Psyllid ID: psy9745

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-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570

TVHSEEITINSPLQVVAARVRSPVLSCPLTVCCLYISHDRKITKDEIYNIKRQLPRPYIICSDMNAHNTIWGGSKIDSNGITKDEIYNIKRQLPRPYIICSDMNAHNTIWGGSKIDSNGVQVEKFLLENDDVCLLNTNEATHFNSSNGTFSAIDLTLASRSITPDLKWSVHDDLYLMLLVLTDIRQGSSLSGDLCNIATSDLPQYIPTVVSHGMFVDDLAIFMRGKDMDHIEETLQNTIQFKENTRYLGLNLDSSLTWKFHIEQTKSKSLKALNVMKILSNRNWGLRRETLRRLYYSFALPILDYGSILYSSASEPNLKKLNVVHHTGVRLISGAFRTSPIVSILAESGIPPLSNLSKREVVHHFLEFKEQHKLDTLCFTDGSKTTDHTGAAFIIRDEICSMKLNPICSIFTAELIAIEKCLEKIKDVVTHDLVTQNFIICSDSKSSLQALQNVYHVSPLVCDIISTIQDIRDLGTRVSFLWIPSHLGIRENDNVDHAARHCNDVPITKVCISDDHKIQFKKIQLGEWSKSWSDNTTTGQKLKKIKPDTRKWKSSMRWKRAEEIVICRLK

cccccEEEEccccEEEEEEEEccccccccEEEEEEccccccccHHHHHHHHHHccccEEEEccccccEEEEEccccccccccHHHHHHHHHHccccEEEEEcccccccccccccccccHHHHHHHHHHccccccccccccccccccccccHHHHHHHHcccccccccccccccccEEEEEEcccccccccHHHHHHHHHcccccccccccccccccccEEEEEccccHHHHHHHHHccccccccEEEEEEEEcccccHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHcccccccccEEEccccccHHHHHHHHcccccccccccccccccEEccccccccccccccccHHHHHHHHHcccccccccccccccccccccccccEEEccccccccccccccHHHHHHHHHHHHHHHHHHHcccccccEEEEEcccHHHHHHHHccccccHHHHHHHHHHHHHHHcccEEEEEEEcccccccccHHHHHHHHccccccccccccHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccHHHHHHHHHcc

ccccEEEEEcccEEEEEEEEEcccccccEEEEEEEccccccccHHHHHHHHHHccccEEEEEccccccccccccccccccccHHHHHHHHHHccccEEEEEcccccccccccccccccccHHHHHEEccccEEEEEcccccEEccccccEEEEEEEEccccccccccEEEcccHEEEEEccccccccHHHHHHHHHHHHHHHHHHHHHHHHcccEEEEEEEEEcccccccccccccccccccccEEEEEEEEccccccHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHcccccccHHHHHHHHHHHHHHcccccccEEEEEcccccccccEEEEEEEccccEcccccccHHHHHHHHHHHHHHHHHHHHcccccccccEEEEEccHHHHHHHHccccccHHHHHHHHHHHHHHHcccEEEEEEEcccccccccHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHcccccccEEEEEccccccccccccccccccEEEHccc

tvhseeitinspLQVVAARVrspvlscpltvcclyishdrkitKDEIYNIkrqlprpyiicsdmnahntiwggskidsngitkdEIYNIkrqlprpyiicsdmnahntiwggskidsngVQVEKFLLENddvcllntneathfnssngtfsaIDLTlasrsitpdlkwsvhdDLYLMLLVLTDirqgsslsgdlcniatsdlpqyiptvvshgmfvddlaifmrgkdmDHIEETLQNTIQFKentrylglnldsslTWKFHIEQTKSKSLKALNVMKILSNRNWGLRRETLRRLYYSFALpildygsilyssasepnlkklNVVHHTGVRlisgafrtsPIVSIlaesgipplsnlskREVVHHFLEFkeqhkldtlcftdgskttdhtgaAFIIRDEICsmklnpicsIFTAELIAIEKCLEKIKDVVTHDLVTQNFIICSDSKSSLQALQnvyhvsplvCDIISTIQDIrdlgtrvsflwipshlgirendnvdhaarhcndvpitkvcisddhkiqfkkiqlgewskswsdntttgqklkkikpdtrkwkSSMRWKRAEEIVICRLK

tvhseeitinsplqvVAARVRSPVLSCPLTVCCLyishdrkitkdeiyNIKRQLPRPYIICSDMNAHNTIWGgskidsngiTKDEIYNIKRQLPRPYIICSDMNAHNTIWGGSKIDSNGVQVEKFLLENDDVCLLNTNEathfnssngtFSAIDLTLASRSITPDLKWSVHDDLYLMLLVLTDIRQGSSLSGDLCNIATSDLPQYIPTVVSHGMFVDDLAIFMRGKDMDHIEETLQNTIQFKENTRYLGLNLDSSLTWKFHIEQTkskslkalnvmkilsnrnwglrrETLRRLYYSFALPILDYGSILYSSASEPNLKKLNVVHHTGVRLISGAFRTSPIVSILAESGIPPLSNLSKREVVHHFLEfkeqhkldtLCFTDGSKTTDHTGAAFIIRDEICSMKLNPICSIFTAELIAIEKCLEKIKDVVTHDLVTQNFIICSDSKSSLQALQNVYHVSPLVCDIISTIQDIRDLGTRVSFLWIPSHLGIRENDNVDHAARHCNDVPITKVCISDDHKIQFKKiqlgewskswsdntttgqklkkikpdtrkwkssmrwkraeeivicrlk

