Psyllid ID: psy16967

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280--
Protein Sequence
MPLSLRRSKMIMNYVSKIGSCHRNPIHNEFFNRNYDFANHPNTPKPLLMRAREITDFIANIDSSEFAPYDKHIPPWSSVVPSIDTSLHSGKKDNVSPSVFQVQFLVNINTKYHDRILCFTDGSKTENSTSCAYTINKNVNSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLVTDSMSSLQAITSKSCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNPSPSFPPLKLCSASDYKPLIKKIVQRNWQSSWNSVPNGNKLKTYRK
Secondary Structure (PSIPRED)
ccHHHHHHHHHHHHHHHHHccccccccHHHHcccccccccccccccHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHccccccEEEEEccccccccccEEEEEcccccEEEccccccHHHHHHHHHHHHHHHHHcccccEEEEEccHHHHHHHHHccccccHHHHHHHHHHHHHHHccccEEEEEcccccccHHHHHHHHHHccccccccccccccHHHHHHHHHHHHHHHHHHHHcccccccccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHHHHHHHcccccccHHHHcccHHHHHcccccccccHHHHHHHHHHHccccccccccccccccccccccccEEEcccccccccccHHHHHHHHHHHHHHHccccEEEEEccccccccEEEEEEEcccccEcccccccHHHHHHHHHHHHHHHHHHHcccccEEEEEccHHHHHHHHccccccHHHHHHHHHHHHHHHcccEEEEEEEcccccccccHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHccccccccEEccc
Coil and Loop (DISEMBL)
MPLSLRRSKMIMNYVSKigschrnpihneffnrnydfanhpntpkplLMRAREITDFIanidssefapydkhippwssvvpsidtslhsgkkdnvspsvFQVQFLVNINTKyhdrilcftdgsktenstscAYTINKNVNSFRLNVVNSVFSAELMAILLCLQnlkylpstkflLVTDSMSSLQAITSKSCNNALLSKIYSTWLDLVAcgkeisfmwcpshcgisgneavdvaaknpspsfpplklcsasdykpLIKKIVQRNWqsswnsvpngnklktyrk
Flexible Loop (DISEMBL)
MPLSLRRSKMIMNYVSKIGSCHRNPIHNEFFNRNYDFANHPNTPKPLLMRAREITDFIANIDSSEFAPYDKHIPPWSSVVPSIDTSLHsgkkdnvspsVFQVQFLVNINTKYHDRILCFTDGSKTENSTSCAYTINKNVNSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLVTDSMSSLQAITSKSCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNPSPSFPPLKLCSASDYKPLIKKIVqrnwqsswnsvpngnklktyrk
Low Complexity Region (SEG)
MPLSLRRSKMIMNYVSKIGSCHRNPIHNEFFNRNYDFANHPNTPKPLLMRAREITDFIANIDSSEFAPYDKHIPPWSSVVPSIDTSLHSGKKDNVSPSVFQVQFLVNINTKYHDRILCFTDGSKTENSTSCAYTINKNVNSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLVTDSMSSLQAITSKSCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNPSPSFPPLKLCSASDYKPLIKKIVQRNWQSSWNSVPNGNKLKTYRK
Disordered region (IsUnstruct)
*********MIMNYVSKIGSCHRNPIHNEFFNRNYDFANHPNTPKPLLMRAREITDFIANIDSSEFAPYDKHIPPWSSVVPSI************SPSVFQVQFLVNINTKYHDRILCFTDGSKTENSTSCAYTINKNVNSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLVTDSMSSLQAITSKSCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVA**********LKLCSASDYKPLIKKIVQRNWQSSW**************
Disordered Region (DISOPRED)
MPLSLRRSKMIMNYVSKIGSCHRNPIHNEFFNR**************LMRAREITDFIANIDSSEFAPYDKHIPPWSSVVPSIDTSLHSGK***VSPSVFQVQFLVNINTKYHDRILCFTDGSKTENSTSCAYTINKNVNSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLVTDSMSSLQAITSKSCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNPSPSFPPLKLCSASDYKPLIKKIVQRNWQSSWNSV***********
Disordered Region (DISEMBL)
MPLSLRRSKMIMNYVSKIGSCHRNPIHNEFFNRNYDFANHPNTPKPLLMRAREITDFIANIDSSEFAPYDKHIPPWSSVVPSIDTSLHSGKKDNVSPSVFQVQFLVNINTKYHDRILCFTDGSKTENSTSCAYTINKNVNSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLVTDSMSSLQAITSKSCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNPSPSFPPLKLCSASDYKPLIKKIVQRNWQSSWNSVPNGNKLKTYRK
Disordered Region (DISPRO)
MPLSLRRSKMIMNYVSKIGSCHRNPIHNEFFNRNYDFANHPNTPKPLLMRAREITDFIANIDSSEFAPYDKHIPPWSSVVPSIDTSLHSGKKDNVSPSVFQVQFLVNINTKYHDRILCFTDGSKTENSTSCAYTINKNVNSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLVTDSMSSLQAITSKSCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNPSPSFPPLKLCSASDYKPLIKKIVQRNWQSSWNSVPNGNKLKTY**
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
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Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MPLSLRRSKMIMNYVSKIGSCHRNPIHNEFFNRNYDFANHPNTPKPLLMRAREITDFIANIDSSEFAPYDKHIPPWSSVVPSIDTSLHSGKKDNVSPSVFQVQFLVNINTKYHDRILCFTDGSKTENSTSCAYTINKNVNSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLVTDSMSSLQAITSKSCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNPSPSFPPLKLCSASDYKPLIKKIVQRNWQSSWNSVPNGNKLKTYRK
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

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	282	2.2.26 [Sep-21-2011]
Q77373	1435	Gag-Pol polyprotein OS=Hu	yes	N/A	0.258	0.050	0.367	0.0001

>sp|Q77373|POL_HV1AN Gag-Pol polyprotein OS=Human immunodeficiency virus type 1 group O (isolate ANT70) GN=gag-pol PE=3 SV=3

 Score = 47.0 bits (110), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 29/79 (36%), Positives = 44/79 (55%), Gaps = 6/79 (7%)

Query: 153  AELMAILLCLQNLKYLPSTKFLLVTDSMSSLQAITSKSCNNALLSKIYSTWLDLVACGKE 212
            AELMAILL LQ+ K   +    +VTDS  +L  I+S+   +   S I    ++ +   ++
Sbjct: 1063 AELMAILLALQDSKETVN----IVTDSQYALGVISSQPTQSE--SPIVQQIIEELTKKEQ 1116

Query: 213  ISFMWCPSHCGISGNEAVD 231
            +   W P+H GI GNE +D
Sbjct: 1117 VYLTWVPAHKGIGGNEKID 1135

Integrase catalyzes viral DNA integration into the host chromosome, by performing a series of DNA cutting and joining reactions. This enzyme activity takes place after virion entry into a cell and reverse transcription of the RNA genome in dsDNA. The first step in the integration process is 3' processing. This step requires a complex comprising the viral genome, matrix protein, Vpr and integrase. This complex is called the pre-integration complex (PIC). The integrase protein removes 2 nucleotides from each 3' end of the viral DNA, leaving recessed CA OH's at the 3' ends. In the second step, the PIC enters cell nucleus. This process is mediated through integrase and Vpr proteins, and allows the virus to infect a non dividing cell. This ability to enter the nucleus is specific of lentiviruses, other retroviruses cannot and rely on cell division to access cell chromosomes. In the third step, termed strand transfer, the integrase protein joins the previously processed 3' ends to the 5' ends of strands of target cellular DNA at the site of integration. The 5'-ends are produced by integrase-catalyzed staggered cuts, 5 bp apart. A Y-shaped, gapped, recombination intermediate results, with the 5'-ends of the viral DNA strands and the 3' ends of target DNA strands remaining unjoined, flanking a gap of 5 bp. The last step is viral DNA integration into host chromosome. This involves host DNA repair synthesis in which the 5 bp gaps between the unjoined strands are filled in and then ligated. Since this process occurs at both cuts flanking the HIV genome, a 5 bp duplication of host DNA is produced at the ends of HIV-1 integration. Alternatively, Integrase may catalyze the excision of viral DNA just after strand transfer, this is termed disintegration.
Homo sapiens (taxid: 9606)
EC: 3EC: .EC: 1EC: .EC: 1EC: 3EC: .EC: 2

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	282
125901787	1222	pol-like protein [Biomphalaria glabrata]	0.936	0.216	0.350	2e-30
443700898	300	hypothetical protein CAPTEDRAFT_212630,	0.968	0.91	0.338	2e-27
443710566	377	hypothetical protein CAPTEDRAFT_186063 [	0.968	0.724	0.338	5e-27
443693558	502	hypothetical protein CAPTEDRAFT_189741,	0.836	0.470	0.336	4e-24
443734745	252	hypothetical protein CAPTEDRAFT_216906 [	0.829	0.928	0.342	2e-22
443723447	225	hypothetical protein CAPTEDRAFT_187673 [	0.765	0.96	0.340	2e-21
443713753	266	hypothetical protein CAPTEDRAFT_215116 [	0.826	0.875	0.315	2e-20
443695973	261	hypothetical protein CAPTEDRAFT_23017, p	0.691	0.747	0.351	5e-19
427791321	1210	Putative tick transposon, partial [Rhipi	0.932	0.217	0.301	2e-18
427791807	1212	Putative tick transposon, partial [Rhipi	0.932	0.216	0.301	2e-18

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

 Score =  139 bits (349), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 97/277 (35%), Positives = 138/277 (49%), Gaps = 13/277 (4%)

Query: 1    MPLSLRRSKMIMNYVSKIGSCHRNPIHNEFFN-RNYDFANH-PNTPKPLLMRARE----I 54
            +P+ +R  K+ M Y+ K+ S   NP  +  FN    +  N  PN  +PL +R RE    +
Sbjct: 841  LPMDIRMKKLAMQYIVKLKSNPTNPAFDSIFNPTEVELYNRRPNVIQPLGLRMREPIQNL 900

Query: 55   TDFIANIDSSEFAPYDKHIPPWSSVVPSIDTSLHSGKKDNVSPSVFQVQFLVNINTKYHD 114
            T  I  I   E  P +   PPW    P ++ SL + KK+N  PS+ QV F   +   Y D
Sbjct: 901  TQPIDQISKIE-TPQN---PPWLMNKPKLNLSLLNFKKENTDPSILQVHFR-ELQESYGD 955

Query: 115  RILCFTDGSKTENSTSCAYTINKNVNSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFL 174
                +TDGSK E   +CA +      S RL    S+F+AEL AILL L  +K    +KF+
Sbjct: 956  CGTIYTDGSKMEGKVACACSFRNKTISRRLPDGCSIFTAELHAILLALMAVKASERSKFI 1015

Query: 175  LVTDSMSSLQAITSKSCNNALLSKIYSTWLDLV-ACGKEISFMWCPSHCGISGNEAVDVA 233
            + +DS S+LQA+     +  L+ K     LDL+ A  ++++F+W PSH GI GNEA D  
Sbjct: 1016 ICSDSKSALQALGRMKTDIPLVHKSLKL-LDLITADRRDVTFIWVPSHVGIEGNEAADRE 1074

Query: 234  AKNPSPSFPPLKLCSASDYKPLIKKIVQRNWQSSWNS 270
            AK              SD +  I     R WQ+ W +
Sbjct: 1075 AKRALNHAVSGTQIPYSDLRQSIASATYREWQNRWEA 1111

Source: Biomphalaria glabrata

Species: Biomphalaria glabrata

Genus: Biomphalaria

Family: Planorbidae

Class: Gastropoda

Phylum: Mollusca

Superkingdom: Eukaryota

>gi|443700898|gb|ELT99633.1| hypothetical protein CAPTEDRAFT_212630, partial [Capitella teleta]

 Score =  129 bits (323), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 96/284 (33%), Positives = 144/284 (50%), Gaps = 11/284 (3%)

Query: 1   MPLSLRRSKMIMNYVSKIGSCHRNPIHNEFFNRNYD--FANHPNTPKPLLMRAREITDFI 58
           MP+++R+  + + +  ++ S   NP H   FN N D  + + PN  +PL +R +E    I
Sbjct: 1   MPMTIRQKLLSVQFALRVCSDTTNPAHQCIFNYNNDRFYLSKPNAIRPLALRIKEDLQTI 60

Query: 59  ANIDSSEFAPYDK-HIPPWSSVVPSIDTSL-HSGKKDNVSPSVFQVQFLVNINTKYHDRI 116
              D     P    +IP W    P +D SL H GKK   +P+        N+  KY D  
Sbjct: 61  CP-DIKAITPNQLFNIPYWLLRPPELDISLIHFGKK-TANPNYTLRNEFYNLMDKYPDHK 118

Query: 117 LCFTDGSKTENSTSCAYTINKNVNSFRLNVVNSVFSAELMAI--LLCLQNLKYLPSTKFL 174
           + FTDGSK++++ +C+ T +      RL    S+FSAEL+AI  +L L         +FL
Sbjct: 119 VIFTDGSKSDSAVACSATADNLRIQIRLPDSASIFSAELLAIYQVLTLLECSANDQQQFL 178

Query: 175 LVTDSMSSLQAITSKSCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAA 234
           + TDS+SSLQAI + +  +  + KI      L   G  +   WCPSH G+ GNE  D+ A
Sbjct: 179 IATDSLSSLQAIGNFNIKHPYVFKILQKCTLLHKKGIYLVMAWCPSHVGVMGNERADLLA 238

Query: 235 KNPSPSFPPLKL-CSASDYKPLIKKIVQRNWQSSWNSVPNGNKL 277
           K  + SF    +   +SD+KP+  +  +  WQ  W+S    NKL
Sbjct: 239 KE-ALSFTTCTIRVPSSDFKPITHEFYKEKWQEQWSS-EQENKL 280

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|443710566|gb|ELU04776.1| hypothetical protein CAPTEDRAFT_186063 [Capitella teleta]

 Score =  127 bits (319), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 96/284 (33%), Positives = 143/284 (50%), Gaps = 11/284 (3%)

Query: 1   MPLSLRRSKMIMNYVSKIGSCHRNPIHNEFFNRNYD--FANHPNTPKPLLMRAREITDFI 58
           MP+++R+  + + +  ++ S   NP H   FN N D  + + PN  +PL +R +E    I
Sbjct: 70  MPMAIRQKLLSVQFALRVCSDTTNPAHQCIFNYNNDRFYLSKPNAIRPLALRIKEDLQTI 129

Query: 59  ANIDSSEFAPYDK-HIPPWSSVVPSIDTSL-HSGKKDNVSPSVFQVQFLVNINTKYHDRI 116
              D     P    +IP W    P +D SL H GKK   +P+        N+  KY D  
Sbjct: 130 CP-DIKAITPNQLFNIPYWLLRPPELDISLIHFGKK-TANPNYTLKNEFYNLMDKYPDHK 187

Query: 117 LCFTDGSKTENSTSCAYTINKNVNSFRLNVVNSVFSAELMAI--LLCLQNLKYLPSTKFL 174
           + FTDGSK++++ +C  T +      RL    S+FSAEL+AI  +L L         +FL
Sbjct: 188 VIFTDGSKSDSAVACFATADNLSIQIRLPDSASIFSAELLAIYQVLTLLECSANDQQQFL 247

Query: 175 LVTDSMSSLQAITSKSCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAA 234
           + TDS+SSLQAI + +  +  + KI      L   G  +   WCPSH G+ GNE  D+ A
Sbjct: 248 IATDSLSSLQAIGNFNIKHPYVFKILEKCTLLHKKGIYLVMAWCPSHVGVMGNERADLLA 307

Query: 235 KNPSPSFPPLKL-CSASDYKPLIKKIVQRNWQSSWNSVPNGNKL 277
           K  + SF    +   +SD+KP+  +  +  WQ  W+S    NKL
Sbjct: 308 KE-ALSFTTCTIRIPSSDFKPITHEFFKEKWQEQWSS-EQENKL 349

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 =  117 bits (294), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 84/250 (33%), Positives = 134/250 (53%), Gaps = 14/250 (5%)

Query: 37  FANHPNTPKPLLMRAREITDFIANIDSSEFAPYD-KHIPPWSSVVPSIDTSLHSGKKDNV 95
           + + P+  +PLL R  E    + ++ ++  AP+    +PPW    P +DTS+    KD  
Sbjct: 7   YTSKPSFIRPLLYRTEEA---LESVITAPIAPFKISDVPPWKLRPPEVDTSISKFLKDQ- 62

Query: 96  SPSVFQVQFLVNINTKYHDRILCFTDGSKTENSTSCAYTINKNVNSFRLNVVNSVFSAEL 155
            P++F  Q   N+  KY   I  +TDGSK+ N+ +CA+T +     F L    S+++AEL
Sbjct: 63  HPALFLKQEFYNLIDKYPG-INIYTDGSKSNNAVACAFTCSTYQIQFGLPTQMSIYTAEL 121

Query: 156 MAI---LLCLQNLKYLPSTKFLLVTDSMSSLQAITSKSCNNALLSKIYSTWLDLVACGKE 212
           +AI   L+ ++ +K     +F + +DS+SSL A+++    +  L  I +   +LV  GK 
Sbjct: 122 IAIEQALIFIETVK--DEDQFNICSDSLSSLTALSNCDITHPYLLSILTKQNNLVRKGKL 179

Query: 213 ISFMWCPSHCGISGNEAVDVAAKNPSPSFPPLKL-CSASDYKPLIKKIVQRNWQSSWNSV 271
           + F+WCPSH GI GNE  D  AK  +   P  KL    +DYK  I+  V+  WQ+ W+  
Sbjct: 180 VVFIWCPSHVGILGNEVADRLAKQ-ALVMPVTKLPLPHTDYKSPIRSYVKSLWQNEWDE- 237

Query: 272 PNGNKLKTYR 281
              NKL + +
Sbjct: 238 ETDNKLHSIQ 247

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|443734745|gb|ELU18611.1| hypothetical protein CAPTEDRAFT_216906 [Capitella teleta]

 Score =  112 bits (279), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 83/242 (34%), Positives = 122/242 (50%), Gaps = 8/242 (3%)

Query: 1   MPLSLRRSKMIMNYVSKIGSCHRNPIHNEFFNRNYD--FANHPNTPKPLLMRAREITDFI 58
           MP+++R+  + + +  +  S   NP H   FN N D  + + PN  +PL +R +E    I
Sbjct: 1   MPMAIRQKLLSVQFALRGCSDTTNPAHQCIFNYNNDRFYLSKPNAIRPLALRIKEDLQTI 60

Query: 59  ANIDSSEFAPYDK-HIPPWSSVVPSIDTSL-HSGKKDNVSPSVFQVQFLVNINTKYHDRI 116
              D     P    +IP W    P +D SL H GKK   +P+        N+  KY D  
Sbjct: 61  CP-DIKAITPNQLFNIPYWLLRPPELDISLIHFGKK-TANPNYTLRNEFYNLMDKYPDHK 118

Query: 117 LCFTDGSKTENSTSCAYTINKNVNSFRLNVVNSVFSAELMAI--LLCLQNLKYLPSTKFL 174
           + FTDGSK++++ +C+ T +      RL    S+FSAEL+AI  +L L         +FL
Sbjct: 119 VIFTDGSKSDSAVACSATADNLRIQIRLPDSASIFSAELLAIYQVLTLLECSANDQQQFL 178

Query: 175 LVTDSMSSLQAITSKSCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAA 234
           + TDS+SSLQAI + +  +  + KI      L   G  +   WCPSH G+ GNE  D+ A
Sbjct: 179 IATDSLSSLQAIGNFNIKHPYVFKILEKCTLLHKKGIYLVMAWCPSHVGVMGNERADLLA 238

Query: 235 KN 236
           K 
Sbjct: 239 KE 240

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|443723447|gb|ELU11866.1| hypothetical protein CAPTEDRAFT_187673 [Capitella teleta]

 Score =  108 bits (271), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 78/229 (34%), Positives = 119/229 (51%), Gaps = 13/229 (5%)

Query: 39  NHPNTPKPLLMRAREITDFIANIDSSEFAPYDKH----IPPWSSVVPSIDTSLHSGKKDN 94
           N P+  +P   R   I D I  + S    P   H    IPPW  V P +D SL S KKD+
Sbjct: 2   NKPSYIQPFPYR---IEDHINTVGS---GPVTHHVIPDIPPWHLVQPEVDLSLTSFKKDS 55

