Psyllid ID: psy3897

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
MKRRRRSDEKRLKAKSLTSMSVWERKSLFRKLPPRTGFNPVCTSGLRISALDHVGGINGPLEGYVKTKPRKSPPPNGYGVYALDTEMVYTVHGLEVARVTVVNVDGRLIYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMGFVSKDSIIVGHGLENDLRALKLIHSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQSGTHDSFEDARACIDLILWKLLSDFRYNH
ccccccHHHHHHHcccccccHHHHHHHHHcccccccccccccccccEEEEEEEcccccccccccEEcccccccccccccEEEEEEcEEEEccccEEEEEEEEEccccEEEEEEccccccccccccccccccHHHHcccccccHHHHHHHHHHccccccEEEEEcHHHHHHHHccccccEEEcccccccccccccccHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHcccccc
ccccccHHHHHHHHHHHHHHHHHHHHHHHHccccHHccccccccccEEcccEccccccccccccEEcccccccccccccEEEEEEEEEEEcccEEEEEEEEEEcccEEEEEEEEcccccEEEcccccccccHHHHHccccccHHHHHHHHHHHcccccEEEEcccHHHHHHHHHHcccEEcEEEEcccccccccHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHccccccc
mkrrrrsdekrlkakslTSMSVWERKSlfrklpprtgfnpvctsglrisaldhvggingplegyvktkprkspppngygvyaldtEMVYTVHGLEVARVTVVNVDgrliyntlvkpdceiidyntkysgisakdfirnpyktLKDVQNDLmgfvskdsiivGHGLENDLRALKLIHSniidtsvlfphsfglpyrrSLKSIVSQLLHQSiqsgthdsfeDARACIDLILWKLLSDFRYNH
mkrrrrsdekrlkaksltsmsvwerkslfrklpprtgfnpvCTSGLRISALDHVGGINGPLEgyvktkprkspppNGYGVYALDTEMVYTVHGLEVARVTvvnvdgrliyntlvkpdceiidyntkysgisakdfIRNPYKTLKDVQNDLMGFVSKDSIIVGHGLENDLRALKLIHSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQsgthdsfeDARACIDLILWKLLSDFRYNH
MKRRRRSDEKRLKAKSLTSMSVWERKSLFRKLPPRTGFNPVCTSGLRISALDHVGGINGPLEGYVKTKPRKSPPPNGYGVYALDTEMVYTVHGLEVARVTVVNVDGRLIYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMGFVSKDSIIVGHGLENDLRALKLIHSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQSGTHDSFEDARACIDLILWKLLSDFRYNH
*********************VWERKSLFRKLPPRTGFNPVCTSGLRISALDHVGGINGPLEGYV***********GYGVYALDTEMVYTVHGLEVARVTVVNVDGRLIYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMGFVSKDSIIVGHGLENDLRALKLIHSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQSGTHDSFEDARACIDLILWKLLSDFR***
**********************************************************GPLE*****************VYALDTEMVYTVHGLEVARVTVVNVDGRLIYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMGFVSKDSIIVGHGLENDLRALKLIHSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQSGTHDSFEDARACIDLILWKLLSDFR*N*
**************KSLTSMSVWERKSLFRKLPPRTGFNPVCTSGLRISALDHVGGINGPLEGYVKTKPRKSPPPNGYGVYALDTEMVYTVHGLEVARVTVVNVDGRLIYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMGFVSKDSIIVGHGLENDLRALKLIHSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQSGTHDSFEDARACIDLILWKLLSDFRYNH
*****RSDEKRLKAKSLTSMSVWERKSLFRKLPPRTGFNPVCTSGLRISALDHVGGINGPLEGYVKTKPRKSPPPNGYGVYALDTEMVYTVHGLEVARVTVVNVDGRLIYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMGFVSKDSIIVGHGLENDLRALKLIHSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQSGTHDSFEDARACIDLILWKLLSDF****
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SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooo
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MKRRRRSDEKRLKAKSLTSMSVWERKSLFRKLPPRTGFNPVCTSGLRISALDHVGGINGPLEGYVKTKPRKSPPPNGYGVYALDTEMVYTVHGLEVARVTVVNVDGRLIYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMGFVSKDSIIVGHGLENDLRALKLIHSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQSGTHDSFEDARACIDLILWKLLSDFRYNH
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 ?
Query240 2.2.26 [Sep-21-2011]
Q7TT281213 RNA exonuclease 1 homolog yes N/A 0.725 0.143 0.497 3e-46
A0PJM3583 Putative exonuclease GOR- no N/A 0.712 0.293 0.5 1e-45
Q8IX06675 Exonuclease GOR OS=Homo s yes N/A 0.708 0.251 0.508 2e-45
P48778 690 Exonuclease GOR OS=Pan tr yes N/A 0.637 0.221 0.532 4e-45
Q8N1G11221 RNA exonuclease 1 homolog no N/A 0.725 0.142 0.508 4e-41
P53331 553 RNA exonuclease 1 OS=Sacc yes N/A 0.675 0.292 0.432 6e-37
Q8L7M4 567 Small RNA degrading nucle yes N/A 0.666 0.282 0.439 4e-32
O94443 631 Uncharacterized exonuclea yes N/A 0.704 0.267 0.404 4e-30
Q6CFE7757 RNA exonuclease 3 OS=Yarr no N/A 0.620 0.196 0.417 9e-29
Q101241647 Putative RNA exonuclease no N/A 0.654 0.095 0.392 2e-27
>sp|Q7TT28|REXO1_MOUSE RNA exonuclease 1 homolog OS=Mus musculus GN=Rexo1 PE=1 SV=1 Back     alignment and function desciption
 Score =  184 bits (468), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 88/177 (49%), Positives = 126/177 (71%), Gaps = 3/177 (1%)

Query: 61   LEGYVKTKPRKSPPPNGYGVYALDTEMVYTVHGLEVARVTVVNVDGRLIYNTLVKPDCEI 120
            LEG+V+T  ++ P     GV+ALD EM YT +GLE+ RVTVV+ D +++Y+T VKPD E+
Sbjct: 1033 LEGFVRTFQKELPEDAHAGVFALDCEMSYTTYGLELTRVTVVDTDMQVVYDTFVKPDNEV 1092

Query: 121  IDYNTKYSGISAKDFIRNPYKTLKDVQNDLMGFVSKDSIIVGHGLENDLRALKLIHSNII 180
            +DYNT++SG++  D +     TL+DVQ  L+   S D+I++GH LE+DL ALK+IH  ++
Sbjct: 1093 VDYNTRFSGVTEADLVDTSI-TLRDVQAVLLSMFSADTILIGHSLESDLLALKVIHGTVV 1151

