Psyllid ID: psy663

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-----
Protein Sequence
MYRLTYVYLTCYVANSIPPIQEGIDAKDSVLNKLNAVHHAGIRIATGALRSSPVVSLYVDSGVPPLTLRRSKLMLNYVAKISASPFNPAQKLLYHQDMSGIIFTVNKPKPLYIRFREVANFNNVLESSEVAPYVRFVPPWSNCAPPVDQCLGEEKKSDVAPVVFQQKFSEAINTKYANHTICYTDGSKSPDVTGCAFSIGDMVRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALANVKFSNPLVTKVFSTWRYLKLCNK
Secondary Structure (PSIPRED)
cHHHHHHHHHHHHHHHcHHHHccccccHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHccccHHHHHHHHHHHHHHHHHcccccHHHHHHHHcccccccccccccccHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHcccccEEEEcccccccccccccEEEccccEEEEcccccHHHHHHHHHHHHHHHHHHccccccEEEEEccHHHHHHHHccccccHHHHHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHccccHHHHHHHHHHHHHHHHHcccccccHHHHHHccccHHHccccccccHHHHHHHHHHHcccccccccccccccccccccccccccEEEcHcccccccHHHHHHHHHHHHHHHccccEEEEEccccccccEEEEEEEccEEEEEEccccccHHHHHHHHHHHHHHHHHHcccccEEEEcccHHHHHHHHccccccHHHHHHHHHHHHHHcccc
Coil and Loop (DISEMBL)
MYRLTYVYLTCYvansippiqegidakDSVLNKLNAVHHAGIRIAtgalrsspvvslyvdsgvppltlrRSKLMLNYVAKisaspfnpaqkllyhqdmsgiiftvnkpkplyIRFREVANfnnvlessevapyvrfvppwsncappvdqclgeekksdvapVVFQQKFSEAINTKYANhticytdgskspdvtgcafsIGDMVRstllnpinsIFSAELIAIFLCLEAIlenpsdqfliVSDSRSALAALANvkfsnplvTKVFSTWRYLKLCNK
Flexible Loop (DISEMBL)
MYRLTYVYLTCYVANSIPPIQEGIDAKDSVLNKLNAVHHAGIRIatgalrsspvvsLYVDSGVPPLTLRRSKLMLNYVAKISASPFNPAQKLLYHQDMSGIIFTVNKPKPLYIRFREVANFNNVLESSEVAPYVRFVPPWSNCAPPVDQCLGEEKKSDVAPVVFQQKFSEAINTKYANHTICYTDGSKSPDVTGCAFSIGDMVRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALAnvkfsnplvtkvfstwrylklcnk
Low Complexity Region (SEG)
MYRLTYVYLTCYVANSIPPIQEGIDAKDSVLNKLNAVHHAGIRIATGALRSSPVVSLYVDSGVPPLTLRRSKLMLNYVAKISASPFNPAQKLLYHQDMSGIIFTVNKPKPLYIRFREVANFNNVLESSEVAPYVRFVPPWSNCAPPVDQCLGEEKKSDVAPVVFQQKFSEAINTKYANHTICYTDGSKSPDVTGCAFSIGDMVRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALANVKFSNPLVTKVFSTWRYLKLCNK
Disordered region (IsUnstruct)
*YRLTYVYLTCYVANSIPPIQEGIDAKDSVLNKLNAVHHAGIRIATGALRSSPVVSLYVDSGVPPLTLRRSKLMLNYVAKISASPFNPAQKLLYHQDMSGIIFTVNKPKPLYIRFREVANFNNVLESSEVAPYVRFVPPWSNCAPPVDQCLGEEKKSDVAPVVFQQKFSEAINTKYANHTICYTDGSKSPDVTGCAFSIGDMVRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALANVKFSNPLVTKVFSTWRYLKLC**
Disordered Region (DISOPRED)
**RLTYVYLTCYVANSIPPIQEGIDAKDSVLNKLNAVHHAGIRIATGALRSSPVVSLYVDSGVPPLTLRRSKLMLNYVAKISASPFNPAQKLLYHQDMSG*****NKPKPLYIRFREVANFNNVLESSEVAPYVRFVPPWSNCAPPVDQCLGEEKKSDVAPVVFQQKFSEAINTKYANHTICYTDGSKSPDVTGCAFSIGDMVRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALANVKFSNPLVTKVFSTWRYLKLC**
Disordered Region (DISEMBL)
MYRLTYVYLTCYVANSIPPIQEGIDAKDSVLNKLNAVHHAGIRIATGALRSSPVVSLYVDSGVPPLTLRRSKLMLNYVAKISASPFNPAQKLLYHQDMSGIIFTVNKPKPLYIRFREVANFNNVLESSEVAPYVRFVPPWSNCAPPVDQCLGEEKKSDVAPVVFQQKFSEAINTKYANHTICYTDGSKSPDVTGCAFSIGDMVRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALANVKFSNPLVTKVFSTWRYLKLCNK
Disordered Region (DISPRO)
MYRLTYVYLTCYVANSIPPIQEGIDAKDSVLNKLNAVHHAGIRIATGALRSSPVVSLYVDSGVPPLTLRRSKLMLNYVAKISASPFNPAQKLLYHQDMSGIIFTVNKPKPLYIRFREVANFNNVLESSEVAPYVRFVPPWSNCAPPVDQCLGEEKKSDVAPVVFQQKFSEAINTKYANHTICYTDGSKSPDVTGCAFSIGDMVRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALANVKFSNPLVTKVFSTWRYLKLCNK
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MYRLTYVYLTCYVANSIPPIQEGIDAKDSVLNKLNAVHHAGIRIATGALRSSPVVSLYVDSGVPPLTLRRSKLMLNYVAKISASPFNPAQKLLYHQDMSGIIFTVNKPKPLYIRFREVANFNNVLESSEVAPYVRFVPPWSNCAPPVDQCLGEEKKSDVAPVVFQQKFSEAINTKYANHTICYTDGSKSPDVTGCAFSIGDMVRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALANVKFSNPLVTKVFSTWRYLKLCNK
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	275
427791807	1212	Putative tick transposon, partial [Rhipi	0.854	0.193	0.345	1e-25
427791321	1210	Putative tick transposon, partial [Rhipi	0.854	0.194	0.345	1e-25
125901787	1222	pol-like protein [Biomphalaria glabrata]	0.825	0.185	0.340	2e-24
427791981	1060	Putative tick transposon, partial [Rhipi	0.810	0.210	0.340	2e-23
427792011	1121	Putative tick transposon, partial [Rhipi	0.854	0.209	0.320	1e-19
443710566	377	hypothetical protein CAPTEDRAFT_186063 [	0.850	0.620	0.293	4e-18
427798889	1199	Putative tick transposon, partial [Rhipi	0.850	0.195	0.329	5e-17
427798887	1199	Putative tick transposon, partial [Rhipi	0.850	0.195	0.317	6e-16
427791063	1035	Putative tick transposon, partial [Rhipi	0.854	0.227	0.302	2e-15
189242251	1808	PREDICTED: similar to pol-like protein [	0.690	0.105	0.347	2e-15

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

 Score =  122 bits (307), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 85/246 (34%), Positives = 128/246 (52%), Gaps = 11/246 (4%)

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  VTKVFS 265
            V  + +
Sbjct: 1020 VGDILN 1025

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  122 bits (307), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 85/246 (34%), Positives = 128/246 (52%), Gaps = 11/246 (4%)

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  VTKVFS 265
            V  + +
Sbjct: 1017 VGDILN 1022

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 =  118 bits (296), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 84/247 (34%), Positives = 126/247 (51%), Gaps = 20/247 (8%)

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   --------FNPAQKLLYHQDMSGIIFTVNKPKPLYIRFRE-VANFNNVLES-SEVAPYVR 135
                    FNP +  LY++  + I       +PL +R RE + N    ++  S++     
Sbjct: 863  TNPAFDSIFNPTEVELYNRRPNVI-------QPLGLRMREPIQNLTQPIDQISKIETPQN 915

Query: 136  FVPPWSNCAPPVDQCLGEEKKSDVAPVVFQQKFSEAINTKYANHTICYTDGSKSPDVTGC 195
              PPW    P ++  L   KK +  P + Q  F E +   Y +    YTDGSK      C
Sbjct: 916  --PPWLMNKPKLNLSLLNFKKENTDPSILQVHFRE-LQESYGDCGTIYTDGSKMEGKVAC 972

Query: 196  AFSIGDMVRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALANVKF 255
            A S  +   S  L    SIF+AEL AI L L A+  +   +F+I SDS+SAL AL  +K 
Sbjct: 973  ACSFRNKTISRRLPDGCSIFTAELHAILLALMAVKASERSKFIICSDSKSALQALGRMKT 1032

Query: 256  SNPLVTK 262
              PLV K
Sbjct: 1033 DIPLVHK 1039

Source: Biomphalaria glabrata

Species: Biomphalaria glabrata

Genus: Biomphalaria

Family: Planorbidae

Class: Gastropoda

Phylum: Mollusca

Superkingdom: Eukaryota

>gi|427791981|gb|JAA61442.1| Putative tick transposon, partial [Rhipicephalus pulchellus]

 Score =  115 bits (289), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 79/232 (34%), Positives = 126/232 (54%), Gaps = 9/232 (3%)

Query: 26   AKDSVLNKLNAVHHAGIRIATGALRSSPVVSLYVDSGVPPLTLRRSKLMLNYVAKISASP 85
            A+DS L +L+ VH+ G+R+ATGA R+SP+ SLY +S  P L  RR++LM  YV K+ +SP
Sbjct: 831  ARDSYLKRLDPVHNKGLRLATGAYRTSPIPSLYAESNEPSLEYRRTQLMFTYVLKVRSSP 890

