Psyllid ID: psy5071

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360------
Protein Sequence
MRYVSKIGSCPSNPAHKELYHTNINVNDFPPNKPKPLCVRIKDMSDFLPLITDSEFVPFTRPRPPWSFQVPSIDFSLHLDNKDNIPPIVFQQHFHDLVTNKYSDSVLCFTDGSKTVNSTSCAYSIGNQVHAFKLNKVNSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNCKNDHPLVSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVDIAARNPITNITLKNCTSFDFRPVISSIIHKQWQISWDNVINNKLKRVKPLIVDWETSNRNSRYEEVVITRLRIGHTRVTHDHLFKRDPRPTCGCGDTLTVDHIFNCRTHLQIRASLPSPPALDNNPANIDSALMYLKAIGLYTKI
Secondary Structure (PSIPRED)
cEEEEEccccccccccHHHHHcccccccccccccccHHHHHHHHHHcccccccccccccccccccccccccEEEccccccccccccHHHHHHHHHHHHHccccccEEEEEccccccccccEEEEEcccEEEEEccccccHHHHHHHHHHHHHHHHHccccccEEEEccHHHHHHHHHccccccHHHHHHHHHHHHHHHcccEEEEEEEcccccccccHHHHHHHcccccccccccccccccHHHHHHHHHHHccccccccccccccccccccccccccccccHHHHHHHHHHHHccccccccccccccccccccccccccHHHHccccccHHHHHccccccccccccHHHHHHHHHHHHHcccccc
Secondary Structure Prediction (SSPRO)
ccEEEEEEcccccHHHHHHHcccccccccccccccHHHHHHHHHHHHccccccccccccccccccccccccEEEEEEcccccccccHHHHHHHHHHHHHHHccccEEEEEccccccccEEEEEEEcccEEEcccccccHHHHHHHHHHHHHHHHHHHcccccEEEEEccHHHHHHHHccccccHHHHHHHHHHHHHHHcccEEEEEEEcccccccccHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccHHHHHHHHHHHccccHHHHHHcccccccccccccccccHEEEccHHHHHHHHHHcccccccccHHHHHHHHHHHHHHcHHccc
Coil and Loop (DISEMBL)
mryvskigscpsnpahkelyhtninvndfppnkpkplcvrikdmsdflplitdsefvpftrprppwsfqvpsidfslhldnkdnippivfQQHFHdlvtnkysdsvlcftdgsktvnstscAYSIGNQVHAFKLNKVNSVLSSELMAILLCVKNliflpstnftlISDSMSALLAISnckndhplvSLVYTTWleakdcgknlnfvwcpshcgitgnelvdiaarnpitnitlknctsfdfrpvISSIIHKQWQISWDNVINnklkrvkplivdwetsnrnsryEEVVITRLRIGhtrvthdhlfkrdprptcgcgdtltvdhiFNCRTHLqiraslpsppaldnnpanIDSALMYLKAIGLYTKI
Flexible Loop (DISEMBL)
mryvskigscpsnpahKELYHtninvndfppnKPKPLCVRIKDMSDFLPLITDSEFVPFTRPRPPWSFQVPSIDFSLHLDNKDNIPPIVFQQHFHDLVTNKYSDSVLCFTDGSKTVNSTSCAYSIGNQVHAFKLNKVNSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNCKNDHPLVSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVDIAARNPITNITLKNCTSFDFRPVISSIIHKQWQISWDNVINNKLKRVKplivdwetsnrnsryeeVVITrlrightrvthdhlfkrdprptcgCGDTLTVDHIFNCRTHLQIRASLPSPPALDNNPANIDSALMYLKAIGLYTKI
Low Complexity Region (SEG)
MRYVSKIGSCPSNPAHKELYHTNINVNDFPPNKPKPLCVRIKDMSDFLPLITDSEFVPFTRPRPPWSFQVPSIDFSLHLDNKDNIPPIVFQQHFHDLVTNKYSDSVLCFTDGSKTVNSTSCAYSIGNQVHAFKLNKVNSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNCKNDHPLVSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVDIAARNPITNITLKNCTSFDFRPVISSIIHKQWQISWDNVINNKLKRVKPLIVDWETSNRNSRYEEVVITRLRIGHTRVTHDHLFKRDPRPTCGCGDTLTVDHIFNCRTHLQIRASLPSPPALDNNPANIDSALMYLKAIGLYTKI
Disordered region (IsUnstruct)
******************LYHTNINVNDFP***PKPLCVRIKDMSDFLPLITDSEFVPFTRPRPPWSFQVPSIDFSLHLDNKDNIPPIVFQQHFHDLVTNKYSDSVLCFTDGSKTVNSTSCAYSIGNQVHAFKLNKVNSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNCKNDHPLVSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVDIAARNPITNITLKNCTSFDFRPVISSIIHKQWQISWDNVINNKLKRVKPLIVDWETSNRNSRYEEVVITRLRIGHTRVTHDHLFKRDPRPTCGCGDTLTVDHIFNCRTHLQIRAS************NIDSALMYLKAIGLY***
Disordered Region (DISOPRED)
MRYVSKIGSCPSNPAHKELYHTNINV******KPKPLCVRIKDMSDFLPLITDSEFVPFTRPRPPWSFQVPSIDFSL*************QQHFHDLVTNKYSDSVLCFTDGSKTVNSTSCAYSIGNQVHAFKLNKVNSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNCKNDHPLVSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVDIAARNPITNITLKNCTSFDFRPVISSIIHKQWQISWDNVINNKLKRVKPLIVDWETSNRNSRYEEVVITRLRIGHTRVTHDHLFKRDPRPTCGCGDTLTVDHIFNCRTHLQIRASLPS****DNNPANIDSALMYLKAIGLYTKI
Disordered Region (DISEMBL)
MRYVSKIGSCPSNPAHKELYHTNINVNDFPPNKPKPLCVRIKDMSDFLPLITDSEFVPFTRPRPPWSFQVPSIDFSLHLDNKDNIPPIVFQQHFHDLVTNKYSDSVLCFTDGSKTVNSTSCAYSIGNQVHAFKLNKVNSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNCKNDHPLVSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVDIAARNPITNITLKNCTSFDFRPVISSIIHKQWQISWDNVINNKLKRVKPLIVDWETSNRNSRYEEVVITRLRIGHTRVTHDHLFKRDPRPTCGCGDTLTVDHIFNCRTHLQIRASLPSPPALDNNPANIDSALMYLKAIGLYTKI
Disordered Region (DISPRO)
MRYVSKIGSCPSNPAHKELYHTNINVNDFPPNKPKPLCVRIKDMSDFLPLITDSEFVPFTRPRPPWSFQVPSIDFSLHLDNKDNIPPIVFQQHFHDLVTNKYSDSVLCFTDGSKTVNSTSCAYSIGNQVHAFKLNKVNSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNCKNDHPLVSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVDIAARNPITNITLKNCTSFDFRPVISSIIHKQWQISWDNVINNKLKRVKPLIVDWETSNRNSRYEEVVITRLRIGHTRVTHDHLFKRDPRPTCGCGDTLTVDHIFNCRTHLQIRASLPSPPALDNNPANIDSALMYLKAIGLYTKI
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MRYVSKIGSCPSNPAHKELYHTNINVNDFPPNKPKPLCVRIKDMSDFLPLITDSEFVPFTRPRPPWSFQVPSIDFSLHLDNKDNIPPIVFQQHFHDLVTNKYSDSVLCFTDGSKTVNSTSCAYSIGNQVHAFKLNKVNSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNCKNDHPLVSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVDIAARNPITNITLKNCTSFDFRPVISSIIHKQWQISWDNVINNKLKRVKPLIVDWETSNRNSRYEEVVITRLRIGHTRVTHDHLFKRDPRPTCGCGDTLTVDHIFNCRTHLQIRASLPSPPALDNNPANIDSALMYLKAIGLYTKI
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

No hits with e-value below 0.001 by BLAST

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	366
125901787	1222	pol-like protein [Biomphalaria glabrata]	0.991	0.297	0.320	5e-41
443693558	502	hypothetical protein CAPTEDRAFT_189741,	0.885	0.645	0.331	6e-40
443695973	261	hypothetical protein CAPTEDRAFT_23017, p	0.674	0.946	0.344	8e-35
443712830	397	hypothetical protein CAPTEDRAFT_202466 [	0.704	0.649	0.326	1e-32
443721618	471	hypothetical protein CAPTEDRAFT_200496,	0.672	0.522	0.353	3e-32
427778603	1397	Putative tick transposon [Rhipicephalus	0.778	0.204	0.333	2e-30
443724607	397	hypothetical protein CAPTEDRAFT_208903 [	0.726	0.670	0.321	2e-29
427791321	1210	Putative tick transposon, partial [Rhipi	0.781	0.236	0.309	7e-29
427791807	1212	Putative tick transposon, partial [Rhipi	0.781	0.235	0.309	8e-29
443682433	619	hypothetical protein CAPTEDRAFT_222606 [	0.551	0.326	0.376	1e-27

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

 Score =  174 bits (441), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 120/374 (32%), Positives = 187/374 (50%), Gaps = 11/374 (2%)

Query: 1    MRYVSKIGSCPSNPAHKELYH-TNINVNDFPPNKPKPLCVRIKDMSDFLPLITDSEFVPF 59
            M+Y+ K+ S P+NPA   +++ T + + +  PN  +PL +R+++    L    D      
Sbjct: 852  MQYIVKLKSNPTNPAFDSIFNPTEVELYNRRPNVIQPLGLRMREPIQNLTQPIDQISKIE 911

Query: 60   TRPRPPWSFQVPSIDFSLHLDNKDNIPPIVFQQHFHDLVTNKYSDSVLCFTDGSKTVNST 119
            T   PPW    P ++ SL    K+N  P + Q HF +L    Y D    +TDGSK     
Sbjct: 912  TPQNPPWLMNKPKLNLSLLNFKKENTDPSILQVHFREL-QESYGDCGTIYTDGSKMEGKV 970

Query: 120  SCAYSIGNQVHAFKLNKVNSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNC 179
            +CA S  N+  + +L    S+ ++EL AILL +  +     + F + SDS SAL A+   
Sbjct: 971  ACACSFRNKTISRRLPDGCSIFTAELHAILLALMAVKASERSKFIICSDSKSALQALGRM 1030

Query: 180  KNDHPLV--SLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVDIAARNPITNITLKNCT 237
            K D PLV  SL     + A    +++ F+W PSH GI GNE  D  A+  + +       
Sbjct: 1031 KTDIPLVHKSLKLLDLITADR--RDVTFIWVPSHVGIEGNEAADREAKRALNHAVSGTQI 1088

Query: 238  SF-DFRPVISSIIHKQWQISWDNVINNKLKRVKPLIVDWETSNRNSRYEEVVITRLRIGH 296
             + D R  I+S  +++WQ  W+   ++KL+++   +    TS   +R     ++RLRIGH
Sbjct: 1089 PYSDLRQSIASATYREWQNRWEAETHSKLRQIVADVRWRPTSKGLTRRGSTTMSRLRIGH 1148

Query: 297  TRVTHDHLFKRDPRPTCG-CGDTLTVDHIF-NCRTHLQIRASLPSPPALDNNPANID--S 352
            T +TH  + KR+  P C  C   LTV+HI  +C  +  +RA       L     N+D   
Sbjct: 1149 TYITHSFVLKREEPPLCEYCDSRLTVEHILVDCPRYQDVRAKHFRATNLKTLFNNVDPGK 1208

Query: 353  ALMYLKAIGLYTKI 366
             L ++  +GL TKI
Sbjct: 1209 VLGFILEVGLSTKI 1222

Source: Biomphalaria glabrata

Species: Biomphalaria glabrata

Genus: Biomphalaria

Family: Planorbidae

Class: Gastropoda

Phylum: Mollusca

Superkingdom: Eukaryota

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

 Score =  171 bits (432), Expect = 6e-40,   Method: Compositional matrix adjust.
 Identities = 119/359 (33%), Positives = 185/359 (51%), Gaps = 35/359 (9%)

Query: 31  PNKPKPLCVRIKDMSDFLPLITDSEFVPFT-RPRPPWSFQVPSIDFSLHLDNKDNIPPIV 89
           P+  +PL  R ++    L  +  +   PF     PPW  + P +D S+    KD  P + 
Sbjct: 11  PSFIRPLLYRTEEA---LESVITAPIAPFKISDVPPWKLRPPEVDTSISKFLKDQHPALF 67

Query: 90  FQQHFHDLVTNKYSDSVLCFTDGSKTVNSTSCAYSIGNQVHAFKLNKVNSVLSSELMAIL 149
            +Q F++L+ +KY   +  +TDGSK+ N+ +CA++       F L    S+ ++EL+AI 
Sbjct: 68  LKQEFYNLI-DKYP-GINIYTDGSKSNNAVACAFTCSTYQIQFGLPTQMSIYTAELIAI- 124

Query: 150 LCVKNLIFLPST----NFTLISDSMSALLAISNCKNDHPLVSLVYTTWLEAKDCGKNLNF 205
              + LIF+ +      F + SDS+S+L A+SNC   HP +  + T        GK + F
Sbjct: 125 --EQALIFIETVKDEDQFNICSDSLSSLTALSNCDITHPYLLSILTKQNNLVRKGKLVVF 182

Query: 206 VWCPSHCGITGNELVDIAARN----PITNITLKNCTSFDFRPVISSIIHKQWQISWDNVI 261
           +WCPSH GI GNE+ D  A+     P+T + L +    D++  I S +   WQ  WD   
Sbjct: 183 IWCPSHVGILGNEVADRLAKQALVMPVTKLPLPHT---DYKSPIRSYVKSLWQNEWDEET 239

Query: 262 NNKLKRVKPLIVDWETSNRNSRYEEVVITRLRIGHTRVTHDHLFKRDPRPTC-GCGDTLT 320
           +NKL  ++P+I +W+   +  R  E+V+ R RIGH+ +TH +L +R+  P C  C   LT
Sbjct: 240 DNKLHSIQPVISEWKQGPQIDRRGEIVLARARIGHSHLTHGYLLRREVAPFCIPCQSLLT 299

Query: 321 VDHIF-NC------RTHLQIRASLPSPPALDNNPANI---DSALM---YLKAIGL-YTK 365
           V HI  +C       T+LQ        P  D++ AN+   DS L+   Y   IG+ Y K
Sbjct: 300 VKHILIDCIDFKMSLTYLQYGPFSSFAPVFDSSAANLSEEDSRLLNSTYGDEIGIQYAK 358

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 =  154 bits (388), Expect = 8e-35,   Method: Compositional matrix adjust.
 Identities = 91/264 (34%), Positives = 145/264 (54%), Gaps = 17/264 (6%)

Query: 71  PSIDFSLHLDNKDNIPPIVFQQHFHDLVTNKYSDSVLCFTDGSKTVNSTSCAYSIGNQVH 130
           P +D S+    KD  P +  +Q F++L+ +KY   +  +TDGSK+ ++ +CA++      
Sbjct: 3   PEVDTSISKFLKDQHPALFLKQEFYNLI-DKYP-GINIYTDGSKSNDAVACAFTCSTYQI 60