Query: 181  DTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQSGT--HDSFEDARACIDLILWKLLSD 235
            DTSVLFPH  GLPY+RSL+++++  L Q IQ     H S EDA AC+ L++WK+  D
Sbjct: 1152 DTSVLFPHRLGLPYKRSLRNLMADYLRQIIQDNVDGHSSSEDASACMHLVIWKIRED 1208
Seems to have no detectable effect on transcription elongation in vitro.
Mus musculus (taxid: 10090)
EC: 3EC: .EC: 1EC: .EC: -EC: .EC: -
>sp|A0PJM3|GORL_HUMAN Putative exonuclease GOR-like protein OS=Homo sapiens GN=REXO1L2P PE=5 SV=2 Back     alignment and function description
>sp|Q8IX06|GOR_HUMAN Exonuclease GOR OS=Homo sapiens GN=REXO1L1 PE=2 SV=2 Back     alignment and function description
>sp|P48778|GOR_PANTR Exonuclease GOR OS=Pan troglodytes GN=REXO1L1 PE=2 SV=3 Back     alignment and function description
>sp|Q8N1G1|REXO1_HUMAN RNA exonuclease 1 homolog OS=Homo sapiens GN=REXO1 PE=1 SV=3 Back     alignment and function description
>sp|P53331|REXO1_YEAST RNA exonuclease 1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RNH70 PE=1 SV=1 Back     alignment and function description
>sp|Q8L7M4|SDN5_ARATH Small RNA degrading nuclease 5 OS=Arabidopsis thaliana GN=SDN5 PE=2 SV=2 Back     alignment and function description
>sp|O94443|YFE9_SCHPO Uncharacterized exonuclease C637.09 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPAC637.09 PE=3 SV=2 Back     alignment and function description
>sp|Q6CFE7|REXO3_YARLI RNA exonuclease 3 OS=Yarrowia lipolytica (strain CLIB 122 / E 150) GN=REX3 PE=3 SV=1 Back     alignment and function description
>sp|Q10124|PQE1_CAEEL Putative RNA exonuclease pqe-1 OS=Caenorhabditis elegans GN=pqe-1 PE=2 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 ?
Query240
340721850 688 PREDICTED: hypothetical protein LOC10064 0.766 0.267 0.548 1e-54
383864443 706 PREDICTED: uncharacterized protein LOC10 0.762 0.259 0.545 1e-53
350407949 711 PREDICTED: hypothetical protein LOC10074 0.75 0.253 0.560 1e-53
110761032 709 PREDICTED: hypothetical protein LOC72532 0.775 0.262 0.531 6e-52
322790469 537 hypothetical protein SINV_00717 [Solenop 0.754 0.337 0.550 1e-51
332024765 629 Exonuclease GOR [Acromyrmex echinatior] 0.754 0.287 0.524 2e-50
195059354273 GH17667 [Drosophila grimshawi] gi|193896 0.762 0.670 0.489 2e-49
195134402 902 GI11131 [Drosophila mojavensis] gi|19390 0.729 0.194 0.473 5e-48
195392620 879 GJ19056 [Drosophila virilis] gi|19414946 0.762 0.208 0.459 8e-48
194912654 773 GG12883 [Drosophila erecta] gi|190648225 0.8 0.248 0.474 8e-48
>gi|340721850|ref|XP_003399327.1| PREDICTED: hypothetical protein LOC100646430 [Bombus terrestris] Back     alignment and taxonomy information
 Score =  219 bits (557), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 102/186 (54%), Positives = 141/186 (75%), Gaps = 2/186 (1%)

Query: 56  GINGPLEGYVKTKPRKSPPPNG-YGVYALDTEMVYTVHGLEVARVTVVNVDGRLIYNTLV 114
           G NGP +GYV+T   ++ P +G YGVYALD EM +T HGLE+ +VTVV+++G+++Y+ LV
Sbjct: 503 GYNGPFDGYVRTSLARTVPIDGNYGVYALDCEMCFTKHGLELTKVTVVDINGKVVYDALV 562

Query: 115 KPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMGFVSKDSIIVGHGLENDLRALKL 174
           KPD E+IDYNT++SGI+AKD + N  KTLKDVQ DL GF+  ++I++GHGLENDLRALKL
Sbjct: 563 KPDTEVIDYNTRFSGITAKD-LANATKTLKDVQKDLTGFIHAETILIGHGLENDLRALKL 621

Query: 175 IHSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQSGTHDSFEDARACIDLILWKLLS 234
           +H+ +IDT + +PH  G P+R SLK++   +L + IQ   HDS EDAR  +DL+L KL  
Sbjct: 622 LHATVIDTCIAYPHFLGYPFRSSLKTLARTVLCKEIQVKGHDSVEDARIVMDLMLRKLQH 681

Query: 235 DFRYNH 240
           +  Y+H
Sbjct: 682 EMPYDH 687

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota
>gi|383864443|ref|XP_003707688.1| PREDICTED: uncharacterized protein LOC100880733 [Megachile rotundata] Back     alignment and taxonomy information
>gi|350407949|ref|XP_003488252.1| PREDICTED: hypothetical protein LOC100741380 [Bombus impatiens] Back     alignment and taxonomy information
>gi|110761032|ref|XP_001121184.1| PREDICTED: hypothetical protein LOC725324 [Apis mellifera] Back     alignment and taxonomy information
>gi|322790469|gb|EFZ15347.1| hypothetical protein SINV_00717 [Solenopsis invicta] Back     alignment and taxonomy information
>gi|332024765|gb|EGI64954.1| Exonuclease GOR [Acromyrmex echinatior] Back     alignment and taxonomy information
>gi|195059354|ref|XP_001995617.1| GH17667 [Drosophila grimshawi] gi|193896403|gb|EDV95269.1| GH17667 [Drosophila grimshawi] Back     alignment and taxonomy information
>gi|195134402|ref|XP_002011626.1| GI11131 [Drosophila mojavensis] gi|193906749|gb|EDW05616.1| GI11131 [Drosophila mojavensis] Back     alignment and taxonomy information
>gi|195392620|ref|XP_002054955.1| GJ19056 [Drosophila virilis] gi|194149465|gb|EDW65156.1| GJ19056 [Drosophila virilis] Back     alignment and taxonomy information
>gi|194912654|ref|XP_001982549.1| GG12883 [Drosophila erecta] gi|190648225|gb|EDV45518.1| GG12883 [Drosophila erecta] 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 ?
Query240
UNIPROTKB|A0PJM3583 REXO1L2P "Putative exonuclease 0.754 0.310 0.497 9.7e-46
MGI|MGI:19141821213 Rexo1 "REX1, RNA exonuclease 1 0.770 0.152 0.486 1e-45
UNIPROTKB|F5GW92675 REXO1L10P "Protein REXO1L10P" 0.754 0.268 0.497 2.2e-45
UNIPROTKB|Q8IX06675 REXO1L1 "Exonuclease GOR" [Hom 0.754 0.268 0.497 2.9e-45
UNIPROTKB|F1P0Z11217 REXO1 "Uncharacterized protein 0.8 0.157 0.472 8.2e-45
RGD|1564472465 RGD1564472 "similar to Transcr 0.804 0.415 0.487 1.9e-44
ZFIN|ZDB-GENE-030131-16501207 rexo1 "REX1, RNA exonuclease 1 0.758 0.150 0.489 5.8e-44
FB|FBgn0261548787 CG42666 [Drosophila melanogast 0.8 0.243 0.469 1.1e-43
UNIPROTKB|Q8N1G11221 REXO1 "RNA exonuclease 1 homol 0.770 0.151 0.497 1.6e-43
UNIPROTKB|E2QX021208 REXO1 "Uncharacterized protein 0.795 0.158 0.474 2.5e-43
UNIPROTKB|A0PJM3 REXO1L2P "Putative exonuclease GOR-like protein" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
 Score = 461 (167.3 bits), Expect = 9.7e-46, Sum P(2) = 9.7e-46
 Identities = 93/187 (49%), Positives = 128/187 (68%)

Query:    50 ALDHV-GGINGPLEGYVKTKPRKSPPPNGY-GVYALDTEMVYTVHGLEVARVTVVNVDGR 107
             A  HV  G    L+G+V+T  +K    + Y G+YALD EM YT HGLE+ RVTVV+ D R
Sbjct:   378 AKQHVRDGRKESLDGFVETF-KKELSRDAYPGIYALDCEMCYTTHGLELTRVTVVDADMR 436

Query:   108 LIYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMGFVSKDSIIVGHGLEN 167
             ++Y+T VKPD EI+DYNT++SG++  D  +    TL  VQ  L+ F S  +I++GH LE+
Sbjct:   437 VVYDTFVKPDNEIVDYNTRFSGVTEADVAKTSI-TLPQVQAILLSFFSAQTILIGHSLES 495

Query:   168 DLRALKLIHSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQSGT--HDSFEDARACI 225
             DL ALKLIHS ++DT+VLFPH  G PY+RSL+++ +  L Q IQ     H+S EDA AC+
Sbjct:   496 DLLALKLIHSTVVDTAVLFPHYLGFPYKRSLRNLAADYLAQIIQDSQDGHNSSEDANACL 555

Query:   226 DLILWKL 232
              L++WK+
Sbjct:   556 QLVMWKV 562
GO:0003676 "nucleic acid binding" evidence=IEA
GO:0005622 "intracellular" evidence=IEA
GO:0004527 "exonuclease activity" evidence=IEA
MGI|MGI:1914182 Rexo1 "REX1, RNA exonuclease 1 homolog (S. cerevisiae)" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
UNIPROTKB|F5GW92 REXO1L10P "Protein REXO1L10P" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|Q8IX06 REXO1L1 "Exonuclease GOR" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|F1P0Z1 REXO1 "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
RGD|1564472 RGD1564472 "similar to Transcription elongation factor B polypeptide 3 binding protein 1" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-030131-1650 rexo1 "REX1, RNA exonuclease 1 homolog (S. cerevisiae)" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
FB|FBgn0261548 CG42666 [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
UNIPROTKB|Q8N1G1 REXO1 "RNA exonuclease 1 homolog" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|E2QX02 REXO1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] 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

