Psyllid ID: psy15277

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 (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-------27

MNSKYLDSVVCFSDGSKTPNSTSCAYSIDKQIHSFNLNKVNSVFSAELMAILLCIKNLKFLPHNKFIIISDSMSALQAISNLNSNNSLVPKIYSHWLDLKSCGKNLCFLWCPSHCGIKGNESVDNAARNPNYNTTLRKCTSDDFRPIISTIIMKNWQTSWDNITNNKLKNIKPKIEEWVSSNRDSRYEEIVITRLRIGHTRLTHEFLFNKTPRPSCSCGEPLSVQHLLSCPSHDQARSRLPSVPALINDPINIDSTLSYLKAIGLFTKI

ccccccccEEEEEccccccccEEEEEEEccccEEEEccccccHHHHHHHHHHHHHHHHHcccccEEEEEccHHHHHHHHHccccccccHHHHHHHHHHHHHcccEEEEEEccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHccccccccccccccccccccccccccccHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccHHHHcccccccccccccccHHHHHHHHHHccccccc

cccccccEEEEEEccccccccEEEEEEEEccEEEcccccccHHHHHHHHHHHHHHHHHHHcccccEEEEEccHHHHHHHHccccccHHHHHHHHHHHHHHHcccEEEEEEEcccccccccHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccHHHHHHHHHHccccccHHHHHccccccccccccccccHHHHHccHHHHHHHHHHHHccccccccHcHHHHHHHHHHHcHHccc

mnskyldsvvcfsdgsktpnstscaysIDKQIHSFNLNKVNSVFSAELMAILLCIKnlkflphnkfiIISDSMSALQAISNlnsnnslvpkiYSHWLdlkscgknlcflwcpshcgikgnesvdnaarnpnynttlrkctsddfrPIISTIIMKNWQTSWDNItnnklknikpkIEEWvssnrdsrYEEIVITRLRIghtrltheflfnktprpscscgeplsvqhllscpshdqarsrlpsvpalindpinidSTLSYLKAIGLFTKI

MNSKYLDSVVCFSDGSKTPNSTSCAYSIDKQIHSFNLNKVNSVFSAELMAILLCIKNLKFLPHNKFIIISDSMSALQAISNLNSNNSLVPKIYSHWLDLKSCGKNLCFLWCPSHCgikgnesvdnaarnpnynttlrkctsddfRPIISTIImknwqtswdnitnnklknikpkieewvssnrdsryeEIVITRLRIGHTRLTHEFLFNKTPRPSCSCGEPLSVQHLLSCPSHDQARSRLPSVPALINDPINIDSTLSYLKAIGLFTKI

*******SVVCF**********SCAYSIDKQIHSFNLNKVNSVFSAELMAILLCIKNLKFLPHNKFIIISDSMSALQAISNLNSNNSLVPKIYSHWLDLKSCGKNLCFLWCPSHCGIKGNESVDNAARNPNYNTTLRKCTSDDFRPIISTIIMKNWQTSWDNITNNKLKNIKPKIEEWVSSNRDSRYEEIVITRLRIGHTRLTHEFLFNKTPRPSCSCGEPLSVQHLLS*************VPALINDPINIDSTLSYLKAIGLF***

***KYLDSVVCFSDGSKTPNSTSCAYSIDKQIHSFNLNKVNSVFSAELMAILLCIKNLKFLPHNKFIIISDSMSALQAISNLNSNNSLVPKIYSHWLDLKSCGKNLCFLWCPSHCGIKGNESVDNAARNPNYNTTLRKCTSDDFRPIISTIIMKNWQTSWDNITNNKLKNIKPKIEEWVSSNRDSRYEEIVITRLRIGHTRLTHEFLFNKTPRPSCSCGEPLSVQHLLSCPSHDQARSRLPSVPALINDPINIDSTLSYLKAIGLFTKI

**SKYLDSVVCFSDGSKTPNSTSCAYSIDKQIHSFNLNKVNSVFSAELMAILLCIKNLKFLPHNKFIIISDSMSALQAISNLNSNNSLVPKIYSHWLDLKSCGKNLCFLWCPSHCGIKGNESVDNAARNPNYNTTLRKCTSDDFRPIISTIIMKNWQTSWDNITNNKLKNIKPKIEEWVSSNRDSRYEEIVITRLRIGHTRLTHEFLFNKTPRPSCSCGEPLSVQHLLSCPSHDQARSRLPSVPALINDPINIDSTLSYLKAIGLFTKI

