Citrus Sinensis ID: 019798

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-----

MASSPSHQTHIPLSSDPDGKPIDSVVPIHIVTNASQLPAEFLEPSSERQLVIGFDCEGVDLCRHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYITKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWYLAVRGALYCRCFCINENDYVDWPPLPPVPDYLIVEGDVPEEEILSILDVPPGKMGRIIGRRGSSILAIKESCNAEILIGGAKGPPDKVFIIGPVKQVRKAEAMLRGRMLEMY

cccccccccccccccccccccccccccEEEEEccccccHHHcccccccccEEEEEcccccccccccEEEEEEEEcccEEEEEEEccccccHHHHHHHHcccccEEEEEcccHHHHHHHHHcccccccHHHHHHHHHHHHHHHcccccccccHHHHHHHcccccccccHHHHHHHHHHHcccccccccccccHHHHHHHHHcccHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHcccccccccccccccccccccccccHHHHHHHcccccccccEEEccccccHHHHHcccccEEEEcccccccccEEEEccHHHHHHHHHHHHHcccccc

cccccccccccccccccccccccccccEEEEEccccccHHHHcccccccEEEEEEEcccccccccEEEEEEEEccccEEEEEcccccHHHHHHHHHHHccccEEEEEEccHHHHHHHHHHcccEEEccccHHHHHHHHHHHcccccccccEEcHHHHHHcHHHcccccHHHHHHHHHHHcccHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcEEEEcccHHccccccccccccccccccccHHHHHEEEccccccccEEEcccccHHHHHHHHccEEEEEccccccccEEEEEccHHHHHHHHHHHHHcHHHcc

masspshqthiplssdpdgkpidsvvpihivtnasqlpaeflepsserqlvigfdcegvdlcrhgslcimqlafpDAIYLVDAIQGGETVVKACkpalessyITKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEeqegrkrspddyISFVGlladprycgisyqEKEEVRVLLRqdpqfwtyrpLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWYLAVRGALYCRCfcinendyvdwpplppvpdylivegdvpeeeilsildvppgkmgriigrrGSSILAIKESCNAeiliggakgppdkvfiigpVKQVRKAEAMLRGRMLEMY

masspshqthiplssdpdgkPIDSVVPIHIVTNASQLPAEFLEPSSERQLVIGFDCEGVDLCRHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYITKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIeeqegrkrspDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWYLAVRGALYCRCFCINENDYVDWPPLPPVPDYLIVEGDVPEEEILsildvppgkmgrIIGRRGSSILAIKESCNAEILiggakgppdkvfiigpvkqVRKAEAMLRGRMLEMY

************************VVPIHIVTNASQLPAEFLE***ERQLVIGFDCEGVDLCRHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYITKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEE********DDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWYLAVRGALYCRCFCINENDYVDWPPLPPVPDYLIVEGDVPEEEILSILDVPPGKMGRIIGRRGSSILAIKESCNAEILIGGAKGPPDKVFIIGPVKQV***************

************************VVPIHIVTNASQLPAEFLEPSSERQLVIGFDCEGVDLCRHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYITKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWYLAVRGALYCRCFCINENDYVDWPPLPPVPDYLIVEGDVPEEEILSILDVPPGKMGRIIGRRGSSILAI*ESC*AEILIGGAKGPPDKVFIIGPVKQVRKAEAMLRGRMLEMY

**************SDPDGKPIDSVVPIHIVTNASQLPAEFLEPSSERQLVIGFDCEGVDLCRHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYITKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWYLAVRGALYCRCFCINENDYVDWPPLPPVPDYLIVEGDVPEEEILSILDVPPGKMGRIIGRRGSSILAIKESCNAEILIGGAKGPPDKVFIIGPVKQVRKAEAMLRGRMLEMY

**************S*PDGKPIDSVVPIHIVTNASQLPAEFLEPSSERQLVIGFDCEGVDLCRHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYITKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWYLAVRGALYCRCFCINENDYVDWPPLPPVPDYLIVEGDVPEEEILSILDVPPGKMGRIIGRRGSSILAIKESCNAEILIGGAKGPPDKVFIIGPVKQVRKAEAMLRGRMLEMY

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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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		335	2.2.26 [Sep-21-2011]
Q8CDF7		570	Exonuclease 3'-5' domain-	yes	no	0.459	0.270	0.317	2e-14
Q8NHP7		514	Exonuclease 3'-5' domain-	yes	no	0.444	0.289	0.327	5e-14
Q6NRD5		444	Exonuclease 3'-5' domain-	N/A	no	0.262	0.198	0.404	2e-10
Q0P3U3		378	Exonuclease 3'-5' domain-	yes	no	0.334	0.296	0.327	2e-06
P56960		887	Exosome component 10 OS=M	no	no	0.489	0.184	0.263	1e-05
Q6G329		406	Ribonuclease D OS=Bartone	yes	no	0.408	0.337	0.297	4e-05
Q01780		885	Exosome component 10 OS=H	no	no	0.414	0.157	0.269	9e-05
A5G127		392	Ribonuclease D OS=Acidiph	yes	no	0.391	0.334	0.246	0.0003
A9H9B7		393	Ribonuclease D OS=Glucona	yes	no	0.402	0.343	0.240	0.0007
Q1QLI8		382	Ribonuclease D OS=Nitroba	yes	no	0.2	0.175	0.352	0.0007

>sp\|Q8CDF7\|EXD1_MOUSE Exonuclease 3'-5' domain-containing protein 1 OS=Mus musculus GN=Exd1 PE=2 SV=1	Back alignment and function desciption

 Score = 80.1 bits (196), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 52/164 (31%), Positives = 83/164 (50%), Gaps = 10/164 (6%)

Query: 47  ERQLVIGFDCEGVDLCRHGSLCIMQLAFPDAIYLVDA-IQGGETVVKACKPALESSYITK 105
           ++Q V+    EG ++CRHG LC +Q+A    +YL D  + G        +  LE   I K
Sbjct: 153 KKQSVLSVAAEGANVCRHGKLCWLQVATNSRVYLFDIFLLGSRAFNNGLQMILEDKRILK 212

Query: 106 VIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFV-----GLLAD 160
           VIHDC+  S+ L  Q+GI L+NV DTQ+A  L    E     P+   +        L   
Sbjct: 213 VIHDCRWLSDCLSHQYGIMLNNVFDTQVADVLQFSMETGGFLPNCISTLQESLIRHLKVA 272

Query: 161 PRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRF 204
           PRY  + + E+ + R+  +++P+ W  RPL   +++  A +  +
Sbjct: 273 PRY--LFFLEERQKRI--QENPEIWLTRPLPPSLLKILALETTY 312

Mus musculus (taxid: 10090)

>sp\|Q8NHP7\|EXD1_HUMAN Exonuclease 3'-5' domain-containing protein 1 OS=Homo sapiens GN=EXD1 PE=2 SV=4	Back alignment and function description

>sp\|Q6NRD5\|EXD1_XENLA Exonuclease 3'-5' domain-containing protein 1 OS=Xenopus laevis GN=exd1 PE=2 SV=1	Back alignment and function description

>sp\|Q0P3U3\|EXD1_DANRE Exonuclease 3'-5' domain-containing protein 1 OS=Danio rerio GN=exd1 PE=2 SV=1	Back alignment and function description

>sp\|P56960\|EXOSX_MOUSE Exosome component 10 OS=Mus musculus GN=Exosc10 PE=1 SV=2	Back alignment and function description

>sp\|Q6G329\|RND_BARHE Ribonuclease D OS=Bartonella henselae (strain ATCC 49882 / Houston 1) GN=rnd PE=3 SV=1	Back alignment and function description

>sp\|Q01780\|EXOSX_HUMAN Exosome component 10 OS=Homo sapiens GN=EXOSC10 PE=1 SV=2	Back alignment and function description

>sp\|A5G127\|RND_ACICJ Ribonuclease D OS=Acidiphilium cryptum (strain JF-5) GN=rnd PE=3 SV=1	Back alignment and function description

>sp\|A9H9B7\|RND_GLUDA Ribonuclease D OS=Gluconacetobacter diazotrophicus (strain ATCC 49037 / DSM 5601 / PAl5) GN=rnd PE=3 SV=1	Back alignment and function description

>sp\|Q1QLI8\|RND_NITHX Ribonuclease D OS=Nitrobacter hamburgensis (strain X14 / DSM 10229) GN=rnd PE=3 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		335
225429426		341	PREDICTED: uncharacterized protein LOC10	1.0	0.982	0.844	1e-167
255550866		342	3'-5' exonuclease, putative [Ricinus com	0.997	0.976	0.805	1e-163
224142834		331	predicted protein [Populus trichocarpa]	0.967	0.978	0.814	1e-160
449450328		340	PREDICTED: uncharacterized protein LOC10	0.997	0.982	0.773	1e-156
225442373		336	PREDICTED: uncharacterized protein LOC10	0.988	0.985	0.788	1e-155
297743128		367	unnamed protein product [Vitis vinifera]	0.988	0.901	0.788	1e-155
224088954		378	predicted protein [Populus trichocarpa]	0.982	0.870	0.712	1e-153
82621130		338	3'-5' exonuclease domain-containing prot	0.928	0.920	0.794	1e-150
356564093		343	PREDICTED: uncharacterized protein LOC10	0.994	0.970	0.753	1e-150
297825683		342	hypothetical protein ARALYDRAFT_481448 [	0.991	0.970	0.749	1e-149

>gi\|225429426\|ref\|XP_002276186.1\| PREDICTED: uncharacterized protein LOC100259526 [Vitis vinifera] gi\|147856945\|emb\|CAN82846.1\| hypothetical protein VITISV_007988 [Vitis vinifera] gi\|296081603\|emb\|CBI20608.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

 Score =  592 bits (1527), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 288/341 (84%), Positives = 314/341 (92%), Gaps = 6/341 (1%)

Query: 1   MAS-SPSHQTHIPLSSDPDGKPIDS-----VVPIHIVTNASQLPAEFLEPSSERQLVIGF 54
           MAS SPS  T+IP+ SDP GKPID      +VPIHIVT  SQLP EFLEPS ER+LVIGF
Sbjct: 1   MASPSPSQPTYIPMPSDPGGKPIDHEGLLPLVPIHIVTLPSQLPIEFLEPSPERKLVIGF 60

