Psyllid ID: psy11456

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----

MNDIFDVIKPPLKRVLFIDDLLIIGRGKDLDLLIQRFQHTLDEIHLWAETNGTLFSTDPGKSVCIDFHRLRVARSPILSYNGTPLHFVTNNKFLGLLWDAKMNWSLHIQYIKSRAMNSLNALKMVSCKKFGVRRDVLLKFYKSFTLPILDYGCYIYSSAKDSVLNKLNTVHHAGIRIATGALRSSPVVSLYVDSGIPPLFLRRSKLMLNYVSKISASPFNPAQKVLFHQDMSGTIFTVNKPKPLYVRFREIANFINVLDSSEIAPYVRFVPPWSNCAPPVDQCLGEGKKSDTAPVVFQKMFHEVINIKYPNHTICFTDGSKSPDVTGCAFSIGDMVQSTLLNPINSIFSAELIAIFLCLEAIIDSPSNQFLIVSDSRSALAALANVRFSNPLVTKVFSTWSYLKLCDKEVSFIWCPSHCGIRGNEIVDVAAKNPSDLAPSKLCTPEDLKPFIASLMKTEWQNQWNNVPSTNKLKSIRPYIKHWNTSNQDRRIKEVILTRMRIGHTRLTHNHLFTKSAPPICQCGAPLSVRHILSCHRHDHIRSSLHPPPSLGDDEEGVTSLFTYLQQLDIYHMI

ccccccccccccEEEEEEcccEEEEEcccHHHHHHHHHHHHHHHHHHHHHcccEEcccccEEEEEEEccccccccccEEEccEEEEcccccEEEEEEEcccccHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHcccccccccEEEccccHHHHHHHHHHHHHHHHHHHcccccccccccccccccccHHHHHHHHHHHHHHHHHccccccccHHHccccccccccccccccccHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHcccccEEEEccccccccccEEEEEEcccEEEEEcccccccHHHHHHHHHHHHHHHHccccccEEEEEcHHHHHHHHHcccccHHHHHHHHHHHHHHHHccccEEEEEEccccccccccHHHHHccccccccccccccccccHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccHHHHHcccccccccccHHHHHHHHHHHHHccccccc

ccHHHHHcccccEEEEEEccHHHHHccccHHHHHHHHHHHHHHHHHHHHHcccEEcccccEEEEEEccccccccccEEEEccEEEcccccEEEEEEEEccccccHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHcHHHHccccHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHccccHHHHHHHHHHHHHHHHHccccccHHHHcccccHHHccccccccccHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHccccccEEEEEccccccccEEEEEEEEccccEEEccccccHHHHHHHHHHHHHHHHHHcccccEEEEEccHHHHHHHHccccccHHHHHHHHHHHHHHHcccEEEEEEEcccccccccHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHccccccccEccccccccccccccccHHHHHHHHHHHcccccHHHHHHcccccccccccccccccHHHEccHHHHHHHHHcccccccccccccHHHHHHHHHHHcHHccc

mndifdvikpplkrvlfiDDLLIIGRGKDLDLLIQRFQHTLDEIHLWaetngtlfstdpgksvcidfhrlrvarspilsyngtplhfvtNNKFLGLLWDAKMNWSLHIQYIKSRAMNSLNALKMVSCKKFGVRRDVLLKFYksftlpildygcyiyssaKDSVLNKLNTVHHAGIRIatgalrsspvvslyvdsgipplfLRRSKLMLNYVSkisaspfnpaqkvlfhqdmsgtiftvnkpkplyVRFREIANFINvldsseiapyvrfvppwsncappvdqclgegkksdtapVVFQKMFHEVinikypnhticftdgskspdvtgcafsiGDMVQSTLLNPINSIFSAELIAIFLCLEAiidspsnqflIVSDSRSALAALANVRFSNPLVTKVFSTWSYLklcdkevsfiwcpshcgirgneivdvaaknpsdlapsklctpedlKPFIASLMKTEWqnqwnnvpstnklksirpyikhwntsnqdrRIKEVILTRMRightrlthnhlftksappicqcgaplsvrhILSChrhdhirsslhpppslgddeegVTSLFTYLQQLDIYHMI

mndifdvikpplkrvLFIDDLLIIGRGKDLDLLIQRFQHTLDEIHLWAETNGTLFSTDPGKSVCIDFHRLRVARSpilsyngtplhFVTNNKFLGLLWDAKMNWSLHIQYIKSRAMNSLNALKMVSCKKFGVRRDVLLKFYKSFTLPILDYGCYIYSSAKDSVLNKLNTVHHAGIRIatgalrsspvVSLYVDSGIPPLFLRRSKLMLNYVSKISASPFNPAQKVLFHQDMSGTIFTVNKPKPLYVRFREIANFINVLDSSEIAPYVRFVPPWSNCAPPVDQCLGEGKKSDTAPVVFQKMFHEVINIKYPNHTICFTDGSKSPDVTGCAFSIGDMVQSTLLNPINSIFSAELIAIFLCLEAIIDSPSNQFLIVSDSRSALAALANvrfsnplvTKVFSTWSYLKLCDKEVSFIWCPSHCGIRGNEIVDVAAKNPSDLAPSKLCTPEDLKPFIASLMKTEwqnqwnnvpstnklksirpyikhwntsnqdrriKEVILTRMRIGHTRLTHNHLFTKSAPPICQCGAPLSVRHILSCHRHDHIRSSLHPPPSLGDDEEGVTSLFTYLQqldiyhmi