Query: 131 AFKLNKVNSVLSSELMAILLCVKNLIFLPST----NFTLISDSMSALLAISNCKNDHPLV 186
            F L    S+ ++EL+AI    + LIF+ +      F + SDS+S+L A+SNC   HP +
Sbjct: 61  QFGLPAQMSIYTAELIAI---EQALIFIETVKDEDQFNICSDSLSSLTALSNCDITHPYL 117

Query: 187 SLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVDIAARN----PITNITLKNCTSFDFR 242
             + T        GK + F+WCPSH GI GNE+ D  A+     P+T + L +    D++
Sbjct: 118 LSILTKQNNLVRKGKLVVFIWCPSHVGILGNEVADRLAKQALVMPVTKLPLPHT---DYK 174

Query: 243 PVISSIIHKQWQISWDNVINNKLKRVKPLIVDWETSNRNSRYEEVVITRLRIGHTRVTHD 302
             I S +   WQ  WD   +NKL  ++P+I +W+   +  R  E+V+ R RIGH+ +TH 
Sbjct: 175 SPIRSYVKSLWQNEWDEETDNKLHSIQPVISEWKQGPQIDRRGEIVLARARIGHSHLTHG 234

Query: 303 HLFKRDPRPTC-GCGDTLTVDHIF 325
           +L +R+  P C  C   L+V HI 
Sbjct: 235 YLLRREVAPFCIPCQSLLSVKHIL 258

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score =  146 bits (369), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 98/300 (32%), Positives = 154/300 (51%), Gaps = 42/300 (14%)

Query: 89  VFQQHFHDLVTNKYSDSVLCFTDGSKTVNSTSCAYSIGNQVHAFKLNKVNSVLSSELMAI 148
            F   F++L+ +KY   +  +TDGSK+ ++ +CA++       F L    S+ ++EL+AI
Sbjct: 116 AFNHEFYNLI-DKYP-GINIYTDGSKSNDTVACAFTCSTYQIQFGLPAQMSIYTAELIAI 173

Query: 149 LLCVKNLIFLPST----NFTLISDSMSALLAISNCKNDHPLVSLVYTTWLEAKDCGKNLN 204
               + LIF+ +      F + SDS+S+L A+SNC   HP +  + T        GK + 
Sbjct: 174 ---EQALIFIETVKDEDQFNICSDSLSSLTALSNCDITHPYLLSILTKQNNLVRKGKKVV 230

Query: 205 FVWCPSHCGITGNELVDIAARN----PITNITLKNCTSFDFRPVISSIIHKQWQISWDNV 260
           F+WCPSH GI GNE+ D  A+     P+T + L +    D++  I S +   WQ  WD  
Sbjct: 231 FIWCPSHVGILGNEVADRQAKQALVMPVTKLPLPHT---DYKSPIRSYVKSLWQNEWDGE 287

Query: 261 INNKLKRVKPLIVDWETSNRNSRYEEVVITRLRIGHTRVTHDHLFKRDPRPTC-GCGDTL 319
            +NKL  ++P+I +W+   +  R  E+V+   RIGH+ +TH +L +R+  P C  C   L
Sbjct: 288 TDNKLHIIQPVISEWKQGPQIDRRGEIVLACARIGHSHLTHGYLLRREVAPFCIPCQSLL 347

Query: 320 TVDHI--------------FNCRTHLQIRASLPSPPALDNNPANIDSALMYLKAIGLYTK 365
           TV HI              FN  +  Q+          D +P+ I   L+YLK IGL+ +
Sbjct: 348 TVKHILIDCIDFEISRRKYFNVFSMRQLFE--------DTHPSKI---LLYLKEIGLFYR 396

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score =  145 bits (366), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 89/252 (35%), Positives = 129/252 (51%), Gaps = 6/252 (2%)

Query: 88  IVFQQHFHDLVTNKYSDSVLCFTDGSKTVNSTSCAYSIGNQVHAFKLNKVNSVLSSELMA 147
           +  +  F D + ++Y DS + +TDGSK+ +S +C++         KL    SV +SE++A
Sbjct: 4   LTIRSEFADAL-DRYPDSTVFYTDGSKSEDSVACSFFSSRLKLKMKLPVQMSVFTSEIIA 62

Query: 148 ILLCVKNLIFL-PSTNFTLISDSMSALLAISNCKNDHPLVSLVYTTWLEAKDCGKNLNFV 206
           IL  ++ +        F + SDS+SA++AI      HP V  V           K + F+
Sbjct: 63  ILSALRCVEADNEQHQFVICSDSLSAIMAIHGMDVRHPYVLQVLYAIKSISQQEKIVVFM 122

Query: 207 WCPSHCGITGNELVDIAARNPI--TNITLKNCTSFDFRPVISSIIHKQWQISWDNVINNK 264
           WCPSH GI GNE+ D  A+  +  TN+      + D R +I   I  +WQ  WD   +NK
Sbjct: 123 WCPSHVGIPGNEMADTLAKEALSSTNLAELPVPASDLRCLIKKYIRSRWQHEWDEQHSNK 182

Query: 265 LKRVKPLIVDWETSNRNSRYEEVVITRLRIGHTRVTHDHLFKRDPRPTC-GCGDTLTVDH 323
           L  + P I  W    R  R EE+V+ R+RIGHT  THD++ + D +  C  C   LTV H
Sbjct: 183 LHSIHPTIGPWPPCQREKRREEIVLARIRIGHTHYTHDYIPRGDDQTECVACVCPLTVQH 242

Query: 324 -IFNCRTHLQIR 334
            I  C   L IR
Sbjct: 243 IIIECADFLHIR 254

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score =  139 bits (349), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 100/300 (33%), Positives = 148/300 (49%), Gaps = 15/300 (5%)

Query: 31   PNKPKPLCVRIKDMSDFLPLITDSEFVPFTRPRPPWSFQVPSI-DFSLHLDNKDNIPPIV 89
            P   +P+  ++K   + L  I   E +P      PW  Q P I D+S     K   P  +
Sbjct: 1042 PLAIRPVVEKLKIHFEDLQEIDQVEVIP------PWK-QCPIICDWSFKDLKKKTAPNAL 1094

Query: 90   FQQHFHDLVTNKYSDSVLCFTDGSKTVNSTSCAYSIGNQVHAFKLNKVNSVLSSELMAIL 149
             QQHF  L  +KY  +   F+DGSK+  S SCA    +   A  L+   S+ ++E   IL
Sbjct: 1095 IQQHFLAL-EHKYRSAAF-FSDGSKSQTSVSCAAYGESFSDAKTLHAHTSIFTAEAYGIL 1152

Query: 150  LCVKNLIFLPSTNFTLISDSMSALLAISNCK-NDHPLVSLVYTTWLEAKDCGKNLNFVWC 208
            L V+++         + +DS+S + A+S  K + +P+ + +     EA +   ++   W 
Sbjct: 1153 LIVEHIKQHMIRRSIIYTDSLSVVTALSCGKCSKNPVFNKLLNNMHEAYNQNLSIVLCWV 1212

Query: 209  PSHCGITGNELVDIAARNPITN--ITLKNCTSFDFRPVISSIIHKQWQISWDNVINNKLK 266
            P H GITGNE+VD  AR   +   I + +    D  PV+   +   WQ+ WD  ++NKL 
Sbjct: 1213 PGHAGITGNEMVDKNAREAASRHTIDISSVPGVDLNPVVRRGLRSHWQVEWDKQVDNKLH 1272

Query: 267  RVKPLIVDWETSNRNSRYEEVVITRLRIGHTRVTHDHLFKRDPRPTC-GCGDTLTVDHIF 325
             VKP +        N R+ EV + RLRIGHT  TH HL      PTC  CG+TLT+ H+ 
Sbjct: 1273 LVKPHLSKVLPQKLN-RFTEVTLARLRIGHTYATHKHLLTGTDPPTCIHCGETLTILHVL 1331

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  136 bits (342), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 94/292 (32%), Positives = 148/292 (50%), Gaps = 26/292 (8%)

Query: 89  VFQQHFHDLVTNKYSDSVLCFTDGSKTVNSTSCAYSIGNQVHAFKLNKVNSVLSSELMAI 148
            F   F++L+ +KY   +  +TDGSK+ ++ +CA++       F L    S+ ++EL+AI
Sbjct: 116 AFNHEFYNLI-DKYP-GINIYTDGSKSNDAVACAFTCSTYQIQFGLPAQMSIYTAELIAI 173

Query: 149 LLCVKNLIFLPST----NFTLISDSMSALLAISNCKNDHPLVSLVYTTWLEAKDCGKNLN 204
               + LIF+ +      F + SDS+S+L A+SNC   HP +  + T        GK + 
Sbjct: 174 ---EQALIFIETMKDEDQFNICSDSLSSLTALSNCDITHPYLLSILTKQNNLVRKGKLVV 230

Query: 205 FVWCPSHCGITGNELVDIAARN----PITNITLKNCTSFDFRPVISSIIHKQWQISWDNV 260
           F+WCPSH GI GNE+ D  A+     P+T + L +    D++  I S +    Q  WD  
Sbjct: 231 FIWCPSHVGILGNEVADRLAKQALVMPVTKLPLPHT---DYKSPIRSYVKSLRQNEWDEE 287

Query: 261 INNKLKRVKPLIVDWETSNRNSRYEEVVITRLRIGHTRVTHDHLFKRDPRPTC-GCGDTL 319
            +NKL  ++P+I +W+   +  R  E+V+    IGH+ +TH +L +R+  P C  C   L
Sbjct: 288 TDNKLHTIQPVISEWKQGPQIDRRGEIVLACACIGHSHLTHGYLLRREVAPFCIPCQSLL 347

Query: 320 TVDHI------FNCRTHLQIRASLPSPPALDNNPANIDSALMYLKAIGLYTK 365
           TV HI      F          S       D +P+     L+YLK IGL+ +
Sbjct: 348 TVKHILIDCIDFEISRRKYFNVSSMRQLFEDTHPSK---NLLYLKEIGLFYR 396

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 =  134 bits (337), Expect = 7e-29,   Method: Compositional matrix adjust.
 Identities = 92/297 (30%), Positives = 140/297 (47%), Gaps = 11/297 (3%)

Query: 35   KPLCVRIKDMSDFLPLITDSEFVPFTRPR-PPWSFQVPSIDFSLHLDNKDNIPPIVFQQH 93
            KPL +R ++      +  ++  V    PR PPW       D SL   NK   PP +  Q 
Sbjct: 866  KPLLLRFEEYCRTYVISEETLDVARKPPRIPPWFDLAQLCDISLSHINKKVTPPELIIQE 925

Query: 94   FHDLVTNKYSDSVLCFTDGSKTVNSTSCAYSIGNQVHAFKLNKVNSVLSSELMAILLCVK 153
            F  L   KY D    +TDGSKT +        G    + ++ +  S+ ++E+ A+    +
Sbjct: 926  FRAL-QEKYRDYAEFYTDGSKTRDHVGIGIVTGESAFSVRVPQCISIFTAEVYALYEAAR 984

Query: 154  NLIFLPSTNFTLISDSMSALLAISNCKNDHPLVSLVYTTWLEAKDCGKNLNFVWCPSHCG 213
             +I        + +DS+SAL A+       PLV  +    L       ++ F W PSH G
Sbjct: 985  KIIAGKHKKAIIYTDSLSALKALHIKSECEPLVGDILNMVLINSKV-ISMRFCWVPSHVG 1043

Query: 214  ITGNELVD----IAARNPITNITLKNCTSFDFRPVISSIIHKQWQISWDNVINNKLKRVK 269
            I GNE  D    +AA   +T I +      D +  I   +  +WQ  WD+  +NKL  VK
Sbjct: 1044 IPGNEKADKCASLAAHKTLTKIRI---PLKDSQRTIRLALLAKWQQQWDSCTSNKLHLVK 1100

Query: 270  PLIVDWETSNRNSRYEEVVITRLRIGHTRVTHDHLFKRDPRPTC-GCGDTLTVDHIF 325
            P + +W+      R+ EV++ RLRIGHT +TH+ L  ++ +P C  C + LT+ HI 
Sbjct: 1101 PTLGEWKNCRHQERFIEVILCRLRIGHTHLTHNFLLTKEEQPMCEKCQEPLTLIHIL 1157

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 =  134 bits (336), Expect = 8e-29,   Method: Compositional matrix adjust.
 Identities = 92/297 (30%), Positives = 140/297 (47%), Gaps = 11/297 (3%)

Query: 35   KPLCVRIKDMSDFLPLITDSEFVPFTRPR-PPWSFQVPSIDFSLHLDNKDNIPPIVFQQH 93
            KPL +R ++      +  ++  V    PR PPW       D SL   NK   PP +  Q 
Sbjct: 869  KPLLLRFEEYCRTYVISEETLDVARKPPRIPPWFDLAQLCDISLSHINKKVTPPELIIQE 928

Query: 94   FHDLVTNKYSDSVLCFTDGSKTVNSTSCAYSIGNQVHAFKLNKVNSVLSSELMAILLCVK 153
            F  L   KY D    +TDGSKT +        G    + ++ +  S+ ++E+ A+    +
Sbjct: 929  FRAL-QEKYRDYAEFYTDGSKTRDHVGIGIVTGESAFSVRVPQCISIFTAEVYALYEAAR 987

Query: 154  NLIFLPSTNFTLISDSMSALLAISNCKNDHPLVSLVYTTWLEAKDCGKNLNFVWCPSHCG 213
             +I        + +DS+SAL A+       PLV  +    L       ++ F W PSH G
Sbjct: 988  KIIAGKHKKAIIYTDSLSALKALHIKSECEPLVGDILNMVLINSKV-ISMRFCWVPSHVG 1046

Query: 214  ITGNELVD----IAARNPITNITLKNCTSFDFRPVISSIIHKQWQISWDNVINNKLKRVK 269
            I GNE  D    +AA   +T I +      D +  I   +  +WQ  WD+  +NKL  VK
Sbjct: 1047 IPGNEKADKCASLAAHKTLTKIRIP---LKDSQRTIRLALLAKWQQQWDSCTSNKLHLVK 1103

Query: 270  PLIVDWETSNRNSRYEEVVITRLRIGHTRVTHDHLFKRDPRPTC-GCGDTLTVDHIF 325
            P + +W+      R+ EV++ RLRIGHT +TH+ L  ++ +P C  C + LT+ HI 
Sbjct: 1104 PTLGEWKNCRHQERFIEVILCRLRIGHTHLTHNFLLTKEEQPMCEKCQEPLTLIHIL 1160

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  129 bits (325), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 79/210 (37%), Positives = 112/210 (53%), Gaps = 8/210 (3%)

Query: 111 DGSKTVNSTSCAYSIGNQVHAFKLNKVNSVLSSELMAILLCVKNLIFLPSTNFTLISDSM 170
           DGSK+ ++  CA+   +   A  L    SV ++EL+AI   + ++  LP   F + +DS 
Sbjct: 2   DGSKSEDAVGCAFHSRDFNLALGLPCQMSVYTAELIAINETLTSIALLPYDEFVICTDSF 61

