Citrus Sinensis ID: 009000

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-------

MNFSLCLLGMGLEERVAESCINGHKADCAWTVSVHTFSDITNISPVVFLYLLKECYIHGTCKATRKFRALQQQVSQALCNSPEPGPATFIVRCLYVLPIFGVYSEGFSHLIISALRRHQKTTVNSADSTQAKEIAAYLFLDITGGFVDHDEKLMVKILEAFDVRLTDIEKAITQLKAQNEHRFDTAKTVIEQYIFAMIDSQSYMTAVSLLEHFSIRQSGESFLLKMIQNKEFKAAEKWATFMGKPILLKRLAEKACWDIAEAKTKGDKRLLEYLVYLAMEAGYSEKVDELCERYSLEGFLKTREPEAGFVHSRFLHLKELVVEDIIWVDEVDGLHKAICHIEGCKVVGIDCEWKPNYVKGCKMNKVSIMQIASDEMVFIFDLIKLAEDVPDVLDSCLTRILQSPGILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNVFKEPKGGLSGLAEKILGAGLNKTRRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCSQPTDVSEGHDKIEWKSYIVSHMDNPKKSKKRPTIKKETESGANYH

ccccEEEccccHHHHHHHHcccccccccccEEEEEEccccccccHHHHHHHHHHHHHcccHHHcHHHHHHHHHHHHHHHccccccccEEEEEcccccccccccccccHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHccccccHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHcHHHHHHHccccHHHHHHHHHHHHHccccccHHHHHHcccHHHHcccccccccccccccccccccccccEEEEEcHHHHHHHHHHHHcccEEEEEcccccccccccccccccEEEEEEcccEEEEEccccccccccHHHHHHHHHccccccEEEEEEHHHHHHHHHHHHcccccHHHHHHHHHHHHHcccccccHHHHHHHHccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccHHHHHHHcccccccccccccccccccccccccc

cccEEEEccccccccEcccccccccccccHHEHEEHHcccccccHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHcccccccEEEEEEEEEEEHHcccccHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHcccccHHHEEEEEEEEEEEEcHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHccHHHHHHHHHHHHcHHHHHHHHHHHcccHHHHHHHccHHHHHHHHHHHHHHHcHHHHHHHHHHHccccccccccccccccccccEEEEcccccccEEEEccHHHHHHHHHHHccccEEEEEcccccccccccccccEEEEEEEcccEEEEEEcHHcccccHHHHHHHHHHHHccccEEEEEEccHHHHHHHHHHcccccccHHHHHHHHHHHHHcccccHHHHHHHHHHcccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHccccccccccccccccEEcccccccc

MNFSLCLLGMGLEERVAESCinghkadcawtvsvhtfsditniSPVVFLYLLKECYIHGTCKATRKFRALQQQVSQAlcnspepgpaTFIVRCLYVLpifgvyseGFSHLIISALRRHqkttvnsadSTQAKEIAAYLFLditggfvdhdEKLMVKILEAFDVRLTDIEKAITQLKAQNEHRFDTAKTVIEQYIFAMIDSQSYMTAVSLLEHFSIRQSGESFLLKMIQNKEFKAAEKWATFMGKPILLKRLAEKACWDIAEAKTKGDKRLLEYLVYLAMEAGYSEKVDELCERYSLegflktrepeagfvhSRFLHLKELVVEDIIWVDEVDGLHKAICHIegckvvgidcewkpnyvkgckmnKVSIMQIASDEMVFIFDLIKLAEDVPDVLDSCLTRIlqspgilklgynFQCDIKQLAHsygelecfKHYEMLLDIQNvfkepkgglsGLAEKILGAglnktrrnsnweqrplsqNQLEYAALDAVVLLQIFHHVrscsqptdvseghdkieWKSYIVShmdnpkkskkrptikketesganyh

MNFSLCLLGMGLEERVAESCINGHKADCAWTVSVHTFSDITNISPVVFLYLLKECYIHGTCKATRKFRALQQQVSQALCNSPEPGPATFIVRCLYVLPIFGVYSEGFSHLIISALRRHQKTTVNSADSTQAKEIAAYLFLDITGGFVDHDEKLMVKILEAFDVRLTDIEKAITQlkaqnehrfdtAKTVIEQYIFAMIDSQSYMTAVSLLEHFSIRQSGESFLLKMIQNKEFKAAEKWATFMGKPILLKRLAEKACWDIaeaktkgdkrlLEYLVYLAMEAGYSEKVDELCERYSLEGFLKTREPEAGFVHSRFLHLKELVVEDIIWVDEVDGLHKAICHIEGCKVVGIDCEWKPNYVKGCKMNKVSIMQIASDEMVFIFDLIKLAEDVPDVLDSCLTRILQSPGILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNVFKEPKGGLSGLAEKILGAGLNKTRRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRscsqptdvseghdKIEWKSyivshmdnpkkskkrptikketesganyh

MNFSLCLLGMGLEERVAESCINGHKADCAWTVSVHTFSDITNISPVVFLYLLKECYIHGTCKATRKFRALQQQVSQALCNSPEPGPATFIVRCLYVLPIFGVYSEGFSHLIISALRRHQKTTVNSADSTQAKEIAAYLFLDITGGFVDHDEKLMVKILEAFDVRLTDIEKAITQLKAQNEHRFDTAKTVIEQYIFAMIDSQSYMTAVSLLEHFSIRQSGESFLLKMIQNKEFKAAEKWATFMGKPILLKRLAEKACWDIAEAKTKGDKRLLEYLVYLAMEAGYSEKVDELCERYSLEGFLKTREPEAGFVHSRFLHLKELvvediiwvdevdGLHKAICHIEGCKVVGIDCEWKPNYVKGCKMNKVSIMQIASDEMVFIFDLIKLAEDVPDVLDSCLTRILQSPGILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNVFKEPKGGLSGLAEKILGAGLNKTRRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCSQPTDVSEGHDKIEWKSYIVSHMDNPkkskkrptikkETESGANYH

**FSLCLLGMGLEERVAESCINGHKADCAWTVSVHTFSDITNISPVVFLYLLKECYIHGTCKATRKFRALQQQVSQALCNSPEPGPATFIVRCLYVLPIFGVYSEGFSHLIISALRRHQKTTV*****TQAKEIAAYLFLDITGGFVDHDEKLMVKILEAFDVRLTDIEKAITQLKAQNEHRFDTAKTVIEQYIFAMIDSQSYMTAVSLLEHFSIRQSGESFLLKMIQNKEFKAAEKWATFMGKPILLKRLAEKACWDIAEAKTKGDKRLLEYLVYLAMEAGYSEKVDELCERYSLEGFLKTREPEAGFVHSRFLHLKELVVEDIIWVDEVDGLHKAICHIEGCKVVGIDCEWKPNYVKGCKMNKVSIMQIASDEMVFIFDLIKLAEDVPDVLDSCLTRILQSPGILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNVFKEPKGGLSGLAEKILGAGLN***************NQLEYAALDAVVLLQIFHHVRSCSQPT*****HDKIEWKSYIV**************************

***SLC*LGMGLEER************CAWTVSVHTFSDITNISPVVFLYLLKECYIHGTCKATRKFRALQQQVSQALCNSPEPGPATFIVRCLYVLPIFGVYSEGFSHLIISALRRHQKT*VNSADSTQAKEIAAYLFLDITGGFVDHDEKLMVKILEAFDVRLTDIEKAITQLKAQNEHRFDTAKTVIEQYIFAMIDSQSYMTAVSLLEHFSIRQSGESFLL*MI*******A**WATFMG*******LAEKACWDIAEAKTKGDKRLLEYLVYLAME*G****VDELCERYSLEGFLKTREPEAGFVHSRFLHLKELVVEDIIWVDEVDGLHKAICHIEGCKVVGIDCEWKPNYVKGCKMNKVSIMQIASDEMVFIFDLIKLAEDVPDVLDSCLTRILQSPGILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNVFKEPKGGLSGLAEKILGAGLNKTRRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRS***********************************************

*NFSLCLLGMGLEERVAESCINGHKADCAWTVSVHTFSDITNISPVVFLYLLKECYIHGTCKATRKFRALQQQVSQALCNSPEPGPATFIVRCLYVLPIFGVYSEGFSHLIISALRRHQKTTVNSADSTQAKEIAAYLFLDITGGFVDHDEKLMVKILEAFDVRLTDIEKAITQLKAQNEHRFDTAKTVIEQYIFAMIDSQSYMTAVSLLEHFSIRQSGESFLLKMIQNKEFKAAEKWATFMGKPILLKRLAEKACWDIAEAKTKGDKRLLEYLVYLAMEAGYSEKVDELCERYSLEGFLKTREPEAGFVHSRFLHLKELVVEDIIWVDEVDGLHKAICHIEGCKVVGIDCEWKPNYVKGCKMNKVSIMQIASDEMVFIFDLIKLAEDVPDVLDSCLTRILQSPGILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNVFKEPKGGLSGLAEKILGAGLNKTRRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCSQPTDVSEGHDKIEWKSYIVSHMDNPK*******************

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SSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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MNFSLCLLGMGLEERVAESCINGHKADCAWTVSVHTFSDITNISPVVFLYLLKECYIHGTCKATRKFRALQQQVSQALCNSPEPGPATFIVRCLYVLPIFGVYSEGFSHLIISALRRHQKTTVNSADSTQAKEIAAYLFLDITGGFVDHDEKLMVKIxxxxxxxxxxxxxxxxxxxxxNEHRFDTAKTVIEQYIFAMIDSQSYMTAVSLLEHFSIRQSGESFLLKMIQNKEFKAAEKWATFMGKPILLKRLAEKACWDIAEAKTKGDKRLLEYLVYLAMEAGYSEKVDELCERYSLEGFLKTREPEAGFVHSRFLHLKELVVEDIIWVDEVDGLHKAICHIEGCKVVGIDCEWKPNYVKGCKMNKVSIMQIASDEMVFIFDLIKLAEDVPDVLDSCLTRILQSPGILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNVFKEPKGGLSGLAEKILGAGLNKTRRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCSQPTDVSEGHDKIEWKSYIVSHMDNPKKSKKRPTIKKETESGANYH