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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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		269
125901787		1222	pol-like protein [Biomphalaria glabrata]	0.992	0.218	0.340	5e-33
443721618		471	hypothetical protein CAPTEDRAFT_200496,	0.836	0.477	0.349	6e-33
443682433		619	hypothetical protein CAPTEDRAFT_222606 [	0.754	0.327	0.372	3e-31
443712830		397	hypothetical protein CAPTEDRAFT_202466 [	0.951	0.644	0.338	1e-30
427791321		1210	Putative tick transposon, partial [Rhipi	0.992	0.220	0.318	1e-30
427791807		1212	Putative tick transposon, partial [Rhipi	0.884	0.196	0.338	1e-30
443695973		261	hypothetical protein CAPTEDRAFT_23017, p	0.799	0.823	0.364	5e-30
443693558		502	hypothetical protein CAPTEDRAFT_189741,	0.799	0.428	0.364	5e-30
443724607		397	hypothetical protein CAPTEDRAFT_208903 [	0.951	0.644	0.330	4e-28
427778603		1397	Putative tick transposon [Rhipicephalus	0.970	0.186	0.315	6e-28

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

 Score =  147 bits (371), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 94/276 (34%), Positives = 146/276 (52%), Gaps = 9/276 (3%)

Query: 1    MNSKYLDSVVCFSDGSKTPNSTSCAYSIDKQIHSFNLNKVNSVFSAELMAILLCIKNLKF 60
            +   Y D    ++DGSK     +CA S   +  S  L    S+F+AEL AILL +  +K 
Sbjct: 949  LQESYGDCGTIYTDGSKMEGKVACACSFRNKTISRRLPDGCSIFTAELHAILLALMAVKA 1008

Query: 61   LPHNKFIIISDSMSALQAISNLNSNNSLVPKIYSHWLDLKSCG-KNLCFLWCPSHCGIKG 119
               +KFII SDS SALQA+  + ++  LV K     LDL +   +++ F+W PSH GI+G
Sbjct: 1009 SERSKFIICSDSKSALQALGRMKTDIPLVHKSLK-LLDLITADRRDVTFIWVPSHVGIEG 1067

Query: 120  NESVD-NAARNPNYNTTLRKCTSDDFRPIISTIIMKNWQTSWDNITNNKLKNIKPKIEEW 178
            NE+ D  A R  N+  +  +    D R  I++   + WQ  W+  T++KL+ I   +   
Sbjct: 1068 NEAADREAKRALNHAVSGTQIPYSDLRQSIASATYREWQNRWEAETHSKLRQIVADVRWR 1127

Query: 179  VSSNRDSRYEEIVITRLRIGHTRLTHEFLFNKTPRPSCS-CGEPLSVQHLL-SCPSHDQA 236
             +S   +R     ++RLRIGHT +TH F+  +   P C  C   L+V+H+L  CP +   
Sbjct: 1128 PTSKGLTRRGSTTMSRLRIGHTYITHSFVLKREEPPLCEYCDSRLTVEHILVDCPRYQDV 1187

Query: 237  RS---RLPSVPALINDPINIDSTLSYLKAIGLFTKI 269
            R+   R  ++  L N+ ++    L ++  +GL TKI
Sbjct: 1188 RAKHFRATNLKTLFNN-VDPGKVLGFILEVGLSTKI 1222

Source: Biomphalaria glabrata

Species: Biomphalaria glabrata

Genus: Biomphalaria

Family: Planorbidae

Order:

Class: Gastropoda

Phylum: Mollusca

Superkingdom: Eukaryota

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

>gi\|443682433\|gb\|ELT87030.1\| hypothetical protein CAPTEDRAFT_222606 [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\|443695973\|gb\|ELT96755.1\| hypothetical protein CAPTEDRAFT_23017, partial [Capitella teleta]	Back alignment and taxonomy information

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

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

>gi\|427778603\|gb\|JAA54753.1\| Putative tick transposon [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		269
ASPGD\|ASPL0000075333		486	AN10625 [Emericella nidulans (	0.858	0.475	0.234	1.5e-09

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

 Score = 163 (62.4 bits), Expect = 1.5e-09, P = 1.5e-09
 Identities = 59/252 (23%), Positives = 105/252 (41%)

