Psyllid ID: psy7230

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------
MDQQRKVLLDFPNPTQTSVIAPYVRFIPPWSNSSPPVDLSLCDGKKCDSAPVVFQSLFRDVINSKYTNHTICYTDGSKTPTTTGCAYSVGNVVRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGEFLVVTDSRSSLAALSNVRFTNPLITKVYSTWNYLKLCKKDITFMWCPSHCGIKGNEIVDVAARNPTTGTTPSKLCTPEDFKPFVASIMQSEWQSLWDNIPNTNKLKNIRPSIKAWKTSDQDKRFQELAGNRRERPYHKSVKAPNSKKRASIASNRKKARYRILCSPSFVSGTPPTDREIK
cHHHHHHHHcccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHcccccEEEEEcccccccccEEEEEEcccEEEEEccccccHHHHHHHHHHHHHHHHHccccccEEEEcccHHHHHHHHcccccHHHHHHHHHHHHHHHcccccEEEEcccccccccccHHHHHHHcccccccccccccccccHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccHHHHHHHHHHccccccccccccccccccccccccccEEccccccccccccccccccc
ccccEHHHHHccccccccccccccccccccccccccEEEEccccccccccHHHHHHHHHHHHHHHccccEEEEEccccccccEEEEEEEEccccEcccccccHHHHHHHHHHHHHHHHHHHcccccEEEEEccHHHHHHHHccccccHHHHHHHHHHHHHHHcccEEEEEEEcccccccccHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHcccccccEEEccccccccccccccHHHHHHHHHHHHcccHHHEccccccccccccccccccEEEEEccHHHccccHHHHHHcc
MDQQRKVlldfpnptqtsviapyvrfippwsnssppvdlslcdgkkcdsapvVFQSLFRDVinskytnhticytdgsktptttgcaysvgnvvrstllnpvnsiFSAELIAIFLCLEAildspsgeflvVTDSRSSLAALsnvrftnplITKVYSTWNYLKLCKkditfmwcpshcgikgneivdvaarnpttgttpsklctpedfkPFVASIMQSEWQSlwdnipntnklknirpsikawktsdQDKRFQELAgnrrerpyhksvkapnskkraSIASNRKKARYRilcspsfvsgtpptdreik
MDQQRKvlldfpnptqtsvIAPYVRFIPPWSNSSPPVDLSLCDGKKCDSAPVVFQSLFRDVINSKYTNHTIcytdgsktptTTGCAYSVGNVVRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGEFLVVTDSRSSLaalsnvrftnpliTKVYSTWNYLKLCKKDITFMWCPSHCGIKGNEIVDVAARNPTtgttpsklctpeDFKPFVASIMQSEWQSlwdnipntnklknirpsikawktsdqdkRFQElagnrrerpyhksvkapnskkrasiasnrkkaryrilcspsfvsgtpptdreik
MDQQRKVLLDFPNPTQTSVIAPYVRFIPPWSNSSPPVDLSLCDGKKCDSAPVVFQSLFRDVINSKYTNHTICYTDGSKTPTTTGCAYSVGNVVRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGEFLVVTDSRSSLAALSNVRFTNPLITKVYSTWNYLKLCKKDITFMWCPSHCGIKGNEIVDVAARNPTTGTTPSKLCTPEDFKPFVASIMQSEWQSLWDNIPNTNKLKNIRPSIKAWKTSDQDKRFQELAGNRRERPYHKSVKAPNSKKRASIASNRKKARYRILCSPSFVSGTPPTDREIK
********LDFPNPTQTSVIAPYVRFIPPWSNSSPPVDLSLCDGKKCDSAPVVFQSLFRDVINSKYTNHTICYTDGSKTPTTTGCAYSVGNVVRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGEFLVVTDSRSSLAALSNVRFTNPLITKVYSTWNYLKLCKKDITFMWCPSHCGIKGNEIVDVAARNPTTGT**SKLCTPEDFKPFVASIMQSEWQSLWDNIPNTNKLKNI****************************************************RILC****************
****RKV*LDFPNPTQTSVIAPYVRFIPPWSNSSPPVDLSLCDGK******VVFQSLFRDVINSKYTNHTICYTDGSKTPTTTGCAYSVGNVVRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGEFLVVTDSRSSLAALSNVRFTNPLITKVYSTWNYLKLCKKDITFMWCPSHCGIKGNEIVDVAARNPTTGTTPSKLCTPEDFKPFVASIMQSEWQSLWDNIPNTNKLKNIRPSIKAWKTSDQDKRFQELAGNRRERPYHKSVKAPNSKKRASIASNRKKARYRILCSPSFVSGTP*******
MDQQRKVLLDFPNPTQTSVIAPYVRFIPPWSNSSPPVDLSLCDGKKCDSAPVVFQSLFRDVINSKYTNHTICYTDGSKTPTTTGCAYSVGNVVRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGEFLVVTDSRSSLAALSNVRFTNPLITKVYSTWNYLKLCKKDITFMWCPSHCGIKGNEIVDVAARNPTTGTTPSKLCTPEDFKPFVASIMQSEWQSLWDNIPNTNKLKNIRPSIKAWKTSDQDKRFQELAGNRRER********************RKKARYRILCSPSFVS**********
*DQQRKVLLDFPNPTQTSVIAPYVRFIPPWSNSSPPVDLSLCDGKKCDSAPVVFQSLFRDVINSKYTNHTICYTDGSKTPTTTGCAYSVGNVVRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGEFLVVTDSRSSLAALSNVRFTNPLITKVYSTWNYLKLCKKDITFMWCPSHCGIKGNEIVDVAARNPTTGTTPSKLCTPEDFKPFVASIMQSEWQSLWDNIPNTNKLKNIRPSIKAWKTSDQDKRFQELAGNRRERPYHKSVKAPNSKKRASIASNRKKARYRILCSPSFVSGTPPT*****
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MDQQRKVLLDFPNPTQTSVIAPYVRFIPPWSNSSPPVDLSLCDGKKCDSAPVVFQSLFRDVINSKYTNHTICYTDGSKTPTTTGCAYSVGNVVRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGEFLVVTDSRSSLAALSNVRFTNPLITKVYSTWNYLKLCKKDITFMWCPSHCGIKGNEIVDVAARNPTTGTTPSKLCTPEDFKPFVASIMQSEWQSLWDNIPNTNKLKNIRPSIKAWKTSDQDKRFQELAGNRRERPYHKSVKAPNSKKRASIASNRKKARYRILCSPSFVSGTPPTDREIK
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 ?
Query306
443713753266 hypothetical protein CAPTEDRAFT_215116 [ 0.738 0.849 0.324 2e-27
125901787 1222 pol-like protein [Biomphalaria glabrata] 0.692 0.173 0.344 2e-26
443693558 502 hypothetical protein CAPTEDRAFT_189741, 0.764 0.466 0.364 2e-25
443710566377 hypothetical protein CAPTEDRAFT_186063 [ 0.754 0.612 0.322 2e-25
443721618 471 hypothetical protein CAPTEDRAFT_200496, 0.660 0.428 0.309 2e-24
443700898300 hypothetical protein CAPTEDRAFT_212630, 0.718 0.733 0.323 5e-24
443695973261 hypothetical protein CAPTEDRAFT_23017, p 0.705 0.827 0.364 6e-22
443723447225 hypothetical protein CAPTEDRAFT_187673 [ 0.562 0.764 0.340 8e-22
443712830397 hypothetical protein CAPTEDRAFT_202466 [ 0.692 0.534 0.355 3e-21
443720278 498 hypothetical protein CAPTEDRAFT_219461 [ 0.666 0.409 0.305 3e-20
>gi|443713753|gb|ELU06453.1| hypothetical protein CAPTEDRAFT_215116 [Capitella teleta] Back     alignment and taxonomy information
 Score =  129 bits (323), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 76/234 (32%), Positives = 122/234 (52%), Gaps = 8/234 (3%)

