Psyllid ID: psy18013

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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-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560---
Protein Sequence
MYRLTYVYLTCYVANSIPPIQEGIDAKDSVLNKLNAVHHAGIRIATGALRSSPVVSLYVDSGVPPLTLRRSKLMLNYVAKISASPFNPAQKLLYHQDMSGIIFTVNKPKPLYIRFREVANFNNVLESSEVAPYVRFVPPWSNCAPPVDQCLGEEKKSDVAPVVFQQKFSEAINTKYANHTICYTDGSKSPDVTGCAFSIGDMVRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALANVKFSNPLVTKVFSTWRYLKLCNKEVTFMWCPSHCGIRGNEIVDDAAKNPNVSAPLKLCTPEDLKPFIASIIQSEWQIQWNNVPNTNKLKSIRPNIKQWNTSTQDRRTKEVILTRMRIGHTRLTHNHLFTKGGQTGNRGSLGNREPILREPQAYFEGTNCYTDGSKSPDVTGCAFSIGDMVRSTLLNPISSIFSAELIAIFLCLEAILENPSDQFLIVSMKLIQSVIRYQNLSANGSVNLKKSTGKTNKQQQRSQEMKPFIKGLCFVLNFPLYIGSRSEVLPANHLRVWAKGTLKRNCASKFRFLMFWTQSK
Secondary Structure (PSIPRED)
ccEEHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHcccccHHHHHHHHHHHHHHHHcccccccccHHHcccccccccccccccccccHHHHHHHHcccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHcccccEEEEEccccccccccccEEccccccEEEccccccHHHHHHHHHHHHHHHHHccccccEEEEcccHHHHHHHHccccccHHHHHHHHHHHHHHHcccEEEEEEEccccccccccHHHccccccccccccccccccccHHHHHHHHHHHHHHHHccccccccccccccccccccccccccHHHHHHHHHHHHccccccHHHHHccccccccccccccccccccccccccccccccccccccccccEEEccccHHHHHHHcccccHHHHHHHHHHHHHHHHHHHcccccEEEEHHHHHHHHHHHHHccccccccHHcccccccHHHHccccccccccccEEEccccccccccccccccccHHHHcccccccHHcccccEEEEEcccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHccccHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHccccccccccccccHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHcccccEEEEEccccccccEEEEEEEEcccEEEEccccccHHHHHHHHHHHHHHHHHHcccccEEEEEccHHHHHHHHccccccHHHHHHHHHHHHHHHccccEEEEEEcccccccccHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHccccccccEEEccccccccccccccHHHHHHHHHHHHccccccHHHHHHccccccccccccccccEEEccEEEEEEEccccccccccccEEccccHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHcccccEEEEEHHHHHHHHHHHHcccccccccccccccccHHHHccccccHHHHcEEEEEcccEEEccccccccccHHHHHHHcHHHHHHHHHHEEEEEEcccc
Coil and Loop (DISEMBL)
MYRLTYVYLTCYvansippiqegidakDSVLNKLNAVHHAGIRIAtgalrsspvvslyvdsgvppltlrRSKLMLNYVAKisaspfnpaqkllyhqdmsgiiftvnkpkplyIRFREVANfnnvlessevapyvrfvppwsncappvdqclgeekksdvapVVFQQKFSEAINTKYANhticytdgskspdvtgcafsIGDMVRstllnpinsIFSAELIAIFLCLEAIlenpsdqfliVSDSRSALAALANvkfsnplvTKVFSTWRYLKLCNkevtfmwcpshcgirgneivddaaknpnvsaplklctpedlKPFIASIIQSEWQIqwnnvpntnklksirpnikqwntstqdrrTKEVILTRMrightrlthnhlftkggqtgnrgslgnrepilrepqayfegtncytdgskspdvtgcafsIGDMVRSTLLNPISSIFSAELIAIFLCLEAilenpsdqFLIVSMKLIQSVIRYQnlsangsvnlkkstgktnkqqQRSQEMKPFIKGLCfvlnfplyigsrsevlpanhlrvwakgtlkrncaskFRFLMFWTQSK
Flexible Loop (DISEMBL)
MYRLTYVYLTCYVANSIPPIQEGIDAKDSVLNKLNAVHHAGIRIatgalrsspvvsLYVDSGVPPLTLRRSKLMLNYVAKISASPFNPAQKLLYHQDMSGIIFTVNKPKPLYIRFREVANFNNVLESSEVAPYVRFVPPWSNCAPPVDQCLGEEKKSDVAPVVFQQKFSEAINTKYANHTICYTDGSKSPDVTGCAFSIGDMVRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALanvkfsnplvtKVFSTWRYLKLCNKEVTFMWCPSHCGIRGNEIVDDAAKNPNVSAPLKLCTPEDLKPFIASIIQSEWQIQWNNVPNtnklksirpnikqwntstqdrrtkeVILTrmrightrlthnhlftkggqtgnrgslgnrePILREPQAYFEGTNCYTDGSKSPDVTGCAFSIGDMVRSTLLNPISSIFSAELIAIFLCLEAILENPSDQFLIVSMKLIQSVIRYQNLsangsvnlkkstgktnkqqqrSQEMKPFIKGLCFVLNFPLYIGSRSEVLPANHLRVWAKGTLKRNCASKFRFlmfwtqsk
Low Complexity Region (SEG)
MYRLTYVYLTCYVANSIPPIQEGIDAKDSVLNKLNAVHHAGIRIATGALRSSPVVSLYVDSGVPPLTLRRSKLMLNYVAKISASPFNPAQKLLYHQDMSGIIFTVNKPKPLYIRFREVANFNNVLESSEVAPYVRFVPPWSNCAPPVDQCLGEEKKSDVAPVVFQQKFSEAINTKYANHTICYTDGSKSPDVTGCAFSIGDMVRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALANVKFSNPLVTKVFSTWRYLKLCNKEVTFMWCPSHCGIRGNEIVDDAAKNPNVSAPLKLCTPEDLKPFIASIIQSEWQIQWNNVPNTNKLKSIRPNIKQWNTSTQDRRTKEVILTRMRIGHTRLTHNHLFTKGGQTGNRGSLGNREPILREPQAYFEGTNCYTDGSKSPDVTGCAFSIGDMVRSTLLNPISSIFSAELIAIFLCLEAILENPSDQFLIVSMKLIQSVIRYQNLSANGSVNLKKSTGKTNKQQQRSQEMKPFIKGLCFVLNFPLYIGSRSEVLPANHLRVWAKGTLKRNCASKFRFLMFWTQSK
Disordered region (IsUnstruct)
*YRLTYVYLTCYVANSIPPIQEGIDAKDSVLNKLNAVHHAGIRIATGALRSSPVVSLYVDSGVPPLTLRRSKLMLNYVAKISASPFNPAQKLLYHQDMSGIIFTVNKPKPLYIRFREVANFNNVLESSEVAPYVRFVPPWSNCAPPVDQCLGEEKKSDVAPVVFQQKFSEAINTKYANHTICYTDGSKSPDVTGCAFSIGDMVRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALANVKFSNPLVTKVFSTWRYLKLCNKEVTFMWCPSHCGIRGNEIVDDAAKNPNVSAPLKLCTPEDLKPFIASIIQSEWQIQWNNVPNTNKLKSIRPNIKQWNT*****RTKEVILTRMRIGHTRLTHNHLFTK****************L*EPQAYFEGTNCYTDGSKSPDVTGCAFSIGDMVRSTLLNPISSIFSAELIAIFLCLEAILENPSDQFLIVSMKLIQSVIRYQNLS*************************PFIKGLCFVLNFPLYIGSRSEVLPANHLRVWAKGTLKRNCASKFRFLMFWT***
Disordered Region (DISOPRED)
MYRLTYVYLTCYVANSIPPIQEGIDAKDSVLNKLNAVHHAGIRIATGALRSSPVVSLYVDSGVPPLTLRRSKLMLNYVAKISASPFNPAQKLLYHQDMSGIIFTVNKPKPLYIRFREVANFNNVLESSEVAPYVRFVPPWSNCAPPVDQCLGEEKKSDVAPVVFQQKFSEAINTKYANHTICYTDGSKSPDVTGCAFSIGDMVRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALANVKFSNPLVTKVFSTWRYLKLCNKEVTFMWCPSHCGIRGNEIVDDAAK******PLKLCTPEDLKPFIASIIQSEWQIQWNNVPNTNKLKSIRPNIKQWNTSTQDRRTKEVILTRMRIGHTRLTHNHLFTKGGQTGNRGSLGNREPILREPQAYFEGTNCYTDGSKSPDVTGCAFSIGDMVRSTLLNPISSIFSAELIAIFLCLEAILENPSDQFLIVSMKLIQSVIRYQNL***************************FIKGLCFVLNFPLYIGSRSEVLPANHLRVWAKGTLKRNCASKFRFLMFWTQS*
Disordered Region (DISEMBL)
MYRLTYVYLTCYVANSIPPIQEGIDAKDSVLNKLNAVHHAGIRIATGALRSSPVVSLYVDSGVPPLTLRRSKLMLNYVAKISASPFNPAQKLLYHQDMSGIIFTVNKPKPLYIRFREVANFNNVLESSEVAPYVRFVPPWSNCAPPVDQCLGEEKKSDVAPVVFQQKFSEAINTKYANHTICYTDGSKSPDVTGCAFSIGDMVRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALANVKFSNPLVTKVFSTWRYLKLCNKEVTFMWCPSHCGIRGNEIVDDAAKNPNVSAPLKLCTPEDLKPFIASIIQSEWQIQWNNVPNTNKLKSIRPNIKQWNTSTQDRRTKEVILTRMRIGHTRLTHNHLFTKGGQTGNRGSLGNREPILREPQAYFEGTNCYTDGSKSPDVTGCAFSIGDMVRSTLLNPISSIFSAELIAIFLCLEAILENPSDQFLIVSMKLIQSVIRYQNLSANGSVNLK**************EMKPFIKGLCFVLNFPLYIGSRSEVLPANHLRVWAKGTLKRNCASKFRFLMFWTQSK
Disordered Region (DISPRO)
MYRLTYVYLTCYVANSIPPIQEGIDAKDSVLNKLNAVHHAGIRIATGALRSSPVVSLYVDSGVPPLTLRRSKLMLNYVAKISASPFNPAQKLLYHQDMSGIIFTVNKPKPLYIRFREVANFNNVLESSEVAPYVRFVPPWSNCAPPVDQCLGEEKKSDVAPVVFQQKFSEAINTKYANHTICYTDGSKSPDVTGCAFSIGDMVRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALANVKFSNPLVTKVFSTWRYLKLCNKEVTFMWCPSHCGIRGNEIVDDAAKNPNVSAPLKLCTPEDLKPFIASIIQSEWQIQWNNVPNTNKLKSIRPNIKQWNTSTQDRRTKEVILTRMRIGHTRLTHNHLFTKGGQTGNRGSLGNREPILREPQAYFEGTNCYTDGSKSPDVTGCAFSIGDMVRSTLLNPISSIFSAELIAIFLCLEAILENPSDQFLIVSMKLIQSVIRYQNLSANG*******************EMKPFIKGLCFVLNFPLYIGSRSEVLPANHLRVWAKGTLKRNCASKFRFLMFWTQS*
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MYRLTYVYLTCYVANSIPPIQEGIDAKDSVLNKLNAVHHAGIRIATGALRSSPVVSLYVDSGVPPLTLRRSKLMLNYVAKISASPFNPAQKLLYHQDMSGIIFTVNKPKPLYIRFREVANFNNVLESSEVAPYVRFVPPWSNCAPPVDQCLGEEKKSDVAPVVFQQKFSEAINTKYANHTICYTDGSKSPDVTGCAFSIGDMVRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALANVKFSNPLVTKVFSTWRYLKLCNKEVTFMWCPSHCGIRGNEIVDDAAKNPNVSAPLKLCTPEDLKPFIASIIQSEWQIQWNNVPNTNKLKSIRPNIKQWNTSTQDRRTKEVILTRMRIGHTRLTHNHLFTKGGQTGNRGSLGNREPILREPQAYFEGTNCYTDGSKSPDVTGCAFSIGDMVRSTLLNPISSIFSAELIAIFLCLEAILENPSDQFLIVSMKLIQSVIRYQNLSANGSVNLKKSTGKTNKQQQRSQEMKPFIKGLCFVLNFPLYIGSRSEVLPANHLRVWAKGTLKRNCASKFRFLMFWTQSK
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	563
427791321	1210	Putative tick transposon, partial [Rhipi	0.621	0.289	0.356	1e-46
427791807	1212	Putative tick transposon, partial [Rhipi	0.621	0.288	0.356	1e-46
125901787	1222	pol-like protein [Biomphalaria glabrata]	0.623	0.287	0.336	3e-42
443693558	502	hypothetical protein CAPTEDRAFT_189741,	0.486	0.545	0.378	4e-36
427798889	1199	Putative tick transposon, partial [Rhipi	0.621	0.291	0.333	6e-36
427798887	1199	Putative tick transposon, partial [Rhipi	0.621	0.291	0.325	7e-35
427791063	1035	Putative tick transposon, partial [Rhipi	0.619	0.337	0.311	1e-34
427798885	1199	Putative tick transposon, partial [Rhipi	0.621	0.291	0.322	3e-34
427778603	1397	Putative tick transposon [Rhipicephalus	0.621	0.250	0.286	8e-34
443721618	471	hypothetical protein CAPTEDRAFT_200496,	0.397	0.475	0.373	2e-33

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

 Score =  194 bits (492), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 132/370 (35%), Positives = 191/370 (51%), Gaps = 20/370 (5%)

Query: 26   AKDSVLNKLNAVHHAGIRIATGALRSSPVVSLYVDSGVPPLTLRRSKLMLNYVAKISASP 85
            A++S + +L+ VH+ G+R+++GA R+SPV SLYVD   PPL+ RR+ L L+YV +I +SP
Sbjct: 782  ARESYIRRLDPVHNLGLRLSSGAYRTSPVESLYVDCNEPPLSHRRASLTLSYVLRIRSSP 841

Query: 86   FNPAQKLLYH--QDMSGIIFTVNKP---KPLYIRFREVANFNNVLESS-EVAPYVRFVPP 139
                Q + Y      S  +  +NK    KPL +RF E      + E + +VA     +PP
Sbjct: 842  ----QHICYDIATRCSSRLHYLNKSNLIKPLLLRFEEYCRTYVISEETLDVARKPPRIPP 897

Query: 140  WSNCAPPVDQCLGEEKKSDVAPVVFQQKFSEAINTKYANHTICYTDGSKSPDVTGCAFSI 199
            W + A   D  L    K    P +  Q+F  A+  KY ++   YTDGSK+ D  G     
Sbjct: 898  WFDLAQLCDISLSHINKKVTPPELIIQEF-RALQEKYRDYAEFYTDGSKTRDHVGIGIVT 956

Query: 200  GDMVRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALANVKFSNPL 259
            G+   S  +    SIF+AE+ A++     I+     + +I +DS SAL AL       PL
Sbjct: 957  GESAFSVRVPQCISIFTAEVYALYEAARKIIAGKHKKAIIYTDSLSALKALHIKSECEPL 1016

Query: 260  VTKVFSTWRYLKLCNKEVT---FMWCPSHCGIRGNEIVDDAAKNPNVSAPLKLCTP-EDL 315
            V  + +    + L N +V    F W PSH GI GNE  D  A         K+  P +D 
Sbjct: 1017 VGDILN----MVLINSKVISMRFCWVPSHVGIPGNEKADKCASLAAHKTLTKIRIPLKDS 1072

Query: 316  KPFIASIIQSEWQIQWNNVPNTNKLKSIRPNIKQWNTSTQDRRTKEVILTRMRIGHTRLT 375
            +  I   + ++WQ QW++   +NKL  ++P + +W       R  EVIL R+RIGHT LT
Sbjct: 1073 QRTIRLALLAKWQQQWDSC-TSNKLHLVKPTLGEWKNCRHQERFIEVILCRLRIGHTHLT 1131

Query: 376  HNHLFTKGGQ 385
            HN L TK  Q
Sbjct: 1132 HNFLLTKEEQ 1141

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 =  194 bits (492), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 132/370 (35%), Positives = 191/370 (51%), Gaps = 20/370 (5%)

Query: 26   AKDSVLNKLNAVHHAGIRIATGALRSSPVVSLYVDSGVPPLTLRRSKLMLNYVAKISASP 85
            A++S + +L+ VH+ G+R+++GA R+SPV SLYVD   PPL+ RR+ L L+YV +I +SP
Sbjct: 785  ARESYIRRLDPVHNLGLRLSSGAYRTSPVESLYVDCNEPPLSHRRASLTLSYVLRIRSSP 844

Query: 86   FNPAQKLLYH--QDMSGIIFTVNKP---KPLYIRFREVANFNNVLESS-EVAPYVRFVPP 139
                Q + Y      S  +  +NK    KPL +RF E      + E + +VA     +PP
Sbjct: 845  ----QHICYDIATRCSSRLHYLNKSNLIKPLLLRFEEYCRTYVISEETLDVARKPPRIPP 900

Query: 140  WSNCAPPVDQCLGEEKKSDVAPVVFQQKFSEAINTKYANHTICYTDGSKSPDVTGCAFSI 199
            W + A   D  L    K    P +  Q+F  A+  KY ++   YTDGSK+ D  G     
Sbjct: 901  WFDLAQLCDISLSHINKKVTPPELIIQEF-RALQEKYRDYAEFYTDGSKTRDHVGIGIVT 959