********INSPLQVVAARVRSPVLSCPLTVCCLYISHDRKITKDEIYNIKRQLPRPYIICSDMNAHNTIWGGSKIDSNGITKDEIYNIKRQLPRPYIICSDMNAHNTIWGGSKIDSNGVQVEKFLLENDDVCLLNTNEATHFNSSNGTFSAIDLTLASRSITPDLKWSVHDDLYLMLLVLTDIRQGSSLSGDLCNIATSDLPQYIPTVVSHGMFVDDLAIFMRGKDMDHIEETLQNTIQFKENTRYLGLNLDSSLTWKFHIEQTKSKSLKALNVMKILSNRNWGLRRETLRRLYYSFALPILDYGSILYSSASEPNLKKLNVVHHTGVRLISGAFRTSPIVSILAESGIPPLSNLSKREVVHHFLEFKEQHKLDTLCFTDGSKTTDHTGAAFIIRDEICSMKLNPICSIFTAELIAIEKCLEKIKDVVTHDLVTQNFIICSDSKSSLQALQNVYHVSPLVCDIISTIQDIRDLGTRVSFLWIPSHLGIRENDNVDHAARHCNDVPITKVCISDDHKIQFKKIQLGEWSKSWS***********************RWKRAEEIVIC***

*****EITINSPLQVVAARVRSPVLSCPLTVCCLYISHDRKITKDEIYNIKRQLPRPYIICSDMNAHNTIWGGSKIDSNGITKDEIYNIKRQLPRPYIICSDMNAHNTIWGGSKIDSNGVQVEKFLLENDDVCLLNTNEATHFNSSNGTFSAIDLTLASRSITPDLKWSVHDDLYLMLLVLTDIRQGSSLSGDLCNIATSDLPQYIPTVVSHGMFVDDLAIFMRGKDMDHIEETLQNTIQFKENTRYLGLNLDSSLTWKFHIEQTKSKSLKALNVMKILSNRNWGLRRETLRRLYYSFALPILDYGSILYSSASEPNLKKLNVVHHTGVRLISGAFRTSPIVSILAESGIPPLSNLSKREVVHHFLEFKEQHKLDTLCFTDGSKTTDHTGAAFIIRDEICSMKLNPICSIFTAELIAIEKCLEKIKDVVTHDLVTQNFIICSDSKSSLQALQNVYHVSPLVCDIISTIQDIRDLGTRVSFLWIPSHLGIRENDNVDHAARHCN***I*KVCISDDHKIQFKKIQLGEWSKSWS******QKLKKIKPDTRKWKSSMRWKRAEEIVICRLK

*VHSEEITINSPLQVVAARVRSPVLSCPLTVCCLYISHDRKITKDEIYNIKRQLPRPYIICSDMNAHNTIWGGSKIDSNGITKDEIYNIKRQLPRPYIICSDMNAHNTIWGGSKIDSNGVQVEKFLLENDDVCLLNTNEATHFNSSNGTFSAIDLTLASRSITPDLKWSVHDDLYLMLLVLTDIRQGSSLSGDLCNIATSDLPQYIPTVVSHGMFVDDLAIFMRGKDMDHIEETLQNTIQFKENTRYLGLNLDSSLTWKFHIEQTKSKSLKALNVMKILSNRNWGLRRETLRRLYYSFALPILDYGSILYSSASEPNLKKLNVVHHTGVRLISGAFRTSPIVSILAESGIPPLSNLSKREVVHHFLEFKEQHKLDTLCFTDGSKTTDHTGAAFIIRDEICSMKLNPICSIFTAELIAIEKCLEKIKDVVTHDLVTQNFIICSDSKSSLQALQNVYHVSPLVCDIISTIQDIRDLGTRVSFLWIPSHLGIRENDNVDHAARHCNDVPITKVCISDDHKIQFKKIQLGEWSKSWSDNTTTGQKLKKIKPDTRKWKSSMRWKRAEEIVI**LK

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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		570
427798139		563	Putative tick transposon, partial [Rhipi	0.294	0.298	0.342	5e-27
443720278		498	hypothetical protein CAPTEDRAFT_219461 [	0.426	0.487	0.295	5e-25
328697366		891	PREDICTED: hypothetical protein LOC10057	0.510	0.326	0.322	5e-24
427778603		1397	Putative tick transposon [Rhipicephalus	0.301	0.123	0.355	1e-23
427791807		1212	Putative tick transposon, partial [Rhipi	0.301	0.141	0.325	2e-22
125901787		1222	pol-like protein [Biomphalaria glabrata]	0.326	0.152	0.323	3e-21
2736044		488	reverse transcriptase [Aphonopelma sp. W	0.536	0.627	0.262	1e-19
427791321		1210	Putative tick transposon, partial [Rhipi	0.184	0.086	0.438	4e-19
443695973		261	hypothetical protein CAPTEDRAFT_23017, p	0.326	0.712	0.352	1e-18
427791063		1035	Putative tick transposon, partial [Rhipi	0.171	0.094	0.463	1e-18

>gi\|427798139\|gb\|JAA64521.1\| Putative tick transposon, partial [Rhipicephalus pulchellus]	Back alignment and taxonomy information

 Score =  129 bits (323), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 60/175 (34%), Positives = 104/175 (59%), Gaps = 7/175 (4%)

Query: 1   TVHSEEITINSPLQVVAARVRSPVLSCPLTVCCLYISHDRKITKDEIYNIKRQLPRPYII 60
           ++  +++T+ + L+ ++ RV   + +  +TVC +Y+  + +++K E YN+  QLP PYI+
Sbjct: 74  SIACQQLTLQTELEAISVRV--ILFNRLITVCSIYLPPNCQVSKTEFYNLINQLPEPYIL 131

