Psyllid ID: psy7629

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-------410-------420-------430-------440-------450-------460-------47

MENFEISENSSTDKVNKEFCELLQSAAKLSIPRGKTKRFNYFWNKKLSVLKSERNAARKRAEKSNLLSDTVEWRKRAAILKKEINSSKRSSFNTFVEKMDYRKDGPKAYSFISSIKKGQTSVNKPFSHNGRSISDSKKIASIFNTFYTSKYNIPKHEVLLTTSKTNKQKIEKVQNEALRLVTGAVKTTPINAMYALTQNQSLSDIIEQQALTTYEKLTRLPNNNFWTTYKEDPTKLKTQTGYIQEVKKIKLLTEIPDKKENLLHPPNPMDSFEITHSLFLEETFRKQDVAPLIAKTMALETINTRYPSDDWLHIYTDGSLINPEDGAGAGIFCELFSFYKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAIQSITNCSEDPSIKHNKRLRNEGQGKKWQQILNTHDIIPNLPRKAAVAHFRLLTGHDCLAEHLHRFGLKTSPIGSRDLKTCFDTKS

cccccccccccHHHHHHHHHHHHHHHHHcccccccccccccccHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHcccccccccccccHHHHHccccccccccccHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHcccccccccccccccHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHccccHHHHHHHHHHHHHHHHcccccccccccccccccccccccHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHcccccccccEEEEcccccccccccEEEEEEccEEEEEEccccccHHHHHHHHHHHHHHHHHHHcccccEEEEEEccHHHHHHHHccccccHHHHHHHHHHcccccEEEEEcccccccccccccEEEEccccccccccHHHHHHHccccccccccccccccccccc

cccEEEEccccccHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHccccccccHcHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHcccccccHHcccHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHccccHHHHHHHHHHHHHHHHHcccccccccccccccccccccHHHHHHHHHccccccccccccccccccccccccccccEEEcccccccccccHHHHHHHHHHHHHHHcccccEEEEEEccccccccccEEEEEEcccEEEEEEccccccHHHHHHHHHHHHHHHHHHHHcccccEEEEcccHHHHHHHHHccccccccHcHHHHHccccccHHHHHcHHHHHccccccccEEEEEEccccHHHHHHHHHccccccccccccccccccccc

menfeisensstdkVNKEFCELLQSAAKlsiprgktkrfNYFWNKKLSVLKSERNAARKRAEKSNLLSDTVEWRKRAAILKKEInsskrssfnTFVEkmdyrkdgpkaySFISSikkgqtsvnkpfshngrsisdskKIASIFNTFytskynipkheVLLTTSKTNKQKIEKVQNEALRLVTGAVKTTPINAMYALTQNQSLSDIIEQQALTTYEKltrlpnnnfwttykedptklktqtgyIQEVKKIKLLteipdkkenllhppnpmdsfeiTHSLFLEETFRKQDVAPLIAKTMALETintrypsddwlhiytdgslinpedgagaGIFCELFSFYKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAIQSITncsedpsikhnkrlrnegqgkkWQQILnthdiipnlprKAAVAHFRLLTGHDCLAehlhrfglktspigsrdlktcfdtks

menfeisensstdkvnKEFCELLQSaaklsiprgktkrfnyfwnkklsvlksernaarkraeksnllsdtveWRKRAAILkkeinsskrssfntfvekmdyrkdGPKAYSFISsikkgqtsvnkpfshngrsisdskkIASIFNTFytskynipKHEVLLTTSKTNKQKIEKVQNEALRLVTGAVKTTPINAMYALTQNQSLSDIIEQQALTTYekltrlpnnnfwttykedptklktqtgyiqevkkikllteipdKKENLLHPPNPMDSFEITHSLFLEETFRKQDVAPLIAKTMALETINTRYPSDDWLHIYTDGSLINPEDGAGAGIFCELFSFYKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAIQSItncsedpsikhnKRLRNEGQGKKWQQILNTHDIIPNLPRKAAVAHFRLLTGHDCLAEHLHrfglktspigsrdlktcfdtks