Query: 95  VSPSVFQVQFLVNINTKYHDRILCFTDGSKTENSTSCAYTINKNVNSFRLNVVNSVFSAE 154
            S    + +F   ++ +Y D  L +TDGSK+E+S +C++  N+     +L V  SVF++E
Sbjct: 56  KSALTIRSEFEDALD-RYPDSTLFYTDGSKSEDSVACSFFSNRLRLKMKLPVQMSVFTSE 114

Query: 155 LMAILLCLQNLKYL-PSTKFLLVTDSMSSLQAITSKSCNNALLSKIYSTWLDLVACGKEI 213
           L+AIL  L+ ++      +F++ +D++S++ AI      +  + K+      +    K +
Sbjct: 115 LIAILSALKCVEVDNEQHQFVICSDALSAIMAIHGMDVRHPYVLKVLYAIKSIYQQEKIV 174

Query: 214 SFMWCPSHCGISGNEAVDVAAKNPSPSFPPLKL-CSASDYKPLIKKIVQ 261
            FMWCP H GI GNE  D  AK    S    +L   ASD + LIKK ++
Sbjct: 175 VFMWCPPHVGIPGNEMADTLAKEALSSTNLAELTVRASDLRCLIKKYIR 223

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score =  105 bits (263), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 78/247 (31%), Positives = 127/247 (51%), Gaps = 14/247 (5%)

Query: 39  NHPNTPKPLLMRAREITDFIANIDSSEFAPYDKHI----PPWSSVVPSIDTSLHSGKKDN 94
           N P+  +P   R   I D +  + SS   P   H+    PPW  V P +D SL   KKD+
Sbjct: 2   NKPSFIQPFPYR---IEDHMDTVGSS---PVTHHVIPETPPWHLVQPEVDLSLTFSKKDS 55

Query: 95  VSPSVFQVQFLVNINTKYHDRILCFTDGSKTENSTSCAYTINKNVNSFRLNVVNSVFSAE 154
           +S    + +F   +++ Y    + +TDGSK+E+S + ++  ++     +L V  SVF++E
Sbjct: 56  MSALTIRSEFEDALDS-YPVSTVFYTDGSKSEDSVARSFFSSRLKLKMKLPVQMSVFTSE 114

Query: 155 LMAILLCLQNLKYL-PSTKFLLVTDSMSSLQAITSKSCNNALLSKIYSTWLDLVACGKEI 213
           ++AIL  L+ L+      +F++ +DS+S++ AI     ++  + ++      +    K +
Sbjct: 115 IIAILSALKCLEADNEQHQFVICSDSLSAIMAIHGMDVHHPYVLQVLYAIKSISQQEKIV 174

Query: 214 SFMWCPSHCGISGNEAVDVAAKNPSPSFPPLKL-CSASDYKPLIKKIVQRNWQSSWNSVP 272
            FMWCPSH GI GNE     A+    S    +L   ASD + LIKK ++  WQ  W    
Sbjct: 175 VFMWCPSHVGIPGNEMAHTLAEKALSSTNLAELPVPASDLRGLIKKYIRSQWQHEWEEQH 234

Query: 273 NGNKLKT 279
           N NKL +
Sbjct: 235 N-NKLHS 240

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score =  101 bits (251), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 72/205 (35%), Positives = 112/205 (54%), Gaps = 10/205 (4%)

Query: 81  PSIDTSLHSGKKDNVSPSVFQVQFLVNINTKYHDRILCFTDGSKTENSTSCAYTINKNVN 140
           P +DTS+    KD   P++F  Q   N+  KY   I  +TDGSK+ ++ +CA+T +    
Sbjct: 3   PEVDTSISKFLKDQ-HPALFLKQEFYNLIDKY-PGINIYTDGSKSNDAVACAFTCSTYQI 60

Query: 141 SFRLNVVNSVFSAELMAI---LLCLQNLKYLPSTKFLLVTDSMSSLQAITSKSCNNALLS 197
            F L    S+++AEL+AI   L+ ++ +K     +F + +DS+SSL A+++    +  L 
Sbjct: 61  QFGLPAQMSIYTAELIAIEQALIFIETVK--DEDQFNICSDSLSSLTALSNCDITHPYLL 118

Query: 198 KIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNPSPSFPPLKL-CSASDYKPLI 256
            I +   +LV  GK + F+WCPSH GI GNE  D  AK  +   P  KL    +DYK  I
Sbjct: 119 SILTKQNNLVRKGKLVVFIWCPSHVGILGNEVADRLAKQ-ALVMPVTKLPLPHTDYKSPI 177

Query: 257 KKIVQRNWQSSWNSVPNGNKLKTYR 281
           +  V+  WQ+ W+     NKL + +
Sbjct: 178 RSYVKSLWQNEWDE-ETDNKLHSIQ 201

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score = 99.4 bits (246), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 87/289 (30%), Positives = 134/289 (46%), Gaps = 26/289 (8%)

Query: 2    PLSLRRSKMIMNYVSKIGSCHRNPIHNEFFNR---NYDFANHPNTPKPLLMRAREI-TDF 57
            PLS RR+ + ++YV +I S  ++ I  +   R      + N  N  KPLL+R  E    +
Sbjct: 821  PLSHRRASLTLSYVLRIRSSPQH-ICYDIATRCSSRLHYLNKSNLIKPLLLRFEEYCRTY 879

Query: 58   IANIDSSEFAPYDKHIPPWSSVVPSIDTSL-HSGKKDNVSPSVFQVQFLVNINTKYHDRI 116
            + + ++ + A     IPPW  +    D SL H  KK  V+P    +Q    +  KY D  
Sbjct: 880  VISEETLDVARKPPRIPPWFDLAQLCDISLSHINKK--VTPPELIIQEFRALQEKYRDYA 937

Query: 117  LCFTDGSKTENSTSCAYTINKNVNSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLV 176
              +TDGSKT +         ++  S R+    S+F+AE+ A+    + +      K ++ 
Sbjct: 938  EFYTDGSKTRDHVGIGIVTGESAFSVRVPQCISIFTAEVYALYEAARKIIAGKHKKAIIY 997

Query: 177  TDSMSSLQAITSKSCNNALLSKIYSTWLDLVACGKEI---SFMWCPSHCGISGNEAVD-- 231
            TDS+S+L+A+  KS    L+  I    L++V    ++    F W PSH GI GNE  D  
Sbjct: 998  TDSLSALKALHIKSECEPLVGDI----LNMVLINSKVISMRFCWVPSHVGIPGNEKADKC 1053

Query: 232  ---VAAKNPSPSFPPLKLCSASDYKPLIKKIVQRNWQSSWNSVPNGNKL 277
                A K  +    PLK     D +  I+  +   WQ  W+S    NKL
Sbjct: 1054 ASLAAHKTLTKIRIPLK-----DSQRTIRLALLAKWQQQWDSC-TSNKL 1096

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score = 99.0 bits (245), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 87/289 (30%), Positives = 134/289 (46%), Gaps = 26/289 (8%)

Query: 2    PLSLRRSKMIMNYVSKIGSCHRNPIHNEFFNR---NYDFANHPNTPKPLLMRAREI-TDF 57
            PLS RR+ + ++YV +I S  ++ I  +   R      + N  N  KPLL+R  E    +
Sbjct: 824  PLSHRRASLTLSYVLRIRSSPQH-ICYDIATRCSSRLHYLNKSNLIKPLLLRFEEYCRTY 882

Query: 58   IANIDSSEFAPYDKHIPPWSSVVPSIDTSL-HSGKKDNVSPSVFQVQFLVNINTKYHDRI 116
            + + ++ + A     IPPW  +    D SL H  KK  V+P    +Q    +  KY D  
Sbjct: 883  VISEETLDVARKPPRIPPWFDLAQLCDISLSHINKK--VTPPELIIQEFRALQEKYRDYA 940

Query: 117  LCFTDGSKTENSTSCAYTINKNVNSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLV 176
              +TDGSKT +         ++  S R+    S+F+AE+ A+    + +      K ++ 
Sbjct: 941  EFYTDGSKTRDHVGIGIVTGESAFSVRVPQCISIFTAEVYALYEAARKIIAGKHKKAIIY 1000

Query: 177  TDSMSSLQAITSKSCNNALLSKIYSTWLDLVACGKEI---SFMWCPSHCGISGNEAVD-- 231
            TDS+S+L+A+  KS    L+  I    L++V    ++    F W PSH GI GNE  D  
Sbjct: 1001 TDSLSALKALHIKSECEPLVGDI----LNMVLINSKVISMRFCWVPSHVGIPGNEKADKC 1056

Query: 232  ---VAAKNPSPSFPPLKLCSASDYKPLIKKIVQRNWQSSWNSVPNGNKL 277
                A K  +    PLK     D +  I+  +   WQ  W+S    NKL
Sbjct: 1057 ASLAAHKTLTKIRIPLK-----DSQRTIRLALLAKWQQQWDSC-TSNKL 1099

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	282
ASPGD|ASPL0000075333	486	AN10625 [Emericella nidulans (	0.599	0.347	0.245	2e-05

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

 Score = 128 (50.1 bits), Expect = 2.0e-05, P = 2.0e-05
 Identities = 45/183 (24%), Positives = 78/183 (42%)

Query:   107 NINTKYHDRILCFTDGSKTENSTSCA-----YTINKNVNSFRLNVVNSVFSAELMAILLC 161
             NI  +    I  +TDGS        A     Y I+++ +       ++V+ AEL  ILL 
Sbjct:   174 NILNRAPRPIALYTDGSGINGRVGAAAICPKYLISRS-SYMGQQSESTVYVAELQGILLA 232

Query:   162 LQNLKYLPSTKFLLVTDSMSSLQAITSKSCNNA--LLSKIYSTWLDLVACGKEISFMWCP 219
             L  +        ++ TD+ ++LQA+ +    +   +L  I          G  + F W P
Sbjct:   233 LVIILQRQMQHAVIFTDNQATLQALRNPGSQSGQYILEAIIMALNKGRKAGLNVHFRWIP 292

Query:   220 SHCGISGNEAVDVAAKNPSPSFPPLK-----LCSASDYKPLIKKIVQRNWQSSWNSVPNG 274
             +H G+ GNE  D  AK  +  +  ++     +   S  K    ++V   W++ W S  +G
Sbjct:   293 AHRGVEGNEQADRRAKEAT-GWRRIRGHRGRMTIRSAVKRRAHEVVNARWENDWKSCHHG 351

Query:   275 NKL 277
              +L
Sbjct:   352 REL 354


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        0.318   0.131   0.403    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      282       282   0.00083  115 3  11 22  0.36    34
                                                     33  0.42    37


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  617 (66 KB)
  Total size of DFA:  229 KB (2125 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:  23.95u 0.08s 24.03t   Elapsed:  00:00:37
  Total cpu time:  23.95u 0.08s 24.03t   Elapsed:  00:00:37
  Start:  Thu Aug 15 13:26:54 2013   End:  Thu Aug 15 13:27:31 2013

GO:0008150 "biological_process" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.1.26	0.691
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	282
cd09276	128	cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom	3e-32
pfam00075	126	pfam00075, RNase_H, RNase H	8e-19
cd06222	123	cd06222, RNase_H, RNase H is an endonuclease that	1e-12
cd09273	135	cd09273, RNase_HI_RT_Bel, Bel/Pao family of RNase	2e-07
cd09280	150	cd09280, RNase_HI_eukaryote_like, Eukaryotic RNase	1e-05
COG0328	154	COG0328, RnhA, Ribonuclease HI [DNA replication, r	3e-05

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

 Score =  115 bits (289), Expect = 3e-32
 Identities = 42/123 (34%), Positives = 60/123 (48%), Gaps = 5/123 (4%)

Query: 118 CFTDGSKTENSTSCAYTI---NKNVNSFRLNVVNSVFSAELMAILLCLQNLKYLPS--TK 172
            +TDGSK E  T   + I        S++L    SVF AEL+AIL  LQ          K
Sbjct: 2   IYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRRARK 61

Query: 173 FLLVTDSMSSLQAITSKSCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDV 232
             + +DS ++L+A+ S   ++ L+ +I     +L   G ++   W P H GI GNE  D 
Sbjct: 62  ITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGNERADR 121

Query: 233 AAK 235
            AK
Sbjct: 122 LAK 124

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 = 80.0 bits (198), Expect = 8e-19
 Identities = 34/124 (27%), Positives = 49/124 (39%), Gaps = 9/124 (7%)

Query: 116 ILCFTDGS--KTENSTSCAYTINKNVN-SFRLNVVNSVFSAELMAILLCLQNLKYLPSTK 172
           +  +TDGS           Y  +     S  L    +   AEL+A++  L+ L      K
Sbjct: 4   VTVYTDGSCNGNPGPGGAGYVTDGGKQRSKPLPG-TTNQRAELLALIEALEAL---SGQK 59

Query: 173 FLLVTDSMSSLQAITSKSCNNALLSK-IYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
             + TDS   +  IT         SK I +   +L+    ++   W P H GI GNE  D
Sbjct: 60  VNIYTDSQYVIGGIT-NGWPTKSESKPIKNEIWELLQKKHKVYIQWVPGHSGIPGNELAD 118

Query: 232 VAAK 235
             AK
Sbjct: 119 KLAK 122

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 = 63.1 bits (154), Expect = 1e-12
 Identities = 30/126 (23%), Positives = 42/126 (33%), Gaps = 11/126 (8%)

Query: 119 FTDGSKTENSTSCAY-----TINKNVNSFRL--NVVNSVFSAELMAILLCLQNLKYLPST 171
            TDGS   N                            +   AEL+A+L  L+    L   
Sbjct: 1   NTDGSCKGNPGPAGAGGVLRDHEGAWLFAGSLSIPAATNNEAELLALLEALELALDLGLK 60

Query: 172 KFLLVTDSMSSLQAITSKSCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           K ++ TDS   +  I S S      + +    L L++   +I F   P      GNE  D
Sbjct: 61  KLIIETDSKYVVDLINSWSKGWKKNNLLLWDILLLLSKFIDIRFEHVPR----EGNEVAD 116

Query: 232 VAAKNP 237
             AK  
Sbjct: 117 RLAKEA 122

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 = 49.2 bits (118), Expect = 2e-07
 Identities = 32/139 (23%), Positives = 48/139 (34%), Gaps = 27/139 (19%)

Query: 117 LCFTDGSKTENSTSCA-YTINKNVNSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLL 175
             FTDGS        A  T    +    L    S   AEL+A++  L+  K        +
Sbjct: 1   TVFTDGSSFVRKAGYAVVTGPDVLEIATLPYGTSAQRAELIALIRALELAK---GKPVNI 57

Query: 176 VTDS---MSSLQA----------ITSKSCNNA-LLSKIYSTWLDLVACGKEISFMWCPSH 221
            TDS      L A          +T K    A L+ ++       +   K ++ +   +H
Sbjct: 58  YTDSAYAFGILHALETIWKERGFLTGKPIALASLILQL----QKAIQRPKPVAVIHIRAH 113

Query: 222 CG-----ISGNEAVDVAAK 235
            G       GN   D AA+
Sbjct: 114 SGLPGPLALGNARADQAAR 132

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 = 44.1 bits (105), Expect = 1e-05
 Identities = 28/105 (26%), Positives = 40/105 (38%), Gaps = 26/105 (24%)

Query: 153 AELMAILLCLQNLKYL--PSTKFLLVTDSMSSLQAITS---------------KSCNNA- 194
           AEL A++  L+ +K +    TK ++ TDS   +  +T                K   N  
Sbjct: 46  AELRAVIHALRLIKEVGEGLTKLVIATDSEYVVNGVTEWIPKWKKNGWKTSKGKPVANKD 105

Query: 195 ----LLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAK 235
               L   +     +L   G  + F   P H GI GNE  D  AK
Sbjct: 106 LIKELDKLLE----ELEERGIRVKFWHVPGHSGIYGNEEADRLAK 146

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 = 43.1 bits (102), Expect = 3e-05
 Identities = 24/95 (25%), Positives = 36/95 (37%), Gaps = 12/95 (12%)

Query: 153 AELMAILLCLQNLKYLPSTKFLLVTDSMSSLQAITSKSCNNALLSKIYST---------W 203
           AEL A++  L+ LK L + +  L TDS   ++ IT             +          W
Sbjct: 46  AELRALIEALEALKELGACEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPVKNKDLW 105

Query: 204 LDLVACGK---EISFMWCPSHCGISGNEAVDVAAK 235
            +L    K    + + W   H G   NE  D  A+
Sbjct: 106 EELDELLKRHELVFWEWVKGHAGHPENERADQLAR 140

Length = 154

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	282
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	99.9
PRK06548	161	ribonuclease H; Provisional	99.9
PRK08719	147	ribonuclease H; Reviewed	99.9
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	99.89
PRK00203	150	rnhA ribonuclease H; Reviewed	99.88
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	99.81
KOG3752|consensus	371		99.77
PRK13907	128	rnhA ribonuclease H; Provisional	99.76
PRK07708	219	hypothetical protein; Validated	99.66
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	99.55
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	99.34
.; 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	81.29

>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=99.90  E-value=4.5e-24  Score=170.42  Aligned_cols=117  Identities=33%  Similarity=0.471  Sum_probs=89.9

Q ss_pred             CceEEecCCCCCCC--CceEEEEEcCCe-eeeecCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeCcHHHHHHHhc--
Q psy16967        114 DRILCFTDGSKTEN--STSCAYTINKNV-NSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLVTDSMSSLQAITS--  188 (282)
Q Consensus       114 ~~~~iyTDGS~~~~--~~G~gvv~~~~~-~~~~l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~sDS~~al~~l~~--  188 (282)
                      +.+.||||||+...  ..|+|+++..+. .+..++ ..+++.|||.||..||+.+ .  ...++|+|||++++..+..  
T Consensus         2 ~~~~iytDgS~~~~~~~~~~g~v~~~~~~~~~~~~-~~s~~~aEl~Ai~~AL~~~-~--~~~v~I~tDS~~v~~~l~~~~   77 (132)
T PF00075_consen    2 KAIIIYTDGSCRPNPGKGGAGYVVWGGRNFSFRLG-GQSNNRAELQAIIEALKAL-E--HRKVTIYTDSQYVLNALNKWL   77 (132)
T ss_dssp             TSEEEEEEEEECTTTTEEEEEEEEETTEEEEEEEE-SECHHHHHHHHHHHHHHTH-S--TSEEEEEES-HHHHHHHHTHH
T ss_pred             CcEEEEEeCCccCCCCceEEEEEEECCeEEEeccc-ccchhhhheehHHHHHHHh-h--cccccccccHHHHHHHHHHhc
Confidence            46899999998753  367776555444 555565 8899999999999999944 3  4999999999999998877  


Q ss_pred             ---CCCCc----hHHHHHHHHHHHHHhCCCceEEEecCCcCCC-cccHHHHHHhcCCC
Q psy16967        189 ---KSCNN----ALLSKIYSTWLDLVACGKEISFMWCPSHCGI-SGNEAVDVAAKNPS  238 (282)
Q Consensus       189 ---~~~~~----~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi-~gNe~AD~lAk~a~  238 (282)
                         .+...    ++..+|.+.   + ..+..|.|+|||||+|+ .||+.||+|||+|+
T Consensus        78 ~~~~~~~~~~~~~i~~~i~~~---~-~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~  131 (132)
T PF00075_consen   78 HGNGWKKTSNGRPIKNEIWEL---L-SRGIKVRFRWVPGHSGVPQGNERADRLAKEAA  131 (132)
T ss_dssp             HHTTSBSCTSSSBHTHHHHHH---H-HHSSEEEEEESSSSSSSHHHHHHHHHHHHHHH
T ss_pred             cccccccccccccchhheeec---c-ccceEEeeeeccCcCCCchhHHHHHHHHHHhc
Confidence               33222    244555555   3 45789999999999999 69999999999763

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 ....

