCCCC----cceeeecCceeeeeecccccchHHHHHHHHHHHhcc----CCcE-EeecCcEEE---ecccccCc
Confidence            46788888753    444444433333333334568999999998887665    3344 999998654   33334445


Q ss_pred             cHHHHHHHHHHHHhCCCceEEEEecC
Q psy8412          93 LISKVYSTWSFLKLNNKNVSFMWCPS  118 (271)
Q Consensus        93 ~~~~~~~~~~~l~~~~~~v~~~WVpg  118 (271)
                      |.......+  +   -..+.|..||+
T Consensus       162 W~lac~A~w--i---Lrgts~~yVPS  182 (245)
T PF00336_consen  162 WLLACAANW--I---LRGTSFYYVPS  182 (245)
T ss_pred             HHHHHHHHH--h---hcCceEEEecc
Confidence            533322221  2   23467888996

The domain is always associated with IPR000201 from INTERPRO and .; GO: 0004523 ribonuclease H activity

---

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	271
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	1e-09
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	2e-09
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	1e-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 = 54.7 bits (132), Expect = 1e-09
 Identities = 23/131 (17%), Positives = 39/131 (29%), Gaps = 12/131 (9%)

Query: 17  FTDGS--KTPDSTSCAFSIGDVVHSTLL-------NPVNSIFSAELMAIFLCLEAILESP 67
           +TDGS      + + AF     VH                  + E+ A    ++   +  
Sbjct: 10  YTDGSYVNGQYAWAYAFVKDGKVHYEDADVGKNPAAATMRNVAGEIAAALYAVKKASQLG 69

Query: 68  DHHFLIVSDSKSSLTALFNIRFTNPLISKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNEI 127
                I+ D                  ++ Y     +       SF    +H G   N+ 
Sbjct: 70  -VKIRILHDYAGIAFWATGEWKAKNEFTQAY--AKLMNQYRGIYSFEKVKAHSGNEFNDY 126

Query: 128 VDEAARNAASI 138
           VD  A++A  I
Sbjct: 127 VDMKAKSALGI 137

>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 = 54.5 bits (131), Expect = 2e-09
 Identities = 33/141 (23%), Positives = 56/141 (39%), Gaps = 23/141 (16%)

Query: 11  ANHTICFTDGS--KTPDSTSCAFSIGD---VVHSTLLNPVNSIFSAELMAIFLCLEAILE 65
           A++T  +TDGS            ++     V+ +  L    S   AEL+A+    +A+  
Sbjct: 22  ADYTW-YTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIAL---TQALKM 77

Query: 66  SPDHHFLIVSDSKSSLTALFNIRFTNPLISKVYSTWSFLKL-----NNKNVSFMWCPSHC 120
           +      + +DS+      F     +    ++ +    L L       K +S + CP H 
Sbjct: 78  AEGKKLNVYTDSRY----AFATAHVHSEGREIKNKNEILALLKALFLPKRLSIIHCPGHQ 133

Query: 121 G-----IRGNEIVDEAARNAA 136
                  RGN + D+AAR AA
Sbjct: 134 KGNSAEARGNRMADQAAREAA 154

>2qkb_A Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hybrid; 2.40A {Homo sapiens} PDB: 2qk9_A 2qkk_A* Length = 154

 Score = 40.6 bits (96), Expect = 1e-04
 Identities = 23/110 (20%), Positives = 33/110 (30%), Gaps = 37/110 (33%)

Query: 51  AELMAIFLCLEAILESPDHHFLIVSDSKSSLTALFNIRFTNPLISKVYSTWSFLKLNN-- 108
           AE+ A    +E       +  ++ ++S           FT   I+     W   K N   
Sbjct: 53  AEIHAACKAIEQAKTQNINKLVLYTNSM----------FTINGITNWVQGW---KKNGWK 99

Query: 109 -------KN---------------VSFMWCPSHCGIRGNEIVDEAARNAA 136
                   N               + +M  P H G  GNE  D  AR  A
Sbjct: 100 TSAGKEVINKEDFVALERLTQGMDIQWMHVPGHSGFIGNEEADRLAREGA 149

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	271
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.93
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.92
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.92
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	99.91
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	99.9
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	99.9
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.9
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.89
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	99.87
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	99.86
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	99.85
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	99.84
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	99.83
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	99.82
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	99.44
4htu_A	134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	99.21
1rw3_A	455	POL polyprotein; RNA and DNA dependent DNA polymer	82.6

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

Probab=99.93  E-value=8e-26  Score=183.24  Aligned_cols=130  Identities=18%  Similarity=0.243  Sum_probs=100.8

Q ss_pred             ccCCcEEEEEcCCCCCCC-----eeEEEEECC---eEEEEecCCCCchHHHHHHHHHHHHHHHHcCCCceEEEEeCCHHH
Q psy8412           9 KYANHTICFTDGSKTPDS-----TSCAFSIGD---VVHSTLLNPVNSIFSAELMAIFLCLEAILESPDHHFLIVSDSKSS   80 (271)
Q Consensus         9 ~~~~~~~iytDGS~~~~~-----~G~a~~~~~---~~~~~~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~v~I~tDS~~a   80 (271)
                      .+++.++||||||+..++     +|+|++..+   ......+++..|++.||+.|++.||+.+...+..+|.|+|||++|
T Consensus         3 ~~~~~~~iytDGs~~~n~~~~~~aG~Gvv~~~~~~~~~~~~l~~~~tn~~aEl~A~~~aL~~~~~~~~~~v~i~tDS~~v   82 (154)
T 2qkb_A            3 HMGDFVVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQAKTQNINKLVLYTNSMFT   82 (154)
T ss_dssp             EETTEEEEEEEEEEETTTSSSCEEEEEEECSTTCTTCEEEECCSSCCHHHHHHHHHHHHHHHHHHTTCCEEEEEESCHHH
T ss_pred             CCCCeEEEEEccCcCCCCCCCCcEEEEEEEECCCceeEEeecCCCCchHHHHHHHHHHHHHHHHhCCCceEEEEECcHHH
Confidence            456789999999987643     688888643   123455666789999999999999999988778999999999999


Q ss_pred             HHHHhccc--------c-CCc--c-HHHHHHHHHHHHhCCCceEEEEecCCCCCccchHHHHHHHHhhcCC
Q psy8412          81 LTALFNIR--------F-TNP--L-ISKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNEIVDEAARNAASID  139 (271)
Q Consensus        81 l~~l~~~~--------~-~~~--~-~~~~~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~~  139 (271)
                      ++.|+++.        . ..+  . ...++..+..+.. +..|.|.|||||+|++||+.||+|||+|+..+
T Consensus        83 i~~i~~~~~~w~~~~w~~~~~~~~~n~~l~~~i~~l~~-~~~v~~~~V~~H~g~~~N~~AD~LA~~a~~~~  152 (154)
T 2qkb_A           83 INGITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQ-GMDIQWMHVPGHSGFIGNEEADRLAREGAKQS  152 (154)
T ss_dssp             HHHHHTHHHHHHTTTSBCTTSSBCTTHHHHHHHHHHHT-TCEEEEEECCTTSSCHHHHHHHHHHHHHHTCC
T ss_pred             HhhhhhhHHHHHhccccccCCCccccHHHHHHHHHHHc-CCceEEEEccCCCCCHhHHHHHHHHHHHHHhc
Confidence            99998742        1 111  1 1334444444433 46799999999999999999999999999764

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

Probab=99.92  E-value=4.1e-25  Score=178.34  Aligned_cols=127  Identities=20%  Similarity=0.258  Sum_probs=95.7

Q ss_pred             hhccCCcEEEEEcCCCCCC--CeeEEEEECC-eEEEEecCCCCchHHHHHHHHHHHHHHHHcCCCceEEEEeCCHHHHHH
Q psy8412           7 NNKYANHTICFTDGSKTPD--STSCAFSIGD-VVHSTLLNPVNSIFSAELMAIFLCLEAILESPDHHFLIVSDSKSSLTA   83 (271)
Q Consensus         7 ~~~~~~~~~iytDGS~~~~--~~G~a~~~~~-~~~~~~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~v~I~tDS~~al~~   83 (271)
                      .+++++.++||||||+..+  ..|+|++..+ ......+ ..+|++.||+.|++.||+.+    ..+|.|+|||++|++.
T Consensus         6 ~~P~~~~~~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~-~~~Tnn~aEl~A~i~AL~~~----~~~v~i~tDS~~v~~~   80 (150)
T 3qio_A            6 KEPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTL-TDTTNQKTELQAIYLALQDS----GLEVNIVTDSQYALGI   80 (150)
T ss_dssp             SSCCTTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEEE-SSCCHHHHHHHHHHHHHHHS----CSEEEEEESCHHHHHH
T ss_pred             cCCCCCCEEEEEccCCCCCCCCeEEEEEEEcCCEEEEeC-CCCCHHHHHHHHHHHHHHhC----CCcEEEEeCcHHHHHH
Confidence            4567788999999998764  3678877543 2223333 57899999999999999985    4899999999999999