MENFEISENSSTDKVNKEFCELLQSAAKLSIPRGKTKRFNYFWNKKLSVLKSERNAARKRAEKSNLLSDTVEWRKRAAILKKEINSSKRSSFNTFVEKMDYRKDGPKAYSFISSIKKGQTSVNKPFSHNGRSISDSKKIASIFNTFYTSKYNIPKHEVLLTTSKTNKQKIEKVQNEALRLVTGAVKTTPINAMYALTQNQSLSDIIEQQALTTYEKLTRLPNNNFWTTYKEDPTKLKTQTGYIQEVKKIKLLTEIPDKKENLLHPPNPMDSFEITHSLFLEETFRKQDVAPLIAKTMALETINTRYPSDDWLHIYTDGSLINPEDGAGAGIFCELFSFYKRLGTFTTNFDGEiaaikiallqilNRTNQFERAVILSDSKAAIQSITNCSEDPSIKHNKRLRNEGQGKKWQQILNTHDIIPNLPRKAAVAHFRLLTGHDCLAEHLHRFGLKTSPIGSRDLKTCFDTKS

******************FCELLQSAAKLSIPRGKTKRFNYFWNKKLSVL********************VEWRKRAAIL*********************************************************KIASIFNTFYTSKYNIPKHEVLLTTSKTNKQKIEKVQNEALRLVTGAVKTTPINAMYALTQNQSLSDIIEQQALTTYEKLTRLPNNNFWTTYKEDPTKLKTQTGYIQEVKKIKLLTEIP**************SFEITHSLFLEETFRKQDVAPLIAKTMALETINTRYPSDDWLHIYTDGSLINPEDGAGAGIFCELFSFYKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAIQSI**********************KWQQILNTHDIIPNLPRKAAVAHFRLLTGHDCLAEHLHRFGLKTSPIG************

**************VNKEFCELLQSAAKLSIPRGKTKRFNYFWNKKLS******************LSDTVEWRKRAAILKKEINSSKRSSFNTFVEKMDYRKDGPKAYSFISSIKKGQTSVNKPFSHNGRSISDSKKIASIFNTFYTSKYNIPKHEVLLTTSKTNKQKIEKVQNEALRLVTGAVKTTPINAMYALTQNQSLSDIIEQQALTTYEKLTRLPNNNFWTTYKEDPTKLKTQTGYIQEVKKIKLLTEIPDKKENLLHPPNPMDSFEITHSLFLEETFRKQDVAPLIAKTMALETINTRYPSDDWLHIYTDGSLINPEDGAGAGIFCELFSFYKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAIQSITNC*****IKH*KRLRNEGQGKKWQQILNTHDIIPNLPRKAAVAHFRLLTGHDCLAEHLHRFGLKTSPIGSRDLKTCF****

*************KVNKEFCELLQSAAKLSIPRGKTKRFNYFWNKKLSVLKS************NLLSDTVEWRKRAAILKKEINSSKRSSFNTFVEKMDYRKDGPKAYSFISSIKKGQTSVNKPFSHNGRSISDSKKIASIFNTFYTSKYNIPKHEVLLTTSKTNKQKIEKVQNEALRLVTGAVKTTPINAMYALTQNQSLSDIIEQQALTTYEKLTRLPNNNFWTTYKEDPTKLKTQTGYIQEVKKIKLLTEIPDKKENLLHPPNPMDSFEITHSLFLEETFRKQDVAPLIAKTMALETINTRYPSDDWLHIYTDGSLINPEDGAGAGIFCELFSFYKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAIQSITNCSEDPSIKHNKRLRNEGQGKKWQQILNTHDIIPNLPRKAAVAHFRLLTGHDCLAEHLHRFGLKTSPIGSRDLKTCFDTKS

