Psyllid ID: psy7520

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (MEMSAT_SVM)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

--------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--

MKYCMLLVVLWNILLLVEHEYKKMSKAKGDLSLDLDQLDCACKNGFCPASRYEQFISGKGGLPQGHPDSLLGPPFLLASPLFLKTIFLPYIKPLPPWSFDVPTFDNSLGSDKKDNISSVAFQQHFRDLLYSKYAHFTPCYTDGSKSVNGTSCAYSINNLIVLSTSLNQVVCVYSSELIAIHLCLEHLKFLPSSHFLIISDSKSALTALSNNTSDNPIVAKISVTWRKLKDYGKTVSFLWCPSHSGIAGNEFVDNAARNPVNPHLPLKLCSPLDLKPFAAKLTKTKWQALWDTLPIPNKLKRVKPVIEDWGSSNRDNRYEEVVICRMRIGHTRATHSFLFKRTPPPSCRCGDPLTVLHILSCHLHANIRASLPTPPLLTDSPEGVDSLINYLKAIDTRIYEQE

cccHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHcccccccEEEEcccccccccEEEEEEcccEEEEEccccccccHHHHHHHHHHHHHHHHccccccEEEEcccHHHHHHHHccccccHHHHHHHHHHHHHHccccEEEEEccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccHHHHHHHHHHcccccccccccccccccccccccccccccHHccccccHHHHHcccccccccccHHHHHHHHHHHHHHcccccccc

ccHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHcHcccccHHHHHHHHHHcccccccccccccccccccccccEcccccccccccccccccccccEEEEEcccccccccHHHHHHHHHHHHHHcccccEEEEEccccccccEEEEEEEccccEEEEEcccccHHHHHHHHHHHHHHHHHHHcccccEEEEEccHHHHHHHHccccccHHHHHHHHHHHHHHHcccEEEEEEEcccccccccHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccHHHHHHHHHHcccccHHHHHHcccccccccccccccccEEEEccHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHccc

MKYCMLLVVLWNILLLVEHEYKKMSkakgdlsldldqldcackngfcpasryeqfisgkgglpqghpdsllgppfllasplflktiflpyikplppwsfdvptfdnslgsdkkdnisSVAFQQHFRDLLYskyahftpcytdgsksvngtscaYSINNLIVLSTSLNQVVCVYSSELIAIHLCLEhlkflpsshfliiSDSKSALTALsnntsdnpivAKISVTWRKLKDygktvsflwcpshsgiagnefvdnaarnpvnphlplklcspldlkpFAAKLTKTKWQALwdtlpipnklkrvkpviedwgssnrdnrYEEVVICRMrightrathsflfkrtpppscrcgdpltvLHILSCHLHAniraslptpplltdspegVDSLINYLKAIDTRIYEQE

MKYCMLLVVLWNILLLVEHEYKKMSKAKGDLSLDLDQLDCACKNGFCPASRYEQFISGKGGLPQGHPDSLLGPPFLLASPLFLKTIFLPYIKPLPPWSFDVPTFDNSLGSDKKDNISSVAFQQHFRDLLYSKYAHFTPCYTDGSKSVNGTSCAYSINNLIVLSTSLNQVVCVYSSELIAIHLCLEHLKFLPSSHFLIISDSKSALTAlsnntsdnpivaKISVTWRKLKDYGKTVSFLWCPSHSGIAGNEFVDNAARNPVNPHLPLKLCSPLDLKPFAAKLTKTKWqalwdtlpipnklkrvkpviedwgssnrdnryeEVVICRMRIGHTRATHSFLFKRTPPPSCRCGDPLTVLHILSCHLHANIRASLptpplltdspegVDSLINYLKAIDTRIYEQE