>PRK06548 ribonuclease H; Provisional

Probab=99.90  E-value=2.3e-23  Score=171.66  Aligned_cols=123  Identities=24%  Similarity=0.302  Sum_probs=94.2

Q ss_pred             CCceEEecCCCCCCC--CceEEEEEcCCe-eeeecCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeCcHHHHHHHhc-
Q psy16967        113 HDRILCFTDGSKTEN--STSCAYTINKNV-NSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLVTDSMSSLQAITS-  188 (282)
Q Consensus       113 ~~~~~iyTDGS~~~~--~~G~gvv~~~~~-~~~~l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~sDS~~al~~l~~-  188 (282)
                      +..+.||||||+.++  ..|+|+++.++. .+.. ....|++.|||.|++.||+.+.. ....|.|+|||++|++++.. 
T Consensus         3 ~~~~~IytDGa~~gnpg~~G~g~~~~~~~~~~g~-~~~~TNnraEl~Aii~aL~~~~~-~~~~v~I~TDS~yvi~~i~~W   80 (161)
T PRK06548          3 NNEIIAATDGSSLANPGPSGWAWYVDENTWDSGG-WDIATNNIAELTAVRELLIATRH-TDRPILILSDSKYVINSLTKW   80 (161)
T ss_pred             CCEEEEEEeeccCCCCCceEEEEEEeCCcEEccC-CCCCCHHHHHHHHHHHHHHhhhc-CCceEEEEeChHHHHHHHHHH
Confidence            455999999999874  378886654332 2212 24579999999999999986643 34679999999999999984 


Q ss_pred             --------CCCCch--H-HHHHHHHHHHHHhCCCceEEEecCCcCCCcccHHHHHHhcCCC
Q psy16967        189 --------KSCNNA--L-LSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNPS  238 (282)
Q Consensus       189 --------~~~~~~--~-~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~  238 (282)
                              +...++  + -+++++.+..+... ..|+|.||+||+|++|||.||+||++|+
T Consensus        81 ~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~-~~v~~~wVkgHsg~~gNe~aD~LA~~aa  140 (161)
T PRK06548         81 VYSWKMRKWRKADGKPVLNQEIIQEIDSLMEN-RNIRMSWVNAHTGHPLNEAADSLARQAA  140 (161)
T ss_pred             HHHHHHCCCcccCCCccccHHHHHHHHHHHhc-CceEEEEEecCCCCHHHHHHHHHHHHHH
Confidence                    222333  3 26676666666655 4799999999999999999999999988

>PRK08719 ribonuclease H; Reviewed

Probab=99.90  E-value=3e-23  Score=169.26  Aligned_cols=120  Identities=19%  Similarity=0.253  Sum_probs=91.7

Q ss_pred             CceEEecCCCCCCCC-----ceEEEE-EcC--Ce---eeeecCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeCcHHH
Q psy16967        114 DRILCFTDGSKTENS-----TSCAYT-INK--NV---NSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLVTDSMSS  182 (282)
Q Consensus       114 ~~~~iyTDGS~~~~~-----~G~gvv-~~~--~~---~~~~l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~sDS~~a  182 (282)
                      ..++||||||+.+++     +|+|++ ...  ..   .+..+....|++.|||.|++.||+.+...    ..|+|||+++
T Consensus         3 ~~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~----~~i~tDS~yv   78 (147)
T PRK08719          3 ASYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARDG----DVIYSDSDYC   78 (147)
T ss_pred             ceEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCC----CEEEechHHH
Confidence            468999999997654     489954 332  21   33345556799999999999999998653    3799999999


Q ss_pred             HHHHh--------cCCCCc-h--H-HHHHHHHHHHHHhCCCceEEEecCCcCCCcccHHHHHHhcCCC
Q psy16967        183 LQAIT--------SKSCNN-A--L-LSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNPS  238 (282)
Q Consensus       183 l~~l~--------~~~~~~-~--~-~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~  238 (282)
                      +++++        +.+..+ +  + -..+++.+..+.. ...|+|.|||||+|++|||.||+||++|+
T Consensus        79 i~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~-~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~  145 (147)
T PRK08719         79 VRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRA-RKYVEVEKVTAHSGIEGNEAADMLAQAAA  145 (147)
T ss_pred             HHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhC-CCcEEEEEecCCCCChhHHHHHHHHHHHh
Confidence            99994        444332 2  1 2556666666655 46799999999999999999999999886

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

Probab=99.89  E-value=6e-23  Score=166.64  Aligned_cols=124  Identities=23%  Similarity=0.244  Sum_probs=100.5

Q ss_pred             CceEEecCCCCCCC--CceEEEEEc-CCe---eeeecCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeCcHHHHHHHh
Q psy16967        114 DRILCFTDGSKTEN--STSCAYTIN-KNV---NSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLVTDSMSSLQAIT  187 (282)
Q Consensus       114 ~~~~iyTDGS~~~~--~~G~gvv~~-~~~---~~~~l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~sDS~~al~~l~  187 (282)
                      ..+.||||||+..+  ..|+|+++. +..   .+..+. .+|++.+|++|++.||+.+...+...|.|+|||++++++|.
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            35899999999874  388995543 322   333344 88999999999999999999888999999999999999998


Q ss_pred             cC---CCCc--------h-HHHHHHHHHHHHHhCCCceEEEecCCcCCCcccHHHHHHhcCCC
Q psy16967        188 SK---SCNN--------A-LLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNPS  238 (282)
Q Consensus       188 ~~---~~~~--------~-~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~  238 (282)
                      .+   +...        + ....+++.+.++......|.+.|||||+|.++||.||+||+.|+
T Consensus        81 ~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~~~  143 (154)
T COG0328          81 RWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAREAA  143 (154)
T ss_pred             HHHhhccccCccccccCccccHHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHHHH
Confidence            43   1111        1 24577777777877777999999999999999999999999987

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=99.88  E-value=2.7e-22  Score=164.53  Aligned_cols=122  Identities=22%  Similarity=0.238  Sum_probs=89.7

Q ss_pred             ceEEecCCCCCCC--CceEEEE-EcCCe-eee-ecCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeCcHHHHHHHhcC
Q psy16967        115 RILCFTDGSKTEN--STSCAYT-INKNV-NSF-RLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLVTDSMSSLQAITSK  189 (282)
Q Consensus       115 ~~~iyTDGS~~~~--~~G~gvv-~~~~~-~~~-~l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~sDS~~al~~l~~~  189 (282)
                      .+.||||||+.++  ..|+|++ ...+. ..+ ......|++.|||.|++.||+.+..  ...+.|+|||++++++|..+
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            4899999999864  3788854 33333 222 2234678999999999999998864  46799999999999999862


Q ss_pred             --------CC-Cch--H-HHHHHHHHHHHHhCCCceEEEecCCcCCCcccHHHHHHhcCCCC
Q psy16967        190 --------SC-NNA--L-LSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNPSP  239 (282)
Q Consensus       190 --------~~-~~~--~-~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~  239 (282)
                              +. .++  + -..+++.+.++.. ...|.|.|||||+|++||+.||+||++|+.
T Consensus        81 ~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~-~~~v~~~wV~~H~~~~~N~~AD~lA~~a~~  141 (150)
T PRK00203         81 IHGWKKNGWKTADKKPVKNVDLWQRLDAALK-RHQIKWHWVKGHAGHPENERCDELARAGAE  141 (150)
T ss_pred             HHHHHHcCCcccCCCccccHHHHHHHHHHhc-cCceEEEEecCCCCCHHHHHHHHHHHHHHH
Confidence                    21 121  2 1344444444443 378999999999999999999999998873

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

Probab=99.81  E-value=4.5e-19  Score=138.07  Aligned_cols=122  Identities=26%  Similarity=0.325  Sum_probs=95.2

Q ss_pred             EEecCCCCCCC--CceEEEEE-cCCe----eeeecCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeCcHHHHHHHhcC
Q psy16967        117 LCFTDGSKTEN--STSCAYTI-NKNV----NSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLVTDSMSSLQAITSK  189 (282)
Q Consensus       117 ~iyTDGS~~~~--~~G~gvv~-~~~~----~~~~l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~sDS~~al~~l~~~  189 (282)
                      .+|||||...+  ++|+|++. +.+.    .........+++.+|+.|++.||+.+...+..++.|++||+.++..+.+.
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            48999999875  58888654 3322    11122257799999999999999999888899999999999999999987


Q ss_pred             CCC-chHHHHHHHHHHHHHhCCCceEEEecCCcCCCcccHHHHHHhcCCC
Q psy16967        190 SCN-NALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNPS  238 (282)
Q Consensus       190 ~~~-~~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~  238 (282)
                      ... ......++..+..+...+..+.|.|||+|+|..+|+.||.||++|.
T Consensus        81 ~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~~  130 (130)
T cd06222          81 YEGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKEAA  130 (130)
T ss_pred             ccCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence            652 2223344444444556788999999999999999999999999874

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=99.77  E-value=3.1e-18  Score=154.87  Aligned_cols=126  Identities=22%  Similarity=0.225  Sum_probs=97.2

Q ss_pred             CCceEEecCCCCCCCC-----ceEEEE-EcCCe--eeeecC-CCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeCcHHHH
Q psy16967        113 HDRILCFTDGSKTENS-----TSCAYT-INKNV--NSFRLN-VVNSVFSAELMAILLCLQNLKYLPSTKFLLVTDSMSSL  183 (282)
Q Consensus       113 ~~~~~iyTDGS~~~~~-----~G~gvv-~~~~~--~~~~l~-~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~sDS~~al  183 (282)
                      .+.+++|||||+..+|     +|+||. .++..  .+.++. ..+++|.|||.||..||+.+.+....+++|.|||++++
T Consensus       210 ~~~~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~~~~kv~I~TDS~~~i  289 (371)
T KOG3752|consen  210 IEIQVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSKNINKVVIRTDSEYFI  289 (371)
T ss_pred             ccceEEEecCccccCCCCCCcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHhcCCCcEEEEechHHHH
Confidence            3448999999998754     799954 44444  666764 78999999999999999999988888999999999999


Q ss_pred             HHHhcCCCC-----------ch----HH--HHHHHHHHHHHh--CCCceEEEecCCcCCCcccHHHHHHhcCCC
Q psy16967        184 QAITSKSCN-----------NA----LL--SKIYSTWLDLVA--CGKEISFMWCPSHCGISGNEAVDVAAKNPS  238 (282)
Q Consensus       184 ~~l~~~~~~-----------~~----~~--~~i~~~~~~l~~--~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~  238 (282)
                      ++|+.+.+.           ++    ++  ...+..+.+|.+  .+.+|.+.||+||.|+.||+.||.||+++.
T Consensus       290 ~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs  363 (371)
T KOG3752|consen  290 NSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEMADALARKGS  363 (371)
T ss_pred             HHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHHHHHHHhhhh
Confidence            999865221           11    01  122222233332  468999999999999999999999999875

>PRK13907 rnhA ribonuclease H; Provisional

Probab=99.76  E-value=5.9e-18  Score=134.97  Aligned_cols=119  Identities=20%  Similarity=0.194  Sum_probs=92.9

Q ss_pred             eEEecCCCCCCC--CceEEEEEc-CCe-eeee-cCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeCcHHHHHHHhcCC
Q psy16967        116 ILCFTDGSKTEN--STSCAYTIN-KNV-NSFR-LNVVNSVFSAELMAILLCLQNLKYLPSTKFLLVTDSMSSLQAITSKS  190 (282)
Q Consensus       116 ~~iyTDGS~~~~--~~G~gvv~~-~~~-~~~~-l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~sDS~~al~~l~~~~  190 (282)
                      +.||||||+..+  ..|+|+++. ... ...+ .....+++.||+.|++.||+.+...+..++.|+|||+.++..+++.+
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            689999999874  489996643 322 2222 22457999999999999999999988889999999999999999876


Q ss_pred             CCchHHHHHHHHHHHHHhCCCceEEEecCCcCCCcccHHHHHHhcCCC
Q psy16967        191 CNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNPS  238 (282)
Q Consensus       191 ~~~~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~  238 (282)
                      ..+.-...+.+.+..+......+.|.|||+    ++|+.||.||+.|.
T Consensus        82 ~~~~~~~~l~~~~~~l~~~f~~~~~~~v~r----~~N~~Ad~LA~~a~  125 (128)
T PRK13907         82 AKNKMFAPLLEEALQYIKSFDLFFIKWIPS----SQNKVADELARKAI  125 (128)
T ss_pred             hcChhHHHHHHHHHHHHhcCCceEEEEcCc----hhchhHHHHHHHHH
Confidence            543334555555555667778889999996    59999999999875

>PRK07708 hypothetical protein; Validated

Probab=99.66  E-value=1.4e-15  Score=131.64  Aligned_cols=127  Identities=15%  Similarity=0.070  Sum_probs=94.2

Q ss_pred             CCCceEEecCCCCCC--CCceEEEEE-cC-C-e-ee----eecCCCCchHHHHHHHHHHHHHHhhcCCCCe--EEEEeCc
Q psy16967        112 YHDRILCFTDGSKTE--NSTSCAYTI-NK-N-V-NS----FRLNVVNSVFSAELMAILLCLQNLKYLPSTK--FLLVTDS  179 (282)
Q Consensus       112 ~~~~~~iyTDGS~~~--~~~G~gvv~-~~-~-~-~~----~~l~~~~s~~~AEl~AI~~AL~~~~~~~~~~--i~I~sDS  179 (282)
                      .++.+++|+|||+..  +++|+|+++ +. + . ..    ..++...+++.||+.|++.||+.+...+.+.  |.|++||
T Consensus        70 ep~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~DS  149 (219)
T PRK07708         70 EPHEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFRGDS  149 (219)
T ss_pred             CCCcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHcCCCcceEEEEecc
Confidence            466799999999864  458889543 32 2 2 11    2355567999999999999999999887654  8999999


Q ss_pred             HHHHHHHhcCCCC-chHHHHHHHHHHHHHhC-CCceEEEecCCcCCCcccHHHHHHhcCCCCCCC
Q psy16967        180 MSSLQAITSKSCN-NALLSKIYSTWLDLVAC-GKEISFMWCPSHCGISGNEAVDVAAKNPSPSFP  242 (282)
Q Consensus       180 ~~al~~l~~~~~~-~~~~~~i~~~~~~l~~~-~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~~p  242 (282)
                      +.+++.+++.+.. ++....+.+.+..+.+. ...+.|.|||    +..|+.||+||+.|+...|
T Consensus       150 qlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~Vp----R~~N~~AD~LAk~Al~~~~  210 (219)
T PRK07708        150 QVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPIS----RKQNKEADQLATQALEGTV  210 (219)
T ss_pred             HHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECC----chhhhHHHHHHHHHHhcCC
Confidence            9999999998654 33444454544444333 3458889998    6789999999999995444

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=99.55  E-value=5.7e-14  Score=131.44  Aligned_cols=118  Identities=14%  Similarity=0.178  Sum_probs=93.5

Q ss_pred             eEEecCCCCCCC--CceEEEEE-cC--Ce--ee--eecCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeCcHHHHHHH
Q psy16967        116 ILCFTDGSKTEN--STSCAYTI-NK--NV--NS--FRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLVTDSMSSLQAI  186 (282)
Q Consensus       116 ~~iyTDGS~~~~--~~G~gvv~-~~--~~--~~--~~l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~sDS~~al~~l  186 (282)
                      +.||||||+..+  ..|+|+++ +.  +.  ..  ..++ .+|++.||+.|++.||+.+...+.+.+.|++||+.+++.+
T Consensus         3 ~~i~~DGa~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~-~~tnn~AE~~All~gL~~a~~~g~~~v~i~~DS~lvi~~i   81 (372)
T PRK07238          3 VVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIG-RATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQM   81 (372)
T ss_pred             EEEEecCCCCCCCCceEEEEEEEeCCCCcEEEEeecccC-CCCchHHHHHHHHHHHHHHHhCCCCeEEEEeCcHHHHHHh
Confidence            689999999975  47899553 32  21  12  2233 6788999999999999999998889999999999999999


Q ss_pred             hcCCC-CchHHHHHHHHHHHHHhCCCceEEEecCCcCCCcccHHHHHHhcCCC
Q psy16967        187 TSKSC-NNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNPS  238 (282)
Q Consensus       187 ~~~~~-~~~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~  238 (282)
                      .+.+. .+.-...+.+.+..+.+.+..+.|.|||.    .+|+.||.||+.|.
T Consensus        82 ~~~~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~r----~~N~~AD~LA~~a~  130 (372)
T PRK07238         82 SGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPR----ARNAHADRLANEAM  130 (372)
T ss_pred             CCCCccCChHHHHHHHHHHHHHhcCCceEEEECCc----hhhhHHHHHHHHHH
Confidence            88764 34434455555566777788999999995    78999999999886

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

Probab=99.34  E-value=4.4e-12  Score=93.36  Aligned_cols=84  Identities=25%  Similarity=0.212  Sum_probs=66.7

Q ss_pred             hHHHHHHHHHHHHHHhhcCCCCeEEEEeCcHHHHHHHhcCCCCchHHHHHHHHHHHHHhCCCceEEEecCCcCCCcccHH
Q psy16967        150 VFSAELMAILLCLQNLKYLPSTKFLLVTDSMSSLQAITSKSCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEA  229 (282)
Q Consensus       150 ~~~AEl~AI~~AL~~~~~~~~~~i~I~sDS~~al~~l~~~~~~~~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~  229 (282)
                      +..||+.|+..||+.+...+..+|.|+|||+.++..+++..........+...+..+.+....+.|.|||    .++|..
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            4689999999999999999999999999999999999988543334455555556677778999999999    789999


Q ss_pred             HHHHhcCC
Q psy16967        230 VDVAAKNP  237 (282)
Q Consensus       230 AD~lAk~a  237 (282)
                      ||.|||.|
T Consensus        77 A~~LA~~a   84 (87)
T PF13456_consen   77 ADALAKFA   84 (87)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99999975

>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=81.29  E-value=2.2  Score=36.42  Aligned_cols=90  Identities=22%  Similarity=0.214  Sum_probs=50.2

Q ss_pred             CceEEecCCCCCCCCceEEEEEcCCeeeeecCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeCcHHHHHHHhcCCCCc
Q psy16967        114 DRILCFTDGSKTENSTSCAYTINKNVNSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLVTDSMSSLQAITSKSCNN  193 (282)
Q Consensus       114 ~~~~iyTDGS~~~~~~G~gvv~~~~~~~~~l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~sDS~~al~~l~~~~~~~  193 (282)
                      .--.||+|+.-.    |+|+.+.++...+.....-.+..+||.|...|.-+..    .++ |.|||-.|+..   ....-
T Consensus        93 ~lc~VfaDATpT----gwgi~i~~~~~~~Tfs~~l~IhtaELlaaClAr~~~~----~r~-l~tDnt~Vlsr---kyts~  160 (245)
T PF00336_consen   93 GLCQVFADATPT----GWGISITGQRMRGTFSKPLPIHTAELLAACLARLMSG----ARC-LGTDNTVVLSR---KYTSF  160 (245)
T ss_pred             CCCceeccCCCC----cceeeecCceeeeeecccccchHHHHHHHHHHHhccC----CcE-EeecCcEEEec---ccccC
Confidence            345789998754    4443333333222222344789999999988876552    233 89999876532   12222


Q ss_pred             h-HHHHHHHHHHHHHhCCCceEEEecCCc
Q psy16967        194 A-LLSKIYSTWLDLVACGKEISFMWCPSH  221 (282)
Q Consensus       194 ~-~~~~i~~~~~~l~~~~~~v~~~WVpgH  221 (282)
                      + .....-+.   +.   ..+.|..||+-
T Consensus       161 PW~lac~A~w---iL---rgts~~yVPS~  183 (245)
T PF00336_consen  161 PWLLACAANW---IL---RGTSFYYVPSK  183 (245)
T ss_pred             cHHHHHHHHH---hh---cCceEEEeccc
Confidence            2 22222222   21   34788889964

