Psyllid ID: psy17737

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490---
Protein Sequence
MTNNQSEYFDQLPEELKSCNKVQNVLGLTWDTDIDTLSIKHGELQCSGKLTKRLLLSVYGSIYDVLGLFTPVVLPLKILIQSVWQRNLSWDEELSTEDKITFMKLIEDIKLIHTVHIPRLIGNLIPGTQYELHGFSDASATSYSMVIYLKCITGNSVTSNLVFAKARIAPLSRPTLPRLELLGALIAYRGLKFVGESLKVKDIKYYLWIDSQIVIHWILGNKVLPTFINNRVKEIKNRSFKLDVHYVPTDMNPADIACRGEKLSSLQNNETWWHGPKWLCQSEGHWPQWSFTDEISPQTEVSMDNALSVPAVKQLSKPLARKPIPVDHEKFNSFNKLVNVTCYVLKFIRLCRRQKENKGNISIIEYEESKLSWIKFAQHQKFASTMQELKQGHKDQLSQQLGLVLDENDILRCKGRFVELKVDGKSCFPMLLPRGNHISKIIVNDIHTSGYHTGDKESKKLSNVARGYYLDGNHLERRVLLGSRLLSGWVRLN
Secondary Structure (PSIPRED)
ccccHHHHHHHccccccccccccEEEEEEEcccccEEEEEccccccccccHHHHHHHHHHHcccccccccccccHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHccccccccEEcccccccccEEEEEEEcccccEEEEEEEEEEEEccccEEEEEEEcccccccccccHHHHHHHHHHHHHHcccEEEEccEEccccEEEEEccEEEHHHHHccccccccccHHHHHHHcccccccEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEcccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHcccHHHHHHHHccccccccccccEEEcccccEEEccccccccccccccccEEcccccHHHHHHHHHHHHHcccccHHHHHHHHHHHccEEEcccHHHHHHHccccccEEccccc
Secondary Structure Prediction (SSPRO)
cccccHHHHHHccHHHccccccEEEEEEEEcccccEEEEEEccccccccccHHHHHHHHHHHcccHcHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHcccccEEEEEEEcccccccEEEEEEEEcccHHHEEEEEEEEEEcccccEEEEEEEEccccccccccccHHHHHHHHHHHHHHHHHHHHccccccEEEEEcccHEEEHEEccccccHHHHHHHHHHHHHccccccEEEcccccccHcHHcccccHHHHHcccccccccHHHcccHHcccccccccccccccccccccccccccEEcEEcccccccccccHHHcccHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccEEEEccccccccccHcccccEEEccccHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHcHHHHHHHHHHcEEEEEEEEcc
Coil and Loop (DISEMBL)
MTNNQSEYFDQLPEELKSCNKVQNVLgltwdtdidtlsikhgelqcsgkLTKRLLLSVYGSIYdvlglftpvvLPLKILIQSVWQRNlswdeelsteDKITFMKLIEDIKLIHTVHiprlignlipgtqyelhgfsdasatSYSMVIYLKCITGNSVTSNLVFAKariaplsrptlprLELLGALIAYRGLkfvgeslkvkdikyyLWIDSQIVIHWIlgnkvlptFINNRVKEIKNrsfkldvhyvptdmnpadiacrgeklsslqnnetwwhgpkwlcqseghwpqwsftdeispqtevsmdnalsvpavkqlskplarkpipvdhekfnsfnklVNVTCYVLKFIRLCRRqkenkgniSIIEYEESKLSWIKFAQHQKFASTMQELKQGHKDQLSQQlglvldendilRCKGRFVELkvdgkscfpmllprgnhiskiivndihtsgyhtgdkeskkLSNVArgyyldgnhLERRVLLGSRLLSGWVRLN
Flexible Loop (DISEMBL)
MTNNQSEYFDQLPEELKSCNKVQNVLGLTWDTDIDTLSIKHGELQCSGKLTKRLLLSVYGSIYDVLGLFTPVVLPLKILIQSVWQRNLSWDEELSTEDKITFMKLIEDIKLIHTVHIPRLIGNLIPGTQYELHGFSDASATSYSMVIYLKCITGNSVTSNLVFAKARiaplsrptlpRLELLGALIAYRGLKFVGESLKVKDIKYYLWIDSQIVIHWILGNKVLPTFINNRVKEIKNRSFKLDVHYVPTDMNPADIACRGEKLSSLQNNETWWHGPKWLCQSEGHWPQWSFTDEISPQTEVSMDNALSVPAVKQlskplarkpipvdhekfnsfnklvnVTCYVLKFIRLcrrqkenkgniSIIEYEESKLSWIKFAQHQKFASTMQELKQGHKDQLSQQLGLVLDENDILRCKGRFVELKVDGKSCFPMLLPRGNHISKIIVNDIHTSgyhtgdkeskklsNVARGYyldgnhlerrvllgsrllsgwvrln
Low Complexity Region (SEG)
MTNNQSEYFDQLPEELKSCNKVQNVLGLTWDTDIDTLSIKHGELQCSGKLTKRLLLSVYGSIYDVLGLFTPVVLPLKILIQSVWQRNLSWDEELSTEDKITFMKLIEDIKLIHTVHIPRLIGNLIPGTQYELHGFSDASATSYSMVIYLKCITGNSVTSNLVFAKARIAPLSRPTLPRLELLGALIAYRGLKFVGESLKVKDIKYYLWIDSQIVIHWILGNKVLPTFINNRVKEIKNRSFKLDVHYVPTDMNPADIACRGEKLSSLQNNETWWHGPKWLCQSEGHWPQWSFTDEISPQTEVSMDNALSVPAVKQLSKPLARKPIPVDHEKFNSFNKLVNVTCYVLKFIRLCRRQKENKGNISIIEYEESKLSWIKFAQHQKFASTMQELKQGHKDQLSQQLGLVLDENDILRCKGRFVELKVDGKSCFPMLLPRGNHISKIIVNDIHTSGYHTGDKESKKLSNVARGYYLDGNHlerrvllgsrllsgwvrlN
Disordered region (IsUnstruct)
****************KSCNKVQNVLGLTWDTDIDTLSIKHGELQCSGKLTKRLLLSVYGSIYDVLGLFTPVVLPLKILIQSVWQRNLSWDEELSTEDKITFMKLIEDIKLIHTVHIPRLIGNLIPGTQYELHGFSDASATSYSMVIYLKCITGNSVTSNLVFAKARIAPLSRPTLPRLELLGALIAYRGLKFVGESLKVKDIKYYLWIDSQIVIHWILGNKVLPTFINNRVKEIKNRSFKLDVHYVPTDMNPADIACRGEKLSSLQNNETWWHGPKWLCQSEGHWPQWSFTDEI****************************IPVDHEKFNSFNKLVNVTCYVLKFIRLCRRQKENKGNISIIEYEESKLSWIKFAQHQKFA***************QQLGLVLDENDILRCKGRFVELKVDGKSCFPMLLPRGNHISKIIVNDIHTSGYHTGD****KLSNVARGYYLDGNHLERRVLLGSRLLSGWV***
Disordered Region (DISOPRED)
MTNNQSEYF***************VLGLTWDTDIDTLSIKHGELQCSGKLTKRLLLSVYGSIYDVLGLFTPVVLPLKILIQSVWQRNLSWDEELSTEDKITFMKLIEDIKLIHTVHIPRLIGNLIPGTQYELHGFSDASATSYSMVIYLKCITGNSVTSNLVFAKARIAPLSRPTLPRLELLGALIAYRGLKFVGESLKVKDIKYYLWIDSQIVIHWILGNKVLPTFINNRVKEIKNRSFKLDVHYVPTDMNPADIACRGEKLSSLQNNETWWHGPKWLCQSEGHWPQWSFTDEISPQTEVSMDNALSVPAVKQLSKPLARKPIPVDHEKFNSFNKLVNVTCYVLKFIRLCRRQKENKGNISIIEYEESKLSWIKFAQHQKFASTMQELKQGHK*QLSQQLGLVLDENDILRCKGRFVELKVDGKSCFPMLLPRGNHISKIIVNDIHTSGYHTGDKESKKLSNVARGYYLDGNHLERRVLLGSRLLSGWVRL*
Disordered Region (DISEMBL)
MTNNQSEYFDQLPEELKSCNKVQNVLGLTWDTDIDTLSIKHGELQCSGKLTKRLLLSVYGSIYDVLGLFTPVVLPLKILIQSVWQRNLSWDEELSTEDKITFMKLIEDIKLIHTVHIPRLIGNLIPGTQYELHGFSDASATSYSMVIYLKCITGNSVTSNLVFAKARIAPLSRPTLPRLELLGALIAYRGLKFVGESLKVKDIKYYLWIDSQIVIHWILGNKVLPTFINNRVKEIKNRSFKLDVHYVPTDMNPADIACRGEKLSSLQNNETWWHGPKWLCQSEGHWPQWSFTDEISPQTEVSMDNALSVPAVKQLSKPLARKPIPVDHEKFNSFNKLVNVTCYVLKFIRLCRRQKENKGNISIIEYEESKLSWIKFAQHQKFAST************SQQLGLVLDENDILRCKGRFVELKVDGKSCFPMLLPRGNHISKIIVNDIHTSGYHTGDKESKKLSNVARGYYLDGNHLERRVLLGSRLLSGWVRLN
Disordered Region (DISPRO)
*********DQLP***KSCNKVQNVLGLTWDTDIDTLSIKHGELQCSGKLTKRLLLSVYGSIYDVLGLFTPVVLPLKILIQSVWQRNLSWDEELSTEDKITFMKLIEDIKLIHTVHIPRLIGNLIPGTQYELHGFSDASATSYSMVIYLKCITGNSVTSNLVFAKARIAPLSRPTLPRLELLGALIAYRGLKFVGESLKVKDIKYYLWIDSQIVIHWILGNKVLPTFINNRVKEIKNRSFKLDVHYVPTDMNPADIACRGEKLSSLQNNETWWHGPKWLCQSEGHWPQ****************NALSVPAVKQLSKPLARKPIPVDHEKFNSFNKLVNVTCYVLKFIRLCRRQKENKGNISIIEYEESKLSWIKFAQHQKFASTMQELKQGHKDQLSQQLGLVLDENDILRCKGRFVELKVDGKSCFPMLLPRGNHISKIIVNDIHTSGYHTGDKESKKLSNVARGYYLDGNHLERRVLLGSRLLSGWVRLN
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MTNNQSEYFDQLPEELKSCNKVQNVLGLTWDTDIDTLSIKHGELQCSGKLTKRLLLSVYGSIYDVLGLFTPVVLPLKILIQSVWQRNLSWDEELSTEDKITFMKLIEDIKLIHTVHIPRLIGNLIPGTQYELHGFSDASATSYSMVIYLKCITGNSVTSNLVFAKARIAPLSRPTLPRLELLGALIAYRGLKFVGESLKVKDIKYYLWIDSQIVIHWILGNKVLPTFINNRVKEIKNRSFKLDVHYVPTDMNPADIACRGEKLSSLQNNETWWHGPKWLCQSEGHWPQWSFTDEISPQTEVSMDNALSVPAVKQLSKPLARKPIPVDHEKFNSFNKLVNVTCYVLKFIRLCRRQKENKGNISIIEYEESKLSWIKFAQHQKFASTMQELKQGHKDQLSQQLGLVLDENDILRCKGRFVELKVDGKSCFPMLLPRGNHISKIIVNDIHTSGYHTGDKESKKLSNVARGYYLDGNHLERRVLLGSRLLSGWVRLN
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	493
291230224	1605	PREDICTED: Pao retrotransposon peptidase	0.896	0.275	0.339	9e-65
237845597	1683	Pao retrotransposon peptidase domain-con	0.898	0.263	0.319	1e-61
170580761	863	Pao retrotransposon peptidase family pro	0.898	0.513	0.317	1e-61
170573786	775	Pao retrotransposon peptidase family pro	0.898	0.571	0.323	1e-61
170588121	1811	Pao retrotransposon peptidase family pro	0.898	0.244	0.317	2e-61
170588613	1750	Pao retrotransposon peptidase family pro	0.898	0.253	0.317	2e-61
170586490	1836	Pao retrotransposon peptidase family pro	0.898	0.241	0.317	4e-61
170589333	1566	Pao retrotransposon peptidase family pro	0.898	0.282	0.317	4e-61
339257282	1564	Pao retrotransposon peptidase superfamil	0.910	0.287	0.319	4e-59
339241105	1759	zinc knuckle protein [Trichinella spiral	0.884	0.247	0.314	1e-57

>gi|291230224|ref|XP_002735068.1| PREDICTED: Pao retrotransposon peptidase family protein-like [Saccoglossus kowalevskii]

 Score =  254 bits (648), Expect = 9e-65,   Method: Compositional matrix adjust.
 Identities = 165/486 (33%), Positives = 248/486 (51%), Gaps = 44/486 (9%)

Query: 2    TNNQSEYFDQLPEELKSCNKVQNVLGLTWDTDIDTLSIKHGELQCSGKL-TKRLLLSVYG 60
            +NNQ        + +   +K  ++LG+ W  D D L+          +L TKR ++S   
Sbjct: 780  SNNQQVMDLAEKDNIHEPSKNVSILGIRWKIDGDELTYNKAVKPILTELVTKRDVVSYAS 839

Query: 61   SIYDVLGLFTPVVLPLKILIQSVWQRNLSWDEELSTEDKITFMKLIEDIKLIHTVHIPR- 119
            S+YD +G  +PV++   + IQ +W+   SWDE L+TE    ++K+ E+++    + + R 
Sbjct: 840  SLYDPIGYLSPVLIKAMLFIQLLWKLGFSWDEPLTTELTTQWIKIAENMRETRNITVKRQ 899

Query: 120  LIGNLIPGTQYELHGFSDASATSYSMVIYLKCITGNSVTSNLVFAKARIAPLSRPTLPRL 179
                  P ++ ++H F+DAS+  Y  ++Y+     N   +  V AK R+AP++  TLPRL
Sbjct: 900  YFTENDPQSKVDVHAFADASSVGYGAIVYIT----NQRETAFVTAKTRVAPMTETTLPRL 955

Query: 180  ELLGALIAYRGLKFVGESL--KVKDIKYYLWIDSQIVIHWILGNKVLPTFINNRVKEIKN 237
            EL+ AL+A R  KFV  +L  K      YLW DSQIV+HW+  +K LP F+ NRVKEIK 
Sbjct: 956  ELMAALMASRLTKFVITALSGKFNINNCYLWSDSQIVLHWLNSDKKLPIFVRNRVKEIK- 1014

Query: 238  RSFKLDVHYVPTDMNPADIACRGEKLSSLQNNETWWHGPKWLCQSEGHWPQWSFTD---- 293
              F     YVPT  NPAD+  RG   + L N+  WW+GP WL  +   WP     D    
Sbjct: 1015 -EFSHIYKYVPTLDNPADLLTRGITCAELINSNIWWNGPLWL-NTPNEWPTCEMFDITIL 1072

Query: 294  ----------------------EISPQTEVSMDNALSVPAVKQLSKPLARKPIPVDHEKF 331
                                   IS Q E+ MDN  +    K++          +D  ++
Sbjct: 1073 HAVLERENRDLLSDSAFTETETNISRQREIVMDNDYN----KEIESQEIGLHTVIDISRY 1128

Query: 332  NSFNKLVNVTCYVLKFI-RLCRRQKENKGNISIIEYEESKLSWIKFAQHQKFASTMQELK 390
            NS +KL+ VT YV++FI R+ +    N G I+  E + ++  WI   Q Q+F  T+ ELK
Sbjct: 1129 NSIDKLLRVTAYVMRFISRVKKADTINTGLITADELKRAEHVWILNVQQQEFRDTIHELK 1188

Query: 391  QGHKD--QLSQQLGLVLDENDILRCKGRFVELKVDGKSCFPMLLPRGNHISKIIVNDIHT 448
              H     + QQLGL +DE D+LRC  R     ++  + FP LLP  + ++K+IV   H+
Sbjct: 1189 TKHTKLGPIVQQLGLFIDEEDVLRCGSRIHNAPIEFVTKFPTLLPSNHELTKLIVLKAHS 1248

Query: 449  SGYHTG 454
               H G
Sbjct: 1249 LILHGG 1254

Source: Saccoglossus kowalevskii

Species: Saccoglossus kowalevskii

Genus: Saccoglossus

Family: Harrimaniidae

Class: Enteropneusta

Phylum: Hemichordata

Superkingdom: Eukaryota

>gi|237845597|ref|XP_002372096.1| Pao retrotransposon peptidase domain-containing protein [Toxoplasma gondii ME49] gi|211969760|gb|EEB04956.1| Pao retrotransposon peptidase domain-containing protein [Toxoplasma gondii ME49]

 Score =  244 bits (622), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 159/497 (31%), Positives = 261/497 (52%), Gaps = 54/497 (10%)

Query: 3    NNQSEYFDQLP-EELKSCNKVQNVLGLTW--DTDIDTLSIKHGELQCSGKLTKRLLLSVY 59
            +N  E  ++LP ++    + ++ +LGL W    DI  +++K        KLTKR++L   
Sbjct: 828  SNDQEVNEKLPVQDRAEVSSIKKILGLNWYHKQDIIQVTLKPW---FGKKLTKRIILQFV 884

Query: 60   GSIYDVLGLFTPVVLPLKILIQSVWQRNLSWDEELSTEDKITFMKLIEDIKLIHTVHIPR 119
             S YD LG   P+++  K+ +Q++W+RNLSWD+ +S ED+ T+ KL+ +        +PR
Sbjct: 885  ASQYDPLGFIVPILIRFKLFLQTLWKRNLSWDQTISEEDETTW-KLLTNEWPKKLKDLPR 943

Query: 120  LIGNLIPGTQYELHGFSDASATSYSMVIYLKCITGNSVTSNLVFAKARIAPLSRPTLPRL 179
               N     Q + H F+DAS  +YS  +Y++          LVFAK+RIAP+   ++PRL
Sbjct: 944  FTTNC--SKQVQFHVFTDASTAAYSAALYIRTQEREVF---LVFAKSRIAPIKGMSIPRL 998

Query: 180  ELLGALIAYRGLKFVGESLKVKDIKYYLWIDSQIVIHWIL-GNKVLPTFINNRVKEIKNR 238
            ELL  LI  R ++FV +  +++D+   LW DSQ  +HW+   +++LPTFI NRV+EI  R
Sbjct: 999  ELLAILIGVRMVQFVLKQKELEDVITILWSDSQCALHWVHNSSRLLPTFIQNRVEEI--R 1056

Query: 239  SFKLDVHYVPTDMNPADIACRGEKLSSLQNNETWWHGPKWLCQSEGHWPQWSFTDEISPQ 298
              K+   Y+P++ NPADIA +G   + L+  + WW GPKWL ++E  WPQW +      Q
Sbjct: 1057 KAKIHFRYIPSEQNPADIATKGISPNKLKGYDLWWKGPKWLTENESKWPQWKYNYNEDYQ 1116

Query: 299  TEVSMDNALSVPAVKQLSKPLA--RKPIPVDHEKFNSFNKLVNVTCYVLKFIRLCRRQKE 356
             E           V  +++P+   +    +D  +F+ +++L+  T +VLKFIRL  ++  
Sbjct: 1117 DE---------EIVAHITEPIIINKHFGILDASRFSKWSRLIRTTGWVLKFIRLTMKR-- 1165

Query: 357  NKGNISIIEYEESKLSWIKFAQHQKFASTMQ--ELKQGHKDQLSQQLGLVLDE------- 407
                         ++ W+K A  +K   T Q  EL +    + +Q  G+  DE       
Sbjct: 1166 -------------EIPWLKMATKEKNILTTQDYELSEIVLFKQAQSEGVTKDEIIKWNLF 1212

Query: 408  --NDILRCKGRFVELKVDGKSCFPMLLPRGNHISKIIVNDIHTSGYHTGDKESKKLSNVA 465
              N++ R K R V  ++   +  P+ LPR N I+++ +   H   YH G   +  LSN+ 
Sbjct: 1213 YDNELWRYKSRVVNSEMKESNLHPIYLPRHNTITELFIQQRHEQLYHAGIAHT--LSNLR 1270

Query: 466  RGYYLDGNHLERRVLLG 482
               ++     E + +L 
Sbjct: 1271 STIWIPKGRTEVKRILN 1287

Source: Toxoplasma gondii ME49

Species: Toxoplasma gondii

Genus: Toxoplasma

Family: Sarcocystidae

Order: Eucoccidiorida

Class: Coccidia

Phylum: Apicomplexa

Superkingdom: Eukaryota

>gi|170580761|ref|XP_001895397.1| Pao retrotransposon peptidase family protein [Brugia malayi] gi|158597669|gb|EDP35752.1| Pao retrotransposon peptidase family protein [Brugia malayi]

 Score =  243 bits (621), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 158/497 (31%), Positives = 261/497 (52%), Gaps = 54/497 (10%)

Query: 3   NNQSEYFDQLP-EELKSCNKVQNVLGLTW--DTDIDTLSIKHGELQCSGKLTKRLLLSVY 59
           +N  E  ++LP ++    + ++ +LGL W    DI  +++K        KLTKR++L   
Sbjct: 8   SNDQEVNEKLPVQDRAEVSSIKKILGLNWYHKQDIIQVTLKPW---FGKKLTKRIILQFV 64

Query: 60  GSIYDVLGLFTPVVLPLKILIQSVWQRNLSWDEELSTEDKITFMKLIEDIKLIHTVHIPR 119
            S YD LG   P+++  K+ +Q++W++NLSWD+ +S ED+ T+ KL+ +        +PR
Sbjct: 65  ASQYDPLGFIVPILIRFKLFLQTLWKKNLSWDQTISEEDETTW-KLLTNEWPKKLKDLPR 123

Query: 120 LIGNLIPGTQYELHGFSDASATSYSMVIYLKCITGNSVTSNLVFAKARIAPLSRPTLPRL 179
              N     Q + H F+DAS  +YS  +Y++          LVFAK+RIAP+   ++PRL
Sbjct: 124 FTTNC--SKQVQFHVFTDASTAAYSAALYIRTQEREVF---LVFAKSRIAPIKGMSIPRL 178

Query: 180 ELLGALIAYRGLKFVGESLKVKDIKYYLWIDSQIVIHWIL-GNKVLPTFINNRVKEIKNR 238
           ELL  LI  R ++FV +  +++D+   LW DSQ  +HW+   +++LPTFI NRV+EI  R
Sbjct: 179 ELLAILIGVRMVQFVLKQKELEDVITILWSDSQCALHWVHNSSRLLPTFIQNRVEEI--R 236

