254780818

254780818

DNA polymerase III subunit epsilon

GeneID in NCBI database:8209824Locus tag:CLIBASIA_03545
Protein GI in NCBI database:254780818Protein Accession:YP_003065231.1
Gene range:+(437177, 437914)Protein Length:245aa
Gene description:DNA polymerase III subunit epsilon
COG prediction:[L] DNA polymerase III, epsilon subunit and related 3'-5' exonucleases
KEGG prediction:dnaQ; DNA polymerase III subunit epsilon; K02342 DNA polymerase III subunit epsilon [EC:2.7.7.7]
SEED prediction:DNA polymerase III epsilon subunit (EC 2.7.7.7)
Pathway involved in KEGG:Purine metabolism [PATH:las00230]
Pyrimidine metabolism [PATH:las00240]
DNA replication [PATH:las03030]
Mismatch repair [PATH:las03430]
Homologous recombination [PATH:las03440]
Subsystem involved in SEED:DNA-replication;
sequencesequence profile

Prediction of Local Sequence Properties

SourceSummaryResult
scaler
NCBI Databasesequence
PSIPREDsecondary structure
SSPROsecondary structure
DISEMBLcoil and loop
DISEMBLflexible loop
SEGlow complexity
DISOPREDdisordered
DISEMBLmissing residues
DISPROdisordered
TMHMMnone TM-Helix
TOPPREDnone TM-Helix
HMMTOPnone TM-Helix
MEMSATnone TM-Helix
MEMSAT_SVMnone TM-Helix
PHOBIUSnone TM-Helix
SignalP_HMMno
SignalP_NNno
COILScoiled coil
70% MSAconservation map
90% MSAconservation map
  
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-----
MIRKNKMRKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSSRNDLNSLCKRYGITISHRSKHGALLDSHLLSDVYIKMMVGGSQINFGFKTNEDRFFKEEKKTVPNISLLKRDKPLFTRITKEELDEHDKTIQTLGKNAIWDRYISSNQ
ccccccccEEEEEEccccccccccEEEEEEEEEEccccEEEcEEEEEEccccccccHHHHHHHcccHHHHcccccHHHHHHHHHHHHHHcccEEEEccHHHHHHHHHHHHHHccccccccccEEEHHHHHHHHcccccccHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHccccccccccccccHHHHHHHHcccccccccccccccccccHHHHHHHHHHHHHHccccHHHHcccccc
ccccccccEEEEccccccccccccEEEEEEEEEEEcccccccEEEEEEccccccccHHHHHHHcccHHHHcccccHHHHHHHHHHHHcccccEEEEEcccccHHHHHHHHHHcccccccHcEEEEHHHHHHHHcccccccHHHHHHHccccccccccccHHHHHHHHHHHHHHHHcccccEEEcccccccccccccccccccccccccccccEEcccHHHHHHHHHHHHHHccccHHHHcccccc
mirknkmrKIVFDIEttgldskndriIEIGAVElldysktnrtfqvflcpngrknspealklhgitdeflkdkpsfssIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQrinkdpldpsriidtlsiarrkhpssrndLNSLCKrygitishrskhgalldshLLSDVYIKMMVggsqinfgfktnedrffkeekktvpnisllkrdkplftRITKEELDEHDKTIQTLGKNAIWDRYISSNQ
mirknkmrkivfdiettgldskndrIIEIGAvelldysktnRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQrinkdpldpsrIIDTlsiarrkhpssrndlnsLCKRYGITishrskhgalLDSHLLSDVYIKMMVGGSQINFGFKTNEDRffkeekktvpnisllkrdkplftritkeeldehdktiqtlgknaiwdryissnq
MIRKNKMRKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSSRNDLNSLCKRYGITISHRSKHGALLDSHLLSDVYIKMMVGGSQINFGFKTNEDRFFKEEKKTVPNISLLKRDKPLFTRITKEELDEHDKTIQTLGKNAIWDRYISSNQ
*****KM**IVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSSRNDLNSLCKRYGITISHRSKHGALLDSHLLSDVYIKMMVGGSQI*****************************PLFTRITKEELDEHDKTIQTLGKNAIW*RYI****
MIRKNKMRKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSSRNDLNSLCKRYGITISHRSKHGALLDSHLLSDVYIKMMVGGSQINFGFKTNEDRFFKEEKKTVPNISLLKRDKPLFTRITKEELDEHDKTIQTLGKNAIWDRYISSNQ
*****KMRKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSSRNDLNSLCKRYGITISHRSKHGALLDSHLLSDVYIKMMVGGSQINFGFK**************PNISLLKRDKPLFTRITKEELDEHDKTIQTLGKNAIWDRYI****
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MIRKNKMRKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSSRNDLNSLCKRYGITISHRSKHGALLDSHLLSDVYIKMMVGGSQINFGFKTNEDRFFKEEKKTVPNISLLKRDKPLFTRITKEELDEHDKTIQTLGKNAIWDRYISSNQ
MIRKNKMRKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSSRNDLNSLCKRYGITISHRSKHGALLDSHLLSDVYIKMMVGGSQINFGFKTNEDRFFKEEKKTVPNISLLKRDKPLFTRITKEELDEHDKTIQTLGKNAIWDRYISSNQ
MIRKNKMRKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSSRNDLNSLCKRYGITISHRSKHGALLDSHLLSDVYIKMMVGGSQINFGFKTNEDRFFKEEKKTVPNISLLKRDKPLFTRITKEELDEHDKTIQTLGKNAIWDRYISSNQ