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

ID	Length	Definition	E-value
Query	282
4b3o_A	560	Structures Of Hiv-1 Rt And Rna-dna Complex Reveal A		3e-04
1lwf_A	560	Crystal Structure Of A Mutant Hiv-1 Reverse Transcr		4e-04
1lwe_A	560	Crystal Structure Of M41lT215Y MUTANT HIV-1 Reverse		5e-04
1rt3_A	560	Azt Drug Resistant Hiv-1 Reverse Transcriptase Comp		5e-04
1lw0_A	560	Crystal Structure Of T215y Mutant Hiv-1 Reverse Tra		5e-04
1s1t_A	560	Crystal Structure Of L100i Mutant Hiv-1 Reverse Tra		5e-04
1s1x_A	560	Crystal Structure Of V108i Mutant Hiv-1 Reverse Tra		5e-04
1lwc_A	560	Crystal Structure Of M184v Mutant Hiv-1 Reverse Tra		5e-04
1rev_A	560	Hiv-1 Reverse Transcriptase Length = 560		5e-04
3dm2_A	560	Crystal Structure Of Hiv-1 K103n Mutant Reverse Tra		5e-04
1jle_A	560	Crystal Structure Of Y188c Mutant Hiv-1 Reverse Tra		5e-04
3med_A	560	Hiv-1 K103n Reverse Transcriptase In Complex With T		5e-04
1s1w_A	560	Crystal Structure Of V106a Mutant Hiv-1 Reverse Tra		5e-04
2rki_A	560	Crystal Structure Of Hiv-1 Reverse Transcriptase (R		5e-04
3ffi_A	561	Hiv-1 Rt With Pyridone Non-Nucleoside Inhibitor Len		5e-04
3dlk_A	556	Crystal Structure Of An Engineered Form Of The Hiv-		5e-04
2jle_A	566	Novel Indazole Nnrtis Created Using Molecular Templ		6e-04
3di6_A	561	Hiv-1 Rt With Pyridazinone Non-Nucleoside Inhibitor		6e-04
1s6p_A	560	Crystal Structure Of Human Immunodeficiency Virus T		6e-04
1jkh_A	560	Crystal Structure Of Y181c Mutant Hiv-1 Reverse Tra		6e-04
1qe1_A	558	Crystal Structure Of 3tc-Resistant M184i Mutant Of		6e-04
3ig1_A	555	Hiv-1 Reverse Transcriptase With The Inhibitor Beta		6e-04
1jlf_A	560	Crystal Structure Of Y188c Mutant Hiv-1 Reverse Tra		6e-04
1hni_A	558	Structure Of Hiv-1 Reverse Transcriptase In A Compl		6e-04
2ynf_A	563	Hiv-1 Reverse Transcriptase Y188l Mutant In Complex		6e-04
3kjv_A	560	Hiv-1 Reverse Transcriptase In Complex With Dna Len		6e-04
2rf2_A	563	Hiv Reverse Transcriptase In Complex With Inhibitor		6e-04
3drs_A	563	Hiv Reverse Transcriptase K103n Mutant In Complex W		6e-04
3qo9_A	557	Crystal Structure Of Hiv-1 Reverse Transcriptase (R		6e-04
1hpz_A	560	Human Immunodeficiency Virus Type 1 Length = 560		6e-04
4dg1_A	549	Crystal Structure Of Hiv-1 Reverse Transcriptase (R		6e-04
3dmj_A	560	Crystal Structure Of Hiv-1 V106a And Y181c Mutant R		6e-04
3qlh_A	555	Hiv-1 Reverse Transcriptase In Complex With Manicol		6e-04
2zd1_A	557	Crystal Structure Of Hiv-1 Reverse Transcriptase (R		6e-04
2i5j_A	552	Crystal Structure Of Hiv-1 Reverse Transcriptase (R		6e-04
1dlo_A	556	Human Immunodeficiency Virus Type 1 Length = 556		6e-04
3irx_A	558	Crystal Structure Of Hiv-1 Reverse Transcriptase (R		7e-04
2ze2_A	557	Crystal Structure Of L100iK103N MUTANT HIV-1 Revers		7e-04
1rdh_A	146	Crystallographic Analyses Of An Active Hiv-1 Ribonu		7e-04
3drr_A	563	Hiv Reverse Transcriptase Y181c Mutant In Complex W		7e-04
1hys_A	553	Crystal Structure Of Hiv-1 Reverse Transcriptase In		7e-04
3kle_A	562	Crystal Structure Of Azt-Resistant Hiv-1 Reverse Tr		7e-04
1hmv_A	560	The Structure Of Unliganded Reverse Transcriptase F		7e-04
1n5y_A	558	Hiv-1 Reverse Transcriptase Crosslinked To Post- Tr		7e-04
1hvu_A	554	Human Immunodeficiency Virus Type 1 Reverse Transcr		7e-04
3klh_A	564	Crystal Structure Of Azt-Resistant Hiv-1 Reverse Tr		7e-04
3jsm_A	558	K65r Mutant Hiv-1 Reverse Transcriptase Cross-Linke		7e-04
2iaj_A	560	Crystal Structure Of K103nY181C MUTANT HIV-1 Revers		7e-04
1uwb_A	558	Tyr 181 Cys Hiv-1 Rt8-Cl Tibo Length = 558		7e-04
3hvt_A	556	Structural Basis Of Asymmetry In The Human Immunode		7e-04
2vg5_A	557	Crystal Structures Of Hiv-1 Reverse Transcriptase C		7e-04
3klf_A	557	Crystal Structure Of Wild-Type Hiv-1 Reverse Transc		8e-04
3bgr_A	557	Crystal Structure Of K103nY181C MUTANT HIV-1 Revers		9e-04

>pdb|4B3O|A Chain A, Structures Of Hiv-1 Rt And Rna-dna Complex Reveal A Unique Rt Conformation And Substrate Interface Length = 560

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 30/117 (25%), Positives = 52/117 (44%), Gaps = 12/117 (10%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLV 176
           + DG+ +  +      Y  NK           +    EL AI L LQ+       +  +V
Sbjct: 441 YVDGAASRETKLGKAGYVTNKGRQKVVTLTDTTNQKTELQAIHLALQD----SGLEVNIV 496
Query: 177 TDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           TDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 497 TDSQYALGIIQAQPDQSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|1LWF|A Chain A, Crystal Structure Of A Mutant Hiv-1 Reverse Transcriptase (rtmq+m184v: M41l/d67n/k70r/m184v/t215y) In Complex With Nevirapine Length = 560

Iteration: 1
 Score = 41.6 bits (96), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 29/117 (24%), Positives = 51/117 (43%), Gaps = 12/117 (10%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLV 176
           + DG+    +      Y  N+           +    EL AI L LQ+       +  +V
Sbjct: 441 YVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQD----SGLEVNIV 496
Query: 177 TDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           TDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 497 TDSQYALGIIQAQPDQSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|1LWE|A Chain A, Crystal Structure Of M41lT215Y MUTANT HIV-1 Reverse Transcriptase (Rtmn) In Complex With Nevirapine Length = 560

Iteration: 1
 Score = 41.6 bits (96), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 29/117 (24%), Positives = 51/117 (43%), Gaps = 12/117 (10%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLV 176
           + DG+    +      Y  N+           +    EL AI L LQ+       +  +V
Sbjct: 441 YVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQD----SGLEVNIV 496
Query: 177 TDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           TDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 497 TDSQYALGIIQAQPDQSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|1RT3|A Chain A, Azt Drug Resistant Hiv-1 Reverse Transcriptase Complexed With 1051u91 Length = 560

Iteration: 1
 Score = 41.6 bits (96), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 29/117 (24%), Positives = 51/117 (43%), Gaps = 12/117 (10%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLV 176
           + DG+    +      Y  N+           +    EL AI L LQ+       +  +V
Sbjct: 441 YVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQD----SGLEVNIV 496
Query: 177 TDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           TDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 497 TDSQYALGIIQAQPDQSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|1LW0|A Chain A, Crystal Structure Of T215y Mutant Hiv-1 Reverse Transcriptase In Complex With Nevirapine Length = 560

Iteration: 1
 Score = 41.6 bits (96), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 29/117 (24%), Positives = 51/117 (43%), Gaps = 12/117 (10%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLV 176
           + DG+    +      Y  N+           +    EL AI L LQ+       +  +V
Sbjct: 441 YVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQD----SGLEVNIV 496
Query: 177 TDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           TDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 497 TDSQYALGIIQAQPDQSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|1S1T|A Chain A, Crystal Structure Of L100i Mutant Hiv-1 Reverse Transcriptase In Complex With Uc-781 Length = 560

Iteration: 1
 Score = 41.6 bits (96), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 29/117 (24%), Positives = 51/117 (43%), Gaps = 12/117 (10%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLV 176
           + DG+    +      Y  N+           +    EL AI L LQ+       +  +V
Sbjct: 441 YVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQD----SGLEVNIV 496
Query: 177 TDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           TDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 497 TDSQYALGIIQAQPDQSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|1S1X|A Chain A, Crystal Structure Of V108i Mutant Hiv-1 Reverse Transcriptase In Complex With Nevirapine Length = 560

Iteration: 1
 Score = 41.6 bits (96), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 29/117 (24%), Positives = 51/117 (43%), Gaps = 12/117 (10%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLV 176
           + DG+    +      Y  N+           +    EL AI L LQ+       +  +V
Sbjct: 441 YVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQD----SGLEVNIV 496
Query: 177 TDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           TDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 497 TDSQYALGIIQAQPDQSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|1LWC|A Chain A, Crystal Structure Of M184v Mutant Hiv-1 Reverse Transcriptase In Complex With Nevirapine Length = 560

Iteration: 1
 Score = 41.6 bits (96), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 29/117 (24%), Positives = 51/117 (43%), Gaps = 12/117 (10%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLV 176
           + DG+    +      Y  N+           +    EL AI L LQ+       +  +V
Sbjct: 441 YVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQD----SGLEVNIV 496
Query: 177 TDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           TDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 497 TDSQYALGIIQAQPDQSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|1REV|A Chain A, Hiv-1 Reverse Transcriptase Length = 560

Iteration: 1
 Score = 41.6 bits (96), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 29/117 (24%), Positives = 51/117 (43%), Gaps = 12/117 (10%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLV 176
           + DG+    +      Y  N+           +    EL AI L LQ+       +  +V
Sbjct: 441 YVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQD----SGLEVNIV 496
Query: 177 TDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           TDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 497 TDSQYALGIIQAQPDQSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|3DM2|A Chain A, Crystal Structure Of Hiv-1 K103n Mutant Reverse Transcriptase In Complex With Gw564511. Length = 560

Iteration: 1
 Score = 41.6 bits (96), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 29/117 (24%), Positives = 51/117 (43%), Gaps = 12/117 (10%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLV 176
           + DG+    +      Y  N+           +    EL AI L LQ+       +  +V
Sbjct: 441 YVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQD----SGLEVNIV 496
Query: 177 TDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           TDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 497 TDSQYALGIIQAQPDQSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|1JLE|A Chain A, Crystal Structure Of Y188c Mutant Hiv-1 Reverse Transcriptase Length = 560

Iteration: 1
 Score = 41.6 bits (96), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 29/117 (24%), Positives = 51/117 (43%), Gaps = 12/117 (10%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLV 176
           + DG+    +      Y  N+           +    EL AI L LQ+       +  +V
Sbjct: 441 YVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQD----SGLEVNIV 496
Query: 177 TDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           TDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 497 TDSQYALGIIQAQPDQSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|3MED|A Chain A, Hiv-1 K103n Reverse Transcriptase In Complex With Tmc125 Length = 560

Iteration: 1
 Score = 41.6 bits (96), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 29/117 (24%), Positives = 51/117 (43%), Gaps = 12/117 (10%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLV 176
           + DG+    +      Y  N+           +    EL AI L LQ+       +  +V
Sbjct: 441 YVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQD----SGLEVNIV 496
Query: 177 TDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           TDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 497 TDSQYALGIIQAQPDQSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|1S1W|A Chain A, Crystal Structure Of V106a Mutant Hiv-1 Reverse Transcriptase In Complex With Uc-781 Length = 560

Iteration: 1
 Score = 41.6 bits (96), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 29/117 (24%), Positives = 51/117 (43%), Gaps = 12/117 (10%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLV 176
           + DG+    +      Y  N+           +    EL AI L LQ+       +  +V
Sbjct: 441 YVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQD----SGLEVNIV 496
Query: 177 TDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           TDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 497 TDSQYALGIIQAQPDQSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|2RKI|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In Complex With A Triazole Derived Nnrti Length = 560

Iteration: 1
 Score = 41.6 bits (96), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 29/117 (24%), Positives = 51/117 (43%), Gaps = 12/117 (10%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLV 176
           + DG+    +      Y  N+           +    EL AI L LQ+       +  +V
Sbjct: 441 YVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQD----SGLEVNIV 496
Query: 177 TDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           TDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 497 TDSQYALGIIQAQPDQSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|3FFI|A Chain A, Hiv-1 Rt With Pyridone Non-Nucleoside Inhibitor Length = 561

Iteration: 1
 Score = 41.6 bits (96), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 29/117 (24%), Positives = 51/117 (43%), Gaps = 12/117 (10%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLV 176
           + DG+    +      Y  N+           +    EL AI L LQ+       +  +V
Sbjct: 442 YVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQD----SGLEVNIV 497
Query: 177 TDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           TDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 498 TDSQYALGIIQAQPDQSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 550

>pdb|3DLK|A Chain A, Crystal Structure Of An Engineered Form Of The Hiv-1 Reverse Transcriptase, Rt69a Length = 556

Iteration: 1
 Score = 41.6 bits (96), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 32/119 (26%), Positives = 52/119 (43%), Gaps = 16/119 (13%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSF--RLNVVNSVFSAELMAILLCLQNLKYLPSTKFL 174
           + DG+    +      Y  NK         N  N     EL AI L LQ+       +  
Sbjct: 442 YVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQ--KTELQAIYLALQD----SGLEVN 495
Query: 175 LVTDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           +VTDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 496 IVTDSQYALGIIQAQPDKSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 550

>pdb|2JLE|A Chain A, Novel Indazole Nnrtis Created Using Molecular Template Hybridization Based On Crystallographic Overlays Length = 566

Iteration: 1
 Score = 41.6 bits (96), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 29/117 (24%), Positives = 51/117 (43%), Gaps = 12/117 (10%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLV 176
           + DG+    +      Y  N+           +    EL AI L LQ+       +  +V
Sbjct: 441 YVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQD----SGLEVNIV 496
Query: 177 TDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           TDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 497 TDSQYALGIIQAQPDQSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|3DI6|A Chain A, Hiv-1 Rt With Pyridazinone Non-Nucleoside Inhibitor Length = 561

Iteration: 1
 Score = 41.6 bits (96), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 29/117 (24%), Positives = 51/117 (43%), Gaps = 12/117 (10%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLV 176
           + DG+    +      Y  N+           +    EL AI L LQ+       +  +V
Sbjct: 441 YVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQD----SGLEVNIV 496
Query: 177 TDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           TDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 497 TDSQYALGIIQAQPDQSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|1S6P|A Chain A, Crystal Structure Of Human Immunodeficiency Virus Type 1 Reverse Transcriptase (Rt) In Complex With Janssen-R100943 Length = 560

Iteration: 1
 Score = 41.2 bits (95), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 32/119 (26%), Positives = 52/119 (43%), Gaps = 16/119 (13%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSF--RLNVVNSVFSAELMAILLCLQNLKYLPSTKFL 174
           + DG+    +      Y  NK         N  N     EL AI L LQ+       +  
Sbjct: 441 YVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQ--KTELQAIYLALQD----SGLEVN 494
Query: 175 LVTDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           +VTDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 495 IVTDSQYALGIIQAQPDKSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|1JKH|A Chain A, Crystal Structure Of Y181c Mutant Hiv-1 Reverse Transcriptase In Complex With Dmp-266(Efavirenz) Length = 560

Iteration: 1
 Score = 41.2 bits (95), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 29/117 (24%), Positives = 51/117 (43%), Gaps = 12/117 (10%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLV 176
           + DG+    +      Y  N+           +    EL AI L LQ+       +  +V
Sbjct: 441 YVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQD----SGLEVNIV 496
Query: 177 TDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           TDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 497 TDSQYALGIIQAQPDQSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|1QE1|A Chain A, Crystal Structure Of 3tc-Resistant M184i Mutant Of Hiv-1 Reverse Transcriptase Length = 558

Iteration: 1
 Score = 41.2 bits (95), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 32/119 (26%), Positives = 52/119 (43%), Gaps = 16/119 (13%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSF--RLNVVNSVFSAELMAILLCLQNLKYLPSTKFL 174
           + DG+    +      Y  NK         N  N     EL AI L LQ+       +  
Sbjct: 441 YVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQ--KTELQAIYLALQD----SGLEVN 494
Query: 175 LVTDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           +VTDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 495 IVTDSQYALGIIQAQPDKSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|3IG1|A Chain A, Hiv-1 Reverse Transcriptase With The Inhibitor Beta- Thujaplicinol Bound At The Rnase H Active Site Length = 555

Iteration: 1
 Score = 41.2 bits (95), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 32/119 (26%), Positives = 52/119 (43%), Gaps = 16/119 (13%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSF--RLNVVNSVFSAELMAILLCLQNLKYLPSTKFL 174
           + DG+    +      Y  NK         N  N     EL AI L LQ+       +  
Sbjct: 441 YVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQ--KTELQAIYLALQD----SGLEVN 494
Query: 175 LVTDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           +VTDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 495 IVTDSQYALGIIQAQPDKSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|1JLF|A Chain A, Crystal Structure Of Y188c Mutant Hiv-1 Reverse Transcriptase In Complex With Nevirapine Length = 560

Iteration: 1
 Score = 41.2 bits (95), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 29/117 (24%), Positives = 51/117 (43%), Gaps = 12/117 (10%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLV 176
           + DG+    +      Y  N+           +    EL AI L LQ+       +  +V
Sbjct: 441 YVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQD----SGLEVNIV 496
Query: 177 TDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           TDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 497 TDSQYALGIIQAQPDQSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|1HNI|A Chain A, Structure Of Hiv-1 Reverse Transcriptase In A Complex With The Nonnucleoside Inhibitor Alpha-Apa R 95845 At 2.8 Angstroms Resolution Length = 558

Iteration: 1
 Score = 41.2 bits (95), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 32/119 (26%), Positives = 52/119 (43%), Gaps = 16/119 (13%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSF--RLNVVNSVFSAELMAILLCLQNLKYLPSTKFL 174
           + DG+    +      Y  NK         N  N     EL AI L LQ+       +  
Sbjct: 441 YVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQ--KTELQAIYLALQD----SGLEVN 494
Query: 175 LVTDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           +VTDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 495 IVTDSQYALGIIQAQPDKSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|2YNF|A Chain A, Hiv-1 Reverse Transcriptase Y188l Mutant In Complex With Inhibitor Gsk560 Length = 563

Iteration: 1
 Score = 41.2 bits (95), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 29/117 (24%), Positives = 51/117 (43%), Gaps = 12/117 (10%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLV 176
           + DG+    +      Y  N+           +    EL AI L LQ+       +  +V
Sbjct: 444 YVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQD----SGLEVNIV 499
Query: 177 TDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           TDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 500 TDSQYALGIIQAQPDQSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 552

>pdb|3KJV|A Chain A, Hiv-1 Reverse Transcriptase In Complex With Dna Length = 560

Iteration: 1
 Score = 41.2 bits (95), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 29/117 (24%), Positives = 51/117 (43%), Gaps = 12/117 (10%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLV 176
           + DG+    +      Y  N+           +    EL AI L LQ+       +  +V
Sbjct: 441 YVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQD----SGLEVNIV 496
Query: 177 TDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           TDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 497 TDSQYALGIIQAQPDQSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|2RF2|A Chain A, Hiv Reverse Transcriptase In Complex With Inhibitor 7e (Nnrti) Length = 563

Iteration: 1
 Score = 41.2 bits (95), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 29/117 (24%), Positives = 51/117 (43%), Gaps = 12/117 (10%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLV 176
           + DG+    +      Y  N+           +    EL AI L LQ+       +  +V
Sbjct: 444 YVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQD----SGLEVNIV 499
Query: 177 TDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           TDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 500 TDSQYALGIIQAQPDQSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 552

>pdb|3DRS|A Chain A, Hiv Reverse Transcriptase K103n Mutant In Complex With Inhibitor R8d Length = 563

Iteration: 1
 Score = 41.2 bits (95), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 29/117 (24%), Positives = 51/117 (43%), Gaps = 12/117 (10%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLV 176
           + DG+    +      Y  N+           +    EL AI L LQ+       +  +V
Sbjct: 444 YVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQD----SGLEVNIV 499
Query: 177 TDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           TDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 500 TDSQYALGIIQAQPDQSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 552