Query: 239 SFKLDVHYVPTDMNPADIACRGEKLSSLQNNETWWHGPKWLCQSEGHWPQWSFTDEISPQ 298
             K+   Y+P++ NPADIA +G   + L+  + WW GPKWL ++E  WPQW +      Q
Sbjct: 237 KAKIHFRYIPSEQNPADIATKGISPNKLKGYDLWWKGPKWLTENESKWPQWKYNYNEDYQ 296

Query: 299 TEVSMDNALSVPAVKQLSKPLA--RKPIPVDHEKFNSFNKLVNVTCYVLKFIRLCRRQKE 356
            E           V  +++P+   +    +D  +F+ +++L+  T +VLKFIRL  ++  
Sbjct: 297 DE---------EIVAHITEPIIINKHFGILDASRFSKWSRLIRTTGWVLKFIRLTMKR-- 345

Query: 357 NKGNISIIEYEESKLSWIKFAQHQKFASTMQ--ELKQGHKDQLSQQLGLVLDE------- 407
                        ++ W+K A  +K   T Q  EL +    + +Q  G+  DE       
Sbjct: 346 -------------EIPWLKMATKEKNILTTQDYELSEIVLFKQAQSEGVTKDEIIKWNLF 392

Query: 408 --NDILRCKGRFVELKVDGKSCFPMLLPRGNHISKIIVNDIHTSGYHTGDKESKKLSNVA 465
             N++ R K R V  ++   +  P+ LPR N I+++ +   H   YH G   +  LSN+ 
Sbjct: 393 YDNELWRYKSRVVNSEMKESNLHPIYLPRHNTITELFIQQRHEQLYHAGIAHT--LSNLR 450

Query: 466 RGYYLDGNHLERRVLLG 482
              ++     E + +L 
Sbjct: 451 STIWIPKGRTEVKRILN 467

Source: Brugia malayi

Species: Brugia malayi

Genus: Brugia

Family: Onchocercidae

Order: Spirurida

Class: Chromadorea

Phylum: Nematoda

Superkingdom: Eukaryota

>gi|170573786|ref|XP_001892591.1| Pao retrotransposon peptidase family protein [Brugia malayi] gi|158601760|gb|EDP38577.1| Pao retrotransposon peptidase family protein [Brugia malayi]

 Score =  243 bits (621), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 161/497 (32%), Positives = 260/497 (52%), Gaps = 54/497 (10%)

Query: 3   NNQSEYFDQLP-EELKSCNKVQNVLGLTW--DTDIDTLSIKHGELQCSGKLTKRLLLSVY 59
           +N  E  ++LP ++    + ++ +LGL W    DI  +++K        KLTKR++L   
Sbjct: 8   SNDQEVNEKLPVQDRAEVSSIKKILGLNWYHKQDIIQVTLKPW---FGKKLTKRIILQFV 64

Query: 60  GSIYDVLGLFTPVVLPLKILIQSVWQRNLSWDEELSTEDKITFMKLIEDIKLIHTVHIPR 119
            S YD LG   P+++  K+ +Q++W++NLSWD+ +S ED+ T+ KL+ +        +PR
Sbjct: 65  ASQYDPLGFIVPILIRFKLFLQTLWKKNLSWDQTISEEDETTW-KLLTNEWPKKLKDLPR 123

Query: 120 LIGNLIPGTQYELHGFSDASATSYSMVIYLKCITGNSVTSNLVFAKARIAPLSRPTLPRL 179
              N     Q + H F+DAS  +YS  +Y++          LVFAK+RIAP+   ++PRL
Sbjct: 124 FTTNC--SKQVQFHVFTDASTAAYSAALYIRTQEREVF---LVFAKSRIAPIKGMSIPRL 178

Query: 180 ELLGALIAYRGLKFVGESLKVKDIKYYLWIDSQIVIHWIL-GNKVLPTFINNRVKEIKNR 238
           ELL  LI  R ++FV +  +++D+   LW DSQ  +HW+   +++LPTFI NRV+EI  R
Sbjct: 179 ELLAILIGVRMVQFVLKQKELEDVITILWSDSQCALHWVHNSSRLLPTFIQNRVEEI--R 236

Query: 239 SFKLDVHYVPTDMNPADIACRGEKLSSLQNNETWWHGPKWLCQSEGHWPQWSFTDEISPQ 298
             K+   Y+P++ NPADIA +G   + L+  + WW GPKWL ++E  WPQW +      Q
Sbjct: 237 KAKIHFRYIPSEQNPADIATKGISPNKLKGYDLWWKGPKWLTENESKWPQWKYNYNEDYQ 296

Query: 299 TEVSMDNALSVPAVKQLSKPLA--RKPIPVDHEKFNSFNKLVNVTCYVLKFIRLCRRQKE 356
            E           V  +++P+   +    +D  +F+ +++L+  T +VLKFIRL      
Sbjct: 297 DE---------EIVAHITEPIIINKHFGILDASRFSKWSRLIRTTGWVLKFIRLTM---- 343

Query: 357 NKGNISIIEYEESKLSWIKFAQHQKFASTMQ--ELKQGHKDQLSQQLGLVLDE------- 407
            KG I           W+K A  +K   T Q  EL +    + +Q  G+  DE       
Sbjct: 344 -KGEI----------PWLKMATKEKNILTTQDYELSEIVLFKQAQSEGVTKDEIIKWNLF 392

Query: 408 --NDILRCKGRFVELKVDGKSCFPMLLPRGNHISKIIVNDIHTSGYHTGDKESKKLSNVA 465
             N++ R K R V  ++   +  P+ LPR N I+++ +   H   YH G   +  LSN+ 
Sbjct: 393 YDNELWRYKSRVVNSEMKESNLHPIYLPRHNTITELFIQQRHEQLYHAGIAHT--LSNLR 450

Query: 466 RGYYLDGNHLERRVLLG 482
              ++     E + +L 
Sbjct: 451 STIWIPKGRTEVKRILN 467

Source: Brugia malayi

Species: Brugia malayi

Genus: Brugia

Family: Onchocercidae

Order: Spirurida

Class: Chromadorea

Phylum: Nematoda

Superkingdom: Eukaryota

>gi|170588121|ref|XP_001898822.1| Pao retrotransposon peptidase family protein [Brugia malayi] gi|158593035|gb|EDP31630.1| Pao retrotransposon peptidase family protein [Brugia malayi]

 Score =  243 bits (619), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 158/497 (31%), Positives = 261/497 (52%), Gaps = 54/497 (10%)

Query: 3    NNQSEYFDQLP-EELKSCNKVQNVLGLTW--DTDIDTLSIKHGELQCSGKLTKRLLLSVY 59
            +N  E  ++LP ++    + ++ +LGL W    DI  +++K        KLTKR++L   
Sbjct: 956  SNDQEVNEKLPVQDRAEVSSIKKILGLNWYHKQDIIQVTLKPW---FGKKLTKRIILQFV 1012

Query: 60   GSIYDVLGLFTPVVLPLKILIQSVWQRNLSWDEELSTEDKITFMKLIEDIKLIHTVHIPR 119
             S YD LG   P+++  K+ +Q++W++NLSWD+ +S ED+ T+ KL+ +        +PR
Sbjct: 1013 ASQYDPLGFIVPILIRFKLFLQTLWKKNLSWDQTISEEDETTW-KLLTNEWPKKLKDLPR 1071

Query: 120  LIGNLIPGTQYELHGFSDASATSYSMVIYLKCITGNSVTSNLVFAKARIAPLSRPTLPRL 179
               N     Q + H F+DAS  +YS  +Y++          LVFAK+RIAP+   ++PRL
Sbjct: 1072 FTTNC--SKQVQFHVFTDASTAAYSAALYIRTQEREVF---LVFAKSRIAPIKGMSIPRL 1126

Query: 180  ELLGALIAYRGLKFVGESLKVKDIKYYLWIDSQIVIHWIL-GNKVLPTFINNRVKEIKNR 238
            ELL  LI  R ++FV +  +++D+   LW DSQ  +HW+   +++LPTFI NRV+EI  R
Sbjct: 1127 ELLAILIGVRMVQFVLKQKELEDVITILWSDSQCALHWVHNSSRLLPTFIQNRVEEI--R 1184

Query: 239  SFKLDVHYVPTDMNPADIACRGEKLSSLQNNETWWHGPKWLCQSEGHWPQWSFTDEISPQ 298
              K+   Y+P++ NPADIA +G   + L+  + WW GPKWL ++E  WPQW +      Q
Sbjct: 1185 KAKIHFRYIPSEQNPADIATKGISPNKLKGYDLWWKGPKWLTENESKWPQWKYNYNEDYQ 1244

Query: 299  TEVSMDNALSVPAVKQLSKPLA--RKPIPVDHEKFNSFNKLVNVTCYVLKFIRLCRRQKE 356
             E           V  +++P+   +    +D  +F+ +++L+  T +VLKFIRL  ++  
Sbjct: 1245 DE---------EIVAHITEPIIINKHFGILDASRFSKWSRLIRTTGWVLKFIRLTMKR-- 1293

Query: 357  NKGNISIIEYEESKLSWIKFAQHQKFASTMQ--ELKQGHKDQLSQQLGLVLDE------- 407
                         ++ W+K A  +K   T Q  EL +    + +Q  G+  DE       
Sbjct: 1294 -------------EIPWLKMATKEKNILTTQDYELSEIVLFKQAQSEGVTKDEIIKWNLF 1340

Query: 408  --NDILRCKGRFVELKVDGKSCFPMLLPRGNHISKIIVNDIHTSGYHTGDKESKKLSNVA 465
              N++ R K R V  ++   +  P+ LPR N I+++ +   H   YH G   +  LSN+ 
Sbjct: 1341 YDNELWRYKSRVVNSEMKESNLHPIYLPRHNTITELFIQQRHEQLYHAGIAHT--LSNLR 1398

Query: 466  RGYYLDGNHLERRVLLG 482
               ++     E + +L 
Sbjct: 1399 STIWIPKGRTEVKRILN 1415

Source: Brugia malayi

Species: Brugia malayi

Genus: Brugia

Family: Onchocercidae

Order: Spirurida

Class: Chromadorea

Phylum: Nematoda

Superkingdom: Eukaryota

>gi|170588613|ref|XP_001899068.1| Pao retrotransposon peptidase family protein [Brugia malayi] gi|158593281|gb|EDP31876.1| Pao retrotransposon peptidase family protein [Brugia malayi]

 Score =  242 bits (618), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 158/497 (31%), Positives = 261/497 (52%), Gaps = 54/497 (10%)

Query: 3    NNQSEYFDQLP-EELKSCNKVQNVLGLTW--DTDIDTLSIKHGELQCSGKLTKRLLLSVY 59
            +N  E  ++LP ++    + ++ +LGL W    DI  +++K        KLTKR++L   
Sbjct: 956  SNDQEVNEKLPVQDRAEVSSIKKILGLNWYHKQDIIQVTLKPW---FGKKLTKRIILQFV 1012

Query: 60   GSIYDVLGLFTPVVLPLKILIQSVWQRNLSWDEELSTEDKITFMKLIEDIKLIHTVHIPR 119
             S YD LG   P+++  K+ +Q++W++NLSWD+ +S ED+ T+ KL+ +        +PR
Sbjct: 1013 ASQYDPLGFIVPILIRFKLFLQTLWKKNLSWDQTISEEDETTW-KLLTNEWPKKLKDLPR 1071

Query: 120  LIGNLIPGTQYELHGFSDASATSYSMVIYLKCITGNSVTSNLVFAKARIAPLSRPTLPRL 179
               N     Q + H F+DAS  +YS  +Y++          LVFAK+RIAP+   ++PRL
Sbjct: 1072 FTTNC--SKQVQFHVFTDASTAAYSAALYIRTQEREVF---LVFAKSRIAPIKGMSIPRL 1126

Query: 180  ELLGALIAYRGLKFVGESLKVKDIKYYLWIDSQIVIHWIL-GNKVLPTFINNRVKEIKNR 238
            ELL  LI  R ++FV +  +++D+   LW DSQ  +HW+   +++LPTFI NRV+EI  R
Sbjct: 1127 ELLAILIGVRMVQFVLKQKELEDVITILWSDSQCALHWVHNSSRLLPTFIQNRVEEI--R 1184

Query: 239  SFKLDVHYVPTDMNPADIACRGEKLSSLQNNETWWHGPKWLCQSEGHWPQWSFTDEISPQ 298
              K+   Y+P++ NPADIA +G   + L+  + WW GPKWL ++E  WPQW +      Q
Sbjct: 1185 KAKIHFRYIPSEQNPADIATKGISPNKLKGYDLWWKGPKWLTENESKWPQWKYNYNEDYQ 1244

Query: 299  TEVSMDNALSVPAVKQLSKPLA--RKPIPVDHEKFNSFNKLVNVTCYVLKFIRLCRRQKE 356
             E           V  +++P+   +    +D  +F+ +++L+  T +VLKFIRL  ++  
Sbjct: 1245 DE---------EIVAHITEPIIINKHFGILDASRFSKWSRLIRTTGWVLKFIRLTMKR-- 1293

Query: 357  NKGNISIIEYEESKLSWIKFAQHQKFASTMQ--ELKQGHKDQLSQQLGLVLDE------- 407
                         ++ W+K A  +K   T Q  EL +    + +Q  G+  DE       
Sbjct: 1294 -------------EIPWLKMATKEKNILTTQDYELSEIVLFKQAQSEGVTKDEIIKWNLF 1340

Query: 408  --NDILRCKGRFVELKVDGKSCFPMLLPRGNHISKIIVNDIHTSGYHTGDKESKKLSNVA 465
              N++ R K R V  ++   +  P+ LPR N I+++ +   H   YH G   +  LSN+ 
Sbjct: 1341 YDNELWRYKSRVVNSEMKESNLHPIYLPRHNTITELFIQQRHEQLYHAGIAHT--LSNLR 1398

Query: 466  RGYYLDGNHLERRVLLG 482
               ++     E + +L 
Sbjct: 1399 STIWIPKGRTEVKRILN 1415

Source: Brugia malayi

Species: Brugia malayi

Genus: Brugia

Family: Onchocercidae

Order: Spirurida

Class: Chromadorea

Phylum: Nematoda

Superkingdom: Eukaryota

>gi|170586490|ref|XP_001898012.1| Pao retrotransposon peptidase family protein [Brugia malayi] gi|158594407|gb|EDP32991.1| Pao retrotransposon peptidase family protein [Brugia malayi]

 Score =  242 bits (617), Expect = 4e-61,   Method: Compositional matrix adjust.
 Identities = 158/497 (31%), Positives = 261/497 (52%), Gaps = 54/497 (10%)

Query: 3    NNQSEYFDQLP-EELKSCNKVQNVLGLTW--DTDIDTLSIKHGELQCSGKLTKRLLLSVY 59
            +N  E  ++LP ++    + ++ +LGL W    DI  +++K        KLTKR++L   
Sbjct: 981  SNDQEVNEKLPVQDRAEVSSIKKILGLNWYHKQDIIQVTLKPW---FGKKLTKRIILQFV 1037

Query: 60   GSIYDVLGLFTPVVLPLKILIQSVWQRNLSWDEELSTEDKITFMKLIEDIKLIHTVHIPR 119
             S YD LG   P+++  K+ +Q++W++NLSWD+ +S ED+ T+ KL+ +        +PR
Sbjct: 1038 ASQYDPLGFIVPILIRFKLFLQTLWKKNLSWDQTISEEDETTW-KLLTNEWPKKLKDLPR 1096

Query: 120  LIGNLIPGTQYELHGFSDASATSYSMVIYLKCITGNSVTSNLVFAKARIAPLSRPTLPRL 179
               N     Q + H F+DAS  +YS  +Y++          LVFAK+RIAP+   ++PRL
Sbjct: 1097 FTTNC--SKQVQFHVFTDASTAAYSAALYIRTQEREVF---LVFAKSRIAPIKGMSIPRL 1151

Query: 180  ELLGALIAYRGLKFVGESLKVKDIKYYLWIDSQIVIHWIL-GNKVLPTFINNRVKEIKNR 238
            ELL  LI  R ++FV +  +++D+   LW DSQ  +HW+   +++LPTFI NRV+EI  R
Sbjct: 1152 ELLAILIGVRMVQFVLKQKELEDVITILWSDSQCALHWVHNSSRLLPTFIQNRVEEI--R 1209

Query: 239  SFKLDVHYVPTDMNPADIACRGEKLSSLQNNETWWHGPKWLCQSEGHWPQWSFTDEISPQ 298
              K+   Y+P++ NPADIA +G   + L+  + WW GPKWL ++E  WPQW +      Q
Sbjct: 1210 KAKIHFRYIPSEQNPADIATKGISPNKLKGYDLWWKGPKWLTENESKWPQWKYNYNEDYQ 1269

Query: 299  TEVSMDNALSVPAVKQLSKPLA--RKPIPVDHEKFNSFNKLVNVTCYVLKFIRLCRRQKE 356
             E           V  +++P+   +    +D  +F+ +++L+  T +VLKFIRL  ++  
Sbjct: 1270 DE---------EIVAHITEPIIINKHFGILDASRFSKWSRLIRTTGWVLKFIRLTMKR-- 1318

Query: 357  NKGNISIIEYEESKLSWIKFAQHQKFASTMQ--ELKQGHKDQLSQQLGLVLDE------- 407
                         ++ W+K A  +K   T Q  EL +    + +Q  G+  DE       
Sbjct: 1319 -------------EIPWLKMATKEKNILTTQDYELSEIVLFKQAQSEGVTKDEIIKWNLF 1365

Query: 408  --NDILRCKGRFVELKVDGKSCFPMLLPRGNHISKIIVNDIHTSGYHTGDKESKKLSNVA 465
              N++ R K R V  ++   +  P+ LPR N I+++ +   H   YH G   +  LSN+ 
Sbjct: 1366 YDNELWRYKSRVVNSEMKESNLHPIYLPRHNTITELFIQQRHEQLYHAGIAHT--LSNLR 1423

Query: 466  RGYYLDGNHLERRVLLG 482
               ++     E + +L 
Sbjct: 1424 STIWIPKGRTEVKRILN 1440

Source: Brugia malayi

Species: Brugia malayi

Genus: Brugia

Family: Onchocercidae

Order: Spirurida

Class: Chromadorea

Phylum: Nematoda

Superkingdom: Eukaryota

>gi|170589333|ref|XP_001899428.1| Pao retrotransposon peptidase family protein [Brugia malayi] gi|158593641|gb|EDP32236.1| Pao retrotransposon peptidase family protein [Brugia malayi]

 Score =  242 bits (617), Expect = 4e-61,   Method: Compositional matrix adjust.
 Identities = 158/497 (31%), Positives = 261/497 (52%), Gaps = 54/497 (10%)

Query: 3    NNQSEYFDQLP-EELKSCNKVQNVLGLTW--DTDIDTLSIKHGELQCSGKLTKRLLLSVY 59
            +N  E  ++LP ++    + ++ +LGL W    DI  +++K        KLTKR++L   
Sbjct: 711  SNDQEVNEKLPVQDRAEXSSIKKILGLNWYHKQDIIQVTLKPW---FGKKLTKRIILQFV 767

Query: 60   GSIYDVLGLFTPVVLPLKILIQSVWQRNLSWDEELSTEDKITFMKLIEDIKLIHTVHIPR 119
             S YD LG   P+++  K+ +Q++W++NLSWD+ +S ED+ T+ KL+ +        +PR
Sbjct: 768  ASQYDPLGFIVPILIRFKLFLQTLWKKNLSWDQTISEEDETTW-KLLTNEWPKKLKDLPR 826

Query: 120  LIGNLIPGTQYELHGFSDASATSYSMVIYLKCITGNSVTSNLVFAKARIAPLSRPTLPRL 179
               N     Q + H F+DAS  +YS  +Y++          LVFAK+RIAP+   ++PRL
Sbjct: 827  FTTNC--SKQVQFHVFTDASTAAYSAALYIRTQEREVF---LVFAKSRIAPIKGMSIPRL 881

Query: 180  ELLGALIAYRGLKFVGESLKVKDIKYYLWIDSQIVIHWIL-GNKVLPTFINNRVKEIKNR 238
            ELL  LI  R ++FV +  +++D+   LW DSQ  +HW+   +++LPTFI NRV+EI  R
Sbjct: 882  ELLAILIGVRMVQFVLKQKELEDVITILWSDSQCALHWVHNSSRLLPTFIQNRVEEI--R 939

Query: 239  SFKLDVHYVPTDMNPADIACRGEKLSSLQNNETWWHGPKWLCQSEGHWPQWSFTDEISPQ 298
              K+   Y+P++ NPADIA +G   + L+  + WW GPKWL ++E  WPQW +      Q
Sbjct: 940  KAKIHFRYIPSEQNPADIATKGISPNKLKGYDLWWKGPKWLTENESKWPQWKYNYNEDYQ 999

Query: 299  TEVSMDNALSVPAVKQLSKPLA--RKPIPVDHEKFNSFNKLVNVTCYVLKFIRLCRRQKE 356
             E           V  +++P+   +    +D  +F+ +++L+  T +VLKFIRL  ++  
Sbjct: 1000 DE---------EIVAHITEPIIINKHFGILDASRFSKWSRLIRTTGWVLKFIRLTMKR-- 1048

Query: 357  NKGNISIIEYEESKLSWIKFAQHQKFASTMQ--ELKQGHKDQLSQQLGLVLDE------- 407
                         ++ W+K A  +K   T Q  EL +    + +Q  G+  DE       
Sbjct: 1049 -------------EIPWLKMATKEKNILTTQDYELSEIVLFKQAQSEGVTKDEIIKWNLF 1095

Query: 408  --NDILRCKGRFVELKVDGKSCFPMLLPRGNHISKIIVNDIHTSGYHTGDKESKKLSNVA 465
              N++ R K R V  ++   +  P+ LPR N I+++ +   H   YH G   +  LSN+ 
Sbjct: 1096 YDNELWRYKSRVVNSEMKESNLHPIYLPRHNTITELFIQQRHEQLYHAGIAHT--LSNLR 1153

Query: 466  RGYYLDGNHLERRVLLG 482
               ++     E + +L 
Sbjct: 1154 STIWIPKGRTEVKRILN 1170

Source: Brugia malayi

Species: Brugia malayi

Genus: Brugia

Family: Onchocercidae

Order: Spirurida

Class: Chromadorea

Phylum: Nematoda

Superkingdom: Eukaryota

>gi|339257282|ref|XP_003370011.1| Pao retrotransposon peptidase superfamily [Trichinella spiralis] gi|316965440|gb|EFV50150.1| Pao retrotransposon peptidase superfamily [Trichinella spiralis]

 Score =  235 bits (599), Expect = 4e-59,   Method: Compositional matrix adjust.
 Identities = 150/470 (31%), Positives = 243/470 (51%), Gaps = 21/470 (4%)