MKYCMllvvlwnilllvEHEYKKMSKAKGDLSLDLDQLDCACKNGFCPASRYEQFISGKGGLPQGHPDSLLGPPFLLASPLFLKTIFLPYIKPLPPWSFDVPTFDNSLGSDKKDNISSVAFQQHFRDLLYSKYAHFTPCYTDGSKSVNGTSCAYSINNLIVLSTSLNQVVCVYSSELIAIHLCLEHLKFLPSSHFLIISDSKSALTALSNNTSDNPIVAKISVTWRKLKDYGKTVSFLWCPSHSGIAGNEFVDNAARNPVNPHLPLKLCSPLDLKPFAAKLTKTKWQALWDTLPIPNKLKRVKPVIEDWGSSNRDNRYEEVVICRMRIGHTRATHSFLFKRTPPPSCRCGDPLTVLHILSCHLHANIRASlptpplltDSPEGVDSLINYLKAIDTRIYEQE

**YCMLLVVLWNILLLVEHEYKKMSKAKGDLSLDLDQLDCACKNGFCPASRYEQFISGKGGLPQGHPDSLLGPPFLLASPLFLKTIFLPYIKPLPPWSFDVPTFDNSLG****DNISSVAFQQHFRDLLYSKYAHFTPCYTDGSKSVNGTSCAYSINNLIVLSTSLNQVVCVYSSELIAIHLCLEHLKFLPSSHFLIISDSKSALTALSNNTSDNPIVAKISVTWRKLKDYGKTVSFLWCPSHSGIAGNEFVDNAARNPVNPHLPLKLCSPLDLKPFAAKLTKTKWQALWDTLPIPNKLKRVKPVIEDWGSSNRDNRYEEVVICRMRIGHTRATHSFLFKRTPPPSCRCGDPLTVLHILSCHLHANIRASLPTPPLLTDSPEGVDSLINYLKAIDTRIY***

*KYCMLLVVLWNILLLVEHEYK*********SLDLDQLDCACKNGFCPA***********************PPFLLASPLFLKTIFLPYIKPLPPWSFDVPTFDNSL**************QHFRDLLYSKYAHFTPCYTDGSKSVNGTSCAYSINNLIVLSTSLNQVVCVYSSELIAIHLCLEHLKFLPSSHFLIISDSKSALTALSNNTSDNPIVAKISVTWRKLKDYGKTVSFLWCPSHSGIAGNEFVDNAARNPVNPHLPLKLCSPLDLKPFAAKLTKTKWQALWDTLPIPNKLKRVKPVIEDWGSSNRDNRYEEVVICRMRIGHTRATHSFLFKRTPPPSCRCGDPLTVLHILSCHLHANIRASLPTPPLLTDSPEGVDSLINYLKAIDT******

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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SSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

No hits with e-value below 0.001 by BLAST

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		402
443693558		502	hypothetical protein CAPTEDRAFT_189741,	0.699	0.559	0.360	2e-33
125901787		1222	pol-like protein [Biomphalaria glabrata]	0.676	0.222	0.364	6e-33
427778603		1397	Putative tick transposon [Rhipicephalus	0.703	0.202	0.335	9e-30
443695973		261	hypothetical protein CAPTEDRAFT_23017, p	0.629	0.969	0.367	9e-30
443721618		471	hypothetical protein CAPTEDRAFT_200496,	0.671	0.573	0.329	1e-28
443712830		397	hypothetical protein CAPTEDRAFT_202466 [	0.584	0.591	0.378	5e-27
427791321		1210	Putative tick transposon, partial [Rhipi	0.646	0.214	0.327	7e-26
427791807		1212	Putative tick transposon, partial [Rhipi	0.646	0.214	0.327	7e-26
443724607		397	hypothetical protein CAPTEDRAFT_208903 [	0.567	0.574	0.36	3e-25
427791063		1035	Putative tick transposon, partial [Rhipi	0.646	0.251	0.315	9e-24

>gi\|443693558\|gb\|ELT94903.1\| hypothetical protein CAPTEDRAFT_189741, partial [Capitella teleta]	Back alignment and taxonomy information

 Score =  149 bits (377), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 106/294 (36%), Positives = 145/294 (49%), Gaps = 13/294 (4%)

Query: 74  PFLLASPLFLKTIFLPYIKP-----LPPWSFDVPTFDNSLGSDKKDNISSVAFQQHFRDL 128
           P L  +   L+++    I P     +PPW    P  D S+    KD   ++  +Q F +L
Sbjct: 16  PLLYRTEEALESVITAPIAPFKISDVPPWKLRPPEVDTSISKFLKDQHPALFLKQEFYNL 75