Query: 61  CSDMNAHNTIWGGSKIDSNGITKDEIYNIKRQLPRPYIICSDMNAHNTIWGGSKIDSNGV 120
             D NAHN++WG S+ D  G   +           PYI+  D NAHN++WG S+ D  G 
Sbjct: 132 AGDFNAHNSLWGDSRCDGRGRMIESFLVTS----GPYILAGDFNAHNSLWGDSRCDGRGR 187

Query: 121 QVEKFLLENDDVCLLNTNEATHFNSSNGTFSAIDLTLASRSITPDLKWSVHDDLY 175
            +E FL+     CL N  E T++++ + ++S+IDLT+ S ++ P L+W V  + Y
Sbjct: 188 MIESFLV-TSGACLFNKKEPTYYSTQHNSYSSIDLTIGSAALFPYLEWDVIKNPY 241

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi\|443720278\|gb\|ELU10076.1\| hypothetical protein CAPTEDRAFT_219461 [Capitella teleta]	Back alignment and taxonomy information

>gi\|328697366\|ref\|XP_003240318.1\| PREDICTED: hypothetical protein LOC100575042 [Acyrthosiphon pisum]	Back alignment and taxonomy information

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

>gi\|427791807\|gb\|JAA61355.1\| 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\|2736044\|gb\|AAB94039.1\| reverse transcriptase [Aphonopelma sp. WDB-1998]	Back alignment and taxonomy information

>gi\|427791321\|gb\|JAA61112.1\| 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\|427791063\|gb\|JAA60983.1\| Putative tick transposon, partial [Rhipicephalus pulchellus]	Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		570
FB\|FBgn0045761		888	CHKov1 "CHKov1" [Drosophila me	0.161	0.103	0.372	2.4e-07
ASPGD\|ASPL0000075333		486	AN10625 [Emericella nidulans (	0.292	0.343	0.264	7e-05
ASPGD\|ASPL0000055652		1054	AN0368 [Emericella nidulans (t	0.207	0.111	0.290	0.00012
ASPGD\|ASPL0000062864		520	AN0621 [Emericella nidulans (t	0.226	0.248	0.272	0.00014
ASPGD\|ASPL0000033911		686	AN2796 [Emericella nidulans (t	0.228	0.189	0.274	0.00036
ASPGD\|ASPL0000040226		1538	AN2661 [Emericella nidulans (t	0.549	0.203	0.222	0.00054
ASPGD\|ASPL0000037597		666	AN2711 [Emericella nidulans (t	0.238	0.204	0.260	0.0007
ASPGD\|ASPL0000077547		1581	AN8648 [Emericella nidulans (t	0.226	0.081	0.272	0.00083

FB\|FBgn0045761 CHKov1 "CHKov1" [Drosophila melanogaster (taxid:7227)]	Back alignment and assigned GO terms

 Score = 134 (52.2 bits), Expect = 2.4e-07, Sum P(3) = 2.4e-07
 Identities = 35/94 (37%), Positives = 53/94 (56%)

Query:   243 ENTRYLGLNLDSSLTWKFHIE-QTKSKSLKALNVMKILSNRNWGLRRETLRRLYYSFALP 301
             +   YLG++LD  LTW+ HIE ++K   LKA N+  +++ R+  L  E    LY S   P
Sbjct:   734 DEVTYLGVHLDRRLTWRKHIEAKSKHLKLKARNLHWLINARS-PLSLEFKALLYNSVLKP 792

Query:   302 ILDYGSILYSSASEPNLKKLNVVHHTGVRLISGA 335
             I  YGS L+ +AS  N+  +       +R+I+GA
Sbjct:   793 IWTYGSELWGNASRSNIDIIQRAQSRILRIITGA 826

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

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

GO:0003723 "RNA binding" evidence=IEA

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

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

ASPGD\|ASPL0000062864 AN0621 [Emericella nidulans (taxid:162425)]	Back alignment and assigned GO terms

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

ASPGD\|ASPL0000040226 AN2661 [Emericella nidulans (taxid:162425)]	Back alignment and assigned GO terms

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

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

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

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

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		570
cd09276		128	cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom	1e-33
cd09077		205	cd09077, R1-I-EN, Endonuclease domain encoded by v	4e-16
pfam00075		126	pfam00075, RNase_H, RNase H	1e-12
cd06222		123	cd06222, RNase_H, RNase H is an endonuclease that	1e-08
cd09273		135	cd09273, RNase_HI_RT_Bel, Bel/Pao family of RNase	7e-08
cd09280		150	cd09280, RNase_HI_eukaryote_like, Eukaryotic RNase	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 =  123 bits (312), Expect = 1e-33
 Identities = 46/126 (36%), Positives = 67/126 (53%), Gaps = 6/126 (4%)

Query: 378 CFTDGSKTTDHTGAAFIIRDE---ICSMKLNPICSIFTAELIAIEKCLEKIKDVVTHDLV 434
            +TDGSK    TGA F I  +     S KL P CS+F AEL+AI + L+           
Sbjct: 2   IYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALRE-GRRA- 59

Query: 435 TQNFIICSDSKSSLQALQNVYHVSPLVCDIISTIQDIRDLGTRVSFLWIPSHLGIRENDN 494
            +   I SDS+++L+AL++    SPLV  I   I+++ + G +V   W+P H GI  N+ 
Sbjct: 60  -RKITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGNER 118

Query: 495 VDHAAR 500
            D  A+
Sbjct: 119 ADRLAK 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\|197311 cd09077, R1-I-EN, Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons	Back alignment and domain information