Q ss_pred             Hhcccc---CCcc---------HHHHHHHHHHHHhCCCceEEEEecCCCCCccchHHHHHHHHhhcC
Q psy8412          84 LFNIRF---TNPL---------ISKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNEIVDEAARNAASI  138 (271)
Q Consensus        84 l~~~~~---~~~~---------~~~~~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~  138 (271)
                      |+++..   ..++         ...++..+..+......|.|.|||||+|++|||.||+||++|++.
T Consensus        81 i~~w~~~W~~~gw~~~~g~~v~n~~l~~~l~~~l~~~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~  147 (150)
T 3qio_A           81 ITQWIHNWKKRGWKTADKKPVKNVDLVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRK  147 (150)
T ss_dssp             HHHHHHHHCC------------CHHHHHHHHHHHTTCSEEEEEECCTTSCCHHHHHHHHHHHTTTSC
T ss_pred             HHHHHHHHhhcCcCcCcCcccccHHHHHHHHHHHhhcCceEEEEccCcCCChhHHHHHHHHHHHHHH
Confidence            987621   1111         122333333333568899999999999999999999999999875

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

Probab=99.92  E-value=7.3e-25  Score=175.92  Aligned_cols=125  Identities=23%  Similarity=0.198  Sum_probs=91.6

Q ss_pred             CCcEEEEEcCCCCCCC--eeEEEEE--CCeEE--EEecCCCCchHHHHHHHHHHHHHHHHcCCCceEEEEeCCHHHHHHH
Q psy8412          11 ANHTICFTDGSKTPDS--TSCAFSI--GDVVH--STLLNPVNSIFSAELMAIFLCLEAILESPDHHFLIVSDSKSSLTAL   84 (271)
Q Consensus        11 ~~~~~iytDGS~~~~~--~G~a~~~--~~~~~--~~~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~v~I~tDS~~al~~l   84 (271)
                      .+.++||||||+..++  .|+|++.  .+...  ...+ +.+|++.||+.|++.||+.+.+  ..+|.|+|||++|++.|
T Consensus         2 ~~~i~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~~~~-~~~Tnn~aEl~A~~~AL~~~~~--~~~v~I~tDS~~vi~~i   78 (146)
T 3h08_A            2 EKTITIYTDGAASGNPGKGGWGALLMYGSSRKEISGYD-PATTNNRMELMAAIKGLEALKE--PARVQLYSDSAYLVNAM   78 (146)
T ss_dssp             CCEEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCSS--CCEEEEEESCHHHHHHH
T ss_pred             CceEEEEEecCCCCCCCceEEEEEEEECCeeEEeecCC-CCCcHHHHHHHHHHHHHHhcCc--cCcEEEEeChHHHHHHH
Confidence            4579999999988753  6888764  33222  2222 3688999999999999999976  68999999999999999


Q ss_pred             hc-ccc---------CC--cc-HHHHHHHHHHHHhCCCceEEEEecCCCCCccchHHHHHHHHhhcCC
Q psy8412          85 FN-IRF---------TN--PL-ISKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNEIVDEAARNAASID  139 (271)
Q Consensus        85 ~~-~~~---------~~--~~-~~~~~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~~  139 (271)
                      ++ +..         ..  +. ...++..+..+.. ...|.|.|||||+|+++||.||+|||+|+...
T Consensus        79 ~~~w~~~W~~~~w~~~~~~~v~n~~l~~~~~~~~~-~~~v~~~~V~gH~g~~~N~~AD~LA~~a~~~~  145 (146)
T 3h08_A           79 NEGWLKRWVKNGWKTAAKKPVENIDLWQEILKLTT-LHRVTFHKVKGHSDNPYNSRADELARLAIKEN  145 (146)
T ss_dssp             HSSHHHHHHHTTCC----CCCTTHHHHHHHHHHHH-HSEEEEEECCC-CCSHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHCCCccCCCCCcCCHHHHHHHHHHHh-hCceEEEEcCCcCCcHhHHHHHHHHHHHHHhC
Confidence            88 210         11  11 1334444333333 35799999999999999999999999998753

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

Probab=99.91  E-value=2.9e-25  Score=178.66  Aligned_cols=127  Identities=17%  Similarity=0.090  Sum_probs=95.9

Q ss_pred             cCCcEEEEEcCCCCCCCeeEEEEE--CCeEE--EE-ec--CC--CCchHHHHHHHHHHHHHHHHcCCCceEEEEeCCHHH
Q psy8412          10 YANHTICFTDGSKTPDSTSCAFSI--GDVVH--ST-LL--NP--VNSIFSAELMAIFLCLEAILESPDHHFLIVSDSKSS   80 (271)
Q Consensus        10 ~~~~~~iytDGS~~~~~~G~a~~~--~~~~~--~~-~l--~~--~~s~~~AEl~Ai~~AL~~a~~~~~~~v~I~tDS~~a   80 (271)
                      +++.+.||||||+.++.+|+|++.  .+...  .. ..  +.  ..||+.||+.|++.||+.+.+.+. +|.|+|||+.+
T Consensus         3 ~~~~i~iytDGs~~~g~~G~G~vi~~~g~~~~~~~~~~~~~~~~~~tNn~aEl~A~~~AL~~a~~~~~-~v~I~tDS~~i   81 (147)
T 2kq2_A            3 DRTEYDVYTDGSYVNGQYAWAYAFVKDGKVHYEDADVGKNPAAATMRNVAGEIAAALYAVKKASQLGV-KIRILHDYAGI   81 (147)
T ss_dssp             TTSCCEEECCCCCBTTBCEEEEEEEETTEEEEEEEEECCCGGGGGTCTTHHHHHHHHHHHHHHHHHTC-CCCBSSCCSTH
T ss_pred             CCCeEEEEECCCCCCCCcEEEEEEEECCEEEEEEeccccccccccccHHHHHHHHHHHHHHHHHHCCC-eEEEEECcHHH
Confidence            456799999999998768888764  34322  22 22  22  368999999999999999877666 99999999998


Q ss_pred             HHHHhccccCCc-cHHHHHHHHHHHHhCCCceEEEEecCCCCCccchHHHHHHHHhhcCCC
Q psy8412          81 LTALFNIRFTNP-LISKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNEIVDEAARNAASIDP  140 (271)
Q Consensus        81 l~~l~~~~~~~~-~~~~~~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~~~  140 (271)
                      .+.+.+.+..+. ....+...+..+..   .|.|.|||||+|++|||.||+|||+|+....
T Consensus        82 ~~w~~~~w~~~~~~~~~~~~l~~~l~~---~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~~~  139 (147)
T 2kq2_A           82 AFWATGEWKAKNEFTQAYAKLMNQYRG---IYSFEKVKAHSGNEFNDYVDMKAKSALGIRD  139 (147)
T ss_dssp             HHHTTSSSSCCHHHHHHHHCGGGGGST---TCCBCCCCCCCCCHHHHHHHHHHHHHHTCCC
T ss_pred             HHHHhCCCccCCcchHHHHHHHHHhcC---CeeEEEecCcCCCcchHHHHHHHHHHHhccc
Confidence            888877655432 22333333222322   8999999999999999999999999998764

>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=9.9e-24  Score=171.12  Aligned_cols=126  Identities=21%  Similarity=0.243  Sum_probs=94.0