Query: 200  GDMVRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALANVKFSNPL 259
            G+   S  +    SIF+AE+ A++     I+     + +I +DS SAL AL       PL
Sbjct: 960  GESAFSVRVPQCISIFTAEVYALYEAARKIIAGKHKKAIIYTDSLSALKALHIKSECEPL 1019

Query: 260  VTKVFSTWRYLKLCNKEVT---FMWCPSHCGIRGNEIVDDAAKNPNVSAPLKLCTP-EDL 315
            V  + +    + L N +V    F W PSH GI GNE  D  A         K+  P +D 
Sbjct: 1020 VGDILN----MVLINSKVISMRFCWVPSHVGIPGNEKADKCASLAAHKTLTKIRIPLKDS 1075

Query: 316  KPFIASIIQSEWQIQWNNVPNTNKLKSIRPNIKQWNTSTQDRRTKEVILTRMRIGHTRLT 375
            +  I   + ++WQ QW++   +NKL  ++P + +W       R  EVIL R+RIGHT LT
Sbjct: 1076 QRTIRLALLAKWQQQWDSC-TSNKLHLVKPTLGEWKNCRHQERFIEVILCRLRIGHTHLT 1134

Query: 376  HNHLFTKGGQ 385
            HN L TK  Q
Sbjct: 1135 HNFLLTKEEQ 1144

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  179 bits (454), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 122/363 (33%), Positives = 184/363 (50%), Gaps = 12/363 (3%)

Query: 26   AKDSVLNKLNAVHHAGIRIATGALRSSPVVSLYVDSGVPPLTLRRSKLMLNYVAKISASP 85
            A+ S L  L  + +A +R+  GA R+SP+ SL+V++G  P+ +R  KL + Y+ K+ ++P
Sbjct: 803  ARKSYLKILEPIQNAALRLCLGAFRTSPIPSLHVEAGELPMDIRMKKLAMQYIVKLKSNP 862

Query: 86   FNPAQKLLYHQDMSGIIFTVNKP---KPLYIRFRE-VANFNNVLES-SEVAPYVRFVPPW 140
             NPA   +++   + +     +P   +PL +R RE + N    ++  S++       PPW
Sbjct: 863  TNPAFDSIFNP--TEVELYNRRPNVIQPLGLRMREPIQNLTQPIDQISKIETPQN--PPW 918

Query: 141  SNCAPPVDQCLGEEKKSDVAPVVFQQKFSEAINTKYANHTICYTDGSKSPDVTGCAFSIG 200
                P ++  L   KK +  P + Q  F E +   Y +    YTDGSK      CA S  
Sbjct: 919  LMNKPKLNLSLLNFKKENTDPSILQVHFRE-LQESYGDCGTIYTDGSKMEGKVACACSFR 977

Query: 201  DMVRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALANVKFSNPLV 260
            +   S  L    SIF+AEL AI L L A+  +   +F+I SDS+SAL AL  +K   PLV
Sbjct: 978  NKTISRRLPDGCSIFTAELHAILLALMAVKASERSKFIICSDSKSALQALGRMKTDIPLV 1037

Query: 261  TKVFSTWRYLKLCNKEVTFMWCPSHCGIRGNEIVDDAAKNPNVSAPLKLCTP-EDLKPFI 319
             K       +    ++VTF+W PSH GI GNE  D  AK     A      P  DL+  I
Sbjct: 1038 HKSLKLLDLITADRRDVTFIWVPSHVGIEGNEAADREAKRALNHAVSGTQIPYSDLRQSI 1097

Query: 320  ASIIQSEWQIQWNNVPNTNKLKSIRPNIKQWNTSTQDRRTKEVILTRMRIGHTRLTHNHL 379
            AS    EWQ +W      +KL+ I  +++   TS    R     ++R+RIGHT +TH+ +
Sbjct: 1098 ASATYREWQNRW-EAETHSKLRQIVADVRWRPTSKGLTRRGSTTMSRLRIGHTYITHSFV 1156

Query: 380  FTK 382
              +
Sbjct: 1157 LKR 1159

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 =  159 bits (401), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 112/296 (37%), Positives = 150/296 (50%), Gaps = 22/296 (7%)

Query: 98  MSGIIFTVNKP---KPLYIRFREVANFNNVLESSEVAPYVRF----VPPWSNCAPPVDQC 150
           M+  IF  +KP   +PL  R  E       LES   AP   F    VPPW    P VD  
Sbjct: 1   MANAIFYTSKPSFIRPLLYRTEEA------LESVITAPIAPFKISDVPPWKLRPPEVDTS 54

Query: 151 LGEEKKSDVAPVVFQQKFSEAINTKYANHTICYTDGSKSPDVTGCAFSIGDMVRSTLLNP 210
           + +  K     +  +Q+F   I+ KY    I YTDGSKS +   CAF+         L  
Sbjct: 55  ISKFLKDQHPALFLKQEFYNLID-KYPGINI-YTDGSKSNNAVACAFTCSTYQIQFGLPT 112

Query: 211 INSIFSAELIAI---FLCLEAILENPSDQFLIVSDSRSALAALANVKFSNPLVTKVFSTW 267
             SI++AELIAI    + +E + +   DQF I SDS S+L AL+N   ++P +  + +  
Sbjct: 113 QMSIYTAELIAIEQALIFIETVKDE--DQFNICSDSLSSLTALSNCDITHPYLLSILTKQ 170

Query: 268 RYLKLCNKEVTFMWCPSHCGIRGNEIVDDAAKNPNVSAPLKLCTPE-DLKPFIASIIQSE 326
             L    K V F+WCPSH GI GNE+ D  AK   V    KL  P  D K  I S ++S 
Sbjct: 171 NNLVRKGKLVVFIWCPSHVGILGNEVADRLAKQALVMPVTKLPLPHTDYKSPIRSYVKSL 230

Query: 327 WQIQWNNVPNTNKLKSIRPNIKQWNTSTQDRRTKEVILTRMRIGHTRLTHNHLFTK 382
           WQ +W+   + NKL SI+P I +W    Q  R  E++L R RIGH+ LTH +L  +
Sbjct: 231 WQNEWDEETD-NKLHSIQPVISEWKQGPQIDRRGEIVLARARIGHSHLTHGYLLRR 285

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|427798889|gb|JAA64896.1| Putative tick transposon, partial [Rhipicephalus pulchellus]

 Score =  158 bits (400), Expect = 6e-36,   Method: Compositional matrix adjust.
 Identities = 122/366 (33%), Positives = 180/366 (49%), Gaps = 16/366 (4%)

Query: 26   AKDSVLNKLNAVHHAGIRIATGALRSSPVVSLYVDSGVPPLTLRRSKLMLNYVAKISASP 85
            A  + L  L+ VHH GIR++TGA R+SPV SLYV+S    L L+RS +   Y  K++A  
Sbjct: 809  ASPTALKMLDPVHHLGIRLSTGAFRTSPVESLYVESNEWSLHLQRSYMSFLYYIKVNADK 868

Query: 86   FNPAQKLLYHQDMSGIIFTVNKP--KPLY-IRFREVANFNN--VLESSEVAPYVRFVPPW 140
             +P+   +   D+S      N+P  KP Y +R R++A      + E   +AP   + PPW
Sbjct: 869  EHPSHSTI--NDLSCSTLFENRPSLKPPYSLRVRDLAEQTGLPLFEHRLMAP-AAYPPPW 925

Query: 141  SNCAPPVDQCLGEEKKSDVAPVVFQQKFSEAINTKYANHTICYTDGSKSPDVTGCAFSIG 200
                   D    E  K   AP+   + +   +  KY N    YTD SKS      A    
Sbjct: 926  QWQLIDCDVSFMEVTKH--APIAHIRTYFLELQHKY-NCPAFYTDASKSHTSVSYAAVGP 982

Query: 201  DMVRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALANV-KFSNPL 259
                +  L+P  SIF+AE  AI   ++ I E    + +I +DS S + AL  + K  NP+
Sbjct: 983  SFSAAGALHPNTSIFTAEAYAILAAVKHIRELKLQKAVIYTDSLSVVKALKTLKKHRNPV 1042

Query: 260  VTKVFSTWRYLKLCNKEVTFMWCPSHCGIRGNEIVDD-AAKNPNVSAPLKLCTPE-DLKP 317
            +  ++S    +    + V   W P H  I+GN + D  A    + SA   +  P  DLKP
Sbjct: 1043 LVSLYSLLCTIYTSKQHVVVCWVPGHREIQGNVMADQLAVSAHDSSANTSIAIPALDLKP 1102

Query: 318  FIASIIQSEWQIQWNNVPNTNKLKSIRPNIKQWNTSTQDRRTKEVILTRMRIGHTRLTHN 377
            ++   I++ WQ  W+   + NKL  I+P +  W   ++ R T EV LTR+R GHT  TH 
Sbjct: 1103 YLKRKIRAYWQSTWDRQTH-NKLHVIKPQLGHWPPISKSRYT-EVTLTRLRTGHTHSTHA 1160

Query: 378  HLFTKG 383
            +L + G
Sbjct: 1161 YLLSGG 1166

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|427798887|gb|JAA64895.1| Putative tick transposon, partial [Rhipicephalus pulchellus]

 Score =  155 bits (391), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 119/366 (32%), Positives = 176/366 (48%), Gaps = 16/366 (4%)

Query: 26   AKDSVLNKLNAVHHAGIRIATGALRSSPVVSLYVDSGVPPLTLRRSKLMLNYVAKISASP 85
            A  + L  L+ VHH GIR++TGA R+SPV SLYV+S    L L+RS +   Y  K++A  
Sbjct: 809  ASPTALKMLDPVHHLGIRLSTGAFRTSPVESLYVESNEWSLHLQRSYMSFLYYLKVNADK 868

Query: 86   FNPAQKLLYHQDMSGIIFTVNKPK---PLYIRFREVANFNN--VLESSEVAPYVRFVPPW 140
             +P+   +   D+S      N+P    P  +R R +A      + E   +AP   + PPW
Sbjct: 869  EHPSHSTI--NDLSSSTLFENRPSLRPPYSLRVRGLAEETGLPLFEHRLMAP-AAYPPPW 925

Query: 141  SNCAPPVDQCLGEEKKSDVAPVVFQQKFSEAINTKYANHTICYTDGSKSPDVTGCAFSIG 200
                   D    E  K   AP+   + +   +  KY N    YTD SKS      A    
Sbjct: 926  QWQLIDCDVSFMEVTKH--APIAHIRTYFLELQHKY-NCPAFYTDASKSHTSVSYAAVGP 982

Query: 201  DMVRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALANV-KFSNPL 259
                +  L+P  SIF+AE  AI   ++ I E    + +I +DS S + AL  + K  N +
Sbjct: 983  SFSAAGALHPNTSIFTAEAYAILAAVKHIRELKLQKAVIYTDSLSVVKALKTLKKHKNSI 1042

Query: 260  VTKVFSTWRYLKLCNKEVTFMWCPSHCGIRGNEIVDD-AAKNPNVSAPLKLCTPE-DLKP 317
            +  ++S    +    + V   W P H  I+GN + D  AA   + SA   +  P  DLKP
Sbjct: 1043 LVSLYSLVCTVYTAKQHVVVCWVPGHREIQGNVMADHLAASTHDCSANTSIAIPALDLKP 1102

Query: 318  FIASIIQSEWQIQWNNVPNTNKLKSIRPNIKQWNTSTQDRRTKEVILTRMRIGHTRLTHN 377
             +   +++ WQ  W+   + NKL  I+P +  W   ++ R T EV LTR+R GHT  TH 
Sbjct: 1103 LLKRKLRAYWQSTWDQQTH-NKLHVIKPQLGHWPPISKSRYT-EVTLTRLRTGHTHSTHA 1160

Query: 378  HLFTKG 383
            +L + G
Sbjct: 1161 YLLSGG 1166

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  154 bits (389), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 113/363 (31%), Positives = 179/363 (49%), Gaps = 14/363 (3%)

Query: 26  AKDSVLNKLNAVHHAGIRIATGALRSSPVVSLYVDSGVPPLTLRRSKLMLNYVAKISASP 85
           A  S L  L+ +HH GIR+ATGA R+SPV SLYV+S    L L+RS +   Y  K+ A  
Sbjct: 643 AAPSALKILDPIHHLGIRLATGAFRTSPVQSLYVESNQWSLHLQRSYMSFVYFLKVKAEK 702

Query: 86  FNPAQKLLYHQDMSGIIFTVNKP---KPLYIRFREVANFNNV-LESSEVAPYVRFVPPWS 141
            +PA   +   D+S  +   N+P   +P  +R R++A    + L    +     ++PPW 
Sbjct: 703 EHPAHSTV--NDLSSSVLYHNRPSVRQPYSLRVRDLAEEMGLSLHEHSLMARAAYLPPWQ 760

Query: 142 NCAPPVDQCLGEEKKSDVAPVVFQQKFSEAINTKYANHTICYTDGSKSPDVTGCAFSIGD 201
                 D  +  E+ +  AP      +   +  KY      +TD SK       A     
Sbjct: 761 WQLIECD--VSFEQVTKHAPHAHIYTYFLELQHKYTFPEF-FTDASKFNSSVSYAAVGPS 817

Query: 202 MVRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALANV-KFSNPLV 260
              + +L+   SIF+AE  AIF+ ++ I +      +I +DS S + AL  + K  NP++
Sbjct: 818 FSDAGVLHQNTSIFTAEAYAIFVAVKHIEQLKLPSAVIYTDSLSVVKALKTLKKHKNPVL 877

Query: 261 TKVFSTWRYLKLCNKEVTFMWCPSHCGIRGNEIVDDAAKNPNVSAPLK-LCTPE-DLKPF 318
             ++S    +    + V   W P H  I+GN + D  A + + +A    L  P  DLKP 
Sbjct: 878 ASLYSLLCTVYALKQHVVVCWVPGHREIQGNVLADQLAASAHENAAHTFLAIPALDLKPL 937

Query: 319 IASIIQSEWQIQWNNVPNTNKLKSIRPNIKQWNTSTQDRRTKEVILTRMRIGHTRLTHNH 378
           +   +++ WQ  W +    NKL +I+P + +W  +++ RRT E+ LTR+R GHT  TH +
Sbjct: 938 LKRKLRAYWQSIW-DTQTQNKLHAIKPQLGEWPPASKSRRT-EITLTRLRTGHTHTTHAY 995

Query: 379 LFT 381
           L +
Sbjct: 996 LLS 998

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|427798885|gb|JAA64894.1| Putative tick transposon, partial [Rhipicephalus pulchellus]

 Score =  153 bits (386), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 118/366 (32%), Positives = 176/366 (48%), Gaps = 16/366 (4%)

Query: 26   AKDSVLNKLNAVHHAGIRIATGALRSSPVVSLYVDSGVPPLTLRRSKLMLNYVAKISASP 85
            A  + L  L+ +HH GIR++TGA  +SPV SLYV+S    L L+RS +   Y  K++A  
Sbjct: 809  ASPTALKMLDPIHHLGIRLSTGAFCTSPVESLYVESNEWSLQLQRSYMSFLYYLKVNADK 868

Query: 86   FNPAQKLLYHQDMSGIIFTVNKPK---PLYIRFREVANFNN--VLESSEVAPYVRFVPPW 140
             +P+   +   D+S      N+P    P  +R R +A      + E   +AP   + PPW
Sbjct: 869  EHPSHSTI--NDLSSSTLFENRPSLRPPYSLRVRGLAEETGLPLFEHRLMAP-AAYPPPW 925

Query: 141  SNCAPPVDQCLGEEKKSDVAPVVFQQKFSEAINTKYANHTICYTDGSKSPDVTGCAFSIG 200
                   D    E  K   AP+   + +   +  KY N    YTD SKS      A    
Sbjct: 926  QWQLIDCDVSFMEVTKH--APIAHIRTYFLELQHKY-NCPAFYTDASKSHTSVSYAAVGP 982

Query: 201  DMVRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALANV-KFSNPL 259
                + +L+P  SIF+AE  AI   ++ I E    + +I +DS S + AL  + K  N +
Sbjct: 983  SFSDAGVLHPNTSIFTAEAYAILAAVKHIRELKLQKAVIYTDSLSVVKALKTLKKHKNSI 1042

Query: 260  VTKVFSTWRYLKLCNKEVTFMWCPSHCGIRGNEIVDD-AAKNPNVSAPLKLCTPE-DLKP 317
            +  ++S    L    + V   W P H  I+GN + D  AA   + SA   +  P  DLKP
Sbjct: 1043 LVSLYSLVCTLYTAKQHVVVCWVPGHREIQGNVMADHLAASTHDCSANTSIAIPALDLKP 1102

Query: 318  FIASIIQSEWQIQWNNVPNTNKLKSIRPNIKQWNTSTQDRRTKEVILTRMRIGHTRLTHN 377
             +   +++ WQ  W+   + NKL  I+P +  W   ++ R T EV LTR+R GHT  TH 
Sbjct: 1103 LLKRKLRAYWQSTWDQQTH-NKLHVIKPQLGHWPPISKSRYT-EVTLTRLRTGHTHSTHA 1160

Query: 378  HLFTKG 383
            +L + G
Sbjct: 1161 YLLSGG 1166

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  151 bits (382), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 119/416 (28%), Positives = 181/416 (43%), Gaps = 66/416 (15%)