***IFDVIKPPLKRVLFIDDLLIIGRGKDLDLLIQRFQHTLDEIHLWAETNGTLFSTDPGKSVCIDFHRLRVARSPILSYNGTPLHFVTNNKFLGLLWDAKMNWSLHIQYIKSRAMNSLNALKMVSCKKFGVRRDVLLKFYKSFTLPILDYGCYIYSSAKDSVLNKLNTVHHAGIRIATGALRSSPVVSLYVDSGIPPLFLRRSKLMLNYVSKISASPFNPAQKVLFHQDMSGTIFTVNKPKPLYVRFREIANFINVLDSSEIAPYVRFVPPWSNCAPPVDQCLGEGKKSDTAPVVFQKMFHEVINIKYPNHTICFTDGSKSPDVTGCAFSIGDMVQSTLLNPINSIFSAELIAIFLCLEAIIDSPSNQFLIVSDSRSALAALANVRFSNPLVTKVFSTWSYLKLCDKEVSFIWCPSHCGIRGNEIVDVAAKN*******KLCTPEDLKPFIASLMKTEWQNQWNNVPSTNKLKSIRPYIKHWNTSNQDRRIKEVILTRMRIGHTRLTHNHLFTKSAPPICQCGAPLSVRHILSCHRHDHI****************VTSLFTYLQQLDIYH**

MNDIFD*IKPPLKRVLFIDDLLIIGRGKDLDLLIQRFQHTLDEIHLWAETNGTLFSTDPGKSVCIDFHRLRVARSPILSYNGTPLHFVTNNKFLGLLWDAKMNWSLHIQYIKSRAMNSLNALKMVSCKKFGVRRDVLLKFYKSFTLPILDYGCYIYSSAKDSVLNKLNTVHHAGIRIATGALRSSPVVSLYVDSGIPPLFLRRSKLMLNYVSKISASPFNPAQKVLFHQDMSGTIFTVNKPKPLYVRFREIANFINVLDSSEIAPYVRFVPPWSNCAPPVDQCLGEGKKSDTAPVVFQKMFHEVINIKYPNHTICFTDGSKSPDVTGCAFSIGDMVQSTLLNPINSIFSAELIAIFLCLEAIIDSPSNQFLIVSDSRSALAALANVRFSNPLVTKVFSTWSYLKLCDKEVSFIWCPSHCGIRGNEIVDVAAK**********CTPEDLKPFIASLMKTEWQNQWNNVPSTNKLKSIRPYIKHWNTSNQDRRIKEVILTRMRIGHTRLTHNHLFTKSAPPICQCGAPLSVRHILSCHRHDHIRSSLH*****GDDEEGVTSLFTYLQQLDIYHMI

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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

ID	Alignment graph	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query		574	2.2.26 [Sep-21-2011]
P21328		916	RNA-directed DNA polymera	yes	N/A	0.371	0.232	0.233	3e-08
P16425		1021	Putative 115 kDa protein	yes	N/A	0.360	0.202	0.216	3e-07
Q03269		337	Retrovirus-related Pol po	no	N/A	0.341	0.581	0.207	2e-06
Q03277		1004	Retrovirus-related Pol po	N/A	N/A	0.243	0.139	0.244	1e-05
P21329		916	RNA-directed DNA polymera	N/A	N/A	0.358	0.224	0.196	0.0002
Q9NBX4		908	Probable RNA-directed DNA	yes	N/A	0.273	0.172	0.244	0.0003

>sp\|P21328\|RTJK_DROME RNA-directed DNA polymerase from mobile element jockey OS=Drosophila melanogaster GN=pol PE=1 SV=1	Back alignment and function desciption

 Score = 60.5 bits (145), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 52/223 (23%), Positives = 89/223 (39%), Gaps = 10/223 (4%)

Query: 17  FIDDLLIIGRGKDLDLLIQRFQHTLDEIHLWAETNGTLFSTDPGKSVCIDFHRLRVARSP 76
           + DD  ++ + K +       Q  LD    WAE      + +  K   + F   R    P
Sbjct: 679 YADDTAVLTKSKSILAATSGLQEYLDAFQQWAENWNVRINAE--KCANVTFAN-RTGSCP 735

Query: 77  ILSYNGTPLHFVTNNKFLGLLWDAKMNWSLHIQYIKSRAMNSLNALKMVSCKKFGVRRDV 136
            +S NG  +      K+LG+  D K+ +S HI  I+      +  +  +   +  +    
Sbjct: 736 GVSLNGRLIRHHQAYKYLGITLDRKLTFSRHITNIQQAFRTKVARMSWLIAPRNKLSLGC 795

Query: 137 LLKFYKSFTLPILDYGCYIYSSAKDSVLNKLNTVHHAGIRIATGALRSSPVVSLYVDSGI 196
            +  YKS   P L YG  +Y  A  S LNK+  +    +R  +GA        +  D  +
Sbjct: 796 KVNIYKSILAPCLFYGLQVYGIAAKSHLNKIRILQAKTLRRISGAPWYMRTRDIERDLKV 855

Query: 197 PPLFLRRSKLMLNYVSKISASPFNPAQKVLFHQDMSGTIFTVN 239
           P L  +   +   Y+ +++  P + A+K+       GT   VN
Sbjct: 856 PKLGDKLQNIAQKYMERLNVHPNSLARKL-------GTAAVVN 891