Query:     9 VVCFSDGSKTPNSTSCAYSIDKQIHS----FNLNKVNSVFSAELMAILLCIKNLKFLPHN 64
             +  ++DGS        A    K + S          ++V+ AEL  ILL +  +      
Sbjct:   183 IALYTDGSGINGRVGAAAICPKYLISRSSYMGQQSESTVYVAELQGILLALVIILQRQMQ 242

Query:    65 KFIIISDSMSALQAISNLNSNNS--LVPKIYSHWLDLKSCGKNLCFLWCPSHCGIKGNES 122
               +I +D+ + LQA+ N  S +   ++  I       +  G N+ F W P+H G++GNE 
Sbjct:   243 HAVIFTDNQATLQALRNPGSQSGQYILEAIIMALNKGRKAGLNVHFRWIPAHRGVEGNEQ 302

Query:   123 VDNAARNPNYNTTLRKCTSD-DFRPIIST----IIMKNWQTSWDNITNNK-LKNIKPK-I 175
              D  A+       +R        R  +      ++   W+  W +  + + L  + P   
Sbjct:   303 ADRRAKEATGWRRIRGHRGRMTIRSAVKRRAHEVVNARWENDWKSCHHGRELYELTPTPT 362

Query:   176 EEWVSSNRD-SRYEEIVITRLRIGHTRLTHEFLFNK----TPRPSCSCGEPL-SVQH-LL 228
              + +  ++D  R    +I ++R G   L H +L+ +     P   C CG    SV+H LL
Sbjct:   363 RKVLRVHQDLHRALSTIIVQMRTGKIGLRH-YLYQRGVPDVPNSDCQCGRATQSVRHILL 421

Query:   229 SCPSHDQARSRL 240
             +CP+    R  +
Sbjct:   422 ACPTFSGLREEI 433


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        0.319   0.132   0.409    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      269       269   0.00096  114 3  11 22  0.47    33
                                                     32  0.39    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:  622 (66 KB)
  Total size of DFA:  226 KB (2123 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  25.81u 0.14s 25.95t   Elapsed:  00:00:01
  Total cpu time:  25.81u 0.14s 25.95t   Elapsed:  00:00:01
  Start:  Thu Aug 15 11:45:08 2013   End:  Thu Aug 15 11:45:09 2013

GO:0008150 "biological_process" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

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

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		269
cd09276		128	cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom	1e-32
pfam00075		126	pfam00075, RNase_H, RNase H	5e-14
cd06222		123	cd06222, RNase_H, RNase H is an endonuclease that	6e-10
cd09273		135	cd09273, RNase_HI_RT_Bel, Bel/Pao family of RNase	9e-05
COG0328		154	COG0328, RnhA, Ribonuclease HI [DNA replication, r	5e-04

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

 Score =  116 bits (292), Expect = 1e-32
 Identities = 42/124 (33%), Positives = 62/124 (50%), Gaps = 5/124 (4%)

Query: 10  VCFSDGSKTPNSTSCAYSI---DKQIHSFNLNKVNSVFSAELMAILLCIKNLKFL--PHN 64
           V ++DGSK    T   ++I        S+ L    SVF AEL+AIL  ++          
Sbjct: 1   VIYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRRAR 60

Query: 65  KFIIISDSMSALQAISNLNSNNSLVPKIYSHWLDLKSCGKNLCFLWCPSHCGIKGNESVD 124
           K  I SDS +AL+A+ +  S++ LV +I     +L + G  +   W P H GI+GNE  D
Sbjct: 61  KITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGNERAD 120

Query: 125 NAAR 128
             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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		269
PRK06548		161	ribonuclease H; Provisional	99.91
COG0328		154	RnhA Ribonuclease HI [DNA replication, recombinati	99.91
PF00075		132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	99.9
PRK08719		147	ribonuclease H; Reviewed	99.9
PRK00203		150	rnhA ribonuclease H; Reviewed	99.89
cd06222		130	RnaseH RNase H (RNase HI) is an endonuclease that	99.82
PRK13907		128	rnhA ribonuclease H; Provisional	99.78
KOG3752\|consensus		371		99.77
PRK07708		219	hypothetical protein; Validated	99.69
PRK07238		372	bifunctional RNase H/acid phosphatase; Provisional	99.58
PF13456		87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	99.45
PF13966		86	zf-RVT: zinc-binding in reverse transcriptase	95.21
PF05380		159	Peptidase_A17: Pao retrotransposon peptidase ; Int	90.59
.; GO: 0004523 ribonuclease H activity" target="_blank" href="http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PF00336">PF00336		245	DNA_pol_viral_C: DNA polymerase (viral) C-terminal	84.73