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		547	2.2.26 [Sep-21-2011]
Q8N9H8		876	Probable exonuclease mut-	yes	no	0.358	0.223	0.296	1e-16
P34607		910	Probable exonuclease mut-	yes	no	0.343	0.206	0.282	1e-11
Q179T2		719	Probable exonuclease mut-	N/A	no	0.305	0.232	0.269	3e-11
Q84LH3		288	Werner Syndrome-like exon	no	no	0.259	0.493	0.316	2e-10
Q9VIF1		625	Probable exonuclease mut-	yes	no	0.314	0.275	0.267	4e-10
O67779		574	DNA polymerase I OS=Aquif	yes	no	0.338	0.322	0.235	1e-09
Q9NVH0		621	Exonuclease 3'-5' domain-	no	no	0.351	0.309	0.290	3e-07
O09053		1401	Werner syndrome ATP-depen	no	no	0.263	0.102	0.308	3e-07
P34603		784	Uncharacterized protein Z	no	no	0.323	0.225	0.230	1e-06
Q14191		1432	Werner syndrome ATP-depen	no	no	0.261	0.099	0.293	2e-06

>sp\|Q8N9H8\|MUT7_HUMAN Probable exonuclease mut-7 homolog OS=Homo sapiens GN=EXD3 PE=1 SV=3	Back alignment and function desciption

 Score = 88.6 bits (218), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 67/226 (29%), Positives = 110/226 (48%), Gaps = 30/226 (13%)

Query: 339 CHIEGCKVVGIDCEWKPNYVKGCKMNKVSIMQIASDEMVFIFDLIKLAEDV----PDVLD 394
           CH    +VVG+D EW P +V G +  + S++Q+A +  VF+ D++ L++           
Sbjct: 392 CH----QVVGVDVEWTPVFVAGGR-PRPSLLQVAVEGHVFLLDVLALSQPPTGQGAQAFS 446

Query: 395 SCLTRILQSPGILKLGYNFQCDIKQLAHS-----YGELECFKHYEMLL--DIQNVFKEPK 447
             + ++L  P I KLGY    D+++L  S     + E +     ++LL      V   P 
Sbjct: 447 RLVAQLLSDPSITKLGYGMVGDLQKLGTSCPALAHVEKQILGGMDLLLVHRQMRVASVPA 506

Query: 448 G---------GLSGLAEKILGAGLNKTRRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHV 498
                     GLS L +++LG  L+KT++ SNW++RPL + Q+ YAA DA  LL++  H 
Sbjct: 507 PAVDRARELRGLSLLVQQVLGTALDKTQQLSNWDRRPLCEEQVIYAAADAYCLLEV--HQ 564

Query: 499 RSCSQPTDVSEGHDKIEWKSYIVSHMDNPKKSKKRPTIKKETESGA 544
             C +P       D     S    H + P  ++K P ++K +   A
Sbjct: 565 ALCREPARFHLSEDLA--GSRRPRHRERP-GARKPPGLQKASAPAA 607

Homo sapiens (taxid: 9606)
EC: 3EC: .EC: 1EC: .EC: -EC: .EC: -

>sp\|P34607\|MUT7_CAEEL Probable exonuclease mut-7 OS=Caenorhabditis elegans GN=mut-7 PE=1 SV=1	Back alignment and function description

>sp\|Q179T2\|MUT7_AEDAE Probable exonuclease mut-7 homolog OS=Aedes aegypti GN=AAEL005527 PE=3 SV=1	Back alignment and function description

>sp\|Q84LH3\|WEX_ARATH Werner Syndrome-like exonuclease OS=Arabidopsis thaliana GN=WEX PE=1 SV=1	Back alignment and function description

>sp\|Q9VIF1\|MUT7_DROME Probable exonuclease mut-7 homolog OS=Drosophila melanogaster GN=CG9247 PE=1 SV=1	Back alignment and function description

>sp\|O67779\|DPO1_AQUAE DNA polymerase I OS=Aquifex aeolicus (strain VF5) GN=polA PE=3 SV=1	Back alignment and function description

>sp\|Q9NVH0\|EXD2_HUMAN Exonuclease 3'-5' domain-containing protein 2 OS=Homo sapiens GN=EXD2 PE=1 SV=2	Back alignment and function description

>sp\|O09053\|WRN_MOUSE Werner syndrome ATP-dependent helicase homolog OS=Mus musculus GN=Wrn PE=1 SV=3	Back alignment and function description

>sp\|P34603\|YO63_CAEEL Uncharacterized protein ZK1098.3 OS=Caenorhabditis elegans GN=ZK1098.3 PE=4 SV=2	Back alignment and function description

>sp\|Q14191\|WRN_HUMAN Werner syndrome ATP-dependent helicase OS=Homo sapiens GN=WRN PE=1 SV=2	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		547
255542852		570	3-5 exonuclease, putative [Ricinus commu	0.948	0.910	0.694	0.0
224123698		552	predicted protein [Populus trichocarpa]	0.936	0.927	0.679	0.0
225450638		586	PREDICTED: uncharacterized protein LOC10	0.939	0.877	0.608	0.0
449520229		580	PREDICTED: uncharacterized LOC101205010	0.943	0.889	0.598	0.0
449435970		580	PREDICTED: uncharacterized protein LOC10	0.943	0.889	0.598	0.0
356576837		571	PREDICTED: uncharacterized protein LOC10	0.941	0.901	0.599	0.0
356535024		566	PREDICTED: uncharacterized protein LOC10	0.941	0.909	0.583	0.0
388502398		553	unknown [Medicago truncatula]	0.908	0.898	0.581	1e-176
357441841		553	hypothetical protein MTR_1g083820 [Medic	0.908	0.898	0.579	1e-176
334183377		589	3'-5' exonuclease domain-containing prot	0.974	0.904	0.564	1e-173

>gi\|255542852\|ref\|XP_002512489.1\| 3-5 exonuclease, putative [Ricinus communis] gi\|223548450\|gb\|EEF49941.1\| 3-5 exonuclease, putative [Ricinus communis]	Back alignment and taxonomy information

 Score =  791 bits (2042), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 391/563 (69%), Positives = 454/563 (80%), Gaps = 44/563 (7%)

Query: 10  MGLEERVAESCINGHKADCAWTVSVHTFSDITNISPVVFLYLLKECYIHGTCKATRKFRA 69
           MGLEE +    I   KA+   T+ +H FSD+T +SPVVFLYLLKECYIHG+CKAT+KFRA
Sbjct: 1   MGLEETID---IKKDKANQTLTICLHAFSDLTYVSPVVFLYLLKECYIHGSCKATKKFRA 57

Query: 70  LQQQVSQALCNSPEPGPATFIVRCLYVLPIFGVYSEGFSHLIISALRRHQKTTVNSADST 129
           LQQQV Q L NSP+ GPATF++ CL+VLPIFG+YSEGFSHLI+SALRR  K +  S D+ 
Sbjct: 58  LQQQVHQVLDNSPKSGPATFVIHCLHVLPIFGLYSEGFSHLIVSALRRFLKLSPTSEDTL 117

Query: 130 QAKEIAAYLFLDITGGFVDHDEKLMVKILEAFDVRLTDIEKAITQLKAQNEHRFDTAKTV 189
           QAK +AA LFLDI GG VDHDE+L++KI+EAFDV+LT+IE AI +LKA+N++RFDTAK  
Sbjct: 118 QAKGLAAQLFLDIVGGLVDHDERLLIKIVEAFDVKLTNIEAAIQRLKARNDNRFDTAKKF 177

Query: 190 IEQYIFAMIDSQSYMTAVSLLEHFSIRQSGESFLLKMIQNKEFKAAEKWATFMGKPIL-- 247
           +EQYIF +++SQSYMTAV+LLEHFSIRQSG+SFLLKM+ NK+ +AAEKWATFMGKP+L  
Sbjct: 178 VEQYIFKLVESQSYMTAVTLLEHFSIRQSGQSFLLKMMDNKQSQAAEKWATFMGKPMLCL 237

Query: 248 ----------LKRLAE----------------------------KACWDIAEAKTKGDKR 269
                     LK   E                            KA WD+AEAKT GD++
Sbjct: 238 LVQEYVDRNMLKHAYETIKKNNLKEEFPDIYHKCKESLLKKLAKKALWDLAEAKTHGDRQ 297

Query: 270 LLEYLVYLAMEAGYSEKVDELCERYSLEGFLKTREPEAGFVHSRFLHLKELVVEDIIWVD 329
           L+EYLVYLAMEAGYSEKVDELC+RYSLEGFLK +E E+   H RFL L E  VEDI+WVD
Sbjct: 298 LVEYLVYLAMEAGYSEKVDELCDRYSLEGFLKGKELES-LPHGRFLQLNEFAVEDIVWVD 356

Query: 330 EVDGLHKAICHIEGCKVVGIDCEWKPNYVKGCKMNKVSIMQIASDEMVFIFDLIKLAEDV 389
           EVDGL  A  HIEGCKVVG+DCEWKPN+ KG K NKVSIMQIASD+MVFIFDLIKL EDV
Sbjct: 357 EVDGLCGATGHIEGCKVVGLDCEWKPNFEKGSKPNKVSIMQIASDKMVFIFDLIKLFEDV 416

Query: 390 PDVLDSCLTRILQSPGILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNVFKEPKGG 449
           PD LD+CLTRILQSP ILKLGYNFQCD KQLA SYGEL+CFKHYEMLLDIQNV +EP+GG
Sbjct: 417 PDTLDNCLTRILQSPRILKLGYNFQCDTKQLAQSYGELKCFKHYEMLLDIQNVCREPRGG 476

Query: 450 LSGLAEKILGAGLNKTRRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCSQPTDVSE 509
           LSGLA+K+LGAGLNKTRRNSNWEQRPLSQ+QLEYAALDAVVL+ IFHH+R+ S+P D+SE
Sbjct: 477 LSGLAKKLLGAGLNKTRRNSNWEQRPLSQHQLEYAALDAVVLIHIFHHIRNHSEPADISE 536

Query: 510 GHDKIEWKSYIVSHMDNPKKSKK 532
           GH+KI+WKSYIVSHMDNP+K KK
Sbjct: 537 GHEKIKWKSYIVSHMDNPQKGKK 559

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|224123698\|ref\|XP_002330186.1\| predicted protein [Populus trichocarpa] gi\|222871642\|gb\|EEF08773.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|225450638\|ref\|XP_002278277.1\| PREDICTED: uncharacterized protein LOC100254615 [Vitis vinifera] gi\|296089752\|emb\|CBI39571.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|449520229\|ref\|XP_004167136.1\| PREDICTED: uncharacterized LOC101205010 [Cucumis sativus]	Back alignment and taxonomy information

>gi\|449435970\|ref\|XP_004135767.1\| PREDICTED: uncharacterized protein LOC101205010 [Cucumis sativus]	Back alignment and taxonomy information

>gi\|356576837\|ref\|XP_003556536.1\| PREDICTED: uncharacterized protein LOC100797818 [Glycine max]	Back alignment and taxonomy information