Query: 129 LYSKYAHFTPCYTDGSKSVNGTSCAYSINNLIVLSTSLNQVVCVYSSELIAIHLCLEHLK 188
           +  KY      YTDGSKS N  +CA++ +   +    L   + +Y++ELIAI   L  ++
Sbjct: 76  I-DKYPGIN-IYTDGSKSNNAVACAFTCSTYQI-QFGLPTQMSIYTAELIAIEQALIFIE 132

Query: 189 FLPSS-HFLIISDSKSALTALSNNTSDNPIVAKISVTWRKLKDYGKTVSFLWCPSHSGIA 247
            +     F I SDS S+LTALSN    +P +  I      L   GK V F+WCPSH GI 
Sbjct: 133 TVKDEDQFNICSDSLSSLTALSNCDITHPYLLSILTKQNNLVRKGKLVVFIWCPSHVGIL 192

Query: 248 GNEFVDNAARNP-VNPHLPLKLCSPLDLKPFAAKLTKTKWQALWDTLPIPNKLKRVKPVI 306
           GNE  D  A+   V P   L L    D K       K+ WQ  WD     NKL  ++PVI
Sbjct: 193 GNEVADRLAKQALVMPVTKLPLPHT-DYKSPIRSYVKSLWQNEWDE-ETDNKLHSIQPVI 250

Query: 307 EDWGSSNRDNRYEEVVICRMRIGHTRATHSFLFKRTPPPSCR-CGDPLTVLHIL 359
            +W    + +R  E+V+ R RIGH+  TH +L +R   P C  C   LTV HIL
Sbjct: 251 SEWKQGPQIDRRGEIVLARARIGHSHLTHGYLLRREVAPFCIPCQSLLTVKHIL 304

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi\|125901787\|gb\|ABN58714.1\| pol-like protein [Biomphalaria glabrata]	Back alignment and taxonomy information

>gi\|427778603\|gb\|JAA54753.1\| Putative tick transposon [Rhipicephalus pulchellus]	Back alignment and taxonomy information

>gi\|443695973\|gb\|ELT96755.1\| hypothetical protein CAPTEDRAFT_23017, partial [Capitella teleta]	Back alignment and taxonomy information

>gi\|443721618\|gb\|ELU10867.1\| hypothetical protein CAPTEDRAFT_200496, partial [Capitella teleta]	Back alignment and taxonomy information

>gi\|443712830\|gb\|ELU05953.1\| hypothetical protein CAPTEDRAFT_202466 [Capitella teleta]	Back alignment and taxonomy information

>gi\|427791321\|gb\|JAA61112.1\| Putative tick transposon, partial [Rhipicephalus pulchellus]	Back alignment and taxonomy information

>gi\|427791807\|gb\|JAA61355.1\| Putative tick transposon, partial [Rhipicephalus pulchellus]	Back alignment and taxonomy information

>gi\|443724607\|gb\|ELU12531.1\| hypothetical protein CAPTEDRAFT_208903 [Capitella teleta]	Back alignment and taxonomy information

>gi\|427791063\|gb\|JAA60983.1\| Putative tick transposon, partial [Rhipicephalus pulchellus]	Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		402
ASPGD\|ASPL0000075333		486	AN10625 [Emericella nidulans (	0.664	0.549	0.269	3.8e-10
ASPGD\|ASPL0000055652		1054	AN0368 [Emericella nidulans (t	0.462	0.176	0.271	7e-06
ASPGD\|ASPL0000033911		686	AN2796 [Emericella nidulans (t	0.315	0.185	0.288	0.00056
ASPGD\|ASPL0000077547		1581	AN8648 [Emericella nidulans (t	0.462	0.117	0.266	0.00058
ASPGD\|ASPL0000037597		666	AN2711 [Emericella nidulans (t	0.315	0.190	0.288	0.00063

ASPGD\|ASPL0000075333 AN10625 [Emericella nidulans (taxid:162425)]	Back alignment and assigned GO terms

 Score = 173 (66.0 bits), Expect = 3.8e-10, P = 3.8e-10
 Identities = 79/293 (26%), Positives = 129/293 (44%)