Query: 2    TNNQSEYFDQLPEELKSCNKVQNVLGLTWDTDIDTLSIK-HGELQCSGKLTKRLLLSVYG 60
            ++N     ++LP E    +K    LG++W+   D LS     E+    + TKR +LS   
Sbjct: 847  SSNIPTIMNELPSEKIEEHKQVTTLGMSWNCKNDELSYNISMEIDEKKEYTKREVLSTAS 906

Query: 61   SIYDVLGLFTPVVLPLKILIQSVWQRNLSWDEELSTEDKITFMKLIEDIKLIHTVHIPRL 120
             IYD LG  TP ++  K LIQ +WQR L W++ L  + K T+ + I + K I  V IPR 
Sbjct: 907  RIYDPLGYLTPFIIRAKTLIQELWQRGLHWEDPLPDDLKTTWTRWITEWKKIENVRIPRC 966

Query: 121  I-----GNLIPGTQYELHGFSDASATSYSMVIYLKC--ITGNSVTSNLVFAKARIAPLSR 173
            +      N+I   + ELHGFSDAS  +Y   +Y++   I G  V   L+ AK+++ PL  
Sbjct: 967  LIEIPMKNII---RLELHGFSDASEKAYGGAVYIRMIDIEGKGVIK-LIVAKSKVTPLKS 1022

Query: 174  PTLPRLELLGALIAYRGLKFVGESLKVKDIKYYLWIDSQIVIHWILG-NKVLPTFINNRV 232
             TLPRLEL+ AL+  + +  V + + +   +   W DSQI + WI    +    F+ NRV
Sbjct: 1023 VTLPRLELVAALVTAKLISHVKQVIDLNIDRVCCWSDSQITLCWIRNVARTWKPFVKNRV 1082

Query: 233  KEIKNRSFKLDVHYVPTDMNPADIACRGEKLSSLQNNETWWHGPKWLCQSEGHWPQWSFT 292
            + I       D  Y PT  NPAD+  RG  L  L++N  WW+GPKWL   E  WP+    
Sbjct: 1083 ESIHELVKPEDWRYCPTKDNPADVITRGTTLRKLKDNHLWWNGPKWL-DDESQWPKERLQ 1141

Query: 293  DEISPQTEVSMDNALSVPAVKQLSKPLARKPIPVDHEKFNSFNKLVNVTCYVLKFIRLCR 352
              ++ + +  ++     P V  L+  +   PI  + EKF +F K++ +T Y  +F+  C+
Sbjct: 1142 RTVTKEIQNIIEEERR-PTVIMLNVNVTIPPI-FEFEKFGNFEKMLRLTAYCNRFVSNCK 1199

Query: 353  RQKENKG--NISIIEYEESKLSWIKFAQHQKFASTMQELKQGH---KDQLSQQLGLVLDE 407
               E +    ++  E   ++  W+K  Q  +F   +Q L++G    K+   + L   LDE
Sbjct: 1200 TLPERRKLRELTSEEMITAEKYWLKIVQRNEFHDEIQILQKGRPLPKENRLKTLDPFLDE 1259

Query: 408  NDILRCKGRFVELKVDGKSCFPMLLPRGNHISKIIVNDIHTSGYHTGDKE 457
            + +LR  GR     +D +  +P++LP+ +H+  +I++  H++  H G+ +
Sbjct: 1260 DGLLRVGGRLRLSDLDYEMKYPIILPKKHHVVNLIIDRAHSNTLHAGNTQ 1309

Source: Trichinella spiralis

Species: Trichinella spiralis

Genus: Trichinella

Family: Trichinellidae

Order: Trichocephalida

Class: Enoplea

Phylum: Nematoda

Superkingdom: Eukaryota

>gi|339241105|ref|XP_003376478.1| zinc knuckle protein [Trichinella spiralis] gi|316974804|gb|EFV58277.1| zinc knuckle protein [Trichinella spiralis]

 Score =  230 bits (587), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 144/458 (31%), Positives = 236/458 (51%), Gaps = 22/458 (4%)

Query: 8    YFDQLP--EELKSCNKVQNVLGLTWDTDIDTLSIKHGELQCSGKLTKRLLLSVYGSIYDV 65
            Y   LP  ++ K   ++   LG+ WDT+ D LS +  E+    + TKR LLS+  +I+D 
Sbjct: 858  YDGALPFGKDPKPAGRLLKTLGVLWDTESDQLSFRQPEVDAEEQDTKRTLLSLAATIFDP 917

Query: 66   LGLFTPVVLPLKILIQSVWQRNLSWDEELSTEDKITFMKLIEDIKLIHTVHIPR--LIGN 123
            LG  TP  +  K+L+Q +WQ   SWD+ L    +  +     ++  +  V I R  +  +
Sbjct: 918  LGYLTPFTVRAKMLLQLLWQEGTSWDDPLPVPVEAVWRNWKGELADLSQVSIDRACIKCS 977

Query: 124  LIPGTQYELHGFSDASATSYSMVIYLKCITGNS-VTSNLVFAKARIAPLSRPTLPRLELL 182
            L+     +LHGF+DAS ++Y  V+YL+ + GN  V    + AK+R+AP+ + +LPRLEL+
Sbjct: 978  LMELVHMDLHGFADASGSAYGAVVYLRLVHGNGKVEVRFLAAKSRVAPIKKLSLPRLELM 1037

Query: 183  GALIAYRGLKFVGESLKVKDIKYYLWIDSQIVIHWILGN-KVLPTFINNRVKEIKNRSFK 241
             AL+  R + +V     +     + W DS + + WI  N +    F++NRV++I+  +  
Sbjct: 1038 AALLCARLVAYVKRKADLPIRSCFCWSDSSVALCWIRSNAQRWKPFVSNRVRDIQEITSP 1097

Query: 242  LDVHYVPTDMNPADIACRGEKLSSLQNNETWWHGPKWLCQSEGHWPQWSFTDEISPQTEV 301
                Y PT  NPAD+A RG  LS L     W  GP+WL   E  WP+   +   +P+  +
Sbjct: 1098 DSWRYCPTQDNPADLASRGCPLSKLAAGSLWHSGPRWLQLDESAWPKLKISHGRTPEN-M 1156

Query: 302  SMDNALSVPAVKQLSKPLARKPIPVDHEKFNSFNKLVNVTCYVLKFIRLCR-----RQKE 356
             ++N  +V  +    K   R  +  D  +++S+ KLV VT + L+FI   R     RQK 
Sbjct: 1157 ELENRKTVLVMTTSVKFDLRSVM--DVARYSSYGKLVRVTAWCLRFIFNARSPMELRQKA 1214

Query: 357  NKGNISIIEYEESKLSWIKFAQHQKFASTMQELKQGHKDQLSQQLGLVLDENDILRCKGR 416
                +++ E  E++ +WI+  Q   +          H+ +  QQ    LDE+ ILR  GR
Sbjct: 1215 R--GLTVPEMREAEKTWIRQVQVSAYGPG------SHRRKDLQQFNPYLDEDGILRVGGR 1266

Query: 417  FVELKVDGKSCFPMLLPRGNHISKIIVNDIHTSGYHTG 454
                ++  ++  PMLLP G+ + K+++  +H    H G
Sbjct: 1267 LAFSELPQETRNPMLLPHGDGVVKLLIQHVHEQQLHAG 1304

Source: Trichinella spiralis

Species: Trichinella spiralis

Genus: Trichinella

Family: Trichinellidae

Order: Trichocephalida

Class: Enoplea

Phylum: Nematoda

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

No hits with e-value below 0.001 by BLAST

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	493
pfam05380	159	pfam05380, Peptidase_A17, Pao retrotransposon pept	1e-37

>gnl|CDD|147520 pfam05380, Peptidase_A17, Pao retrotransposon peptidase

 Score =  135 bits (341), Expect = 1e-37
 Identities = 57/158 (36%), Positives = 85/158 (53%), Gaps = 1/158 (0%)

Query: 51  TKRLLLSVYGSIYDVLGLFTPVVLPLKILIQSVWQRNLSWDEELSTEDKITFMKLIEDIK 110
           TKR +LS   SI+D LGL  PV +  KI +Q +W++ L WDEE+  E    ++   + + 
Sbjct: 2   TKREVLSQVASIFDPLGLLAPVTVRAKIFLQEIWRQKLGWDEEIPEELSQRWLAFRKQLS 61

Query: 111 LIHTVHIPRLIGNLIPGTQYELHGFSDASATSYSMVIYLKCITGNSVTSNLVFAKARIAP 170
            +  + +PR +    P    +LHGF DAS  +Y+  +Y +   G  +  +LV AK R+AP
Sbjct: 62  TLQQIRVPRYV-PYSPARNIQLHGFCDASEKAYAAAVYWRVEEGEEIQVSLVAAKTRVAP 120

Query: 171 LSRPTLPRLELLGALIAYRGLKFVGESLKVKDIKYYLW 208
           L   ++PRLEL  AL+  R  + V     VK    Y W
Sbjct: 121 LKTVSIPRLELCAALLLTRLARAVKPEHDVKPTDTYCW 158

Corresponds to Merops family A17. These proteins are homologous to aspartic proteinases encoded by retroposons and retroviruses. Length = 159

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	493
PF05380	159	Peptidase_A17: Pao retrotransposon peptidase ; Int	100.0
PF09337	39	zf-H2C2: His(2)-Cys(2) zinc finger; InterPro: IPR0	98.71
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	98.32
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	98.27
.; GO: 0004523 ribonuclease H activity" target="_blank" href="http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PF00336">PF00336	245	DNA_pol_viral_C: DNA polymerase (viral) C-terminal	98.27
PRK13907	128	rnhA ribonuclease H; Provisional	97.89
PRK07708	219	hypothetical protein; Validated	97.84
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	97.67
PRK00203	150	rnhA ribonuclease H; Reviewed	97.51
PRK08719	147	ribonuclease H; Reviewed	97.43
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	97.31
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	97.15
PRK06548	161	ribonuclease H; Provisional	97.02
KOG3752|consensus	371		92.6

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

Probab=100.00  E-value=8e-47  Score=346.74  Aligned_cols=158  Identities=38%  Similarity=0.678  Sum_probs=148.3

Q ss_pred             ccHhHHHHhHhcccccCCCCcceeecchhhhhhhhhccCCCCccCChhHHHHHHHHHHHHhcccceeceeEEeccCCCCc
Q psy17737         50 LTKRLLLSVYGSIYDVLGLFTPVVLPLKILIQSVWQRNLSWDEELSTEDKITFMKLIEDIKLIHTVHIPRLIGNLIPGTQ  129 (493)
Q Consensus        50 ~TkR~ilS~ias~yDPLGl~~p~~l~~K~llq~l~~~~~~WD~~i~~e~~~~w~~~~~~l~~~~~~~iPR~~~~~~~~~~  129 (493)
                      +|||+++|.+|++|||||+++|+++++|+++|++|+.+++||++||+++.+.|.+|.+++..++++.|||++ .......
T Consensus         1 pTKR~ils~ia~~yDPlGl~~p~~i~~K~llq~lw~~~l~WD~~lp~el~~~w~~~~~~l~~~~~i~iPR~i-~~~~~~~   79 (159)
T PF05380_consen    1 PTKRQILSFIASIYDPLGLLAPIIIRAKLLLQKLWQSKLDWDDPLPDELRKEWKKWLKELESLSPIRIPRCI-PISDYRS   79 (159)
T ss_pred             CChHHHHHHHHHHcCcchhhHHHHHHHHHHHHhhhccccchhhhhhHHHHHHHHHHHHHHhhcccccCCccc-ccccccc
Confidence            599999999999999999999999999999999999999999999999999999999999998889999987 3222223


Q ss_pred             eeEEeecccccccceeeEEEEEeeCCCcee-eeeecccccCCCCCCccchhhhhHHHHHhhhhHHHhhhhcccceeEEEe
Q psy17737        130 YELHGFSDASATSYSMVIYLKCITGNSVTS-NLVFAKARIAPLSRPTLPRLELLGALIAYRGLKFVGESLKVKDIKYYLW  208 (493)
Q Consensus       130 ~~L~vF~DAS~~a~gav~y~r~~~~~g~~~-~ll~aksrv~P~k~~tIpRlEL~a~~~~~~l~~~~~~~l~~~~~~~~~~  208 (493)
                      .+||+|||||+.|||||+|+|. ..||... ++++||+||+|+|..|||||||+|+++|++++.++.+++++++.++++|
T Consensus        80 ~~L~~F~DAS~~aygavvYlr~-~~~~~~~~~ll~aKsrv~P~k~~tIPRlEL~a~~l~~~l~~~~~~~l~~~~~~~~~w  158 (159)
T PF05380_consen   80 VELHVFCDASESAYGAVVYLRS-YSDGSVQVRLLFAKSRVAPLKTVTIPRLELLAALLGVRLANTVKKELDIEISQVVFW  158 (159)
T ss_pred             eeeeEeecccccceeeEeEeee-ccCCceeeeeeeecccccCCCCCcHHHHHHHHHHHHHHHHHHHHHHcCCCcceeEEe
Confidence            8999999999999999999999 6777777 9999999999999899999999999999999999999999999999999


Q ss_pred             c
Q psy17737        209 I  209 (493)
Q Consensus       209 t  209 (493)
                      |
T Consensus       159 t  159 (159)
T PF05380_consen  159 T  159 (159)
T ss_pred             C
Confidence            7

>PF09337 zf-H2C2: His(2)-Cys(2) zinc finger; InterPro: IPR015416 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=98.71  E-value=6.9e-09  Score=71.80  Aligned_cols=38  Identities=18%  Similarity=0.229  Sum_probs=35.6

Q ss_pred             HHhCCCCChhhhhHHHHHHhhhc-cccchHHHHHhcCCcccc
Q psy17737        447 HTSGYHTGDKESKKLSNVARGYY-LDGNHLERRVLLGSRLLS  487 (493)
Q Consensus       447 H~~~~H~G~~~t~~l~~lr~~yW-~~~r~~vr~vi~~C~~C~  487 (493)
                      |+. +|.|.+.|  ++.|+++|| |+|+..|+++|+.|..||
T Consensus         1 H~~-~H~Gi~kT--~~~i~~~y~W~gm~~~V~~~ir~C~~Cq   39 (39)
T PF09337_consen    1 HNQ-GHPGINKT--TAKISQRYHWPGMKKDVRRVIRSCPQCQ   39 (39)
T ss_pred             CCc-cCCCHHHH--HHHHHHhheecCHHHHHHHHHhcCcccC
Confidence            454 59999999  999999999 999999999999999997

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents an H2C2-type zinc finger that binds to histone upstream activating sequence (UAS) elements found in histone gene promoters []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].

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

Probab=98.32  E-value=1.8e-06  Score=73.84  Aligned_cols=112  Identities=21%  Similarity=0.214  Sum_probs=75.7

Q ss_pred             eecccccc------cceeeEEEEEeeCCCceeeeeecccccCCCCCCccchhhhhHHHHHhhhhHHHhhhhcccceeEEE
Q psy17737        134 GFSDASAT------SYSMVIYLKCITGNSVTSNLVFAKARIAPLSRPTLPRLELLGALIAYRGLKFVGESLKVKDIKYYL  207 (493)
Q Consensus       134 vF~DAS~~------a~gav~y~r~~~~~g~~~~ll~aksrv~P~k~~tIpRlEL~a~~~~~~l~~~~~~~l~~~~~~~~~  207 (493)
                      +|+|||-.      |||++  ++.  .++..   ........  ...|.-..|+.|++.|++.+.      ......+.+
T Consensus         2 ~~~Dgs~~~~~~~~g~g~v--~~~--~~~~~---~~~~~~~~--~~~s~~~aEl~al~~al~~~~------~~~~~~i~i   66 (130)
T cd06222           2 IYTDGSCRGNPGPAGAGVV--LRD--PGGEV---LLSGGLLG--GNTTNNRAELLALIEALELAL------ELGGKKVNI   66 (130)
T ss_pred             EEecccCCCCCCceEEEEE--EEe--CCCeE---EEeccccC--CCCcHHHHHHHHHHHHHHHHH------hCCCceEEE
Confidence            79999987      55543  332  22221   21111111  577889999999999998876      346789999


Q ss_pred             ecchhhhHHHHhcCCc-cChhhhHHHHHHHHhc---cccceEEecC----CCC-CCcccccc
Q psy17737        208 WIDSQIVIHWILGNKV-LPTFINNRVKEIKNRS---FKLDVHYVPT----DMN-PADIACRG  260 (493)
Q Consensus       208 ~tDS~i~l~~l~~~~~-~~~fv~nRv~~I~~~~---~~~~~~hv~~----~~N-pAD~~SRg  260 (493)
                      +|||..++..+.+... ...-....+..|++..   ..+.+.|||+    ..| .||.++|.
T Consensus        67 ~~Ds~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~  128 (130)
T cd06222          67 YTDSQYVINALTGWYEGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKE  128 (130)
T ss_pred             EECHHHHHHHhhccccCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHh
Confidence            9999999999998722 2223344445555544   5688999999    666 69988764

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.

>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=98.27  E-value=9.4e-07  Score=77.78  Aligned_cols=100  Identities=21%  Similarity=0.251  Sum_probs=65.4

Q ss_pred             eEEeeccccc------ccceeeEEEEEeeCCCceeeeeecccccCCCCCCccchhhhhHHHHHhhhhHHHhhhhccccee
Q psy17737        131 ELHGFSDASA------TSYSMVIYLKCITGNSVTSNLVFAKARIAPLSRPTLPRLELLGALIAYRGLKFVGESLKVKDIK  204 (493)
Q Consensus       131 ~L~vF~DAS~------~a~gav~y~r~~~~~g~~~~ll~aksrv~P~k~~tIpRlEL~a~~~~~~l~~~~~~~l~~~~~~  204 (493)
                      .+.+|+|||-      .|+|+|++      +|. .  .     -.++...|..+.||.|+..|++.+..         ..
T Consensus         3 ~~~iytDgS~~~~~~~~~~g~v~~------~~~-~--~-----~~~~~~~s~~~aEl~Ai~~AL~~~~~---------~~   59 (132)
T PF00075_consen    3 AIIIYTDGSCRPNPGKGGAGYVVW------GGR-N--F-----SFRLGGQSNNRAELQAIIEALKALEH---------RK   59 (132)
T ss_dssp             SEEEEEEEEECTTTTEEEEEEEEE------TTE-E--E-----EEEEESECHHHHHHHHHHHHHHTHST---------SE
T ss_pred             cEEEEEeCCccCCCCceEEEEEEE------CCe-E--E-----EecccccchhhhheehHHHHHHHhhc---------cc
Confidence            5899999993      35554322      221 1  0     11122778999999999999994421         68


Q ss_pred             EEEecchhhhHHHHhc-----CC--c-cChhhhHHHHHHHHhccccceEEecCCCCC
Q psy17737        205 YYLWIDSQIVIHWILG-----NK--V-LPTFINNRVKEIKNRSFKLDVHYVPTDMNP  253 (493)
Q Consensus       205 ~~~~tDS~i~l~~l~~-----~~--~-~~~fv~nRv~~I~~~~~~~~~~hv~~~~Np  253 (493)
                      +.++|||+.++.+|..     ..  + ...-+.+++.+.......+.++||||..|-
T Consensus        60 v~I~tDS~~v~~~l~~~~~~~~~~~~~~~~~i~~~i~~~~~~~~~v~~~~V~~H~~~  116 (132)
T PF00075_consen   60 VTIYTDSQYVLNALNKWLHGNGWKKTSNGRPIKNEIWELLSRGIKVRFRWVPGHSGV  116 (132)
T ss_dssp             EEEEES-HHHHHHHHTHHHHTTSBSCTSSSBHTHHHHHHHHHSSEEEEEESSSSSSS
T ss_pred             ccccccHHHHHHHHHHhccccccccccccccchhheeeccccceEEeeeeccCcCCC
Confidence            8999999999998887     31  1 111234455555444456899999999765

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 ....