ID ?Name ?Annotated EC number ?Identity ?Query coverage ?Hit coverage ?RBH(Q2H) ?RBH(H2Q) ?
P48778GOR_PANTR3, ., 1, ., -, ., -0.53200.63750.2217yesN/A
Q8IX06GOR_HUMAN3, ., 1, ., -, ., -0.50850.70830.2518yesN/A

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query240
cd06145150 cd06145, REX1_like, DEDDh 3'-5' exonuclease domain 2e-78
cd06137161 cd06137, DEDDh_RNase, DEDDh 3'-5' exonuclease doma 4e-44
cd06144152 cd06144, REX4_like, DEDDh 3'-5' exonuclease domain 2e-35
smart00479169 smart00479, EXOIII, exonuclease domain in DNA-poly 3e-34
cd06149157 cd06149, ISG20, DEDDh 3'-5' exonuclease domain of 1e-25
pfam00929161 pfam00929, RNase_T, Exonuclease 4e-24
cd06143174 cd06143, PAN2_exo, DEDDh 3'-5' exonuclease domain 5e-21
cd06127159 cd06127, DEDDh, DEDDh 3'-5' exonuclease domain fam 2e-11
cd06141170 cd06141, WRN_exo, DEDDy 3'-5' exonuclease domain o 3e-05
COG0847243 COG0847, DnaQ, DNA polymerase III, epsilon subunit 1e-04
>gnl|CDD|99848 cd06145, REX1_like, DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins Back     alignment and domain information 
 Score =  232 bits (594), Expect = 2e-78
 Identities = 79/151 (52%), Positives = 109/151 (72%), Gaps = 3/151 (1%)

Query: 81  YALDTEMVYTVHGLEVARVTVVNVDGRLIYNTLVKPDCEIIDYNTKYSGISAKDFIRNPY 140
           +ALD EM YT  GLE+ RVTVV+ +G+++ + LVKPD EI+DYNT++SGI+ +       
Sbjct: 1   FALDCEMCYTTDGLELTRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEMLENVT- 59

Query: 141 KTLKDVQNDLMGFVSKDSIIVGHGLENDLRALKLIHSNIIDTSVLFPHSFGLPYRRSLKS 200
            TL+DVQ  L+  +S D+I+VGH LENDL+ALKLIH  +IDT++LFPH  G PY+ SLK+
Sbjct: 60  TTLEDVQKKLLSLISPDTILVGHSLENDLKALKLIHPRVIDTAILFPHPRGPPYKPSLKN 119

Query: 201 IVSQLLHQSIQ--SGTHDSFEDARACIDLIL 229
           +  + L + IQ   G HDS EDARA ++L+ 
Sbjct: 120 LAKKYLGRDIQQGEGGHDSVEDARAALELVK 150

This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T. Length = 150
>gnl|CDD|99840 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
>gnl|CDD|99847 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
>gnl|CDD|214685 smart00479, EXOIII, exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases Back     alignment and domain information
>gnl|CDD|99852 cd06149, ISG20, DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins Back     alignment and domain information
>gnl|CDD|216200 pfam00929, RNase_T, Exonuclease Back     alignment and domain information
>gnl|CDD|99846 cd06143, PAN2_exo, DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2 Back     alignment and domain information
>gnl|CDD|176648 cd06127, DEDDh, DEDDh 3'-5' exonuclease domain family 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|223916 COG0847, DnaQ, DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair] Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 240
cd06143174 PAN2_exo DEDDh 3'-5' exonuclease domain of the euk 100.0
KOG2248|consensus380 100.0
cd06145150 REX1_like DEDDh 3'-5' exonuclease domain of RNA ex 100.0
KOG2249|consensus280 100.0
cd06137161 DEDDh_RNase DEDDh 3'-5' exonuclease domain of the 100.0
cd06149157 ISG20 DEDDh 3'-5' exonuclease domain of Interferon 100.0
cd06144152 REX4_like DEDDh 3'-5' exonuclease domain of RNA ex 100.0
PRK07247195 DNA polymerase III subunit epsilon; Validated 99.96
PRK07740244 hypothetical protein; Provisional 99.96
PRK09146239 DNA polymerase III subunit epsilon; Validated 99.95
cd06130156 DNA_pol_III_epsilon_like an uncharacterized bacter 99.95
PRK06309232 DNA polymerase III subunit epsilon; Validated 99.95
PRK06310250 DNA polymerase III subunit epsilon; Validated 99.95
PRK05711240 DNA polymerase III subunit epsilon; Provisional 99.95
TIGR01406225 dnaQ_proteo DNA polymerase III, epsilon subunit, P 99.95
smart00479169 EXOIII exonuclease domain in DNA-polymerase alpha 99.95
PRK09145202 DNA polymerase III subunit epsilon; Validated 99.95
PRK06807 313 DNA polymerase III subunit epsilon; Validated 99.94
PRK07942232 DNA polymerase III subunit epsilon; Provisional 99.94
PRK07983219 exodeoxyribonuclease X; Provisional 99.94
TIGR00573217 dnaq exonuclease, DNA polymerase III, epsilon subu 99.94
PRK06063 313 DNA polymerase III subunit epsilon; Provisional 99.94
PRK08517257 DNA polymerase III subunit epsilon; Provisional 99.94
cd06131167 DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonucl 99.94
PRK06195 309 DNA polymerase III subunit epsilon; Validated 99.94
cd06136177 TREX1_2 DEDDh 3'-5' exonuclease domain of three pr 99.94
PRK07748207 sporulation inhibitor KapD; Provisional 99.94
PRK07246 820 bifunctional ATP-dependent DNA helicase/DNA polyme 99.93
TIGR01298200 RNaseT ribonuclease T. in gamma-subdivision Proteo 99.93
PRK07883 557 hypothetical protein; Validated 99.92
cd06134189 RNaseT DEDDh 3'-5' exonuclease domain of RNase T. 99.92
PRK05168211 ribonuclease T; Provisional 99.92
PRK06722281 exonuclease; Provisional 99.92
PRK08074 928 bifunctional ATP-dependent DNA helicase/DNA polyme 99.91
TIGR01407 850 dinG_rel DnaQ family exonuclease/DinG family helic 99.91
cd06133176 ERI-1_3'hExo_like DEDDh 3'-5' exonuclease domain o 99.91
cd06127159 DEDDh DEDDh 3'-5' exonuclease domain family. DEDDh 99.91
COG2176 1444 PolC DNA polymerase III, alpha subunit (gram-posit 99.9
TIGR01405 1213 polC_Gram_pos DNA polymerase III, alpha chain, Gra 99.9
PRK09182294 DNA polymerase III subunit epsilon; Validated 99.9
PRK05601 377 DNA polymerase III subunit epsilon; Validated 99.9
COG0847243 DnaQ DNA polymerase III, epsilon subunit and relat 99.89
cd06138183 ExoI_N N-terminal DEDDh 3'-5' exonuclease domain o 99.89
PF00929164 RNase_T: Exonuclease; InterPro: IPR013520 This ent 99.88
PTZ00315 582 2'-phosphotransferase; Provisional 99.85
PRK00448 1437 polC DNA polymerase III PolC; Validated 99.83
PRK11779 476 sbcB exonuclease I; Provisional 99.82
PRK05359181 oligoribonuclease; Provisional 99.82
cd06135173 Orn DEDDh 3'-5' exonuclease domain of oligoribonuc 99.81
KOG1275|consensus1118 99.77
COG5018210 KapD Inhibitor of the KinA pathway to sporulation, 99.23
KOG0542|consensus280 99.18
COG1949184 Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA 99.0
KOG3242|consensus208 98.99
cd05160199 DEDDy_DNA_polB_exo DEDDy 3'-5' exonuclease domain 98.95
cd06139193 DNA_polA_I_Ecoli_like_exo DEDDy 3'-5' exonuclease 98.74
COG2925 475 SbcB Exonuclease I [DNA replication, recombination 98.67
PF01612176 DNA_pol_A_exo1: 3'-5' exonuclease; InterPro: IPR00 98.52
cd0612596 DnaQ_like_exo DnaQ-like (or DEDD) 3'-5' exonucleas 98.47
cd06146193 mut-7_like_exo DEDDy 3'-5' exonuclease domain of C 98.4
PRK05755 880 DNA polymerase I; Provisional 98.22
cd05780195 DNA_polB_Kod1_like_exo DEDDy 3'-5' exonuclease dom 98.14
PF04857262 CAF1: CAF1 family ribonuclease; InterPro: IPR00694 97.94
cd06129161 RNaseD_like DEDDy 3'-5' exonuclease domain of RNas 97.87
cd06141170 WRN_exo DEDDy 3'-5' exonuclease domain of WRN and 97.85
cd00007155 35EXOc 3'-5' exonuclease. The 35EXOc domain is res 97.73
PRK10829 373 ribonuclease D; Provisional 97.73
cd05779204 DNA_polB_epsilon_exo DEDDy 3'-5' exonuclease domai 97.6
cd05781188 DNA_polB_B3_exo DEDDy 3'-5' exonuclease domain of 97.48
cd05784193 DNA_polB_II_exo DEDDy 3'-5' exonuclease domain of 97.43
COG0349 361 Rnd Ribonuclease D [Translation, ribosomal structu 97.42
PF13482164 RNase_H_2: RNase_H superfamily; PDB: 1TKD_A 1TK5_A 97.39
TIGR01388 367 rnd ribonuclease D. This model describes ribonucle 97.32
cd06148197 Egl_like_exo DEDDy 3'-5' exonuclease domain of Dro 97.23
cd05783204 DNA_polB_B1_exo DEDDy 3'-5' exonuclease domain of 97.21
cd05777230 DNA_polB_delta_exo DEDDy 3'-5' exonuclease domain 96.76
cd05785207 DNA_polB_like2_exo Uncharacterized bacterial subgr 96.42
cd06142178 RNaseD_exo DEDDy 3'-5' exonuclease domain of Ribon 96.31
cd05778231 DNA_polB_zeta_exo inactive DEDDy 3'-5' exonuclease 96.3
PHA02570220 dexA exonuclease; Provisional 96.18
smart00474172 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proo 96.1
PF10108209 DNA_pol_B_exo2: Predicted 3'-5' exonuclease relate 95.96
PRK05762 786 DNA polymerase II; Reviewed 95.77
KOG4793|consensus318 95.65
cd05782208 DNA_polB_like1_exo Uncharacterized bacterial subgr 95.63
PTZ00166 1054 DNA polymerase delta catalytic subunit; Provisiona 95.48
cd06140178 DNA_polA_I_Bacillus_like_exo inactive DEDDy 3'-5' 94.86
PF03104325 DNA_pol_B_exo1: DNA polymerase family B, exonuclea 94.73
cd05776234 DNA_polB_alpha_exo inactive DEDDy 3'-5' exonucleas 94.52
COG3359278 Predicted exonuclease [DNA replication, recombinat 94.25
COG0749 593 PolA DNA polymerase I - 3'-5' exonuclease and poly 94.14
TIGR00593 887 pola DNA polymerase I. This family is based on the 93.8
PHA02528 881 43 DNA polymerase; Provisional 93.47
KOG3657|consensus 1075 92.94
smart00486 471 POLBc DNA polymerase type-B family. DNA polymerase 92.94
KOG0304|consensus239 92.92
cd06147192 Rrp6p_like_exo DEDDy 3'-5' exonuclease domain of y 92.41
KOG1798|consensus 2173 91.95
cd09018150 DEDDy_polA_RNaseD_like_exo DEDDy 3'-5' exonuclease 88.64
COG0417 792 PolB DNA polymerase elongation subunit (family B) 88.09
TIGR00592 1172 pol2 DNA polymerase (pol2). This family is based o 86.99
PRK05761 787 DNA polymerase I; Reviewed 86.02
TIGR03491457 RecB family nuclease, putative, TM0106 family. Mem 85.3
PHA02524 498 43A DNA polymerase subunit A; Provisional 83.21
PF00843533 Arena_nucleocap: Arenavirus nucleocapsid protein; 81.51
>cd06143 PAN2_exo DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2 Back     alignment and domain information 
Probab=100.00  E-value=6.6e-40  Score=270.96  Aligned_cols=146  Identities=36%  Similarity=0.490  Sum_probs=132.0