Q ss_pred             CcEEEEEcCCCCCC--CeeEEEEE--CCeEE--EEecCCCCchHHHHHHHHHHHHHHHHcCCCceEEEEeCCHHHHHHHh
Q psy8412          12 NHTICFTDGSKTPD--STSCAFSI--GDVVH--STLLNPVNSIFSAELMAIFLCLEAILESPDHHFLIVSDSKSSLTALF   85 (271)
Q Consensus        12 ~~~~iytDGS~~~~--~~G~a~~~--~~~~~--~~~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~v~I~tDS~~al~~l~   85 (271)
                      ..+.||||||+..+  .+|+|++.  .+...  ...+ +..|++.||+.|++.||+.+..  ..+|.|+|||++|++.|+
T Consensus         3 ~~~~iytDGs~~~n~~~~G~G~v~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~~~~--~~~v~I~tDS~~vi~~i~   79 (155)
T 1jl1_A            3 KQVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGY-TRTTNNRMELMAAIVALEALKE--HAEVILSTDSQYVRQGIT   79 (155)
T ss_dssp             CCEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCCS--CCEEEEEECCHHHHHHHH
T ss_pred             ceEEEEEccccCCCCCceEEEEEEEECCeEEEEecCC-CCCcHHHHHHHHHHHHHHHhCc--CCcEEEEeCHHHHHHHHH
Confidence            46899999999864  36888764  33221  2223 3578999999999999999976  489999999999999999


Q ss_pred             ccc---------cCC--ccH-HHHHHHHHHHHhCCCceEEEEecCCCCCccchHHHHHHHHhhcCCCC
Q psy8412          86 NIR---------FTN--PLI-SKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNEIVDEAARNAASIDPY  141 (271)
Q Consensus        86 ~~~---------~~~--~~~-~~~~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~~~~  141 (271)
                      ++.         ...  +.. ..++..+..+.. ...|.|.|||||+|++||+.||+|||+|+..+..
T Consensus        80 ~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~-~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~~~~  146 (155)
T 1jl1_A           80 QWIHNWKKRGWKTADKKPVKNVDLWQRLDAALG-QHQIKWEWVKGHAGHPENERADELARAAAMNPTL  146 (155)
T ss_dssp             TTHHHHHHTTTBCTTSCBCTTHHHHHHHHHHTT-TCEEEEEECCSSTTCHHHHHHHHHHHHHHHSCCB
T ss_pred             HHHHHHhhcccccccCCccCCHHHHHHHHHHHc-cCceEEEEcCCCCCCHHHHHHHHHHHHHHhccch
Confidence            732         111  111 233443333433 4689999999999999999999999999987643

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

Probab=99.90  E-value=2e-23  Score=170.83  Aligned_cols=124  Identities=23%  Similarity=0.245  Sum_probs=91.1

Q ss_pred             cEEEEEcCCCCC--CCeeEEEE--ECCe-EEEEecCCCCchHHHHHHHHHHHHHHHHcCCCceEEEEeCCHHHHHHHhcc
Q psy8412          13 HTICFTDGSKTP--DSTSCAFS--IGDV-VHSTLLNPVNSIFSAELMAIFLCLEAILESPDHHFLIVSDSKSSLTALFNI   87 (271)
Q Consensus        13 ~~~iytDGS~~~--~~~G~a~~--~~~~-~~~~~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~v~I~tDS~~al~~l~~~   87 (271)
                      .+.||||||+..  +..|+|++  ..+. .....++..+|++.||+.|++.||+.+ .  ..+|.|+|||++|++.+-..
T Consensus        23 ~i~iytDGs~~~npG~~g~G~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~-~--~~~v~I~tDS~~vi~~iw~~   99 (165)
T 3p1g_A           23 DYTWYTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMA-E--GKKLNVYTDSRYAFATAHVH   99 (165)
T ss_dssp             SEEEEEEEEEEEETTEEEEEEEEECSSCEEEEEEECTTCCHHHHHHHHHHHHHHHT-B--TSEEEEEECCHHHHHHHHSC
T ss_pred             CEEEEEEcccCCCCCceEEEEEEEECCEEEEEecCCCCCcHHHHHHHHHHHHHHHc-c--CceEEEEEchHHHHhhhhcc
Confidence            499999999974  44677754  3332 223345678899999999999999998 3  68999999999999998321


Q ss_pred             ccCCcc-HHHHHHHHHHHHhCCCceEEEEecCCCC-----CccchHHHHHHHHhhcCC
Q psy8412          88 RFTNPL-ISKVYSTWSFLKLNNKNVSFMWCPSHCG-----IRGNEIVDEAARNAASID  139 (271)
Q Consensus        88 ~~~~~~-~~~~~~~~~~l~~~~~~v~~~WVpgH~g-----i~gNe~AD~lAk~a~~~~  139 (271)
                      ....+. -..++..+......+..|.|.|||||+|     ++|||.||+|||+|+...
T Consensus       100 ~~g~~v~n~dl~~~l~~~l~~~~~v~~~wVkgH~g~~~~~~~gNe~AD~LA~~aa~~~  157 (165)
T 3p1g_A          100 SEGREIKNKNEILALLKALFLPKRLSIIHCPGHQKGNSAEARGNRMADQAAREAAMKA  157 (165)
T ss_dssp             CCSCCCSSHHHHHHHHHHTTSBSEEEEEECCSSCCSCSHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCcccCHHHHHHHHHHHhcCCceEEEEecCCCCCCcCcchHHHHHHHHHHHHHhcC
Confidence            112222 1232322222223678999999999999     999999999999999765

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

Probab=99.90  E-value=8.5e-24  Score=172.04  Aligned_cols=123  Identities=23%  Similarity=0.306  Sum_probs=92.2

Q ss_pred             CcEEEEEcCCCCCC--CeeEEEEE--CCeEE--EEecCCCCchHHHHHHHHHHHHHHHHcCCCceEEEEeCCHHHHHHHh
Q psy8412          12 NHTICFTDGSKTPD--STSCAFSI--GDVVH--STLLNPVNSIFSAELMAIFLCLEAILESPDHHFLIVSDSKSSLTALF   85 (271)
Q Consensus        12 ~~~~iytDGS~~~~--~~G~a~~~--~~~~~--~~~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~v~I~tDS~~al~~l~   85 (271)
                      ..++||||||+..+  .+|+|++.  .+...  ...+ +..|++.||+.|++.||+.+..  ..+|.|+|||++|++.|.
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-SLTTNNRMELLAPIVALEALKE--PCKIILTSDSQYMRQGIM   81 (158)
T ss_dssp             CEEEEEEEEEESSSSEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCSS--CCEEEEEECCHHHHHHHH
T ss_pred             CeEEEEEcccccCCCCcEEEEEEEEECCEEEEEecCc-CCCccHHHHHHHHHHHHHHhcc--CCeEEEEeCHHHHHHHHH
Confidence            46999999999854  36888764  33321  2223 3578999999999999999865  389999999999999998


Q ss_pred             cc--------cc-CC--cc-HHHHHHHHHHHHhCCCceEEEEecCCCCCccchHHHHHHHHhhcC
Q psy8412          86 NI--------RF-TN--PL-ISKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNEIVDEAARNAASI  138 (271)
Q Consensus        86 ~~--------~~-~~--~~-~~~~~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~  138 (271)
                      ++        +. ..  +. ...++..+..+.. ...|.|.|||||+|++||+.||+|||+|+..
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            82        21 11  11 1233333334443 4699999999999999999999999999987

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

Probab=99.89  E-value=9.5e-24  Score=173.14  Aligned_cols=127  Identities=20%  Similarity=0.160  Sum_probs=94.1

Q ss_pred             CcEEEEEcCCCCCC--CeeEEEEEC--CeEEEEe-cCCCCchHHHHHHHHHHHHHHHHcCCCceEEEEeCCHHHHHHHhc
Q psy8412          12 NHTICFTDGSKTPD--STSCAFSIG--DVVHSTL-LNPVNSIFSAELMAIFLCLEAILESPDHHFLIVSDSKSSLTALFN   86 (271)
Q Consensus        12 ~~~~iytDGS~~~~--~~G~a~~~~--~~~~~~~-l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~v~I~tDS~~al~~l~~   86 (271)
                      ..++||||||+..+  ..|+|++..  +....+. .....|++.||+.|++.||+.+..  ..+|.|+|||++|++.|.+
T Consensus         7 ~~i~iytDGs~~~n~g~~G~G~v~~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~~~--~~~v~I~tDS~~vi~~i~~   84 (166)
T 1ril_A            7 KRVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKE--PCEVDLYTDSHYLKKAFTE   84 (166)
T ss_dssp             CCCCEEEEEEESSTTEEEEEEEEECBTTBCCEECCEEEEECHHHHHHHHHHHHHHSCCS--CCEEEEECCCHHHHHHHHS
T ss_pred             ccEEEEECccccCCCCCEEEEEEEEECCEEEEEecCCCCCcHHHHHHHHHHHHHHHhcc--CCeEEEEeChHHHHHHHhh
Confidence            57899999999864  378887753  2211111 113578999999999999998865  3599999999999999998