>pdb|3QO9|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In Complex With Tsao-T, A Non-Nucleoside Rt Inhibitor (Nnrti) Length = 557

Iteration: 1
 Score = 41.2 bits (95), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 32/119 (26%), Positives = 52/119 (43%), Gaps = 16/119 (13%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSF--RLNVVNSVFSAELMAILLCLQNLKYLPSTKFL 174
           + DG+    +      Y  NK         N  N     EL AI L LQ+       +  
Sbjct: 443 YVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQ--KTELQAIYLALQD----SGLEVN 496
Query: 175 LVTDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           +VTDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 497 IVTDSQYALGIIQAQPDKSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 551

>pdb|1HPZ|A Chain A, Human Immunodeficiency Virus Type 1 Length = 560

Iteration: 1
 Score = 41.2 bits (95), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 32/119 (26%), Positives = 52/119 (43%), Gaps = 16/119 (13%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSF--RLNVVNSVFSAELMAILLCLQNLKYLPSTKFL 174
           + DG+    +      Y  NK         N  N     EL AI L LQ+       +  
Sbjct: 441 YVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQ--KTELQAIYLALQD----SGLEVN 494
Query: 175 LVTDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           +VTDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 495 IVTDSQYALGIIQAQPDKSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|4DG1|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) With Polymorphism Mutation K172a And K173a Length = 549

Iteration: 1
 Score = 41.2 bits (95), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 32/119 (26%), Positives = 52/119 (43%), Gaps = 16/119 (13%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSF--RLNVVNSVFSAELMAILLCLQNLKYLPSTKFL 174
           + DG+    +      Y  NK         N  N     EL AI L LQ+       +  
Sbjct: 441 YVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQ--KTELQAIYLALQD----SGLEVN 494
Query: 175 LVTDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           +VTDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 495 IVTDSQYALGIIQAQPDKSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|3DMJ|A Chain A, Crystal Structure Of Hiv-1 V106a And Y181c Mutant Reverse Transcriptase In Complex With Gw564511 Length = 560

Iteration: 1
 Score = 41.2 bits (95), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 29/117 (24%), Positives = 51/117 (43%), Gaps = 12/117 (10%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLV 176
           + DG+    +      Y  N+           +    EL AI L LQ+       +  +V
Sbjct: 441 YVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQD----SGLEVNIV 496
Query: 177 TDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           TDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 497 TDSQYALGIIQAQPDQSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|3QLH|A Chain A, Hiv-1 Reverse Transcriptase In Complex With Manicol At The Rnase H Active Site And Tmc278 (rilpivirine) At The Nnrti Binding Pocket Length = 555

Iteration: 1
 Score = 41.2 bits (95), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 32/119 (26%), Positives = 52/119 (43%), Gaps = 16/119 (13%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSF--RLNVVNSVFSAELMAILLCLQNLKYLPSTKFL 174
           + DG+    +      Y  NK         N  N     EL AI L LQ+       +  
Sbjct: 442 YVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQ--KTELQAIYLALQD----SGLEVN 495
Query: 175 LVTDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           +VTDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 496 IVTDSQYALGIIQAQPDKSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 550

>pdb|2ZD1|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In Complex With Tmc278 (Rilpivirine), A Non-Nucleoside Rt Inhibitor Length = 557

Iteration: 1
 Score = 41.2 bits (95), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 32/119 (26%), Positives = 52/119 (43%), Gaps = 16/119 (13%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSF--RLNVVNSVFSAELMAILLCLQNLKYLPSTKFL 174
           + DG+    +      Y  NK         N  N     EL AI L LQ+       +  
Sbjct: 443 YVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQ--KTELQAIYLALQD----SGLEVN 496
Query: 175 LVTDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           +VTDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 497 IVTDSQYALGIIQAQPDKSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 551

>pdb|2I5J|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In Complex With Dhbnh, An Rnase H Inhibitor Length = 552

Iteration: 1
 Score = 41.2 bits (95), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 32/119 (26%), Positives = 52/119 (43%), Gaps = 16/119 (13%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSF--RLNVVNSVFSAELMAILLCLQNLKYLPSTKFL 174
           + DG+    +      Y  NK         N  N     EL AI L LQ+       +  
Sbjct: 441 YVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQ--KTELQAIYLALQD----SGLEVN 494
Query: 175 LVTDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           +VTDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 495 IVTDSQYALGIIQAQPDKSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|1DLO|A Chain A, Human Immunodeficiency Virus Type 1 Length = 556

Iteration: 1
 Score = 41.2 bits (95), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 32/119 (26%), Positives = 52/119 (43%), Gaps = 16/119 (13%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSF--RLNVVNSVFSAELMAILLCLQNLKYLPSTKFL 174
           + DG+    +      Y  NK         N  N     EL AI L LQ+       +  
Sbjct: 441 YVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQ--KTELQAIYLALQD----SGLEVN 494
Query: 175 LVTDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           +VTDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 495 IVTDSQYALGIIQAQPDKSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|3IRX|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In Complex With The Non-Nucleoside Rt Inhibitor (E)-S-Methyl 5-(1-(3,7-Dimethyl-2-Oxo-2, 3-Dihydrobenzo[d]oxazol-5-Yl)-5- (5-Methyl-1,3,4-Oxadiazol-2-Yl)pent-1-Enyl)-2-Methoxy-3- Methylbenzothioate. Length = 558

Iteration: 1
 Score = 41.2 bits (95), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 32/119 (26%), Positives = 52/119 (43%), Gaps = 16/119 (13%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSF--RLNVVNSVFSAELMAILLCLQNLKYLPSTKFL 174
           + DG+    +      Y  NK         N  N     EL AI L LQ+       +  
Sbjct: 444 YVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQ--KTELQAIYLALQD----SGLEVN 497
Query: 175 LVTDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           +VTDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 498 IVTDSQYALGIIQAQPDKSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 552

>pdb|2ZE2|A Chain A, Crystal Structure Of L100iK103N MUTANT HIV-1 Reverse Transcriptase (Rt) In Complex With Tmc278 (Rilpivirine), A Non-Nucleoside Rt Inhibitor Length = 557

Iteration: 1
 Score = 41.2 bits (95), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 32/119 (26%), Positives = 52/119 (43%), Gaps = 16/119 (13%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSF--RLNVVNSVFSAELMAILLCLQNLKYLPSTKFL 174
           + DG+    +      Y  NK         N  N     EL AI L LQ+       +  
Sbjct: 443 YVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQ--KTELQAIYLALQD----SGLEVN 496
Query: 175 LVTDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           +VTDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 497 IVTDSQYALGIIQAQPDKSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 551

>pdb|1RDH|A Chain A, Crystallographic Analyses Of An Active Hiv-1 Ribonuclease H Domain Show Structural Features That Distinguish It From The Inactive Form Length = 146

Iteration: 1
 Score = 41.2 bits (95), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 31/117 (26%), Positives = 51/117 (43%), Gaps = 12/117 (10%)
Query: 119 FTDGSKTENS--TSCAYTINKNVNSF--RLNVVNSVFSAELMAILLCLQNLKYLPSTKFL 174
           + DG+    +      Y  NK         N  N     EL AI L LQ+       +  
Sbjct: 27  YVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQ--KTELQAIYLALQD----SGLEVN 80
Query: 175 LVTDSMSSLQAITSKSCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           +VTDS  +L  I ++   +   S++ +  ++ +   +++   W P+H GI GNE VD
Sbjct: 81  IVTDSQYALGIIQAQPDKSE--SELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVD 135

>pdb|3DRR|A Chain A, Hiv Reverse Transcriptase Y181c Mutant In Complex With Inhibitor R8e Length = 563

Iteration: 1
 Score = 41.2 bits (95), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 29/117 (24%), Positives = 51/117 (43%), Gaps = 12/117 (10%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLV 176
           + DG+    +      Y  N+           +    EL AI L LQ+       +  +V
Sbjct: 444 YVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQD----SGLEVNIV 499
Query: 177 TDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           TDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 500 TDSQYALGIIQAQPDQSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 552

>pdb|1HYS|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase In Complex With A Polypurine Tract Rna:dna Length = 553

Iteration: 1
 Score = 41.2 bits (95), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 32/119 (26%), Positives = 52/119 (43%), Gaps = 16/119 (13%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSF--RLNVVNSVFSAELMAILLCLQNLKYLPSTKFL 174
           + DG+    +      Y  NK         N  N     EL AI L LQ+       +  
Sbjct: 441 YVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQ--KTELQAIYLALQD----SGLEVN 494
Query: 175 LVTDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           +VTDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 495 IVTDSQYALGIIQAQPDKSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|3KLE|A Chain A, Crystal Structure Of Azt-Resistant Hiv-1 Reverse Transcriptase Crosslinked To A Dsdna With A Bound Excision Product, Aztppppa Length = 562

Iteration: 1
 Score = 41.2 bits (95), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 32/119 (26%), Positives = 52/119 (43%), Gaps = 16/119 (13%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSF--RLNVVNSVFSAELMAILLCLQNLKYLPSTKFL 174
           + DG+    +      Y  NK         N  N     EL AI L LQ+       +  
Sbjct: 443 YVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQ--KTELQAIYLALQD----SGLEVN 496
Query: 175 LVTDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           +VTDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 497 IVTDSQYALGIIQAQPDKSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 551

>pdb|1HMV|A Chain A, The Structure Of Unliganded Reverse Transcriptase From The Human Immunodeficiency Virus Type 1 Length = 560

Iteration: 1
 Score = 41.2 bits (95), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 32/119 (26%), Positives = 52/119 (43%), Gaps = 16/119 (13%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSF--RLNVVNSVFSAELMAILLCLQNLKYLPSTKFL 174
           + DG+    +      Y  NK         N  N     EL AI L LQ+       +  
Sbjct: 441 YVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQ--KTELQAIYLALQD----SGLEVN 494
Query: 175 LVTDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           +VTDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 495 IVTDSQYALGIIQAQPDKSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|1N5Y|A Chain A, Hiv-1 Reverse Transcriptase Crosslinked To Post- Translocation Aztmp-Terminated Dna (Complex P) Length = 558

Iteration: 1
 Score = 41.2 bits (95), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 32/119 (26%), Positives = 52/119 (43%), Gaps = 16/119 (13%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSF--RLNVVNSVFSAELMAILLCLQNLKYLPSTKFL 174
           + DG+    +      Y  NK         N  N     EL AI L LQ+       +  
Sbjct: 441 YVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQ--KTELQAIYLALQD----SGLEVN 494
Query: 175 LVTDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           +VTDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 495 IVTDSQYALGIIQAQPDKSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|1HVU|A Chain A, Human Immunodeficiency Virus Type 1 Reverse Transcriptase Complexed With A 33-Base Nucleotide Rna Pseudoknot Length = 554

Iteration: 1
 Score = 41.2 bits (95), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 32/119 (26%), Positives = 52/119 (43%), Gaps = 16/119 (13%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSF--RLNVVNSVFSAELMAILLCLQNLKYLPSTKFL 174
           + DG+    +      Y  NK         N  N     EL AI L LQ+       +  
Sbjct: 441 YVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQ--KTELQAIYLALQD----SGLEVN 494
Query: 175 LVTDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           +VTDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 495 IVTDSQYALGIIQAQPDKSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|3KLH|A Chain A, Crystal Structure Of Azt-Resistant Hiv-1 Reverse Transcriptase Crosslinked To Post-Translocation Aztmp-Terminated Dna (Complex P) Length = 564

Iteration: 1
 Score = 41.2 bits (95), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 32/119 (26%), Positives = 52/119 (43%), Gaps = 16/119 (13%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSF--RLNVVNSVFSAELMAILLCLQNLKYLPSTKFL 174
           + DG+    +      Y  NK         N  N     EL AI L LQ+       +  
Sbjct: 443 YVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQ--KTELQAIYLALQD----SGLEVN 496
Query: 175 LVTDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           +VTDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 497 IVTDSQYALGIIQAQPDKSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 551

>pdb|3JSM|A Chain A, K65r Mutant Hiv-1 Reverse Transcriptase Cross-Linked To Ds-Dna And Complexed With Tenofovir-Diphosphate As The Incoming Nucleotide Substrate Length = 558

Iteration: 1
 Score = 41.2 bits (95), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 32/119 (26%), Positives = 52/119 (43%), Gaps = 16/119 (13%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSF--RLNVVNSVFSAELMAILLCLQNLKYLPSTKFL 174
           + DG+    +      Y  NK         N  N     EL AI L LQ+       +  
Sbjct: 441 YVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQ--KTELQAIYLALQD----SGLEVN 494
Query: 175 LVTDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           +VTDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 495 IVTDSQYALGIIQAQPDKSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|2IAJ|A Chain A, Crystal Structure Of K103nY181C MUTANT HIV-1 Reverse Transcriptase (Rt) In Complex With Atp Length = 560

Iteration: 1
 Score = 41.2 bits (95), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 32/119 (26%), Positives = 52/119 (43%), Gaps = 16/119 (13%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSF--RLNVVNSVFSAELMAILLCLQNLKYLPSTKFL 174
           + DG+    +      Y  NK         N  N     EL AI L LQ+       +  
Sbjct: 441 YVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQ--KTELQAIYLALQD----SGLEVN 494
Query: 175 LVTDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           +VTDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 495 IVTDSQYALGIIQAQPDKSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|1UWB|A Chain A, Tyr 181 Cys Hiv-1 Rt8-Cl Tibo Length = 558

Iteration: 1
 Score = 41.2 bits (95), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 32/119 (26%), Positives = 52/119 (43%), Gaps = 16/119 (13%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSF--RLNVVNSVFSAELMAILLCLQNLKYLPSTKFL 174
           + DG+    +      Y  NK         N  N     EL AI L LQ+       +  
Sbjct: 441 YVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQ--KTELQAIYLALQD----SGLEVN 494
Query: 175 LVTDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           +VTDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 495 IVTDSQYALGIIQAQPDKSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|3HVT|A Chain A, Structural Basis Of Asymmetry In The Human Immunodeficiency Virus Type 1 Reverse Transcriptase Heterodimer Length = 556

Iteration: 1
 Score = 41.2 bits (95), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 32/119 (26%), Positives = 52/119 (43%), Gaps = 16/119 (13%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSF--RLNVVNSVFSAELMAILLCLQNLKYLPSTKFL 174
           + DG+    +      Y  NK         N  N     EL AI L LQ+       +  
Sbjct: 441 YVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQ--KTELQAIYLALQD----SGLEVN 494
Query: 175 LVTDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           +VTDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 495 IVTDSQYALGIIQAQPDKSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|2VG5|A Chain A, Crystal Structures Of Hiv-1 Reverse Transcriptase Complexes With Thiocarbamate Non-Nucleoside Inhibitors Length = 557

Iteration: 1
 Score = 40.8 bits (94), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 32/119 (26%), Positives = 52/119 (43%), Gaps = 16/119 (13%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSF--RLNVVNSVFSAELMAILLCLQNLKYLPSTKFL 174
           + DG+    +      Y  NK         N  N     EL AI L LQ+       +  
Sbjct: 441 YVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQ--KTELQAIYLALQD----SGLEVN 494
Query: 175 LVTDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           +VTDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 495 IVTDSQYALGIIQAQPDKSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|3KLF|A Chain A, Crystal Structure Of Wild-Type Hiv-1 Reverse Transcriptase Crosslinked To A Dsdna With A Bound Excision Product, Aztppppa Length = 557

Iteration: 1
 Score = 40.8 bits (94), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 32/119 (26%), Positives = 52/119 (43%), Gaps = 16/119 (13%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSF--RLNVVNSVFSAELMAILLCLQNLKYLPSTKFL 174
           + DG+    +      Y  NK         N  N     EL AI L LQ+       +  
Sbjct: 443 YVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQ--KTELQAIYLALQD----SGLEVN 496
Query: 175 LVTDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           +VTDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 497 IVTDSQYALGIIQAQPDKSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 551

>pdb|3BGR|A Chain A, Crystal Structure Of K103nY181C MUTANT HIV-1 Reverse Transcriptase (Rt) In Complex With Tmc278 (Rilpivirine), A Non-Nucleoside Rt Inhibitor Length = 557

Iteration: 1
 Score = 40.8 bits (94), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 32/119 (26%), Positives = 52/119 (43%), Gaps = 16/119 (13%)
Query: 119 FTDGSKTENST--SCAYTINKNVNSF--RLNVVNSVFSAELMAILLCLQNLKYLPSTKFL 174
           + DG+    +      Y  NK         N  N     EL AI L LQ+       +  
Sbjct: 443 YVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQ--KTELQAIYLALQD----SGLEVN 496
Query: 175 LVTDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD 231
           +VTDS  +L  I ++     + L+++I    ++ +   +++   W P+H GI GNE VD
Sbjct: 497 IVTDSQYALGIIQAQPDKSESELVNQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVD 551

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	282
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	2e-08
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	1e-06
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	2e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-05
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	6e-05
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	3e-04
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	4e-04

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

 Score = 51.8 bits (124), Expect = 2e-08
 Identities = 28/130 (21%), Positives = 44/130 (33%), Gaps = 18/130 (13%)

Query: 119 FTDGSKTENS--TSCAYTI---NKNVNSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKF 173
           +TDGS             +    + + +  L    S   AEL+A+   L+  +     K 
Sbjct: 27  YTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMAE---GKKL 83

Query: 174 LLVTDSMSSLQAITSKSCNNALLSKIYSTW---LDLVACGKEISFMWCPSHCG-----IS 225
            + TDS  +       S       K  +     L  +   K +S + CP H         
Sbjct: 84  NVYTDSRYAFATAHVHSEGRE--IKNKNEILALLKALFLPKRLSIIHCPGHQKGNSAEAR 141

Query: 226 GNEAVDVAAK 235
           GN   D AA+
Sbjct: 142 GNRMADQAAR 151

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

 Score = 46.4 bits (111), Expect = 1e-06
 Identities = 25/101 (24%), Positives = 39/101 (38%), Gaps = 23/101 (22%)

Query: 153 AELMAILLCLQNLKYLPSTKFLLVTDSMSSLQAITS-----KSCN----------NALLS 197
           AE+ A    ++  K     K +L T+SM ++  IT+     K             N    
Sbjct: 53  AEIHAACKAIEQAKTQNINKLVLYTNSMFTINGITNWVQGWKKNGWKTSAGKEVINKED- 111

Query: 198 KIYSTW--LDLVACGKEISFMWCPSHCGISGNEAVDVAAKN 236
                +  L+ +  G +I +M  P H G  GNE  D  A+ 
Sbjct: 112 -----FVALERLTQGMDIQWMHVPGHSGFIGNEEADRLARE 147

>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 = 42.7 bits (101), Expect = 2e-05
 Identities = 24/137 (17%), Positives = 38/137 (27%), Gaps = 24/137 (17%)

Query: 114 DRILCFTDGSKTENSTSCAY-TINKNVNSFRL--------NVVNSVFSAELMAILLCLQN 164
                +TDGS      + AY  +      +                 + E+ A L  ++ 
Sbjct: 5   TEYDVYTDGSYVNGQYAWAYAFVKDGKVHYEDADVGKNPAAATMRNVAGEIAAALYAVKK 64

Query: 165 LKYLPSTKFLLVTDSMSSLQAITS------KSCNNALLSKIYSTWLDLVACGKEISFMWC 218
              L   K  ++ D       I        K+  N                    SF   
Sbjct: 65  ASQLGV-KIRILHDY----AGIAFWATGEWKA-KNEFTQAYAKLMNQY---RGIYSFEKV 115

Query: 219 PSHCGISGNEAVDVAAK 235
            +H G   N+ VD+ AK
Sbjct: 116 KAHSGNEFNDYVDMKAK 132

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

 Score = 44.1 bits (103), Expect = 4e-05
 Identities = 47/320 (14%), Positives = 85/320 (26%), Gaps = 108/320 (33%)

Query: 28  NEFFNRNYDF-----ANHPNTPKPLLMRAREITDFIANIDSSEFAPYDKHIPPW------ 76
            E    NY F           P  +     E  D + N D+  FA Y+            
Sbjct: 84  EEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYN-DNQVFAKYNVSRLQPYLKLRQ 142

Query: 77  --SSVVPSIDTSLH----SGKKDNVSPSVFQVQFLVNINTKYHDRILCFTDGSKTENSTS 130
               + P+ +  +     SGK      +      +       +                 
Sbjct: 143 ALLELRPAKNVLIDGVLGSGK------TW-----VALDVCLSYKVQCKMDFK-------- 183