Query: 55  DCEGVDLCRHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYITKVIHDCKRDS 114
           DCEGVDLCRHG+LCIMQ+AFPDAIYLVDAIQGGE ++KACKPALESSYITKVIHDCKRDS
Sbjct: 61  DCEGVDLCRHGTLCIMQIAFPDAIYLVDAIQGGEMLMKACKPALESSYITKVIHDCKRDS 120

Query: 115 EALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEV 174
           EALYFQFGIKLHNVVDTQIAYSLIEEQEGRKR  DDYISFVGLLADPRYCG+SY EK+EV
Sbjct: 121 EALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRLVDDYISFVGLLADPRYCGVSYLEKQEV 180

Query: 175 RVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWYLAVRGALYCRC 234
           R LLRQ+P FWT+RPL++LMVRAAADDVRFL YIYH MM+KLN++SLWYLAVRGALYCRC
Sbjct: 181 RDLLRQNPDFWTHRPLSDLMVRAAADDVRFLLYIYHKMMEKLNERSLWYLAVRGALYCRC 240

Query: 235 FCINENDYVDWPPLPPVPDYLIVEGDVPEEEILSILDVPPGKMGRIIGRRGSSILAIKES 294
           FCIN+NDY DWPPLPP+PD LIVEG+ PEEEILS+L VPPGKMGR+IGRRG+SIL++KES
Sbjct: 241 FCINDNDYADWPPLPPIPDNLIVEGNAPEEEILSVLHVPPGKMGRVIGRRGASILSVKES 300

Query: 295 CNAEILIGGAKGPPDKVFIIGPVKQVRKAEAMLRGRMLEMY 335
           CNAEILIGGAKGPPDKVFIIGPVKQVRKAEA+LRGRMLEMY
Sbjct: 301 CNAEILIGGAKGPPDKVFIIGPVKQVRKAEAILRGRMLEMY 341

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|255550866\|ref\|XP_002516481.1\| 3'-5' exonuclease, putative [Ricinus communis] gi\|223544301\|gb\|EEF45822.1\| 3'-5' exonuclease, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|224142834\|ref\|XP_002324746.1\| predicted protein [Populus trichocarpa] gi\|222866180\|gb\|EEF03311.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|449450328\|ref\|XP_004142915.1\| PREDICTED: uncharacterized protein LOC101214970 [Cucumis sativus] gi\|449522022\|ref\|XP_004168027.1\| PREDICTED: uncharacterized protein LOC101223734 [Cucumis sativus]	Back alignment and taxonomy information

>gi\|225442373\|ref\|XP_002281479.1\| PREDICTED: uncharacterized protein LOC100263418 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|297743128\|emb\|CBI35995.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|224088954\|ref\|XP_002308585.1\| predicted protein [Populus trichocarpa] gi\|222854561\|gb\|EEE92108.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|82621130\|gb\|ABB86253.1\| 3'-5' exonuclease domain-containing protein-like [Solanum tuberosum]	Back alignment and taxonomy information

>gi\|356564093\|ref\|XP_003550291.1\| PREDICTED: uncharacterized protein LOC100788577 [Glycine max]	Back alignment and taxonomy information

>gi\|297825683\|ref\|XP_002880724.1\| hypothetical protein ARALYDRAFT_481448 [Arabidopsis lyrata subsp. lyrata] gi\|297326563\|gb\|EFH56983.1\| hypothetical protein ARALYDRAFT_481448 [Arabidopsis lyrata subsp. lyrata]	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		335
TAIR\|locus:2043555		342	AT2G25910 [Arabidopsis thalian	0.991	0.970	0.746	1.7e-139
FB\|FBgn0000562		1004	egl "egalitarian" [Drosophila	0.516	0.172	0.318	5e-18
DICTYBASE\|DDB_G0282387		390	DDB_G0282387 "3'-5' exonucleas	0.507	0.435	0.306	1.1e-16
GENEDB_PFALCIPARUM\|MAL8P1.35		406	MAL8P1.35 "exonuclease, putati	0.552	0.455	0.300	9.9e-16
UNIPROTKB\|Q8IB75		406	MAL8P1.35 "Exonuclease, putati	0.552	0.455	0.300	9.9e-16
UNIPROTKB\|F1SSV1		568	LOC100621282 "Uncharacterized	0.462	0.272	0.327	5.2e-14
UNIPROTKB\|E2RJB4		569	EXD1 "Uncharacterized protein"	0.474	0.279	0.329	6.9e-14
UNIPROTKB\|Q8NHP7		514	EXD1 "Exonuclease 3'-5' domain	0.462	0.301	0.327	9.6e-14
MGI\|MGI:3045306		570	Exd1 "exonuclease 3'-5' domain	0.462	0.271	0.327	1.2e-13
UNIPROTKB\|B7Z839		572	EXD1 "cDNA FLJ55584" [Homo sap	0.462	0.270	0.327	1.2e-13

TAIR\|locus:2043555 AT2G25910 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 1365 (485.6 bits), Expect = 1.7e-139, P = 1.7e-139
 Identities = 253/339 (74%), Positives = 297/339 (87%)

Query:     2 ASSPSHQTHIPLSSDPDGK-PIDSV----VPIHIVTNASQLPAEFLEPSSERQLVIGFDC 56
             +SSP+   H+P+  +P G+ P        VPI+IVT+  QLPA+FL PS E++LVIGFDC
Sbjct:     3 SSSPTQLAHVPIPPEPGGRSPTQEANEPPVPIYIVTDPFQLPADFLNPSPEKKLVIGFDC 62

Query:    57 EGVDLCRHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYITKVIHDCKRDSEA 116
             EGVDLCRHG LCIMQ+AF +AIYLVD I+GGE ++KACKPALES+YITKVIHDCKRDSEA
Sbjct:    63 EGVDLCRHGKLCIMQIAFSNAIYLVDVIEGGEVIMKACKPALESNYITKVIHDCKRDSEA 122

Query:   117 LYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRV 176
             LYFQFGI+LHNVVDTQIAYSLIEEQEGR+R  DDYISFV LLADPRYCGISY+EKEEVRV
Sbjct:   123 LYFQFGIRLHNVVDTQIAYSLIEEQEGRRRPLDDYISFVSLLADPRYCGISYEEKEEVRV 182

Query:   177 LLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWYLAVRGALYCRCFC 236
             L+RQDP+FWTYRP+TELM+RAAADDVRFL Y+YH MM KLNQ+SLW+LAVRGALYCRC C
Sbjct:   183 LMRQDPKFWTYRPMTELMIRAAADDVRFLLYLYHKMMGKLNQRSLWHLAVRGALYCRCLC 242

Query:   237 -INENDYVDWPPLPPVPDYLIVEGDVPEEEILSILDVPPGKMGRIIGRRGSSILAIKESC 295
              +N+ D+ DWP +PP+PD L  E    EEEILS+LDVPPGKMGR+IGR+G+SILAIKE+C
Sbjct:   243 CMNDADFADWPTVPPIPDNLKSEDQCLEEEILSVLDVPPGKMGRVIGRKGASILAIKEAC 302

Query:   296 N-AEILIGGAKGPPDKVFIIGPVKQVRKAEAMLRGRMLE 333
             N AEILIGGAKGPPDK+F+IGPV++VRKAEA+LRGRM++
Sbjct:   303 NSAEILIGGAKGPPDKIFVIGPVREVRKAEAILRGRMID 341

GO:0003676 "nucleic acid binding" evidence=IEA;ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005622 "intracellular" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISM

GO:0006139 "nucleobase-containing compound metabolic process" evidence=IEA

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

GO:0006623 "protein targeting to vacuole" evidence=RCA

GO:0016192 "vesicle-mediated transport" evidence=RCA

FB\|FBgn0000562 egl "egalitarian" [Drosophila melanogaster (taxid:7227)]	Back alignment and assigned GO terms

DICTYBASE\|DDB_G0282387 DDB_G0282387 "3'-5' exonuclease domain-containing protein" [Dictyostelium discoideum (taxid:44689)]	Back alignment and assigned GO terms

GENEDB_PFALCIPARUM\|MAL8P1.35 MAL8P1.35 "exonuclease, putative" [Plasmodium falciparum (taxid:5833)]	Back alignment and assigned GO terms

UNIPROTKB\|Q8IB75 MAL8P1.35 "Exonuclease, putative" [Plasmodium falciparum 3D7 (taxid:36329)]	Back alignment and assigned GO terms

UNIPROTKB\|F1SSV1 LOC100621282 "Uncharacterized protein" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

UNIPROTKB\|E2RJB4 EXD1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

UNIPROTKB\|Q8NHP7 EXD1 "Exonuclease 3'-5' domain-containing protein 1" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

MGI\|MGI:3045306 Exd1 "exonuclease 3'-5' domain containing 1" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

UNIPROTKB\|B7Z839 EXD1 "cDNA FLJ55584" [Homo sapiens (taxid:9606)]	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

Your Input:
	GSVIVG00032148001	SubName- Full=Putative uncharacterized protein (Chromosome chr4 scaffold_6, whole genome shotgun sequence); (341 aa)
		(Vitis vinifera)
Predicted Functional Partners:
		Sorry, there are no predicted associations at the current settings.