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

No hits with e-value below 0.05

Close Homologs Detected BLAST or PSI-BLAST in the First 2 Iterations

IdentityAlignment graphLength Definition Round E-value
Target245 DNA polymerase III subunit epsilon [Candidatus Liberiba
315122041244 DNA polymerase III subunit epsilon [Candidatus Liberiba 1 1e-116
150398405242 DNA polymerase III subunit epsilon [Sinorhizobium medic 1 4e-64
15963758242 DNA polymerase III subunit epsilon [Sinorhizobium melil 1 4e-64
209551510245 DNA polymerase III subunit epsilon [Rhizobium leguminos 1 4e-63
227823864232 DNA polymerase III subunit epsilon [Sinorhizobium fredi 1 1e-62
86355674240 DNA polymerase III subunit epsilon [Rhizobium etli CFN 1 4e-62
222147020236 DNA polymerase III subunit epsilon [Agrobacterium vitis 1 5e-62
325291458233 DNA polymerase III epsilon chain [Agrobacterium sp. H13 1 6e-61
218660611238 DNA polymerase III subunit epsilon [Rhizobium etli IE47 1 6e-61
116249771240 DNA polymerase III subunit epsilon [Rhizobium leguminos 1 8e-61
>gi|315122041|ref|YP_004062530.1| DNA polymerase III subunit epsilon [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 244 Back     alignment and organism information
 Score =  420 bits (1080), Expect = e-116,   Method: Compositional matrix adjust.
 Identities = 199/242 (82%), Positives = 221/242 (91%)

Query: 4   KNKMRKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLH 63
           KNKMRKI+FDIETTGLD KNDRIIEIGAVELLDYSKT RTFQVFL P+G+K +PEALKLH
Sbjct: 3   KNKMRKIIFDIETTGLDKKNDRIIEIGAVELLDYSKTGRTFQVFLSPDGKKVNPEALKLH 62

Query: 64  GITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRI 123
           GITDEFL+DKP FS+IF EFWDFFN++NAEWIAHNAKFDVGFINAELQRINKDPLDPSRI
Sbjct: 63  GITDEFLRDKPFFSAIFPEFWDFFNDKNAEWIAHNAKFDVGFINAELQRINKDPLDPSRI 122

Query: 124 IDTLSIARRKHPSSRNDLNSLCKRYGITISHRSKHGALLDSHLLSDVYIKMMVGGSQINF 183
           +DTLSIARRKHPSSRNDLNSLCKRYGITISHRSKHGALLDSHLL+DVY++MMVGGSQI+F
Sbjct: 123 VDTLSIARRKHPSSRNDLNSLCKRYGITISHRSKHGALLDSHLLADVYVQMMVGGSQIDF 182