Query: 26   AKDSVLNKLNAVHHAGIRIATGALRSSPVVSLYVDSGVPPLTLRRSKLMLNYVAKISASP 85
            A  + L  L+ V+H GIR+A GA R+SPV SLY +S   PL  +R+ L + Y  +I +  
Sbjct: 902  ASKTALKLLDPVYHLGIRLALGAFRTSPVQSLYAESDQWPLDYQRTYLGVTYATRIMSLK 961

Query: 86   FNPAQKLLYHQDMSGIIFTVNKPK-----PLYIR---------FREVANFNNV------- 124
             +P + L+   D+S     +N+P      PL IR         F ++   + V       
Sbjct: 962  QHPCKSLM--NDVSTTQLYINRPSISPPFPLAIRPVVEKLKIHFEDLQEIDQVEXQHPCK 1019

Query: 125  ------------------------------------LESSEVAPYVRFVPPWSNCAPPVD 148
                                                 E  +    V  +PPW  C    D
Sbjct: 1020 ALMNDVSTTQLYINRPSISPPFPLAIRPVVEKLKIHFEDLQEIDQVEVIPPWKQCPIICD 1079

Query: 149  QCLGEEKKSDVAPVVFQQKFSEAINTKYANHTICYTDGSKSPDVTGCAFSIGDMVRSTLL 208
                + KK      + QQ F  A+  KY +    ++DGSKS     CA        +  L
Sbjct: 1080 WSFKDLKKKTAPNALIQQHFL-ALEHKYRSAAF-FSDGSKSQTSVSCAAYGESFSDAKTL 1137

Query: 209  NPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALANVKFS-NPLVTKVFSTW 267
            +   SIF+AE   I L +E I ++   + +I +DS S + AL+  K S NP+  K+ +  
Sbjct: 1138 HAHTSIFTAEAYGILLIVEHIKQHMIRRSIIYTDSLSVVTALSCGKCSKNPVFNKLLNNM 1197

Query: 268  RYLKLCNKEVTFMWCPSHCGIRGNEIVDDAAKNPNVSAPLKLCTPE--DLKPFIASIIQS 325
                  N  +   W P H GI GNE+VD  A+       + + +    DL P +   ++S
Sbjct: 1198 HEAYNQNLSIVLCWVPGHAGITGNEMVDKNAREAASRHTIDISSVPGVDLNPVVRRGLRS 1257

Query: 326  EWQIQWNNVPNTNKLKSIRPNIKQWNTSTQDRRTKEVILTRMRIGHTRLTHNHLFT 381
             WQ++W+   + NKL  ++P++ +      +R T EV L R+RIGHT  TH HL T
Sbjct: 1258 HWQVEWDKQVD-NKLHLVKPHLSKVLPQKLNRFT-EVTLARLRIGHTYATHKHLLT 1311

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  150 bits (379), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 87/233 (37%), Positives = 133/233 (57%), Gaps = 9/233 (3%)

Query: 159 VAPVVFQQKFSEAINTKYANHTICYTDGSKSPDVTGCAFSIGDMVRSTLLNPINSIFSAE 218
           ++ +  + +F++A++ +Y + T+ YTDGSKS D   C+F    +     L    S+F++E
Sbjct: 1   MSALTIRSEFADALD-RYPDSTVFYTDGSKSEDSVACSFFSSRLKLKMKLPVQMSVFTSE 59

Query: 219 LIAIF---LCLEAILENPSDQFLIVSDSRSALAALANVKFSNPLVTKVFSTWRYLKLCNK 275
           +IAI     C+EA  +N   QF+I SDS SA+ A+  +   +P V +V    + +    K
Sbjct: 60  IIAILSALRCVEA--DNEQHQFVICSDSLSAIMAIHGMDVRHPYVLQVLYAIKSISQQEK 117

Query: 276 EVTFMWCPSHCGIRGNEIVDDAAKNPNVSAPL-KLCTP-EDLKPFIASIIQSEWQIQWNN 333
            V FMWCPSH GI GNE+ D  AK    S  L +L  P  DL+  I   I+S WQ +W+ 
Sbjct: 118 IVVFMWCPSHVGIPGNEMADTLAKEALSSTNLAELPVPASDLRCLIKKYIRSRWQHEWDE 177

Query: 334 VPNTNKLKSIRPNIKQWNTSTQDRRTKEVILTRMRIGHTRLTHNHLFTKGGQT 386
             ++NKL SI P I  W    +++R +E++L R+RIGHT  TH+++     QT
Sbjct: 178 -QHSNKLHSIHPTIGPWPPCQREKRREEIVLARIRIGHTHYTHDYIPRGDDQT 229

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	563
ASPGD|ASPL0000075333	486	AN10625 [Emericella nidulans (	0.355	0.411	0.238	7.6e-06
ASPGD|ASPL0000010587	342	AN3980 [Emericella nidulans (t	0.284	0.467	0.254	0.00051
ASPGD|ASPL0000077547	1581	AN8648 [Emericella nidulans (t	0.296	0.105	0.271	0.00054

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

 Score = 137 (53.3 bits), Expect = 7.6e-06, P = 7.6e-06
 Identities = 51/214 (23%), Positives = 90/214 (42%)

Query:   183 YTDGSKSPDVTGCAFSIGDMV--RSTLLNPIN--SIFSAELIAIFLCLEAILENPSDQFL 238
             YTDGS      G A      +  RS+ +   +  +++ AEL  I L L  IL+      +
Sbjct:   186 YTDGSGINGRVGAAAICPKYLISRSSYMGQQSESTVYVAELQGILLALVIILQRQMQHAV 245

Query:   239 IVSDSRSALAALANV--KFSNPLVTKVFSTWRYLKLCNKEVTFMWCPSHCGIRGNEIVDD 296
             I +D+++ L AL N   +    ++  +       +     V F W P+H G+ GNE  D 
Sbjct:   246 IFTDNQATLQALRNPGSQSGQYILEAIIMALNKGRKAGLNVHFRWIPAHRGVEGNEQADR 305

Query:   297 AAKNPNVSAPLK-----LCTPEDLKPFIASIIQSEWQIQWNNVPNTNKLKSIRPN-IKQW 350
              AK       ++     +     +K     ++ + W+  W +  +  +L  + P   ++ 
Sbjct:   306 RAKEATGWRRIRGHRGRMTIRSAVKRRAHEVVNARWENDWKSCHHGRELYELTPTPTRKV 365

Query:   351 NTSTQD-RRTKEVILTRMRIGHTRLTHNHLFTKG 383
                 QD  R    I+ +MR G   L H +L+ +G
Sbjct:   366 LRVHQDLHRALSTIIVQMRTGKIGLRH-YLYQRG 398

GO:0008150 "biological_process" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

ASPGD|ASPL0000010587 AN3980 [Emericella nidulans (taxid:162425)]

 Score = 118 (46.6 bits), Expect = 0.00051, P = 0.00051
 Identities = 47/185 (25%), Positives = 83/185 (44%)

Query:   210 PINSIFSAELIAIFLCLEAILENP----SDQFLIVSDSRSALAALANVK--FSNPLVTKV 263
             P   ++ AE+I     L A L  P    S Q +I+ D+ +A + LA+ +       +++ 
Sbjct:    84 PRTEVYDAEIIGAVEGLRAALGQPCMGYSTQLVILLDNLAAASLLASYRPTLHRHRLSES 143

Query:   264 FST-----WRYLKLCNKEVTFMWCPSHCGIRGNEIVDDAAK-NPNVSAPLKLCTPEDLKP 317
             F       W+ L++C       W P H GI GN++ D  AK   ++ +P    +P  L+ 
Sbjct:   144 FGQLATQPWKPLQVC-------WIPGHSGIAGNKLADKLAKLGSSIYSPNIPPSPAYLQR 196

Query:   318 FIASIIQSEWQIQW-NNVPNTNKLKSIRPNIKQWNTSTQDRRTKEVILTRM---RIGHTR 373
                  +++E    + +  P   K   IRP+ K+  + T++ +    +L R+   R GH  
Sbjct:   197 ETKQQLRTETYTAYASKAPQAYKTLDIRPHTKE--SRTREHKLPRWVLGRLVAARTGHGD 254

Query:   374 LTHNH 378
              T  H
Sbjct:   255 FTAYH 259

GO:0008150 "biological_process" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

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

 Score = 126 (49.4 bits), Expect = 0.00054, P = 0.00054
 Identities = 51/188 (27%), Positives = 85/188 (45%)

Query:   210 PINSIFSAELIAIFLCLEAILENP----SDQFLIVSDSRSALAALANVKFSNPL---VTK 262
             P   ++ AE++     L A L  P    S Q +I+ D+ +A + LA+ +   P    +++
Sbjct:  1313 PRTEVYDAEIMGAVEGLRAALGQPCVGYSTQLVILLDNLAAASLLASYR-PTPHRHGLSE 1371

Query:   263 VFST----WR----YLKLCNKEVTFMWCPSHCGIRGNEIVDDAAK-NPNVSAPLKLCTPE 313
              FS     W      L +  K +   W P H GI GNE+ D  AK   ++ +P    +P 
Sbjct:  1372 TFSQLAAQWMESPSILTMQRKPLQVRWIPGHSGIAGNELADKLAKLGSSIYSPDIPPSPA 1431

Query:   314 DLKPFIASIIQSEWQIQW-NNVPNTNKLKSIRPNIKQWNTSTQDRRTKEVI--LTRMRIG 370
              L+      +++E    + N  P T K  +IRP+ K+ + S + +  + V+  L   R G
Sbjct:  1432 YLRREAKQWLRTETYTAYANKAPETYKALNIRPHTKE-SRSREHKLPRWVLGRLVAARTG 1490

Query:   371 HTRLTHNH 378
             H   T  H
Sbjct:  1491 HGDFTAYH 1498


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.320   0.134   0.405    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      563       563    0.0010  119 3  11 22  0.38    34
                                                     35  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:  3
  No. of states in DFA:  628 (67 KB)
  Total size of DFA:  322 KB (2162 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:  45.68u 0.11s 45.79t   Elapsed:  00:00:03
  Total cpu time:  45.68u 0.11s 45.79t   Elapsed:  00:00:03
  Start:  Thu Aug 15 16:21:07 2013   End:  Thu Aug 15 16:21:10 2013

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

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

GO:0003723 "RNA binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.1.26.4	LOW CONFIDENCE prediction!
3rd Layer	3.1.26	0.691

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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	563
cd09276	128	cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom	2e-35
pfam00075	126	pfam00075, RNase_H, RNase H	9e-13
cd09276	128	cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom	1e-11
cd09273	135	cd09273, RNase_HI_RT_Bel, Bel/Pao family of RNase	3e-08
cd06222	123	cd06222, RNase_H, RNase H is an endonuclease that	1e-06
COG0328	154	COG0328, RnhA, Ribonuclease HI [DNA replication, r	0.004

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

 Score =  128 bits (324), Expect = 2e-35
 Identities = 50/124 (40%), Positives = 65/124 (52%), Gaps = 5/124 (4%)

Query: 181 ICYTDGSKSPDVTGCAFSI---GDMVRSTLLNPINSIFSAELIAIFLCLEAILENPSD-- 235
           + YTDGSK    TG  F+I   G + RS  L P  S+F AEL+AI   L+  L       
Sbjct: 1   VIYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRRAR 60

Query: 236 QFLIVSDSRSALAALANVKFSNPLVTKVFSTWRYLKLCNKEVTFMWCPSHCGIRGNEIVD 295
           +  I SDS++AL AL + + S+PLV ++    R L     +V   W P H GI GNE  D
Sbjct: 61  KITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGNERAD 120

Query: 296 DAAK 299
             AK
Sbjct: 121 RLAK 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 = 65.0 bits (159), Expect = 9e-13
 Identities = 35/126 (27%), Positives = 49/126 (38%), Gaps = 9/126 (7%)

Query: 178 NHTICYTDGS--KSPDVTGCAFSI-GDMVRSTLLNPINSIFSAELIAIFLCLEAILENPS 234
                YTDGS   +P   G  +   G   RS  L P  +   AEL+A+   +EA+     
Sbjct: 2   EAVTVYTDGSCNGNPGPGGAGYVTDGGKQRSKPL-PGTTNQRAELLAL---IEALEALSG 57

Query: 235 DQFLIVSDSRSAL-AALANVKFSNPLVTKVFSTWRYLKLCNKEVTFMWCPSHCGIRGNEI 293
            +  I +DS+  +          +         W  L     +V   W P H GI GNE+
Sbjct: 58  QKVNIYTDSQYVIGGITNGWPTKSESKPIKNEIWE-LLQKKHKVYIQWVPGHSGIPGNEL 116

Query: 294 VDDAAK 299
            D  AK
Sbjct: 117 ADKLAK 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|187700 cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI domain of reverse transcriptases

 Score = 61.9 bits (151), Expect = 1e-11
 Identities = 24/56 (42%), Positives = 29/56 (51%), Gaps = 3/56 (5%)

Query: 411 CYTDGSKSPDVTGCAFSI---GDMVRSTLLNPISSIFSAELIAIFLCLEAILENPS 463
            YTDGSK    TG  F+I   G + RS  L P  S+F AEL+AI   L+  L    
Sbjct: 2   IYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGR 57

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

 Score = 51.9 bits (125), Expect = 3e-08
 Identities = 33/134 (24%), Positives = 48/134 (35%), Gaps = 19/134 (14%)

Query: 182 CYTDGSKSPDVTGCA-FSIGDMVRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIV 240
            +TDGS      G A  +  D++    L    S   AELIA+   + A+         I 
Sbjct: 2   VFTDGSSFVRKAGYAVVTGPDVLEIATLPYGTSAQRAELIAL---IRALELAKGKPVNIY 58

Query: 241 SDSR---SALAALANVKFSNPLVT----KVFSTWRYLK---LCNKEVTFMWCPSHCG--- 287
           +DS      L AL  +      +T     + S    L+      K V  +   +H G   
Sbjct: 59  TDSAYAFGILHALETIWKERGFLTGKPIALASLILQLQKAIQRPKPVAVIHIRAHSGLPG 118

Query: 288 --IRGNEIVDDAAK 299
               GN   D AA+
Sbjct: 119 PLALGNARADQAAR 132

Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryote. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamatic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. Bel/Pao family has been described only in metazoan genomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription. Length = 135

>gnl|CDD|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 = 47.3 bits (113), Expect = 1e-06
 Identities = 29/128 (22%), Positives = 48/128 (37%), Gaps = 15/128 (11%)

Query: 183 YTDGSKSPDVTGCAFSIGDMVR---------STLLNPINSIFSAELIAIFLCLEAILENP 233
            TDGS   +  G A   G ++R          +L  P  +   AEL+A+   LE  L+  
Sbjct: 1   NTDGSCKGNP-GPA-GAGGVLRDHEGAWLFAGSLSIPAATNNEAELLALLEALELALDLG 58

Query: 234 SDQFLIVSDSRSALAALANVKFSNPLVTKVFSTWRYLKLCNKEVTFMWCPSHCGIRGNEI 293
             + +I +DS+  +  + +          +      L     ++ F   P      GNE+
Sbjct: 59  LKKLIIETDSKYVVDLINSWSKGWKKNNLLLWDILLLLSKFIDIRFEHVPRE----GNEV 114

Query: 294 VDDAAKNP 301
            D  AK  
Sbjct: 115 ADRLAKEA 122

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

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

 Score = 38.1 bits (89), Expect = 0.004
 Identities = 27/105 (25%), Positives = 37/105 (35%), Gaps = 16/105 (15%)

Query: 217 AELIAIFLCLEAILENPSDQFLIVSDS---RSALAALANVKFSNPLVT------KVFSTW 267
           AEL A+   LEA+ E  + +  + +DS      +         N   T      K    W
Sbjct: 46  AELRALIEALEALKELGACEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPVKNKDLW 105

Query: 268 RYLKLCNK---EVTFMWCPSHCGIRGNEIVD----DAAKNPNVSA 305
             L    K    V + W   H G   NE  D    +AA+    SA
Sbjct: 106 EELDELLKRHELVFWEWVKGHAGHPENERADQLAREAARAAKKSA 150

Length = 154

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	563
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	99.81
PRK06548	161	ribonuclease H; Provisional	99.8
PRK08719	147	ribonuclease H; Reviewed	99.8
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	99.77
PRK00203	150	rnhA ribonuclease H; Reviewed	99.76
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	99.7
KOG3752|consensus	371		99.6
PRK13907	128	rnhA ribonuclease H; Provisional	99.57
PRK07708	219	hypothetical protein; Validated	99.35
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	99.26
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	98.98
PF13966	86	zf-RVT: zinc-binding in reverse transcriptase	82.06

>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=99.81  E-value=5.9e-20  Score=166.21  Aligned_cols=116  Identities=33%  Similarity=0.420  Sum_probs=88.3