>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\|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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		570
PRK06548		161	ribonuclease H; Provisional	99.87
COG0328		154	RnhA Ribonuclease HI [DNA replication, recombinati	99.87
PRK08719		147	ribonuclease H; Reviewed	99.86
PF00075		132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	99.84
PRK00203		150	rnhA ribonuclease H; Reviewed	99.83
cd06222		130	RnaseH RNase H (RNase HI) is an endonuclease that	99.71
PRK13907		128	rnhA ribonuclease H; Provisional	99.69
KOG3752\|consensus		371		99.67
PRK07708		219	hypothetical protein; Validated	99.55
PRK07238		372	bifunctional RNase H/acid phosphatase; Provisional	99.4
PF14529		119	Exo_endo_phos_2: Endonuclease-reverse transcriptas	99.25
PF13456		87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	99.11
cd03487		214	RT_Bac_retron_II RT_Bac_retron_II: Reverse transcr	98.93
cd01651		226	RT_G2_intron RT_G2_intron: Reverse transcriptases	98.92
cd01648		119	TERT TERT: Telomerase reverse transcriptase (TERT)	98.92
cd01650		220	RT_nLTR_like RT_nLTR: Non-LTR (long terminal repea	98.91
PF00078		214	RVT_1: Reverse transcriptase (RNA-dependent DNA po	98.64
cd01646		158	RT_Bac_retron_I RT_Bac_retron_I: Reverse transcrip	98.54
cd00304		98	RT_like RT_like: Reverse transcriptase (RT, RNA-de	98.37
cd01709		346	RT_like_1 RT_like_1: A subfamily of reverse transc	98.33
KOG4768\|consensus		796		97.4
cd01645		213	RT_Rtv RT_Rtv: Reverse transcriptases (RTs) from r	97.33
cd03714		119	RT_DIRS1 RT_DIRS1: Reverse transcriptases (RTs) oc	96.98
cd03715		210	RT_ZFREV_like RT_ZFREV_like: A subfamily of revers	96.74
PRK13911		250	exodeoxyribonuclease III; Provisional	95.92
KOG1005\|consensus		888		95.89
TIGR00633		255	xth exodeoxyribonuclease III (xth). This family is	95.6
COG0708		261	XthA Exonuclease III [DNA replication, recombinati	94.88
cd01647		177	RT_LTR RT_LTR: Reverse transcriptases (RTs) from r	94.85
TIGR00195		254	exoDNase_III exodeoxyribonuclease III. The model b	92.62
PF14529		119	Exo_endo_phos_2: Endonuclease-reverse transcriptas	92.27
cd01644		213	RT_pepA17 RT_pepA17: Reverse transcriptase (RTs) i	92.08
PRK11756		268	exonuclease III; Provisional	91.65
PF03372		249	Exo_endo_phos: Endonuclease/Exonuclease/phosphatas	89.69
PF09004		42	DUF1891: Domain of unknown function (DUF1891); Int	83.23
PF05380		159	Peptidase_A17: Pao retrotransposon peptidase ; Int	81.44

>PRK06548 ribonuclease H; Provisional	Back alignment and domain information

Probab=99.87  E-value=5.4e-22  Score=179.53  Aligned_cols=127  Identities=22%  Similarity=0.296  Sum_probs=98.5

Q ss_pred             CCCeEEEecCCCCC--CCceEEEEEeceeeeeccCCccccchhhHHHHHHHHHHHHhhhcccCCcceEEEEecCHHHHHH
Q psy9745         373 KLDTLCFTDGSKTT--DHTGAAFIIRDEICSMKLNPICSIFTAELIAIEKCLEKIKDVVTHDLVTQNFIICSDSKSSLQA  450 (570)
Q Consensus       373 ~~~~~iytDGS~~~--~~~G~g~~~~~~~~~~~~~~~~s~~~aEl~ai~~al~~~~~~~~~~~~~~~v~I~tDs~~al~~  450 (570)
                      +..+.||||||+..  +..|+|+++............+|+++||++|++.||+.+..      ....|.|+|||++|+++
T Consensus         3 ~~~~~IytDGa~~gnpg~~G~g~~~~~~~~~~g~~~~~TNnraEl~Aii~aL~~~~~------~~~~v~I~TDS~yvi~~   76 (161)
T PRK06548          3 NNEIIAATDGSSLANPGPSGWAWYVDENTWDSGGWDIATNNIAELTAVRELLIATRH------TDRPILILSDSKYVINS   76 (161)
T ss_pred             CCEEEEEEeeccCCCCCceEEEEEEeCCcEEccCCCCCCHHHHHHHHHHHHHHhhhc------CCceEEEEeChHHHHHH
Confidence            34589999999864  56889988854322222234689999999999999986542      34579999999999999


Q ss_pred             Hhc---------CCCCChh--H-HHHHHHHHHHHHhCCceEEEeecCCCCCCccchhchhhhhccCCC
Q psy9745         451 LQN---------VYHVSPL--V-CDIISTIQDIRDLGTRVSFLWIPSHLGIRENDNVDHAARHCNDVP  506 (570)
Q Consensus       451 l~~---------~~~~~~~--~-~~~~~~~~~l~~~~~~v~~~WVp~H~gi~gNe~AD~lAk~a~~~~  506 (570)
                      ++.         +...++.  . +++++.+.++.+. ..|+|.|||||+|++|||.||+||++|+...
T Consensus        77 i~~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~-~~v~~~wVkgHsg~~gNe~aD~LA~~aa~~~  143 (161)
T PRK06548         77 LTKWVYSWKMRKWRKADGKPVLNQEIIQEIDSLMEN-RNIRMSWVNAHTGHPLNEAADSLARQAANNF  143 (161)
T ss_pred             HHHHHHHHHHCCCcccCCCccccHHHHHHHHHHHhc-CceEEEEEecCCCCHHHHHHHHHHHHHHHHh
Confidence            983         3333333  2 6788888888776 5799999999999999999999999988543