Query: 28  PPWSNSSPPVDLSLCDGKKCDSAPVVFQSLFRDVINSKYTNHTICYTDGSKTPTTTGCAY 87
           PPW    P VDLSL   KK   + +  +S F D ++S Y   T+ YTDGSK+  +   ++
Sbjct: 35  PPWHLVQPEVDLSLTFSKKDSMSALTIRSEFEDALDS-YPVSTVFYTDGSKSEDSVARSF 93

Query: 88  SVGNVVRSTLLNPVNSIFSAELIAIF---LCLEAILDSPSGEFLVVTDSRSSLAALSNVR 144
               +     L    S+F++E+IAI     CLEA  D+   +F++ +DS S++ A+  + 
Sbjct: 94  FSSRLKLKMKLPVQMSVFTSEIIAILSALKCLEA--DNEQHQFVICSDSLSAIMAIHGMD 151

Query: 145 FTNPLITKVYSTWNYLKLCKKDITFMWCPSHCGIKGNEIVDVAARNPTTGTTPSKLCTP- 203
             +P + +V      +   +K + FMWCPSH GI GNE+    A    + T  ++L  P 
Sbjct: 152 VHHPYVLQVLYAIKSISQQEKIVVFMWCPSHVGIPGNEMAHTLAEKALSSTNLAELPVPA 211

Query: 204 EDFKPFVASIMQSEWQSLWDNIPNTNKLKNIRPSIKAWKTSDQDKRFQELAGNR 257
            D +  +   ++S+WQ  W+   N NKL +I P+I  W    ++KR +E+   R
Sbjct: 212 SDLRGLIKKYIRSQWQHEWEEQHN-NKLHSIHPTIGPWPPCQREKRREEIVLVR 264

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|443693558|gb|ELT94903.1| hypothetical protein CAPTEDRAFT_189741, partial [Capitella teleta] Back     alignment and taxonomy information
>gi|443710566|gb|ELU04776.1| hypothetical protein CAPTEDRAFT_186063 [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|443700898|gb|ELT99633.1| hypothetical protein CAPTEDRAFT_212630, partial [Capitella teleta] Back     alignment and taxonomy information
>gi|443695973|gb|ELT96755.1| hypothetical protein CAPTEDRAFT_23017, partial [Capitella teleta] Back     alignment and taxonomy information
>gi|443723447|gb|ELU11866.1| hypothetical protein CAPTEDRAFT_187673 [Capitella teleta] Back     alignment and taxonomy information
>gi|443712830|gb|ELU05953.1| hypothetical protein CAPTEDRAFT_202466 [Capitella teleta] Back     alignment and taxonomy information
>gi|443720278|gb|ELU10076.1| hypothetical protein CAPTEDRAFT_219461 [Capitella teleta] 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 ?
Query306
ASPGD|ASPL0000075333486 AN10625 [Emericella nidulans ( 0.581 0.366 0.222 0.00012
ASPGD|ASPL0000075333 AN10625 [Emericella nidulans (taxid:162425)] Back     alignment and assigned GO terms
 Score = 122 (48.0 bits), Expect = 0.00012, P = 0.00012
 Identities = 42/189 (22%), Positives = 82/189 (43%)

Query:    59 RDVINSKYTNHTICYTDGSKTPTTTGCAYSVGN--VVRSTLLNPVN--SIFSAELIAIFL 114
             R+++N +       YTDGS      G A       + RS+ +   +  +++ AEL  I L
Sbjct:   173 RNILN-RAPRPIALYTDGSGINGRVGAAAICPKYLISRSSYMGQQSESTVYVAELQGILL 231

Query:   115 CLEAILDSPSGEFLVVTDSRSSLAALSNVRFTNP--LITKVYSTWNYLKLCKKDITFMWC 172
              L  IL       ++ TD++++L AL N    +   ++  +    N  +    ++ F W 
Sbjct:   232 ALVIILQRQMQHAVIFTDNQATLQALRNPGSQSGQYILEAIIMALNKGRKAGLNVHFRWI 291

Query:   173 PSHCGIKGNEIVDVAARNPTTGTT----PSKLCTPEDFKPFVASIMQSEWQSLWDNIPNT 228
             P+H G++GNE  D  A+  T          ++      K     ++ + W++ W +  + 
Sbjct:   292 PAHRGVEGNEQADRRAKEATGWRRIRGHRGRMTIRSAVKRRAHEVVNARWENDWKSCHHG 351

Query:   229 NKLKNIRPS 237
              +L  + P+
Sbjct:   352 RELYELTPT 360


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.318   0.131   0.406    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      306       306   0.00099  115 3  11 22  0.40    34
                                                     33  0.45    37


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  618 (66 KB)
  Total size of DFA:  236 KB (2127 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:01
  No. of threads or processors used:  24
  Search cpu time:  26.83u 0.08s 26.91t   Elapsed:  00:00:16
  Total cpu time:  26.83u 0.08s 26.91t   Elapsed:  00:00:17
  Start:  Thu Aug 15 11:23:43 2013   End:  Thu Aug 15 11:24:00 2013
GO:0008150 "biological_process" evidence=ND
GO:0003676 "nucleic acid binding" evidence=IEA
GO:0004523 "ribonuclease H activity" evidence=IEA
GO:0005575 "cellular_component" evidence=ND

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries ?

