Psyllid ID: psy5480

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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------
Protein Sequence
HILNKLNPVHNSGIRIATGALRSSPIPSLLVESGVPPLQLRRSQLAMSYAVKIASCPANPTYSLLFPDNIDADIYPLNKPKPLCLRVRELALFSRTLQNSEFAPYCKFFPPWSIATPVIDNALSFDKKENVSSVVFQQRFHELVQSKYQDFTLCFTDGSKTANNTSCAYIIDKTLISSFVLNNVNSVYTSELIAVLLCLKHLKFLPKEKFVVISDSKSTLLALSNPSNTNPIVSLIHSCWTDLLCYGKQLAFLWCPSHTGIQGNEAVDRAARNPSASLPPLKLCSPEDFKPFICKLIKDLWQNSWSNIPNSEAVDRAARNPSASLPPLKLCSPEDFKPFIMIGRTGSIKPVIGPWPSSDRQSRYEEVVICRMRIGHTRATHGHLFKRAPPSTCRCGETLSVQHILTCTLHGHIRASLPAPPALTDDVESVDSMLKYLKKLNLYAKI
Secondary Structure (PSIPRED)
cHHHHHHHHHHHHHHHHHcccccccHHHHHHHcccccHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHccccccEEEEcccccccccccEEEEEccccEEEEEEcccccccHHHHHHHHHHHHHHHccccccEEEEccHHHHHHHHcccccccHHHHHHHHHHHHHHHcccEEEEEEccccccccHHHHHHHHHccccccccccccccccccHHHHHHHHHHHHHcccccccccHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEEEccccccHHccccccccccccccccccHHHHccccccHHHHHcccccccccccHHHHHHHHHHHHHHcccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHHHHHHHcccccccHHHHHHHHccccHHHHHHHHHHHHHHHHHcccccccHHHHcccccccccccccccccccHHHHHHHcccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHcccccEEEEEccccccccEEEEEEEEccccEEEccccccHHHHHHHHHHHHHHHHHHHcccccEEEEEccHHHHHHHHcccccHHHHHHHHHHHHHHHHcccEEEEEEEcccccccccHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHcccHHHHcccccccccHccccccccccccccccccccccHHHHHHHHHHHcccccHHHHHHccccccccccccccccccEEEccHHHHHHHHHccccccccccHHHHHHHHHHHHHccHHHcc
Coil and Loop (DISEMBL)
hilnklnpvhnsgiriatgalrsspipsllvesgvpplqlrRSQLAMSYAVKiascpanptysllfpdnidadiyplnkpkplcLRVRELALFSRtlqnsefapyckffppwsiatpvidnalsfdkkenvsSVVFQQRFHELVQSKYQDftlcftdgsktanntscayIIDKTLISSFVLNNVNSVYTSELIAVLLCLKhlkflpkekfvvisDSKSTLlalsnpsntnpiVSLIHSCWTDLLcygkqlaflwcpshtgiqgneavdraarnpsaslpplklcspedfkPFICKLIKDLWqnswsnipnseavdraarnpsaslpplklcspedfkpfimigrtgsikpvigpwpssdrqsrYEEVVICRMRightrathghlfkrappstcrcgetlsvQHILTCTLHghiraslpappaltddvESVDSMLKYLKKLNLYAKI
Flexible Loop (DISEMBL)
hilnklnpvhnSGIRIATGALRSSPIPSLLVESGVPPLQLRRSQLAMSYAVKIASCPANPTYSLLFPDNIDADIYPLNKPKPLCLRVRELALFSRTLQNSEFAPYCKFFPPWSIATPVIDNALSFDKKENVSSVVFQQRFHELVQSKYQDFTLCFTDGSKTANNTSCAYIIDKTLISSFVLNNVNSVYTSELIAVLLCLKHLKFLPKEKFVVISDSKSTLLALSNPSNTNPIVSLIHSCWTDLLCYGKQLAFLWCPSHTGIQGNEAVDRAARNPSAslpplklcspeDFKPFICKLIKDLWQNSWSNIPNSEAVDRAARNPSaslpplklcspeDFKPFIMIGRtgsikpvigpwpssdrqsrYEEVVICRMRIGHtrathghlfkrappstcRCGETLSVQHILTCTLHGHIRASLPAPPALTDDVESVDSMLKYLKKLNLYAKI
Low Complexity Region (SEG)
HILNKLNPVHNSGIRIATGALRSSPIPSLLVESGVPPLQLRRSQLAMSYAVKIASCPANPTYSLLFPDNIDADIYPLNKPKPLCLRVRELALFSRTLQNSEFAPYCKFFPPWSIATPVIDNALSFDKKENVSSVVFQQRFHELVQSKYQDFTLCFTDGSKTANNTSCAYIIDKTLISSFVLNNVNSVYTSELIAVLLCLKHLKFLPKEKFVVISDSKSTLLALSNPSNTNPIVSLIHSCWTDLLCYGKQLAFLWCPSHTGIQGNEAVDRAARNPSASLPPLKLCSPEDFKPFICKLIKDLWQNSWSNIPNSEAVDRAARNPSASLPPLKLCSPEDFKPFIMIGRTGSIKPVIGPWPSSDRQSRYEEVVICRMRIGHTRATHGHLFKRAPPSTCRCGETLSVQHILTCTLHGHIRASLPAPPALTDDVESVDSMlkylkklnlyakI
Disordered region (IsUnstruct)
*************IRIATG********SLLVESGVPPLQLRRSQLAMSYAVKIASCPANPTYSLLFPDNIDADIYPLNKPKPLCLRVRELALFSRTLQNSEFAPYCKFFPPWSIATPVIDNALSFDKKENVSSVVFQQRFHELVQSKYQDFTLCFTDGSKTANNTSCAYIIDKTLISSFVLNNVNSVYTSELIAVLLCLKHLKFLPKEKFVVISDSKSTLLALSNPSNTNPIVSLIHSCWTDLLCYGKQLAFLWCPSHTGIQG******************KLCSPEDFKPFICKLIKDLWQNSWSNI*********************LCSPEDFKPFIMIGRTGSIKPVIGPWPS**RQSRYEEVVICRMRIGHTRATHGHLFKRAPPSTCRCGETLSVQHILTCTLHGHIRASLPAPPALTDDVESVDSMLKYLKKLNLY***
Disordered Region (DISOPRED)
HILNKLNPVHNSGIRIATGALRSSPIPSLLVESGVPPLQLRRSQLAMSYAVKIASCPANPTYSLLFPDNIDADIYPLNKPKPLCLRVRELALFSRTLQNSEFAPYCKFFPPWSIATPVIDNALSFDKKENVSSVVFQQRFHELVQSKYQDFTLCFTDGSKTANNTSCAYIIDKTLISSFVLNNVNSVYTSELIAVLLCLKHLKFLPKEKFVVISDSKSTLLALSNPSNTNPIVSLIHSCWTDLLCYGKQLAFLWCPSHTGIQGNEAVDRAARNPSASLPPLKLCSPEDFKPFICKLIKDLWQNSWSNIPNSEAVDRAARNPSASLPPLKLCSPEDFKPFIMIGRTGSIKPVIGPWPSSDRQSRYEEVVICRMRIGHTRATHGHLFKRAPPSTCRCGETLSVQHILTCTLHGHIRASLPAPPALTDDVESVDSMLKYLKKLNLYAKI
Disordered Region (DISEMBL)
HILNKLNPVHNSGIRIATGALRSSPIPSLLVESGVPPLQLRRSQLAMSYAVKIASCPANPTYSLLFPDNIDADIYPLNKPKPLCLRVRELALFSRTLQNSEFAPYCKFFPPWSIATPVIDNALSFDKKENVSSVVFQQRFHELVQSKYQDFTLCFTDGSKTANNTSCAYIIDKTLISSFVLNNVNSVYTSELIAVLLCLKHLKFLPKEKFVVISDSKSTLLALSNPSNTNPIVSLIHSCWTDLLCYGKQLAFLWCPSHTGIQGNEAVDRAARNPSASLPPLKLCSPEDFKPFICKLIKDLWQNSWSNIPNSEAVDRAARNPSASLPPLKLCSPEDFKPFIMIGRTGSIKPVIGPWPSSDRQSRYEEVVICRMRIGHTRATHGHLFKRAPPSTCRCGETLSVQHILTCTLHGHIRASLPAPPALTDDVESVDSMLKYLKKLNLYAKI
Disordered Region (DISPRO)
HILNKLNPVHNSGIRIATGALRSSPIPSLLVESGVPPLQLRRSQLAMSYAVKIASCPANPTYSLLFPDNI*******N*PKPLCLRVRELALFSRTLQNSEFAPYCKFFPPWSIATPVIDNALSFDKKENVSSVVFQQRFHELVQSKYQDFTLCFTDGSKTANNTSCAYIIDKTLISSFVLNNVNSVYTSELIAVLLCLKHLKFLPKEKFVVISDSKSTLLALSNPSNTNPIVSLIHSCWTDLLCYGKQLAFLWCPSHTGIQGNEAVDRAARNPSASLPPLKLCSPEDFKPFICKLIKDLWQNSWSNIPNSEAVDRAARNPSASLPPLKLCSPEDFKPFIMIGRTGSIKPVIGPWPSSDRQSRYEEVVICRMRIGHTRATHGHLFKRAPPSTCRCGETLSVQHILTCTLHGHIRASLPAPPALTDDVESVDSMLKYLKKLNLYAKI
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
HILNKLNPVHNSGIRIATGALRSSPIPSLLVESGVPPLQLRRSQLAMSYAVKIASCPANPTYSLLFPDNIDADIYPLNKPKPLCLRVRELALFSRTLQNSEFAPYCKFFPPWSIATPVIDNALSFDKKENVSSVVFQQRFHELVQSKYQDFTLCFTDGSKTANNTSCAYIIDKTLISSFVLNNVNSVYTSELIAVLLCLKHLKFLPKEKFVVISDSKSTLLALSNPSNTNPIVSLIHSCWTDLLCYGKQLAFLWCPSHTGIQGNEAVDRAARNPSASLPPLKLCSPEDFKPFICKLIKDLWQNSWSNIPNSEAVDRAARNPSASLPPLKLCSPEDFKPFIMIGRTGSIKPVIGPWPSSDRQSRYEEVVICRMRIGHTRATHGHLFKRAPPSTCRCGETLSVQHILTCTLHGHIRASLPAPPALTDDVESVDSMLKYLKKLNLYAKI
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	446
125901787	1222	pol-like protein [Biomphalaria glabrata]	0.894	0.326	0.310	3e-42
427791063	1035	Putative tick transposon, partial [Rhipi	0.813	0.350	0.291	1e-37
427798889	1199	Putative tick transposon, partial [Rhipi	0.804	0.299	0.301	5e-37
427791321	1210	Putative tick transposon, partial [Rhipi	0.807	0.297	0.299	5e-36
427791807	1212	Putative tick transposon, partial [Rhipi	0.807	0.297	0.299	6e-36
427798887	1199	Putative tick transposon, partial [Rhipi	0.791	0.294	0.296	2e-34
427798885	1199	Putative tick transposon, partial [Rhipi	0.791	0.294	0.296	2e-34
443693558	502	hypothetical protein CAPTEDRAFT_189741,	0.650	0.577	0.333	8e-34
427778603	1397	Putative tick transposon [Rhipicephalus	0.905	0.289	0.269	1e-32
443695973	261	hypothetical protein CAPTEDRAFT_23017, p	0.567	0.969	0.342	4e-30

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

 Score =  179 bits (453), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 143/460 (31%), Positives = 204/460 (44%), Gaps = 61/460 (13%)

Query: 3    LNKLNPVHNSGIRIATGALRSSPIPSLLVESGVPPLQLRRSQLAMSYAVKIASCPANPTY 62
            L  L P+ N+ +R+  GA R+SPIPSL VE+G  P+ +R  +LAM Y VK+ S P NP +
Sbjct: 808  LKILEPIQNAALRLCLGAFRTSPIPSLHVEAGELPMDIRMKKLAMQYIVKLKSNPTNPAF 867

Query: 63   SLLF-PDNIDADIYPLNKPKPLCLRVRE--------LALFSR--TLQNSEFAPYCKFFPP 111
              +F P  ++      N  +PL LR+RE        +   S+  T QN          PP
Sbjct: 868  DSIFNPTEVELYNRRPNVIQPLGLRMREPIQNLTQPIDQISKIETPQN----------PP 917

Query: 112  WSIATPVIDNALSFDKKENVSSVVFQQRFHELVQSKYQDFTLCFTDGSKTANNTSCAYII 171
            W +  P ++ +L   KKEN    + Q  F EL Q  Y D    +TDGSK     +CA   
Sbjct: 918  WLMNKPKLNLSLLNFKKENTDPSILQVHFREL-QESYGDCGTIYTDGSKMEGKVACACSF 976

Query: 172  DKTLISSFVLNNVNSVYTSELIAVLLCLKHLKFLPKEKFVVISDSKSTLLALSNPSNTNP 231
                IS  + +   S++T+EL A+LL L  +K   + KF++ SDSKS L AL       P
Sbjct: 977  RNKTISRRLPDGC-SIFTAELHAILLALMAVKASERSKFIICSDSKSALQALGRMKTDIP 1035

Query: 232  IVSLIHSCWTDLLCYGKQLAFLWCPSHTGIQGNEAVDRAARNPSASLPPLKLCSPEDFKP 291
            +V         +    + + F+W PSH GI+GNEA DR A+               D + 
Sbjct: 1036 LVHKSLKLLDLITADRRDVTFIWVPSHVGIEGNEAADREAKRALNHAVSGTQIPYSDLRQ 1095

Query: 292  FICKLIKDLWQNSWSNIPNSEAVDRAARNPSASLPPLKLCSPEDFKPFIMIGRTGSIKPV 351
             I       WQN W    +S+     A                D +              
Sbjct: 1096 SIASATYREWQNRWEAETHSKLRQIVA----------------DVR-------------- 1125

Query: 352  IGPW-PSSDRQSRYEEVVICRMRIGHTRATHGHLFKRAPPSTCR-CGETLSVQHILT-CT 408
               W P+S   +R     + R+RIGHT  TH  + KR  P  C  C   L+V+HIL  C 
Sbjct: 1126 ---WRPTSKGLTRRGSTTMSRLRIGHTYITHSFVLKREEPPLCEYCDSRLTVEHILVDCP 1182

Query: 409  LHGHIRASLPAPPALTDDVESVD--SMLKYLKKLNLYAKI 446
             +  +RA       L     +VD   +L ++ ++ L  KI
Sbjct: 1183 RYQDVRAKHFRATNLKTLFNNVDPGKVLGFILEVGLSTKI 1222

Source: Biomphalaria glabrata

Species: Biomphalaria glabrata

Genus: Biomphalaria

Family: Planorbidae

Class: Gastropoda

Phylum: Mollusca

Superkingdom: Eukaryota

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

 Score =  164 bits (414), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 120/411 (29%), Positives = 198/411 (48%), Gaps = 48/411 (11%)

Query: 3    LNKLNPVHNSGIRIATGALRSSPIPSLLVESGVPPLQLRRSQLAMSYAVKIASCPANPTY 62
            L  L+P+H+ GIR+ATGA R+SP+ SL VES    L L+RS ++  Y +K+ +   +P +
Sbjct: 648  LKILDPIHHLGIRLATGAFRTSPVQSLYVESNQWSLHLQRSYMSFVYFLKVKAEKEHPAH 707

Query: 63   SLLFPDNIDADIYPLNKP---KPLCLRVRELA-LFSRTLQNSEFAPYCKFFPPWSIATPV 118
            S +  +++ + +   N+P   +P  LRVR+LA     +L          + PPW     +
Sbjct: 708  STV--NDLSSSVLYHNRPSVRQPYSLRVRDLAEEMGLSLHEHSLMARAAYLPPWQWQ--L 763

Query: 119  IDNALSFDKKENVSSVVFQQRFHELVQSKYQDFTLCFTDGSKTANNTSCAY-IIDKTLIS 177
            I+  +SF++    +       +   +Q KY  F   FTD SK   N+S +Y  +  +   
Sbjct: 764  IECDVSFEQVTKHAPHAHIYTYFLELQHKY-TFPEFFTDASKF--NSSVSYAAVGPSFSD 820