Query:   114 DNISSVAFQQHFRDLLYSKYAHFTPCYTDGSKSVNGTSCAYSI--NNLIVLSTSLNQVV- 170
             D  +  A + H R++L ++       YTDGS  +NG   A +I    LI  S+ + Q   
Sbjct:   162 DGDAETAIETH-RNIL-NRAPRPIALYTDGS-GINGRVGAAAICPKYLISRSSYMGQQSE 218

Query:   171 -CVYSSELIAIHLCLEHLKFLPSSHFLIISDSKSALTALSN--NTSDNPIVAKISVTWRK 227
               VY +EL  I L L  +      H +I +D+++ L AL N  + S   I+  I +   K
Sbjct:   219 STVYVAELQGILLALVIILQRQMQHAVIFTDNQATLQALRNPGSQSGQYILEAIIMALNK 278

Query:   228 LKDYGKTVSFLWCPSHSGIAGNEFVDNAARNP-----VNPHLPLKLCSPLDLKPFAAKLT 282
              +  G  V F W P+H G+ GNE  D  A+       +  H   ++     +K  A ++ 
Sbjct:   279 GRKAGLNVHFRWIPAHRGVEGNEQADRRAKEATGWRRIRGHRG-RMTIRSAVKRRAHEVV 337

Query:   283 KTKWQALWDTLPIPNKLKRVKPV-IEDWGSSNRD-NRYEEVVICRMRIGHTRATHSFLFK 340
               +W+  W +     +L  + P         ++D +R    +I +MR G     H +L++
Sbjct:   338 NARWENDWKSCHHGRELYELTPTPTRKVLRVHQDLHRALSTIIVQMRTGKIGLRH-YLYQ 396

Query:   341 RTPP--PS--CRCGDPL-TVLHIL-SCHLHANIRASXXXXXXXXDSPEGVDSL 387
             R  P  P+  C+CG    +V HIL +C   + +R            PEG  S+
Sbjct:   397 RGVPDVPNSDCQCGRATQSVRHILLACPTFSGLREEIFGGRSG--GPEGEGSV 447

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\|ASPL0000055652 AN0368 [Emericella nidulans (taxid:162425)]	Back alignment and assigned GO terms

ASPGD\|ASPL0000033911 AN2796 [Emericella nidulans (taxid:162425)]	Back alignment and assigned GO terms

ASPGD\|ASPL0000077547 AN8648 [Emericella nidulans (taxid:162425)]	Back alignment and assigned GO terms

ASPGD\|ASPL0000037597 AN2711 [Emericella nidulans (taxid:162425)]	Back alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

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

Prediction of Functionally Associated Proteins

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Alignment Graph	Length	Definition	E-value
Query		402
cd09276		128	cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom	1e-28
pfam00075		126	pfam00075, RNase_H, RNase H	3e-15
cd06222		123	cd06222, RNase_H, RNase H is an endonuclease that	4e-08
cd09273		135	cd09273, RNase_HI_RT_Bel, Bel/Pao family of RNase	3e-07
cd09278		139	cd09278, RNase_HI_prokaryote_like, RNase HI family	1e-04
COG0328		154	COG0328, RnhA, Ribonuclease HI [DNA replication, r	4e-04

>gnl\|CDD\|187700 cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI domain of reverse transcriptases	Back alignment and domain information

 Score =  108 bits (272), Expect = 1e-28
 Identities = 44/123 (35%), Positives = 60/123 (48%), Gaps = 4/123 (3%)

Query: 139 CYTDGSKSVNGTSCAYSI--NNLIVLSTSLNQVVCVYSSELIAIHLCLEHLKFLPSSH-- 194
            YTDGSK    T   ++I     I  S  L     V+ +EL+AI   L+           
Sbjct: 2   IYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRRARK 61

Query: 195 FLIISDSKSALTALSNNTSDNPIVAKISVTWRKLKDYGKTVSFLWCPSHSGIAGNEFVDN 254
             I SDS++AL AL +  S +P+V +I    R+L ++G  V   W P HSGI GNE  D 
Sbjct: 62  ITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGNERADR 121

Query: 255 AAR 257
            A+
Sbjct: 122 LAK 124

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

>gnl\|CDD\|215695 pfam00075, RNase_H, RNase H	Back alignment and domain information