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software ?

Prediction LevelEC numberConfidence of Prediction
3rd Layer3.1.260.691
3rd Layer3.1.26.4LOW 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 ?
Query306
cd09276128 cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom 1e-31
pfam00075126 pfam00075, RNase_H, RNase H 2e-17
cd06222123 cd06222, RNase_H, RNase H is an endonuclease that 2e-09
cd09273135 cd09273, RNase_HI_RT_Bel, Bel/Pao family of RNase 1e-07
COG0328154 COG0328, RnhA, Ribonuclease HI [DNA replication, r 4e-04
cd09277133 cd09277, RNase_HI_bacteria_HBD, Bacterial RNase HI 7e-04
>gnl|CDD|187700 cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI domain of reverse transcriptases Back     alignment and domain information 
 Score =  114 bits (287), Expect = 1e-31
 Identities = 41/124 (33%), Positives = 64/124 (51%), Gaps = 5/124 (4%)

Query: 71  ICYTDGSKTPTTTGCAYSV---GNVVRSTLLNPVNSIFSAELIAIFLCLEAILDSPSG-- 125
           + YTDGSK    TG  +++   G + RS  L P  S+F AEL+AI   L+  L       
Sbjct: 1   VIYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRRAR 60

Query: 126 EFLVVTDSRSSLAALSNVRFTNPLITKVYSTWNYLKLCKKDITFMWCPSHCGIKGNEIVD 185
           +  + +DS+++L AL + R ++PL+ ++      L      +   W P H GI+GNE  D
Sbjct: 61  KITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGNERAD 120

Query: 186 VAAR 189
             A+
Sbjct: 121 RLAK 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|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|187701 cd09277, RNase_HI_bacteria_HBD, Bacterial RNase HI containing a hybrid binding domain (HBD) at the N-terminus Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 306
PRK06548161 ribonuclease H; Provisional 99.9
PRK08719147 ribonuclease H; Reviewed 99.89
PF00075132 RNase_H: RNase H; InterPro: IPR002156 The RNase H 99.89
COG0328154 RnhA Ribonuclease HI [DNA replication, recombinati 99.89
PRK00203150 rnhA ribonuclease H; Reviewed 99.88
cd06222130 RnaseH RNase H (RNase HI) is an endonuclease that 99.8
KOG3752|consensus371 99.77
PRK13907128 rnhA ribonuclease H; Provisional 99.73
PRK07708219 hypothetical protein; Validated 99.58
PRK07238 372 bifunctional RNase H/acid phosphatase; Provisional 99.48
PF1345687 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH 99.27
PF05380159 Peptidase_A17: Pao retrotransposon peptidase ; Int 89.16
COG3341225 Predicted double-stranded RNA/RNA-DNA hybrid bindi 85.83
>PRK06548 ribonuclease H; Provisional Back     alignment and domain information 
Probab=99.90  E-value=2.8e-23  Score=176.60  Aligned_cols=127  Identities=24%  Similarity=0.281  Sum_probs=93.5

Q ss_pred             CcEEEEEcCCCCCC--ccceEEEeCCeEEEEcCCCCCcHHHHHHHHHHHHHHHHHhCCCCeEEEEeChHHHHHHHhc---
Q psy7230          68 NHTICYTDGSKTPT--TTGCAYSVGNVVRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGEFLVVTDSRSSLAALSN---  142 (306)
Q Consensus        68 ~~~~iyTDGS~~~~--g~G~av~~~~~~~~~~l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~sDS~sal~~l~~---  142 (306)
                      ..+.||||||+.++  ..|+|++..+..........+||++|||+||+.||+.+.. ....|.|+|||++|+++|+.   
T Consensus         4 ~~~~IytDGa~~gnpg~~G~g~~~~~~~~~~g~~~~~TNnraEl~Aii~aL~~~~~-~~~~v~I~TDS~yvi~~i~~W~~   82 (161)
T PRK06548          4 NEIIAATDGSSLANPGPSGWAWYVDENTWDSGGWDIATNNIAELTAVRELLIATRH-TDRPILILSDSKYVINSLTKWVY   82 (161)
T ss_pred             CEEEEEEeeccCCCCCceEEEEEEeCCcEEccCCCCCCHHHHHHHHHHHHHHhhhc-CCceEEEEeChHHHHHHHHHHHH
Confidence            45999999999864  3788865433212222234689999999999999986653 44579999999999999994   


Q ss_pred             ------cccCCh--hH-HHHHHHHHHHHhCCCceEEEecCCCCCCccchHHHHHHcCcCCCCC
Q psy7230         143 ------VRFTNP--LI-TKVYSTWNYLKLCKKDITFMWCPSHCGIKGNEIVDVAARNPTTGTT  196 (306)
Q Consensus       143 ------~~~~s~--~~-~~i~~~~~~l~~~~~~V~~~WVPgH~gi~gNE~AD~lAk~A~~~~~  196 (306)
                            ++..++  .. ++++.++..+... ..|+|.|||||+|++|||.||+||++|+....
T Consensus        83 ~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~-~~v~~~wVkgHsg~~gNe~aD~LA~~aa~~~~  144 (161)
T PRK06548         83 SWKMRKWRKADGKPVLNQEIIQEIDSLMEN-RNIRMSWVNAHTGHPLNEAADSLARQAANNFS  144 (161)
T ss_pred             HHHHCCCcccCCCccccHHHHHHHHHHHhc-CceEEEEEecCCCCHHHHHHHHHHHHHHHHhc
Confidence                  333333  22 4455555444433 57999999999999999999999999986544