>gi\|356535024\|ref\|XP_003536049.1\| PREDICTED: uncharacterized protein LOC100788595 [Glycine max]	Back alignment and taxonomy information

>gi\|388502398\|gb\|AFK39265.1\| unknown [Medicago truncatula]	Back alignment and taxonomy information

>gi\|357441841\|ref\|XP_003591198.1\| hypothetical protein MTR_1g083820 [Medicago truncatula] gi\|355480246\|gb\|AES61449.1\| hypothetical protein MTR_1g083820 [Medicago truncatula]	Back alignment and taxonomy information

>gi\|334183377\|ref\|NP_176027.2\| 3'-5' exonuclease domain-containing protein [Arabidopsis thaliana] gi\|332195255\|gb\|AEE33376.1\| 3'-5' exonuclease domain-containing protein [Arabidopsis thaliana]	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		547
UNIPROTKB\|E1BWV5		725	EXD3 "Uncharacterized protein"	0.127	0.096	0.402	2.8e-13
ZFIN\|ZDB-GENE-091204-349		861	exd3 "exonuclease 3'-5' domain	0.085	0.054	0.553	2e-10
TAIR\|locus:2119525		288	WRNEXO "Werner syndrome-like e	0.252	0.479	0.331	2.7e-10
UNIPROTKB\|F1RVW3		863	EXD3 "Uncharacterized protein"	0.206	0.130	0.335	1.8e-08
UNIPROTKB\|E1BEQ0		628	EXD2 "Uncharacterized protein"	0.329	0.286	0.290	1.9e-08
UNIPROTKB\|F1Q045		850	EXD3 "Uncharacterized protein"	0.208	0.134	0.348	2.3e-08
RGD\|1564788		1448	Wrn "Werner syndrome, RecQ hel	0.290	0.109	0.304	3.4e-08
WB\|WBGene00013256		710	Y57A10A.13 [Caenorhabditis ele	0.085	0.066	0.489	4.4e-08
UNIPROTKB\|G3X7J6		724	G3X7J6 "Uncharacterized protei	0.206	0.156	0.328	4.9e-08
UNIPROTKB\|F1NAR0		1367	F1NAR0 "Uncharacterized protei	0.266	0.106	0.308	5.3e-08

UNIPROTKB\|E1BWV5 EXD3 "Uncharacterized protein" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

 Score = 141 (54.7 bits), Expect = 2.8e-13, Sum P(2) = 2.8e-13
 Identities = 29/72 (40%), Positives = 43/72 (59%)

Query:   444 KEPKGGLSGLAEKILGAGLNKTRRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCSQ 503
             ++P+ GLS L + +LG  L+KT + SNWE+RPL + Q+ YAA DA  LL+++  +  C  
Sbjct:   510 RQPEKGLSLLVQHVLGKPLDKTEQMSNWEKRPLREEQILYAASDAYCLLEVYEKL--CKD 567

Query:   504 PTDVSEGHDKIE 515
             P       D  E
Sbjct:   568 PESFGLSSDLTE 579

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0008408 "3'-5' exonuclease activity" evidence=IEA

ZFIN\|ZDB-GENE-091204-349 exd3 "exonuclease 3'-5' domain containing 3" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

TAIR\|locus:2119525 WRNEXO "Werner syndrome-like exonuclease" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

UNIPROTKB\|F1RVW3 EXD3 "Uncharacterized protein" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

UNIPROTKB\|E1BEQ0 EXD2 "Uncharacterized protein" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|F1Q045 EXD3 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

RGD\|1564788 Wrn "Werner syndrome, RecQ helicase-like" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

 Score = 164 (62.8 bits), Expect = 3.4e-08, P = 3.4e-08
 Identities = 53/174 (30%), Positives = 85/174 (48%)

Query:   340 HIEGCKVVGIDCEWKPNYVKGCKMNKVSIMQIA-SDEMVFIFDLIKLAEDVPDVLDSCLT 398
             H+    VVG D EW P Y +G K ++V+++Q+  S+   ++F +  ++     V    L 
Sbjct:    73 HLSDGDVVGFDMEWPPIYKQG-KRSRVAVIQLCVSESKCYLFHISSMS-----VFPQGLK 126

Query:   399 RILQSPGILKLGYNFQCDIKQLAHSYG-ELECFKHYEMLLDIQN-VFK-EPKGGLSGLAE 455
              +L++  I K G   + D  +L   +  +LE F     L D+ N   K      L+GL +
Sbjct:   127 MLLENKSIRKAGVGIEGDQWKLLRDFDVKLESFVE---LTDVANRKLKCAETWSLNGLVK 183

Query:   456 KILGAGL--NKTRRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCSQPTDV 507
              +LG  L  +K+ R SNW   PLS++Q  YAA DA   L I+  + +      V
Sbjct:   184 HVLGKQLLKDKSIRCSNWSDFPLSEDQKLYAATDAYAGLIIYQKLENLGDAVQV 237

GO:0000287 "magnesium ion binding" evidence=ISO

GO:0000403 "Y-form DNA binding" evidence=ISO

GO:0000405 "bubble DNA binding" evidence=ISO

GO:0000723 "telomere maintenance" evidence=ISO

GO:0000731 "DNA synthesis involved in DNA repair" evidence=ISO

GO:0001302 "replicative cell aging" evidence=ISO

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003677 "DNA binding" evidence=ISO

GO:0003678 "DNA helicase activity" evidence=ISO

GO:0004003 "ATP-dependent DNA helicase activity" evidence=ISO

GO:0004386 "helicase activity" evidence=ISO

GO:0004527 "exonuclease activity" evidence=ISO

GO:0005524 "ATP binding" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

GO:0005654 "nucleoplasm" evidence=ISO

GO:0005730 "nucleolus" evidence=ISO

GO:0005813 "centrosome" evidence=ISO

GO:0006200 "ATP catabolic process" evidence=ISO

GO:0006259 "DNA metabolic process" evidence=ISO

GO:0006260 "DNA replication" evidence=IEA;ISO

GO:0006281 "DNA repair" evidence=IEA

GO:0006284 "base-excision repair" evidence=ISO

GO:0006302 "double-strand break repair" evidence=ISO

GO:0006310 "DNA recombination" evidence=IEA

GO:0006974 "response to DNA damage stimulus" evidence=ISO

GO:0006979 "response to oxidative stress" evidence=ISO

GO:0007569 "cell aging" evidence=ISO

GO:0008408 "3'-5' exonuclease activity" evidence=IEA;ISO

GO:0009267 "cellular response to starvation" evidence=ISO

GO:0009378 "four-way junction helicase activity" evidence=ISO

GO:0010225 "response to UV-C" evidence=ISO

GO:0010259 "multicellular organismal aging" evidence=ISO

GO:0016887 "ATPase activity" evidence=ISO

GO:0030145 "manganese ion binding" evidence=ISO

GO:0031297 "replication fork processing" evidence=ISO

GO:0032066 "nucleolus to nucleoplasm transport" evidence=ISO

GO:0032403 "protein complex binding" evidence=ISO

GO:0032508 "DNA duplex unwinding" evidence=ISO

GO:0040009 "regulation of growth rate" evidence=ISO

GO:0042803 "protein homodimerization activity" evidence=ISO

GO:0042981 "regulation of apoptotic process" evidence=ISO

GO:0043138 "3'-5' DNA helicase activity" evidence=ISO

GO:0043140 "ATP-dependent 3'-5' DNA helicase activity" evidence=IEA

GO:0051345 "positive regulation of hydrolase activity" evidence=ISO

GO:0051880 "G-quadruplex DNA binding" evidence=ISO

GO:0071480 "cellular response to gamma radiation" evidence=ISO

GO:0032389 "MutLalpha complex" evidence=ISO

WB\|WBGene00013256 Y57A10A.13 [Caenorhabditis elegans (taxid:6239)]	Back alignment and assigned GO terms

UNIPROTKB\|G3X7J6 G3X7J6 "Uncharacterized protein" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|F1NAR0 F1NAR0 "Uncharacterized protein" [Gallus gallus (taxid:9031)]	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 Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		547
cd06146		193	cd06146, mut-7_like_exo, DEDDy 3'-5' exonuclease d	3e-57
cd06141		170	cd06141, WRN_exo, DEDDy 3'-5' exonuclease domain o	4e-36
pfam01612		172	pfam01612, DNA_pol_A_exo1, 3'-5' exonuclease	8e-21
cd06142		178	cd06142, RNaseD_exo, DEDDy 3'-5' exonuclease domai	1e-19
cd06129		161	cd06129, RNaseD_like, DEDDy 3'-5' exonuclease doma	4e-15
COG0349		361	COG0349, Rnd, Ribonuclease D [Translation, ribosom	8e-15
smart00474		172	smart00474, 35EXOc, 3'-5' exonuclease	7e-14
cd09018		150	cd09018, DEDDy_polA_RNaseD_like_exo, DEDDy 3'-5' e	5e-11
cd06148		197	cd06148, Egl_like_exo, DEDDy 3'-5' exonuclease dom	5e-10
cd06147		192	cd06147, Rrp6p_like_exo, DEDDy 3'-5' exonuclease d	2e-09
TIGR01388		367	TIGR01388, rnd, ribonuclease D	6e-07
PRK10829		373	PRK10829, PRK10829, ribonuclease D; Provisional	4e-04

>gnl\|CDD\|176655 cd06146, mut-7_like_exo, DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins	Back alignment and domain information

 Score =  189 bits (482), Expect = 3e-57
 Identities = 69/195 (35%), Positives = 117/195 (60%), Gaps = 18/195 (9%)

Query: 322 VEDIIWVDEVDGLHKAICHIEGCKVVGIDCEWKPNYVKGCKMNKVSIMQIASDEMVFIFD 381
           +  +   +E++ L  A+  +E  +VVGID EWKP+++      +V+I+Q+A+++ VF+ D
Sbjct: 1   IHIVDSEEELEALLLAL-SLEAGRVVGIDSEWKPSFLGDSD-PRVAILQLATEDEVFLLD 58

Query: 382 LIKLAEDVPDVLDSCLTRILQSPGILKLGYNFQCDIKQLAHSYGELEC-FKHYEMLLDIQ 440
           L+ L     +  D  L R+ + P +LKLG+ F+ D+K L+ SY  L+C F+  + +LD+Q
Sbjct: 59  LLALENLESEDWDRLLKRLFEDPDVLKLGFGFKQDLKALSASYPALKCMFERVQNVLDLQ 118

Query: 441 NVFKEPK---------------GGLSGLAEKILGAGLNKTRRNSNWEQRPLSQNQLEYAA 485
           N+ KE +                GL+ L +++LG  L+K+ + SNWE+RPL + Q+ YAA
Sbjct: 119 NLAKELQKSDMGRLKGNLPSKTKGLADLVQEVLGKPLDKSEQCSNWERRPLREEQILYAA 178