Query: 86   FNPAQKLLYHQDMSGIIFTVNKP---KPLYIRFREVANFNNV-LESSEVAPYVRFVPPWS 141
             +    ++   D    +   NKP   KPL +RF E  +  N+  E+  +A   R + PWS
Sbjct: 891  DHICYSIVTRSDQR--LHYANKPNAIKPLILRFEEKFHALNIPNEALSIAKRPRSLAPWS 948

Query: 142  NCAPPVDQCLGEEKKSDVAPVVFQQKFSEAINTKYANHTICYTDGSKSPDVTGCAFSIGD 201
            + +  +D  L   KK         Q+F   +  KY      YTDGSK+    G +  +G+
Sbjct: 949  DFSMFLDFSLTHIKKQGTPREHILQEF-RTLQEKYHTFNEFYTDGSKASAYVGSSV-VGE 1006

Query: 202  MVRSTLLNP-INSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALAN 252
            +    +  P   S+++AE  A+++ +  I+ +   + +I SDS SAL AL++
Sbjct: 1007 IYEEVVRLPQFVSVYTAECYALWIAVRNIINSNHKKAVIFSDSLSALRALSS 1058

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|427792011|gb|JAA61457.1| Putative tick transposon, partial [Rhipicephalus pulchellus]

 Score =  103 bits (256), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 78/243 (32%), Positives = 115/243 (47%), Gaps = 8/243 (3%)

Query: 26   AKDSVLNKLNAVHHAGIRIATGALRSSPVVSLYVDSGVPPLTLRRSKLMLNYVAKISASP 85
            A  + +  L+ V+H GIR+ATGA R+SPV SLYV++   P+ L R    L Y  K+++ P
Sbjct: 803  ASKTAVKMLDPVYHLGIRLATGAFRTSPVSSLYVEANEWPMQLEREYCTLMYTLKVTSIP 862

Query: 86   FNPAQKLLYHQDMSGIIFTVNKP---KPLYIRFREVANFNNV-LESSEVAPYVRFVPPWS 141
             +P  KL+   D S + F   +P   KP  +     A    + L+    AP + ++PPW 
Sbjct: 863  THPCAKLV--ADTSALRFFEKRPSLSKPFSLTCTATAAQAEIPLQQVAKAPSMEWLPPWE 920

Query: 142  NCAPPVDQCLGEEKKSDVAPVVFQQKFSEAINTKYANHTICYTDGSKSPDVTGCAFSIGD 201
                  D       K        QQ F  ++  KY      YTD SK+ D    A    +
Sbjct: 921  KTRIKCDMSFCHIDKQRHPRAAIQQHFL-SLQYKYRGCHQFYTDASKTRDSVSAAAVGPE 979

Query: 202  MVRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALANVK-FSNPLV 260
               S  LN   SIF+AE  AI + ++ IL +   + +I +DS S + AL   K   NP++
Sbjct: 980  FTTSERLNVHTSIFTAEAYAILIAIKYILNHNITKSVIFTDSLSVVRALHTGKPNKNPVL 1039

Query: 261  TKV 263
              V
Sbjct: 1040 CDV 1042

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score = 97.8 bits (242), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 73/249 (29%), Positives = 123/249 (49%), Gaps = 15/249 (6%)

Query: 26  AKDSVLNKLNAVHHAGIRIATGALRSSPVVSLYVDSGVPPLTLRRSKLMLNYVAKISASP 85
           A+ S L +L  + +   R+  GA R SPV SL+ ++   P+ +R+  L + +  ++ +  
Sbjct: 32  ARISYLERLKPIQNQAFRLCLGAFRISPVTSLHTEANEMPMAIRQKLLSVQFALRVCSDT 91

Query: 86  FNPAQKLLYHQDMSGIIFTVNKP---KPLYIRFREVANFNNVL-ESSEVAPYVRF-VPPW 140
            NPA + +++ +     F ++KP   +PL +R +E  +   +  +   + P   F +P W
Sbjct: 92  TNPAHQCIFNYNNDR--FYLSKPNAIRPLALRIKE--DLQTICPDIKAITPNQLFNIPYW 147

Query: 141 SNCAPPVDQCLGEEKKSDVAP-VVFQQKFSEAINTKYANHTICYTDGSKSPDVTGCAFSI 199
               P +D  L    K    P    + +F   ++ KY +H + +TDGSKS     C  + 
Sbjct: 148 LLRPPELDISLIHFGKKTANPNYTLKNEFYNLMD-KYPDHKVIFTDGSKSDSAVACFATA 206

Query: 200 GDMVRSTLLNPINSIFSAELIAIFLCLEAILE---NPSDQFLIVSDSRSALAALANVKFS 256
            ++     L    SIFSAEL+AI+  L  +LE   N   QFLI +DS S+L A+ N    
Sbjct: 207 DNLSIQIRLPDSASIFSAELLAIYQVL-TLLECSANDQQQFLIATDSLSSLQAIGNFNIK 265

Query: 257 NPLVTKVFS 265
           +P V K+  
Sbjct: 266 HPYVFKILE 274

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 = 94.4 bits (233), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 81/246 (32%), Positives = 120/246 (48%), Gaps = 12/246 (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  VTKVFS 265
            +  ++S
Sbjct: 1043 LVSLYS 1048

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 = 90.9 bits (224), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 78/246 (31%), Positives = 116/246 (47%), Gaps = 12/246 (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  VTKVFS 265
            +  ++S
Sbjct: 1043 LVSLYS 1048

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 = 89.4 bits (220), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 74/245 (30%), Positives = 117/245 (47%), Gaps = 10/245 (4%)

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 TKVFS 265
             ++S
Sbjct: 878 ASLYS 882

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|189242251|ref|XP_001808188.1| PREDICTED: similar to pol-like protein [Tribolium castaneum]

 Score = 89.0 bits (219), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 67/193 (34%), Positives = 97/193 (50%), Gaps = 3/193 (1%)

Query: 26   AKDSVLNKLNAVHHAGIRIATGALRSSPVVSLYVDSGVPPLTLRRSKLMLNYVAKISASP 85
            AK  +LNKLN + +  IR A GA  ++PV SLY  S +P L  RRS+L+L Y AKISA+ 
Sbjct: 1208 AKPHILNKLNPIQNTSIRTALGAYCTTPVESLYALSDIPSLEARRSELILRYAAKISANK 1267

Query: 86   FNPAQKLLYHQDMSGIIFTVNKPKPLYIRFREVANFNNVLESSEVAPYVRF-VPPWSNCA 144
             NPA  +++      +     K  P   R  ++A+ N  L      P+ R   PPW+   
Sbjct: 1268 TNPAHNMMFPNRKEDLFSRKVKLTPPAYRRIKIASVNLNLSLPITYPFQRSKTPPWTYNK 1327

Query: 145  PPVDQCLGEEKKSDVAPVVFQQKFSEAINTKYANHTICYTDGSKSPDVTGCAFSIGDMVR 204
            P V   L    K      V + K + A+ T  +++ I YTD SKS D  G A+   D  +
Sbjct: 1328 PRVHTELLNLVKDKPLKSVLKTKLA-ALLTSISSNYIFYTDASKS-DTVGAAYVTNDTQQ 1385

Query: 205  STLLNPINSIFSA 217
            +  L+P + +  A
Sbjct: 1386 AFRLSPESKLREA 1398

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

No hits with e-value below 0.001 by BLAST

---

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

No EC number assignment, probably not an enzyme!

---

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	275
cd09276	128	cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom	3e-19
cd06222	123	cd06222, RNase_H, RNase H is an endonuclease that	2e-04
cd09273	135	cd09273, RNase_HI_RT_Bel, Bel/Pao family of RNase	0.001

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

 Score = 80.8 bits (200), Expect = 3e-19
 Identities = 38/100 (38%), Positives = 52/100 (52%), Gaps = 5/100 (5%)

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 QFLIVSDSRSALAALANVKFSNPLVTKVFSTWRYLKLCNK 275
           +  I SDS++AL AL + + S+PLV ++    R L     
Sbjct: 61  KITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGV 100

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|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 = 39.6 bits (93), Expect = 2e-04
 Identities = 20/79 (25%), Positives = 35/79 (44%), Gaps = 11/79 (13%)

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

Query: 234 SDQFLIVSDSRSALAALAN 252
             + +I +DS+  +  + +
Sbjct: 59  LKKLIIETDSKYVVDLINS 77

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

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

 Score = 38.0 bits (89), Expect = 0.001
 Identities = 22/84 (26%), Positives = 32/84 (38%), Gaps = 7/84 (8%)

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

Query: 241 SDSR---SALAALANVKFSNPLVT 261
           +DS      L AL  +      +T
Sbjct: 59  TDSAYAFGILHALETIWKERGFLT 82

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	275
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	99.11
PRK06548	161	ribonuclease H; Provisional	98.98
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	98.93
PRK08719	147	ribonuclease H; Reviewed	98.92
PRK00203	150	rnhA ribonuclease H; Reviewed	98.92
PRK13907	128	rnhA ribonuclease H; Provisional	98.88
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	98.73
KOG3752|consensus	371		98.59
PRK07708	219	hypothetical protein; Validated	98.31
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	98.19
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	97.57
PF05380	159	Peptidase_A17: Pao retrotransposon peptidase ; Int	88.57

>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=99.11  E-value=1.6e-10  Score=92.57  Aligned_cols=86  Identities=30%  Similarity=0.344  Sum_probs=60.8