Q ss_pred             EEEEEeecCCCC--------Cc---------cEEEEEEEE----cCCcEEEEEEEcCCCcccccceecCCCCHHhhccCC
Q psy3897          81 YALDTEMVYTVH--------GL---------EVARVTVVN----VDGRLIYNTLVKPDCEIIDYNTKYSGISAKDFIRNP  139 (240)
Q Consensus        81 valD~E~tg~~~--------g~---------ei~~v~vv~----~~g~~~~d~lVkP~~~I~~~~t~~~GIt~edl~~a~  139 (240)
                      ||+||||+++++        |.         +++||++||    .+|+++||.||+|..+|.||+|+|||||+++|.++.
T Consensus         1 ~a~d~e~v~~~~~~~~~~~~g~~~~~~~~~~~LaRVsiVd~~~~~~g~vllD~~VkP~~~V~DYrT~~SGIt~~~L~~a~   80 (174)
T cd06143           1 VAIDAEFVKLKPEETEIRSDGTKSTIRPSQMSLARVSVVRGEGELEGVPFIDDYISTTEPVVDYLTRFSGIKPGDLDPKT   80 (174)
T ss_pred             CceeeeEEEecchhceecCCCcEeeeccCCceeEEEEEEcCCCCcCCCEEEeeeECCCCCccCcCccccccCHHHcCccc
Confidence            578888888776        32         699999999    689999999999999999999999999999999875


Q ss_pred             C----CCHHHHHHHHHhhhcCCcEEEEEchHHHHHHHhccCC--CeeeccccCcccCCCCCCccHHHHHHHHcCCCCCCC
Q psy3897         140 Y----KTLKDVQNDLMGFVSKDSIIVGHGLENDLRALKLIHS--NIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQSG  213 (240)
Q Consensus       140 ~----~~~~ev~~~l~~~i~~~~iLVGH~~~~Dl~~L~~~~~--~~iDT~~l~~~~~~~~~~~sL~~L~~~~L~~~iq~~  213 (240)
                      .    .+++++++++.++++.++|||||+++|||++|++.|+  .+|||+.+|+...+  .++||+.|++.+||++||.+
T Consensus        81 ~~~~~~t~~~v~~~l~~li~~~tILVGHsL~nDL~aL~l~hp~~~viDTa~l~~~~~~--r~~sLk~La~~~L~~~IQ~~  158 (174)
T cd06143          81 SSKNLTTLKSAYLKLRLLVDLGCIFVGHGLAKDFRVINIQVPKEQVIDTVELFHLPGQ--RKLSLRFLAWYLLGEKIQSE  158 (174)
T ss_pred             cccccCCHHHHHHHHHHHcCCCCEEEeccchhHHHHhcCcCCCcceEEcHHhccCCCC--CChhHHHHHHHHcCCcccCC
Confidence            2    2399999999999988999999999999999999966  79999999987543  36899999999999999998


Q ss_pred             CCChHHHHHHHHHHH
Q psy3897         214 THDSFEDARACIDLI  228 (240)
Q Consensus       214 ~H~A~eDA~at~~L~  228 (240)
                      +|||+|||+|||+||
T Consensus       159 ~HdSvEDArAam~Ly  173 (174)
T cd06143         159 THDSIEDARTALKLY  173 (174)
T ss_pred             CcCcHHHHHHHHHHh
Confidence            999999999999997

PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. PAN catalyzes the deadenylation of poly(A) tails, which are initially synthesized to default lengths of 70 to 90, to mRNA-specific lengths of 55 to 71. Pab1p and PAN also play a role in the export and decay of mRNA. PAN2 contains a DEDDh-type DnaQ-like 3'-5' exonuclease domain with three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.
>KOG2248|consensus 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
>KOG2249|consensus 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
>cd06149 ISG20 DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins 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
>PRK07247 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK07740 hypothetical protein; Provisional Back     alignment and domain information
>PRK09146 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
>PRK06309 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK06310 DNA polymerase III subunit epsilon; Validated 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
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases Back     alignment and domain information
>PRK09145 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK06807 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK07942 DNA polymerase III subunit epsilon; Provisional Back     alignment and domain information
>PRK07983 exodeoxyribonuclease X; Provisional Back     alignment and domain information
>TIGR00573 dnaq exonuclease, DNA polymerase III, epsilon subunit family Back     alignment and domain information
>PRK06063 DNA polymerase III subunit epsilon; Provisional Back     alignment and domain information
>PRK08517 DNA polymerase III subunit epsilon; Provisional Back     alignment and domain information
>cd06131 DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins Back     alignment and domain information
>PRK06195 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>cd06136 TREX1_2 DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins Back     alignment and domain information
>PRK07748 sporulation inhibitor KapD; Provisional Back     alignment and domain information
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>TIGR01298 RNaseT ribonuclease T Back     alignment and domain information
>PRK07883 hypothetical protein; Validated Back     alignment and domain information
>cd06134 RNaseT DEDDh 3'-5' exonuclease domain of RNase T Back     alignment and domain information
>PRK05168 ribonuclease T; Provisional Back     alignment and domain information
>PRK06722 exonuclease; Provisional Back     alignment and domain information
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative Back     alignment and domain information
>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
>cd06127 DEDDh DEDDh 3'-5' exonuclease domain family 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
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type Back     alignment and domain information
>PRK09182 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK05601 DNA polymerase III subunit epsilon; Validated 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
>cd06138 ExoI_N N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins Back     alignment and domain information
>PF00929 RNase_T: Exonuclease; InterPro: IPR013520 This entry includes a variety of exonuclease proteins, such as ribonuclease T [] and the epsilon subunit of DNA polymerase III Back     alignment and domain information
>PTZ00315 2'-phosphotransferase; Provisional Back     alignment and domain information
>PRK00448 polC DNA polymerase III PolC; Validated Back     alignment and domain information
>PRK11779 sbcB exonuclease I; Provisional Back     alignment and domain information
>PRK05359 oligoribonuclease; Provisional Back     alignment and domain information
>cd06135 Orn DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins Back     alignment and domain information
>KOG1275|consensus Back     alignment and domain information
>COG5018 KapD Inhibitor of the KinA pathway to sporulation, predicted exonuclease [General function prediction only] Back     alignment and domain information
>KOG0542|consensus Back     alignment and domain information
>COG1949 Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification] Back     alignment and domain information
>KOG3242|consensus 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
>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
>COG2925 SbcB Exonuclease I [DNA replication, recombination, and repair] 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
>cd06125 DnaQ_like_exo DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily 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
>PRK05755 DNA polymerase I; Provisional 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
>PF04857 CAF1: CAF1 family ribonuclease; InterPro: IPR006941 CAF1 is an RNase of the DEDD superfamily, and a subunit of the Ccr4-Not complex that mediates 3' to 5' mRNA deadenylation 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
>cd00007 35EXOc 3'-5' exonuclease Back     alignment and domain information
>PRK10829 ribonuclease D; Provisional 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
>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
>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
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis] 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
>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
>cd05783 DNA_polB_B1_exo DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal family-B DNA polymerases Back     alignment and domain information
>cd05777 DNA_polB_delta_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase 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
>cd06142 RNaseD_exo DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins Back     alignment and domain information
>cd05778 DNA_polB_zeta_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA polymerase Back     alignment and domain information
>PHA02570 dexA exonuclease; Provisional Back     alignment and domain information
>smart00474 35EXOc 3'-5' exonuclease 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
>PRK05762 DNA polymerase II; Reviewed Back     alignment and domain information
>KOG4793|consensus 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
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional 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
>PF03104 DNA_pol_B_exo1: DNA polymerase family B, exonuclease domain Several related DNA polymerases were too dissimilar to be included Back     alignment and domain information
>cd05776 DNA_polB_alpha_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA polymerase Back     alignment and domain information
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair] 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
>TIGR00593 pola DNA polymerase I Back     alignment and domain information
>PHA02528 43 DNA polymerase; Provisional Back     alignment and domain information
>KOG3657|consensus Back     alignment and domain information
>smart00486 POLBc DNA polymerase type-B family Back     alignment and domain information
>KOG0304|consensus 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
>KOG1798|consensus 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
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair] Back     alignment and domain information
>TIGR00592 pol2 DNA polymerase (pol2) Back     alignment and domain information
>PRK05761 DNA polymerase I; Reviewed Back     alignment and domain information
>TIGR03491 RecB family nuclease, putative, TM0106 family Back     alignment and domain information
>PHA02524 43A DNA polymerase subunit A; Provisional Back     alignment and domain information
>PF00843 Arena_nucleocap: Arenavirus nucleocapsid protein; InterPro: IPR000229 Arenaviruses are single stranded RNA viruses 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 ?
Query240
1wlj_A189 Human Isg20 Length = 189 6e-14
2p1j_A186 Crystal Structure Of A Polc-Type Dna Polymerase Iii 5e-04
>pdb|1WLJ|A Chain A, Human Isg20 Length = 189 Back     alignment and structure 
Iteration: 1

 Score = 73.9 bits (180), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 58/161 (36%), Positives = 89/161 (55%), Gaps = 19/161 (11%)
Query: 80  VYALDTEMV----YTVHGLEVARVTVVNVDGRLIYNTLVKPDCEIIDYNTKYSGISAKDF 135
           V A+D EMV    +   GL  AR ++VNV G ++Y+  ++P+ EI DY T+ SG++ +  
Sbjct: 7   VVAMDCEMVGLGPHRESGL--ARCSLVNVHGAVLYDKFIRPEGEITDYRTRVSGVTPQHM 64
Query: 136 I-RNPYKTLKDVQNDLMGFVSKDSIIVGHGLENDLRALKLIHS--NIIDTSV--LFPHSF 190
           +   P+   +     L+    K  ++VGH L++D +ALK   S   I DTS   L     
Sbjct: 65  VGATPFAVARLEILQLL----KGKLVVGHDLKHDFQALKEDMSGYTIYDTSTDRLLWREA 120
Query: 191 GLPY--RRSLKSIVSQLLHQSIQSGT--HDSFEDARACIDL 227
            L +  R SL+ +  +LLH+SIQ+    H S EDARA ++L
Sbjct: 121 KLDHCRRVSLRVLSERLLHKSIQNSLLGHSSVEDARATMEL 161
>pdb|2P1J|A Chain A, Crystal Structure Of A Polc-Type Dna Polymerase Iii Exonuclease Domain From Thermotoga Maritima Length = 186 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 ?
Query240
1wlj_A189 Interferon stimulated gene 20KDA; exoribonuclease, 3e-60
2p1j_A186 POLIII, DNA polymerase III POLC-type; structural g 2e-04
3mxm_B242 Three prime repair exonuclease 1; RNAse H-like fol 6e-04
1y97_A238 Three prime repair exonuclease 2; TREX2, hydrolase 6e-04
>1wlj_A Interferon stimulated gene 20KDA; exoribonuclease, hydrolase; HET: U5P; 1.90A {Homo sapiens} SCOP: c.55.3.5 Length = 189 Back     alignment and structure
 Score =  187 bits (476), Expect = 3e-60
 Identities = 52/168 (30%), Positives = 83/168 (49%), Gaps = 13/168 (7%)

Query: 75  PNGYGVYALDTEMVYTVHGLE--VARVTVVNVDGRLIYNTLVKPDCEIIDYNTKYSGISA 132
                V A+D EMV      E  +AR ++VNV G ++Y+  ++P+ EI DY T+ SG++ 
Sbjct: 2   AGSREVVAMDCEMVGLGPHRESGLARCSLVNVHGAVLYDKFIRPEGEITDYRTRVSGVTP 61

Query: 133 KDFIRNPYKTLKDVQNDLMGFVSKDSIIVGHGLENDLRALKLIH--SNIIDTSV----LF 186
           +             + +++  + K  ++VGH L++D +ALK       I DTS       
Sbjct: 62  QHM--VGATPFAVARLEILQLL-KGKLVVGHDLKHDFQALKEDMSGYTIYDTSTDRLLWR 118