>PF00336 DNA_pol_viral_C: DNA polymerase (viral) C-terminal domain; InterPro: IPR001462 This domain is at the C terminus of hepatitis B-type viruses P proteins and represents a functional domain that controls the RNase H activities of the protein

Probab=98.27  E-value=1.6e-06  Score=80.26  Aligned_cols=102  Identities=25%  Similarity=0.223  Sum_probs=64.3

Q ss_pred             EEeecccccccceeeEEEEEeeCCCceeeeeecccccCCCCCCccchhhhhHHHHHhhhhHHHhhhhcccceeEEEecch
Q psy17737        132 LHGFSDASATSYSMVIYLKCITGNSVTSNLVFAKARIAPLSRPTLPRLELLGALIAYRGLKFVGESLKVKDIKYYLWIDS  211 (493)
Q Consensus       132 L~vF~DAS~~a~gav~y~r~~~~~g~~~~ll~aksrv~P~k~~tIpRlEL~a~~~~~~l~~~~~~~l~~~~~~~~~~tDS  211 (493)
                      =-||+||+..|||.++-      .|.. +.-+++       ..-|--.||+|+.+|--...           .-.+-|||
T Consensus        95 c~VfaDATpTgwgi~i~------~~~~-~~Tfs~-------~l~IhtaELlaaClAr~~~~-----------~r~l~tDn  149 (245)
T PF00336_consen   95 CQVFADATPTGWGISIT------GQRM-RGTFSK-------PLPIHTAELLAACLARLMSG-----------ARCLGTDN  149 (245)
T ss_pred             CceeccCCCCcceeeec------Ccee-eeeecc-------cccchHHHHHHHHHHHhccC-----------CcEEeecC
Confidence            35899999999997631      1211 222222       34566789999866543322           22377999


Q ss_pred             hhhHHHHhcCCccChhhhHHHHHHHHhccccceEEecCCCCCCccccccccc
Q psy17737        212 QIVIHWILGNKVLPTFINNRVKEIKNRSFKLDVHYVPTDMNPADIACRGEKL  263 (493)
Q Consensus       212 ~i~l~~l~~~~~~~~fv~nRv~~I~~~~~~~~~~hv~~~~NpAD~~SRg~~~  263 (493)
                      +.|++     +++..|-=+---.-..++...++.||||+.||||..|||..+
T Consensus       150 t~Vls-----rkyts~PW~lac~A~wiLrgts~~yVPS~~NPAD~PsR~~~~  196 (245)
T PF00336_consen  150 TVVLS-----RKYTSFPWLLACAANWILRGTSFYYVPSKYNPADDPSRGKLG  196 (245)
T ss_pred             cEEEe-----cccccCcHHHHHHHHHhhcCceEEEeccccCcCCCCCCCccc
Confidence            99986     344443111111112235678999999999999999999754

The domain is always associated with IPR000201 from INTERPRO and .; GO: 0004523 ribonuclease H activity

>PRK13907 rnhA ribonuclease H; Provisional

Probab=97.89  E-value=5.1e-05  Score=66.85  Aligned_cols=111  Identities=16%  Similarity=0.110  Sum_probs=73.1

Q ss_pred             EEeecccccc------cceeeEEEEEeeCCCceeeeeecccccCCCCCCccchhhhhHHHHHhhhhHHHhhhhcccceeE
Q psy17737        132 LHGFSDASAT------SYSMVIYLKCITGNSVTSNLVFAKARIAPLSRPTLPRLELLGALIAYRGLKFVGESLKVKDIKY  205 (493)
Q Consensus       132 L~vF~DAS~~------a~gav~y~r~~~~~g~~~~ll~aksrv~P~k~~tIpRlEL~a~~~~~~l~~~~~~~l~~~~~~~  205 (493)
                      +++|+|||-.      |||+|+  +  +.+|...  . +    .+....|=.+-|+.|++.|++++..+      .+..+
T Consensus         2 ~~iy~DGa~~~~~g~~G~G~vi--~--~~~~~~~--~-~----~~~~~~tn~~AE~~All~aL~~a~~~------g~~~v   64 (128)
T PRK13907          2 IEVYIDGASKGNPGPSGAGVFI--K--GVQPAVQ--L-S----LPLGTMSNHEAEYHALLAALKYCTEH------NYNIV   64 (128)
T ss_pred             EEEEEeeCCCCCCCccEEEEEE--E--ECCeeEE--E-E----ecccccCCcHHHHHHHHHHHHHHHhC------CCCEE
Confidence            5789998864      556554  3  2233221  1 1    12234577899999999999988743      34579


Q ss_pred             EEecchhhhHHHHhcC-CccChhhhHHHHHHHHh---ccccceEEecCCCCC-Ccccccc
Q psy17737        206 YLWIDSQIVIHWILGN-KVLPTFINNRVKEIKNR---SFKLDVHYVPTDMNP-ADIACRG  260 (493)
Q Consensus       206 ~~~tDS~i~l~~l~~~-~~~~~fv~nRv~~I~~~---~~~~~~~hv~~~~Np-AD~~SRg  260 (493)
                      .++|||+.++.++.+. ++- .-...-+.+++.+   ...+.+.|||...|- ||.+.|.
T Consensus        65 ~i~sDS~~vi~~~~~~~~~~-~~~~~l~~~~~~l~~~f~~~~~~~v~r~~N~~Ad~LA~~  123 (128)
T PRK13907         65 SFRTDSQLVERAVEKEYAKN-KMFAPLLEEALQYIKSFDLFFIKWIPSSQNKVADELARK  123 (128)
T ss_pred             EEEechHHHHHHHhHHHhcC-hhHHHHHHHHHHHHhcCCceEEEEcCchhchhHHHHHHH
Confidence            9999999999999986 211 1123334555444   345667999999995 9987664

>PRK07708 hypothetical protein; Validated

Probab=97.84  E-value=6.5e-05  Score=72.52  Aligned_cols=121  Identities=18%  Similarity=0.148  Sum_probs=76.2

Q ss_pred             eEEeeccccc------ccceeeEEEEEeeCCCceeeeeecccccCCCCCCccchhhhhHHHHHhhhhHHHhhhhccccee
Q psy17737        131 ELHGFSDASA------TSYSMVIYLKCITGNSVTSNLVFAKARIAPLSRPTLPRLELLGALIAYRGLKFVGESLKVKDIK  204 (493)
Q Consensus       131 ~L~vF~DAS~------~a~gav~y~r~~~~~g~~~~ll~aksrv~P~k~~tIpRlEL~a~~~~~~l~~~~~~~l~~~~~~  204 (493)
                      .+++|+|||-      .|+|+|++.    .+|.....+.....+.+  ..|=..-|+.|++.|++++..+    ++.-..
T Consensus        73 ~~~vY~DGs~~~n~g~aG~GvVI~~----~~g~~~~~~~~~~~l~~--~~TNN~AEy~Ali~aL~~A~e~----g~~~~~  142 (219)
T PRK07708         73 EILVYFDGGFDKETKLAGLGIVIYY----KQGNKRYRIRRNAYIEG--IYDNNEAEYAALYYAMQELEEL----GVKHEP  142 (219)
T ss_pred             cEEEEEeeccCCCCCCcEEEEEEEE----CCCCEEEEEEeeccccc--cccCcHHHHHHHHHHHHHHHHc----CCCcce
Confidence            5789999976      456666554    22322211211122332  3577888999999999988743    333345


Q ss_pred             EEEecchhhhHHHHhcC-CccChhhhHHHHHHHHhcc----ccceEEecCCCCC-Cccccccc
Q psy17737        205 YYLWIDSQIVIHWILGN-KVLPTFINNRVKEIKNRSF----KLDVHYVPTDMNP-ADIACRGE  261 (493)
Q Consensus       205 ~~~~tDS~i~l~~l~~~-~~~~~fv~nRv~~I~~~~~----~~~~~hv~~~~Np-AD~~SRg~  261 (493)
                      |.+++||+.++.|+.+. +....-...-+.+|++...    .+.+.|||-+.|- ||.+.+-.
T Consensus       143 V~I~~DSqlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~VpR~~N~~AD~LAk~A  205 (219)
T PRK07708        143 VTFRGDSQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPISRKQNKEADQLATQA  205 (219)
T ss_pred             EEEEeccHHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECCchhhhHHHHHHHHH
Confidence            89999999999999988 3322222223344443332    3667899999995 99776543

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

Probab=97.67  E-value=0.00027  Score=64.11  Aligned_cols=113  Identities=22%  Similarity=0.265  Sum_probs=74.7

Q ss_pred             eEEeeccccc------ccceeeEEEEEeeCCCceeeeeecccccCCCCCCccchhhhhHHHHHhhhhHHHhhhhccccee
Q psy17737        131 ELHGFSDASA------TSYSMVIYLKCITGNSVTSNLVFAKARIAPLSRPTLPRLELLGALIAYRGLKFVGESLKVKDIK  204 (493)
Q Consensus       131 ~L~vF~DAS~------~a~gav~y~r~~~~~g~~~~ll~aksrv~P~k~~tIpRlEL~a~~~~~~l~~~~~~~l~~~~~~  204 (493)
                      .+++|+|+|.      -|||+|++    +.++...       -..+...-|=.|+||.|++.|++.+..      .....
T Consensus         3 ~v~if~DGa~~gNpG~gG~g~vl~----~~~~~~~-------~s~~~~~tTNNraEl~A~i~AL~~l~~------~~~~~   65 (154)
T COG0328           3 KVEIFTDGACLGNPGPGGWGAVLR----YGDGEKE-------LSGGEGRTTNNRAELRALIEALEALKE------LGACE   65 (154)
T ss_pred             ceEEEecCccCCCCCCceEEEEEE----cCCceEE-------EeeeeecccChHHHHHHHHHHHHHHHh------cCCce
Confidence            5789999985      67888766    2233221       112223678899999999999998885      35678


Q ss_pred             EEEecchhhhHH----HHhcC--CccC----hhhhHH--HHHHHHhc---cccceEEecCCCC-C----Ccccccc
Q psy17737        205 YYLWIDSQIVIH----WILGN--KVLP----TFINNR--VKEIKNRS---FKLDVHYVPTDMN-P----ADIACRG  260 (493)
Q Consensus       205 ~~~~tDS~i~l~----~l~~~--~~~~----~fv~nR--v~~I~~~~---~~~~~~hv~~~~N-p----AD~~SRg  260 (493)
                      +.+||||+.+..    |+.+.  ..|+    ..|.|+  ..++.++.   ..+.|.+|+|..+ |    ||.+-|.
T Consensus        66 v~l~tDS~yv~~~i~~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~  141 (154)
T COG0328          66 VTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLARE  141 (154)
T ss_pred             EEEEecHHHHHHHHHHHHhhccccCccccccCccccHHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHH
Confidence            999999987764    44333  3444    345443  44454444   4579999997665 2    6665554

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=97.51  E-value=0.00052  Score=62.31  Aligned_cols=110  Identities=19%  Similarity=0.195  Sum_probs=67.5

Q ss_pred             eEEeeccccc------ccceeeEEEEEeeCCCceeeeeecccccCCCCCCccchhhhhHHHHHhhhhHHHhhhhccccee
Q psy17737        131 ELHGFSDASA------TSYSMVIYLKCITGNSVTSNLVFAKARIAPLSRPTLPRLELLGALIAYRGLKFVGESLKVKDIK  204 (493)
Q Consensus       131 ~L~vF~DAS~------~a~gav~y~r~~~~~g~~~~ll~aksrv~P~k~~tIpRlEL~a~~~~~~l~~~~~~~l~~~~~~  204 (493)
                      .+.+|+|+|.      .|||+|+..    .++.. . +. .    +....|-.|.||.|++.|++.+..        ...
T Consensus         3 ~v~iytDGs~~~n~~~~g~g~v~~~----~~~~~-~-~~-~----~~~~~TN~~aEL~Ai~~AL~~~~~--------~~~   63 (150)
T PRK00203          3 QVEIYTDGACLGNPGPGGWGAILRY----KGHEK-E-LS-G----GEALTTNNRMELMAAIEALEALKE--------PCE   63 (150)
T ss_pred             eEEEEEEecccCCCCceEEEEEEEE----CCeeE-E-Ee-c----CCCCCcHHHHHHHHHHHHHHHcCC--------CCe
Confidence            4789999997      456655432    22211 1 11 1    123678899999999999885531        256


Q ss_pred             EEEecchhhhHHHHhcC------Ccc----ChhhhHH--HHHHHHhcc--ccceEEecCCC----C-CCccccc
Q psy17737        205 YYLWIDSQIVIHWILGN------KVL----PTFINNR--VKEIKNRSF--KLDVHYVPTDM----N-PADIACR  259 (493)
Q Consensus       205 ~~~~tDS~i~l~~l~~~------~~~----~~fv~nR--v~~I~~~~~--~~~~~hv~~~~----N-pAD~~SR  259 (493)
                      +.++|||+.++.=|..-      +.|    ..-|+|+  +.+|.++..  .+.|.|||+-.    | -||.+.|
T Consensus        64 v~I~tDS~yvi~~i~~w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~~~~v~~~wV~~H~~~~~N~~AD~lA~  137 (150)
T PRK00203         64 VTLYTDSQYVRQGITEWIHGWKKNGWKTADKKPVKNVDLWQRLDAALKRHQIKWHWVKGHAGHPENERCDELAR  137 (150)
T ss_pred             EEEEECHHHHHHHHHHHHHHHHHcCCcccCCCccccHHHHHHHHHHhccCceEEEEecCCCCCHHHHHHHHHHH
Confidence            89999998877544421      122    2345554  456655543  58899999665    3 2775544

>PRK08719 ribonuclease H; Reviewed

Probab=97.43  E-value=0.00019  Score=65.00  Aligned_cols=108  Identities=17%  Similarity=0.160  Sum_probs=66.3

Q ss_pred             eeEEeecccccc---------cceeeEEEEEeeCCCcee-eeeecccccCCCC-CCccchhhhhHHHHHhhhhHHHhhhh
Q psy17737        130 YELHGFSDASAT---------SYSMVIYLKCITGNSVTS-NLVFAKARIAPLS-RPTLPRLELLGALIAYRGLKFVGESL  198 (493)
Q Consensus       130 ~~L~vF~DAS~~---------a~gav~y~r~~~~~g~~~-~ll~aksrv~P~k-~~tIpRlEL~a~~~~~~l~~~~~~~l  198 (493)
                      ..+.+|||+|..         |+|+++|.    ++|... ...      .|+. ..|-.|.||.|+..|++.+..     
T Consensus         3 ~~~~iYtDGs~~~n~~~~~~~G~G~vv~~----~~~~~~~~~~------~~~~~~~Tnn~aEl~A~~~aL~~~~~-----   67 (147)
T PRK08719          3 ASYSIYIDGAAPNNQHGCVRGGIGLVVYD----EAGEIVDEQS------ITVNRYTDNAELELLALIEALEYARD-----   67 (147)
T ss_pred             ceEEEEEecccCCCCCCCCCcEEEEEEEe----CCCCeeEEEE------ecCCCCccHHHHHHHHHHHHHHHcCC-----
Confidence            468999998882         67766553    234322 111      1222 469999999999999987652     


Q ss_pred             cccceeEEEecchhhhHHHH--------hcC-C-ccChhhhHH--HHHHHHhc--cccceEEecC----CCC-CCccc
Q psy17737        199 KVKDIKYYLWIDSQIVIHWI--------LGN-K-VLPTFINNR--VKEIKNRS--FKLDVHYVPT----DMN-PADIA  257 (493)
Q Consensus       199 ~~~~~~~~~~tDS~i~l~~l--------~~~-~-~~~~fv~nR--v~~I~~~~--~~~~~~hv~~----~~N-pAD~~  257 (493)
                           ...++|||+-++.=|        ++. + +-...|.|+  ..+|.++.  ..++|.|||+    ..| -||.+
T Consensus        68 -----~~~i~tDS~yvi~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~~~~i~~~~VkgH~g~~~Ne~aD~l  140 (147)
T PRK08719         68 -----GDVIYSDSDYCVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRARKYVEVEKVTAHSGIEGNEAADML  140 (147)
T ss_pred             -----CCEEEechHHHHHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhCCCcEEEEEecCCCCChhHHHHHHH
Confidence                 126999998887655        333 1 223445553  33444433  3588999999    344 26643

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

Probab=97.31  E-value=0.00016  Score=58.45  Aligned_cols=76  Identities=22%  Similarity=0.154  Sum_probs=55.6

Q ss_pred             hhhhHHHHHhhhhHHHhhhhcccceeEEEecchhhhHHHHhcCCccChhhhHHHHHHHHhcc---ccceEEecCCCCC-C
Q psy17737        179 LELLGALIAYRGLKFVGESLKVKDIKYYLWIDSQIVIHWILGNKVLPTFINNRVKEIKNRSF---KLDVHYVPTDMNP-A  254 (493)
Q Consensus       179 lEL~a~~~~~~l~~~~~~~l~~~~~~~~~~tDS~i~l~~l~~~~~~~~fv~nRv~~I~~~~~---~~~~~hv~~~~Np-A  254 (493)
                      .|+.|+..|++++..      ..+.++.+.|||..++..|++...........+.+|+.+..   .+.++|||-+.|- |
T Consensus         4 aE~~al~~al~~a~~------~g~~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~r~~N~~A   77 (87)
T PF13456_consen    4 AEALALLEALQLAWE------LGIRKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDRFWNVSVSHIPREQNKVA   77 (87)
T ss_dssp             HHHHHHHHHHHHHHC------CT-SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCCCSCEEEEE--GGGSHHH
T ss_pred             HHHHHHHHHHHHHHH------CCCCEEEEEecCccccccccccccccccccccchhhhhhhccccceEEEEEChHHhHHH
Confidence            589999999988873      35679999999999999999883332366677777777664   5889999999995 9


Q ss_pred             cccccc
Q psy17737        255 DIACRG  260 (493)
Q Consensus       255 D~~SRg  260 (493)
                      |.+.|-
T Consensus        78 ~~LA~~   83 (87)
T PF13456_consen   78 DALAKF   83 (87)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            877653

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=97.15  E-value=0.0012  Score=69.06  Aligned_cols=117  Identities=16%  Similarity=0.237  Sum_probs=75.3

Q ss_pred             eEEeecccccc------cceeeEEEEEeeCCCceeeeeecccccCCCCCCccchhhhhHHHHHhhhhHHHhhhhccccee
Q psy17737        131 ELHGFSDASAT------SYSMVIYLKCITGNSVTSNLVFAKARIAPLSRPTLPRLELLGALIAYRGLKFVGESLKVKDIK  204 (493)
Q Consensus       131 ~L~vF~DAS~~------a~gav~y~r~~~~~g~~~~ll~aksrv~P~k~~tIpRlEL~a~~~~~~l~~~~~~~l~~~~~~  204 (493)
                      .++||+|||..      |+|+++..    .+|..  .+...+  .++...|-...|+.|++.|++++..+      .+..
T Consensus         2 ~~~i~~DGa~~~n~g~aG~G~vi~~----~~~~~--~~~~~~--~~~~~~tnn~AE~~All~gL~~a~~~------g~~~   67 (372)
T PRK07238          2 KVVVEADGGSRGNPGPAGYGAVVWD----ADRGE--VLAERA--EAIGRATNNVAEYRGLIAGLEAAAEL------GATE   67 (372)
T ss_pred             eEEEEecCCCCCCCCceEEEEEEEe----CCCCc--EEEEee--cccCCCCchHHHHHHHHHHHHHHHhC------CCCe
Confidence            57899999876      44544332    23211  111111  12225677889999999999988754      3457


Q ss_pred             EEEecchhhhHHHHhcC-CccChhhh---HHHHHHHHhccccceEEecCCCCC-Cccccccc
Q psy17737        205 YYLWIDSQIVIHWILGN-KVLPTFIN---NRVKEIKNRSFKLDVHYVPTDMNP-ADIACRGE  261 (493)
Q Consensus       205 ~~~~tDS~i~l~~l~~~-~~~~~fv~---nRv~~I~~~~~~~~~~hv~~~~Np-AD~~SRg~  261 (493)
                      +.+++||..++.-+.+. +.-..=..   ..+.++.+.+..+.+.|||...|- ||.+.+..
T Consensus        68 v~i~~DS~lvi~~i~~~~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~r~~N~~AD~LA~~a  129 (372)
T PRK07238         68 VEVRMDSKLVVEQMSGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPRARNAHADRLANEA  129 (372)
T ss_pred             EEEEeCcHHHHHHhCCCCccCChHHHHHHHHHHHHHhcCCceEEEECCchhhhHHHHHHHHH
Confidence            99999999999998876 21111111   233444444567899999999995 99877754

>PRK06548 ribonuclease H; Provisional

Probab=97.02  E-value=0.0043  Score=57.02  Aligned_cols=110  Identities=20%  Similarity=0.178  Sum_probs=67.1

Q ss_pred             eeEEeecccccc------cceeeEEEEEeeCCCceeeeeecccccCCCCCCccchhhhhHHHHHhhhhHHHhhhhcccce
Q psy17737        130 YELHGFSDASAT------SYSMVIYLKCITGNSVTSNLVFAKARIAPLSRPTLPRLELLGALIAYRGLKFVGESLKVKDI  203 (493)
Q Consensus       130 ~~L~vF~DAS~~------a~gav~y~r~~~~~g~~~~ll~aksrv~P~k~~tIpRlEL~a~~~~~~l~~~~~~~l~~~~~  203 (493)
                      .++++|||||..      |||+  |+.   .++   .      ...+....|=.|.||.|+..|++...       ....
T Consensus         4 ~~~~IytDGa~~gnpg~~G~g~--~~~---~~~---~------~~g~~~~~TNnraEl~Aii~aL~~~~-------~~~~   62 (161)
T PRK06548          4 NEIIAATDGSSLANPGPSGWAW--YVD---ENT---W------DSGGWDIATNNIAELTAVRELLIATR-------HTDR   62 (161)
T ss_pred             CEEEEEEeeccCCCCCceEEEE--EEe---CCc---E------EccCCCCCCHHHHHHHHHHHHHHhhh-------cCCc
Confidence            368999998865      3444  332   111   1      11222356889999999988765322       1223


Q ss_pred             eEEEecchhhhHHHHhc--------C--CccChhhhHH--HHHHHHhc--cccceEEecCCC----CC-Ccccccc
Q psy17737        204 KYYLWIDSQIVIHWILG--------N--KVLPTFINNR--VKEIKNRS--FKLDVHYVPTDM----NP-ADIACRG  260 (493)
Q Consensus       204 ~~~~~tDS~i~l~~l~~--------~--~~~~~fv~nR--v~~I~~~~--~~~~~~hv~~~~----Np-AD~~SRg  260 (493)
                      .+.++|||+.++.-+..        .  ++-..-|.|+  +.+|.++.  ..++|.||+|-.    |- ||.+-|-
T Consensus        63 ~v~I~TDS~yvi~~i~~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~~~v~~~wVkgHsg~~gNe~aD~LA~~  138 (161)
T PRK06548         63 PILILSDSKYVINSLTKWVYSWKMRKWRKADGKPVLNQEIIQEIDSLMENRNIRMSWVNAHTGHPLNEAADSLARQ  138 (161)
T ss_pred             eEEEEeChHHHHHHHHHHHHHHHHCCCcccCCCccccHHHHHHHHHHHhcCceEEEEEecCCCCHHHHHHHHHHHH
Confidence            68999999999966663        2  2223557776  44554444  258899999855    32 6755443

>KOG3752|consensus

Probab=92.60  E-value=0.71  Score=47.51  Aligned_cols=113  Identities=22%  Similarity=0.228  Sum_probs=68.6

Q ss_pred             eEEeeccccccc-------ceeeEEEEEeeCCCceeeeeecccccCCCC--CCccchhhhhHHHHHhhhhHHHhhhhccc
Q psy17737        131 ELHGFSDASATS-------YSMVIYLKCITGNSVTSNLVFAKARIAPLS--RPTLPRLELLGALIAYRGLKFVGESLKVK  201 (493)
Q Consensus       131 ~L~vF~DAS~~a-------~gav~y~r~~~~~g~~~~ll~aksrv~P~k--~~tIpRlEL~a~~~~~~l~~~~~~~l~~~  201 (493)
                      .+.|+||+|-.+       -|.++|.-    +|..-.      .-.|+.  ..|-.|-||.|+..|++-+..      .+
T Consensus       212 ~~vvytDGS~~~ng~~~~~AGyGvywg----~~~e~N------~s~pv~~g~qtNnrAEl~Av~~ALkka~~------~~  275 (371)
T KOG3752|consen  212 IQVVYTDGSSSGNGRKSSRAGYGVYWG----PGHELN------VSGPLAGGRQTNNRAELIAAIEALKKARS------KN  275 (371)
T ss_pred             ceEEEecCccccCCCCCCcceeEEeeC----CCCccc------ccccCCCCcccccHHHHHHHHHHHHHHHh------cC
Confidence            378999998755       23335763    332111      123332  789999999999888776553      34


Q ss_pred             ceeEEEecchhhhHHHHhcC------Ccc---------Chhhh-----HHHHHHHHh--ccccceEEecCCCC-----CC
Q psy17737        202 DIKYYLWIDSQIVIHWILGN------KVL---------PTFIN-----NRVKEIKNR--SFKLDVHYVPTDMN-----PA  254 (493)
Q Consensus       202 ~~~~~~~tDS~i~l~~l~~~------~~~---------~~fv~-----nRv~~I~~~--~~~~~~~hv~~~~N-----pA  254 (493)
                      +.++++.|||.-++.||..-      +.|         ..+|.     +.+.+..+-  -..++|.||+|...     .|
T Consensus       276 ~~kv~I~TDS~~~i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~A  355 (371)
T KOG3752|consen  276 INKVVIRTDSEYFINSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEMA  355 (371)
T ss_pred             CCcEEEEechHHHHHHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHHH
Confidence            56999999999888777633      111         11222     222332222  24589999998743     25