Query: 178  SFVLNNVNSVYTSELIAVLLCLKHLKFLPKEKFVVISDSKSTLLALSN-PSNTNPIVSLI 236
            + VL+   S++T+E  A+ + +KH++ L     V+ +DS S + AL     + NP+++ +
Sbjct: 821  AGVLHQNTSIFTAEAYAIFVAVKHIEQLKLPSAVIYTDSLSVVKALKTLKKHKNPVLASL 880

Query: 237  HSCWTDLLCYGKQLAFLWCPSHTGIQGNEAVDRAARNPSASLPPLKLCSPE-DFKPFICK 295
            +S    +    + +   W P H  IQGN   D+ A +   +     L  P  D KP + +
Sbjct: 881  YSLLCTVYALKQHVVVCWVPGHREIQGNVLADQLAASAHENAAHTFLAIPALDLKPLLKR 940

Query: 296  LIKDLWQNSWSNIPNSEAVDRAARNPSASLPPLKLCSPEDFKPFIMIGRTGSIKPVIGPW 355
             ++  WQ+ W         D   +N                       +  +IKP +G W
Sbjct: 941  KLRAYWQSIW---------DTQTQN-----------------------KLHAIKPQLGEW 968

Query: 356  PSSDRQSRYEEVVICRMRIGHTRATHGHLFKRAPPSTC-RCGETLSVQHIL 405
            P + + SR  E+ + R+R GHT  TH +L     P  C RCGE L+V HIL
Sbjct: 969  PPASK-SRRTEITLTRLRTGHTHTTHAYLLSGNDPPRCERCGEPLTVLHIL 1018

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  161 bits (408), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 125/415 (30%), Positives = 201/415 (48%), Gaps = 56/415 (13%)

Query: 3    LNKLNPVHNSGIRIATGALRSSPIPSLLVESGVPPLQLRRSQLAMSYAVKIASCPANPTY 62
            L  L+PVH+ GIR++TGA R+SP+ SL VES    L L+RS ++  Y +K+ +   +P++
Sbjct: 814  LKMLDPVHHLGIRLSTGAFRTSPVESLYVESNEWSLHLQRSYMSFLYYIKVNADKEHPSH 873

Query: 63   SLLFPDNIDADIYPLNKPK---PLCLRVRELA------LFSRTLQNSEFAPYCKFFPPWS 113
            S +  +++       N+P    P  LRVR+LA      LF   L     AP   + PPW 
Sbjct: 874  STI--NDLSCSTLFENRPSLKPPYSLRVRDLAEQTGLPLFEHRL----MAP-AAYPPPWQ 926

Query: 114  IATPVIDNALSFDKKENVSSVVFQQRFHELVQSKYQDFTLCFTDGSKTANNTSCAYIIDK 173
                +ID  +SF +    + +   + +   +Q KY +    +TD SK+  + S A  +  
Sbjct: 927  WQ--LIDCDVSFMEVTKHAPIAHIRTYFLELQHKY-NCPAFYTDASKSHTSVSYA-AVGP 982

Query: 174  TLISSFVLNNVNSVYTSELIAVLLCLKHLKFLPKEKFVVISDSKSTLLALSN-PSNTNPI 232
            +  ++  L+   S++T+E  A+L  +KH++ L  +K V+ +DS S + AL     + NP+
Sbjct: 983  SFSAAGALHPNTSIFTAEAYAILAAVKHIRELKLQKAVIYTDSLSVVKALKTLKKHRNPV 1042

Query: 233  VSLIHSCWTDLLCYGKQLAFLWCPSHTGIQGNEAVDRAARNPSASLPPLKLCSPE-DFKP 291
            +  ++S    +    + +   W P H  IQGN   D+ A +   S     +  P  D KP
Sbjct: 1043 LVSLYSLLCTIYTSKQHVVVCWVPGHREIQGNVMADQLAVSAHDSSANTSIAIPALDLKP 1102

Query: 292  FICKLIKDLWQNSWSNIPNSEAVDRAARNPSASLPPLKLCSPEDFKPFIMIGRTGSIKPV 351
            ++ + I+  WQ++W         DR   N                       +   IKP 
Sbjct: 1103 YLKRKIRAYWQSTW---------DRQTHN-----------------------KLHVIKPQ 1130

Query: 352  IGPWPSSDRQSRYEEVVICRMRIGHTRATHGHLFKRAPPSTC-RCGETLSVQHIL 405
            +G WP   + SRY EV + R+R GHT +TH +L        C +CGE L+V HIL
Sbjct: 1131 LGHWPPISK-SRYTEVTLTRLRTGHTHSTHAYLLSGGDAPFCDKCGEPLTVIHIL 1184

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 =  158 bits (400), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 124/414 (29%), Positives = 196/414 (47%), Gaps = 54/414 (13%)

Query: 3    LNKLNPVHNSGIRIATGALRSSPIPSLLVESGVPPLQLRRSQLAMSYAVKIASCPANPTY 62
            + +L+PVHN G+R+++GA R+SP+ SL V+   PPL  RR+ L +SY ++I S P +  Y
Sbjct: 787  IRRLDPVHNLGLRLSSGAYRTSPVESLYVDCNEPPLSHRRASLTLSYVLRIRSSPQHICY 846

Query: 63   SLLFPDNIDADIYPLNKP---KPLCLRVRELALFSRTLQNSE----FAPYCKFFPPWSIA 115
             +       + ++ LNK    KPL LR  E   + RT   SE     A      PPW   
Sbjct: 847  DI--ATRCSSRLHYLNKSNLIKPLLLRFEE---YCRTYVISEETLDVARKPPRIPPWFDL 901

Query: 116  TPVIDNALSFDKKENVSSVVFQQRFHELVQSKYQDFTLCFTDGSKTANNTSCAYIIDKTL 175
              + D +LS   K+     +  Q F  L Q KY+D+   +TDGSKT ++     +  ++ 
Sbjct: 902  AQLCDISLSHINKKVTPPELIIQEFRAL-QEKYRDYAEFYTDGSKTRDHVGIGIVTGESA 960

Query: 176  ISSFVLNNVNSVYTSELIAVLLCLKHLKFLPKEKFVVISDSKSTLLALSNPSNTNPIVSL 235
             S  V   + S++T+E+ A+    + +     +K ++ +DS S L AL   S   P+V  
Sbjct: 961  FSVRVPQCI-SIFTAEVYALYEAARKIIAGKHKKAIIYTDSLSALKALHIKSECEPLVGD 1019

Query: 236  IHSCWTDLLCYGK--QLAFLWCPSHTGIQGNEAVDR-AARNPSASLPPLKLCSPEDFKPF 292
            I +    +L   K   + F W PSH GI GNE  D+ A+     +L  +++   +  +  
Sbjct: 1020 ILNM---VLINSKVISMRFCWVPSHVGIPGNEKADKCASLAAHKTLTKIRIPLKDSQRTI 1076

Query: 293  ICKLIKDLWQNSWSNIPNSEAVDRAARNPSASLPPLKLCSPEDFKPFIMIGRTGSIKPVI 352
               L+   WQ  W +  +++               L L                 +KP +
Sbjct: 1077 RLALLAK-WQQQWDSCTSNK---------------LHL-----------------VKPTL 1103

Query: 353  GPWPSSDRQSRYEEVVICRMRIGHTRATHGHLFKRAPPSTC-RCGETLSVQHIL 405
            G W +   Q R+ EV++CR+RIGHT  TH  L  +     C +C E L++ HIL
Sbjct: 1104 GEWKNCRHQERFIEVILCRLRIGHTHLTHNFLLTKEEQPMCEKCQEPLTLIHIL 1157

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  158 bits (399), Expect = 6e-36,   Method: Compositional matrix adjust.
 Identities = 124/414 (29%), Positives = 196/414 (47%), Gaps = 54/414 (13%)

Query: 3    LNKLNPVHNSGIRIATGALRSSPIPSLLVESGVPPLQLRRSQLAMSYAVKIASCPANPTY 62
            + +L+PVHN G+R+++GA R+SP+ SL V+   PPL  RR+ L +SY ++I S P +  Y
Sbjct: 790  IRRLDPVHNLGLRLSSGAYRTSPVESLYVDCNEPPLSHRRASLTLSYVLRIRSSPQHICY 849

Query: 63   SLLFPDNIDADIYPLNKP---KPLCLRVRELALFSRTLQNSE----FAPYCKFFPPWSIA 115
             +       + ++ LNK    KPL LR  E   + RT   SE     A      PPW   
Sbjct: 850  DI--ATRCSSRLHYLNKSNLIKPLLLRFEE---YCRTYVISEETLDVARKPPRIPPWFDL 904

Query: 116  TPVIDNALSFDKKENVSSVVFQQRFHELVQSKYQDFTLCFTDGSKTANNTSCAYIIDKTL 175
              + D +LS   K+     +  Q F  L Q KY+D+   +TDGSKT ++     +  ++ 
Sbjct: 905  AQLCDISLSHINKKVTPPELIIQEFRAL-QEKYRDYAEFYTDGSKTRDHVGIGIVTGESA 963

Query: 176  ISSFVLNNVNSVYTSELIAVLLCLKHLKFLPKEKFVVISDSKSTLLALSNPSNTNPIVSL 235
             S  V   + S++T+E+ A+    + +     +K ++ +DS S L AL   S   P+V  
Sbjct: 964  FSVRVPQCI-SIFTAEVYALYEAARKIIAGKHKKAIIYTDSLSALKALHIKSECEPLVGD 1022

Query: 236  IHSCWTDLLCYGK--QLAFLWCPSHTGIQGNEAVDR-AARNPSASLPPLKLCSPEDFKPF 292
            I +    +L   K   + F W PSH GI GNE  D+ A+     +L  +++   +  +  
Sbjct: 1023 ILNM---VLINSKVISMRFCWVPSHVGIPGNEKADKCASLAAHKTLTKIRIPLKDSQRTI 1079

Query: 293  ICKLIKDLWQNSWSNIPNSEAVDRAARNPSASLPPLKLCSPEDFKPFIMIGRTGSIKPVI 352
               L+   WQ  W +  +++               L L                 +KP +
Sbjct: 1080 RLALLAK-WQQQWDSCTSNK---------------LHL-----------------VKPTL 1106

Query: 353  GPWPSSDRQSRYEEVVICRMRIGHTRATHGHLFKRAPPSTC-RCGETLSVQHIL 405
            G W +   Q R+ EV++CR+RIGHT  TH  L  +     C +C E L++ HIL
Sbjct: 1107 GEWKNCRHQERFIEVILCRLRIGHTHLTHNFLLTKEEQPMCEKCQEPLTLIHIL 1160

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 =  153 bits (386), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 125/421 (29%), Positives = 200/421 (47%), Gaps = 68/421 (16%)

Query: 3    LNKLNPVHNSGIRIATGALRSSPIPSLLVESGVPPLQLRRSQLAMSYAVKIASCPANPTY 62
            L  L+PVH+ GIR++TGA R+SP+ SL VES    L L+RS ++  Y +K+ +   +P++
Sbjct: 814  LKMLDPVHHLGIRLSTGAFRTSPVESLYVESNEWSLHLQRSYMSFLYYLKVNADKEHPSH 873

Query: 63   SLLFPDNIDADIYPLNKPK---PLCLRVRELA------LFSRTLQNSEFAPYCKFFPPWS 113
            S +  +++ +     N+P    P  LRVR LA      LF   L     AP   + PPW 
Sbjct: 874  STI--NDLSSSTLFENRPSLRPPYSLRVRGLAEETGLPLFEHRL----MAP-AAYPPPWQ 926

Query: 114  IATPVIDNALSFDKKENVSSVVFQQRFHELVQSKYQDFTLCFTDGSKTANNTSCAYIIDK 173
                +ID  +SF +    + +   + +   +Q KY +    +TD SK+  + S A  +  
Sbjct: 927  WQ--LIDCDVSFMEVTKHAPIAHIRTYFLELQHKY-NCPAFYTDASKSHTSVSYA-AVGP 982

Query: 174  TLISSFVLNNVNSVYTSELIAVLLCLKHLKFLPKEKFVVISDSKSTLLALSN-PSNTNPI 232
            +  ++  L+   S++T+E  A+L  +KH++ L  +K V+ +DS S + AL     + N I
Sbjct: 983  SFSAAGALHPNTSIFTAEAYAILAAVKHIRELKLQKAVIYTDSLSVVKALKTLKKHKNSI 1042

Query: 233  VSLIHSCWTDLLCYGKQLAFLWCPSHTGIQGNEAVDRAA-------RNPSASLPPLKLCS 285
            +  ++S    +    + +   W P H  IQGN   D  A        N S ++P L    
Sbjct: 1043 LVSLYSLVCTVYTAKQHVVVCWVPGHREIQGNVMADHLAASTHDCSANTSIAIPAL---- 1098

Query: 286  PEDFKPFICKLIKDLWQNSWSNIPNSEAVDRAARNPSASLPPLKLCSPEDFKPFIMIGRT 345
              D KP + + ++  WQ++W         D+   N                       + 
Sbjct: 1099 --DLKPLLKRKLRAYWQSTW---------DQQTHN-----------------------KL 1124

Query: 346  GSIKPVIGPWPSSDRQSRYEEVVICRMRIGHTRATHGHLFKRAPPSTC-RCGETLSVQHI 404
              IKP +G WP   + SRY EV + R+R GHT +TH +L        C +CGE L+V HI
Sbjct: 1125 HVIKPQLGHWPPISK-SRYTEVTLTRLRTGHTHSTHAYLLSGGDAPFCDKCGEPLTVIHI 1183

Query: 405  L 405
            L
Sbjct: 1184 L 1184

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 =  152 bits (385), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 125/421 (29%), Positives = 198/421 (47%), Gaps = 68/421 (16%)

Query: 3    LNKLNPVHNSGIRIATGALRSSPIPSLLVESGVPPLQLRRSQLAMSYAVKIASCPANPTY 62
            L  L+P+H+ GIR++TGA  +SP+ SL VES    LQL+RS ++  Y +K+ +   +P++
Sbjct: 814  LKMLDPIHHLGIRLSTGAFCTSPVESLYVESNEWSLQLQRSYMSFLYYLKVNADKEHPSH 873

Query: 63   SLLFPDNIDADIYPLNKPK---PLCLRVRELA------LFSRTLQNSEFAPYCKFFPPWS 113
            S +  +++ +     N+P    P  LRVR LA      LF   L      P     PPW 
Sbjct: 874  STI--NDLSSSTLFENRPSLRPPYSLRVRGLAEETGLPLFEHRLMAPAAYP-----PPWQ 926

Query: 114  IATPVIDNALSFDKKENVSSVVFQQRFHELVQSKYQDFTLCFTDGSKTANNTSCAYIIDK 173
                +ID  +SF +    + +   + +   +Q KY +    +TD SK+  + S A  +  
Sbjct: 927  WQ--LIDCDVSFMEVTKHAPIAHIRTYFLELQHKY-NCPAFYTDASKSHTSVSYA-AVGP 982

Query: 174  TLISSFVLNNVNSVYTSELIAVLLCLKHLKFLPKEKFVVISDSKSTLLALSN-PSNTNPI 232
            +   + VL+   S++T+E  A+L  +KH++ L  +K V+ +DS S + AL     + N I
Sbjct: 983  SFSDAGVLHPNTSIFTAEAYAILAAVKHIRELKLQKAVIYTDSLSVVKALKTLKKHKNSI 1042

Query: 233  VSLIHSCWTDLLCYGKQLAFLWCPSHTGIQGNEAVDRAA-------RNPSASLPPLKLCS 285
            +  ++S    L    + +   W P H  IQGN   D  A        N S ++P L    
Sbjct: 1043 LVSLYSLVCTLYTAKQHVVVCWVPGHREIQGNVMADHLAASTHDCSANTSIAIPAL---- 1098

Query: 286  PEDFKPFICKLIKDLWQNSWSNIPNSEAVDRAARNPSASLPPLKLCSPEDFKPFIMIGRT 345
              D KP + + ++  WQ++W         D+   N                       + 
Sbjct: 1099 --DLKPLLKRKLRAYWQSTW---------DQQTHN-----------------------KL 1124

Query: 346  GSIKPVIGPWPSSDRQSRYEEVVICRMRIGHTRATHGHLFKRAPPSTC-RCGETLSVQHI 404
              IKP +G WP   + SRY EV + R+R GHT +TH +L        C +CGE L+V HI
Sbjct: 1125 HVIKPQLGHWPPISK-SRYTEVTLTRLRTGHTHSTHAYLLSGGDAPFCDKCGEPLTVIHI 1183