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		335
cd06148		197	cd06148, Egl_like_exo, DEDDy 3'-5' exonuclease dom	2e-80
cd06142		178	cd06142, RNaseD_exo, DEDDy 3'-5' exonuclease domai	2e-26
smart00474		172	smart00474, 35EXOc, 3'-5' exonuclease	8e-23
pfam01612		172	pfam01612, DNA_pol_A_exo1, 3'-5' exonuclease	1e-21
COG0349		361	COG0349, Rnd, Ribonuclease D [Translation, ribosom	3e-13
cd06129		161	cd06129, RNaseD_like, DEDDy 3'-5' exonuclease doma	3e-12
TIGR01388		367	TIGR01388, rnd, ribonuclease D	2e-10
cd06146		193	cd06146, mut-7_like_exo, DEDDy 3'-5' exonuclease d	7e-10
smart00322		68	smart00322, KH, K homology RNA-binding domain	1e-09
cd00105		64	cd00105, KH-I, K homology RNA-binding domain, type	2e-09
pfam00013		59	pfam00013, KH_1, KH domain	5e-09
cd09018		150	cd09018, DEDDy_polA_RNaseD_like_exo, DEDDy 3'-5' e	2e-08
cd02394		62	cd02394, vigilin_like_KH, K homology RNA-binding d	3e-08
cd06147		192	cd06147, Rrp6p_like_exo, DEDDy 3'-5' exonuclease d	6e-08
PRK05755		880	PRK05755, PRK05755, DNA polymerase I; Provisional	3e-07
cd06141		170	cd06141, WRN_exo, DEDDy 3'-5' exonuclease domain o	4e-07
cd06139		193	cd06139, DNA_polA_I_Ecoli_like_exo, DEDDy 3'-5' ex	7e-05
cd06140		178	cd06140, DNA_polA_I_Bacillus_like_exo, inactive DE	8e-05
pfam13014		42	pfam13014, KH_3, KH domain	4e-04
PRK10829		373	PRK10829, PRK10829, ribonuclease D; Provisional	0.002
cd02396		65	cd02396, PCBP_like_KH, K homology RNA-binding doma	0.002
pfam13083		71	pfam13083, KH_4, KH domain	0.003

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

 Score =  242 bits (620), Expect = 2e-80
 Identities = 89/198 (44%), Positives = 117/198 (59%), Gaps = 4/198 (2%)

Query: 41  FLEPSSERQLVIGFDCEGVDLCRHGSLCIMQLAFP-DAIYLVDAIQGGETVV-KACKPAL 98
                 ++Q VIG DCEGV+L R G LC++Q+A     IYL D ++ G  V     K  L
Sbjct: 2   EAIIHLKKQKVIGLDCEGVNLGRKGKLCLVQIATRTGQIYLFDILKLGSIVFINGLKDIL 61

Query: 99  ESSYITKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLL 158
           ES  I KVIHDC+RDS+ALY Q+GIKL+NV DTQ+A +L++EQE    +PD  IS V LL
Sbjct: 62  ESKKILKVIHDCRRDSDALYHQYGIKLNNVFDTQVADALLQEQETGGFNPDRVISLVQLL 121

Query: 159 ADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQ 218
               Y  IS   KE+V+ L+R+DP+FW  RPLTE M+R AA DV  L  +Y+ M+  L  
Sbjct: 122 DKYLYISIS--LKEDVKKLMREDPKFWALRPLTEDMIRYAALDVLCLLPLYYAMLDALIS 179

Query: 219 QSLWYLAVRGALYCRCFC 236
           + L  +            
Sbjct: 180 KFLKAVFKYLNTERNLSE 197

The Egalitarian (Egl) protein subfamily is composed of Drosophila Egl and similar proteins. Egl is a component of an mRNA-binding complex which is required for oocyte specification. Egl 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. The 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. The conservation of this subfamily throughout eukaryotes suggests that its members may be part of ancient RNA processing complexes that are likely to participate in the regulated processing of specific mRNAs. Some members of this subfamily do not have a completely conserved YX(3)D pattern at the ExoIII motif. Length = 197

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

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

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

>gnl\|CDD\|223426 COG0349, Rnd, Ribonuclease D [Translation, ribosomal structure and biogenesis]	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\|130455 TIGR01388, rnd, ribonuclease D	Back alignment and domain information

>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

>gnl\|CDD\|197652 smart00322, KH, K homology RNA-binding domain	Back alignment and domain information

>gnl\|CDD\|238053 cd00105, KH-I, K homology RNA-binding domain, type I	Back alignment and domain information

>gnl\|CDD\|215657 pfam00013, KH_1, KH domain	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\|239087 cd02394, vigilin_like_KH, K homology RNA-binding domain_vigilin_like	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\|235591 PRK05755, PRK05755, DNA polymerase I; Provisional	Back alignment and domain information

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

>gnl\|CDD\|176651 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

>gnl\|CDD\|176652 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

>gnl\|CDD\|221895 pfam13014, KH_3, KH domain	Back alignment and domain information

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

>gnl\|CDD\|239089 cd02396, PCBP_like_KH, K homology RNA-binding domain, PCBP_like	Back alignment and domain information

>gnl\|CDD\|221909 pfam13083, KH_4, KH domain	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		335
PRK10829		373	ribonuclease D; Provisional	100.0
COG0349		361	Rnd Ribonuclease D [Translation, ribosomal structu	100.0
TIGR01388		367	rnd ribonuclease D. This model describes ribonucle	99.98
cd06148		197	Egl_like_exo DEDDy 3'-5' exonuclease domain of Dro	99.97
cd06146		193	mut-7_like_exo DEDDy 3'-5' exonuclease domain of C	99.96
cd06129		161	RNaseD_like DEDDy 3'-5' exonuclease domain of RNas	99.96
cd06141		170	WRN_exo DEDDy 3'-5' exonuclease domain of WRN and	99.95
PF01612		176	DNA_pol_A_exo1: 3'-5' exonuclease; InterPro: IPR00	99.95
COG0749		593	PolA DNA polymerase I - 3'-5' exonuclease and poly	99.91
PRK05755		880	DNA polymerase I; Provisional	99.91
KOG2206		687	consensus Exosome 3'-5' exoribonuclease complex, s	99.9
cd06142		178	RNaseD_exo DEDDy 3'-5' exonuclease domain of Ribon	99.88
cd06140		178	DNA_polA_I_Bacillus_like_exo inactive DEDDy 3'-5'	99.86
TIGR00593		887	pola DNA polymerase I. This family is based on the	99.84
smart00474		172	35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proo	99.83
PRK14975		553	bifunctional 3'-5' exonuclease/DNA polymerase; Pro	99.82
cd06147		192	Rrp6p_like_exo DEDDy 3'-5' exonuclease domain of y	99.81
cd06139		193	DNA_polA_I_Ecoli_like_exo DEDDy 3'-5' exonuclease	99.8
cd00007		155	35EXOc 3'-5' exonuclease. The 35EXOc domain is res	99.76
cd09018		150	DEDDy_polA_RNaseD_like_exo DEDDy 3'-5' exonuclease	99.74
KOG2207		617	consensus Predicted 3'-5' exonuclease [Replication	99.4
cd06128		151	DNA_polA_exo DEDDy 3'-5' exonuclease domain of fam	99.29
KOG2405		458	consensus Predicted 3'-5' exonuclease [Replication	98.91
KOG2405		458	consensus Predicted 3'-5' exonuclease [Replication	98.25
KOG4373		319	consensus Predicted 3'-5' exonuclease [General fun	97.92
cd06125		96	DnaQ_like_exo DnaQ-like (or DEDD) 3'-5' exonucleas	97.89
PRK07740		244	hypothetical protein; Provisional	97.79
PRK06063		313	DNA polymerase III subunit epsilon; Provisional	97.67
PRK07942		232	DNA polymerase III subunit epsilon; Provisional	97.45
cd06144		152	REX4_like DEDDh 3'-5' exonuclease domain of RNA ex	97.45
cd06149		157	ISG20 DEDDh 3'-5' exonuclease domain of Interferon	97.37
cd06137		161	DEDDh_RNase DEDDh 3'-5' exonuclease domain of the	97.31
cd06145		150	REX1_like DEDDh 3'-5' exonuclease domain of RNA ex	97.28
PRK07246		820	bifunctional ATP-dependent DNA helicase/DNA polyme	97.24
PRK06309		232	DNA polymerase III subunit epsilon; Validated	97.24
TIGR00573		217	dnaq exonuclease, DNA polymerase III, epsilon subu	97.24
TIGR01405		1213	polC_Gram_pos DNA polymerase III, alpha chain, Gra	97.19
PRK06310		250	DNA polymerase III subunit epsilon; Validated	97.16
COG2176		1444	PolC DNA polymerase III, alpha subunit (gram-posit	97.07
PRK06807		313	DNA polymerase III subunit epsilon; Validated	97.05
PRK09146		239	DNA polymerase III subunit epsilon; Validated	97.02
PRK07883		557	hypothetical protein; Validated	97.02
PRK06195		309	DNA polymerase III subunit epsilon; Validated	96.97
cd06131		167	DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonucl	96.86
PRK05601		377	DNA polymerase III subunit epsilon; Validated	96.83
cd06130		156	DNA_pol_III_epsilon_like an uncharacterized bacter	96.8
PRK05711		240	DNA polymerase III subunit epsilon; Provisional	96.78
TIGR01406		225	dnaQ_proteo DNA polymerase III, epsilon subunit, P	96.78
PRK05168		211	ribonuclease T; Provisional	96.78
PRK08517		257	DNA polymerase III subunit epsilon; Provisional	96.74
KOG2249		280	consensus 3'-5' exonuclease [Replication, recombin	96.73
PRK08074		928	bifunctional ATP-dependent DNA helicase/DNA polyme	96.72
cd05160		199	DEDDy_DNA_polB_exo DEDDy 3'-5' exonuclease domain	96.7
smart00479		169	EXOIII exonuclease domain in DNA-polymerase alpha	96.65
cd06136		177	TREX1_2 DEDDh 3'-5' exonuclease domain of three pr	96.6
TIGR01407		850	dinG_rel DnaQ family exonuclease/DinG family helic	96.51
cd05780		195	DNA_polB_Kod1_like_exo DEDDy 3'-5' exonuclease dom	96.48
cd02394		62	vigilin_like_KH K homology RNA-binding domain_vigi	96.4
cd06134		189	RNaseT DEDDh 3'-5' exonuclease domain of RNase T.	96.39
PRK09145		202	DNA polymerase III subunit epsilon; Validated	96.29
cd06127		159	DEDDh DEDDh 3'-5' exonuclease domain family. DEDDh	96.24
TIGR01298		200	RNaseT ribonuclease T. in gamma-subdivision Proteo	96.21
PRK00448		1437	polC DNA polymerase III PolC; Validated	96.11
cd06143		174	PAN2_exo DEDDh 3'-5' exonuclease domain of the euk	95.71
PF13482		164	RNase_H_2: RNase_H superfamily; PDB: 1TKD_A 1TK5_A	95.55
PRK07247		195	DNA polymerase III subunit epsilon; Validated	95.27
PRK09182		294	DNA polymerase III subunit epsilon; Validated	94.81
PF09281		138	Taq-exonuc: Taq polymerase, exonuclease; InterPro:	94.47
cd00105		64	KH-I K homology RNA-binding domain, type I. KH bin	94.32
PRK07748		207	sporulation inhibitor KapD; Provisional	93.97
PRK07983		219	exodeoxyribonuclease X; Provisional	93.12
cd05785		207	DNA_polB_like2_exo Uncharacterized bacterial subgr	93.1
smart00322		69	KH K homology RNA-binding domain.	93.1
KOG3657		1075	consensus Mitochondrial DNA polymerase gamma, cata	92.88
PRK11779		476	sbcB exonuclease I; Provisional	92.85
cd02396		65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	92.38
PF00013		60	KH_1: KH domain syndrome, contains KH motifs.; Int	92.11
cd05784		193	DNA_polB_II_exo DEDDy 3'-5' exonuclease domain of	91.34
cd06133		176	ERI-1_3'hExo_like DEDDh 3'-5' exonuclease domain o	91.25
PF10108		209	DNA_pol_B_exo2: Predicted 3'-5' exonuclease relate	90.94
cd05781		188	DNA_polB_B3_exo DEDDy 3'-5' exonuclease domain of	90.48
cd02393		61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	90.33
COG0847		243	DnaQ DNA polymerase III, epsilon subunit and relat	90.1
cd05782		208	DNA_polB_like1_exo Uncharacterized bacterial subgr	89.12
PRK06722		281	exonuclease; Provisional	88.71
cd06138		183	ExoI_N N-terminal DEDDh 3'-5' exonuclease domain o	88.3
KOG2248		380	consensus 3'-5' exonuclease [Replication, recombin	88.09
cd05779		204	DNA_polB_epsilon_exo DEDDy 3'-5' exonuclease domai	81.44