Q ss_pred             CcEEEEecCCCCC--CcceEEEEeC-CeeeeeecCCCCcchhHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHHHhc--
Q psy18013        178 NHTICYTDGSKSP--DVTGCAFSIG-DMVRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALAN--  252 (563)
Q Consensus       178 ~~i~IyTDGS~~~--~~vG~gvv~~-~~~~~~~L~~~~sv~~AEL~AI~~AL~~a~~~~~~~i~I~tDS~sal~aL~~--  252 (563)
                      ..+.||||||...  +..|+|+++. +...++.++ ..+++.|||.||..||+.+ .  ...++|+|||++++..+..  
T Consensus         2 ~~~~iytDgS~~~~~~~~~~g~v~~~~~~~~~~~~-~~s~~~aEl~Ai~~AL~~~-~--~~~v~I~tDS~~v~~~l~~~~   77 (132)
T PF00075_consen    2 KAIIIYTDGSCRPNPGKGGAGYVVWGGRNFSFRLG-GQSNNRAELQAIIEALKAL-E--HRKVTIYTDSQYVLNALNKWL   77 (132)
T ss_dssp             TSEEEEEEEEECTTTTEEEEEEEEETTEEEEEEEE-SECHHHHHHHHHHHHHHTH-S--TSEEEEEES-HHHHHHHHTHH
T ss_pred             CcEEEEEeCCccCCCCceEEEEEEECCeEEEeccc-ccchhhhheehHHHHHHHh-h--cccccccccHHHHHHHHHHhc
Confidence            4789999999764  3356666543 334445566 7899999999999999944 3  4999999999999998777  


Q ss_pred             ---cCCCC----hhHHHHHHHHHHHhhcCCeEEEEeecCccCC-cCChHHHHHhcCC
Q psy18013        253 ---VKFSN----PLVTKVFSTWRYLKLCNKEVTFMWCPSHCGI-RGNEIVDDAAKNP  301 (563)
Q Consensus       253 ---~~~~s----~~~~~I~~~i~~L~~~~~~V~~~WVPgH~gi-~GNE~AD~lAK~A  301 (563)
                         .....    ++..+|++.+    ..+..|.|.|||||+|+ .|||.||+|||+|
T Consensus        78 ~~~~~~~~~~~~~i~~~i~~~~----~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a  130 (132)
T PF00075_consen   78 HGNGWKKTSNGRPIKNEIWELL----SRGIKVRFRWVPGHSGVPQGNERADRLAKEA  130 (132)
T ss_dssp             HHTTSBSCTSSSBHTHHHHHHH----HHSSEEEEEESSSSSSSHHHHHHHHHHHHHH
T ss_pred             cccccccccccccchhheeecc----ccceEEeeeeccCcCCCchhHHHHHHHHHHh
Confidence               33221    3445555533    55889999999999999 6999999999987

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

>PRK06548 ribonuclease H; Provisional

Probab=99.80  E-value=2.7e-19  Score=168.99  Aligned_cols=123  Identities=25%  Similarity=0.317  Sum_probs=95.1

Q ss_pred             CCcEEEEecCCCCCC--cceEEEEeCCe-eeeeecCCCCcchhHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHHHhc-
Q psy18013        177 ANHTICYTDGSKSPD--VTGCAFSIGDM-VRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALAN-  252 (563)
Q Consensus       177 ~~~i~IyTDGS~~~~--~vG~gvv~~~~-~~~~~L~~~~sv~~AEL~AI~~AL~~a~~~~~~~i~I~tDS~sal~aL~~-  252 (563)
                      +..+.||||||+..+  ..|+|+++... ..+... ...|++.|||.||+.||+.+.. ....|.|+|||+++++++.. 
T Consensus         3 ~~~~~IytDGa~~gnpg~~G~g~~~~~~~~~~g~~-~~~TNnraEl~Aii~aL~~~~~-~~~~v~I~TDS~yvi~~i~~W   80 (161)
T PRK06548          3 NNEIIAATDGSSLANPGPSGWAWYVDENTWDSGGW-DIATNNIAELTAVRELLIATRH-TDRPILILSDSKYVINSLTKW   80 (161)
T ss_pred             CCEEEEEEeeccCCCCCceEEEEEEeCCcEEccCC-CCCCHHHHHHHHHHHHHHhhhc-CCceEEEEeChHHHHHHHHHH
Confidence            356999999998864  47888776543 122122 3579999999999999986653 34579999999999999983 


Q ss_pred             --------cCCCC--hhH-HHHHHHHHHHhhcCCeEEEEeecCccCCcCChHHHHHhcCCC
Q psy18013        253 --------VKFSN--PLV-TKVFSTWRYLKLCNKEVTFMWCPSHCGIRGNEIVDDAAKNPN  302 (563)
Q Consensus       253 --------~~~~s--~~~-~~I~~~i~~L~~~~~~V~~~WVPgH~gi~GNE~AD~lAK~Aa  302 (563)
                              +...+  ++. +++++++..+..+ ..|+|.|||||+|++|||.||+||++|+
T Consensus        81 ~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~-~~v~~~wVkgHsg~~gNe~aD~LA~~aa  140 (161)
T PRK06548         81 VYSWKMRKWRKADGKPVLNQEIIQEIDSLMEN-RNIRMSWVNAHTGHPLNEAADSLARQAA  140 (161)
T ss_pred             HHHHHHCCCcccCCCccccHHHHHHHHHHHhc-CceEEEEEecCCCCHHHHHHHHHHHHHH
Confidence                    32222  343 6788888877765 4799999999999999999999999993

>PRK08719 ribonuclease H; Reviewed

Probab=99.80  E-value=3e-19  Score=166.72  Aligned_cols=119  Identities=23%  Similarity=0.255  Sum_probs=92.7

Q ss_pred             CcEEEEecCCCCCCc-----ceEEEEeC--C--e--eeeeecCCCCcchhHHHHHHHHHHHHHHcCCCCeEEEEeccHHH
Q psy18013        178 NHTICYTDGSKSPDV-----TGCAFSIG--D--M--VRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSA  246 (563)
Q Consensus       178 ~~i~IyTDGS~~~~~-----vG~gvv~~--~--~--~~~~~L~~~~sv~~AEL~AI~~AL~~a~~~~~~~i~I~tDS~sa  246 (563)
                      ..++||||||+.+++     .|+|+++.  +  .  ..+..+....|++.||+.|+..||+.+.+.    ..|+|||+++
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            568999999997643     48887642  2  1  234445556899999999999999998753    3799999999


Q ss_pred             HHHHh--------ccCCCC---hh-HHHHHHHHHHHhhcCCeEEEEeecCccCCcCChHHHHHhcCC
Q psy18013        247 LAALA--------NVKFSN---PL-VTKVFSTWRYLKLCNKEVTFMWCPSHCGIRGNEIVDDAAKNP  301 (563)
Q Consensus       247 l~aL~--------~~~~~s---~~-~~~I~~~i~~L~~~~~~V~~~WVPgH~gi~GNE~AD~lAK~A  301 (563)
                      ++.+.        +.+..+   ++ -.++++.+..|.. ...|+|.|||||+|++|||.||+||++|
T Consensus        79 i~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~-~~~i~~~~VkgH~g~~~Ne~aD~lA~~a  144 (147)
T PRK08719         79 VRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRA-RKYVEVEKVTAHSGIEGNEAADMLAQAA  144 (147)
T ss_pred             HHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhC-CCcEEEEEecCCCCChhHHHHHHHHHHH
Confidence            99983        443322   22 2577777777766 4679999999999999999999999998

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

Probab=99.77  E-value=3.8e-18  Score=159.11  Aligned_cols=123  Identities=21%  Similarity=0.212  Sum_probs=101.1

Q ss_pred             CcEEEEecCCCCCC--cceEEEEeC--Cee--eeeecCCCCcchhHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHHHh
Q psy18013        178 NHTICYTDGSKSPD--VTGCAFSIG--DMV--RSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALA  251 (563)
Q Consensus       178 ~~i~IyTDGS~~~~--~vG~gvv~~--~~~--~~~~L~~~~sv~~AEL~AI~~AL~~a~~~~~~~i~I~tDS~sal~aL~  251 (563)
                      ..+.||||||+..+  ..|+|++..  +..  .+..+. .+|++.||+.|++.||+++.+.+...|.|+|||+++++.|.
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            35899999998864  478886654  222  334444 78999999999999999999888999999999999999998


Q ss_pred             ccCC---C--------Ch-hHHHHHHHHHHHhhcCCeEEEEeecCccCCcCChHHHHHhcCC
Q psy18013        252 NVKF---S--------NP-LVTKVFSTWRYLKLCNKEVTFMWCPSHCGIRGNEIVDDAAKNP  301 (563)
Q Consensus       252 ~~~~---~--------s~-~~~~I~~~i~~L~~~~~~V~~~WVPgH~gi~GNE~AD~lAK~A  301 (563)
                      .+..   .        .| -..++++++.++..+...|.+.|||||.|.++||.||+||+.|
T Consensus        81 ~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~~  142 (154)
T COG0328          81 RWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAREA  142 (154)
T ss_pred             HHHhhccccCccccccCccccHHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHHH
Confidence            4311   1        12 2468888888888888899999999999999999999999999

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=99.76  E-value=2.3e-18  Score=161.18  Aligned_cols=122  Identities=19%  Similarity=0.220  Sum_probs=91.3

Q ss_pred             cEEEEecCCCCCC--cceEEEEeC--Cee--eeeecCCCCcchhHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHHHhc
Q psy18013        179 HTICYTDGSKSPD--VTGCAFSIG--DMV--RSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALAN  252 (563)
Q Consensus       179 ~i~IyTDGS~~~~--~vG~gvv~~--~~~--~~~~L~~~~sv~~AEL~AI~~AL~~a~~~~~~~i~I~tDS~sal~aL~~  252 (563)
                      .+.||||||+..+  ..|+|++..  +..  .+... ...|++.|||.|+..||+.+.+  ...+.|+|||+++++.|..
T Consensus         3 ~v~iytDGs~~~n~~~~g~g~v~~~~~~~~~~~~~~-~~~TN~~aEL~Ai~~AL~~~~~--~~~v~I~tDS~yvi~~i~~   79 (150)
T PRK00203          3 QVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGE-ALTTNNRMELMAAIEALEALKE--PCEVTLYTDSQYVRQGITE   79 (150)
T ss_pred             eEEEEEEecccCCCCceEEEEEEEECCeeEEEecCC-CCCcHHHHHHHHHHHHHHHcCC--CCeEEEEECHHHHHHHHHH
Confidence            4899999998854  478886653  222  22223 3578999999999999998865  4679999999999999985


Q ss_pred             c--------C-CC--Chh-HHHHHHHHHHHhhcCCeEEEEeecCccCCcCChHHHHHhcCCCccC
Q psy18013        253 V--------K-FS--NPL-VTKVFSTWRYLKLCNKEVTFMWCPSHCGIRGNEIVDDAAKNPNVSA  305 (563)
Q Consensus       253 ~--------~-~~--s~~-~~~I~~~i~~L~~~~~~V~~~WVPgH~gi~GNE~AD~lAK~Aa~~~  305 (563)
                      +        . ..  .++ -.++++.+..+... ..|.|.|||||+|++|||.||+|||+| ...
T Consensus        80 w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~~-~~v~~~wV~~H~~~~~N~~AD~lA~~a-~~~  142 (150)
T PRK00203         80 WIHGWKKNGWKTADKKPVKNVDLWQRLDAALKR-HQIKWHWVKGHAGHPENERCDELARAG-AEE  142 (150)
T ss_pred             HHHHHHHcCCcccCCCccccHHHHHHHHHHhcc-CceEEEEecCCCCCHHHHHHHHHHHHH-HHH
Confidence            2        1 11  122 24566666666543 789999999999999999999999999 543

>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=99.70  E-value=2.2e-16  Score=138.22  Aligned_cols=121  Identities=30%  Similarity=0.350  Sum_probs=96.7

Q ss_pred             EEEecCCCCCC--cceEEEEeCCe--e---eeeecCCCCcchhHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHHHhcc
Q psy18013        181 ICYTDGSKSPD--VTGCAFSIGDM--V---RSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALANV  253 (563)
Q Consensus       181 ~IyTDGS~~~~--~vG~gvv~~~~--~---~~~~L~~~~sv~~AEL~AI~~AL~~a~~~~~~~i~I~tDS~sal~aL~~~  253 (563)
                      .+|||||...+  ++|+|++..+.  .   .........+++.+|+.|+..||+.+......++.|++||+.++..+.+.
T Consensus         1 ~~~~Dgs~~~~~~~~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~~~~~~~i~i~~Ds~~~~~~~~~~   80 (130)
T cd06222           1 VIYTDGSCRGNPGPAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALELGGKKVNIYTDSQYVINALTGW   80 (130)
T ss_pred             CEEecccCCCCCCceEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHHhCCCceEEEEECHHHHHHHhhcc
Confidence            48999998865  68888776542  1   11122246899999999999999999988899999999999999999987


Q ss_pred             CC-CChhHHHHHHHHHHHhhcCCeEEEEeecCccCCcCChHHHHHhcCC
Q psy18013        254 KF-SNPLVTKVFSTWRYLKLCNKEVTFMWCPSHCGIRGNEIVDDAAKNP  301 (563)
Q Consensus       254 ~~-~s~~~~~I~~~i~~L~~~~~~V~~~WVPgH~gi~GNE~AD~lAK~A  301 (563)
                      .. .......++..+..+...+..+.|.|||+|+|+.+|+.||.|||+|
T Consensus        81 ~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~  129 (130)
T cd06222          81 YEGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKEA  129 (130)
T ss_pred             ccCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHhh
Confidence            65 2233445555555555678899999999999999999999999987

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=99.60  E-value=3.5e-15  Score=154.69  Aligned_cols=127  Identities=26%  Similarity=0.265  Sum_probs=101.1

Q ss_pred             cCCcEEEEecCCCCCC-----cceEEEEeCCe---eeeeecC-CCCcchhHHHHHHHHHHHHHHcCCCCeEEEEeccHHH
Q psy18013        176 YANHTICYTDGSKSPD-----VTGCAFSIGDM---VRSTLLN-PINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSA  246 (563)
Q Consensus       176 ~~~~i~IyTDGS~~~~-----~vG~gvv~~~~---~~~~~L~-~~~sv~~AEL~AI~~AL~~a~~~~~~~i~I~tDS~sa  246 (563)
                      .-+..++|||||...+     .+|+|+++++.   ..++.+. ..+++|.|||.||..||+.+.+.+..+++|.|||..+
T Consensus       209 ~~~~~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~~~~kv~I~TDS~~~  288 (371)
T KOG3752|consen  209 EIEIQVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSKNINKVVIRTDSEYF  288 (371)
T ss_pred             cccceEEEecCccccCCCCCCcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHhcCCCcEEEEechHHH
Confidence            4455999999998874     38999998753   5667764 7899999999999999999999888899999999999


Q ss_pred             HHHHhccCCC-----------Ch----h--HHHHHHHHHHHhh--cCCeEEEEeecCccCCcCChHHHHHhcCCC
Q psy18013        247 LAALANVKFS-----------NP----L--VTKVFSTWRYLKL--CNKEVTFMWCPSHCGIRGNEIVDDAAKNPN  302 (563)
Q Consensus       247 l~aL~~~~~~-----------s~----~--~~~I~~~i~~L~~--~~~~V~~~WVPgH~gi~GNE~AD~lAK~Aa  302 (563)
                      ++.|+.+-+.           ++    +  .+..+..+.+|.+  ++..|.+.|||||.|+.|||.||.+|++++
T Consensus       289 i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs  363 (371)
T KOG3752|consen  289 INSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEMADALARKGS  363 (371)
T ss_pred             HHHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHHHHHHHhhhh
Confidence            9998765321           12    1  1233344444443  368999999999999999999999999983

>PRK13907 rnhA ribonuclease H; Provisional

Probab=99.57  E-value=1.7e-14  Score=130.92  Aligned_cols=117  Identities=20%  Similarity=0.192  Sum_probs=94.7

Q ss_pred             EEEEecCCCCCC--cceEEEEeCCe----eeeeecCCCCcchhHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHHHhcc
Q psy18013        180 TICYTDGSKSPD--VTGCAFSIGDM----VRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALANV  253 (563)
Q Consensus       180 i~IyTDGS~~~~--~vG~gvv~~~~----~~~~~L~~~~sv~~AEL~AI~~AL~~a~~~~~~~i~I~tDS~sal~aL~~~  253 (563)
                      +.||||||...+  ..|+|+++.+.    ..++.. ...++..||+.|++.||+.+...+..++.|++||+.+++.+.+.
T Consensus         2 ~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~~~~-~~~tn~~AE~~All~aL~~a~~~g~~~v~i~sDS~~vi~~~~~~   80 (128)
T PRK13907          2 IEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLPL-GTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEKE   80 (128)
T ss_pred             EEEEEeeCCCCCCCccEEEEEEEECCeeEEEEecc-cccCCcHHHHHHHHHHHHHHHhCCCCEEEEEechHHHHHHHhHH
Confidence            679999998763  58999887542    122222 35789999999999999999998888999999999999999986


Q ss_pred             CCCChhHHHHHHHHHHHhhcCCeEEEEeecCccCCcCChHHHHHhcCC
Q psy18013        254 KFSNPLVTKVFSTWRYLKLCNKEVTFMWCPSHCGIRGNEIVDDAAKNP  301 (563)
Q Consensus       254 ~~~s~~~~~I~~~i~~L~~~~~~V~~~WVPgH~gi~GNE~AD~lAK~A  301 (563)
                      ...+.....+++.+..|..+...+.+.|||.    +.|+.||.+|+.|
T Consensus        81 ~~~~~~~~~l~~~~~~l~~~f~~~~~~~v~r----~~N~~Ad~LA~~a  124 (128)
T PRK13907         81 YAKNKMFAPLLEEALQYIKSFDLFFIKWIPS----SQNKVADELARKA  124 (128)
T ss_pred             HhcChhHHHHHHHHHHHHhcCCceEEEEcCc----hhchhHHHHHHHH
Confidence            6544445666776777777778888999997    5999999999988