Q ss_pred             ccccc
Q psy17737        255 DIACR  259 (493)
Q Consensus       255 D~~SR  259 (493)
                      |.+.|
T Consensus       356 d~lAR  360 (371)
T KOG3752|consen  356 DALAR  360 (371)
T ss_pred             HHHHh
Confidence            65555

---

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	493
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-08

>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 = 54.5 bits (130), Expect = 6e-08
 Identities = 82/587 (13%), Positives = 170/587 (28%), Gaps = 198/587 (33%)

Query: 1   MTNNQSEYFDQLPEELKS------CNKVQNVL-GLTWDTDID-TLSIKHGELQCSGKLTK 52
              +Q +Y D L     +      C  VQ++   +    +ID  +  K          T 
Sbjct: 11  TGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSG-----TL 65

Query: 53  RL---LLSVYGSIYDVLGLFTPVVLPLKILIQSVWQRNLSW-DEELSTEDKITFM----- 103
           RL   LLS    +              +  ++ V + N  +    + TE +   M     
Sbjct: 66  RLFWTLLSKQEEMV-------------QKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMY 112

Query: 104 -----KLIEDIKLIHTVHIPRL---------IGNLIPGTQYELHG--------FSDASAT 141
                +L  D ++    ++ RL         +  L P     + G         +     
Sbjct: 113 IEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCL 172

Query: 142 SYSM-------VIYL---KCITGNSVTSNLVFAKARIAP-----LSRPTLPRLEL----- 181
           SY +       + +L    C +  +V   L     +I P         +  +L +     
Sbjct: 173 SYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQA 232

Query: 182 -LGALIAYRGLKFVGESLKVKDIKYYLWIDSQIVIHWILGNKVLPT----FINNRVKEIK 236
            L  L+  +  +     L V      +  +++    + L  K+L T     + + +    
Sbjct: 233 ELRRLLKSKPYE---NCLLVLL---NVQ-NAKAWNAFNLSCKILLTTRFKQVTDFLSAAT 285

Query: 237 NRSFKLDVHYVP-------------TDMNPADI---ACRGEKLS------SLQNN-ETWW 273
                LD H +               D  P D+                 S+++   TW 
Sbjct: 286 TTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATW- 344

Query: 274 HGPKWLCQSEGHWPQWSFTDEISPQTEVSMDNALSVPAVKQLSKPLARKPIPVDHEKFNS 333
                      +W      D+++   E S++  L     +++   L+   +         
Sbjct: 345 ----------DNWKH-VNCDKLTTIIESSLNV-LEPAEYRKMFDRLS---V--------- 380

Query: 334 FNKLVNVTCYVL-----------------KFIRLC---RRQKENKGNISIIEYEESKLSW 373
           F    ++   +L                 K  +     ++ KE+   ISI          
Sbjct: 381 FPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKEST--ISI---------- 428

Query: 374 IKFAQHQKFASTMQELKQGHKDQLSQ-QLGLVLDENDILRCKGRFVELKVDGKSCFPMLL 432
              + + +    ++     H+  +    +    D +D        +   +D         
Sbjct: 429 --PSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDD-------LIPPYLDQYFY----- 474

Query: 433 PRGNHISKIIVNDIHTSGYHTGDKESKKLSNVARGYYLDGNHLERRV 479
              +HI           G+H  + E  +   + R  +LD   LE+++
Sbjct: 475 ---SHI-----------GHHLKNIEHPERMTLFRMVFLDFRFLEQKI 507

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	493
1rw3_A	455	POL polyprotein; RNA and DNA dependent DNA polymer	99.11
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	98.43
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	98.39
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	98.36
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	98.23
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	98.14
3oym_A	395	PFV integrase, P42IN; protein-DNA complex; HET: DN	98.03
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	97.82
2zd1_B	428	P51 RT; P51/P66, hetero dimer, NNRTI, nonnucleosid	97.82
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	97.71
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	97.65
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	97.61
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	97.61
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	97.6
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	97.53
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	97.48
3nnq_A	114	Integrase P46, N-terminal domain of moloney murine	97.4
4htu_A	134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	97.36
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	96.96
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	96.89

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

Probab=99.11  E-value=9.1e-12  Score=131.65  Aligned_cols=175  Identities=10%  Similarity=0.048  Sum_probs=120.6

Q ss_pred             CCCcceEeEEEecCCCeEEEecCC----ccCCCCccHhHHHHhHhcccccCCCCcceeecchhhhhhhhh-----ccCCC
Q psy17737         20 NKVQNVLGLTWDTDIDTLSIKHGE----LQCSGKLTKRLLLSVYGSIYDVLGLFTPVVLPLKILIQSVWQ-----RNLSW   90 (493)
Q Consensus        20 ~~~~k~LG~~W~~~~D~l~~~~~~----~~~~~~~TkR~ilS~ias~yDPLGl~~p~~l~~K~llq~l~~-----~~~~W   90 (493)
                      ....+.||+.++..  .+......    ..-+.+.|++++.|+++.    +|++..++-....+++-|++     ..+.|
T Consensus       244 ~~~~~fLG~~i~~~--gi~~~~~kv~~i~~~~~p~t~k~l~~flG~----~~y~r~fi~~~~~~~~pL~~llkk~~~~~W  317 (455)
T 1rw3_A          244 QKQVKYLGYLLKEG--QRWLTEARKETVMGQPTPKTPRQLREFLGT----AGFCRLWIPGFAEMAAPLYPLTKTGTLFNW  317 (455)
T ss_dssp             BSSCEETTEEESSS--EECCCTTCCCCCCCCCTTTHHHHHHHTTTT----TCCCSSCCCCCGGGCCTTCC--------CC
T ss_pred             ccceeEeeeeccCC--eeEEChhHhhhhccCCCCCCHHHhhhhccc----chHHHHHHhhhhhhcccHHHHhcCCCCcCc
Confidence            45679999999863  33332211    112456799999999864    45555555554444444433     25788


Q ss_pred             CccCChhHHHHHHHHHHHHhcccceeceeEEeccCCCCceeEEeecccccccceeeEEEEEeeCCCcee-eeeecccccC
Q psy17737         91 DEELSTEDKITFMKLIEDIKLIHTVHIPRLIGNLIPGTQYELHGFSDASATSYSMVIYLKCITGNSVTS-NLVFAKARIA  169 (493)
Q Consensus        91 D~~i~~e~~~~w~~~~~~l~~~~~~~iPR~~~~~~~~~~~~L~vF~DAS~~a~gav~y~r~~~~~g~~~-~ll~aksrv~  169 (493)
                      ++.    ..+.|+++.+.+.+.+.+..|+.-        .++++|||||..|+|||++..   .+|... ....||+...
T Consensus       318 ~~~----~~~af~~lK~~l~~~pvL~~p~~~--------~~~~l~~DAS~~~~gavL~q~---~~~~~~~i~y~Sk~l~~  382 (455)
T 1rw3_A          318 GPD----QQKAYQEIKQALLTAPALGLPDLT--------KPFELFVDEKQGYAKGVLTQK---LGPWRRPVAYLSKKLDP  382 (455)
T ss_dssp             CCC----CSSSCCHHHHHTCSSCCSCCSSSC--------CTTSCEEEEEECSSSBEECCB---CTTTTCCCCCCCBCSCS
T ss_pred             hHH----HHHHHHHHHHHhhcCcccccCCCC--------CcEEEEEeccCCcceeEEEEe---cCCcEEEEEEEcccCCc
Confidence            874    566788899999887555555532        578999999999999988764   244444 4455666445


Q ss_pred             CCCCCccchhhhhHHHHHhhhhHHHhhhhcccceeEEEecchhhhHHHHhcC
Q psy17737        170 PLSRPTLPRLELLGALIAYRGLKFVGESLKVKDIKYYLWIDSQIVIHWILGN  221 (493)
Q Consensus       170 P~k~~tIpRlEL~a~~~~~~l~~~~~~~l~~~~~~~~~~tDS~i~l~~l~~~  221 (493)
                      +.++++++.+||+|++.|++.+......     ..++++||+. +++|+.+.
T Consensus       383 ~e~~ys~~ekEllAi~~a~~~~~~yl~g-----~~~~v~tDh~-~~~~l~~~  428 (455)
T 1rw3_A          383 VAAGWPPCLRMVAAIAVLTKDAGKLTMG-----QPLVIKAPHA-VEALVKQP  428 (455)
T ss_dssp             SCSSSCCSSHHHHHHHHHHHHHHGGGCS-----SCEEEECSSC-TTTTSSST
T ss_pred             cccccchHHHHHHHHHHHHHHHHHHcCC-----CcEEEEecCh-HHHHhCCC
Confidence            5569999999999999999988754333     4789999998 88888876

>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=98.43  E-value=2.3e-07  Score=81.48  Aligned_cols=114  Identities=17%  Similarity=0.199  Sum_probs=77.2

Q ss_pred             eEEeecccccc------cceeeEEEEEeeCC-CceeeeeecccccCCCCCCccchhhhhHHHHHhhhhHHHhhhhcccce
Q psy17737        131 ELHGFSDASAT------SYSMVIYLKCITGN-SVTSNLVFAKARIAPLSRPTLPRLELLGALIAYRGLKFVGESLKVKDI  203 (493)
Q Consensus       131 ~L~vF~DAS~~------a~gav~y~r~~~~~-g~~~~ll~aksrv~P~k~~tIpRlEL~a~~~~~~l~~~~~~~l~~~~~  203 (493)
                      .+.+|+|||-.      |||++++.    .+ |....-+ +.    +....|-.+.||.|++.|++++..+      .+.
T Consensus         3 ~~~iy~DGs~~~~~g~~g~G~v~~~----~~~~~~~~~~-~~----~~~~~tn~~aEl~A~~~aL~~a~~~------~~~   67 (141)
T 3hst_B            3 KVVIEADGGSRGNPGPAGYGAVVWT----ADHSTVLAES-KQ----AIGRATNNVAEYRGLIAGLDDAVKL------GAT   67 (141)
T ss_dssp             EEEEEEEEEESSSSEEEEEEEEEEE----TTSCSEEEEE-EE----EEEEECHHHHHHHHHHHHHHHHHHH------TCS
T ss_pred             EEEEEEecCCCCCCCCcEEEEEEEe----CCCCcEEEee-ec----cCCCCchHHHHHHHHHHHHHHHHHC------CCc
Confidence            68899999965      66665442    22 3221111 11    1125688999999999999988642      347


Q ss_pred             eEEEecchhhhHHHHhcC-CccChhhhHHHHHHHHhc---cccceEEecCCCCC-Cccccc
Q psy17737        204 KYYLWIDSQIVIHWILGN-KVLPTFINNRVKEIKNRS---FKLDVHYVPTDMNP-ADIACR  259 (493)
Q Consensus       204 ~~~~~tDS~i~l~~l~~~-~~~~~fv~nRv~~I~~~~---~~~~~~hv~~~~Np-AD~~SR  259 (493)
                      ++.++|||+.++.++.+. +.-..-....+.+|+++.   ..+.|.|||...|- ||.+.+
T Consensus        68 ~v~i~tDS~~vv~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~v~~~~V~~~~N~~AD~LA~  128 (141)
T 3hst_B           68 EAAVLMDSKLVVEQMSGRWKVKHPDLLKLYVQAQALASQFRRINYEWVPRARNTYADRLAN  128 (141)
T ss_dssp             EEEEEESCHHHHHHHTTSSCCCSHHHHHHHHHHHHHHTTSSEEEEEECCGGGCHHHHHHHH
T ss_pred             eEEEEeChHHHHHHHhCCcccCCHHHHHHHHHHHHHHhcCCeEEEEEcCCcccHHHHHHHH
Confidence            899999999999999975 222222334445555544   46899999999994 997765

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

Probab=98.39  E-value=4.2e-07  Score=80.93  Aligned_cols=117  Identities=21%  Similarity=0.209  Sum_probs=77.1

Q ss_pred             EEeecccccc-------c-ceeeEEEEEeeCCCceeeeeecccccCCC-CCCccchhhhhHHHHHhhhhHHHhhhhcccc
Q psy17737        132 LHGFSDASAT-------S-YSMVIYLKCITGNSVTSNLVFAKARIAPL-SRPTLPRLELLGALIAYRGLKFVGESLKVKD  202 (493)
Q Consensus       132 L~vF~DAS~~-------a-~gav~y~r~~~~~g~~~~ll~aksrv~P~-k~~tIpRlEL~a~~~~~~l~~~~~~~l~~~~  202 (493)
                      +.+|+|||-.       | ||++++.     +|.... -+++ .+.|. ...|-.+.||.|++.|++++..+      .+
T Consensus         2 ~~iy~DGs~~~~n~g~~G~~G~vi~~-----~g~~~~-~~~~-~~~~~~~~~tnn~aEl~A~~~aL~~a~~~------g~   68 (149)
T 2ehg_A            2 IIGYFDGLCEPKNPGGIATFGFVIYL-----DNRKIE-GYGL-AEKPFSINSTNNVAEYSGLICLMETMLRL------GI   68 (149)
T ss_dssp             CEEEEEEEEESSSSSSEEEEEEEEEC-----SSCEEE-EEEE-CSCTTCTTCCHHHHHHHHHHHHHHHHHHH------TC
T ss_pred             EEEEEeeccCCCCCChheEEEEEEEE-----CCEEEE-Eecc-ccCCCCCCccHHHHHHHHHHHHHHHHHHc------CC
Confidence            4689999876       3 5766542     343211 1111 13343 26789999999999999988643      34


Q ss_pred             eeEEEecchhhhHHHHhcC-CccChhhhHHHHHHHHhcc--ccceEEecCCCC-CCccccccc
Q psy17737        203 IKYYLWIDSQIVIHWILGN-KVLPTFINNRVKEIKNRSF--KLDVHYVPTDMN-PADIACRGE  261 (493)
Q Consensus       203 ~~~~~~tDS~i~l~~l~~~-~~~~~fv~nRv~~I~~~~~--~~~~~hv~~~~N-pAD~~SRg~  261 (493)
                      .++.++|||+.++.++.+. +.-..-...-+.+|+++..  .+.|.|||+..| .||.+.|-.
T Consensus        69 ~~v~i~tDS~~vi~~i~~~w~~~~~~~~~l~~~i~~l~~~~~v~~~~V~~~~N~~AD~LA~~a  131 (149)
T 2ehg_A           69 SSPIIKGDSQLVIKQMNGEYKVKAKRIIPLYEKAIELKKKLNATLIWVPREENKEADRLSRVA  131 (149)
T ss_dssp             CSCEEEESCHHHHHHHTTSSCCCCTTHHHHHHHHHHHHHHHTCEEEECCGGGCHHHHHHHHHH
T ss_pred             CEEEEEeChHHHHHHHhCccccCCHHHHHHHHHHHHHHhcCCEEEEEcCCcccHHHHHHHHHH
Confidence            6899999999999999986 2111112233344443322  589999999999 499887643

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

Probab=98.36  E-value=4.8e-07  Score=79.04  Aligned_cols=118  Identities=21%  Similarity=0.257  Sum_probs=74.8

Q ss_pred             eEEeecccccc------cceeeEEEEEeeCCCceeeeeecccccCCCCCCccchhhhhHHHHHhhhhHHHhhhhccccee
Q psy17737        131 ELHGFSDASAT------SYSMVIYLKCITGNSVTSNLVFAKARIAPLSRPTLPRLELLGALIAYRGLKFVGESLKVKDIK  204 (493)
Q Consensus       131 ~L~vF~DAS~~------a~gav~y~r~~~~~g~~~~ll~aksrv~P~k~~tIpRlEL~a~~~~~~l~~~~~~~l~~~~~~  204 (493)
                      .+.+|+|||-.      |||++++    +.+|....-+ +. .+   ...|..+.||.|++.|++++...-  .......
T Consensus         3 ~~~iy~DGs~~~n~g~~G~G~v~~----~~~g~~~~~~-~~-~~---~~~tn~~aEl~A~~~aL~~a~~~~--~~~~~~~   71 (140)
T 3u3g_D            3 KIIIYTDGGARGNPGPAGIGVVIT----DEKGNTLHES-SA-YI---GETTNNVAEYEALIRALEDLQMFG--DKLVDME   71 (140)
T ss_dssp             EEEEEEEEEESSTTEEEEEEEEEE----CTTSCEEEEE-EE-EE---EEECHHHHHHHHHHHHHHHHGGGG--GGGTTCE
T ss_pred             eEEEEEecCCCCCCCCcEEEEEEE----eCCCCEEEEE-Ee-eC---CCCchHHHHHHHHHHHHHHHHHcC--CCCCCce
Confidence            58899999973      5665443    2345332111 11 11   135889999999999999876431  0001238


Q ss_pred             EEEecchhhhHHHHhcC-CccChhhh---HHHHHH-HHhccccceEEecCCCCC-Cccccc
Q psy17737        205 YYLWIDSQIVIHWILGN-KVLPTFIN---NRVKEI-KNRSFKLDVHYVPTDMNP-ADIACR  259 (493)
Q Consensus       205 ~~~~tDS~i~l~~l~~~-~~~~~fv~---nRv~~I-~~~~~~~~~~hv~~~~Np-AD~~SR  259 (493)
                      +.++|||+.++.++.+. +.-..-..   .++.++ .+....+.|.|||...|- ||.+.+
T Consensus        72 v~i~tDS~~vi~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~~v~~~~V~~~~N~~AD~LA~  132 (140)
T 3u3g_D           72 VEVRMDSELIVRQMQGVYKVKEPTLKEKFAKIAHIKMERVPNLVFVHIPREKNARADELVN  132 (140)
T ss_dssp             EEEEESCHHHHHHHTTSSCCCCGGGHHHHHHHHHHHHHHCTTCEEEECCGGGGHHHHHHHH
T ss_pred             EEEEeChHHHHHHhCCCcccCCHHHHHHHHHHHHHhhcCCCcEEEEEcCchhhHHHHHHHH
Confidence            99999999999999986 21111122   333333 344457999999999994 887654

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

Probab=98.23  E-value=7.7e-06  Score=88.34  Aligned_cols=112  Identities=12%  Similarity=0.070  Sum_probs=69.2

Q ss_pred             CCCcceEeEEEecCCCeEEEecCCccCCCCccHhHHHHhHhc--ccccCCCCcceeecchhhhhhhhh-----ccCCCCc
Q psy17737         20 NKVQNVLGLTWDTDIDTLSIKHGELQCSGKLTKRLLLSVYGS--IYDVLGLFTPVVLPLKILIQSVWQ-----RNLSWDE   92 (493)
Q Consensus        20 ~~~~k~LG~~W~~~~D~l~~~~~~~~~~~~~TkR~ilS~ias--~yDPLGl~~p~~l~~K~llq~l~~-----~~~~WD~   92 (493)
                      ....+.||+....  +.+.+....++....+|++++-++++.  +|-.  ++..+.  ++-|.+.|-.     ..+.|++
T Consensus       226 ~~~~~fLG~~i~~--~gi~~~~~k~~~~~~~t~k~lr~flG~~~~yrr--fi~~~~--~~pl~~ll~~~~~~~~~~~Wt~  299 (557)
T 2zd1_A          226 EPPFLWMGYELHP--DKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQ--IYPGIK--VRQLSKLLRGTKALTEVIPLTE  299 (557)
T ss_dssp             CSSEEETTEEECS--SCEEESCCCCCCCSCEEHHHHHHHHHHHHHHTT--TSTTCC--CHHHHGGGTTCCCTTCEECCCH
T ss_pred             CCceEEeeEEEcc--CcEEEcceecccccCCCHHHHHHHhhHHHhhhh--hccchh--HHHHHHHhcccCCCCCceecCH
Confidence            4456789999765  555554434455566799999998762  1111  111111  1222222222     2477877


Q ss_pred             cCChhHHHHHHHHHHHHhcccceeceeEEeccCCCCceeEEeeccccccc-ceeeEEE
Q psy17737         93 ELSTEDKITFMKLIEDIKLIHTVHIPRLIGNLIPGTQYELHGFSDASATS-YSMVIYL  149 (493)
Q Consensus        93 ~i~~e~~~~w~~~~~~l~~~~~~~iPR~~~~~~~~~~~~L~vF~DAS~~a-~gav~y~  149 (493)
                          +..+.++++++.|.+.+.+..|..        +..+.++||||..| +|+|++.
T Consensus       300 ----~~~~af~~lK~~L~~~p~L~~pd~--------~~~~~l~~das~~g~~g~vl~q  345 (557)
T 2zd1_A          300 ----EAELELAENREILKEPVHGVYYDP--------SKDLIAEIQKQGQGQWTYQIYQ  345 (557)
T ss_dssp             ----HHHHHHHHHHHHTSSCCCBCCCCT--------TSCCEEEEEEEETTEEEEEEEE
T ss_pred             ----HHHHHHHHHHHHHhCccceeecCC--------CCCEEEEEecCCCCcEEEEEec
Confidence                889999999999987644433332        25789999999975 5887655

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

Probab=98.14  E-value=7.1e-06  Score=88.60  Aligned_cols=113  Identities=12%  Similarity=0.078  Sum_probs=69.8

Q ss_pred             CCCCcceEeEEEecCCCeEEEecCCccCCCCccHhHHHHhHhcc--cccCCCCcceeecchhhhhhhhh-----ccCCCC
Q psy17737         19 CNKVQNVLGLTWDTDIDTLSIKHGELQCSGKLTKRLLLSVYGSI--YDVLGLFTPVVLPLKILIQSVWQ-----RNLSWD   91 (493)
Q Consensus        19 ~~~~~k~LG~~W~~~~D~l~~~~~~~~~~~~~TkR~ilS~ias~--yDPLGl~~p~~l~~K~llq~l~~-----~~~~WD   91 (493)
                      .....+.||+....  +.+.+....++...+.|++++-++++.+  |-.  ++..+.  ++-|...+-.     ..+.|+
T Consensus       223 ~~~~~~fLG~~i~~--~gi~~~~~ki~~i~~~t~k~lr~flG~~~~~rr--fi~~~~--~~pL~~llk~~~~~~~~~~wt  296 (555)
T 1mu2_A          223 KDPPYHWMGYELWP--TKWKLQKIQLPQKEIWTVNDIQKLVGVLNWAAQ--LYPGIK--TKHLCRLISGKMTLTEEVQWT  296 (555)
T ss_dssp             CSSSEEETTEEECS--SEEEECCCCCCCCSSCBHHHHHHHHHHHHHHHH--HSTTCC--CHHHHTTSCSSSCTTCBCCCC
T ss_pred             cCCceeEEeEEEeC--CceeccccccCcCCCCCHHHHHhHhhhhhhhhh--ccCccc--hHHHHHHhccCCCCCCcccCC
Confidence            34567899998765  6666554344444677999988887531  110  011111  2222211111     357787


Q ss_pred             ccCChhHHHHHHHHHHHHhcccceeceeEEeccCCCCceeEEeeccccccc-ceeeEEE
Q psy17737         92 EELSTEDKITFMKLIEDIKLIHTVHIPRLIGNLIPGTQYELHGFSDASATS-YSMVIYL  149 (493)
Q Consensus        92 ~~i~~e~~~~w~~~~~~l~~~~~~~iPR~~~~~~~~~~~~L~vF~DAS~~a-~gav~y~  149 (493)
                      +    +..+.++++++.|.+.+.+..|..        +..+.++||||..| +|||++.
T Consensus       297 ~----~~~~af~~lK~~L~~~p~L~~p~~--------~~~~~l~~das~~ga~g~vl~Q  343 (555)
T 1mu2_A          297 E----LAEAELEENRIILSQEQEGHYYQE--------EKELEATVQKDQDNQWTYKIHQ  343 (555)
T ss_dssp             H----HHHHHHHHHHHHHSCCEEEECBCT--------TSCCEEEEEECSSSCEEEEEEE
T ss_pred             H----HHHHHHHHHHHHHhhCccccccCC--------CCCEEEEEecCCCCcEEEEEee
Confidence            6    889999999999987633333332        25899999999995 9988654

>3oym_A PFV integrase, P42IN; protein-DNA complex; HET: DNA; 2.02A {Human spumaretrovirus} PDB: 3oyn_A* 3s3o_A* 4be2_A* 3l2q_A 3l2s_A 3l2r_A* 3l2u_A* 3l2v_A* 3l2w_A* 3l2t_A* 3os1_A* 3os2_A* 3os0_A* 3oya_A* 3oy9_A* 3oyc_A* 3oyd_A* 3oye_A* 3oyb_A* 3oyg_A* ...