Q ss_pred             CceEEEecCCCCC--CceeEEEEe-CcceeeeecCCccchhHHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHHHhC--
Q psy663          178 NHTICYTDGSKSP--DVTGCAFSI-GDMVRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALAN--  252 (275)
Q Consensus       178 ~~~~IyTDGSk~~--~~~G~a~~~-~~~~~~~~l~~~~sif~AEl~aI~~al~~~~~~~~~~~~I~sDS~sal~al~n--  252 (275)
                      +.+.||||||...  +..|+|++. .+...+..++ ..|++.||+.||.+||+.+   ....++|+|||++++..|..  
T Consensus         2 ~~~~iytDgS~~~~~~~~~~g~v~~~~~~~~~~~~-~~s~~~aEl~Ai~~AL~~~---~~~~v~I~tDS~~v~~~l~~~~   77 (132)
T PF00075_consen    2 KAIIIYTDGSCRPNPGKGGAGYVVWGGRNFSFRLG-GQSNNRAELQAIIEALKAL---EHRKVTIYTDSQYVLNALNKWL   77 (132)
T ss_dssp             TSEEEEEEEEECTTTTEEEEEEEEETTEEEEEEEE-SECHHHHHHHHHHHHHHTH---STSEEEEEES-HHHHHHHHTHH
T ss_pred             CcEEEEEeCCccCCCCceEEEEEEECCeEEEeccc-ccchhhhheehHHHHHHHh---hcccccccccHHHHHHHHHHhc
Confidence            5789999999543  335666544 3333444566 8899999999999999944   33999999999999998877  


Q ss_pred             ---CC-CC--C-HHHHHHHHHH
Q psy663          253 ---VK-FS--N-PLVTKVFSTW  267 (275)
Q Consensus       253 ---~~-~~--~-~i~~~I~~~~  267 (275)
                         .. ..  . ++..+|.+.+
T Consensus        78 ~~~~~~~~~~~~~i~~~i~~~~   99 (132)
T PF00075_consen   78 HGNGWKKTSNGRPIKNEIWELL   99 (132)
T ss_dssp             HHTTSBSCTSSSBHTHHHHHHH
T ss_pred             cccccccccccccchhheeecc
Confidence               22 11  2 4666666655

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=98.98  E-value=5e-09  Score=88.07  Aligned_cols=73  Identities=29%  Similarity=0.267  Sum_probs=54.6

Q ss_pred             CceEEEecCCCCCC--ceeEEEEeCcceeeeecCCccchhHHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHHHh
Q psy663          178 NHTICYTDGSKSPD--VTGCAFSIGDMVRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALA  251 (275)
Q Consensus       178 ~~~~IyTDGSk~~~--~~G~a~~~~~~~~~~~l~~~~sif~AEl~aI~~al~~~~~~~~~~~~I~sDS~sal~al~  251 (275)
                      ..++||||||...+  ..|+|++..+......-....|...||+.|+..||+.+.. ....+.|+|||+.++.++.
T Consensus         4 ~~~~IytDGa~~gnpg~~G~g~~~~~~~~~~g~~~~~TNnraEl~Aii~aL~~~~~-~~~~v~I~TDS~yvi~~i~   78 (161)
T PRK06548          4 NEIIAATDGSSLANPGPSGWAWYVDENTWDSGGWDIATNNIAELTAVRELLIATRH-TDRPILILSDSKYVINSLT   78 (161)
T ss_pred             CEEEEEEeeccCCCCCceEEEEEEeCCcEEccCCCCCCHHHHHHHHHHHHHHhhhc-CCceEEEEeChHHHHHHHH
Confidence            45899999998765  3788877643221111224578899999999999986542 3457999999999999999

>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=98.93  E-value=1.3e-08  Score=78.89  Aligned_cols=75  Identities=29%  Similarity=0.276  Sum_probs=59.8

Q ss_pred             EEEecCCCCCC--ceeEEEEeCc--ceee---eecCCccchhHHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHHHhCC
Q psy663          181 ICYTDGSKSPD--VTGCAFSIGD--MVRS---TLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALANV  253 (275)
Q Consensus       181 ~IyTDGSk~~~--~~G~a~~~~~--~~~~---~~l~~~~sif~AEl~aI~~al~~~~~~~~~~~~I~sDS~sal~al~n~  253 (275)
                      .+|||||...+  +.|+|++..+  ....   .......|++.||+.|++.||+++......++.|++||+.++..+.+.
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            48999998876  5788876532  1111   122257899999999999999999988889999999999999999987


Q ss_pred             CC
Q psy663          254 KF  255 (275)
Q Consensus       254 ~~  255 (275)
                      ..
T Consensus        81 ~~   82 (130)
T cd06222          81 YE   82 (130)
T ss_pred             cc
Confidence            54

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.

>PRK08719 ribonuclease H; Reviewed

Probab=98.92  E-value=9.4e-09  Score=85.26  Aligned_cols=69  Identities=22%  Similarity=0.264  Sum_probs=53.5

Q ss_pred             CceEEEecCCCCCCc-----eeEEEEe--Cc--c--eeeeecCCccchhHHHHHHHHHHHHHHHcCCCCeEEEEeccHHH
Q psy663          178 NHTICYTDGSKSPDV-----TGCAFSI--GD--M--VRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSA  246 (275)
Q Consensus       178 ~~~~IyTDGSk~~~~-----~G~a~~~--~~--~--~~~~~l~~~~sif~AEl~aI~~al~~~~~~~~~~~~I~sDS~sa  246 (275)
                      ..+.||||||...++     .|+|++.  ++  .  ..+..+....|...||+.|+..||+.+...    .+|+|||+.+
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            468999999997653     3788653  22  1  234445566899999999999999998653    3799999999


Q ss_pred             HHHH
Q psy663          247 LAAL  250 (275)
Q Consensus       247 l~al  250 (275)
                      +.++
T Consensus        79 i~~i   82 (147)
T PRK08719         79 VRGF   82 (147)
T ss_pred             HHHH
Confidence            9998

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=98.92  E-value=5.9e-09  Score=86.49  Aligned_cols=72  Identities=19%  Similarity=0.190  Sum_probs=54.1

Q ss_pred             ceEEEecCCCCCC--ceeEEEEe--Cccee-eeecCCccchhHHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHHHhC
Q psy663          179 HTICYTDGSKSPD--VTGCAFSI--GDMVR-STLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALAN  252 (275)
Q Consensus       179 ~~~IyTDGSk~~~--~~G~a~~~--~~~~~-~~~l~~~~sif~AEl~aI~~al~~~~~~~~~~~~I~sDS~sal~al~n  252 (275)
                      ++.||||||...+  ..|+|++.  ++... ........|...||+.|+..||+.+..  ...+.|+|||+.++.+|..
T Consensus         3 ~v~iytDGs~~~n~~~~g~g~v~~~~~~~~~~~~~~~~~TN~~aEL~Ai~~AL~~~~~--~~~v~I~tDS~yvi~~i~~   79 (150)
T PRK00203          3 QVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGEALTTNNRMELMAAIEALEALKE--PCEVTLYTDSQYVRQGITE   79 (150)
T ss_pred             eEEEEEEecccCCCCceEEEEEEEECCeeEEEecCCCCCcHHHHHHHHHHHHHHHcCC--CCeEEEEECHHHHHHHHHH
Confidence            4899999998754  27777664  23221 122234678899999999999998854  4679999999999999984

>PRK13907 rnhA ribonuclease H; Provisional

Probab=98.88  E-value=1.4e-08  Score=81.75  Aligned_cols=74  Identities=20%  Similarity=0.133  Sum_probs=58.4

Q ss_pred             eEEEecCCCCCC--ceeEEEEeCcc----eeeeecCCccchhHHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHHHhCC
Q psy663          180 TICYTDGSKSPD--VTGCAFSIGDM----VRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALANV  253 (275)
Q Consensus       180 ~~IyTDGSk~~~--~~G~a~~~~~~----~~~~~l~~~~sif~AEl~aI~~al~~~~~~~~~~~~I~sDS~sal~al~n~  253 (275)
                      ++||||||-..+  ..|+|++..+.    ..++. ....+...||+.|++.||+.+......++.|++||+.++..+.+.
T Consensus         2 ~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~~~-~~~~tn~~AE~~All~aL~~a~~~g~~~v~i~sDS~~vi~~~~~~   80 (128)
T PRK13907          2 IEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLP-LGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEKE   80 (128)
T ss_pred             EEEEEeeCCCCCCCccEEEEEEEECCeeEEEEec-ccccCCcHHHHHHHHHHHHHHHhCCCCEEEEEechHHHHHHHhHH
Confidence            579999997754  47888775332    12222 245688999999999999999988888999999999999999874


Q ss_pred             C
Q psy663          254 K  254 (275)
Q Consensus       254 ~  254 (275)
                      .
T Consensus        81 ~   81 (128)
T PRK13907         81 Y   81 (128)
T ss_pred             H
Confidence            3

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

Probab=98.73  E-value=6.7e-08  Score=80.39  Aligned_cols=74  Identities=23%  Similarity=0.194  Sum_probs=59.6

Q ss_pred             CceEEEecCCCCCC-c-eeEEEEe--Ccce--eeeecCCccchhHHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHHHh
Q psy663          178 NHTICYTDGSKSPD-V-TGCAFSI--GDMV--RSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALA  251 (275)
Q Consensus       178 ~~~~IyTDGSk~~~-~-~G~a~~~--~~~~--~~~~l~~~~sif~AEl~aI~~al~~~~~~~~~~~~I~sDS~sal~al~  251 (275)
                      ..++||||||...+ | -|+|+|.  ++..  .+..+. .+|...||+.|+.+||+++.+.+...+.|+|||+.+++.|.
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            35799999998765 3 6777654  3322  333444 88999999999999999999988999999999999999998


Q ss_pred             C
Q psy663          252 N  252 (275)
Q Consensus       252 n  252 (275)
                      .
T Consensus        81 ~   81 (154)
T COG0328          81 R   81 (154)
T ss_pred             H
Confidence            3

>KOG3752|consensus

Probab=98.59  E-value=1.7e-07  Score=87.18  Aligned_cols=77  Identities=26%  Similarity=0.245  Sum_probs=65.3