********NSSTDKVNKEFCELLQSAAKLSIPRGKTKRFNYFWNKKLSVLKSERNAAR*******LLSDTVEWRKRAAILKKEINSSKRSSFNTFVEKMDYRKDGPKAYSFISSIKKGQTSVNKPFSHNGRSISDSKKIASIFNTFYTSKYNIPKHEVLLTTSKTNKQKIEKVQNEALRLVTGAVKTTPINAMYALTQNQSLSDIIEQQALTTYEKLTRLPNNNFWTTYKEDPTKLKTQTGYIQEVKKIKLLTEIPDKKENLLHPPNPMDSFEITHSLFLEETFRKQDVAPLIAKTMALETINTRYPSDDWLHIYTDGSLINPEDGAGAGIFCELFSFYKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAIQSITNCSEDPSIKHNKRLRNEGQGKKWQQILNTHDIIPNLPRKAAVAHFRLLTGHDCLAEHLHRFGLKTSPIGSRDLKTC*****

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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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		468
427783061		460	Putative tick transposon [Rhipicephalus	0.476	0.484	0.267	2e-10
427783063		460	Putative tick transposon [Rhipicephalus	0.476	0.484	0.267	2e-10
427783065		456	Putative tick transposon [Rhipicephalus	0.476	0.489	0.267	3e-09
357621647		1133	putative pol-like protein [Danaus plexip	0.465	0.192	0.264	6e-07
427784665		455	Putative tick transposon [Rhipicephalus	0.555	0.571	0.243	9e-07
427791981		1060	Putative tick transposon, partial [Rhipi	0.514	0.227	0.249	5e-06
427798837		1174	Putative tick transposon, partial [Rhipi	0.474	0.189	0.258	1e-05
125901787		1222	pol-like protein [Biomphalaria glabrata]	0.585	0.224	0.243	1e-05
427798001		1259	Putative tick transposon, partial [Rhipi	0.474	0.176	0.258	1e-05
427791921		993	Putative tick transposon, partial [Rhipi	0.561	0.264	0.219	3e-05

>gi\|427783061\|gb\|JAA56982.1\| Putative tick transposon [Rhipicephalus pulchellus]	Back alignment and taxonomy information

 Score = 73.6 bits (179), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 64/239 (26%), Positives = 110/239 (46%), Gaps = 16/239 (6%)

Query: 150 KYNIPKHEVLLTTSKTNKQKIEKVQNEALRLVTGAVKTTPINAMYALTQNQSLSDIIEQQ 209
           +Y++P   VL  T KTN + ++  Q +ALR+  G  K  P  A  A+ ++Q +   I  +
Sbjct: 19  RYSLP---VLTNTCKTNLRILQAAQAQALRVCLGLPKCAPTEATIAIAKDQPIQTHIALE 75

Query: 210 ALTTYEK-LTRLPNNNFWTTYKEDPTKLKTQTGYIQEVKKIKLLTEIPDKKENLLHPP-N 267
           AL  + +   R P+++  T   E P     Q  Y   + +      +P        PP  
Sbjct: 76  ALRAHVRHFARAPSHHLATLPSERP-----QASYCATISRYS--ANLPSGFSPAAKPPIP 128

Query: 268 PMDSFEITHSLFLEETFRKQDVAPLIAKTMALETINTRYPSDDWLHIYTDGSLINPEDGA 327
           P         L +    +K +++  + K ++L  ++ +Y   D +HIYTDGS        
Sbjct: 129 PWCLIRPAVHLSVPGIKKKAELSSPVLKQLSLRLMHEKY--TDHVHIYTDGSTTIRSSSG 186

Query: 328 GAGIFCELFSFYKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAIQSI 386
              +     +   +    T++   E+AA++ AL  +LNR  Q +R  I +DSKAA+QS+
Sbjct: 187 AVVVPARGVTVSFKTDHPTSSTAAELAALRTALC-VLNR-EQPQRWSIFTDSKAALQSL 243