Q ss_pred             -c---------ccCCc--c-HHHHHHHHHHHHhCCCceEEEEecCCCCCccchHHHHHHHHhhcCCCC
Q psy8412          87 -I---------RFTNP--L-ISKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNEIVDEAARNAASIDPY  141 (271)
Q Consensus        87 -~---------~~~~~--~-~~~~~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~~~~  141 (271)
                       +         ...++  . ...++..+..+.. ...|.|.|||||+|+++|+.||+|||+|+.....
T Consensus        85 ~w~~~W~~~~w~~~~g~~v~n~~l~~~i~~l~~-~~~v~~~wV~gH~g~~~Ne~AD~LAk~a~~~~~~  151 (166)
T 1ril_A           85 GWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMA-PHRVRFHFVKGHTGHPENERVDREARRQAQSQAK  151 (166)
T ss_dssp             SHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHT-TSEEECCCCCGGGSCTHHHHHHHHHHHHHTSSCC
T ss_pred             hHHHHHHhcccccccCCccCcHHHHHHHHHHHh-cCeEEEEEeeCCCCchhHHHHHHHHHHHHHHhhc
Confidence             2         22221  1 1234444444443 3699999999999999999999999999988753

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

Probab=99.87  E-value=7.1e-22  Score=161.50  Aligned_cols=126  Identities=16%  Similarity=0.169  Sum_probs=91.3

Q ss_pred             CcEEEEEcCCCCCC--C-----eeEEEEEC--C----eEEEEec-CCCCchHHHHHHHHHHHHHHHHcCCCceEEEEeCC
Q psy8412          12 NHTICFTDGSKTPD--S-----TSCAFSIG--D----VVHSTLL-NPVNSIFSAELMAIFLCLEAILESPDHHFLIVSDS   77 (271)
Q Consensus        12 ~~~~iytDGS~~~~--~-----~G~a~~~~--~----~~~~~~l-~~~~s~~~AEl~Ai~~AL~~a~~~~~~~v~I~tDS   77 (271)
                      ..++||||||+..+  +     .|+|++..  +    ....... .+..+++.||+.|+..||+.++..+ .+|.|+|||
T Consensus         6 ~evviYTDGsc~gNpgp~~~~~aG~Gv~~~~~~~~~~~~~~~~~~tnn~te~~Aei~Al~~al~~al~~~-~~v~I~TDS   84 (165)
T 2lsn_A            6 YEGVFYTDGSAIKSPDPTKSNNAGMGIVHATYKPEYQVLNQWSIPLGNHTAQMAEIAAVEFACKKALKIP-GPVLVITDS   84 (165)
T ss_dssp             CSEEEEEEEEEEECSSCTTCEEEEEEEEEECCSSSCCEEEEEEEEESSCCHHHHHHHHHHHHHHHHHHSS-SCEEEEESC
T ss_pred             ceEEEEEcCCCCCCCCCCCCCcEEEEEEEEECCCccEEeccccCCchHHHHHHHHHHHHHHHHHHHhcCC-CeEEEEeCh
Confidence            45899999998753  2     68888742  1    2233333 3567899999999999999887644 579999999


Q ss_pred             HHHHHHHhcccc---------CC--cc-HHHHHHHHHHHHhCCCceEEEEecCCCCC------ccchHHHHHHHHhhcC
Q psy8412          78 KSSLTALFNIRF---------TN--PL-ISKVYSTWSFLKLNNKNVSFMWCPSHCGI------RGNEIVDEAARNAASI  138 (271)
Q Consensus        78 ~~al~~l~~~~~---------~~--~~-~~~~~~~~~~l~~~~~~v~~~WVpgH~gi------~gNe~AD~lAk~a~~~  138 (271)
                      ++|++.|+.+..         ..  |. -.+++..+..+......|.|.|||||+|.      +|||+||+||++|+..
T Consensus        85 ~Yvi~~it~w~~~Wk~ngw~~~~~~pVkN~dL~~~l~~~~~~~~~v~~~~VkgH~g~~~~~~~~gNe~AD~LA~~gA~~  163 (165)
T 2lsn_A           85 FYVAESANKELPYWKSNGFVNNKKKPLKHISKWKSIAECLSMKPDITIQHEKGHQPTNTSIHTEGNALADKLATQGSYV  163 (165)
T ss_dssp             HHHHHHHHTHHHHHHHTTSCSCSSSCCSSHHHHHHHHHHHHHCTTCEEEECCSSSCSSSCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhhhhhhhhhheeccccccCCCcccCHHHHHHHHHHHhCCCCEEEEEEeCCCCccCCCCChHHHHHHHHHHHhhhh
Confidence            999999986421         11  11 13333444444445678999999999994      5899999999999853

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

Probab=99.86  E-value=3.4e-21  Score=152.47  Aligned_cols=122  Identities=19%  Similarity=0.229  Sum_probs=94.0

Q ss_pred             CcEEEEEcCCCCCC--CeeEEEEEC--C--eE-E-EEecCCCCchHHHHHHHHHHHHHHHHcCCCc----eEEEEeCCHH
Q psy8412          12 NHTICFTDGSKTPD--STSCAFSIG--D--VV-H-STLLNPVNSIFSAELMAIFLCLEAILESPDH----HFLIVSDSKS   79 (271)
Q Consensus        12 ~~~~iytDGS~~~~--~~G~a~~~~--~--~~-~-~~~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~----~v~I~tDS~~   79 (271)
                      ..++||||||+..+  .+|+|++..  +  .. . ...+ +.+|++.||+.|++.||+.+...+..    +|.|+|||++
T Consensus         2 ~~~~iy~DGs~~~n~g~~G~G~v~~~~~g~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~a~~~~~~~~~~~v~i~tDS~~   80 (140)
T 3u3g_D            2 NKIIIYTDGGARGNPGPAGIGVVITDEKGNTLHESSAYI-GETTNNVAEYEALIRALEDLQMFGDKLVDMEVEVRMDSEL   80 (140)
T ss_dssp             CEEEEEEEEEESSTTEEEEEEEEEECTTSCEEEEEEEEE-EEECHHHHHHHHHHHHHHHHGGGGGGGTTCEEEEEESCHH
T ss_pred             ceEEEEEecCCCCCCCCcEEEEEEEeCCCCEEEEEEeeC-CCCchHHHHHHHHHHHHHHHHHcCCCCCCceEEEEeChHH
Confidence            46899999999764  478887742  1  22 1 2222 35799999999999999999887777    9999999999


Q ss_pred             HHHHHhcccc-CCccHHHHHHHHHHH-HhCCCceEEEEecCCCCCccchHHHHHHHHhhcC
Q psy8412          80 SLTALFNIRF-TNPLISKVYSTWSFL-KLNNKNVSFMWCPSHCGIRGNEIVDEAARNAASI  138 (271)
Q Consensus        80 al~~l~~~~~-~~~~~~~~~~~~~~l-~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~  138 (271)
                      +++.+++++. .++....++..+..+ ......|.|.|||    .++|+.||+|||+|++.
T Consensus        81 vi~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~~v~~~~V~----~~~N~~AD~LA~~a~~~  137 (140)
T 3u3g_D           81 IVRQMQGVYKVKEPTLKEKFAKIAHIKMERVPNLVFVHIP----REKNARADELVNEAIDK  137 (140)
T ss_dssp             HHHHHTTSSCCCCGGGHHHHHHHHHHHHHHCTTCEEEECC----GGGGHHHHHHHHHHHHH
T ss_pred             HHHHhCCCcccCCHHHHHHHHHHHHHhhcCCCcEEEEEcC----chhhHHHHHHHHHHHHh
Confidence            9999998764 333344455555555 5666799999999    48999999999999864

>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=99.85  E-value=3.3e-21  Score=153.08  Aligned_cols=122  Identities=16%  Similarity=0.223  Sum_probs=94.4