>PRK10829 ribonuclease D; Provisional	Back alignment and domain information

Probab=100.00  E-value=6e-35  Score=279.90  Aligned_cols=249  Identities=24%  Similarity=0.319  Sum_probs=211.8

Q ss_pred             CeEEeCCccchhHHHhhhhccCCceEEEEEeecCCC-ccCcEEEEEEEeCCceEEEEccCCChhhHHHHHHHHcCCCceE
Q 019798           27 PIHIVTNASQLPAEFLEPSSERQLVIGFDCEGVDLC-RHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYITK  105 (335)
Q Consensus        27 ~~~~I~t~~~L~~~~l~~~~~~~~~ia~D~E~~~~~-~~~~l~~lqla~~~~~~lid~~~~~~~~~~~Lk~lLe~~~i~K  105 (335)
                      .|.+|+|+++|.+ +++. +.+.+.+|||||+.+.. +++++|+|||++++.+|+||++...+  +..|+++|+|+.+.|
T Consensus         2 ~~~~I~t~~~L~~-~~~~-l~~~~~lalDtEf~~~~ty~~~l~LiQl~~~~~~~LiD~l~~~d--~~~L~~ll~~~~ivK   77 (373)
T PRK10829          2 NYQMITTDDALAS-VCEA-ARAFPAIALDTEFVRTRTYYPQLGLIQLYDGEQLSLIDPLGITD--WSPFKALLRDPQVTK   77 (373)
T ss_pred             CcEEeCCHHHHHH-HHHH-HhcCCeEEEecccccCccCCCceeEEEEecCCceEEEecCCccc--hHHHHHHHcCCCeEE
Confidence            5789999999997 9988 47899999999999875 78899999999988999999987753  678999999999999


Q ss_pred             EEEechhcHHHHHHHcCCccceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCcccchhHHHHHHhcCCCCCC
Q 019798          106 VIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFW  185 (335)
Q Consensus       106 V~hd~k~D~~~L~~~~gi~l~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l~~k~~~~~~~~~~~~~w  185 (335)
                      |+|++++|+..|++.+|+.+.++||||+|+.+++.+.        .+||+.|++  +|||++++| ++.+       +||
T Consensus        78 V~H~~~~Dl~~l~~~~g~~p~~~fDTqiaa~~lg~~~--------~~gl~~Lv~--~~lgv~ldK-~~~~-------sDW  139 (373)
T PRK10829         78 FLHAGSEDLEVFLNAFGELPQPLIDTQILAAFCGRPL--------SCGFASMVE--EYTGVTLDK-SESR-------TDW  139 (373)
T ss_pred             EEeChHhHHHHHHHHcCCCcCCeeeHHHHHHHcCCCc--------cccHHHHHH--HHhCCccCc-cccc-------CCC
Confidence            9999999999998899999999999999999998642        249999999  999999985 3322       499


Q ss_pred             ccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhccccHHHHHHhhh-hcc----cc-------cc------cCCc------
Q 019798          186 TYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWYLAVRGAL-YCR----CF-------CI------NEND------  241 (335)
Q Consensus       186 ~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~~~l~~l~~~~e~-~~~----vL-------~m------e~~g------  241 (335)
                      ..|||+++|+.|||.||.+++.||+.|..+|.+.|.+.++.+..- .+.    ..       .+      ...+      
T Consensus       140 ~~RPLs~~ql~YAa~Dv~~L~~l~~~L~~~L~~~g~~~w~~ee~~~l~~~~~~~~~~~~~~~~ik~~~~L~~~~lavl~~  219 (373)
T PRK10829        140 LARPLSERQCEYAAADVFYLLPIAAKLMAETEAAGWLPAALDECRLLCQRRQEVLAPEEAYRDITNAWQLRTRQLACLQL  219 (373)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHhccccCCChHHHHHHhccccCCCHHHHHHHHH
Confidence            999999999999999999999999999999999999888765432 110    00       11      1111      


Q ss_pred             cCCCCCCCCCCCcccccCCCCHHHHHhhhcCCCCccc---------cccccccccHHHHHHHhhh
Q 019798          242 YVDWPPLPPVPDYLIVEGDVPEEEILSILDVPPGKMG---------RIIGRRGSSILAIKESCNA  297 (335)
Q Consensus       242 ~~d~~~L~~~~~~l~~~~~~~e~~i~~lAg~~~~~~~---------~~~~~~~~~~~~~~~~~~~  297 (335)
                      ...||+..++..|.++.....++.++++|..+|.+..         ..++++|.+|+.+++.+.+
T Consensus       220 L~~WRe~~Ar~~d~p~~~Vl~d~~L~~lA~~~P~~~~~L~~~~~~~~~~r~~g~~ll~~i~~a~~  284 (373)
T PRK10829        220 LADWRLRKARERDLAVNFVVREEHLWQVARYMPGSLGELDSLGLSGSEIRFHGKTLLALVAKAQA  284 (373)
T ss_pred             HHHHHHHHHHHhCCCcceecChHHHHHHHHhCCCCHHHHHhccCChHhHHhhHHHHHHHHHHHhc
Confidence            2378888899999999999999999999999997754         4677889999999999854

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

>TIGR01388 rnd ribonuclease D	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

>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

>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

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

>PRK05755 DNA polymerase I; Provisional	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

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

>TIGR00593 pola DNA polymerase I	Back alignment and domain information

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

>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional	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

>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

>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

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

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

>KOG2405 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]	Back alignment and domain information

>KOG2405 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]	Back alignment and domain information

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

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

>PRK07942 DNA polymerase III subunit epsilon; Provisional	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

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

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

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

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

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

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

>PRK06310 DNA polymerase III subunit epsilon; Validated	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

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

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

>PRK07883 hypothetical protein; Validated	Back alignment and domain information

>PRK06195 DNA polymerase III subunit epsilon; Validated	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

>PRK05601 DNA polymerase III subunit epsilon; Validated	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

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

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

>PRK05168 ribonuclease T; Provisional	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

>PRK08074 bifunctional ATP-dependent DNA helicase/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

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

>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative	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

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like	Back alignment and domain information

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

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

>cd06127 DEDDh DEDDh 3'-5' exonuclease domain family	Back alignment and domain information

>TIGR01298 RNaseT ribonuclease T	Back alignment and domain information

>PRK00448 polC DNA polymerase III PolC; Validated	Back alignment and domain information

>cd06143 PAN2_exo DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2	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

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

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

>PF09281 Taq-exonuc: Taq polymerase, exonuclease; InterPro: IPR015361 This domain is found in prokaryotic Taq DNA polymerase (thermostable), where it assumes a ribonuclease H-like motif	Back alignment and domain information

>cd00105 KH-I K homology RNA-binding domain, type I	Back alignment and domain information

>PRK07748 sporulation inhibitor KapD; Provisional	Back alignment and domain information

>PRK07983 exodeoxyribonuclease X; 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

>smart00322 KH K homology RNA-binding domain	Back alignment and domain information

>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]	Back alignment and domain information

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

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like	Back alignment and domain information

>PF00013 KH_1: KH domain syndrome, contains KH motifs	Back alignment and domain information

>cd05784 DNA_polB_II_exo DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial family-B DNA polymerases	Back alignment and domain information

>cd06133 ERI-1_3'hExo_like DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins	Back alignment and domain information

>PF10108 DNA_pol_B_exo2: Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; InterPro: IPR019288 This entry represents various prokaryotic 3'-5' exonucleases and hypothetical 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

>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH)	Back alignment and domain information

>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]	Back alignment and domain information

>cd05782 DNA_polB_like1_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases	Back alignment and domain information

>PRK06722 exonuclease; Provisional	Back alignment and domain information

>cd06138 ExoI_N N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins	Back alignment and domain information

>KOG2248 consensus 3'-5' exonuclease [Replication, recombination and repair]	Back alignment and domain information

>cd05779 DNA_polB_epsilon_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase	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		335
3sah_A		428	Crystal Structure Of The Human Rrp6 Catalytic Domai		1e-06
2hbj_A		410	Structure Of The Yeast Nuclear Exosome Component, R		6e-06
3saf_A		428	Crystal Structure Of The Human Rrp6 Catalytic Domai		1e-05

>pdb|3SAH|A Chain A, Crystal Structure Of The Human Rrp6 Catalytic Domain With Y436a Mutation In The Catalytic Site Length = 428

Back alignment and structure

Iteration: 1

Score = 50.8 bits (120), Expect = 1e-06, Method: Compositional matrix adjust. Identities = 46/167 (27%), Positives = 70/167 (41%), Gaps = 28/167 (16%) Query: 54 FDCE--GVDLCRH------GSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYITK 105 +C+ VDL H G C+MQ++ +++D ++ + +L I K Sbjct: 127 LNCQEFAVDLEHHSYRSFLGLTCLMQISTRTEDFIIDTLELRSDMY-ILNESLTDPAIVK 185 Query: 106 VIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCG 165 V H D E L FG+ + N+ DT A L+ GR S D + YC Sbjct: 186 VFHGADSDIEWLQKDFGLYVVNMFDTHQAARLL--NLGR-HSLDHLLKL--------YCN 234 Query: 166 ISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNM 212 + ++ ++ W RPL E M+ AA DD +L YIY M Sbjct: 235 VDSNKQYQLAD--------WRIRPLPEEMLSAARDDTHYLLYIYDKM 273