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi\|427783063\|gb\|JAA56983.1\| Putative tick transposon [Rhipicephalus pulchellus]	Back alignment and taxonomy information

>gi\|427783065\|gb\|JAA56984.1\| Putative tick transposon [Rhipicephalus pulchellus]	Back alignment and taxonomy information

>gi\|357621647\|gb\|EHJ73416.1\| putative pol-like protein [Danaus plexippus]	Back alignment and taxonomy information

>gi\|427784665\|gb\|JAA57784.1\| Putative tick transposon [Rhipicephalus pulchellus]	Back alignment and taxonomy information

>gi\|427791981\|gb\|JAA61442.1\| Putative tick transposon, partial [Rhipicephalus pulchellus]	Back alignment and taxonomy information

>gi\|427798837\|gb\|JAA64870.1\| Putative tick transposon, partial [Rhipicephalus pulchellus]	Back alignment and taxonomy information

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

>gi\|427798001\|gb\|JAA64452.1\| Putative tick transposon, partial [Rhipicephalus pulchellus]	Back alignment and taxonomy information

>gi\|427791921\|gb\|JAA61412.1\| 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)

No hits with e-value below 0.001 by BLAST

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.1.26.4	LOW CONFIDENCE prediction!
3rd Layer	3.1.26	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		468
cd09276		128	cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom	1e-12
cd09280		150	cd09280, RNase_HI_eukaryote_like, Eukaryotic RNase	8e-08
cd06222		123	cd06222, RNase_H, RNase H is an endonuclease that	3e-06
pfam00075		126	pfam00075, RNase_H, RNase H	1e-05
COG0328		154	COG0328, RnhA, Ribonuclease HI [DNA replication, r	3e-04

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

 Score = 64.6 bits (158), Expect = 1e-12
 Identities = 28/91 (30%), Positives = 41/91 (45%), Gaps = 5/91 (5%)

Query: 313 HIYTDGSLINPEDGAGAGIFCELFSFYKR---LGTFTTNFDGEIAAIKIALLQILNRTNQ 369
            IYTDGS +  E   GAG          R   LG + + FD E+ AI  AL   L    +
Sbjct: 1   VIYTDGSKL--EGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRR 58

Query: 370 FERAVILSDSKAAIQSITNCSEDPSIKHNKR 400
             +  I SDS+AA++++ +      +    R
Sbjct: 59  ARKITIFSDSQAALKALRSPRSSSPLVLRIR 89

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\|187704 cd09280, RNase_HI_eukaryote_like, Eukaryotic RNase H is longer and more complex than their prokaryotic counterparts and unlike prokaryote, RNase H are essential in higher eukaryote	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\|215695 pfam00075, RNase_H, RNase H	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		468
PRK06548		161	ribonuclease H; Provisional	99.97
COG0328		154	RnhA Ribonuclease HI [DNA replication, recombinati	99.96
PRK00203		150	rnhA ribonuclease H; Reviewed	99.94
PRK08719		147	ribonuclease H; Reviewed	99.94
KOG3752\|consensus		371		99.87
PF00075		132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	99.84
PRK13907		128	rnhA ribonuclease H; Provisional	99.78
PRK07708		219	hypothetical protein; Validated	99.66
cd06222		130	RnaseH RNase H (RNase HI) is an endonuclease that	99.65
PRK07238		372	bifunctional RNase H/acid phosphatase; Provisional	99.59
PF13456		87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	98.88
.; 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	82.21

>PRK06548 ribonuclease H; Provisional	Back alignment and domain information

Probab=99.97  E-value=7.3e-30  Score=235.97  Aligned_cols=133  Identities=23%  Similarity=0.233  Sum_probs=114.3