Q ss_pred             CCceEEEecCCCCCCc-----eeEEEEeCc---ceeeeecC-CccchhHHHHHHHHHHHHHHHcCCCCeEEEEeccHHHH
Q psy663          177 ANHTICYTDGSKSPDV-----TGCAFSIGD---MVRSTLLN-PINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSAL  247 (275)
Q Consensus       177 ~~~~~IyTDGSk~~~~-----~G~a~~~~~---~~~~~~l~-~~~sif~AEl~aI~~al~~~~~~~~~~~~I~sDS~sal  247 (275)
                      .+..++|||||-..+|     +|+|++.++   ...+..+. .-.+.|.||+.||.+||+-+.+....+++|.|||.-.+
T Consensus       210 ~~~~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~~~~kv~I~TDS~~~i  289 (371)
T KOG3752|consen  210 IEIQVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSKNINKVVIRTDSEYFI  289 (371)
T ss_pred             ccceEEEecCccccCCCCCCcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHhcCCCcEEEEechHHHH
Confidence            3458999999988754     799998754   25556665 77899999999999999999998888999999999999


Q ss_pred             HHHhCC
Q psy663          248 AALANV  253 (275)
Q Consensus       248 ~al~n~  253 (275)
                      ++|+.+
T Consensus       290 ~~l~~w  295 (371)
T KOG3752|consen  290 NSLTLW  295 (371)
T ss_pred             HHHHHH
Confidence            999743

>PRK07708 hypothetical protein; Validated

Probab=98.31  E-value=9.5e-06  Score=71.61  Aligned_cols=92  Identities=16%  Similarity=0.196  Sum_probs=64.4

Q ss_pred             cCCceEEEecCCCC--CCceeEEEEe--Cccee------eeecCCccchhHHHHHHHHHHHHHHHcCCCC--eEEEEecc
Q psy663          176 YANHTICYTDGSKS--PDVTGCAFSI--GDMVR------STLLNPINSIFSAELIAIFLCLEAILENPSD--QFLIVSDS  243 (275)
Q Consensus       176 ~~~~~~IyTDGSk~--~~~~G~a~~~--~~~~~------~~~l~~~~sif~AEl~aI~~al~~~~~~~~~--~~~I~sDS  243 (275)
                      .++.+.+|+|||-.  .++.|+|++.  .+...      ...++..++...||..|++.||+.+...+.+  .+.|++||
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            45679999999964  3457777654  22111      1245556799999999999999999887654  48999999


Q ss_pred             HHHHHHHhCCC-CCCHHHHHHHHHH
Q psy663          244 RSALAALANVK-FSNPLVTKVFSTW  267 (275)
Q Consensus       244 ~sal~al~n~~-~~~~i~~~I~~~~  267 (275)
                      +-++..+.+.. ..++..+..++.+
T Consensus       150 qlVi~qi~g~wk~~~~~l~~y~~~i  174 (219)
T PRK07708        150 QVVLNQLAGEWPCYDEHLNHWLDRI  174 (219)
T ss_pred             HHHHHHhCCCceeCChhHHHHHHHH
Confidence            99999998653 2333333444333

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=98.19  E-value=1.7e-05  Score=74.98  Aligned_cols=91  Identities=18%  Similarity=0.174  Sum_probs=64.4

Q ss_pred             ceEEEecCCCCCC--ceeEEEEe--Cc-c----eeeeecCCccchhHHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHH
Q psy663          179 HTICYTDGSKSPD--VTGCAFSI--GD-M----VRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAA  249 (275)
Q Consensus       179 ~~~IyTDGSk~~~--~~G~a~~~--~~-~----~~~~~l~~~~sif~AEl~aI~~al~~~~~~~~~~~~I~sDS~sal~a  249 (275)
                      .+.||||||...+  ..|+|++.  .+ .    .....++ .+|...||+.|++.||+.+.+....++.|++||+.++..
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            3689999998765  37888664  22 1    1122333 677889999999999999998888899999999999999


Q ss_pred             HhCCC-CCCHHHHHHHHHHHHH
Q psy663          250 LANVK-FSNPLVTKVFSTWRYL  270 (275)
Q Consensus       250 l~n~~-~~~~i~~~I~~~~~~l  270 (275)
                      +.+.. ..++-....+..++.|
T Consensus        81 i~~~~~~~~~~l~~~~~~i~~l  102 (372)
T PRK07238         81 MSGRWKVKHPDMKPLAAQAREL  102 (372)
T ss_pred             hCCCCccCChHHHHHHHHHHHH
Confidence            97643 2333233344444443

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

Probab=97.57  E-value=0.00022  Score=52.32  Aligned_cols=41  Identities=22%  Similarity=0.260  Sum_probs=35.6

Q ss_pred             hHHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHHHhCCCC
Q psy663          215 FSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALANVKF  255 (275)
Q Consensus       215 f~AEl~aI~~al~~~~~~~~~~~~I~sDS~sal~al~n~~~  255 (275)
                      ..||+.|++.||+++.+.+..+++|.|||+.++..|.+...
T Consensus         2 ~~aE~~al~~al~~a~~~g~~~i~v~sDs~~vv~~i~~~~~   42 (87)
T PF13456_consen    2 LEAEALALLEALQLAWELGIRKIIVESDSQLVVDAINGRSS   42 (87)
T ss_dssp             HHHHHHHHHHHHHHHHCCT-SCEEEEES-HHHHHHHTTSS-
T ss_pred             cHHHHHHHHHHHHHHHHCCCCEEEEEecCcccccccccccc
Confidence            57999999999999999999999999999999999987743

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

Probab=88.57  E-value=2  Score=35.73  Aligned_cols=52  Identities=17%  Similarity=0.149  Sum_probs=34.5

Q ss_pred             CceEEEecCCCCCCceeEEEEeC---cceee-------eecC--CccchhHHHHHHHHHHHHHHHc
Q psy663          178 NHTICYTDGSKSPDVTGCAFSIG---DMVRS-------TLLN--PINSIFSAELIAIFLCLEAILE  231 (275)
Q Consensus       178 ~~~~IyTDGSk~~~~~G~a~~~~---~~~~~-------~~l~--~~~sif~AEl~aI~~al~~~~~  231 (275)
                      ..+++|+|+|+  .+.|+.++..   +....       .+..  ...||=.-||.|+..|.+++..
T Consensus        80 ~~L~~F~DAS~--~aygavvYlr~~~~~~~~~~ll~aKsrv~P~k~~tIPRlEL~a~~l~~~l~~~  143 (159)
T PF05380_consen   80 VELHVFCDASE--SAYGAVVYLRSYSDGSVQVRLLFAKSRVAPLKTVTIPRLELLAALLGVRLANT  143 (159)
T ss_pred             eeeeEeecccc--cceeeEeEeeeccCCceeeeeeeecccccCCCCCcHHHHHHHHHHHHHHHHHH
Confidence            46899999995  4556655531   11111       1221  3459999999999999999854

---

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	275
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-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 = 41.0 bits (95), Expect = 3e-04
 Identities = 46/272 (16%), Positives = 82/272 (30%), Gaps = 61/272 (22%)

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 PSDQFLIVSDSRSALAALANVKFSNPLVTKVF 264
                L      + L  L NV   N      F
Sbjct: 234 LRR-LLKSKPYENCLLVLLNV--QNAKAWNAF 262

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	275
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.22
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	99.14
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	99.14
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.09
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	98.98
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	98.98
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	98.96
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	98.96
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	98.94
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	98.9
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	98.88
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	98.69
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	98.63
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	98.61
4htu_A	134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	98.6
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	98.55
1rw3_A	455	POL polyprotein; RNA and DNA dependent DNA polymer	88.52

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

Probab=99.22  E-value=4.1e-11  Score=98.39  Aligned_cols=76  Identities=18%  Similarity=0.217  Sum_probs=62.6

Q ss_pred             CCceEEEecCCCCCCc-----eeEEEEeCcc---eeeeecCCccchhHHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHH
Q psy663          177 ANHTICYTDGSKSPDV-----TGCAFSIGDM---VRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALA  248 (275)
Q Consensus       177 ~~~~~IyTDGSk~~~~-----~G~a~~~~~~---~~~~~l~~~~sif~AEl~aI~~al~~~~~~~~~~~~I~sDS~sal~  248 (275)
                      .+.+.||||||...++     .|+|++..+.   ..+..++..+|.+.||+.|+..||+.+......++.|+|||+.++.
T Consensus         5 ~~~~~iytDGs~~~n~~~~~~aG~Gvv~~~~~~~~~~~~l~~~~tn~~aEl~A~~~aL~~~~~~~~~~v~i~tDS~~vi~   84 (154)
T 2qkb_A            5 GDFVVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQAKTQNINKLVLYTNSMFTIN   84 (154)
T ss_dssp             TTEEEEEEEEEEETTTSSSCEEEEEEECSTTCTTCEEEECCSSCCHHHHHHHHHHHHHHHHHHTTCCEEEEEESCHHHHH
T ss_pred             CCeEEEEEccCcCCCCCCCCcEEEEEEEECCCceeEEeecCCCCchHHHHHHHHHHHHHHHHhCCCceEEEEECcHHHHh
Confidence            4678999999987543     7888876431   2345666678999999999999999998877789999999999999


Q ss_pred             HHhC
Q psy663          249 ALAN  252 (275)
Q Consensus       249 al~n  252 (275)
                      .|..
T Consensus        85 ~i~~   88 (154)
T 2qkb_A           85 GITN   88 (154)
T ss_dssp             HHHT
T ss_pred             hhhh
Confidence            9986

>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=99.14  E-value=1.6e-10  Score=92.56  Aligned_cols=92  Identities=14%  Similarity=0.200  Sum_probs=68.3