Query: 405  L 405
            L
Sbjct: 1184 L 1184

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  151 bits (381), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 114/342 (33%), Positives = 165/342 (48%), Gaps = 52/342 (15%)

Query: 74  IYPLNKP---KPLCLRVRELALFSRTLQNSEFAPYCKF----FPPWSIATPVIDNALSFD 126
           I+  +KP   +PL  R  E       L++   AP   F     PPW +  P +D ++S  
Sbjct: 5   IFYTSKPSFIRPLLYRTEE------ALESVITAPIAPFKISDVPPWKLRPPEVDTSISKF 58

Query: 127 KKENVSSVVFQQRFHELVQSKYQDFTLCFTDGSKTANNTSCAYIIDKTLISSFVLNNVNS 186
            K+   ++  +Q F+ L+  KY    + +TDGSK+ N  +CA+      I  F L    S
Sbjct: 59  LKDQHPALFLKQEFYNLI-DKYPGINI-YTDGSKSNNAVACAFTCSTYQIQ-FGLPTQMS 115

Query: 187 VYTSELIAVLLCLKHLKFLPKE-KFVVISDSKSTLLALSNPSNTNPIVSLIHSCWTDLLC 245
           +YT+ELIA+   L  ++ +  E +F + SDS S+L ALSN   T+P +  I +   +L+ 
Sbjct: 116 IYTAELIAIEQALIFIETVKDEDQFNICSDSLSSLTALSNCDITHPYLLSILTKQNNLVR 175

Query: 246 YGKQLAFLWCPSHTGIQGNEAVDRAARNPSASLPPLKLCSPE-DFKPFICKLIKDLWQNS 304
            GK + F+WCPSH GI GNE  DR A+  +  +P  KL  P  D+K  I   +K LWQN 
Sbjct: 176 KGKLVVFIWCPSHVGILGNEVADRLAKQ-ALVMPVTKLPLPHTDYKSPIRSYVKSLWQNE 234

Query: 305 WSNIPNSEAVDRAARNPSASLPPLKLCSPEDFKPFIMIGRTGSIKPVIGPWPSSDRQSRY 364
           W      E  D                            +  SI+PVI  W    +  R 
Sbjct: 235 W-----DEETD---------------------------NKLHSIQPVISEWKQGPQIDRR 262

Query: 365 EEVVICRMRIGHTRATHGHLFKRAPPSTCR-CGETLSVQHIL 405
            E+V+ R RIGH+  THG+L +R     C  C   L+V+HIL
Sbjct: 263 GEIVLARARIGHSHLTHGYLLRREVAPFCIPCQSLLTVKHIL 304

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score =  147 bits (370), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 140/519 (26%), Positives = 219/519 (42%), Gaps = 115/519 (22%)

Query: 3    LNKLNPVHNSGIRIATGALRSSPIPSLLVESGVPPLQLRRSQLAMSYAVKIASCPANPTY 62
            L  L+PV++ GIR+A GA R+SP+ SL  ES   PL  +R+ L ++YA +I S   +P  
Sbjct: 907  LKLLDPVYHLGIRLALGAFRTSPVQSLYAESDQWPLDYQRTYLGVTYATRIMSLKQHPCK 966

Query: 63   SLL------------------FP---------------------------------DNID 71
            SL+                  FP                                 +++ 
Sbjct: 967  SLMNDVSTTQLYINRPSISPPFPLAIRPVVEKLKIHFEDLQEIDQVEXQHPCKALMNDVS 1026

Query: 72   ADIYPLNKPK-----PLCLR--VRELALFSRTLQNSEFAPYCKFFPPWSIATPVIDNALS 124
                 +N+P      PL +R  V +L +    LQ  +     +  PPW     + D +  
Sbjct: 1027 TTQLYINRPSISPPFPLAIRPVVEKLKIHFEDLQEID---QVEVIPPWKQCPIICDWSFK 1083

Query: 125  FDKKENVSSVVFQQRFHELVQSKYQDFTLCFTDGSKTANNTSCAYIIDKTLISSFVLNNV 184
              KK+   + + QQ F  L + KY+     F+DGSK+  + SCA    ++   +  L+  
Sbjct: 1084 DLKKKTAPNALIQQHFLAL-EHKYRSAAF-FSDGSKSQTSVSCA-AYGESFSDAKTLHAH 1140

Query: 185  NSVYTSELIAVLLCLKHLKFLPKEKFVVISDSKSTLLALS-NPSNTNPIVSLIHSCWTDL 243
             S++T+E   +LL ++H+K     + ++ +DS S + ALS    + NP+ + + +   + 
Sbjct: 1141 TSIFTAEAYGILLIVEHIKQHMIRRSIIYTDSLSVVTALSCGKCSKNPVFNKLLNNMHEA 1200

Query: 244  LCYGKQLAFLWCPSHTGIQGNEAVDRAARNPSASLPPLKLCS--PEDFKPFICKLIKDLW 301
                  +   W P H GI GNE VD+ AR  +AS   + + S    D  P + + ++  W
Sbjct: 1201 YNQNLSIVLCWVPGHAGITGNEMVDKNARE-AASRHTIDISSVPGVDLNPVVRRGLRSHW 1259

Query: 302  QNSWSNIPNSEAVDRAARNPSASLPPLKLCSPEDFKPFIMIGRTGSIKPVIGPWPSSDRQ 361
            Q  W         D+   N       L L  P   K                      + 
Sbjct: 1260 QVEW---------DKQVDN------KLHLVKPHLSKVL------------------PQKL 1286

Query: 362  SRYEEVVICRMRIGHTRATHGHLFKRAPPSTC-RCGETLSVQHIL-TC-TLHGH------ 412
            +R+ EV + R+RIGHT ATH HL     P TC  CGETL++ H+L  C  LH        
Sbjct: 1287 NRFTEVTLARLRIGHTYATHKHLLTGTDPPTCIHCGETLTILHVLIECPGLHQERLTHFR 1346

Query: 413  --IRASLPAPPAL---TDDVESVDSMLKYLKKLNLYAKI 446
               R  +P  PAL    D +  +  +L YL K+N  A +
Sbjct: 1347 ELYRYHIPPHPALFLSLDPMFKLKRLLHYLAKVNFLAMV 1385

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  138 bits (348), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 100/292 (34%), Positives = 145/292 (49%), Gaps = 39/292 (13%)

Query: 117 PVIDNALSFDKKENVSSVVFQQRFHELVQSKYQDFTLCFTDGSKTANNTSCAYIIDKTLI 176
           P +D ++S   K+   ++  +Q F+ L+  KY    + +TDGSK+ +  +CA+      I
Sbjct: 3   PEVDTSISKFLKDQHPALFLKQEFYNLI-DKYPGINI-YTDGSKSNDAVACAFTCSTYQI 60

Query: 177 SSFVLNNVNSVYTSELIAVLLCLKHLKFLPKE-KFVVISDSKSTLLALSNPSNTNPIVSL 235
             F L    S+YT+ELIA+   L  ++ +  E +F + SDS S+L ALSN   T+P +  
Sbjct: 61  Q-FGLPAQMSIYTAELIAIEQALIFIETVKDEDQFNICSDSLSSLTALSNCDITHPYLLS 119

Query: 236 IHSCWTDLLCYGKQLAFLWCPSHTGIQGNEAVDRAARNPSASLPPLKLCSPE-DFKPFIC 294
           I +   +L+  GK + F+WCPSH GI GNE  DR A+  +  +P  KL  P  D+K  I 
Sbjct: 120 ILTKQNNLVRKGKLVVFIWCPSHVGILGNEVADRLAKQ-ALVMPVTKLPLPHTDYKSPIR 178

Query: 295 KLIKDLWQNSWSNIPNSEAVDRAARNPSASLPPLKLCSPEDFKPFIMIGRTGSIKPVIGP 354
             +K LWQN W      E  D                            +  SI+PVI  
Sbjct: 179 SYVKSLWQNEW-----DEETD---------------------------NKLHSIQPVISE 206

Query: 355 WPSSDRQSRYEEVVICRMRIGHTRATHGHLFKRAPPSTCR-CGETLSVQHIL 405
           W    +  R  E+V+ R RIGH+  THG+L +R     C  C   LSV+HIL
Sbjct: 207 WKQGPQIDRRGEIVLARARIGHSHLTHGYLLRREVAPFCIPCQSLLSVKHIL 258

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	446
ASPGD|ASPL0000075333	486	AN10625 [Emericella nidulans (	0.264	0.242	0.325	1.4e-06

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

 Score = 142 (55.0 bits), Expect = 1.4e-06, P = 1.4e-06
 Identities = 40/123 (32%), Positives = 63/123 (51%)

Query:   155 FTDGSKTANNTSCAYIIDKTLIS--SFV-LNNVNSVYTSELIAVLLCLKHLKFLPKEKFV 211
             +TDGS        A I  K LIS  S++   + ++VY +EL  +LL L  +     +  V
Sbjct:   186 YTDGSGINGRVGAAAICPKYLISRSSYMGQQSESTVYVAELQGILLALVIILQRQMQHAV 245

Query:   212 VISDSKSTLLALSNPSNTNP--IVSLIHSCWTDLLCYGKQLAFLWCPSHTGIQGNEAVDR 269
             + +D+++TL AL NP + +   I+  I          G  + F W P+H G++GNE  DR
Sbjct:   246 IFTDNQATLQALRNPGSQSGQYILEAIIMALNKGRKAGLNVHFRWIPAHRGVEGNEQADR 305

Query:   270 AAR 272
              A+
Sbjct:   306 RAK 308


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        0.321   0.135   0.420    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      446       434   0.00087  118 3  11 22  0.37    34
                                                     34  0.45    37


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  611 (65 KB)
  Total size of DFA:  274 KB (2143 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  36.16u 0.07s 36.23t   Elapsed:  00:00:25
  Total cpu time:  36.16u 0.07s 36.23t   Elapsed:  00:00:25
  Start:  Thu Aug 15 13:31:03 2013   End:  Thu Aug 15 13:31:28 2013

GO:0008150 "biological_process" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	446
cd09276	128	cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom	5e-30
pfam00075	126	pfam00075, RNase_H, RNase H	5e-18
cd06222	123	cd06222, RNase_H, RNase H is an endonuclease that	2e-10
cd09273	135	cd09273, RNase_HI_RT_Bel, Bel/Pao family of RNase	1e-09
cd09278	139	cd09278, RNase_HI_prokaryote_like, RNase HI family	5e-06

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

 Score =  112 bits (283), Expect = 5e-30
 Identities = 43/123 (34%), Positives = 68/123 (55%), Gaps = 4/123 (3%)

Query: 154 CFTDGSKTANNTSCAY-IIDKTLIS-SFVLNNVNSVYTSELIAVLLCLKHLKFLPKE--K 209
            +TDGSK    T   + I+ K  IS S+ L    SV+ +EL+A+L  L+      +   K
Sbjct: 2   IYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRRARK 61

Query: 210 FVVISDSKSTLLALSNPSNTNPIVSLIHSCWTDLLCYGKQLAFLWCPSHTGIQGNEAVDR 269
             + SDS++ L AL +P +++P+V  I     +L  +G ++   W P H+GI+GNE  DR
Sbjct: 62  ITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGNERADR 121

Query: 270 AAR 272
            A+
Sbjct: 122 LAK 124

Ribonuclease H (RNase H) is classified into two families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). Ribonuclease HI (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as an adjunct domain to the reverse transcriptase gene in retroviruses, long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamatic acid residue (DEDD), are unvaried across all RNase H domains. The position of the RNase domain of non-LTR and LTR transposons is at the carboxyl terminal of the reverse transcriptase (RT) domain and their RNase domains group together, indicating a common evolutionary origin. Many non-LTR transposons have lost the RNase domain because their activity is at the nucleus and cellular RNase may suffice; however LTR retotransposons always encode their own RNase domain because it requires RNase activity in RNA-protein particles in the cytoplasm. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription. Length = 128

>gnl|CDD|215695 pfam00075, RNase_H, RNase H

 Score = 79.6 bits (197), Expect = 5e-18
 Identities = 32/125 (25%), Positives = 52/125 (41%), Gaps = 14/125 (11%)

Query: 154 CFTDGS--KTANNTSCAYIIDKTLISSFVLNNVNSVYTSELIAVLLCLKHLKFLPKEKFV 211
            +TDGS           Y+ D     S  L    +   +EL+A++  L+ L     +K  
Sbjct: 6   VYTDGSCNGNPGPGGAGYVTDGGKQRSKPLPG-TTNQRAELLALIEALEAL---SGQKVN 61

Query: 212 VISDSKST----LLALSNPSNTNPIVSLIHSCWTDLLCYGKQLAFLWCPSHTGIQGNEAV 267
           + +DS+             S + PI + I     +LL    ++   W P H+GI GNE  
Sbjct: 62  IYTDSQYVIGGITNGWPTKSESKPIKNEIW----ELLQKKHKVYIQWVPGHSGIPGNELA 117

Query: 268 DRAAR 272
           D+ A+
Sbjct: 118 DKLAK 122

RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral replication cycle, and often found as a domain associated with reverse transcriptases. Structure is a mixed alpha+beta fold with three a/b/a layers. Length = 126

>gnl|CDD|187690 cd06222, RNase_H, RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner

 Score = 58.1 bits (141), Expect = 2e-10
 Identities = 29/128 (22%), Positives = 51/128 (39%), Gaps = 14/128 (10%)

Query: 155 FTDGSKTAN--NTSCAYII---DKTLISSFVLNNVNSVYTS---ELIAVLLCLKHLKFLP 206
            TDGS   N        ++   +   + +  L+      T+   EL+A+L  L+    L 
Sbjct: 1   NTDGSCKGNPGPAGAGGVLRDHEGAWLFAGSLSI--PAATNNEAELLALLEALELALDLG 58

Query: 207 KEKFVVISDSKSTLLALSNPSNTNPIVSLIHSCWTDLLCYGKQLAFLWCPSHTGIQGNEA 266
            +K ++ +DSK  +  +++ S      +L+      LL     + F   P      GNE 
Sbjct: 59  LKKLIIETDSKYVVDLINSWSKGWKKNNLLLWDILLLLSKFIDIRFEHVPRE----GNEV 114

Query: 267 VDRAARNP 274
            DR A+  
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|187697 cd09273, RNase_HI_RT_Bel, Bel/Pao family of RNase HI in long-term repeat retroelements

 Score = 55.7 bits (135), Expect = 1e-09
 Identities = 30/139 (21%), Positives = 49/139 (35%), Gaps = 26/139 (18%)

Query: 153 LCFTDGSKTANNTSCAYIIDKTLISSFVLNNVNSVYTSELIAVLLCLKHLKFLPKEKFVV 212
             FTDGS        A +    ++    L    S   +ELIA++  L+  K    +   +
Sbjct: 1   TVFTDGSSFVRKAGYAVVTGPDVLEIATLPYGTSAQRAELIALIRALELAKG---KPVNI 57

Query: 213 ISDSK---STLLAL-----------SNPSNTNPIVSLIHSCWTDLLCYGKQLAFLWCPSH 258
            +DS      L AL             P     ++  +       +   K +A +   +H
Sbjct: 58  YTDSAYAFGILHALETIWKERGFLTGKPIALASLILQL----QKAIQRPKPVAVIHIRAH 113

Query: 259 TG-----IQGNEAVDRAAR 272
           +G       GN   D+AAR
Sbjct: 114 SGLPGPLALGNARADQAAR 132

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

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

 Score = 45.6 bits (109), Expect = 5e-06
 Identities = 34/142 (23%), Positives = 52/142 (36%), Gaps = 35/142 (24%)

Query: 155 FTDGSKTANNTS--CAYIID-----KTLISSFVL--NNVNSVYTSELIAVLLCLKHLKFL 205
           +TDG+   N      A I+      K L        NN       EL AV+  L+ LK  
Sbjct: 5   YTDGACLGNPGPGGWAAILRYGDHEKELSGGEAGTTNNR-----MELTAVIEALEALK-- 57

Query: 206 PKEKFVVISDSKSTLLALSN-----------PSNTNPI--VSLIHSCWTDL--LCYGKQL 250
                ++ +DS+  +  ++             ++  P+  V L    W +L  L    Q+
Sbjct: 58  EPCPVLLYTDSQYVINGITKWIHGWKKNGWKTADGKPVKNVDL----WQELDALLAKHQV 113