Q ss_pred             CcEEEEEeccccCCCCceEEEEEEecCeE-EeecCccccchHHHHHHHHHHHHHHHhhcCCCceEEEEecCHHHHHHhhc
Q psy7629         310 DWLHIYTDGSLINPEDGAGAGIFCELFSF-YKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAIQSITN  388 (468)
Q Consensus       310 ~~i~IYTDGS~~~n~~~aG~GVv~~~~~~-~~~L~~~~Tn~~AEL~AIl~ALe~a~~~~~~~~~v~I~TDSqyai~~I~~  388 (468)
                      ..++|||||||.+|++++|||+++.+... ....+ .+|||+|||+||++||+.+..   ...+|.|+|||+||+++|+.
T Consensus         4 ~~~~IytDGa~~gnpg~~G~g~~~~~~~~~~g~~~-~~TNnraEl~Aii~aL~~~~~---~~~~v~I~TDS~yvi~~i~~   79 (161)
T PRK06548          4 NEIIAATDGSSLANPGPSGWAWYVDENTWDSGGWD-IATNNIAELTAVRELLIATRH---TDRPILILSDSKYVINSLTK   79 (161)
T ss_pred             CEEEEEEeeccCCCCCceEEEEEEeCCcEEccCCC-CCCHHHHHHHHHHHHHHhhhc---CCceEEEEeChHHHHHHHHH
Confidence            36999999999999999999998765432 33333 459999999999999986642   34579999999999999999


Q ss_pred             ccCCchhhhccCcccCCCCcchHHHHHHHH-hcCCCCCCCcceEEEEEcchh-----HHHHHHHHHhhhcC
Q psy7629         389 CSEDPSIKHNKRLRNEGQGKKWQQILNTHD-IIPNLPRKAAVAHFRLLTGHD-----CLAEHLHRFGLKTS  453 (468)
Q Consensus       389 ~~~~~~Wk~ngW~ts~G~~V~n~~li~~I~-li~~l~~~g~~V~f~WVpgH~-----E~AD~LAK~Aa~~~  453 (468)
                      |..+  |++|||++++|+||+|++||++|+ ++..     ..|+|.|||||+     |.||+||++|+...
T Consensus        80 W~~~--Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~-----~~v~~~wVkgHsg~~gNe~aD~LA~~aa~~~  143 (161)
T PRK06548         80 WVYS--WKMRKWRKADGKPVLNQEIIQEIDSLMEN-----RNIRMSWVNAHTGHPLNEAADSLARQAANNF  143 (161)
T ss_pred             HHHH--HHHCCCcccCCCccccHHHHHHHHHHHhc-----CceEEEEEecCCCCHHHHHHHHHHHHHHHHh
Confidence            9998  999999999999999999999998 5543     269999999999     99999999999754

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

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

>PRK08719 ribonuclease H; Reviewed	Back alignment and domain information

>KOG3752\|consensus	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

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

>PRK07708 hypothetical protein; Validated	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

>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

>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		468
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-10
2kq2_A		147	Ribonuclease H-related protein; PSI, NESG, protein	4e-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 = 61.4 bits (148), Expect = 3e-10
 Identities = 75/530 (14%), Positives = 146/530 (27%), Gaps = 144/530 (27%)

Query: 3   NFEISENSSTDKVNKEFCELLQSAAKLSIPRGKTKRFNYFWNKKLSVLKSERN----AAR 58
           +FE  E        K+   + + A                 +   S+L  E       ++
Sbjct: 8   DFETGE---HQYQYKDILSVFEDAFV------DNFDCKDVQDMPKSILSKEEIDHIIMSK 58

Query: 59  KRAEKSNLLSDTVEWRKRAAILKKEINSSKRSSFNTFVEKMDYRKDGPKAYSFISSIKKG 118
                +  L  T+   K+  +++K            FVE++  R +    Y F+ S    
Sbjct: 59  DAVSGTLRLFWTLL-SKQEEMVQK------------FVEEVL-RIN----YKFLMS--PI 98