Q ss_pred             ceEEEecCCCCCC--ceeEEEEe--Cc---c--eeeeecCCccchhHHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHH
Q psy663          179 HTICYTDGSKSPD--VTGCAFSI--GD---M--VRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAA  249 (275)
Q Consensus       179 ~~~IyTDGSk~~~--~~G~a~~~--~~---~--~~~~~l~~~~sif~AEl~aI~~al~~~~~~~~~~~~I~sDS~sal~a  249 (275)
                      .+.||||||...+  ..|+|++.  .+   .  ..+..+ ..+|.+.||+.|+..||+++.+.+..+++|++||+.++..
T Consensus         3 ~~~iy~DGs~~~~~g~~g~G~v~~~~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~a~~~~~~~v~i~tDS~~vv~~   81 (141)
T 3hst_B            3 KVVIEADGGSRGNPGPAGYGAVVWTADHSTVLAESKQAI-GRATNNVAEYRGLIAGLDDAVKLGATEAAVLMDSKLVVEQ   81 (141)
T ss_dssp             EEEEEEEEEESSSSEEEEEEEEEEETTSCSEEEEEEEEE-EEECHHHHHHHHHHHHHHHHHHHTCSEEEEEESCHHHHHH
T ss_pred             EEEEEEecCCCCCCCCcEEEEEEEeCCCCcEEEeeeccC-CCCchHHHHHHHHHHHHHHHHHCCCceEEEEeChHHHHHH
Confidence            5799999998754  47888764  22   1  112223 4789999999999999999988778899999999999999


Q ss_pred             HhCC-CCCCHHHHHHHHHHHHHH
Q psy663          250 LANV-KFSNPLVTKVFSTWRYLK  271 (275)
Q Consensus       250 l~n~-~~~~~i~~~I~~~~~~l~  271 (275)
                      +... ...++....++..+..|.
T Consensus        82 i~~~~~~~~~~l~~~~~~i~~l~  104 (141)
T 3hst_B           82 MSGRWKVKHPDLLKLYVQAQALA  104 (141)
T ss_dssp             HTTSSCCCSHHHHHHHHHHHHHH
T ss_pred             HhCCcccCCHHHHHHHHHHHHHH
Confidence            9874 344554555666555543

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

Probab=99.14  E-value=1.2e-10  Score=92.91  Aligned_cols=92  Identities=21%  Similarity=0.217  Sum_probs=65.5

Q ss_pred             ceEEEecCCCCCC--ceeEEEEeCc----ce-eeeecCCccchhHHHHHHHHHHHHHHHcCCCC----eEEEEeccHHHH
Q psy663          179 HTICYTDGSKSPD--VTGCAFSIGD----MV-RSTLLNPINSIFSAELIAIFLCLEAILENPSD----QFLIVSDSRSAL  247 (275)
Q Consensus       179 ~~~IyTDGSk~~~--~~G~a~~~~~----~~-~~~~l~~~~sif~AEl~aI~~al~~~~~~~~~----~~~I~sDS~sal  247 (275)
                      .+.||||||...+  ..|+|++..+    .. ........+|.+.||+.|+..||+++.+.+..    +++|+|||+.++
T Consensus         3 ~~~iy~DGs~~~n~g~~G~G~v~~~~~g~~~~~~~~~~~~~tn~~aEl~A~~~aL~~a~~~~~~~~~~~v~i~tDS~~vi   82 (140)
T 3u3g_D            3 KIIIYTDGGARGNPGPAGIGVVITDEKGNTLHESSAYIGETTNNVAEYEALIRALEDLQMFGDKLVDMEVEVRMDSELIV   82 (140)
T ss_dssp             EEEEEEEEEESSTTEEEEEEEEEECTTSCEEEEEEEEEEEECHHHHHHHHHHHHHHHHGGGGGGGTTCEEEEEESCHHHH
T ss_pred             eEEEEEecCCCCCCCCcEEEEEEEeCCCCEEEEEEeeCCCCchHHHHHHHHHHHHHHHHHcCCCCCCceEEEEeChHHHH
Confidence            5899999998764  3788876522    11 11122235799999999999999999876655    999999999999


Q ss_pred             HHHhCCCC-CCHHHHHHHHHHHHH
Q psy663          248 AALANVKF-SNPLVTKVFSTWRYL  270 (275)
Q Consensus       248 ~al~n~~~-~~~i~~~I~~~~~~l  270 (275)
                      ..+..... .+.-...++..+..|
T Consensus        83 ~~i~~~~~~~~~~l~~~~~~i~~l  106 (140)
T 3u3g_D           83 RQMQGVYKVKEPTLKEKFAKIAHI  106 (140)
T ss_dssp             HHHTTSSCCCCGGGHHHHHHHHHH
T ss_pred             HHhCCCcccCCHHHHHHHHHHHHH
Confidence            99987542 343333445555444

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

Probab=99.09  E-value=1.5e-10  Score=94.12  Aligned_cols=72  Identities=28%  Similarity=0.292  Sum_probs=56.5

Q ss_pred             CceEEEecCCCCCCc--eeEEEEe--Ccce--eeeecCCccchhHHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHHHh
Q psy663          178 NHTICYTDGSKSPDV--TGCAFSI--GDMV--RSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALA  251 (275)
Q Consensus       178 ~~~~IyTDGSk~~~~--~G~a~~~--~~~~--~~~~l~~~~sif~AEl~aI~~al~~~~~~~~~~~~I~sDS~sal~al~  251 (275)
                      +.+.||||||...++  .|+|++.  ++..  .+..+ ..+|...||+.|+..||+.+.+  ..++.|+|||+.++..|.
T Consensus         3 ~~i~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~~~~-~~~Tnn~aEl~A~~~AL~~~~~--~~~v~I~tDS~~vi~~i~   79 (146)
T 3h08_A            3 KTITIYTDGAASGNPGKGGWGALLMYGSSRKEISGYD-PATTNNRMELMAAIKGLEALKE--PARVQLYSDSAYLVNAMN   79 (146)
T ss_dssp             CEEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCSS--CCEEEEEESCHHHHHHHH
T ss_pred             ceEEEEEecCCCCCCCceEEEEEEEECCeeEEeecCC-CCCcHHHHHHHHHHHHHHhcCc--cCcEEEEeChHHHHHHHH
Confidence            468999999977653  7888764  3221  12223 4678999999999999999865  579999999999999998


Q ss_pred             C
Q psy663          252 N  252 (275)
Q Consensus       252 n  252 (275)
                      .
T Consensus        80 ~   80 (146)
T 3h08_A           80 E   80 (146)
T ss_dssp             S
T ss_pred             H
Confidence            7

>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=98.98  E-value=2e-10  Score=93.76  Aligned_cols=93  Identities=13%  Similarity=0.038  Sum_probs=64.1

Q ss_pred             cCCceEEEecCCCCCCceeEEEEe--Ccce--eee-ec--CC--ccchhHHHHHHHHHHHHHHHcCCCCeEEEEeccHHH
Q psy663          176 YANHTICYTDGSKSPDVTGCAFSI--GDMV--RST-LL--NP--INSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSA  246 (275)
Q Consensus       176 ~~~~~~IyTDGSk~~~~~G~a~~~--~~~~--~~~-~l--~~--~~sif~AEl~aI~~al~~~~~~~~~~~~I~sDS~sa  246 (275)
                      +++.+.||||||...+..|+|++.  .+..  .+. ..  +.  .++++.||+.|+..||+++.+.+. ++.|+|||+.+
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            346789999999988668999765  2221  222 22  22  368999999999999999876555 99999999987


Q ss_pred             HHHHhCCC-CCCHHHHHHHHHHHH
Q psy663          247 LAALANVK-FSNPLVTKVFSTWRY  269 (275)
Q Consensus       247 l~al~n~~-~~~~i~~~I~~~~~~  269 (275)
                      ..-+.+.. ...+..+..++.+++
T Consensus        82 ~~w~~~~w~~~~~~~~~~~~l~~~  105 (147)
T 2kq2_A           82 AFWATGEWKAKNEFTQAYAKLMNQ  105 (147)
T ss_dssp             HHHTTSSSSCCHHHHHHHHCGGGG
T ss_pred             HHHHhCCCccCCcchHHHHHHHHH
Confidence            77665432 333344444444443

>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=98.98  E-value=1.6e-09  Score=90.31  Aligned_cols=71  Identities=25%  Similarity=0.242  Sum_probs=55.1

Q ss_pred             CceEEEecCCCCC--CceeEEEEe--Ccc-eeeeecCCccchhHHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHHHh
Q psy663          178 NHTICYTDGSKSP--DVTGCAFSI--GDM-VRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALA  251 (275)
Q Consensus       178 ~~~~IyTDGSk~~--~~~G~a~~~--~~~-~~~~~l~~~~sif~AEl~aI~~al~~~~~~~~~~~~I~sDS~sal~al~  251 (275)
                      ..+.||||||...  +..|+|++.  ++. .....+...+|++.||+.|+..||+++   ...++.|+|||+.++..|-
T Consensus        22 ~~i~iytDGs~~~npG~~g~G~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~---~~~~v~I~tDS~~vi~~iw   97 (165)
T 3p1g_A           22 ADYTWYTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMA---EGKKLNVYTDSRYAFATAH   97 (165)
T ss_dssp             CSEEEEEEEEEEEETTEEEEEEEEECSSCEEEEEEECTTCCHHHHHHHHHHHHHHHT---BTSEEEEEECCHHHHHHHH
T ss_pred             CCEEEEEEcccCCCCCceEEEEEEEECCEEEEEecCCCCCcHHHHHHHHHHHHHHHc---cCceEEEEEchHHHHhhhh
Confidence            3589999999873  336676543  332 222256678899999999999999998   3689999999999999994

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

Probab=98.96  E-value=2.2e-09  Score=87.24  Aligned_cols=74  Identities=18%  Similarity=0.138  Sum_probs=57.2