Drosophila melanogaster (taxid: 7227)
EC: 2EC: .EC: 7EC: .EC: 7EC: .EC: 4EC: 9

>sp\|P16425\|Y2R2_DROME Putative 115 kDa protein in type-1 retrotransposable element R1DM OS=Drosophila melanogaster PE=4 SV=1	Back alignment and function description

>sp\|Q03269\|PO11_NASVI Retrovirus-related Pol polyprotein from type-1 retrotransposable element R1 (Fragment) OS=Nasonia vitripennis PE=4 SV=1	Back alignment and function description

>sp\|Q03277\|PO11_SCICO Retrovirus-related Pol polyprotein from type-1 retrotransposable element R1 (Fragment) OS=Sciara coprophila PE=4 SV=1	Back alignment and function description

>sp\|P21329\|RTJK_DROFU RNA-directed DNA polymerase from mobile element jockey OS=Drosophila funebris GN=jockey\pol PE=1 SV=1	Back alignment and function description

>sp\|Q9NBX4\|RTXE_DROME Probable RNA-directed DNA polymerase from transposon X-element OS=Drosophila melanogaster GN=X-element\ORF2 PE=3 SV=1	Back alignment and function description

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		574
125901787		1222	pol-like protein [Biomphalaria glabrata]	0.935	0.439	0.356	4e-78
427791807		1212	Putative tick transposon, partial [Rhipi	0.947	0.448	0.348	1e-76
427791321		1210	Putative tick transposon, partial [Rhipi	0.951	0.451	0.331	7e-73
427791063		1035	Putative tick transposon, partial [Rhipi	0.928	0.514	0.315	5e-68
427798889		1199	Putative tick transposon, partial [Rhipi	0.935	0.447	0.331	2e-66
427798887		1199	Putative tick transposon, partial [Rhipi	0.935	0.447	0.326	2e-65
427798885		1199	Putative tick transposon, partial [Rhipi	0.935	0.447	0.327	5e-65
427778603		1397	Putative tick transposon [Rhipicephalus	0.914	0.375	0.289	2e-60
427792011		1121	Putative tick transposon, partial [Rhipi	0.811	0.415	0.288	9e-50
427791981		1060	Putative tick transposon, partial [Rhipi	0.660	0.357	0.333	4e-47

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

 Score =  298 bits (764), Expect = 4e-78,   Method: Compositional matrix adjust.
 Identities = 196/550 (35%), Positives = 295/550 (53%), Gaps = 13/550 (2%)

Query: 1    MNDIFDVIKPPLKRVLFIDDLLIIGRGKDLDLLIQRFQHTLDEIHLWAETNGTLFSTDPG 60
            +N I + + P ++  L++DD +I+  GK+++ L ++ Q  L++I  WA  NG  FS    
Sbjct: 646  INSIINALSPGIECSLYVDDFVILTYGKNMNTLERKLQLCLNKIQGWANYNGFKFSD--S 703

Query: 61   KSVCIDFHRLR-VARSPILSYNGTPLHFVTNNKFLGLLWDAKMNWSLHIQYIKSRAMNSL 119
            K+V + F  LR +   P L  +   +  V   KFLGL  D+K N+  HI+ +K +   SL
Sbjct: 704  KTVSMHFCNLRGLHPDPELFIHKKKIPVVKTTKFLGLTLDSKFNFLPHIKELKKKCQKSL 763

Query: 120  NALKMVSCKKFGVRRDVLLKFYKSFTLPILDYGCYIYSSAKDSVLNKLNTVHHAGIRIAT 179
            N L+++S   +G  RD LL  Y+S     LDYG  IY +A+ S L  L  + +A +R+  
Sbjct: 764  NILRVLSHTDWGADRDTLLLLYRSLIRSKLDYGSIIYGAARKSYLKILEPIQNAALRLCL 823

Query: 180  GALRSSPVVSLYVDSGIPPLFLRRSKLMLNYVSKISASPFNPAQKVLFH-QDMSGTIFTV 238
            GA R+SP+ SL+V++G  P+ +R  KL + Y+ K+ ++P NPA   +F+  ++       
Sbjct: 824  GAFRTSPIPSLHVEAGELPMDIRMKKLAMQYIVKLKSNPTNPAFDSIFNPTEVELYNRRP 883

Query: 239  NKPKPLYVRFRE-IANFINVLDS-SEIAPYVRFVPPWSNCAPPVDQCLGEGKKSDTAPVV 296
            N  +PL +R RE I N    +D  S+I       PPW    P ++  L   KK +T P +
Sbjct: 884  NVIQPLGLRMREPIQNLTQPIDQISKIETPQN--PPWLMNKPKLNLSLLNFKKENTDPSI 941

Query: 297  FQKMFHEVINIKYPNHTICFTDGSKSPDVTGCAFSIGDMVQSTLLNPINSIFSAELIAIF 356
             Q  F E +   Y +    +TDGSK      CA S  +   S  L    SIF+AEL AI 
Sbjct: 942  LQVHFRE-LQESYGDCGTIYTDGSKMEGKVACACSFRNKTISRRLPDGCSIFTAELHAIL 1000

