Psyllid ID: psy556

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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-----
Protein Sequence
MGRRIAVKCNNLISNFKGLENGLVQGSSLSTLLFAVFMNDIFHVINLPTRGLLFVDDLLLTIRGKILEQLGSRNPTLPLIMLNGNQLKFDNTAKFLGLIWDRKMSWKQHVKYTKIKALTALNALKIVMLDYGSPIYGSAKDHVIAKLNTEHHIGIRIVTGALRTSPVPSLYVESGIPPLVIRRQKLLLNYVTKISACPSNPVYNILFPTSLRRRLGIYEFTRTPKPLFVRFRAIEAYVQELDRCDMMEYKDLTPPWSDDMSEVIDLWRNLTSNNIKLTFIWCPSHCGIEGNEEVDRAANRDGHTQAINICSPDDLKTMVKKLAYNNWQVLWNQTDPLNKLKQIKPIISTWKTSQQSRRYDEVVLSRLRIGHTRVTHSYLFERTTPPLCSCGENLLTVKHLLDCVHHAPVRSTLSSKPSLLDEPEGVKATNANVKK
Secondary Structure (PSIPRED)
cccEEEEEEccEEccEEEcccccccccccHHHHHHHHHHHHHHcccccccEEEEEcHHHHHHHHHHHHHccccccccccccccccEEccccccccccEEEcccccHHHHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHccccHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccHHHHHHHccccccccccccccccccccHHHHHHHHccccccccccEEEcccccccccHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccEEEEEEHHccccccccccccccccccccccccccccccEEccccccHHHHHHHcccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccEEEEEEcccccccccccccccccccHHHHHHHHHHHHHHHHccccccEEEEEccHHHHHccccHHHHHHccccccEEEccccEccccccEEEEEEEEccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHccccHHHHHHHHHHHHHHHHHHcccccHHHHccccHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHcccccccccccccccHHHHHHHHHHHcccccEEEEEEEcccccccccHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccEEEEHEHEcccccHHHHHHHccccccccccccccEEEEEEEccHHHHHHHHHHHcccccccHHcccccccccccc
Coil and Loop (DISEMBL)
MGRRIAVKCNNLISNFKGlenglvqgsSLSTLLFAVFMNDIfhvinlptrgllfvDDLLLTIRGKILEqlgsrnptlplimlngnqlkfdnTAKFLGLIWDRKMSWKQHVKYTKIKALTALNALKIVMLDygspiygsaKDHVIAKLNtehhigirivtgalrtspvpslyvesgipplvIRRQKLLLNYVTkisacpsnpvynilfptslrrrlgiyeftrtpkplfVRFRAIEAYVQEldrcdmmeykdltppwsddmSEVIDLWRNLTsnnikltfiwcpshcgiegneevdraanrdghtqainicspDDLKTMVKKLAYNNWQVLwnqtdplnklkqikpiistwktsqqsrrydEVVLSRLRightrvthsylferttpplcscgenllTVKHLLDcvhhapvrstlsskpslldepegvkatnanvkk
Flexible Loop (DISEMBL)
MGRRIAVKCNNLISNFKGLENGLVQGSSLSTLLFAVFMNDIFHVINLPTRGLLFVDDLLLTIRGKILeqlgsrnptlPLIMLNGNQLKFDNTAKFLGLIWDRKMSWKQHVKYTKIKALTALNALKIVMLDYGSPIYGSAKDHVIAKLNTEHHIGIRIVTGALRTSPVPSLYVESGIPPLVIRRQKLLLNYVTkisacpsnpvyniLFPTSLRRRLGIYEFtrtpkplfvrfRAIEAYVQELDRCDMMEYKDLTPPWSDDMSEVIDLWRNLTSNNIKLTFIWCPSHCGIEGNEEVDRAANRDGHTQAINICSPDDLKTMVKKLAYNNWQVLWNQTDPLNKLKQIKPiistwktsqqsrrydEVVLSRLRightrvthsylferttpplcSCGENLLTVKHLLDCVHHAPvrstlsskpslldepegvkatnanvkk
Low Complexity Region (SEG)
MGRRIAVKCNNLISNFKGLENGLVQGSSLSTLLFAVFMNDIFHVINLPTRGLLFVDDLLLTIRGKILEQLGSRNPTLPLIMLNGNQLKFDNTAKFLGLIWDRKMSWKQHVKYTKIKALTALNALKIVMLDYGSPIYGSAKDHVIAKLNTEHHIGIRIVTGALRTSPVPSLYVESGIPPLVIRRQKLLLNYVTKISACPSNPVYNILFPTSLRRRLGIYEFTRTPKPLFVRFRAIEAYVQELDRCDMMEYKDLTPPWSDDMSEVIDLWRNLTSNNIKLTFIWCPSHCGIEGNEEVDRAANRDGHTQAINICSPDDLKTMVKKLAYNNWQVLWNQTDPLNKLKQIKPIISTWKTSQQSRRYDEVVLSRLRIGHTRVTHSYLFERTTPPLCSCGENLLTVKHLLDCVHHAPVRSTLSSKPSLLDEPEGVKATNANVKK
Disordered region (IsUnstruct)
****IAVKCNNLISNFKGLENGLVQGSSLSTLLFAVFMNDIFHVINLPTRGLLFVDDLLLTIRGKILEQLGSRNPTLPLIMLNGNQLKFDNTAKFLGLIWDRKMSWKQHVKYTKIKALTALNALKIVMLDYGSPIYGSAKDHVIAKLNTEHHIGIRIVTGALRTSPVPSLYVESGIPPLVIRRQKLLLNYVTKISACPSNPVYNILFPTSLRRRLGIYEFTRTPKPLFVRFRAIEAYVQELDRCDMMEYKDLTPPWSDDMSEVIDLWRNLTSNNIKLTFIWCPSHCGIEGNEEVDRAANRDGHTQAINICSPDDLKTMVKKLAYNNWQVLWNQTDPLNKLKQIKPIISTWKTSQQSRRYDEVVLSRLRIGHTRVTHSYLFERTTPPLCSCGENLLTVKHLLDCVHHAPV**************************
Disordered Region (DISOPRED)
MGRRIAVKCNNLISNFKGLENGLVQGSSLSTLLFAVFMNDIFHVINLPTRGLLFVDDLLLTIRGKILEQLGSRNPTLPLIMLNGNQLKFDNTAKFLGLIWDRKMSWKQHVKYTKIKALTALNALKIVMLDYGSPIYGSAKDHVIAKLNTEHHIGIRIVTGALRTSPVPSLYVESGIPPLVIRRQKLLLNYVTKISACPSNPVYNILFPTSLRRRLGIYEFTRTPKPLFVRFRAIEAYVQELDRCDMMEYKDLTPPWSDDMSEVIDLWRNLTSNNIKLTFIWCPSHCGIEGNEEVDRAANRDGHTQAINICSPDDLKTMVKKLAYNNWQVLWNQTDPLNKLKQIKPIISTWKTSQQSRRYDEVVLSRLRIGHTRVTHSYLFERTTPPLCSCGENLLTVKHLLDCVHHAPVRSTLSS********************
Disordered Region (DISEMBL)
MGRRIAVKCNNLISNFKGLENGLVQGSSLSTLLFAVFMNDIFHVINLPTRGLLFVDDLLLTIRGKILEQLGSRNPTLPLIMLNGNQLKFDNTAKFLGLIWDRKMSWKQHVKYTKIKALTALNALKIVMLDYGSPIYGSAKDHVIAKLNTEHHIGIRIVTGALRTSPVPSLYVESGIPPLVIRRQKLLLNYVTKISACPSNPVYNILFPTSLRRRLGIYEFTRTPKPLFVRFRAIEAYVQELDRCDMMEYKDLTPPWSDDMSEVIDLWRNLTSNNIKLTFIWCPSHCGIEGNEEVDRAANRDGHTQAINICSPDDLKTMVKKLAYNNWQVLWNQTDPLNKLKQIKPIISTW********YDEVVLSRLRIGHTRVTHSYLFERTTPPLCSCGENLLTVKHLLDCVHHAPVRSTLSSKPSLLDEPEGVKATNANVKK
Disordered Region (DISPRO)
*GRRIAVKCNNLISNFKGLENGLVQGSSLSTLLFAVFMNDIFHVINLPTRGLLFVDDLLLTIRGKILEQLGSRNPTLPLIMLNGNQLKFDNTAKFLGLIWDRKMSWKQHVKYTKIKALTALNALKIVMLDYGSPIYGSAKDHVIAKLNTEHHIGIRIVTGALRTSPVPSLYVESGIPPLVIRRQKLLLNYVTKISACPSNPVYNILFPTSLRRRLGIYEFTRTPKPLFVRFRAIEAYVQELDRCDMMEYKDLTPPWSDDMSEVIDLWRNLTSNNIKLTFIWCPSHCGIEGNEEVDRAANRDGHTQAINICSPDDLKTMVKKLAYNNWQVLWNQTDPLNKLKQIKPIISTWKTSQQSRRYDEVVLSRLRIGHTRVTHSYLFERTTPPLCSCGENLLTVKHLLDCVHHAPVRSTLSSKPSLLD**************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGRRIAVKCNNLISNFKGLENGLVQGSSLSTLLFAVFMNDIFHVINLPTRGLLFVDDLLLTIRGKILEQLGSRNPTLPLIMLNGNQLKFDNTAKFLGLIWDRKMSWKQHVKYTKIKALTALNALKIVMLDYGSPIYGSAKDHVIAKLNTEHHIGIRIVTGALRTSPVPSLYVESGIPPLVIRRQKLLLNYVTKISACPSNPVYNILFPTSLRRRLGIYEFTRTPKPLFVRFRAIEAYVQELDRCDMMEYKDLTPPWSDDMSEVIDLWRNLTSNNIKLTFIWCPSHCGIEGNEEVDRAANRDGHTQAINICSPDDLKTMVKKLAYNNWQVLWNQTDPLNKLKQIKPIISTWKTSQQSRRYDEVVLSRLRIGHTRVTHSYLFERTTPPLCSCGENLLTVKHLLDCVHHAPVRSTLSSKPSLLDEPEGVKATNANVKK
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

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	435	2.2.26 [Sep-21-2011]
Q9NBX4	908	Probable RNA-directed DNA	no	N/A	0.360	0.172	0.233	0.0005

>sp|Q9NBX4|RTXE_DROME Probable RNA-directed DNA polymerase from transposon X-element OS=Drosophila melanogaster GN=X-element\ORF2 PE=3 SV=1

 Score = 46.2 bits (108), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 51/218 (23%), Positives = 89/218 (40%), Gaps = 61/218 (27%)

Query: 2   GRRIAVKCNNLISNFKGLENGLVQGSSLSTLLFAVFMNDIFHV-INLPTRGLL--FVDDL 58
           GRR AV+ ++ IS    +  G+ QGS L  LL+ ++ +D+    ++L  + +L  F DD+
Sbjct: 619 GRRFAVRFHSAISTEHNVAAGVPQGSVLGPLLYCLYSHDMPQPDVSLYGKSMLATFADDV 678

Query: 59  LLTIRGK----------------------------------ILEQLGSRNPTLPLIMLNG 84
            +T R +                                  +   L  R P  P + +  
Sbjct: 679 CVTYRSRCEHDAADGIQDFAYRFSEWARRWNIGINSSKSNNVCFTLKRRTP--PPVYIEE 736

Query: 85  NQLKFDNTAKFLGLIWDRKMSWKQHVK--YTKIKALTA--------------LNALKIVM 128
             +   N AK+LG++ DR++++ +HV    T+++A  A               N L I  
Sbjct: 737 VPVPQPNAAKYLGVLLDRRLTFSKHVTDIRTRLRAKVAKHYWLLSSRSKLSLSNKLTIYK 796

Query: 129 ------LDYGSPIYGSAKDHVIAKLNTEHHIGIRIVTG 160
                   YG  I+G A D  I ++    +   R++TG
Sbjct: 797 QILAPNWKYGCQIWGLACDSHIKRIQAIQNKVARLITG 834

Drosophila melanogaster (taxid: 7227)
EC: 2EC: .EC: 7EC: .EC: 7EC: .EC: 4EC: 9

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	435
189242251	1808	PREDICTED: similar to pol-like protein [	0.777	0.186	0.298	4e-30
427791807	1212	Putative tick transposon, partial [Rhipi	0.622	0.223	0.315	4e-28
427791981	1060	Putative tick transposon, partial [Rhipi	0.521	0.214	0.305	4e-25
125901787	1222	pol-like protein [Biomphalaria glabrata]	0.565	0.201	0.294	2e-23
427792011	1121	Putative tick transposon, partial [Rhipi	0.577	0.223	0.288	2e-22
427791321	1210	Putative tick transposon, partial [Rhipi	0.450	0.161	0.339	2e-22
427791063	1035	Putative tick transposon, partial [Rhipi	0.595	0.250	0.297	5e-22
427778603	1397	Putative tick transposon [Rhipicephalus	0.595	0.185	0.290	1e-21
443693558	502	hypothetical protein CAPTEDRAFT_189741,	0.342	0.296	0.401	4e-21
443712830	397	hypothetical protein CAPTEDRAFT_202466 [	0.342	0.375	0.401	1e-20

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

 Score =  139 bits (349), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 116/388 (29%), Positives = 180/388 (46%), Gaps = 50/388 (12%)

Query: 52   LLFVDDLLLTIRGKILEQLGSRNPTLPLIMLNGNQLKFDNTAKFLGLIWDRKMSWKQHVK 111
            L F+ + L   +  I  +     P  P I L    L F +  K+LG+I+D K++W+ H+ 
Sbjct: 1101 LAFIKNFLKKTKCVIFSKRKKIQP--PEITLYHKILSFCDEIKYLGIIFDSKLNWQNHIT 1158

Query: 112  YTKIKALTALNALKIVM----------------------LDYGSPIYGSAKDHVIAKLNT 149
            Y + +    +  LK+++                      LDYG+  Y SAK H++ KLN 
Sbjct: 1159 YLRKECCNRIRLLKMLVHQHWGADTTILLRLYKILIRSKLDYGATAYASAKPHILNKLNP 1218

Query: 150  EHHIGIRIVTGALRTSPVPSLYVESGIPPLVIRRQKLLLNYVTKISACPSNPVYNILFPT 209
              +  IR   GA  T+PV SLY  S IP L  RR +L+L Y  KISA  +NP +N++FP 
Sbjct: 1219 IQNTSIRTALGAYCTTPVESLYALSDIPSLEARRSELILRYAAKISANKTNPAHNMMFPN 1278

Query: 210  SLRRRLGIYEFTRTPKPLFVRFRAIEAYVQELDRCDMMEY---KDLTPPWSDDMSEVIDL 266
               R+  +  F+R  K     +R I+     L+    + Y   +  TPPW+ +   V   
Sbjct: 1279 ---RKEDL--FSRKVKLTPPAYRRIKIASVNLNLSLPITYPFQRSKTPPWTYNKPRVHTE 1333

Query: 267  WRNLTSNNIKLTFIWCPSHCGIEGNEEVDRAANRDGHTQAINICSPDDLKTMVKKLAY-- 324
              NL  +         P    ++      + A       +  I   D  K+     AY  
Sbjct: 1334 LLNLVKDK--------PLKSVLKT-----KLAALLTSISSNYIFYTDASKSDTVGAAYVT 1380

Query: 325  NNWQVLWNQTDPLNKLKQIKPIISTWKTSQQSRRYDEVVLSRLRIGHTRVTHSYLFERTT 384
            N+ Q  + +  P +KL++  P I  W  S   +R +EV ++RLR+GHTR+T  Y  ++  
Sbjct: 1381 NDTQQAF-RLSPESKLREAYPDIKKWPPSNL-KRGEEVTINRLRLGHTRLTQEYHLKKVD 1438

Query: 385  PPLCSCGENLLTVKH-LLDCVHHAPVRS 411
            PP C   E  LTV+H LL+C  +  +R+
Sbjct: 1439 PPTCCYCEGRLTVRHILLECPKYHDIRN 1466

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  132 bits (332), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 105/333 (31%), Positives = 153/333 (45%), Gaps = 62/333 (18%)

Query: 3   RRIAVKCNNLISNFKGLENGLVQGSSLSTLLFAVFMNDIFHVINLPTRGLLFVDDLLLTI 62
           R   V+   ++S     ENG+ QG  LST LF V MN I  VI       ++VDDL +  
Sbjct: 593 RTFQVRLGTVLSRIFVQENGVPQGCILSTTLFIVKMNSINKVIPPTVMHSIYVDDLQIAC 652

Query: 63  RGKIL------------------EQLGSRNPTL----------------PLIMLNGNQLK 88
           R   L                  +Q G R  T                 P + LN   L 
Sbjct: 653 RASSLSSCERQLQITINKLTKWADQNGFRFSTQKTTAVLFTQKRGLFPDPALKLNNIDLP 712

Query: 89  FDNTAKFLGLIWDRKMSWKQHVKYTKIKALTALNALKIV--------------------- 127
                KFLG+ +D+K+++  H+   K+KA  ALN LK++                     
Sbjct: 713 VKREYKFLGVTFDQKLNFLSHINALKVKANKALNLLKVLSHKHWGSDRLCLLRIYRSIVR 772

Query: 128 -MLDYGSPIYGSAKDHVIAKLNTEHHIGIRIVTGALRTSPVPSLYVESGIPPLVIRRQKL 186
            +LDYG  +YGSA++  I +L+  H++G+R+ +GA RTSPV SLYV+   PPL  RR  L
Sbjct: 773 SILDYGCVVYGSARESYIRRLDPVHNLGLRLSSGAYRTSPVESLYVDCNEPPLSHRRASL 832

Query: 187 LLNYVTKISACPSNPVYNILFPTSLRRRLGIYEFTRTPKPLFVRFRA-IEAYVQELDRCD 245
            L+YV +I + P +  Y+I   T    RL     +   KPL +RF      YV   +  D
Sbjct: 833 TLSYVLRIRSSPQHICYDI--ATRCSSRLHYLNKSNLIKPLLLRFEEYCRTYVISEETLD 890

Query: 246 MMEYKDLTPPWSDDMSEVIDLWRNLTSNNIKLT 278
           +       PPW  D++++ D+  +L+  N K+T
Sbjct: 891 VARKPPRIPPWF-DLAQLCDI--SLSHINKKVT 920

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  122 bits (305), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 95/311 (30%), Positives = 135/311 (43%), Gaps = 84/311 (27%)

Query: 3   RRIAVKCNNLISNFKGLENGLVQGSSLSTLLFAVFMNDIFHVINLPTRGLLFVDDLLLTI 62
           R   V+  +++S+    ENG+ QG  LST LF V MN +  VI       L+VDDL +  
Sbjct: 613 RTFQVRLGSILSHPVTQENGVPQGCILSTTLFVVKMNSVNQVIPSTLMHSLYVDDLQIAC 672

Query: 63  RGK--------------ILEQLGSRNPTL--------------------PLIMLNGNQLK 88
           R                 L Q  ++N                       P++ LN   L 
Sbjct: 673 RSSNMATCERQIQIALNKLTQWANKNGFRFSEEKTVAVAFSQKRGLQPDPVLKLNETLLP 732

Query: 89  FDNTAKFLGLIWDRKMSWKQHVKYTKIKALTALNALKIV--------------------- 127
             +  KFLG+I+D+K+++  H+   KIKA  ALN LK++                     
Sbjct: 733 IQHEQKFLGVIFDKKLNFLSHINKLKIKANKALNVLKVLSRKRWGSDXXKLKVKANKALN 792

Query: 128 ---------------------------MLDYGSPIYGSAKDHVIAKLNTEHHIGIRIVTG 160
                                       LDYGS IYGSA+D  + +L+  H+ G+R+ TG
Sbjct: 793 VLKVLSRKRWGSDRKCLLHIYRSLVRSKLDYGSIIYGSARDSYLKRLDPVHNKGLRLATG 852

Query: 161 ALRTSPVPSLYVESGIPPLVIRRQKLLLNYVTKISACPSNPVYNILFPTSLRRRLGIYEF 220
           A RTSP+PSLY ES  P L  RR +L+  YV K+ + P +  Y+I+  T   +RL     
Sbjct: 853 AYRTSPIPSLYAESNEPSLEYRRTQLMFTYVLKVRSSPDHICYSIV--TRSDQRLHYANK 910