Query: 486 LDAVVLLQIFHHVRS 500
           LDA  LL++F  +  
Sbjct: 179 LDAYCLLEVFDKLLE 193

The mut-7 subfamily is composed of Caenorhabditis elegans mut-7 and similar proteins found in plants and metazoans. Mut-7 is implicated in posttranscriptional gene silencing. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs, termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Length = 193

>gnl\|CDD\|176653 cd06141, WRN_exo, DEDDy 3'-5' exonuclease domain of WRN and similar proteins	Back alignment and domain information

>gnl\|CDD\|216604 pfam01612, DNA_pol_A_exo1, 3'-5' exonuclease	Back alignment and domain information

>gnl\|CDD\|176654 cd06142, RNaseD_exo, DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins	Back alignment and domain information

>gnl\|CDD\|176650 cd06129, RNaseD_like, DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins	Back alignment and domain information

>gnl\|CDD\|223426 COG0349, Rnd, Ribonuclease D [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>gnl\|CDD\|214681 smart00474, 35EXOc, 3'-5' exonuclease	Back alignment and domain information

>gnl\|CDD\|176656 cd09018, DEDDy_polA_RNaseD_like_exo, DEDDy 3'-5' exonuclease domain of family-A DNA polymerases, RNase D, WRN, and similar proteins	Back alignment and domain information

>gnl\|CDD\|99851 cd06148, Egl_like_exo, DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins	Back alignment and domain information

>gnl\|CDD\|99850 cd06147, Rrp6p_like_exo, DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen 100kDa, and similar proteins	Back alignment and domain information

>gnl\|CDD\|130455 TIGR01388, rnd, ribonuclease D	Back alignment and domain information

>gnl\|CDD\|236771 PRK10829, PRK10829, ribonuclease D; Provisional	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		547
KOG2207		617	consensus Predicted 3'-5' exonuclease [Replication	100.0
cd06146		193	mut-7_like_exo DEDDy 3'-5' exonuclease domain of C	99.94
cd06129		161	RNaseD_like DEDDy 3'-5' exonuclease domain of RNas	99.92
cd06141		170	WRN_exo DEDDy 3'-5' exonuclease domain of WRN and	99.9
PRK10829		373	ribonuclease D; Provisional	99.89
PF01612		176	DNA_pol_A_exo1: 3'-5' exonuclease; InterPro: IPR00	99.89
cd06148		197	Egl_like_exo DEDDy 3'-5' exonuclease domain of Dro	99.87
TIGR01388		367	rnd ribonuclease D. This model describes ribonucle	99.85
COG0349		361	Rnd Ribonuclease D [Translation, ribosomal structu	99.83
PRK05755		880	DNA polymerase I; Provisional	99.7
cd06142		178	RNaseD_exo DEDDy 3'-5' exonuclease domain of Ribon	99.68
smart00474		172	35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proo	99.62
cd06147		192	Rrp6p_like_exo DEDDy 3'-5' exonuclease domain of y	99.59
TIGR00593		887	pola DNA polymerase I. This family is based on the	99.55
cd00007		155	35EXOc 3'-5' exonuclease. The 35EXOc domain is res	99.48
cd09018		150	DEDDy_polA_RNaseD_like_exo DEDDy 3'-5' exonuclease	99.46
KOG2206		687	consensus Exosome 3'-5' exoribonuclease complex, s	99.35
cd06140		178	DNA_polA_I_Bacillus_like_exo inactive DEDDy 3'-5'	99.29
COG0749		593	PolA DNA polymerase I - 3'-5' exonuclease and poly	99.29
cd06139		193	DNA_polA_I_Ecoli_like_exo DEDDy 3'-5' exonuclease	99.19
PRK14975		553	bifunctional 3'-5' exonuclease/DNA polymerase; Pro	98.94
cd06128		151	DNA_polA_exo DEDDy 3'-5' exonuclease domain of fam	98.45
KOG4373		319	consensus Predicted 3'-5' exonuclease [General fun	97.94
cd06149		157	ISG20 DEDDh 3'-5' exonuclease domain of Interferon	96.12
cd06125		96	DnaQ_like_exo DnaQ-like (or DEDD) 3'-5' exonucleas	95.95
cd06137		161	DEDDh_RNase DEDDh 3'-5' exonuclease domain of the	95.94
PRK08517		257	DNA polymerase III subunit epsilon; Provisional	95.36
KOG2249		280	consensus 3'-5' exonuclease [Replication, recombin	95.31
cd06144		152	REX4_like DEDDh 3'-5' exonuclease domain of RNA ex	94.98
PRK06310		250	DNA polymerase III subunit epsilon; Validated	94.83
PRK07740		244	hypothetical protein; Provisional	94.82
PRK06063		313	DNA polymerase III subunit epsilon; Provisional	94.74
PRK07883		557	hypothetical protein; Validated	94.72
PRK07942		232	DNA polymerase III subunit epsilon; Provisional	94.61
cd06143		174	PAN2_exo DEDDh 3'-5' exonuclease domain of the euk	94.15
PRK05711		240	DNA polymerase III subunit epsilon; Provisional	94.12
cd06131		167	DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonucl	93.6
TIGR01406		225	dnaQ_proteo DNA polymerase III, epsilon subunit, P	93.6
TIGR00573		217	dnaq exonuclease, DNA polymerase III, epsilon subu	93.15
cd06130		156	DNA_pol_III_epsilon_like an uncharacterized bacter	92.95
PRK07246		820	bifunctional ATP-dependent DNA helicase/DNA polyme	92.87
PRK09145		202	DNA polymerase III subunit epsilon; Validated	92.85
cd05160		199	DEDDy_DNA_polB_exo DEDDy 3'-5' exonuclease domain	92.68
cd06145		150	REX1_like DEDDh 3'-5' exonuclease domain of RNA ex	92.65
TIGR01405		1213	polC_Gram_pos DNA polymerase III, alpha chain, Gra	92.53
PRK06807		313	DNA polymerase III subunit epsilon; Validated	92.5
smart00479		169	EXOIII exonuclease domain in DNA-polymerase alpha	92.02
PRK09146		239	DNA polymerase III subunit epsilon; Validated	91.86
TIGR01407		850	dinG_rel DnaQ family exonuclease/DinG family helic	91.39
PRK06309		232	DNA polymerase III subunit epsilon; Validated	90.28
cd05780		195	DNA_polB_Kod1_like_exo DEDDy 3'-5' exonuclease dom	90.17
PRK08074		928	bifunctional ATP-dependent DNA helicase/DNA polyme	89.63
cd06136		177	TREX1_2 DEDDh 3'-5' exonuclease domain of three pr	89.31
cd05781		188	DNA_polB_B3_exo DEDDy 3'-5' exonuclease domain of	88.87
PRK05601		377	DNA polymerase III subunit epsilon; Validated	86.76
TIGR01298		200	RNaseT ribonuclease T. in gamma-subdivision Proteo	85.59
cd06134		189	RNaseT DEDDh 3'-5' exonuclease domain of RNase T.	85.24
PRK07983		219	exodeoxyribonuclease X; Provisional	84.74
PRK07247		195	DNA polymerase III subunit epsilon; Validated	84.18
PRK06195		309	DNA polymerase III subunit epsilon; Validated	82.31
PRK09182		294	DNA polymerase III subunit epsilon; Validated	82.03
PF13482		164	RNase_H_2: RNase_H superfamily; PDB: 1TKD_A 1TK5_A	81.71
COG2176		1444	PolC DNA polymerase III, alpha subunit (gram-posit	81.34
PRK11779		476	sbcB exonuclease I; Provisional	81.32
PRK05168		211	ribonuclease T; Provisional	81.12
cd05785		207	DNA_polB_like2_exo Uncharacterized bacterial subgr	80.63

>KOG2207 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]	Back alignment and domain information

Probab=100.00  E-value=1.3e-43  Score=381.30  Aligned_cols=520  Identities=27%  Similarity=0.368  Sum_probs=411.3

Q ss_pred             ccchhhhhhhhcccCCccccceEeeeecccCCCcchHHHHHHHHhhhhcccchhchhHHHHHHHHHHHhhCCCCCCCcee
Q 009000           10 MGLEERVAESCINGHKADCAWTVSVHTFSDITNISPVVFLYLLKECYIHGTCKATRKFRALQQQVSQALCNSPEPGPATF   89 (547)
Q Consensus        10 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   89 (547)
                      ||.+....++++...+.+++.+.|.|.+|+.++++++||.+..|+||-+++-+.+.+|..++.+.|.+.++.|+++|+++
T Consensus         1 M~~~s~~~~l~~a~~e~~e~N~~~~~~~s~~k~~~~i~~~~~~k~~~~~~i~ak~~eff~~~~~s~~~~~g~~~~~~lll   80 (617)
T KOG2207|consen    1 MGNTSALQDLHNAEYERKEANLKALLVKSTDKYLKDIVFGSFSKKFDESTIIAKDAEFFPLDYESHIYANGFPPVNPLLL   80 (617)
T ss_pred             CCCchhhhhccchhhhhhhhhHHHHHhhhhhhHHHHhhhhhhhcccchhhHHHhhHHHHHHHHHHHHHhcCCCCCChHHH
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeeeeeeccccc-ccccchhHHHHHHHHhhhcc---cCCccchhHHHHHHHH-HHHHHhcCCCCChhHHHHHHH-HHhcc
Q 009000           90 IVRCLYVLPIFG-VYSEGFSHLIISALRRHQKT---TVNSADSTQAKEIAAY-LFLDITGGFVDHDEKLMVKIL-EAFDV  163 (547)
Q Consensus        90 ~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~r~~~~l~-e~f~~  163 (547)
                      |+.||+-+|-+| +++|++||.+++++++++|.   .+..+|...+..+|+. .++=..+++.-+++.+-+-.+ .|+|+
T Consensus        81 ~l~~l~~lPd~~~v~g~~lS~~vl~~~~~~~kd~~~~~~~~d~~lt~~~~~~~~~v~t~g~~~ll~e~~~i~~~~~~~Di  160 (617)
T KOG2207|consen   81 ILIMLSQLPDRSKVFGESLSHWVLEDVGELLKDGSRMTESEDVALTGKIAFKADFVCTSGTLTLLGEIFKIQKLKQTLDI  160 (617)
T ss_pred             HHHHHHhCccccCcchhhhHHHHHHHHHHHhccCcccccccchHhhhhhhhccceeEecchHHHHHHHhcchhhhhhHhH
Confidence            999999999999 99999999999999999998   7889999888888887 677777888888899999888 99999