Query: 187 PHSFGLPYRRSLKSIVSQLLHQSIQSGT--HDSFEDARACIDLILWKL 232
                   R SL+ +  +LLH+SIQ+    H S EDARA ++L     
Sbjct: 119 EAKLDHCRRVSLRVLSERLLHKSIQNSLLGHSSVEDARATMELYQISQ 166
>2p1j_A POLIII, DNA polymerase III POLC-type; structural genomics, exonuclease, PSI-2, protein structure initiative; HET: DNA; 2.50A {Thermotoga maritima MSB8} Length = 186 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} PDB: 3mxj_B 2ioc_B 3mxi_B* 3b6o_A* 2o4g_A* 3b6p_A* 2o4i_A 2oa8_A Length = 242 Back     alignment and structure
>1y97_A Three prime repair exonuclease 2; TREX2, hydrolase; 2.50A {Homo sapiens} SCOP: c.55.3.5 Length = 238 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query240
1wlj_A189 Interferon stimulated gene 20KDA; exoribonuclease, 100.0
2p1j_A186 POLIII, DNA polymerase III POLC-type; structural g 99.97
2gui_A194 DNA polymerase III epsilon subunit; DNA polymerase 99.96
1w0h_A204 3'-5' exonuclease ERI1; nuclease domain, hydrolase 99.95
3mxm_B242 Three prime repair exonuclease 1; RNAse H-like fol 99.94
2xri_A224 ERI1 exoribonuclease 3; hydrolase, metal binding; 99.94
1zbh_A299 3'-5' exonuclease ERI1; histone mRNA 3'-END-specif 99.94
2f96_A224 Ribonuclease T; RNAse, RNT, RNAse T, tRNA hydrolas 99.93
1y97_A238 Three prime repair exonuclease 2; TREX2, hydrolase 99.93
3u3y_B314 Three prime repair exonuclease 1; RNAse H fold, 3' 99.93
2igi_A180 Oligoribonuclease; RNAse, exoribonuclease, exonucl 99.93
3cg7_A308 CRN-4, cell death-related nuclease 4; hydrolase, a 99.92
1zbu_A349 ERI-1 homolog, 3'-5' exonuclease ERI1; hydrolase; 99.92
3v9w_A235 Ribonuclease T; DEDD nucleases family, EXO-nucleas 99.92
2gbz_A194 Oligoribonuclease; ORN, deddh, structural genomics 99.91
3tr8_A186 Oligoribonuclease; transcription, hydrolase; 2.50A 99.89
2qxf_A 482 Exodeoxyribonuclease I; alpha-beta domain, DNAQ su 99.89
4hec_A190 Putative uncharacterized protein; ssgcid, structur 99.05
2kfn_A 605 Klenow fragment of DNA polymerase I; complex (poly 98.81
1x9m_A 698 DNA polymerase; DNA ploymerase, N-2-acetylaminoflu 98.5
4gmj_B285 CCR4-NOT transcription complex subunit 7; mRNA dec 98.06
3saf_A 428 Exosome component 10; exoribonuclease, RNA exosome 97.89
4dfk_A 540 DNA polymerase I, thermostable; DNA polymerase, tr 97.82
1vk0_A206 Hypothetical protein; homohexamer, AT5G06450, stru 97.67
1qht_A 775 Protein (DNA polymerase); archaea, hyperthermostab 97.64
2e6m_A208 Werner syndrome ATP-dependent helicase homolog; AP 97.4
2d5r_A252 CCR4-NOT transcription complex subunit 7; poly(A) 97.35
1noy_A388 Protein (DNA polymerase (E.C.2.7.7.7)); exonucleas 97.33
2p51_A333 SPCC18.06C protein; DEDD nuclease fold, hydrolase, 97.27
1yt3_A 375 Ribonuclease D, RNAse D; exoribonuclease, exonucle 97.26
1uoc_A289 POP2; hydrolase, DEDD nuclease, mRNA degradation, 97.11
2hbj_A 410 Exosome complex exonuclease RRP6; RNA metabolism, 97.05
1s5j_A 847 DNA polymerase I; replication, disulfide bonds, tr 96.94
3k59_A 786 POL II, DNA polymerase II; protein-DNA complex, DN 96.82
3pv8_A 592 DNA polymerase I; DNA polymerase I, protein-DNA co 96.75
2a1r_A430 Poly(A)-specific ribonuclease PARN; DEDD, nuclease 96.71
3cym_A 440 Uncharacterized protein BAD_0989; structural genom 96.55
3qex_A 903 DNA polymerase, GP43; difluorotoluene nucleoside; 96.5
3iay_A 919 DNA polymerase delta catalytic subunit; protein-DN 96.46
3d45_A 507 Poly(A)-specific ribonuclease PARN; CAP analogue, 96.39
2gv9_A 1193 DNA polymerase; polymerase alpha fold, transferase 95.53
2py5_A 575 DNA polymerase; protein-DNA complex, replication, 88.47
3q7c_A243 Nucleoprotein; deddh exonuclease, 3' exonuclease, 84.1
>1wlj_A Interferon stimulated gene 20KDA; exoribonuclease, hydrolase; HET: U5P; 1.90A {Homo sapiens} SCOP: c.55.3.5 Back     alignment and structure
Probab=100.00  E-value=2.8e-33  Score=233.94  Aligned_cols=155  Identities=34%  Similarity=0.465  Sum_probs=133.9

Q ss_pred             CCcEEEEEEeecCCCCC--ccEEEEEEEEcCCcEEEEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHHHHHHhhh
Q psy3897          77 GYGVYALDTEMVYTVHG--LEVARVTVVNVDGRLIYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMGFV  154 (240)
Q Consensus        77 ~~~~valD~E~tg~~~g--~ei~~v~vv~~~g~~~~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~~~l~~~i  154 (240)
                      ..++|+|||||||+++.  .+|++|++|+.+|+++|++||+|..+|+++++++||||++++.++|+  +++|+++|.+|+
T Consensus         4 ~~~~vviD~ETTGl~~~~~~~iiei~~v~~~g~~i~~~lV~P~~~i~~~~~~i~GIt~~~l~~a~~--~~~v~~~~~~~l   81 (189)
T 1wlj_A            4 SREVVAMDCEMVGLGPHRESGLARCSLVNVHGAVLYDKFIRPEGEITDYRTRVSGVTPQHMVGATP--FAVARLEILQLL   81 (189)
T ss_dssp             --CEEEEEEEEEEETTTTEEEEEEEEEECTTCCEEEEEEEECSSCEEECCHHHHCCCHHHHTTCEE--HHHHHHHHHHHH
T ss_pred             CCeEEEEEeECcCcCCCCCceEEEEEEEeCCCCEEEeeEecCCCCCCccccCCCCCCHHHHcCCCC--HHHHHHHHHHHH
Confidence            45799999999999865  47899999999999999999999999999999999999999999988  999999999999


Q ss_pred             cCCcEEEEEchHHHHHHHhccCCC--eeeccccCcccC--CCC--CCccHHHHHHHHcCCCCCCC--CCChHHHHHHHHH
Q psy3897         155 SKDSIIVGHGLENDLRALKLIHSN--IIDTSVLFPHSF--GLP--YRRSLKSIVSQLLHQSIQSG--THDSFEDARACID  226 (240)
Q Consensus       155 ~~~~iLVGH~~~~Dl~~L~~~~~~--~iDT~~l~~~~~--~~~--~~~sL~~L~~~~L~~~iq~~--~H~A~eDA~at~~  226 (240)
                      + +.+|||||+.||+++|+..++.  ++||+.+++...  +.+  .+++|+.|++.+||++++.+  +|+|++||++|++
T Consensus        82 ~-~~~lV~hn~~fD~~~L~~~~~~~~~idt~~~~~~~~~~~~p~~~~~~L~~l~~~~lgi~~~~~~~~H~Al~Da~ata~  160 (189)
T 1wlj_A           82 K-GKLVVGHDLKHDFQALKEDMSGYTIYDTSTDRLLWREAKLDHCRRVSLRVLSERLLHKSIQNSLLGHSSVEDARATME  160 (189)
T ss_dssp             T-TSEEEESSHHHHHHHTTCCCTTCEEEEGGGCHHHHHHHTC-----CCHHHHHHHHTCCCCSCCTTCCCHHHHHHHHHH
T ss_pred             C-CCEEEECCcHHHHHHHHHhCCCCceechHhhhhhhhcccCCCCCCccHHHHHHHHcCCCCCCCCCCcCcHHHHHHHHH
Confidence            5 8999999999999999987764  899998754221  221  35799999986689888765  8999999999999