Q ss_pred             cEEEEEcCCCCCC--CeeEEEEE--CC---eE--EEEecCCCCchHHHHHHHHHHHHHHHHcCCCceEEEEeCCHHHHHH
Q psy8412          13 HTICFTDGSKTPD--STSCAFSI--GD---VV--HSTLLNPVNSIFSAELMAIFLCLEAILESPDHHFLIVSDSKSSLTA   83 (271)
Q Consensus        13 ~~~iytDGS~~~~--~~G~a~~~--~~---~~--~~~~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~v~I~tDS~~al~~   83 (271)
                      .++||||||+..+  .+|+|++.  .+   ..  ....+ +..|++.||+.|++.||+.+...+..+|.|+|||+++++.
T Consensus         3 ~~~iy~DGs~~~~~g~~g~G~v~~~~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~a~~~~~~~v~i~tDS~~vv~~   81 (141)
T 3hst_B            3 KVVIEADGGSRGNPGPAGYGAVVWTADHSTVLAESKQAI-GRATNNVAEYRGLIAGLDDAVKLGATEAAVLMDSKLVVEQ   81 (141)
T ss_dssp             EEEEEEEEEESSSSEEEEEEEEEEETTSCSEEEEEEEEE-EEECHHHHHHHHHHHHHHHHHHHTCSEEEEEESCHHHHHH
T ss_pred             EEEEEEecCCCCCCCCcEEEEEEEeCCCCcEEEeeeccC-CCCchHHHHHHHHHHHHHHHHHCCCceEEEEeChHHHHHH
Confidence            5899999998864  47888764  22   12  12223 4789999999999999999998888999999999999999


Q ss_pred             Hhcccc-CCccHHHHHHHHHHHHhCCCceEEEEecCCCCCccchHHHHHHHHhhcCC
Q psy8412          84 LFNIRF-TNPLISKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNEIVDEAARNAASID  139 (271)
Q Consensus        84 l~~~~~-~~~~~~~~~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~~  139 (271)
                      +++.+. .++....++..+..+...+..|.|.|||+    ++|+.||+|||+|+...
T Consensus        82 i~~~~~~~~~~l~~~~~~i~~l~~~~~~v~~~~V~~----~~N~~AD~LA~~a~~~~  134 (141)
T 3hst_B           82 MSGRWKVKHPDLLKLYVQAQALASQFRRINYEWVPR----ARNTYADRLANDAMDAA  134 (141)
T ss_dssp             HTTSSCCCSHHHHHHHHHHHHHHTTSSEEEEEECCG----GGCHHHHHHHHHHHHHH
T ss_pred             HhCCcccCCHHHHHHHHHHHHHHhcCCeEEEEEcCC----cccHHHHHHHHHHHHHh
Confidence            998654 33333344444445666779999999994    79999999999998653

>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=99.84  E-value=1.1e-20  Score=182.14  Aligned_cols=122  Identities=20%  Similarity=0.242  Sum_probs=92.8

Q ss_pred             hccCCcEEEEEcCCCCCCC--eeEEEEEC-CeEEEEecCCCCchHHHHHHHHHHHHHHHHcCCCceEEEEeCCHHHHHHH
Q psy8412           8 NKYANHTICFTDGSKTPDS--TSCAFSIG-DVVHSTLLNPVNSIFSAELMAIFLCLEAILESPDHHFLIVSDSKSSLTAL   84 (271)
Q Consensus         8 ~~~~~~~~iytDGS~~~~~--~G~a~~~~-~~~~~~~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~v~I~tDS~~al~~l   84 (271)
                      +..++.+.||||||+..++  .|+|++.. +......+ ..+||+.||+.|++.||+.    ...++.|+|||++|++.+
T Consensus       431 ~p~~~~~~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~-~~~TNn~aEl~A~i~aL~~----~~~~v~I~tDS~~v~~~i  505 (555)
T 1mu2_A          431 DPIPGAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKL-EQTTNQQAELEAFAMALTD----SGPKVNIIVDSQYVMGIV  505 (555)
T ss_dssp             SCCTTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEEE-SSCCHHHHHHHHHHHHHHT----SCSEEEEEESCHHHHHHH
T ss_pred             CCCCCceEEEEcccccCCCCCceEEEEEEeCCEeeccC-CCCCHHHHHHHHHHHHHHc----CCCeEEEEEehHHHHHHH
Confidence            3445679999999988643  67887753 22222333 4689999999999999998    478999999999999999


Q ss_pred             hccccCCccHHHHHHHHHHHHhCCCceEEEEecCCCCCccchHHHHHHHHhh
Q psy8412          85 FNIRFTNPLISKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNEIVDEAARNAA  136 (271)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~  136 (271)
                      +++......  .+...+.++...+..|.|.|||||+|++|||.||+|||+|+
T Consensus       506 ~~~~~~~~~--~l~~~~~~~~~~~~~v~~~wV~~H~g~~~Ne~AD~LA~~a~  555 (555)
T 1mu2_A          506 ASQPTESES--KIVNQIIEEMIKKEAIYVAWVPAHKGIGGNQEVDHLVSQGI  555 (555)
T ss_dssp             HTCCSEESC--HHHHHHHHHHHHCSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             hcccccccH--HHHHHHHHHhccCCcEEEEEEECCCCChhHHHHHHHHHhhC
Confidence            987643221  23333333333467899999999999999999999999884

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

Probab=99.83  E-value=4.1e-20  Score=148.48  Aligned_cols=121  Identities=19%  Similarity=0.190  Sum_probs=91.0

Q ss_pred             EEEEEcCCCC-C--CCeeE-EEEE--CC-eEEEE--ecC---CCCchHHHHHHHHHHHHHHHHcCCCceEEEEeCCHHHH
Q psy8412          14 TICFTDGSKT-P--DSTSC-AFSI--GD-VVHST--LLN---PVNSIFSAELMAIFLCLEAILESPDHHFLIVSDSKSSL   81 (271)
Q Consensus        14 ~~iytDGS~~-~--~~~G~-a~~~--~~-~~~~~--~l~---~~~s~~~AEl~Ai~~AL~~a~~~~~~~v~I~tDS~~al   81 (271)
                      ++||||||+. .  +++|+ |++.  .+ .....  .++   ...|++.||+.|++.||+.+...+..+|.|+|||++++
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            6899999987 2  45775 7653  22 22222  222   37899999999999999999988889999999999999


Q ss_pred             HHHhccccC-CccHHHHHHHHHHHHhCCCceEEEEecCCCCCccchHHHHHHHHhhcCC
Q psy8412          82 TALFNIRFT-NPLISKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNEIVDEAARNAASID  139 (271)
Q Consensus        82 ~~l~~~~~~-~~~~~~~~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~~  139 (271)
                      +.+++++.. ++....+...+..+.... .|.|.|||+    ++|+.||+|||+|+...
T Consensus        82 ~~i~~~w~~~~~~~~~l~~~i~~l~~~~-~v~~~~V~~----~~N~~AD~LA~~a~~~~  135 (149)
T 2ehg_A           82 KQMNGEYKVKAKRIIPLYEKAIELKKKL-NATLIWVPR----EENKEADRLSRVAYELV  135 (149)
T ss_dssp             HHHTTSSCCCCTTHHHHHHHHHHHHHHH-TCEEEECCG----GGCHHHHHHHHHHHHHH
T ss_pred             HHHhCccccCCHHHHHHHHHHHHHHhcC-CEEEEEcCC----cccHHHHHHHHHHHHhh
Confidence            999998653 333444444444443333 599999998    49999999999998764

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

Probab=99.82  E-value=1.1e-20  Score=182.18  Aligned_cols=121  Identities=21%  Similarity=0.278  Sum_probs=89.3