Q ss_pred             cccchHHHHhhhhhccccchhHHHHHH-----HHHHHHHHhhchhhHHHHHHHhhh-ccccchHHHHHHHhccchHHHHH
Q 009000          164 RLTDIEKAITQLKAQNEHRFDTAKTVI-----EQYIFAMIDSQSYMTAVSLLEHFS-IRQSGESFLLKMIQNKEFKAAEK  237 (547)
Q Consensus       164 ~~~~~~~a~~~~~~~~~~~~~~~~~~~-----~~~i~~~~~~~~~~~~~~li~~f~-~~~~~~~~l~~~~~~~~~~~a~~  237 (547)
                      .+.-++.++.....+--...+.-..++     ++|+.-+|-+++...|..+++|+. +|+...+|++.|+.- ++...++
T Consensus       161 ~l~~i~e~lq~~~f~e~a~~~ik~~l~~~~~~e~~~ldlIls~k~q~a~~ll~~~~~~q~p~v~fld~~v~~-~~~v~e~  239 (617)
T KOG2207|consen  161 TLCKIDEYLQNQRFGEAAPKAIKSLLLSDNAFEQLMLDLILSKKLQIADELLRHLTELQKPYVEFLDQMVLD-NFIVDER  239 (617)
T ss_pred             hcchhHHHHHhHHHHHHHHHHHHhhhhhhhhHHHHhccHhhccchhHHHHHHhhhhhhhhhHHHHHHHHHHH-HHHHHHH
Confidence            999999998766665543344444444     999999999999999999999999 888899999999986 8899999


Q ss_pred             HHHhcCc-----hHH------------------------------------------HHHHhhhcc-hHHHHHHhhcch-
Q 009000          238 WATFMGK-----PIL------------------------------------------LKRLAEKAC-WDIAEAKTKGDK-  268 (547)
Q Consensus       238 ~~~~~~~-----~~~------------------------------------------~~~l~~k~~-wd~a~~~~~~D~-  268 (547)
                      |+.+++.     +.+                                          -.+++.|+. |++++.....|. 
T Consensus       240 ~~~~~e~~~~~~~tl~~~v~~i~~rn~~~~~f~~~~~~n~v~~~~~kal~~~~~~~e~~~~~~~~f~~~~~~~~t~~~d~  319 (617)
T KOG2207|consen  240 CAHLLERTINLPKTLTILVQEIINRNQKKYTFSDEYAKNYVQNKNCKALHYIRSEREKGQMADKGFVQHVVETKTKPDDE  319 (617)
T ss_pred             HHHHHhhccCCCchhhhhHHHHHhccchhhhhhhhhhhhHhhcccHHHHHHHHHHhhhhhhHHHhhchhheeecccccch
Confidence            9999998     211                                          456777888 999999998887 


Q ss_pred             hHHHHHHHHh--hccCCHHHHH---------HHHHHcCCccccccc-----CcccCCcccccccccccCCcCeEEEcCHH
Q 009000          269 RLLEYLVYLA--MEAGYSEKVD---------ELCERYSLEGFLKTR-----EPEAGFVHSRFLHLKELVVEDIIWVDEVD  332 (547)
Q Consensus       269 ~l~~~lv~L~--~~~~d~~~L~---------~l~~ryef~sll~el-----~~~~~~~~~~~~~l~~~~~~~y~~Idt~e  332 (547)
                      ++..||.+..  .++...+...         +|.+++.-++.-+++     ....+......+.......+.+.+|+++.
T Consensus       320 ~~lkyLw~~~~~iEai~~~~~~~i~~~d~~~el~~~~s~~~~~k~~~~~~~~~~~pl~~~~~~~~~~~~~~~i~~V~~e~  399 (617)
T KOG2207|consen  320 NLLKYLWSFGEHIEAIYLATYDNIDPKDDAKELEKRTSRRGAGKTLFNQRMTTNVPLVCEDLFLFEPPWVESIGMVGNEK  399 (617)
T ss_pred             hHHHHHHHHHHhhhhhhhhhhhcCCCchhHHHHhchhhhcccChhhhhcccccccCccchhhhccCCCcccceeeeCCHH
Confidence            8888988887  3322222221         444444333222221     00000111112222224456789999999


Q ss_pred             HHHHHH-HHhhCC-CeEEEEeeeecCCccCCcCCceeEEEEEeCCeEEEEEcCcccCCCchHHHHHHHHhhcCCCceEEE
Q 009000          333 GLHKAI-CHIEGC-KVVGIDCEWKPNYVKGCKMNKVSIMQIASDEMVFIFDLIKLAEDVPDVLDSCLTRILQSPGILKLG  410 (547)
Q Consensus       333 eL~~ll-e~L~~a-~vIgfDtE~~~l~~~~~~~~~VsLlQLAt~~~a~~Idl~~l~~~~p~~Ll~~Lk~LLed~~I~KVG  410 (547)
                      ++..++ +.+... -.||+|.||.|.  .+...++++++|++.++.+|++|..++.....+-+...+..+|+++++.|||
T Consensus       400 El~~l~l~~l~~e~~yVGiDsEwkps--~~v~dsk~~IlQif~~~~v~Lidc~~l~~~~se~w~~~~s~if~s~~i~kvG  477 (617)
T KOG2207|consen  400 ELRDLLLESLSEELRYVGIDSEWKPS--KKVSDSKLAILQIFFKDCVYLIDCVKLENLASEIWHLLLSQIFESKSILKVG  477 (617)
T ss_pred             HHHHHHHHHhhhcCEEEEEccccCcc--cCCChhHHHHHHHHhcCeEEEeehHHhhhchHHHHHHHHHHHccCCceeeee
Confidence            998876 455555 789999999987  1223679999999999999999998875433333556788899999999999


Q ss_pred             echHHHHHHHHHHhCCc-cccc--ccchhh-hHHHh------------hcCCCCCHHHHHHHHhCCCCCCCcccccCCCC
Q 009000          411 YNFQCDIKQLAHSYGEL-ECFK--HYEMLL-DIQNV------------FKEPKGGLSGLAEKILGAGLNKTRRNSNWEQR  474 (547)
Q Consensus       411 hnlK~Dl~vLa~~~GIl-~~~~--~~~~vf-DtmLA------------l~~~~~gLd~LAer~Lg~~L~K~e~~SdW~~r  474 (547)
                      +++..|++++.++-|-+ .+++  ....++ ++.++            +++...+|.+|+...+|..++|++++|+|..|
T Consensus       478 f~~~eDL~~l~~s~pa~~~q~ki~~~~l~~~~~kl~e~~~~~~~~i~n~~~~~~~L~~Lt~~llg~~lnKteqcsnWqcr  557 (617)
T KOG2207|consen  478 FSMREDLEVLEASSPALRFQMKIEGLQLVSCVLKLAENVIDLPLSIENLNEATKGLADLTDCLLGKKLNKTEQCSNWQCR  557 (617)
T ss_pred             cchhhhHHHHHhhhhhhhhcccccchHHHHHHHHHHHHHhcccchhhhhcchhhhhhhhhHHHhhhhcccccccchhhcC
Confidence            99999999998533310 0000  011111 12222            12457899999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCCCcccchhHHHHHhhccCcccccCCCCcccc
Q 009000          475 PLSQNQLEYAALDAVVLLQIFHHVRSCSQPTDVSEGHDKIEWKSYIVSHMDNPKKSKKRPTIKKE  539 (547)
Q Consensus       475 pLt~~Qi~YAAeDA~vlLrL~~~L~~rLee~~~~~~~~~~~w~s~~~~~~~~~~k~~~~~~~~~~  539 (547)
                      ||+.+|+-|||.||.++..++..+....+. .+  ..+|..|+|    |+..++|.|-..++.|.
T Consensus       558 pLr~nQi~yaalDa~~~~~ifkkv~~vv~~-~~--~~ek~i~es----~~~~~~~~~~~~s~~~~  615 (617)
T KOG2207|consen  558 PLRRNQIYYAALDAVVLVEIFKKVCSVVEH-DA--DIEKFICES----HLGRPKKKKEHCSVWNR  615 (617)
T ss_pred             CchhhHHHHHHhcchhhHHHHHHHHhhcch-hh--HHHHHHHHH----hcCCccccccccccccc
Confidence            999999999999999999999999998885 33  455666665    67777777777776654

>cd06146 mut-7_like_exo DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins	Back alignment and domain information

>cd06129 RNaseD_like DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins	Back alignment and domain information

>cd06141 WRN_exo DEDDy 3'-5' exonuclease domain of WRN and similar proteins	Back alignment and domain information

>PRK10829 ribonuclease D; Provisional	Back alignment and domain information

>PF01612 DNA_pol_A_exo1: 3'-5' exonuclease; InterPro: IPR002562 This domain is responsible for the 3'-5' exonuclease proofreading activity of Escherichia coli DNA polymerase I (polI) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides	Back alignment and domain information

>cd06148 Egl_like_exo DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins	Back alignment and domain information

>TIGR01388 rnd ribonuclease D	Back alignment and domain information

>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>PRK05755 DNA polymerase I; Provisional	Back alignment and domain information

>cd06142 RNaseD_exo DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins	Back alignment and domain information

>smart00474 35EXOc 3'-5' exonuclease	Back alignment and domain information

>cd06147 Rrp6p_like_exo DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen 100kDa, and similar proteins	Back alignment and domain information

>TIGR00593 pola DNA polymerase I	Back alignment and domain information

>cd00007 35EXOc 3'-5' exonuclease	Back alignment and domain information

>cd09018 DEDDy_polA_RNaseD_like_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases, RNase D, WRN, and similar proteins	Back alignment and domain information

>KOG2206 consensus Exosome 3'-5' exoribonuclease complex, subunit PM/SCL-100 (Rrp6) [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>cd06140 DNA_polA_I_Bacillus_like_exo inactive DEDDy 3'-5' exonuclease domain of Bacillus stearothermophilus DNA polymerase I and similar family-A DNA polymerases	Back alignment and domain information

>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]	Back alignment and domain information

>cd06139 DNA_polA_I_Ecoli_like_exo DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases	Back alignment and domain information

>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional	Back alignment and domain information

>cd06128 DNA_polA_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases	Back alignment and domain information

>KOG4373 consensus Predicted 3'-5' exonuclease [General function prediction only]	Back alignment and domain information

>cd06149 ISG20 DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins	Back alignment and domain information

>cd06125 DnaQ_like_exo DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily	Back alignment and domain information

>cd06137 DEDDh_RNase DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins	Back alignment and domain information

>PRK08517 DNA polymerase III subunit epsilon; Provisional	Back alignment and domain information