Query: 251 AFLWCPSHTGIQGNEAVDRAAR 272
            + W   H G  GNE  D  A 
Sbjct: 114 TWHWVKGHAGHPGNERADELAN 135

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	446
PRK06548	161	ribonuclease H; Provisional	99.87
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	99.87
PRK08719	147	ribonuclease H; Reviewed	99.86
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	99.85
PRK00203	150	rnhA ribonuclease H; Reviewed	99.83
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	99.74
KOG3752|consensus	371		99.69
PRK13907	128	rnhA ribonuclease H; Provisional	99.69
PRK07708	219	hypothetical protein; Validated	99.57
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	99.44
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	99.15
PF13966	86	zf-RVT: zinc-binding in reverse transcriptase	95.36

>PRK06548 ribonuclease H; Provisional

Probab=99.87  E-value=9.5e-22  Score=174.87  Aligned_cols=123  Identities=26%  Similarity=0.316  Sum_probs=92.4

Q ss_pred             CcEEEEEcCCcCCC--CceEEEEEcCCeEEEEecCCccchhHHHHHHHHHHHHHhhcCCCCceEEEechHHHHHHhcC--
Q psy5480         150 DFTLCFTDGSKTAN--NTSCAYIIDKTLISSFVLNNVNSVYTSELIAVLLCLKHLKFLPKEKFVVISDSKSTLLALSN--  225 (446)
Q Consensus       150 ~~~~iyTDGS~~~~--~~G~g~v~~~~~~~~~~l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~~--  225 (446)
                      ..+.||||||+..+  .+|+|+++......+.. ....||+.|||+||+.||+.+.. ....|.|+|||+++++++..  
T Consensus         4 ~~~~IytDGa~~gnpg~~G~g~~~~~~~~~~g~-~~~~TNnraEl~Aii~aL~~~~~-~~~~v~I~TDS~yvi~~i~~W~   81 (161)
T PRK06548          4 NEIIAATDGSSLANPGPSGWAWYVDENTWDSGG-WDIATNNIAELTAVRELLIATRH-TDRPILILSDSKYVINSLTKWV   81 (161)
T ss_pred             CEEEEEEeeccCCCCCceEEEEEEeCCcEEccC-CCCCCHHHHHHHHHHHHHHhhhc-CCceEEEEeChHHHHHHHHHHH
Confidence            45899999998754  47888665443222222 34689999999999999986643 34579999999999999983  


Q ss_pred             -------CCCCC--hh-HHHHHHHHHHHHhcCceEEEEEcCCCCCCccchHhHHHhcCCC
Q psy5480         226 -------PSNTN--PI-VSLIHSCWTDLLCYGKQLAFLWCPSHTGIQGNEAVDRAARNPS  275 (446)
Q Consensus       226 -------~~~~~--~~-~~~i~~~~~~l~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a~  275 (446)
                             +...+  ++ -+++.+.+..+... ..|+|.|||||+|++|||.||+||++++
T Consensus        82 ~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~-~~v~~~wVkgHsg~~gNe~aD~LA~~aa  140 (161)
T PRK06548         82 YSWKMRKWRKADGKPVLNQEIIQEIDSLMEN-RNIRMSWVNAHTGHPLNEAADSLARQAA  140 (161)
T ss_pred             HHHHHCCCcccCCCccccHHHHHHHHHHHhc-CceEEEEEecCCCCHHHHHHHHHHHHHH
Confidence                   32222  32 35666666666444 4799999999999999999999999953

>PF00075 RNase_H: RNase H; InterPro: IPR002156 The RNase H domain is responsible for hydrolysis of the RNA portion of RNA x DNA hybrids, and this activity requires the presence of divalent cations (Mg2+ or Mn2+) that bind its active site

Probab=99.87  E-value=6.2e-22  Score=171.47  Aligned_cols=117  Identities=32%  Similarity=0.433  Sum_probs=90.1

Q ss_pred             CcEEEEEcCCcCCC--CceEEEEEcCCeEEEEecCCccchhHHHHHHHHHHHHHhhcCCCCceEEEechHHHHHHhcC--
Q psy5480         150 DFTLCFTDGSKTAN--NTSCAYIIDKTLISSFVLNNVNSVYTSELIAVLLCLKHLKFLPKEKFVVISDSKSTLLALSN--  225 (446)
Q Consensus       150 ~~~~iyTDGS~~~~--~~G~g~v~~~~~~~~~~l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~~--  225 (446)
                      +.+.||||||+..+  ..|+||++..+...+..++ ..|++.|||+||.+||+ +..  ..+++|+|||+++++.+..  
T Consensus         2 ~~~~iytDgS~~~~~~~~~~g~v~~~~~~~~~~~~-~~s~~~aEl~Ai~~AL~-~~~--~~~v~I~tDS~~v~~~l~~~~   77 (132)
T PF00075_consen    2 KAIIIYTDGSCRPNPGKGGAGYVVWGGRNFSFRLG-GQSNNRAELQAIIEALK-ALE--HRKVTIYTDSQYVLNALNKWL   77 (132)
T ss_dssp             TSEEEEEEEEECTTTTEEEEEEEEETTEEEEEEEE-SECHHHHHHHHHHHHHH-THS--TSEEEEEES-HHHHHHHHTHH
T ss_pred             CcEEEEEeCCccCCCCceEEEEEEECCeEEEeccc-ccchhhhheehHHHHHH-Hhh--cccccccccHHHHHHHHHHhc
Confidence            46899999997643  3677876554444455556 89999999999999999 443  3899999999999997777  


Q ss_pred             ---CCCCC----hhHHHHHHHHHHHHhcCceEEEEEcCCCCCC-ccchHhHHHhcCC
Q psy5480         226 ---PSNTN----PIVSLIHSCWTDLLCYGKQLAFLWCPSHTGI-QGNEAVDRAARNP  274 (446)
Q Consensus       226 ---~~~~~----~~~~~i~~~~~~l~~~~~~V~~~WVpgH~gi-~gNe~AD~lAk~a  274 (446)
                         .....    ++..+|.+.+    ..+..|.|.|||||+|+ .|||.||+|||+|
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               33222    3445555554    55889999999999999 6999999999983

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

>PRK08719 ribonuclease H; Reviewed

Probab=99.86  E-value=2.1e-21  Score=171.19  Aligned_cols=120  Identities=21%  Similarity=0.220  Sum_probs=91.3

Q ss_pred             CcEEEEEcCCcCCCC-----ceEEEEE-cC--Ce--EEEEecCCccchhHHHHHHHHHHHHHhhcCCCCceEEEechHHH
Q psy5480         150 DFTLCFTDGSKTANN-----TSCAYII-DK--TL--ISSFVLNNVNSVYTSELIAVLLCLKHLKFLPKEKFVVISDSKST  219 (446)
Q Consensus       150 ~~~~iyTDGS~~~~~-----~G~g~v~-~~--~~--~~~~~l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~a  219 (446)
                      +.++||||||+..++     +|+|+++ +.  ..  ..+..+....|++.||+.|++.||+.+.+.    ..|+|||+++
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            568999999996543     5888654 32  21  344456667899999999999999998652    4899999999


Q ss_pred             HHHh--------cCCCCCC-h---hHHHHHHHHHHHHhcCceEEEEEcCCCCCCccchHhHHHhcCC
Q psy5480         220 LLAL--------SNPSNTN-P---IVSLIHSCWTDLLCYGKQLAFLWCPSHTGIQGNEAVDRAARNP  274 (446)
Q Consensus       220 i~~l--------~~~~~~~-~---~~~~i~~~~~~l~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a  274 (446)
                      ++++        ++.+..+ +   ...++++.+..+.. ...|.|.|||||+|++|||.||+||++|
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            9998        3444322 2   13556666666645 5679999999999999999999999984

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

Probab=99.85  E-value=5.8e-21  Score=166.93  Aligned_cols=124  Identities=22%  Similarity=0.180  Sum_probs=99.0

Q ss_pred             CcEEEEEcCCcCCC--CceEEEEEc-CCe--EEEEecCCccchhHHHHHHHHHHHHHhhcCCCCceEEEechHHHHHHhc
Q psy5480         150 DFTLCFTDGSKTAN--NTSCAYIID-KTL--ISSFVLNNVNSVYTSELIAVLLCLKHLKFLPKEKFVVISDSKSTLLALS  224 (446)
Q Consensus       150 ~~~~iyTDGS~~~~--~~G~g~v~~-~~~--~~~~~l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~  224 (446)
                      ..+.||||||+..+  ..|+|+|+. +..  ..+.... .+||+.+|++|++.||+.+.+.+...|.|+|||++++++|.
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            35899999999754  488996653 322  2444444 89999999999999999999888999999999999999998


Q ss_pred             CCCC---C--------Ch-hHHHHHHHHHHHHhcCceEEEEEcCCCCCCccchHhHHHhcCC
Q psy5480         225 NPSN---T--------NP-IVSLIHSCWTDLLCYGKQLAFLWCPSHTGIQGNEAVDRAARNP  274 (446)
Q Consensus       225 ~~~~---~--------~~-~~~~i~~~~~~l~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a  274 (446)
                      .+..   .        .| ...+++..+.++......|.+.|||||+|.++||.||+||+.+
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            3311   1        12 2456677777776777799999999999999999999999993

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=99.83  E-value=3.8e-20  Score=164.30  Aligned_cols=121  Identities=21%  Similarity=0.193  Sum_probs=88.0

Q ss_pred             cEEEEEcCCcCCC--CceEEEEE-cCCeEE-EEecCCccchhHHHHHHHHHHHHHhhcCCCCceEEEechHHHHHHhcCC
Q psy5480         151 FTLCFTDGSKTAN--NTSCAYII-DKTLIS-SFVLNNVNSVYTSELIAVLLCLKHLKFLPKEKFVVISDSKSTLLALSNP  226 (446)
Q Consensus       151 ~~~iyTDGS~~~~--~~G~g~v~-~~~~~~-~~~l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~~~  226 (446)
                      .+.||||||+..+  .+|+|+|+ .++... ........|++.|||.|++.||+.+.+  ...+.|+|||++++++|..+
T Consensus         3 ~v~iytDGs~~~n~~~~g~g~v~~~~~~~~~~~~~~~~~TN~~aEL~Ai~~AL~~~~~--~~~v~I~tDS~yvi~~i~~w   80 (150)
T PRK00203          3 QVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGEALTTNNRMELMAAIEALEALKE--PCEVTLYTDSQYVRQGITEW   80 (150)
T ss_pred             eEEEEEEecccCCCCceEEEEEEEECCeeEEEecCCCCCcHHHHHHHHHHHHHHHcCC--CCeEEEEECHHHHHHHHHHH
Confidence            4899999999743  47888654 333221 222234789999999999999998865  46799999999999998852


Q ss_pred             --------C-CC--Chh-HHHHHHHHHHHHhcCceEEEEEcCCCCCCccchHhHHHhcCC
Q psy5480         227 --------S-NT--NPI-VSLIHSCWTDLLCYGKQLAFLWCPSHTGIQGNEAVDRAARNP  274 (446)
Q Consensus       227 --------~-~~--~~~-~~~i~~~~~~l~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a  274 (446)
                              + ..  .++ ..++.+.+..+.. ...|.|.|||||+|++||+.||+|||++
T Consensus        81 ~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~-~~~v~~~wV~~H~~~~~N~~AD~lA~~a  139 (150)
T PRK00203         81 IHGWKKNGWKTADKKPVKNVDLWQRLDAALK-RHQIKWHWVKGHAGHPENERCDELARAG  139 (150)
T ss_pred             HHHHHHcCCcccCCCccccHHHHHHHHHHhc-cCceEEEEecCCCCCHHHHHHHHHHHHH
Confidence                    1 11  122 2334444444433 3789999999999999999999999994

>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=99.74  E-value=4.7e-17  Score=137.75  Aligned_cols=121  Identities=25%  Similarity=0.304  Sum_probs=94.3

Q ss_pred             EEEEcCCcCCC--CceEEEEEc-CCe--E-EEEecCCccchhHHHHHHHHHHHHHhhcCCCCceEEEechHHHHHHhcCC
Q psy5480         153 LCFTDGSKTAN--NTSCAYIID-KTL--I-SSFVLNNVNSVYTSELIAVLLCLKHLKFLPKEKFVVISDSKSTLLALSNP  226 (446)
Q Consensus       153 ~iyTDGS~~~~--~~G~g~v~~-~~~--~-~~~~l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~~~  226 (446)
                      ++|||||...+  ++|+|+++. .+.  . .........+++.+|+.|++.||+.+...+..++.|++||+.++..+.+.
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            48999998765  588886553 222  1 11112257899999999999999999888899999999999999999987


Q ss_pred             CC-CChhHHHHHHHHHHHHhcCceEEEEEcCCCCCCccchHhHHHhcC
Q psy5480         227 SN-TNPIVSLIHSCWTDLLCYGKQLAFLWCPSHTGIQGNEAVDRAARN  273 (446)
Q Consensus       227 ~~-~~~~~~~i~~~~~~l~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~  273 (446)
                      .. .......+...+..+...+..+.|.|||+|+|+.+|+.||.|||+
T Consensus        81 ~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~  128 (130)
T cd06222          81 YEGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKE  128 (130)
T ss_pred             ccCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHh
Confidence            65 223344444444444467889999999999999999999999998

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=99.69  E-value=6.4e-17  Score=157.68  Aligned_cols=126  Identities=24%  Similarity=0.215  Sum_probs=96.4

Q ss_pred             CCcEEEEEcCCcCCC-----CceEEEE-EcCC-eEEEEecC-CccchhHHHHHHHHHHHHHhhcCCCCceEEEechHHHH
Q psy5480         149 QDFTLCFTDGSKTAN-----NTSCAYI-IDKT-LISSFVLN-NVNSVYTSELIAVLLCLKHLKFLPKEKFVVISDSKSTL  220 (446)
Q Consensus       149 ~~~~~iyTDGS~~~~-----~~G~g~v-~~~~-~~~~~~l~-~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai  220 (446)
                      .+.++||||||+..+     .+|+||+ ..+. ...+..+. ..+++|.|||.||..||+.|.+....+|+|.|||++++
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            345899999999764     3899954 4332 35566664 78999999999999999999998888999999999999


Q ss_pred             HHhcCCCCC-----------Ch------hHHHHHHHHHHHHh--cCceEEEEEcCCCCCCccchHhHHHhcCC
Q psy5480         221 LALSNPSNT-----------NP------IVSLIHSCWTDLLC--YGKQLAFLWCPSHTGIQGNEAVDRAARNP  274 (446)
Q Consensus       221 ~~l~~~~~~-----------~~------~~~~i~~~~~~l~~--~~~~V~~~WVpgH~gi~gNe~AD~lAk~a  274 (446)
                      +.|+.+...           ++      ........+.+|.+  .+.+|.+.||+||.|+.|||.||.||+++
T Consensus       290 ~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~Ad~lARkg  362 (371)
T KOG3752|consen  290 NSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEMADALARKG  362 (371)
T ss_pred             HHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHHHHHHHhhh
Confidence            998754321           12      01223333444433  36899999999999999999999999994

>PRK13907 rnhA ribonuclease H; Provisional

Probab=99.69  E-value=2.2e-16  Score=136.37  Aligned_cols=118  Identities=19%  Similarity=0.134  Sum_probs=93.6

Q ss_pred             EEEEEcCCcCCC--CceEEEEEcC-Ce--EEEEecCCccchhHHHHHHHHHHHHHhhcCCCCceEEEechHHHHHHhcCC
Q psy5480         152 TLCFTDGSKTAN--NTSCAYIIDK-TL--ISSFVLNNVNSVYTSELIAVLLCLKHLKFLPKEKFVVISDSKSTLLALSNP  226 (446)
Q Consensus       152 ~~iyTDGS~~~~--~~G~g~v~~~-~~--~~~~~l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~~~  226 (446)
                      +.||||||+..+  .+|+|+|+.+ ..  ..... ....|++.||+.|++.||+.+.+.+..++.|+|||+.+++.+++.
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            689999998753  5899976633 22  22222 346799999999999999999998888999999999999999987