Query: 357  LCLEAIIDSPSNQFLIVSDSRSALAALANVRFSNPLVTKVFSTWSYLKLCDKEVSFIWCP 416
            L L A+  S  ++F+I SDS+SAL AL  ++   PLV K       +    ++V+FIW P
Sbjct: 1001 LALMAVKASERSKFIICSDSKSALQALGRMKTDIPLVHKSLKLLDLITADRRDVTFIWVP 1060

Query: 417  SHCGIRGNEIVDVAAKNPSDLAPSKLCTP-EDLKPFIASLMKTEWQNQWNNVPSTNKLKS 475
            SH GI GNE  D  AK   + A S    P  DL+  IAS    EWQN+W    + +KL+ 
Sbjct: 1061 SHVGIEGNEAADREAKRALNHAVSGTQIPYSDLRQSIASATYREWQNRW-EAETHSKLRQ 1119

Query: 476  IRPYIKHWNTSNQDRRIKEVILTRMRIGHTRLTHNHLFTKSAPPICQ-CGAPLSVRHIL- 533
            I   ++   TS    R     ++R+RIGHT +TH+ +  +  PP+C+ C + L+V HIL 
Sbjct: 1120 IVADVRWRPTSKGLTRRGSTTMSRLRIGHTYITHSFVLKREEPPLCEYCDSRLTVEHILV 1179

Query: 534  SCHRHDHIRS 543
             C R+  +R+
Sbjct: 1180 DCPRYQDVRA 1189

Source: Biomphalaria glabrata

Species: Biomphalaria glabrata

Genus: Biomphalaria

Family: Planorbidae

Order:

Class: Gastropoda

Phylum: Mollusca

Superkingdom: Eukaryota

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

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

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

>gi\|427798889\|gb\|JAA64896.1\| Putative tick transposon, partial [Rhipicephalus pulchellus]	Back alignment and taxonomy information

>gi\|427798887\|gb\|JAA64895.1\| Putative tick transposon, partial [Rhipicephalus pulchellus]	Back alignment and taxonomy information

>gi\|427798885\|gb\|JAA64894.1\| Putative tick transposon, partial [Rhipicephalus pulchellus]	Back alignment and taxonomy information

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

>gi\|427792011\|gb\|JAA61457.1\| Putative tick transposon, partial [Rhipicephalus pulchellus]	Back alignment and taxonomy information

>gi\|427791981\|gb\|JAA61442.1\| 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		574
ASPGD\|ASPL0000055652		1054	AN0368 [Emericella nidulans (t	0.331	0.180	0.265	5.6e-13
ASPGD\|ASPL0000077547		1581	AN8648 [Emericella nidulans (t	0.331	0.120	0.269	5.7e-12
ASPGD\|ASPL0000040226		1538	AN2661 [Emericella nidulans (t	0.332	0.124	0.266	8.3e-11
ASPGD\|ASPL0000075333		486	AN10625 [Emericella nidulans (	0.452	0.534	0.252	8.9e-11
ASPGD\|ASPL0000037597		666	AN2711 [Emericella nidulans (t	0.332	0.286	0.266	6.2e-10
ASPGD\|ASPL0000033911		686	AN2796 [Emericella nidulans (t	0.219	0.183	0.288	1.4e-09
ASPGD\|ASPL0000010587		342	AN3980 [Emericella nidulans (t	0.327	0.549	0.270	4e-07

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

 Score = 146 (56.5 bits), Expect = 5.6e-13, Sum P(2) = 5.6e-13
 Identities = 57/215 (26%), Positives = 92/215 (42%)

Query:   343 PINSIFSAELIAIFLCLEAIIDSP----SNQFLIVSDSRSALAALANVRFSNPL---VTK 395
             P   ++ AE++     L   +  P    S Q +I+ D+ +A + LA+ R   P    +++
Sbjct:   786 PRTEVYDAEIMGAVEGLRTALGQPCVGYSTQLVILLDNLAAASLLASYR-PTPHRHGLSE 844

Query:   396 VFST----W----SYLKLCDKEVSFIWCPSHCGIRGNEIVDVAAKNPSDL-APSKLCTPE 446
              FS     W    S L +  K +   W P H GI GNE+ D  AK  S + +P    +P 
Sbjct:   845 TFSQLAAQWMESPSILTMQWKPLQVRWIPGHSGIAGNELADKLAKLGSSIYSPDIPPSPA 904

Query:   447 DLKPFIASLMKTEWQNQW-NNVPSTNKLKSIRPYIKHWNTSNQDRRIKEVILTRM---RI 502
              L+      ++TE    + N  P T K  +IRP+ K   + +++ ++   +L R+   R 
Sbjct:   905 YLRQEAKQWLRTETYTAYANKAPETYKALNIRPHTKE--SRSREHKLPRWVLGRLVAART 962

Query:   503 GHTRLT--HNHLFTKSAPPICQCGAPLSVRHILSC 535
             GH   T  H           C CG   +  H   C
Sbjct:   963 GHGDFTAYHQRFDHTDYLESCTCGKAKTPVHFFFC 997

GO:0005575 "cellular_component" evidence=ND

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

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

GO:0003723 "RNA binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

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

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

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

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

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

ASPGD\|ASPL0000010587 AN3980 [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		574
cd09276		128	cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom	4e-33
pfam00075		126	pfam00075, RNase_H, RNase H	3e-13
cd09273		135	cd09273, RNase_HI_RT_Bel, Bel/Pao family of RNase	1e-10
cd06222		123	cd06222, RNase_H, RNase H is an endonuclease that	5e-05
cd01650		220	cd01650, RT_nLTR_like, RT_nLTR: Non-LTR (long term	2e-04