Q ss_pred             hccCCcEEEEEcCCCCCC--CeeEEEEEC-CeEEEEecCCCCchHHHHHHHHHHHHHHHHcCCCceEEEEeCCHHHHHHH
Q psy8412           8 NKYANHTICFTDGSKTPD--STSCAFSIG-DVVHSTLLNPVNSIFSAELMAIFLCLEAILESPDHHFLIVSDSKSSLTAL   84 (271)
Q Consensus         8 ~~~~~~~~iytDGS~~~~--~~G~a~~~~-~~~~~~~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~v~I~tDS~~al~~l   84 (271)
                      +...+.+.||||||+..+  ..|+|++.. +....... ..+||+.||+.|++.||+.+    ..++.|+|||++|++.+
T Consensus       434 ep~~~~~~iytDGs~~~n~g~~g~g~v~~~~~~~~~~~-~~~TNn~aEl~Ai~~aL~~~----~~~v~I~tDS~~vi~~i  508 (557)
T 2zd1_A          434 EPIVGAETFYVDGAANRETKLGKAGYVTNKGRQKVVPL-TNTTNQKTELQAIYLALQDS----GLEVNIVTDSQYALGII  508 (557)
T ss_dssp             SCCTTSCEEEEEEEECTTTCCEEEEEEETTSCEEEEEE-CSCCHHHHHHHHHHHHHHHS----CSEEEEEECCHHHHHHH
T ss_pred             CCCCCCEEEEEccCCCCCCCceEEEEEEECCcEEEecC-CCCCHHHHHHHHHHHHHHhC----CCcEEEEeChHHHHHHH
Confidence            344567999999998754  367777653 22222333 46899999999999999998    58999999999999999


Q ss_pred             hccccCCccHHHHHHHHHHHHhCCCceEEEEecCCCCCccchHHHHHHHHh
Q psy8412          85 FNIRFTNPLISKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNEIVDEAARNA  135 (271)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a  135 (271)
                      +++...+..  .+...+.+.......|.|.|||||+|++|||.||+|||+|
T Consensus       509 ~~~~~~~~~--~l~~~~~~~l~~~~~v~~~wV~~H~g~~~Ne~AD~LA~~a  557 (557)
T 2zd1_A          509 QAQPDKSES--ELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAG  557 (557)
T ss_dssp             TTCCSEESS--HHHHHHHHHHHHCSEEEEEECCSSSCCTTCCGGGGCC---
T ss_pred             hcCCccCCH--HHHHHHHHHHhcCCCEEEEEcCCCCCChhHHHHHHHHhcC
Confidence            997654221  2333333222234689999999999999999999999986

>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=99.44  E-value=2.9e-14  Score=113.38  Aligned_cols=118  Identities=12%  Similarity=-0.044  Sum_probs=81.7

Q ss_pred             cCCcEEEEEcCCCCCC--CeeEEEEEC--CeEEEEec-CCCCchHHHHHHHHHHHHHHHHcCCCceEEEEeCCHHHHHHH
Q psy8412          10 YANHTICFTDGSKTPD--STSCAFSIG--DVVHSTLL-NPVNSIFSAELMAIFLCLEAILESPDHHFLIVSDSKSSLTAL   84 (271)
Q Consensus        10 ~~~~~~iytDGS~~~~--~~G~a~~~~--~~~~~~~l-~~~~s~~~AEl~Ai~~AL~~a~~~~~~~v~I~tDS~~al~~l   84 (271)
                      .++.+.||||||+..+  .+|+|++..  +....... -..+|++.||+.|++.||+.+.+.+. +|.|+|||++|++.+
T Consensus         8 ~~~~~~iy~DGa~~gNpG~~G~G~vl~~~g~~~~~~~~~~~~TNN~aEl~A~i~aL~~~~~~~~-~v~i~tDS~~vi~w~   86 (142)
T 1zbf_A            8 EIIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERNS-RKPIYSNSQTAIKWV   86 (142)
T ss_dssp             CCCSSSEEEEEEECSSSEEEEEEEEETTTCCEEEECCCEEEECHHHHHHHHHHHHHHHHHHTTC-CCCEEESCHHHHHHH
T ss_pred             CCCeEEEEEeeccCCCCCCeEEEEEEEeCCEEEEEecccCCcCcHHHHHHHHHHHHHHHHhCCC-eEEEEEehHHHHHHH
Confidence            4467899999998754  478888764  22221111 12578999999999999999998766 999999999999999


Q ss_pred             hccccC-C---c-cHHHHHHHHHH----HHhCCCceEEEEecCCCCCccchHHHH
Q psy8412          85 FNIRFT-N---P-LISKVYSTWSF----LKLNNKNVSFMWCPSHCGIRGNEIVDE  130 (271)
Q Consensus        85 ~~~~~~-~---~-~~~~~~~~~~~----l~~~~~~v~~~WVpgH~gi~gNe~AD~  130 (271)
                      ++.... +   + ....++..+..    +..  ..++...|+-|++.-||..||.
T Consensus        87 ~~~~~k~~~~~~v~n~dLw~~l~~~~~w~~~--~~~~~~~~kw~~~~~ge~pad~  139 (142)
T 1zbf_A           87 KDKKAKSTLVRNEETALIWKLVDEAEEWLNT--HTYETPILKWQTDKWGEIKADY  139 (142)
T ss_dssp             HHTCCCCCCCCSTTTHHHHHHHHHHHHHHHH--CCCCCCEEECCHHHHCSCTTCC
T ss_pred             HcCCccCCCCCCcccHHHHHHHHHHHHHHhh--CCCceeEEEeccCccCcCcccc
Confidence            987621 1   1 12233333222    333  3455556777888889988884

>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=99.21  E-value=1.4e-11  Score=96.50  Aligned_cols=75  Identities=13%  Similarity=0.038  Sum_probs=56.6

Q ss_pred             CCcEEEEEcCCCCCC--CeeEEEEE-CC-e-E-EEEecCCCCchHHHHHHHHHHHHHHHHcCCCceEEEEeCCHHHHHHH
Q psy8412          11 ANHTICFTDGSKTPD--STSCAFSI-GD-V-V-HSTLLNPVNSIFSAELMAIFLCLEAILESPDHHFLIVSDSKSSLTAL   84 (271)
Q Consensus        11 ~~~~~iytDGS~~~~--~~G~a~~~-~~-~-~-~~~~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~v~I~tDS~~al~~l   84 (271)
                      +....||||||+..+  ..|+|+|. .+ . . ....+ +.+||+.||++|++.||+.+.+.+.. +.|+|||++|++.|
T Consensus         3 p~~~~iytDGac~GNPGp~G~ggV~~~~g~~~~~~g~~-~~tTNN~aEl~A~i~aL~~l~~~~~~-v~i~tDSqyVi~wi   80 (134)
T 4htu_A            3 IIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPI-PIGTNNMGEFLAIVHGLRYLKERNSR-KPIYSNSQTAIKWV   80 (134)
T ss_dssp             CCSSSEEEEEEEETTTEEEEEEEEETTTCCEEEEEEEE-EEECHHHHHHHHHHHHHHHHHHTTCC-CCEEESCHHHHHHH
T ss_pred             ccceEEEEeeccCCCCCCeEEEEEEEECCEEEEEecCC-CCCchHHHHHHHHHHHHHHHHhCCCC-EEEEcchHHHHHHH
Confidence            456789999998865  36775443 22 1 1 22223 36899999999999999999875544 89999999999999


Q ss_pred             hcc
Q psy8412          85 FNI   87 (271)
Q Consensus        85 ~~~   87 (271)
                      .++
T Consensus        81 ~~~   83 (134)
T 4htu_A           81 KDK   83 (134)
T ss_dssp             HHT
T ss_pred             HcC
Confidence            875

>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=82.60  E-value=0.15  Score=47.14  Aligned_cols=72  Identities=11%  Similarity=-0.106  Sum_probs=46.4

Q ss_pred             CcEEEEEcCCCCCCCeeEEEE-ECC---e--E--EEEec---CCCCchHHHHHHHHHHHHHHHHcC-CCceEEEEeCCHH
Q psy8412          12 NHTICFTDGSKTPDSTSCAFS-IGD---V--V--HSTLL---NPVNSIFSAELMAIFLCLEAILES-PDHHFLIVSDSKS   79 (271)
Q Consensus        12 ~~~~iytDGS~~~~~~G~a~~-~~~---~--~--~~~~l---~~~~s~~~AEl~Ai~~AL~~a~~~-~~~~v~I~tDS~~   79 (271)
                      ..+.+|||+|..  ++|+ ++ +..   .  .  .+..+   ....+++..|+.||..|++..... ....++|+||+. 
T Consensus       345 ~~~~l~~DAS~~--~~ga-vL~q~~~~~~~~i~y~Sk~l~~~e~~ys~~ekEllAi~~a~~~~~~yl~g~~~~v~tDh~-  420 (455)
T 1rw3_A          345 KPFELFVDEKQG--YAKG-VLTQKLGPWRRPVAYLSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLTMGQPLVIKAPHA-  420 (455)
T ss_dssp             CTTSCEEEEEEC--SSSB-EECCBCTTTTCCCCCCCBCSCSSCSSSCCSSHHHHHHHHHHHHHHGGGCSSCEEEECSSC-
T ss_pred             CcEEEEEeccCC--ccee-EEEEecCCcEEEEEEEcccCCccccccchHHHHHHHHHHHHHHHHHHcCCCcEEEEecCh-
Confidence            457899999853  3333 33 211   0  1  12222   235567889999999999887653 467999999996 