Q ss_pred             eEEEecCCCC-C--CceeE-EEEeC--cc-eeee--ecC---CccchhHHHHHHHHHHHHHHHcCCCCeEEEEeccHHHH
Q psy663          180 TICYTDGSKS-P--DVTGC-AFSIG--DM-VRST--LLN---PINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSAL  247 (275)
Q Consensus       180 ~~IyTDGSk~-~--~~~G~-a~~~~--~~-~~~~--~l~---~~~sif~AEl~aI~~al~~~~~~~~~~~~I~sDS~sal  247 (275)
                      +.||||||.. .  +..|+ |++..  +. ...+  .++   +.+|.+.||+.|+..||+.+......++.|++||+.++
T Consensus         2 ~~iy~DGs~~~~n~g~~G~~G~vi~~~g~~~~~~~~~~~~~~~~~tnn~aEl~A~~~aL~~a~~~g~~~v~i~tDS~~vi   81 (149)
T 2ehg_A            2 IIGYFDGLCEPKNPGGIATFGFVIYLDNRKIEGYGLAEKPFSINSTNNVAEYSGLICLMETMLRLGISSPIIKGDSQLVI   81 (149)
T ss_dssp             CEEEEEEEEESSSSSSEEEEEEEEECSSCEEEEEEECSCTTCTTCCHHHHHHHHHHHHHHHHHHHTCCSCEEEESCHHHH
T ss_pred             EEEEEeeccCCCCCChheEEEEEEEECCEEEEEeccccCCCCCCccHHHHHHHHHHHHHHHHHHcCCCEEEEEeChHHHH
Confidence            5799999987 2  44775 76542  21 1222  222   37889999999999999999887778999999999999


Q ss_pred             HHHhCC
Q psy663          248 AALANV  253 (275)
Q Consensus       248 ~al~n~  253 (275)
                      ..+..+
T Consensus        82 ~~i~~~   87 (149)
T 2ehg_A           82 KQMNGE   87 (149)
T ss_dssp             HHHTTS
T ss_pred             HHHhCc
Confidence            999876

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

Probab=98.96  E-value=1.1e-09  Score=90.42  Aligned_cols=72  Identities=22%  Similarity=0.245  Sum_probs=55.8

Q ss_pred             CceEEEecCCCCCC-c-eeEEEEe--Ccce--eeeecCCccchhHHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHHHh
Q psy663          178 NHTICYTDGSKSPD-V-TGCAFSI--GDMV--RSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALA  251 (275)
Q Consensus       178 ~~~~IyTDGSk~~~-~-~G~a~~~--~~~~--~~~~l~~~~sif~AEl~aI~~al~~~~~~~~~~~~I~sDS~sal~al~  251 (275)
                      ..+.||||||...+ + .|+|++.  .+..  .+..+ +.+|.+.||+.|+..||+.+..  ..++.|+|||+.++..|.
T Consensus         5 ~~i~iytDGs~~~n~g~~G~G~v~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~AL~~~~~--~~~v~I~tDS~~vi~~i~   81 (158)
T 2e4l_A            5 KLIHIFTDGSCLGNPGPGGYGIVMNYKGHTKEMSDGF-SLTTNNRMELLAPIVALEALKE--PCKIILTSDSQYMRQGIM   81 (158)
T ss_dssp             CEEEEEEEEEESSSSEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCSS--CCEEEEEECCHHHHHHHH
T ss_pred             CeEEEEEcccccCCCCcEEEEEEEEECCEEEEEecCc-CCCccHHHHHHHHHHHHHHhcc--CCeEEEEeCHHHHHHHHH
Confidence            46899999998754 3 7888765  2221  12233 3578999999999999998754  389999999999999998


Q ss_pred             C
Q psy663          252 N  252 (275)
Q Consensus       252 n  252 (275)
                      .
T Consensus        82 ~   82 (158)
T 2e4l_A           82 T   82 (158)
T ss_dssp             T
T ss_pred             H
Confidence            7

>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=98.94  E-value=9.4e-10  Score=90.47  Aligned_cols=71  Identities=20%  Similarity=0.206  Sum_probs=55.7

Q ss_pred             ceEEEecCCCCCC-c-eeEEEEeC--cc--eeeeecCCccchhHHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHHHhC
Q psy663          179 HTICYTDGSKSPD-V-TGCAFSIG--DM--VRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALAN  252 (275)
Q Consensus       179 ~~~IyTDGSk~~~-~-~G~a~~~~--~~--~~~~~l~~~~sif~AEl~aI~~al~~~~~~~~~~~~I~sDS~sal~al~n  252 (275)
                      .+.||||||...+ + .|+|++..  +.  ..+..+ ..+|.+.||+.|+..||+.+.+  ..++.|+|||+.++..|..
T Consensus         4 ~~~iytDGs~~~n~~~~G~G~v~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~~~~--~~~v~I~tDS~~vi~~i~~   80 (155)
T 1jl1_A            4 QVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGY-TRTTNNRMELMAAIVALEALKE--HAEVILSTDSQYVRQGITQ   80 (155)
T ss_dssp             CEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCCS--CCEEEEEECCHHHHHHHHT
T ss_pred             eEEEEEccccCCCCCceEEEEEEEECCeEEEEecCC-CCCcHHHHHHHHHHHHHHHhCc--CCcEEEEeCHHHHHHHHHH
Confidence            5899999998764 3 78887652  22  122233 4678999999999999999865  3799999999999999986

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

Probab=98.90  E-value=1.9e-09  Score=89.75  Aligned_cols=72  Identities=21%  Similarity=0.087  Sum_probs=55.6

Q ss_pred             CceEEEecCCCCCC-c-eeEEEEeC--cce--eeeecCCccchhHHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHHHh
Q psy663          178 NHTICYTDGSKSPD-V-TGCAFSIG--DMV--RSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALA  251 (275)
Q Consensus       178 ~~~~IyTDGSk~~~-~-~G~a~~~~--~~~--~~~~l~~~~sif~AEl~aI~~al~~~~~~~~~~~~I~sDS~sal~al~  251 (275)
                      ..+.||||||...+ + .|+|++..  +..  .+... ..+|.+.||+.|+..||+.+...  .++.|+|||+.++..|.
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            46899999998865 3 78887753  221  11122 46789999999999999987543  58999999999999998


Q ss_pred             C
Q psy663          252 N  252 (275)
Q Consensus       252 n  252 (275)
                      .
T Consensus        84 ~   84 (166)
T 1ril_A           84 E   84 (166)
T ss_dssp             S
T ss_pred             h
Confidence            8

>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=98.88  E-value=5.4e-09  Score=85.66  Aligned_cols=73  Identities=22%  Similarity=0.279  Sum_probs=56.6

Q ss_pred             cCCceEEEecCCCCCCc--eeEEEEeCc-ceeeeecCCccchhHHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHHHhC
Q psy663          176 YANHTICYTDGSKSPDV--TGCAFSIGD-MVRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALAN  252 (275)
Q Consensus       176 ~~~~~~IyTDGSk~~~~--~G~a~~~~~-~~~~~~l~~~~sif~AEl~aI~~al~~~~~~~~~~~~I~sDS~sal~al~n  252 (275)
                      ..+.+.||||||...+.  .|+|++..+ ....+.+ ..+|...||+.|+..||+.+    ..++.|+|||+.++..|..
T Consensus         9 ~~~~~~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~-~~~Tnn~aEl~A~i~AL~~~----~~~v~i~tDS~~v~~~i~~   83 (150)
T 3qio_A            9 IVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTL-TDTTNQKTELQAIYLALQDS----GLEVNIVTDSQYALGIITQ   83 (150)
T ss_dssp             CTTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEEE-SSCCHHHHHHHHHHHHHHHS----CSEEEEEESCHHHHHHHHH
T ss_pred             CCCCEEEEEccCCCCCCCCeEEEEEEEcCCEEEEeC-CCCCHHHHHHHHHHHHHHhC----CCcEEEEeCcHHHHHHHHH
Confidence            34678999999976543  677776533 2223344 46899999999999999984    4899999999999999986


Q ss_pred             C
Q psy663          253 V  253 (275)
Q Consensus       253 ~  253 (275)
                      +
T Consensus        84 w   84 (150)
T 3qio_A           84 W   84 (150)
T ss_dssp             H
T ss_pred             H
Confidence            4

>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=98.69  E-value=4.9e-08  Score=95.59  Aligned_cols=85  Identities=21%  Similarity=0.274  Sum_probs=64.5

Q ss_pred             CceEEEecCCCCCCc--eeEEEEeC-cceeeeecCCccchhHHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHHHhCCC
Q psy663          178 NHTICYTDGSKSPDV--TGCAFSIG-DMVRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALANVK  254 (275)
Q Consensus       178 ~~~~IyTDGSk~~~~--~G~a~~~~-~~~~~~~l~~~~sif~AEl~aI~~al~~~~~~~~~~~~I~sDS~sal~al~n~~  254 (275)
                      +.+.||||||...++  .|+|++.. +....+.+ ..+|.+.||+.|+..||+.+    ..++.|+|||+.++..|..+.
T Consensus       438 ~~~~iytDGs~~~n~g~~g~g~v~~~~~~~~~~~-~~~TNn~aEl~Ai~~aL~~~----~~~v~I~tDS~~vi~~i~~~~  512 (557)
T 2zd1_A          438 GAETFYVDGAANRETKLGKAGYVTNKGRQKVVPL-TNTTNQKTELQAIYLALQDS----GLEVNIVTDSQYALGIIQAQP  512 (557)
T ss_dssp             TSCEEEEEEEECTTTCCEEEEEEETTSCEEEEEE-CSCCHHHHHHHHHHHHHHHS----CSEEEEEECCHHHHHHHTTCC
T ss_pred             CCEEEEEccCCCCCCCceEEEEEEECCcEEEecC-CCCCHHHHHHHHHHHHHHhC----CCcEEEEeChHHHHHHHhcCC
Confidence            568999999976543  67776653 22233333 46789999999999999998    679999999999999999876