>PRK08719 ribonuclease H; Reviewed Back     alignment and domain information
>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
>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
>PF05380 Peptidase_A17: Pao retrotransposon peptidase ; InterPro: IPR008042 This signature identifies members of the Pao retrotransposon family Back     alignment and domain information
>COG3341 Predicted double-stranded RNA/RNA-DNA hybrid binding protein [General function prediction only] Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query306
1hni_A558 Structure Of Hiv-1 Reverse Transcriptase In A Compl 8e-05
1hys_A553 Crystal Structure Of Hiv-1 Reverse Transcriptase In 8e-05
3dlk_A556 Crystal Structure Of An Engineered Form Of The Hiv- 8e-05
1qe1_A558 Crystal Structure Of 3tc-Resistant M184i Mutant Of 9e-05
3ig1_A555 Hiv-1 Reverse Transcriptase With The Inhibitor Beta 9e-05
2i5j_A552 Crystal Structure Of Hiv-1 Reverse Transcriptase (R 9e-05
1dlo_A556 Human Immunodeficiency Virus Type 1 Length = 556 9e-05
4dg1_A549 Crystal Structure Of Hiv-1 Reverse Transcriptase (R 9e-05
1uwb_A558 Tyr 181 Cys Hiv-1 Rt8-Cl Tibo Length = 558 9e-05
3qo9_A557 Crystal Structure Of Hiv-1 Reverse Transcriptase (R 9e-05
1s6p_A560 Crystal Structure Of Human Immunodeficiency Virus T 1e-04
3qlh_A555 Hiv-1 Reverse Transcriptase In Complex With Manicol 1e-04
2zd1_A557 Crystal Structure Of Hiv-1 Reverse Transcriptase (R 1e-04
1hpz_A560 Human Immunodeficiency Virus Type 1 Length = 560 1e-04
2ze2_A557 Crystal Structure Of L100iK103N MUTANT HIV-1 Revers 1e-04
3jsm_A558 K65r Mutant Hiv-1 Reverse Transcriptase Cross-Linke 1e-04
1hvu_A554 Human Immunodeficiency Virus Type 1 Reverse Transcr 1e-04
1n5y_A558 Hiv-1 Reverse Transcriptase Crosslinked To Post- Tr 1e-04
1s1w_A560 Crystal Structure Of V106a Mutant Hiv-1 Reverse Tra 1e-04
3irx_A558 Crystal Structure Of Hiv-1 Reverse Transcriptase (R 1e-04
2vg5_A557 Crystal Structures Of Hiv-1 Reverse Transcriptase C 1e-04
1s1t_A560 Crystal Structure Of L100i Mutant Hiv-1 Reverse Tra 1e-04
1jle_A560 Crystal Structure Of Y188c Mutant Hiv-1 Reverse Tra 1e-04
3kle_A562 Crystal Structure Of Azt-Resistant Hiv-1 Reverse Tr 1e-04
1hmv_A560 The Structure Of Unliganded Reverse Transcriptase F 1e-04
3dm2_A560 Crystal Structure Of Hiv-1 K103n Mutant Reverse Tra 1e-04
1lwf_A560 Crystal Structure Of A Mutant Hiv-1 Reverse Transcr 1e-04
1rt3_A560 Azt Drug Resistant Hiv-1 Reverse Transcriptase Comp 1e-04
1lwc_A560 Crystal Structure Of M184v Mutant Hiv-1 Reverse Tra 1e-04
1lwe_A560 Crystal Structure Of M41lT215Y MUTANT HIV-1 Reverse 1e-04
3hvt_A556 Structural Basis Of Asymmetry In The Human Immunode 1e-04
1rev_A560 Hiv-1 Reverse Transcriptase Length = 560 1e-04
1lw0_A560 Crystal Structure Of T215y Mutant Hiv-1 Reverse Tra 1e-04
1s1x_A560 Crystal Structure Of V108i Mutant Hiv-1 Reverse Tra 1e-04
2iaj_A560 Crystal Structure Of K103nY181C MUTANT HIV-1 Revers 1e-04
3klf_A557 Crystal Structure Of Wild-Type Hiv-1 Reverse Transc 1e-04
1jkh_A560 Crystal Structure Of Y181c Mutant Hiv-1 Reverse Tra 1e-04
1jlf_A560 Crystal Structure Of Y188c Mutant Hiv-1 Reverse Tra 1e-04
2rki_A560 Crystal Structure Of Hiv-1 Reverse Transcriptase (R 1e-04
3ffi_A561 Hiv-1 Rt With Pyridone Non-Nucleoside Inhibitor Len 1e-04
3dmj_A560 Crystal Structure Of Hiv-1 V106a And Y181c Mutant R 1e-04
2ynf_A563 Hiv-1 Reverse Transcriptase Y188l Mutant In Complex 1e-04
3drs_A563 Hiv Reverse Transcriptase K103n Mutant In Complex W 1e-04
2rf2_A563 Hiv Reverse Transcriptase In Complex With Inhibitor 1e-04
3med_A560 Hiv-1 K103n Reverse Transcriptase In Complex With T 1e-04
3kjv_A560 Hiv-1 Reverse Transcriptase In Complex With Dna Len 1e-04
3di6_A561 Hiv-1 Rt With Pyridazinone Non-Nucleoside Inhibitor 1e-04
3klh_A564 Crystal Structure Of Azt-Resistant Hiv-1 Reverse Tr 1e-04
3bgr_A557 Crystal Structure Of K103nY181C MUTANT HIV-1 Revers 1e-04
2jle_A566 Novel Indazole Nnrtis Created Using Molecular Templ 1e-04
3drr_A563 Hiv Reverse Transcriptase Y181c Mutant In Complex W 1e-04
1o1w_A138 Solution Structure Of The Rnase H Domain Of The Hiv 2e-04
3k2p_A136 Hiv-1 Reverse Transcriptase Isolated Rnaseh Domain 2e-04
1bqn_A558 Tyr 188 Leu Hiv-1 RtHBY 097 Length = 558 2e-04
2ykn_A562 Crystal Structure Of Hiv-1 Reverse Transcriptase (R 2e-04
1rdh_A146 Crystallographic Analyses Of An Active Hiv-1 Ribonu 2e-04
3lp3_A138 P15 Hiv Rnaseh Domain With Inhibitor Mk3 Length = 1 2e-04
2ykm_A562 Crystal Structure Of Hiv-1 Reverse Transcriptase (R 2e-04
1hrh_A136 Crystal Structure Of The Ribonuclease H Domain Of H 2e-04
1eet_A557 Hiv-1 Reverse Transcriptase In Complex With The Inh 2e-04
1ikw_A560 Wild Type Hiv-1 Reverse Transcriptase In Complex Wi 3e-04
1ikv_A560 K103n Mutant Hiv-1 Reverse Transcriptase In Complex 3e-04
4b3o_A560 Structures Of Hiv-1 Rt And Rna-dna Complex Reveal A 4e-04
2opr_A547 Crystal Structure Of K101e Mutant Hiv-1 Reverse Tra 5e-04
3v4i_A556 Crystal Structure Of Hiv-1 Reverse Transcriptase (R 5e-04
3hyf_A150 Crystal Structure Of Hiv-1 Rnase H P15 With Enginee 8e-04
>pdb|1HNI|A Chain A, Structure Of Hiv-1 Reverse Transcriptase In A Complex With The Nonnucleoside Inhibitor Alpha-Apa R 95845 At 2.8 Angstroms Resolution Length = 558 Back     alignment and structure 
Iteration: 1