Q ss_pred             HHHHHHhh
Q psy3897         227 LILWKLLS  234 (240)
Q Consensus       227 L~~~~l~~  234 (240)
                      ||.+++++
T Consensus       161 l~~~l~~~  168 (189)
T 1wlj_A          161 LYQISQRI  168 (189)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99987765
>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
>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
>1w0h_A 3'-5' exonuclease ERI1; nuclease domain, hydrolase; HET: AMP; 1.59A {Homo sapiens} SCOP: c.55.3.5 Back     alignment and structure
>3mxm_B Three prime repair exonuclease 1; RNAse H-like fold, polyproline type II helix, hydrolase-DNA; HET: DNA; 1.75A {Mus musculus} SCOP: c.55.3.5 PDB: 3mxj_B 2ioc_B 3mxi_B* 3b6o_A* 2o4g_A* 3b6p_A* 2o4i_A 2oa8_A Back     alignment and structure
>2xri_A ERI1 exoribonuclease 3; hydrolase, metal binding; 2.15A {Homo sapiens} 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
>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
>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
>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
>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
>1zbu_A ERI-1 homolog, 3'-5' exonuclease ERI1; hydrolase; HET: AMP; 3.00A {Homo sapiens} 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
>2gbz_A Oligoribonuclease; ORN, deddh, structural genomics, hydrolase; 2.30A {Xanthomonas campestris PV} Back     alignment and structure
>3tr8_A Oligoribonuclease; transcription, hydrolase; 2.50A {Coxiella burnetii} 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
>4hec_A Putative uncharacterized protein; ssgcid, structural genomics, SEA structural genomics center for infectious disease, unknown; 1.80A {Mycobacterium tuberculosis} 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
>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
>4gmj_B CCR4-NOT transcription complex subunit 7; mRNA decay, deadenylase, RNA bindin; HET: GOL; 2.70A {Homo sapiens} Back     alignment and structure
>3saf_A Exosome component 10; exoribonuclease, RNA exosome, hydrolase; 2.50A {Homo sapiens} PDB: 3sag_A 3sah_A 2cpr_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
>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
>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
>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
>2d5r_A CCR4-NOT transcription complex subunit 7; poly(A) deadenylase, antiproliferative protein, transcription; 2.50A {Homo sapiens} SCOP: c.55.3.9 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
>2p51_A SPCC18.06C protein; DEDD nuclease fold, hydrolase, gene regulation; 1.40A {Schizosaccharomyces pombe} PDB: 3g0z_A 3g10_A Back     alignment and structure
>1yt3_A Ribonuclease D, RNAse D; exoribonuclease, exonuclease, hydrolase, tRNA processing, hydrolase,translation; 1.60A {Escherichia coli} SCOP: a.60.8.3 a.60.8.3 c.55.3.5 Back     alignment and structure
>1uoc_A POP2; hydrolase, DEDD nuclease, mRNA degradation, poly(A) tail, transcription regulation, repressor, phosphorylation.; 2.3A {Saccharomyces cerevisiae} SCOP: c.55.3.9 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
>1s5j_A DNA polymerase I; replication, disulfide bonds, transferase; HET: DNA; 2.40A {Sulfolobus solfataricus} SCOP: c.55.3.5 e.8.1.1 Back     alignment and structure
>3k59_A POL II, DNA polymerase II; protein-DNA complex, DNA damage, DNA repair, DNA-binding; HET: DNA DOC DCP; 1.92A {Escherichia coli} PDB: 3k57_A* 3k58_A* 3k5l_A* 3k5m_A* 3k5n_A* 3k5o_A* 3maq_A* 1q8i_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
>2a1r_A Poly(A)-specific ribonuclease PARN; DEDD, nuclease domain, hydrolase-RNA complex; 2.60A {Homo sapiens} PDB: 2a1s_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
>3qex_A DNA polymerase, GP43; difluorotoluene nucleoside; HET: DNA DOC DGT; 1.73A {Enterobacteria phage RB69} PDB: 3qei_A* 3qer_A* 3qes_A* 3qet_A* 3qep_A* 3qew_A* 3qev_A* 3s9h_A* 3sq0_A* 4dtn_A* 4dto_A* 4dtp_A* 4dtr_A* 4dts_A* 4dtu_A* 4dtx_A* 4e3s_A* 4fjm_A* 4fjl_A* 3spz_A* ... Back     alignment and structure
>3iay_A DNA polymerase delta catalytic subunit; protein-DNA complex, DNA replication, DNA-BI DNA-directed DNA polymerase, exonuclease, hydrolase; HET: DNA DOC DCP; 2.00A {Saccharomyces cerevisiae} Back     alignment and structure
>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus} Back     alignment and structure
>2gv9_A DNA polymerase; polymerase alpha fold, transferase; HET: DNA; 2.68A {Human herpesvirus 1} PDB: 1dml_B* Back     alignment and structure
>2py5_A DNA polymerase; protein-DNA complex, replication, transferase/DNA complex; HET: DNA; 1.60A {Bacillus phage PHI29} SCOP: c.55.3.5 e.8.1.1 PDB: 1xhz_A* 1xhx_A* 2ex3_A* 1xi1_A* 2pyj_A* 2pyl_A* 2pzs_A* Back     alignment and structure
>3q7c_A Nucleoprotein; deddh exonuclease, 3' exonuclease, hydrolase; 1.50A {Lassa virus} PDB: 3q7b_A 4fvu_A Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 240
d1wlja_173 c.55.3.5 (A:) Interferon-stimulated gene 20 kDa pr 2e-17
d3b6oa1226 c.55.3.5 (A:9-234) Three prime repair exonuclease 8e-04
d1w0ha_200 c.55.3.5 (A:) Exonuclease ERI1 {Human (Homo sapien 0.002
>d1wlja_ c.55.3.5 (A:) Interferon-stimulated gene 20 kDa protein, ISG20 {Human (Homo sapiens) [TaxId: 9606]} Length = 173 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: Interferon-stimulated gene 20 kDa protein, ISG20
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 75.0 bits (183), Expect = 2e-17
 Identities = 51/171 (29%), Positives = 86/171 (50%), Gaps = 15/171 (8%)

Query: 80  VYALDTEMVYTVHGLE--VARVTVVNVDGRLIYNTLVKPDCEIIDYNTKYSGISAKDFIR 137
           V A+D EMV      E  +AR ++VNV G ++Y+  ++P+ EI DY T+ SG++      
Sbjct: 2   VVAMDCEMVGLGPHRESGLARCSLVNVHGAVLYDKFIRPEGEITDYRTRVSGVT--PQHM 59

Query: 138 NPYKTLKDVQNDLMGFVSKDSIIVGHGLENDLRALKL------IHSNIIDTSVLFPHSFG 191
                    + +++  + K  ++VGH L++D +ALK       I+    D  +       
Sbjct: 60  VGATPFAVARLEILQLL-KGKLVVGHDLKHDFQALKEDMSGYTIYDTSTDRLLWREAKLD 118