Query: 171 SALLAISNCKNDHPLVS--LVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVDIAARNPI 228
           S++LAIS+    H  V   L   T L  +D  K + F+WCPSH GI GNE  D  A+   
Sbjct: 62  SSILAISSIDLIHSYVQSILQKCTNLAGRD--KRIIFIWCPSHVGIPGNETADTLAQQA- 118

Query: 229 TNITLKNCT--SFDFRPVISSIIHKQWQISWDNVINNKLKRVKPLIVDWETSNRNSRYEE 286
           + + + NC     DF+P+  S +  QWQ   D    NKL  ++P I  W    R  R +E
Sbjct: 119 SGMNILNCPIPHTDFKPITRSFVETQWQSESDQETGNKLHDIEPDIGSWPPCQREKRRDE 178

Query: 287 VVITRLRIGHTRVTHDHLFKRDPRPTC-GC 315
           +VI RLRIGHT +T+ HL   +  P C GC
Sbjct: 179 IVIARLRIGHTFLTYSHLLSGNDAPMCYGC 208

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	366
ASPGD|ASPL0000075333	486	AN10625 [Emericella nidulans (	0.658	0.495	0.204	4.7e-05

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

 Score = 127 (49.8 bits), Expect = 4.7e-05, P = 4.7e-05
 Identities = 54/264 (20%), Positives = 108/264 (40%)

Query:    95 HDLVTNKYSDSVLCFTDGSKTVNSTSCA-----YSIGNQVHAFKLNKVNSVLSSELMAIL 149
             H  + N+    +  +TDGS        A     Y I    +  + ++ ++V  +EL  IL
Sbjct:   172 HRNILNRAPRPIALYTDGSGINGRVGAAAICPKYLISRSSYMGQQSE-STVYVAELQGIL 230

Query:   150 LCVKNLIFLPSTNFTLISDSMSALLAISN--CKNDHPLVSLVYTTWLEAKDCGKNLNFVW 207
             L +  ++     +  + +D+ + L A+ N   ++   ++  +     + +  G N++F W
Sbjct:   231 LALVIILQRQMQHAVIFTDNQATLQALRNPGSQSGQYILEAIIMALNKGRKAGLNVHFRW 290

Query:   208 CPSHCGITGNELVDIAARNPITNITLKNCTS-FDFRPVIS----SIIHKQWQISWDNVIN 262
              P+H G+ GNE  D  A+       ++        R  +      +++ +W+  W +  +
Sbjct:   291 IPAHRGVEGNEQADRRAKEATGWRRIRGHRGRMTIRSAVKRRAHEVVNARWENDWKSCHH 350

Query:   263 NK-LKRVKPLIVD--WETSNRNSRYEEVVITRLRIGHTRVTHDHLFKRD----PRPTCGC 315
              + L  + P              R    +I ++R G   + H +L++R     P   C C
Sbjct:   351 GRELYELTPTPTRKVLRVHQDLHRALSTIIVQMRTGKIGLRH-YLYQRGVPDVPNSDCQC 409

Query:   316 GD-TLTVDHIF-NCRTHLQIRASL 337
             G  T +V HI   C T   +R  +
Sbjct:   410 GRATQSVRHILLACPTFSGLREEI 433


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        0.322   0.136   0.432    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      366       366   0.00084  117 3  11 22  0.37    34
                                                     34  0.45    37


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  622 (66 KB)
  Total size of DFA:  275 KB (2143 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:  30.41u 0.13s 30.54t   Elapsed:  00:00:04
  Total cpu time:  30.41u 0.13s 30.54t   Elapsed:  00:00:04
  Start:  Thu Aug 15 16:49:06 2013   End:  Thu Aug 15 16:49:10 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	366
cd09276	128	cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom	8e-28
pfam00075	126	pfam00075, RNase_H, RNase H	1e-09
cd06222	123	cd06222, RNase_H, RNase H is an endonuclease that	1e-09
cd09273	135	cd09273, RNase_HI_RT_Bel, Bel/Pao family of RNase	2e-04

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

 Score =  105 bits (264), Expect = 8e-28
 Identities = 39/123 (31%), Positives = 59/123 (47%), Gaps = 5/123 (4%)

Query: 108 CFTDGSKTVNSTSCAYSI---GNQVHAFKLNKVNSVLSSELMAILLCVKNLIFLPS--TN 162
            +TDGSK    T   ++I   G    ++KL    SV  +EL+AIL  ++  +        
Sbjct: 2   IYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRRARK 61

Query: 163 FTLISDSMSALLAISNCKNDHPLVSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVDI 222
            T+ SDS +AL A+ + ++  PLV  +     E  + G  +   W P H GI GNE  D 
Sbjct: 62  ITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGNERADR 121

Query: 223 AAR 225
            A+
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 = 55.3 bits (134), Expect = 1e-09
 Identities = 28/128 (21%), Positives = 49/128 (38%), Gaps = 13/128 (10%)

Query: 104 DSVLCFTDGSKTVNS-TSCAYSIGNQVHAFKLNK-VNSVLSSELMAILLCVKNLIFLPST 161
           ++V  +TDGS   N     A  + +            +   +EL+A++  ++ L      
Sbjct: 2   EAVTVYTDGSCNGNPGPGGAGYVTDGGKQRSKPLPGTTNQRAELLALIEALEAL---SGQ 58

Query: 162 NFTLISDSMSALLAISN-CKNDH---PLVSLVYTTWLEAKDCGKNLNFVWCPSHCGITGN 217
              + +DS   +  I+N         P+ + +     E       +   W P H GI GN
Sbjct: 59  KVNIYTDSQYVIGGITNGWPTKSESKPIKNEI----WELLQKKHKVYIQWVPGHSGIPGN 114

Query: 218 ELVDIAAR 225
           EL D  A+
Sbjct: 115 ELADKLAK 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 = 55.1 bits (133), Expect = 1e-09
 Identities = 25/127 (19%), Positives = 45/127 (35%), Gaps = 11/127 (8%)

Query: 109 FTDGSKTVNSTSCAYSI------GNQVHAFKLNKVN-SVLSSELMAILLCVKNLIFLPST 161
            TDGS   N              G  + A  L+    +   +EL+A+L  ++  + L   
Sbjct: 1   NTDGSCKGNPGPAGAGGVLRDHEGAWLFAGSLSIPAATNNEAELLALLEALELALDLGLK 60

Query: 162 NFTLISDSMSALLAISNCKNDHPLVSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVD 221
              + +DS   +  I++        +L+    L       ++ F   P      GNE+ D
Sbjct: 61  KLIIETDSKYVVDLINSWSKGWKKNNLLLWDILLLLSKFIDIRFEHVPRE----GNEVAD 116

Query: 222 IAARNPI 228
             A+   
Sbjct: 117 RLAKEAA 123

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

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

 Score = 40.3 bits (95), Expect = 2e-04
 Identities = 31/136 (22%), Positives = 46/136 (33%), Gaps = 21/136 (15%)

Query: 107 LCFTDGSKTVNSTSCA-YSIGNQVHAFKLNKVNSVLSSELMAILLCVKNLIFLPSTNFTL 165
             FTDGS  V     A  +  + +    L    S   +EL+A++     L         +
Sbjct: 1   TVFTDGSSFVRKAGYAVVTGPDVLEIATLPYGTSAQRAELIALIRA---LELAKGKPVNI 57

Query: 166 ISDS------MSALLAI-----SNCKNDHPLVSLVYTTWLEAKDCGKNLNFVWCPSHCG- 213
            +DS      + AL  I             L SL+     +A    K +  +   +H G 
Sbjct: 58  YTDSAYAFGILHALETIWKERGFLTGKPIALASLILQLQ-KAIQRPKPVAVIHIRAHSGL 116

Query: 214 ----ITGNELVDIAAR 225
                 GN   D AAR
Sbjct: 117 PGPLALGNARADQAAR 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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	366
PRK06548	161	ribonuclease H; Provisional	99.88
PRK08719	147	ribonuclease H; Reviewed	99.88
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	99.87
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	99.86
PRK00203	150	rnhA ribonuclease H; Reviewed	99.85
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	99.75
KOG3752|consensus	371		99.7
PRK13907	128	rnhA ribonuclease H; Provisional	99.68
PRK07708	219	hypothetical protein; Validated	99.53
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	99.42
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	99.23
PF13966	86	zf-RVT: zinc-binding in reverse transcriptase	96.3
PF05380	159	Peptidase_A17: Pao retrotransposon peptidase ; Int	87.2

>PRK06548 ribonuclease H; Provisional

Probab=99.88  E-value=3.1e-22  Score=172.40  Aligned_cols=125  Identities=18%  Similarity=0.223  Sum_probs=95.1

Q ss_pred             CceEEEecCCCCCC-C-cceEEEeCCeEeeeecCCCCchHHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHHhc---
Q psy5071         104 DSVLCFTDGSKTVN-S-TSCAYSIGNQVHAFKLNKVNSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISN---  178 (366)
Q Consensus       104 ~~~~iytDgS~~~~-~-~G~a~~~~~~~~~~~l~~~~s~~~AEl~AI~~aL~~~~~~~~~~i~I~sDs~~al~~l~~---  178 (366)
                      ..+.||||||+.++ | .|+|++..+..........+|++.|||.|++.||+.+.. ....|.|+|||++|++.+..   
T Consensus         4 ~~~~IytDGa~~gnpg~~G~g~~~~~~~~~~g~~~~~TNnraEl~Aii~aL~~~~~-~~~~v~I~TDS~yvi~~i~~W~~   82 (161)
T PRK06548          4 NEIIAATDGSSLANPGPSGWAWYVDENTWDSGGWDIATNNIAELTAVRELLIATRH-TDRPILILSDSKYVINSLTKWVY   82 (161)
T ss_pred             CEEEEEEeeccCCCCCceEEEEEEeCCcEEccCCCCCCHHHHHHHHHHHHHHhhhc-CCceEEEEeChHHHHHHHHHHHH
Confidence            45899999999954 3 678866543221111124689999999999999986643 34579999999999999993   


Q ss_pred             ------CCCCch--H-HHHHHHHHHHHHhcCCcceEEEecccCCCccchhHHHHHcCcccC
Q psy5071         179 ------CKNDHP--L-VSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVDIAARNPITN  230 (366)
Q Consensus       179 ------~~~~s~--~-~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~A~~~  230 (366)
                            +...++  + -+++|+.+.++... ..|+|.|||||+|++|||.||+||++|+..
T Consensus        83 ~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~-~~v~~~wVkgHsg~~gNe~aD~LA~~aa~~  142 (161)
T PRK06548         83 SWKMRKWRKADGKPVLNQEIIQEIDSLMEN-RNIRMSWVNAHTGHPLNEAADSLARQAANN  142 (161)
T ss_pred             HHHHCCCcccCCCccccHHHHHHHHHHHhc-CceEEEEEecCCCCHHHHHHHHHHHHHHHH
Confidence                  333333  3 36777888777544 479999999999999999999999999864

>PRK08719 ribonuclease H; Reviewed

Probab=99.88  E-value=4.8e-22  Score=169.63  Aligned_cols=121  Identities=18%  Similarity=0.181  Sum_probs=92.3

Q ss_pred             CceEEEecCCCCCCC-----cceEEEe--CC--eE--eeeecCCCCchHHHHHHHHHHHHHHhhhCCCCeEEEEeccHHH
Q psy5071         104 DSVLCFTDGSKTVNS-----TSCAYSI--GN--QV--HAFKLNKVNSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSA  172 (366)
Q Consensus       104 ~~~~iytDgS~~~~~-----~G~a~~~--~~--~~--~~~~l~~~~s~~~AEl~AI~~aL~~~~~~~~~~i~I~sDs~~a  172 (366)
                      ..++||||||+.+++     .|+|++.  .+  ..  .+..+....|++.|||.|+..||+.+...    ..|+|||+++
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            468999999998543     3777653  22  12  33445556899999999999999998653    4899999999


Q ss_pred             HHHH--------hcCCCCch---H-HHHHHHHHHHHHhcCCcceEEEecccCCCccchhHHHHHcCccc
Q psy5071         173 LLAI--------SNCKNDHP---L-VSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVDIAARNPIT  229 (366)
Q Consensus       173 l~~l--------~~~~~~s~---~-~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~A~~  229 (366)
                      +++|        ++.+..+.   + -.++|+.+..+.. ...|+|.|||||+|++|||.||+||++|++
T Consensus        79 i~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~-~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~  146 (147)
T PRK08719         79 VRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRA-RKYVEVEKVTAHSGIEGNEAADMLAQAAAE  146 (147)
T ss_pred             HHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhC-CCcEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence            9999        45554332   1 2556677766644 567999999999999999999999999875

>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=99.87  E-value=3e-22  Score=167.58  Aligned_cols=117  Identities=27%  Similarity=0.448  Sum_probs=87.9

Q ss_pred             CceEEEecCCCCCC-C-cceEE-EeCCeEeeeecCCCCchHHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHHhc--
Q psy5071         104 DSVLCFTDGSKTVN-S-TSCAY-SIGNQVHAFKLNKVNSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISN--  178 (366)
Q Consensus       104 ~~~~iytDgS~~~~-~-~G~a~-~~~~~~~~~~l~~~~s~~~AEl~AI~~aL~~~~~~~~~~i~I~sDs~~al~~l~~--  178 (366)
                      ..+.||||||+..+ + .|+|+ +..+...+..++ ..+++.|||.||..||+ +..  ...++|+|||++++..+..  
T Consensus         2 ~~~~iytDgS~~~~~~~~~~g~v~~~~~~~~~~~~-~~s~~~aEl~Ai~~AL~-~~~--~~~v~I~tDS~~v~~~l~~~~   77 (132)
T PF00075_consen    2 KAIIIYTDGSCRPNPGKGGAGYVVWGGRNFSFRLG-GQSNNRAELQAIIEALK-ALE--HRKVTIYTDSQYVLNALNKWL   77 (132)
T ss_dssp             TSEEEEEEEEECTTTTEEEEEEEEETTEEEEEEEE-SECHHHHHHHHHHHHHH-THS--TSEEEEEES-HHHHHHHHTHH
T ss_pred             CcEEEEEeCCccCCCCceEEEEEEECCeEEEeccc-ccchhhhheehHHHHHH-Hhh--cccccccccHHHHHHHHHHhc
Confidence            46899999997732 2 35554 444544455566 88999999999999999 442  3899999999999998877  


Q ss_pred             ---CCCCc----hHHHHHHHHHHHHHhcCCcceEEEecccCCC-ccchhHHHHHcCcc
Q psy5071         179 ---CKNDH----PLVSLVYTTWLEAKDCGKNLNFVWCPSHCGI-TGNELVDIAARNPI  228 (366)
Q Consensus       179 ---~~~~s----~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi-~gNe~AD~lAk~A~  228 (366)
                         .+...    ++..+|++    +...+..|.|+|||||+|+ .|||.||+|||+|+
T Consensus        78 ~~~~~~~~~~~~~i~~~i~~----~~~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~  131 (132)
T PF00075_consen   78 HGNGWKKTSNGRPIKNEIWE----LLSRGIKVRFRWVPGHSGVPQGNERADRLAKEAA  131 (132)
T ss_dssp             HHTTSBSCTSSSBHTHHHHH----HHHHSSEEEEEESSSSSSSHHHHHHHHHHHHHHH
T ss_pred             cccccccccccccchhheee----ccccceEEeeeeccCcCCCchhHHHHHHHHHHhc
Confidence               33222    24444433    3346899999999999999 69999999999885

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 ....