Q ss_pred             CC--CHHHHHHHHHH
Q psy663          255 FS--NPLVTKVFSTW  267 (275)
Q Consensus       255 ~~--~~i~~~I~~~~  267 (275)
                      ..  .++.+++.+.+
T Consensus       513 ~~~~~~l~~~~~~~l  527 (557)
T 2zd1_A          513 DKSESELVNQIIEQL  527 (557)
T ss_dssp             SEESSHHHHHHHHHH
T ss_pred             ccCCHHHHHHHHHHH
Confidence            54  56666665544

>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=98.63  E-value=7e-08  Score=78.39  Aligned_cols=76  Identities=20%  Similarity=0.106  Sum_probs=58.2

Q ss_pred             CCceEEEecCCCCCC--ceeEEEEeCc--cee--eeecCCccchhHHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHHH
Q psy663          177 ANHTICYTDGSKSPD--VTGCAFSIGD--MVR--STLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAAL  250 (275)
Q Consensus       177 ~~~~~IyTDGSk~~~--~~G~a~~~~~--~~~--~~~l~~~~sif~AEl~aI~~al~~~~~~~~~~~~I~sDS~sal~al  250 (275)
                      ...+.||||||...+  ..|+|++...  ...  +..+ ..+|...||+.|+..||+.+.+... ++.|+|||+.++..+
T Consensus         9 ~~~~~iy~DGa~~gNpG~~G~G~vl~~~g~~~~~~~~~-~~~TNN~aEl~A~i~aL~~~~~~~~-~v~i~tDS~~vi~w~   86 (142)
T 1zbf_A            9 IIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPI-PIGTNNMGEFLAIVHGLRYLKERNS-RKPIYSNSQTAIKWV   86 (142)
T ss_dssp             CCSSSEEEEEEECSSSEEEEEEEEETTTCCEEEECCCE-EEECHHHHHHHHHHHHHHHHHHTTC-CCCEEESCHHHHHHH
T ss_pred             CCeEEEEEeeccCCCCCCeEEEEEEEeCCEEEEEeccc-CCcCcHHHHHHHHHHHHHHHHhCCC-eEEEEEehHHHHHHH
Confidence            356799999997654  3788887632  111  1122 2578999999999999999987655 899999999999999


Q ss_pred             hCCC
Q psy663          251 ANVK  254 (275)
Q Consensus       251 ~n~~  254 (275)
                      ++..
T Consensus        87 ~~~~   90 (142)
T 1zbf_A           87 KDKK   90 (142)
T ss_dssp             HHTC
T ss_pred             HcCC
Confidence            8664

>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=98.61  E-value=1.2e-07  Score=92.80  Aligned_cols=86  Identities=19%  Similarity=0.223  Sum_probs=64.1

Q ss_pred             CCceEEEecCCCCCCc--eeEEEEeCc-ceeeeecCCccchhHHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHHHhCC
Q psy663          177 ANHTICYTDGSKSPDV--TGCAFSIGD-MVRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALANV  253 (275)
Q Consensus       177 ~~~~~IyTDGSk~~~~--~G~a~~~~~-~~~~~~l~~~~sif~AEl~aI~~al~~~~~~~~~~~~I~sDS~sal~al~n~  253 (275)
                      .+.+.||||||...++  .|+|++... ......+ ..+|...||+.|+..||+.    ...++.|+|||+.++..|..+
T Consensus       434 ~~~~~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~-~~~TNn~aEl~A~i~aL~~----~~~~v~I~tDS~~v~~~i~~~  508 (555)
T 1mu2_A          434 PGAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKL-EQTTNQQAELEAFAMALTD----SGPKVNIIVDSQYVMGIVASQ  508 (555)
T ss_dssp             TTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEEE-SSCCHHHHHHHHHHHHHHT----SCSEEEEEESCHHHHHHHHTC
T ss_pred             CCceEEEEcccccCCCCCceEEEEEEeCCEeeccC-CCCCHHHHHHHHHHHHHHc----CCCeEEEEEehHHHHHHHhcc
Confidence            3568999999987653  677776532 2223333 4678999999999999998    567999999999999999987


Q ss_pred             CC--CCHHHHHHHHHH
Q psy663          254 KF--SNPLVTKVFSTW  267 (275)
Q Consensus       254 ~~--~~~i~~~I~~~~  267 (275)
                      ..  ..++.+++.+.+
T Consensus       509 ~~~~~~~l~~~~~~~~  524 (555)
T 1mu2_A          509 PTESESKIVNQIIEEM  524 (555)
T ss_dssp             CSEESCHHHHHHHHHH
T ss_pred             cccccHHHHHHHHHHh
Confidence            53  356666655543

>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=98.60  E-value=1.2e-07  Score=76.17  Aligned_cols=76  Identities=18%  Similarity=0.065  Sum_probs=55.6

Q ss_pred             CCceEEEecCCCCCC-c-eeEEEEe-Cc-c--eeeeecCCccchhHHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHHH
Q psy663          177 ANHTICYTDGSKSPD-V-TGCAFSI-GD-M--VRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAAL  250 (275)
Q Consensus       177 ~~~~~IyTDGSk~~~-~-~G~a~~~-~~-~--~~~~~l~~~~sif~AEl~aI~~al~~~~~~~~~~~~I~sDS~sal~al  250 (275)
                      +....||||||...+ | .|+|.|. .+ .  .....+ ..+|...||+.|+..||+.+.+.... +.|+|||+.++.-|
T Consensus         3 p~~~~iytDGac~GNPGp~G~ggV~~~~g~~~~~~g~~-~~tTNN~aEl~A~i~aL~~l~~~~~~-v~i~tDSqyVi~wi   80 (134)
T 4htu_A            3 IIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPI-PIGTNNMGEFLAIVHGLRYLKERNSR-KPIYSNSQTAIKWV   80 (134)
T ss_dssp             CCSSSEEEEEEEETTTEEEEEEEEETTTCCEEEEEEEE-EEECHHHHHHHHHHHHHHHHHHTTCC-CCEEESCHHHHHHH
T ss_pred             ccceEEEEeeccCCCCCCeEEEEEEEECCEEEEEecCC-CCCchHHHHHHHHHHHHHHHHhCCCC-EEEEcchHHHHHHH
Confidence            456789999997654 3 7785443 22 1  122223 36899999999999999999875433 79999999999999


Q ss_pred             hCCC
Q psy663          251 ANVK  254 (275)
Q Consensus       251 ~n~~  254 (275)
                      .+..
T Consensus        81 ~~~~   84 (134)
T 4htu_A           81 KDKK   84 (134)
T ss_dssp             HHTC
T ss_pred             HcCC
Confidence            8643

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

Probab=98.55  E-value=1e-07  Score=79.27  Aligned_cols=74  Identities=18%  Similarity=0.188  Sum_probs=52.2

Q ss_pred             CceEEEecCCCCCC--c-----eeEEEEeC--cc----eeeeecC-CccchhHHHHHHHHHHHHHHHcCCCCeEEEEecc
Q psy663          178 NHTICYTDGSKSPD--V-----TGCAFSIG--DM----VRSTLLN-PINSIFSAELIAIFLCLEAILENPSDQFLIVSDS  243 (275)
Q Consensus       178 ~~~~IyTDGSk~~~--~-----~G~a~~~~--~~----~~~~~l~-~~~sif~AEl~aI~~al~~~~~~~~~~~~I~sDS  243 (275)
                      ..++||||||...+  .     .|+|++..  +.    ...+..+ ...+-..||+.|+..||+.+... +.++.|+|||
T Consensus         6 ~evviYTDGsc~gNpgp~~~~~aG~Gv~~~~~~~~~~~~~~~~~~tnn~te~~Aei~Al~~al~~al~~-~~~v~I~TDS   84 (165)
T 2lsn_A            6 YEGVFYTDGSAIKSPDPTKSNNAGMGIVHATYKPEYQVLNQWSIPLGNHTAQMAEIAAVEFACKKALKI-PGPVLVITDS   84 (165)
T ss_dssp             CSEEEEEEEEEEECSSCTTCEEEEEEEEEECCSSSCCEEEEEEEEESSCCHHHHHHHHHHHHHHHHHHS-SSCEEEEESC
T ss_pred             ceEEEEEcCCCCCCCCCCCCCcEEEEEEEEECCCccEEeccccCCchHHHHHHHHHHHHHHHHHHHhcC-CCeEEEEeCh
Confidence            45799999997643  2     68887742  21    2223332 45567778888888888877653 3579999999


Q ss_pred             HHHHHHHhC
Q psy663          244 RSALAALAN  252 (275)
Q Consensus       244 ~sal~al~n  252 (275)
                      +.++..|..
T Consensus        85 ~Yvi~~it~   93 (165)
T 2lsn_A           85 FYVAESANK   93 (165)
T ss_dssp             HHHHHHHHT
T ss_pred             HHHHhhhhh
Confidence            999999963

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

Probab=88.52  E-value=0.15  Score=48.09  Aligned_cols=73  Identities=10%  Similarity=-0.092  Sum_probs=48.2

Q ss_pred             CceEEEecCCCCCCceeEEEEe-Cc---c----eeeeecC---CccchhHHHHHHHHHHHHHHHcC-CCCeEEEEeccHH
Q psy663          178 NHTICYTDGSKSPDVTGCAFSI-GD---M----VRSTLLN---PINSIFSAELIAIFLCLEAILEN-PSDQFLIVSDSRS  245 (275)
Q Consensus       178 ~~~~IyTDGSk~~~~~G~a~~~-~~---~----~~~~~l~---~~~sif~AEl~aI~~al~~~~~~-~~~~~~I~sDS~s  245 (275)
                      ....+|||+|.  +++|+ +.. .+   .    ..+-++.   ...+++..|+.||..|++.+... .+..++|+||+. 
T Consensus       345 ~~~~l~~DAS~--~~~ga-vL~q~~~~~~~~i~y~Sk~l~~~e~~ys~~ekEllAi~~a~~~~~~yl~g~~~~v~tDh~-  420 (455)
T 1rw3_A          345 KPFELFVDEKQ--GYAKG-VLTQKLGPWRRPVAYLSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLTMGQPLVIKAPHA-  420 (455)
T ss_dssp             CTTSCEEEEEE--CSSSB-EECCBCTTTTCCCCCCCBCSCSSCSSSCCSSHHHHHHHHHHHHHHGGGCSSCEEEECSSC-
T ss_pred             CcEEEEEeccC--Cccee-EEEEecCCcEEEEEEEcccCCccccccchHHHHHHHHHHHHHHHHHHcCCCcEEEEecCh-
Confidence            45689999985  34443 332 11   0    1111222   34578999999999999988653 567999999996 