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

>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

>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

>PF14529 Exo_endo_phos_2: Endonuclease-reverse transcriptase ; PDB: 2EI9_A 1WDU_B	Back alignment and domain information

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

>cd03487 RT_Bac_retron_II RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons	Back alignment and domain information

>cd01651 RT_G2_intron RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin	Back alignment and domain information

>cd01648 TERT TERT: Telomerase reverse transcriptase (TERT)	Back alignment and domain information

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

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

>cd01646 RT_Bac_retron_I RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons	Back alignment and domain information

>cd00304 RT_like RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family	Back alignment and domain information

>cd01709 RT_like_1 RT_like_1: A subfamily of reverse transcriptases (RTs)	Back alignment and domain information

>KOG4768\|consensus	Back alignment and domain information

>cd01645 RT_Rtv RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs)	Back alignment and domain information

>cd03714 RT_DIRS1 RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons	Back alignment and domain information

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

>PRK13911 exodeoxyribonuclease III; Provisional	Back alignment and domain information

>KOG1005\|consensus	Back alignment and domain information

>TIGR00633 xth exodeoxyribonuclease III (xth)	Back alignment and domain information

>COG0708 XthA Exonuclease III [DNA replication, recombination, and repair]	Back alignment and domain information

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

>TIGR00195 exoDNase_III exodeoxyribonuclease III	Back alignment and domain information

>PF14529 Exo_endo_phos_2: Endonuclease-reverse transcriptase ; PDB: 2EI9_A 1WDU_B	Back alignment and domain information

>cd01644 RT_pepA17 RT_pepA17: Reverse transcriptase (RTs) in retrotransposons	Back alignment and domain information

>PRK11756 exonuclease III; Provisional	Back alignment and domain information

>PF03372 Exo_endo_phos: Endonuclease/Exonuclease/phosphatase family Subset of Pfam family Subset of Pfam family; InterPro: IPR005135 This domain is found in a large number of proteins including magnesium dependent endonucleases and phosphatases involved in intracellular signalling []	Back alignment and domain information

>PF09004 DUF1891: Domain of unknown function (DUF1891); InterPro: IPR015095 This domain is found at the extreme N terminus of eukaryotic alkylated DNA repair protein homologs	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

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		570
3p1g_A		165	Xenotropic murine leukemia virus-related virus (X	1e-05
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-05
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-05
1wdu_A		245	TRAS1 ORF2P; four-layered alpha/beta sandwich, RNA	4e-05
2ei9_A		240	Non-LTR retrotransposon R1BMKS ORF2 protein; four	7e-05

>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 = 44.8 bits (106), Expect = 1e-05
 Identities = 30/133 (22%), Positives = 47/133 (35%), Gaps = 19/133 (14%)

Query: 379 FTDGSKTTD----HTGAAFIIRDEICSMK-LNPICSIFTAELIAIEKCLEKIKDVVTHDL 433
           +TDGS          GAA     E+   + L    S   AELIA+ + L+  +       
Sbjct: 27  YTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMAEG------ 80

Query: 434 VTQNFIICSDSKSSLQALQNVYHVSPLVC-DIISTIQDIRDLGTRVSFLWIPSHLG---- 488
             +   + +DS+ +            +   + I  +     L  R+S +  P H      
Sbjct: 81  --KKLNVYTDSRYAFATAHVHSEGREIKNKNEILALLKALFLPKRLSIIHCPGHQKGNSA 138

Query: 489 -IRENDNVDHAAR 500
             R N   D AAR
Sbjct: 139 EARGNRMADQAAR 151

PyMOL of 3p1g

>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

>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

>1wdu_A TRAS1 ORF2P; four-layered alpha/beta sandwich, RNA binding protein; 2.40A {Bombyx mori} SCOP: d.151.1.1 Length = 245	Back alignment and structure