Q ss_pred             CCCChhHHHHHHHHHHHHhcCceEEEEEcCCCCCCccchHhHHHhcCC
Q psy5480         227 SNTNPIVSLIHSCWTDLLCYGKQLAFLWCPSHTGIQGNEAVDRAARNP  274 (446)
Q Consensus       227 ~~~~~~~~~i~~~~~~l~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a  274 (446)
                      ...+.....+...+..+......+.|.|||+    ++|+.||.||+.+
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            6555445556666666667778888999996    5999999999983

>PRK07708 hypothetical protein; Validated

Probab=99.57  E-value=3.8e-14  Score=132.77  Aligned_cols=125  Identities=14%  Similarity=0.072  Sum_probs=92.3

Q ss_pred             cCCCcEEEEEcCCcC--CCCceEEEEEc-C--CeEE----EEecCCccchhHHHHHHHHHHHHHhhcCCCCc--eEEEec
Q psy5480         147 KYQDFTLCFTDGSKT--ANNTSCAYIID-K--TLIS----SFVLNNVNSVYTSELIAVLLCLKHLKFLPKEK--FVVISD  215 (446)
Q Consensus       147 ~~~~~~~iyTDGS~~--~~~~G~g~v~~-~--~~~~----~~~l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~--i~I~tD  215 (446)
                      ..++.+++|+|||..  ++++|+|+|+. .  +...    ...++...|++.||+.|++.||+.+.+.+.+.  |.|++|
T Consensus        69 ~ep~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~D  148 (219)
T PRK07708         69 EEPHEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFRGD  148 (219)
T ss_pred             cCCCcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHcCCCcceEEEEec
Confidence            345679999999986  45689996552 2  2221    23455568999999999999999999887654  899999


Q ss_pred             hHHHHHHhcCCCCC-ChhHHHHHHHHHHHHh-cCceEEEEEcCCCCCCccchHhHHHhcCCC
Q psy5480         216 SKSTLLALSNPSNT-NPIVSLIHSCWTDLLC-YGKQLAFLWCPSHTGIQGNEAVDRAARNPS  275 (446)
Q Consensus       216 S~~ai~~l~~~~~~-~~~~~~i~~~~~~l~~-~~~~V~~~WVpgH~gi~gNe~AD~lAk~a~  275 (446)
                      |+.+++.+.+.+.. ++....+.+.+..+.. -...+.|.|||    ...|+.||+||++|.
T Consensus       149 SqlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~Vp----R~~N~~AD~LAk~Al  206 (219)
T PRK07708        149 SQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPIS----RKQNKEADQLATQAL  206 (219)
T ss_pred             cHHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECC----chhhhHHHHHHHHHH
Confidence            99999999987754 3444444444443322 34468889998    578999999999954

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=99.44  E-value=8.6e-13  Score=134.39  Aligned_cols=119  Identities=17%  Similarity=0.178  Sum_probs=94.0

Q ss_pred             cEEEEEcCCcCCC--CceEEEEE-cC--Ce---EEEEecCCccchhHHHHHHHHHHHHHhhcCCCCceEEEechHHHHHH
Q psy5480         151 FTLCFTDGSKTAN--NTSCAYII-DK--TL---ISSFVLNNVNSVYTSELIAVLLCLKHLKFLPKEKFVVISDSKSTLLA  222 (446)
Q Consensus       151 ~~~iyTDGS~~~~--~~G~g~v~-~~--~~---~~~~~l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~  222 (446)
                      .+.||||||+..+  .+|+|+++ +.  +.   .....++ ..|++.||+.|++.||+.+.+.+...|.|++||+.+++.
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            3789999998764  48899665 32  21   1223333 789999999999999999999888999999999999999


Q ss_pred             hcCCCC-CChhHHHHHHHHHHHHhcCceEEEEEcCCCCCCccchHhHHHhcCC
Q psy5480         223 LSNPSN-TNPIVSLIHSCWTDLLCYGKQLAFLWCPSHTGIQGNEAVDRAARNP  274 (446)
Q Consensus       223 l~~~~~-~~~~~~~i~~~~~~l~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a  274 (446)
                      +.+.+. +++-...+...+..+......+.|.|||.    .+|+.||.||+.|
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            998764 44445555555666667778999999995    7999999999983

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

Probab=99.15  E-value=1.9e-10  Score=91.66  Aligned_cols=83  Identities=22%  Similarity=0.138  Sum_probs=66.7

Q ss_pred             hhHHHHHHHHHHHHHhhcCCCCceEEEechHHHHHHhcCCCCCChhHHHHHHHHHHHHhcCceEEEEEcCCCCCCccchH
Q psy5480         187 VYTSELIAVLLCLKHLKFLPKEKFVVISDSKSTLLALSNPSNTNPIVSLIHSCWTDLLCYGKQLAFLWCPSHTGIQGNEA  266 (446)
Q Consensus       187 ~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~~~~~~~~~~~~i~~~~~~l~~~~~~V~~~WVpgH~gi~gNe~  266 (446)
                      +..||+.|+..||+.+.+.+..+|.|.|||+.+++.+++..........+...+..+.+....+.|.|||    .++|..
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            4689999999999999999999999999999999999988654435556666666666778999999999    799999


Q ss_pred             hHHHhcC
Q psy5480         267 VDRAARN  273 (446)
Q Consensus       267 AD~lAk~  273 (446)
                      ||.|||.
T Consensus        77 A~~LA~~   83 (87)
T PF13456_consen   77 ADALAKF   83 (87)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9999997

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

Probab=95.36  E-value=0.0072  Score=48.11  Aligned_cols=29  Identities=21%  Similarity=0.515  Sum_probs=23.8

Q ss_pred             ccCCCCCCCcc-CC-CCCccchhhc-cccchH
Q psy5480         384 LFKRAPPSTCR-CG-ETLSVQHILT-CTLHGH  412 (446)
Q Consensus       384 ~~~~~~~~~C~-Cg-~~~t~~Hil~-Cp~~~~  412 (446)
                      +.+...++.|. || +.||++|+|+ ||...+
T Consensus        53 ~r~~~~~~~C~~C~~~~Et~~Hlf~~C~~a~~   84 (86)
T PF13966_consen   53 RRGIQVDPICPLCGNEEETIEHLFFHCPFARE   84 (86)
T ss_pred             ccCCccCCccccCCCccccccceeccCcCccc
Confidence            34556789999 99 6999999999 997643

---

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	446
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	2e-09
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	2e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	9e-05

>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 = 55.2 bits (133), Expect = 2e-09
 Identities = 35/134 (26%), Positives = 53/134 (39%), Gaps = 16/134 (11%)

Query: 150 DFTLCFTDGSKTANN----TSCAYIIDKTLISSFVLNNVNSVYTSELIAVLLCLKHLKFL 205
           D+T  +TDGS            A   +  +I +  L    S   +ELIA+   LK  +  
Sbjct: 23  DYTW-YTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMAE-- 79

Query: 206 PKEKFVVISDSKSTLLALSNPSNTNPI--VSLIHSCWTDLLCYGKQLAFLWCPSHTG--- 260
             +K  V +DS+         S    I   + I +     L   K+L+ + CP H     
Sbjct: 80  -GKKLNVYTDSRYAFATAHVHSEGREIKNKNEILAL-LKALFLPKRLSIIHCPGHQKGNS 137

Query: 261 --IQGNEAVDRAAR 272
              +GN   D+AAR
Sbjct: 138 AEARGNRMADQAAR 151

>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 = 46.6 bits (111), Expect = 2e-06
 Identities = 23/137 (16%), Positives = 37/137 (27%), Gaps = 33/137 (24%)

Query: 155 FTDGSKTANNTSCAYII-----DKTLISSFVL---NNVNSVYTSELIAVLLCLKHLKFLP 206
           +TDGS      + AY            +                E+ A L  +K      
Sbjct: 10  YTDGSYVNGQYAWAYAFVKDGKVHYEDADVGKNPAAATMRNVAGEIAAALYAVKKAS-QL 68

Query: 207 KEKFVVISDSKSTLLALSNPSNTNPIVSLIHSCW----------TDLL-CYGKQLAFLWC 255
             K  ++ D                I       W            L+  Y    +F   
Sbjct: 69  GVKIRILHDYAG-------------IAFWATGEWKAKNEFTQAYAKLMNQYRGIYSFEKV 115

Query: 256 PSHTGIQGNEAVDRAAR 272
            +H+G + N+ VD  A+
Sbjct: 116 KAHSGNEFNDYVDMKAK 132

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

 Score = 44.1 bits (103), Expect = 9e-05
 Identities = 39/229 (17%), Positives = 70/229 (30%), Gaps = 58/229 (25%)

Query: 23  SSPIP----SLL---VESGVPPL---QLRRSQLAMSYAVKIASCPANPTYSLLFPDNIDA 72
           S+ IP    SL+   V      +   +L +  L           P   T S+        
Sbjct: 384 SAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQ-------PKESTISIP------- 429

Query: 73  DIYPLNKPKPLCLRVRELALFSRTLQNSEFAPYCKFFPPWSIATPVIDN------ALSFD 126
            IY   K K     +       R++ +    P    F    +  P +D            
Sbjct: 430 SIYLELKVK-----LENEYALHRSIVDHYNIPKT--FDSDDLIPPYLDQYFYSHIGHHLK 482

Query: 127 KKENVSSVVFQQRFHELVQSKYQDF-----TLCFTDGSKTANNTSCAYIIDKTLISSFVL 181
             E+       +R   L +  + DF      +     +  A+ +    +        ++ 
Sbjct: 483 NIEH------PERM-TLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYIC 535

Query: 182 NNVNSVYTSELIAVLLCLKHLKFLPK-EKFVVISDSKSTL-LALSNPSN 228
           +N +  Y   + A+      L FLPK E+ ++ S     L +AL     
Sbjct: 536 DN-DPKYERLVNAI------LDFLPKIEENLICSKYTDLLRIALMAEDE 577

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	446
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.89
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.88
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	99.88
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.87
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	99.85
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.85
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	99.85
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.84
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	99.8
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	99.78
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	99.78
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	99.76
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	99.76
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	99.73
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	99.36
4htu_A	134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	99.15

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

Probab=99.89  E-value=7.2e-23  Score=180.37  Aligned_cols=125  Identities=19%  Similarity=0.282  Sum_probs=93.3

Q ss_pred             hcCCCcEEEEEcCCcCCC--CceEEEEEcCCeEEEEecCCccchhHHHHHHHHHHHHHhhcCCCCceEEEechHHHHHHh
Q psy5480         146 SKYQDFTLCFTDGSKTAN--NTSCAYIIDKTLISSFVLNNVNSVYTSELIAVLLCLKHLKFLPKEKFVVISDSKSTLLAL  223 (446)
Q Consensus       146 ~~~~~~~~iyTDGS~~~~--~~G~g~v~~~~~~~~~~l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l  223 (446)
                      .+..+.+.||||||+..+  ..|+|+++..+......+ ..+|++.||+.|++.||+.+    ..+|.|+|||+++++.|
T Consensus         7 ~P~~~~~~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~-~~~Tnn~aEl~A~i~AL~~~----~~~v~i~tDS~~v~~~i   81 (150)
T 3qio_A            7 EPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTL-TDTTNQKTELQAIYLALQDS----GLEVNIVTDSQYALGII   81 (150)
T ss_dssp             SCCTTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEEE-SSCCHHHHHHHHHHHHHHHS----CSEEEEEESCHHHHHHH
T ss_pred             CCCCCCEEEEEccCCCCCCCCeEEEEEEEcCCEEEEeC-CCCCHHHHHHHHHHHHHHhC----CCcEEEEeCcHHHHHHH
Confidence            456678999999998754  378887765443333344 47899999999999999985    47899999999999999


Q ss_pred             cCCC-----------CCCh-hHHHHHHHHHHHHhcCceEEEEEcCCCCCCccchHhHHHhcCCC
Q psy5480         224 SNPS-----------NTNP-IVSLIHSCWTDLLCYGKQLAFLWCPSHTGIQGNEAVDRAARNPS  275 (446)
Q Consensus       224 ~~~~-----------~~~~-~~~~i~~~~~~l~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a~  275 (446)
                      ..+.           ...+ ...++...+..+......|.|.|||||+|++|||.||+|||+|+
T Consensus        82 ~~w~~~W~~~gw~~~~g~~v~n~~l~~~l~~~l~~~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~  145 (150)
T 3qio_A           82 TQWIHNWKKRGWKTADKKPVKNVDLVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGI  145 (150)
T ss_dssp             HHHHHHHCC------------CHHHHHHHHHHHTTCSEEEEEECCTTSCCHHHHHHHHHHHTTT
T ss_pred             HHHHHHHhhcCcCcCcCcccccHHHHHHHHHHHhhcCceEEEEccCcCCChhHHHHHHHHHHHH
Confidence            7641           1111 12233333333235678999999999999999999999999953

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

Probab=99.88  E-value=5.2e-23  Score=182.30  Aligned_cols=127  Identities=23%  Similarity=0.295  Sum_probs=97.0

Q ss_pred             cCCCcEEEEEcCCcCCCC-----ceEEEEEcCC--eEEEEecCCccchhHHHHHHHHHHHHHhhcCCCCceEEEechHHH
Q psy5480         147 KYQDFTLCFTDGSKTANN-----TSCAYIIDKT--LISSFVLNNVNSVYTSELIAVLLCLKHLKFLPKEKFVVISDSKST  219 (446)
Q Consensus       147 ~~~~~~~iyTDGS~~~~~-----~G~g~v~~~~--~~~~~~l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~a  219 (446)
                      .+.+.++||||||+..++     +|+|+++..+  ...+..+...+|++.||+.|++.||+.+.+.+..+|.|+|||+++
T Consensus         3 ~~~~~~~iytDGs~~~n~~~~~~aG~Gvv~~~~~~~~~~~~l~~~~tn~~aEl~A~~~aL~~~~~~~~~~v~i~tDS~~v   82 (154)
T 2qkb_A            3 HMGDFVVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQAKTQNINKLVLYTNSMFT   82 (154)
T ss_dssp             EETTEEEEEEEEEEETTTSSSCEEEEEEECSTTCTTCEEEECCSSCCHHHHHHHHHHHHHHHHHHTTCCEEEEEESCHHH
T ss_pred             CCCCeEEEEEccCcCCCCCCCCcEEEEEEEECCCceeEEeecCCCCchHHHHHHHHHHHHHHHHhCCCceEEEEECcHHH
Confidence            345789999999987543     6888765432  234455655789999999999999999988778899999999999


Q ss_pred             HHHhcCCC---------CCC--h-hHHHHHHHHHHHHhcCceEEEEEcCCCCCCccchHhHHHhcCC
Q psy5480         220 LLALSNPS---------NTN--P-IVSLIHSCWTDLLCYGKQLAFLWCPSHTGIQGNEAVDRAARNP  274 (446)
Q Consensus       220 i~~l~~~~---------~~~--~-~~~~i~~~~~~l~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a  274 (446)
                      ++.|.++.         ...  + ....+...+..+.. +..|.|.|||||+|++|||.||+|||+|
T Consensus        83 i~~i~~~~~~w~~~~w~~~~~~~~~n~~l~~~i~~l~~-~~~v~~~~V~~H~g~~~N~~AD~LA~~a  148 (154)
T 2qkb_A           83 INGITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQ-GMDIQWMHVPGHSGFIGNEEADRLAREG  148 (154)
T ss_dssp             HHHHHTHHHHHHTTTSBCTTSSBCTTHHHHHHHHHHHT-TCEEEEEECCTTSSCHHHHHHHHHHHHH
T ss_pred             HhhhhhhHHHHHhccccccCCCccccHHHHHHHHHHHc-CCceEEEEccCCCCCHhHHHHHHHHHHH
Confidence            99998731         111  1 22344444444433 4579999999999999999999999994

>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=99.88  E-value=1.7e-23  Score=184.02  Aligned_cols=124  Identities=17%  Similarity=0.128  Sum_probs=96.6

Q ss_pred             CCCcEEEEEcCCcCCCCceEEEEE-cCCeE--EEE-ec--CC--ccchhHHHHHHHHHHHHHhhcCCCCceEEEechHHH
Q psy5480         148 YQDFTLCFTDGSKTANNTSCAYII-DKTLI--SSF-VL--NN--VNSVYTSELIAVLLCLKHLKFLPKEKFVVISDSKST  219 (446)
Q Consensus       148 ~~~~~~iyTDGS~~~~~~G~g~v~-~~~~~--~~~-~l--~~--~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~a  219 (446)
                      +++.+.||||||+..+.+|+|+++ +++..  .+. ..  +.  ..||+.||+.|++.||+.+.+.+. +|.|+|||+.+
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            457799999999998779999655 44332  222 22  22  369999999999999998877666 99999999998