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

 Score =  122 bits (308), Expect = 4e-33
 Identities = 47/124 (37%), Positives = 65/124 (52%), Gaps = 5/124 (4%)

Query: 314 ICFTDGSKSPDVTGCAFSI---GDMVQSTLLNPINSIFSAELIAIFLCLEAII--DSPSN 368
           + +TDGSK    TG  F+I   G + +S  L P  S+F AEL+AI   L+  +     + 
Sbjct: 1   VIYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRRAR 60

Query: 369 QFLIVSDSRSALAALANVRFSNPLVTKVFSTWSYLKLCDKEVSFIWCPSHCGIRGNEIVD 428
           +  I SDS++AL AL + R S+PLV ++      L     +V   W P H GI GNE  D
Sbjct: 61  KITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGNERAD 120

Query: 429 VAAK 432
             AK
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\|187697 cd09273, RNase_HI_RT_Bel, Bel/Pao family of RNase HI in long-term repeat retroelements	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\|238827 cd01650, RT_nLTR_like, RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT)	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		574
PF00075		132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	99.8
PRK08719		147	ribonuclease H; Reviewed	99.8
PRK06548		161	ribonuclease H; Provisional	99.76
PRK00203		150	rnhA ribonuclease H; Reviewed	99.73
COG0328		154	RnhA Ribonuclease HI [DNA replication, recombinati	99.7
cd06222		130	RnaseH RNase H (RNase HI) is an endonuclease that	99.67
KOG3752\|consensus		371		99.54
PRK13907		128	rnhA ribonuclease H; Provisional	99.45
PRK07708		219	hypothetical protein; Validated	99.28
PRK07238		372	bifunctional RNase H/acid phosphatase; Provisional	99.07
PF13456		87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	98.77
cd01650		220	RT_nLTR_like RT_nLTR: Non-LTR (long terminal repea	98.6
cd01651		226	RT_G2_intron RT_G2_intron: Reverse transcriptases	97.67
PF00078		214	RVT_1: Reverse transcriptase (RNA-dependent DNA po	97.66
cd01648		119	TERT TERT: Telomerase reverse transcriptase (TERT)	97.65
cd00304		98	RT_like RT_like: Reverse transcriptase (RT, RNA-de	97.55
cd03487		214	RT_Bac_retron_II RT_Bac_retron_II: Reverse transcr	97.36
cd01646		158	RT_Bac_retron_I RT_Bac_retron_I: Reverse transcrip	97.27
cd03714		119	RT_DIRS1 RT_DIRS1: Reverse transcriptases (RTs) oc	96.93
cd01709		346	RT_like_1 RT_like_1: A subfamily of reverse transc	95.54
cd01645		213	RT_Rtv RT_Rtv: Reverse transcriptases (RTs) from r	95.37
PF13966		86	zf-RVT: zinc-binding in reverse transcriptase	95.22
cd03715		210	RT_ZFREV_like RT_ZFREV_like: A subfamily of revers	94.22
KOG4768\|consensus		796		87.67
PF09004		42	DUF1891: Domain of unknown function (DUF1891); Int	86.62
cd01647		177	RT_LTR RT_LTR: Reverse transcriptases (RTs) from r	85.84

>PF00075 RNase_H: RNase H; InterPro: IPR002156 The RNase H domain is responsible for hydrolysis of the RNA portion of RNA x DNA hybrids, and this activity requires the presence of divalent cations (Mg2+ or Mn2+) that bind its active site	Back alignment and domain information

Probab=99.80  E-value=3.9e-20  Score=164.74  Aligned_cols=117  Identities=31%  Similarity=0.401  Sum_probs=88.8

Q ss_pred             CceEEEecCCCCC--CCeeEEEEec-ceeeeeeCCCCccchHHHHHHHHHHHHHHHcCCCCcEEEEeccHHHHHHHhc--
Q psy11456        311 NHTICFTDGSKSP--DVTGCAFSIG-DMVQSTLLNPINSIFSAELIAIFLCLEAIIDSPSNQFLIVSDSRSALAALAN--  385 (574)
Q Consensus       311 ~~~~i~tDGS~~~--~~~G~~~~~~-~~~~~~~l~~~~sv~~aE~~ai~~al~~~~~~~~~~~~I~~Ds~sa~~~l~~--  385 (574)
                      .++.||||||...  +..|+|++.. .....+.++ ..|++.||+.||..||+.+   ...++.|+|||+.++..+..  
T Consensus         2 ~~~~iytDgS~~~~~~~~~~g~v~~~~~~~~~~~~-~~s~~~aEl~Ai~~AL~~~---~~~~v~I~tDS~~v~~~l~~~~   77 (132)
T PF00075_consen    2 KAIIIYTDGSCRPNPGKGGAGYVVWGGRNFSFRLG-GQSNNRAELQAIIEALKAL---EHRKVTIYTDSQYVLNALNKWL   77 (132)
T ss_dssp             TSEEEEEEEEECTTTTEEEEEEEEETTEEEEEEEE-SECHHHHHHHHHHHHHHTH---STSEEEEEES-HHHHHHHHTHH
T ss_pred             CcEEEEEeCCccCCCCceEEEEEEECCeEEEeccc-ccchhhhheehHHHHHHHh---hcccccccccHHHHHHHHHHhc
Confidence            4789999999664  3356776543 333445556 8999999999999999944   33999999999999998877  