PyMOL of 3sah

>pdb|2HBJ|A Chain A, Structure Of The Yeast Nuclear Exosome Component, Rrp6p, Reveals An Interplay Between The Active Site And The Hrdc Domain Length = 410

Back alignment and structure

>pdb|3SAF|A Chain A, Crystal Structure Of The Human Rrp6 Catalytic Domain With D313n Mutation In The Active Site Length = 428

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		335
3saf_A		428	Exosome component 10; exoribonuclease, RNA exosome	3e-25
2hbj_A		410	Exosome complex exonuclease RRP6; RNA metabolism,	5e-24
1yt3_A		375	Ribonuclease D, RNAse D; exoribonuclease, exonucle	8e-24
2e6m_A		208	Werner syndrome ATP-dependent helicase homolog; AP	2e-22
3cym_A		440	Uncharacterized protein BAD_0989; structural genom	9e-21
2ctj_A		95	Vigilin; K homology type I domain, RNA-binding, ce	6e-10
1vig_A		71	Vigilin; RNA-binding protein, ribonucleoprotein; N	6e-10
2ctk_A		104	Vigilin; K homology type I domain, RNA-binding, ce	7e-10
2cte_A		94	Vigilin; K homology type I domain, RNA-binding, ce	2e-09
1j5k_A		89	Heterogeneous nuclear ribonucleoprotein K; single-	3e-09
1x4m_A		94	FAR upstream element binding protein 1; KH domain,	5e-09
2ctm_A		95	Vigilin; K homology type I domain, RNA-binding, ce	6e-09
3krm_A		163	Insulin-like growth factor 2 mRNA-binding protein	7e-09
3krm_A		163	Insulin-like growth factor 2 mRNA-binding protein	7e-09
2p2r_A		76	Poly(RC)-binding protein 2; protein-DNA complex, R	9e-09
1zzk_A		82	Heterogeneous nuclear ribonucleoprotein K; KH domi	1e-08
2axy_A		73	Poly(RC)-binding protein 2; protein-DNA complex, D	1e-08
1x4n_A		92	FAR upstream element binding protein 1; KH domain,	1e-08
1ec6_A		87	RNA-binding protein NOVA-2; KH domain, alpha-beta	1e-08
2opv_A		85	KHSRP protein; KH domain, RNA binding protein, KSR	2e-08
1wvn_A		82	Poly(RC)-binding protein 1; KH domain, RNA binding	2e-08
1dtj_A		76	RNA-binding neurooncological ventral antigen 2; KH	2e-08
1we8_A		104	Tudor and KH domain containing protein; structural	3e-08
2hh2_A		107	KH-type splicing regulatory protein; KH-RNA bindin	3e-08
2jzx_A		160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	3e-08
2jzx_A		160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	2e-07
2ctl_A		97	Vigilin; K homology type I domain, RNA-binding, ce	4e-08
2anr_A		178	Neuro-oncological ventral antigen 1; protein-RNA c	4e-08
2anr_A		178	Neuro-oncological ventral antigen 1; protein-RNA c	2e-06
2jvz_A		164	KH type-splicing, FAR upstream element-binding pro	6e-08
2jvz_A		164	KH type-splicing, FAR upstream element-binding pro	6e-07
1j4w_A		174	FUSE binding protein; single-stranded DNA binding	5e-07
1j4w_A		174	FUSE binding protein; single-stranded DNA binding	8e-07
2hh3_A		106	KH-type splicing regulatory protein; KH-RNA bindin	5e-07
1vk0_A		206	Hypothetical protein; homohexamer, AT5G06450, stru	1e-06
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-06
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-05
2e3u_A		219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	3e-05
2qnd_A		144	FMR1 protein; KH domain, eukaryotic KH domains, ta	7e-05
2ctf_A		102	Vigilin; K homology type I domain, RNA-binding, ce	2e-04
2dgr_A		83	Ring finger and KH domain-containing protein 1; st	2e-04
2kfn_A		605	Klenow fragment of DNA polymerase I; complex (poly	8e-04

>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

 Score =  104 bits (260), Expect = 3e-25
 Identities = 50/240 (20%), Positives = 84/240 (35%), Gaps = 26/240 (10%)

Query: 14  SSDPDGKPIDSVVPIHIVTNASQLPAEFLEPSSERQLVIGFDCEGVDLCR-HGSLCIMQL 72
                 +PI+   P H +++  +L  E  E           + E        G  C+MQ+
Sbjct: 97  PQPQLYRPIEET-PCHFISSLDEL-VELNE-KLLNCQEFAVNLEHHSYRSFLGLTCLMQI 153

Query: 73  AFPDAIYLVDAIQGGETVVKACKPALESSYITKVIHDCKRDSEALYFQFGIKLHNVVDTQ 132
           +     +++D ++    +      +L    I KV H    D E L   FG+ + N+ DT 
Sbjct: 154 STRTEDFIIDTLELRSDM-YILNESLTDPAIVKVFHGADSDIEWLQKDFGLYVVNMFDTH 212

Query: 133 IAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTE 192
            A  L+              S   LL    YC +   ++ +       D   W  RPL E
Sbjct: 213 QAARLLNLGR---------HSLDHLLK--LYCNVDSNKQYQ-----LAD---WRIRPLPE 253

Query: 193 LMVRAAADDVRFLPYIYHNMMKKLNQQSL--WYLAVRGALYCRCFCINENDYVDWPPLPP 250
            M+  A DD  +L YIY  M  ++ ++               R  C+ +     +     
Sbjct: 254 EMLSYARDDTHYLLYIYDKMRLEMWERGNGQPVQLQVVWQRSRDICLKKFIKPIFTDESY 313

PyMOL of 3saf

>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

>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

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

>2ctj_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 95	Back alignment and structure

>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1vih_A Length = 71	Back alignment and structure

>2ctk_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 104	Back alignment and structure

>2cte_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 94	Back alignment and structure

>1j5k_A Heterogeneous nuclear ribonucleoprotein K; single-stranded DNA binding protein, transcription factor, hnRNP K, CT element, C-MYC oncogene; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1khm_A Length = 89	Back alignment and structure

>1x4m_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 Length = 94	Back alignment and structure

>2ctm_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 95	Back alignment and structure

>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain, cell projection, cytoplasm, nucleus, phosphoprotein, translation regulation; 2.75A {Homo sapiens} Length = 163	Back alignment and structure

>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain, cell projection, cytoplasm, nucleus, phosphoprotein, translation regulation; 2.75A {Homo sapiens} Length = 163	Back alignment and structure

>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA binding protein/DNA complex; 1.60A {Homo sapiens} Length = 76	Back alignment and structure

>1zzk_A Heterogeneous nuclear ribonucleoprotein K; KH domian, alpha-beta fold, DNA binding protein; 0.95A {Homo sapiens} SCOP: d.51.1.1 PDB: 1zzj_A 1zzi_A Length = 82	Back alignment and structure

>2axy_A Poly(RC)-binding protein 2; protein-DNA complex, DNA binding protein-DNA complex; 1.70A {Homo sapiens} SCOP: d.51.1.1 PDB: 2pqu_A 2py9_A 1ztg_A 3vke_A* Length = 73	Back alignment and structure

>1x4n_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 PDB: 2opu_A Length = 92	Back alignment and structure

>1ec6_A RNA-binding protein NOVA-2; KH domain, alpha-beta fold, RNA-binding motif, protein/RNA structure, RNA binding protein/RNA complex; 2.40A {Homo sapiens} SCOP: d.51.1.1 Length = 87	Back alignment and structure

>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens} Length = 85	Back alignment and structure

>1wvn_A Poly(RC)-binding protein 1; KH domain, RNA binding domain, RNA binding protein; 2.10A {Homo sapiens} SCOP: d.51.1.1 Length = 82	Back alignment and structure

>1dtj_A RNA-binding neurooncological ventral antigen 2; KH domain, alpha-beta fold RNA-binding motif, immune system; 2.00A {Homo sapiens} SCOP: d.51.1.1 PDB: 1dt4_A Length = 76	Back alignment and structure

>1we8_A Tudor and KH domain containing protein; structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.51.1.1 Length = 104	Back alignment and structure

>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Length = 107	Back alignment and structure

>2jzx_A Poly(RC)-binding protein 2; PCBP2, KH domains, RNA binding, DNA-binding, nucleus, phosph ribonucleoprotein, RNA-binding, RNA binding protein; NMR {Homo sapiens} Length = 160	Back alignment and structure

>2jzx_A Poly(RC)-binding protein 2; PCBP2, KH domains, RNA binding, DNA-binding, nucleus, phosph ribonucleoprotein, RNA-binding, RNA binding protein; NMR {Homo sapiens} Length = 160	Back alignment and structure

>2ctl_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 97	Back alignment and structure

>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A* Length = 178	Back alignment and structure

>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A* Length = 178	Back alignment and structure

>2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA binding protein, KH domain, KSRP, posttranscriptional regulation, mRNA decay; NMR {Homo sapiens} Length = 164	Back alignment and structure

>2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA binding protein, KH domain, KSRP, posttranscriptional regulation, mRNA decay; NMR {Homo sapiens} Length = 164	Back alignment and structure

>1j4w_A FUSE binding protein; single-stranded DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: d.51.1.1 d.51.1.1 Length = 174	Back alignment and structure

>1j4w_A FUSE binding protein; single-stranded DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: d.51.1.1 d.51.1.1 Length = 174	Back alignment and structure

>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Length = 106	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 Length = 206	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

>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

>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii} PDB: 3aev_B Length = 219	Back alignment and structure

>2qnd_A FMR1 protein; KH domain, eukaryotic KH domains, tandem KH domains, type I domains, fragIle X mental retardation protein, RNA BI protein; 1.90A {Homo sapiens} PDB: 2fmr_A Length = 144	Back alignment and structure

>2ctf_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 102	Back alignment and structure