>2ei9_A Non-LTR retrotransposon R1BMKS ORF2 protein; four layered alpha beta sandwich, gene regulation; 2.00A {Bombyx mori} Length = 240	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		570
2qkb_A		154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.87
2kq2_A		147	Ribonuclease H-related protein; PSI, NESG, protein	99.87
2zd1_A		557	Reverse transcriptase/ribonuclease H; P51/P66, het	99.87
3qio_A		150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.87
1mu2_A		555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	99.86
3h08_A		146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.85
3p1g_A		165	Xenotropic murine leukemia virus-related virus (X	99.84
1jl1_A		155	Ribonuclease HI; RNAse HI, protein stability, ther	99.83
2e4l_A		158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.83
1ril_A		166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.82
2lsn_A		165	Reverse transcriptase; RNAse H, viral protein; NMR	99.81
3hst_B		141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	99.78
3u3g_D		140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	99.77
2ehg_A		149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	99.74
1zbf_A		142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	99.28
4htu_A		134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	99.0
2ei9_A		240	Non-LTR retrotransposon R1BMKS ORF2 protein; four	98.78
3kyl_A		596	Telomerase reverse transcriptase; reverse transcri	98.77
1wdu_A		245	TRAS1 ORF2P; four-layered alpha/beta sandwich, RNA	98.74
1rw3_A		455	POL polyprotein; RNA and DNA dependent DNA polymer	98.19
1vyb_A		238	ORF2 contains A reverse transcriptase domain; endo	97.93
2zd1_B		428	P51 RT; P51/P66, hetero dimer, NNRTI, nonnucleosid	97.78
3g91_A		265	MTH0212, exodeoxyribonuclease; double-strand speci	97.19
3fsi_A		255	RT, reverse transcriptase domain; transferase/DNA	96.65
2j63_A		467	AP-endonuclease; base excision repair, lyase; 2.48	96.23
2o3h_A		285	DNA-(apurinic or apyrimidinic site) lyase; APE, en	95.41
1ako_A		268	Exonuclease III; AP-endonuclease, DNA repair; 1.70	94.63
2voa_A		257	AF_EXO, XTHA, exodeoxyribonuclease III; EXOIII, AP	94.45
2jc4_A		256	Exodeoxyribonuclease III; hydrolase, repair phosph	93.66
2jc5_A		259	Exodeoxyribonuclease; hydrolase, repair phosphodie	89.84
3g6s_A		267	Putative endonuclease/exonuclease/phosphatase fami	89.42
1hd7_A		318	DNA-(apurinic or apyrimidinic site) lyase; DNA rep	89.13
4fva_A		256	5'-tyrosyl-DNA phosphodiesterase; 5'-phosphotyrosy	88.23
4gz1_A		256	Tyrosyl-DNA phosphodiesterase 2; protein-DNA compl	88.0
4f1h_A		250	Tyrosyl-DNA phosphodiesterase 2; hydrolase-DNA com	86.94
4gew_A		362	5'-tyrosyl-DNA phosphodiesterase; 5'-phosphotyrosy	86.41
3teb_A		266	Endonuclease/exonuclease/phosphatase; PSI-biology,	85.03
2jc5_A		259	Exodeoxyribonuclease; hydrolase, repair phosphodie	83.09
3i41_A		317	Beta-hemolysin; beta toxin, sphingomyelinase, toxi	83.08
1zwx_A		301	SMCL, sphingomyelinase-C; dnase1-like fold, beta-h	81.29
2ddr_A		306	Sphingomyelin phosphodiesterase; DNAse I like fold	81.25

>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=99.87  E-value=1.4e-22  Score=184.03  Aligned_cols=128  Identities=16%  Similarity=0.249  Sum_probs=101.8

Q ss_pred             CCCeEEEecCCCCCC-----CceEEEEEece---eeeeccCCccccchhhHHHHHHHHHHHHhhhcccCCcceEEEEecC
Q psy9745         373 KLDTLCFTDGSKTTD-----HTGAAFIIRDE---ICSMKLNPICSIFTAELIAIEKCLEKIKDVVTHDLVTQNFIICSDS  444 (570)
Q Consensus       373 ~~~~~iytDGS~~~~-----~~G~g~~~~~~---~~~~~~~~~~s~~~aEl~ai~~al~~~~~~~~~~~~~~~v~I~tDs  444 (570)
                      .+.+.||||||+..+     .+|+|+++...   ..+..+.+.+|++.||++|++.||+.+.+.     +..+|.|+|||
T Consensus         5 ~~~~~iytDGs~~~n~~~~~~aG~Gvv~~~~~~~~~~~~l~~~~tn~~aEl~A~~~aL~~~~~~-----~~~~v~i~tDS   79 (154)
T 2qkb_A            5 GDFVVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQAKTQ-----NINKLVLYTNS   79 (154)
T ss_dssp             TTEEEEEEEEEEETTTSSSCEEEEEEECSTTCTTCEEEECCSSCCHHHHHHHHHHHHHHHHHHT-----TCCEEEEEESC
T ss_pred             CCeEEEEEccCcCCCCCCCCcEEEEEEEECCCceeEEeecCCCCchHHHHHHHHHHHHHHHHhC-----CCceEEEEECc
Confidence            456889999998643     27999888532   244556567899999999999999999875     67899999999


Q ss_pred             HHHHHHHhcC--------CCC-Ch---hHHHHHHHHHHHHHhCCceEEEeecCCCCCCccchhchhhhhccCCC
Q psy9745         445 KSSLQALQNV--------YHV-SP---LVCDIISTIQDIRDLGTRVSFLWIPSHLGIRENDNVDHAARHCNDVP  506 (570)
Q Consensus       445 ~~al~~l~~~--------~~~-~~---~~~~~~~~~~~l~~~~~~v~~~WVp~H~gi~gNe~AD~lAk~a~~~~  506 (570)
                      +++++.|+++        +.. .+   ...++++.+.++... ..|.|.|||||+|++|||+||+|||+|+..+
T Consensus        80 ~~vi~~i~~~~~~w~~~~w~~~~~~~~~n~~l~~~i~~l~~~-~~v~~~~V~~H~g~~~N~~AD~LA~~a~~~~  152 (154)
T 2qkb_A           80 MFTINGITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQG-MDIQWMHVPGHSGFIGNEEADRLAREGAKQS  152 (154)
T ss_dssp             HHHHHHHHTHHHHHHTTTSBCTTSSBCTTHHHHHHHHHHHTT-CEEEEEECCTTSSCHHHHHHHHHHHHHHTCC
T ss_pred             HHHHhhhhhhHHHHHhccccccCCCccccHHHHHHHHHHHcC-CceEEEEccCCCCCHhHHHHHHHHHHHHHhc
Confidence            9999999872        221 11   124677777776664 5799999999999999999999999998765

PyMOL of 2qkb

>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

>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

>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

>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

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

>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

>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

>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

>2ei9_A Non-LTR retrotransposon R1BMKS ORF2 protein; four layered alpha beta sandwich, gene regulation; 2.00A {Bombyx mori}	Back alignment and structure

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

>1wdu_A TRAS1 ORF2P; four-layered alpha/beta sandwich, RNA binding protein; 2.40A {Bombyx mori} SCOP: d.151.1.1	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