 Score = 44.3 bits (103), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 48/170 (28%), Positives = 70/170 (41%), Gaps = 40/170 (23%)
Query: 26  FIPPWS--NSSPPVDLSLCDGKKCDSAPVVFQSLFRDVINSKYTNHTICYTDGSKT-PTT 82
           +IP W   N+ P V L      + +  P+V    F              Y DG+    T 
Sbjct: 410 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 451
Query: 83  TGCAYSVGNVVRSTLLNPVNSI-FSAELIAIFLCLEAILDSPSGEFLVVTDSRSSLAAL- 140
            G A  V N  R  ++   N+     EL AI+L L+   DS   E  +VTDS+ +L  + 
Sbjct: 452 LGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQ---DS-GLEVNIVTDSQYALGIIQ 507
Query: 141 -----SNVRFTNPLITKVYSTWNYLKLCKKDITFMWCPSHCGIKGNEIVD 185
                S     N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 508 AQPDKSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 549
>pdb|1HYS|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase In Complex With A Polypurine Tract Rna:dna Length = 553 Back     alignment and structure
>pdb|3DLK|A Chain A, Crystal Structure Of An Engineered Form Of The Hiv-1 Reverse Transcriptase, Rt69a Length = 556 Back     alignment and structure
>pdb|1QE1|A Chain A, Crystal Structure Of 3tc-Resistant M184i Mutant Of Hiv-1 Reverse Transcriptase Length = 558 Back     alignment and structure
>pdb|3IG1|A Chain A, Hiv-1 Reverse Transcriptase With The Inhibitor Beta- Thujaplicinol Bound At The Rnase H Active Site Length = 555 Back     alignment and structure
>pdb|2I5J|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In Complex With Dhbnh, An Rnase H Inhibitor Length = 552 Back     alignment and structure
>pdb|1DLO|A Chain A, Human Immunodeficiency Virus Type 1 Length = 556 Back     alignment and structure
>pdb|4DG1|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) With Polymorphism Mutation K172a And K173a Length = 549 Back     alignment and structure
>pdb|1UWB|A Chain A, Tyr 181 Cys Hiv-1 Rt8-Cl Tibo Length = 558 Back     alignment and structure
>pdb|3QO9|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In Complex With Tsao-T, A Non-Nucleoside Rt Inhibitor (Nnrti) Length = 557 Back     alignment and structure
>pdb|1S6P|A Chain A, Crystal Structure Of Human Immunodeficiency Virus Type 1 Reverse Transcriptase (Rt) In Complex With Janssen-R100943 Length = 560 Back     alignment and structure
>pdb|3QLH|A Chain A, Hiv-1 Reverse Transcriptase In Complex With Manicol At The Rnase H Active Site And Tmc278 (rilpivirine) At The Nnrti Binding Pocket Length = 555 Back     alignment and structure
>pdb|2ZD1|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In Complex With Tmc278 (Rilpivirine), A Non-Nucleoside Rt Inhibitor Length = 557 Back     alignment and structure
>pdb|1HPZ|A Chain A, Human Immunodeficiency Virus Type 1 Length = 560 Back     alignment and structure
>pdb|2ZE2|A Chain A, Crystal Structure Of L100iK103N MUTANT HIV-1 Reverse Transcriptase (Rt) In Complex With Tmc278 (Rilpivirine), A Non-Nucleoside Rt Inhibitor Length = 557 Back     alignment and structure
>pdb|3JSM|A Chain A, K65r Mutant Hiv-1 Reverse Transcriptase Cross-Linked To Ds-Dna And Complexed With Tenofovir-Diphosphate As The Incoming Nucleotide Substrate Length = 558 Back     alignment and structure
>pdb|1HVU|A Chain A, Human Immunodeficiency Virus Type 1 Reverse Transcriptase Complexed With A 33-Base Nucleotide Rna Pseudoknot Length = 554 Back     alignment and structure
>pdb|1N5Y|A Chain A, Hiv-1 Reverse Transcriptase Crosslinked To Post- Translocation Aztmp-Terminated Dna (Complex P) Length = 558 Back     alignment and structure
>pdb|1S1W|A Chain A, Crystal Structure Of V106a Mutant Hiv-1 Reverse Transcriptase In Complex With Uc-781 Length = 560 Back     alignment and structure
>pdb|3IRX|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In Complex With The Non-Nucleoside Rt Inhibitor (E)-S-Methyl 5-(1-(3,7-Dimethyl-2-Oxo-2, 3-Dihydrobenzo[d]oxazol-5-Yl)-5- (5-Methyl-1,3,4-Oxadiazol-2-Yl)pent-1-Enyl)-2-Methoxy-3- Methylbenzothioate. Length = 558 Back     alignment and structure
>pdb|2VG5|A Chain A, Crystal Structures Of Hiv-1 Reverse Transcriptase Complexes With Thiocarbamate Non-Nucleoside Inhibitors Length = 557 Back     alignment and structure
>pdb|1S1T|A Chain A, Crystal Structure Of L100i Mutant Hiv-1 Reverse Transcriptase In Complex With Uc-781 Length = 560 Back     alignment and structure
>pdb|1JLE|A Chain A, Crystal Structure Of Y188c Mutant Hiv-1 Reverse Transcriptase Length = 560 Back     alignment and structure
>pdb|3KLE|A Chain A, Crystal Structure Of Azt-Resistant Hiv-1 Reverse Transcriptase Crosslinked To A Dsdna With A Bound Excision Product, Aztppppa Length = 562 Back     alignment and structure
>pdb|1HMV|A Chain A, The Structure Of Unliganded Reverse Transcriptase From The Human Immunodeficiency Virus Type 1 Length = 560 Back     alignment and structure
>pdb|3DM2|A Chain A, Crystal Structure Of Hiv-1 K103n Mutant Reverse Transcriptase In Complex With Gw564511. Length = 560 Back     alignment and structure
>pdb|1LWF|A Chain A, Crystal Structure Of A Mutant Hiv-1 Reverse Transcriptase (rtmq+m184v: M41l/d67n/k70r/m184v/t215y) In Complex With Nevirapine Length = 560 Back     alignment and structure
>pdb|1RT3|A Chain A, Azt Drug Resistant Hiv-1 Reverse Transcriptase Complexed With 1051u91 Length = 560 Back     alignment and structure
>pdb|1LWC|A Chain A, Crystal Structure Of M184v Mutant Hiv-1 Reverse Transcriptase In Complex With Nevirapine Length = 560 Back     alignment and structure
>pdb|1LWE|A Chain A, Crystal Structure Of M41lT215Y MUTANT HIV-1 Reverse Transcriptase (Rtmn) In Complex With Nevirapine Length = 560 Back     alignment and structure
>pdb|3HVT|A Chain A, Structural Basis Of Asymmetry In The Human Immunodeficiency Virus Type 1 Reverse Transcriptase Heterodimer Length = 556 Back     alignment and structure
>pdb|1REV|A Chain A, Hiv-1 Reverse Transcriptase Length = 560 Back     alignment and structure