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

Probab=99.86  E-value=2.4e-21  Score=164.22  Aligned_cols=127  Identities=21%  Similarity=0.201  Sum_probs=101.6

Q ss_pred             CceEEEecCCCCCC-C-cceEEEe--CCeEe--eeecCCCCchHHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHHh
Q psy5071         104 DSVLCFTDGSKTVN-S-TSCAYSI--GNQVH--AFKLNKVNSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSALLAIS  177 (366)
Q Consensus       104 ~~~~iytDgS~~~~-~-~G~a~~~--~~~~~--~~~l~~~~s~~~AEl~AI~~aL~~~~~~~~~~i~I~sDs~~al~~l~  177 (366)
                      ..+.||||||+.++ | .|+|++.  ++..+  +.... .+|++.||++|++.||+++.+.+...|.|+|||+++++.|.
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            35899999999954 3 5666543  33333  33334 89999999999999999999888899999999999999998


Q ss_pred             cC---CCCc--------h-HHHHHHHHHHHHHhcCCcceEEEecccCCCccchhHHHHHcCcccCC
Q psy5071         178 NC---KNDH--------P-LVSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVDIAARNPITNI  231 (366)
Q Consensus       178 ~~---~~~s--------~-~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~A~~~~  231 (366)
                      .+   +...        + ...++|+++.++..+...|.+.|||||+|.++||.||+||+.|++..
T Consensus        81 ~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~~~~~~  146 (154)
T COG0328          81 RWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAREAARAA  146 (154)
T ss_pred             HHHhhccccCccccccCccccHHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHHHHHhh
Confidence            43   1111        1 24577888888877777999999999999999999999999998754

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=99.85  E-value=7.4e-21  Score=163.36  Aligned_cols=124  Identities=20%  Similarity=0.206  Sum_probs=92.1

Q ss_pred             ceEEEecCCCCCC-C-cceEEEe--CCeEeeee-cCCCCchHHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHHhcC
Q psy5071         105 SVLCFTDGSKTVN-S-TSCAYSI--GNQVHAFK-LNKVNSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNC  179 (366)
Q Consensus       105 ~~~iytDgS~~~~-~-~G~a~~~--~~~~~~~~-l~~~~s~~~AEl~AI~~aL~~~~~~~~~~i~I~sDs~~al~~l~~~  179 (366)
                      .+.||||||+.++ + .|+|++.  .+....+. .....|++.|||.|+..||+.+..  ...+.|+|||+++++.|..+
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            4899999999854 3 5666543  33332222 134678999999999999998865  45799999999999999862


Q ss_pred             --------CC-Cc--hH-HHHHHHHHHHHHhcCCcceEEEecccCCCccchhHHHHHcCcccCC
Q psy5071         180 --------KN-DH--PL-VSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVDIAARNPITNI  231 (366)
Q Consensus       180 --------~~-~s--~~-~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~A~~~~  231 (366)
                              +. .+  ++ -..+|+.+.++. ....|.|.|||||+|++||+.||+|||+|+...
T Consensus        81 ~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~-~~~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~~  143 (150)
T PRK00203         81 IHGWKKNGWKTADKKPVKNVDLWQRLDAAL-KRHQIKWHWVKGHAGHPENERCDELARAGAEEA  143 (150)
T ss_pred             HHHHHHcCCcccCCCccccHHHHHHHHHHh-ccCceEEEEecCCCCCHHHHHHHHHHHHHHHHh
Confidence                    21 11  22 244556666654 347899999999999999999999999998753

>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=99.75  E-value=2.3e-17  Score=134.86  Aligned_cols=122  Identities=20%  Similarity=0.278  Sum_probs=95.8

Q ss_pred             EEEecCCCCCC--CcceEEEeCC--eEeee---ecCCCCchHHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHHhcC
Q psy5071         107 LCFTDGSKTVN--STSCAYSIGN--QVHAF---KLNKVNSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNC  179 (366)
Q Consensus       107 ~iytDgS~~~~--~~G~a~~~~~--~~~~~---~l~~~~s~~~AEl~AI~~aL~~~~~~~~~~i~I~sDs~~al~~l~~~  179 (366)
                      .+|||||...+  +.|+|++..+  ....+   ......+++.+|+.|+..||+++...+..++.|++||+.++..+.+.
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            48999999865  4777766432  22111   12257899999999999999999888899999999999999999987


Q ss_pred             CC-CchHHHHHHHHHHHHHhcCCcceEEEecccCCCccchhHHHHHcCcc
Q psy5071         180 KN-DHPLVSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVDIAARNPI  228 (366)
Q Consensus       180 ~~-~s~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~A~  228 (366)
                      .. .......+++.+..+...+..+.|.|||+|+|+.+|+.||.|||.|.
T Consensus        81 ~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~~  130 (130)
T cd06222          81 YEGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKEAA  130 (130)
T ss_pred             ccCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence            65 22234444466666556789999999999999999999999999873

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=99.70  E-value=5.7e-17  Score=153.16  Aligned_cols=127  Identities=20%  Similarity=0.187  Sum_probs=100.4

Q ss_pred             CCceEEEecCCCCCCC-----cceEEEeCCe---EeeeecC-CCCchHHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHH
Q psy5071         103 SDSVLCFTDGSKTVNS-----TSCAYSIGNQ---VHAFKLN-KVNSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSAL  173 (366)
Q Consensus       103 ~~~~~iytDgS~~~~~-----~G~a~~~~~~---~~~~~l~-~~~s~~~AEl~AI~~aL~~~~~~~~~~i~I~sDs~~al  173 (366)
                      .+.+++|||||+..+|     +|+||+.++.   ..++.+. ..++++.|||.||..||+.+.+....+++|.|||++++
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            3448999999998654     7999998654   4577774 89999999999999999999988888999999999999


Q ss_pred             HHHhcCCCC-----------ch----H--HHHHHHHHHHHHh--cCCcceEEEecccCCCccchhHHHHHcCccc
Q psy5071         174 LAISNCKND-----------HP----L--VSLVYTTWLEAKD--CGKNLNFVWCPSHCGITGNELVDIAARNPIT  229 (366)
Q Consensus       174 ~~l~~~~~~-----------s~----~--~~~i~~~~~~l~~--~~~~v~~~WVpgH~gi~gNe~AD~lAk~A~~  229 (366)
                      ++|+.+.+.           ++    +  .+..+..+.+|.+  ++..|.+.||+||.|+.|||+||.||+++..
T Consensus       290 ~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs~  364 (371)
T KOG3752|consen  290 NSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEMADALARKGST  364 (371)
T ss_pred             HHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHHHHHHHhhhhh
Confidence            999865331           11    0  1122234444432  4689999999999999999999999998854

>PRK13907 rnhA ribonuclease H; Provisional

Probab=99.68  E-value=2.3e-16  Score=131.73  Aligned_cols=120  Identities=18%  Similarity=0.143  Sum_probs=94.0

Q ss_pred             eEEEecCCCCCC--CcceEEEeCC--eEeeee-cCCCCchHHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHHhcCC
Q psy5071         106 VLCFTDGSKTVN--STSCAYSIGN--QVHAFK-LNKVNSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNCK  180 (366)
Q Consensus       106 ~~iytDgS~~~~--~~G~a~~~~~--~~~~~~-l~~~~s~~~AEl~AI~~aL~~~~~~~~~~i~I~sDs~~al~~l~~~~  180 (366)
                      +.||||||+..+  ..|+|++..+  .....+ .....++..||+.|++.||+.+...+..++.|+|||+.++..+.+.+
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            689999999853  3677766432  222222 12467899999999999999999988889999999999999999866


Q ss_pred             CCchHHHHHHHHHHHHHhcCCcceEEEecccCCCccchhHHHHHcCccc
Q psy5071         181 NDHPLVSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVDIAARNPIT  229 (366)
Q Consensus       181 ~~s~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~A~~  229 (366)
                      ....-...+++.+..+......+.|.|||.    ++|+.||.||+.|..
T Consensus        82 ~~~~~~~~l~~~~~~l~~~f~~~~~~~v~r----~~N~~Ad~LA~~a~~  126 (128)
T PRK13907         82 AKNKMFAPLLEEALQYIKSFDLFFIKWIPS----SQNKVADELARKAIL  126 (128)
T ss_pred             hcChhHHHHHHHHHHHHhcCCceEEEEcCc----hhchhHHHHHHHHHh
Confidence            443334556677777766778888999996    599999999998864

>PRK07708 hypothetical protein; Validated

Probab=99.53  E-value=1.5e-13  Score=124.69  Aligned_cols=127  Identities=12%  Similarity=0.020  Sum_probs=92.0

Q ss_pred             CCCceEEEecCCCCC--CCcceEEEe--CCe--Ee----eeecCCCCchHHHHHHHHHHHHHHhhhCCCCe--EEEEecc
Q psy5071         102 YSDSVLCFTDGSKTV--NSTSCAYSI--GNQ--VH----AFKLNKVNSVLSSELMAILLCVKNLIFLPSTN--FTLISDS  169 (366)
Q Consensus       102 ~~~~~~iytDgS~~~--~~~G~a~~~--~~~--~~----~~~l~~~~s~~~AEl~AI~~aL~~~~~~~~~~--i~I~sDs  169 (366)
                      .++.+++|+|||...  ++.|+|++.  .+.  ..    ...++...+++.||+.|++.||+.+...+.+.  |.|++||
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            345799999999874  346777543  222  11    12345568999999999999999999876554  8999999


Q ss_pred             HHHHHHHhcCCCC-chHHHHHHHHHHHHHhc-CCcceEEEecccCCCccchhHHHHHcCcccCCC
Q psy5071         170 MSALLAISNCKND-HPLVSLVYTTWLEAKDC-GKNLNFVWCPSHCGITGNELVDIAARNPITNIT  232 (366)
Q Consensus       170 ~~al~~l~~~~~~-s~~~~~i~~~~~~l~~~-~~~v~~~WVpgH~gi~gNe~AD~lAk~A~~~~~  232 (366)
                      +.+++.+.+.+.. ++..+..+..+.++... ...+.+.|||    ...|+.||+||+.|++...
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            9999999987654 33344444555544322 3357788998    5789999999999998543

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=99.42  E-value=1.7e-12  Score=127.71  Aligned_cols=121  Identities=17%  Similarity=0.164  Sum_probs=93.8

Q ss_pred             ceEEEecCCCCCC-C-cceEEEe--CC-e-E-e--eeecCCCCchHHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHH
Q psy5071         105 SVLCFTDGSKTVN-S-TSCAYSI--GN-Q-V-H--AFKLNKVNSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSALLA  175 (366)
Q Consensus       105 ~~~iytDgS~~~~-~-~G~a~~~--~~-~-~-~--~~~l~~~~s~~~AEl~AI~~aL~~~~~~~~~~i~I~sDs~~al~~  175 (366)
                      .+.||||||+.++ | .|+|++.  .+ . . .  ...++ ..+++.||+.|++.||+.+.+.+...+.|++||+.+++.
T Consensus         2 ~~~i~~DGa~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~-~~tnn~AE~~All~gL~~a~~~g~~~v~i~~DS~lvi~~   80 (372)
T PRK07238          2 KVVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIG-RATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQ   80 (372)
T ss_pred             eEEEEecCCCCCCCCceEEEEEEEeCCCCcEEEEeecccC-CCCchHHHHHHHHHHHHHHHhCCCCeEEEEeCcHHHHHH
Confidence            3789999999964 3 6777654  22 1 1 1  22333 678899999999999999999888999999999999999


Q ss_pred             HhcCCC-CchHHHHHHHHHHHHHhcCCcceEEEecccCCCccchhHHHHHcCcccC
Q psy5071         176 ISNCKN-DHPLVSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVDIAARNPITN  230 (366)
Q Consensus       176 l~~~~~-~s~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~A~~~  230 (366)
                      +.+.+. ++.-...++..+..+..+...+.+.|||.    .+|+.||.||+.|...
T Consensus        81 i~~~~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~r----~~N~~AD~LA~~a~~~  132 (372)
T PRK07238         81 MSGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPR----ARNAHADRLANEAMDA  132 (372)
T ss_pred             hCCCCccCChHHHHHHHHHHHHHhcCCceEEEECCc----hhhhHHHHHHHHHHHh
Confidence            998664 33333444466667666778999999995    7899999999999764

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

Probab=99.23  E-value=3e-11  Score=93.13  Aligned_cols=85  Identities=19%  Similarity=0.114  Sum_probs=68.3

Q ss_pred             hHHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHHhcCCCCchHHHHHHHHHHHHHhcCCcceEEEecccCCCccchh
Q psy5071         140 VLSSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNCKNDHPLVSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNEL  219 (366)
Q Consensus       140 ~~~AEl~AI~~aL~~~~~~~~~~i~I~sDs~~al~~l~~~~~~s~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~  219 (366)
                      +..||+.|+..||+++.+.+..+|.|.|||+.++..|.+..........++..+..+......+.+.|||    .++|..
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            4689999999999999999999999999999999999987543223455557777777788999999999    799999


Q ss_pred             HHHHHcCcc
Q psy5071         220 VDIAARNPI  228 (366)
Q Consensus       220 AD~lAk~A~  228 (366)
                      ||.|||.|.
T Consensus        77 A~~LA~~a~   85 (87)
T PF13456_consen   77 ADALAKFAL   85 (87)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHh
Confidence            999999875

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

Probab=96.30  E-value=0.0025  Score=49.07  Aligned_cols=41  Identities=29%  Similarity=0.498  Sum_probs=29.8

Q ss_pred             eeecCcccc-h--hhcccCCCCCCCcc-CCC-CCCcceeec-CcccH
Q psy5071         291 RLRIGHTRV-T--HDHLFKRDPRPTCG-CGD-TLTVDHIFN-CRTHL  331 (366)
Q Consensus       291 qlRTGH~~l-~--h~~~~~~~~~~~C~-CG~-~etv~HiL~-Cp~~~  331 (366)
                      --|.-|.++ +  -+.+.+...++.|. ||. .||++|+|+ ||...
T Consensus        37 ~W~~~~~rL~t~~~l~~r~~~~~~~C~~C~~~~Et~~Hlf~~C~~a~   83 (86)
T PF13966_consen   37 LWRALHNRLPTKDNLQRRGIQVDPICPLCGNEEETIEHLFFHCPFAR   83 (86)
T ss_pred             eeeeccccchhhhhhhccCCccCCccccCCCccccccceeccCcCcc
Confidence            344455555 2  24445567789999 997 999999999 99764