>PRK07708 hypothetical protein; Validated

Probab=99.35  E-value=8.4e-12  Score=123.92  Aligned_cols=124  Identities=15%  Similarity=0.106  Sum_probs=93.2

Q ss_pred             cCCcEEEEecCCCCC--CcceEEEEeC--Ce--ee----eeecCCCCcchhHHHHHHHHHHHHHHcCCCC--eEEEEecc
Q psy18013        176 YANHTICYTDGSKSP--DVTGCAFSIG--DM--VR----STLLNPINSIFSAELIAIFLCLEAILENPSD--QFLIVSDS  243 (563)
Q Consensus       176 ~~~~i~IyTDGS~~~--~~vG~gvv~~--~~--~~----~~~L~~~~sv~~AEL~AI~~AL~~a~~~~~~--~i~I~tDS  243 (563)
                      .++.+.+|+|||...  ++.|+|+++.  +.  ..    ...++...+++.||+.|++.||+.+.+.+.+  .|.|++||
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            456899999999864  4588887653  21  11    1235556899999999999999999987654  48999999


Q ss_pred             HHHHHHHhccCC-CChhHHHHHHHHHHHhhc-CCeEEEEeecCccCCcCChHHHHHhcCCCcc
Q psy18013        244 RSALAALANVKF-SNPLVTKVFSTWRYLKLC-NKEVTFMWCPSHCGIRGNEIVDDAAKNPNVS  304 (563)
Q Consensus       244 ~sal~aL~~~~~-~s~~~~~I~~~i~~L~~~-~~~V~~~WVPgH~gi~GNE~AD~lAK~Aa~~  304 (563)
                      +.+++.+.+.+. .++..+.+.+.+..+.++ ...+.+.|||    .+.|+.||+||+.| .+
T Consensus       150 qlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~Vp----R~~N~~AD~LAk~A-l~  207 (219)
T PRK07708        150 QVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPIS----RKQNKEADQLATQA-LE  207 (219)
T ss_pred             HHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECC----chhhhHHHHHHHHH-Hh
Confidence            999999998764 345555555655544433 4468889998    46899999999999 55

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=99.26  E-value=3.7e-11  Score=128.29  Aligned_cols=118  Identities=19%  Similarity=0.205  Sum_probs=94.9

Q ss_pred             cEEEEecCCCCCC--cceEEEEeCCe-------eeeeecCCCCcchhHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHH
Q psy18013        179 HTICYTDGSKSPD--VTGCAFSIGDM-------VRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAA  249 (563)
Q Consensus       179 ~i~IyTDGS~~~~--~vG~gvv~~~~-------~~~~~L~~~~sv~~AEL~AI~~AL~~a~~~~~~~i~I~tDS~sal~a  249 (563)
                      .+.||||||...+  ..|+|+++.+.       ..+..++ ..+++.||+.|++.||+.+.+.....+.|++||+.+++.
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            4789999998865  47888776431       1122344 578889999999999999999888899999999999999


Q ss_pred             HhccCC-CChhHHHHHHHHHHHhhcCCeEEEEeecCccCCcCChHHHHHhcCC
Q psy18013        250 LANVKF-SNPLVTKVFSTWRYLKLCNKEVTFMWCPSHCGIRGNEIVDDAAKNP  301 (563)
Q Consensus       250 L~~~~~-~s~~~~~I~~~i~~L~~~~~~V~~~WVPgH~gi~GNE~AD~lAK~A  301 (563)
                      +.+... +++-...+.+.+..|.++...+.+.|||.    ++|+.||.||+.|
T Consensus        81 i~~~~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~r----~~N~~AD~LA~~a  129 (372)
T PRK07238         81 MSGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPR----ARNAHADRLANEA  129 (372)
T ss_pred             hCCCCccCChHHHHHHHHHHHHHhcCCceEEEECCc----hhhhHHHHHHHHH
Confidence            988654 44445556666777777778899999996    7899999999998

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

Probab=98.98  E-value=1.6e-09  Score=90.51  Aligned_cols=84  Identities=21%  Similarity=0.180  Sum_probs=67.8

Q ss_pred             chhHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHHHhccCCCChhHHHHHHHHHHHhhcCCeEEEEeecCccCCcCChH
Q psy18013        214 IFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALANVKFSNPLVTKVFSTWRYLKLCNKEVTFMWCPSHCGIRGNEI  293 (563)
Q Consensus       214 v~~AEL~AI~~AL~~a~~~~~~~i~I~tDS~sal~aL~~~~~~s~~~~~I~~~i~~L~~~~~~V~~~WVPgH~gi~GNE~  293 (563)
                      +..||+.|+..||+.+.+.+.++|.|.|||+.+++.|.+..........+...+..+.+....+.+.|||    .++|..
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            4579999999999999999999999999999999999988543224556666677788888999999999    589999


Q ss_pred             HHHHhcCC
Q psy18013        294 VDDAAKNP  301 (563)
Q Consensus       294 AD~lAK~A  301 (563)
                      ||.|||.|
T Consensus        77 A~~LA~~a   84 (87)
T PF13456_consen   77 ADALAKFA   84 (87)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99999987

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

Probab=82.06  E-value=0.73  Score=38.84  Aligned_cols=18  Identities=11%  Similarity=0.146  Sum_probs=15.9

Q ss_pred             CCCCCC-CCCcCceeccCC
Q psy18013        408 GTNCYT-DGSKSPDVTGCA  425 (563)
Q Consensus       408 C~~C~~-~~tv~Hil~~C~  425 (563)
                      |..|+. .||+.|++++||
T Consensus        62 C~~C~~~~Et~~Hlf~~C~   80 (86)
T PF13966_consen   62 CPLCGNEEETIEHLFFHCP   80 (86)
T ss_pred             cccCCCccccccceeccCc
Confidence            777775 799999999999

---

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	563
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-09
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	5e-08
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	2e-07
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	2e-04

>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 = 57.9 bits (139), Expect = 7e-09
 Identities = 67/377 (17%), Positives = 114/377 (30%), Gaps = 94/377 (24%)

Query: 18  PPIQEGIDAKD------SVLNK------LNAVHH-AGIRIATGALRSSP--VVSLYVDSG 62
               +  D KD      S+L+K      + +    +G       L S    +V  +V+  
Sbjct: 27  DAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEV 86

Query: 63  VPPLTLRRSKLMLNY---VAKISASPFNPAQKLLYHQDMSGIIFTVNKP-KPLYI-RFRE 117
                     L +NY   ++ I      P+     + +    ++  N+      + R + 
Sbjct: 87  ----------LRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQP 136

Query: 118 VANFNNVLESSEVAPYVRFVPPWSNCAPPVDQCLGEEKKSDVAPVVFQQKFSEAINTK-- 175
                  L     A  V            +D  LG  K      V    K    ++ K  
Sbjct: 137 YLKLRQALLELRPAKNV-----------LIDGVLGSGKTWVALDVCLSYKVQCKMDFKIF 185

Query: 176 YANHTICYTDGSKSPDVTGCAFSIGDMVRSTLLNPINSIFSAEL---IAIFLCLEAILEN 232
           + N   C      SP+      ++ +M+   LL  I+  +++       I L + +I   
Sbjct: 186 WLNLKNC-----NSPE------TVLEML-QKLLYQIDPNWTSRSDHSSNIKLRIHSIQAE 233

Query: 233 PSDQFLIVSDSRSALAALANVKFSNPLVTKVFS-------TWRYLKLCNKEVTFMWCPSH 285
                L      + L  L NV   N      F+       T R      K+VT     + 
Sbjct: 234 LRR-LLKSKPYENCLLVLLNV--QNAKAWNAFNLSCKILLTTR-----FKQVTDFLSAAT 285

Query: 286 CGIRGNEIVDDAAKNPNVSAPLKL------CTPEDLK-------PFIASII---QSEWQI 329
                +  +D  +          L      C P+DL        P   SII     +   
Sbjct: 286 ---TTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLA 342

Query: 330 QWNNVP--NTNKLKSIR 344
            W+N    N +KL +I 
Sbjct: 343 TWDNWKHVNCDKLTTII 359

>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 = 51.2 bits (123), Expect = 5e-08
 Identities = 20/129 (15%), Positives = 34/129 (26%), Gaps = 18/129 (13%)

Query: 183 YTDGSKSPDVTGCAFSI-----------GDMVRSTLLNPINSIFSAELIAIFLCLEAILE 231
           YTDGS        A++                            + E+ A    ++   +
Sbjct: 10  YTDGSYVNGQYAWAYAFVKDGKVHYEDADVGKNPA--AATMRNVAGEIAAALYAVKKASQ 67

Query: 232 NPSDQFLIVSDSRSALAALANV-KFSNPLVTKVFSTWRYLKLCNKEVTFMWCPSHCGIRG 290
               +  I+ D            K  N          + +       +F    +H G   
Sbjct: 68  LGV-KIRILHDYAGIAFWATGEWKAKNEFTQAY---AKLMNQYRGIYSFEKVKAHSGNEF 123

Query: 291 NEIVDDAAK 299
           N+ VD  AK
Sbjct: 124 NDYVDMKAK 132

>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 = 50.2 bits (120), Expect = 2e-07
 Identities = 35/136 (25%), Positives = 52/136 (38%), Gaps = 19/136 (13%)

Query: 177 ANHTICYTDGSKS----PDVTGCAFSIGDMVR-STLLNPINSIFSAELIAIFLCLEAILE 231
           A++T  YTDGS          G A +    V  +  L    S   AELIA+    +A+  
Sbjct: 22  ADYTW-YTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIAL---TQALKM 77

Query: 232 NPSDQFLIVSDSRSALAALANVKFSNPLVTKVFSTWRYL--KLCNKE-VTFMWCPSHCG- 287
               +  + +DSR A A             K  +    L   L   + ++ + CP H   
Sbjct: 78  AEGKKLNVYTDSRYAFATAHVHSEGRE--IKNKNEILALLKALFLPKRLSIIHCPGHQKG 135

Query: 288 ----IRGNEIVDDAAK 299
                RGN + D AA+
Sbjct: 136 NSAEARGNRMADQAAR 151

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

 Score = 43.2 bits (102), Expect = 2e-04
 Identities = 28/82 (34%), Positives = 42/82 (51%), Gaps = 12/82 (14%)

Query: 217 AELIAIFLCLEAILENPSDQFLIVSDSRSALAALAN--VKFSNPLVTKVFSTWRYLKLCN 274
            EL AI+L L+    +   +  IV+DS+ AL  +     K  + LV ++       +L  
Sbjct: 479 TELQAIYLALQ----DSGLEVNIVTDSQYALGIIQAQPDKSESELVNQIIE-----QLIK 529

Query: 275 KEVTFM-WCPSHCGIRGNEIVD 295
           KE  ++ W P+H GI GNE VD
Sbjct: 530 KEKVYLAWVPAHKGIGGNEQVD 551

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	563
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.84
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.82
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	99.81
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.81
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	99.78
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	99.78
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.77
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.75
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	99.71
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	99.7
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	99.7
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	99.66
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	99.66
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	99.64
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	99.03
4htu_A	134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	98.67

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

Probab=99.84  E-value=5.5e-21  Score=177.79  Aligned_cols=127  Identities=20%  Similarity=0.262  Sum_probs=100.3

Q ss_pred             cCCcEEEEecCCCCCCc-----ceEEEEeCCe---eeeeecCCCCcchhHHHHHHHHHHHHHHcCCCCeEEEEeccHHHH
Q psy18013        176 YANHTICYTDGSKSPDV-----TGCAFSIGDM---VRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSAL  247 (563)
Q Consensus       176 ~~~~i~IyTDGS~~~~~-----vG~gvv~~~~---~~~~~L~~~~sv~~AEL~AI~~AL~~a~~~~~~~i~I~tDS~sal  247 (563)
                      ..+.+.||||||+..++     .|+|+++.+.   ..+..+...++++.||+.|+..||+.+.+.+..+|.|+|||++++
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            45789999999987542     7899887542   244556557899999999999999999987789999999999999


Q ss_pred             HHHhccC---------CCC--hh-HHHHHHHHHHHhhcCCeEEEEeecCccCCcCChHHHHHhcCCCcc
Q psy18013        248 AALANVK---------FSN--PL-VTKVFSTWRYLKLCNKEVTFMWCPSHCGIRGNEIVDDAAKNPNVS  304 (563)
Q Consensus       248 ~aL~~~~---------~~s--~~-~~~I~~~i~~L~~~~~~V~~~WVPgH~gi~GNE~AD~lAK~Aa~~  304 (563)
                      +.|..+.         ..+  +. ...+++.+..+.. +..|.|.|||||+|++|||.||+|||+| +.
T Consensus        84 ~~i~~~~~~w~~~~w~~~~~~~~~n~~l~~~i~~l~~-~~~v~~~~V~~H~g~~~N~~AD~LA~~a-~~  150 (154)
T 2qkb_A           84 NGITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQ-GMDIQWMHVPGHSGFIGNEEADRLAREG-AK  150 (154)
T ss_dssp             HHHHTHHHHHHTTTSBCTTSSBCTTHHHHHHHHHHHT-TCEEEEEECCTTSSCHHHHHHHHHHHHH-HT
T ss_pred             hhhhhhHHHHHhccccccCCCccccHHHHHHHHHHHc-CCceEEEEccCCCCCHhHHHHHHHHHHH-HH
Confidence            9998731         111  11 2455666666555 4679999999999999999999999999 44

>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=99.82  E-value=2.5e-20  Score=173.18  Aligned_cols=123  Identities=23%  Similarity=0.302  Sum_probs=93.1

Q ss_pred             ccCCcEEEEecCCCCCC--cceEEEEeCCe-eeeeecCCCCcchhHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHHHh
Q psy18013        175 KYANHTICYTDGSKSPD--VTGCAFSIGDM-VRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALA  251 (563)
Q Consensus       175 ~~~~~i~IyTDGS~~~~--~vG~gvv~~~~-~~~~~L~~~~sv~~AEL~AI~~AL~~a~~~~~~~i~I~tDS~sal~aL~  251 (563)
                      +.++.+.||||||+..+  ..|+|++..+. .....+ ..++++.||+.|+..||+.+    ..++.|+|||+++++.|.
T Consensus         8 P~~~~~~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~-~~~Tnn~aEl~A~i~AL~~~----~~~v~i~tDS~~v~~~i~   82 (150)
T 3qio_A            8 PIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTL-TDTTNQKTELQAIYLALQDS----GLEVNIVTDSQYALGIIT   82 (150)
T ss_dssp             CCTTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEEE-SSCCHHHHHHHHHHHHHHHS----CSEEEEEESCHHHHHHHH
T ss_pred             CCCCCEEEEEccCCCCCCCCeEEEEEEEcCCEEEEeC-CCCCHHHHHHHHHHHHHHhC----CCcEEEEeCcHHHHHHHH
Confidence            35678999999998764  37888776542 223334 36899999999999999985    489999999999999998


Q ss_pred             ccC-----------CCChh-HHHHHHHHHHHhhcCCeEEEEeecCccCCcCChHHHHHhcCCC
Q psy18013        252 NVK-----------FSNPL-VTKVFSTWRYLKLCNKEVTFMWCPSHCGIRGNEIVDDAAKNPN  302 (563)
Q Consensus       252 ~~~-----------~~s~~-~~~I~~~i~~L~~~~~~V~~~WVPgH~gi~GNE~AD~lAK~Aa  302 (563)
                      .+.           ...++ -+++++.+..+..++..|.|.|||||+|++|||.||+||++|+
T Consensus        83 ~w~~~W~~~gw~~~~g~~v~n~~l~~~l~~~l~~~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~  145 (150)
T 3qio_A           83 QWIHNWKKRGWKTADKKPVKNVDLVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGI  145 (150)
T ss_dssp             HHHHHHCC------------CHHHHHHHHHHHTTCSEEEEEECCTTSCCHHHHHHHHHHHTTT
T ss_pred             HHHHHHhhcCcCcCcCcccccHHHHHHHHHHHhhcCceEEEEccCcCCChhHHHHHHHHHHHH
Confidence            751           11111 1345554444444678999999999999999999999999993

>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=99.81  E-value=1.6e-21  Score=180.44  Aligned_cols=126  Identities=14%  Similarity=0.055  Sum_probs=97.2

Q ss_pred             cCCcEEEEecCCCCCCcceEEEEeC--Ce--eeee-ec--CC--CCcchhHHHHHHHHHHHHHHcCCCCeEEEEeccHHH
Q psy18013        176 YANHTICYTDGSKSPDVTGCAFSIG--DM--VRST-LL--NP--INSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSA  246 (563)
Q Consensus       176 ~~~~i~IyTDGS~~~~~vG~gvv~~--~~--~~~~-~L--~~--~~sv~~AEL~AI~~AL~~a~~~~~~~i~I~tDS~sa  246 (563)
                      +++.+.||||||+..+..|+|+++.  +.  ..+. ..  +.  .++++.||+.|+..||+.+.+.+. +|.|+|||+.+
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            4578999999999987799997763  22  2233 22  22  368999999999999999877656 99999999988