Query: 221 TRTPKPLFVRF 231
               KPL +RF
Sbjct: 911 PNAIKPLILRF 921

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  116 bits (291), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 93/316 (29%), Positives = 142/316 (44%), Gaps = 70/316 (22%)

Query: 3   RRIAVKCNNLISNFKGLENGLVQGSSLSTLLFAVFMNDIFHVINLPTRGLLFVDDLLLTI 62
           R+  V+  N  S+    E G+ QGS LS  LF + +N I + ++      L+VDD ++  
Sbjct: 611 RKFQVRVGNSASDTHDQEMGVPQGSILSVTLFNIKINSIINALSPGIECSLYVDDFVILT 670

Query: 63  RGKILEQLGSRNPTLPLIMLNG----NQLKFDN--------------------------- 91
            GK +  L  R   L L  + G    N  KF +                           
Sbjct: 671 YGKNMNTL-ERKLQLCLNKIQGWANYNGFKFSDSKTVSMHFCNLRGLHPDPELFIHKKKI 729

Query: 92  ----TAKFLGLIWDRKMSWKQHVKYTKIKALTALNALKIV-------------------- 127
               T KFLGL  D K ++  H+K  K K   +LN L+++                    
Sbjct: 730 PVVKTTKFLGLTLDSKFNFLPHIKELKKKCQKSLNILRVLSHTDWGADRDTLLLLYRSLI 789

Query: 128 --MLDYGSPIYGSAKDHVIAKLNTEHHIGIRIVTGALRTSPVPSLYVESGIPPLVIRRQK 185
              LDYGS IYG+A+   +  L    +  +R+  GA RTSP+PSL+VE+G  P+ IR +K
Sbjct: 790 RSKLDYGSIIYGAARKSYLKILEPIQNAALRLCLGAFRTSPIPSLHVEAGELPMDIRMKK 849

Query: 186 LLLNYVTKISACPSNPVYNILF-PTSLRRRLGIYEFTRTP---KPLFVRFRA-IEAYVQE 240
           L + Y+ K+ + P+NP ++ +F PT       +  + R P   +PL +R R  I+   Q 
Sbjct: 850 LAMQYIVKLKSNPTNPAFDSIFNPTE------VELYNRRPNVIQPLGLRMREPIQNLTQP 903

Query: 241 LDRCDMMEYKDLTPPW 256
           +D+   +E     PPW
Sbjct: 904 IDQISKIETPQ-NPPW 918

Source: Biomphalaria glabrata

Species: Biomphalaria glabrata

Genus: Biomphalaria

Family: Planorbidae

Class: Gastropoda

Phylum: Mollusca

Superkingdom: Eukaryota

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

 Score =  113 bits (283), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 90/312 (28%), Positives = 137/312 (43%), Gaps = 61/312 (19%)

Query: 3   RRIAVKCNNLISNFKGLENGLVQGSSLSTLLFAVFMNDIFHVINLPTRGLLFVDDLLLTI 62
           R+  V+    +S     ENG+ QG  LS  LF V MN +   +       ++VDD+ ++ 
Sbjct: 611 RKFRVRVGTALSKTYIQENGVPQGGVLSCTLFIVKMNSLRTALPPTISYSVYVDDVQVSF 670

Query: 63  RG---KILE---QLGSRNPT----------------------------LPLIMLNGNQLK 88
           R     I E   QLG    +                             P I +NG+ + 
Sbjct: 671 RSCNLSICERQIQLGVNRLSKWANENGFAVNVDKTVCVLFNKCKGVRPAPCIKINGSPIC 730

Query: 89  FDNTAKFLGLIWDRKMSWKQHVKYTKIKALTALNALKIVM-------------------- 128
             N  KFLGLI+D +MS+  H+K  K+K L  +N LK++                     
Sbjct: 731 VKNEHKFLGLIFDNRMSFIPHIKALKLKCLQTMNLLKLLSRPSWGTDKKCLMSLFNSLIK 790

Query: 129 --LDYGSPIYGSAKDHVIAKLNTEHHIGIRIVTGALRTSPVPSLYVESGIPPLVIRRQKL 186
             L+YG  +Y SA    +  L+  +H+GIR+ TGA RTSPV SLYVE+   P+ + R+  
Sbjct: 791 SRLNYGCIVYQSASKTAVKMLDPVYHLGIRLATGAFRTSPVSSLYVEANEWPMQLEREYC 850

Query: 187 LLNYVTKISACPSNPVYNILFPTSLRRRLGIYEFTRTPKPLFVRFRAIEAYV--QELDRC 244
            L Y  K+++ P++P   ++  TS  R          P  L     A +A +  Q++ + 
Sbjct: 851 TLMYTLKVTSIPTHPCAKLVADTSALRFFEKRPSLSKPFSLTCTATAAQAEIPLQQVAKA 910

Query: 245 DMMEYKDLTPPW 256
             ME+    PPW
Sbjct: 911 PSMEW---LPPW 919

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  113 bits (283), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 76/224 (33%), Positives = 116/224 (51%), Gaps = 28/224 (12%)

Query: 78  PLIMLNGNQLKFDNTAKFLGLIWDRKMSWKQHVKYTKIKALTALNALKIV---------- 127
           P + LN   L      KFLG+ +D+K+++  H+   K+KA  ALN LK++          
Sbjct: 699 PALKLNNIGLPVKREYKFLGVTFDQKLNFLSHINALKVKANKALNLLKVLSHKHWGSDRL 758

Query: 128 ------------MLDYGSPIYGSAKDHVIAKLNTEHHIGIRIVTGALRTSPVPSLYVESG 175
                       +LDYG  +YGSA++  I +L+  H++G+R+ +GA RTSPV SLYV+  
Sbjct: 759 CLLRIYRSIVRSILDYGCVVYGSARESYIRRLDPVHNLGLRLSSGAYRTSPVESLYVDCN 818

Query: 176 IPPLVIRRQKLLLNYVTKISACPSNPVYNILFPTSLRRRLGIYEFTRTPKPLFVRFRA-I 234
            PPL  RR  L L+YV +I + P +  Y+I   T    RL     +   KPL +RF    
Sbjct: 819 EPPLSHRRASLTLSYVLRIRSSPQHICYDI--ATRCSSRLHYLNKSNLIKPLLLRFEEYC 876

Query: 235 EAYVQELDRCDMMEYKDLTPPWSDDMSEVIDLWRNLTSNNIKLT 278
             YV   +  D+       PPW  D++++ D+  +L+  N K+T
Sbjct: 877 RTYVISEETLDVARKPPRIPPWF-DLAQLCDI--SLSHINKKVT 917

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  112 bits (279), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 94/316 (29%), Positives = 135/316 (42%), Gaps = 57/316 (18%)

Query: 3   RRIAVKCNNLISNFKGLENGLVQGSSLSTLLFAVFMNDIFHVINLPTRGLLFVDDLLLTI 62
           R   V+  N++S     E G+ QG  LS  LF V MN +  VI+      ++VDD+ +  
Sbjct: 451 RTFRVRVANVLSKLFTQETGVPQGGVLSCTLFIVKMNSLRAVISPAMFYCVYVDDVQIGF 510

Query: 63  RG------------------KILEQLGSR-NP---------------TLPLIMLNGNQLK 88
           +                   K   + G + NP               + P + L+G  ++
Sbjct: 511 KSCNISSCERQVQLALNKVSKWANENGFKINPLKSSCVLFNRKRGLVSDPQVNLDGQHIQ 570

Query: 89  FDNTAKFLGLIWDRKMSWKQHVKYTKIKALTALNALKIVM-------------------- 128
            +N  KFLG+I D K+S+  H+KY K K L  +N LKI+                     
Sbjct: 571 INNEHKFLGVILDSKLSFIPHIKYLKTKCLKTMNILKILSHTTWGSDRKCLMDIYKSLVR 630

Query: 129 --LDYGSPIYGSAKDHVIAKLNTEHHIGIRIVTGALRTSPVPSLYVESGIPPLVIRRQKL 186
             LDYGS +Y SA    +  L+  HH+GIR+ TGA RTSPV SLYVES    L ++R  +
Sbjct: 631 TRLDYGSVVYHSAAPSALKILDPIHHLGIRLATGAFRTSPVQSLYVESNQWSLHLQRSYM 690

Query: 187 LLNYVTKISACPSNPVYNILFPTSLRRRLGIYEFTRTPKPLFVRFRAIEAYVQELDRCDM 246
              Y  K+ A   +P ++ +   S           R P  L VR  A E  +  L    +
Sbjct: 691 SFVYFLKVKAEKEHPAHSTVNDLSSSVLYHNRPSVRQPYSLRVRDLAEEMGL-SLHEHSL 749

Query: 247 MEYKDLTPPWSDDMSE 262
           M      PPW   + E
Sbjct: 750 MARAAYLPPWQWQLIE 765

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  110 bits (275), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 92/317 (29%), Positives = 142/317 (44%), Gaps = 58/317 (18%)

Query: 3    RRIAVKCNNLISNFKGLENGLVQGSSLSTLLFAVFMNDIFHVINLPTRGLLFVDDLLLTI 62
            R+  V+  +++S     ENG+ QG  LS  LF V MN +  VI       ++VDD+ ++ 
Sbjct: 710  RKFRVRIGSVLSRSFIQENGVPQGGVLSCTLFIVKMNSLRSVIPPAISYSVYVDDIQISF 769

Query: 63   RG---KILE---QLG-------------------------SRNPTL---PLIMLNGNQLK 88
            +     I E   QLG                         SR   +   P I++NG  L 
Sbjct: 770  KSCNLTICERQIQLGVNRLAKWADENGFKINTEKTTCVLFSRRRGIHPDPCILMNGESLV 829

Query: 89   FDNTAKFLGLIWDRKMSWKQHVKYTKIKALTALNALKIV--------------------- 127
                 KFLG+I+D K+++ QH+K  K+K L  +N LKI+                     
Sbjct: 830  IAKEQKFLGVIFDAKLTFIQHIKQLKLKCLKTMNLLKILSHQSWGTDRYCLITLFRSLVL 889

Query: 128  -MLDYGSPIYGSAKDHVIAKLNTEHHIGIRIVTGALRTSPVPSLYVESGIPPLVIRRQKL 186
              +DYGS IY SA    +  L+  +H+GIR+  GA RTSPV SLY ES   PL  +R  L
Sbjct: 890  SRIDYGSIIYQSASKTALKLLDPVYHLGIRLALGAFRTSPVQSLYAESDQWPLDYQRTYL 949

Query: 187  LLNYVTKISACPSNPVYNILFPTSLRRRLGIYEFTRTPKPLFVR--FRAIEAYVQELDRC 244
             + Y T+I +   +P  +++   S  +          P PL +R     ++ + ++L   
Sbjct: 950  GVTYATRIMSLKQHPCKSLMNDVSTTQLYINRPSISPPFPLAIRPVVEKLKIHFEDLQEI 1009

Query: 245  DMMEYKDLTPPWSDDMS 261
            D +E +       +D+S
Sbjct: 1010 DQVEXQHPCKALMNDVS 1026

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  108 bits (271), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 63/157 (40%), Positives = 87/157 (55%), Gaps = 8/157 (5%)

Query: 251 DLTPPWSDDMSEVIDLWRNLTSNNIKLTFIWCPSHCGIEGNEEVDRAANRDGHTQAINIC 310
           D+T P+   +  ++    NL      + FIWCPSH GI GNE  DR A +        + 
Sbjct: 157 DITHPY---LLSILTKQNNLVRKGKLVVFIWCPSHVGILGNEVADRLAKQALVMPVTKLP 213

Query: 311 SPD-DLKTMVKKLAYNNWQVLWNQ-TDPLNKLKQIKPIISTWKTSQQSRRYDEVVLSRLR 368
            P  D K+ ++    + WQ  W++ TD  NKL  I+P+IS WK   Q  R  E+VL+R R
Sbjct: 214 LPHTDYKSPIRSYVKSLWQNEWDEETD--NKLHSIQPVISEWKQGPQIDRRGEIVLARAR 271

Query: 369 IGHTRVTHSYLFERTTPPLCSCGENLLTVKH-LLDCV 404
           IGH+ +TH YL  R   P C   ++LLTVKH L+DC+
Sbjct: 272 IGHSHLTHGYLLRREVAPFCIPCQSLLTVKHILIDCI 308

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score =  107 bits (267), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 63/157 (40%), Positives = 87/157 (55%), Gaps = 8/157 (5%)

Query: 251 DLTPPWSDDMSEVIDLWRNLTSNNIKLTFIWCPSHCGIEGNEEVDRAANRDGHTQAINIC 310
           D+T P+   +  ++    NL     K+ FIWCPSH GI GNE  DR A +        + 
Sbjct: 206 DITHPY---LLSILTKQNNLVRKGKKVVFIWCPSHVGILGNEVADRQAKQALVMPVTKLP 262

Query: 311 SPD-DLKTMVKKLAYNNWQVLWN-QTDPLNKLKQIKPIISTWKTSQQSRRYDEVVLSRLR 368
            P  D K+ ++    + WQ  W+ +TD  NKL  I+P+IS WK   Q  R  E+VL+  R
Sbjct: 263 LPHTDYKSPIRSYVKSLWQNEWDGETD--NKLHIIQPVISEWKQGPQIDRRGEIVLACAR 320

Query: 369 IGHTRVTHSYLFERTTPPLCSCGENLLTVKH-LLDCV 404
           IGH+ +TH YL  R   P C   ++LLTVKH L+DC+
Sbjct: 321 IGHSHLTHGYLLRREVAPFCIPCQSLLTVKHILIDCI 357

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	435
ASPGD|ASPL0000075333	486	AN10625 [Emericella nidulans (	0.340	0.304	0.260	2.3e-05
ASPGD|ASPL0000033911	686	AN2796 [Emericella nidulans (t	0.275	0.174	0.284	0.00044

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

 Score = 131 (51.2 bits), Expect = 2.3e-05, P = 2.3e-05
 Identities = 43/165 (26%), Positives = 71/165 (43%)

Query:   275 IKLTFIWCPSHCGIEGNEEVDRAANRD-------GHTQAINICSPDDLKTMVKKLAYNNW 327
             + + F W P+H G+EGNE+ DR A          GH   + I S   +K    ++    W
Sbjct:   284 LNVHFRWIPAHRGVEGNEQADRRAKEATGWRRIRGHRGRMTIRSA--VKRRAHEVVNARW 341

Query:   328 QVLWNQTDPLNKLKQIKPIIS--TWKTSQQSRRYDEVVLSRLRIGHTRVTHSYLFERTTP 385
             +  W       +L ++ P  +    +  Q   R    ++ ++R G   + H YL++R  P
Sbjct:   342 ENDWKSCHHGRELYELTPTPTRKVLRVHQDLHRALSTIIVQMRTGKIGLRH-YLYQRGVP 400

Query:   386 PL----CSCGENLLTVKH-LLDCVHHAPVRSTLSSKPSLLDEPEG 425
              +    C CG    +V+H LL C   + +R  +    S   E EG
Sbjct:   401 DVPNSDCQCGRATQSVRHILLACPTFSGLREEIFGGRSGGPEGEG 445

GO:0008150 "biological_process" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

ASPGD|ASPL0000033911 AN2796 [Emericella nidulans (taxid:162425)]

 Score = 88 (36.0 bits), Expect = 0.00044, Sum P(4) = 0.00044
 Identities = 37/130 (28%), Positives = 50/130 (38%)

Query:   281 WCPSHCGIEGNEEVDRAANRDGHTQAINIC-SPDDLKTMVKK-LAYNNWQVLWNQTDPLN 338
             W P H GI GNE  D+ A       + NI  SP  L+   K+ L    +    ++     
Sbjct:   503 WIPGHSGIAGNELADKLAKLGSSIYSPNIPPSPAYLRREAKQWLRTEAYTAYASKAPQAY 562

Query:   339 KLKQIKPIISTWKTSQQSRRYDEVVLSRL---RIGHTRVT--HSYLFERTTPPLCSCGEN 393
             K   I+P   T ++  +  +    VL RL   R GH   T  H           CSCG+ 
Sbjct:   563 KTLDIRP--HTKESRTREHKLPRWVLGRLVAARTGHGDFTAYHQRFNHSDYLESCSCGKT 620

Query:   394 LLTVKHLLDC 403
                V H   C
Sbjct:   621 KTPV-HFFFC 629

GO:0005575 "cellular_component" evidence=ND

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

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

GO:0003723 "RNA binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	435
cd09276	128	cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom	2e-10
cd01650	220	cd01650, RT_nLTR_like, RT_nLTR: Non-LTR (long term	1e-05
pfam00075	126	pfam00075, RNase_H, RNase H	2e-05
cd09278	139	cd09278, RNase_HI_prokaryote_like, RNase HI family	2e-04
pfam00078	194	pfam00078, RVT_1, Reverse transcriptase (RNA-depen	3e-04
cd09280	150	cd09280, RNase_HI_eukaryote_like, Eukaryotic RNase	0.003

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

 Score = 58.0 bits (141), Expect = 2e-10
 Identities = 15/34 (44%), Positives = 19/34 (55%)

Query: 267 WRNLTSNNIKLTFIWCPSHCGIEGNEEVDRAANR 300
            R L ++ +K+   W P H GIEGNE  DR A  
Sbjct: 92  IRELANHGVKVRLHWVPGHSGIEGNERADRLAKE 125

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

>gnl|CDD|238827 cd01650, RT_nLTR_like, RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT)

 Score = 46.1 bits (110), Expect = 1e-05
 Identities = 28/114 (24%), Positives = 45/114 (39%), Gaps = 36/114 (31%)

Query: 22  GLVQGSSLSTLLFAVFMNDIFHVINLPTRG---------LLFVDDLLLTIRGK---ILEQ 69
           G+ QG  LS LLF + ++D+  ++N              L + DD++L   GK   + E 
Sbjct: 106 GVRQGDPLSPLLFNLALDDLLRLLNKEEEIKLGGPGITHLAYADDIVLFSEGKSRKLQEL 165

Query: 70  L------------------------GSRNPTLPLIMLNGNQLKFDNTAKFLGLI 99
           L                        G++   L  I LNG  ++   T K+LG+ 
Sbjct: 166 LQRLQEWSKESGLKINPSKSKVMLIGNKKKRLKDITLNGTPIEAVETFKYLGVT 219

This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities. Length = 220

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

 Score = 43.4 bits (103), Expect = 2e-05
 Identities = 13/34 (38%), Positives = 17/34 (50%), Gaps = 1/34 (2%)

Query: 265 DLWRNLTSNNIKLTFIWCPSHCGIEGNEEVDRAA 298
           ++W  L     K+   W P H GI GNE  D+ A
Sbjct: 89  EIWELL-QKKHKVYIQWVPGHSGIPGNELADKLA 121

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

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

 Score = 40.6 bits (96), Expect = 2e-04
 Identities = 14/39 (35%), Positives = 19/39 (48%), Gaps = 2/39 (5%)

Query: 264 IDLWRNL--TSNNIKLTFIWCPSHCGIEGNEEVDRAANR 300
           +DLW+ L       ++T+ W   H G  GNE  D  AN 
Sbjct: 98  VDLWQELDALLAKHQVTWHWVKGHAGHPGNERADELANA 136

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

>gnl|CDD|215698 pfam00078, RVT_1, Reverse transcriptase (RNA-dependent DNA polymerase)

 Score = 41.6 bits (98), Expect = 3e-04
 Identities = 21/66 (31%), Positives = 30/66 (45%), Gaps = 4/66 (6%)

Query: 3   RRIAVKCNNLISNFKGLENGLVQGSSLSTLLFAVFMNDIFHVINLPTRG---LLFVDDLL 59
           R  +V  N           GL QGS LS LLF +FMN++   +     G   L + DD+L
Sbjct: 89  RTFSVLVNGNPGGRY-EWRGLPQGSVLSPLLFNLFMNELLRPLRKRFPGLTYLRYADDIL 147

Query: 60  LTIRGK 65
           +  +  
Sbjct: 148 IFSKSP 153

A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. Length = 194

>gnl|CDD|187704 cd09280, RNase_HI_eukaryote_like, Eukaryotic RNase H is longer and more complex than their prokaryotic counterparts and unlike prokaryote, RNase H are essential in higher eukaryote