Q ss_pred             ---CCCCc----HHHHHHHHHHHHhhhcCceEEEEEecCCCCC-CcchhhhhhhcCCC
Q psy11456        386 ---VRFSN----PLVTKVFSTWSYLKLCDKEVSFIWCPSHCGI-RGNEIVDVAAKNPS  435 (574)
Q Consensus       386 ---~~~~~----~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi-~gNe~AD~~Ak~a~  435 (574)
                         .....    ++..+|.+.+    ..+..|.|.|||||+|+ .|||.||+|||.|+
T Consensus        78 ~~~~~~~~~~~~~i~~~i~~~~----~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~  131 (132)
T PF00075_consen   78 HGNGWKKTSNGRPIKNEIWELL----SRGIKVRFRWVPGHSGVPQGNERADRLAKEAA  131 (132)
T ss_dssp             HHTTSBSCTSSSBHTHHHHHHH----HHSSEEEEEESSSSSSSHHHHHHHHHHHHHHH
T ss_pred             cccccccccccccchhheeecc----ccceEEeeeeccCcCCCchhHHHHHHHHHHhc
Confidence               33222    3555555543    45889999999999999 69999999999774

This domain is a part of a large family of homologous RNase H enzymes of which the RNase HI protein from Escherichia coli is the best characterised []. Secondary structure predictions for the enzymes from E. coli, yeast, human liver and diverse retroviruses (such as Rous sarcoma virus and the Foamy viruses) supported, in every case, the five beta-strands (1 to 5) and four or five alpha-helices (A, B/C, D, E) that have been identified by crystallography in the RNase H domain of Human immunodeficiency virus 1 (HIV-1) reverse transcriptase and in E. coli RNase H []. Reverse transcriptase (RT) is a modular enzyme carrying polymerase and ribonuclease H (RNase H) activities in separable domains. Reverse transcriptase (RT) converts the single-stranded RNA genome of a retrovirus into a double-stranded DNA copy for integration into the host genome. This process requires ribonuclease H as well as RNA- and DNA-directed DNA polymerase activities. Retroviral RNase H is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. Bacterial RNase H 3.1.26.4 from EC catalyses endonucleolytic cleavage to 5'-phosphomonoester acting on RNA-DNA hybrids. The 3D structure of the RNase H domain from diverse bacteria and retroviruses has been solved [, , ]. All have four beta strands and four to five alpha helices. The E. coli RNase H1 protein binds a single Mg2+ ion cofactor in the active site of the enzyme. The divalent cation is bound by the carboxyl groups of four acidic residues, Asp-10, Glu-48, Asp-70, and Asp-134 []. The first three acidic residues are highly conserved in all bacterial and retroviral RNase H sequences. ; GO: 0003676 nucleic acid binding, 0004523 ribonuclease H activity; PDB: 3LP3_B 2KW4_A 3P1G_A 1RIL_A 2RPI_A 4EQJ_G 4EP2_B 3OTY_P 3U3G_D 2ZQB_D ....

>PRK08719 ribonuclease H; Reviewed	Back alignment and domain information

>PRK06548 ribonuclease H; Provisional	Back alignment and domain information

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

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

>cd06222 RnaseH RNase H (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a not sequence-specific manner	Back alignment and domain information

>KOG3752\|consensus	Back alignment and domain information

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

>PRK07708 hypothetical protein; Validated	Back alignment and domain information

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

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

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

>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

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

>cd00304 RT_like RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family	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

>cd01646 RT_Bac_retron_I RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons	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

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

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

>PF13966 zf-RVT: zinc-binding in reverse transcriptase	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

>KOG4768\|consensus	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

>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

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		574
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-08
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	9e-05
3p1g_A		165	Xenotropic murine leukemia virus-related virus (X	8e-07
2zd1_A		557	Reverse transcriptase/ribonuclease H; P51/P66, het	1e-05
2kq2_A		147	Ribonuclease H-related protein; PSI, NESG, protein	2e-05
1mu2_A		555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	4e-05

>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 = 56.0 bits (134), Expect = 3e-08
 Identities = 85/568 (14%), Positives = 154/568 (27%), Gaps = 186/568 (32%)

Query: 134 RDVLLKFYKSFTLPILDYGCY--------IYSSAK-DSVLNKLNTVHHAGIRIATGALRS 184
           +D+L  F  +F   + ++ C         I S  + D ++   + V  +G       L S
Sbjct: 19  KDILSVFEDAF---VDNFDCKDVQDMPKSILSKEEIDHIIMSKDAV--SGTLRLFWTLLS 73

Query: 185 SP--VVSLYVDSGIPPLFLRRSKLMLNY---VSKISASPFNPAQKVLFHQDMSGTIFTVN 239
               +V  +V+  +            NY   +S I      P+     + +    ++  N
Sbjct: 74  KQEEMVQKFVEEVLRI----------NYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDN 123

Query: 240 KP-KPLYV-RFREIANFINVLDSSEIAPYVRFVPPWSNCAPPVDQCLGEGKKSDTAPV-- 295
           +      V R +        L     A  V            +D  LG GK      V  
Sbjct: 124 QVFAKYNVSRLQPYLKLRQALLELRPAKNV-----------LIDGVLGSGKTWVALDVCL 172