Probab=98.03  E-value=3.7e-06  Score=86.30  Aligned_cols=76  Identities=16%  Similarity=0.028  Sum_probs=61.6

Q ss_pred             ceeeccCCcEEeccccccccCCCCCCCceEecCCCcchhHHHHHHHHhCCCCChhhhhHHHHHHhhhc-cccchHHHHHh
Q psy17737        402 GLVLDENDILRCKGRFVELKVDGKSCFPMLLPRGNHISKIIVNDIHTSGYHTGDKESKKLSNVARGYY-LDGNHLERRVL  480 (493)
Q Consensus       402 ~pflD~~GllRv~gRl~~s~l~~~~k~Pillp~~~~lt~Lii~~~H~~~~H~G~~~t~~l~~lr~~yW-~~~r~~vr~vi  480 (493)
                      ..|..+||+|++.+.          ++..++|++ .+...|+..+|+ .+|.|...|  ...|++.|| +++++.+++++
T Consensus        31 ~~y~~~~g~ly~~~~----------~g~~~~~~~-~~~~~il~~~H~-~gH~g~~~~--~~~l~~~~~~~~~~~~v~~~~   96 (395)
T 3oym_A           31 YTYFLEDGKVKVSRP----------EGVKIIPPQ-SDRQKIVLQAHN-LAHTGREAT--LLKIANLYWWPNMRKDVVKQL   96 (395)
T ss_dssp             SCEEEETTEEEEEET----------TEEEECCCH-HHHHHHHHHHHH-TTTCCHHHH--HHHHHTTBCCTTHHHHHHHHH
T ss_pred             CcEEEECCEEEEEcC----------CCcEEECCH-HHHHHHHHHHHh-cCCCCHHHH--HHHHhCCeECCCHHHHHHHhC
Confidence            346666898887541          122445543 468889999999 899999999  999999999 99999999999


Q ss_pred             cCCcccccccc
Q psy17737        481 LGSRLLSGWVR  491 (493)
Q Consensus       481 ~~C~~C~r~~~  491 (493)
                      +.|..||+.|.
T Consensus        97 ~~C~~C~~~k~  107 (395)
T 3oym_A           97 GRCQQCLITNA  107 (395)
T ss_dssp             TTCHHHHHHSC
T ss_pred             ccChhhcccCC
Confidence            99999998764

>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=97.82  E-value=1.4e-05  Score=71.02  Aligned_cols=116  Identities=15%  Similarity=0.085  Sum_probs=72.8

Q ss_pred             eeEEeeccccc----ccceeeEEEEEeeCCCceeeeeecc-cccCCC-CCCccchhhhhHHHHHhhhhHHHhhhhcccce
Q psy17737        130 YELHGFSDASA----TSYSMVIYLKCITGNSVTSNLVFAK-ARIAPL-SRPTLPRLELLGALIAYRGLKFVGESLKVKDI  203 (493)
Q Consensus       130 ~~L~vF~DAS~----~a~gav~y~r~~~~~g~~~~ll~ak-srv~P~-k~~tIpRlEL~a~~~~~~l~~~~~~~l~~~~~  203 (493)
                      ..+.+|+|+|-    .|||++++.     +|.... + +. ....|. ...|-.|.||.|+..|++++...      .. 
T Consensus         5 ~~i~iytDGs~~~g~~G~G~vi~~-----~g~~~~-~-~~~~~~~~~~~~~tNn~aEl~A~~~AL~~a~~~------~~-   70 (147)
T 2kq2_A            5 TEYDVYTDGSYVNGQYAWAYAFVK-----DGKVHY-E-DADVGKNPAAATMRNVAGEIAAALYAVKKASQL------GV-   70 (147)
T ss_dssp             SCCEEECCCCCBTTBCEEEEEEEE-----TTEEEE-E-EEEECCCGGGGGTCTTHHHHHHHHHHHHHHHHH------TC-
T ss_pred             CeEEEEECCCCCCCCcEEEEEEEE-----CCEEEE-E-EeccccccccccccHHHHHHHHHHHHHHHHHHC------CC-
Confidence            36789999997    567765542     343211 1 11 111121 14689999999999999975432      23 


Q ss_pred             eEEEecchhhhHHHHhcC-Cc-cChhhhHHHHHHHHhccccceEEecCCC----C-CCcccccc
Q psy17737        204 KYYLWIDSQIVIHWILGN-KV-LPTFINNRVKEIKNRSFKLDVHYVPTDM----N-PADIACRG  260 (493)
Q Consensus       204 ~~~~~tDS~i~l~~l~~~-~~-~~~fv~nRv~~I~~~~~~~~~~hv~~~~----N-pAD~~SRg  260 (493)
                      .+.++|||+.+..|+.+. +. -+..+.++ ..++++...+.|.||||-.    | -||.+.|-
T Consensus        71 ~v~I~tDS~~i~~w~~~~w~~~~~~~~~~~-~l~~~l~~~v~~~wV~gH~g~~~Ne~AD~LA~~  133 (147)
T 2kq2_A           71 KIRILHDYAGIAFWATGEWKAKNEFTQAYA-KLMNQYRGIYSFEKVKAHSGNEFNDYVDMKAKS  133 (147)
T ss_dssp             CCCBSSCCSTHHHHTTSSSSCCHHHHHHHH-CGGGGGSTTCCBCCCCCCCCCHHHHHHHHHHHH
T ss_pred             eEEEEECcHHHHHHHhCCCccCCcchHHHH-HHHHHhcCCeeEEEecCcCCCcchHHHHHHHHH
Confidence            789999999999999875 21 11223222 2344444478999999854    4 48876653

>2zd1_B P51 RT; P51/P66, hetero dimer, NNRTI, nonnucleoside inhibitor, AIDS, HIV, rilpivirine, diarylpyrimidine, DAPY, DNA recombination; HET: T27; 1.80A {Human immunodeficiency virus 1} SCOP: e.8.1.2 PDB: 2ykm_B* 2ykn_B* 2ze2_B* 3bgr_B* 3ig1_B* 3irx_B* 3is9_B* 3qo9_B* 3v4i_B* 3v6d_B* 3v81_B* 3klf_B* 3kk1_B* 3kjv_B* 3kk2_B* 3kk3_B* 2be2_B* 1n5y_B* 1bqm_B* 1n6q_B* ...

Probab=97.82  E-value=2.6e-05  Score=81.51  Aligned_cols=170  Identities=10%  Similarity=0.009  Sum_probs=104.7

Q ss_pred             CCCcceEeEEEecCCCeEEEecCCccCCCCccHhHHHHhHhc--ccccCCCCcceeecchhhhhhhhhc-----cCCCCc
Q psy17737         20 NKVQNVLGLTWDTDIDTLSIKHGELQCSGKLTKRLLLSVYGS--IYDVLGLFTPVVLPLKILIQSVWQR-----NLSWDE   92 (493)
Q Consensus        20 ~~~~k~LG~~W~~~~D~l~~~~~~~~~~~~~TkR~ilS~ias--~yDPLGl~~p~~l~~K~llq~l~~~-----~~~WD~   92 (493)
                      ....+.||+....  +.+.+....++...+.|++++-|+++.  +|-.  ++..+.  ++-|.+.+-..     .+.|++
T Consensus       224 ~~~~~fLG~~i~~--~~i~~~~~ki~~~~~~t~k~lr~flG~~~yyrr--Fi~~~s--~~pL~~llkk~~~~~~~~~Wt~  297 (428)
T 2zd1_B          224 EPPFLWMGYELHP--DKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQ--IYPGIK--VRQLSKLLRGTKALTEVIPLTE  297 (428)
T ss_dssp             ---CTTCCEEECG--GGCCCCCCCCCCCSSEEHHHHHHHHHHHHHHTT--TCTTCC--CHHHHHTTCSCCCTTCEECCCH
T ss_pred             cceEEEeccEecC--CceEecccccccccccCHHHHHHHhhhHHHHHH--hcCCcc--HHHHHHHHccCCCCCCeecCCH
Confidence            3446789999775  333332222334456799999888752  2211  111111  33333222222     367876


Q ss_pred             cCChhHHHHHHHHHHHHhcccceeceeEEeccCCCCceeEEeecccccc-cceeeEEEEEeeCCCceeeeeecccccCCC
Q psy17737         93 ELSTEDKITFMKLIEDIKLIHTVHIPRLIGNLIPGTQYELHGFSDASAT-SYSMVIYLKCITGNSVTSNLVFAKARIAPL  171 (493)
Q Consensus        93 ~i~~e~~~~w~~~~~~l~~~~~~~iPR~~~~~~~~~~~~L~vF~DAS~~-a~gav~y~r~~~~~g~~~~ll~aksrv~P~  171 (493)
                          +..++++++++.|.+.+.+..|.        .+..+.+.||||.. ++|+|++.    ++|.   .+.+++ +.+.
T Consensus       298 ----~~~~af~~lK~~L~~~p~l~~pd--------~~~~~~l~~das~~g~~g~vl~q----~~~~---~~~s~~-~~~~  357 (428)
T 2zd1_B          298 ----EAELELAENREILKEPVHGVYYD--------PSKDLIAEIQKQGQGQWTYQIYQ----EPFK---NLKTGK-YARM  357 (428)
T ss_dssp             ----HHHHHHHHHHHHTTSCCTTCCCC--------TTSCCEEEEEEEETTEEEEEEES----STTC---EEEEEE-EECC
T ss_pred             ----HHHHHHHHHHHHHhcchhccccC--------CCCCEEEEEecCCCCcEEEEEec----CCCc---eeeecc-cchh
Confidence                88999999999998753333332        22689999999995 66887764    2332   234443 4466


Q ss_pred             CCCccchhhhhH-HHHHhhhhH-HHhhhhcccceeEEEecchhhhHHHHh
Q psy17737        172 SRPTLPRLELLG-ALIAYRGLK-FVGESLKVKDIKYYLWIDSQIVIHWIL  219 (493)
Q Consensus       172 k~~tIpRlEL~a-~~~~~~l~~-~~~~~l~~~~~~~~~~tDS~i~l~~l~  219 (493)
                      +++++..+|++| ++.+++-.. ++.   |...+.++++||++. +.|+.
T Consensus       358 ~~y~~~~~e~la~vv~al~~~r~yl~---G~~~~~~i~~td~~~-~~~~~  403 (428)
T 2zd1_B          358 RGAHTNDVKQLTEAVQKITTESIVIW---GKTPKFKLPIQKETW-ETWWT  403 (428)
T ss_dssp             SSCTTCHHHHHHHHHHHHHHHHHHHH---SSCCEEEESSCHHHH-HHHHH
T ss_pred             hhcccchHHHHHHHHHHhhccceEEE---CCCCcEECCccHHHH-HHHHH
Confidence            799999999999 999988777 443   333456788999995 44444

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

Probab=97.71  E-value=4.3e-05  Score=68.28  Aligned_cols=115  Identities=21%  Similarity=0.157  Sum_probs=71.3

Q ss_pred             eeEEeeccccccc-------ceeeEEEEEeeCCCceeeeeecccccCCCCCCccchhhhhHHHHHhhhhHHHhhhhcccc
Q psy17737        130 YELHGFSDASATS-------YSMVIYLKCITGNSVTSNLVFAKARIAPLSRPTLPRLELLGALIAYRGLKFVGESLKVKD  202 (493)
Q Consensus       130 ~~L~vF~DAS~~a-------~gav~y~r~~~~~g~~~~ll~aksrv~P~k~~tIpRlEL~a~~~~~~l~~~~~~~l~~~~  202 (493)
                      ..+.+|+|+|-.+       .|+.++++    ++....  .++ ++..  ..|..+.||.|++.|++++..      ...
T Consensus         6 ~~~~iytDGs~~~n~~~~~~aG~Gvv~~----~~~~~~--~~~-~l~~--~~tn~~aEl~A~~~aL~~~~~------~~~   70 (154)
T 2qkb_A            6 DFVVVYTDGCCSSNGRRRPRAGIGVYWG----PGHPLN--VGI-RLPG--RQTNQRAEIHAACKAIEQAKT------QNI   70 (154)
T ss_dssp             TEEEEEEEEEEETTTSSSCEEEEEEECS----TTCTTC--EEE-ECCS--SCCHHHHHHHHHHHHHHHHHH------TTC
T ss_pred             CeEEEEEccCcCCCCCCCCcEEEEEEEE----CCCcee--EEe-ecCC--CCchHHHHHHHHHHHHHHHHh------CCC
Confidence            3688999999642       23333433    221111  111 1211  578999999999999998863      245


Q ss_pred             eeEEEecchhhhHHHHhcC------CccC----hhhhHH--HHHHHHhcc--ccceEEecCCC----C-CCccccc
Q psy17737        203 IKYYLWIDSQIVIHWILGN------KVLP----TFINNR--VKEIKNRSF--KLDVHYVPTDM----N-PADIACR  259 (493)
Q Consensus       203 ~~~~~~tDS~i~l~~l~~~------~~~~----~fv~nR--v~~I~~~~~--~~~~~hv~~~~----N-pAD~~SR  259 (493)
                      ..+.++|||+.++.-|.+-      +.|+    ..+.|+  +.+|.++..  .+.|.|||+-.    | -||.+.+
T Consensus        71 ~~v~i~tDS~~vi~~i~~~~~~w~~~~w~~~~~~~~~n~~l~~~i~~l~~~~~v~~~~V~~H~g~~~N~~AD~LA~  146 (154)
T 2qkb_A           71 NKLVLYTNSMFTINGITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQGMDIQWMHVPGHSGFIGNEEADRLAR  146 (154)
T ss_dssp             CEEEEEESCHHHHHHHHTHHHHHHTTTSBCTTSSBCTTHHHHHHHHHHHTTCEEEEEECCTTSSCHHHHHHHHHHH
T ss_pred             ceEEEEECcHHHHhhhhhhHHHHHhccccccCCCccccHHHHHHHHHHHcCCceEEEEccCCCCCHhHHHHHHHHH
Confidence            7899999999888666542      1222    223332  556655543  48899999854    5 4786654

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

Probab=97.65  E-value=9.6e-05  Score=66.40  Aligned_cols=112  Identities=28%  Similarity=0.294  Sum_probs=70.0

Q ss_pred             eEEeecccccc------cceeeEEEEEeeCCCceeeeeecccccCCCCCCccchhhhhHHHHHhhhhHHHhhhhccccee
Q psy17737        131 ELHGFSDASAT------SYSMVIYLKCITGNSVTSNLVFAKARIAPLSRPTLPRLELLGALIAYRGLKFVGESLKVKDIK  204 (493)
Q Consensus       131 ~L~vF~DAS~~------a~gav~y~r~~~~~g~~~~ll~aksrv~P~k~~tIpRlEL~a~~~~~~l~~~~~~~l~~~~~~  204 (493)
                      .+.+|+|+|-.      |||++++.     +|.... +.+.  +   ...|-.+.||.|++.|++++..        ...
T Consensus         6 ~i~iytDGs~~~n~g~~G~G~v~~~-----~~~~~~-~~~~--~---~~~tn~~aEl~A~~~AL~~~~~--------~~~   66 (158)
T 2e4l_A            6 LIHIFTDGSCLGNPGPGGYGIVMNY-----KGHTKE-MSDG--F---SLTTNNRMELLAPIVALEALKE--------PCK   66 (158)
T ss_dssp             EEEEEEEEEESSSSEEEEEEEEEEE-----TTEEEE-EEEE--E---EEECHHHHHHHHHHHHHHTCSS--------CCE
T ss_pred             eEEEEEcccccCCCCcEEEEEEEEE-----CCEEEE-EecC--c---CCCccHHHHHHHHHHHHHHhcc--------CCe
Confidence            68899999975      56654432     232111 1111  1   1457889999999999987642        168


Q ss_pred             EEEecchhhhHHHHhcC------Ccc----ChhhhHH--HHHHHHhcc--ccceEEecCC----CC-CCccccccc
Q psy17737        205 YYLWIDSQIVIHWILGN------KVL----PTFINNR--VKEIKNRSF--KLDVHYVPTD----MN-PADIACRGE  261 (493)
Q Consensus       205 ~~~~tDS~i~l~~l~~~------~~~----~~fv~nR--v~~I~~~~~--~~~~~hv~~~----~N-pAD~~SRg~  261 (493)
                      +.++|||+.++.-|..-      +.|    ...+.|+  +.+|.++..  .+.|.||||-    .| -||.+.+-.
T Consensus        67 v~I~tDS~~vi~~i~~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~~~~v~~~wV~gH~g~~~Ne~AD~LAk~a  142 (158)
T 2e4l_A           67 IILTSDSQYMRQGIMTWIHGWKKKGWMTSNRTPVKNVDLWKRLDKAAQLHQIDWRWVKGHAGHAENERCDQLARAA  142 (158)
T ss_dssp             EEEEECCHHHHHHHHTHHHHHHHTTTBCTTSSBCTTHHHHHHHHHHHTTSEEEEEECCTTCCCHHHHHHHHHHHHH
T ss_pred             EEEEeCHHHHHHHHHHHHHHHHHccccccCCCcccCHHHHHHHHHHHccCcEEEEEccCCCCchhHHHHHHHHHHH
Confidence            99999999998855541      112    1234443  345555443  5889999965    45 488766543

>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=97.61  E-value=1.4e-05  Score=71.42  Aligned_cols=107  Identities=20%  Similarity=0.167  Sum_probs=66.6

Q ss_pred             eeEEeeccccc------ccceeeEEEEEeeCCCceeeeeecccccCCCCCCccchhhhhHHHHHhhhhHHHhhhhcccce
Q psy17737        130 YELHGFSDASA------TSYSMVIYLKCITGNSVTSNLVFAKARIAPLSRPTLPRLELLGALIAYRGLKFVGESLKVKDI  203 (493)
Q Consensus       130 ~~L~vF~DAS~------~a~gav~y~r~~~~~g~~~~ll~aksrv~P~k~~tIpRlEL~a~~~~~~l~~~~~~~l~~~~~  203 (493)
                      ..+.+|+|+|-      .|||+|++      +|.... +       +....|-.|.||.|++.|++..          ..
T Consensus        11 ~~~~iytDGs~~~n~g~~g~G~v~~------~~~~~~-~-------~~~~~Tnn~aEl~A~i~AL~~~----------~~   66 (150)
T 3qio_A           11 GAETFYVDGAANRETKLGKAGYVTN------RGRQKV-V-------TLTDTTNQKTELQAIYLALQDS----------GL   66 (150)
T ss_dssp             TCEEEEEEEEECTTTCCEEEEEEET------TSCEEE-E-------EESSCCHHHHHHHHHHHHHHHS----------CS
T ss_pred             CCEEEEEccCCCCCCCCeEEEEEEE------cCCEEE-E-------eCCCCCHHHHHHHHHHHHHHhC----------CC
Confidence            46899999995      35554332      222111 1       1246799999999999999863          26


Q ss_pred             eEEEecchhhhHHHHhcC------CccC----hhhhHH--HHHHHHh---ccccceEEecCCC----C-CCcccccc
Q psy17737        204 KYYLWIDSQIVIHWILGN------KVLP----TFINNR--VKEIKNR---SFKLDVHYVPTDM----N-PADIACRG  260 (493)
Q Consensus       204 ~~~~~tDS~i~l~~l~~~------~~~~----~fv~nR--v~~I~~~---~~~~~~~hv~~~~----N-pAD~~SRg  260 (493)
                      .+.++|||+.++.-|.+-      +.|+    ..|.|+  +.+|.+.   ...+.|.||||..    | -||.+.|-
T Consensus        67 ~v~i~tDS~~v~~~i~~w~~~W~~~gw~~~~g~~v~n~~l~~~l~~~l~~~~~v~~~wV~gH~g~~~Ne~AD~LA~~  143 (150)
T 3qio_A           67 EVNIVTDSQYALGIITQWIHNWKKRGWKTADKKPVKNVDLVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSA  143 (150)
T ss_dssp             EEEEEESCHHHHHHHHHHHHHHCC------------CHHHHHHHHHHHTTCSEEEEEECCTTSCCHHHHHHHHHHHT
T ss_pred             cEEEEeCcHHHHHHHHHHHHHHhhcCcCcCcCcccccHHHHHHHHHHHhhcCceEEEEccCcCCChhHHHHHHHHHH
Confidence            899999999988755542      1222    234443  3344332   2458999999997    6 48876553

>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=97.61  E-value=0.00013  Score=65.36  Aligned_cols=111  Identities=23%  Similarity=0.228  Sum_probs=71.0