>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]	Back alignment and domain information

>cd06144 REX4_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins	Back alignment and domain information

>PRK06310 DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>PRK07740 hypothetical protein; Provisional	Back alignment and domain information

>PRK06063 DNA polymerase III subunit epsilon; Provisional	Back alignment and domain information

>PRK07883 hypothetical protein; Validated	Back alignment and domain information

>PRK07942 DNA polymerase III subunit epsilon; Provisional	Back alignment and domain information

>cd06143 PAN2_exo DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2	Back alignment and domain information

>PRK05711 DNA polymerase III subunit epsilon; Provisional	Back alignment and domain information

>cd06131 DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins	Back alignment and domain information

>TIGR01406 dnaQ_proteo DNA polymerase III, epsilon subunit, Proteobacterial	Back alignment and domain information

>TIGR00573 dnaq exonuclease, DNA polymerase III, epsilon subunit family	Back alignment and domain information

>cd06130 DNA_pol_III_epsilon_like an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III	Back alignment and domain information

>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>PRK09145 DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>cd05160 DEDDy_DNA_polB_exo DEDDy 3'-5' exonuclease domain of family-B DNA polymerases	Back alignment and domain information

>cd06145 REX1_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins	Back alignment and domain information

>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type	Back alignment and domain information

>PRK06807 DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases	Back alignment and domain information

>PRK09146 DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative	Back alignment and domain information

>PRK06309 DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>cd05780 DNA_polB_Kod1_like_exo DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B DNA polymerases	Back alignment and domain information

>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>cd06136 TREX1_2 DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins	Back alignment and domain information

>cd05781 DNA_polB_B3_exo DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar archaeal family-B DNA polymerases	Back alignment and domain information

>PRK05601 DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>TIGR01298 RNaseT ribonuclease T	Back alignment and domain information

>cd06134 RNaseT DEDDh 3'-5' exonuclease domain of RNase T	Back alignment and domain information

>PRK07983 exodeoxyribonuclease X; Provisional	Back alignment and domain information

>PRK07247 DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>PRK06195 DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>PRK09182 DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>PF13482 RNase_H_2: RNase_H superfamily; PDB: 1TKD_A 1TK5_A 2AJQ_F 1T8E_A 1T7P_A 1SKR_A 1X9W_A 1TK8_A 1TK0_A 1SL2_A	Back alignment and domain information

>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]	Back alignment and domain information

>PRK11779 sbcB exonuclease I; Provisional	Back alignment and domain information

>PRK05168 ribonuclease T; Provisional	Back alignment and domain information

>cd05785 DNA_polB_like2_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Alignment Graph	Length	Definition	E-value
Query		547
2e6l_A		208	Structure Of Mouse Wrn Exonuclease Domain Length =		3e-08
2fbt_A		205	Wrn Exonuclease Length = 205		9e-08
1yt3_A		375	Crystal Structure Of Escherichia Coli Rnase D, An E		3e-05

>pdb|2E6L|A Chain A, Structure Of Mouse Wrn Exonuclease Domain Length = 208

Back alignment and structure

Iteration: 1

Score = 57.0 bits (136), Expect = 3e-08, Method: Compositional matrix adjust. Identities = 50/168 (29%), Positives = 82/168 (48%), Gaps = 15/168 (8%) Query: 346 VVGIDCEWKPNYVKGCKMNKVSIMQI-ASDEMVFIFDLIKLAEDVPDVLDSCLTRILQSP 404 VVG D EW P Y G K ++V+++Q+ S+ ++F + ++ V L +L++ Sbjct: 42 VVGFDMEWPPIYKPG-KRSRVAVIQLCVSESKCYLFHISSMS-----VFPQGLKMLLENK 95 Query: 405 GILKLGYNFQCDIKQLAHSYG-ELECFKHYEMLLDIQN--VFKEPKGGLSGLAEKILGAG 461 I K G + D +L + +LE F L D+ N + L+GL + +LG Sbjct: 96 SIKKAGVGIEGDQWKLLRDFDVKLESFVE---LTDVANEKLKCAETWSLNGLVKHVLGKQ 152 Query: 462 L--NKTRRNSNWEQRPLSQNQLEYAALDAVVLLQIFHHVRSCSQPTDV 507 L +K+ R SNW PL+++Q YAA DA L I+ + + V Sbjct: 153 LLKDKSIRCSNWSNFPLTEDQKLYAATDAYAGLIIYQKLGNLGDTVQV 200

PyMOL of 2e6l

>pdb|2FBT|A Chain A, Wrn Exonuclease Length = 205

Back alignment and structure

>pdb|1YT3|A Chain A, Crystal Structure Of Escherichia Coli Rnase D, An Exoribonuclease Involved In Structured Rna Processing Length = 375

Back alignment and structure

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		547
2e6m_A		208	Werner syndrome ATP-dependent helicase homolog; AP	2e-39
1vk0_A		206	Hypothetical protein; homohexamer, AT5G06450, stru	2e-27
3saf_A		428	Exosome component 10; exoribonuclease, RNA exosome	7e-22
2hbj_A		410	Exosome complex exonuclease RRP6; RNA metabolism,	2e-20
1yt3_A		375	Ribonuclease D, RNAse D; exoribonuclease, exonucle	2e-18
3cym_A		440	Uncharacterized protein BAD_0989; structural genom	1e-15
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	9e-08

>2e6m_A Werner syndrome ATP-dependent helicase homolog; APO form, hydrolase; 2.00A {Mus musculus} PDB: 2e6l_A 2fby_A 2fbv_A 2fbx_A 2fbt_A 2fc0_A* Length = 208	Back alignment and structure

 Score =  141 bits (357), Expect = 2e-39
 Identities = 48/186 (25%), Positives = 80/186 (43%), Gaps = 23/186 (12%)

Query: 324 DIIWVDEVDGLHKA----ICHIEGCKVVGIDCEWKPNYVKGCKMNKVSIMQIA-SDEMVF 378
            I++  E              +    VVG D EW P Y  G K ++V+++Q+  S+   +
Sbjct: 16  SIVYSYEASDCSFLSEDISMRLSDGDVVGFDMEWPPIYKPG-KRSRVAVIQLCVSESKCY 74

Query: 379 IFDLIKLAEDVPDVLDSCLTRILQSPGILKLGYNFQCDIKQLAHSYGELECFKHYEMLLD 438
           +F +  +      V    L  +L++  I K G   + D  +L   +         E  ++
Sbjct: 75  LFHISSM-----SVFPQGLKMLLENKSIKKAGVGIEGDQWKLLRDFDV-----KLESFVE 124

Query: 439 IQNVFKEPKG-----GLSGLAEKILGAGLNKTR--RNSNWEQRPLSQNQLEYAALDAVVL 491
           + +V  E         L+GL + +LG  L K +  R SNW   PL+++Q  YAA DA   
Sbjct: 125 LTDVANEKLKCAETWSLNGLVKHVLGKQLLKDKSIRCSNWSNFPLTEDQKLYAATDAYAG 184

Query: 492 LQIFHH 497
           L I+  
Sbjct: 185 LIIYQK 190

PyMOL of 2e6m

>1vk0_A Hypothetical protein; homohexamer, AT5G06450, struc genomics, protein structure initiative, center for eukaryot structural genomics, CESG; 2.10A {Arabidopsis thaliana} SCOP: c.55.3.5 PDB: 2q3s_A Length = 206	Back alignment and structure

>3saf_A Exosome component 10; exoribonuclease, RNA exosome, hydrolase; 2.50A {Homo sapiens} PDB: 3sag_A 3sah_A 2cpr_A Length = 428	Back alignment and structure

>2hbj_A Exosome complex exonuclease RRP6; RNA metabolism, RNA surveillance, RNA processing, hydrolase, gene regulation; 2.10A {Saccharomyces cerevisiae} SCOP: a.60.8.4 c.55.3.5 PDB: 2hbk_A 2hbl_A* 2hbm_A* Length = 410	Back alignment and structure

>1yt3_A Ribonuclease D, RNAse D; exoribonuclease, exonuclease, hydrolase, tRNA processing, hydrolase,translation; 1.60A {Escherichia coli} SCOP: a.60.8.3 a.60.8.3 c.55.3.5 Length = 375	Back alignment and structure

>3cym_A Uncharacterized protein BAD_0989; structural genomics, unknown function; 2.10A {Bifidobacterium adolescentis atcc 1570ORGANISM_TAXID} Length = 440	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

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		547
3saf_A		428	Exosome component 10; exoribonuclease, RNA exosome	99.91
2e6m_A		208	Werner syndrome ATP-dependent helicase homolog; AP	99.88
1vk0_A		206	Hypothetical protein; homohexamer, AT5G06450, stru	99.87
2hbj_A		410	Exosome complex exonuclease RRP6; RNA metabolism,	99.83
1yt3_A		375	Ribonuclease D, RNAse D; exoribonuclease, exonucle	99.82
3cym_A		440	Uncharacterized protein BAD_0989; structural genom	99.7
2kfn_A		605	Klenow fragment of DNA polymerase I; complex (poly	99.62
3pv8_A		592	DNA polymerase I; DNA polymerase I, protein-DNA co	99.47
1x9m_A		698	DNA polymerase; DNA ploymerase, N-2-acetylaminoflu	99.05
1bgx_T		832	TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhi	98.76
4dfk_A		540	DNA polymerase I, thermostable; DNA polymerase, tr	98.46
3v9w_A		235	Ribonuclease T; DEDD nucleases family, EXO-nucleas	97.71
1wlj_A		189	Interferon stimulated gene 20KDA; exoribonuclease,	96.27
2p1j_A		186	POLIII, DNA polymerase III POLC-type; structural g	96.19
2f96_A		224	Ribonuclease T; RNAse, RNT, RNAse T, tRNA hydrolas	94.82
2gui_A		194	DNA polymerase III epsilon subunit; DNA polymerase	93.91
2qxf_A		482	Exodeoxyribonuclease I; alpha-beta domain, DNAQ su	86.19
3u3y_B		314	Three prime repair exonuclease 1; RNAse H fold, 3'	85.53
1y97_A		238	Three prime repair exonuclease 2; TREX2, hydrolase	85.43
3mxm_B		242	Three prime repair exonuclease 1; RNAse H-like fol	83.4

>3saf_A Exosome component 10; exoribonuclease, RNA exosome, hydrolase; 2.50A {Homo sapiens} PDB: 3sag_A 3sah_A 2cpr_A	Back alignment and structure

Probab=99.91  E-value=1.2e-23  Score=224.97  Aligned_cols=198  Identities=19%  Similarity=0.219  Sum_probs=166.3