 Score = 38.0 bits (89), Expect = 0.003
 Identities = 17/43 (39%), Positives = 22/43 (51%)

Query: 258 DDMSEVIDLWRNLTSNNIKLTFIWCPSHCGIEGNEEVDRAANR 300
           D + E+  L   L    I++ F   P H GI GNEE DR A +
Sbjct: 105 DLIKELDKLLEELEERGIRVKFWHVPGHSGIYGNEEADRLAKK 147

Ribonuclease H (RNase H) is classified into two families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H is widely present in various organisms, including bacteria, archaea and eukaryote and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, Type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD) residues and have the same catalytic mechanism and functions in cells. Eukaryotic RNase H is longer and more complex than in prokaryotes. Almost all eukaryotic RNase HI have highly conserved regions at the N-terminal called hybrid binding domain (HBD). It is speculated that the HBD contributes to binding the RNA/DNA hybrid. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability, but RNase H is essential in higher eukaryotes. RNase H knockout mice lack mitochondrial DNA replication and die as embryos. Length = 150

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	435
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	99.25
PRK08719	147	ribonuclease H; Reviewed	99.23
cd01648	119	TERT TERT: Telomerase reverse transcriptase (TERT)	99.23
PRK00203	150	rnhA ribonuclease H; Reviewed	99.23
PRK06548	161	ribonuclease H; Provisional	99.22
cd01650	220	RT_nLTR_like RT_nLTR: Non-LTR (long terminal repea	99.06
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	98.92
cd01651	226	RT_G2_intron RT_G2_intron: Reverse transcriptases	98.86
PF00078	214	RVT_1: Reverse transcriptase (RNA-dependent DNA po	98.85
cd03487	214	RT_Bac_retron_II RT_Bac_retron_II: Reverse transcr	98.82
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	98.66
cd00304	98	RT_like RT_like: Reverse transcriptase (RT, RNA-de	98.62
cd01646	158	RT_Bac_retron_I RT_Bac_retron_I: Reverse transcrip	98.53
KOG3752|consensus	371		98.29
cd01645	213	RT_Rtv RT_Rtv: Reverse transcriptases (RTs) from r	97.77
cd01709	346	RT_like_1 RT_like_1: A subfamily of reverse transc	97.71
cd03714	119	RT_DIRS1 RT_DIRS1: Reverse transcriptases (RTs) oc	97.68
PRK13907	128	rnhA ribonuclease H; Provisional	97.56
KOG1005|consensus	888		97.12
cd03715	210	RT_ZFREV_like RT_ZFREV_like: A subfamily of revers	96.76
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	96.54
PRK07708	219	hypothetical protein; Validated	96.51
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	96.49
PF13966	86	zf-RVT: zinc-binding in reverse transcriptase	95.58
KOG4768|consensus	796		95.06
cd01647	177	RT_LTR RT_LTR: Reverse transcriptases (RTs) from r	92.68
cd01644	213	RT_pepA17 RT_pepA17: Reverse transcriptase (RTs) i	92.39

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

Probab=99.25  E-value=3.6e-12  Score=108.15  Aligned_cols=61  Identities=26%  Similarity=0.464  Sum_probs=48.4

Q ss_pred             CCCChh--hhhcc-----------cccccCCHHHHHHhhc-----cCCCC----C------------ceEEEEEecccCC
Q psy556          242 DRCDMM--EYKDL-----------TPPWSDDMSEVIDLWR-----NLTSN----N------------IKLTFIWCPSHCG  287 (435)
Q Consensus       242 ~~~~v~--El~ai-----------~~i~sDs~sa~~~l~~-----~~~~~----~------------i~v~~~Wvp~H~g  287 (435)
                      +..+++  ||.||           +.|+|||++++..+..     .....    .            +.|.|.|||||+|
T Consensus        36 ~~~s~~~aEl~Ai~~AL~~~~~~~v~I~tDS~~v~~~l~~~~~~~~~~~~~~~~~i~~~i~~~~~~~~~v~~~~V~~H~~  115 (132)
T PF00075_consen   36 GGQSNNRAELQAIIEALKALEHRKVTIYTDSQYVLNALNKWLHGNGWKKTSNGRPIKNEIWELLSRGIKVRFRWVPGHSG  115 (132)
T ss_dssp             ESECHHHHHHHHHHHHHHTHSTSEEEEEES-HHHHHHHHTHHHHTTSBSCTSSSBHTHHHHHHHHHSSEEEEEESSSSSS
T ss_pred             cccchhhhheehHHHHHHHhhcccccccccHHHHHHHHHHhccccccccccccccchhheeeccccceEEeeeeccCcCC
Confidence            355665  98888           5899999999998866     22111    1            3899999999999


Q ss_pred             C-CcchHHhHHHhhcc
Q psy556          288 I-EGNEEVDRAANRDG  302 (435)
Q Consensus       288 i-~gNe~AD~~Ak~a~  302 (435)
                      + .|||.||++||+|+
T Consensus       116 ~~~~N~~aD~lAk~a~  131 (132)
T PF00075_consen  116 VPQGNERADRLAKEAA  131 (132)
T ss_dssp             SHHHHHHHHHHHHHHH
T ss_pred             CchhHHHHHHHHHHhc
Confidence            9 69999999999986

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

>PRK08719 ribonuclease H; Reviewed

Probab=99.23  E-value=1.1e-11  Score=106.76  Aligned_cols=61  Identities=25%  Similarity=0.257  Sum_probs=50.4

Q ss_pred             CCChh--hhhcc----------cccccCCHHHHHHh--------hccCCCCC------------c-------eEEEEEec
Q psy556          243 RCDMM--EYKDL----------TPPWSDDMSEVIDL--------WRNLTSNN------------I-------KLTFIWCP  283 (435)
Q Consensus       243 ~~~v~--El~ai----------~~i~sDs~sa~~~l--------~~~~~~~~------------i-------~v~~~Wvp  283 (435)
                      ..|..  |+.|+          ..|+|||+++++.+        ++.+..++            |       .|+|.|||
T Consensus        47 ~~Tnn~aEl~A~~~aL~~~~~~~~i~tDS~yvi~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~~~~i~~~~Vk  126 (147)
T PRK08719         47 YTDNAELELLALIEALEYARDGDVIYSDSDYCVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRARKYVEVEKVT  126 (147)
T ss_pred             CccHHHHHHHHHHHHHHHcCCCCEEEechHHHHHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhCCCcEEEEEec
Confidence            35555  99988          67999999999999        45544332            1       79999999


Q ss_pred             ccCCCCcchHHhHHHhhccC
Q psy556          284 SHCGIEGNEEVDRAANRDGH  303 (435)
Q Consensus       284 ~H~gi~gNe~AD~~Ak~a~~  303 (435)
                      ||+|++|||.||++|++|++
T Consensus       127 gH~g~~~Ne~aD~lA~~a~~  146 (147)
T PRK08719        127 AHSGIEGNEAADMLAQAAAE  146 (147)
T ss_pred             CCCCChhHHHHHHHHHHHhh
Confidence            99999999999999999974

>cd01648 TERT TERT: Telomerase reverse transcriptase (TERT)

Probab=99.23  E-value=7.9e-12  Score=104.14  Aligned_cols=89  Identities=22%  Similarity=0.217  Sum_probs=62.3

Q ss_pred             cccceeccCCCCCCCchhHHHHHHHHHhhhhhcC-------CCcceeeeccceeEEEecCCHhHhh----ccCC-CCCce
Q psy556           13 ISNFKGLENGLVQGSSLSTLLFAVFMNDIFHVIN-------LPTRGLLFVDDLLLTIRGKILEQLG----SRNP-TLPLI   80 (435)
Q Consensus        13 ~s~~~~i~~GvpQGs~LSP~Lf~l~~~~l~~~~~-------~~~~~~~yADD~~i~~~~~~~~~l~----k~~~-~~~~~   80 (435)
                      .+..+...+|+|||++|||+||++|++.+.+.+.       .......||||+.+++......+..    +..+ ....+
T Consensus        10 ~~~~~~~~~GlpQG~~lSp~L~nl~l~~l~~~~~~~~~~~~~~~~~~rYaDD~li~~~~~~~~~~~~~~l~~~l~~~~gl   89 (119)
T cd01648          10 IPQYYRQKVGIPQGSPLSSLLCSLYYADLENKYLSFLDVIDKDSLLLRLVDDFLLITTSLDKAIKFLNLLLRGFINQYKT   89 (119)
T ss_pred             hhhhhhhcCcccCCcchHHHHHHHHHHHHHHHHHhhcccCCCCceEEEEeCcEEEEeCCHHHHHHHHHHHHHhhHHhhCe
Confidence            3345677889999999999999999999987742       3456899999999887765433211    2222 33455


Q ss_pred             EeCCeeee---------ccCcceeeceeec
Q psy556           81 MLNGNQLK---------FDNTAKFLGLIWD  101 (435)
Q Consensus        81 ~l~~~~I~---------~~~~~kyLGv~ld  101 (435)
                      .+|..+.+         ..+.+.|||+.|+
T Consensus        90 ~iN~~Kt~~~~~~~~~~~~~~~~flG~~i~  119 (119)
T cd01648          90 FVNFDKTQINFSFAQLDSSDLIPWCGLLIN  119 (119)
T ss_pred             EECcccceeeccccccCCCCccCceeEeeC
Confidence            55543332         3567999999885

Telomerase is a ribonucleoprotein (RNP) that synthesizes telomeric DNA repeats. The telomerase RNA subunit provides the template for synthesis of these repeats. The catalytic subunit of RNP is known as telomerase reverse transcriptase (TERT). The reverse transcriptase (RT) domain is located in the C-terminal region of the TERT polypeptide. Single amino acid substitutions in this region lead to telomere shortening and senescence. Telomerase is an enzyme that, in certain cells, maintains the physical ends of chromosomes (telomeres) during replication. In somatic cells, replication of the lagging strand requires the continual presence of an RNA primer approximately 200 nucleotides upstream, which is complementary to the template strand. Since there is a region of DNA less than 200 base pairs from the end of the chromosome where this is not possible, the chromosome is continually shortened. However, a surplus of repetitive DNA at

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=99.23  E-value=7.7e-12  Score=108.64  Aligned_cols=64  Identities=16%  Similarity=0.215  Sum_probs=50.5

Q ss_pred             CCCChh--hhhcc------------cccccCCHHHHHHhhc--------cC-CCCC------------------ceEEEE
Q psy556          242 DRCDMM--EYKDL------------TPPWSDDMSEVIDLWR--------NL-TSNN------------------IKLTFI  280 (435)
Q Consensus       242 ~~~~v~--El~ai------------~~i~sDs~sa~~~l~~--------~~-~~~~------------------i~v~~~  280 (435)
                      ...|..  ||.|+            +.|+|||+++++.|..        .. ..++                  ..|.|.
T Consensus        39 ~~~TN~~aEL~Ai~~AL~~~~~~~~v~I~tDS~yvi~~i~~w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~~~~v~~~  118 (150)
T PRK00203         39 ALTTNNRMELMAAIEALEALKEPCEVTLYTDSQYVRQGITEWIHGWKKNGWKTADKKPVKNVDLWQRLDAALKRHQIKWH  118 (150)
T ss_pred             CCCcHHHHHHHHHHHHHHHcCCCCeEEEEECHHHHHHHHHHHHHHHHHcCCcccCCCccccHHHHHHHHHHhccCceEEE
Confidence            334443  99888            6799999999999964        22 1222                  279999


Q ss_pred             EecccCCCCcchHHhHHHhhccCCC
Q psy556          281 WCPSHCGIEGNEEVDRAANRDGHTQ  305 (435)
Q Consensus       281 Wvp~H~gi~gNe~AD~~Ak~a~~~~  305 (435)
                      |||||+|++|||.||++||+|+..+
T Consensus       119 wV~~H~~~~~N~~AD~lA~~a~~~~  143 (150)
T PRK00203        119 WVKGHAGHPENERCDELARAGAEEA  143 (150)
T ss_pred             EecCCCCCHHHHHHHHHHHHHHHHh
Confidence            9999999999999999999998654

>PRK06548 ribonuclease H; Provisional

Probab=99.22  E-value=1.2e-11  Score=107.60  Aligned_cols=57  Identities=21%  Similarity=0.275  Sum_probs=48.1

Q ss_pred             hhhcc-------------cccccCCHHHHHHhh---------ccCCCCC-----------c-------eEEEEEecccCC
Q psy556          248 EYKDL-------------TPPWSDDMSEVIDLW---------RNLTSNN-----------I-------KLTFIWCPSHCG  287 (435)
Q Consensus       248 El~ai-------------~~i~sDs~sa~~~l~---------~~~~~~~-----------i-------~v~~~Wvp~H~g  287 (435)
                      ||.|+             +.|+|||+++++.+.         +....+|           |       .|+|.|||||+|
T Consensus        46 El~Aii~aL~~~~~~~~~v~I~TDS~yvi~~i~~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~~~v~~~wVkgHsg  125 (161)
T PRK06548         46 ELTAVRELLIATRHTDRPILILSDSKYVINSLTKWVYSWKMRKWRKADGKPVLNQEIIQEIDSLMENRNIRMSWVNAHTG  125 (161)
T ss_pred             HHHHHHHHHHhhhcCCceEEEEeChHHHHHHHHHHHHHHHHCCCcccCCCccccHHHHHHHHHHHhcCceEEEEEecCCC
Confidence            98888             679999999999997         3333333           1       799999999999


Q ss_pred             CCcchHHhHHHhhccCC
Q psy556          288 IEGNEEVDRAANRDGHT  304 (435)
Q Consensus       288 i~gNe~AD~~Ak~a~~~  304 (435)
                      ++|||.||++|++|+..
T Consensus       126 ~~gNe~aD~LA~~aa~~  142 (161)
T PRK06548        126 HPLNEAADSLARQAANN  142 (161)
T ss_pred             CHHHHHHHHHHHHHHHH
Confidence            99999999999998754

>cd01650 RT_nLTR_like RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT)

Probab=99.06  E-value=1.2e-10  Score=107.56  Aligned_cols=79  Identities=37%  Similarity=0.558  Sum_probs=59.7

Q ss_pred             CCCCCCchhHHHHHHHHHhhhhhcC---------CCcceeeeccceeEEEecCC-HhH--hh-----------ccCCC--
Q psy556           22 GLVQGSSLSTLLFAVFMNDIFHVIN---------LPTRGLLFVDDLLLTIRGKI-LEQ--LG-----------SRNPT--   76 (435)
Q Consensus        22 GvpQGs~LSP~Lf~l~~~~l~~~~~---------~~~~~~~yADD~~i~~~~~~-~~~--l~-----------k~~~~--   76 (435)
                      |+|||++|||+||++|++++.+.+.         ..+....||||+++++.+.. ..+  +.           +.+..  
T Consensus       106 GipQG~~lSp~l~~l~~~~l~~~~~~~~~~~~~~~~~~~~~yaDD~~i~~~~~~~~~~~~~~~~~~~~~~~gl~in~~Kt  185 (220)
T cd01650         106 GVRQGDPLSPLLFNLALDDLLRLLNKEEEIKLGGPGITHLAYADDIVLFSEGKSRKLQELLQRLQEWSKESGLKINPSKS  185 (220)
T ss_pred             CCccCCcccHHHHHHHHHHHHHHHHhhccccCCCCccceEEeccceeeeccCCHHHHHHHHHHHHHHHHHcCCEEChhhe
Confidence            9999999999999999999988753         56789999999999988886 221  11           11111  


Q ss_pred             -----------CCceEeCCeeeeccCcceeeceee
Q psy556           77 -----------LPLIMLNGNQLKFDNTAKFLGLIW  100 (435)
Q Consensus        77 -----------~~~~~l~~~~I~~~~~~kyLGv~l  100 (435)
                                 ...+.+++..+..+..+||||+.|
T Consensus       186 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~kyLG~~i  220 (220)
T cd01650         186 KVMLIGNKKKRLKDITLNGTPIEAVETFKYLGVTI  220 (220)
T ss_pred             EEEEecCCCcchhhhhhcCCcccCCCCCeeccccC
Confidence                       111345667778889999999975

This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.

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

Probab=98.92  E-value=7.4e-10  Score=94.70  Aligned_cols=53  Identities=21%  Similarity=0.287  Sum_probs=42.8

Q ss_pred             cccccCCHHHHHHhhcc---CCCCC------------------------c-eEEEEEecccCCCCcchHHhHHHhhccCC
Q psy556          253 TPPWSDDMSEVIDLWRN---LTSNN------------------------I-KLTFIWCPSHCGIEGNEEVDRAANRDGHT  304 (435)
Q Consensus       253 ~~i~sDs~sa~~~l~~~---~~~~~------------------------i-~v~~~Wvp~H~gi~gNe~AD~~Ak~a~~~  304 (435)
                      +.|+|||+.+++.|..-   +...+                        . .|.+.|||||.|.++||.||++|++|+..
T Consensus        66 v~l~tDS~yv~~~i~~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~~~~~  145 (154)
T COG0328          66 VTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAREAARA  145 (154)
T ss_pred             EEEEecHHHHHHHHHHHHhhccccCccccccCccccHHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHHHHHh
Confidence            78999999999999611   11111                        1 89999999999999999999999999865


Q ss_pred             C
Q psy556          305 Q  305 (435)
Q Consensus       305 ~  305 (435)
                      .
T Consensus       146 ~  146 (154)
T COG0328         146 A  146 (154)
T ss_pred             h
Confidence            4

>cd01651 RT_G2_intron RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin

Probab=98.86  E-value=2.8e-09  Score=98.80  Aligned_cols=87  Identities=20%  Similarity=0.351  Sum_probs=59.8

Q ss_pred             ccceeccCCCCCCCchhHHHHHHHHHhhhhhcC--------------CCcceeeeccceeEEEecCCHhH-hh---ccCC
Q psy556           14 SNFKGLENGLVQGSSLSTLLFAVFMNDIFHVIN--------------LPTRGLLFVDDLLLTIRGKILEQ-LG---SRNP   75 (435)
Q Consensus        14 s~~~~i~~GvpQGs~LSP~Lf~l~~~~l~~~~~--------------~~~~~~~yADD~~i~~~~~~~~~-l~---k~~~   75 (435)
                      +..+....|||||+++||+||++|++++...+.              .++....||||+++++.+....+ ..   ..-+
T Consensus       118 ~~~~~~~~GlpqG~~lSp~L~~~~l~~ld~~l~~~~~~~~~~~~~~~~~~~~~rY~DD~~i~~~~~~~~~~~~~~i~~~~  197 (226)
T cd01651         118 GKLVETEKGTPQGGVISPLLANIYLHELDKFVEEKLKEYYDTSDPKFRRLRYVRYADDFVIGVRGPKEAEEIKELIREFL  197 (226)
T ss_pred             CeEeCCCCCcCCCccHHHHHHHHHHHHHHHHHHHhhhhcccccccccCceEEEEecCceEEecCCHHHHHHHHHHHHHHH
Confidence            456678899999999999999999999977643              55779999999999988877432 11   0000


Q ss_pred             CCCceEeC--Ceeeec--cCcceeeceee
Q psy556           76 TLPLIMLN--GNQLKF--DNTAKFLGLIW  100 (435)
Q Consensus        76 ~~~~~~l~--~~~I~~--~~~~kyLGv~l  100 (435)
                      ....+.++  ...+-.  .+.+.|||+.|
T Consensus       198 ~~~gl~ln~~Kt~i~~~~~~~~~fLG~~~  226 (226)
T cd01651         198 EELGLELNPEKTRITHFKSEGFDFLGFTF  226 (226)
T ss_pred             HHcCCeechhhcceeecCCCCCeeCCeEC
Confidence            11122222  222222  57899999875

RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).