Query: 131 CAYTINKNVNSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLVTDSMSSLQA----- 185
             + +N          + +  S E   +L  LQ L Y     +   +D  S+++      
Sbjct: 184 -IFWLN----------LKNCNSPE--TVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSI 230

Query: 186 -------ITSKSCNNALLSKIYSTWLDLVACGKEI--SFMWCPSHC-------------G 223
                  + SK   N LL  +    L  V    +   +F      C              
Sbjct: 231 QAELRRLLKSKPYENCLL--V----LLNV-QNAKAWNAF---NLSCKILLTTRFKQVTDF 280

Query: 224 ISGNEAVDVAAKNPSPSFPP---LKL------CSASDYKPLIKKI----------VQRNW 264
           +S      ++  + S +  P     L      C   D    +               R+ 
Sbjct: 281 LSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDG 340

Query: 265 QSSWNSVP--NGNKLKTYRK 282
            ++W++    N +KL T  +
Sbjct: 341 LATWDNWKHVNCDKLTTIIE 360

>2zd1_A Reverse transcriptase/ribonuclease H; P51/P66, hetero dimer, NNRTI, nonnucleoside inhibitor, AIDS, HIV, rilpivirine, diarylpyrimidine, DAPY, DNA recombination; HET: T27; 1.80A {Human immunodeficiency virus 1} PDB: 3is9_A* 3irx_A* 2ze2_A* 3bgr_A* 3qlh_A* 3klf_A* 3qo9_A* 1dlo_A 1bqm_A 2be2_A* 1s6q_A* 1s6p_A* 1s9g_A* 1suq_A* 2b5j_A* 2b6a_A* 2ban_A* 1s9e_A* 1hni_A* 1hnv_A* ... Length = 557

 Score = 43.2 bits (102), Expect = 6e-05
 Identities = 27/82 (32%), Positives = 43/82 (52%), Gaps = 12/82 (14%)

Query: 153 AELMAILLCLQNLKYLPSTKFLLVTDS---MSSLQAITSKSCNNALLSKIYSTWLDLVAC 209
            EL AI L LQ+       +  +VTDS   +  +QA   KS  + L+++I    ++ +  
Sbjct: 479 TELQAIYLALQDSG----LEVNIVTDSQYALGIIQAQPDKS-ESELVNQI----IEQLIK 529

Query: 210 GKEISFMWCPSHCGISGNEAVD 231
            +++   W P+H GI GNE VD
Sbjct: 530 KEKVYLAWVPAHKGIGGNEQVD 551

>1mu2_A HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polymerase, drug design, transferase; 2.35A {Human immunodeficiency virus 2} SCOP: c.55.3.1 e.8.1.2 PDB: 1mu2_B Length = 555

 Score = 40.9 bits (96), Expect = 3e-04
 Identities = 21/82 (25%), Positives = 38/82 (46%), Gaps = 12/82 (14%)

Query: 153 AELMAILLCLQNLKYLPSTKFLLVTDSMSSLQAITSK--SCNNALLSKIYSTWLDLVACG 210
           AEL A  + L +       K  ++ DS   +  + S+     + ++++I    +      
Sbjct: 476 AELEAFAMALTD----SGPKVNIIVDSQYVMGIVASQPTESESKIVNQIIEEMI-----K 526

Query: 211 KEISFM-WCPSHCGISGNEAVD 231
           KE  ++ W P+H GI GN+ VD
Sbjct: 527 KEAIYVAWVPAHKGIGGNQEVD 548

>3qio_A GAG-POL polyprotein; RNAse H, inhibitor, nuclease, transferase, hydrolase- complex; HET: QID; 1.40A {Hiv-1 M} PDB: 3qin_A* 3hyf_A* 1o1w_A 3lp3_A* 1hrh_A 3k2p_A* 1rdh_A Length = 150

 Score = 38.7 bits (91), Expect = 4e-04
 Identities = 27/102 (26%), Positives = 38/102 (37%), Gaps = 28/102 (27%)

Query: 153 AELMAILLCLQNLKYLPSTKFLLVTDSMSSLQAITS-----KSCN----------NALLS 197
            EL AI L LQ+       +  +VTDS  +L  IT      K             N  L 
Sbjct: 52  TELQAIYLALQDSG----LEVNIVTDSQYALGIITQWIHNWKKRGWKTADKKPVKNVDL- 106

Query: 198 KIYSTW---LDLVACGKEISFMWCPSHCGISGNEAVDVAAKN 236
                    ++ +   +++   W P+H GI GNE VD     
Sbjct: 107 -----VNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSA 143

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	282
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.92
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.91
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	99.91
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.91
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	99.89
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.89
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	99.89
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.88
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	99.85
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	99.84
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	99.83
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	99.81
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	99.81
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	99.8
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	99.41
4htu_A	134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	99.24
1rw3_A	455	POL polyprotein; RNA and DNA dependent DNA polymer	85.06

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

Probab=99.92  E-value=5.6e-25  Score=179.94  Aligned_cols=127  Identities=24%  Similarity=0.295  Sum_probs=97.8

Q ss_pred             CCCceEEecCCCCCCCC-----ceEEEEEc-CCe--eeeecCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeCcHHHH
Q psy16967        112 YHDRILCFTDGSKTENS-----TSCAYTIN-KNV--NSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLVTDSMSSL  183 (282)
Q Consensus       112 ~~~~~~iyTDGS~~~~~-----~G~gvv~~-~~~--~~~~l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~sDS~~al  183 (282)
                      ..+.+.||||||+..++     +|+||++. ++.  .+..+...+|++.|||.|++.||+.+...+..+|.|+|||++++
T Consensus         4 ~~~~~~iytDGs~~~n~~~~~~aG~Gvv~~~~~~~~~~~~l~~~~tn~~aEl~A~~~aL~~~~~~~~~~v~i~tDS~~vi   83 (154)
T 2qkb_A            4 MGDFVVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQAKTQNINKLVLYTNSMFTI   83 (154)
T ss_dssp             ETTEEEEEEEEEEETTTSSSCEEEEEEECSTTCTTCEEEECCSSCCHHHHHHHHHHHHHHHHHHTTCCEEEEEESCHHHH
T ss_pred             CCCeEEEEEccCcCCCCCCCCcEEEEEEEECCCceeEEeecCCCCchHHHHHHHHHHHHHHHHhCCCceEEEEECcHHHH
Confidence            35679999999998643     68886653 322  45556557899999999999999999887789999999999999


Q ss_pred             HHHhcC--------CC-Cch---HHHHHHHHHHHHHhCCCceEEEecCCcCCCcccHHHHHHhcCCCC
Q psy16967        184 QAITSK--------SC-NNA---LLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNPSP  239 (282)
Q Consensus       184 ~~l~~~--------~~-~~~---~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~  239 (282)
                      +.|..+        +. .++   ....+++.+..+.. +..|.|.|||||+|++||+.||+||++|+.
T Consensus        84 ~~i~~~~~~w~~~~w~~~~~~~~~n~~l~~~i~~l~~-~~~v~~~~V~~H~g~~~N~~AD~LA~~a~~  150 (154)
T 2qkb_A           84 NGITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQ-GMDIQWMHVPGHSGFIGNEEADRLAREGAK  150 (154)
T ss_dssp             HHHHTHHHHHHTTTSBCTTSSBCTTHHHHHHHHHHHT-TCEEEEEECCTTSSCHHHHHHHHHHHHHHT
T ss_pred             hhhhhhHHHHHhccccccCCCccccHHHHHHHHHHHc-CCceEEEEccCCCCCHhHHHHHHHHHHHHH
Confidence            999873        11 111   12344444444444 467999999999999999999999998863

>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=99.91  E-value=3.2e-24  Score=174.70  Aligned_cols=123  Identities=24%  Similarity=0.318  Sum_probs=92.7

Q ss_pred             CCCceEEecCCCCCCCC--ceEEEEEcCCe-eeeecCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeCcHHHHHHHhc
Q psy16967        112 YHDRILCFTDGSKTENS--TSCAYTINKNV-NSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLVTDSMSSLQAITS  188 (282)
Q Consensus       112 ~~~~~~iyTDGS~~~~~--~G~gvv~~~~~-~~~~l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~sDS~~al~~l~~  188 (282)
                      ..+.+.||||||+..++  .|+|+++..+. ....+ ..+|++.||+.|++.||+.+    ..+|.|+|||++++++|..
T Consensus         9 ~~~~~~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~-~~~Tnn~aEl~A~i~AL~~~----~~~v~i~tDS~~v~~~i~~   83 (150)
T 3qio_A            9 IVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTL-TDTTNQKTELQAIYLALQDS----GLEVNIVTDSQYALGIITQ   83 (150)
T ss_dssp             CTTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEEE-SSCCHHHHHHHHHHHHHHHS----CSEEEEEESCHHHHHHHHH
T ss_pred             CCCCEEEEEccCCCCCCCCeEEEEEEEcCCEEEEeC-CCCCHHHHHHHHHHHHHHhC----CCcEEEEeCcHHHHHHHHH
Confidence            46779999999997643  78887654433 33344 46899999999999999985    4899999999999999987


Q ss_pred             CC---CCc------h--H-HHHHHHHHHHHHhCCCceEEEecCCcCCCcccHHHHHHhcCCCC
Q psy16967        189 KS---CNN------A--L-LSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNPSP  239 (282)
Q Consensus       189 ~~---~~~------~--~-~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~  239 (282)
                      +.   ..+      +  + -..+++.+..+...+..|.|.|||||+|++|||.||+||++|+.
T Consensus        84 w~~~W~~~gw~~~~g~~v~n~~l~~~l~~~l~~~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~  146 (150)
T 3qio_A           84 WIHNWKKRGWKTADKKPVKNVDLVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIR  146 (150)
T ss_dssp             HHHHHCC------------CHHHHHHHHHHHTTCSEEEEEECCTTSCCHHHHHHHHHHHTTTS
T ss_pred             HHHHHhhcCcCcCcCcccccHHHHHHHHHHHhhcCceEEEEccCcCCChhHHHHHHHHHHHHH
Confidence            51   111      1  1 12333333333346789999999999999999999999999984

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

Probab=99.91  E-value=1.5e-25  Score=182.11  Aligned_cols=126  Identities=17%  Similarity=0.092  Sum_probs=98.8

Q ss_pred             CCCceEEecCCCCCCCCceEEEEE-cCCe---eee-ec--CC--CCchHHHHHHHHHHHHHHhhcCCCCeEEEEeCcHHH
Q psy16967        112 YHDRILCFTDGSKTENSTSCAYTI-NKNV---NSF-RL--NV--VNSVFSAELMAILLCLQNLKYLPSTKFLLVTDSMSS  182 (282)
Q Consensus       112 ~~~~~~iyTDGS~~~~~~G~gvv~-~~~~---~~~-~l--~~--~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~sDS~~a  182 (282)
                      +++.+.||||||+.++.+|+|+++ +.+.   .+. ..  +.  .+|++.|||.|++.||+.+...+. +|.|+|||+.+
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            457799999999999669999654 3332   333 22  22  369999999999999998877666 99999999999


Q ss_pred             HHHHhcCCCCc-hHHHHHHHHHHHHHhCCCceEEEecCCcCCCcccHHHHHHhcCCCCCC
Q psy16967        183 LQAITSKSCNN-ALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNPSPSF  241 (282)
Q Consensus       183 l~~l~~~~~~~-~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~~  241 (282)
                      ...+.+.+..+ +....+.+++++|..   .|.|.|||||+|++|||.||+||++|+...
T Consensus        82 ~~w~~~~w~~~~~~~~~~~~l~~~l~~---~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~~  138 (147)
T 2kq2_A           82 AFWATGEWKAKNEFTQAYAKLMNQYRG---IYSFEKVKAHSGNEFNDYVDMKAKSALGIR  138 (147)
T ss_dssp             HHHTTSSSSCCHHHHHHHHCGGGGGST---TCCBCCCCCCCCCHHHHHHHHHHHHHHTCC
T ss_pred             HHHHhCCCccCCcchHHHHHHHHHhcC---CeeEEEecCcCCCcchHHHHHHHHHHHhcc
Confidence            88888766544 355666666665543   899999999999999999999999998433

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

Probab=99.91  E-value=1.5e-24  Score=175.77  Aligned_cols=121  Identities=20%  Similarity=0.150  Sum_probs=89.0

Q ss_pred             CceEEecCCCCCCCC--ceEEEE-EcCCe---eeeecCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeCcHHHHHHHh
Q psy16967        114 DRILCFTDGSKTENS--TSCAYT-INKNV---NSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLVTDSMSSLQAIT  187 (282)
Q Consensus       114 ~~~~iyTDGS~~~~~--~G~gvv-~~~~~---~~~~l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~sDS~~al~~l~  187 (282)
                      ..++||||||+..++  +|+|++ .+++.   .+..+ ..+|++.|||.|++.||+.+..  ..+|.|+|||+++++.|.
T Consensus         3 ~~i~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~~~~-~~~Tnn~aEl~A~~~AL~~~~~--~~~v~I~tDS~~vi~~i~   79 (146)
T 3h08_A            3 KTITIYTDGAASGNPGKGGWGALLMYGSSRKEISGYD-PATTNNRMELMAAIKGLEALKE--PARVQLYSDSAYLVNAMN   79 (146)
T ss_dssp             CEEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCSS--CCEEEEEESCHHHHHHHH
T ss_pred             ceEEEEEecCCCCCCCceEEEEEEEECCeeEEeecCC-CCCcHHHHHHHHHHHHHHhcCc--cCcEEEEeChHHHHHHHH
Confidence            468999999998754  788855 34433   22333 3579999999999999999876  589999999999999998


Q ss_pred             cCC---------C-Cch---HHHHHHHHHHHHHhCCCceEEEecCCcCCCcccHHHHHHhcCCC
Q psy16967        188 SKS---------C-NNA---LLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNPS  238 (282)
Q Consensus       188 ~~~---------~-~~~---~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~  238 (282)
                      ..+         . .++   ....+++.+..+... ..|.|.|||||+|++|||.||+|||+|+
T Consensus        80 ~~w~~~W~~~~w~~~~~~~v~n~~l~~~~~~~~~~-~~v~~~~V~gH~g~~~N~~AD~LA~~a~  142 (146)
T 3h08_A           80 EGWLKRWVKNGWKTAAKKPVENIDLWQEILKLTTL-HRVTFHKVKGHSDNPYNSRADELARLAI  142 (146)
T ss_dssp             SSHHHHHHHTTCC----CCCTTHHHHHHHHHHHHH-SEEEEEECCC-CCSHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCccCCCCCcCCHHHHHHHHHHHhh-CceEEEEcCCcCCcHhHHHHHHHHHHHH
Confidence            721         1 111   113333333333332 4699999999999999999999999886

>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=99.89  E-value=2e-23  Score=170.95  Aligned_cols=121  Identities=23%  Similarity=0.266  Sum_probs=91.6

Q ss_pred             ceEEecCCCCCCCC--ceEEEEE-cCCe---eeeecCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeCcHHHHHHHhc
Q psy16967        115 RILCFTDGSKTENS--TSCAYTI-NKNV---NSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLVTDSMSSLQAITS  188 (282)
Q Consensus       115 ~~~iyTDGS~~~~~--~G~gvv~-~~~~---~~~~l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~sDS~~al~~l~~  188 (282)
                      .+.||||||+..++  +|+|+++ +.+.   .+..+ ..+|++.|||.|++.||+.+..  ..+|.|+|||+++++.|..
T Consensus         4 ~~~iytDGs~~~n~~~~G~G~v~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~~~~--~~~v~I~tDS~~vi~~i~~   80 (155)
T 1jl1_A            4 QVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGY-TRTTNNRMELMAAIVALEALKE--HAEVILSTDSQYVRQGITQ   80 (155)
T ss_dssp             CEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCCS--CCEEEEEECCHHHHHHHHT
T ss_pred             eEEEEEccccCCCCCceEEEEEEEECCeEEEEecCC-CCCcHHHHHHHHHHHHHHHhCc--CCcEEEEeCHHHHHHHHHH
Confidence            58999999998653  7888654 3332   33333 3568999999999999999875  3899999999999999987


Q ss_pred             C--------CC-Cc--hH-HHHHHHHHHHHHhCCCceEEEecCCcCCCcccHHHHHHhcCCCC
Q psy16967        189 K--------SC-NN--AL-LSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNPSP  239 (282)
Q Consensus       189 ~--------~~-~~--~~-~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~  239 (282)
                      +        +. .+  ++ ...+++.+..+.. ...|.|.|||||+|++||+.||+||++|+.
T Consensus        81 w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~-~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~  142 (155)
T 1jl1_A           81 WIHNWKKRGWKTADKKPVKNVDLWQRLDAALG-QHQIKWEWVKGHAGHPENERADELARAAAM  142 (155)
T ss_dssp             THHHHHHTTTBCTTSCBCTTHHHHHHHHHHTT-TCEEEEEECCSSTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHhhcccccccCCccCCHHHHHHHHHHHc-cCceEEEEcCCCCCCHHHHHHHHHHHHHHh
Confidence            2        21 11  11 1344444444544 368999999999999999999999999983

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

Probab=99.89  E-value=2.2e-23  Score=171.28  Aligned_cols=123  Identities=24%  Similarity=0.289  Sum_probs=91.9

Q ss_pred             CceEEecCCCCCCCC--ceEEEEE-cCCe---eeeecCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeCcHHHHHHHh
Q psy16967        114 DRILCFTDGSKTENS--TSCAYTI-NKNV---NSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLVTDSMSSLQAIT  187 (282)
Q Consensus       114 ~~~~iyTDGS~~~~~--~G~gvv~-~~~~---~~~~l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~sDS~~al~~l~  187 (282)
                      ..+.||||||+..++  +|+|+++ +++.   .+..+ ..+|++.|||.|++.||+.+..  ..+|.|+|||+++++.|.
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            458999999998643  7888654 3333   23333 3578999999999999999865  389999999999999998


Q ss_pred             c--------CCCC-c--hH-HHHHHHHHHHHHhCCCceEEEecCCcCCCcccHHHHHHhcCCCCC
Q psy16967        188 S--------KSCN-N--AL-LSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNPSPS  240 (282)
Q Consensus       188 ~--------~~~~-~--~~-~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~  240 (282)
                      .        .+.. .  ++ -..+++.+..+.. ...|.|.|||||+|++||+.||+||++|+..
T Consensus        82 ~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~-~~~v~~~wV~gH~g~~~Ne~AD~LAk~a~~~  145 (158)
T 2e4l_A           82 TWIHGWKKKGWMTSNRTPVKNVDLWKRLDKAAQ-LHQIDWRWVKGHAGHAENERCDQLARAAAEA  145 (158)
T ss_dssp             THHHHHHHTTTBCTTSSBCTTHHHHHHHHHHHT-TSEEEEEECCTTCCCHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHccccccCCCcccCHHHHHHHHHHHc-cCcEEEEEccCCCCchhHHHHHHHHHHHHHh
Confidence            8        2221 1  11 1334444444444 3689999999999999999999999999843

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

Probab=99.89  E-value=3.4e-23  Score=171.12  Aligned_cols=121  Identities=22%  Similarity=0.218  Sum_probs=89.3

Q ss_pred             CceEEecCCCCCC--CCceEEEE-EcCCe--eeeecCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeCcHHHHHHHhc
Q psy16967        114 DRILCFTDGSKTE--NSTSCAYT-INKNV--NSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLVTDSMSSLQAITS  188 (282)
Q Consensus       114 ~~~~iyTDGS~~~--~~~G~gvv-~~~~~--~~~~l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~sDS~~al~~l~~  188 (282)
                      ..+.||||||+..  |..|+|++ ..++.  ....+...+|++.||+.|++.||+.+   ...++.|+|||+++++.+-.
T Consensus        22 ~~i~iytDGs~~~npG~~g~G~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~---~~~~v~I~tDS~~vi~~iw~   98 (165)
T 3p1g_A           22 ADYTWYTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMA---EGKKLNVYTDSRYAFATAHV   98 (165)
T ss_dssp             CSEEEEEEEEEEEETTEEEEEEEEECSSCEEEEEEECTTCCHHHHHHHHHHHHHHHT---BTSEEEEEECCHHHHHHHHS
T ss_pred             CCEEEEEEcccCCCCCceEEEEEEEECCEEEEEecCCCCCcHHHHHHHHHHHHHHHc---cCceEEEEEchHHHHhhhhc
Confidence            4589999999984  33788864 34333  22245567899999999999999998   36899999999999999832