Q ss_pred             cCCcCeEEEcCHHHHHHHHHHhhCCCeEEEEeeeecCCccCCcCCceeEEEEEeCCeEEEEEcCcccCCCchHHHHHHHH
Q 009000          320 LVVEDIIWVDEVDGLHKAICHIEGCKVVGIDCEWKPNYVKGCKMNKVSIMQIASDEMVFIFDLIKLAEDVPDVLDSCLTR  399 (547)
Q Consensus       320 ~~~~~y~~Idt~eeL~~lle~L~~a~vIgfDtE~~~l~~~~~~~~~VsLlQLAt~~~a~~Idl~~l~~~~p~~Ll~~Lk~  399 (547)
                      .....|.+|++.+++..+++.+..++.+|||+||.+..   +....++++||++++++++||+.....    . ...|++
T Consensus       105 ~~~~~y~~I~t~e~L~~~l~~L~~~~~vavDtE~~~~~---~~~~~l~lIQLa~~~~~~lidpl~l~~----~-l~~L~~  176 (428)
T 3saf_A          105 IEETPCHFISSLDELVELNEKLLNCQEFAVNLEHHSYR---SFLGLTCLMQISTRTEDFIIDTLELRS----D-MYILNE  176 (428)
T ss_dssp             GGGSCEEEECSHHHHHHHHHHHTTCSEEEEEEEEECTT---CSSCEEEEEEEECSSCEEEEETTTTGG----G-GGGGHH
T ss_pred             CCCCCcEEECCHHHHHHHHHHHhcCCeEEEEEEecCCC---CCCCeEEEEEEEeCCcEEEEEeccchh----h-HHHHHH
Confidence            44568999999999999999999999999999998752   235689999999988899999876421    1 246899


Q ss_pred             hhcCCCceEEEechHHHHHHHHHHhCCcccccccchhhhHHHhh---cCCCCCHHHHHHHHhCCCCCCCcccccCCCCCC
Q 009000          400 ILQSPGILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNVF---KEPKGGLSGLAEKILGAGLNKTRRNSNWEQRPL  476 (547)
Q Consensus       400 LLed~~I~KVGhnlK~Dl~vLa~~~GIl~~~~~~~~vfDtmLAl---~~~~~gLd~LAer~Lg~~L~K~e~~SdW~~rpL  476 (547)
                      +|+|+++.|||||+|+|+++|.+.+|+..     .++||||++.   +..++||+.|+++|||..++|+++.++|++|||
T Consensus       177 lL~dp~i~KV~H~~k~Dl~~L~~~~Gi~~-----~~~fDT~lAa~lL~~~~~gL~~Lv~~~Lg~~l~K~~~~sdW~~rpL  251 (428)
T 3saf_A          177 SLTDPAIVKVFHGADSDIEWLQKDFGLYV-----VNMFDTHQAARLLNLGRHSLDHLLKLYCNVDSNKQYQLADWRIRPL  251 (428)
T ss_dssp             HHTCTTSEEEESSCHHHHHHHHHHHCCCC-----SSEEEHHHHHHHTTCSCCSHHHHHHHHHCCCCCCTTTTSCTTCSSC
T ss_pred             HHcCCCceEEEeehHHHHHHHHHHcCCCc-----CceeechhHHHHhCCCCCCHHHHHHHHcCCCCCccccccccccCCC
Confidence            99999999999999999999976699853     5689999993   444689999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCCCcccchhHHHHHhhccCcccccCCC
Q 009000          477 SQNQLEYAALDAVVLLQIFHHVRSCSQPTDVSEGHDKIEWKSYIVSHMDNPKKSKKRP  534 (547)
Q Consensus       477 t~~Qi~YAAeDA~vlLrL~~~L~~rLee~~~~~~~~~~~w~s~~~~~~~~~~k~~~~~  534 (547)
                      +++|+.|||.||+++++||+.|.++|++.+.    ....|...+..+++..+..+..+
T Consensus       252 s~~q~~YAA~DA~~ll~L~~~L~~~L~~~g~----~~~~~~~~~~~~~~~~~~~~~~~  305 (428)
T 3saf_A          252 PEEMLSYARDDTHYLLYIYDKMRLEMWERGN----GQPVQLQVVWQRSRDICLKKFIK  305 (428)
T ss_dssp             CHHHHHHHHHHHHTHHHHHHHHHHHHHHHTT----SCSHHHHHHHHHHHHHTTCCCCC
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC----ccccHHHHHHHHHHHHHHHhhcC
Confidence            9999999999999999999999999987553    22457777777776666555443

PyMOL of 3saf

>2e6m_A Werner syndrome ATP-dependent helicase homolog; APO form, hydrolase; 2.00A {Mus musculus} PDB: 2e6l_A 2fby_A 2fbv_A 2fbx_A 2fbt_A 2fc0_A*	Back alignment and structure

>1vk0_A Hypothetical protein; homohexamer, AT5G06450, struc genomics, protein structure initiative, center for eukaryot structural genomics, CESG; 2.10A {Arabidopsis thaliana} SCOP: c.55.3.5 PDB: 2q3s_A	Back alignment and structure

>2hbj_A Exosome complex exonuclease RRP6; RNA metabolism, RNA surveillance, RNA processing, hydrolase, gene regulation; 2.10A {Saccharomyces cerevisiae} SCOP: a.60.8.4 c.55.3.5 PDB: 2hbk_A 2hbl_A* 2hbm_A*	Back alignment and structure

>1yt3_A Ribonuclease D, RNAse D; exoribonuclease, exonuclease, hydrolase, tRNA processing, hydrolase,translation; 1.60A {Escherichia coli} SCOP: a.60.8.3 a.60.8.3 c.55.3.5	Back alignment and structure

>3cym_A Uncharacterized protein BAD_0989; structural genomics, unknown function; 2.10A {Bifidobacterium adolescentis atcc 1570ORGANISM_TAXID}	Back alignment and structure

>2kfn_A Klenow fragment of DNA polymerase I; complex (polymerase/DNA), exonuclease, transferase, transferase/DNA complex; HET: US1; 2.03A {Escherichia coli} SCOP: c.55.3.5 e.8.1.1 PDB: 1d9f_A* 1d9d_A* 1krp_A* 1ksp_A* 1qsl_A* 1kfs_A* 2kfz_A* 2kzm_A* 2kzz_A* 1dpi_A* 1kfd_A* 1kln_A* 1d8y_A*	Back alignment and structure

>3pv8_A DNA polymerase I; DNA polymerase I, protein-DNA complex, thymine-adenine, CLOS conformation; HET: DNA 2DT D3T; 1.52A {Geobacillus kaustophilus} PDB: 3px0_A* 3px4_A* 3px6_A* 3thv_A* 3ti0_A* 4dse_A* 4dsf_A* 4ds4_A* 4dqp_A* 4dqi_A* 4ds5_A* 4e0d_A* 4dqr_A* 4dqq_A* 3tan_A* 3tap_A* 3taq_A* 3tar_A* 4dqs_A* 3hp6_A* ...	Back alignment and structure

>1x9m_A DNA polymerase; DNA ploymerase, N-2-acetylaminofluorene, replication block, mutagenesis, transferase/electron transport/DNA complex; HET: DNA 2DT 8FG; 2.10A {Enterobacteria phage T7} SCOP: c.55.3.5 e.8.1.1 PDB: 1skr_A* 1skw_A* 1sl0_A* 1sks_A* 1sl2_A* 1t7p_A* 1t8e_A* 1tk0_A* 1tk5_A* 1tk8_A* 1tkd_A* 1sl1_A* 1x9s_A* 1x9w_A* 1zyq_A* 2ajq_A*	Back alignment and structure

>1bgx_T TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhibition, helix-coil dynamics, inhibitor design, complex (polymerase/inhibitor); 2.30A {Thermus aquaticus} SCOP: a.60.7.1 c.120.1.2 c.55.3.5 e.8.1.1 PDB: 1cmw_A 1tau_A* 1taq_A*	Back alignment and structure

>4dfk_A DNA polymerase I, thermostable; DNA polymerase, transferase-DNA complex; HET: DNA DOC 0L5; 1.65A {Thermus aquaticus} PDB: 1jxe_A* 3ktq_A* 3lwl_A* 3lwm_A* 3m8s_A* 3m8r_A* 3oju_A* 3rr7_A* 3rr8_A* 3rrg_A* 3ojs_A* 3rtv_A* 3sv3_A* 3sv4_A* 3syz_A* 3sz2_A* 3t3f_A* 4df4_A* 4df8_A* 4dfj_A* ...	Back alignment and structure

>3v9w_A Ribonuclease T; DEDD nucleases family, EXO-nucleases, hydrolase-DNA complex; HET: DNA; 1.70A {Escherichia coli} PDB: 3ngy_A 3v9u_A* 3ngz_A* 3va3_A* 3v9z_A* 3nh0_A 3nh2_A 3nh1_A* 3v9s_A* 3v9x_A* 3va0_A* 2is3_A	Back alignment and structure

>1wlj_A Interferon stimulated gene 20KDA; exoribonuclease, hydrolase; HET: U5P; 1.90A {Homo sapiens} SCOP: c.55.3.5	Back alignment and structure

>2p1j_A POLIII, DNA polymerase III POLC-type; structural genomics, exonuclease, PSI-2, protein structure initiative; HET: DNA; 2.50A {Thermotoga maritima MSB8}	Back alignment and structure

>2f96_A Ribonuclease T; RNAse, RNT, RNAse T, tRNA hydrolase, SAD, PS protein structure initiative, midwest center for structural genomics; 2.09A {Pseudomonas aeruginosa} SCOP: c.55.3.5	Back alignment and structure

>2gui_A DNA polymerase III epsilon subunit; DNA polymerase proofreading domain, transferase; HET: DNA U5P; 1.60A {Escherichia coli} SCOP: c.55.3.5 PDB: 1j54_A* 1j53_A* 2ido_A* 2xy8_A*	Back alignment and structure

>2qxf_A Exodeoxyribonuclease I; alpha-beta domain, DNAQ superfamily, SH3-like domain, produc structure, DNA damage, DNA repair, exonuclease; HET: TMP; 1.50A {Escherichia coli} SCOP: c.55.3.5 PDB: 1fxx_A* 3c94_A 3c95_A 3hl8_A* 3hp9_A*	Back alignment and structure

>3u3y_B Three prime repair exonuclease 1; RNAse H fold, 3' exonuclease, homodimer, hydrolase-DNA compl; HET: BU1; 2.28A {Mus musculus} PDB: 3u6f_B*	Back alignment and structure

>1y97_A Three prime repair exonuclease 2; TREX2, hydrolase; 2.50A {Homo sapiens} SCOP: c.55.3.5	Back alignment and structure