>PF00078 RVT_1: Reverse transcriptase (RNA-dependent DNA polymerase); InterPro: IPR000477 The use of an RNA template to produce DNA, for integration into the host genome and exploitation of a host cell, is a strategy employed in the replication of retroid elements, such as the retroviruses and bacterial retrons

Probab=98.85  E-value=1.6e-09  Score=99.29  Aligned_cols=95  Identities=27%  Similarity=0.291  Sum_probs=63.7

Q ss_pred             EEEEECCccccceeccCCCCCCCchhHHHHHHHHHhhhhhcC----CCcceeeeccceeEEEecCCHhHhh----ccCCC
Q psy556            5 IAVKCNNLISNFKGLENGLVQGSSLSTLLFAVFMNDIFHVIN----LPTRGLLFVDDLLLTIRGKILEQLG----SRNPT   76 (435)
Q Consensus         5 ~~v~~~g~~s~~~~i~~GvpQGs~LSP~Lf~l~~~~l~~~~~----~~~~~~~yADD~~i~~~~~~~~~l~----k~~~~   76 (435)
                      ..+.+++.. .......|+|||+++||+||++|++++.+.+.    +++.+..||||+.+++......+..    ..-+.
T Consensus       109 ~~~~~~~~~-~~~~~~~glpqG~~~S~~l~~~~l~~l~~~~~~~~~~~~~~~rY~DD~~i~~~~~~~~~~~~~~i~~~~~  187 (214)
T PF00078_consen  109 AKVYLDGDL-SPYFQKRGLPQGSPLSPLLFNIYLDDLDRELQQELNPDISYLRYADDILIISKSKEELQKILEKISQWLE  187 (214)
T ss_dssp             H-EECGCSS-SEEEEESBS-TTSTCHHHHHHHHHHHHHHHHHHHS-TTSEEEEETTEEEEEESSHHHHHHHHHHHHHHHH
T ss_pred             ccccccccc-ccccccccccccccccchhhccccccccccccccccccccceEeccccEEEECCHHHHHHHHHHHHHHHH
Confidence            345666665 77889999999999999999999999988743    5788999999999998874432111    00000


Q ss_pred             CCceEeCCeeee---ccCcceeeceee
Q psy556           77 LPLIMLNGNQLK---FDNTAKFLGLIW  100 (435)
Q Consensus        77 ~~~~~l~~~~I~---~~~~~kyLGv~l  100 (435)
                      ...+.++..+.+   ..++++|||+.|
T Consensus       188 ~~gl~ln~~Kt~~~~~~~~~~~lG~~i  214 (214)
T PF00078_consen  188 ELGLKLNPEKTKILHPSDSVKFLGYVI  214 (214)
T ss_dssp             HTTSBCSSTTTSCS--ESSEEETTEEE
T ss_pred             HCCCEEChHHEEEEeCCCCEEEEeEEC
Confidence            112233322211   468899999975

The enzyme catalysing polymerisation is an RNA-directed DNA-polymerase, or reverse trancriptase (RT) (2.7.7.49 from EC). Reverse transcriptase occurs in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. Retroviral reverse transcriptase 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. The discovery of retroelements in the prokaryotes raises intriguing questions concerning their roles in bacteria and the origin and evolution of reverse transcriptases and whether the bacterial reverse transcriptases are older than eukaryotic reverse transcriptases [].; GO: 0003723 RNA binding, 0003964 RNA-directed DNA polymerase activity, 0006278 RNA-dependent DNA replication; PDB: 1MU2_B 3RWE_C 3DU6_B 3DU5_A 3KYL_A 2WOM_B 1DTQ_A 2OPS_A 3FFI_A 1VRU_B ....

>cd03487 RT_Bac_retron_II RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons

Probab=98.82  E-value=4.2e-09  Score=97.12  Aligned_cols=85  Identities=14%  Similarity=0.138  Sum_probs=59.9

Q ss_pred             ccCCCCCCCchhHHHHHHHHHhhhhhcC-----CCcceeeeccceeEEEecCCH---hHhh---ccCCCCCceEeCCee-
Q psy556           19 LENGLVQGSSLSTLLFAVFMNDIFHVIN-----LPTRGLLFVDDLLLTIRGKIL---EQLG---SRNPTLPLIMLNGNQ-   86 (435)
Q Consensus        19 i~~GvpQGs~LSP~Lf~l~~~~l~~~~~-----~~~~~~~yADD~~i~~~~~~~---~~l~---k~~~~~~~~~l~~~~-   86 (435)
                      ...|||||+++||+||++|++++...+.     .++....||||+++++.....   +++.   ..-+....+.++..+ 
T Consensus       100 ~~~GlpQG~~lSp~Lanl~l~~~d~~l~~~~~~~~~~~~RYaDD~~i~~~~~~~~~~~~~~~~i~~~l~~~gL~ln~~Kt  179 (214)
T cd03487         100 YNGHLPQGAPTSPALSNLVFRKLDERLSKLAKSNGLTYTRYADDITFSSNKKLKEALDKLLEIIRSILSEEGFKINKSKT  179 (214)
T ss_pred             CCCCcCCCCcccHHHHHHHHHHHHHHHHHHHHHcCCeEEEEeccEEEEccccchhHHHHHHHHHHHHHHHCCceeCCCce
Confidence            4459999999999999999999887653     567899999999999888762   2211   111112344554432 


Q ss_pred             -e-eccCcceeeceeecCc
Q psy556           87 -L-KFDNTAKFLGLIWDRK  103 (435)
Q Consensus        87 -I-~~~~~~kyLGv~ld~~  103 (435)
                       + ...+.+.+||+.+.++
T Consensus       180 ~i~~~~~~~~~~G~~i~~~  198 (214)
T cd03487         180 RISSKGSRQIVTGLVVNNG  198 (214)
T ss_pred             EEccCCCCcEEEEEEEeCC
Confidence             2 2345799999999864

The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.

>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=98.66  E-value=3.9e-08  Score=81.56  Aligned_cols=60  Identities=28%  Similarity=0.389  Sum_probs=50.3

Q ss_pred             CCChh--hhhcc--------------cccccCCHHHHHHhhccCCCCC-----------------ceEEEEEecccCCCC
Q psy556          243 RCDMM--EYKDL--------------TPPWSDDMSEVIDLWRNLTSNN-----------------IKLTFIWCPSHCGIE  289 (435)
Q Consensus       243 ~~~v~--El~ai--------------~~i~sDs~sa~~~l~~~~~~~~-----------------i~v~~~Wvp~H~gi~  289 (435)
                      ..+++  |+.|+              +.|++||+.++..+.+......                 ..++|.|||+|+|+.
T Consensus        38 ~~s~~~aEl~al~~al~~~~~~~~~~i~i~~Ds~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~  117 (130)
T cd06222          38 NTTNNRAELLALIEALELALELGGKKVNIYTDSQYVINALTGWYEGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHSGIE  117 (130)
T ss_pred             CCcHHHHHHHHHHHHHHHHHhCCCceEEEEECHHHHHHHhhccccCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCc
Confidence            55665  98888              6899999999999987654211                 289999999999999


Q ss_pred             cchHHhHHHhhcc
Q psy556          290 GNEEVDRAANRDG  302 (435)
Q Consensus       290 gNe~AD~~Ak~a~  302 (435)
                      +|+.||.+||+|.
T Consensus       118 ~n~~ad~la~~~~  130 (130)
T cd06222         118 GNERADALAKEAA  130 (130)
T ss_pred             chHHHHHHHHhhC
Confidence            9999999999874

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.

>cd00304 RT_like RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family

Probab=98.62  E-value=4.2e-08  Score=78.49  Aligned_cols=78  Identities=24%  Similarity=0.285  Sum_probs=55.0

Q ss_pred             CCCCCchhHHHHHHHHHhhhhhc---CCCcceeeeccceeEEEecCCHhHhh---ccCCCCCceEeCCeeee---ccCcc
Q psy556           23 LVQGSSLSTLLFAVFMNDIFHVI---NLPTRGLLFVDDLLLTIRGKILEQLG---SRNPTLPLIMLNGNQLK---FDNTA   93 (435)
Q Consensus        23 vpQGs~LSP~Lf~l~~~~l~~~~---~~~~~~~~yADD~~i~~~~~~~~~l~---k~~~~~~~~~l~~~~I~---~~~~~   93 (435)
                      +|||+++||.||+++++.+...+   ..++....|+||+.+++.........   ...+....+.++..+.+   ....+
T Consensus        12 lPqG~~~Sp~l~~~~~~~l~~~~~~~~~~~~~~~Y~DD~~i~~~~~~~~~~~~~l~~~l~~~gl~ln~~Kt~~~~~~~~~   91 (98)
T cd00304          12 LPQGSPLSPALANLYMEKLEAPILKQLLDITLIRYVDDLVVIAKSEQQAVKKRELEEFLARLGLNLSDEKTQFTEKEKKF   91 (98)
T ss_pred             cCCCCchHHHHHHHHHHHHHHHHHHhcCCceEEEeeCcEEEEeCcHHHHHHHHHHHHHHHHcCcEEChheeEEecCCCCe
Confidence            99999999999999999998875   35778999999999998776111111   11111234455544433   56789


Q ss_pred             eeeceee
Q psy556           94 KFLGLIW  100 (435)
Q Consensus        94 kyLGv~l  100 (435)
                      +|||+.+
T Consensus        92 ~flG~~~   98 (98)
T cd00304          92 KFLGILV   98 (98)
T ss_pred             eeeceeC
Confidence            9999864

An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.

>cd01646 RT_Bac_retron_I RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons

Probab=98.53  E-value=6.3e-08  Score=84.86  Aligned_cols=90  Identities=23%  Similarity=0.269  Sum_probs=60.1

Q ss_pred             ccceeccCCCCCCCchhHHHHHHHHHhhhhhcC---CCcceeeeccceeEEEecCCHhH-hh---ccCCCCCceEeCCee
Q psy556           14 SNFKGLENGLVQGSSLSTLLFAVFMNDIFHVIN---LPTRGLLFVDDLLLTIRGKILEQ-LG---SRNPTLPLIMLNGNQ   86 (435)
Q Consensus        14 s~~~~i~~GvpQGs~LSP~Lf~l~~~~l~~~~~---~~~~~~~yADD~~i~~~~~~~~~-l~---k~~~~~~~~~l~~~~   86 (435)
                      +.......|+|||+++||+|+++|+.++...+.   .++....||||+++++......+ ..   ..-+....+.++..+
T Consensus        45 ~~~~~~~~GlpqG~~lS~~L~~~~l~~~d~~i~~~~~~~~~~RY~DD~~i~~~~~~~~~~~~~~i~~~l~~~gL~ln~~K  124 (158)
T cd01646          45 SSQYGQTNGLPIGPLTSRFLANIYLNDVDHELKSKLKGVDYVRYVDDIRIFADSKEEAEEILEELKEFLAELGLSLNLSK  124 (158)
T ss_pred             hccCCCCceEccCcchHHHHHHHHHHHHHHHHHhccCCceEEEecCcEEEEcCCHHHHHHHHHHHHHHHHHCCCEEChhh
Confidence            345567789999999999999999999987753   57889999999999986554331 11   000111233333221


Q ss_pred             ---eecc---CcceeeceeecCc
Q psy556           87 ---LKFD---NTAKFLGLIWDRK  103 (435)
Q Consensus        87 ---I~~~---~~~kyLGv~ld~~  103 (435)
                         ....   ..+.+||..+...
T Consensus       125 t~~~~~~~~~~~~~flg~~~~~~  147 (158)
T cd01646         125 TEILPLPEGTASKDFLGYRFSPI  147 (158)
T ss_pred             ceeeecCCCCccccccceEeehh
Confidence               1222   2489999999754

The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.

>KOG3752|consensus

Probab=98.29  E-value=7.9e-07  Score=85.45  Aligned_cols=61  Identities=21%  Similarity=0.143  Sum_probs=48.3

Q ss_pred             CCCChh--hhhcc--------------cccccCCHHHHHHhhcc--------CCC---CC--------------------
Q psy556          242 DRCDMM--EYKDL--------------TPPWSDDMSEVIDLWRN--------LTS---NN--------------------  274 (435)
Q Consensus       242 ~~~~v~--El~ai--------------~~i~sDs~sa~~~l~~~--------~~~---~~--------------------  274 (435)
                      ..+|.+  ||.|+              +.|.|||+..++.|+.-        ...   +.                    
T Consensus       252 g~qtNnrAEl~Av~~ALkka~~~~~~kv~I~TDS~~~i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q  331 (371)
T KOG3752|consen  252 GRQTNNRAELIAAIEALKKARSKNINKVVIRTDSEYFINSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQ  331 (371)
T ss_pred             CcccccHHHHHHHHHHHHHHHhcCCCcEEEEechHHHHHHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHh
Confidence            445555  99888              78999999999998421        111   11                    


Q ss_pred             ----ceEEEEEecccCCCCcchHHhHHHhhcc
Q psy556          275 ----IKLTFIWCPSHCGIEGNEEVDRAANRDG  302 (435)
Q Consensus       275 ----i~v~~~Wvp~H~gi~gNe~AD~~Ak~a~  302 (435)
                          ..|.+.|||||.||.|||+||.+|++++
T Consensus       332 ~~~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs  363 (371)
T KOG3752|consen  332 EISNKKVQQEYVGGHSGILGNEMADALARKGS  363 (371)
T ss_pred             hhccCceEEEEecCcCCcchHHHHHHHHhhhh
Confidence                1799999999999999999999999985

>cd01645 RT_Rtv RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs)

Probab=97.77  E-value=1.2e-05  Score=73.97  Aligned_cols=78  Identities=15%  Similarity=0.154  Sum_probs=57.3

Q ss_pred             CCCCCCCchhHHHHHHHHHhhhhhcC---CCcceeeeccceeEEEecCCHhHhh------ccCCCCCceEeCCeeeeccC
Q psy556           21 NGLVQGSSLSTLLFAVFMNDIFHVIN---LPTRGLLFVDDLLLTIRGKILEQLG------SRNPTLPLIMLNGNQLKFDN   91 (435)
Q Consensus        21 ~GvpQGs~LSP~Lf~l~~~~l~~~~~---~~~~~~~yADD~~i~~~~~~~~~l~------k~~~~~~~~~l~~~~I~~~~   91 (435)
                      +.+|||...||.+|+.+|+.++..+.   .++.+..|+||+.+.+...  ++..      ...+....+.++..+.....
T Consensus       127 ~~lP~Gl~~SP~~f~~~m~~~l~~~~~~~~~~~~~~Y~DDili~s~~~--~~~~~~l~~v~~~l~~~gl~ln~~K~~~~~  204 (213)
T cd01645         127 KVLPQGMKNSPTICQSFVAQALEPFRKQYPDIVIYHYMDDILIASDLE--GQLREIYEELRQTLLRWGLTIPPEKVQKEP  204 (213)
T ss_pred             EEeCCCCcChHHHHHHHHHHHHHHHHHHCCCeEEEEEcCCEEEEcCCH--HHHHHHHHHHHHHHHHCCCEeCHHHEeCCC
Confidence            57999999999999999999987643   3456899999999875443  3222      22233456677766666678


Q ss_pred             cceeeceee
Q psy556           92 TAKFLGLIW  100 (435)
Q Consensus        92 ~~kyLGv~l  100 (435)
                      +++|||+.+
T Consensus       205 ~v~fLG~~i  213 (213)
T cd01645         205 PFQYLGYEL  213 (213)
T ss_pred             CeEeccEeC
Confidence            899999864

RTs catalyze the conversion of single-stranded RNA into double-stranded viral DNA for integration into host chromosomes. Proteins in this subfamily contain long terminal repeats (LTRs) and are multifunctional enzymes with RNA-directed DNA polymerase, DNA directed DNA polymerase, and ribonuclease hybrid (RNase H) activities. The viral RNA genome enters the cytoplasm as part of a nucleoprotein complex, and the process of reverse transcription generates in the cytoplasm forming a linear DNA duplex via an intricate series of steps. This duplex DNA is colinear with its RNA template, but contains terminal duplications known as LTRs that are not present in viral RNA. It has been proposed that two specialized template switches, known as strand-transfer reactions or "jumps", are required to generate the LTRs.

>cd01709 RT_like_1 RT_like_1: A subfamily of reverse transcriptases (RTs)

Probab=97.71  E-value=4.5e-05  Score=73.61  Aligned_cols=49  Identities=14%  Similarity=-0.013  Sum_probs=40.6

Q ss_pred             cceeccCCCCCCCchhHHHHHHHHHhhhhhcC---CCcceeeeccceeEEEe
Q psy556           15 NFKGLENGLVQGSSLSTLLFAVFMNDIFHVIN---LPTRGLLFVDDLLLTIR   63 (435)
Q Consensus        15 ~~~~i~~GvpQGs~LSP~Lf~l~~~~l~~~~~---~~~~~~~yADD~~i~~~   63 (435)
                      ....-.+|+|||+++||+|=|+|+..+...++   +++.+.-||||+.++.+
T Consensus        76 ~~r~r~rGtPqGgviSplLaNiyL~~lD~~v~~~~~g~~l~RYaDD~vi~~~  127 (346)
T cd01709          76 PPRIRKRGTPMSHALSDVFGELVLFCLDFAVNQATDGGLLYRLHDDLWFWGQ  127 (346)
T ss_pred             cccccCCccCCCchhhHHHHHHHHHHHHHHHHhcCCCceEEEEcCeEEEEcC
Confidence            44556679999999999999999997765554   57889999999999944

An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.

>cd03714 RT_DIRS1 RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons

Probab=97.68  E-value=3.1e-05  Score=64.35  Aligned_cols=78  Identities=23%  Similarity=0.221  Sum_probs=55.5

Q ss_pred             CCCCCchhHHHHHHHHHhhhhhcC-CCcceeeeccceeEEEecCCHhHhh----cc-CCCCCceEeCCeeee--ccCcce
Q psy556           23 LVQGSSLSTLLFAVFMNDIFHVIN-LPTRGLLFVDDLLLTIRGKILEQLG----SR-NPTLPLIMLNGNQLK--FDNTAK   94 (435)
Q Consensus        23 vpQGs~LSP~Lf~l~~~~l~~~~~-~~~~~~~yADD~~i~~~~~~~~~l~----k~-~~~~~~~~l~~~~I~--~~~~~k   94 (435)
                      +|||...||.+|.-+|+.++..+. .+..+..|+||+.+.+......+..    +. -+....+.++..+..  +.++++
T Consensus        34 mp~Gl~~sp~~f~~~~~~i~~~~~~~~~~v~~Y~DDili~~~~~~~~~~~~~~l~~~~l~~~gl~ln~~K~~~~~~~~v~  113 (119)
T cd03714          34 LPFGLSLAPRVFTKVVEALLAPLRLLGVRIFSYLDDLLIIASSIKTSEAVLRHLRATLLANLGFTLNLEKSKLGPTQRIT  113 (119)
T ss_pred             cCCcccchHHHHHHHHHHHHHHhhcCCeEEEEEecCeEEEeCcHHHHHHHHHHHHHHHHHHcCCccChhhcEecCCCcEE
Confidence            899999999999999999988653 4567899999999987752211111    11 123445666655555  578899


Q ss_pred             eeceee
Q psy556           95 FLGLIW  100 (435)
Q Consensus        95 yLGv~l  100 (435)
                      |||..|
T Consensus       114 fLG~~~  119 (119)
T cd03714         114 FLGLEL  119 (119)
T ss_pred             ECcEeC
Confidence            999865

Members of the subfamily include the Dictyostelium DIRS-1, Volvox carteri kangaroo, and Panagrellus redivivus PAT elements. These elements differ from LTR and conventional non-LTR retrotransposons. They contain split direct repeat (SDR) termini, and have been proposed to integrate via double-stranded closed-circle DNA intermediates assisted by an encoded recombinase which is similar to gamma-site-specific integrase.