Query: 119 QTSVNKPFSHNGRSISDSKKIASIFNTFYTSKYNIPKHEVLLTTSKTNKQKIEKVQNEAL 178
           +T   +P       I    ++ +    F  +KYN+ + +  L      +Q + +++    
Sbjct: 99  KTEQRQPSMMTRMYIEQRDRLYNDNQVF--AKYNVSRLQPYLKL----RQALLELRPAKN 152

Query: 179 RLV---TGAVKTTPINAMYALTQNQSLSDIIEQQALTTYEKLTRLPNNNFWTT---YKED 232
            L+    G+ KT        +                +Y+   ++    FW         
Sbjct: 153 VLIDGVLGSGKTW-------VAL----------DVCLSYKVQCKMDFKIFWLNLKNCNSP 195

Query: 233 PTKLKTQTGYIQEVKKIKLLTEI-PDKKENLLHPPNPMDSFEITHS----LFLEETFRK- 286
            T L+            KLL +I P+      H  N         +    L   + +   
Sbjct: 196 ETVLEMLQ---------KLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENC 246

Query: 287 ----QDVA-PLIAKTMALE---TINTRYPSD-DWL--HIYTDGSLINPEDGAGAGIFCEL 335
                +V          L     + TR+    D+L     T  SL +            L
Sbjct: 247 LLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSL 306

Query: 336 FSFYKRLGTFTTNFDGEIAAIKIALLQI----------LNRTNQFERAVILSDSKAAIQS 385
               K L     +   E   +     ++          L   + ++  V        I+S
Sbjct: 307 LL--KYLDCRPQDLPRE--VLTTNPRRLSIIAESIRDGLATWDNWKH-VNCDKLTTIIES 361

Query: 386 ITNCSEDPSIKHN---------------KRLRNEGQGKKWQQIL--NTHDIIPNLPRKAA 428
             N  E    +                   L        W  ++  +   ++  L + + 
Sbjct: 362 SLNVLEPAEYRKMFDRLSVFPPSAHIPTILL-----SLIWFDVIKSDVMVVVNKLHKYSL 416

Query: 429 VA-------------HFRLLTGHDCLAEHLHRFGLKTSPIGSRDLKTCFD 465
           V              +  L    +     LHR     S +   ++   FD
Sbjct: 417 VEKQPKESTISIPSIYLELKVKLENEYA-LHR-----SIVDHYNIPKTFD 460

PyMOL of 1vt4

>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

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		468
3h08_A		146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.96
2qkb_A		154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.96
2lsn_A		165	Reverse transcriptase; RNAse H, viral protein; NMR	99.96
3qio_A		150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.95
1jl1_A		155	Ribonuclease HI; RNAse HI, protein stability, ther	99.95
2e4l_A		158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.95
1ril_A		166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.94
3p1g_A		165	Xenotropic murine leukemia virus-related virus (X	99.9
2kq2_A		147	Ribonuclease H-related protein; PSI, NESG, protein	99.86
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
2ehg_A		149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	99.83
1mu2_A		555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	99.73
4htu_A		134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	99.71
2zd1_A		557	Reverse transcriptase/ribonuclease H; P51/P66, het	99.7
1zbf_A		142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	99.68
1rw3_A		455	POL polyprotein; RNA and DNA dependent DNA polymer	80.18

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

Probab=99.96  E-value=1.5e-29  Score=227.26  Aligned_cols=132  Identities=20%  Similarity=0.150  Sum_probs=110.3