>pdb|1LW0|A Chain A, Crystal Structure Of T215y Mutant Hiv-1 Reverse Transcriptase In Complex With Nevirapine Length = 560 Back     alignment and structure
>pdb|1S1X|A Chain A, Crystal Structure Of V108i Mutant Hiv-1 Reverse Transcriptase In Complex With Nevirapine Length = 560 Back     alignment and structure
>pdb|2IAJ|A Chain A, Crystal Structure Of K103nY181C MUTANT HIV-1 Reverse Transcriptase (Rt) In Complex With Atp Length = 560 Back     alignment and structure
>pdb|3KLF|A Chain A, Crystal Structure Of Wild-Type Hiv-1 Reverse Transcriptase Crosslinked To A Dsdna With A Bound Excision Product, Aztppppa Length = 557 Back     alignment and structure
>pdb|1JKH|A Chain A, Crystal Structure Of Y181c Mutant Hiv-1 Reverse Transcriptase In Complex With Dmp-266(Efavirenz) Length = 560 Back     alignment and structure
>pdb|1JLF|A Chain A, Crystal Structure Of Y188c Mutant Hiv-1 Reverse Transcriptase In Complex With Nevirapine Length = 560 Back     alignment and structure
>pdb|2RKI|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In Complex With A Triazole Derived Nnrti Length = 560 Back     alignment and structure
>pdb|3FFI|A Chain A, Hiv-1 Rt With Pyridone Non-Nucleoside Inhibitor Length = 561 Back     alignment and structure
>pdb|3DMJ|A Chain A, Crystal Structure Of Hiv-1 V106a And Y181c Mutant Reverse Transcriptase In Complex With Gw564511 Length = 560 Back     alignment and structure
>pdb|2YNF|A Chain A, Hiv-1 Reverse Transcriptase Y188l Mutant In Complex With Inhibitor Gsk560 Length = 563 Back     alignment and structure
>pdb|3DRS|A Chain A, Hiv Reverse Transcriptase K103n Mutant In Complex With Inhibitor R8d Length = 563 Back     alignment and structure
>pdb|2RF2|A Chain A, Hiv Reverse Transcriptase In Complex With Inhibitor 7e (Nnrti) Length = 563 Back     alignment and structure
>pdb|3MED|A Chain A, Hiv-1 K103n Reverse Transcriptase In Complex With Tmc125 Length = 560 Back     alignment and structure
>pdb|3KJV|A Chain A, Hiv-1 Reverse Transcriptase In Complex With Dna Length = 560 Back     alignment and structure
>pdb|3DI6|A Chain A, Hiv-1 Rt With Pyridazinone Non-Nucleoside Inhibitor Length = 561 Back     alignment and structure
>pdb|3KLH|A Chain A, Crystal Structure Of Azt-Resistant Hiv-1 Reverse Transcriptase Crosslinked To Post-Translocation Aztmp-Terminated Dna (Complex P) Length = 564 Back     alignment and structure
>pdb|3BGR|A Chain A, Crystal Structure Of K103nY181C MUTANT HIV-1 Reverse Transcriptase (Rt) In Complex With Tmc278 (Rilpivirine), A Non-Nucleoside Rt Inhibitor Length = 557 Back     alignment and structure
>pdb|2JLE|A Chain A, Novel Indazole Nnrtis Created Using Molecular Template Hybridization Based On Crystallographic Overlays Length = 566 Back     alignment and structure
>pdb|3DRR|A Chain A, Hiv Reverse Transcriptase Y181c Mutant In Complex With Inhibitor R8e Length = 563 Back     alignment and structure
>pdb|1O1W|A Chain A, Solution Structure Of The Rnase H Domain Of The Hiv-1 Reverse Transcriptase In The Presence Of Magnesium Length = 138 Back     alignment and structure
>pdb|3K2P|A Chain A, Hiv-1 Reverse Transcriptase Isolated Rnaseh Domain With The Inhibitor Beta-Thujaplicinol Bound At The Active Site Length = 136 Back     alignment and structure
>pdb|1BQN|A Chain A, Tyr 188 Leu Hiv-1 RtHBY 097 Length = 558 Back     alignment and structure
>pdb|2YKN|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In Complex With A Difluoromethylbenzoxazole (Dfmb) Pyrimidine Thioether Derivative, A Non-Nucleoside Rt Inhibitor (Nnrti) Length = 562 Back     alignment and structure
>pdb|1RDH|A Chain A, Crystallographic Analyses Of An Active Hiv-1 Ribonuclease H Domain Show Structural Features That Distinguish It From The Inactive Form Length = 146 Back     alignment and structure
>pdb|3LP3|A Chain A, P15 Hiv Rnaseh Domain With Inhibitor Mk3 Length = 138 Back     alignment and structure
>pdb|2YKM|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In Complex With A Difluoromethylbenzoxazole (Dfmb) Pyrimidine Thioether Derivative, A Non-Nucleoside Rt Inhibitor (Nnrti) Length = 562 Back     alignment and structure
>pdb|1HRH|A Chain A, Crystal Structure Of The Ribonuclease H Domain Of Hiv-1 Reverse Transcriptase Length = 136 Back     alignment and structure
>pdb|1EET|A Chain A, Hiv-1 Reverse Transcriptase In Complex With The Inhibitor Msc204 Length = 557 Back     alignment and structure
>pdb|1IKW|A Chain A, Wild Type Hiv-1 Reverse Transcriptase In Complex With Efavirenz Length = 560 Back     alignment and structure
>pdb|1IKV|A Chain A, K103n Mutant Hiv-1 Reverse Transcriptase In Complex With Efivarenz Length = 560 Back     alignment and structure
>pdb|4B3O|A Chain A, Structures Of Hiv-1 Rt And Rna-dna Complex Reveal A Unique Rt Conformation And Substrate Interface Length = 560 Back     alignment and structure
>pdb|2OPR|A Chain A, Crystal Structure Of K101e Mutant Hiv-1 Reverse Transcriptase In Complex With Gw420867x Length = 547 Back     alignment and structure
>pdb|3V4I|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) With Dna And Azttp Length = 556 Back     alignment and structure
>pdb|3HYF|A Chain A, Crystal Structure Of Hiv-1 Rnase H P15 With Engineered E. Coli Loop And Active Site Inhibitor Length = 150 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query306
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 2e-09
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 3e-04
2kq2_A147 Ribonuclease H-related protein; PSI, NESG, protein 3e-09
3p1g_A165 Xenotropic murine leukemia virus-related virus (X 5e-08
2zd1_A557 Reverse transcriptase/ribonuclease H; P51/P66, het 3e-05
1mu2_A555 HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym 1e-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 Back     alignment and structure
 Score = 57.6 bits (138), Expect = 2e-09
 Identities = 45/282 (15%), Positives = 80/282 (28%), Gaps = 90/282 (31%)