Q ss_pred             HHHHHhcc
Q psy8412          80 SLTALFNI   87 (271)
Q Consensus        80 al~~l~~~   87 (271)
                      ++..+.+.
T Consensus       421 ~~~~l~~~  428 (455)
T 1rw3_A          421 VEALVKQP  428 (455)
T ss_dssp             TTTTSSST
T ss_pred             HHHHhCCC
Confidence            55555543

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	271
d1mu2a1	126	c.55.3.1 (A:430-555) HIV RNase H (Domain of revers	1e-06
d1rila_	147	c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermoph	1e-04
d1jl1a_	152	c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli	2e-04

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

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

 Score = 44.9 bits (105), Expect = 1e-06
 Identities = 23/121 (19%), Positives = 41/121 (33%), Gaps = 8/121 (6%)

Query: 17  FTDGS--KTPDSTSCAFSIGDVVHSTLLNPVNSIFSAELMAIFLCLEAILESPDHHFLIV 74
           +TDGS  +        +               +   AEL A  + L            I+
Sbjct: 11  YTDGSCNRQSKEGKAGYVTDRGKDKVKKLEQTTNQQAELEAFAMALT----DSGPKVNII 66

Query: 75  SDSKSSLTALFNIRFTNPLISKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNEIVDEAARN 134
            DS+  +  + +    +   SK+ +      +  + +   W P+H GI GN+ VD     
Sbjct: 67  VDSQYVMGIVASQPTESE--SKIVNQIIEEMIKKEAIYVAWVPAHKGIGGNQEVDHLVSQ 124

Query: 135 A 135
            
Sbjct: 125 G 125

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

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

 Score = 38.8 bits (89), Expect = 1e-04
 Identities = 26/135 (19%), Positives = 42/135 (31%), Gaps = 15/135 (11%)

Query: 17  FTDGS--KTPDSTSCAFSIGDVVHSTLLNPVNSIFSAELMAIFLCLEAILESPDHHFLIV 74
           FTDG+    P     A  +    H  LL+   +  +   M +   +E +    +   + +
Sbjct: 7   FTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKEPCEVDL 66

Query: 75  SDSKSSLTALFNIRFTNPLISKVYST-------------WSFLKLNNKNVSFMWCPSHCG 121
                 L   F   +      + + T                L +    V F +   H G
Sbjct: 67  YTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPHRVRFHFVKGHTG 126

Query: 122 IRGNEIVDEAARNAA 136
              NE VD  AR  A
Sbjct: 127 HPENERVDREARRQA 141

>d1jl1a_ c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli [TaxId: 562]} Length = 152

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]

 Score = 38.5 bits (88), Expect = 2e-04
 Identities = 24/134 (17%), Positives = 39/134 (29%), Gaps = 14/134 (10%)

Query: 17  FTDGS--KTPDSTSCAFSIGDVVHSTLLNPVNSIFSAELMAIFLCLEAILESPDHHFLIV 74
           FT GS    P        +         +   +  +   M +   + A+    +H  +I+
Sbjct: 6   FTAGSALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKEHAEVIL 65

Query: 75  SDSKSSLTALFNIRFTN------------PLISKVYSTWSFLKLNNKNVSFMWCPSHCGI 122
           S     +         N            P+ +          L    + + W   H G 
Sbjct: 66  STDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVKGHAGH 125

Query: 123 RGNEIVDEAARNAA 136
             NE  DE AR AA
Sbjct: 126 PENERADELARAAA 139

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	271
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.94
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	99.91
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.9
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	99.81
d1zbfa1	132	BH0863-like Ribonuclease H {Bacillus halodurans [T	99.56

>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=99.94  E-value=8.3e-27  Score=181.00  Aligned_cols=121  Identities=19%  Similarity=0.229  Sum_probs=90.5

Q ss_pred             ccCCcEEEEEcCCCCCC-C-eeEEEEECC-eEEEEecCCCCchHHHHHHHHHHHHHHHHcCCCceEEEEeCCHHHHHHHh
Q psy8412           9 KYANHTICFTDGSKTPD-S-TSCAFSIGD-VVHSTLLNPVNSIFSAELMAIFLCLEAILESPDHHFLIVSDSKSSLTALF   85 (271)
Q Consensus         9 ~~~~~~~iytDGS~~~~-~-~G~a~~~~~-~~~~~~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~v~I~tDS~~al~~l~   85 (271)
                      +.++..++|||||+..+ + .|+|++... ......++ ..|++.|||.||+.||+..    ...+.|+|||++|++.++
T Consensus         3 p~~~~~t~YTDGS~~~n~~~~~~g~~~~~~~~~~~~~~-~~tnn~AEl~Ai~~al~~~----~~~i~I~tDS~~v~~~~~   77 (126)
T d1mu2a1           3 PIPGAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKLE-QTTNQQAELEAFAMALTDS----GPKVNIIVDSQYVMGIVA   77 (126)
T ss_dssp             CCTTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEEES-SCCHHHHHHHHHHHHHHTS----CSEEEEEESCHHHHHHHH
T ss_pred             CCCCCcEEEEcCCCCCCCCcEEEEEEecCCCEEEEecC-CCcchHHHHHHHHHHhccC----CcceEEEechHHHHHHHh
Confidence            45667899999998754 3 566666543 33334443 5799999999999999854    678999999999999999


Q ss_pred             ccccCCccHHHHHHHHHHHHhCCCceEEEEecCCCCCccchHHHHHHHHhh
Q psy8412          86 NIRFTNPLISKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNEIVDEAARNAA  136 (271)
Q Consensus        86 ~~~~~~~~~~~~~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~  136 (271)
                      ++...+..  .......+.......|.|.|||||+|++|||.||+||++|.
T Consensus        78 ~~~~~~~~--~~~~~~~~~~~~~~~v~~~wV~gH~g~~gNe~AD~LA~~ai  126 (126)
T d1mu2a1          78 SQPTESES--KIVNQIIEEMIKKEAIYVAWVPAHKGIGGNQEVDHLVSQGI  126 (126)
T ss_dssp             TCCSEESC--HHHHHHHHHHHHCSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             cCCccccc--hHHHHHHHHhhhcceeEEEEEeCCCCCcchHHHHHHHHhhC
Confidence            98764322  12222222223456999999999999999999999999873

>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=99.91  E-value=2.9e-24  Score=171.08  Aligned_cols=129  Identities=20%  Similarity=0.221  Sum_probs=93.4

Q ss_pred             cEEEEEcCCCCCC--CeeEEEEE--CCeEEEEe-cCCCCchHHHHHHHHHHHHHHHHcCCCceEEEEeCCHHHHHHHhcc
Q psy8412          13 HTICFTDGSKTPD--STSCAFSI--GDVVHSTL-LNPVNSIFSAELMAIFLCLEAILESPDHHFLIVSDSKSSLTALFNI   87 (271)
Q Consensus        13 ~~~iytDGS~~~~--~~G~a~~~--~~~~~~~~-l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~v~I~tDS~~al~~l~~~   87 (271)
                      .+.||||||+.++  .+|+|++.  .+....+. ..+..|++.||+.|++.||+++..  ...+.|+|||++++..+..+
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            5899999998865  36888663  44332222 124578999999999999998754  67899999999999998755