>3mxm_B Three prime repair exonuclease 1; RNAse H-like fold, polyproline type II helix, hydrolase-DNA; HET: DNA; 1.75A {Mus musculus} SCOP: c.55.3.5 PDB: 3mxj_B 2ioc_B 3mxi_B* 3b6o_A* 2o4g_A* 3b6p_A* 2o4i_A 2oa8_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		547
d1vk0a_		206	c.55.3.5 (A:) Hypothetical protein AT5G06450 {Thal	1e-28
d2hbka2		292	c.55.3.5 (A:129-420) Exosome complex exonuclease R	2e-16
d1yt3a3		193	c.55.3.5 (A:1-193) Ribonuclease D, catalytic domai	1e-09
d1kfsa1		195	c.55.3.5 (A:324-518) Exonuclease domain of prokary	6e-09

>d1vk0a_ c.55.3.5 (A:) Hypothetical protein AT5G06450 {Thale-cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 206	Back information, alignment and structure


class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: DnaQ-like 3'-5' exonuclease
domain: Hypothetical protein AT5G06450
species: Thale-cress (Arabidopsis thaliana) [TaxId: 3702]

 Score =  110 bits (277), Expect = 1e-28
 Identities = 31/193 (16%), Positives = 69/193 (35%), Gaps = 19/193 (9%)

Query: 321 VVEDIIWVDEVDGLHKAICHI------EGCKVVGIDCEWKPNYVKG-----CKMNKVSIM 369
           V    I V     +   +  I       G + V  D  W   + +           +S +
Sbjct: 17  VQTKTIDVGSSTDISPYLSLIREDSILNGNRAVIFDVYWDVGFPETETKTKTSGWSLSSV 76

Query: 370 QIASDEMVFIFDLIKLAEDVPDVLDSCLTRILQSPGILKLGYNFQCDIKQLAHSYGELE- 428
           ++++  +     L K   D    L     R   S  +  +G   + D+  L  ++G +  
Sbjct: 77  KLSTRNLCLFLRLPKPFHDNLKDL----YRFFASKFVTFVGVQIEEDLDLLRENHGLVIR 132

Query: 429 -CFKHYEMLLDIQNVFKEPKGGLSGLAEKILGAGLNKT-RRNSNWEQRPLSQNQLEYAAL 486
                 ++  + +        G   LA ++L + L +     + WE +   + QLE AA+
Sbjct: 133 NAINVGKLAAEARGTLVLEFLGTRELAHRVLWSDLGQLDSIEAKWE-KAGPEEQLEAAAI 191

Query: 487 DAVVLLQIFHHVR 499
           +  +++ ++  + 
Sbjct: 192 EGWLIVNVWDQLS 204

PyMOL of d1vk0a_

>d2hbka2 c.55.3.5 (A:129-420) Exosome complex exonuclease RRP6 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 292	Back information, alignment and structure

>d1yt3a3 c.55.3.5 (A:1-193) Ribonuclease D, catalytic domain {Escherichia coli [TaxId: 562]} Length = 193	Back information, alignment and structure

>d1kfsa1 c.55.3.5 (A:324-518) Exonuclease domain of prokaryotic DNA polymerase {Escherichia coli [TaxId: 562]} Length = 195	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		547
d1yt3a3		193	Ribonuclease D, catalytic domain {Escherichia coli	99.95
d2hbka2		292	Exosome complex exonuclease RRP6 {Baker's yeast (S	99.95
d1vk0a_		206	Hypothetical protein AT5G06450 {Thale-cress (Arabi	99.86
d1kfsa1		195	Exonuclease domain of prokaryotic DNA polymerase {	99.84
d2hhva1		171	Exonuclease domain of prokaryotic DNA polymerase {	99.62
d1wlja_		173	Interferon-stimulated gene 20 kDa protein, ISG20 {	97.75
d1x9ma1		204	Exonuclease domain of T7 DNA polymerase {Bacteriop	94.67
d1tgoa1		347	Exonuclease domain of family B DNA polymerases {Ar	91.8
d3b6oa1		226	Three prime repair exonuclease 1, TREX1 {Mouse (Mu	90.73
d1y97a1		228	Three prime repair exonuclease 2, TREX2 {Human (Ho	86.96
d2guia1		174	N-terminal exonuclease domain of the epsilon subun	86.5

>d1yt3a3 c.55.3.5 (A:1-193) Ribonuclease D, catalytic domain {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: DnaQ-like 3'-5' exonuclease
domain: Ribonuclease D, catalytic domain
species: Escherichia coli [TaxId: 562]

Probab=99.95  E-value=1.3e-27  Score=227.43  Aligned_cols=185  Identities=22%  Similarity=0.319  Sum_probs=158.9

Q ss_pred             CeEEEcCHHHHHHHHHHhhCCCeEEEEeeeecCCccCCcCCceeEEEEEeCCeEEEEEcCcccCCCchHHHHHHHHhhcC
Q 009000          324 DIIWVDEVDGLHKAICHIEGCKVVGIDCEWKPNYVKGCKMNKVSIMQIASDEMVFIFDLIKLAEDVPDVLDSCLTRILQS  403 (547)
Q Consensus       324 ~y~~Idt~eeL~~lle~L~~a~vIgfDtE~~~l~~~~~~~~~VsLlQLAt~~~a~~Idl~~l~~~~p~~Ll~~Lk~LLed  403 (547)
                      +|++|++.+++..+++.+..++++|||+||.+..   ++.++++++|+++++.+|+||+....  .+    ..++++|+|
T Consensus         2 ~y~~I~t~~~l~~~~~~l~~~~~i~~DtE~~~~~---~~~~~l~liQi~~~~~~~~id~~~~~--~~----~~l~~ll~~   72 (193)
T d1yt3a3           2 NYQMITTDDALASLCEAVRAFPAIALDTEFVRTR---TYYPQLGLIQLFDGEHLALIDPLGIT--DW----SPLKAILRD   72 (193)
T ss_dssp             CCEEECSHHHHHHHHHHHTTSSEEEEEEEEECCS---CSSCEEEEEEEECSSCEEEECGGGCS--CC----HHHHHHHHC
T ss_pred             eEEEECCHHHHHHHHHHHhcCCeEEEECcccCCC---cCCCcEEEEEEecCCcceeehhcchh--hh----HHHHHHhcC
Confidence            6899999999999999999999999999999873   23568999999999999999987542  22    357899999


Q ss_pred             CCceEEEechHHHHHHHHHHhCCcccccccchhhhHHHhh---c-CCCCCHHHHHHHHhCCCCCCCcccccCCCCCCCHH
Q 009000          404 PGILKLGYNFQCDIKQLAHSYGELECFKHYEMLLDIQNVF---K-EPKGGLSGLAEKILGAGLNKTRRNSNWEQRPLSQN  479 (547)
Q Consensus       404 ~~I~KVGhnlK~Dl~vLa~~~GIl~~~~~~~~vfDtmLAl---~-~~~~gLd~LAer~Lg~~L~K~e~~SdW~~rpLt~~  479 (547)
                      +++.|||||+++|+..|.+.+|+..     .+++|||++.   + ..++||..|++++||++++|.++.|||+.|||+++
T Consensus        73 ~~i~Kv~hn~~~D~~~L~~~~g~~~-----~~~~Dt~~~~~~l~~~~~~~L~~l~~~~lg~~ldK~~q~sdW~~rPL~~~  147 (193)
T d1yt3a3          73 PSITKFLHAGSEDLEVFLNVFGELP-----QPLIDTQILAAFCGRPMSWGFASMVEEYSGVTLDKSESRTDWLARPLTER  147 (193)
T ss_dssp             TTSEEEESSCHHHHHHHHHHHSSCC-----SSEEEHHHHHHHTTCCTTCCHHHHHHHHHCCCCCCTTTTSCTTSSSCCHH
T ss_pred             CCceEEEecchhhhhhhhhhcCccc-----cccchhhHHHhhhccccccchhhHHhhhccccccchhhccccccccccHH
Confidence            9999999999999999988788843     7889999994   3 56799999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHhccCCCCCCCCcccchhHHHHHhhccCccccc
Q 009000          480 QLEYAALDAVVLLQIFHHVRSCSQPTDVSEGHDKIEWKSYIVSHMDNPKKSK  531 (547)
Q Consensus       480 Qi~YAAeDA~vlLrL~~~L~~rLee~~~~~~~~~~~w~s~~~~~~~~~~k~~  531 (547)
                      |+.|||.||+++++||+.|..++++.         +|...+...++...++|
T Consensus       148 qi~YAA~Dv~~ll~L~~~L~~~l~~~---------~~l~~~~~e~~~l~~~~  190 (193)
T d1yt3a3         148 QCEYAAADVWYLLPITAKLMVETEAS---------GWLPAALDECRLMQMRR  190 (193)
T ss_dssp             HHHHHHHHHHTHHHHHHHHHHHHHHT---------TCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhHHHHHHHHHHHHHHHHhC---------CcHHHHHHHHHHHHHhh
Confidence            99999999999999999999998653         35555666666555444

PyMOL of d1yt3a3

>d2hbka2 c.55.3.5 (A:129-420) Exosome complex exonuclease RRP6 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d1vk0a_ c.55.3.5 (A:) Hypothetical protein AT5G06450 {Thale-cress (Arabidopsis thaliana) [TaxId: 3702]}	Back information, alignment and structure

>d1kfsa1 c.55.3.5 (A:324-518) Exonuclease domain of prokaryotic DNA polymerase {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d2hhva1 c.55.3.5 (A:298-468) Exonuclease domain of prokaryotic DNA polymerase {Bacillus stearothermophilus, newly identified strain as yet unnamed [TaxId: 1422]}	Back information, alignment and structure

>d1wlja_ c.55.3.5 (A:) Interferon-stimulated gene 20 kDa protein, ISG20 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1x9ma1 c.55.3.5 (A:1-210) Exonuclease domain of T7 DNA polymerase {Bacteriophage T7 [TaxId: 10760]}	Back information, alignment and structure

>d1tgoa1 c.55.3.5 (A:1-347) Exonuclease domain of family B DNA polymerases {Archaeon Thermococcus gorgonarius [TaxId: 71997]}	Back information, alignment and structure

>d3b6oa1 c.55.3.5 (A:9-234) Three prime repair exonuclease 1, TREX1 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1y97a1 c.55.3.5 (A:1-228) Three prime repair exonuclease 2, TREX2 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2guia1 c.55.3.5 (A:7-180) N-terminal exonuclease domain of the epsilon subunit of DNA polymerase III {Escherichia coli [TaxId: 562]}	Back information, alignment and structure