Q ss_pred             HHHhcCCCCCC-hhHHHHHHHHHHHHhcCceEEEEEcCCCCCCccchHhHHHhcCCC
Q psy5480         220 LLALSNPSNTN-PIVSLIHSCWTDLLCYGKQLAFLWCPSHTGIQGNEAVDRAARNPS  275 (446)
Q Consensus       220 i~~l~~~~~~~-~~~~~i~~~~~~l~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a~  275 (446)
                      ...+.+.+..+ +....+.++++++..   .|.|.|||||+|++|||.||+|||+|+
T Consensus        82 ~~w~~~~w~~~~~~~~~~~~l~~~l~~---~v~~~wV~gH~g~~~Ne~AD~LA~~a~  135 (147)
T 2kq2_A           82 AFWATGEWKAKNEFTQAYAKLMNQYRG---IYSFEKVKAHSGNEFNDYVDMKAKSAL  135 (147)
T ss_dssp             HHHTTSSSSCCHHHHHHHHCGGGGGST---TCCBCCCCCCCCCHHHHHHHHHHHHHH
T ss_pred             HHHHhCCCccCCcchHHHHHHHHHhcC---CeeEEEecCcCCCcchHHHHHHHHHHH
Confidence            88887765544 345556666665533   899999999999999999999999953

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

Probab=99.87  E-value=7.7e-23  Score=179.55  Aligned_cols=121  Identities=19%  Similarity=0.108  Sum_probs=88.1

Q ss_pred             CcEEEEEcCCcCCCC--ceEEEEE-cCCe--EEEEecCCccchhHHHHHHHHHHHHHhhcCCCCceEEEechHHHHHHhc
Q psy5480         150 DFTLCFTDGSKTANN--TSCAYII-DKTL--ISSFVLNNVNSVYTSELIAVLLCLKHLKFLPKEKFVVISDSKSTLLALS  224 (446)
Q Consensus       150 ~~~~iyTDGS~~~~~--~G~g~v~-~~~~--~~~~~l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~  224 (446)
                      +.++||||||+..++  +|+|+++ .++.  ..+..+ ..+|++.||+.|++.||+.+.+  ..+|.|+|||+++++.|.
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            468999999988653  7888654 4332  222233 4689999999999999999876  579999999999999998


Q ss_pred             CCC------------CCCh-hHHHHHHHHHHHHhcCceEEEEEcCCCCCCccchHhHHHhcCC
Q psy5480         225 NPS------------NTNP-IVSLIHSCWTDLLCYGKQLAFLWCPSHTGIQGNEAVDRAARNP  274 (446)
Q Consensus       225 ~~~------------~~~~-~~~~i~~~~~~l~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a  274 (446)
                      ..+            ...+ ....+...+..+.. ...|.|.|||||+|++|||.||+|||+|
T Consensus        80 ~~w~~~W~~~~w~~~~~~~v~n~~l~~~~~~~~~-~~~v~~~~V~gH~g~~~N~~AD~LA~~a  141 (146)
T 3h08_A           80 EGWLKRWVKNGWKTAAKKPVENIDLWQEILKLTT-LHRVTFHKVKGHSDNPYNSRADELARLA  141 (146)
T ss_dssp             SSHHHHHHHTTCC----CCCTTHHHHHHHHHHHH-HSEEEEEECCC-CCSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCccCCCCCcCCHHHHHHHHHHHh-hCceEEEEcCCcCCcHhHHHHHHHHHHH
Confidence            721            1111 12333333333323 2479999999999999999999999984

>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=99.85  E-value=2.7e-21  Score=172.70  Aligned_cols=120  Identities=28%  Similarity=0.310  Sum_probs=89.2

Q ss_pred             cEEEEEcCCcC--CCCceEEEEE-cCCe-EEEEecCCccchhHHHHHHHHHHHHHhhcCCCCceEEEechHHHHHHhcCC
Q psy5480         151 FTLCFTDGSKT--ANNTSCAYII-DKTL-ISSFVLNNVNSVYTSELIAVLLCLKHLKFLPKEKFVVISDSKSTLLALSNP  226 (446)
Q Consensus       151 ~~~iyTDGS~~--~~~~G~g~v~-~~~~-~~~~~l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~~~  226 (446)
                      .+.||||||+.  ++.+|+|+++ .++. .....+...+||+.||+.|++.||+.+   ...+|.|+|||+++++.+-..
T Consensus        23 ~i~iytDGs~~~npG~~g~G~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~---~~~~v~I~tDS~~vi~~iw~~   99 (165)
T 3p1g_A           23 DYTWYTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMA---EGKKLNVYTDSRYAFATAHVH   99 (165)
T ss_dssp             SEEEEEEEEEEEETTEEEEEEEEECSSCEEEEEEECTTCCHHHHHHHHHHHHHHHT---BTSEEEEEECCHHHHHHHHSC
T ss_pred             CEEEEEEcccCCCCCceEEEEEEEECCEEEEEecCCCCCcHHHHHHHHHHHHHHHc---cCceEEEEEchHHHHhhhhcc
Confidence            58999999997  3447888654 3332 222245568899999999999999998   368999999999999998322


Q ss_pred             CCCChh-HHH-HHHHHHHHHhcCceEEEEEcCCCCC-----CccchHhHHHhcCC
Q psy5480         227 SNTNPI-VSL-IHSCWTDLLCYGKQLAFLWCPSHTG-----IQGNEAVDRAARNP  274 (446)
Q Consensus       227 ~~~~~~-~~~-i~~~~~~l~~~~~~V~~~WVpgH~g-----i~gNe~AD~lAk~a  274 (446)
                      ....++ ..+ +.+++..+ ..+..|.|.|||||+|     ++|||.||+|||+|
T Consensus       100 ~~g~~v~n~dl~~~l~~~l-~~~~~v~~~wVkgH~g~~~~~~~gNe~AD~LA~~a  153 (165)
T 3p1g_A          100 SEGREIKNKNEILALLKAL-FLPKRLSIIHCPGHQKGNSAEARGNRMADQAAREA  153 (165)
T ss_dssp             CCSCCCSSHHHHHHHHHHT-TSBSEEEEEECCSSCCSCSHHHHHHHHHHHHHHHH
T ss_pred             cCCCcccCHHHHHHHHHHH-hcCCceEEEEecCCCCCCcCcchHHHHHHHHHHHH
Confidence            222222 223 22232333 3678999999999999     99999999999994

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

Probab=99.85  E-value=2e-21  Score=172.74  Aligned_cols=122  Identities=24%  Similarity=0.236  Sum_probs=90.3

Q ss_pred             CcEEEEEcCCcCCC--CceEEEEE-cCCe--EEEEecCCccchhHHHHHHHHHHHHHhhcCCCCceEEEechHHHHHHhc
Q psy5480         150 DFTLCFTDGSKTAN--NTSCAYII-DKTL--ISSFVLNNVNSVYTSELIAVLLCLKHLKFLPKEKFVVISDSKSTLLALS  224 (446)
Q Consensus       150 ~~~~iyTDGS~~~~--~~G~g~v~-~~~~--~~~~~l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~  224 (446)
                      ..+.||||||+..+  .+|+|+|+ +++.  ..+..+ ..+|++.||+.|++.||+.+.+  ..+|.|+|||+++++.|.
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            46899999999754  37888655 3332  222233 3679999999999999999865  389999999999999998


Q ss_pred             C--------CCCC---Ch-hHHHHHHHHHHHHhcCceEEEEEcCCCCCCccchHhHHHhcCCC
Q psy5480         225 N--------PSNT---NP-IVSLIHSCWTDLLCYGKQLAFLWCPSHTGIQGNEAVDRAARNPS  275 (446)
Q Consensus       225 ~--------~~~~---~~-~~~~i~~~~~~l~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a~  275 (446)
                      .        .+..   .+ ....+...+..+.. ...|.|.|||||+|++|||.||+|||+|+
T Consensus        82 ~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~-~~~v~~~wV~gH~g~~~Ne~AD~LAk~a~  143 (158)
T 2e4l_A           82 TWIHGWKKKGWMTSNRTPVKNVDLWKRLDKAAQ-LHQIDWRWVKGHAGHAENERCDQLARAAA  143 (158)
T ss_dssp             THHHHHHHTTTBCTTSSBCTTHHHHHHHHHHHT-TSEEEEEECCTTCCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHccccccCCCcccCHHHHHHHHHHHc-cCcEEEEEccCCCCchhHHHHHHHHHHHH
Confidence            7        2211   11 12334444444433 46899999999999999999999999943

>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=99.85  E-value=2e-21  Score=172.25  Aligned_cols=120  Identities=22%  Similarity=0.243  Sum_probs=90.1

Q ss_pred             cEEEEEcCCcCCC--CceEEEEE-cCCe--EEEEecCCccchhHHHHHHHHHHHHHhhcCCCCceEEEechHHHHHHhcC
Q psy5480         151 FTLCFTDGSKTAN--NTSCAYII-DKTL--ISSFVLNNVNSVYTSELIAVLLCLKHLKFLPKEKFVVISDSKSTLLALSN  225 (446)
Q Consensus       151 ~~~iyTDGS~~~~--~~G~g~v~-~~~~--~~~~~l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~~  225 (446)
                      .+.||||||+..+  .+|+|+++ +.+.  ..+..+ ..+|++.||+.|++.||+.+.+  ..+|.|+|||+++++.|..
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            5899999999754  37888655 3332  223333 4679999999999999999876  3799999999999999987


Q ss_pred             C--------CC-C--Chh-HHHHHHHHHHHHhcCceEEEEEcCCCCCCccchHhHHHhcCC
Q psy5480         226 P--------SN-T--NPI-VSLIHSCWTDLLCYGKQLAFLWCPSHTGIQGNEAVDRAARNP  274 (446)
Q Consensus       226 ~--------~~-~--~~~-~~~i~~~~~~l~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a  274 (446)
                      +        +. .  .+. ...+...+..+.. ...|.|.|||||+|++|||.||+|||+|
T Consensus        81 w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~-~~~v~~~wV~gH~g~~~Ne~AD~LA~~a  140 (155)
T 1jl1_A           81 WIHNWKKRGWKTADKKPVKNVDLWQRLDAALG-QHQIKWEWVKGHAGHPENERADELARAA  140 (155)
T ss_dssp             THHHHHHTTTBCTTSCBCTTHHHHHHHHHHTT-TCEEEEEECCSSTTCHHHHHHHHHHHHH
T ss_pred             HHHHHhhcccccccCCccCCHHHHHHHHHHHc-cCceEEEEcCCCCCCHHHHHHHHHHHHH
Confidence            2        21 1  121 2344444444433 4689999999999999999999999994

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

Probab=99.84  E-value=1.7e-21  Score=174.57  Aligned_cols=122  Identities=23%  Similarity=0.171  Sum_probs=90.1

Q ss_pred             CcEEEEEcCCcCCC--CceEEEEE-cCCe--EEEEecCCccchhHHHHHHHHHHHHHhhcCCCCceEEEechHHHHHHhc
Q psy5480         150 DFTLCFTDGSKTAN--NTSCAYII-DKTL--ISSFVLNNVNSVYTSELIAVLLCLKHLKFLPKEKFVVISDSKSTLLALS  224 (446)
Q Consensus       150 ~~~~iyTDGS~~~~--~~G~g~v~-~~~~--~~~~~l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~  224 (446)
                      ..+.||||||+..+  .+|+|+|+ +.+.  ..+... ...|++.||+.|++.||+.+.+.  .+|.|+|||+++++.|.
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            57899999999854  37888765 3322  222222 36799999999999999988663  58999999999999998


Q ss_pred             C----------CCCCCh--h-HHHHHHHHHHHHhcCceEEEEEcCCCCCCccchHhHHHhcCCC
Q psy5480         225 N----------PSNTNP--I-VSLIHSCWTDLLCYGKQLAFLWCPSHTGIQGNEAVDRAARNPS  275 (446)
Q Consensus       225 ~----------~~~~~~--~-~~~i~~~~~~l~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a~  275 (446)
                      +          +...++  + ...+...+..+.. ...|.|.|||||+|++|||.||+|||+|.
T Consensus        84 ~~w~~~W~~~~w~~~~g~~v~n~~l~~~i~~l~~-~~~v~~~wV~gH~g~~~Ne~AD~LAk~a~  146 (166)
T 1ril_A           84 EGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMA-PHRVRFHFVKGHTGHPENERVDREARRQA  146 (166)
T ss_dssp             SSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHT-TSEEECCCCCGGGSCTHHHHHHHHHHHHH
T ss_pred             hhHHHHHHhcccccccCCccCcHHHHHHHHHHHh-cCeEEEEEeeCCCCchhHHHHHHHHHHHH
Confidence            8          222211  1 2334444444433 35899999999999999999999999943

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

Probab=99.80  E-value=7e-20  Score=163.36  Aligned_cols=125  Identities=17%  Similarity=0.186  Sum_probs=87.9

Q ss_pred             CCcEEEEEcCCcCCC--C-----ceEEEEE-cC-C---eEEEEec-CCccchhHHHHHHHHHHHHHhhcCCCCceEEEec
Q psy5480         149 QDFTLCFTDGSKTAN--N-----TSCAYII-DK-T---LISSFVL-NNVNSVYTSELIAVLLCLKHLKFLPKEKFVVISD  215 (446)
Q Consensus       149 ~~~~~iyTDGS~~~~--~-----~G~g~v~-~~-~---~~~~~~l-~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~tD  215 (446)
                      +..++|||||||..+  +     +|+|+++ .+ .   ....+.. ....+++.||+.|+..||+.++.. ..+|.|+||
T Consensus         5 ~~evviYTDGsc~gNpgp~~~~~aG~Gv~~~~~~~~~~~~~~~~~~tnn~te~~Aei~Al~~al~~al~~-~~~v~I~TD   83 (165)
T 2lsn_A            5 QYEGVFYTDGSAIKSPDPTKSNNAGMGIVHATYKPEYQVLNQWSIPLGNHTAQMAEIAAVEFACKKALKI-PGPVLVITD   83 (165)
T ss_dssp             CCSEEEEEEEEEEECSSCTTCEEEEEEEEEECCSSSCCEEEEEEEEESSCCHHHHHHHHHHHHHHHHHHS-SSCEEEEES
T ss_pred             CceEEEEEcCCCCCCCCCCCCCcEEEEEEEEECCCccEEeccccCCchHHHHHHHHHHHHHHHHHHHhcC-CCeEEEEeC
Confidence            356899999998743  2     6888654 22 1   2233333 346788899999999999887664 357999999


Q ss_pred             hHHHHHHhcCC---------CC--CChh-HHHHHHHHHHHHhcCceEEEEEcCCCCCC------ccchHhHHHhcCC
Q psy5480         216 SKSTLLALSNP---------SN--TNPI-VSLIHSCWTDLLCYGKQLAFLWCPSHTGI------QGNEAVDRAARNP  274 (446)
Q Consensus       216 S~~ai~~l~~~---------~~--~~~~-~~~i~~~~~~l~~~~~~V~~~WVpgH~gi------~gNe~AD~lAk~a  274 (446)
                      |++++++|..+         ..  ..++ -.+++..+.++.....+|.|.|||||+|+      +|||.||+||+++
T Consensus        84 S~Yvi~~it~w~~~Wk~ngw~~~~~~pVkN~dL~~~l~~~~~~~~~v~~~~VkgH~g~~~~~~~~gNe~AD~LA~~g  160 (165)
T 2lsn_A           84 SFYVAESANKELPYWKSNGFVNNKKKPLKHISKWKSIAECLSMKPDITIQHEKGHQPTNTSIHTEGNALADKLATQG  160 (165)
T ss_dssp             CHHHHHHHHTHHHHHHHTTSCSCSSSCCSSHHHHHHHHHHHHHCTTCEEEECCSSSCSSSCHHHHHHHHHHHHHHHH
T ss_pred             hHHHHhhhhhhhhhheeccccccCCCcccCHHHHHHHHHHHhCCCCEEEEEEeCCCCccCCCCChHHHHHHHHHHHh
Confidence            99999999642         11  1121 23444444444455678999999999995      5899999999984