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

Probab=87.20  E-value=2.6  Score=36.25  Aligned_cols=52  Identities=19%  Similarity=0.171  Sum_probs=34.7

Q ss_pred             CceEEEecCCCCCCCcceEEEeCC---eEeee-------ec--CCCCchHHHHHHHHHHHHHHhhh
Q psy5071         104 DSVLCFTDGSKTVNSTSCAYSIGN---QVHAF-------KL--NKVNSVLSSELMAILLCVKNLIF  157 (366)
Q Consensus       104 ~~~~iytDgS~~~~~~G~a~~~~~---~~~~~-------~l--~~~~s~~~AEl~AI~~aL~~~~~  157 (366)
                      ..+++|+|+|.  .+.|+++|...   .....       ++  -...|+-.-||.|+..|.+++..
T Consensus        80 ~~L~~F~DAS~--~aygavvYlr~~~~~~~~~~ll~aKsrv~P~k~~tIPRlEL~a~~l~~~l~~~  143 (159)
T PF05380_consen   80 VELHVFCDASE--SAYGAVVYLRSYSDGSVQVRLLFAKSRVAPLKTVTIPRLELLAALLGVRLANT  143 (159)
T ss_pred             eeeeEeecccc--cceeeEeEeeeccCCceeeeeeeecccccCCCCCcHHHHHHHHHHHHHHHHHH
Confidence            46899999994  55676665321   11111       11  13459999999999999988753

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	366
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	3e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-04
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-04
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	6e-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 = 48.7 bits (116), Expect = 3e-07
 Identities = 29/143 (20%), Positives = 48/143 (33%), Gaps = 16/143 (11%)

Query: 109 FTDGSKTVNS--TSCAYSIG---NQVHAFKLNKVNSVLSSELMAILLCVKNLIFLPSTNF 163
           +TDGS  +         ++      + A  L    S   +EL+A+    + L        
Sbjct: 27  YTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALT---QALKMAEGKKL 83

Query: 164 TLISDSMSALLAISNC--KNDHPLVSLVYTTWLEAKDCGKNLNFVWCPSHCG-----ITG 216
            + +DS  A           +    + +    L+A    K L+ + CP H         G
Sbjct: 84  NVYTDSRYAFATAHVHSEGREIKNKNEI-LALLKALFLPKRLSIIHCPGHQKGNSAEARG 142

Query: 217 NELVDIAARNPITNITLKNCTSF 239
           N + D AAR       L+  T  
Sbjct: 143 NRMADQAAREAAMKAVLETSTLL 165

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

 Score = 42.9 bits (100), Expect = 2e-04
 Identities = 47/306 (15%), Positives = 92/306 (30%), Gaps = 93/306 (30%)

Query: 73  IDFS---LHLDNKDNIPPIVFQQHF-HDLVTNKYSDSVLCFTDGSKTVNSTSCAYSIGNQ 128
           +DF         KD +   VF+  F  +       D         K++ S      I   
Sbjct: 7   MDFETGEHQYQYKDILS--VFEDAFVDNFDCKDVQDMP-------KSILSKEEIDHI--- 54

Query: 129 VHAFKLNKVNSVLSSELMAILLCVKN----LIFLPS---TNFTLISDSMSALLAISNCKN 181
                +   ++V  +  +   L  K       F+      N+  +   +         + 
Sbjct: 55  -----IMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKT-------EQ 102

Query: 182 DHPLVSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVDIAARNPITNITLKNCTSFDF 241
             P  S++   ++E +D   N N V+   +  ++  +              L+     + 
Sbjct: 103 RQP--SMMTRMYIEQRDRLYNDNQVFAKYN--VSRLQPYL----------KLRQALL-EL 147

Query: 242 RPVISSIIH------KQW-----------------QISWDNVINNK-----LKRVKPLIV 273
           RP  + +I       K W                 +I W N+ N       L+ ++ L+ 
Sbjct: 148 RPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLY 207

Query: 274 DWETSNRNSRYEEVVITRLRIGHTRVTHDHLFKRDPRPTCGCGDTLTVDHI--------- 324
             +  N  SR +     +LRI   +     L K  P   C     L + ++         
Sbjct: 208 QID-PNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENC----LLVLLNVQNAKAWNAF 262

Query: 325 -FNCRT 329
             +C+ 
Sbjct: 263 NLSCKI 268

>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 = 40.6 bits (94), Expect = 8e-04
 Identities = 46/291 (15%), Positives = 88/291 (30%), Gaps = 69/291 (23%)

Query: 74  DFSLHLDNKDNIPPIV--FQQHFHDLVTNK-YSDSVLCFTDGSKTVNSTSCAYSIGNQVH 130
           +++   D+  NI   +   Q     L+ +K Y + +L   +    V +           +
Sbjct: 212 NWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLN----VQNAKA-------WN 260

Query: 131 AFKLN-KV-----NSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNCK-NDH 183
           AF L+ K+        ++  L A      +L     T  T   +  S LL   +C+  D 
Sbjct: 261 AFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMT-LTP-DEVKSLLLKYLDCRPQDL 318

Query: 184 PLVSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVDIAAR---------NPITNI--- 231
           P          E             P    I    + D  A          + +T I   
Sbjct: 319 PR---------EVLTTN--------PRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIES 361

Query: 232 TLKNCTSFDFR---------PVISSIIHKQWQISWDNV-------INNKLKRVKPLIVDW 275
           +L      ++R         P  + I      + W +V       + NKL +   L+   
Sbjct: 362 SLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHK-YSLVEKQ 420

Query: 276 ETSNRNSRYEEVVITRLRIGHTRVTHDHLFKRDPRPTCGCGDTLTVDHIFN 326
              +  S     +  ++++ +    H  +      P     D L   ++  
Sbjct: 421 PKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQ 471

>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 = 38.9 bits (91), Expect = 6e-04
 Identities = 22/133 (16%), Positives = 40/133 (30%), Gaps = 14/133 (10%)

Query: 103 SDSVLCFTDGSKTVNSTSCAYSI---GNQVHAFKL------NKVNSVLSSELMAILLCVK 153
                 +TDGS      + AY+    G   +                ++ E+ A L  VK
Sbjct: 4   RTEYDVYTDGSYVNGQYAWAYAFVKDGKVHYEDADVGKNPAAATMRNVAGEIAAALYAVK 63

Query: 154 NLIFLPSTNFTLISDSMSALLAISNC-KNDHPLVSLVYTTWLEAKDCGKNLNFVWCPSHC 212
               L      ++ D        +   K  +           + +      +F    +H 
Sbjct: 64  KASQLGV-KIRILHDYAGIAFWATGEWKAKNEFTQAYAKLMNQYR---GIYSFEKVKAHS 119

Query: 213 GITGNELVDIAAR 225
           G   N+ VD+ A+
Sbjct: 120 GNEFNDYVDMKAK 132

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	366
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.9
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.89
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.87
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	99.87
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	99.86
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	99.86
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.86
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.85
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	99.82
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	99.79
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	99.79
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	99.78
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	99.77
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	99.75
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	99.28
4htu_A	134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	98.97
1rw3_A	455	POL polyprotein; RNA and DNA dependent DNA polymer	82.68

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

Probab=99.90  E-value=1.3e-23  Score=180.07  Aligned_cols=128  Identities=20%  Similarity=0.259  Sum_probs=100.8

Q ss_pred             CCCceEEEecCCCCCCC-----cceEEEeCCe---EeeeecCCCCchHHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHH
Q psy5071         102 YSDSVLCFTDGSKTVNS-----TSCAYSIGNQ---VHAFKLNKVNSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSAL  173 (366)
Q Consensus       102 ~~~~~~iytDgS~~~~~-----~G~a~~~~~~---~~~~~l~~~~s~~~AEl~AI~~aL~~~~~~~~~~i~I~sDs~~al  173 (366)
                      +.+.+.||||||+..++     .|+|++..+.   ..+..+...+|++.|||.|+..||+.+...+..+|.|+|||++++
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            45679999999998543     6888876432   234556557899999999999999999887788999999999999


Q ss_pred             HHHhcC--------CC-Cc--h-HHHHHHHHHHHHHhcCCcceEEEecccCCCccchhHHHHHcCcccC
Q psy5071         174 LAISNC--------KN-DH--P-LVSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVDIAARNPITN  230 (366)
Q Consensus       174 ~~l~~~--------~~-~s--~-~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~A~~~  230 (366)
                      +.|.++        +. ..  + ..+.+++.+.++.. +..|.|.|||||+|++|||.||+|||+|+..
T Consensus        84 ~~i~~~~~~w~~~~w~~~~~~~~~n~~l~~~i~~l~~-~~~v~~~~V~~H~g~~~N~~AD~LA~~a~~~  151 (154)
T 2qkb_A           84 NGITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQ-GMDIQWMHVPGHSGFIGNEEADRLAREGAKQ  151 (154)
T ss_dssp             HHHHTHHHHHHTTTSBCTTSSBCTTHHHHHHHHHHHT-TCEEEEEECCTTSSCHHHHHHHHHHHHHHTC
T ss_pred             hhhhhhHHHHHhccccccCCCccccHHHHHHHHHHHc-CCceEEEEccCCCCCHhHHHHHHHHHHHHHh
Confidence            999873        11 11  1 12455666666543 5679999999999999999999999999875

>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=99.89  E-value=3e-23  Score=176.87  Aligned_cols=126  Identities=21%  Similarity=0.311  Sum_probs=95.9

Q ss_pred             ccCCCceEEEecCCCCCCC--cceEEEeCC-eEeeeecCCCCchHHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHH
Q psy5071         100 NKYSDSVLCFTDGSKTVNS--TSCAYSIGN-QVHAFKLNKVNSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSALLAI  176 (366)
Q Consensus       100 ~~~~~~~~iytDgS~~~~~--~G~a~~~~~-~~~~~~l~~~~s~~~AEl~AI~~aL~~~~~~~~~~i~I~sDs~~al~~l  176 (366)
                      +...+.+.||||||+..++  .|+|++..+ ......+ ..+|++.||+.|+..||+.+    ..++.|+|||+++++.|
T Consensus         7 ~P~~~~~~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~-~~~Tnn~aEl~A~i~AL~~~----~~~v~i~tDS~~v~~~i   81 (150)
T 3qio_A            7 EPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTL-TDTTNQKTELQAIYLALQDS----GLEVNIVTDSQYALGII   81 (150)
T ss_dssp             SCCTTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEEE-SSCCHHHHHHHHHHHHHHHS----CSEEEEEESCHHHHHHH
T ss_pred             CCCCCCEEEEEccCCCCCCCCeEEEEEEEcCCEEEEeC-CCCCHHHHHHHHHHHHHHhC----CCcEEEEeCcHHHHHHH
Confidence            3556789999999998543  577766533 2333344 57899999999999999986    47999999999999999


Q ss_pred             hcCC-----------CCch-HHHHHHHHHHHHHhcCCcceEEEecccCCCccchhHHHHHcCcccC
Q psy5071         177 SNCK-----------NDHP-LVSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVDIAARNPITN  230 (366)
Q Consensus       177 ~~~~-----------~~s~-~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~A~~~  230 (366)
                      .++.           .+.+ .-+.+++.+.++......|.|.|||||+|++|||.||+||++|+..
T Consensus        82 ~~w~~~W~~~gw~~~~g~~v~n~~l~~~l~~~l~~~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~  147 (150)
T 3qio_A           82 TQWIHNWKKRGWKTADKKPVKNVDLVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRK  147 (150)
T ss_dssp             HHHHHHHCC------------CHHHHHHHHHHHTTCSEEEEEECCTTSCCHHHHHHHHHHHTTTSC
T ss_pred             HHHHHHHhhcCcCcCcCcccccHHHHHHHHHHHhhcCceEEEEccCcCCChhHHHHHHHHHHHHHH
Confidence            8751           1111 1244556665544577899999999999999999999999999875

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

Probab=99.87  E-value=1e-22  Score=172.88  Aligned_cols=123  Identities=20%  Similarity=0.157  Sum_probs=91.1

Q ss_pred             CceEEEecCCCCCCC--cceEEEe--CCeEe--eeecCCCCchHHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHHh
Q psy5071         104 DSVLCFTDGSKTVNS--TSCAYSI--GNQVH--AFKLNKVNSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSALLAIS  177 (366)
Q Consensus       104 ~~~~iytDgS~~~~~--~G~a~~~--~~~~~--~~~l~~~~s~~~AEl~AI~~aL~~~~~~~~~~i~I~sDs~~al~~l~  177 (366)
                      ..++||||||+..++  .|+|++.  ++...  +..+ ..+|++.|||.|+..||+.+.+  ..+|.|+|||+++++.|.
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            468999999998653  6777653  33322  2233 3678999999999999999976  579999999999999998


Q ss_pred             cCC---------C---Cch-HHHHHHHHHHHHHhcCCcceEEEecccCCCccchhHHHHHcCcccC
Q psy5071         178 NCK---------N---DHP-LVSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVDIAARNPITN  230 (366)
Q Consensus       178 ~~~---------~---~s~-~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~A~~~  230 (366)
                      +.+         .   ..+ ..+.+++.+.++... ..|.|.|||||+|++|||.||+|||+|+..
T Consensus        80 ~~w~~~W~~~~w~~~~~~~v~n~~l~~~~~~~~~~-~~v~~~~V~gH~g~~~N~~AD~LA~~a~~~  144 (146)
T 3h08_A           80 EGWLKRWVKNGWKTAAKKPVENIDLWQEILKLTTL-HRVTFHKVKGHSDNPYNSRADELARLAIKE  144 (146)
T ss_dssp             SSHHHHHHHTTCC----CCCTTHHHHHHHHHHHHH-SEEEEEECCC-CCSHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCccCCCCCcCCHHHHHHHHHHHhh-CceEEEEcCCcCCcHhHHHHHHHHHHHHHh
Confidence            721         1   111 123455555555433 579999999999999999999999999764

>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=99.87  E-value=5.1e-23  Score=174.98  Aligned_cols=127  Identities=17%  Similarity=0.148  Sum_probs=94.6

Q ss_pred             CCCceEEEecCCCCCCCcceEEEe--CCeE--eee-ec--CC--CCchHHHHHHHHHHHHHHhhhCCCCeEEEEeccHHH
Q psy5071         102 YSDSVLCFTDGSKTVNSTSCAYSI--GNQV--HAF-KL--NK--VNSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSA  172 (366)
Q Consensus       102 ~~~~~~iytDgS~~~~~~G~a~~~--~~~~--~~~-~l--~~--~~s~~~AEl~AI~~aL~~~~~~~~~~i~I~sDs~~a  172 (366)
                      +.+.+.||||||+.++..|+|++.  .+..  .+. ..  +.  .++++.||+.|+..||+++.+.+. +|.|+|||+.+
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            456799999999998557888654  3332  233 22  21  368999999999999999877666 99999999988