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

>gnl\|CDD\|187697 cd09273, RNase_HI_RT_Bel, Bel/Pao family of RNase HI in long-term repeat retroelements	Back alignment and domain information

>gnl\|CDD\|187702 cd09278, RNase_HI_prokaryote_like, RNase HI family found mainly in prokaryotes	Back alignment and domain information

>gnl\|CDD\|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and repair]	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		402
PF00075		132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	99.87
PRK08719		147	ribonuclease H; Reviewed	99.86
PRK06548		161	ribonuclease H; Provisional	99.85
COG0328		154	RnhA Ribonuclease HI [DNA replication, recombinati	99.83
PRK00203		150	rnhA ribonuclease H; Reviewed	99.82
cd06222		130	RnaseH RNase H (RNase HI) is an endonuclease that	99.75
KOG3752\|consensus		371		99.66
PRK13907		128	rnhA ribonuclease H; Provisional	99.65
PRK07708		219	hypothetical protein; Validated	99.48
PRK07238		372	bifunctional RNase H/acid phosphatase; Provisional	99.37
PF13456		87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	99.1
PF13966		86	zf-RVT: zinc-binding in reverse transcriptase	93.85

>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	Back alignment and domain information

Probab=99.87  E-value=1.2e-22  Score=174.62  Aligned_cols=118  Identities=31%  Similarity=0.356  Sum_probs=91.7

Q ss_pred             CceEEEeccCccCC--CceEEEEeeCCEEEEEecCCcccchHHHHHHHHHHHHHhhhCCCCceEEEeccHHHHHHhcC--
Q psy7520         135 HFTPCYTDGSKSVN--GTSCAYSINNLIVLSTSLNQVVCVYSSELIAIHLCLEHLKFLPSSHFLIISDSKSALTALSN--  210 (402)
Q Consensus       135 ~~~~iyTDGS~~~~--~~G~gv~~~~~~~~~~~l~~~~sv~~AEl~AI~~AL~~~~~~~~~~v~I~tDS~sal~~l~~--  210 (402)
                      +.++||||||+..+  ..|+|+++..+......++ ..+++.||+.||..||+.+ .  ...++|+|||+++++.+..  
T Consensus         2 ~~~~iytDgS~~~~~~~~~~g~v~~~~~~~~~~~~-~~s~~~aEl~Ai~~AL~~~-~--~~~v~I~tDS~~v~~~l~~~~   77 (132)
T PF00075_consen    2 KAIIIYTDGSCRPNPGKGGAGYVVWGGRNFSFRLG-GQSNNRAELQAIIEALKAL-E--HRKVTIYTDSQYVLNALNKWL   77 (132)
T ss_dssp             TSEEEEEEEEECTTTTEEEEEEEEETTEEEEEEEE-SECHHHHHHHHHHHHHHTH-S--TSEEEEEES-HHHHHHHHTHH
T ss_pred             CcEEEEEeCCccCCCCceEEEEEEECCeEEEeccc-ccchhhhheehHHHHHHHh-h--cccccccccHHHHHHHHHHhc
Confidence            47899999997643  3577776665555555666 8999999999999999944 3  4999999999999998877  


Q ss_pred             ---CCCCc----hHHHHHHHHHHHHHhCCceEEEEEcCCCCCC-CCChHHHHHhcCCC
Q psy7520         211 ---NTSDN----PIVAKISVTWRKLKDYGKTVSFLWCPSHSGI-AGNEFVDNAARNPV  260 (402)
Q Consensus       211 ---~~~~s----~i~~~I~~~~~~l~~~~~~V~~~WVPgH~Gi-~gNE~AD~lAk~A~  260 (402)
                         .+...    ++..+|++.+    ..+..|.|+|||||+|+ .|||.||+|||+|+
T Consensus        78 ~~~~~~~~~~~~~i~~~i~~~~----~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~  131 (132)
T PF00075_consen   78 HGNGWKKTSNGRPIKNEIWELL----SRGIKVRFRWVPGHSGVPQGNERADRLAKEAA  131 (132)
T ss_dssp             HHTTSBSCTSSSBHTHHHHHHH----HHSSEEEEEESSSSSSSHHHHHHHHHHHHHHH
T ss_pred             cccccccccccccchhheeecc----ccceEEeeeeccCcCCCchhHHHHHHHHHHhc
Confidence               33222    3555666533    55899999999999999 69999999999874