>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=99.78  E-value=7.8e-19  Score=152.54  Aligned_cols=119  Identities=17%  Similarity=0.189  Sum_probs=94.8

Q ss_pred             cEEEEEcCCcCCC--CceEEEEE-cC--C-e--EEEEecCCccchhHHHHHHHHHHHHHhhcCCCCceEEEechHHHHHH
Q psy5480         151 FTLCFTDGSKTAN--NTSCAYII-DK--T-L--ISSFVLNNVNSVYTSELIAVLLCLKHLKFLPKEKFVVISDSKSTLLA  222 (446)
Q Consensus       151 ~~~iyTDGS~~~~--~~G~g~v~-~~--~-~--~~~~~l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~  222 (446)
                      .++||||||+..+  .+|+|+++ +.  + .  ..+..+ ..+|++.||+.|++.||+.+.+.+..+|.|+|||+++++.
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            5899999998854  47888654 32  2 1  222333 4789999999999999999998888999999999999999


Q ss_pred             hcCCCC-CChhHHHHHHHHHHHHhcCceEEEEEcCCCCCCccchHhHHHhcCC
Q psy5480         223 LSNPSN-TNPIVSLIHSCWTDLLCYGKQLAFLWCPSHTGIQGNEAVDRAARNP  274 (446)
Q Consensus       223 l~~~~~-~~~~~~~i~~~~~~l~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a  274 (446)
                      +.+.+. .++.+..+...+..+...+..|.|.|||+    ++|+.||+|||+|
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 45555566666666667778999999994    8999999999983

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

Probab=99.78  E-value=1e-18  Score=151.35  Aligned_cols=119  Identities=18%  Similarity=0.231  Sum_probs=92.1

Q ss_pred             cEEEEEcCCcCCC--CceEEEEE-c-CC-e--EEEEecCCccchhHHHHHHHHHHHHHhhcCCCC----ceEEEechHHH
Q psy5480         151 FTLCFTDGSKTAN--NTSCAYII-D-KT-L--ISSFVLNNVNSVYTSELIAVLLCLKHLKFLPKE----KFVVISDSKST  219 (446)
Q Consensus       151 ~~~iyTDGS~~~~--~~G~g~v~-~-~~-~--~~~~~l~~~~t~~~AEl~Ai~~AL~~~~~~~~~----~i~I~tDS~~a  219 (446)
                      .++||||||+..+  .+|+|+++ + ++ .  ..+..+ ..+|++.||+.|++.||+.+.+.+..    +|.|+|||+++
T Consensus         3 ~~~iy~DGs~~~n~g~~G~G~v~~~~~g~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~a~~~~~~~~~~~v~i~tDS~~v   81 (140)
T 3u3g_D            3 KIIIYTDGGARGNPGPAGIGVVITDEKGNTLHESSAYI-GETTNNVAEYEALIRALEDLQMFGDKLVDMEVEVRMDSELI   81 (140)
T ss_dssp             EEEEEEEEEESSTTEEEEEEEEEECTTSCEEEEEEEEE-EEECHHHHHHHHHHHHHHHHGGGGGGGTTCEEEEEESCHHH
T ss_pred             eEEEEEecCCCCCCCCcEEEEEEEeCCCCEEEEEEeeC-CCCchHHHHHHHHHHHHHHHHHcCCCCCCceEEEEeChHHH
Confidence            5899999999754  48888665 3 22 2  222233 35799999999999999999887666    99999999999


Q ss_pred             HHHhcCCCC-CChhHHHHHHHHHHH-HhcCceEEEEEcCCCCCCccchHhHHHhcCC
Q psy5480         220 LLALSNPSN-TNPIVSLIHSCWTDL-LCYGKQLAFLWCPSHTGIQGNEAVDRAARNP  274 (446)
Q Consensus       220 i~~l~~~~~-~~~~~~~i~~~~~~l-~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a  274 (446)
                      ++.+.+.+. .++.+..+...+..+ ......|.|.|||    .++||.||+|||+|
T Consensus        82 i~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~~v~~~~V~----~~~N~~AD~LA~~a  134 (140)
T 3u3g_D           82 VRQMQGVYKVKEPTLKEKFAKIAHIKMERVPNLVFVHIP----REKNARADELVNEA  134 (140)
T ss_dssp             HHHHTTSSCCCCGGGHHHHHHHHHHHHHHCTTCEEEECC----GGGGHHHHHHHHHH
T ss_pred             HHHhCCCcccCCHHHHHHHHHHHHHhhcCCCcEEEEEcC----chhhHHHHHHHHHH
Confidence            999998764 444444555555555 5666799999999    48999999999983

>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=99.76  E-value=2e-18  Score=183.01  Aligned_cols=118  Identities=23%  Similarity=0.309  Sum_probs=92.9

Q ss_pred             CCCcEEEEEcCCcCCCC--ceEEEEEcCCeEEEEecCCccchhHHHHHHHHHHHHHhhcCCCCceEEEechHHHHHHhcC
Q psy5480         148 YQDFTLCFTDGSKTANN--TSCAYIIDKTLISSFVLNNVNSVYTSELIAVLLCLKHLKFLPKEKFVVISDSKSTLLALSN  225 (446)
Q Consensus       148 ~~~~~~iyTDGS~~~~~--~G~g~v~~~~~~~~~~l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~~  225 (446)
                      ..+.+.||||||+..++  +|+|+++..+....... ..+||+.||+.|++.||+.    ...++.|+|||++|++.+.+
T Consensus       433 ~~~~~~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~-~~~TNn~aEl~A~i~aL~~----~~~~v~I~tDS~~v~~~i~~  507 (555)
T 1mu2_A          433 IPGAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKL-EQTTNQQAELEAFAMALTD----SGPKVNIIVDSQYVMGIVAS  507 (555)
T ss_dssp             CTTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEEE-SSCCHHHHHHHHHHHHHHT----SCSEEEEEESCHHHHHHHHT
T ss_pred             CCCceEEEEcccccCCCCCceEEEEEEeCCEeeccC-CCCCHHHHHHHHHHHHHHc----CCCeEEEEEehHHHHHHHhc
Confidence            35679999999987543  78887764433333333 4789999999999999998    46799999999999999998


Q ss_pred             CCCC--ChhHHHHHHHHHHHHhcCceEEEEEcCCCCCCccchHhHHHhcCC
Q psy5480         226 PSNT--NPIVSLIHSCWTDLLCYGKQLAFLWCPSHTGIQGNEAVDRAARNP  274 (446)
Q Consensus       226 ~~~~--~~~~~~i~~~~~~l~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a  274 (446)
                      +...  .++..++.+.+    ..+..|.|.|||||+|++|||.||+|||+|
T Consensus       508 ~~~~~~~~l~~~~~~~~----~~~~~v~~~wV~~H~g~~~Ne~AD~LA~~a  554 (555)
T 1mu2_A          508 QPTESESKIVNQIIEEM----IKKEAIYVAWVPAHKGIGGNQEVDHLVSQG  554 (555)
T ss_dssp             CCSEESCHHHHHHHHHH----HHCSEEEEEECCSSSCCTTHHHHHHHHHTT
T ss_pred             ccccccHHHHHHHHHHh----ccCCcEEEEEEECCCCChhHHHHHHHHHhh
Confidence            6532  34555544443    346789999999999999999999999984

>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=99.76  E-value=1.1e-18  Score=185.22  Aligned_cols=117  Identities=21%  Similarity=0.334  Sum_probs=91.0

Q ss_pred             CCCcEEEEEcCCcCCC--CceEEEEEcCCeEEEEecCCccchhHHHHHHHHHHHHHhhcCCCCceEEEechHHHHHHhcC
Q psy5480         148 YQDFTLCFTDGSKTAN--NTSCAYIIDKTLISSFVLNNVNSVYTSELIAVLLCLKHLKFLPKEKFVVISDSKSTLLALSN  225 (446)
Q Consensus       148 ~~~~~~iyTDGS~~~~--~~G~g~v~~~~~~~~~~l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~~  225 (446)
                      ..+.+.||||||+..+  .+|+|+++..+....... ..+||+.||+.|++.||+.+    ..++.|+|||++|++.+.+
T Consensus       436 ~~~~~~iytDGs~~~n~g~~g~g~v~~~~~~~~~~~-~~~TNn~aEl~Ai~~aL~~~----~~~v~I~tDS~~vi~~i~~  510 (557)
T 2zd1_A          436 IVGAETFYVDGAANRETKLGKAGYVTNKGRQKVVPL-TNTTNQKTELQAIYLALQDS----GLEVNIVTDSQYALGIIQA  510 (557)
T ss_dssp             CTTSCEEEEEEEECTTTCCEEEEEEETTSCEEEEEE-CSCCHHHHHHHHHHHHHHHS----CSEEEEEECCHHHHHHHTT
T ss_pred             CCCCEEEEEccCCCCCCCceEEEEEEECCcEEEecC-CCCCHHHHHHHHHHHHHHhC----CCcEEEEeChHHHHHHHhc
Confidence            3467999999998754  378887765543333333 47899999999999999998    5789999999999999999


Q ss_pred             CCCC--ChhHHHHHHHHHHHHhcCceEEEEEcCCCCCCccchHhHHHhcC
Q psy5480         226 PSNT--NPIVSLIHSCWTDLLCYGKQLAFLWCPSHTGIQGNEAVDRAARN  273 (446)
Q Consensus       226 ~~~~--~~~~~~i~~~~~~l~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~  273 (446)
                      +...  .++..++.+.+    .....|.|.|||||+|++|||.||+|||+
T Consensus       511 ~~~~~~~~l~~~~~~~l----~~~~~v~~~wV~~H~g~~~Ne~AD~LA~~  556 (557)
T 2zd1_A          511 QPDKSESELVNQIIEQL----IKKEKVYLAWVPAHKGIGGNEQVDKLVSA  556 (557)
T ss_dssp             CCSEESSHHHHHHHHHH----HHCSEEEEEECCSSSCCTTCCGGGGCC--
T ss_pred             CCccCCHHHHHHHHHHH----hcCCCEEEEEcCCCCCChhHHHHHHHHhc
Confidence            7654  24555544433    23568999999999999999999999997

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

Probab=99.73  E-value=1.1e-17  Score=146.91  Aligned_cols=118  Identities=13%  Similarity=0.186  Sum_probs=88.9

Q ss_pred             EEEEEcCCcC-C--CCceE-EEEE-cCCe-EEEE--ecC---CccchhHHHHHHHHHHHHHhhcCCCCceEEEechHHHH
Q psy5480         152 TLCFTDGSKT-A--NNTSC-AYII-DKTL-ISSF--VLN---NVNSVYTSELIAVLLCLKHLKFLPKEKFVVISDSKSTL  220 (446)
Q Consensus       152 ~~iyTDGS~~-~--~~~G~-g~v~-~~~~-~~~~--~l~---~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai  220 (446)
                      +.||||||+. .  +++|+ |+++ +++. ....  .++   ...|++.||+.|++.||+.+.+.+..+|.|+|||++++
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 8654 3332 2222  222   37899999999999999999988888999999999999


Q ss_pred             HHhcCCCCC-ChhHHHHHHHHHHHHhcCceEEEEEcCCCCCCccchHhHHHhcCC
Q psy5480         221 LALSNPSNT-NPIVSLIHSCWTDLLCYGKQLAFLWCPSHTGIQGNEAVDRAARNP  274 (446)
Q Consensus       221 ~~l~~~~~~-~~~~~~i~~~~~~l~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a  274 (446)
                      +.+.+++.. ++....+.+.+..+.... .|.|.|||+    ++|+.||+|||+|
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            999997543 344445555454443433 599999998    5999999999994

>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=99.36  E-value=2.8e-13  Score=117.46  Aligned_cols=120  Identities=13%  Similarity=0.020  Sum_probs=81.9

Q ss_pred             cCCCcEEEEEcCCcCCC--CceEEEEEc-CCeEE--EEecCCccchhHHHHHHHHHHHHHhhcCCCCceEEEechHHHHH
Q psy5480         147 KYQDFTLCFTDGSKTAN--NTSCAYIID-KTLIS--SFVLNNVNSVYTSELIAVLLCLKHLKFLPKEKFVVISDSKSTLL  221 (446)
Q Consensus       147 ~~~~~~~iyTDGS~~~~--~~G~g~v~~-~~~~~--~~~l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~  221 (446)
                      .+.+.+.||||||+..+  .+|+|+|+. ++...  +..++ .+||+.||++|++.||+.+.+.+. +|.|+|||+++++
T Consensus         7 ~~~~~~~iy~DGa~~gNpG~~G~G~vl~~~g~~~~~~~~~~-~~TNN~aEl~A~i~aL~~~~~~~~-~v~i~tDS~~vi~   84 (142)
T 1zbf_A            7 EEIIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIP-IGTNNMGEFLAIVHGLRYLKERNS-RKPIYSNSQTAIK   84 (142)
T ss_dssp             -CCCSSSEEEEEEECSSSEEEEEEEEETTTCCEEEECCCEE-EECHHHHHHHHHHHHHHHHHHTTC-CCCEEESCHHHHH
T ss_pred             CCCCeEEEEEeeccCCCCCCeEEEEEEEeCCEEEEEecccC-CcCcHHHHHHHHHHHHHHHHhCCC-eEEEEEehHHHHH
Confidence            34567899999999754  478887663 22222  12222 679999999999999999988666 9999999999999


Q ss_pred             HhcCCCCC-----ChhHHHHHHHHHHHH--hcCceEEEEEcCCCCCCccchHhH
Q psy5480         222 ALSNPSNT-----NPIVSLIHSCWTDLL--CYGKQLAFLWCPSHTGIQGNEAVD  268 (446)
Q Consensus       222 ~l~~~~~~-----~~~~~~i~~~~~~l~--~~~~~V~~~WVpgH~gi~gNe~AD  268 (446)
                      .+.+....     .....++.+.+.++.  .+...+....|+-|++.-||..||
T Consensus        85 w~~~~~~k~~~~~~v~n~dLw~~l~~~~~w~~~~~~~~~~~kw~~~~~ge~pad  138 (142)
T 1zbf_A           85 WVKDKKAKSTLVRNEETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKAD  138 (142)
T ss_dssp             HHHHTCCCCCCCCSTTTHHHHHHHHHHHHHHHHCCCCCCEEECCHHHHCSCTTC
T ss_pred             HHHcCCccCCCCCCcccHHHHHHHHHHHHHHhhCCCceeEEEeccCccCcCccc
Confidence            99877632     112333333333221  112344555577788888999888

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

Probab=99.15  E-value=8.3e-11  Score=100.21  Aligned_cols=77  Identities=12%  Similarity=0.041  Sum_probs=57.9

Q ss_pred             CCcEEEEEcCCcCCC--CceEE-EEEcCCe--EEEEecCCccchhHHHHHHHHHHHHHhhcCCCCceEEEechHHHHHHh
Q psy5480         149 QDFTLCFTDGSKTAN--NTSCA-YIIDKTL--ISSFVLNNVNSVYTSELIAVLLCLKHLKFLPKEKFVVISDSKSTLLAL  223 (446)
Q Consensus       149 ~~~~~iyTDGS~~~~--~~G~g-~v~~~~~--~~~~~l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l  223 (446)
                      +....||||||+..+  .+|+| |+...+.  .....+ ..+||+.||++|++.||+.+.+.+.. +.|+|||++|++.+
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            456789999999754  37885 4444332  222233 37899999999999999999875443 89999999999999


Q ss_pred             cCCC
Q psy5480         224 SNPS  227 (446)
Q Consensus       224 ~~~~  227 (446)
                      .+..
T Consensus        81 ~~~~   84 (134)
T 4htu_A           81 KDKK   84 (134)
T ss_dssp             HHTC
T ss_pred             HcCC
Confidence            8643

---

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	446
d1mu2a1	126	c.55.3.1 (A:430-555) HIV RNase H (Domain of revers	7e-07
d1rila_	147	c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermoph	6e-04
d1jl1a_	152	c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli	0.003

>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 = 46.1 bits (108), Expect = 7e-07
 Identities = 27/122 (22%), Positives = 47/122 (38%), Gaps = 13/122 (10%)