Q ss_pred             HHHHhcCCCCch-HHHHHHHHHHHHHhcCCcceEEEecccCCCccchhHHHHHcCcccCCC
Q psy5071         173 LLAISNCKNDHP-LVSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVDIAARNPITNIT  232 (366)
Q Consensus       173 l~~l~~~~~~s~-~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~A~~~~~  232 (366)
                      ...+.+.+..+. ......+.+.++.  . .|.|.|||||+|++|||.||+|||+|+....
T Consensus        82 ~~w~~~~w~~~~~~~~~~~~l~~~l~--~-~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~~~  139 (147)
T 2kq2_A           82 AFWATGEWKAKNEFTQAYAKLMNQYR--G-IYSFEKVKAHSGNEFNDYVDMKAKSALGIRD  139 (147)
T ss_dssp             HHHTTSSSSCCHHHHHHHHCGGGGGS--T-TCCBCCCCCCCCCHHHHHHHHHHHHHHTCCC
T ss_pred             HHHHhCCCccCCcchHHHHHHHHHhc--C-CeeEEEecCcCCCcchHHHHHHHHHHHhccc
Confidence            888877665543 3333322222321  2 8999999999999999999999999988643

>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=99.86  E-value=5.4e-22  Score=170.15  Aligned_cols=126  Identities=22%  Similarity=0.224  Sum_probs=95.3

Q ss_pred             CceEEEecCCCCCCC--cceEEEe--CCeEe--eeecCCCCchHHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHHh
Q psy5071         104 DSVLCFTDGSKTVNS--TSCAYSI--GNQVH--AFKLNKVNSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSALLAIS  177 (366)
Q Consensus       104 ~~~~iytDgS~~~~~--~G~a~~~--~~~~~--~~~l~~~~s~~~AEl~AI~~aL~~~~~~~~~~i~I~sDs~~al~~l~  177 (366)
                      ..+.||||||+.+++  .|+|++.  .+...  +..+ ..+|++.|||.|+..||+.+..  ..++.|+|||+++++.|.
T Consensus         3 ~~~~iytDGs~~~n~~~~G~G~v~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~~~~--~~~v~I~tDS~~vi~~i~   79 (155)
T 1jl1_A            3 KQVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGY-TRTTNNRMELMAAIVALEALKE--HAEVILSTDSQYVRQGIT   79 (155)
T ss_dssp             CCEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCCS--CCEEEEEECCHHHHHHHH
T ss_pred             ceEEEEEccccCCCCCceEEEEEEEECCeEEEEecCC-CCCcHHHHHHHHHHHHHHHhCc--CCcEEEEeCHHHHHHHHH
Confidence            358999999998643  6777654  33322  2233 3578999999999999999976  379999999999999999


Q ss_pred             cC--------CC-Cc--hH-HHHHHHHHHHHHhcCCcceEEEecccCCCccchhHHHHHcCcccCCCC
Q psy5071         178 NC--------KN-DH--PL-VSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVDIAARNPITNITL  233 (366)
Q Consensus       178 ~~--------~~-~s--~~-~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~A~~~~~~  233 (366)
                      ++        +. .+  ++ ...+++.+.++. ....|.|.|||||+|++|||.||+|||+|+..+..
T Consensus        80 ~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~-~~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~~~~  146 (155)
T 1jl1_A           80 QWIHNWKKRGWKTADKKPVKNVDLWQRLDAAL-GQHQIKWEWVKGHAGHPENERADELARAAAMNPTL  146 (155)
T ss_dssp             TTHHHHHHTTTBCTTSCBCTTHHHHHHHHHHT-TTCEEEEEECCSSTTCHHHHHHHHHHHHHHHSCCB
T ss_pred             HHHHHHhhcccccccCCccCCHHHHHHHHHHH-ccCceEEEEcCCCCCCHHHHHHHHHHHHHHhccch
Confidence            72        21 11  11 244556666654 34689999999999999999999999999987543

>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=99.86  E-value=1.2e-21  Score=169.36  Aligned_cols=124  Identities=23%  Similarity=0.259  Sum_probs=92.8

Q ss_pred             ceEEEecCCCCC-CC-cceEE--EeCCeEe-eeecCCCCchHHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHHhcC
Q psy5071         105 SVLCFTDGSKTV-NS-TSCAY--SIGNQVH-AFKLNKVNSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNC  179 (366)
Q Consensus       105 ~~~iytDgS~~~-~~-~G~a~--~~~~~~~-~~~l~~~~s~~~AEl~AI~~aL~~~~~~~~~~i~I~sDs~~al~~l~~~  179 (366)
                      .+.||||||+.. .| .|+|+  +.++... ...+...++++.||+.|+..||+++   ...++.|+|||+++++.+-..
T Consensus        23 ~i~iytDGs~~~npG~~g~G~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~---~~~~v~I~tDS~~vi~~iw~~   99 (165)
T 3p1g_A           23 DYTWYTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMA---EGKKLNVYTDSRYAFATAHVH   99 (165)
T ss_dssp             SEEEEEEEEEEEETTEEEEEEEEECSSCEEEEEEECTTCCHHHHHHHHHHHHHHHT---BTSEEEEEECCHHHHHHHHSC
T ss_pred             CEEEEEEcccCCCCCceEEEEEEEECCEEEEEecCCCCCcHHHHHHHHHHHHHHHc---cCceEEEEEchHHHHhhhhcc
Confidence            589999999983 34 55554  3333332 2245568899999999999999999   368999999999999998322


Q ss_pred             CCCchH-HHHHHHHHHHHHhcCCcceEEEecccCC-----CccchhHHHHHcCcccCC
Q psy5071         180 KNDHPL-VSLVYTTWLEAKDCGKNLNFVWCPSHCG-----ITGNELVDIAARNPITNI  231 (366)
Q Consensus       180 ~~~s~~-~~~i~~~~~~l~~~~~~v~~~WVpgH~g-----i~gNe~AD~lAk~A~~~~  231 (366)
                      ..+.++ -+.+|+.+......+..|.|.|||||+|     ++|||.||+|||+|+...
T Consensus       100 ~~g~~v~n~dl~~~l~~~l~~~~~v~~~wVkgH~g~~~~~~~gNe~AD~LA~~aa~~~  157 (165)
T 3p1g_A          100 SEGREIKNKNEILALLKALFLPKRLSIIHCPGHQKGNSAEARGNRMADQAAREAAMKA  157 (165)
T ss_dssp             CCSCCCSSHHHHHHHHHHTTSBSEEEEEECCSSCCSCSHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCcccCHHHHHHHHHHHhcCCceEEEEecCCCCCCcCcchHHHHHHHHHHHHHhcC
Confidence            222221 2344565544434678999999999999     999999999999998753

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

Probab=99.86  E-value=7.6e-22  Score=169.75  Aligned_cols=123  Identities=20%  Similarity=0.213  Sum_probs=93.4

Q ss_pred             CceEEEecCCCCCCC--cceEEEe--CCeEe--eeecCCCCchHHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHHh
Q psy5071         104 DSVLCFTDGSKTVNS--TSCAYSI--GNQVH--AFKLNKVNSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSALLAIS  177 (366)
Q Consensus       104 ~~~~iytDgS~~~~~--~G~a~~~--~~~~~--~~~l~~~~s~~~AEl~AI~~aL~~~~~~~~~~i~I~sDs~~al~~l~  177 (366)
                      ..+.||||||+.+++  .|+|++.  .+...  +..+ ..+|++.|||.|+..||+.+..  ..+|.|+|||+++++.|.
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            468999999998543  6777654  33322  2233 3578999999999999999865  389999999999999998


Q ss_pred             c--------CCCC-c--h-HHHHHHHHHHHHHhcCCcceEEEecccCCCccchhHHHHHcCcccC
Q psy5071         178 N--------CKND-H--P-LVSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVDIAARNPITN  230 (366)
Q Consensus       178 ~--------~~~~-s--~-~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~A~~~  230 (366)
                      +        .+.. .  + .-..+++.+.++.. ...|.|.|||||+|++|||.||+|||+|+..
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        3221 1  1 12345555655543 4689999999999999999999999999986

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

Probab=99.85  E-value=3.9e-22  Score=172.91  Aligned_cols=125  Identities=22%  Similarity=0.161  Sum_probs=94.7

Q ss_pred             CceEEEecCCCCCCC--cceEEEeC--CeEe--eeecCCCCchHHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHHh
Q psy5071         104 DSVLCFTDGSKTVNS--TSCAYSIG--NQVH--AFKLNKVNSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSALLAIS  177 (366)
Q Consensus       104 ~~~~iytDgS~~~~~--~G~a~~~~--~~~~--~~~l~~~~s~~~AEl~AI~~aL~~~~~~~~~~i~I~sDs~~al~~l~  177 (366)
                      ..+.||||||+..++  .|+|++..  +...  +... ..+|++.|||.|+..||+.+...  .+|.|+|||++++..|.
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            578999999998653  67887653  2221  2222 35789999999999999988663  58999999999999999


Q ss_pred             c----------CCCCch--H-HHHHHHHHHHHHhcCCcceEEEecccCCCccchhHHHHHcCcccCCC
Q psy5071         178 N----------CKNDHP--L-VSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVDIAARNPITNIT  232 (366)
Q Consensus       178 ~----------~~~~s~--~-~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~A~~~~~  232 (366)
                      +          +...++  + ...+++.+.++.. ...|.|.|||||+|++|||.||+|||+|+....
T Consensus        84 ~~w~~~W~~~~w~~~~g~~v~n~~l~~~i~~l~~-~~~v~~~wV~gH~g~~~Ne~AD~LAk~a~~~~~  150 (166)
T 1ril_A           84 EGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMA-PHRVRFHFVKGHTGHPENERVDREARRQAQSQA  150 (166)
T ss_dssp             SSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHT-TSEEECCCCCGGGSCTHHHHHHHHHHHHHTSSC
T ss_pred             hhHHHHHHhcccccccCCccCcHHHHHHHHHHHh-cCeEEEEEeeCCCCchhHHHHHHHHHHHHHHhh
Confidence            8          222221  1 2345566666543 468999999999999999999999999988654

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

Probab=99.82  E-value=5.2e-20  Score=158.94  Aligned_cols=126  Identities=16%  Similarity=0.176  Sum_probs=91.7

Q ss_pred             CCceEEEecCCCCCC-C------cceEEEeC--Ce----Eeeeec-CCCCchHHHHHHHHHHHHHHhhhCCCCeEEEEec
Q psy5071         103 SDSVLCFTDGSKTVN-S------TSCAYSIG--NQ----VHAFKL-NKVNSVLSSELMAILLCVKNLIFLPSTNFTLISD  168 (366)
Q Consensus       103 ~~~~~iytDgS~~~~-~------~G~a~~~~--~~----~~~~~l-~~~~s~~~AEl~AI~~aL~~~~~~~~~~i~I~sD  168 (366)
                      ...++||||||+..+ |      .|+|++..  +.    ...+.. ....+.+.||+.|+..||+.+...+ .+|.|+||
T Consensus         5 ~~evviYTDGsc~gNpgp~~~~~aG~Gv~~~~~~~~~~~~~~~~~~tnn~te~~Aei~Al~~al~~al~~~-~~v~I~TD   83 (165)
T 2lsn_A            5 QYEGVFYTDGSAIKSPDPTKSNNAGMGIVHATYKPEYQVLNQWSIPLGNHTAQMAEIAAVEFACKKALKIP-GPVLVITD   83 (165)
T ss_dssp             CCSEEEEEEEEEEECSSCTTCEEEEEEEEEECCSSSCCEEEEEEEEESSCCHHHHHHHHHHHHHHHHHHSS-SCEEEEES
T ss_pred             CceEEEEEcCCCCCCCCCCCCCcEEEEEEEEECCCccEEeccccCCchHHHHHHHHHHHHHHHHHHHhcCC-CeEEEEeC
Confidence            346899999999843 2      57887642  21    223333 3567889999999999999887644 57999999


Q ss_pred             cHHHHHHHhcC--------CCC---chH-HHHHHHHHHHHHhcCCcceEEEecccCCC------ccchhHHHHHcCccc
Q psy5071         169 SMSALLAISNC--------KND---HPL-VSLVYTTWLEAKDCGKNLNFVWCPSHCGI------TGNELVDIAARNPIT  229 (366)
Q Consensus       169 s~~al~~l~~~--------~~~---s~~-~~~i~~~~~~l~~~~~~v~~~WVpgH~gi------~gNe~AD~lAk~A~~  229 (366)
                      |+++++.|..+        +..   .++ -.++|+.+.++......|.|.|||||+|+      +|||.||+||++|+.
T Consensus        84 S~Yvi~~it~w~~~Wk~ngw~~~~~~pVkN~dL~~~l~~~~~~~~~v~~~~VkgH~g~~~~~~~~gNe~AD~LA~~gA~  162 (165)
T 2lsn_A           84 SFYVAESANKELPYWKSNGFVNNKKKPLKHISKWKSIAECLSMKPDITIQHEKGHQPTNTSIHTEGNALADKLATQGSY  162 (165)
T ss_dssp             CHHHHHHHHTHHHHHHHTTSCSCSSSCCSSHHHHHHHHHHHHHCTTCEEEECCSSSCSSSCHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHhhhhhhhhhheeccccccCCCcccCHHHHHHHHHHHhCCCCEEEEEEeCCCCccCCCCChHHHHHHHHHHHhhh
Confidence            99999999752        111   111 24455666665555678999999999995      589999999999864

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

Probab=99.79  E-value=3.3e-19  Score=149.21  Aligned_cols=121  Identities=16%  Similarity=0.198  Sum_probs=93.2

Q ss_pred             CceEEEecCCCCCC-C-cceEEEeC--Ce--E--eeeecCCCCchHHHHHHHHHHHHHHhhhCCCC----eEEEEeccHH
Q psy5071         104 DSVLCFTDGSKTVN-S-TSCAYSIG--NQ--V--HAFKLNKVNSVLSSELMAILLCVKNLIFLPST----NFTLISDSMS  171 (366)
Q Consensus       104 ~~~~iytDgS~~~~-~-~G~a~~~~--~~--~--~~~~l~~~~s~~~AEl~AI~~aL~~~~~~~~~----~i~I~sDs~~  171 (366)
                      ..+.||||||+..+ | .|+|++..  +.  .  .+..+ ..+|++.||+.|+..||+++...+..    ++.|+|||++
T Consensus         2 ~~~~iy~DGs~~~n~g~~G~G~v~~~~~g~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~a~~~~~~~~~~~v~i~tDS~~   80 (140)
T 3u3g_D            2 NKIIIYTDGGARGNPGPAGIGVVITDEKGNTLHESSAYI-GETTNNVAEYEALIRALEDLQMFGDKLVDMEVEVRMDSEL   80 (140)
T ss_dssp             CEEEEEEEEEESSTTEEEEEEEEEECTTSCEEEEEEEEE-EEECHHHHHHHHHHHHHHHHGGGGGGGTTCEEEEEESCHH
T ss_pred             ceEEEEEecCCCCCCCCcEEEEEEEeCCCCEEEEEEeeC-CCCchHHHHHHHHHHHHHHHHHcCCCCCCceEEEEeChHH
Confidence            35899999999854 2 67776642  21  1  12223 34799999999999999999887666    9999999999