Query: 296 ---VFQKMFHEV--INIKYPN---------HTICFT---------DGSKSPDVTGCAFSI 332
              V  KM  ++  +N+K  N           + +          D S +  +     SI
Sbjct: 173 SYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLR--IHSI 230

Query: 333 GDMVQSTLLNPI--NS------IFSAELIAIFL--C--L-----EAIIDSPSNQF----- 370
              ++  L +    N       + +A+    F   C  L     + + D  S        
Sbjct: 231 QAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHIS 290

Query: 371 -------LIVSDSRSALAALANVRFS---------NPLVTKVF--------STWSYLK-- 404
                  L   + +S L    + R           NP    +         +TW   K  
Sbjct: 291 LDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHV 350

Query: 405 LCDKEVSFIWCPSHCGIRGNEIVD--VAAKNPSDLAPS-KLCT--PEDLK-PFIASLMKT 458
            CDK                 I++  +    P++        +  P     P    L+  
Sbjct: 351 NCDKL--------------TTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIP--TILLSL 394

Query: 459 EWQNQWNNVPS--TNKLKSIRPYIKHWNTSNQDRRIKEVIL-TRMRIGHTRLTHNHLFTK 515
            W +   +      NKL       K    S     I  + L  ++++ +    H  +   
Sbjct: 395 IWFDVIKSDVMVVVNKLHKYSLVEKQPKEST--ISIPSIYLELKVKLENEYALHRSIVDH 452

Query: 516 SAPPICQCGAPLS------------VRHILSCHRHD--------------------HIRS 543
              P       L               H+ +    +                    H  +
Sbjct: 453 YNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDST 512

Query: 544 SLHPPPSLGDDEEGVTSLFTYLQQLDIY 571
           + +   S+ +           LQQL  Y
Sbjct: 513 AWNASGSILNT----------LQQLKFY 530

PyMOL of 1vt4

>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

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

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

>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

>1mu2_A HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polymerase, drug design, transferase; 2.35A {Human immunodeficiency virus 2} SCOP: c.55.3.1 e.8.1.2 PDB: 1mu2_B Length = 555	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		574
2qkb_A		154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.83
2kq2_A		147	Ribonuclease H-related protein; PSI, NESG, protein	99.82
3h08_A		146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.8
3qio_A		150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.8
1jl1_A		155	Ribonuclease HI; RNAse HI, protein stability, ther	99.77
3p1g_A		165	Xenotropic murine leukemia virus-related virus (X	99.77
2e4l_A		158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.76
1ril_A		166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.73
3hst_B		141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	99.64
2lsn_A		165	Reverse transcriptase; RNAse H, viral protein; NMR	99.64
3u3g_D		140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	99.63
2zd1_A		557	Reverse transcriptase/ribonuclease H; P51/P66, het	99.63
1mu2_A		555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	99.62
2ehg_A		149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	99.59
1zbf_A		142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	98.87
4htu_A		134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	98.47
3fsi_A		255	RT, reverse transcriptase domain; transferase/DNA	95.9
1rw3_A		455	POL polyprotein; RNA and DNA dependent DNA polymer	94.42
1mu2_A		555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	91.81
2zd1_B		428	P51 RT; P51/P66, hetero dimer, NNRTI, nonnucleosid	90.29
2zd1_A		557	Reverse transcriptase/ribonuclease H; P51/P66, het	89.95

>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=99.83  E-value=1.5e-20  Score=170.66  Aligned_cols=127  Identities=20%  Similarity=0.241  Sum_probs=97.0

Q ss_pred             CCceEEEecCCCCCCC-----eeEEEEecce---eeeeeCCCCccchHHHHHHHHHHHHHHHcCCCCcEEEEeccHHHHH
Q psy11456        310 PNHTICFTDGSKSPDV-----TGCAFSIGDM---VQSTLLNPINSIFSAELIAIFLCLEAIIDSPSNQFLIVSDSRSALA  381 (574)
Q Consensus       310 ~~~~~i~tDGS~~~~~-----~G~~~~~~~~---~~~~~l~~~~sv~~aE~~ai~~al~~~~~~~~~~~~I~~Ds~sa~~  381 (574)
                      .+.+.||||||...++     .|+|++..+.   ..+..++..+|++.||+.|+..||+.+.+.+..++.|+|||+.+++
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            4678999999987542     6889886532   2445666678999999999999999999888899999999999999


Q ss_pred             HHhcC--------CC-Cc--HH-HHHHHHHHHHhhhcCceEEEEEecCCCCCCcchhhhhhhcCCCCC
Q psy11456        382 ALANV--------RF-SN--PL-VTKVFSTWSYLKLCDKEVSFIWCPSHCGIRGNEIVDVAAKNPSDL  437 (574)
Q Consensus       382 ~l~~~--------~~-~~--~~-~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~~Ak~a~~~  437 (574)
                      .|.+.        .. ..  +. .+.+...+..+.. +..|.|.|||||+|++|||.||+|||+|+..
T Consensus        85 ~i~~~~~~w~~~~w~~~~~~~~~n~~l~~~i~~l~~-~~~v~~~~V~~H~g~~~N~~AD~LA~~a~~~  151 (154)
T 2qkb_A           85 GITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQ-GMDIQWMHVPGHSGFIGNEEADRLAREGAKQ  151 (154)
T ss_dssp             HHHTHHHHHHTTTSBCTTSSBCTTHHHHHHHHHHHT-TCEEEEEECCTTSSCHHHHHHHHHHHHHHTC
T ss_pred             hhhhhHHHHHhccccccCCCccccHHHHHHHHHHHc-CCceEEEEccCCCCCHhHHHHHHHHHHHHHh
Confidence            99861        11 11  11 1223333333332 4679999999999999999999999998765