Query: 155 FTDGSKTANNT--SCAYIIDKTLISSFVLNNVNSVYTSELIAVLLCLKHLKFLPKEKFVV 212
           +TDGS    +      Y+ D+       L    +   +EL A  + L         K  +
Sbjct: 11  YTDGSCNRQSKEGKAGYVTDRGKDKVKKLEQT-TNQQAELEAFAMALTD----SGPKVNI 65

Query: 213 ISDSKSTLLALSN--PSNTNPIVSLIHSCWTDLLCYGKQLAFLWCPSHTGIQGNEAVDRA 270
           I DS+  +  +++    + + IV+ I           + +   W P+H GI GN+ VD  
Sbjct: 66  IVDSQYVMGIVASQPTESESKIVNQIIEEM----IKKEAIYVAWVPAHKGIGGNQEVDHL 121

Query: 271 AR 272
             
Sbjct: 122 VS 123

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

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

 Score = 38.0 bits (87), Expect = 6e-04
 Identities = 28/135 (20%), Positives = 42/135 (31%), Gaps = 18/135 (13%)

Query: 155 FTDGSKTANNTSCAY----IIDKTLISSFVLNNVNSVYTSELIAVLLCLKHLKFLPKEKF 210
           FTDG+   N     +                    +    EL A +  LK LK     + 
Sbjct: 7   FTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKE--PCEV 64

Query: 211 VVISDSKSTLLALSNP------------SNTNPIVSLIHSCWTDLLCYGKQLAFLWCPSH 258
            + +DS     A +              +   P+ +        L     ++ F +   H
Sbjct: 65  DLYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPHRVRFHFVKGH 124

Query: 259 TGIQGNEAVDRAARN 273
           TG   NE VDR AR 
Sbjct: 125 TGHPENERVDREARR 139

>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 = 36.1 bits (82), Expect = 0.003
 Identities = 14/57 (24%), Positives = 23/57 (40%), Gaps = 1/57 (1%)

Query: 226 PSNTNPIVSLIHSCWTDLLCYGKQLAFLWCPSHTGIQGNEAVDRAARNPSASLPPLK 282
            ++  P+ ++      D      Q+ + W   H G   NE  D  AR  +A  P L+
Sbjct: 90  TADKKPVKNVDLWQRLDAALGQHQIKWEWVKGHAGHPENERADELARA-AAMNPTLE 145

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	446
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.9
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	99.86
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.85
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	99.74
d1zbfa1	132	BH0863-like Ribonuclease H {Bacillus halodurans [T	99.48

>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=99.90  E-value=8.2e-24  Score=179.11  Aligned_cols=117  Identities=22%  Similarity=0.324  Sum_probs=89.4

Q ss_pred             CCcEEEEEcCCcCCC-C-ceEEEEEcCCeEEEEecCCccchhHHHHHHHHHHHHHhhcCCCCceEEEechHHHHHHhcCC
Q psy5480         149 QDFTLCFTDGSKTAN-N-TSCAYIIDKTLISSFVLNNVNSVYTSELIAVLLCLKHLKFLPKEKFVVISDSKSTLLALSNP  226 (446)
Q Consensus       149 ~~~~~iyTDGS~~~~-~-~G~g~v~~~~~~~~~~l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~~~  226 (446)
                      ++..++|||||+..+ + +|+||++..+......++ ..|++.|||.||++||+..    ..++.|+|||+++++.+.+.
T Consensus         5 ~~~~t~YTDGS~~~n~~~~~~g~~~~~~~~~~~~~~-~~tnn~AEl~Ai~~al~~~----~~~i~I~tDS~~v~~~~~~~   79 (126)
T d1mu2a1           5 PGAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKLE-QTTNQQAELEAFAMALTDS----GPKVNIIVDSQYVMGIVASQ   79 (126)
T ss_dssp             TTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEEES-SCCHHHHHHHHHHHHHHTS----CSEEEEEESCHHHHHHHHTC
T ss_pred             CCCcEEEEcCCCCCCCCcEEEEEEecCCCEEEEecC-CCcchHHHHHHHHHHhccC----CcceEEEechHHHHHHHhcC
Confidence            456799999998754 3 667777665555555554 6799999999999999853    57899999999999999987


Q ss_pred             CCCC--hhHHHHHHHHHHHHhcCceEEEEEcCCCCCCccchHhHHHhcCC
Q psy5480         227 SNTN--PIVSLIHSCWTDLLCYGKQLAFLWCPSHTGIQGNEAVDRAARNP  274 (446)
Q Consensus       227 ~~~~--~~~~~i~~~~~~l~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a  274 (446)
                      ...+  ....   ..+..+ .....|.|.|||||+|++|||.||+||++|
T Consensus        80 ~~~~~~~~~~---~~~~~~-~~~~~v~~~wV~gH~g~~gNe~AD~LA~~a  125 (126)
T d1mu2a1          80 PTESESKIVN---QIIEEM-IKKEAIYVAWVPAHKGIGGNQEVDHLVSQG  125 (126)
T ss_dssp             CSEESCHHHH---HHHHHH-HHCSEEEEEECCSSSCCTTHHHHHHHHHTT
T ss_pred             CccccchHHH---HHHHHh-hhcceeEEEEEeCCCCCcchHHHHHHHHhh
Confidence            6532  2222   222222 335689999999999999999999999983

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

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

Probab=99.86  E-value=5e-22  Score=173.06  Aligned_cols=131  Identities=21%  Similarity=0.191  Sum_probs=92.3

Q ss_pred             cEEEEEcCCcCCCC--ceEEEEE-cCCeE--EEEecCCccchhHHHHHHHHHHHHHhhcCCCCceEEEechHHHHHHhcC
Q psy5480         151 FTLCFTDGSKTANN--TSCAYII-DKTLI--SSFVLNNVNSVYTSELIAVLLCLKHLKFLPKEKFVVISDSKSTLLALSN  225 (446)
Q Consensus       151 ~~~iyTDGS~~~~~--~G~g~v~-~~~~~--~~~~l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~~  225 (446)
                      .|.||||||+..++  +|+|+++ ..+..  .+.. ....|++.||++|++.||+++..  ...+.|++||++++..+..
T Consensus         2 ~I~IYtDGS~~~N~g~aG~G~vi~~~~~~~~~~~~-~~~~tnn~aE~~Ai~~Al~~~~~--~~~i~i~tds~~~i~~~~~   78 (152)
T d1jl1a_           2 QVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAG-YTRTTNNRMELMAAIVALEALKE--HAEVILSTDSQYVRQGITQ   78 (152)
T ss_dssp             CEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEE-EEEECHHHHHHHHHHHHHHTCCS--CCEEEEEECCHHHHHHHHT
T ss_pred             EEEEEEeCCCCCCCCcEEEEEEEEECCeEEEeccc-cCcccHHHHHHhhhhhhhhhhcc--cceEEEeecceeeEEcccc
Confidence            48999999987653  7888554 44332  2222 34678999999999999998654  5678999999999988864


Q ss_pred             CCC---------CC--h-hHHHHHHHHHHHHhcCceEEEEEcCCCCCCccchHhHHHhcCCCCCCCCCccCCCc
Q psy5480         226 PSN---------TN--P-IVSLIHSCWTDLLCYGKQLAFLWCPSHTGIQGNEAVDRAARNPSASLPPLKLCSPE  287 (446)
Q Consensus       226 ~~~---------~~--~-~~~~i~~~~~~l~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a~a~~~~~~~~~~~  287 (446)
                      ...         ..  + ....+...+..+ ....+|.|.|||||+|++|||.||+|||+  |...|.....++
T Consensus        79 ~~~~~~~~~~~~~~~~~~~n~~~~~~i~~~-~~~~~V~~~wV~gH~g~~gNe~AD~LAk~--aa~~~~~~d~~~  149 (152)
T d1jl1a_          79 WIHNWKKRGWKTADKKPVKNVDLWQRLDAA-LGQHQIKWEWVKGHAGHPENERADELARA--AAMNPTLEDTGY  149 (152)
T ss_dssp             THHHHHHTTTBCTTSCBCTTHHHHHHHHHH-TTTCEEEEEECCSSTTCHHHHHHHHHHHH--HHHSCCBCCTTC
T ss_pred             hhhHhHhccchhcccCeeecHHHHHHHHHH-hhcceeEEEEecccCCCccHHHHHHHHHH--HHhCCCCCccCC
Confidence            421         11  1 112233333333 34568999999999999999999999999  444454444444

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

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

Probab=99.85  E-value=3.4e-22  Score=173.52  Aligned_cols=121  Identities=23%  Similarity=0.148  Sum_probs=86.9

Q ss_pred             cEEEEEcCCcCCCC--ceEEEEE-cCC-eEEEEecCCccchhHHHHHHHHHHHHHhhcCCCCceEEEechHHHHHHhcCC
Q psy5480         151 FTLCFTDGSKTANN--TSCAYII-DKT-LISSFVLNNVNSVYTSELIAVLLCLKHLKFLPKEKFVVISDSKSTLLALSNP  226 (446)
Q Consensus       151 ~~~iyTDGS~~~~~--~G~g~v~-~~~-~~~~~~l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~~~  226 (446)
                      .|+||||||+..++  +|+|+++ ..+ ...........|++.||+.||+.||+.+..  ...+.|++||++++..+...
T Consensus         3 ~i~iytDGs~~~N~g~~G~g~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~~~--~~~i~i~tds~~~~~~~~~~   80 (147)
T d1rila_           3 RVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKE--PCEVDLYTDSHYLKKAFTEG   80 (147)
T ss_dssp             CCCEEEEEEESSTTEEEEEEEEECBTTBCCEECCEEEEECHHHHHHHHHHHHHHSCCS--CCEEEEECCCHHHHHHHHSS
T ss_pred             EEEEEEccCCCCCCCccEEEEEEEECCcceEEecccccccHHHHHHHHHHHHhhhccC--CceEEEecchhhhhcccccc
Confidence            58999999998653  7888654 332 222222234679999999999999997653  56799999999999988653


Q ss_pred             CC----------C--Chh-HHHHHHHHHHHHhcCceEEEEEcCCCCCCccchHhHHHhcCC
Q psy5480         227 SN----------T--NPI-VSLIHSCWTDLLCYGKQLAFLWCPSHTGIQGNEAVDRAARNP  274 (446)
Q Consensus       227 ~~----------~--~~~-~~~i~~~~~~l~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a  274 (446)
                      ..          .  .++ -.+++..+..+ .....|.|.|||||+|++|||.||+|||+|
T Consensus        81 ~~~~~~~~~~~~~~~~~v~n~dL~~~l~~~-~~~~~v~~~wVkgHsg~~gNe~AD~LAk~a  140 (147)
T d1rila_          81 WLEGWRKRGWRTAEGKPVKNRDLWEALLLA-MAPHRVRFHFVKGHTGHPENERVDREARRQ  140 (147)
T ss_dssp             HHHHHHHTTSBCTTSSBCTTHHHHHHHHHH-HTTSEEECCCCCGGGSCTHHHHHHHHHHHH
T ss_pred             chhhhhhccccccccccchhHHHHHHHHHH-hhhcccceEEccCCCCCcchHHHHHHHHHH
Confidence            21          1  111 12333333333 345689999999999999999999999994

>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=99.74  E-value=5.4e-18  Score=139.03  Aligned_cols=103  Identities=17%  Similarity=0.285  Sum_probs=77.5

Q ss_pred             cCCCcEEEEEcCCcCCCC--ceEEEEEcCCeEEEEecCCccchhHHHHHHHHHHHHHhhcCCCCceEEEechHHHHHHhc
Q psy5480         147 KYQDFTLCFTDGSKTANN--TSCAYIIDKTLISSFVLNNVNSVYTSELIAVLLCLKHLKFLPKEKFVVISDSKSTLLALS  224 (446)
Q Consensus       147 ~~~~~~~iyTDGS~~~~~--~G~g~v~~~~~~~~~~l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~  224 (446)
                      +.++..++|||||+..++  +|+|++...+......++ .+||+.|||.||++||+..    ..++.|+|||+++++++.
T Consensus         4 Pi~~~~t~ytDGs~~~n~~~g~~g~~~~~~~~~~~~~~-~~TNn~aEl~Avi~aL~~~----~~~v~I~TDS~yvi~~i~   78 (110)
T d1s1ta1           4 PIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLT-DTTNQKTELQAIYLALQDS----GLEVNIVTDSQYALGIIQ   78 (110)
T ss_dssp             CCTTSEEEEEEEEEETTTTEEEEEEEETTSCEEEEEES-SCCHHHHHHHHHHHHHHHS----CSEEEEEECCHHHHHHHH
T ss_pred             CCCCCcEEEEeCCCCCCCCCcEEEEEEecCCeEEEecc-cCcHHHHHHHHHHHHHHhC----CCeEEEEEehHHHHHHHh
Confidence            345667899999986543  666776665544455554 6799999999999999853    568999999999999999


Q ss_pred             CCCCC--ChhHHHHHHHHHHHHhcCceEEEEEcCCC
Q psy5480         225 NPSNT--NPIVSLIHSCWTDLLCYGKQLAFLWCPSH  258 (446)
Q Consensus       225 ~~~~~--~~~~~~i~~~~~~l~~~~~~V~~~WVpgH  258 (446)
                      .....  .....+|.+.+    .....|.|.|||||
T Consensus        79 ~~~~~~~~~l~~~il~~l----~~~~~v~i~WVpgH  110 (110)
T d1s1ta1          79 AQPDQSESELVNQIIEQL----IKKEKVYLAWVPAH  110 (110)
T ss_dssp             HCCSEESCHHHHHHHHHH----HHCSEEEEEECCSS
T ss_pred             cCccccchHHHHHHHHHH----hcCCceEEEEeCCC
Confidence            87653  34555554444    34678999999999

>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=99.48  E-value=7.5e-15  Score=122.51  Aligned_cols=115  Identities=13%  Similarity=0.001  Sum_probs=81.0

Q ss_pred             EEEEcCCcCCC--CceEEEEEcC-CeEEEEe-cCCccchhHHHHHHHHHHHHHhhcCCCCceEEEechHHHHHHhcCCCC
Q psy5480         153 LCFTDGSKTAN--NTSCAYIIDK-TLISSFV-LNNVNSVYTSELIAVLLCLKHLKFLPKEKFVVISDSKSTLLALSNPSN  228 (446)
Q Consensus       153 ~iyTDGS~~~~--~~G~g~v~~~-~~~~~~~-l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~tDS~~ai~~l~~~~~  228 (446)
                      .||||||+..+  .+|+|+|+.. +...... .-...||+.||++|++.||+.+.+.+ .++.|+|||+++++.+.+...
T Consensus         6 sIy~DGa~~GNPGp~g~g~v~~~~~~~~~~sg~~~~~TNN~aEl~A~i~aL~~~~~~~-~~i~I~tDS~yvi~wv~~~~~   84 (132)
T d1zbfa1           6 SLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERN-SRKPIYSNSQTAIKWVKDKKA   84 (132)
T ss_dssp             SEEEEEEECSSSEEEEEEEEETTTCCEEEECCCEEEECHHHHHHHHHHHHHHHHHHTT-CCCCEEESCHHHHHHHHHTCC
T ss_pred             eEEEeecCCCCCchheEEEEEEcCCEEEEEEcCcCccchHHHHHHHHHHHHHHhhcCC-ceEEEEeccHHHHHHHHhCce
Confidence            48999999854  3788866533 3222221 12478999999999999999998754 679999999999999976553


Q ss_pred             CC-----hhHHHHHHHHHHHH--hcCceEEEEEcCCCCCCccchHhH
Q psy5480         229 TN-----PIVSLIHSCWTDLL--CYGKQLAFLWCPSHTGIQGNEAVD  268 (446)
Q Consensus       229 ~~-----~~~~~i~~~~~~l~--~~~~~V~~~WVpgH~gi~gNe~AD  268 (446)
                      ..     ..-.++.+++.++.  -+...+.+.||+.|+..-||..||
T Consensus        85 kt~~~~~vkN~~l~~~i~~a~~~lk~h~~~~~~~KW~~~~wG~i~AD  131 (132)
T d1zbfa1          85 KSTLVRNEETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKAD  131 (132)
T ss_dssp             CCCCCCSTTTHHHHHHHHHHHHHHHHCCCCCCEEECCHHHHCSCTTC
T ss_pred             ecCcCCCcccHHHHHHHHHHHHHHHhCCcCceeEEecCcccccCCCC
Confidence            21     12334444443221  224568899999999999999988