>2dgr_A Ring finger and KH domain-containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 83	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* Length = 605	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		335
3saf_A		428	Exosome component 10; exoribonuclease, RNA exosome	100.0
1yt3_A		375	Ribonuclease D, RNAse D; exoribonuclease, exonucle	99.98
2hbj_A		410	Exosome complex exonuclease RRP6; RNA metabolism,	99.97
2e6m_A		208	Werner syndrome ATP-dependent helicase homolog; AP	99.95
2kfn_A		605	Klenow fragment of DNA polymerase I; complex (poly	99.94
3pv8_A		592	DNA polymerase I; DNA polymerase I, protein-DNA co	99.94
1vk0_A		206	Hypothetical protein; homohexamer, AT5G06450, stru	99.93
3cym_A		440	Uncharacterized protein BAD_0989; structural genom	99.92
1x9m_A		698	DNA polymerase; DNA ploymerase, N-2-acetylaminoflu	99.85
4dfk_A		540	DNA polymerase I, thermostable; DNA polymerase, tr	99.83
1bgx_T		832	TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhi	99.62
3v9w_A		235	Ribonuclease T; DEDD nucleases family, EXO-nucleas	98.72
2p1j_A		186	POLIII, DNA polymerase III POLC-type; structural g	97.68
1wlj_A		189	Interferon stimulated gene 20KDA; exoribonuclease,	97.62
2f96_A		224	Ribonuclease T; RNAse, RNT, RNAse T, tRNA hydrolas	97.53
3mxm_B		242	Three prime repair exonuclease 1; RNAse H-like fol	97.42
1y97_A		238	Three prime repair exonuclease 2; TREX2, hydrolase	97.3
3u3y_B		314	Three prime repair exonuclease 1; RNAse H fold, 3'	96.99
2gui_A		194	DNA polymerase III epsilon subunit; DNA polymerase	96.6
2qxf_A		482	Exodeoxyribonuclease I; alpha-beta domain, DNAQ su	96.27
1vig_A		71	Vigilin; RNA-binding protein, ribonucleoprotein; N	95.72
1w0h_A		204	3'-5' exonuclease ERI1; nuclease domain, hydrolase	95.59
2axy_A		73	Poly(RC)-binding protein 2; protein-DNA complex, D	94.89
1zbh_A		299	3'-5' exonuclease ERI1; histone mRNA 3'-END-specif	94.87
1zzk_A		82	Heterogeneous nuclear ribonucleoprotein K; KH domi	94.59
1we8_A		104	Tudor and KH domain containing protein; structural	94.21
2cte_A		94	Vigilin; K homology type I domain, RNA-binding, ce	94.17
2ctm_A		95	Vigilin; K homology type I domain, RNA-binding, ce	94.04
1dtj_A		76	RNA-binding neurooncological ventral antigen 2; KH	94.01
1wvn_A		82	Poly(RC)-binding protein 1; KH domain, RNA binding	93.38
2ctj_A		95	Vigilin; K homology type I domain, RNA-binding, ce	93.36
2ctk_A		104	Vigilin; K homology type I domain, RNA-binding, ce	93.14
1qht_A		775	Protein (DNA polymerase); archaea, hyperthermostab	93.1
2ctl_A		97	Vigilin; K homology type I domain, RNA-binding, ce	93.09
1j5k_A		89	Heterogeneous nuclear ribonucleoprotein K; single-	92.64
2p2r_A		76	Poly(RC)-binding protein 2; protein-DNA complex, R	92.48
2hh2_A		107	KH-type splicing regulatory protein; KH-RNA bindin	92.43
1x4m_A		94	FAR upstream element binding protein 1; KH domain,	92.23
1ec6_A		87	RNA-binding protein NOVA-2; KH domain, alpha-beta	91.98
1x4n_A		92	FAR upstream element binding protein 1; KH domain,	91.88
2hh3_A		106	KH-type splicing regulatory protein; KH-RNA bindin	91.61
2opv_A		85	KHSRP protein; KH domain, RNA binding protein, KSR	91.47
3cg7_A		308	CRN-4, cell death-related nuclease 4; hydrolase, a	91.06
2jzx_A		160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	90.87
2xri_A		224	ERI1 exoribonuclease 3; hydrolase, metal binding;	89.52
3krm_A		163	Insulin-like growth factor 2 mRNA-binding protein	87.18
1j4w_A		174	FUSE binding protein; single-stranded DNA binding	86.65
2jvz_A		164	KH type-splicing, FAR upstream element-binding pro	86.45
3ikm_A		1172	DNA polymerase subunit gamma-1; human mitochondria	86.36
2jvz_A		164	KH type-splicing, FAR upstream element-binding pro	85.91
3tr8_A		186	Oligoribonuclease; transcription, hydrolase; 2.50A	84.43
2jzx_A		160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	84.19
3krm_A		163	Insulin-like growth factor 2 mRNA-binding protein	83.88
2dgr_A		83	Ring finger and KH domain-containing protein 1; st	82.68
1noy_A		388	Protein (DNA polymerase (E.C.2.7.7.7)); exonucleas	81.58
1j4w_A		174	FUSE binding protein; single-stranded DNA binding	81.24
2anr_A		178	Neuro-oncological ventral antigen 1; protein-RNA c	81.23
2igi_A		180	Oligoribonuclease; RNAse, exoribonuclease, exonucl	80.92
1zbu_A		349	ERI-1 homolog, 3'-5' exonuclease ERI1; hydrolase;	80.32

>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=100.00  E-value=1.2e-32  Score=268.17  Aligned_cols=260  Identities=20%  Similarity=0.271  Sum_probs=212.4

Q ss_pred             cCeEEeCCccchhHHHhhhhccCCceEEEEEeecCCC-ccCcEEEEEEEeCCceEEEEccCCChhhHHHHHHHHcCCCce
Q 019798           26 VPIHIVTNASQLPAEFLEPSSERQLVIGFDCEGVDLC-RHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYIT  104 (335)
Q Consensus        26 ~~~~~I~t~~~L~~~~l~~~~~~~~~ia~D~E~~~~~-~~~~l~~lqla~~~~~~lid~~~~~~~~~~~Lk~lLe~~~i~  104 (335)
                      .+|++|+|.+++.+ +++.+ ..+..+|||+||.+.. +.+.+|+||||+.+++|+||+..++. .+..|+++|+|+++.
T Consensus       108 ~~y~~I~t~e~L~~-~l~~L-~~~~~vavDtE~~~~~~~~~~l~lIQLa~~~~~~lidpl~l~~-~l~~L~~lL~dp~i~  184 (428)
T 3saf_A          108 TPCHFISSLDELVE-LNEKL-LNCQEFAVNLEHHSYRSFLGLTCLMQISTRTEDFIIDTLELRS-DMYILNESLTDPAIV  184 (428)
T ss_dssp             SCEEEECSHHHHHH-HHHHH-TTCSEEEEEEEEECTTCSSCEEEEEEEECSSCEEEEETTTTGG-GGGGGHHHHTCTTSE
T ss_pred             CCcEEECCHHHHHH-HHHHH-hcCCeEEEEEEecCCCCCCCeEEEEEEEeCCcEEEEEeccchh-hHHHHHHHHcCCCce
Confidence            67899999999997 99884 6788999999999875 78999999999988999999987743 468899999999999


Q ss_pred             EEEEechhcHHHHHHHcCCccceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCcccchhHHHHHHhcCCCCC
Q 019798          105 KVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQF  184 (335)
Q Consensus       105 KV~hd~k~D~~~L~~~~gi~l~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l~~k~~~~~~~~~~~~~  184 (335)
                      ||+||+|+|+++|++.+|+.+.++||||+|+|+++++  ++       ||+.|++  +|||+++++. .       ..++
T Consensus       185 KV~H~~k~Dl~~L~~~~Gi~~~~~fDT~lAa~lL~~~--~~-------gL~~Lv~--~~Lg~~l~K~-~-------~~sd  245 (428)
T 3saf_A          185 KVFHGADSDIEWLQKDFGLYVVNMFDTHQAARLLNLG--RH-------SLDHLLK--LYCNVDSNKQ-Y-------QLAD  245 (428)
T ss_dssp             EEESSCHHHHHHHHHHHCCCCSSEEEHHHHHHHTTCS--CC-------SHHHHHH--HHHCCCCCCT-T-------TTSC
T ss_pred             EEEeehHHHHHHHHHHcCCCcCceeechhHHHHhCCC--CC-------CHHHHHH--HHcCCCCCcc-c-------cccc
Confidence            9999999999999778999999999999999999974  23       8999999  9999998742 2       2359


Q ss_pred             CccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhccccH------HHHHHhhhh-ccc-----c-c-------------cc
Q 019798          185 WTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLW------YLAVRGALY-CRC-----F-C-------------IN  238 (335)
Q Consensus       185 w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~~~l~------~l~~~~e~~-~~v-----L-~-------------me  238 (335)
                      |..|||+++|+.|||.||+++++||+.|.++|.+.|.+      .++.+.+.. .+.     . .             +.
T Consensus       246 W~~rpLs~~q~~YAA~DA~~ll~L~~~L~~~L~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  325 (428)
T 3saf_A          246 WRIRPLPEEMLSYARDDTHYLLYIYDKMRLEMWERGNGQPVQLQVVWQRSRDICLKKFIKPIFTDESYLELYRKQKKHLN  325 (428)
T ss_dssp             TTCSSCCHHHHHHHHHHHHTHHHHHHHHHHHHHHHTTSCSHHHHHHHHHHHHHTTCCCCCCCCCTTGGGHHHHTTCCCCC
T ss_pred             cccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHHHHHHHHHHHHhhcCCCCCcccHHHHHHHhccCCC
Confidence            99999999999999999999999999999999988751      233333321 111     1 0             00


Q ss_pred             CCc------cCCCCCCCCCCCcccccCCCCHHHHHhhhcCCCCccc----------cccccccccHHHHHHHhhhhhhhc
Q 019798          239 END------YVDWPPLPPVPDYLIVEGDVPEEEILSILDVPPGKMG----------RIIGRRGSSILAIKESCNAEILIG  302 (335)
Q Consensus       239 ~~g------~~d~~~L~~~~~~l~~~~~~~e~~i~~lAg~~~~~~~----------~~~~~~~~~~~~~~~~~~~~~~~~  302 (335)
                      ..+      ...||.-.++..+.++..+..++.++++|..+|.++.          ..++++|..|+.+++.+.+.    
T Consensus       326 ~~~l~l~~~L~~wR~~~Ar~~d~p~~~V~~d~~L~~iA~~~P~~~~~L~~i~g~~~~~~r~~g~~~l~~I~~a~~~----  401 (428)
T 3saf_A          326 TQQLTAFQLLFAWRDKTARREDESYGYVLPNHMMLKIAEELPKEPQGIIACCNPVPPLVRQQINEMHLLIQQAREM----  401 (428)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTCCHHHHCCHHHHHHHHHHCCSSHHHHHTTCSSCCHHHHHTHHHHHHHHHHHHTS----
T ss_pred             hHHHHHHHHHHHHHHHHHHHcCCCcCEEECHHHHHHHHHHCCCCHHHHHhccCCCHHHHHHHHHHHHHHHHHHHhC----
Confidence            000      1267777788899999999999999999999997753          57789999999999998543    