Q ss_pred             HHHHhccCCCC-hhHHHHHHHHHHHhhcCCeEEEEeecCccCCcCChHHHHHhcCCCccCC
Q psy18013        247 LAALANVKFSN-PLVTKVFSTWRYLKLCNKEVTFMWCPSHCGIRGNEIVDDAAKNPNVSAP  306 (563)
Q Consensus       247 l~aL~~~~~~s-~~~~~I~~~i~~L~~~~~~V~~~WVPgH~gi~GNE~AD~lAK~Aa~~~p  306 (563)
                      ...+.+.+..+ +....+.+.++.|..   .|.|.|||||+|++|||.||+|||+| +..+
T Consensus        82 ~~w~~~~w~~~~~~~~~~~~l~~~l~~---~v~~~wV~gH~g~~~Ne~AD~LA~~a-~~~~  138 (147)
T 2kq2_A           82 AFWATGEWKAKNEFTQAYAKLMNQYRG---IYSFEKVKAHSGNEFNDYVDMKAKSA-LGIR  138 (147)
T ss_dssp             HHHTTSSSSCCHHHHHHHHCGGGGGST---TCCBCCCCCCCCCHHHHHHHHHHHHH-HTCC
T ss_pred             HHHHhCCCccCCcchHHHHHHHHHhcC---CeeEEEecCcCCCcchHHHHHHHHHH-Hhcc
Confidence            88777755443 344555555555543   79999999999999999999999999 5543

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

Probab=99.81  E-value=1.2e-20  Score=173.77  Aligned_cols=121  Identities=22%  Similarity=0.142  Sum_probs=90.3

Q ss_pred             CcEEEEecCCCCCC--cceEEEEeCC--e--eeeeecCCCCcchhHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHHHh
Q psy18013        178 NHTICYTDGSKSPD--VTGCAFSIGD--M--VRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALA  251 (563)
Q Consensus       178 ~~i~IyTDGS~~~~--~vG~gvv~~~--~--~~~~~L~~~~sv~~AEL~AI~~AL~~a~~~~~~~i~I~tDS~sal~aL~  251 (563)
                      ..+.||||||+..+  ..|+|+++..  .  ..+..++ .++++.||+.|++.||+.+.+  ..+|.|+|||+++++.|.
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 KTITIYTDGAASGNPGKGGWGALLMYGSSRKEISGYDP-ATTNNRMELMAAIKGLEALKE--PARVQLYSDSAYLVNAMN   79 (146)
T ss_dssp             CEEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEEE-EECHHHHHHHHHHHHHHTCSS--CCEEEEEESCHHHHHHHH
T ss_pred             ceEEEEEecCCCCCCCceEEEEEEEECCeeEEeecCCC-CCcHHHHHHHHHHHHHHhcCc--cCcEEEEeChHHHHHHHH
Confidence            46899999998765  3788877542  2  2223333 578999999999999999976  589999999999999998


Q ss_pred             ccC------------CCCh-hHHHHHHHHHHHhhcCCeEEEEeecCccCCcCChHHHHHhcCCC
Q psy18013        252 NVK------------FSNP-LVTKVFSTWRYLKLCNKEVTFMWCPSHCGIRGNEIVDDAAKNPN  302 (563)
Q Consensus       252 ~~~------------~~s~-~~~~I~~~i~~L~~~~~~V~~~WVPgH~gi~GNE~AD~lAK~Aa  302 (563)
                      ..+            ...+ .-+.+++.+..+... ..|.|.|||||+|++|||.||+|||+|+
T Consensus        80 ~~w~~~W~~~~w~~~~~~~v~n~~l~~~~~~~~~~-~~v~~~~V~gH~g~~~N~~AD~LA~~a~  142 (146)
T 3h08_A           80 EGWLKRWVKNGWKTAAKKPVENIDLWQEILKLTTL-HRVTFHKVKGHSDNPYNSRADELARLAI  142 (146)
T ss_dssp             SSHHHHHHHTTCC----CCCTTHHHHHHHHHHHHH-SEEEEEECCC-CCSHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCccCCCCCcCCHHHHHHHHHHHhh-CceEEEEcCCcCCcHhHHHHHHHHHHHH
Confidence            721            0111 124455555555443 4799999999999999999999999993

>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=99.78  E-value=1.6e-19  Score=168.25  Aligned_cols=124  Identities=19%  Similarity=0.257  Sum_probs=93.8

Q ss_pred             CcEEEEecCCCCCC--cceEEEEeC--Ce--eeeeecCCCCcchhHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHHHh
Q psy18013        178 NHTICYTDGSKSPD--VTGCAFSIG--DM--VRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALA  251 (563)
Q Consensus       178 ~~i~IyTDGS~~~~--~vG~gvv~~--~~--~~~~~L~~~~sv~~AEL~AI~~AL~~a~~~~~~~i~I~tDS~sal~aL~  251 (563)
                      ..+.||||||+..+  ..|+|+++.  +.  ..+..+ ...+++.||+.|+..||+.+.+  ..++.|+|||+++++.|.
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            35899999999864  378887764  22  222233 3578999999999999999876  379999999999999998


Q ss_pred             cc--------C-CC--Chh-HHHHHHHHHHHhhcCCeEEEEeecCccCCcCChHHHHHhcCCCccCC
Q psy18013        252 NV--------K-FS--NPL-VTKVFSTWRYLKLCNKEVTFMWCPSHCGIRGNEIVDDAAKNPNVSAP  306 (563)
Q Consensus       252 ~~--------~-~~--s~~-~~~I~~~i~~L~~~~~~V~~~WVPgH~gi~GNE~AD~lAK~Aa~~~p  306 (563)
                      .+        . ..  .++ -..+++.+..+.+ ...|.|.|||||+|++|||.||+|||+| +..|
T Consensus        80 ~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~-~~~v~~~wV~gH~g~~~Ne~AD~LA~~a-~~~~  144 (155)
T 1jl1_A           80 QWIHNWKKRGWKTADKKPVKNVDLWQRLDAALG-QHQIKWEWVKGHAGHPENERADELARAA-AMNP  144 (155)
T ss_dssp             TTHHHHHHTTTBCTTSCBCTTHHHHHHHHHHTT-TCEEEEEECCSSTTCHHHHHHHHHHHHH-HHSC
T ss_pred             HHHHHHhhcccccccCCccCCHHHHHHHHHHHc-cCceEEEEcCCCCCCHHHHHHHHHHHHH-Hhcc
Confidence            72        1 11  122 1455665666655 3689999999999999999999999999 5543

>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=99.78  E-value=3.5e-19  Score=168.04  Aligned_cols=121  Identities=25%  Similarity=0.287  Sum_probs=89.2

Q ss_pred             CcEEEEecCCCCC--CcceEEEEeC--Cee-eeeecCCCCcchhHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHHHhc
Q psy18013        178 NHTICYTDGSKSP--DVTGCAFSIG--DMV-RSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALAN  252 (563)
Q Consensus       178 ~~i~IyTDGS~~~--~~vG~gvv~~--~~~-~~~~L~~~~sv~~AEL~AI~~AL~~a~~~~~~~i~I~tDS~sal~aL~~  252 (563)
                      ..+.||||||+..  +..|+|+++.  +.. ....+...++++.||+.|+..||+.+   ...++.|+|||+++++.+-.
T Consensus        22 ~~i~iytDGs~~~npG~~g~G~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~---~~~~v~I~tDS~~vi~~iw~   98 (165)
T 3p1g_A           22 ADYTWYTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMA---EGKKLNVYTDSRYAFATAHV   98 (165)
T ss_dssp             CSEEEEEEEEEEEETTEEEEEEEEECSSCEEEEEEECTTCCHHHHHHHHHHHHHHHT---BTSEEEEEECCHHHHHHHHS
T ss_pred             CCEEEEEEcccCCCCCceEEEEEEEECCEEEEEecCCCCCcHHHHHHHHHHHHHHHc---cCceEEEEEchHHHHhhhhc
Confidence            3699999999974  4477776542  222 22245567899999999999999998   36899999999999999832


Q ss_pred             cCCCChh-HHHHHHHH-HHHhhcCCeEEEEeecCccC-----CcCChHHHHHhcCCC
Q psy18013        253 VKFSNPL-VTKVFSTW-RYLKLCNKEVTFMWCPSHCG-----IRGNEIVDDAAKNPN  302 (563)
Q Consensus       253 ~~~~s~~-~~~I~~~i-~~L~~~~~~V~~~WVPgH~g-----i~GNE~AD~lAK~Aa  302 (563)
                      .....++ -.+++..+ ..+. .+..|.|.|||||+|     ++|||.||+|||+|+
T Consensus        99 ~~~g~~v~n~dl~~~l~~~l~-~~~~v~~~wVkgH~g~~~~~~~gNe~AD~LA~~aa  154 (165)
T 3p1g_A           99 HSEGREIKNKNEILALLKALF-LPKRLSIIHCPGHQKGNSAEARGNRMADQAAREAA  154 (165)
T ss_dssp             CCCSCCCSSHHHHHHHHHHTT-SBSEEEEEECCSSCCSCSHHHHHHHHHHHHHHHHH
T ss_pred             ccCCCcccCHHHHHHHHHHHh-cCCceEEEEecCCCCCCcCcchHHHHHHHHHHHHH
Confidence            2222222 13333333 2333 578999999999999     999999999999993

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

Probab=99.77  E-value=3.2e-19  Score=166.86  Aligned_cols=123  Identities=21%  Similarity=0.286  Sum_probs=92.8

Q ss_pred             CcEEEEecCCCCCC--cceEEEEeC--Ce--eeeeecCCCCcchhHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHHHh
Q psy18013        178 NHTICYTDGSKSPD--VTGCAFSIG--DM--VRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALA  251 (563)
Q Consensus       178 ~~i~IyTDGS~~~~--~vG~gvv~~--~~--~~~~~L~~~~sv~~AEL~AI~~AL~~a~~~~~~~i~I~tDS~sal~aL~  251 (563)
                      ..+.||||||+..+  ..|+|+++.  +.  ..+..++ .++++.||+.|+..||+.+.+  ..+|.|+|||+++++.|.
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 KLIHIFTDGSCLGNPGPGGYGIVMNYKGHTKEMSDGFS-LTTNNRMELLAPIVALEALKE--PCKIILTSDSQYMRQGIM   81 (158)
T ss_dssp             CEEEEEEEEEESSSSEEEEEEEEEEETTEEEEEEEEEE-EECHHHHHHHHHHHHHHTCSS--CCEEEEEECCHHHHHHHH
T ss_pred             CeEEEEEcccccCCCCcEEEEEEEEECCEEEEEecCcC-CCccHHHHHHHHHHHHHHhcc--CCeEEEEeCHHHHHHHHH
Confidence            46899999999854  378887763  22  1222333 478999999999999999865  389999999999999998


Q ss_pred             c--------cCC-C--Chh-HHHHHHHHHHHhhcCCeEEEEeecCccCCcCChHHHHHhcCCCccC
Q psy18013        252 N--------VKF-S--NPL-VTKVFSTWRYLKLCNKEVTFMWCPSHCGIRGNEIVDDAAKNPNVSA  305 (563)
Q Consensus       252 ~--------~~~-~--s~~-~~~I~~~i~~L~~~~~~V~~~WVPgH~gi~GNE~AD~lAK~Aa~~~  305 (563)
                      .        ... .  .++ -..+++.+..+.+. ..|.|.|||||+|++|||.||+|||+| +..
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 TWIHGWKKKGWMTSNRTPVKNVDLWKRLDKAAQL-HQIDWRWVKGHAGHAENERCDQLARAA-AEA  145 (158)
T ss_dssp             THHHHHHHTTTBCTTSSBCTTHHHHHHHHHHHTT-SEEEEEECCTTCCCHHHHHHHHHHHHH-HHS
T ss_pred             HHHHHHHHccccccCCCcccCHHHHHHHHHHHcc-CcEEEEEccCCCCchhHHHHHHHHHHH-HHh
Confidence            8        221 1  111 23555555555543 689999999999999999999999999 543

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

Probab=99.75  E-value=4.6e-19  Score=167.19  Aligned_cols=122  Identities=20%  Similarity=0.174  Sum_probs=92.6

Q ss_pred             CcEEEEecCCCCCC--cceEEEEeCC--e--eeeeecCCCCcchhHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHHHh
Q psy18013        178 NHTICYTDGSKSPD--VTGCAFSIGD--M--VRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALA  251 (563)
Q Consensus       178 ~~i~IyTDGS~~~~--~vG~gvv~~~--~--~~~~~L~~~~sv~~AEL~AI~~AL~~a~~~~~~~i~I~tDS~sal~aL~  251 (563)
                      ..+.||||||+..+  ..|+|+++..  .  ..+... ...+++.||+.|++.||+.+.+.  .+|.|+|||+++++.|.
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            56899999999864  3788987642  1  122222 35789999999999999988653  58999999999999998


Q ss_pred             c----------cCCCC--hh-HHHHHHHHHHHhhcCCeEEEEeecCccCCcCChHHHHHhcCCCcc
Q psy18013        252 N----------VKFSN--PL-VTKVFSTWRYLKLCNKEVTFMWCPSHCGIRGNEIVDDAAKNPNVS  304 (563)
Q Consensus       252 ~----------~~~~s--~~-~~~I~~~i~~L~~~~~~V~~~WVPgH~gi~GNE~AD~lAK~Aa~~  304 (563)
                      .          +...+  ++ -..+++.+..+... ..|.|.|||||+|++|||.||+|||+| +.
T Consensus        84 ~~w~~~W~~~~w~~~~g~~v~n~~l~~~i~~l~~~-~~v~~~wV~gH~g~~~Ne~AD~LAk~a-~~  147 (166)
T 1ril_A           84 EGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAP-HRVRFHFVKGHTGHPENERVDREARRQ-AQ  147 (166)
T ss_dssp             SSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHTT-SEEECCCCCGGGSCTHHHHHHHHHHHH-HT
T ss_pred             hhHHHHHHhcccccccCCccCcHHHHHHHHHHHhc-CeEEEEEeeCCCCchhHHHHHHHHHHH-HH
Confidence            8          22111  12 23556656566553 589999999999999999999999999 44

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

Probab=99.71  E-value=8.4e-18  Score=158.57  Aligned_cols=125  Identities=18%  Similarity=0.181  Sum_probs=89.8

Q ss_pred             CCcEEEEecCCCCCC--c-----ceEEEEeC--Ce----eeeeec-CCCCcchhHHHHHHHHHHHHHHcCCCCeEEEEec
Q psy18013        177 ANHTICYTDGSKSPD--V-----TGCAFSIG--DM----VRSTLL-NPINSIFSAELIAIFLCLEAILENPSDQFLIVSD  242 (563)
Q Consensus       177 ~~~i~IyTDGS~~~~--~-----vG~gvv~~--~~----~~~~~L-~~~~sv~~AEL~AI~~AL~~a~~~~~~~i~I~tD  242 (563)
                      ...++||||||+..+  .     .|+|+++.  +.    ...+.. ....+.+.||+.|+..||+.++..+ .+|.|+||
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            356899999998754  2     78998753  11    222332 2456778899999999998877643 57999999


Q ss_pred             cHHHHHHHhccC---------C--CChh-HHHHHHHHHHHhhcCCeEEEEeecCccCC------cCChHHHHHhcCCC
Q psy18013        243 SRSALAALANVK---------F--SNPL-VTKVFSTWRYLKLCNKEVTFMWCPSHCGI------RGNEIVDDAAKNPN  302 (563)
Q Consensus       243 S~sal~aL~~~~---------~--~s~~-~~~I~~~i~~L~~~~~~V~~~WVPgH~gi------~GNE~AD~lAK~Aa  302 (563)
                      |+++++.+..+.         .  ..++ -.++++.+..+......|.|.|||||+|+      +|||.||+||++||
T Consensus        84 S~Yvi~~it~w~~~Wk~ngw~~~~~~pVkN~dL~~~l~~~~~~~~~v~~~~VkgH~g~~~~~~~~gNe~AD~LA~~gA  161 (165)
T 2lsn_A           84 SFYVAESANKELPYWKSNGFVNNKKKPLKHISKWKSIAECLSMKPDITIQHEKGHQPTNTSIHTEGNALADKLATQGS  161 (165)
T ss_dssp             CHHHHHHHHTHHHHHHHTTSCSCSSSCCSSHHHHHHHHHHHHHCTTCEEEECCSSSCSSSCHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHhhhhhhhhhheeccccccCCCcccCHHHHHHHHHHHhCCCCEEEEEEeCCCCccCCCCChHHHHHHHHHHHhh
Confidence            999999997521         1  1122 24555555555555568999999999995      58999999999984

>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=99.70  E-value=2.4e-17  Score=149.65  Aligned_cols=118  Identities=14%  Similarity=0.198  Sum_probs=96.4