>PRK06548 ribonuclease H; Provisional	Back alignment and domain information

Probab=99.91  E-value=7e-24  Score=170.19  Aligned_cols=127  Identities=20%  Similarity=0.288  Sum_probs=94.0

Q ss_pred             CCceEEEecCCCCCC--CeeEEEEeCCeEEEeeCCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeCcHHHHHHHhc--
Q psy15277          6 LDSVVCFSDGSKTPN--STSCAYSIDKQIHSFNLNKVNSVFSAELMAILLCIKNLKFLPHNKFIIISDSMSALQAISN--   81 (269)
Q Consensus         6 ~~~~~i~tDGS~~~~--~~G~~~~~~~~~~~~~~~~~~s~~~aEl~Ai~~aL~~~~~~~~~~v~I~sDS~~~i~~l~~--   81 (269)
                      ++.++||||||+.++  ..|+|++..............|+++|||.||+.||+.+.. +..+|.|+|||++++++++.  
T Consensus         3 ~~~~~IytDGa~~gnpg~~G~g~~~~~~~~~~g~~~~~TNnraEl~Aii~aL~~~~~-~~~~v~I~TDS~yvi~~i~~W~   81 (161)
T PRK06548          3 NNEIIAATDGSSLANPGPSGWAWYVDENTWDSGGWDIATNNIAELTAVRELLIATRH-TDRPILILSDSKYVINSLTKWV   81 (161)
T ss_pred             CCEEEEEEeeccCCCCCceEEEEEEeCCcEEccCCCCCCHHHHHHHHHHHHHHhhhc-CCceEEEEeChHHHHHHHHHHH
Confidence            456999999999874  4788876533211122234689999999999999986643 44579999999999999994  


Q ss_pred             -------CCCCC--Cc-HHHHHHHHHHHhhcCCcEEEEEeCCCCCCccccccchhhcCCCCCC
Q psy15277         82 -------LNSNN--SL-VPKIYSHWLDLKSCGKNLCFLWCPSHCGIKGNESVDNAARNPNYNT  134 (269)
Q Consensus        82 -------~~~~~--~~-~~~i~~~~~~l~~~~~~v~~~wvp~H~g~~gNe~AD~lAk~a~~~~  134 (269)
                             +...+  +. -.++.+.+..+.+. ..|+|.|||||+|.+|||.||.||++|+...
T Consensus        82 ~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~-~~v~~~wVkgHsg~~gNe~aD~LA~~aa~~~  143 (161)
T PRK06548         82 YSWKMRKWRKADGKPVLNQEIIQEIDSLMEN-RNIRMSWVNAHTGHPLNEAADSLARQAANNF  143 (161)
T ss_pred             HHHHHCCCcccCCCccccHHHHHHHHHHHhc-CceEEEEEecCCCCHHHHHHHHHHHHHHHHh
Confidence                   22222  22 25666655555544 4799999999999999999999999987543

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

>PRK08719 ribonuclease H; Reviewed	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

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

>KOG3752\|consensus	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

>PF05380 Peptidase_A17: Pao retrotransposon peptidase ; InterPro: IPR008042 This signature identifies members of the Pao retrotransposon family	Back alignment and domain information

>PF00336 DNA_pol_viral_C: DNA polymerase (viral) C-terminal domain; InterPro: IPR001462 This domain is at the C terminus of hepatitis B-type viruses P proteins and represents a functional domain that controls the RNase H activities of the protein	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		269
3p1g_A		165	Xenotropic murine leukemia virus-related virus (X	8e-07
2kq2_A		147	Ribonuclease H-related protein; PSI, NESG, protein	4e-06
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-04
2zd1_A		557	Reverse transcriptase/ribonuclease H; P51/P66, het	2e-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 = 46.8 bits (111), Expect = 8e-07
 Identities = 31/133 (23%), Positives = 50/133 (37%), Gaps = 18/133 (13%)

Query: 9   VVCFSDGS--KTPNSTSCAYSI---DKQIHSFNLNKVNSVFSAELMAILLCIKNLKFLPH 63
              ++DGS            ++    + I +  L    S   AEL+A+    + LK    
Sbjct: 24  YTWYTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIAL---TQALKMAEG 80

Query: 64  NKFIIISDSMSALQAISNLNSNNSLVPKIYSHW---LDLKSCGKNLCFLWCPSHCG---- 116
            K  + +DS  A  A ++++S    + K  +     L      K L  + CP H      
Sbjct: 81  KKLNVYTDSRYAF-ATAHVHSEGREI-KNKNEILALLKALFLPKRLSIIHCPGHQKGNSA 138