>PRK13907 rnhA ribonuclease H; Provisional

Probab=97.56  E-value=7e-05  Score=63.02  Aligned_cols=46  Identities=17%  Similarity=0.174  Sum_probs=37.0

Q ss_pred             cccccCCHHHHHHhhccCCCCC--------c--------eEEEEEecccCCCCcchHHhHHHhhcc
Q psy556          253 TPPWSDDMSEVIDLWRNLTSNN--------I--------KLTFIWCPSHCGIEGNEEVDRAANRDG  302 (435)
Q Consensus       253 ~~i~sDs~sa~~~l~~~~~~~~--------i--------~v~~~Wvp~H~gi~gNe~AD~~Ak~a~  302 (435)
                      +.|++||+..+..+.+......        +        .+.+.|||.+    .|+.||.+|+.|.
T Consensus        64 v~i~sDS~~vi~~~~~~~~~~~~~~~l~~~~~~l~~~f~~~~~~~v~r~----~N~~Ad~LA~~a~  125 (128)
T PRK13907         64 VSFRTDSQLVERAVEKEYAKNKMFAPLLEEALQYIKSFDLFFIKWIPSS----QNKVADELARKAI  125 (128)
T ss_pred             EEEEechHHHHHHHhHHHhcChhHHHHHHHHHHHHhcCCceEEEEcCch----hchhHHHHHHHHH
Confidence            6799999999999987443221        1        6778999994    7999999999986

>KOG1005|consensus

Probab=97.12  E-value=0.00059  Score=72.07  Aligned_cols=60  Identities=27%  Similarity=0.271  Sum_probs=47.5

Q ss_pred             EEEECCccccceeccCCCCCCCchhHHHHHHHHHhhhhhc-C---CC--cceeeeccceeEEEecCCHh
Q psy556            6 AVKCNNLISNFKGLENGLVQGSSLSTLLFAVFMNDIFHVI-N---LP--TRGLLFVDDLLLTIRGKILE   68 (435)
Q Consensus         6 ~v~~~g~~s~~~~i~~GvpQGs~LSP~Lf~l~~~~l~~~~-~---~~--~~~~~yADD~~i~~~~~~~~   68 (435)
                      -|+++|   ..+....|+||||+||-+|-.+|+++|.+.. .   .+  +.++-|+||..++++..+..
T Consensus       621 ~vki~~---k~yvq~~GIpQGs~LSslLc~lyy~dle~~y~~~~~~~g~~vLlR~vDDFLfITt~~~~a  686 (888)
T KOG1005|consen  621 YVKIGG---KSYVQKKGIPQGSILSSLLCHLYYGDLEDKYFSFEKEDGSIVLLRYVDDFLFITTENDQA  686 (888)
T ss_pred             eEEECC---eEEEEecCccCCCchhHHHHHHHHHhHHHHHhhcccCCCcEEEEEeecceEEEecCHHHH
Confidence            366666   3355677999999999999999999999872 2   22  36899999999998777655

>cd03715 RT_ZFREV_like RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the intact endogenous retrovirus ZFERV from zebrafish and to Moloney murine leukemia virus RT

Probab=96.76  E-value=0.00085  Score=61.57  Aligned_cols=79  Identities=25%  Similarity=0.218  Sum_probs=54.2

Q ss_pred             cCCCCCCCchhHHHHHHHHHhhhhhcC---CCcceeeeccceeEEEecCCHhHhh------ccCCCCCceEeCCeeeec-
Q psy556           20 ENGLVQGSSLSTLLFAVFMNDIFHVIN---LPTRGLLFVDDLLLTIRGKILEQLG------SRNPTLPLIMLNGNQLKF-   89 (435)
Q Consensus        20 ~~GvpQGs~LSP~Lf~l~~~~l~~~~~---~~~~~~~yADD~~i~~~~~~~~~l~------k~~~~~~~~~l~~~~I~~-   89 (435)
                      ..-+|||...||.+|+-++..++..+.   .+..+..|.||+.+++.  +.++..      ...+....+.++..+... 
T Consensus       122 ~~~lp~Gl~~sp~~f~~~~~~~l~~~~~~~~~~~~~~Y~DDili~s~--~~~e~~~~l~~v~~~l~~~gl~l~~~K~~~~  199 (210)
T cd03715         122 FTRLPQGFKNSPTLFHEALARDLAPFPLEHEGTILLQYVDDLLLAAD--SEEDCLKGTDALLTHLGELGYKVSPKKAQIC  199 (210)
T ss_pred             EEEEeccccCcHHHHHHHHHHHHHHHHhhCCCeEEEEECCcEEEecC--CHHHHHHHHHHHHHHHHHCCCCcCHHHeeCC
Confidence            457899999999999999999988753   45678899999999854  444322      111223334444333332 


Q ss_pred             cCcceeeceee
Q psy556           90 DNTAKFLGLIW  100 (435)
Q Consensus        90 ~~~~kyLGv~l  100 (435)
                      .++++|||..+
T Consensus       200 ~~~v~fLG~~~  210 (210)
T cd03715         200 RAEVKFLGVVW  210 (210)
T ss_pred             CCceEEeeEEC
Confidence            57899999874

An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs. Phylogenetic analysis suggests that ZFERV belongs to a distinct group of retroviruses.

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

Probab=96.54  E-value=0.0021  Score=49.55  Aligned_cols=47  Identities=21%  Similarity=0.073  Sum_probs=35.3

Q ss_pred             cccccCCHHHHHHhhccCCC-CC-------c--------eEEEEEecccCCCCcchHHhHHHhhccC
Q psy556          253 TPPWSDDMSEVIDLWRNLTS-NN-------I--------KLTFIWCPSHCGIEGNEEVDRAANRDGH  303 (435)
Q Consensus       253 ~~i~sDs~sa~~~l~~~~~~-~~-------i--------~v~~~Wvp~H~gi~gNe~AD~~Ak~a~~  303 (435)
                      +.+.|||+.+++.+++.... +.       |        .+.+.|||-    .+|..||.+||.|.+
T Consensus        24 i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~r----~~N~~A~~LA~~a~~   86 (87)
T PF13456_consen   24 IIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDRFWNVSVSHIPR----EQNKVADALAKFALS   86 (87)
T ss_dssp             EEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCCCSCEEEEE--G----GGSHHHHHHHHHHHH
T ss_pred             EEEEecCccccccccccccccccccccchhhhhhhccccceEEEEECh----HHhHHHHHHHHHHhh
Confidence            78999999999999877433 23       1        799999997    679999999998853

>PRK07708 hypothetical protein; Validated

Probab=96.51  E-value=0.0034  Score=57.78  Aligned_cols=48  Identities=13%  Similarity=0.046  Sum_probs=37.5

Q ss_pred             cccccCCHHHHHHhhccCCCCC------------------ceEEEEEecccCCCCcchHHhHHHhhccCC
Q psy556          253 TPPWSDDMSEVIDLWRNLTSNN------------------IKLTFIWCPSHCGIEGNEEVDRAANRDGHT  304 (435)
Q Consensus       253 ~~i~sDs~sa~~~l~~~~~~~~------------------i~v~~~Wvp~H~gi~gNe~AD~~Ak~a~~~  304 (435)
                      +.|++||+.++..+.+-.....                  +++.+.|||-.    -|+.||++|+.|...
T Consensus       143 V~I~~DSqlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~VpR~----~N~~AD~LAk~Al~~  208 (219)
T PRK07708        143 VTFRGDSQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPISRK----QNKEADQLATQALEG  208 (219)
T ss_pred             EEEEeccHHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECCch----hhhHHHHHHHHHHhc
Confidence            4689999999999987543222                  25778899874    499999999999864

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=96.49  E-value=0.0034  Score=62.93  Aligned_cols=48  Identities=21%  Similarity=0.292  Sum_probs=38.8

Q ss_pred             cccccCCHHHHHHhhccCCCCC---------c--------eEEEEEecccCCCCcchHHhHHHhhccCC
Q psy556          253 TPPWSDDMSEVIDLWRNLTSNN---------I--------KLTFIWCPSHCGIEGNEEVDRAANRDGHT  304 (435)
Q Consensus       253 ~~i~sDs~sa~~~l~~~~~~~~---------i--------~v~~~Wvp~H~gi~gNe~AD~~Ak~a~~~  304 (435)
                      +.|++||+.+++.+.+......         |        .+++.|||.    .+|+.||.+|+.|...
T Consensus        68 v~i~~DS~lvi~~i~~~~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~r----~~N~~AD~LA~~a~~~  132 (372)
T PRK07238         68 VEVRMDSKLVVEQMSGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPR----ARNAHADRLANEAMDA  132 (372)
T ss_pred             EEEEeCcHHHHHHhCCCCccCChHHHHHHHHHHHHHhcCCceEEEECCc----hhhhHHHHHHHHHHHh
Confidence            6799999999999976543221         1        799999998    6799999999998644

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

Probab=95.58  E-value=0.005  Score=47.84  Aligned_cols=31  Identities=23%  Similarity=0.329  Sum_probs=25.7

Q ss_pred             cccccCCCCCCCCCCCc-ccchhHH-hhccCcH
Q psy556          377 SYLFERTTPPLCSCGEN-LLTVKHL-LDCVHHA  407 (435)
Q Consensus       377 ~~~~~~~~~~~C~~c~~-~et~~H~-~~Cp~~~  407 (435)
                      +.+.+...++.|..|+. .||++|+ ++||...
T Consensus        51 l~~r~~~~~~~C~~C~~~~Et~~Hlf~~C~~a~   83 (86)
T PF13966_consen   51 LQRRGIQVDPICPLCGNEEETIEHLFFHCPFAR   83 (86)
T ss_pred             hhccCCccCCccccCCCccccccceeccCcCcc
Confidence            45666678899998886 7999999 9999764

>KOG4768|consensus

Probab=95.06  E-value=0.019  Score=58.94  Aligned_cols=23  Identities=30%  Similarity=0.517  Sum_probs=20.9

Q ss_pred             CCCCCCCchhHHHHHHHHHhhhh
Q psy556           21 NGLVQGSSLSTLLFAVFMNDIFH   43 (435)
Q Consensus        21 ~GvpQGs~LSP~Lf~l~~~~l~~   43 (435)
                      =|+||||+.||+|-|+|+..|.+
T Consensus       416 lGtpqgsvvspil~nifL~~LDk  438 (796)
T KOG4768|consen  416 LGTPQGSVVSPILCNIFLRELDK  438 (796)
T ss_pred             ccccccccCCchhHHHHHHHHHH
Confidence            39999999999999999988864

>cd01647 RT_LTR RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long terminal repeats (LTRs) in their DNA copies but not in their RNA template

Probab=92.68  E-value=0.087  Score=45.84  Aligned_cols=43  Identities=19%  Similarity=0.225  Sum_probs=35.1

Q ss_pred             CCCCCCCchhHHHHHHHHHhhhhhcCCCcceeeeccceeEEEec
Q psy556           21 NGLVQGSSLSTLLFAVFMNDIFHVINLPTRGLLFVDDLLLTIRG   64 (435)
Q Consensus        21 ~GvpQGs~LSP~Lf~l~~~~l~~~~~~~~~~~~yADD~~i~~~~   64 (435)
                      ..+|||...||.+|.-.+..++..+. +..+..|+||+.+....
T Consensus        94 ~~~p~G~~~s~~~~~~~~~~~l~~~~-~~~~~~y~DDi~i~~~~  136 (177)
T cd01647          94 TRMPFGLKNAPATFQRLMNKILGDLL-GDFVEVYLDDILVYSKT  136 (177)
T ss_pred             EEecCCCccHHHHHHHHHHhhhcccc-ccccEEEecCccccCCC
Confidence            46999999999999999998887642 33578899999998554

RT catalyzes DNA replication from an RNA template, and is responsible for the replication of retroelements. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs are present in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and Caulimoviruses.

>cd01644 RT_pepA17 RT_pepA17: Reverse transcriptase (RTs) in retrotransposons

Probab=92.39  E-value=0.11  Score=47.67  Aligned_cols=47  Identities=13%  Similarity=0.069  Sum_probs=37.6

Q ss_pred             eccCCCCCCCchhHHHHHHHHHhhhhhcCC-----CcceeeeccceeEEEec
Q psy556           18 GLENGLVQGSSLSTLLFAVFMNDIFHVINL-----PTRGLLFVDDLLLTIRG   64 (435)
Q Consensus        18 ~i~~GvpQGs~LSP~Lf~l~~~~l~~~~~~-----~~~~~~yADD~~i~~~~   64 (435)
                      .--.-+|+|-.-||.+|+.+++.+++.+..     .+....|+||+.+.+..
T Consensus        99 Y~~~~~pFG~~~AP~~~~~~~~~~~~~~~~~~~~~~i~~~~YvDDili~~~s  150 (213)
T cd01644          99 YRMTVVPFGAASAPFLANRALKQHAEDHPHEAAAKIIKRNFYVDDILVSTDT  150 (213)
T ss_pred             EEEEEEccCCccchHHHHHHHHHHHhhcchhhHHHHHHHeeecccceecCCC
Confidence            344569999999999999999999987553     23467999999997444

This subfamily represents the RT domain of a multifunctional enzyme. C-terminal to the RT domain is a domain homologous to aspartic proteinases (corresponding to Merops family A17) encoded by retrotransposons and retroviruses. RT catalyzes DNA replication from an RNA template and is responsible for the replication of retroelements.

---

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	435
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-08
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	1e-04
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	5e-04

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

 Score = 55.2 bits (132), Expect = 3e-08
 Identities = 64/477 (13%), Positives = 145/477 (30%), Gaps = 133/477 (27%)

Query: 26  GSSLSTLLFAV---------FMNDIFHVINLPTRGLLFVDDLLLTIRGKILEQLGSRNPT 76
           GS  + +   V             IF  +NL         + +L +  K+L Q+     +
Sbjct: 160 GSGKTWVALDVCLSYKVQCKMDFKIFW-LNL---KNCNSPETVLEMLQKLLYQIDPNWTS 215

Query: 77  LPLIMLNGNQLKFDNTAKFLGLIWDRKMSWKQHVKYTKIKALTALNALKIVMLDYGSPIY 136
                 N  +L+  +    L     R +  K +            N L +V+L+  +   
Sbjct: 216 RSDHSSN-IKLRIHSIQAEL----RRLLKSKPYE-----------NCL-LVLLNVQNA-- 256

Query: 137 GSAKDHVIAKLNTEHHIGIRI--------VTGALRTSPVPSLYVESGIPPLVIRRQK-LL 187
                      N    +  +I        VT  L  +    + ++     L     K LL
Sbjct: 257 -----KAWNAFN----LSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLL 307

Query: 188 LNYV-TKIS-----ACPSNPVYNILFPTSLRRRLGIYEFTRTPKPLFVRF-RAIEAYVQE 240
           L Y+  +          +NP    +   S+R  L  ++  +       +    IE+ +  
Sbjct: 308 LKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWK--HVNCDKLTTIIESSLNV 365

Query: 241 LDRCDMME-YKDLT--PPWSDDMSEVID-LWRNLTSNNIKLTFIWCPSHCGIEGNEEVDR 296
           L+  +  + +  L+  PP +   + ++  +W ++  +++ +             N+    
Sbjct: 366 LEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVV-----------NKLHKY 414

Query: 297 A-ANRDGHTQAINI--------CSPDDLKTMVKKL--------AYNNWQVLWNQTDP--- 336
           +   +      I+I           ++   + + +         +++  ++    D    
Sbjct: 415 SLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFY 474

Query: 337 ------LNKLKQ----------------IKPIISTWKTSQQSRRYDEVVLSRLRIGHTRV 374
                 L  ++                 ++  I    T+  +       L +L+     +
Sbjct: 475 SHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYI 534

Query: 375 T-HSYLFERTTPP----LCSCGENLLTVKHLLDCVHHAPVRSTLSSKPSLLDEPEGV 426
             +   +ER        L    ENL+  K+  D +  A           L+ E E +
Sbjct: 535 CDNDPKYERLVNAILDFLPKIEENLICSKY-TDLLRIA-----------LMAEDEAI 579

>2qkb_A Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hybrid; 2.40A {Homo sapiens} PDB: 2qk9_A 2qkk_A* Length = 154

 Score = 41.4 bits (98), Expect = 1e-04
 Identities = 11/39 (28%), Positives = 18/39 (46%), Gaps = 2/39 (5%)

Query: 264 IDLWRNL--TSNNIKLTFIWCPSHCGIEGNEEVDRAANR 300
            + +  L   +  + + ++  P H G  GNEE DR A  
Sbjct: 109 KEDFVALERLTQGMDIQWMHVPGHSGFIGNEEADRLARE 147

>2kq2_A Ribonuclease H-related protein; PSI, NESG, protein structure, APO enzyme, structural genomics, protein structure initiative; NMR {Desulfitobacterium hafniense dcb-2} PDB: 2kw4_A Length = 147

 Score = 39.3 bits (92), Expect = 5e-04
 Identities = 10/46 (21%), Positives = 16/46 (34%), Gaps = 5/46 (10%)

Query: 264 IDLWRNLTSNNIKLTFIWCPSHCGIEGNEEVDRAANRDGHTQAINI 309
               + +       +F    +H G E N+ VD  A       A+ I
Sbjct: 97  QAYAKLMNQYRGIYSFEKVKAHSGNEFNDYVDMKAK-----SALGI 137

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	435
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	99.42
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	99.41
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.28
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.28
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	99.26
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.25
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	99.23
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.23
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.17
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	98.95
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	98.89
3kyl_A	596	Telomerase reverse transcriptase; reverse transcri	98.62
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	98.54
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	98.42
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	98.12
3fsi_A	255	RT, reverse transcriptase domain; transferase/DNA	96.69
2zd1_B	428	P51 RT; P51/P66, hetero dimer, NNRTI, nonnucleosid	96.43
1rw3_A	455	POL polyprotein; RNA and DNA dependent DNA polymer	95.51
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	85.54

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

Probab=99.42  E-value=1.2e-13  Score=143.68  Aligned_cols=84  Identities=15%  Similarity=0.086  Sum_probs=56.9

Q ss_pred             cCCCCCCCchhHHHHHHHHHhhhhhcC---CCcceeeeccceeEEEecCCHhHhh-----ccCCCCCceEeCCeeeeccC
Q psy556           20 ENGLVQGSSLSTLLFAVFMNDIFHVIN---LPTRGLLFVDDLLLTIRGKILEQLG-----SRNPTLPLIMLNGNQLKFDN   91 (435)
Q Consensus        20 ~~GvpQGs~LSP~Lf~l~~~~l~~~~~---~~~~~~~yADD~~i~~~~~~~~~l~-----k~~~~~~~~~l~~~~I~~~~   91 (435)
                      ...+|||-.-||.+|.-+|+.++..+.   +++.+..|.||+.|.+.....+.+.     ...+....+.++..+...++
T Consensus       146 ~~~mPfGl~napa~fq~~m~~il~~~~~~~~~~~v~~Y~DDIli~s~~~~~eh~~~l~~v~~~l~~~gl~l~~~K~~~~~  225 (555)
T 1mu2_A          146 YKVLPQGWKGSPAIFQHTMRQVLEPFRKANKDVIIIQYMDDILIASDRTDLEHDRVVLQLKELLNGLGFSTPDEKFQKDP  225 (555)
T ss_dssp             ESBCCTTCTTHHHHHHHHHHHHHHHHHHHCTTSEEEEETTEEEEEECSCHHHHHHHHHHHHHHHHHTTCBCCSTTEECSS
T ss_pred             EEEeCCCCCCcHHHHHHHHHHHHHHHHhhCCCcEEEEEecceEEecCCCHHHHHHHHHHHHHHHHHcCCccCHHHhccCC
Confidence            457899999999999999999998743   4667899999999986522222111     11111223344434444577


Q ss_pred             cceeeceeecCc
Q psy556           92 TAKFLGLIWDRK  103 (435)
Q Consensus        92 ~~kyLGv~ld~~  103 (435)
                      +++|||..++.+
T Consensus       226 ~~~fLG~~i~~~  237 (555)
T 1mu2_A          226 PYHWMGYELWPT  237 (555)
T ss_dssp             SEEETTEEECSS
T ss_pred             ceeEEeEEEeCC
Confidence            899999998764

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

Probab=99.41  E-value=4e-13  Score=139.93  Aligned_cols=84  Identities=15%  Similarity=0.063  Sum_probs=56.5

Q ss_pred             cCCCCCCCchhHHHHHHHHHhhhhhcC---CCcceeeeccceeEEEecCCHhHhh-----ccCCCCCceEeCCeeeeccC
Q psy556           20 ENGLVQGSSLSTLLFAVFMNDIFHVIN---LPTRGLLFVDDLLLTIRGKILEQLG-----SRNPTLPLIMLNGNQLKFDN   91 (435)
Q Consensus        20 ~~GvpQGs~LSP~Lf~l~~~~l~~~~~---~~~~~~~yADD~~i~~~~~~~~~l~-----k~~~~~~~~~l~~~~I~~~~   91 (435)
                      -..+|||-.-||.+|.-+|+.++..+.   +++.+..|.||+.+.+.....+.+.     ...+....+.++..+.....
T Consensus       148 ~~~mPfGl~nap~~fq~~m~~il~~~~~~~~~~~v~~Y~DDIli~s~~~~~eh~~~l~~v~~~l~~~gl~l~~~Kc~f~~  227 (557)
T 2zd1_A          148 YNVLPQGWKGSPAIFQSSMTKILEPFAAQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEP  227 (557)
T ss_dssp             ESBCCTTCTTHHHHHHHHHHHHHHHHHHTCTTEEEEEETTEEEEEECSCHHHHHHHHHHHHHHHHTTTCCCCCSCCSCCS
T ss_pred             EEeeCCCCCCHHHHHHHHHHHHHHHhhhcCCCceEEEEecCEEEecCchHHHHHHHHHHHHHHHHHcCCccChhhcCCCC
Confidence            457899999999999999999998742   4566899999999987532222111     11111223444444444456