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

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

>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

>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

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

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

>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

>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

>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

>1mu2_A HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polymerase, drug design, transferase; 2.35A {Human immunodeficiency virus 2} SCOP: c.55.3.1 e.8.1.2 PDB: 1mu2_B	Back alignment and structure

>2zd1_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

>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

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		574
d1mu2a1		126	c.55.3.1 (A:430-555) HIV RNase H (Domain of revers	2e-06
d1jl1a_		152	c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli	0.004

>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 = 45.3 bits (106), Expect = 2e-06
 Identities = 23/125 (18%), Positives = 44/125 (35%), Gaps = 8/125 (6%)

Query: 310 PNHTICFTDGSKS--PDVTGCAFSIGDMVQSTLLNPINSIFSAELIAIFLCLEAIIDSPS 367
           P     +TDGS +         +               +   AEL A  +     +    
Sbjct: 5   PGAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKLEQTTNQQAELEAFAMA----LTDSG 60

Query: 368 NQFLIVSDSRSALAALANVRFSNPLVTKVFSTWSYLKLCDKEVSFIWCPSHCGIRGNEIV 427
            +  I+ DS+  +  +A+    +   +K+ +      +  + +   W P+H GI GN+ V
Sbjct: 61  PKVNIIVDSQYVMGIVASQPTESE--SKIVNQIIEEMIKKEAIYVAWVPAHKGIGGNQEV 118

Query: 428 DVAAK 432
           D    
Sbjct: 119 DHLVS 123

PyMOL of d1mu2a1

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

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		574
d1mu2a1		126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.84
d1jl1a_		152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	99.75
d1rila_		147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.75
d1s1ta1		110	HIV RNase H (Domain of reverse transcriptase) {Hum	99.5
d1zbfa1		132	BH0863-like Ribonuclease H {Bacillus halodurans [T	99.01
d1ztwa1		255	MMLV reverse transcriptase {Moloney murine leukemi	95.34
d2zd1b1		424	HIV-1 reverse transcriptase {Human immunodeficienc	87.62
d1mu2a2		427	HIV-1 reverse transcriptase {Human immunodeficienc	84.44

>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=99.84  E-value=2.4e-21  Score=167.55  Aligned_cols=117  Identities=21%  Similarity=0.281  Sum_probs=86.9

Q ss_pred             CCceEEEecCCCCCC-C-eeEEEEecce-eeeeeCCCCccchHHHHHHHHHHHHHHHcCCCCcEEEEeccHHHHHHHhcC
Q psy11456        310 PNHTICFTDGSKSPD-V-TGCAFSIGDM-VQSTLLNPINSIFSAELIAIFLCLEAIIDSPSNQFLIVSDSRSALAALANV  386 (574)
Q Consensus       310 ~~~~~i~tDGS~~~~-~-~G~~~~~~~~-~~~~~l~~~~sv~~aE~~ai~~al~~~~~~~~~~~~I~~Ds~sa~~~l~~~  386 (574)
                      ++...+|||||.... + .|+|++.... .....++ ..|++.||+.||..||+.    ...++.|+|||+.+++.+.+.
T Consensus         5 ~~~~t~YTDGS~~~n~~~~~~g~~~~~~~~~~~~~~-~~tnn~AEl~Ai~~al~~----~~~~i~I~tDS~~v~~~~~~~   79 (126)
T d1mu2a1           5 PGAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKLE-QTTNQQAELEAFAMALTD----SGPKVNIIVDSQYVMGIVASQ   79 (126)
T ss_dssp             TTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEEES-SCCHHHHHHHHHHHHHHT----SCSEEEEEESCHHHHHHHHTC
T ss_pred             CCCcEEEEcCCCCCCCCcEEEEEEecCCCEEEEecC-CCcchHHHHHHHHHHhcc----CCcceEEEechHHHHHHHhcC
Confidence            456789999997653 3 4566665443 3334444 579999999999999875    467899999999999999986


Q ss_pred             CCCc--HHHHHHHHHHHHhhhcCceEEEEEecCCCCCCcchhhhhhhcCCC
Q psy11456        387 RFSN--PLVTKVFSTWSYLKLCDKEVSFIWCPSHCGIRGNEIVDVAAKNPS  435 (574)
Q Consensus       387 ~~~~--~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~~Ak~a~  435 (574)
                      ....  .....   .+..+. ....|.|.|||||+|++|||.||+||++|.
T Consensus        80 ~~~~~~~~~~~---~~~~~~-~~~~v~~~wV~gH~g~~gNe~AD~LA~~ai  126 (126)
T d1mu2a1          80 PTESESKIVNQ---IIEEMI-KKEAIYVAWVPAHKGIGGNQEVDHLVSQGI  126 (126)
T ss_dssp             CSEESCHHHHH---HHHHHH-HCSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             CccccchHHHH---HHHHhh-hcceeEEEEEeCCCCCcchHHHHHHHHhhC
Confidence            5433  22222   222332 246899999999999999999999999874

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

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

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