Q ss_pred             CCCCchH-HHHHHH-HHHHHHhCCCceEEEecCCcCC-----CcccHHHHHHhcCCC
Q psy16967        189 KSCNNAL-LSKIYS-TWLDLVACGKEISFMWCPSHCG-----ISGNEAVDVAAKNPS  238 (282)
Q Consensus       189 ~~~~~~~-~~~i~~-~~~~l~~~~~~v~~~WVpgH~g-----i~gNe~AD~lAk~a~  238 (282)
                      .....++ -..+++ ++..+ ..+..|.|+|||||+|     ++|||.||+||++|+
T Consensus        99 ~~~g~~v~n~dl~~~l~~~l-~~~~~v~~~wVkgH~g~~~~~~~gNe~AD~LA~~aa  154 (165)
T 3p1g_A           99 HSEGREIKNKNEILALLKAL-FLPKRLSIIHCPGHQKGNSAEARGNRMADQAAREAA  154 (165)
T ss_dssp             CCCSCCCSSHHHHHHHHHHT-TSBSEEEEEECCSSCCSCSHHHHHHHHHHHHHHHHH
T ss_pred             ccCCCcccCHHHHHHHHHHH-hcCCceEEEEecCCCCCCcCcchHHHHHHHHHHHHH
Confidence            1111221 122222 22223 3578999999999999     999999999999988

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

Probab=99.88  E-value=2.4e-23  Score=172.35  Aligned_cols=122  Identities=25%  Similarity=0.206  Sum_probs=91.8

Q ss_pred             CceEEecCCCCCCCC--ceEEEEE-cCCe---eeeecCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeCcHHHHHHHh
Q psy16967        114 DRILCFTDGSKTENS--TSCAYTI-NKNV---NSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLVTDSMSSLQAIT  187 (282)
Q Consensus       114 ~~~~iyTDGS~~~~~--~G~gvv~-~~~~---~~~~l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~sDS~~al~~l~  187 (282)
                      ..+.||||||+..++  +|+|+++ +.+.   .+... ..+|++.|||.|++.||+.+...  .+|.|+|||+++++.|.
T Consensus         7 ~~i~iytDGs~~~n~g~~G~G~v~~~~~~~~~~~~~~-~~~Tnn~aEl~Ai~~AL~~~~~~--~~v~I~tDS~~vi~~i~   83 (166)
T 1ril_A            7 KRVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGE-ACTTNNRMELKAAIEGLKALKEP--CEVDLYTDSHYLKKAFT   83 (166)
T ss_dssp             CCCCEEEEEEESSTTEEEEEEEEECBTTBCCEECCEE-EEECHHHHHHHHHHHHHHSCCSC--CEEEEECCCHHHHHHHH
T ss_pred             ccEEEEECccccCCCCCEEEEEEEEECCEEEEEecCC-CCCcHHHHHHHHHHHHHHHhccC--CeEEEEeChHHHHHHHh
Confidence            568999999998753  7888664 3332   22222 35789999999999999988653  58999999999999998


Q ss_pred             c----------CCCCch--H-HHHHHHHHHHHHhCCCceEEEecCCcCCCcccHHHHHHhcCCCC
Q psy16967        188 S----------KSCNNA--L-LSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNPSP  239 (282)
Q Consensus       188 ~----------~~~~~~--~-~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~  239 (282)
                      .          +...++  + ...+++.+..+... ..|.|.|||||+|++||+.||+||++|+.
T Consensus        84 ~~w~~~W~~~~w~~~~g~~v~n~~l~~~i~~l~~~-~~v~~~wV~gH~g~~~Ne~AD~LAk~a~~  147 (166)
T 1ril_A           84 EGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAP-HRVRFHFVKGHTGHPENERVDREARRQAQ  147 (166)
T ss_dssp             SSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHTT-SEEECCCCCGGGSCTHHHHHHHHHHHHHT
T ss_pred             hhHHHHHHhcccccccCCccCcHHHHHHHHHHHhc-CeEEEEEeeCCCCchhHHHHHHHHHHHHH
Confidence            8          222221  1 13344444444443 58999999999999999999999999984

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

Probab=99.85  E-value=1.7e-21  Score=160.73  Aligned_cols=125  Identities=17%  Similarity=0.180  Sum_probs=88.4

Q ss_pred             CCceEEecCCCCCCC--C-----ceEEEEE-cC-Ce----eeeec-CCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeC
Q psy16967        113 HDRILCFTDGSKTEN--S-----TSCAYTI-NK-NV----NSFRL-NVVNSVFSAELMAILLCLQNLKYLPSTKFLLVTD  178 (282)
Q Consensus       113 ~~~~~iyTDGS~~~~--~-----~G~gvv~-~~-~~----~~~~l-~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~sD  178 (282)
                      .-.++||||||+..+  +     .|+||++ .. ..    ..+.. ....+++.||+.|+..||+.+... ..+|.|+||
T Consensus         5 ~~evviYTDGsc~gNpgp~~~~~aG~Gv~~~~~~~~~~~~~~~~~~tnn~te~~Aei~Al~~al~~al~~-~~~v~I~TD   83 (165)
T 2lsn_A            5 QYEGVFYTDGSAIKSPDPTKSNNAGMGIVHATYKPEYQVLNQWSIPLGNHTAQMAEIAAVEFACKKALKI-PGPVLVITD   83 (165)
T ss_dssp             CCSEEEEEEEEEEECSSCTTCEEEEEEEEEECCSSSCCEEEEEEEEESSCCHHHHHHHHHHHHHHHHHHS-SSCEEEEES
T ss_pred             CceEEEEEcCCCCCCCCCCCCCcEEEEEEEEECCCccEEeccccCCchHHHHHHHHHHHHHHHHHHHhcC-CCeEEEEeC
Confidence            345899999999764  2     6888654 22 21    22233 356789999999999999887664 357999999


Q ss_pred             cHHHHHHHhcC--------CCC-c--hH-HHHHHHHHHHHHhCCCceEEEecCCcCCC------cccHHHHHHhcCCC
Q psy16967        179 SMSSLQAITSK--------SCN-N--AL-LSKIYSTWLDLVACGKEISFMWCPSHCGI------SGNEAVDVAAKNPS  238 (282)
Q Consensus       179 S~~al~~l~~~--------~~~-~--~~-~~~i~~~~~~l~~~~~~v~~~WVpgH~gi------~gNe~AD~lAk~a~  238 (282)
                      |++++++|..+        +.. .  ++ -..+++.+.++......|.|.|||||+|+      +|||.||+||++|+
T Consensus        84 S~Yvi~~it~w~~~Wk~ngw~~~~~~pVkN~dL~~~l~~~~~~~~~v~~~~VkgH~g~~~~~~~~gNe~AD~LA~~gA  161 (165)
T 2lsn_A           84 SFYVAESANKELPYWKSNGFVNNKKKPLKHISKWKSIAECLSMKPDITIQHEKGHQPTNTSIHTEGNALADKLATQGS  161 (165)
T ss_dssp             CHHHHHHHHTHHHHHHHTTSCSCSSSCCSSHHHHHHHHHHHHHCTTCEEEECCSSSCSSSCHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHhhhhhhhhhheeccccccCCCcccCHHHHHHHHHHHhCCCCEEEEEEeCCCCccCCCCChHHHHHHHHHHHhh
Confidence            99999999753        111 1  11 13344444444444568999999999994      68999999999875

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

Probab=99.84  E-value=7.2e-21  Score=151.98  Aligned_cols=119  Identities=16%  Similarity=0.220  Sum_probs=91.9

Q ss_pred             ceEEecCCCCCCC--CceEEEEE-cCC--e---eeeecCCCCchHHHHHHHHHHHHHHhhcCCCC----eEEEEeCcHHH
Q psy16967        115 RILCFTDGSKTEN--STSCAYTI-NKN--V---NSFRLNVVNSVFSAELMAILLCLQNLKYLPST----KFLLVTDSMSS  182 (282)
Q Consensus       115 ~~~iyTDGS~~~~--~~G~gvv~-~~~--~---~~~~l~~~~s~~~AEl~AI~~AL~~~~~~~~~----~i~I~sDS~~a  182 (282)
                      .+.||||||+..+  .+|+|+++ +.+  .   .+..+ ..+|++.||+.|++.||+.+...+..    +|.|+|||+++
T Consensus         3 ~~~iy~DGs~~~n~g~~G~G~v~~~~~g~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~a~~~~~~~~~~~v~i~tDS~~v   81 (140)
T 3u3g_D            3 KIIIYTDGGARGNPGPAGIGVVITDEKGNTLHESSAYI-GETTNNVAEYEALIRALEDLQMFGDKLVDMEVEVRMDSELI   81 (140)
T ss_dssp             EEEEEEEEEESSTTEEEEEEEEEECTTSCEEEEEEEEE-EEECHHHHHHHHHHHHHHHHGGGGGGGTTCEEEEEESCHHH
T ss_pred             eEEEEEecCCCCCCCCcEEEEEEEeCCCCEEEEEEeeC-CCCchHHHHHHHHHHHHHHHHHcCCCCCCceEEEEeChHHH
Confidence            5899999999865  37888654 422  2   22223 34799999999999999999887767    99999999999


Q ss_pred             HHHHhcCCC-CchHHHHHHHHHHHH-HhCCCceEEEecCCcCCCcccHHHHHHhcCCC
Q psy16967        183 LQAITSKSC-NNALLSKIYSTWLDL-VACGKEISFMWCPSHCGISGNEAVDVAAKNPS  238 (282)
Q Consensus       183 l~~l~~~~~-~~~~~~~i~~~~~~l-~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~  238 (282)
                      ++.+.+.+. .+.-...+++.+..+ ......|.|.|||    .++|+.||+||++|+
T Consensus        82 i~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~~v~~~~V~----~~~N~~AD~LA~~a~  135 (140)
T 3u3g_D           82 VRQMQGVYKVKEPTLKEKFAKIAHIKMERVPNLVFVHIP----REKNARADELVNEAI  135 (140)
T ss_dssp             HHHHTTSSCCCCGGGHHHHHHHHHHHHHHCTTCEEEECC----GGGGHHHHHHHHHHH
T ss_pred             HHHhCCCcccCCHHHHHHHHHHHHHhhcCCCcEEEEEcC----chhhHHHHHHHHHHH
Confidence            999999764 344344455555555 5666799999999    489999999999875

>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=99.83  E-value=1.6e-20  Score=150.52  Aligned_cols=119  Identities=18%  Similarity=0.223  Sum_probs=95.3

Q ss_pred             ceEEecCCCCCCC--CceEEEE-EcCC---e---eeeecCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeCcHHHHHH
Q psy16967        115 RILCFTDGSKTEN--STSCAYT-INKN---V---NSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLVTDSMSSLQA  185 (282)
Q Consensus       115 ~~~iyTDGS~~~~--~~G~gvv-~~~~---~---~~~~l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~sDS~~al~~  185 (282)
                      .++||||||+..+  .+|+|++ .+.+   .   .+..+ ..+|++.||+.|++.||+.+...+..+|.|+|||+++++.
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            4799999999865  3788855 3432   2   22223 3679999999999999999988888999999999999999


Q ss_pred             HhcCCC-CchHHHHHHHHHHHHHhCCCceEEEecCCcCCCcccHHHHHHhcCCC
Q psy16967        186 ITSKSC-NNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNPS  238 (282)
Q Consensus       186 l~~~~~-~~~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~  238 (282)
                      +.+.+. .+.....+++.+..+...+..|.|.|||+    ++|+.||+||++|+
T Consensus        82 i~~~~~~~~~~l~~~~~~i~~l~~~~~~v~~~~V~~----~~N~~AD~LA~~a~  131 (141)
T 3hst_B           82 MSGRWKVKHPDLLKLYVQAQALASQFRRINYEWVPR----ARNTYADRLANDAM  131 (141)
T ss_dssp             HTTSSCCCSHHHHHHHHHHHHHHTTSSEEEEEECCG----GGCHHHHHHHHHHH
T ss_pred             HhCCcccCCHHHHHHHHHHHHHHhcCCeEEEEEcCC----cccHHHHHHHHHHH
Confidence            998653 44445566666667777788999999994    89999999999887

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

Probab=99.81  E-value=6.8e-20  Score=178.24  Aligned_cols=117  Identities=23%  Similarity=0.369  Sum_probs=92.2

Q ss_pred             CCceEEecCCCCCCCC--ceEEEEEcC-CeeeeecCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeCcHHHHHHHhcC
Q psy16967        113 HDRILCFTDGSKTENS--TSCAYTINK-NVNSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLVTDSMSSLQAITSK  189 (282)
Q Consensus       113 ~~~~~iyTDGS~~~~~--~G~gvv~~~-~~~~~~l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~sDS~~al~~l~~~  189 (282)
                      .+.+.||||||+..++  +|+|+++.. +.....+ ..+||+.||+.|++.||+.    ...++.|+|||++|+++++++
T Consensus       434 ~~~~~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~-~~~TNn~aEl~A~i~aL~~----~~~~v~I~tDS~~v~~~i~~~  508 (555)
T 1mu2_A          434 PGAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKL-EQTTNQQAELEAFAMALTD----SGPKVNIIVDSQYVMGIVASQ  508 (555)
T ss_dssp             TTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEEE-SSCCHHHHHHHHHHHHHHT----SCSEEEEEESCHHHHHHHHTC
T ss_pred             CCceEEEEcccccCCCCCceEEEEEEeCCEeeccC-CCCCHHHHHHHHHHHHHHc----CCCeEEEEEehHHHHHHHhcc
Confidence            4569999999998654  788876543 3333333 4679999999999999998    468999999999999999986


Q ss_pred             CCC--chHHHHHHHHHHHHHhCCCceEEEecCCcCCCcccHHHHHHhcCCC
Q psy16967        190 SCN--NALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNPS  238 (282)
Q Consensus       190 ~~~--~~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~  238 (282)
                      ...  .++..++.+.   +. .+..|.|.|||||+|++|||.||+||++|+
T Consensus       509 ~~~~~~~l~~~~~~~---~~-~~~~v~~~wV~~H~g~~~Ne~AD~LA~~a~  555 (555)
T 1mu2_A          509 PTESESKIVNQIIEE---MI-KKEAIYVAWVPAHKGIGGNQEVDHLVSQGI  555 (555)
T ss_dssp             CSEESCHHHHHHHHH---HH-HCSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             cccccHHHHHHHHHH---hc-cCCcEEEEEEECCCCChhHHHHHHHHHhhC
Confidence            533  2355544443   33 357899999999999999999999999985

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

Probab=99.81  E-value=7.3e-20  Score=148.43  Aligned_cols=118  Identities=13%  Similarity=0.220  Sum_probs=89.0

Q ss_pred             eEEecCCCCC-C--CCceE-EEE-EcCCe--eee--ecC---CCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeCcHHHH
Q psy16967        116 ILCFTDGSKT-E--NSTSC-AYT-INKNV--NSF--RLN---VVNSVFSAELMAILLCLQNLKYLPSTKFLLVTDSMSSL  183 (282)
Q Consensus       116 ~~iyTDGS~~-~--~~~G~-gvv-~~~~~--~~~--~l~---~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~sDS~~al  183 (282)
                      +.||||||+. .  +.+|+ |++ .+.+.  ..+  .++   ..+|++.||+.|++.||+.+...+..+|.|+|||++++
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            6899999998 3  44785 854 44322  222  222   37899999999999999999887888999999999999


Q ss_pred             HHHhcCCCC-chHHHHHHHHHHHHHhCCCceEEEecCCcCCCcccHHHHHHhcCCC
Q psy16967        184 QAITSKSCN-NALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNPS  238 (282)
Q Consensus       184 ~~l~~~~~~-~~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~  238 (282)
                      +.+.+++.. ++....+.+.+..+.... .|.|.|||+    ++|+.||+||++|+
T Consensus        82 ~~i~~~w~~~~~~~~~l~~~i~~l~~~~-~v~~~~V~~----~~N~~AD~LA~~a~  132 (149)
T 2ehg_A           82 KQMNGEYKVKAKRIIPLYEKAIELKKKL-NATLIWVPR----EENKEADRLSRVAY  132 (149)
T ss_dssp             HHHTTSSCCCCTTHHHHHHHHHHHHHHH-TCEEEECCG----GGCHHHHHHHHHHH
T ss_pred             HHHhCccccCCHHHHHHHHHHHHHHhcC-CEEEEEcCC----cccHHHHHHHHHHH
Confidence            999998653 233344444444444433 599999998    59999999999988

>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=99.80  E-value=7.8e-20  Score=177.92  Aligned_cols=116  Identities=28%  Similarity=0.415  Sum_probs=89.5

Q ss_pred             CCceEEecCCCCCCCC--ceEEEEEcCCe-eeeecCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeCcHHHHHHHhcC
Q psy16967        113 HDRILCFTDGSKTENS--TSCAYTINKNV-NSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLVTDSMSSLQAITSK  189 (282)
Q Consensus       113 ~~~~~iyTDGS~~~~~--~G~gvv~~~~~-~~~~l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~sDS~~al~~l~~~  189 (282)
                      .+.+.||||||+..++  +|+|+++..+. ..... ..+||+.||+.|++.||+.+    ..++.|+|||++|++++.++
T Consensus       437 ~~~~~iytDGs~~~n~g~~g~g~v~~~~~~~~~~~-~~~TNn~aEl~Ai~~aL~~~----~~~v~I~tDS~~vi~~i~~~  511 (557)
T 2zd1_A          437 VGAETFYVDGAANRETKLGKAGYVTNKGRQKVVPL-TNTTNQKTELQAIYLALQDS----GLEVNIVTDSQYALGIIQAQ  511 (557)
T ss_dssp             TTSCEEEEEEEECTTTCCEEEEEEETTSCEEEEEE-CSCCHHHHHHHHHHHHHHHS----CSEEEEEECCHHHHHHHTTC
T ss_pred             CCCEEEEEccCCCCCCCceEEEEEEECCcEEEecC-CCCCHHHHHHHHHHHHHHhC----CCcEEEEeChHHHHHHHhcC
Confidence            4569999999997643  78887655333 33333 46799999999999999998    57999999999999999997


Q ss_pred             CCCc--hHHHHHHHHHHHHHhCCCceEEEecCCcCCCcccHHHHHHhcCC
Q psy16967        190 SCNN--ALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNP  237 (282)
Q Consensus       190 ~~~~--~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a  237 (282)
                      ...+  ++..++.+.   +.. ...|.|.|||||+|++|||.||+||++|
T Consensus       512 ~~~~~~~l~~~~~~~---l~~-~~~v~~~wV~~H~g~~~Ne~AD~LA~~a  557 (557)
T 2zd1_A          512 PDKSESELVNQIIEQ---LIK-KEKVYLAWVPAHKGIGGNEQVDKLVSAG  557 (557)
T ss_dssp             CSEESSHHHHHHHHH---HHH-CSEEEEEECCSSSCCTTCCGGGGCC---
T ss_pred             CccCCHHHHHHHHHH---Hhc-CCCEEEEEcCCCCCChhHHHHHHHHhcC
Confidence            6542  355554443   433 4689999999999999999999999986

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

Probab=99.41  E-value=9.9e-14  Score=111.38  Aligned_cols=116  Identities=14%  Similarity=-0.006  Sum_probs=81.8