>1vyb_A ORF2 contains A reverse transcriptase domain; endonuclease, APE-1 type, retrotransposition, retrotransposon, transferase; 1.8A {Homo sapiens} SCOP: d.151.1.1 PDB: 2v0s_A 2v0r_A	Back alignment and structure

>2zd1_B P51 RT; P51/P66, hetero dimer, NNRTI, nonnucleoside inhibitor, AIDS, HIV, rilpivirine, diarylpyrimidine, DAPY, DNA recombination; HET: T27; 1.80A {Human immunodeficiency virus 1} SCOP: e.8.1.2 PDB: 2ykm_B* 2ykn_B* 2ze2_B* 3bgr_B* 3ig1_B* 3irx_B* 3is9_B* 3qo9_B* 3v4i_B* 3v6d_B* 3v81_B* 3klf_B* 3kk1_B* 3kjv_B* 3kk2_B* 3kk3_B* 2be2_B* 1n5y_B* 1bqm_B* 1n6q_B* ...	Back alignment and structure

>3g91_A MTH0212, exodeoxyribonuclease; double-strand specific 3'-5' exonuclease, AP endonuclease; HET: PG4; 1.23A {Methanothermobacter thermautotrophicusorganism_taxid} PDB: 3fzi_A 3g0a_A 3g1k_A 3g2c_A 3g3c_A* 3g3y_A* 3g4t_A* 3g00_A 3g0r_A* 3g2d_A* 3g38_A 3g8v_A* 3ga6_A	Back alignment and structure

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

>2j63_A AP-endonuclease; base excision repair, lyase; 2.48A {Leishmania major}	Back alignment and structure

>2o3h_A DNA-(apurinic or apyrimidinic site) lyase; APE, endonuclease; 1.90A {Homo sapiens} PDB: 1bix_A 1dew_A* 1de8_B* 1de9_A* 2o3c_A	Back alignment and structure

>1ako_A Exonuclease III; AP-endonuclease, DNA repair; 1.70A {Escherichia coli} SCOP: d.151.1.1	Back alignment and structure

>2voa_A AF_EXO, XTHA, exodeoxyribonuclease III; EXOIII, AP endonuclease, lyase; 1.7A {Archaeoglobus fulgidus}	Back alignment and structure

>2jc4_A Exodeoxyribonuclease III; hydrolase, repair phosphodiesterase, DNA repair, exonuclease, endonuclease; HET: 1PE; 1.90A {Neisseria meningitidis}	Back alignment and structure

>2jc5_A Exodeoxyribonuclease; hydrolase, repair phosphodiesterase, DNA repair, exonuclease, endonuclease; HET: BCN DIO GOL; 1.50A {Neisseria meningitidis}	Back alignment and structure

>3g6s_A Putative endonuclease/exonuclease/phosphatase family protein; alpha-beta protein, structural genomics, PSI-2; 2.50A {Bacteroides vulgatus atcc 8482}	Back alignment and structure

>1hd7_A DNA-(apurinic or apyrimidinic site) lyase; DNA repair, endonuclease, APE1, HAP1, REF-1; 1.95A {Homo sapiens} SCOP: d.151.1.1 PDB: 1e9n_A 3u8u_A 2isi_A	Back alignment and structure

>4fva_A 5'-tyrosyl-DNA phosphodiesterase; 5'-phosphotyrosyl-DNA diesterase, hydrolase; HET: EDO; 2.07A {Caenorhabditis elegans}	Back alignment and structure

>4gz1_A Tyrosyl-DNA phosphodiesterase 2; protein-DNA complex, DNA repair, 5'-DNA END processing, endonuclease/exonuclease/phosphatase domain; HET: DNA EPE; 1.50A {Mus musculus} PDB: 4gyz_A* 4gz0_A* 4gz2_A*	Back alignment and structure

>4f1h_A Tyrosyl-DNA phosphodiesterase 2; hydrolase-DNA complex; HET: DNA; 1.66A {Danio rerio} PDB: 4fpv_A* 4f1h_B*	Back alignment and structure

>4gew_A 5'-tyrosyl-DNA phosphodiesterase; 5'-phosphotyrosyl-DNA diesterase, hydrolase; 2.35A {Caenorhabditis elegans} PDB: 4f1i_A	Back alignment and structure

>3teb_A Endonuclease/exonuclease/phosphatase; PSI-biology, MCSG, midwest center for structural genomics; 2.99A {Leptotrichia buccalis c-1013-b}	Back alignment and structure

>2jc5_A Exodeoxyribonuclease; hydrolase, repair phosphodiesterase, DNA repair, exonuclease, endonuclease; HET: BCN DIO GOL; 1.50A {Neisseria meningitidis}	Back alignment and structure

>3i41_A Beta-hemolysin; beta toxin, sphingomyelinase, toxin; 1.75A {Staphylococcus aureus} PDB: 3i46_A 3i48_A 3i5v_A* 3k55_A	Back alignment and structure

>1zwx_A SMCL, sphingomyelinase-C; dnase1-like fold, beta-hairpin, hydrolase; 1.90A {Listeria ivanovii} SCOP: d.151.1.3	Back alignment and structure

>2ddr_A Sphingomyelin phosphodiesterase; DNAse I like folding, riken structural genomics/proteomics initiative, RSGI, structural genomics, hydrolase; 1.40A {Bacillus cereus} SCOP: d.151.1.3 PDB: 2dds_A 2ddt_A* 2uyr_X	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		570
d1mu2a1		126	c.55.3.1 (A:430-555) HIV RNase H (Domain of revers	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 = 42.2 bits (98), Expect = 2e-05
 Identities = 25/124 (20%), Positives = 41/124 (33%), Gaps = 13/124 (10%)