Q ss_pred             HHHHHhcCCC-CchHHHHHHHHHHHH-HhcCCcceEEEecccCCCccchhHHHHHcCccc
Q psy5071         172 ALLAISNCKN-DHPLVSLVYTTWLEA-KDCGKNLNFVWCPSHCGITGNELVDIAARNPIT  229 (366)
Q Consensus       172 al~~l~~~~~-~s~~~~~i~~~~~~l-~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~A~~  229 (366)
                      +++.+.+.+. .+.....+++.+.++ ......|.|.|||    .++||.||+|||+|+.
T Consensus        81 vi~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~~v~~~~V~----~~~N~~AD~LA~~a~~  136 (140)
T 3u3g_D           81 IVRQMQGVYKVKEPTLKEKFAKIAHIKMERVPNLVFVHIP----REKNARADELVNEAID  136 (140)
T ss_dssp             HHHHHTTSSCCCCGGGHHHHHHHHHHHHHHCTTCEEEECC----GGGGHHHHHHHHHHHH
T ss_pred             HHHHhCCCcccCCHHHHHHHHHHHHHhhcCCCcEEEEEcC----chhhHHHHHHHHHHHH
Confidence            9999998764 333334445667666 5666799999999    4899999999999875

>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=99.79  E-value=2.2e-19  Score=150.78  Aligned_cols=121  Identities=16%  Similarity=0.221  Sum_probs=95.4

Q ss_pred             ceEEEecCCCCCC--CcceEEEe--CC-e--E--eeeecCCCCchHHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHH
Q psy5071         105 SVLCFTDGSKTVN--STSCAYSI--GN-Q--V--HAFKLNKVNSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSALLA  175 (366)
Q Consensus       105 ~~~iytDgS~~~~--~~G~a~~~--~~-~--~--~~~~l~~~~s~~~AEl~AI~~aL~~~~~~~~~~i~I~sDs~~al~~  175 (366)
                      .+.||||||+..+  ..|+|++.  .+ .  .  .+..+ ..+|++.||+.|+..||+++...+..++.|+|||+++++.
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            5899999999854  26777553  22 1  1  22233 3689999999999999999998888999999999999999


Q ss_pred             HhcCCC-CchHHHHHHHHHHHHHhcCCcceEEEecccCCCccchhHHHHHcCcccC
Q psy5071         176 ISNCKN-DHPLVSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVDIAARNPITN  230 (366)
Q Consensus       176 l~~~~~-~s~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~A~~~  230 (366)
                      +.+.+. .+.....+++.+..+......|.|.|||+    ++|+.||+|||+|+..
T Consensus        82 i~~~~~~~~~~l~~~~~~i~~l~~~~~~v~~~~V~~----~~N~~AD~LA~~a~~~  133 (141)
T 3hst_B           82 MSGRWKVKHPDLLKLYVQAQALASQFRRINYEWVPR----ARNTYADRLANDAMDA  133 (141)
T ss_dssp             HTTSSCCCSHHHHHHHHHHHHHHTTSSEEEEEECCG----GGCHHHHHHHHHHHHH
T ss_pred             HhCCcccCCHHHHHHHHHHHHHHhcCCeEEEEEcCC----cccHHHHHHHHHHHHH
Confidence            998653 34444555577777766778999999994    8999999999999764

>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=99.78  E-value=4.3e-19  Score=181.56  Aligned_cols=119  Identities=22%  Similarity=0.307  Sum_probs=91.0

Q ss_pred             CCceEEEecCCCCCCC--cceEEEeC-CeEeeeecCCCCchHHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHHhcC
Q psy5071         103 SDSVLCFTDGSKTVNS--TSCAYSIG-NQVHAFKLNKVNSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNC  179 (366)
Q Consensus       103 ~~~~~iytDgS~~~~~--~G~a~~~~-~~~~~~~l~~~~s~~~AEl~AI~~aL~~~~~~~~~~i~I~sDs~~al~~l~~~  179 (366)
                      .+.+.||||||+..++  .|+|++.. +...+..+ ..+||+.||+.|+..||+.    ...++.|+|||++|++.+.++
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            4569999999998543  57776643 22333333 4678999999999999998    467999999999999999986


Q ss_pred             CCCchHHHHHHHHHHHHHhcCCcceEEEecccCCCccchhHHHHHcCcc
Q psy5071         180 KNDHPLVSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVDIAARNPI  228 (366)
Q Consensus       180 ~~~s~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~A~  228 (366)
                      ...+.  ..+++.+.++...+..|.|.|||||+|++|||.||+|||+|+
T Consensus       509 ~~~~~--~~l~~~~~~~~~~~~~v~~~wV~~H~g~~~Ne~AD~LA~~a~  555 (555)
T 1mu2_A          509 PTESE--SKIVNQIIEEMIKKEAIYVAWVPAHKGIGGNQEVDHLVSQGI  555 (555)
T ss_dssp             CSEES--CHHHHHHHHHHHHCSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             ccccc--HHHHHHHHHHhccCCcEEEEEEECCCCChhHHHHHHHHHhhC
Confidence            54332  223333333333568899999999999999999999999985

>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=99.77  E-value=3.4e-19  Score=182.38  Aligned_cols=116  Identities=22%  Similarity=0.331  Sum_probs=87.5

Q ss_pred             CCceEEEecCCCCCC-C-cceEEEeC-CeEeeeecCCCCchHHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHHhcC
Q psy5071         103 SDSVLCFTDGSKTVN-S-TSCAYSIG-NQVHAFKLNKVNSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNC  179 (366)
Q Consensus       103 ~~~~~iytDgS~~~~-~-~G~a~~~~-~~~~~~~l~~~~s~~~AEl~AI~~aL~~~~~~~~~~i~I~sDs~~al~~l~~~  179 (366)
                      .+.+.||||||+..+ | .|+|++.. +....... ..+||+.||+.|+..||+.+    ..++.|+|||++|++.|.++
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            456999999999754 3 56676543 33333333 46899999999999999998    57999999999999999997


Q ss_pred             CCCc--hHHHHHHHHHHHHHhcCCcceEEEecccCCCccchhHHHHHcCc
Q psy5071         180 KNDH--PLVSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVDIAARNP  227 (366)
Q Consensus       180 ~~~s--~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~A  227 (366)
                      ...+  ++.+++++.+    .....|.|.|||||+|++|||.||+||++|
T Consensus       512 ~~~~~~~l~~~~~~~l----~~~~~v~~~wV~~H~g~~~Ne~AD~LA~~a  557 (557)
T 2zd1_A          512 PDKSESELVNQIIEQL----IKKEKVYLAWVPAHKGIGGNEQVDKLVSAG  557 (557)
T ss_dssp             CSEESSHHHHHHHHHH----HHCSEEEEEECCSSSCCTTCCGGGGCC---
T ss_pred             CccCCHHHHHHHHHHH----hcCCCEEEEEcCCCCCChhHHHHHHHHhcC
Confidence            6653  2444432222    345689999999999999999999999986

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

Probab=99.75  E-value=3.3e-18  Score=145.33  Aligned_cols=120  Identities=15%  Similarity=0.201  Sum_probs=90.7

Q ss_pred             eEEEecCCCC-CC--Ccce-EEEe--CCeE-eee--ecC---CCCchHHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHH
Q psy5071         106 VLCFTDGSKT-VN--STSC-AYSI--GNQV-HAF--KLN---KVNSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSAL  173 (366)
Q Consensus       106 ~~iytDgS~~-~~--~~G~-a~~~--~~~~-~~~--~l~---~~~s~~~AEl~AI~~aL~~~~~~~~~~i~I~sDs~~al  173 (366)
                      +.||||||+. ++  +.|+ |++.  .+.. ..+  .++   ..++++.||+.|+..||+.+...+..++.|+|||++++
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            6899999997 33  3675 7543  2222 222  222   37899999999999999999987788999999999999


Q ss_pred             HHHhcCCCC-chHHHHHHHHHHHHHhcCCcceEEEecccCCCccchhHHHHHcCcccC
Q psy5071         174 LAISNCKND-HPLVSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVDIAARNPITN  230 (366)
Q Consensus       174 ~~l~~~~~~-s~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~A~~~  230 (366)
                      ..+.+++.. ++....+++.+..+.... .|.|.|||+    ++|+.||+|||+|+..
T Consensus        82 ~~i~~~w~~~~~~~~~l~~~i~~l~~~~-~v~~~~V~~----~~N~~AD~LA~~a~~~  134 (149)
T 2ehg_A           82 KQMNGEYKVKAKRIIPLYEKAIELKKKL-NATLIWVPR----EENKEADRLSRVAYEL  134 (149)
T ss_dssp             HHHTTSSCCCCTTHHHHHHHHHHHHHHH-TCEEEECCG----GGCHHHHHHHHHHHHH
T ss_pred             HHHhCccccCCHHHHHHHHHHHHHHhcC-CEEEEEcCC----cccHHHHHHHHHHHHh
Confidence            999997653 233455556666554443 599999998    5999999999999864

>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=99.28  E-value=2.3e-12  Score=108.14  Aligned_cols=119  Identities=14%  Similarity=-0.042  Sum_probs=84.6

Q ss_pred             CCCceEEEecCCCCCC-C-cceEEEeCC--eEee--eecCCCCchHHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHH
Q psy5071         102 YSDSVLCFTDGSKTVN-S-TSCAYSIGN--QVHA--FKLNKVNSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSALLA  175 (366)
Q Consensus       102 ~~~~~~iytDgS~~~~-~-~G~a~~~~~--~~~~--~~l~~~~s~~~AEl~AI~~aL~~~~~~~~~~i~I~sDs~~al~~  175 (366)
                      ..+.+.||||||+..+ | .|+|++...  ....  ..+ ..+|++.||++|++.||+.+.+.+. ++.|+|||++++..
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 EIIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPI-PIGTNNMGEFLAIVHGLRYLKERNS-RKPIYSNSQTAIKW   85 (142)
T ss_dssp             CCCSSSEEEEEEECSSSEEEEEEEEETTTCCEEEECCCE-EEECHHHHHHHHHHHHHHHHHHTTC-CCCEEESCHHHHHH
T ss_pred             CCCeEEEEEeeccCCCCCCeEEEEEEEeCCEEEEEeccc-CCcCcHHHHHHHHHHHHHHHHhCCC-eEEEEEehHHHHHH
Confidence            3467899999999854 3 688877632  2221  222 2578999999999999999998766 89999999999999


Q ss_pred             HhcCCCC-c---h-HHHHHHHHHHHH--HhcCCcceEEEecccCCCccchhHHH
Q psy5071         176 ISNCKND-H---P-LVSLVYTTWLEA--KDCGKNLNFVWCPSHCGITGNELVDI  222 (366)
Q Consensus       176 l~~~~~~-s---~-~~~~i~~~~~~l--~~~~~~v~~~WVpgH~gi~gNe~AD~  222 (366)
                      +.+.+.. +   + ...++|+.+.++  ......++...|.-|++.-||..||.
T Consensus        86 ~~~~~~k~~~~~~v~n~dLw~~l~~~~~w~~~~~~~~~~~kw~~~~~ge~pad~  139 (142)
T 1zbf_A           86 VKDKKAKSTLVRNEETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKADY  139 (142)
T ss_dssp             HHHTCCCCCCCCSTTTHHHHHHHHHHHHHHHHCCCCCCEEECCHHHHCSCTTCC
T ss_pred             HHcCCccCCCCCCcccHHHHHHHHHHHHHHhhCCCceeEEEeccCccCcCcccc
Confidence            9987632 1   1 233444444332  12345667777888888899999983

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

Probab=98.97  E-value=9.3e-10  Score=90.78  Aligned_cols=74  Identities=15%  Similarity=0.015  Sum_probs=55.6

Q ss_pred             CceEEEecCCCCCC-C-cceEEE-eCC-eE--eeeecCCCCchHHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHHh
Q psy5071         104 DSVLCFTDGSKTVN-S-TSCAYS-IGN-QV--HAFKLNKVNSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSALLAIS  177 (366)
Q Consensus       104 ~~~~iytDgS~~~~-~-~G~a~~-~~~-~~--~~~~l~~~~s~~~AEl~AI~~aL~~~~~~~~~~i~I~sDs~~al~~l~  177 (366)
                      ....||||||+..+ | .|+|++ ..+ ..  .+..+ ..+|++.||++|+..||+.+.+.+.. +.|+|||++++..|.
T Consensus         4 ~~~~iytDGac~GNPGp~G~ggV~~~~g~~~~~~g~~-~~tTNN~aEl~A~i~aL~~l~~~~~~-v~i~tDSqyVi~wi~   81 (134)
T 4htu_A            4 IWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPI-PIGTNNMGEFLAIVHGLRYLKERNSR-KPIYSNSQTAIKWVK   81 (134)
T ss_dssp             CSSSEEEEEEEETTTEEEEEEEEETTTCCEEEEEEEE-EEECHHHHHHHHHHHHHHHHHHTTCC-CCEEESCHHHHHHHH
T ss_pred             cceEEEEeeccCCCCCCeEEEEEEEECCEEEEEecCC-CCCchHHHHHHHHHHHHHHHHhCCCC-EEEEcchHHHHHHHH
Confidence            45689999999854 3 677444 322 21  12223 36899999999999999999886544 899999999999998


Q ss_pred             cC
Q psy5071         178 NC  179 (366)
Q Consensus       178 ~~  179 (366)
                      +.
T Consensus        82 ~~   83 (134)
T 4htu_A           82 DK   83 (134)
T ss_dssp             HT
T ss_pred             cC
Confidence            75

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

Probab=82.68  E-value=0.18  Score=49.50  Aligned_cols=74  Identities=9%  Similarity=-0.050  Sum_probs=47.1

Q ss_pred             CCceEEEecCCCCCCCcceEEEeCC----eE---eeeec---CCCCchHHHHHHHHHHHHHHhhh-CCCCeEEEEeccHH
Q psy5071         103 SDSVLCFTDGSKTVNSTSCAYSIGN----QV---HAFKL---NKVNSVLSSELMAILLCVKNLIF-LPSTNFTLISDSMS  171 (366)
Q Consensus       103 ~~~~~iytDgS~~~~~~G~a~~~~~----~~---~~~~l---~~~~s~~~AEl~AI~~aL~~~~~-~~~~~i~I~sDs~~  171 (366)
                      ...+.+|||+|.  .++|+......    ..   .+..+   ....+.+..|++||..|++.... .....++|+||+. 
T Consensus       344 ~~~~~l~~DAS~--~~~gavL~q~~~~~~~~i~y~Sk~l~~~e~~ys~~ekEllAi~~a~~~~~~yl~g~~~~v~tDh~-  420 (455)
T 1rw3_A          344 TKPFELFVDEKQ--GYAKGVLTQKLGPWRRPVAYLSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLTMGQPLVIKAPHA-  420 (455)
T ss_dssp             CCTTSCEEEEEE--CSSSBEECCBCTTTTCCCCCCCBCSCSSCSSSCCSSHHHHHHHHHHHHHHGGGCSSCEEEECSSC-
T ss_pred             CCcEEEEEeccC--CcceeEEEEecCCcEEEEEEEcccCCccccccchHHHHHHHHHHHHHHHHHHcCCCcEEEEecCh-
Confidence            345789999984  34443332221    11   12223   23456788999999999988765 3457899999996 