Q ss_pred             cceeeceeecCc
Q psy556           92 TAKFLGLIWDRK  103 (435)
Q Consensus        92 ~~kyLGv~ld~~  103 (435)
                      +++|||..++.+
T Consensus       228 ~~~fLG~~i~~~  239 (557)
T 2zd1_A          228 PFLWMGYELHPD  239 (557)
T ss_dssp             SEEETTEEECSS
T ss_pred             ceEEeeEEEccC
Confidence            788999998764

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

Probab=99.28  E-value=1.1e-12  Score=112.40  Aligned_cols=61  Identities=18%  Similarity=0.066  Sum_probs=48.4

Q ss_pred             CCChh--hhhcc------------cccccCCHHHHHHhhccC---------------CCCC-------------ceEEEE
Q psy556          243 RCDMM--EYKDL------------TPPWSDDMSEVIDLWRNL---------------TSNN-------------IKLTFI  280 (435)
Q Consensus       243 ~~~v~--El~ai------------~~i~sDs~sa~~~l~~~~---------------~~~~-------------i~v~~~  280 (435)
                      .+|..  |+.|+            +.|+|||+++++.|....               +...             +.|.|.
T Consensus        41 ~~Tnn~aEl~A~~~AL~~~~~~~~v~I~tDS~~vi~~i~~~w~~~W~~~~w~~~~~~~v~n~~l~~~~~~~~~~~~v~~~  120 (146)
T 3h08_A           41 ATTNNRMELMAAIKGLEALKEPARVQLYSDSAYLVNAMNEGWLKRWVKNGWKTAAKKPVENIDLWQEILKLTTLHRVTFH  120 (146)
T ss_dssp             EECHHHHHHHHHHHHHHTCSSCCEEEEEESCHHHHHHHHSSHHHHHHHTTCC----CCCTTHHHHHHHHHHHHHSEEEEE
T ss_pred             CCcHHHHHHHHHHHHHHhcCccCcEEEEeChHHHHHHHHHHHHHHHHHCCCccCCCCCcCCHHHHHHHHHHHhhCceEEE
Confidence            34554  88888            789999999999997621               1111             289999


Q ss_pred             EecccCCCCcchHHhHHHhhccC
Q psy556          281 WCPSHCGIEGNEEVDRAANRDGH  303 (435)
Q Consensus       281 Wvp~H~gi~gNe~AD~~Ak~a~~  303 (435)
                      |||||+|++|||.||+|||+|+.
T Consensus       121 ~V~gH~g~~~N~~AD~LA~~a~~  143 (146)
T 3h08_A          121 KVKGHSDNPYNSRADELARLAIK  143 (146)
T ss_dssp             ECCC-CCSHHHHHHHHHHHHHHH
T ss_pred             EcCCcCCcHhHHHHHHHHHHHHH
Confidence            99999999999999999999974

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

Probab=99.28  E-value=1.5e-12  Score=111.79  Aligned_cols=63  Identities=22%  Similarity=0.293  Sum_probs=50.5

Q ss_pred             CCCChh--hhhcc----------cccccCCHHHHHHhhcc-----------CCC---CC--------------ceEEEEE
Q psy556          242 DRCDMM--EYKDL----------TPPWSDDMSEVIDLWRN-----------LTS---NN--------------IKLTFIW  281 (435)
Q Consensus       242 ~~~~v~--El~ai----------~~i~sDs~sa~~~l~~~-----------~~~---~~--------------i~v~~~W  281 (435)
                      ..+|..  |+.|+          +.|+|||+++++.+...           ...   ..              ..|.|.|
T Consensus        45 ~~~Tnn~aEl~A~i~AL~~~~~~v~i~tDS~~v~~~i~~w~~~W~~~gw~~~~g~~v~n~~l~~~l~~~l~~~~~v~~~w  124 (150)
T 3qio_A           45 TDTTNQKTELQAIYLALQDSGLEVNIVTDSQYALGIITQWIHNWKKRGWKTADKKPVKNVDLVNQIIEQLIKKEKVYLAW  124 (150)
T ss_dssp             SSCCHHHHHHHHHHHHHHHSCSEEEEEESCHHHHHHHHHHHHHHCC------------CHHHHHHHHHHHTTCSEEEEEE
T ss_pred             CCCCHHHHHHHHHHHHHHhCCCcEEEEeCcHHHHHHHHHHHHHHhhcCcCcCcCcccccHHHHHHHHHHHhhcCceEEEE
Confidence            455655  99988          78999999999999653           011   11              2899999


Q ss_pred             ecccCCCCcchHHhHHHhhccCC
Q psy556          282 CPSHCGIEGNEEVDRAANRDGHT  304 (435)
Q Consensus       282 vp~H~gi~gNe~AD~~Ak~a~~~  304 (435)
                      ||||+|++|||.||++|++|+..
T Consensus       125 V~gH~g~~~Ne~AD~LA~~a~~~  147 (150)
T 3qio_A          125 VPAHKGIGGNEQVDKLVSAGIRK  147 (150)
T ss_dssp             CCTTSCCHHHHHHHHHHHTTTSC
T ss_pred             ccCcCCChhHHHHHHHHHHHHHH
Confidence            99999999999999999999864

>1jl1_A Ribonuclease HI; RNAse HI, protein stability, thermostability, hydrogen exchange, cooperativity, hydrolase; 1.30A {Escherichia coli} SCOP: c.55.3.1 PDB: 1f21_A 1jxb_A 1g15_A 1rch_A 1rdd_A 1rnh_A* 2rn2_A 1rda_A 1law_A 1rdb_A 1lav_A 3aa4_A 1rbu_A 1gob_A 1rdc_A 1kvc_A 3aa3_A 3aa2_A 3aa5_X 1rbv_A ...

Probab=99.26  E-value=1.9e-12  Score=111.96  Aligned_cols=65  Identities=17%  Similarity=0.203  Sum_probs=52.7

Q ss_pred             CCChh--hhhcc------------cccccCCHHHHHHhhc--------c-CCCCC------------------ceEEEEE
Q psy556          243 RCDMM--EYKDL------------TPPWSDDMSEVIDLWR--------N-LTSNN------------------IKLTFIW  281 (435)
Q Consensus       243 ~~~v~--El~ai------------~~i~sDs~sa~~~l~~--------~-~~~~~------------------i~v~~~W  281 (435)
                      .+|..  |+.|+            +.|+|||+++++.|..        . ...++                  ..|.|.|
T Consensus        41 ~~tn~~aEl~A~~~aL~~~~~~~~v~I~tDS~~vi~~i~~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~~~~v~~~w  120 (155)
T 1jl1_A           41 RTTNNRMELMAAIVALEALKEHAEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWEW  120 (155)
T ss_dssp             EECHHHHHHHHHHHHHHTCCSCCEEEEEECCHHHHHHHHTTHHHHHHTTTBCTTSCBCTTHHHHHHHHHHTTTCEEEEEE
T ss_pred             CCcHHHHHHHHHHHHHHHhCcCCcEEEEeCHHHHHHHHHHHHHHHhhcccccccCCccCCHHHHHHHHHHHccCceEEEE
Confidence            34555  98888            6899999999999975        2 11111                  2899999


Q ss_pred             ecccCCCCcchHHhHHHhhccCCCCC
Q psy556          282 CPSHCGIEGNEEVDRAANRDGHTQAI  307 (435)
Q Consensus       282 vp~H~gi~gNe~AD~~Ak~a~~~~~~  307 (435)
                      ||||+|++|||.||+|||+|+..+.+
T Consensus       121 V~gH~g~~~Ne~AD~LA~~a~~~~~~  146 (155)
T 1jl1_A          121 VKGHAGHPENERADELARAAAMNPTL  146 (155)
T ss_dssp             CCSSTTCHHHHHHHHHHHHHHHSCCB
T ss_pred             cCCCCCCHHHHHHHHHHHHHHhccch
Confidence            99999999999999999999987643

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

Probab=99.25  E-value=4.4e-12  Score=109.51  Aligned_cols=63  Identities=24%  Similarity=0.353  Sum_probs=51.4

Q ss_pred             CCChh--hhhcc--------------cccccCCHHHHHHhhcc--------C-CCCC------------------ceEEE
Q psy556          243 RCDMM--EYKDL--------------TPPWSDDMSEVIDLWRN--------L-TSNN------------------IKLTF  279 (435)
Q Consensus       243 ~~~v~--El~ai--------------~~i~sDs~sa~~~l~~~--------~-~~~~------------------i~v~~  279 (435)
                      .+|.+  |+.|+              +.|+|||+++++.|...        + ..++                  +.|.|
T Consensus        47 ~~tn~~aEl~A~~~aL~~~~~~~~~~v~i~tDS~~vi~~i~~~~~~w~~~~w~~~~~~~~~n~~l~~~i~~l~~~~~v~~  126 (154)
T 2qkb_A           47 RQTNQRAEIHAACKAIEQAKTQNINKLVLYTNSMFTINGITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQGMDIQW  126 (154)
T ss_dssp             SCCHHHHHHHHHHHHHHHHHHTTCCEEEEEESCHHHHHHHHTHHHHHHTTTSBCTTSSBCTTHHHHHHHHHHHTTCEEEE
T ss_pred             CCchHHHHHHHHHHHHHHHHhCCCceEEEEECcHHHHhhhhhhHHHHHhccccccCCCccccHHHHHHHHHHHcCCceEE
Confidence            45666  98888              78999999999999651        1 1111                  28999


Q ss_pred             EEecccCCCCcchHHhHHHhhccCCC
Q psy556          280 IWCPSHCGIEGNEEVDRAANRDGHTQ  305 (435)
Q Consensus       280 ~Wvp~H~gi~gNe~AD~~Ak~a~~~~  305 (435)
                      .|||||+|++|||.||+|||+|+..+
T Consensus       127 ~~V~~H~g~~~N~~AD~LA~~a~~~~  152 (154)
T 2qkb_A          127 MHVPGHSGFIGNEEADRLAREGAKQS  152 (154)
T ss_dssp             EECCTTSSCHHHHHHHHHHHHHHTCC
T ss_pred             EEccCCCCCHhHHHHHHHHHHHHHhc
Confidence            99999999999999999999998754

>3p1g_A Xenotropic murine leukemia virus-related virus (X H domain; XMRV, RNAse H, reverse transcriptase, transcription; 1.50A {Xenotropic mulv-related virus} PDB: 3v1q_A 3v1o_A 3v1r_A* 2hb5_A 4e89_A

Probab=99.23  E-value=3.8e-12  Score=110.80  Aligned_cols=64  Identities=20%  Similarity=0.276  Sum_probs=51.5

Q ss_pred             CCCChh--hhhcc-----------cccccCCHHHHHHhhccCCCCC-----------------ceEEEEEecccCC----
Q psy556          242 DRCDMM--EYKDL-----------TPPWSDDMSEVIDLWRNLTSNN-----------------IKLTFIWCPSHCG----  287 (435)
Q Consensus       242 ~~~~v~--El~ai-----------~~i~sDs~sa~~~l~~~~~~~~-----------------i~v~~~Wvp~H~g----  287 (435)
                      ..+|..  |+.|+           +.|+|||+++++.+........                 .+|.|.|||||+|    
T Consensus        59 ~~~Tnn~aEl~Ai~~AL~~~~~~~v~I~tDS~~vi~~iw~~~~g~~v~n~dl~~~l~~~l~~~~~v~~~wVkgH~g~~~~  138 (165)
T 3p1g_A           59 AGTSAQRAELIALTQALKMAEGKKLNVYTDSRYAFATAHVHSEGREIKNKNEILALLKALFLPKRLSIIHCPGHQKGNSA  138 (165)
T ss_dssp             TTCCHHHHHHHHHHHHHHHTBTSEEEEEECCHHHHHHHHSCCCSCCCSSHHHHHHHHHHTTSBSEEEEEECCSSCCSCSH
T ss_pred             CCCcHHHHHHHHHHHHHHHccCceEEEEEchHHHHhhhhcccCCCcccCHHHHHHHHHHHhcCCceEEEEecCCCCCCcC
Confidence            455666  99988           7899999999999943222111                 2899999999999    


Q ss_pred             -CCcchHHhHHHhhccCCC
Q psy556          288 -IEGNEEVDRAANRDGHTQ  305 (435)
Q Consensus       288 -i~gNe~AD~~Ak~a~~~~  305 (435)
                       ++|||+||++||+|+..+
T Consensus       139 ~~~gNe~AD~LA~~aa~~~  157 (165)
T 3p1g_A          139 EARGNRMADQAAREAAMKA  157 (165)
T ss_dssp             HHHHHHHHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHhcC
Confidence             999999999999998653

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

Probab=99.23  E-value=3.1e-12  Score=110.90  Aligned_cols=62  Identities=21%  Similarity=0.191  Sum_probs=51.0

Q ss_pred             CCChh--hhhcc------------cccccCCHHHHHHhhc--------cC-CCCC------------------ceEEEEE
Q psy556          243 RCDMM--EYKDL------------TPPWSDDMSEVIDLWR--------NL-TSNN------------------IKLTFIW  281 (435)
Q Consensus       243 ~~~v~--El~ai------------~~i~sDs~sa~~~l~~--------~~-~~~~------------------i~v~~~W  281 (435)
                      .+|..  |+.|+            +.|+|||+++++.|..        .. ..++                  ..|.|.|
T Consensus        43 ~~tn~~aEl~A~~~AL~~~~~~~~v~I~tDS~~vi~~i~~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~~~~v~~~w  122 (158)
T 2e4l_A           43 LTTNNRMELLAPIVALEALKEPCKIILTSDSQYMRQGIMTWIHGWKKKGWMTSNRTPVKNVDLWKRLDKAAQLHQIDWRW  122 (158)
T ss_dssp             EECHHHHHHHHHHHHHHTCSSCCEEEEEECCHHHHHHHHTHHHHHHHTTTBCTTSSBCTTHHHHHHHHHHHTTSEEEEEE
T ss_pred             CCccHHHHHHHHHHHHHHhccCCeEEEEeCHHHHHHHHHHHHHHHHHccccccCCCcccCHHHHHHHHHHHccCcEEEEE
Confidence            35555  98888            6899999999999976        22 1111                  2899999


Q ss_pred             ecccCCCCcchHHhHHHhhccCC
Q psy556          282 CPSHCGIEGNEEVDRAANRDGHT  304 (435)
Q Consensus       282 vp~H~gi~gNe~AD~~Ak~a~~~  304 (435)
                      ||||+|++|||.||+|||+|+..
T Consensus       123 V~gH~g~~~Ne~AD~LAk~a~~~  145 (158)
T 2e4l_A          123 VKGHAGHAENERCDQLARAAAEA  145 (158)
T ss_dssp             CCTTCCCHHHHHHHHHHHHHHHS
T ss_pred             ccCCCCchhHHHHHHHHHHHHHh
Confidence            99999999999999999999876

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

Probab=99.17  E-value=5.2e-12  Score=110.34  Aligned_cols=63  Identities=24%  Similarity=0.254  Sum_probs=51.7

Q ss_pred             CCChh--hhhcc------------cccccCCHHHHHHhhc----------cCCCCC------------------ceEEEE
Q psy556          243 RCDMM--EYKDL------------TPPWSDDMSEVIDLWR----------NLTSNN------------------IKLTFI  280 (435)
Q Consensus       243 ~~~v~--El~ai------------~~i~sDs~sa~~~l~~----------~~~~~~------------------i~v~~~  280 (435)
                      .+|..  |+.|+            +.|+|||+++++.|..          ....++                  ..|.|.
T Consensus        45 ~~Tnn~aEl~Ai~~AL~~~~~~~~v~I~tDS~~vi~~i~~~w~~~W~~~~w~~~~g~~v~n~~l~~~i~~l~~~~~v~~~  124 (166)
T 1ril_A           45 CTTNNRMELKAAIEGLKALKEPCEVDLYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPHRVRFH  124 (166)
T ss_dssp             EECHHHHHHHHHHHHHHSCCSCCEEEEECCCHHHHHHHHSSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHTTSEEECC
T ss_pred             CCcHHHHHHHHHHHHHHHhccCCeEEEEeChHHHHHHHhhhHHHHHHhcccccccCCccCcHHHHHHHHHHHhcCeEEEE
Confidence            34555  98888            7899999999999987          122222                  279999


Q ss_pred             EecccCCCCcchHHhHHHhhccCCC
Q psy556          281 WCPSHCGIEGNEEVDRAANRDGHTQ  305 (435)
Q Consensus       281 Wvp~H~gi~gNe~AD~~Ak~a~~~~  305 (435)
                      |||||+|++|||.||+|||+|+...
T Consensus       125 wV~gH~g~~~Ne~AD~LAk~a~~~~  149 (166)
T 1ril_A          125 FVKGHTGHPENERVDREARRQAQSQ  149 (166)
T ss_dssp             CCCGGGSCTHHHHHHHHHHHHHTSS
T ss_pred             EeeCCCCchhHHHHHHHHHHHHHHh
Confidence            9999999999999999999999775

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

Probab=98.95  E-value=3.7e-10  Score=98.07  Aligned_cols=51  Identities=16%  Similarity=0.128  Sum_probs=40.5

Q ss_pred             cccccCCHHHHHHhhc--------cCCC-CC-------------------ceEEEEEecccCCC------CcchHHhHHH
Q psy556          253 TPPWSDDMSEVIDLWR--------NLTS-NN-------------------IKLTFIWCPSHCGI------EGNEEVDRAA  298 (435)
Q Consensus       253 ~~i~sDs~sa~~~l~~--------~~~~-~~-------------------i~v~~~Wvp~H~gi------~gNe~AD~~A  298 (435)
                      +.|+|||+++++.+..        .+.. ++                   ..|.|.|||||+|+      +|||+||+||
T Consensus        78 v~I~TDS~Yvi~~it~w~~~Wk~ngw~~~~~~pVkN~dL~~~l~~~~~~~~~v~~~~VkgH~g~~~~~~~~gNe~AD~LA  157 (165)
T 2lsn_A           78 VLVITDSFYVAESANKELPYWKSNGFVNNKKKPLKHISKWKSIAECLSMKPDITIQHEKGHQPTNTSIHTEGNALADKLA  157 (165)
T ss_dssp             EEEEESCHHHHHHHHTHHHHHHHTTSCSCSSSCCSSHHHHHHHHHHHHHCTTCEEEECCSSSCSSSCHHHHHHHHHHHHH
T ss_pred             EEEEeChHHHHhhhhhhhhhheeccccccCCCcccCHHHHHHHHHHHhCCCCEEEEEEeCCCCccCCCCChHHHHHHHHH
Confidence            6899999999999943        2111 11                   17999999999996      4899999999


Q ss_pred             hhccC
Q psy556          299 NRDGH  303 (435)
Q Consensus       299 k~a~~  303 (435)
                      ++|+.
T Consensus       158 ~~gA~  162 (165)
T 2lsn_A          158 TQGSY  162 (165)
T ss_dssp             HHHHH
T ss_pred             HHhhh
Confidence            99873

>2kq2_A Ribonuclease H-related protein; PSI, NESG, protein structure, APO enzyme, structural genomics, protein structure initiative; NMR {Desulfitobacterium hafniense dcb-2} PDB: 2kw4_A

Probab=98.89  E-value=1.9e-10  Score=98.32  Aligned_cols=62  Identities=18%  Similarity=0.031  Sum_probs=50.3