Q ss_pred             HHHHHhCCC
Q psy663          246 ALAALANVK  254 (275)
Q Consensus       246 al~al~n~~  254 (275)
                      ++.-+.++.
T Consensus       421 ~~~~l~~~~  429 (455)
T 1rw3_A          421 VEALVKQPP  429 (455)
T ss_dssp             TTTTSSSTT
T ss_pred             HHHHhCCCc
Confidence            666665543

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	275
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	99.24
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.18
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	98.84
d1zbfa1	132	BH0863-like Ribonuclease H {Bacillus halodurans [T	98.75
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	98.63

>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=99.24  E-value=1.6e-11  Score=93.90  Aligned_cols=86  Identities=21%  Similarity=0.264  Sum_probs=62.0

Q ss_pred             CceEEEecCCCCCC-c-eeEEEEeCc-ceeeeecCCccchhHHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHHHhCCC
Q psy663          178 NHTICYTDGSKSPD-V-TGCAFSIGD-MVRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALANVK  254 (275)
Q Consensus       178 ~~~~IyTDGSk~~~-~-~G~a~~~~~-~~~~~~l~~~~sif~AEl~aI~~al~~~~~~~~~~~~I~sDS~sal~al~n~~  254 (275)
                      +...+|||||...+ + .|+|++..+ ......++ ..|...||+.||.+||+.    ...++.|+|||+.++.++....
T Consensus         7 ~~~t~ytDGs~~~n~~~g~~g~~~~~~~~~~~~~~-~~TNn~aEl~Avi~aL~~----~~~~v~I~TDS~yvi~~i~~~~   81 (110)
T d1s1ta1           7 GAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLT-DTTNQKTELQAIYLALQD----SGLEVNIVTDSQYALGIIQAQP   81 (110)
T ss_dssp             TSEEEEEEEEEETTTTEEEEEEEETTSCEEEEEES-SCCHHHHHHHHHHHHHHH----SCSEEEEEECCHHHHHHHHHCC
T ss_pred             CCcEEEEeCCCCCCCCCcEEEEEEecCCeEEEecc-cCcHHHHHHHHHHHHHHh----CCCeEEEEEehHHHHHHHhcCc
Confidence            45689999996544 3 455555443 23334444 568999999999999974    4568999999999999998755


Q ss_pred             C--CCHHHHHHHHHHH
Q psy663          255 F--SNPLVTKVFSTWR  268 (275)
Q Consensus       255 ~--~~~i~~~I~~~~~  268 (275)
                      .  .+.+.++|.+.+.
T Consensus        82 ~~~~~~l~~~il~~l~   97 (110)
T d1s1ta1          82 DQSESELVNQIIEQLI   97 (110)
T ss_dssp             SEESCHHHHHHHHHHH
T ss_pred             cccchHHHHHHHHHHh
Confidence            4  3677777766554

>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=99.18  E-value=5e-11  Score=92.78  Aligned_cols=73  Identities=21%  Similarity=0.201  Sum_probs=54.9

Q ss_pred             CceEEEecCCCCCC-c-eeEEEEeCcc-eeeeecCCccchhHHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHHHhCCC
Q psy663          178 NHTICYTDGSKSPD-V-TGCAFSIGDM-VRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALANVK  254 (275)
Q Consensus       178 ~~~~IyTDGSk~~~-~-~G~a~~~~~~-~~~~~l~~~~sif~AEl~aI~~al~~~~~~~~~~~~I~sDS~sal~al~n~~  254 (275)
                      ....||||||...+ + .|+|++.... .....++ ..|++.||+.||.+||+.    ...++.|+|||+.++..+.+..
T Consensus         6 ~~~t~YTDGS~~~n~~~~~~g~~~~~~~~~~~~~~-~~tnn~AEl~Ai~~al~~----~~~~i~I~tDS~~v~~~~~~~~   80 (126)
T d1mu2a1           6 GAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKLE-QTTNQQAELEAFAMALTD----SGPKVNIIVDSQYVMGIVASQP   80 (126)
T ss_dssp             TCEEEEEEEEECTTTCCEEEEEEETTSCEEEEEES-SCCHHHHHHHHHHHHHHT----SCSEEEEEESCHHHHHHHHTCC
T ss_pred             CCcEEEEcCCCCCCCCcEEEEEEecCCCEEEEecC-CCcchHHHHHHHHHHhcc----CCcceEEEechHHHHHHHhcCC
Confidence            44689999996554 4 5566655443 3333444 578999999999999874    4678999999999999999865


Q ss_pred             C
Q psy663          255 F  255 (275)
Q Consensus       255 ~  255 (275)
                      .
T Consensus        81 ~   81 (126)
T d1mu2a1          81 T   81 (126)
T ss_dssp             S
T ss_pred             c
Confidence            4

>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=98.84  E-value=1.6e-09  Score=85.94  Aligned_cols=73  Identities=18%  Similarity=0.058  Sum_probs=54.0

Q ss_pred             CceEEEecCCCCCC-c-eeEEEEe--Cc-ceeeeecCCccchhHHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHHHhC
Q psy663          178 NHTICYTDGSKSPD-V-TGCAFSI--GD-MVRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALAN  252 (275)
Q Consensus       178 ~~~~IyTDGSk~~~-~-~G~a~~~--~~-~~~~~~l~~~~sif~AEl~aI~~al~~~~~~~~~~~~I~sDS~sal~al~n  252 (275)
                      ..++||||||...+ | .|+|++.  .+ ....+.....+|..+||+.|+++||+++.  ....+.|++||+.++..+..
T Consensus         2 ~~i~iytDGs~~~N~g~~G~g~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~~--~~~~i~i~tds~~~~~~~~~   79 (147)
T d1rila_           2 KRVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALK--EPCEVDLYTDSHYLKKAFTE   79 (147)
T ss_dssp             CCCCEEEEEEESSTTEEEEEEEEECBTTBCCEECCEEEEECHHHHHHHHHHHHHHSCC--SCCEEEEECCCHHHHHHHHS
T ss_pred             CEEEEEEccCCCCCCCccEEEEEEEECCcceEEecccccccHHHHHHHHHHHHhhhcc--CCceEEEecchhhhhccccc
Confidence            35899999998765 3 6788764  22 22222223456899999999999998653  45689999999999988865

>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=98.75  E-value=1.2e-08  Score=79.80  Aligned_cols=73  Identities=19%  Similarity=0.053  Sum_probs=54.8

Q ss_pred             EEEecCCCCCC-c-eeEEEEeCc--ceeeeecC-CccchhHHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHHHhCCC
Q psy663          181 ICYTDGSKSPD-V-TGCAFSIGD--MVRSTLLN-PINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALANVK  254 (275)
Q Consensus       181 ~IyTDGSk~~~-~-~G~a~~~~~--~~~~~~l~-~~~sif~AEl~aI~~al~~~~~~~~~~~~I~sDS~sal~al~n~~  254 (275)
                      -||||||...+ | .|+|+|...  ....++-+ +..|...||+.|+..||+++.+.. .++.|+|||+.++..+.+..
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 SLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERN-SRKPIYSNSQTAIKWVKDKK   83 (132)
T ss_dssp             SEEEEEEECSSSEEEEEEEEETTTCCEEEECCCEEEECHHHHHHHHHHHHHHHHHHTT-CCCCEEESCHHHHHHHHHTC
T ss_pred             eEEEeecCCCCCchheEEEEEEcCCEEEEEEcCcCccchHHHHHHHHHHHHHHhhcCC-ceEEEEeccHHHHHHHHhCc
Confidence            48999997765 3 788877532  22222211 467889999999999999998744 57899999999999997654

>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=98.63  E-value=2.6e-08  Score=78.66  Aligned_cols=73  Identities=16%  Similarity=0.178  Sum_probs=53.4

Q ss_pred             ceEEEecCCCCCCc--eeEEEEe--Ccceeeeec-CCccchhHHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHHHhCC
Q psy663          179 HTICYTDGSKSPDV--TGCAFSI--GDMVRSTLL-NPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALANV  253 (275)
Q Consensus       179 ~~~IyTDGSk~~~~--~G~a~~~--~~~~~~~~l-~~~~sif~AEl~aI~~al~~~~~~~~~~~~I~sDS~sal~al~n~  253 (275)
                      .+.||||||...++  .|+|++.  ++....+.. .+..|...||+.|+..||+++.  ....+.|.+||+.++..+...
T Consensus         2 ~I~IYtDGS~~~N~g~aG~G~vi~~~~~~~~~~~~~~~~tnn~aE~~Ai~~Al~~~~--~~~~i~i~tds~~~i~~~~~~   79 (152)
T d1jl1a_           2 QVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALK--EHAEVILSTDSQYVRQGITQW   79 (152)
T ss_dssp             CEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEEEEECHHHHHHHHHHHHHHTCC--SCCEEEEEECCHHHHHHHHTT
T ss_pred             EEEEEEeCCCCCCCCcEEEEEEEEECCeEEEeccccCcccHHHHHHhhhhhhhhhhc--ccceEEEeecceeeEEcccch
Confidence            47999999977653  7888764  333222222 2456889999999999998753  456789999999999888643