Q ss_pred             CCCCCCCcc
Q 019798          303 GAKGPPDKV  311 (335)
Q Consensus       303 ~~~~~~~~~  311 (335)
                      +..+|+...
T Consensus       402 p~~~~~~~~  410 (428)
T 3saf_A          402 PLLKSEVAA  410 (428)
T ss_dssp             CCCHHHHCC
T ss_pred             CCcCcchhh
Confidence            555555543

PyMOL of 3saf

>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

>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

>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

>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

>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

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

>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

>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

>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

>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

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

>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

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

>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

>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1vih_A	Back alignment and structure

>1w0h_A 3'-5' exonuclease ERI1; nuclease domain, hydrolase; HET: AMP; 1.59A {Homo sapiens} SCOP: c.55.3.5	Back alignment and structure

>2axy_A Poly(RC)-binding protein 2; protein-DNA complex, DNA binding protein-DNA complex; 1.70A {Homo sapiens} SCOP: d.51.1.1 PDB: 2pqu_A 2py9_A 1ztg_A 3vke_A*	Back alignment and structure

>1zbh_A 3'-5' exonuclease ERI1; histone mRNA 3'-END-specific recognition, structures of 3'- exonuclease and ITS RNA complex, hydrolase/RNA complex; HET: AMP; 3.00A {Homo sapiens}	Back alignment and structure

>1zzk_A Heterogeneous nuclear ribonucleoprotein K; KH domian, alpha-beta fold, DNA binding protein; 0.95A {Homo sapiens} SCOP: d.51.1.1 PDB: 1zzj_A 1zzi_A	Back alignment and structure

>1we8_A Tudor and KH domain containing protein; structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.51.1.1	Back alignment and structure

>2cte_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1	Back alignment and structure

>2ctm_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1	Back alignment and structure

>1dtj_A RNA-binding neurooncological ventral antigen 2; KH domain, alpha-beta fold RNA-binding motif, immune system; 2.00A {Homo sapiens} SCOP: d.51.1.1 PDB: 1dt4_A	Back alignment and structure

>1wvn_A Poly(RC)-binding protein 1; KH domain, RNA binding domain, RNA binding protein; 2.10A {Homo sapiens} SCOP: d.51.1.1	Back alignment and structure

>2ctj_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1	Back alignment and structure

>2ctk_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1	Back alignment and structure

>1qht_A Protein (DNA polymerase); archaea, hyperthermostable, family B polymer alpha family polymerase, transferase; 2.10A {Thermococcus SP} SCOP: c.55.3.5 e.8.1.1 PDB: 1tgo_A 2xhb_A* 2vwj_A* 2vwk_A* 1wns_A* 1wn7_A 1qqc_A* 4ahc_A* 4ail_C* 3a2f_A* 2jgu_A* 1d5a_A	Back alignment and structure

>2ctl_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1	Back alignment and structure

>1j5k_A Heterogeneous nuclear ribonucleoprotein K; single-stranded DNA binding protein, transcription factor, hnRNP K, CT element, C-MYC oncogene; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1khm_A	Back alignment and structure

>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA binding protein/DNA complex; 1.60A {Homo sapiens}	Back alignment and structure

>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens}	Back alignment and structure

>1x4m_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1	Back alignment and structure

>1ec6_A RNA-binding protein NOVA-2; KH domain, alpha-beta fold, RNA-binding motif, protein/RNA structure, RNA binding protein/RNA complex; 2.40A {Homo sapiens} SCOP: d.51.1.1	Back alignment and structure

>1x4n_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 PDB: 2opu_A	Back alignment and structure

>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens}	Back alignment and structure

>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens}	Back alignment and structure

>3cg7_A CRN-4, cell death-related nuclease 4; hydrolase, apoptosis, 3'-5' exonuclease, deddh; 2.50A {Caenorhabditis elegans} PDB: 3cm5_A 3cm6_A	Back alignment and structure

>2jzx_A Poly(RC)-binding protein 2; PCBP2, KH domains, RNA binding, DNA-binding, nucleus, phosph ribonucleoprotein, RNA-binding, RNA binding protein; NMR {Homo sapiens}	Back alignment and structure

>2xri_A ERI1 exoribonuclease 3; hydrolase, metal binding; 2.15A {Homo sapiens}	Back alignment and structure

>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain, cell projection, cytoplasm, nucleus, phosphoprotein, translation regulation; 2.75A {Homo sapiens}	Back alignment and structure

>1j4w_A FUSE binding protein; single-stranded DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: d.51.1.1 d.51.1.1	Back alignment and structure

>2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA binding protein, KH domain, KSRP, posttranscriptional regulation, mRNA decay; NMR {Homo sapiens}	Back alignment and structure

>3ikm_A DNA polymerase subunit gamma-1; human mitochondrial DNA polymerase, disease mutation, DNA replication, DNA-binding, DNA-directed DNA polymerase; HET: DNA; 3.24A {Homo sapiens}	Back alignment and structure

>2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA binding protein, KH domain, KSRP, posttranscriptional regulation, mRNA decay; NMR {Homo sapiens}	Back alignment and structure

>3tr8_A Oligoribonuclease; transcription, hydrolase; 2.50A {Coxiella burnetii}	Back alignment and structure

>2jzx_A Poly(RC)-binding protein 2; PCBP2, KH domains, RNA binding, DNA-binding, nucleus, phosph ribonucleoprotein, RNA-binding, RNA binding protein; NMR {Homo sapiens}	Back alignment and structure

>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain, cell projection, cytoplasm, nucleus, phosphoprotein, translation regulation; 2.75A {Homo sapiens}	Back alignment and structure

>2dgr_A Ring finger and KH domain-containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>1noy_A Protein (DNA polymerase (E.C.2.7.7.7)); exonuclease, DNA-binding, complex (nucleotidyltransferase/DNA); HET: DNA; 2.20A {Enterobacteria phage T4} SCOP: c.55.3.5 PDB: 1noz_A*	Back alignment and structure

>1j4w_A FUSE binding protein; single-stranded DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: d.51.1.1 d.51.1.1	Back alignment and structure

>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A*	Back alignment and structure

>2igi_A Oligoribonuclease; RNAse, exoribonuclease, exonuclease, hydrolase, mRNA decay; 1.70A {Escherichia coli} SCOP: c.55.3.5 PDB: 1yta_A 1j9a_A	Back alignment and structure

>1zbu_A ERI-1 homolog, 3'-5' exonuclease ERI1; hydrolase; HET: AMP; 3.00A {Homo sapiens}	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		335
d1vk0a_		206	c.55.3.5 (A:) Hypothetical protein AT5G06450 {Thal	1e-19
d2hbka2		292	c.55.3.5 (A:129-420) Exosome complex exonuclease R	1e-15
d2ctea1		81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	9e-11
d2axya1		71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	3e-10
d1viga_		71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	6e-10
d2ctka1		91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	3e-09
d1dtja_		74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	7e-09
d1wvna1		70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	8e-09
d1x4ma1		81	d.51.1.1 (A:8-88) Far upstream binding element, FB	8e-09
d1yt3a3		193	c.55.3.5 (A:1-193) Ribonuclease D, catalytic domai	1e-08
d1x4na1		79	d.51.1.1 (A:8-86) Far upstream binding element, FB	5e-08
d1we8a_		104	d.51.1.1 (A:) Tudor and KH domain containing prote	1e-07
d1zzka1		75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	1e-07
d2ctla1		84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	1e-07
d2ba0a3		84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	2e-07
d2ctja1		82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	2e-07
d2ctma1		81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	2e-07
d2hhva1		171	c.55.3.5 (A:298-468) Exonuclease domain of prokary	4e-07
d2je6i3		69	d.51.1.1 (I:153-221) Exosome complex RNA-binding p	1e-06
d1j4wa1		74	d.51.1.1 (A:1-74) Far upstream binding element, FB	1e-06
d1j4wa2		71	d.51.1.1 (A:104-174) Far upstream binding element,	2e-06
d2z0sa2		87	d.51.1.1 (A:148-234) Exosome complex RNA-binding p	7e-06
d1kfsa1		195	c.55.3.5 (A:324-518) Exonuclease domain of prokary	7e-06
d1tuaa2		104	d.51.1.1 (A:85-188) Hypothetical protein APE0754 {	1e-05
d2cpqa1		78	d.51.1.1 (A:212-289) Fragile X mental retardation	3e-04
d1tuaa1		84	d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Ae	0.004

>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 = 83.5 bits (206), Expect = 1e-19
 Identities = 20/176 (11%), Positives = 51/176 (28%), Gaps = 24/176 (13%)

Query: 49  QLVIGFDCE---------GVDLCRHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALE 99
              + FD                   SL  ++L+  +    +   +     +K       
Sbjct: 46  NRAVIFDVYWDVGFPETETKTKTSGWSLSSVKLSTRNLCLFLRLPKPFHDNLKDLYRFFA 105

Query: 100 SSYITKVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLA 159
           S ++T V    + D + L    G+ + N ++     +        +     ++    L  
Sbjct: 106 SKFVTFVGVQIEEDLDLLRENHGLVIRNAINVGKLAAEARGTLVLE-----FLGTRELAH 160

Query: 160 DPRYCGISYQEKEEVRVLLRQDPQFWTYRPLTELMVRAAADDVRFLPYIYHNMMKK 215
             R       + + +          W  +   E  + AAA +   +  ++  +  +
Sbjct: 161 --RVLWSDLGQLDSIE-------AKWE-KAGPEEQLEAAAIEGWLIVNVWDQLSDE 206

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

>d2ctea1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81	Back information, alignment and structure

>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 71	Back information, alignment and structure

>d1viga_ d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 71	Back information, alignment and structure

>d2ctka1 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 91	Back information, alignment and structure

>d1dtja_ d.51.1.1 (A:) Neuro-oncological ventral antigen 2, nova-2, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 74	Back information, alignment and structure

>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 70	Back information, alignment and structure

>d1x4ma1 d.51.1.1 (A:8-88) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 81	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

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 79	Back information, alignment and structure

>d1we8a_ d.51.1.1 (A:) Tudor and KH domain containing protein, Tdrkh {Mouse (Mus musculus) [TaxId: 10090]} Length = 104	Back information, alignment and structure

>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 75	Back information, alignment and structure