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	Back alignment and domain information

>PRK06548 ribonuclease H; Provisional	Back alignment and domain information

>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]	Back alignment and domain information

>PRK00203 rnhA ribonuclease H; Reviewed	Back alignment and domain information

>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	Back alignment and domain information

>KOG3752\|consensus	Back alignment and domain information

>PRK13907 rnhA ribonuclease H; Provisional	Back alignment and domain information

>PRK07708 hypothetical protein; Validated	Back alignment and domain information

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional	Back alignment and domain information

>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B	Back alignment and domain information

>PF13966 zf-RVT: zinc-binding in reverse transcriptase	Back alignment and domain information

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	Alignment Graph	Length	Definition	E-value
Query		402
3p1g_A		165	Xenotropic murine leukemia virus-related virus (X	2e-08
2kq2_A		147	Ribonuclease H-related protein; PSI, NESG, protein	8e-06
2zd1_A		557	Reverse transcriptase/ribonuclease H; P51/P66, het	2e-05
1mu2_A		555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	1e-04
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-04

>3p1g_A Xenotropic murine leukemia virus-related virus (X H domain; XMRV, RNAse H, reverse transcriptase, transcription; 1.50A {Xenotropic mulv-related virus} PDB: 3v1q_A 3v1o_A 3v1r_A* 2hb5_A Length = 165	Back alignment and structure

 Score = 52.5 bits (126), Expect = 2e-08
 Identities = 29/130 (22%), Positives = 46/130 (35%), Gaps = 17/130 (13%)

Query: 140 YTDGSKSVN----GTSCAYSINNLIVLSTSLNQVVCVYSSELIAIHLCLEHLKFLPSSHF 195
           YTDGS  +         A +    ++ + +L        +ELIA+   L+  +       
Sbjct: 27  YTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMAE---GKKL 83

Query: 196 LIISDSKSALTALSNNTSDNPIVAKISVTWRKLKDY---GKTVSFLWCPSHSG-----IA 247
            + +DS+ A      ++    I  K       L       K +S + CP H         
Sbjct: 84  NVYTDSRYAFATAHVHSEGREI--KNKNEILALLKALFLPKRLSIIHCPGHQKGNSAEAR 141

Query: 248 GNEFVDNAAR 257
           GN   D AAR
Sbjct: 142 GNRMADQAAR 151

PyMOL of 3p1g

>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	Back alignment and structure

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

>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 Length = 555	Back alignment and structure

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

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		402
3qio_A		150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.88
2qkb_A		154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.88
2kq2_A		147	Ribonuclease H-related protein; PSI, NESG, protein	99.87
3h08_A		146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.86
1jl1_A		155	Ribonuclease HI; RNAse HI, protein stability, ther	99.84
3p1g_A		165	Xenotropic murine leukemia virus-related virus (X	99.84
2e4l_A		158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.84
1ril_A		166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.82
2lsn_A		165	Reverse transcriptase; RNAse H, viral protein; NMR	99.78
3hst_B		141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	99.77
3u3g_D		140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	99.76
2zd1_A		557	Reverse transcriptase/ribonuclease H; P51/P66, het	99.75
1mu2_A		555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	99.75
2ehg_A		149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	99.72
1zbf_A		142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	99.22
4htu_A		134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	98.99
1rw3_A		455	POL polyprotein; RNA and DNA dependent DNA polymer	80.06

>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	Back alignment and structure

Probab=99.88  E-value=1.1e-22  Score=179.08  Aligned_cols=126  Identities=23%  Similarity=0.275  Sum_probs=95.5