Q ss_pred             cEEEEecCCCCCC--cceEEEEeCCe-------eeeeecCCCCcchhHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHH
Q psy18013        179 HTICYTDGSKSPD--VTGCAFSIGDM-------VRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAA  249 (563)
Q Consensus       179 ~i~IyTDGS~~~~--~vG~gvv~~~~-------~~~~~L~~~~sv~~AEL~AI~~AL~~a~~~~~~~i~I~tDS~sal~a  249 (563)
                      .+.||||||...+  ..|+|+++.+.       ..+..++ .++++.||+.|++.||+.+.+.+..++.|+|||+++++.
T Consensus         3 ~~~iy~DGs~~~~~g~~g~G~v~~~~~~~~~~~~~~~~~~-~~tn~~aEl~A~~~aL~~a~~~~~~~v~i~tDS~~vv~~   81 (141)
T 3hst_B            3 KVVIEADGGSRGNPGPAGYGAVVWTADHSTVLAESKQAIG-RATNNVAEYRGLIAGLDDAVKLGATEAAVLMDSKLVVEQ   81 (141)
T ss_dssp             EEEEEEEEEESSSSEEEEEEEEEEETTSCSEEEEEEEEEE-EECHHHHHHHHHHHHHHHHHHHTCSEEEEEESCHHHHHH
T ss_pred             EEEEEEecCCCCCCCCcEEEEEEEeCCCCcEEEeeeccCC-CCchHHHHHHHHHHHHHHHHHCCCceEEEEeChHHHHHH
Confidence            5899999998864  47888776321       1222333 678999999999999999998778899999999999999


Q ss_pred             HhccCC-CChhHHHHHHHHHHHhhcCCeEEEEeecCccCCcCChHHHHHhcCC
Q psy18013        250 LANVKF-SNPLVTKVFSTWRYLKLCNKEVTFMWCPSHCGIRGNEIVDDAAKNP  301 (563)
Q Consensus       250 L~~~~~-~s~~~~~I~~~i~~L~~~~~~V~~~WVPgH~gi~GNE~AD~lAK~A  301 (563)
                      +.+.+. .++....+++.+..|..+...|.|.|||+    ++||.||+|||+|
T Consensus        82 i~~~~~~~~~~l~~~~~~i~~l~~~~~~v~~~~V~~----~~N~~AD~LA~~a  130 (141)
T 3hst_B           82 MSGRWKVKHPDLLKLYVQAQALASQFRRINYEWVPR----ARNTYADRLANDA  130 (141)
T ss_dssp             HTTSSCCCSHHHHHHHHHHHHHHTTSSEEEEEECCG----GGCHHHHHHHHHH
T ss_pred             HhCCcccCCHHHHHHHHHHHHHHhcCCeEEEEEcCC----cccHHHHHHHHHH
Confidence            998653 45556667777778877789999999995    8999999999998

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

Probab=99.70  E-value=2.7e-17  Score=148.61  Aligned_cols=119  Identities=20%  Similarity=0.235  Sum_probs=93.8

Q ss_pred             CcEEEEecCCCCCC--cceEEEEeCC----e--eeeeecCCCCcchhHHHHHHHHHHHHHHcCCCC----eEEEEeccHH
Q psy18013        178 NHTICYTDGSKSPD--VTGCAFSIGD----M--VRSTLLNPINSIFSAELIAIFLCLEAILENPSD----QFLIVSDSRS  245 (563)
Q Consensus       178 ~~i~IyTDGS~~~~--~vG~gvv~~~----~--~~~~~L~~~~sv~~AEL~AI~~AL~~a~~~~~~----~i~I~tDS~s  245 (563)
                      ..+.||||||...+  ..|+|+++.+    .  ..+..++ .++++.||+.|+..||+.+.+.+..    ++.|+|||++
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 NKIIIYTDGGARGNPGPAGIGVVITDEKGNTLHESSAYIG-ETTNNVAEYEALIRALEDLQMFGDKLVDMEVEVRMDSEL   80 (140)
T ss_dssp             CEEEEEEEEEESSTTEEEEEEEEEECTTSCEEEEEEEEEE-EECHHHHHHHHHHHHHHHHGGGGGGGTTCEEEEEESCHH
T ss_pred             ceEEEEEecCCCCCCCCcEEEEEEEeCCCCEEEEEEeeCC-CCchHHHHHHHHHHHHHHHHHcCCCCCCceEEEEeChHH
Confidence            35899999998764  4888877643    1  1222333 4789999999999999999886666    9999999999


Q ss_pred             HHHHHhccCC-CChhHHHHHHHHHHH-hhcCCeEEEEeecCccCCcCChHHHHHhcCC
Q psy18013        246 ALAALANVKF-SNPLVTKVFSTWRYL-KLCNKEVTFMWCPSHCGIRGNEIVDDAAKNP  301 (563)
Q Consensus       246 al~aL~~~~~-~s~~~~~I~~~i~~L-~~~~~~V~~~WVPgH~gi~GNE~AD~lAK~A  301 (563)
                      +++.+.+.+. .+.-...+++.+..+ .++...|.|.|||+    ++||.||+|||+|
T Consensus        81 vi~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~~v~~~~V~~----~~N~~AD~LA~~a  134 (140)
T 3u3g_D           81 IVRQMQGVYKVKEPTLKEKFAKIAHIKMERVPNLVFVHIPR----EKNARADELVNEA  134 (140)
T ss_dssp             HHHHHTTSSCCCCGGGHHHHHHHHHHHHHHCTTCEEEECCG----GGGHHHHHHHHHH
T ss_pred             HHHHhCCCcccCCHHHHHHHHHHHHHhhcCCCcEEEEEcCc----hhhHHHHHHHHHH
Confidence            9999998764 444445566666666 66667899999994    8999999999998

>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=99.66  E-value=9.6e-17  Score=178.02  Aligned_cols=116  Identities=26%  Similarity=0.370  Sum_probs=88.6

Q ss_pred             CCcEEEEecCCCCCC--cceEEEEeCCe-eeeeecCCCCcchhHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHHHhcc
Q psy18013        177 ANHTICYTDGSKSPD--VTGCAFSIGDM-VRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALANV  253 (563)
Q Consensus       177 ~~~i~IyTDGS~~~~--~vG~gvv~~~~-~~~~~L~~~~sv~~AEL~AI~~AL~~a~~~~~~~i~I~tDS~sal~aL~~~  253 (563)
                      .+.+.||||||+..+  ..|+|++..+. ...... ..+|++.||+.|++.||+.+    ..++.|+|||++|++.+..+
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            456999999998754  36788776532 222333 35799999999999999998    57999999999999999987


Q ss_pred             CCC--ChhHHHHHHHHHHHhhcCCeEEEEeecCccCCcCChHHHHHhcCC
Q psy18013        254 KFS--NPLVTKVFSTWRYLKLCNKEVTFMWCPSHCGIRGNEIVDDAAKNP  301 (563)
Q Consensus       254 ~~~--s~~~~~I~~~i~~L~~~~~~V~~~WVPgH~gi~GNE~AD~lAK~A  301 (563)
                      ...  .++.+++.+   .+.+ ...|.|.|||||+|++|||.||+|||+|
T Consensus       512 ~~~~~~~l~~~~~~---~l~~-~~~v~~~wV~~H~g~~~Ne~AD~LA~~a  557 (557)
T 2zd1_A          512 PDKSESELVNQIIE---QLIK-KEKVYLAWVPAHKGIGGNEQVDKLVSAG  557 (557)
T ss_dssp             CSEESSHHHHHHHH---HHHH-CSEEEEEECCSSSCCTTCCGGGGCC---
T ss_pred             CccCCHHHHHHHHH---HHhc-CCCEEEEEcCCCCCChhHHHHHHHHhcC
Confidence            654  245554443   3333 4689999999999999999999999986

>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=99.66  E-value=1.4e-16  Score=176.68  Aligned_cols=116  Identities=22%  Similarity=0.317  Sum_probs=91.0

Q ss_pred             CCcEEEEecCCCCCCc--ceEEEEeCC-eeeeeecCCCCcchhHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHHHhcc
Q psy18013        177 ANHTICYTDGSKSPDV--TGCAFSIGD-MVRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALANV  253 (563)
Q Consensus       177 ~~~i~IyTDGS~~~~~--vG~gvv~~~-~~~~~~L~~~~sv~~AEL~AI~~AL~~a~~~~~~~i~I~tDS~sal~aL~~~  253 (563)
                      ++.+.||||||+..++  .|+|++... ...+..+. .++++.||+.|+..||+.    ...++.|+|||+++++.+.++
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 PGAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKLE-QTTNQQAELEAFAMALTD----SGPKVNIIVDSQYVMGIVASQ  508 (555)
T ss_dssp             TTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEEES-SCCHHHHHHHHHHHHHHT----SCSEEEEEESCHHHHHHHHTC
T ss_pred             CCceEEEEcccccCCCCCceEEEEEEeCCEeeccCC-CCCHHHHHHHHHHHHHHc----CCCeEEEEEehHHHHHHHhcc
Confidence            4679999999988643  688877643 22233333 578999999999999998    468999999999999999986


Q ss_pred             CCC--ChhHHHHHHHHHHHhhcCCeEEEEeecCccCCcCChHHHHHhcCC
Q psy18013        254 KFS--NPLVTKVFSTWRYLKLCNKEVTFMWCPSHCGIRGNEIVDDAAKNP  301 (563)
Q Consensus       254 ~~~--s~~~~~I~~~i~~L~~~~~~V~~~WVPgH~gi~GNE~AD~lAK~A  301 (563)
                      ...  .++.+++.+    +...+..|.|.|||||+|++|||.||+|||+|
T Consensus       509 ~~~~~~~l~~~~~~----~~~~~~~v~~~wV~~H~g~~~Ne~AD~LA~~a  554 (555)
T 1mu2_A          509 PTESESKIVNQIIE----EMIKKEAIYVAWVPAHKGIGGNQEVDHLVSQG  554 (555)
T ss_dssp             CSEESCHHHHHHHH----HHHHCSEEEEEECCSSSCCTTHHHHHHHHHTT
T ss_pred             cccccHHHHHHHHH----HhccCCcEEEEEEECCCCChhHHHHHHHHHhh
Confidence            532  345554443    32336789999999999999999999999998

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

Probab=99.64  E-value=2.3e-16  Score=145.29  Aligned_cols=117  Identities=17%  Similarity=0.152  Sum_probs=90.1

Q ss_pred             EEEEecCCCC-C--CcceE-EEEeCC--e-ee--eeecC---CCCcchhHHHHHHHHHHHHHHcCCCCeEEEEeccHHHH
Q psy18013        180 TICYTDGSKS-P--DVTGC-AFSIGD--M-VR--STLLN---PINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSAL  247 (563)
Q Consensus       180 i~IyTDGS~~-~--~~vG~-gvv~~~--~-~~--~~~L~---~~~sv~~AEL~AI~~AL~~a~~~~~~~i~I~tDS~sal  247 (563)
                      +.||||||.. .  +..|+ |+++.+  . ..  +..++   ...+++.||+.|+..||+.+.+.+..++.|+|||+.++
T Consensus         2 ~~iy~DGs~~~~n~g~~G~~G~vi~~~g~~~~~~~~~~~~~~~~~tnn~aEl~A~~~aL~~a~~~g~~~v~i~tDS~~vi   81 (149)
T 2ehg_A            2 IIGYFDGLCEPKNPGGIATFGFVIYLDNRKIEGYGLAEKPFSINSTNNVAEYSGLICLMETMLRLGISSPIIKGDSQLVI   81 (149)
T ss_dssp             CEEEEEEEEESSSSSSEEEEEEEEECSSCEEEEEEECSCTTCTTCCHHHHHHHHHHHHHHHHHHHTCCSCEEEESCHHHH
T ss_pred             EEEEEeeccCCCCCChheEEEEEEEECCEEEEEeccccCCCCCCccHHHHHHHHHHHHHHHHHHcCCCEEEEEeChHHHH
Confidence            6899999987 2  45785 866532  1 11  12233   36889999999999999999987778999999999999


Q ss_pred             HHHhccCC-CChhHHHHHHHHHHHhhcCCeEEEEeecCccCCcCChHHHHHhcCC
Q psy18013        248 AALANVKF-SNPLVTKVFSTWRYLKLCNKEVTFMWCPSHCGIRGNEIVDDAAKNP  301 (563)
Q Consensus       248 ~aL~~~~~-~s~~~~~I~~~i~~L~~~~~~V~~~WVPgH~gi~GNE~AD~lAK~A  301 (563)
                      +.+.+++. .++....+++.+..+.++. .|.|.|||+    ++|+.||+|||+|
T Consensus        82 ~~i~~~w~~~~~~~~~l~~~i~~l~~~~-~v~~~~V~~----~~N~~AD~LA~~a  131 (149)
T 2ehg_A           82 KQMNGEYKVKAKRIIPLYEKAIELKKKL-NATLIWVPR----EENKEADRLSRVA  131 (149)
T ss_dssp             HHHTTSSCCCCTTHHHHHHHHHHHHHHH-TCEEEECCG----GGCHHHHHHHHHH
T ss_pred             HHHhCccccCCHHHHHHHHHHHHHHhcC-CEEEEEcCC----cccHHHHHHHHHH
Confidence            99999754 3344556666666555544 499999998    5999999999999

>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=99.03  E-value=1.1e-10  Score=107.22  Aligned_cols=117  Identities=15%  Similarity=0.031  Sum_probs=83.5

Q ss_pred             cCCcEEEEecCCCCCC--cceEEEEeCCe--e--eeeecCCCCcchhHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHH
Q psy18013        176 YANHTICYTDGSKSPD--VTGCAFSIGDM--V--RSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAA  249 (563)
Q Consensus       176 ~~~~i~IyTDGS~~~~--~vG~gvv~~~~--~--~~~~L~~~~sv~~AEL~AI~~AL~~a~~~~~~~i~I~tDS~sal~a  249 (563)
                      .+..+.||||||+..+  ..|+|+++...  .  .+..++ ..|++.||+.|++.||+.+.+... ++.|+|||+.+++.
T Consensus         8 ~~~~~~iy~DGa~~gNpG~~G~G~vl~~~g~~~~~~~~~~-~~TNN~aEl~A~i~aL~~~~~~~~-~v~i~tDS~~vi~w   85 (142)
T 1zbf_A            8 EIIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIP-IGTNNMGEFLAIVHGLRYLKERNS-RKPIYSNSQTAIKW   85 (142)
T ss_dssp             CCCSSSEEEEEEECSSSEEEEEEEEETTTCCEEEECCCEE-EECHHHHHHHHHHHHHHHHHHTTC-CCCEEESCHHHHHH
T ss_pred             CCCeEEEEEeeccCCCCCCeEEEEEEEeCCEEEEEecccC-CcCcHHHHHHHHHHHHHHHHhCCC-eEEEEEehHHHHHH
Confidence            3467889999998754  47899887521  1  122233 478999999999999999998666 99999999999999


Q ss_pred             HhccCCCC-----hhHHHHHHHHH----HHhhcCCeEEEEeecCccCCcCChHHHH
Q psy18013        250 LANVKFSN-----PLVTKVFSTWR----YLKLCNKEVTFMWCPSHCGIRGNEIVDD  296 (563)
Q Consensus       250 L~~~~~~s-----~~~~~I~~~i~----~L~~~~~~V~~~WVPgH~gi~GNE~AD~  296 (563)
                      +.+.....     ..-.++++.+.    -++.  ..++...|.-|++.-||..||.
T Consensus        86 ~~~~~~k~~~~~~v~n~dLw~~l~~~~~w~~~--~~~~~~~~kw~~~~~ge~pad~  139 (142)
T 1zbf_A           86 VKDKKAKSTLVRNEETALIWKLVDEAEEWLNT--HTYETPILKWQTDKWGEIKADY  139 (142)
T ss_dssp             HHHTCCCCCCCCSTTTHHHHHHHHHHHHHHHH--CCCCCCEEECCHHHHCSCTTCC
T ss_pred             HHcCCccCCCCCCcccHHHHHHHHHHHHHHhh--CCCceeEEEeccCccCcCcccc
Confidence            98876211     12234444433    3433  4456666777898999999984

>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=98.67  E-value=3.7e-08  Score=89.34  Aligned_cols=75  Identities=16%  Similarity=0.038  Sum_probs=56.8

Q ss_pred             CCcEEEEecCCCCCC--cceEEEEeCC-e---eeeeecCCCCcchhHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHHH
Q psy18013        177 ANHTICYTDGSKSPD--VTGCAFSIGD-M---VRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAAL  250 (563)
Q Consensus       177 ~~~i~IyTDGS~~~~--~vG~gvv~~~-~---~~~~~L~~~~sv~~AEL~AI~~AL~~a~~~~~~~i~I~tDS~sal~aL  250 (563)
                      +....||||||+..+  ..|+|+|+.. .   ..+..++ .+|++.||+.|++.||+.+.+.+.. +.|+|||+++++.+
T Consensus         3 p~~~~iytDGac~GNPGp~G~ggV~~~~g~~~~~~g~~~-~tTNN~aEl~A~i~aL~~l~~~~~~-v~i~tDSqyVi~wi   80 (134)
T 4htu_A            3 IIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIP-IGTNNMGEFLAIVHGLRYLKERNSR-KPIYSNSQTAIKWV   80 (134)
T ss_dssp             CCSSSEEEEEEEETTTEEEEEEEEETTTCCEEEEEEEEE-EECHHHHHHHHHHHHHHHHHHTTCC-CCEEESCHHHHHHH
T ss_pred             ccceEEEEeeccCCCCCCeEEEEEEEECCEEEEEecCCC-CCchHHHHHHHHHHHHHHHHhCCCC-EEEEcchHHHHHHH
Confidence            456789999998764  3788544432 1   2222333 5799999999999999999885444 89999999999999


Q ss_pred             hcc
Q psy18013        251 ANV  253 (563)
Q Consensus       251 ~~~  253 (563)
                      .+.
T Consensus        81 ~~~   83 (134)
T 4htu_A           81 KDK   83 (134)
T ss_dssp             HHT
T ss_pred             HcC
Confidence            874