Q ss_pred             CCCceEEecCCCCCCC--CceEEEEEcC--Ce--eeeecCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeCcHHHHHH
Q psy16967        112 YHDRILCFTDGSKTEN--STSCAYTINK--NV--NSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLVTDSMSSLQA  185 (282)
Q Consensus       112 ~~~~~~iyTDGS~~~~--~~G~gvv~~~--~~--~~~~l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~sDS~~al~~  185 (282)
                      ..+.+.||||||+..+  .+|+|+++..  ..  .+..++ .+|++.||++|++.||+.+...+. ++.|+|||+++++.
T Consensus         8 ~~~~~~iy~DGa~~gNpG~~G~G~vl~~~g~~~~~~~~~~-~~TNN~aEl~A~i~aL~~~~~~~~-~v~i~tDS~~vi~w   85 (142)
T 1zbf_A            8 EIIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIP-IGTNNMGEFLAIVHGLRYLKERNS-RKPIYSNSQTAIKW   85 (142)
T ss_dssp             CCCSSSEEEEEEECSSSEEEEEEEEETTTCCEEEECCCEE-EECHHHHHHHHHHHHHHHHHHTTC-CCCEEESCHHHHHH
T ss_pred             CCCeEEEEEeeccCCCCCCeEEEEEEEeCCEEEEEecccC-CcCcHHHHHHHHHHHHHHHHhCCC-eEEEEEehHHHHHH
Confidence            3567899999999864  3788866532  22  222232 578999999999999999988766 99999999999999


Q ss_pred             HhcCCCC-c--------hHHHHHHHHHHHHHhCCCceEEEecCCcCCCcccHHHH
Q psy16967        186 ITSKSCN-N--------ALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVD  231 (282)
Q Consensus       186 l~~~~~~-~--------~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD  231 (282)
                      +.+.+.. +        .+.+.|..+..-+..+  .+....|.-|++.-||..||
T Consensus        86 ~~~~~~k~~~~~~v~n~dLw~~l~~~~~w~~~~--~~~~~~~kw~~~~~ge~pad  138 (142)
T 1zbf_A           86 VKDKKAKSTLVRNEETALIWKLVDEAEEWLNTH--TYETPILKWQTDKWGEIKAD  138 (142)
T ss_dssp             HHHTCCCCCCCCSTTTHHHHHHHHHHHHHHHHC--CCCCCEEECCHHHHCSCTTC
T ss_pred             HHcCCccCCCCCCcccHHHHHHHHHHHHHHhhC--CCceeEEEeccCccCcCccc
Confidence            9987632 1        1334444443334444  34555566688788888887

>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=99.24  E-value=1.8e-11  Score=96.80  Aligned_cols=75  Identities=15%  Similarity=0.059  Sum_probs=58.2

Q ss_pred             CCceEEecCCCCCCCC--ceEE-EEEcCCe---eeeecCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeCcHHHHHHH
Q psy16967        113 HDRILCFTDGSKTENS--TSCA-YTINKNV---NSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLVTDSMSSLQAI  186 (282)
Q Consensus       113 ~~~~~iyTDGS~~~~~--~G~g-vv~~~~~---~~~~l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~sDS~~al~~l  186 (282)
                      +....||||||+..+.  .|+| |+...+.   .+..+ ..+||+.||++|++.||+.+.+.+.. +.|+|||++|+..+
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            5667899999998754  7885 5544322   22233 36799999999999999999876544 89999999999999


Q ss_pred             hcC
Q psy16967        187 TSK  189 (282)
Q Consensus       187 ~~~  189 (282)
                      .+.
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=85.06  E-value=0.18  Score=47.02  Aligned_cols=72  Identities=11%  Similarity=-0.005  Sum_probs=47.1

Q ss_pred             CceEEecCCCCCCCCceEEEEEcC---Ce-----eeeec---CCCCchHHHHHHHHHHHHHHhhcC-CCCeEEEEeCcHH
Q psy16967        114 DRILCFTDGSKTENSTSCAYTINK---NV-----NSFRL---NVVNSVFSAELMAILLCLQNLKYL-PSTKFLLVTDSMS  181 (282)
Q Consensus       114 ~~~~iyTDGS~~~~~~G~gvv~~~---~~-----~~~~l---~~~~s~~~AEl~AI~~AL~~~~~~-~~~~i~I~sDS~~  181 (282)
                      ..+.+|||+|..  ++| ||....   ..     .+..+   ....+++..|+.||..|++..... ....++|+||+. 
T Consensus       345 ~~~~l~~DAS~~--~~g-avL~q~~~~~~~~i~y~Sk~l~~~e~~ys~~ekEllAi~~a~~~~~~yl~g~~~~v~tDh~-  420 (455)
T 1rw3_A          345 KPFELFVDEKQG--YAK-GVLTQKLGPWRRPVAYLSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLTMGQPLVIKAPHA-  420 (455)
T ss_dssp             CTTSCEEEEEEC--SSS-BEECCBCTTTTCCCCCCCBCSCSSCSSSCCSSHHHHHHHHHHHHHHGGGCSSCEEEECSSC-
T ss_pred             CcEEEEEeccCC--cce-eEEEEecCCcEEEEEEEcccCCccccccchHHHHHHHHHHHHHHHHHHcCCCcEEEEecCh-
Confidence            447899999853  333 344321   11     22233   234578899999999999877543 457999999996 


Q ss_pred             HHHHHhcC
Q psy16967        182 SLQAITSK  189 (282)
Q Consensus       182 al~~l~~~  189 (282)
                      ++..+.+.
T Consensus       421 ~~~~l~~~  428 (455)
T 1rw3_A          421 VEALVKQP  428 (455)
T ss_dssp             TTTTSSST
T ss_pred             HHHHhCCC
Confidence            66555554

---

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	282
d1mu2a1	126	c.55.3.1 (A:430-555) HIV RNase H (Domain of revers	4e-08
d1s1ta1	110	c.55.3.1 (A:430-539) HIV RNase H (Domain of revers	3e-06
d1rila_	147	c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermoph	4e-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 = 48.8 bits (115), Expect = 4e-08
 Identities = 28/119 (23%), Positives = 49/119 (41%), Gaps = 8/119 (6%)

Query: 119 FTDGSKTENST--SCAYTINKNVNSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLV 176
           +TDGS    S      Y  ++  +  +     +   AEL A  + L +       K  ++
Sbjct: 11  YTDGSCNRQSKEGKAGYVTDRGKDKVKKLEQTTNQQAELEAFAMALTDSG----PKVNII 66

Query: 177 TDSMSSLQAITSKSCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAK 235
            DS   +  + S+   +   SKI +  ++ +   + I   W P+H GI GN+ VD    
Sbjct: 67  VDSQYVMGIVASQPTESE--SKIVNQIIEEMIKKEAIYVAWVPAHKGIGGNQEVDHLVS 123

>d1s1ta1 c.55.3.1 (A:430-539) HIV RNase H (Domain of reverse transcriptase) {Human immunodeficiency virus type 1 [TaxId: 11676]} Length = 110

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]

 Score = 43.0 bits (101), Expect = 3e-06
 Identities = 22/107 (20%), Positives = 43/107 (40%), Gaps = 12/107 (11%)

Query: 119 FTDGSKTENSTS--CAYTINKNVNSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLV 176
           + DG+    +      Y  N+           +    EL AI L LQ+       +  +V
Sbjct: 12  YVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSG----LEVNIV 67

Query: 177 TDSMSSLQAITS--KSCNNALLSKIYSTWLDLVACGKEISFMWCPSH 221
           TDS  +L  I +      + L+++I    ++ +   +++   W P+H
Sbjct: 68  TDSQYALGIIQAQPDQSESELVNQI----IEQLIKKEKVYLAWVPAH 110

>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 = 37.6 bits (86), Expect = 4e-04
 Identities = 29/139 (20%), Positives = 41/139 (29%), Gaps = 19/139 (13%)

Query: 115 RILCFTDGSKTENSTSCAYTI-----NKNVNSFRLNVVNSVFSAELMAILLCLQNLKYLP 169
           R+  FTDG+   N     +                    +    EL A +  L+ LK   
Sbjct: 3   RVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKE-- 60

Query: 170 STKFLLVTDSMSSLQAITSKSCNNAL----------LSKIYSTWLDLVACGKE--ISFMW 217
             +  L TDS    +A T                    K    W  L+       + F +
Sbjct: 61  PCEVDLYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPHRVRFHF 120

Query: 218 CPSHCGISGNEAVDVAAKN 236
              H G   NE VD  A+ 
Sbjct: 121 VKGHTGHPENERVDREARR 139

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	282
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.92
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.88
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	99.88
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	99.77
d1zbfa1	132	BH0863-like Ribonuclease H {Bacillus halodurans [T	99.53

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

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

Probab=99.92  E-value=1.2e-25  Score=175.99  Aligned_cols=117  Identities=21%  Similarity=0.357  Sum_probs=89.2

Q ss_pred             CCceEEecCCCCCCC-C-ceEEEEEcCCe-eeeecCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeCcHHHHHHHhcC
Q psy16967        113 HDRILCFTDGSKTEN-S-TSCAYTINKNV-NSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLVTDSMSSLQAITSK  189 (282)
Q Consensus       113 ~~~~~iyTDGS~~~~-~-~G~gvv~~~~~-~~~~l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~sDS~~al~~l~~~  189 (282)
                      ++..++|||||+..+ + .|+|++...+. ....++ ..|++.|||.||++||+..    ...+.|+|||++++..+.+.
T Consensus         5 ~~~~t~YTDGS~~~n~~~~~~g~~~~~~~~~~~~~~-~~tnn~AEl~Ai~~al~~~----~~~i~I~tDS~~v~~~~~~~   79 (126)
T d1mu2a1           5 PGAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKLE-QTTNQQAELEAFAMALTDS----GPKVNIIVDSQYVMGIVASQ   79 (126)
T ss_dssp             TTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEEES-SCCHHHHHHHHHHHHHHTS----CSEEEEEESCHHHHHHHHTC
T ss_pred             CCCcEEEEcCCCCCCCCcEEEEEEecCCCEEEEecC-CCcchHHHHHHHHHHhccC----CcceEEEechHHHHHHHhcC
Confidence            455799999998764 3 56666655444 444453 5799999999999999863    57899999999999999997


Q ss_pred             CCCch--HHHHHHHHHHHHHhCCCceEEEecCCcCCCcccHHHHHHhcCCC
Q psy16967        190 SCNNA--LLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNPS  238 (282)
Q Consensus       190 ~~~~~--~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~  238 (282)
                      ...+.  ....   .+..+.. ...|.|.|||||+|++|||.||+||++|.
T Consensus        80 ~~~~~~~~~~~---~~~~~~~-~~~v~~~wV~gH~g~~gNe~AD~LA~~ai  126 (126)
T d1mu2a1          80 PTESESKIVNQ---IIEEMIK-KEAIYVAWVPAHKGIGGNQEVDHLVSQGI  126 (126)
T ss_dssp             CSEESCHHHHH---HHHHHHH-CSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             CccccchHHHH---HHHHhhh-cceeEEEEEeCCCCCcchHHHHHHHHhhC
Confidence            65432  2222   2233433 46899999999999999999999999984

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

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

Probab=99.88  E-value=5.7e-24  Score=170.50  Aligned_cols=122  Identities=23%  Similarity=0.199  Sum_probs=88.0

Q ss_pred             ceEEecCCCCCCCC--ceEEEEE-cCCe--eeeecCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeCcHHHHHHHhcC
Q psy16967        115 RILCFTDGSKTENS--TSCAYTI-NKNV--NSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLVTDSMSSLQAITSK  189 (282)
Q Consensus       115 ~~~iyTDGS~~~~~--~G~gvv~-~~~~--~~~~l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~sDS~~al~~l~~~  189 (282)
                      .|+||||||+.+++  +|+|+++ ..+.  ..+.....+|++.||+.|++.||+.+..  ...+.|+|||++++..+...
T Consensus         3 ~i~iytDGs~~~N~g~~G~g~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~~~--~~~i~i~tds~~~~~~~~~~   80 (147)
T d1rila_           3 RVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKE--PCEVDLYTDSHYLKKAFTEG   80 (147)
T ss_dssp             CCCEEEEEEESSTTEEEEEEEEECBTTBCCEECCEEEEECHHHHHHHHHHHHHHSCCS--CCEEEEECCCHHHHHHHHSS
T ss_pred             EEEEEEccCCCCCCCccEEEEEEEECCcceEEecccccccHHHHHHHHHHHHhhhccC--CceEEEecchhhhhcccccc
Confidence            58999999998754  7888554 3332  2222223469999999999999998653  57899999999999988664


Q ss_pred             CC----------Cc--hH-HHHHHHHHHHHHhCCCceEEEecCCcCCCcccHHHHHHhcCCCC
Q psy16967        190 SC----------NN--AL-LSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNPSP  239 (282)
Q Consensus       190 ~~----------~~--~~-~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~  239 (282)
                      ..          ..  ++ -..+.+.+..+. ....|.|+|||||+|++|||.||+||++|+.
T Consensus        81 ~~~~~~~~~~~~~~~~~v~n~dL~~~l~~~~-~~~~v~~~wVkgHsg~~gNe~AD~LAk~aa~  142 (147)
T d1rila_          81 WLEGWRKRGWRTAEGKPVKNRDLWEALLLAM-APHRVRFHFVKGHTGHPENERVDREARRQAQ  142 (147)
T ss_dssp             HHHHHHHTTSBCTTSSBCTTHHHHHHHHHHH-TTSEEECCCCCGGGSCTHHHHHHHHHHHHHT
T ss_pred             chhhhhhccccccccccchhHHHHHHHHHHh-hhcccceEEccCCCCCcchHHHHHHHHHHHH
Confidence            21          11  11 122333333333 3568999999999999999999999999873

>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=99.88  E-value=4.7e-23  Score=165.53  Aligned_cols=122  Identities=23%  Similarity=0.259  Sum_probs=88.6

Q ss_pred             ceEEecCCCCCCCC--ceEEEE-EcCCe-eeee-cCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeCcHHHHHHHhcC
Q psy16967        115 RILCFTDGSKTENS--TSCAYT-INKNV-NSFR-LNVVNSVFSAELMAILLCLQNLKYLPSTKFLLVTDSMSSLQAITSK  189 (282)
Q Consensus       115 ~~~iyTDGS~~~~~--~G~gvv-~~~~~-~~~~-l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~sDS~~al~~l~~~  189 (282)
                      .|.||||||+.+++  +|+|++ ..++. ..+. .....|++.||+.|++.||+++..  ...+.++|||++++..+...
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            48999999998754  789954 44443 2222 124568999999999999998653  57899999999999988754


Q ss_pred             CC---------Cch---HHHHHHHHHHHHHhCCCceEEEecCCcCCCcccHHHHHHhcCCCC
Q psy16967        190 SC---------NNA---LLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNPSP  239 (282)
Q Consensus       190 ~~---------~~~---~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~  239 (282)
                      ..         ..+   ....+...+..+. ....|.|+|||||+|++|||.||+|||+|+.
T Consensus        80 ~~~~~~~~~~~~~~~~~~n~~~~~~i~~~~-~~~~V~~~wV~gH~g~~gNe~AD~LAk~aa~  140 (152)
T d1jl1a_          80 IHNWKKRGWKTADKKPVKNVDLWQRLDAAL-GQHQIKWEWVKGHAGHPENERADELARAAAM  140 (152)
T ss_dssp             HHHHHHTTTBCTTSCBCTTHHHHHHHHHHT-TTCEEEEEECCSSTTCHHHHHHHHHHHHHHH
T ss_pred             hhHhHhccchhcccCeeecHHHHHHHHHHh-hcceeEEEEecccCCCccHHHHHHHHHHHHh
Confidence            21         111   1122333333333 3468999999999999999999999999984

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

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

Probab=99.77  E-value=6e-19  Score=134.13  Aligned_cols=100  Identities=24%  Similarity=0.395  Sum_probs=75.1

Q ss_pred             CCceEEecCCCCCCCC--ceEEEEEcCCe-eeeecCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeCcHHHHHHHhcC
Q psy16967        113 HDRILCFTDGSKTENS--TSCAYTINKNV-NSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLVTDSMSSLQAITSK  189 (282)
Q Consensus       113 ~~~~~iyTDGS~~~~~--~G~gvv~~~~~-~~~~l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~sDS~~al~~l~~~  189 (282)
                      .+..++|||||+..++  .|+|++...+. ....+ ..+|++.|||.||+.||+..    ..++.|+|||+++++++...
T Consensus         6 ~~~~t~ytDGs~~~n~~~g~~g~~~~~~~~~~~~~-~~~TNn~aEl~Avi~aL~~~----~~~v~I~TDS~yvi~~i~~~   80 (110)
T d1s1ta1           6 VGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTL-TDTTNQKTELQAIYLALQDS----GLEVNIVTDSQYALGIIQAQ   80 (110)
T ss_dssp             TTSEEEEEEEEEETTTTEEEEEEEETTSCEEEEEE-SSCCHHHHHHHHHHHHHHHS----CSEEEEEECCHHHHHHHHHC
T ss_pred             CCCcEEEEeCCCCCCCCCcEEEEEEecCCeEEEec-ccCcHHHHHHHHHHHHHHhC----CCeEEEEEehHHHHHHHhcC
Confidence            4667899999987653  56665554433 44444 35699999999999999864    56899999999999999987


Q ss_pred             CCC--chHHHHHHHHHHHHHhCCCceEEEecCCc
Q psy16967        190 SCN--NALLSKIYSTWLDLVACGKEISFMWCPSH  221 (282)
Q Consensus       190 ~~~--~~~~~~i~~~~~~l~~~~~~v~~~WVpgH  221 (282)
                      ...  ..+.+++.+.   +.. ...|.|.|||||
T Consensus        81 ~~~~~~~l~~~il~~---l~~-~~~v~i~WVpgH  110 (110)
T d1s1ta1          81 PDQSESELVNQIIEQ---LIK-KEKVYLAWVPAH  110 (110)
T ss_dssp             CSEESCHHHHHHHHH---HHH-CSEEEEEECCSS
T ss_pred             ccccchHHHHHHHHH---Hhc-CCceEEEEeCCC
Confidence            654  3355665544   433 478999999999

>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=99.53  E-value=1.7e-15  Score=117.45  Aligned_cols=111  Identities=14%  Similarity=0.048  Sum_probs=79.9

Q ss_pred             EEecCCCCCCCC--ceEEEEEcC-Ce---eeeecCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeCcHHHHHHHhcCC
Q psy16967        117 LCFTDGSKTENS--TSCAYTINK-NV---NSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLVTDSMSSLQAITSKS  190 (282)
Q Consensus       117 ~iyTDGS~~~~~--~G~gvv~~~-~~---~~~~l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~sDS~~al~~l~~~~  190 (282)
                      .||||||+..+.  +|+|+|+.. +.   .+..+ ...|++.||++|++.||+.+...+ .++.|+|||++|+..+.+..
T Consensus         6 sIy~DGa~~GNPGp~g~g~v~~~~~~~~~~sg~~-~~~TNN~aEl~A~i~aL~~~~~~~-~~i~I~tDS~yvi~wv~~~~   83 (132)
T d1zbfa1           6 SLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPI-PIGTNNMGEFLAIVHGLRYLKERN-SRKPIYSNSQTAIKWVKDKK   83 (132)
T ss_dssp             SEEEEEEECSSSEEEEEEEEETTTCCEEEECCCE-EEECHHHHHHHHHHHHHHHHHHTT-CCCCEEESCHHHHHHHHHTC
T ss_pred             eEEEeecCCCCCchheEEEEEEcCCEEEEEEcCc-CccchHHHHHHHHHHHHHHhhcCC-ceEEEEeccHHHHHHHHhCc
Confidence            489999999754  788865432 22   22223 456899999999999999998754 57999999999999998764


Q ss_pred             CCc----h-HHHHHHHHHHH----HHhCCCceEEEecCCcCCCcccHHHH
Q psy16967        191 CNN----A-LLSKIYSTWLD----LVACGKEISFMWCPSHCGISGNEAVD  231 (282)
Q Consensus       191 ~~~----~-~~~~i~~~~~~----l~~~~~~v~~~WVpgH~gi~gNe~AD  231 (282)
                      ...    + -.+.+++++.+    +.  ...+.+.||..|+..-||..||
T Consensus        84 ~kt~~~~~vkN~~l~~~i~~a~~~lk--~h~~~~~~~KW~~~~wG~i~AD  131 (132)
T d1zbfa1          84 AKSTLVRNEETALIWKLVDEAEEWLN--THTYETPILKWQTDKWGEIKAD  131 (132)
T ss_dssp             CCCCCCCSTTTHHHHHHHHHHHHHHH--HCCCCCCEEECCHHHHCSCTTC
T ss_pred             eecCcCCCcccHHHHHHHHHHHHHHH--hCCcCceeEEecCcccccCCCC
Confidence            221    1 22333333332    33  3558889999999999999887