Q ss_pred             cEEEEEeccccCCCCceEEEEEEecCe----EEeecCccccchHHHHHHHHHHHHHHHhhcCCCceEEEEecCHHHHHHh
Q psy7629         311 WLHIYTDGSLINPEDGAGAGIFCELFS----FYKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAIQSI  386 (468)
Q Consensus       311 ~i~IYTDGS~~~n~~~aG~GVv~~~~~----~~~~L~~~~Tn~~AEL~AIl~ALe~a~~~~~~~~~v~I~TDSqyai~~I  386 (468)
                      .++|||||||.+|++.+|+|+++.++.    ++..++ .+||++|||.|++.||+.+.+    ..+|.|+|||+||+++|
T Consensus         4 ~i~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~~~~~-~~Tnn~aEl~A~~~AL~~~~~----~~~v~I~tDS~~vi~~i   78 (146)
T 3h08_A            4 TITIYTDGAASGNPGKGGWGALLMYGSSRKEISGYDP-ATTNNRMELMAAIKGLEALKE----PARVQLYSDSAYLVNAM   78 (146)
T ss_dssp             EEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEEE-EECHHHHHHHHHHHHHHTCSS----CCEEEEEESCHHHHHHH
T ss_pred             eEEEEEecCCCCCCCceEEEEEEEECCeeEEeecCCC-CCcHHHHHHHHHHHHHHhcCc----cCcEEEEeChHHHHHHH
Confidence            789999999998888899999876543    244444 469999999999999999853    57899999999999999


Q ss_pred             hc-ccCCchhhhccCcccCCCCcchHHHHHHHH-hcCCCCCCCcceEEEEEcchh-----HHHHHHHHHhhhcCC
Q psy7629         387 TN-CSEDPSIKHNKRLRNEGQGKKWQQILNTHD-IIPNLPRKAAVAHFRLLTGHD-----CLAEHLHRFGLKTSP  454 (468)
Q Consensus       387 ~~-~~~~~~Wk~ngW~ts~G~~V~n~~li~~I~-li~~l~~~g~~V~f~WVpgH~-----E~AD~LAK~Aa~~~p  454 (468)
                      +. |...  |+++||+++.|.+|+|+++++.|. ++..+     .|.|.|||||+     |.||+||++|+...|
T Consensus        79 ~~~w~~~--W~~~~w~~~~~~~v~n~~l~~~~~~~~~~~-----~v~~~~V~gH~g~~~N~~AD~LA~~a~~~~p  146 (146)
T 3h08_A           79 NEGWLKR--WVKNGWKTAAKKPVENIDLWQEILKLTTLH-----RVTFHKVKGHSDNPYNSRADELARLAIKENS  146 (146)
T ss_dssp             HSSHHHH--HHHTTCC----CCCTTHHHHHHHHHHHHHS-----EEEEEECCC-CCSHHHHHHHHHHHHHHHHC-
T ss_pred             HHHHHHH--HHHCCCccCCCCCcCCHHHHHHHHHHHhhC-----ceEEEEcCCcCCcHhHHHHHHHHHHHHHhCc
Confidence            99 9888  999999999999999999999998 65543     69999999998     999999999998765

PyMOL of 3h08

>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

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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>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		468
d1s1ta1		110	c.55.3.1 (A:430-539) HIV RNase H (Domain of revers	2e-05
d1mu2a1		126	c.55.3.1 (A:430-555) HIV RNase H (Domain of revers	0.002

>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


class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: HIV RNase H (Domain of reverse transcriptase)
species: Human immunodeficiency virus type 1 [TaxId: 11676]

 Score = 41.1 bits (96), Expect = 2e-05
 Identities = 20/82 (24%), Positives = 27/82 (32%), Gaps = 6/82 (7%)

Query: 307 PSDDWLHIYTDGSLINPEDGAGAGIFCELFSFYKRLGTFTTNFDGEIAAIKIALLQILNR 366
           P       Y DG+         AG             T TTN   E+ AI +AL      
Sbjct: 4   PIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSG-- 61

Query: 367 TNQFERAVILSDSKAAIQSITN 388
                   I++DS+ A+  I  
Sbjct: 62  ----LEVNIVTDSQYALGIIQA 79

PyMOL of d1s1ta1

>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

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		468
d1jl1a_		152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	99.94
d1rila_		147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.94
d1mu2a1		126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.87
d1s1ta1		110	HIV RNase H (Domain of reverse transcriptase) {Hum	99.83
d1zbfa1		132	BH0863-like Ribonuclease H {Bacillus halodurans [T	99.78