Q ss_pred             eEEeecccccc------cceeeEEEEEeeCCCceeeeeecccccCCCCCCccchhhhhHHHHHhhhhHHHhhhhccccee
Q psy17737        131 ELHGFSDASAT------SYSMVIYLKCITGNSVTSNLVFAKARIAPLSRPTLPRLELLGALIAYRGLKFVGESLKVKDIK  204 (493)
Q Consensus       131 ~L~vF~DAS~~------a~gav~y~r~~~~~g~~~~ll~aksrv~P~k~~tIpRlEL~a~~~~~~l~~~~~~~l~~~~~~  204 (493)
                      .+.+|+|+|..      |||++++.     ++. ...+.+.  +   ...|-.+.||.|++.|++++..        ...
T Consensus         4 ~~~iytDGs~~~n~~~~G~G~v~~~-----~~~-~~~~~~~--~---~~~tn~~aEl~A~~~aL~~~~~--------~~~   64 (155)
T 1jl1_A            4 QVEIFTAGSALGNPGPGGYGAILRY-----RGR-EKTFSAG--Y---TRTTNNRMELMAAIVALEALKE--------HAE   64 (155)
T ss_dssp             CEEEEEEEEESSTTEEEEEEEEEEE-----TTE-EEEEEEE--E---EEECHHHHHHHHHHHHHHTCCS--------CCE
T ss_pred             eEEEEEccccCCCCCceEEEEEEEE-----CCe-EEEEecC--C---CCCcHHHHHHHHHHHHHHHhCc--------CCc
Confidence            57899999874      45554332     221 1111111  1   2457889999999999987753        268


Q ss_pred             EEEecchhhhHHHHhcC------Ccc----ChhhhHH--HHHHHHhcc--ccceEEecCC----CC-CCcccccc
Q psy17737        205 YYLWIDSQIVIHWILGN------KVL----PTFINNR--VKEIKNRSF--KLDVHYVPTD----MN-PADIACRG  260 (493)
Q Consensus       205 ~~~~tDS~i~l~~l~~~------~~~----~~fv~nR--v~~I~~~~~--~~~~~hv~~~----~N-pAD~~SRg  260 (493)
                      +.++|||+.++.-|.+-      +.|    ...|.|+  +.+|.++..  .+.|.||||-    .| -||.+.+-
T Consensus        65 v~I~tDS~~vi~~i~~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~~~~v~~~wV~gH~g~~~Ne~AD~LA~~  139 (155)
T 1jl1_A           65 VILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVKGHAGHPENERADELARA  139 (155)
T ss_dssp             EEEEECCHHHHHHHHTTHHHHHHTTTBCTTSCBCTTHHHHHHHHHHTTTCEEEEEECCSSTTCHHHHHHHHHHHH
T ss_pred             EEEEeCHHHHHHHHHHHHHHHhhcccccccCCccCCHHHHHHHHHHHccCceEEEEcCCCCCCHHHHHHHHHHHH
Confidence            99999999999777752      112    2244443  455666554  5889999965    45 48877654

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

Probab=97.60  E-value=9.3e-05  Score=65.38  Aligned_cols=111  Identities=20%  Similarity=0.226  Sum_probs=65.7

Q ss_pred             eeEEeeccccc------ccceeeEEEEEeeCCCceeeeeecccccCCCCCCccchhhhhHHHHHhhhhHHHhhhhcccce
Q psy17737        130 YELHGFSDASA------TSYSMVIYLKCITGNSVTSNLVFAKARIAPLSRPTLPRLELLGALIAYRGLKFVGESLKVKDI  203 (493)
Q Consensus       130 ~~L~vF~DAS~------~a~gav~y~r~~~~~g~~~~ll~aksrv~P~k~~tIpRlEL~a~~~~~~l~~~~~~~l~~~~~  203 (493)
                      ..+.+|+|+|-      .|||++++  .   ++ ...-+.+     +....|-.+.||.|++.|++.+..        ..
T Consensus         3 ~~i~iytDGs~~~n~g~~g~G~v~~--~---~~-~~~~~~~-----~~~~~Tnn~aEl~A~~~AL~~~~~--------~~   63 (146)
T 3h08_A            3 KTITIYTDGAASGNPGKGGWGALLM--Y---GS-SRKEISG-----YDPATTNNRMELMAAIKGLEALKE--------PA   63 (146)
T ss_dssp             CEEEEEEEEEESSTTEEEEEEEEEE--E---TT-EEEEEEE-----EEEEECHHHHHHHHHHHHHHTCSS--------CC
T ss_pred             ceEEEEEecCCCCCCCceEEEEEEE--E---CC-eeEEeec-----CCCCCcHHHHHHHHHHHHHHhcCc--------cC
Confidence            36899999994      35554433  2   12 1111111     112567889999999999998753        47


Q ss_pred             eEEEecchhhhHHHHhcC-------CccC----hhhhHH--HHHHHHhc--cccceEEecCC----CC-CCccccc
Q psy17737        204 KYYLWIDSQIVIHWILGN-------KVLP----TFINNR--VKEIKNRS--FKLDVHYVPTD----MN-PADIACR  259 (493)
Q Consensus       204 ~~~~~tDS~i~l~~l~~~-------~~~~----~fv~nR--v~~I~~~~--~~~~~~hv~~~----~N-pAD~~SR  259 (493)
                      .+.++|||+.++.-|.+.       +.|+    .-+.|+  +.+|.++.  ..+.|.||||-    .| -||.+.+
T Consensus        64 ~v~I~tDS~~vi~~i~~~w~~~W~~~~w~~~~~~~v~n~~l~~~~~~~~~~~~v~~~~V~gH~g~~~N~~AD~LA~  139 (146)
T 3h08_A           64 RVQLYSDSAYLVNAMNEGWLKRWVKNGWKTAAKKPVENIDLWQEILKLTTLHRVTFHKVKGHSDNPYNSRADELAR  139 (146)
T ss_dssp             EEEEEESCHHHHHHHHSSHHHHHHHTTCC----CCCTTHHHHHHHHHHHHHSEEEEEECCC-CCSHHHHHHHHHHH
T ss_pred             cEEEEeChHHHHHHHHHHHHHHHHHCCCccCCCCCcCCHHHHHHHHHHHhhCceEEEEcCCcCCcHhHHHHHHHHH
Confidence            899999999988766551       1121    112222  33333332  24889999954    44 3665543

>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=97.53  E-value=0.00023  Score=64.52  Aligned_cols=99  Identities=14%  Similarity=0.148  Sum_probs=63.8

Q ss_pred             eeEEeecccccc------cceeeEEEEEeeCCCceeeeeecccccCCCCCCccchhhhhHHHHHhhhhHHHhhhhcccce
Q psy17737        130 YELHGFSDASAT------SYSMVIYLKCITGNSVTSNLVFAKARIAPLSRPTLPRLELLGALIAYRGLKFVGESLKVKDI  203 (493)
Q Consensus       130 ~~L~vF~DAS~~------a~gav~y~r~~~~~g~~~~ll~aksrv~P~k~~tIpRlEL~a~~~~~~l~~~~~~~l~~~~~  203 (493)
                      ..+.+|+|+|..      |||+++|.     +|....  .+  .. + ...|..|.||.|++.|++.+.         ..
T Consensus        22 ~~i~iytDGs~~~npG~~g~G~vi~~-----~~~~~~--~~--~~-~-~~~Tnn~aEl~Ai~~AL~~~~---------~~   81 (165)
T 3p1g_A           22 ADYTWYTDGSSFLQEGQRRAGAAVTT-----ETEVIW--AR--AL-P-AGTSAQRAELIALTQALKMAE---------GK   81 (165)
T ss_dssp             CSEEEEEEEEEEEETTEEEEEEEEEC-----SSCEEE--EE--EE-C-TTCCHHHHHHHHHHHHHHHTB---------TS
T ss_pred             CCEEEEEEcccCCCCCceEEEEEEEE-----CCEEEE--Ee--cC-C-CCCcHHHHHHHHHHHHHHHcc---------Cc
Confidence            469999999985      46655542     232111  11  11 1 256999999999999999771         46


Q ss_pred             eEEEecchhhhHHHH--hcCCccChhhhHH--HHHHHH-h--ccccceEEecCCC
Q psy17737        204 KYYLWIDSQIVIHWI--LGNKVLPTFINNR--VKEIKN-R--SFKLDVHYVPTDM  251 (493)
Q Consensus       204 ~~~~~tDS~i~l~~l--~~~~~~~~fv~nR--v~~I~~-~--~~~~~~~hv~~~~  251 (493)
                      .+.+||||+.++.-|  .+.   +..|.|+  +.++.. +  ...+.|.||||-.
T Consensus        82 ~v~I~tDS~~vi~~iw~~~~---g~~v~n~dl~~~l~~~l~~~~~v~~~wVkgH~  133 (165)
T 3p1g_A           82 KLNVYTDSRYAFATAHVHSE---GREIKNKNEILALLKALFLPKRLSIIHCPGHQ  133 (165)
T ss_dssp             EEEEEECCHHHHHHHHSCCC---SCCCSSHHHHHHHHHHTTSBSEEEEEECCSSC
T ss_pred             eEEEEEchHHHHhhhhcccC---CCcccCHHHHHHHHHHHhcCCceEEEEecCCC
Confidence            899999999877644  322   2234443  334422 2  2458999999977

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

Probab=97.48  E-value=2.6e-05  Score=70.74  Aligned_cols=111  Identities=16%  Similarity=0.175  Sum_probs=69.3

Q ss_pred             eEEeecccccc------cceeeEEEEEeeCCCceeeeeecccccCCCCCCccchhhhhHHHHHhhhhHHHhhhhccccee
Q psy17737        131 ELHGFSDASAT------SYSMVIYLKCITGNSVTSNLVFAKARIAPLSRPTLPRLELLGALIAYRGLKFVGESLKVKDIK  204 (493)
Q Consensus       131 ~L~vF~DAS~~------a~gav~y~r~~~~~g~~~~ll~aksrv~P~k~~tIpRlEL~a~~~~~~l~~~~~~~l~~~~~~  204 (493)
                      .+.+|+|+|..      |||+++  +.  .++.. . + +..    ....|-.+.||.|++.|++++..        ...
T Consensus         8 ~i~iytDGs~~~n~g~~G~G~v~--~~--~~~~~-~-~-~~~----~~~~Tnn~aEl~Ai~~AL~~~~~--------~~~   68 (166)
T 1ril_A            8 RVALFTDGACLGNPGPGGWAALL--RF--HAHEK-L-L-SGG----EACTTNNRMELKAAIEGLKALKE--------PCE   68 (166)
T ss_dssp             CCCEEEEEEESSTTEEEEEEEEE--CB--TTBCC-E-E-CCE----EEEECHHHHHHHHHHHHHHSCCS--------CCE
T ss_pred             cEEEEECccccCCCCCEEEEEEE--EE--CCEEE-E-E-ecC----CCCCcHHHHHHHHHHHHHHHhcc--------CCe
Confidence            57899999975      455433  21  12211 1 1 111    12468889999999999987653        147


Q ss_pred             EEEecchhhhHHHHhcC-------CccC----hhhhH--HHHHHHHhcc--ccceEEecC----CCC-CCcccccc
Q psy17737        205 YYLWIDSQIVIHWILGN-------KVLP----TFINN--RVKEIKNRSF--KLDVHYVPT----DMN-PADIACRG  260 (493)
Q Consensus       205 ~~~~tDS~i~l~~l~~~-------~~~~----~fv~n--Rv~~I~~~~~--~~~~~hv~~----~~N-pAD~~SRg  260 (493)
                      +.++|||+.++.-|.+.       +.|+    ..+.|  -+.+|.++..  .+.|.||||    ..| -||.+.+-
T Consensus        69 v~I~tDS~~vi~~i~~~w~~~W~~~~w~~~~g~~v~n~~l~~~i~~l~~~~~v~~~wV~gH~g~~~Ne~AD~LAk~  144 (166)
T 1ril_A           69 VDLYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPHRVRFHFVKGHTGHPENERVDREARR  144 (166)
T ss_dssp             EEEECCCHHHHHHHHSSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHTTSEEECCCCCGGGSCTHHHHHHHHHHH
T ss_pred             EEEEeChHHHHHHHhhhHHHHHHhcccccccCCccCcHHHHHHHHHHHhcCeEEEEEeeCCCCchhHHHHHHHHHH
Confidence            99999999998766551       1222    33444  2455555544  588899994    456 48876653

>3nnq_A Integrase P46, N-terminal domain of moloney murine leukemia VIRU integrase; retroviral integrase, Zn finger; 2.69A {Moloney murine leukemia virus}

Probab=97.40  E-value=6.2e-05  Score=63.02  Aligned_cols=71  Identities=13%  Similarity=0.239  Sum_probs=59.0

Q ss_pred             eeeccC-CcEEeccccccccCCCCCCCceEecCCCcchhHHHHHHHHhCCCCChhhhhHHHHHHhh---hc-cccchHHH
Q psy17737        403 LVLDEN-DILRCKGRFVELKVDGKSCFPMLLPRGNHISKIIVNDIHTSGYHTGDKESKKLSNVARG---YY-LDGNHLER  477 (493)
Q Consensus       403 pflD~~-GllRv~gRl~~s~l~~~~k~Pillp~~~~lt~Lii~~~H~~~~H~G~~~t~~l~~lr~~---yW-~~~r~~vr  477 (493)
                      -..|+. +-+...||+             ++|  ..++..+|...|... |.|.+.+  .+.|++.   || ++..+.+|
T Consensus        28 ~~y~~~~~~w~~~Gk~-------------vlP--~~~~~eli~~lH~lT-HLg~~kl--~~Ll~r~e~~~~i~~~~~~~~   89 (114)
T 3nnq_A           28 AIYDKTKKYWVYQGKP-------------VMP--DQFTFELLDFLHQLT-HLSFSKM--KALLERSHSPYYMLNRDRTLK   89 (114)
T ss_dssp             CEEETTTTEEEETTEE-------------EEC--HHHHHHHHHHHHHHH-CCCHHHH--HHHHHHHCCSSEETTHHHHHH
T ss_pred             ceecCCCceeccCCCC-------------cCC--HHHHHHHHHHHHHHh-ccCHHHH--HHHHHhhccceeeeCHHHHHH
Confidence            345544 456666766             377  458999999999986 9999999  9999886   89 99999999


Q ss_pred             HHhcCCcccccccc
Q psy17737        478 RVLLGSRLLSGWVR  491 (493)
Q Consensus       478 ~vi~~C~~C~r~~~  491 (493)
                      .|+.+|..|++.+.
T Consensus        90 ~Vt~sC~aCaqvNa  103 (114)
T 3nnq_A           90 NITETCKACAQVNA  103 (114)
T ss_dssp             HHHHHCHHHHHHHC
T ss_pred             HHHHHHHHHHHhCC
Confidence            99999999998765

>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=97.36  E-value=3.9e-05  Score=66.98  Aligned_cols=72  Identities=19%  Similarity=0.116  Sum_probs=50.1

Q ss_pred             EEeeccccc------ccceeeEEEEEeeCCCceeeeeecccccCCCCCCccchhhhhHHHHHhhhhHHHhhhhcccceeE
Q psy17737        132 LHGFSDASA------TSYSMVIYLKCITGNSVTSNLVFAKARIAPLSRPTLPRLELLGALIAYRGLKFVGESLKVKDIKY  205 (493)
Q Consensus       132 L~vF~DAS~------~a~gav~y~r~~~~~g~~~~ll~aksrv~P~k~~tIpRlEL~a~~~~~~l~~~~~~~l~~~~~~~  205 (493)
                      ..+|+|||-      .|||+|++     .+|..... .  .   +....|-.|.||.|++.|++++...    +.   .+
T Consensus         6 ~~iytDGac~GNPGp~G~ggV~~-----~~g~~~~~-~--g---~~~~tTNN~aEl~A~i~aL~~l~~~----~~---~v   67 (134)
T 4htu_A            6 ESLSVDVGSQGNPGIVEYKGVDT-----KTGEVLFE-R--E---PIPIGTNNMGEFLAIVHGLRYLKER----NS---RK   67 (134)
T ss_dssp             SSEEEEEEEETTTEEEEEEEEET-----TTCCEEEE-E--E---EEEEECHHHHHHHHHHHHHHHHHHT----TC---CC
T ss_pred             eEEEEeeccCCCCCCeEEEEEEE-----ECCEEEEE-e--c---CCCCCchHHHHHHHHHHHHHHHHhC----CC---CE
Confidence            468999986      46766542     13432211 1  1   2235799999999999999987642    22   37


Q ss_pred             EEecchhhhHHHHhcC
Q psy17737        206 YLWIDSQIVIHWILGN  221 (493)
Q Consensus       206 ~~~tDS~i~l~~l~~~  221 (493)
                      .++|||+.++.||++.
T Consensus        68 ~i~tDSqyVi~wi~~~   83 (134)
T 4htu_A           68 PIYSNSQTAIKWVKDK   83 (134)
T ss_dssp             CEEESCHHHHHHHHHT
T ss_pred             EEEcchHHHHHHHHcC
Confidence            8999999999999976

>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=96.96  E-value=0.0011  Score=58.51  Aligned_cols=73  Identities=19%  Similarity=0.123  Sum_probs=52.1

Q ss_pred             eEEeecccccc------cceeeEEEEEeeCCCceeeeeecccccCCCCCCccchhhhhHHHHHhhhhHHHhhhhccccee
Q psy17737        131 ELHGFSDASAT------SYSMVIYLKCITGNSVTSNLVFAKARIAPLSRPTLPRLELLGALIAYRGLKFVGESLKVKDIK  204 (493)
Q Consensus       131 ~L~vF~DAS~~------a~gav~y~r~~~~~g~~~~ll~aksrv~P~k~~tIpRlEL~a~~~~~~l~~~~~~~l~~~~~~  204 (493)
                      .+.+|+|+|-.      |||+|++     .+|...  ..+ .   +....|-.|.||.|++.|++++...    +  + .
T Consensus        11 ~~~iy~DGa~~gNpG~~G~G~vl~-----~~g~~~--~~~-~---~~~~~TNN~aEl~A~i~aL~~~~~~----~--~-~   72 (142)
T 1zbf_A           11 WESLSVDVGSQGNPGIVEYKGVDT-----KTGEVL--FER-E---PIPIGTNNMGEFLAIVHGLRYLKER----N--S-R   72 (142)
T ss_dssp             SSSEEEEEEECSSSEEEEEEEEET-----TTCCEE--EEC-C---CEEEECHHHHHHHHHHHHHHHHHHT----T--C-C
T ss_pred             eEEEEEeeccCCCCCCeEEEEEEE-----eCCEEE--EEe-c---ccCCcCcHHHHHHHHHHHHHHHHhC----C--C-e
Confidence            56789999863      5665443     244321  111 1   2224689999999999999988742    2  2 7


Q ss_pred             EEEecchhhhHHHHhcC
Q psy17737        205 YYLWIDSQIVIHWILGN  221 (493)
Q Consensus       205 ~~~~tDS~i~l~~l~~~  221 (493)
                      +.++|||+.++.|+++.
T Consensus        73 v~i~tDS~~vi~w~~~~   89 (142)
T 1zbf_A           73 KPIYSNSQTAIKWVKDK   89 (142)
T ss_dssp             CCEEESCHHHHHHHHHT
T ss_pred             EEEEEehHHHHHHHHcC
Confidence            89999999999999988

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

Probab=96.89  E-value=0.0028  Score=57.31  Aligned_cols=108  Identities=13%  Similarity=-0.018  Sum_probs=60.1

Q ss_pred             eeEEeeccccc-----------ccceeeEEEEEeeCCCceeeeeecccccCCCCCCccchhhhhHHHHHhhhhHHHhhhh
Q psy17737        130 YELHGFSDASA-----------TSYSMVIYLKCITGNSVTSNLVFAKARIAPLSRPTLPRLELLGALIAYRGLKFVGESL  198 (493)
Q Consensus       130 ~~L~vF~DAS~-----------~a~gav~y~r~~~~~g~~~~ll~aksrv~P~k~~tIpRlEL~a~~~~~~l~~~~~~~l  198 (493)
                      .++++|||+|-           .|||+  ++...   +....+..+-.      .-|=.|.|+.|.+.|+..+...  ++
T Consensus         6 ~evviYTDGsc~gNpgp~~~~~aG~Gv--~~~~~---~~~~~~~~~~~------~~tnn~te~~Aei~Al~~al~~--al   72 (165)
T 2lsn_A            6 YEGVFYTDGSAIKSPDPTKSNNAGMGI--VHATY---KPEYQVLNQWS------IPLGNHTAQMAEIAAVEFACKK--AL   72 (165)
T ss_dssp             CSEEEEEEEEEEECSSCTTCEEEEEEE--EEECC---SSSCCEEEEEE------EEESSCCHHHHHHHHHHHHHHH--HH
T ss_pred             ceEEEEEcCCCCCCCCCCCCCcEEEEE--EEEEC---CCccEEecccc------CCchHHHHHHHHHHHHHHHHHH--Hh
Confidence            67899999994           35664  44321   11112221111      1133577888888887755421  22


Q ss_pred             cccceeEEEecchhhhHHHHh--------cC--CccChhhhHH--HHHHHHh---ccccceEEecCCC
Q psy17737        199 KVKDIKYYLWIDSQIVIHWIL--------GN--KVLPTFINNR--VKEIKNR---SFKLDVHYVPTDM  251 (493)
Q Consensus       199 ~~~~~~~~~~tDS~i~l~~l~--------~~--~~~~~fv~nR--v~~I~~~---~~~~~~~hv~~~~  251 (493)
                      . ....+.++|||+-++.-|.        +.  ..-+.-|.|+  +.+|.++   ...+.|.||+|-.
T Consensus        73 ~-~~~~v~I~TDS~Yvi~~it~w~~~Wk~ngw~~~~~~pVkN~dL~~~l~~~~~~~~~v~~~~VkgH~  139 (165)
T 2lsn_A           73 K-IPGPVLVITDSFYVAESANKELPYWKSNGFVNNKKKPLKHISKWKSIAECLSMKPDITIQHEKGHQ  139 (165)
T ss_dssp             H-SSSCEEEEESCHHHHHHHHTHHHHHHHTTSCSCSSSCCSSHHHHHHHHHHHHHCTTCEEEECCSSS
T ss_pred             c-CCCeEEEEeChHHHHhhhhhhhhhheeccccccCCCcccCHHHHHHHHHHHhCCCCEEEEEEeCCC
Confidence            1 1246999999998875333        22  1222335554  3344433   3468999999864

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	493
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	97.86
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	97.56
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	97.14
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	97.12
d1zbfa1	132	BH0863-like Ribonuclease H {Bacillus halodurans [T	96.62
d2zd1b1	424	HIV-1 reverse transcriptase {Human immunodeficienc	91.73
d1mu2a2	427	HIV-1 reverse transcriptase {Human immunodeficienc	84.77
d1k6ya1	46	N-terminal Zn binding domain of HIV integrase {Hum	82.37

>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=97.86  E-value=6e-06  Score=67.86  Aligned_cols=94  Identities=18%  Similarity=0.233  Sum_probs=58.6