Query: 84  GCAYSV--GNVVRS--TLLNPVNSIF---------SAELIAIF--LC------LEAILDS 122
           G   +    +V  S          IF            ++ +   L         +  D 
Sbjct: 160 GSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDH 219

Query: 123 PSGEFLVVTDSRSSLAAL-SNVRFTNPLIT--KVYS--TWNYLKL-CK-------KDITF 169
            S   L +   ++ L  L  +  + N L+    V +   WN   L CK       K +T 
Sbjct: 220 SSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTD 279

Query: 170 MWCPSHCGIKGNEIVDVAARNPTTGTTPSKL---------CTPEDFK-------PFVASI 213
                   +       ++  + +   TP ++         C P+D         P   SI
Sbjct: 280 F-------LSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSI 332

Query: 214 ---MQSEWQSLWDNIP--NTNKLKN-IRPSIKAWKTSDQDKRFQELAGNRRERPYHKSVK 267
                 +  + WDN    N +KL   I  S+   + ++  K F  L+       +  S  
Sbjct: 333 IAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLS------VFPPSAH 386

Query: 268 APNS---------------------KKRASIASNRKKARYRI 288
            P                        K + +    K++   I
Sbjct: 387 IPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISI 428
>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
>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
>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
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query306
2qkb_A154 Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy 99.92
3qio_A150 GAG-POL polyprotein; RNAse H, inhibitor, nuclease, 99.91
2kq2_A147 Ribonuclease H-related protein; PSI, NESG, protein 99.89
3h08_A146 RNH (ribonuclease H); RNAse H, 3D-structure, endon 99.89
1jl1_A155 Ribonuclease HI; RNAse HI, protein stability, ther 99.88
3p1g_A165 Xenotropic murine leukemia virus-related virus (X 99.88
2e4l_A158 Ribonuclease HI, RNAse HI; hydrolase, endoribonucl 99.88
1ril_A166 Ribonuclease H; hydrolase(endoribonuclease); 2.80A 99.87
2lsn_A165 Reverse transcriptase; RNAse H, viral protein; NMR 99.85
3u3g_D140 Ribonuclease H, RNAse H1; hydrolase, cleave the RN 99.82
3hst_B141 Protein RV2228C/MT2287; ribonuclease H1, RV2228C N 99.82
1mu2_A555 HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym 99.81
2zd1_A557 Reverse transcriptase/ribonuclease H; P51/P66, het 99.79
2ehg_A149 Ribonuclease HI; RNAse HI, hyperthermophilic archa 99.78
1zbf_A142 Ribonuclease H-related protein; RNAse H, RNA/DNA h 99.38
4htu_A134 Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine, 99.11
1rw3_A455 POL polyprotein; RNA and DNA dependent DNA polymer 84.37
>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
Probab=99.92  E-value=6.9e-25  Score=184.36  Aligned_cols=130  Identities=21%  Similarity=0.255  Sum_probs=99.6

Q ss_pred             cCCCcEEEEEcCCCCCCc-----cceEEEeCC---eEEEEcCCCCCcHHHHHHHHHHHHHHHHHhCCCCeEEEEeChHHH
Q psy7230          65 KYTNHTICYTDGSKTPTT-----TGCAYSVGN---VVRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGEFLVVTDSRSS  136 (306)
Q Consensus        65 ~~~~~~~iyTDGS~~~~g-----~G~av~~~~---~~~~~~l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~sDS~sa  136 (306)
                      +..+.+.||||||+..++     +|+|++...   ...+..+...+|++.||+.|++.||+.+.+.+..+|.|+|||+++
T Consensus         3 ~~~~~~~iytDGs~~~n~~~~~~aG~Gvv~~~~~~~~~~~~l~~~~tn~~aEl~A~~~aL~~~~~~~~~~v~i~tDS~~v   82 (154)
T 2qkb_A            3 HMGDFVVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQAKTQNINKLVLYTNSMFT   82 (154)
T ss_dssp             EETTEEEEEEEEEEETTTSSSCEEEEEEECSTTCTTCEEEECCSSCCHHHHHHHHHHHHHHHHHHTTCCEEEEEESCHHH
T ss_pred             CCCCeEEEEEccCcCCCCCCCCcEEEEEEEECCCceeEEeecCCCCchHHHHHHHHHHHHHHHHhCCCceEEEEECcHHH
Confidence            456789999999998543     688876432   123445655789999999999999999998888999999999999