---

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	563
d1mu2a1	126	c.55.3.1 (A:430-555) HIV RNase H (Domain of revers	1e-07
d1jl1a_	152	c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli	8e-05
d1s1ta1	110	c.55.3.1 (A:430-539) HIV RNase H (Domain of revers	5e-04
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 = 48.8 bits (115), Expect = 1e-07
 Identities = 24/119 (20%), Positives = 44/119 (36%), Gaps = 8/119 (6%)

Query: 183 YTDGSKS--PDVTGCAFSIGDMVRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIV 240
           YTDGS +         +               +   AEL A  + L     +   +  I+
Sbjct: 11  YTDGSCNRQSKEGKAGYVTDRGKDKVKKLEQTTNQQAELEAFAMALT----DSGPKVNII 66

Query: 241 SDSRSALAALANVKFSNPLVTKVFSTWRYLKLCNKEVTFMWCPSHCGIRGNEIVDDAAK 299
            DS+  +  +A+    +   +K+ +      +  + +   W P+H GI GN+ VD    
Sbjct: 67  VDSQYVMGIVASQPTESE--SKIVNQIIEEMIKKEAIYVAWVPAHKGIGGNQEVDHLVS 123

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

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: RNase H (RNase HI)
species: Escherichia coli [TaxId: 562]

 Score = 40.8 bits (94), Expect = 8e-05
 Identities = 28/138 (20%), Positives = 39/138 (28%), Gaps = 18/138 (13%)

Query: 183 YTDGSKS--PDVTGCAFSI---GDMVRSTLLNPINSIFSAE-------LIAIFLCLEAIL 230
           +T GS    P   G    +   G     +      +    E       L A+    E IL
Sbjct: 6   FTAGSALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKEHAEVIL 65

Query: 231 ENPSDQFLIVSDSRSALAALANVKFSNPLVTKVFSTWRYLK--LCNKEVTFMWCPSHCGI 288
              S                   K ++    K    W+ L   L   ++ + W   H G 
Sbjct: 66  STDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVKGHAGH 125

Query: 289 RGNEIVD----DAAKNPN 302
             NE  D     AA NP 
Sbjct: 126 PENERADELARAAAMNPT 143

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

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

 Score = 37.7 bits (87), Expect = 5e-04
 Identities = 21/107 (19%), Positives = 42/107 (39%), Gaps = 12/107 (11%)

Query: 183 YTDGS--KSPDVTGCAFSIGDMVRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIV 240
           Y DG+  +   +    +      +  +     +    EL AI+L L+        +  IV
Sbjct: 12  YVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDS----GLEVNIV 67

Query: 241 SDSRSALAALANVKFSNPLVTKVFSTWRYLKLCNK--EVTFMWCPSH 285
           +DS+ AL  +     + P  ++     + ++   K  +V   W P+H
Sbjct: 68  TDSQYALGIIQ----AQPDQSESELVNQIIEQLIKKEKVYLAWVPAH 110

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

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

 Score = 37.2 bits (85), Expect = 0.002
 Identities = 26/133 (19%), Positives = 40/133 (30%), Gaps = 15/133 (11%)

Query: 183 YTDGSKS--PDVTGCAFSIGDMVRSTLLN---PINSIFSAELIAIFLCLEA--------I 229
           +TDG+    P   G A  +       LL+      +    EL A    L+A        +
Sbjct: 7   FTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKEPCEVDL 66

Query: 230 LENPSDQFLIVSDSRSALAALANVKFSNPLVTKVFSTWRYLKLCNKE--VTFMWCPSHCG 287
             +        ++           + +     K    W  L L      V F +   H G
Sbjct: 67  YTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPHRVRFHFVKGHTG 126

Query: 288 IRGNEIVDDAAKN 300
              NE VD  A+ 
Sbjct: 127 HPENERVDREARR 139

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	563
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.85
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	99.79
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.78
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	99.59
d1zbfa1	132	BH0863-like Ribonuclease H {Bacillus halodurans [T	99.21

>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=99.85  E-value=9.1e-22  Score=175.02  Aligned_cols=116  Identities=22%  Similarity=0.287  Sum_probs=88.1

Q ss_pred             CCcEEEEecCCCCCC-c-ceEEEEeCCe-eeeeecCCCCcchhHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHHHhcc
Q psy18013        177 ANHTICYTDGSKSPD-V-TGCAFSIGDM-VRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALANV  253 (563)
Q Consensus       177 ~~~i~IyTDGS~~~~-~-vG~gvv~~~~-~~~~~L~~~~sv~~AEL~AI~~AL~~a~~~~~~~i~I~tDS~sal~aL~~~  253 (563)
                      ++...||||||+..+ + .|+|++.... .....++ ..|++.|||.||.+||+.    ...++.|+|||++++..+.+.
T Consensus         5 ~~~~t~YTDGS~~~n~~~~~~g~~~~~~~~~~~~~~-~~tnn~AEl~Ai~~al~~----~~~~i~I~tDS~~v~~~~~~~   79 (126)
T d1mu2a1           5 PGAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKLE-QTTNQQAELEAFAMALTD----SGPKVNIIVDSQYVMGIVASQ   79 (126)
T ss_dssp             TTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEEES-SCCHHHHHHHHHHHHHHT----SCSEEEEEESCHHHHHHHHTC
T ss_pred             CCCcEEEEcCCCCCCCCcEEEEEEecCCCEEEEecC-CCcchHHHHHHHHHHhcc----CCcceEEEechHHHHHHHhcC
Confidence            356799999997654 3 5666666543 3334444 578999999999999975    467899999999999999987


Q ss_pred             CCC--ChhHHHHHHHHHHHhhcCCeEEEEeecCccCCcCChHHHHHhcCC
Q psy18013        254 KFS--NPLVTKVFSTWRYLKLCNKEVTFMWCPSHCGIRGNEIVDDAAKNP  301 (563)
Q Consensus       254 ~~~--s~~~~~I~~~i~~L~~~~~~V~~~WVPgH~gi~GNE~AD~lAK~A  301 (563)
                      ...  .....   ..+..+.+ ...|.|.|||||+|++|||.||+||++|
T Consensus        80 ~~~~~~~~~~---~~~~~~~~-~~~v~~~wV~gH~g~~gNe~AD~LA~~a  125 (126)
T d1mu2a1          80 PTESESKIVN---QIIEEMIK-KEAIYVAWVPAHKGIGGNQEVDHLVSQG  125 (126)
T ss_dssp             CSEESCHHHH---HHHHHHHH-CSEEEEEECCSSSCCTTHHHHHHHHHTT
T ss_pred             CccccchHHH---HHHHHhhh-cceeEEEEEeCCCCCcchHHHHHHHHhh
Confidence            653  22322   22333433 4689999999999999999999999998

>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=99.79  E-value=4.5e-20  Score=167.80  Aligned_cols=131  Identities=18%  Similarity=0.219  Sum_probs=93.6

Q ss_pred             cEEEEecCCCCCC--cceEEEEeC--Cee--eeeecCCCCcchhHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHHHhc
Q psy18013        179 HTICYTDGSKSPD--VTGCAFSIG--DMV--RSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALAN  252 (563)
Q Consensus       179 ~i~IyTDGS~~~~--~vG~gvv~~--~~~--~~~~L~~~~sv~~AEL~AI~~AL~~a~~~~~~~i~I~tDS~sal~aL~~  252 (563)
                      .|.||||||+.++  ..|+|+++.  +..  .+... ...+++.||+.|+..||+++..  ...+.|++||+.++..+..
T Consensus         2 ~I~IYtDGS~~~N~g~aG~G~vi~~~~~~~~~~~~~-~~~tnn~aE~~Ai~~Al~~~~~--~~~i~i~tds~~~i~~~~~   78 (152)
T d1jl1a_           2 QVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGY-TRTTNNRMELMAAIVALEALKE--HAEVILSTDSQYVRQGITQ   78 (152)
T ss_dssp             CEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCCS--CCEEEEEECCHHHHHHHHT
T ss_pred             EEEEEEeCCCCCCCCcEEEEEEEEECCeEEEecccc-CcccHHHHHHhhhhhhhhhhcc--cceEEEeecceeeEEcccc
Confidence            4899999998765  378887653  322  22223 3468899999999999987643  6789999999999988865


Q ss_pred             cCC---------C--Chh-HHHHHHHHHHHhhcCCeEEEEeecCccCCcCChHHHHHhcCCCccCCCCCCCCCc
Q psy18013        253 VKF---------S--NPL-VTKVFSTWRYLKLCNKEVTFMWCPSHCGIRGNEIVDDAAKNPNVSAPLKLCTPED  314 (563)
Q Consensus       253 ~~~---------~--s~~-~~~I~~~i~~L~~~~~~V~~~WVPgH~gi~GNE~AD~lAK~Aa~~~p~~~~~p~~  314 (563)
                      ...         .  .++ ..+.+..+..+.. ...|.|+|||||+|++|||.||+|||+| +..|..+..+++
T Consensus        79 ~~~~~~~~~~~~~~~~~~~n~~~~~~i~~~~~-~~~V~~~wV~gH~g~~gNe~AD~LAk~a-a~~~~~~d~~~~  150 (152)
T d1jl1a_          79 WIHNWKKRGWKTADKKPVKNVDLWQRLDAALG-QHQIKWEWVKGHAGHPENERADELARAA-AMNPTLEDTGYQ  150 (152)
T ss_dssp             THHHHHHTTTBCTTSCBCTTHHHHHHHHHHTT-TCEEEEEECCSSTTCHHHHHHHHHHHHH-HHSCCBCCTTCC
T ss_pred             hhhHhHhccchhcccCeeecHHHHHHHHHHhh-cceeEEEEecccCCCccHHHHHHHHHHH-HhCCCCCccCCC
Confidence            421         0  111 1234444444433 4689999999999999999999999999 555655544443

>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=99.78  E-value=4.2e-20  Score=167.95  Aligned_cols=121  Identities=20%  Similarity=0.158  Sum_probs=87.9

Q ss_pred             cEEEEecCCCCCC--cceEEEEeCC--e-eeeeecCCCCcchhHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHHHhcc
Q psy18013        179 HTICYTDGSKSPD--VTGCAFSIGD--M-VRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALANV  253 (563)
Q Consensus       179 ~i~IyTDGS~~~~--~vG~gvv~~~--~-~~~~~L~~~~sv~~AEL~AI~~AL~~a~~~~~~~i~I~tDS~sal~aL~~~  253 (563)
                      .++||||||+.++  ..|+|+++..  . .........+|++.||+.||..||+++..  ...+.|++||+++++.+...
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            5899999998875  3788876532  1 11111122468999999999999987643  56899999999999988653


Q ss_pred             CC----------C--ChhH-HHHHHHHHHHhhcCCeEEEEeecCccCCcCChHHHHHhcCCC
Q psy18013        254 KF----------S--NPLV-TKVFSTWRYLKLCNKEVTFMWCPSHCGIRGNEIVDDAAKNPN  302 (563)
Q Consensus       254 ~~----------~--s~~~-~~I~~~i~~L~~~~~~V~~~WVPgH~gi~GNE~AD~lAK~Aa  302 (563)
                      ..          .  .++. .+++..+..+.. ...|.|.|||||+|++|||.||+|||+||
T Consensus        81 ~~~~~~~~~~~~~~~~~v~n~dL~~~l~~~~~-~~~v~~~wVkgHsg~~gNe~AD~LAk~aa  141 (147)
T d1rila_          81 WLEGWRKRGWRTAEGKPVKNRDLWEALLLAMA-PHRVRFHFVKGHTGHPENERVDREARRQA  141 (147)
T ss_dssp             HHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHT-TSEEECCCCCGGGSCTHHHHHHHHHHHHH
T ss_pred             chhhhhhccccccccccchhHHHHHHHHHHhh-hcccceEEccCCCCCcchHHHHHHHHHHH
Confidence            21          0  1121 344444544443 57899999999999999999999999994

>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=99.59  E-value=1.4e-15  Score=131.90  Aligned_cols=100  Identities=23%  Similarity=0.339  Sum_probs=74.0

Q ss_pred             CCcEEEEecCCCCCC-c-ceEEEEeCCe-eeeeecCCCCcchhHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHHHhcc
Q psy18013        177 ANHTICYTDGSKSPD-V-TGCAFSIGDM-VRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALANV  253 (563)
Q Consensus       177 ~~~i~IyTDGS~~~~-~-vG~gvv~~~~-~~~~~L~~~~sv~~AEL~AI~~AL~~a~~~~~~~i~I~tDS~sal~aL~~~  253 (563)
                      ++..++|||||+..+ + .|+|++..+. .....++ .+|++.|||.||+.||+.    ...++.|+|||+++++++...
T Consensus         6 ~~~~t~ytDGs~~~n~~~g~~g~~~~~~~~~~~~~~-~~TNn~aEl~Avi~aL~~----~~~~v~I~TDS~yvi~~i~~~   80 (110)
T d1s1ta1           6 VGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLT-DTTNQKTELQAIYLALQD----SGLEVNIVTDSQYALGIIQAQ   80 (110)
T ss_dssp             TTSEEEEEEEEEETTTTEEEEEEEETTSCEEEEEES-SCCHHHHHHHHHHHHHHH----SCSEEEEEECCHHHHHHHHHC
T ss_pred             CCCcEEEEeCCCCCCCCCcEEEEEEecCCeEEEecc-cCcHHHHHHHHHHHHHHh----CCCeEEEEEehHHHHHHHhcC
Confidence            456789999997654 3 5666665542 3444454 579999999999999985    356899999999999999987


Q ss_pred             CCC--ChhHHHHHHHHHHHhhcCCeEEEEeecCc
Q psy18013        254 KFS--NPLVTKVFSTWRYLKLCNKEVTFMWCPSH  285 (563)
Q Consensus       254 ~~~--s~~~~~I~~~i~~L~~~~~~V~~~WVPgH  285 (563)
                      ...  ..+.++|.+   .|. ....|.+.|||||
T Consensus        81 ~~~~~~~l~~~il~---~l~-~~~~v~i~WVpgH  110 (110)
T d1s1ta1          81 PDQSESELVNQIIE---QLI-KKEKVYLAWVPAH  110 (110)
T ss_dssp             CSEESCHHHHHHHH---HHH-HCSEEEEEECCSS
T ss_pred             ccccchHHHHHHHH---HHh-cCCceEEEEeCCC
Confidence            653  345555544   333 3578999999999

>d1zbfa1 c.55.3.1 (A:62-193) BH0863-like Ribonuclease H {Bacillus halodurans [TaxId: 86665]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: BH0863-like Ribonuclease H
species: Bacillus halodurans [TaxId: 86665]

Probab=99.21  E-value=4.8e-12  Score=112.27  Aligned_cols=113  Identities=16%  Similarity=0.067  Sum_probs=81.3

Q ss_pred             EEEecCCCCCC--cceEEEEeCCe--e--eeeecCCCCcchhHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHHHhccC
Q psy18013        181 ICYTDGSKSPD--VTGCAFSIGDM--V--RSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALANVK  254 (563)
Q Consensus       181 ~IyTDGS~~~~--~vG~gvv~~~~--~--~~~~L~~~~sv~~AEL~AI~~AL~~a~~~~~~~i~I~tDS~sal~aL~~~~  254 (563)
                      .||||||+..+  ..|+|+|+...  .  .+..+ ...|++.||+.|++.||+.+.+.+ .++.|+|||++++..+.+..
T Consensus         6 sIy~DGa~~GNPGp~g~g~v~~~~~~~~~~sg~~-~~~TNN~aEl~A~i~aL~~~~~~~-~~i~I~tDS~yvi~wv~~~~   83 (132)
T d1zbfa1           6 SLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPI-PIGTNNMGEFLAIVHGLRYLKERN-SRKPIYSNSQTAIKWVKDKK   83 (132)
T ss_dssp             SEEEEEEECSSSEEEEEEEEETTTCCEEEECCCE-EEECHHHHHHHHHHHHHHHHHHTT-CCCCEEESCHHHHHHHHHTC
T ss_pred             eEEEeecCCCCCchheEEEEEEcCCEEEEEEcCc-CccchHHHHHHHHHHHHHHhhcCC-ceEEEEeccHHHHHHHHhCc
Confidence            38999998865  48888776532  1  22223 357899999999999999998754 57999999999999998754


Q ss_pred             CC-----ChhHHHHHHHHHHHh--hcCCeEEEEeecCccCCcCChHHH
Q psy18013        255 FS-----NPLVTKVFSTWRYLK--LCNKEVTFMWCPSHCGIRGNEIVD  295 (563)
Q Consensus       255 ~~-----s~~~~~I~~~i~~L~--~~~~~V~~~WVPgH~gi~GNE~AD  295 (563)
                      -.     ..--+++++.+.++.  -+...+.+.||..|++.-||..||
T Consensus        84 ~kt~~~~~vkN~~l~~~i~~a~~~lk~h~~~~~~~KW~~~~wG~i~AD  131 (132)
T d1zbfa1          84 AKSTLVRNEETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKAD  131 (132)
T ss_dssp             CCCCCCCSTTTHHHHHHHHHHHHHHHHCCCCCCEEECCHHHHCSCTTC
T ss_pred             eecCcCCCcccHHHHHHHHHHHHHHHhCCcCceeEEecCcccccCCCC
Confidence            21     112244444444321  123568899999999999999998