Q ss_pred             EEeecccccc---cceeeEEEEEeeCCCceeeeeecccccCCCCCCccchhhhhHHHHHhhhhHHHhhhhcccceeEEEe
Q psy17737        132 LHGFSDASAT---SYSMVIYLKCITGNSVTSNLVFAKARIAPLSRPTLPRLELLGALIAYRGLKFVGESLKVKDIKYYLW  208 (493)
Q Consensus       132 L~vF~DAS~~---a~gav~y~r~~~~~g~~~~ll~aksrv~P~k~~tIpRlEL~a~~~~~~l~~~~~~~l~~~~~~~~~~  208 (493)
                      ..+|||+|..   +-|++.|..   .+|...        +.++..-|-.|.||.|++.|++.          ....+.++
T Consensus         9 ~t~ytDGs~~~n~~~g~~g~~~---~~~~~~--------~~~~~~~TNn~aEl~Avi~aL~~----------~~~~v~I~   67 (110)
T d1s1ta1           9 ETFYVDGAANRETKLGKAGYVT---NRGRQK--------VVTLTDTTNQKTELQAIYLALQD----------SGLEVNIV   67 (110)
T ss_dssp             EEEEEEEEEETTTTEEEEEEEE---TTSCEE--------EEEESSCCHHHHHHHHHHHHHHH----------SCSEEEEE
T ss_pred             cEEEEeCCCCCCCCCcEEEEEE---ecCCeE--------EEecccCcHHHHHHHHHHHHHHh----------CCCeEEEE
Confidence            4689999843   223333432   233221        11223458999999999998642          23579999


Q ss_pred             cchhhhHHHHhcC-CccChhhhHHHHHHHHh---ccccceEEecC
Q psy17737        209 IDSQIVIHWILGN-KVLPTFINNRVKEIKNR---SFKLDVHYVPT  249 (493)
Q Consensus       209 tDS~i~l~~l~~~-~~~~~fv~nRv~~I~~~---~~~~~~~hv~~  249 (493)
                      |||+-++.-+.+. ..+.   .+-+.+|.+.   ...+.+.||||
T Consensus        68 TDS~yvi~~i~~~~~~~~---~~l~~~il~~l~~~~~v~i~WVpg  109 (110)
T d1s1ta1          68 TDSQYALGIIQAQPDQSE---SELVNQIIEQLIKKEKVYLAWVPA  109 (110)
T ss_dssp             ECCHHHHHHHHHCCSEES---CHHHHHHHHHHHHCSEEEEEECCS
T ss_pred             EehHHHHHHHhcCccccc---hHHHHHHHHHHhcCCceEEEEeCC
Confidence            9999999988876 3332   2223333332   24588999997

>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=97.56  E-value=9.4e-05  Score=61.67  Aligned_cols=98  Identities=18%  Similarity=0.227  Sum_probs=61.9

Q ss_pred             EEeecccccc---cceeeEEEEEeeCCCceeeeeecccccCCCCCCccchhhhhHHHHHhhhhHHHhhhhcccceeEEEe
Q psy17737        132 LHGFSDASAT---SYSMVIYLKCITGNSVTSNLVFAKARIAPLSRPTLPRLELLGALIAYRGLKFVGESLKVKDIKYYLW  208 (493)
Q Consensus       132 L~vF~DAS~~---a~gav~y~r~~~~~g~~~~ll~aksrv~P~k~~tIpRlEL~a~~~~~~l~~~~~~~l~~~~~~~~~~  208 (493)
                      ..+|||+|..   +-|+..|..   .+|...        ..++...|-.+-||.|++.|++.          ....+.++
T Consensus         8 ~t~YTDGS~~~n~~~~~~g~~~---~~~~~~--------~~~~~~~tnn~AEl~Ai~~al~~----------~~~~i~I~   66 (126)
T d1mu2a1           8 ETFYTDGSCNRQSKEGKAGYVT---DRGKDK--------VKKLEQTTNQQAELEAFAMALTD----------SGPKVNII   66 (126)
T ss_dssp             EEEEEEEEECTTTCCEEEEEEE---TTSCEE--------EEEESSCCHHHHHHHHHHHHHHT----------SCSEEEEE
T ss_pred             cEEEEcCCCCCCCCcEEEEEEe---cCCCEE--------EEecCCCcchHHHHHHHHHHhcc----------CCcceEEE
Confidence            5799999943   223333332   233221        11223468899999999888653          23578999


Q ss_pred             cchhhhHHHHhcC-Ccc-ChhhhHHHHHHHHhccccceEEecCCC
Q psy17737        209 IDSQIVIHWILGN-KVL-PTFINNRVKEIKNRSFKLDVHYVPTDM  251 (493)
Q Consensus       209 tDS~i~l~~l~~~-~~~-~~fv~nRv~~I~~~~~~~~~~hv~~~~  251 (493)
                      |||+-++.++.+. +.+ .......+.+..+. ..+.+.||||-.
T Consensus        67 tDS~~v~~~~~~~~~~~~~~~~~~~~~~~~~~-~~v~~~wV~gH~  110 (126)
T d1mu2a1          67 VDSQYVMGIVASQPTESESKIVNQIIEEMIKK-EAIYVAWVPAHK  110 (126)
T ss_dssp             ESCHHHHHHHHTCCSEESCHHHHHHHHHHHHC-SEEEEEECCSSS
T ss_pred             echHHHHHHHhcCCccccchHHHHHHHHhhhc-ceeEEEEEeCCC
Confidence            9999999999987 333 23333334443332 368899999865

>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=97.14  E-value=0.00047  Score=58.69  Aligned_cols=110  Identities=23%  Similarity=0.274  Sum_probs=67.1

Q ss_pred             eEEeeccccc------ccceeeEEEEEeeCCCceeeeeecccccCCCCCCccchhhhhHHHHHhhhhHHHhhhhccccee
Q psy17737        131 ELHGFSDASA------TSYSMVIYLKCITGNSVTSNLVFAKARIAPLSRPTLPRLELLGALIAYRGLKFVGESLKVKDIK  204 (493)
Q Consensus       131 ~L~vF~DAS~------~a~gav~y~r~~~~~g~~~~ll~aksrv~P~k~~tIpRlEL~a~~~~~~l~~~~~~~l~~~~~~  204 (493)
                      ++.||||+|.      .|||++++.     +|....+  +..    ....|=.+-||.|++.|++.+.        ....
T Consensus         2 ~I~IYtDGS~~~N~g~aG~G~vi~~-----~~~~~~~--~~~----~~~~tnn~aE~~Ai~~Al~~~~--------~~~~   62 (152)
T d1jl1a_           2 QVEIFTAGSALGNPGPGGYGAILRY-----RGREKTF--SAG----YTRTTNNRMELMAAIVALEALK--------EHAE   62 (152)
T ss_dssp             CEEEEEEEEESSTTEEEEEEEEEEE-----TTEEEEE--EEE----EEEECHHHHHHHHHHHHHHTCC--------SCCE
T ss_pred             EEEEEEeCCCCCCCCcEEEEEEEEE-----CCeEEEe--ccc----cCcccHHHHHHhhhhhhhhhhc--------ccce
Confidence            5789999884      467876543     2322111  111    1234667899999999876432        2356


Q ss_pred             EEEecchhhhHHHHhcC----------CccChhhhH--HHHHHHHhcc--ccceEEecCCCC-C----Cccccc
Q psy17737        205 YYLWIDSQIVIHWILGN----------KVLPTFINN--RVKEIKNRSF--KLDVHYVPTDMN-P----ADIACR  259 (493)
Q Consensus       205 ~~~~tDS~i~l~~l~~~----------~~~~~fv~n--Rv~~I~~~~~--~~~~~hv~~~~N-p----AD~~SR  259 (493)
                      +.++|||..++..+...          ......+.|  .+.+|.++..  .+.|.||||-.+ +    ||.+-+
T Consensus        63 i~i~tds~~~i~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~i~~~~~~~~V~~~wV~gH~g~~gNe~AD~LAk  136 (152)
T d1jl1a_          63 VILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVKGHAGHPENERADELAR  136 (152)
T ss_dssp             EEEEECCHHHHHHHHTTHHHHHHTTTBCTTSCBCTTHHHHHHHHHHTTTCEEEEEECCSSTTCHHHHHHHHHHH
T ss_pred             EEEeecceeeEEcccchhhHhHhccchhcccCeeecHHHHHHHHHHhhcceeEEEEecccCCCccHHHHHHHHH
Confidence            78999999888766544          112233444  3556666554  588999998542 2    775443

>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=97.12  E-value=0.00013  Score=62.39  Aligned_cols=101  Identities=17%  Similarity=0.225  Sum_probs=60.2

Q ss_pred             eEEeeccccc------ccceeeEEEEEeeCCCceeeeeecccccCCCCCCccchhhhhHHHHHhhhhHHHhhhhccccee
Q psy17737        131 ELHGFSDASA------TSYSMVIYLKCITGNSVTSNLVFAKARIAPLSRPTLPRLELLGALIAYRGLKFVGESLKVKDIK  204 (493)
Q Consensus       131 ~L~vF~DAS~------~a~gav~y~r~~~~~g~~~~ll~aksrv~P~k~~tIpRlEL~a~~~~~~l~~~~~~~l~~~~~~  204 (493)
                      .++||||+|.      .|||++++.     +|.. ..+...     ....|-.|.||.|++.|++...        ....
T Consensus         3 ~i~iytDGs~~~N~g~~G~g~vi~~-----~~~~-~~~~~~-----~~~~Tnn~aEl~Ai~~AL~~~~--------~~~~   63 (147)
T d1rila_           3 RVALFTDGACLGNPGPGGWAALLRF-----HAHE-KLLSGG-----EACTTNNRMELKAAIEGLKALK--------EPCE   63 (147)
T ss_dssp             CCCEEEEEEESSTTEEEEEEEEECB-----TTBC-CEECCE-----EEEECHHHHHHHHHHHHHHSCC--------SCCE
T ss_pred             EEEEEEccCCCCCCCccEEEEEEEE-----CCcc-eEEecc-----cccccHHHHHHHHHHHHhhhcc--------CCce
Confidence            5789999884      356654321     2221 112111     1234889999999999976432        3357


Q ss_pred             EEEecchhhhHHHHhcC-----------CccChhhhHH--HHHHHHhcc--ccceEEecCC
Q psy17737        205 YYLWIDSQIVIHWILGN-----------KVLPTFINNR--VKEIKNRSF--KLDVHYVPTD  250 (493)
Q Consensus       205 ~~~~tDS~i~l~~l~~~-----------~~~~~fv~nR--v~~I~~~~~--~~~~~hv~~~  250 (493)
                      +.++|||..++.-+...           ..-...+.|+  +.+|.++..  .++|.||||-
T Consensus        64 i~i~tds~~~~~~~~~~~~~~~~~~~~~~~~~~~v~n~dL~~~l~~~~~~~~v~~~wVkgH  124 (147)
T d1rila_          64 VDLYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPHRVRFHFVKGH  124 (147)
T ss_dssp             EEEECCCHHHHHHHHSSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHTTSEEECCCCCGG
T ss_pred             EEEecchhhhhccccccchhhhhhccccccccccchhHHHHHHHHHHhhhcccceEEccCC
Confidence            88999999887544332           1122334553  445555443  4788999864

>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=96.62  E-value=0.00047  Score=57.78  Aligned_cols=70  Identities=21%  Similarity=0.206  Sum_probs=48.7

Q ss_pred             eecccccc------cceeeEEEEEeeCCCceeeeeecccccCCCCCCccchhhhhHHHHHhhhhHHHhhhhcccceeEEE
Q psy17737        134 GFSDASAT------SYSMVIYLKCITGNSVTSNLVFAKARIAPLSRPTLPRLELLGALIAYRGLKFVGESLKVKDIKYYL  207 (493)
Q Consensus       134 vF~DAS~~------a~gav~y~r~~~~~g~~~~ll~aksrv~P~k~~tIpRlEL~a~~~~~~l~~~~~~~l~~~~~~~~~  207 (493)
                      +|+|||..      |||+|+ .    .+|..  +.. .   .|....|=.|.||.|++.|++++..-       ..++.+
T Consensus         7 Iy~DGa~~GNPGp~g~g~v~-~----~~~~~--~~~-s---g~~~~~TNN~aEl~A~i~aL~~~~~~-------~~~i~I   68 (132)
T d1zbfa1           7 LSVDVGSQGNPGIVEYKGVD-T----KTGEV--LFE-R---EPIPIGTNNMGEFLAIVHGLRYLKER-------NSRKPI   68 (132)
T ss_dssp             EEEEEEECSSSEEEEEEEEE-T----TTCCE--EEE-C---CCEEEECHHHHHHHHHHHHHHHHHHT-------TCCCCE
T ss_pred             EEEeecCCCCCchheEEEEE-E----cCCEE--EEE-E---cCcCccchHHHHHHHHHHHHHHhhcC-------CceEEE
Confidence            68999886      588643 2    12321  111 1   13345688999999999999887531       135789


Q ss_pred             ecchhhhHHHHhcC
Q psy17737        208 WIDSQIVIHWILGN  221 (493)
Q Consensus       208 ~tDS~i~l~~l~~~  221 (493)
                      +|||+.++.|+++-
T Consensus        69 ~tDS~yvi~wv~~~   82 (132)
T d1zbfa1          69 YSNSQTAIKWVKDK   82 (132)
T ss_dssp             EESCHHHHHHHHHT
T ss_pred             EeccHHHHHHHHhC
Confidence            99999999999876

>d2zd1b1 e.8.1.2 (B:5-428) HIV-1 reverse transcriptase {Human immunodeficiency virus type 1 [TaxId: 11676]}

class: Multi-domain proteins (alpha and beta)
fold: DNA/RNA polymerases
superfamily: DNA/RNA polymerases
family: Reverse transcriptase
domain: HIV-1 reverse transcriptase
species: Human immunodeficiency virus type 1 [TaxId: 11676]

Probab=91.73  E-value=0.11  Score=51.43  Aligned_cols=117  Identities=10%  Similarity=0.019  Sum_probs=64.7

Q ss_pred             CCCCCcceEeEEEecCCCeEEEecCCccCCCCccHhHHHHhHhc--ccccCCCCcceee-cchhhhhhhh--hccCCCCc
Q psy17737         18 SCNKVQNVLGLTWDTDIDTLSIKHGELQCSGKLTKRLLLSVYGS--IYDVLGLFTPVVL-PLKILIQSVW--QRNLSWDE   92 (493)
Q Consensus        18 ~~~~~~k~LG~~W~~~~D~l~~~~~~~~~~~~~TkR~ilS~ias--~yDPLGl~~p~~l-~~K~llq~l~--~~~~~WD~   92 (493)
                      ....+.+.||+.-..  +.+++....++...+.|.+++-++++.  +|-..  +..+.+ +.-.+|+.+-  ...+.|+ 
T Consensus       218 f~~~~v~~LG~~is~--~gi~~~~~kl~~~~p~t~kelq~fLG~~n~~r~f--Ip~~s~~~L~~ll~~~~~~~~~~~Wt-  292 (424)
T d2zd1b1         218 QKEPPFLWMGYELHP--DKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQI--YPGIKVRQLSKLLRGTKALTEVIPLT-  292 (424)
T ss_dssp             -----CTTCCEEECG--GGCCCCCCCCCCCSSEEHHHHHHHHHHHHHHTTT--CTTCCCHHHHHTTCSCCCTTCEECCC-
T ss_pred             hhhcccccceeeecC--CcEeCCHHHhccccCCCHHHHHHHHHHHHHHHHh--cccchHHHHHHHhhhhccCCCCccCC-
Confidence            345567899998665  444443333344677899999888763  22211  111111 1111121111  1124454 


Q ss_pred             cCChhHHHHHHHHHHHHhcccceeceeEEeccCCCCceeEEeecccccccceeeEEEEEe
Q psy17737         93 ELSTEDKITFMKLIEDIKLIHTVHIPRLIGNLIPGTQYELHGFSDASATSYSMVIYLKCI  152 (493)
Q Consensus        93 ~i~~e~~~~w~~~~~~l~~~~~~~iPR~~~~~~~~~~~~L~vF~DAS~~a~gav~y~r~~  152 (493)
                         ++..++++++.+.+.+...+..|+        ...+|.+.+|||  |+|++.|+..+
T Consensus       293 ---~e~~~af~~lK~~l~~~p~L~~~D--------p~kp~~~~~das--~~g~~~~~~~q  339 (424)
T d2zd1b1         293 ---EEAELELAENREILKEPVHGVYYD--------PSKDLIAEIQKQ--GQGQWTYQIYQ  339 (424)
T ss_dssp             ---HHHHHHHHHHHHHTTSCCTTCCCC--------TTSCCEEEEEEE--ETTEEEEEEES
T ss_pred             ---HHHHHHHHHHHHHhcccccccCCC--------CCCCEEEEEecC--CCCceEEEEEc
Confidence               588999999999998753333222        226899999999  56666787764

>d1mu2a2 e.8.1.2 (A:3-429) HIV-1 reverse transcriptase {Human immunodeficiency virus type 2 [TaxId: 11709]}

class: Multi-domain proteins (alpha and beta)
fold: DNA/RNA polymerases
superfamily: DNA/RNA polymerases
family: Reverse transcriptase
domain: HIV-1 reverse transcriptase
species: Human immunodeficiency virus type 2 [TaxId: 11709]

Probab=84.77  E-value=1.4  Score=43.14  Aligned_cols=139  Identities=13%  Similarity=0.078  Sum_probs=77.4

Q ss_pred             CCCCCcceEeEEEecCCCeEEEecCCccCCCCccHhHHHHhHhc-----ccccCCCCc-ceeecchhhhhhhhh--ccCC
Q psy17737         18 SCNKVQNVLGLTWDTDIDTLSIKHGELQCSGKLTKRLLLSVYGS-----IYDVLGLFT-PVVLPLKILIQSVWQ--RNLS   89 (493)
Q Consensus        18 ~~~~~~k~LG~~W~~~~D~l~~~~~~~~~~~~~TkR~ilS~ias-----~yDPLGl~~-p~~l~~K~llq~l~~--~~~~   89 (493)
                      ....+.+.||+.-.  .|.+.+....++...+.|+.++-++++.     -|=| |+-. ++   ++ .|+.+-.  ..+.
T Consensus       220 ~~~~~v~~LG~~i~--~~~~k~~~i~l~~~~p~tvkelq~fLG~~n~~r~fIp-~~~~~~l---~~-pL~~~~~~~~~~~  292 (427)
T d1mu2a2         220 QKDPPYHWMGYELW--PTKWKLQKIQLPQKEIWTVNDIQKLVGVLNWAAQLYP-GIKTKHL---CR-LISGKMTLTEEVQ  292 (427)
T ss_dssp             ECSSSEEETTEEEC--SSEEEECCCCCCCCSSCBHHHHHHHHHHHHHHHHHST-TCCCHHH---HT-TSCSSSCTTCBCC
T ss_pred             hceeeeeeeeeEec--CCccccCccccCCCCCCCHHHHHHHhhHHHHHHHhhC-CCchhhH---HH-HHHhhhcCCCCcc
Confidence            44567899999854  4666665433344567799988888752     2222 2110 11   11 1222211  2455


Q ss_pred             CCccCChhHHHHHHHHHHHHhcccceeceeEEeccCCCCceeEEeecccccccc-eeeEEEEEeeCCCceeeeeeccccc
Q psy17737         90 WDEELSTEDKITFMKLIEDIKLIHTVHIPRLIGNLIPGTQYELHGFSDASATSY-SMVIYLKCITGNSVTSNLVFAKARI  168 (493)
Q Consensus        90 WD~~i~~e~~~~w~~~~~~l~~~~~~~iPR~~~~~~~~~~~~L~vF~DAS~~a~-gav~y~r~~~~~g~~~~ll~aksrv  168 (493)
                      |.+    +..+++++..+.|.+......|.        ....|.+.+|+|..|. +.++|.     ++...  -.++  .
T Consensus       293 Wt~----e~q~afe~lK~~L~~~~~l~~~d--------p~kpl~~~i~~~~~~~~~~~~~q-----~~~~l--~~~~--~  351 (427)
T d1mu2a2         293 WTE----LAEAELEENRIILSQEQEGHYYQ--------EEKELEATVQKDQDNQWTYKIHQ-----EEKIL--KVGK--Y  351 (427)
T ss_dssp             CCH----HHHHHHHHHHHHHSCCEEEECBC--------TTSCCEEEEEECSSSCEEEEEEE-----TTEEE--EEEE--E
T ss_pred             CCH----HHHHHHHHHHHHhccCcccccCC--------CCCCEEEEEEcCCCCcEEEEEEc-----cCCce--eeee--e
Confidence            654    88999999999998753322222        2257888999997665 434432     23222  1122  1


Q ss_pred             CCCCCCccchhhhhHH
Q psy17737        169 APLSRPTLPRLELLGA  184 (493)
Q Consensus       169 ~P~k~~tIpRlEL~a~  184 (493)
                      +-.+..+.+-+|++|.
T Consensus       352 ~~~~~~~~~~~~~l~~  367 (427)
T d1mu2a2         352 AKVKNTHTNGIRLLAQ  367 (427)
T ss_dssp             CCC--CEECHHHHHHH
T ss_pred             cccccccCCHHHHHHH
Confidence            2234666788888775

>d1k6ya1 a.4.10.1 (A:1-46) N-terminal Zn binding domain of HIV integrase {Human immunodeficiency virus type 1 [TaxId: 11676]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: N-terminal Zn binding domain of HIV integrase
family: N-terminal Zn binding domain of HIV integrase
domain: N-terminal Zn binding domain of HIV integrase
species: Human immunodeficiency virus type 1 [TaxId: 11676]

Probab=82.37  E-value=0.36  Score=32.01  Aligned_cols=37  Identities=11%  Similarity=0.188  Sum_probs=29.4

Q ss_pred             HHHHHHhCCCCChhhhhHHHHHHhhhc-cccchHHHHHhcCCccccc
Q psy17737        443 VNDIHTSGYHTGDKESKKLSNVARGYY-LDGNHLERRVLLGSRLLSG  488 (493)
Q Consensus       443 i~~~H~~~~H~G~~~t~~l~~lr~~yW-~~~r~~vr~vi~~C~~C~r  488 (493)
                      ..+.|+. .|.+.+.+      +++|= |+  ..+|.++..|..||.
T Consensus         8 Aqe~H~k-~H~n~~~L------~~~F~ip~--~vAr~IV~~C~~Cq~   45 (46)
T d1k6ya1           8 AQEEHEK-YHSNWRAM------ASDFNLPP--VVAKEIVASCDKCQL   45 (46)
T ss_dssp             HHHHHHH-HCCCHHHH------HHHHTCCH--HHHHHHHHHCTTCCC
T ss_pred             HHHHHHH-HhcCHHHH------HHHcCCCH--HHHHHHHHHHHHhcC
Confidence            4667887 88886654      77888 74  688999999999985