Query: 117 -IKGNESVDNAAR 128
             +GN   D AAR
Sbjct: 139 EARGNRMADQAAR 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

>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

>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

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		269
2qkb_A		154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.93
3qio_A		150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.92
3h08_A		146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.91
2kq2_A		147	Ribonuclease H-related protein; PSI, NESG, protein	99.91
1jl1_A		155	Ribonuclease HI; RNAse HI, protein stability, ther	99.9
3p1g_A		165	Xenotropic murine leukemia virus-related virus (X	99.9
2e4l_A		158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.89
1ril_A		166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.88
2lsn_A		165	Reverse transcriptase; RNAse H, viral protein; NMR	99.87
3hst_B		141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	99.85
3u3g_D		140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	99.85
2zd1_A		557	Reverse transcriptase/ribonuclease H; P51/P66, het	99.83
1mu2_A		555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	99.83
2ehg_A		149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	99.81
1zbf_A		142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	99.51
4htu_A		134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	99.31
1rw3_A		455	POL polyprotein; RNA and DNA dependent DNA polymer	83.52

>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=99.93  E-value=1.1e-25  Score=180.04  Aligned_cols=128  Identities=23%  Similarity=0.295  Sum_probs=98.9

Q ss_pred             CCceEEEecCCCCCCC-----eeEEEEeCC---eEEEeeCCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeCcHHHHH
Q psy15277          6 LDSVVCFSDGSKTPNS-----TSCAYSIDK---QIHSFNLNKVNSVFSAELMAILLCIKNLKFLPHNKFIIISDSMSALQ   77 (269)
Q Consensus         6 ~~~~~i~tDGS~~~~~-----~G~~~~~~~---~~~~~~~~~~~s~~~aEl~Ai~~aL~~~~~~~~~~v~I~sDS~~~i~   77 (269)
                      ++.++||||||+..++     +|+|++...   ...+..+...+|++.||+.|++.||+.+...+..+|.|+|||+++++
T Consensus         5 ~~~~~iytDGs~~~n~~~~~~aG~Gvv~~~~~~~~~~~~l~~~~tn~~aEl~A~~~aL~~~~~~~~~~v~i~tDS~~vi~   84 (154)
T 2qkb_A            5 GDFVVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQAKTQNINKLVLYTNSMFTIN   84 (154)
T ss_dssp             TTEEEEEEEEEEETTTSSSCEEEEEEECSTTCTTCEEEECCSSCCHHHHHHHHHHHHHHHHHHTTCCEEEEEESCHHHHH
T ss_pred             CCeEEEEEccCcCCCCCCCCcEEEEEEEECCCceeEEeecCCCCchHHHHHHHHHHHHHHHHhCCCceEEEEECcHHHHh
Confidence            4568999999997643     788877532   12455566678999999999999999999888899999999999999


Q ss_pred             HHhcCC---------CCC--Cc-HHHHHHHHHHHhhcCCcEEEEEeCCCCCCccccccchhhcCCCCCC
Q psy15277         78 AISNLN---------SNN--SL-VPKIYSHWLDLKSCGKNLCFLWCPSHCGIKGNESVDNAARNPNYNT  134 (269)
Q Consensus        78 ~l~~~~---------~~~--~~-~~~i~~~~~~l~~~~~~v~~~wvp~H~g~~gNe~AD~lAk~a~~~~  134 (269)
                      .|+++.         ...  +. ...+.+.+..+.. +..|.|.|||||+|++|||.||+|||+|+..+
T Consensus        85 ~i~~~~~~w~~~~w~~~~~~~~~n~~l~~~i~~l~~-~~~v~~~~V~~H~g~~~N~~AD~LA~~a~~~~  152 (154)
T 2qkb_A           85 GITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQ-GMDIQWMHVPGHSGFIGNEEADRLAREGAKQS  152 (154)
T ss_dssp             HHHTHHHHHHTTTSBCTTSSBCTTHHHHHHHHHHHT-TCEEEEEECCTTSSCHHHHHHHHHHHHHHTCC
T ss_pred             hhhhhHHHHHhccccccCCCccccHHHHHHHHHHHc-CCceEEEEccCCCCCHhHHHHHHHHHHHHHhc
Confidence            998731         111  11 2344444444433 46799999999999999999999999987653