Q ss_pred             CChh--hhhcc-------------cccccCCHHHHHHhhccCCCCC------------c--eEEEEEecccCCCCcchHH
Q psy556          244 CDMM--EYKDL-------------TPPWSDDMSEVIDLWRNLTSNN------------I--KLTFIWCPSHCGIEGNEEV  294 (435)
Q Consensus       244 ~~v~--El~ai-------------~~i~sDs~sa~~~l~~~~~~~~------------i--~v~~~Wvp~H~gi~gNe~A  294 (435)
                      +|++  |+.|+             +.|++||+++..-+.+.+..+.            +  .|.|.|||||+|++|||+|
T Consensus        48 ~tNn~aEl~A~~~AL~~a~~~~~~v~I~tDS~~i~~w~~~~w~~~~~~~~~~~~l~~~l~~~v~~~wV~gH~g~~~Ne~A  127 (147)
T 2kq2_A           48 MRNVAGEIAAALYAVKKASQLGVKIRILHDYAGIAFWATGEWKAKNEFTQAYAKLMNQYRGIYSFEKVKAHSGNEFNDYV  127 (147)
T ss_dssp             TCTTHHHHHHHHHHHHHHHHHTCCCCBSSCCSTHHHHTTSSSSCCHHHHHHHHCGGGGGSTTCCBCCCCCCCCCHHHHHH
T ss_pred             ccHHHHHHHHHHHHHHHHHHCCCeEEEEECcHHHHHHHhCCCccCCcchHHHHHHHHHhcCCeeEEEecCcCCCcchHHH
Confidence            3555  98888             7899999987776665443332            1  6999999999999999999


Q ss_pred             hHHHhhccCCC
Q psy556          295 DRAANRDGHTQ  305 (435)
Q Consensus       295 D~~Ak~a~~~~  305 (435)
                      |+|||+|+..+
T Consensus       128 D~LA~~a~~~~  138 (147)
T 2kq2_A          128 DMKAKSALGIR  138 (147)
T ss_dssp             HHHHHHHHTCC
T ss_pred             HHHHHHHHhcc
Confidence            99999999775

>3kyl_A Telomerase reverse transcriptase; reverse transcriptase; 2.70A {Tribolium castaneum} PDB: 3du5_A 3du6_A

Probab=98.62  E-value=1.5e-08  Score=100.08  Aligned_cols=93  Identities=19%  Similarity=0.136  Sum_probs=60.2

Q ss_pred             EEECCccccceeccCCCCCCCchhHHHHHHHHHhhhhhc----CCCcceeeeccceeEEEecCCHhHhh----c----cC
Q psy556            7 VKCNNLISNFKGLENGLVQGSSLSTLLFAVFMNDIFHVI----NLPTRGLLFVDDLLLTIRGKILEQLG----S----RN   74 (435)
Q Consensus         7 v~~~g~~s~~~~i~~GvpQGs~LSP~Lf~l~~~~l~~~~----~~~~~~~~yADD~~i~~~~~~~~~l~----k----~~   74 (435)
                      |.++|.   ...-+.|+|||++|||+|-|+|++++.+.+    ..+..++-||||.++++......+..    +    .+
T Consensus       293 V~igGk---~y~qekGTPQGGVISPLLANIYLheLDkel~~~l~kd~~LVRYADDFVIi~~Ske~Aerfl~~Lkg~leLN  369 (596)
T 3kyl_A          293 VAFRRK---IYKWNHGLLQGDPLSGCLCELYMAFMDRLYFSNLDKDAFIHRTVDDYFFCSPHPHKVYDFELLIKGVYQVN  369 (596)
T ss_dssp             EESSSS---EEEECSSSCBTCTTHHHHHHHHHHHHHHHHSTTSCTTSEEEECSSEEEEEESCHHHHHHHHHHHHHHSCEE
T ss_pred             EEECCE---EEecCCcccCCcchhHHHHHHHHHHHHHHHHHhhccCceEEEEcCcEEEEECCHHHHHHHHHHhhCcceEC
Confidence            444553   345678999999999999999999998774    24667899999999998765443211    0    00


Q ss_pred             CCCCceEeCCeeeeccCcceeeceeecCc
Q psy556           75 PTLPLIMLNGNQLKFDNTAKFLGLIWDRK  103 (435)
Q Consensus        75 ~~~~~~~l~~~~I~~~~~~kyLGv~ld~~  103 (435)
                      .....+......+ +...+.|+|+.||.+
T Consensus       370 pEKTrInF~~~~l-p~~~fpwCGLLIDtk  397 (596)
T 3kyl_A          370 PTKTRTNLPTHRH-PQDEIPYCGKIFNLT  397 (596)
T ss_dssp             EEEEEECCTTSSS-CCSEEEETTEEEETT
T ss_pred             chhceeecccccC-CCceeeeeeEEEECC
Confidence            0000111111111 236689999999875

>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=98.54  E-value=4e-08  Score=82.96  Aligned_cols=57  Identities=23%  Similarity=0.323  Sum_probs=46.3

Q ss_pred             CCChh--hhhcc--------------cccccCCHHHHHHhhccCCCCC-----------------ceEEEEEecccCCCC
Q psy556          243 RCDMM--EYKDL--------------TPPWSDDMSEVIDLWRNLTSNN-----------------IKLTFIWCPSHCGIE  289 (435)
Q Consensus       243 ~~~v~--El~ai--------------~~i~sDs~sa~~~l~~~~~~~~-----------------i~v~~~Wvp~H~gi~  289 (435)
                      .+|..  |+.|+              +.|++||+.+++.+.+.+....                 ..|.|.|||+    +
T Consensus        43 ~~tn~~aEl~A~~~aL~~a~~~~~~~v~i~tDS~~vv~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~v~~~~V~~----~  118 (141)
T 3hst_B           43 RATNNVAEYRGLIAGLDDAVKLGATEAAVLMDSKLVVEQMSGRWKVKHPDLLKLYVQAQALASQFRRINYEWVPR----A  118 (141)
T ss_dssp             EECHHHHHHHHHHHHHHHHHHHTCSEEEEEESCHHHHHHHTTSSCCCSHHHHHHHHHHHHHHTTSSEEEEEECCG----G
T ss_pred             CCchHHHHHHHHHHHHHHHHHCCCceEEEEeChHHHHHHHhCCcccCCHHHHHHHHHHHHHHhcCCeEEEEEcCC----c
Confidence            44555  88888              7899999999999987543322                 2799999996    8


Q ss_pred             cchHHhHHHhhccC
Q psy556          290 GNEEVDRAANRDGH  303 (435)
Q Consensus       290 gNe~AD~~Ak~a~~  303 (435)
                      +||.||++||+|+.
T Consensus       119 ~N~~AD~LA~~a~~  132 (141)
T 3hst_B          119 RNTYADRLANDAMD  132 (141)
T ss_dssp             GCHHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHH
Confidence            99999999999864

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

Probab=98.42  E-value=8.7e-08  Score=80.61  Aligned_cols=46  Identities=20%  Similarity=0.155  Sum_probs=38.0

Q ss_pred             ccccCCHHHHHHhhccCCCCC------------------ceEEEEEecccCCCCcchHHhHHHhhccC
Q psy556          254 PPWSDDMSEVIDLWRNLTSNN------------------IKLTFIWCPSHCGIEGNEEVDRAANRDGH  303 (435)
Q Consensus       254 ~i~sDs~sa~~~l~~~~~~~~------------------i~v~~~Wvp~H~gi~gNe~AD~~Ak~a~~  303 (435)
                      .|++||+++++.+.+......                  ..|.|.|||.    ++||.||++||+|+.
T Consensus        73 ~i~tDS~~vi~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~~v~~~~V~~----~~N~~AD~LA~~a~~  136 (140)
T 3u3g_D           73 EVRMDSELIVRQMQGVYKVKEPTLKEKFAKIAHIKMERVPNLVFVHIPR----EKNARADELVNEAID  136 (140)
T ss_dssp             EEEESCHHHHHHHTTSSCCCCGGGHHHHHHHHHHHHHHCTTCEEEECCG----GGGHHHHHHHHHHHH
T ss_pred             EEEeChHHHHHHhCCCcccCCHHHHHHHHHHHHHhhcCCCcEEEEEcCc----hhhHHHHHHHHHHHH
Confidence            599999999999987654222                  1799999995    899999999999863

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

Probab=98.12  E-value=1.5e-06  Score=74.06  Aligned_cols=58  Identities=22%  Similarity=0.299  Sum_probs=47.0

Q ss_pred             CCChh--hhhcc--------------cccccCCHHHHHHhhccCCCC-C---------------ceEEEEEecccCCCCc
Q psy556          243 RCDMM--EYKDL--------------TPPWSDDMSEVIDLWRNLTSN-N---------------IKLTFIWCPSHCGIEG  290 (435)
Q Consensus       243 ~~~v~--El~ai--------------~~i~sDs~sa~~~l~~~~~~~-~---------------i~v~~~Wvp~H~gi~g  290 (435)
                      .+|..  |+.|+              +.|++||+.+++.+.+....+ +               ..|.|.|||+    .+
T Consensus        45 ~~tnn~aEl~A~~~aL~~a~~~g~~~v~i~tDS~~vi~~i~~~w~~~~~~~~~l~~~i~~l~~~~~v~~~~V~~----~~  120 (149)
T 2ehg_A           45 NSTNNVAEYSGLICLMETMLRLGISSPIIKGDSQLVIKQMNGEYKVKAKRIIPLYEKAIELKKKLNATLIWVPR----EE  120 (149)
T ss_dssp             TCCHHHHHHHHHHHHHHHHHHHTCCSCEEEESCHHHHHHHTTSSCCCCTTHHHHHHHHHHHHHHHTCEEEECCG----GG
T ss_pred             CccHHHHHHHHHHHHHHHHHHcCCCEEEEEeChHHHHHHHhCccccCCHHHHHHHHHHHHHHhcCCEEEEEcCC----cc
Confidence            45665  98887              789999999999998864432 2               1699999999    48


Q ss_pred             chHHhHHHhhccCC
Q psy556          291 NEEVDRAANRDGHT  304 (435)
Q Consensus       291 Ne~AD~~Ak~a~~~  304 (435)
                      ||.||++||+|+..
T Consensus       121 N~~AD~LA~~a~~~  134 (149)
T 2ehg_A          121 NKEADRLSRVAYEL  134 (149)
T ss_dssp             CHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHh
Confidence            99999999998743

>3fsi_A RT, reverse transcriptase domain; transferase/DNA MMLV RT, protein-DNA complex, drug-DNA complex; HET: OWL; 1.75A {Moloney murine leukemia virus} SCOP: e.8.1.2 PDB: 1d1u_A 1n4l_A* 1ztt_A 2fjv_A* 2fjw_A 2fjx_A* 2fvp_A 2fvq_A 2fvr_A 2fvs_A 2r2r_A* 2r2s_A* 2r2t_A* 2r2u_A* 1ztw_A* 1i6j_A 1qaj_A* 1d0e_A* 1nnd_A 1mml_A ...

Probab=96.69  E-value=0.00056  Score=63.42  Aligned_cols=81  Identities=20%  Similarity=0.146  Sum_probs=53.8

Q ss_pred             CCCCCCCchhHHHHHHHHHhhhhhcC---CCcceeeeccceeEEEecCCHhHhh------ccCCCCCceEeCCeeeec-c
Q psy556           21 NGLVQGSSLSTLLFAVFMNDIFHVIN---LPTRGLLFVDDLLLTIRGKILEQLG------SRNPTLPLIMLNGNQLKF-D   90 (435)
Q Consensus        21 ~GvpQGs~LSP~Lf~l~~~~l~~~~~---~~~~~~~yADD~~i~~~~~~~~~l~------k~~~~~~~~~l~~~~I~~-~   90 (435)
                      .-+|||-.-||.+|+-+|+.+++.+.   .++.+..|+||+.+.+.  +.++..      ...+....+.++..+... .
T Consensus       163 ~~mPfGl~~sP~~fq~~m~~il~~~~~~~~~~~v~~Y~DDili~s~--~~eeh~~~l~~v~~~L~~~gl~l~~~Kc~f~~  240 (255)
T 3fsi_A          163 TRLPQGFKNSPTLFDEALHRDLADFRIQHPDLILLQYVDDLLLAAT--SELDCQQGTRALLQTLGNLGYRASAKKAQICQ  240 (255)
T ss_dssp             SBCCTTCTTHHHHHHHHHHHHTHHHHHHCTTCEEEEETTEEEEEES--SHHHHHHHHHHHHHHHHHHTCCBCTTTCEEEE
T ss_pred             EEeCCCCCCcHHHHHHHHHHHHHHHHHhCcCcEEEEEcCCeEEEeC--CHHHHHHHHHHHHHHHHHCCeEECHHHhcccC
Confidence            34699999999999999999988742   55678999999998854  333321      000111122232222222 4


Q ss_pred             CcceeeceeecCc
Q psy556           91 NTAKFLGLIWDRK  103 (435)
Q Consensus        91 ~~~kyLGv~ld~~  103 (435)
                      ++++|||..++.+
T Consensus       241 ~~~~fLG~~i~~~  253 (255)
T 3fsi_A          241 KQVKYLGYLLKEG  253 (255)
T ss_dssp             SEEEETTEEEETT
T ss_pred             CceEEEEEEEeCC
Confidence            6799999999875

>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=96.43  E-value=0.00086  Score=67.04  Aligned_cols=84  Identities=15%  Similarity=0.067  Sum_probs=50.5

Q ss_pred             cCCCCCCCchhHHHHHHHHHhhhhhcC---CCcceeeeccceeEEEecCCHhHhh-----ccCCCCCceEeCCeeeeccC
Q psy556           20 ENGLVQGSSLSTLLFAVFMNDIFHVIN---LPTRGLLFVDDLLLTIRGKILEQLG-----SRNPTLPLIMLNGNQLKFDN   91 (435)
Q Consensus        20 ~~GvpQGs~LSP~Lf~l~~~~l~~~~~---~~~~~~~yADD~~i~~~~~~~~~l~-----k~~~~~~~~~l~~~~I~~~~   91 (435)
                      -.-+|||-.-||.+|+-+|+.+++.+.   +++.+..|+||+.+.+.....+...     ...+....+.++..+.....
T Consensus       146 ~~vmPfGl~nsPa~fq~~m~~il~~~~~~~~~~~v~vY~DDIlI~s~~~~~eh~~~l~~v~~~l~~~gL~l~~~Kc~~~~  225 (428)
T 2zd1_B          146 YNVLPQGWKGSPAIFQSSMTKILEPFKKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEP  225 (428)
T ss_dssp             ESBCCTTCTHHHHHHHHHHHHHHHHHHHHCTTCEEEEETTEEEEEECSCHHHHHHHHHHHHHHHHHHHC-----------
T ss_pred             EEeeCCCCcchHHHHHHHHHHHHHHHhhcCCCceEEEEecceEEecCCcHHHHHHHHHHHHHHHHHhCCccChhHccccc
Confidence            456899999999999999999998742   4566899999999987543222211     00111112333333333456


Q ss_pred             cceeeceeecCc
Q psy556           92 TAKFLGLIWDRK  103 (435)
Q Consensus        92 ~~kyLGv~ld~~  103 (435)
                      +++|||..++++
T Consensus       226 ~~~fLG~~i~~~  237 (428)
T 2zd1_B          226 PFLWMGYELHPD  237 (428)
T ss_dssp             -CTTCCEEECGG
T ss_pred             eEEEeccEecCC
Confidence            789999999865

>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=95.51  E-value=0.0053  Score=61.77  Aligned_cols=81  Identities=20%  Similarity=0.155  Sum_probs=52.8

Q ss_pred             CCCCCCCchhHHHHHHHHHhhhhhcC---CCcceeeeccceeEEEecCCHhHhh------ccCCCCCceEeCCeeeec-c
Q psy556           21 NGLVQGSSLSTLLFAVFMNDIFHVIN---LPTRGLLFVDDLLLTIRGKILEQLG------SRNPTLPLIMLNGNQLKF-D   90 (435)
Q Consensus        21 ~GvpQGs~LSP~Lf~l~~~~l~~~~~---~~~~~~~yADD~~i~~~~~~~~~l~------k~~~~~~~~~l~~~~I~~-~   90 (435)
                      .-+|||-.-||.+|+-+|+.+++.+.   .+..+..|+||+.+.+..  .++..      ...+....+.++-.+... .
T Consensus       167 ~~mpfGl~naP~~fq~~m~~~l~~~~~~~~~~~v~~YvDDili~s~~--~~e~~~~l~~v~~~l~~~gl~l~~~K~~f~~  244 (455)
T 1rw3_A          167 TRLPQGFKNSPTLFDEALHRDLADFRIQHPDLILLQYVDDLLLAATS--ELDCQQGTRALLQTLGNLGYRASAKKAQICQ  244 (455)
T ss_dssp             SBCCSSCTTHHHHHHHHHHHHHHHHHHTCTTCEEEEETTEEEEEESS--HHHHHHHHHHHHHHHHHHTCCBCGGGCCCSB
T ss_pred             EecCCCCCCcHHHHHHHHHHHHHHhhhhCCCceEEEEcCCEEEecCC--HHHHHHHHHHHHHHHHHcCCccCccchhhhc
Confidence            45899999999999999999988742   456788999999888544  33321      000001112222222211 4


Q ss_pred             CcceeeceeecCc
Q psy556           91 NTAKFLGLIWDRK  103 (435)
Q Consensus        91 ~~~kyLGv~ld~~  103 (435)
                      ++++|||..++.+
T Consensus       245 ~~~~fLG~~i~~~  257 (455)
T 1rw3_A          245 KQVKYLGYLLKEG  257 (455)
T ss_dssp             SSCEETTEEESSS
T ss_pred             cceeEeeeeccCC
Confidence            6789999999865

>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=85.54  E-value=0.082  Score=44.03  Aligned_cols=48  Identities=10%  Similarity=0.082  Sum_probs=33.7

Q ss_pred             hhhcc-------------cccccCCHHHHHHhhccCCC-C-C-----------c----------eEEEEEecccCCCCcc
Q psy556          248 EYKDL-------------TPPWSDDMSEVIDLWRNLTS-N-N-----------I----------KLTFIWCPSHCGIEGN  291 (435)
Q Consensus       248 El~ai-------------~~i~sDs~sa~~~l~~~~~~-~-~-----------i----------~v~~~Wvp~H~gi~gN  291 (435)
                      |+.|+             +.|+|||+.+++-+++.... + +           +          .++...+.-|++.-||
T Consensus        55 El~A~i~aL~~~~~~~~~v~i~tDS~~vi~w~~~~~~k~~~~~~v~n~dLw~~l~~~~~w~~~~~~~~~~~kw~~~~~ge  134 (142)
T 1zbf_A           55 EFLAIVHGLRYLKERNSRKPIYSNSQTAIKWVKDKKAKSTLVRNEETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGE  134 (142)
T ss_dssp             HHHHHHHHHHHHHHTTCCCCEEESCHHHHHHHHHTCCCCCCCCSTTTHHHHHHHHHHHHHHHHCCCCCCEEECCHHHHCS
T ss_pred             HHHHHHHHHHHHHhCCCeEEEEEehHHHHHHHHcCCccCCCCCCcccHHHHHHHHHHHHHHhhCCCceeEEEeccCccCc
Confidence            88887             67999999999999876421 1 1           1          4455556666666777


Q ss_pred             hHHh
Q psy556          292 EEVD  295 (435)
Q Consensus       292 e~AD  295 (435)
                      +.||
T Consensus       135 ~pad  138 (142)
T 1zbf_A          135 IKAD  138 (142)
T ss_dssp             CTTC
T ss_pred             Cccc
Confidence            7776

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	435
d1mu2a1	126	c.55.3.1 (A:430-555) HIV RNase H (Domain of revers	2e-05
d1rila_	147	c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermoph	2e-05
d1jl1a_	152	c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli	0.002

>d1mu2a1 c.55.3.1 (A:430-555) HIV RNase H (Domain of reverse transcriptase) {Human immunodeficiency virus type 2 [TaxId: 11709]} Length = 126

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: HIV RNase H (Domain of reverse transcriptase)
species: Human immunodeficiency virus type 2 [TaxId: 11709]

 Score = 41.8 bits (97), Expect = 2e-05
 Identities = 11/49 (22%), Positives = 23/49 (46%)

Query: 252 LTPPWSDDMSEVIDLWRNLTSNNIKLTFIWCPSHCGIEGNEEVDRAANR 300
           +    ++  S++++           +   W P+H GI GN+EVD   ++
Sbjct: 76  VASQPTESESKIVNQIIEEMIKKEAIYVAWVPAHKGIGGNQEVDHLVSQ 124