Q ss_pred             HHHHHhcC
Q psy5071         172 ALLAISNC  179 (366)
Q Consensus       172 al~~l~~~  179 (366)
                      ++..+.+.
T Consensus       421 ~~~~l~~~  428 (455)
T 1rw3_A          421 VEALVKQP  428 (455)
T ss_dssp             TTTTSSST
T ss_pred             HHHHhCCC
Confidence            65555544

---

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	366
d1mu2a1	126	c.55.3.1 (A:430-555) HIV RNase H (Domain of revers	5e-06
d1rila_	147	c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermoph	0.002

>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 = 43.4 bits (101), Expect = 5e-06
 Identities = 24/124 (19%), Positives = 44/124 (35%), Gaps = 8/124 (6%)

Query: 104 DSVLCFTDGSKTVNST--SCAYSIGNQVHAFKLNKVNSVLSSELMAILLCVKNLIFLPST 161
            +   +TDGS    S      Y         K  +  +   +EL A  + + +       
Sbjct: 6   GAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKLEQTTNQQAELEAFAMALTD----SGP 61

Query: 162 NFTLISDSMSALLAISNCKNDHPLVSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVD 221
              +I DS   +  +++   +    S +    +E     + +   W P+H GI GN+ VD
Sbjct: 62  KVNIIVDSQYVMGIVASQPTESE--SKIVNQIIEEMIKKEAIYVAWVPAHKGIGGNQEVD 119

Query: 222 IAAR 225
               
Sbjct: 120 HLVS 123

>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 = 36.1 bits (82), Expect = 0.002
 Identities = 25/138 (18%), Positives = 38/138 (27%), Gaps = 19/138 (13%)

Query: 106 VLCFTDGSKTVNSTSCAYSI-----GNQVHAFKLNKVNSVLSSELMAILLCVKNLIFLPS 160
           V  FTDG+   N     ++       ++          +    EL A +  +K       
Sbjct: 4   VALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLK--ALKEP 61

Query: 161 TNFTLISDSMSALLAISNCKNDHPLVSLVYT----------TWLEAKDCGKN--LNFVWC 208
               L +DS     A +    +        T           W           + F + 
Sbjct: 62  CEVDLYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPHRVRFHFV 121

Query: 209 PSHCGITGNELVDIAARN 226
             H G   NE VD  AR 
Sbjct: 122 KGHTGHPENERVDREARR 139

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	366
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.91
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	99.86
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.85
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	99.76
d1zbfa1	132	BH0863-like Ribonuclease H {Bacillus halodurans [T	99.43

>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=99.91  E-value=5.6e-25  Score=180.30  Aligned_cols=117  Identities=21%  Similarity=0.296  Sum_probs=87.8

Q ss_pred             CCceEEEecCCCCCC-C-cceEEEeCC-eEeeeecCCCCchHHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHHhcC
Q psy5071         103 SDSVLCFTDGSKTVN-S-TSCAYSIGN-QVHAFKLNKVNSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNC  179 (366)
Q Consensus       103 ~~~~~iytDgS~~~~-~-~G~a~~~~~-~~~~~~l~~~~s~~~AEl~AI~~aL~~~~~~~~~~i~I~sDs~~al~~l~~~  179 (366)
                      ++..++|||||+..+ + .|+|++... ......+ ..+|++.|||.||.+||+..    ...+.|+|||++++..+.+.
T Consensus         5 ~~~~t~YTDGS~~~n~~~~~~g~~~~~~~~~~~~~-~~~tnn~AEl~Ai~~al~~~----~~~i~I~tDS~~v~~~~~~~   79 (126)
T d1mu2a1           5 PGAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKL-EQTTNQQAELEAFAMALTDS----GPKVNIIVDSQYVMGIVASQ   79 (126)
T ss_dssp             TTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEEE-SSCCHHHHHHHHHHHHHHTS----CSEEEEEESCHHHHHHHHTC
T ss_pred             CCCcEEEEcCCCCCCCCcEEEEEEecCCCEEEEec-CCCcchHHHHHHHHHHhccC----CcceEEEechHHHHHHHhcC
Confidence            455799999998754 4 455555443 3334444 36799999999999999854    57899999999999999997


Q ss_pred             CCCch--HHHHHHHHHHHHHhcCCcceEEEecccCCCccchhHHHHHcCcc
Q psy5071         180 KNDHP--LVSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVDIAARNPI  228 (366)
Q Consensus       180 ~~~s~--~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~A~  228 (366)
                      ...+.  ...   +.+..+ .....|.|.|||||+|++|||.||+||++|.
T Consensus        80 ~~~~~~~~~~---~~~~~~-~~~~~v~~~wV~gH~g~~gNe~AD~LA~~ai  126 (126)
T d1mu2a1          80 PTESESKIVN---QIIEEM-IKKEAIYVAWVPAHKGIGGNQEVDHLVSQGI  126 (126)
T ss_dssp             CSEESCHHHH---HHHHHH-HHCSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             CccccchHHH---HHHHHh-hhcceeEEEEEeCCCCCcchHHHHHHHHhhC
Confidence            66432  222   222222 3456899999999999999999999999984

>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=99.86  E-value=4.2e-22  Score=167.69  Aligned_cols=131  Identities=22%  Similarity=0.214  Sum_probs=94.8

Q ss_pred             ceEEEecCCCCCCC--cceEEE--eCCeEeeeec-CCCCchHHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHHhcC
Q psy5071         105 SVLCFTDGSKTVNS--TSCAYS--IGNQVHAFKL-NKVNSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNC  179 (366)
Q Consensus       105 ~~~iytDgS~~~~~--~G~a~~--~~~~~~~~~l-~~~~s~~~AEl~AI~~aL~~~~~~~~~~i~I~sDs~~al~~l~~~  179 (366)
                      .|.||||||+.+++  .|+|++  ..+....+.. ....|++.||++|+..||+++..  ...+.|++||++++..+...
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            48999999998653  677755  3544433322 24578999999999999998754  56899999999999888654


Q ss_pred             CC---------Cc--h-HHHHHHHHHHHHHhcCCcceEEEecccCCCccchhHHHHHcCcccCCCCCCcCc
Q psy5071         180 KN---------DH--P-LVSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVDIAARNPITNITLKNCTS  238 (366)
Q Consensus       180 ~~---------~s--~-~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~A~~~~~~~~~~~  238 (366)
                      ..         ..  . .....++.+..+ .....|.|+|||||+|++|||.||+|||+|+..+...+.++
T Consensus        80 ~~~~~~~~~~~~~~~~~~n~~~~~~i~~~-~~~~~V~~~wV~gH~g~~gNe~AD~LAk~aa~~~~~~d~~~  149 (152)
T d1jl1a_          80 IHNWKKRGWKTADKKPVKNVDLWQRLDAA-LGQHQIKWEWVKGHAGHPENERADELARAAAMNPTLEDTGY  149 (152)
T ss_dssp             HHHHHHTTTBCTTSCBCTTHHHHHHHHHH-TTTCEEEEEECCSSTTCHHHHHHHHHHHHHHHSCCBCCTTC
T ss_pred             hhHhHhccchhcccCeeecHHHHHHHHHH-hhcceeEEEEecccCCCccHHHHHHHHHHHHhCCCCCccCC
Confidence            21         11  1 112233455444 34578999999999999999999999999998776554433

>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=99.85  E-value=1.4e-22  Score=170.10  Aligned_cols=124  Identities=23%  Similarity=0.162  Sum_probs=90.6

Q ss_pred             ceEEEecCCCCCCC--cceEEEe--CCeEee-eecCCCCchHHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHHhcC
Q psy5071         105 SVLCFTDGSKTVNS--TSCAYSI--GNQVHA-FKLNKVNSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNC  179 (366)
Q Consensus       105 ~~~iytDgS~~~~~--~G~a~~~--~~~~~~-~~l~~~~s~~~AEl~AI~~aL~~~~~~~~~~i~I~sDs~~al~~l~~~  179 (366)
                      .++||||||+.+++  .|+|++.  .+.... +.....+|++.||+.||..||+++..  ...+.|++||++++..+...
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            58999999998653  5777654  222211 11123568999999999999997654  56899999999999988664


Q ss_pred             CC----------Cc--hH-HHHHHHHHHHHHhcCCcceEEEecccCCCccchhHHHHHcCcccCC
Q psy5071         180 KN----------DH--PL-VSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVDIAARNPITNI  231 (366)
Q Consensus       180 ~~----------~s--~~-~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~A~~~~  231 (366)
                      +.          ..  ++ -.++++.+..+. ....|.|.|||||+|++|||.||+|||+|+.+.
T Consensus        81 ~~~~~~~~~~~~~~~~~v~n~dL~~~l~~~~-~~~~v~~~wVkgHsg~~gNe~AD~LAk~aa~~~  144 (147)
T d1rila_          81 WLEGWRKRGWRTAEGKPVKNRDLWEALLLAM-APHRVRFHFVKGHTGHPENERVDREARRQAQSQ  144 (147)
T ss_dssp             HHHHHHHTTSBCTTSSBCTTHHHHHHHHHHH-TTSEEECCCCCGGGSCTHHHHHHHHHHHHHTSS
T ss_pred             chhhhhhccccccccccchhHHHHHHHHHHh-hhcccceEEccCCCCCcchHHHHHHHHHHHHHh
Confidence            21          11  11 133455555543 567899999999999999999999999998754

>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=99.76  E-value=1.1e-18  Score=138.80  Aligned_cols=101  Identities=20%  Similarity=0.325  Sum_probs=73.8

Q ss_pred             CCCceEEEecCCCCCC-C-cceEEEeCC-eEeeeecCCCCchHHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHHhc
Q psy5071         102 YSDSVLCFTDGSKTVN-S-TSCAYSIGN-QVHAFKLNKVNSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISN  178 (366)
Q Consensus       102 ~~~~~~iytDgS~~~~-~-~G~a~~~~~-~~~~~~l~~~~s~~~AEl~AI~~aL~~~~~~~~~~i~I~sDs~~al~~l~~  178 (366)
                      -.+..++|||||+..+ + .|+|++..+ ......+ ..+|++.|||.||+.||+..    ..++.|+|||++++.++.+
T Consensus         5 i~~~~t~ytDGs~~~n~~~g~~g~~~~~~~~~~~~~-~~~TNn~aEl~Avi~aL~~~----~~~v~I~TDS~yvi~~i~~   79 (110)
T d1s1ta1           5 IVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTL-TDTTNQKTELQAIYLALQDS----GLEVNIVTDSQYALGIIQA   79 (110)
T ss_dssp             CTTSEEEEEEEEEETTTTEEEEEEEETTSCEEEEEE-SSCCHHHHHHHHHHHHHHHS----CSEEEEEECCHHHHHHHHH
T ss_pred             CCCCcEEEEeCCCCCCCCCcEEEEEEecCCeEEEec-ccCcHHHHHHHHHHHHHHhC----CCeEEEEEehHHHHHHHhc
Confidence            3466899999998754 4 344444433 3444444 36799999999999999854    5689999999999999998


Q ss_pred             CCCCc--hHHHHHHHHHHHHHhcCCcceEEEeccc
Q psy5071         179 CKNDH--PLVSLVYTTWLEAKDCGKNLNFVWCPSH  211 (366)
Q Consensus       179 ~~~~s--~~~~~i~~~~~~l~~~~~~v~~~WVpgH  211 (366)
                      .....  .+.++|    .++......|.+.|||||
T Consensus        80 ~~~~~~~~l~~~i----l~~l~~~~~v~i~WVpgH  110 (110)
T d1s1ta1          80 QPDQSESELVNQI----IEQLIKKEKVYLAWVPAH  110 (110)
T ss_dssp             CCSEESCHHHHHH----HHHHHHCSEEEEEECCSS
T ss_pred             CccccchHHHHHH----HHHHhcCCceEEEEeCCC
Confidence            77643  244444    333334678999999999

>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=99.43  E-value=3.6e-14  Score=114.64  Aligned_cols=114  Identities=14%  Similarity=-0.018  Sum_probs=81.5

Q ss_pred             EEEecCCCCCC-C-cceEEEeCC--eEeeeec-CCCCchHHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHHhcCCC
Q psy5071         107 LCFTDGSKTVN-S-TSCAYSIGN--QVHAFKL-NKVNSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNCKN  181 (366)
Q Consensus       107 ~iytDgS~~~~-~-~G~a~~~~~--~~~~~~l-~~~~s~~~AEl~AI~~aL~~~~~~~~~~i~I~sDs~~al~~l~~~~~  181 (366)
                      .||||||+..+ | .|+|++...  ....++- -..+|++.||++|+..||+.+.+.+ .++.|+|||++|+..+.+..-
T Consensus         6 sIy~DGa~~GNPGp~g~g~v~~~~~~~~~~sg~~~~~TNN~aEl~A~i~aL~~~~~~~-~~i~I~tDS~yvi~wv~~~~~   84 (132)
T d1zbfa1           6 SLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERN-SRKPIYSNSQTAIKWVKDKKA   84 (132)
T ss_dssp             SEEEEEEECSSSEEEEEEEEETTTCCEEEECCCEEEECHHHHHHHHHHHHHHHHHHTT-CCCCEEESCHHHHHHHHHTCC
T ss_pred             eEEEeecCCCCCchheEEEEEEcCCEEEEEEcCcCccchHHHHHHHHHHHHHHhhcCC-ceEEEEeccHHHHHHHHhCce
Confidence            48999999954 4 677766532  2222221 1467899999999999999998754 579999999999999987542


Q ss_pred             Cc-----hHHHHHHHHHHHH--HhcCCcceEEEecccCCCccchhHH
Q psy5071         182 DH-----PLVSLVYTTWLEA--KDCGKNLNFVWCPSHCGITGNELVD  221 (366)
Q Consensus       182 ~s-----~~~~~i~~~~~~l--~~~~~~v~~~WVpgH~gi~gNe~AD  221 (366)
                      ..     .--+++|+.+.++  .-....+.+.||..|+..-||..||
T Consensus        85 kt~~~~~vkN~~l~~~i~~a~~~lk~h~~~~~~~KW~~~~wG~i~AD  131 (132)
T d1zbfa1          85 KSTLVRNEETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKAD  131 (132)
T ss_dssp             CCCCCCSTTTHHHHHHHHHHHHHHHHCCCCCCEEECCHHHHCSCTTC
T ss_pred             ecCcCCCcccHHHHHHHHHHHHHHHhCCcCceeEEecCcccccCCCC
Confidence            11     1234444444332  1245679999999999999999998