Q ss_pred             HHHHhccc---------cCCh--h-HHHHHHHHHHHHhCCCceEEEecCCCCCCccchHHHHHHcCcCCCC
Q psy7230         137 LAALSNVR---------FTNP--L-ITKVYSTWNYLKLCKKDITFMWCPSHCGIKGNEIVDVAARNPTTGT  195 (306)
Q Consensus       137 l~~l~~~~---------~~s~--~-~~~i~~~~~~l~~~~~~V~~~WVPgH~gi~gNE~AD~lAk~A~~~~  195 (306)
                      ++.|+.+.         ...+  . -.+++..+..+. .+..|.|.|||||+|++|||+||+|||+|+..+
T Consensus        83 i~~i~~~~~~w~~~~w~~~~~~~~~n~~l~~~i~~l~-~~~~v~~~~V~~H~g~~~N~~AD~LA~~a~~~~  152 (154)
T 2qkb_A           83 INGITNWVQGWKKNGWKTSAGKEVINKEDFVALERLT-QGMDIQWMHVPGHSGFIGNEEADRLAREGAKQS  152 (154)
T ss_dssp             HHHHHTHHHHHHTTTSBCTTSSBCTTHHHHHHHHHHH-TTCEEEEEECCTTSSCHHHHHHHHHHHHHHTCC
T ss_pred             HhhhhhhHHHHHhccccccCCCccccHHHHHHHHHHH-cCCceEEEEccCCCCCHhHHHHHHHHHHHHHhc
Confidence            99998742         1111  1 123333333332 356799999999999999999999999998764
>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
>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
>3u3g_D Ribonuclease H, RNAse H1; hydrolase, cleave the RNA strand of RNA/DNA hybrid; 1.40A {Uncultured organism} 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
>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
>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
>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 306
d1mu2a1126 c.55.3.1 (A:430-555) HIV RNase H (Domain of revers 9e-07
d1s1ta1110 c.55.3.1 (A:430-539) HIV RNase H (Domain of revers 0.001
d1jl1a_152 c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli 0.001
>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 = 44.9 bits (105), Expect = 9e-07
 Identities = 25/119 (21%), Positives = 44/119 (36%), Gaps = 8/119 (6%)

Query: 73  YTDGS--KTPTTTGCAYSVGNVVRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGEFLVV 130
           YTDGS  +        Y               +   AEL A  + L         +  ++
Sbjct: 11  YTDGSCNRQSKEGKAGYVTDRGKDKVKKLEQTTNQQAELEAFAMALT----DSGPKVNII 66

Query: 131 TDSRSSLAALSNVRFTNPLITKVYSTWNYLKLCKKDITFMWCPSHCGIKGNEIVDVAAR 189
            DS+  +  +++    +   +K+ +      + K+ I   W P+H GI GN+ VD    
Sbjct: 67  VDSQYVMGIVASQPTESE--SKIVNQIIEEMIKKEAIYVAWVPAHKGIGGNQEVDHLVS 123
>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
>d1jl1a_ c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli [TaxId: 562]} Length = 152 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 ?
Query306
d1mu2a1126 HIV RNase H (Domain of reverse transcriptase) {Hum 99.92
d1rila_147 RNase H (RNase HI) {Thermus thermophilus [TaxId: 2 99.89
d1jl1a_152 RNase H (RNase HI) {Escherichia coli [TaxId: 562]} 99.88
d1s1ta1110 HIV RNase H (Domain of reverse transcriptase) {Hum 99.76
d1zbfa1132 BH0863-like Ribonuclease H {Bacillus halodurans [T 99.55
>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=99.92  E-value=9.3e-26  Score=181.64  Aligned_cols=121  Identities=21%  Similarity=0.253  Sum_probs=88.0

Q ss_pred             cCCCcEEEEEcCCCCCC-c-cceEEEeCC-eEEEEcCCCCCcHHHHHHHHHHHHHHHHHhCCCCeEEEEeChHHHHHHHh
Q psy7230          65 KYTNHTICYTDGSKTPT-T-TGCAYSVGN-VVRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGEFLVVTDSRSSLAALS  141 (306)
Q Consensus        65 ~~~~~~~iyTDGS~~~~-g-~G~av~~~~-~~~~~~l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~sDS~sal~~l~  141 (306)
                      |..+...+|||||+..+ + .|+|++... ......++ ..|+++|||.||++||+.    ....+.|+|||++++..+.
T Consensus         3 p~~~~~t~YTDGS~~~n~~~~~~g~~~~~~~~~~~~~~-~~tnn~AEl~Ai~~al~~----~~~~i~I~tDS~~v~~~~~   77 (126)
T d1mu2a1           3 PIPGAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKLE-QTTNQQAELEAFAMALTD----SGPKVNIIVDSQYVMGIVA   77 (126)
T ss_dssp             CCTTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEEES-SCCHHHHHHHHHHHHHHT----SCSEEEEEESCHHHHHHHH
T ss_pred             CCCCCcEEEEcCCCCCCCCcEEEEEEecCCCEEEEecC-CCcchHHHHHHHHHHhcc----CCcceEEEechHHHHHHHh
Confidence            34566899999998754 3 456654332 23333343 579999999999999985    4668999999999999999


Q ss_pred             ccccCChhHHHHHHHHHHHHhCCCceEEEecCCCCCCccchHHHHHHcCcC
Q psy7230         142 NVRFTNPLITKVYSTWNYLKLCKKDITFMWCPSHCGIKGNEIVDVAARNPT  192 (306)
Q Consensus       142 ~~~~~s~~~~~i~~~~~~l~~~~~~V~~~WVPgH~gi~gNE~AD~lAk~A~  192 (306)
                      ++...+.. ......+..+. ....|.|.|||||+|++|||+||+||++|+
T Consensus        78 ~~~~~~~~-~~~~~~~~~~~-~~~~v~~~wV~gH~g~~gNe~AD~LA~~ai  126 (126)
T d1mu2a1          78 SQPTESES-KIVNQIIEEMI-KKEAIYVAWVPAHKGIGGNQEVDHLVSQGI  126 (126)
T ss_dssp             TCCSEESC-HHHHHHHHHHH-HCSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             cCCccccc-hHHHHHHHHhh-hcceeEEEEEeCCCCCcchHHHHHHHHhhC
Confidence            87643221 11111122332 357999999999999999999999999985
>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