Q ss_pred             hcCCceEEEeccCccCC--CceEEEEeeCCEEEEEecCCcccchHHHHHHHHHHHHHhhhCCCCceEEEeccHHHHHHhc
Q psy7520         132 KYAHFTPCYTDGSKSVN--GTSCAYSINNLIVLSTSLNQVVCVYSSELIAIHLCLEHLKFLPSSHFLIISDSKSALTALS  209 (402)
Q Consensus       132 ~~~~~~~iyTDGS~~~~--~~G~gv~~~~~~~~~~~l~~~~sv~~AEl~AI~~AL~~~~~~~~~~v~I~tDS~sal~~l~  209 (402)
                      +..+.+.||||||+..+  ..|+|+++.++......+ ..+|+++||+.|+..||+.+    ..+|.|+|||+++++.|.
T Consensus         8 P~~~~~~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~-~~~Tnn~aEl~A~i~AL~~~----~~~v~i~tDS~~v~~~i~   82 (150)
T 3qio_A            8 PIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTL-TDTTNQKTELQAIYLALQDS----GLEVNIVTDSQYALGIIT   82 (150)
T ss_dssp             CCTTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEEE-SSCCHHHHHHHHHHHHHHHS----CSEEEEEESCHHHHHHHH
T ss_pred             CCCCCEEEEEccCCCCCCCCeEEEEEEEcCCEEEEeC-CCCCHHHHHHHHHHHHHHhC----CCcEEEEeCcHHHHHHHH
Confidence            45678999999998744  378888765543333344 47899999999999999985    488999999999999998


Q ss_pred             CCC-----------CCchH-HHHHHHHHHHHHhCCceEEEEEcCCCCCCCCChHHHHHhcCCCCC
Q psy7520         210 NNT-----------SDNPI-VAKISVTWRKLKDYGKTVSFLWCPSHSGIAGNEFVDNAARNPVNP  262 (402)
Q Consensus       210 ~~~-----------~~s~i-~~~I~~~~~~l~~~~~~V~~~WVPgH~Gi~gNE~AD~lAk~A~~~  262 (402)
                      .+.           ...++ -+++++.+..+..++..|.|.|||||+|++|||.||+||++|+..
T Consensus        83 ~w~~~W~~~gw~~~~g~~v~n~~l~~~l~~~l~~~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~  147 (150)
T 3qio_A           83 QWIHNWKKRGWKTADKKPVKNVDLVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRK  147 (150)
T ss_dssp             HHHHHHCC------------CHHHHHHHHHHHTTCSEEEEEECCTTSCCHHHHHHHHHHHTTTSC
T ss_pred             HHHHHHhhcCcCcCcCcccccHHHHHHHHHHHhhcCceEEEEccCcCCChhHHHHHHHHHHHHHH
Confidence            751           11111 234444443333467899999999999999999999999999875

PyMOL of 3qio

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

>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	Back alignment and structure

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

>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 ...	Back alignment and structure

>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	Back alignment and structure

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

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

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

>3hst_B Protein RV2228C/MT2287; ribonuclease H1, RV2228C N-terminal domain, fusion protein, maltose binding protein, HYDR; HET: MLR TAR; 2.25A {Mycobacterium tuberculosis}	Back alignment and structure

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

>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* ...	Back alignment and structure

>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	Back alignment and structure

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

>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*	Back alignment and structure

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

>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	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Alignment Graph	Length	Definition	E-value
Query		402
d1mu2a1		126	c.55.3.1 (A:430-555) HIV RNase H (Domain of revers	3e-08
d1rila_		147	c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermoph	3e-04
d1jl1a_		152	c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli	4e-04
d1s1ta1		110	c.55.3.1 (A:430-539) HIV RNase H (Domain of revers	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	Back information, alignment and structure


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 = 49.5 bits (117), Expect = 3e-08
 Identities = 25/122 (20%), Positives = 42/122 (34%), Gaps = 13/122 (10%)

Query: 140 YTDGSKSVNGT--SCAYSINNLIVLSTSLNQVVCVYSSELIAIHLCLEHLKFLPSSHFLI 197
           YTDGS +         Y  +        L Q     +          +           I
Sbjct: 11  YTDGSCNRQSKEGKAGYVTDRGKDKVKKLEQTTNQQAELEAFAMALTDS-----GPKVNI 65