>d2ctla1 d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 84	Back information, alignment and structure

>d2ba0a3 d.51.1.1 (A:136-219) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 84	Back information, alignment and structure

>d2ctja1 d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 82	Back information, alignment and structure

>d2ctma1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81	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]} Length = 171	Back information, alignment and structure

>d2je6i3 d.51.1.1 (I:153-221) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]} Length = 69	Back information, alignment and structure

>d1j4wa1 d.51.1.1 (A:1-74) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 74	Back information, alignment and structure

>d1j4wa2 d.51.1.1 (A:104-174) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 71	Back information, alignment and structure

>d2z0sa2 d.51.1.1 (A:148-234) Exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]} Length = 87	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

>d1tuaa2 d.51.1.1 (A:85-188) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]} Length = 104	Back information, alignment and structure

>d2cpqa1 d.51.1.1 (A:212-289) Fragile X mental retardation syndrome related protein 1, FXR1 {Human (Homo sapiens) [TaxId: 9606]} Length = 78	Back information, alignment and structure

>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]} Length = 84	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		335
d2hbka2		292	Exosome complex exonuclease RRP6 {Baker's yeast (S	100.0
d1yt3a3		193	Ribonuclease D, catalytic domain {Escherichia coli	100.0
d1vk0a_		206	Hypothetical protein AT5G06450 {Thale-cress (Arabi	99.93
d1kfsa1		195	Exonuclease domain of prokaryotic DNA polymerase {	99.92
d2hhva1		171	Exonuclease domain of prokaryotic DNA polymerase {	99.9
d1wlja_		173	Interferon-stimulated gene 20 kDa protein, ISG20 {	98.17
d1x9ma1		204	Exonuclease domain of T7 DNA polymerase {Bacteriop	97.93
d3b6oa1		226	Three prime repair exonuclease 1, TREX1 {Mouse (Mu	96.7
d1viga_		71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	95.91
d2axya1		71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	95.54
d2ctka1		91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	95.52
d2ctea1		81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	95.46
d1y97a1		228	Three prime repair exonuclease 2, TREX2 {Human (Ho	95.45
d2ctma1		81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	95.38
d1zzka1		75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	95.37
d1tgoa1		347	Exonuclease domain of family B DNA polymerases {Ar	95.23
d1wvna1		70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	95.13
d2ctla1		84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	94.89
d1j4wa2		71	Far upstream binding element, FBP {Human (Homo sap	94.79
d1qtma1		130	Exonuclease domain of prokaryotic DNA polymerase {	94.36
d1x4ma1		81	Far upstream binding element, FBP {Mouse (Mus musc	94.36
d2f96a1		202	Ribonuclease T {Pseudomonas aeruginosa [TaxId: 287	94.35
d2guia1		174	N-terminal exonuclease domain of the epsilon subun	94.3
d1qtma2		409	DNA polymerase I (Klenow fragment) {Thermus aquati	94.14
d1we8a_		104	Tudor and KH domain containing protein, Tdrkh {Mou	93.69
d2ba0a3		84	Exosome complex RNA-binding protein 1, ECR1 {Archa	93.65
d2ctja1		82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	93.18
d1kfsa2		410	DNA polymerase I (Klenow fragment) {Escherichia co	91.85
d1j4wa1		74	Far upstream binding element, FBP {Human (Homo sap	91.75
d1x4na1		79	Far upstream binding element, FBP {Mouse (Mus musc	91.37
d1dtja_		74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	91.23
d2cpqa1		78	Fragile X mental retardation syndrome related prot	91.16
d2je6i3		69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	89.73
d2hhva2		408	DNA polymerase I (Klenow fragment) {Bacillus stear	87.81
d2z0sa2		87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	87.37
d2cpra1		113	Exosome component 10, EXOSC10 {Human (Homo sapiens	84.88
d2ctfa1		90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	82.04
d1yt3a1		101	Ribonuclease D {Escherichia coli [TaxId: 562]}	81.7
d1tuaa2		104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	80.44

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

Probab=100.00  E-value=2e-33  Score=258.05  Aligned_cols=179  Identities=26%  Similarity=0.314  Sum_probs=159.9

Q ss_pred             cCeEEeCCccchhHHHhhhhccCCceEEEEEeecCCC-ccCcEEEEEEEeCCceEEEEccCCChhhHHHHHHHHcCCCce
Q 019798           26 VPIHIVTNASQLPAEFLEPSSERQLVIGFDCEGVDLC-RHGSLCIMQLAFPDAIYLVDAIQGGETVVKACKPALESSYIT  104 (335)
Q Consensus        26 ~~~~~I~t~~~L~~~~l~~~~~~~~~ia~D~E~~~~~-~~~~l~~lqla~~~~~~lid~~~~~~~~~~~Lk~lLe~~~i~  104 (335)
                      .++.+|+|.++|.+ +++.+ +++..+|||+|+.+.. +.|.+|+||||+.+++|+||+..+... +..|+++|+|++|.
T Consensus        83 t~~~~Vdt~e~L~~-li~~L-~~~~~iavDtE~~~~~s~~g~l~LiQiat~~~~~iiD~~~l~~~-l~~L~~ll~d~~I~  159 (292)
T d2hbka2          83 SVPIWVDTSTELES-MLEDL-KNTKEIAVDLEHHDYRSYYGIVCLMQISTRERDYLVDTLKLREN-LHILNEVFTNPSIV  159 (292)
T ss_dssp             CCCEEECSHHHHHH-HHHHH-TTCSEEEEEEEEECSSSSSCEEEEEEEECSSCEEEEETTTTTTT-GGGGHHHHTCTTSE
T ss_pred             CCcEEeCCHHHHHH-HHHHH-hcCCcEEEEEEeCcCcccCCeEEEEEEEeCCccEEEEecccccc-hHHHHHHHhccCeE
Confidence            56889999999997 99984 8899999999999885 789999999999999999999887643 57899999999999


Q ss_pred             EEEEechhcHHHHHHHcCCccceEeehhHHHHhhhhccCCCCCCCCcccHHhhhcCCcccCcccchhHHHHHHhcCCCCC
Q 019798          105 KVIHDCKRDSEALYFQFGIKLHNVVDTQIAYSLIEEQEGRKRSPDDYISFVGLLADPRYCGISYQEKEEVRVLLRQDPQF  184 (335)
Q Consensus       105 KV~hd~k~D~~~L~~~~gi~l~~vfDt~lAayLL~~~~~~~~l~~~~~sL~~L~~~~~~L~~~l~~k~~~~~~~~~~~~~  184 (335)
                      ||+||+++|+.+|++.+|+.+.++||||+|+++++..  +       .||+.|++  +|||++++|+.+        .+|
T Consensus       160 KV~H~~~~Di~~L~~~~g~~~~n~fDT~~aa~~l~~~--~-------~sL~~L~~--~yl~~~ldK~~q--------~Sd  220 (292)
T d2hbka2         160 KVFHGAFMDIIWLQRDLGLYVVGLFDTYHASKAIGLP--R-------HSLAYLLE--NFANFKTSKKYQ--------LAD  220 (292)
T ss_dssp             EEESSCHHHHHHHHHHHCCCCSSEEEHHHHHHHHTCS--C-------CSHHHHHH--HHHCCCCCCTTT--------TSC
T ss_pred             EEeechHhhhhhhhhcccccccchHHHHHHHHHhCcc--c-------cchHHHHH--Hhhhhccccccc--------ccc
Confidence            9999999999999999999999999999999999753  2       38999999  999999985332        259


Q ss_pred             CccCCCCHHHHHHHHhhhhHHHHHHHHHHHHHhccccHHHHH
Q 019798          185 WTYRPLTELMVRAAADDVRFLPYIYHNMMKKLNQQSLWYLAV  226 (335)
Q Consensus       185 w~~rpL~~~~~~YAa~Da~~ll~L~~~L~~~L~~~~l~~l~~  226 (335)
                      |..|||+++|+.|||.||++++.||+.|+.+|.+.|...+..
T Consensus       221 W~~RPLs~~qi~YAa~Da~~Ll~ly~~L~~~L~~~~~l~~v~  262 (292)
T d2hbka2         221 WRIRPLSKPMTAAARADTHFLLNIYDQLRNKLIESNKLAGVL  262 (292)
T ss_dssp             TTCSSCCHHHHHHHHHHHHTHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             cccCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHH
Confidence            999999999999999999999999999999999888655443

PyMOL of d2hbka2

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

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

>d1viga_ d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2ctka1 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2ctea1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]}	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

>d2ctma1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	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

>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2ctla1 d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1j4wa2 d.51.1.1 (A:104-174) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1qtma1 c.55.3.5 (A:293-422) Exonuclease domain of prokaryotic DNA polymerase {Thermus aquaticus [TaxId: 271]}	Back information, alignment and structure

>d1x4ma1 d.51.1.1 (A:8-88) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2f96a1 c.55.3.5 (A:19-220) Ribonuclease T {Pseudomonas aeruginosa [TaxId: 287]}	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

>d1qtma2 e.8.1.1 (A:423-831) DNA polymerase I (Klenow fragment) {Thermus aquaticus [TaxId: 271]}	Back information, alignment and structure

>d1we8a_ d.51.1.1 (A:) Tudor and KH domain containing protein, Tdrkh {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2ba0a3 d.51.1.1 (A:136-219) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]}	Back information, alignment and structure

>d2ctja1 d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1kfsa2 e.8.1.1 (A:519-928) DNA polymerase I (Klenow fragment) {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1j4wa1 d.51.1.1 (A:1-74) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1dtja_ d.51.1.1 (A:) Neuro-oncological ventral antigen 2, nova-2, KH3 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cpqa1 d.51.1.1 (A:212-289) Fragile X mental retardation syndrome related protein 1, FXR1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2je6i3 d.51.1.1 (I:153-221) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]}	Back information, alignment and structure

>d2hhva2 e.8.1.1 (A:469-876) DNA polymerase I (Klenow fragment) {Bacillus stearothermophilus, newly identified strain as yet unnamed [TaxId: 1422]}	Back information, alignment and structure

>d2z0sa2 d.51.1.1 (A:148-234) Exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]}	Back information, alignment and structure

>d2cpra1 a.60.8.4 (A:483-595) Exosome component 10, EXOSC10 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2ctfa1 d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1yt3a1 a.60.8.3 (A:194-294) Ribonuclease D {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1tuaa2 d.51.1.1 (A:85-188) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]}	Back information, alignment and structure