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

Probab=99.94  E-value=8.6e-27  Score=206.88  Aligned_cols=139  Identities=19%  Similarity=0.212  Sum_probs=117.7

Q ss_pred             cEEEEEeccccCCCCceEEEEEEecCe----EEeecCccccchHHHHHHHHHHHHHHHhhcCCCceEEEEecCHHHHHHh
Q psy7629         311 WLHIYTDGSLINPEDGAGAGIFCELFS----FYKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAIQSI  386 (468)
Q Consensus       311 ~i~IYTDGS~~~n~~~aG~GVv~~~~~----~~~~L~~~~Tn~~AEL~AIl~ALe~a~~~~~~~~~v~I~TDSqyai~~I  386 (468)
                      .+.|||||||.+|++.+|||+|+...+    ++...+ .+||++||++|++.||+.+.    ....+.|+|||++++.++
T Consensus         2 ~I~IYtDGS~~~N~g~aG~G~vi~~~~~~~~~~~~~~-~~tnn~aE~~Ai~~Al~~~~----~~~~i~i~tds~~~i~~~   76 (152)
T d1jl1a_           2 QVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGYT-RTTNNRMELMAAIVALEALK----EHAEVILSTDSQYVRQGI   76 (152)
T ss_dssp             CEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEEE-EECHHHHHHHHHHHHHHTCC----SCCEEEEEECCHHHHHHH
T ss_pred             EEEEEEeCCCCCCCCcEEEEEEEEECCeEEEeccccC-cccHHHHHHhhhhhhhhhhc----ccceEEEeecceeeEEcc
Confidence            589999999999998899998874433    234444 45999999999999998763    456789999999999999


Q ss_pred             hcccCCchhhhccCcccCCCCcchHHHHHHHH-hcCCCCCCCcceEEEEEcchh-----HHHHHHHHHhhhcCCCCCCCc
Q psy7629         387 TNCSEDPSIKHNKRLRNEGQGKKWQQILNTHD-IIPNLPRKAAVAHFRLLTGHD-----CLAEHLHRFGLKTSPIGSRDL  460 (468)
Q Consensus       387 ~~~~~~~~Wk~ngW~ts~G~~V~n~~li~~I~-li~~l~~~g~~V~f~WVpgH~-----E~AD~LAK~Aa~~~pi~~r~~  460 (468)
                      +.+...  |..++|+...|++++|.++++.+. +...     ..|.|+|||||+     |+||+|||+|+..+++.+...
T Consensus        77 ~~~~~~--~~~~~~~~~~~~~~~n~~~~~~i~~~~~~-----~~V~~~wV~gH~g~~gNe~AD~LAk~aa~~~~~~d~~~  149 (152)
T d1jl1a_          77 TQWIHN--WKKRGWKTADKKPVKNVDLWQRLDAALGQ-----HQIKWEWVKGHAGHPENERADELARAAAMNPTLEDTGY  149 (152)
T ss_dssp             HTTHHH--HHHTTTBCTTSCBCTTHHHHHHHHHHTTT-----CEEEEEECCSSTTCHHHHHHHHHHHHHHHSCCBCCTTC
T ss_pred             cchhhH--hHhccchhcccCeeecHHHHHHHHHHhhc-----ceeEEEEecccCCCccHHHHHHHHHHHHhCCCCCccCC
Confidence            999877  999999999999999999999988 5433     479999999999     999999999999888776554


Q ss_pred             c
Q psy7629         461 K  461 (468)
Q Consensus       461 ~  461 (468)
                      +
T Consensus       150 ~  150 (152)
T d1jl1a_         150 Q  150 (152)
T ss_dssp             C
T ss_pred             C
Confidence            4

PyMOL of d1jl1a_

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

>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

>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