Query: 192 LPYRRSLKSIVSQLLHQSIQSGT--HDSFEDARACIDLILWKLLSDFRYNH 240
              R SL+ +  +LLH+SIQ+    H S EDARA ++  L+++    R   
Sbjct: 119 HCRRVSLRVLSERLLHKSIQNSLLGHSSVEDARATME--LYQISQRIRARR 167
>d3b6oa1 c.55.3.5 (A:9-234) Three prime repair exonuclease 1, TREX1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 226 Back     information, alignment and structure
>d1w0ha_ c.55.3.5 (A:) Exonuclease ERI1 {Human (Homo sapiens) [TaxId: 9606]} Length = 200 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 ?
Query240
d1wlja_173 Interferon-stimulated gene 20 kDa protein, ISG20 { 100.0
d2guia1174 N-terminal exonuclease domain of the epsilon subun 99.93
d3b6oa1226 Three prime repair exonuclease 1, TREX1 {Mouse (Mu 99.9
d1y97a1228 Three prime repair exonuclease 2, TREX2 {Human (Ho 99.88
d1w0ha_200 Exonuclease ERI1 {Human (Homo sapiens) [TaxId: 960 99.85
d2f96a1202 Ribonuclease T {Pseudomonas aeruginosa [TaxId: 287 99.69
d2qxfa1 467 Exonuclease I {Escherichia coli K12 (Escherichia c 99.67
d2igia1180 Oligoribonuclease {Escherichia coli [TaxId: 562]} 99.46
d1kfsa1195 Exonuclease domain of prokaryotic DNA polymerase { 98.75
d1yt3a3193 Ribonuclease D, catalytic domain {Escherichia coli 98.55
d2d5ra1252 CCR4-NOT transcription complex subunit 7, CAF1 {Hu 98.48
d2hbka2292 Exosome complex exonuclease RRP6 {Baker's yeast (S 98.13
d2hhva1171 Exonuclease domain of prokaryotic DNA polymerase { 97.97
d1vk0a_206 Hypothetical protein AT5G06450 {Thale-cress (Arabi 97.95
d1x9ma1204 Exonuclease domain of T7 DNA polymerase {Bacteriop 97.53
d1tgoa1347 Exonuclease domain of family B DNA polymerases {Ar 97.33
d1uoca_286 Pop2 RNase D domain {Baker's yeast (Saccharomyces 97.28
d1s5ja1410 Exonuclease domain of family B DNA polymerases {Su 96.61
d1q8ia1388 Exonuclease domain of family B DNA polymerases {Es 96.25
d2py5a1183 Exonuclease domain of phi29 DNA polymerase {Bacter 92.57
d1ih7a1375 Exonuclease domain of family B DNA polymerases {Ba 88.62
d1noya_372 Exonuclease domain of family B DNA polymerases {Ba 86.7
>d1wlja_ c.55.3.5 (A:) Interferon-stimulated gene 20 kDa protein, ISG20 {Human (Homo sapiens) [TaxId: 9606]} 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: Interferon-stimulated gene 20 kDa protein, ISG20
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=8.7e-33  Score=223.30  Aligned_cols=152  Identities=32%  Similarity=0.477  Sum_probs=127.8

Q ss_pred             cEEEEEEeecCCCCCc-c-EEEEEEEEcCCcEEEEEEEcCCCcccccceecCCCCHHhhccCCCCCHHHHHHHHHhhhcC
Q psy3897          79 GVYALDTEMVYTVHGL-E-VARVTVVNVDGRLIYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMGFVSK  156 (240)
Q Consensus        79 ~~valD~E~tg~~~g~-e-i~~v~vv~~~g~~~~d~lVkP~~~I~~~~t~~~GIt~edl~~a~~~~~~ev~~~l~~~i~~  156 (240)
                      ++|||||||||++++. + |..+++++.+|.++|++||+|..||+++++++||||++++.++++  ++++.++|.++++ 
T Consensus         1 ~~v~iD~EttGl~~~~~~ii~~~~iv~~~g~~i~~~~v~p~~~i~~~~~~i~GIt~e~~~~~~~--~~~~~~~~~~~~~-   77 (173)
T d1wlja_           1 EVVAMDCEMVGLGPHRESGLARCSLVNVHGAVLYDKFIRPEGEITDYRTRVSGVTPQHMVGATP--FAVARLEILQLLK-   77 (173)
T ss_dssp             CEEEEEEEEEEETTTTEEEEEEEEEECTTCCEEEEEEEECSSCEEECCHHHHCCCHHHHTTCEE--HHHHHHHHHHHHT-
T ss_pred             CEEEEEEEcCCCCCCCCcEEEEEEEEEecCeEEEEEeeecccccCcceeEEecCcchhhhcCCc--HHHHHHHHHhhcc-
Confidence            4899999999999775 3 667999999999999999999999999999999999999999988  9999999999995 


Q ss_pred             CcEEEEEchHHHHHHHhccCC------CeeeccccCcccCCCCCCccHHHHHHHHcCCCCCCC--CCChHHHHHHHHHHH
Q psy3897         157 DSIIVGHGLENDLRALKLIHS------NIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQSG--THDSFEDARACIDLI  228 (240)
Q Consensus       157 ~~iLVGH~~~~Dl~~L~~~~~------~~iDT~~l~~~~~~~~~~~sL~~L~~~~L~~~iq~~--~H~A~eDA~at~~L~  228 (240)
                      +.++||||+.||+++|+...+      .++||..+++...+...+++|+.|++.+++..++..  +|+|++||++|++||
T Consensus        78 ~~~lv~hn~~fD~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~~~~~~~~i~~~~~~H~Al~Da~at~~l~  157 (173)
T d1wlja_          78 GKLVVGHDLKHDFQALKEDMSGYTIYDTSTDRLLWREAKLDHCRRVSLRVLSERLLHKSIQNSLLGHSSVEDARATMELY  157 (173)
T ss_dssp             TSEEEESSHHHHHHHTTCCCTTCEEEEGGGCHHHHHHHTC-----CCHHHHHHHHTCCCCSCCTTCCCHHHHHHHHHHHH
T ss_pred             cceEEeechHhHHHHHHHhhccCcccchhHHHHHHHHHhhcccCCcCHHHHHHHHhCCcccCCCCCCChHHHHHHHHHHH
Confidence            899999999999999998543      345666665554444446799999998899888643  799999999999998


Q ss_pred             HHHHh
Q psy3897         229 LWKLL  233 (240)
Q Consensus       229 ~~~l~  233 (240)
                      ....+
T Consensus       158 ~~~~~  162 (173)
T d1wlja_         158 QISQR  162 (173)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            65444
>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
>d3b6oa1 c.55.3.5 (A:9-234) Three prime repair exonuclease 1, TREX1 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1y97a1 c.55.3.5 (A:1-228) Three prime repair exonuclease 2, TREX2 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1w0ha_ c.55.3.5 (A:) Exonuclease ERI1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2f96a1 c.55.3.5 (A:19-220) Ribonuclease T {Pseudomonas aeruginosa [TaxId: 287]} Back     information, alignment and structure
>d2qxfa1 c.55.3.5 (A:8-474) Exonuclease I {Escherichia coli K12 (Escherichia coli K-12) [TaxId: 83333]} Back     information, alignment and structure
>d2igia1 c.55.3.5 (A:1-180) Oligoribonuclease {Escherichia coli [TaxId: 562]} 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
>d1yt3a3 c.55.3.5 (A:1-193) Ribonuclease D, catalytic domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2d5ra1 c.55.3.9 (A:11-262) CCR4-NOT transcription complex subunit 7, CAF1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2hbka2 c.55.3.5 (A:129-420) Exosome complex exonuclease RRP6 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} 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
>d1vk0a_ c.55.3.5 (A:) Hypothetical protein AT5G06450 {Thale-cress (Arabidopsis thaliana) [TaxId: 3702]} Back     information, alignment and structure
>d1x9ma1 c.55.3.5 (A:1-210) Exonuclease domain of T7 DNA polymerase {Bacteriophage T7 [TaxId: 10760]} Back     information, alignment and structure
>d1tgoa1 c.55.3.5 (A:1-347) Exonuclease domain of family B DNA polymerases {Archaeon Thermococcus gorgonarius [TaxId: 71997]} Back     information, alignment and structure
>d1uoca_ c.55.3.9 (A:) Pop2 RNase D domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1s5ja1 c.55.3.5 (A:40-449) Exonuclease domain of family B DNA polymerases {Sulfolobus solfataricus [TaxId: 2287]} Back     information, alignment and structure
>d1q8ia1 c.55.3.5 (A:2-389) Exonuclease domain of family B DNA polymerases {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2py5a1 c.55.3.5 (A:5-187) Exonuclease domain of phi29 DNA polymerase {Bacteriophage phi-29 [TaxId: 10756]} Back     information, alignment and structure
>d1ih7a1 c.55.3.5 (A:1-375) Exonuclease domain of family B DNA polymerases {Bacteriophage RB69 [TaxId: 12353]} Back     information, alignment and structure
>d1noya_ c.55.3.5 (A:) Exonuclease domain of family B DNA polymerases {Bacteriophage T4 [TaxId: 10665]} Back     information, alignment and structure