Query: 198 ISDSKSALTALSNN--TSDNPIVAKISVTWRKLKDYGKTVSFLWCPSHSGIAGNEFVDNA 255
           I DS+  +  +++    S++ IV +I           + +   W P+H GI GN+ VD+ 
Sbjct: 66  IVDSQYVMGIVASQPTESESKIVNQIIEEMI----KKEAIYVAWVPAHKGIGGNQEVDHL 121

Query: 256 AR 257
             
Sbjct: 122 VS 123

PyMOL of d1mu2a1

>d1rila_ c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermophilus [TaxId: 274]} Length = 147	Back information, alignment and structure

>d1jl1a_ c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli [TaxId: 562]} Length = 152	Back information, alignment and structure

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

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		402
d1mu2a1		126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.9
d1rila_		147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.84
d1jl1a_		152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	99.84
d1s1ta1		110	HIV RNase H (Domain of reverse transcriptase) {Hum	99.72
d1zbfa1		132	BH0863-like Ribonuclease H {Bacillus halodurans [T	99.38

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

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

Probab=99.90  E-value=3.2e-24  Score=181.17  Aligned_cols=119  Identities=22%  Similarity=0.330  Sum_probs=91.3

Q ss_pred             cCCceEEEeccCccCC-C-ceEEEEeeCCEEEEEecCCcccchHHHHHHHHHHHHHhhhCCCCceEEEeccHHHHHHhcC
Q psy7520         133 YAHFTPCYTDGSKSVN-G-TSCAYSINNLIVLSTSLNQVVCVYSSELIAIHLCLEHLKFLPSSHFLIISDSKSALTALSN  210 (402)
Q Consensus       133 ~~~~~~iyTDGS~~~~-~-~G~gv~~~~~~~~~~~l~~~~sv~~AEl~AI~~AL~~~~~~~~~~v~I~tDS~sal~~l~~  210 (402)
                      .++..++|||||+..+ + .|+|+++..+......++ ..|+++||+.||+.||+.    ....+.|+|||++++..+.+
T Consensus         4 ~~~~~t~YTDGS~~~n~~~~~~g~~~~~~~~~~~~~~-~~tnn~AEl~Ai~~al~~----~~~~i~I~tDS~~v~~~~~~   78 (126)
T d1mu2a1           4 IPGAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKLE-QTTNQQAELEAFAMALTD----SGPKVNIIVDSQYVMGIVAS   78 (126)
T ss_dssp             CTTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEEES-SCCHHHHHHHHHHHHHHT----SCSEEEEEESCHHHHHHHHT
T ss_pred             CCCCcEEEEcCCCCCCCCcEEEEEEecCCCEEEEecC-CCcchHHHHHHHHHHhcc----CCcceEEEechHHHHHHHhc
Confidence            3556799999997643 3 567776665554555554 579999999999999975    36789999999999999999


Q ss_pred             CCCCc--hHHHHHHHHHHHHHhCCceEEEEEcCCCCCCCCChHHHHHhcCCC
Q psy7520         211 NTSDN--PIVAKISVTWRKLKDYGKTVSFLWCPSHSGIAGNEFVDNAARNPV  260 (402)
Q Consensus       211 ~~~~s--~i~~~I~~~~~~l~~~~~~V~~~WVPgH~Gi~gNE~AD~lAk~A~  260 (402)
                      .+..+  .....   .+..+.. ...|.|.|||||+|++|||.||+||++|.
T Consensus        79 ~~~~~~~~~~~~---~~~~~~~-~~~v~~~wV~gH~g~~gNe~AD~LA~~ai  126 (126)
T d1mu2a1          79 QPTESESKIVNQ---IIEEMIK-KEAIYVAWVPAHKGIGGNQEVDHLVSQGI  126 (126)
T ss_dssp             CCSEESCHHHHH---HHHHHHH-CSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             CCccccchHHHH---HHHHhhh-cceeEEEEEeCCCCCcchHHHHHHHHhhC
Confidence            87543  23222   2223333 46999999999999999999999999984

PyMOL of d1mu2a1

>d1rila_ c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermophilus [TaxId: 274]}	Back information, alignment and structure

>d1jl1a_ c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1s1ta1 c.55.3.1 (A:430-539) HIV RNase H (Domain of reverse transcriptase) {Human immunodeficiency virus type 1 [TaxId: 11676]}	Back information, alignment and structure

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