PyMOL of 2qkb

>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

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

>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		269
d1mu2a1		126	c.55.3.1 (A:430-555) HIV RNase H (Domain of revers	6e-08
d1rila_		147	c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermoph	2e-05

>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 = 48.4 bits (114), Expect = 6e-08
 Identities = 25/124 (20%), Positives = 49/124 (39%), Gaps = 8/124 (6%)

Query: 7   DSVVCFSDGS--KTPNSTSCAYSIDKQIHSFNLNKVNSVFSAELMAILLCIKNLKFLPHN 64
            +   ++DGS  +        Y  D+        +  +   AEL A  + + +       
Sbjct: 6   GAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKLEQTTNQQAELEAFAMALTD----SGP 61

Query: 65  KFIIISDSMSALQAISNLNSNNSLVPKIYSHWLDLKSCGKNLCFLWCPSHCGIKGNESVD 124
           K  II DS   +  +++  + +    KI +  ++     + +   W P+H GI GN+ VD
Sbjct: 62  KVNIIVDSQYVMGIVASQPTES--ESKIVNQIIEEMIKKEAIYVAWVPAHKGIGGNQEVD 119

Query: 125 NAAR 128
           +   
Sbjct: 120 HLVS 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

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		269
d1mu2a1		126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.94
d1jl1a_		152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	99.9
d1rila_		147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.89
d1s1ta1		110	HIV RNase H (Domain of reverse transcriptase) {Hum	99.8
d1zbfa1		132	BH0863-like Ribonuclease H {Bacillus halodurans [T	99.62

>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=99.94  E-value=1.5e-26  Score=176.96  Aligned_cols=120  Identities=21%  Similarity=0.284  Sum_probs=89.4

Q ss_pred             CCCceEEEecCCCCCCC--eeEEEEeCC-eEEEeeCCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeCcHHHHHHHhc
Q psy15277          5 YLDSVVCFSDGSKTPNS--TSCAYSIDK-QIHSFNLNKVNSVFSAELMAILLCIKNLKFLPHNKFIIISDSMSALQAISN   81 (269)
Q Consensus         5 ~~~~~~i~tDGS~~~~~--~G~~~~~~~-~~~~~~~~~~~s~~~aEl~Ai~~aL~~~~~~~~~~v~I~sDS~~~i~~l~~   81 (269)
                      +++..++|||||+..++  .|+|++... ......+ ...|++.|||.||++||+..    ..++.|+|||+++++.+++
T Consensus         4 ~~~~~t~YTDGS~~~n~~~~~~g~~~~~~~~~~~~~-~~~tnn~AEl~Ai~~al~~~----~~~i~I~tDS~~v~~~~~~   78 (126)
T d1mu2a1           4 IPGAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKL-EQTTNQQAELEAFAMALTDS----GPKVNIIVDSQYVMGIVAS   78 (126)
T ss_dssp             CTTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEEE-SSCCHHHHHHHHHHHHHHTS----CSEEEEEESCHHHHHHHHT
T ss_pred             CCCCcEEEEcCCCCCCCCcEEEEEEecCCCEEEEec-CCCcchHHHHHHHHHHhccC----CcceEEEechHHHHHHHhc
Confidence            46778999999987643  666665432 2223333 35799999999999999864    6789999999999999999


Q ss_pred             CCCCCCcHHHHHHHHHHHhhcCCcEEEEEeCCCCCCccccccchhhcCCC
Q psy15277         82 LNSNNSLVPKIYSHWLDLKSCGKNLCFLWCPSHCGIKGNESVDNAARNPN  131 (269)
Q Consensus        82 ~~~~~~~~~~i~~~~~~l~~~~~~v~~~wvp~H~g~~gNe~AD~lAk~a~  131 (269)
                      ....+.. ......+..+. ....|.|.|||||+|++|||+||+||++|.
T Consensus        79 ~~~~~~~-~~~~~~~~~~~-~~~~v~~~wV~gH~g~~gNe~AD~LA~~ai  126 (126)
T d1mu2a1          79 QPTESES-KIVNQIIEEMI-KKEAIYVAWVPAHKGIGGNQEVDHLVSQGI  126 (126)
T ss_dssp             CCSEESC-HHHHHHHHHHH-HCSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             CCccccc-hHHHHHHHHhh-hcceeEEEEEeCCCCCcchHHHHHHHHhhC
Confidence            7654332 11222222333 356899999999999999999999999984

PyMOL of d1mu2a1

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

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