Query: 379 FTDGS--KTTDHTGAAFIIRDEICSMKLNPICSIFTAELIAIEKCLEKIKDVVTHDLVTQ 436
           +TDGS  + +    A ++       +K     +   AEL A    L              
Sbjct: 11  YTDGSCNRQSKEGKAGYVTDRGKDKVKKLEQTTNQQAELEAFAMALTDSG---------P 61

Query: 437 NFIICSDSKSSLQALQNVYHVSPLVCDIISTIQDIRDLGTRVSFLWIPSHLGIRENDNVD 496
              I  DS+  +  + +    S          + I+     +   W+P+H GI  N  VD
Sbjct: 62  KVNIIVDSQYVMGIVASQPTESESKIVNQIIEEMIKK--EAIYVAWVPAHKGIGGNQEVD 119

Query: 497 HAAR 500
           H   
Sbjct: 120 HLVS 123

PyMOL of d1mu2a1

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		570
d1mu2a1		126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.89
d1rila_		147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.84
d1jl1a_		152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	99.83
d1s1ta1		110	HIV RNase H (Domain of reverse transcriptase) {Hum	99.69
d1zbfa1		132	BH0863-like Ribonuclease H {Bacillus halodurans [T	99.48
d1wdua_		228	Endonuclease domain of TRAS1 retrotransposon (ORF2	98.81
d1vyba_		236	Endonuclease domain of LINE-1 reverse transcriptas	97.61
d1ztwa1		255	MMLV reverse transcriptase {Moloney murine leukemi	96.29
d1mu2a2		427	HIV-1 reverse transcriptase {Human immunodeficienc	94.9
d2zd1b1		424	HIV-1 reverse transcriptase {Human immunodeficienc	94.26
d1hara_		216	HIV-1 reverse transcriptase {Human immunodeficienc	85.42

>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=99.89  E-value=8.8e-24  Score=183.17  Aligned_cols=122  Identities=20%  Similarity=0.202  Sum_probs=90.0

Q ss_pred             cCCCCeEEEecCCCCC--CCceEEEEEeceeeeeccCCccccchhhHHHHHHHHHHHHhhhcccCCcceEEEEecCHHHH
Q psy9745         371 QHKLDTLCFTDGSKTT--DHTGAAFIIRDEICSMKLNPICSIFTAELIAIEKCLEKIKDVVTHDLVTQNFIICSDSKSSL  448 (570)
Q Consensus       371 ~~~~~~~iytDGS~~~--~~~G~g~~~~~~~~~~~~~~~~s~~~aEl~ai~~al~~~~~~~~~~~~~~~v~I~tDs~~al  448 (570)
                      +.+....+|||||+..  +.+|+|+++..........+..|+++||+.|+++||+.         ....+.|+|||++++
T Consensus         3 p~~~~~t~YTDGS~~~n~~~~~~g~~~~~~~~~~~~~~~~tnn~AEl~Ai~~al~~---------~~~~i~I~tDS~~v~   73 (126)
T d1mu2a1           3 PIPGAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKLEQTTNQQAELEAFAMALTD---------SGPKVNIIVDSQYVM   73 (126)
T ss_dssp             CCTTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEEESSCCHHHHHHHHHHHHHHT---------SCSEEEEEESCHHHH
T ss_pred             CCCCCcEEEEcCCCCCCCCcEEEEEEecCCCEEEEecCCCcchHHHHHHHHHHhcc---------CCcceEEEechHHHH
Confidence            3456678999999753  34677777754322222234679999999999999874         356799999999999


Q ss_pred             HHHhcCCCCChhHHHHHHHHHHHHHhCCceEEEeecCCCCCCccchhchhhhhcc
Q psy9745         449 QALQNVYHVSPLVCDIISTIQDIRDLGTRVSFLWIPSHLGIRENDNVDHAARHCN  503 (570)
Q Consensus       449 ~~l~~~~~~~~~~~~~~~~~~~l~~~~~~v~~~WVp~H~gi~gNe~AD~lAk~a~  503 (570)
                      ..+++.+...... ...+.+..+.+ ...|.|.|||||+|++|||+||+||++|.
T Consensus        74 ~~~~~~~~~~~~~-~~~~~~~~~~~-~~~v~~~wV~gH~g~~gNe~AD~LA~~ai  126 (126)
T d1mu2a1          74 GIVASQPTESESK-IVNQIIEEMIK-KEAIYVAWVPAHKGIGGNQEVDHLVSQGI  126 (126)
T ss_dssp             HHHHTCCSEESCH-HHHHHHHHHHH-CSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             HHHhcCCccccch-HHHHHHHHhhh-cceeEEEEEeCCCCCcchHHHHHHHHhhC
Confidence            9999876533221 12333444433 47999999999999999999999999984

PyMOL of d1mu2a1

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

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

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

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

>d1wdua_ d.151.1.1 (A:) Endonuclease domain of TRAS1 retrotransposon (ORF2) {Silkworm (Bombyx mori) [TaxId: 7091]}	Back information, alignment and structure

>d1vyba_ d.151.1.1 (A:) Endonuclease domain of LINE-1 reverse transcriptase homolog {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

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

>d1mu2a2 e.8.1.2 (A:3-429) HIV-1 reverse transcriptase {Human immunodeficiency virus type 2 [TaxId: 11709]}	Back information, alignment and structure

>d2zd1b1 e.8.1.2 (B:5-428) HIV-1 reverse transcriptase {Human immunodeficiency virus type 1 [TaxId: 11676]}	Back information, alignment and structure

>d1hara_ e.8.1.2 (A:) HIV-1 reverse transcriptase {Human immunodeficiency virus type 1 [TaxId: 11676]}	Back information, alignment and structure