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

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

 Score = 42.2 bits (98), Expect = 2e-05
 Identities = 17/88 (19%), Positives = 24/88 (27%), Gaps = 4/88 (4%)

Query: 217 IYEFTRTPKPLFVRFRAIEAY----VQELDRCDMMEYKDLTPPWSDDMSEVIDLWRNLTS 272
           I       +P  V       Y      E       +    T       +  +     L  
Sbjct: 52  IEGLKALKEPCEVDLYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAM 111

Query: 273 NNIKLTFIWCPSHCGIEGNEEVDRAANR 300
              ++ F +   H G   NE VDR A R
Sbjct: 112 APHRVRFHFVKGHTGHPENERVDREARR 139

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

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

 Score = 36.1 bits (82), Expect = 0.002
 Identities = 7/34 (20%), Positives = 11/34 (32%)

Query: 267 WRNLTSNNIKLTFIWCPSHCGIEGNEEVDRAANR 300
             +      ++ + W   H G   NE  D  A  
Sbjct: 104 RLDAALGQHQIKWEWVKGHAGHPENERADELARA 137

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	435
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.53
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	99.36
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.27
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	98.29
d1mu2a2	427	HIV-1 reverse transcriptase {Human immunodeficienc	97.14
d2zd1b1	424	HIV-1 reverse transcriptase {Human immunodeficienc	96.72
d1ztwa1	255	MMLV reverse transcriptase {Moloney murine leukemi	96.11
d1zbfa1	132	BH0863-like Ribonuclease H {Bacillus halodurans [T	95.44
d1hara_	216	HIV-1 reverse transcriptase {Human immunodeficienc	90.59

>d1mu2a1 c.55.3.1 (A:430-555) HIV RNase H (Domain of reverse transcriptase) {Human immunodeficiency virus type 2 [TaxId: 11709]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: HIV RNase H (Domain of reverse transcriptase)
species: Human immunodeficiency virus type 2 [TaxId: 11709]

Probab=99.53  E-value=1.9e-15  Score=124.29  Aligned_cols=61  Identities=21%  Similarity=0.273  Sum_probs=52.5

Q ss_pred             CCCChh--hhhcc----------cccccCCHHHHHHhhccCCCCC--------------ceEEEEEecccCCCCcchHHh
Q psy556          242 DRCDMM--EYKDL----------TPPWSDDMSEVIDLWRNLTSNN--------------IKLTFIWCPSHCGIEGNEEVD  295 (435)
Q Consensus       242 ~~~~v~--El~ai----------~~i~sDs~sa~~~l~~~~~~~~--------------i~v~~~Wvp~H~gi~gNe~AD  295 (435)
                      ..+|+.  |+.||          +.|++||++++..+.+....+.              ..|.|.|||||+|++|||+||
T Consensus        40 ~~~tnn~AEl~Ai~~al~~~~~~i~I~tDS~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~wV~gH~g~~gNe~AD  119 (126)
T d1mu2a1          40 EQTTNQQAELEAFAMALTDSGPKVNIIVDSQYVMGIVASQPTESESKIVNQIIEEMIKKEAIYVAWVPAHKGIGGNQEVD  119 (126)
T ss_dssp             SSCCHHHHHHHHHHHHHHTSCSEEEEEESCHHHHHHHHTCCSEESCHHHHHHHHHHHHCSEEEEEECCSSSCCTTHHHHH
T ss_pred             CCCcchHHHHHHHHHHhccCCcceEEEechHHHHHHHhcCCccccchHHHHHHHHhhhcceeEEEEEeCCCCCcchHHHH
Confidence            666776  99999          8899999999999987544332              289999999999999999999


Q ss_pred             HHHhhcc
Q psy556          296 RAANRDG  302 (435)
Q Consensus       296 ~~Ak~a~  302 (435)
                      +||++|.
T Consensus       120 ~LA~~ai  126 (126)
T d1mu2a1         120 HLVSQGI  126 (126)
T ss_dssp             HHHHTTC
T ss_pred             HHHHhhC
Confidence            9999984

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

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

Probab=99.36  E-value=1.1e-13  Score=117.24  Aligned_cols=70  Identities=16%  Similarity=0.156  Sum_probs=53.7

Q ss_pred             CCCChh--hhhcc------------cccccCCHHHHHHhhcc---------CCCCC------------------ceEEEE
Q psy556          242 DRCDMM--EYKDL------------TPPWSDDMSEVIDLWRN---------LTSNN------------------IKLTFI  280 (435)
Q Consensus       242 ~~~~v~--El~ai------------~~i~sDs~sa~~~l~~~---------~~~~~------------------i~v~~~  280 (435)
                      ..+|..  |+.|+            +.+++||+.++..+...         ....+                  ..|.|+
T Consensus        38 ~~~tnn~aE~~Ai~~Al~~~~~~~~i~i~tds~~~i~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~i~~~~~~~~V~~~  117 (152)
T d1jl1a_          38 TRTTNNRMELMAAIVALEALKEHAEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWE  117 (152)
T ss_dssp             EEECHHHHHHHHHHHHHHTCCSCCEEEEEECCHHHHHHHHTTHHHHHHTTTBCTTSCBCTTHHHHHHHHHHTTTCEEEEE
T ss_pred             CcccHHHHHHhhhhhhhhhhcccceEEEeecceeeEEcccchhhHhHhccchhcccCeeecHHHHHHHHHHhhcceeEEE
Confidence            444444  88777            67899999998877422         11111                  179999


Q ss_pred             EecccCCCCcchHHhHHHhhccCCCCCCCCC
Q psy556          281 WCPSHCGIEGNEEVDRAANRDGHTQAINICS  311 (435)
Q Consensus       281 Wvp~H~gi~gNe~AD~~Ak~a~~~~~~~~~~  311 (435)
                      |||||+|++|||+||+|||+|+..|.+...+
T Consensus       118 wV~gH~g~~gNe~AD~LAk~aa~~~~~~d~~  148 (152)
T d1jl1a_         118 WVKGHAGHPENERADELARAAAMNPTLEDTG  148 (152)
T ss_dssp             ECCSSTTCHHHHHHHHHHHHHHHSCCBCCTT
T ss_pred             EecccCCCccHHHHHHHHHHHHhCCCCCccC
Confidence            9999999999999999999999988766554

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

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

Probab=99.27  E-value=3.8e-13  Score=113.23  Aligned_cols=58  Identities=26%  Similarity=0.339  Sum_probs=47.0

Q ss_pred             hhhcc------------cccccCCHHHHHHhhcc----------CCCCC------------------ceEEEEEecccCC
Q psy556          248 EYKDL------------TPPWSDDMSEVIDLWRN----------LTSNN------------------IKLTFIWCPSHCG  287 (435)
Q Consensus       248 El~ai------------~~i~sDs~sa~~~l~~~----------~~~~~------------------i~v~~~Wvp~H~g  287 (435)
                      |+.|+            +.|++||+.++..+...          ....+                  ..|+|.|||||+|
T Consensus        47 El~Ai~~AL~~~~~~~~i~i~tds~~~~~~~~~~~~~~~~~~~~~~~~~~~v~n~dL~~~l~~~~~~~~v~~~wVkgHsg  126 (147)
T d1rila_          47 ELKAAIEGLKALKEPCEVDLYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPHRVRFHFVKGHTG  126 (147)
T ss_dssp             HHHHHHHHHHSCCSCCEEEEECCCHHHHHHHHSSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHTTSEEECCCCCGGGS
T ss_pred             HHHHHHHHhhhccCCceEEEecchhhhhccccccchhhhhhccccccccccchhHHHHHHHHHHhhhcccceEEccCCCC
Confidence            88888            67999999999877432          11111                  2899999999999


Q ss_pred             CCcchHHhHHHhhccCCC
Q psy556          288 IEGNEEVDRAANRDGHTQ  305 (435)
Q Consensus       288 i~gNe~AD~~Ak~a~~~~  305 (435)
                      ++|||.||+|||+|+.+.
T Consensus       127 ~~gNe~AD~LAk~aa~~~  144 (147)
T d1rila_         127 HPENERVDREARRQAQSQ  144 (147)
T ss_dssp             CTHHHHHHHHHHHHHTSS
T ss_pred             CcchHHHHHHHHHHHHHh
Confidence            999999999999998753

>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=98.29  E-value=1.1e-07  Score=74.76  Aligned_cols=44  Identities=16%  Similarity=0.243  Sum_probs=35.6

Q ss_pred             CCCChh--hhhcc----------cccccCCHHHHHHhhccCCCCC------c--------eEEEEEeccc
Q psy556          242 DRCDMM--EYKDL----------TPPWSDDMSEVIDLWRNLTSNN------I--------KLTFIWCPSH  285 (435)
Q Consensus       242 ~~~~v~--El~ai----------~~i~sDs~sa~~~l~~~~~~~~------i--------~v~~~Wvp~H  285 (435)
                      ..+|..  ||.||          +.|+|||+++++.+........      |        .|.+.|||||
T Consensus        41 ~~~TNn~aEl~Avi~aL~~~~~~v~I~TDS~yvi~~i~~~~~~~~~~l~~~il~~l~~~~~v~i~WVpgH  110 (110)
T d1s1ta1          41 TDTTNQKTELQAIYLALQDSGLEVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAH  110 (110)
T ss_dssp             SSCCHHHHHHHHHHHHHHHSCSEEEEEECCHHHHHHHHHCCSEESCHHHHHHHHHHHHCSEEEEEECCSS
T ss_pred             ccCcHHHHHHHHHHHHHHhCCCeEEEEEehHHHHHHHhcCccccchHHHHHHHHHHhcCCceEEEEeCCC
Confidence            455665  99999          8999999999999987544333      1        8999999999

>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=97.14  E-value=0.00011  Score=70.63  Aligned_cols=87  Identities=16%  Similarity=0.102  Sum_probs=61.3

Q ss_pred             eeccCCCCCCCchhHHHHHHHHHhhhhhc---CCCcceeeeccceeEEEecCCHhHhh-----ccCCCCCceEeCCeeee
Q psy556           17 KGLENGLVQGSSLSTLLFAVFMNDIFHVI---NLPTRGLLFVDDLLLTIRGKILEQLG-----SRNPTLPLIMLNGNQLK   88 (435)
Q Consensus        17 ~~i~~GvpQGs~LSP~Lf~l~~~~l~~~~---~~~~~~~~yADD~~i~~~~~~~~~l~-----k~~~~~~~~~l~~~~I~   88 (435)
                      ..--+-+|||-.-||.+|.-+|+.++..+   .+++.++.|+||+.|.+.....+...     +..+....+.++...+.
T Consensus       141 ~y~~~vLP~GlknsPa~fQ~~m~~iL~~~~~~~~~~~i~~Y~DDIlI~S~~~~~eH~~~v~~l~~~l~~~g~~~~~kK~~  220 (427)
T d1mu2a2         141 RYIYKVLPQGWKGSPAIFQHTMRQVLEPFRKANKDVIIIQYMDDILIASDRTDLEHDRVVLQLKELLNGLGFSTPDEKFQ  220 (427)
T ss_dssp             EEEESBCCTTCTTHHHHHHHHHHHHHHHHHHHCTTSEEEEETTEEEEEECSCHHHHHHHHHHHHHHHHHTTCBCCSTTEE
T ss_pred             eEEEeecCCCCcCcHHHHHHHHHHHHHHHHhhcccceeEeeeeeeEeeccchhHHHHHHHHHHHHHHHHhcchhhhhhhh
Confidence            33445699999999999999999999874   35677899999999987543323221     11111223445555566


Q ss_pred             ccCcceeeceeecCc
Q psy556           89 FDNTAKFLGLIWDRK  103 (435)
Q Consensus        89 ~~~~~kyLGv~ld~~  103 (435)
                      ...+++|||..++++
T Consensus       221 ~~~~v~~LG~~i~~~  235 (427)
T d1mu2a2         221 KDPPYHWMGYELWPT  235 (427)
T ss_dssp             CSSSEEETTEEECSS
T ss_pred             ceeeeeeeeeEecCC
Confidence            677899999999765

>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=96.72  E-value=0.0002  Score=68.69  Aligned_cols=84  Identities=15%  Similarity=0.067  Sum_probs=51.0

Q ss_pred             cCCCCCCCchhHHHHHHHHHhhhhhcC---CCcceeeeccceeEEEecCCHhHhh-----ccCCCCCceEeCCeeeeccC
Q psy556           20 ENGLVQGSSLSTLLFAVFMNDIFHVIN---LPTRGLLFVDDLLLTIRGKILEQLG-----SRNPTLPLIMLNGNQLKFDN   91 (435)
Q Consensus        20 ~~GvpQGs~LSP~Lf~l~~~~l~~~~~---~~~~~~~yADD~~i~~~~~~~~~l~-----k~~~~~~~~~l~~~~I~~~~   91 (435)
                      .+-+|||-.-||.+|.-+|+.++..+.   .++-+..|+||+.|.+.....+...     ...+....+.++.......+
T Consensus       142 ~~vlPfGl~nsPa~Fqr~m~~il~~~~~~~~~~~i~~Y~DDIlI~S~~~~eeH~~~l~~vl~~L~~~gl~l~~Kk~f~~~  221 (424)
T d2zd1b1         142 YNVLPQGWKGSPAIFQSSMTKILEPFKKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEP  221 (424)
T ss_dssp             ESBCCTTCTHHHHHHHHHHHHHHHHHHHHCTTCEEEEETTEEEEEECSCHHHHHHHHHHHHHHHHHHHC-----------
T ss_pred             EEecCCcccCcHHHHHHHHHHHcccccccCcceeEEeccceEEEecCchhHHHHHHHHHHHHHHHHhCCccchhhhhhhc
Confidence            456899999999999999999997642   4566899999999876433232211     11111223444555556677


Q ss_pred             cceeeceeecCc
Q psy556           92 TAKFLGLIWDRK  103 (435)
Q Consensus        92 ~~kyLGv~ld~~  103 (435)
                      +++|||..++++
T Consensus       222 ~v~~LG~~is~~  233 (424)
T d2zd1b1         222 PFLWMGYELHPD  233 (424)
T ss_dssp             -CTTCCEEECGG
T ss_pred             ccccceeeecCC
Confidence            899999999865

>d1ztwa1 e.8.1.2 (A:24-278) MMLV reverse transcriptase {Moloney murine leukemia virus, MoMLV [TaxId: 11801]}

class: Multi-domain proteins (alpha and beta)
fold: DNA/RNA polymerases
superfamily: DNA/RNA polymerases
family: Reverse transcriptase
domain: MMLV reverse transcriptase
species: Moloney murine leukemia virus, MoMLV [TaxId: 11801]

Probab=96.11  E-value=0.0011  Score=59.32  Aligned_cols=82  Identities=20%  Similarity=0.119  Sum_probs=54.2

Q ss_pred             cCCCCCCCchhHHHHHHHHHhhhhhcC---CCcceeeeccceeEEEecCCHhHhh------ccCCCCCceEeCCeeee-c
Q psy556           20 ENGLVQGSSLSTLLFAVFMNDIFHVIN---LPTRGLLFVDDLLLTIRGKILEQLG------SRNPTLPLIMLNGNQLK-F   89 (435)
Q Consensus        20 ~~GvpQGs~LSP~Lf~l~~~~l~~~~~---~~~~~~~yADD~~i~~~~~~~~~l~------k~~~~~~~~~l~~~~I~-~   89 (435)
                      .+.+|||..-||..|.-+|+.++..+.   .++.+..|.||+.+.+.  +.++..      ...+....+.++-.+.+ .
T Consensus       162 ~~~lPfGl~~spa~fq~~~~~il~~~~~~~~~~~~~~Y~DDili~s~--t~~eh~~~l~~vl~~l~~~gl~~~~~K~~~~  239 (255)
T d1ztwa1         162 WTRLPQGFKNSPTLFDEALHRDLADFRIQHPDLILLQYVDDLLLAAT--SELDCQQGTRALLQTLGNLGYRASAKKAQIC  239 (255)
T ss_dssp             ESBCCTTCTTHHHHHHHHHHHHTHHHHHHCTTCEEEEETTEEEEEES--SHHHHHHHHHHHHHHHHHHTCCBCTTTCEEE
T ss_pred             EeeeehhcccchhhhHHHHHHHHHHhhccCCceEEEEEeeeeeccCC--CHHHHHHHHHHHHHHHHHCcCEeCHHHeECC
Confidence            456999999999999999999887642   56678899999999744  444322      00001112233322222 2


Q ss_pred             cCcceeeceeecCc
Q psy556           90 DNTAKFLGLIWDRK  103 (435)
Q Consensus        90 ~~~~kyLGv~ld~~  103 (435)
                      .++++|||..++..
T Consensus       240 ~~~v~fLG~~I~~G  253 (255)
T d1ztwa1         240 QKQVKYLGYLLKEG  253 (255)
T ss_dssp             ESEEEETTEEEETT
T ss_pred             CCCcEEeEEEEeCC
Confidence            56799999999764

>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=95.44  E-value=0.00055  Score=54.28  Aligned_cols=48  Identities=10%  Similarity=0.058  Sum_probs=37.8

Q ss_pred             hhhcc-------------cccccCCHHHHHHhhccCCC--CC-----------c----------eEEEEEecccCCCCcc
Q psy556          248 EYKDL-------------TPPWSDDMSEVIDLWRNLTS--NN-----------I----------KLTFIWCPSHCGIEGN  291 (435)
Q Consensus       248 El~ai-------------~~i~sDs~sa~~~l~~~~~~--~~-----------i----------~v~~~Wvp~H~gi~gN  291 (435)
                      |+.|+             +.|+|||+.++.-+.+-...  .+           |          .+.+.|+..|+.--||
T Consensus        48 El~A~i~aL~~~~~~~~~i~I~tDS~yvi~wv~~~~~kt~~~~~vkN~~l~~~i~~a~~~lk~h~~~~~~~KW~~~~wG~  127 (132)
T d1zbfa1          48 EFLAIVHGLRYLKERNSRKPIYSNSQTAIKWVKDKKAKSTLVRNEETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGE  127 (132)
T ss_dssp             HHHHHHHHHHHHHHTTCCCCEEESCHHHHHHHHHTCCCCCCCCSTTTHHHHHHHHHHHHHHHHCCCCCCEEECCHHHHCS
T ss_pred             HHHHHHHHHHHhhcCCceEEEEeccHHHHHHHHhCceecCcCCCcccHHHHHHHHHHHHHHHhCCcCceeEEecCccccc
Confidence            88888             78999999999998653211  11           1          7888899999988888


Q ss_pred             hHHh
Q psy556          292 EEVD  295 (435)
Q Consensus       292 e~AD  295 (435)
                      ..||
T Consensus       128 i~AD  131 (132)
T d1zbfa1         128 IKAD  131 (132)
T ss_dssp             CTTC
T ss_pred             CCCC
Confidence            8887

>d1hara_ e.8.1.2 (A:) 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=90.59  E-value=0.11  Score=44.25  Aligned_cols=44  Identities=25%  Similarity=0.190  Sum_probs=37.1

Q ss_pred             ccCCCCCCCchhHHHHHHHHHhhhhhcC---CCcceeeeccceeEEE
Q psy556           19 LENGLVQGSSLSTLLFAVFMNDIFHVIN---LPTRGLLFVDDLLLTI   62 (435)
Q Consensus        19 i~~GvpQGs~LSP~Lf~l~~~~l~~~~~---~~~~~~~yADD~~i~~   62 (435)
                      -.+-+|||-.-||..|.=+|+.++..+.   .++-++.|.||+.|++
T Consensus       145 ~~~~lPfGl~naPa~fqr~m~~~l~~~~~~~~~~~v~~YlDDIlI~S  191 (216)
T d1hara_         145 QYNVLPQGWKGSPAIFQSSMTKILAPFKAANPDIVIYQYMDDLYVGS  191 (216)
T ss_dssp             EESBCCTTCTTHHHHHHHHHHHHHHHHHHHCTTSEEEEETTEEEEEE
T ss_pred             EEEEcCCcccCcHHHHHHHHHHHHHHHhhcCCCeEEEEECceEEEcc
Confidence            3567999999999999999999998753   4566889999999875