Q ss_pred             cc---------CCc--cH-HHHHHHHHHHHhCCCceEEEEecCCCCCccchHHHHHHHHhhcCCCCCCC
Q psy8412          88 RF---------TNP--LI-SKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNEIVDEAARNAASIDPYKLC  144 (271)
Q Consensus        88 ~~---------~~~--~~-~~~~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~~~~~~~  144 (271)
                      ..         ..+  .. ......+..+ .....|+|+|||||+|++|||.||+|||+|+..++..+.
T Consensus        80 ~~~~~~~~~~~~~~~~~~n~~~~~~i~~~-~~~~~V~~~wV~gH~g~~gNe~AD~LAk~aa~~~~~~d~  147 (152)
T d1jl1a_          80 IHNWKKRGWKTADKKPVKNVDLWQRLDAA-LGQHQIKWEWVKGHAGHPENERADELARAAAMNPTLEDT  147 (152)
T ss_dssp             HHHHHHTTTBCTTSCBCTTHHHHHHHHHH-TTTCEEEEEECCSSTTCHHHHHHHHHHHHHHHSCCBCCT
T ss_pred             hhHhHhccchhcccCeeecHHHHHHHHHH-hhcceeEEEEecccCCCccHHHHHHHHHHHHhCCCCCcc
Confidence            31         111  11 1222222222 345789999999999999999999999999998866544

>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=99.90  E-value=1e-24  Score=173.29  Aligned_cols=126  Identities=21%  Similarity=0.188  Sum_probs=90.4

Q ss_pred             CcEEEEEcCCCCCCC--eeEEEEE--CCe-EEEEecCCCCchHHHHHHHHHHHHHHHHcCCCceEEEEeCCHHHHHHHhc
Q psy8412          12 NHTICFTDGSKTPDS--TSCAFSI--GDV-VHSTLLNPVNSIFSAELMAIFLCLEAILESPDHHFLIVSDSKSSLTALFN   86 (271)
Q Consensus        12 ~~~~iytDGS~~~~~--~G~a~~~--~~~-~~~~~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~v~I~tDS~~al~~l~~   86 (271)
                      ..++||||||+.+++  .|+|++.  .+. ..........|++.||+.||+.||+++..  ...+.|+|||+++++.+..
T Consensus         2 ~~i~iytDGs~~~N~g~~G~g~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~~~--~~~i~i~tds~~~~~~~~~   79 (147)
T d1rila_           2 KRVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKE--PCEVDLYTDSHYLKKAFTE   79 (147)
T ss_dssp             CCCCEEEEEEESSTTEEEEEEEEECBTTBCCEECCEEEEECHHHHHHHHHHHHHHSCCS--CCEEEEECCCHHHHHHHHS
T ss_pred             CEEEEEEccCCCCCCCccEEEEEEEECCcceEEecccccccHHHHHHHHHHHHhhhccC--CceEEEecchhhhhccccc
Confidence            468999999998753  6778764  222 12112223568999999999999997654  6789999999999998876


Q ss_pred             ccc----------CC--ccH-HHHHHHHHHHHhCCCceEEEEecCCCCCccchHHHHHHHHhhcCCC
Q psy8412          87 IRF----------TN--PLI-SKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNEIVDEAARNAASIDP  140 (271)
Q Consensus        87 ~~~----------~~--~~~-~~~~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~~~  140 (271)
                      ...          ..  +.. .+++..+..+ .....|+|.|||||+|++|||.||+|||+|++...
T Consensus        80 ~~~~~~~~~~~~~~~~~~v~n~dL~~~l~~~-~~~~~v~~~wVkgHsg~~gNe~AD~LAk~aa~~~~  145 (147)
T d1rila_          80 GWLEGWRKRGWRTAEGKPVKNRDLWEALLLA-MAPHRVRFHFVKGHTGHPENERVDREARRQAQSQA  145 (147)
T ss_dssp             SHHHHHHHTTSBCTTSSBCTTHHHHHHHHHH-HTTSEEECCCCCGGGSCTHHHHHHHHHHHHHTSSC
T ss_pred             cchhhhhhccccccccccchhHHHHHHHHHH-hhhcccceEEccCCCCCcchHHHHHHHHHHHHHhc
Confidence            421          11  111 1222222222 35678999999999999999999999999998753

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

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

Probab=99.81  E-value=4.9e-20  Score=138.93  Aligned_cols=105  Identities=18%  Similarity=0.254  Sum_probs=76.3

Q ss_pred             hccCCcEEEEEcCCCCCC-C-eeEEEEECC-eEEEEecCCCCchHHHHHHHHHHHHHHHHcCCCceEEEEeCCHHHHHHH
Q psy8412           8 NKYANHTICFTDGSKTPD-S-TSCAFSIGD-VVHSTLLNPVNSIFSAELMAIFLCLEAILESPDHHFLIVSDSKSSLTAL   84 (271)
Q Consensus         8 ~~~~~~~~iytDGS~~~~-~-~G~a~~~~~-~~~~~~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~v~I~tDS~~al~~l   84 (271)
                      ++.++..++|||||+..+ + .|+|++..+ ......+ ...||+.|||.||+.||+..    ..++.|+|||++|++++
T Consensus         3 ~Pi~~~~t~ytDGs~~~n~~~g~~g~~~~~~~~~~~~~-~~~TNn~aEl~Avi~aL~~~----~~~v~I~TDS~yvi~~i   77 (110)
T d1s1ta1           3 EPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTL-TDTTNQKTELQAIYLALQDS----GLEVNIVTDSQYALGII   77 (110)
T ss_dssp             SCCTTSEEEEEEEEEETTTTEEEEEEEETTSCEEEEEE-SSCCHHHHHHHHHHHHHHHS----CSEEEEEECCHHHHHHH
T ss_pred             CCCCCCcEEEEeCCCCCCCCCcEEEEEEecCCeEEEec-ccCcHHHHHHHHHHHHHHhC----CCeEEEEEehHHHHHHH
Confidence            456677899999997754 3 456665533 3333444 35799999999999999854    57899999999999999


Q ss_pred             hccccCCccHHHHHHHHHHHHhCCCceEEEEecCC
Q psy8412          85 FNIRFTNPLISKVYSTWSFLKLNNKNVSFMWCPSH  119 (271)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~~l~~~~~~v~~~WVpgH  119 (271)
                      +++.....  .+.+.++.+.......|.|.|||||
T Consensus        78 ~~~~~~~~--~~l~~~il~~l~~~~~v~i~WVpgH  110 (110)
T d1s1ta1          78 QAQPDQSE--SELVNQIIEQLIKKEKVYLAWVPAH  110 (110)
T ss_dssp             HHCCSEES--CHHHHHHHHHHHHCSEEEEEECCSS
T ss_pred             hcCccccc--hHHHHHHHHHHhcCCceEEEEeCCC
Confidence            98876432  2334343333344678999999999

>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=99.56  E-value=5.4e-16  Score=119.11  Aligned_cols=114  Identities=14%  Similarity=0.007  Sum_probs=79.7

Q ss_pred             EEEEcCCCCCC--CeeEEEEECC--eEEEEec-CCCCchHHHHHHHHHHHHHHHHcCCCceEEEEeCCHHHHHHHhcccc
Q psy8412          15 ICFTDGSKTPD--STSCAFSIGD--VVHSTLL-NPVNSIFSAELMAIFLCLEAILESPDHHFLIVSDSKSSLTALFNIRF   89 (271)
Q Consensus        15 ~iytDGS~~~~--~~G~a~~~~~--~~~~~~l-~~~~s~~~AEl~Ai~~AL~~a~~~~~~~v~I~tDS~~al~~l~~~~~   89 (271)
                      .||||||+.++  ..|+|+|...  .....+. -+..|++.||+.|++.||+.+...+ .++.|+|||++|++.+.++.-
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            48999999865  3788877532  2222221 2467999999999999999998754 679999999999999987642


Q ss_pred             C-----CccHHHHHHHHHHHH--hCCCceEEEEecCCCCCccchHHH
Q psy8412          90 T-----NPLISKVYSTWSFLK--LNNKNVSFMWCPSHCGIRGNEIVD  129 (271)
Q Consensus        90 ~-----~~~~~~~~~~~~~l~--~~~~~v~~~WVpgH~gi~gNe~AD  129 (271)
                      .     ...-..++..+.++.  -....+.+.|++.|+..-||..||
T Consensus        85 kt~~~~~vkN~~l~~~i~~a~~~lk~h~~~~~~~KW~~~~wG~i~AD  131 (132)
T d1zbfa1          85 KSTLVRNEETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKAD  131 (132)
T ss_dssp             CCCCCCSTTTHHHHHHHHHHHHHHHHCCCCCCEEECCHHHHCSCTTC
T ss_pred             ecCcCCCcccHHHHHHHHHHHHHHHhCCcCceeEEecCcccccCCCC
Confidence            1     111233443333211  123467888999999888998887