Query: 184 GFKTNEDRFFKEEKKTVPNISLLKRDKPLFTRITKEELDEHDKTIQTLGKNAIWDRYISS 243
           GFK NED  F +++    NIS LKR+KPL  RIT+EE+ EH KTIQ +GKN+IW+RY SS
Sbjct: 183 GFKANEDFLFGKDENIAQNISFLKREKPLSLRITEEEIAEHTKTIQMIGKNSIWNRYTSS 242

Query: 244 NQ 245
           NQ
Sbjct: 243 NQ 244


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|150398405|ref|YP_001328872.1| DNA polymerase III subunit epsilon [Sinorhizobium medicae WSM419] Length = 242 Back     alignment and organism information
>gi|15963758|ref|NP_384111.1| DNA polymerase III subunit epsilon [Sinorhizobium meliloti 1021] Length = 242 Back     alignment and organism information
>gi|209551510|ref|YP_002283427.1| DNA polymerase III subunit epsilon [Rhizobium leguminosarum bv. trifolii WSM2304] Length = 245 Back     alignment and organism information
>gi|227823864|ref|YP_002827837.1| DNA polymerase III subunit epsilon [Sinorhizobium fredii NGR234] Length = 232 Back     alignment and organism information
>gi|86355674|ref|YP_467566.1| DNA polymerase III subunit epsilon [Rhizobium etli CFN 42] Length = 240 Back     alignment and organism information
>gi|222147020|ref|YP_002547977.1| DNA polymerase III subunit epsilon [Agrobacterium vitis S4] Length = 236 Back     alignment and organism information
>gi|325291458|ref|YP_004277322.1| DNA polymerase III epsilon chain [Agrobacterium sp. H13-3] Length = 233 Back     alignment and organism information
>gi|218660611|ref|ZP_03516541.1| DNA polymerase III subunit epsilon [Rhizobium etli IE4771] Length = 238 Back     alignment and organism information
>gi|116249771|ref|YP_765609.1| DNA polymerase III subunit epsilon [Rhizobium leguminosarum bv. viciae 3841] Length = 240 Back     alignment and organism information

Conserved Domains in CDD Database
Detected by RPS-BLAST and HHsearch

Conserved Domains in CDD Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target245 DNA polymerase III subunit epsilon [Candidatus Liberiba
PRK05711240 PRK05711, PRK05711, DNA polymerase III subunit epsilon; 1e-69
TIGR01406225 TIGR01406, dnaQ_proteo, DNA polymerase III, epsilon sub 1e-57
COG0847243 COG0847, DnaQ, DNA polymerase III, epsilon subunit and 2e-36
TIGR00573217 TIGR00573, dnaq, exonuclease, DNA polymerase III, epsil 3e-40
cd06127159 cd06127, DEDDh, DEDDh 3'-5' exonuclease domain family 4e-35
smart00479169 smart00479, EXOIII, exonuclease domain in DNA-polymeras 3e-33
PRK00448 1437 PRK00448, polC, DNA polymerase III PolC; Validated 2e-29
pfam00929162 pfam00929, Exonuc_X-T, Exonuclease 7e-26
TIGR01405 1213 TIGR01405, polC_Gram_pos, DNA polymerase III, alpha cha 1e-24
COG2176 1444 COG2176, PolC, DNA polymerase III, alpha subunit (gram- 2e-24
PRK07883 557 PRK07883, PRK07883, hypothetical protein; Validated 2e-24
PRK08074 928 PRK08074, PRK08074, bifunctional ATP-dependent DNA heli 6e-19
PRK07740244 PRK07740, PRK07740, hypothetical protein; Provisional 6e-18
PRK06309232 PRK06309, PRK06309, DNA polymerase III subunit epsilon; 4e-17
PRK08517257 PRK08517, PRK08517, DNA polymerase III subunit epsilon; 1e-16
PRK06310250 PRK06310, PRK06310, DNA polymerase III subunit epsilon; 1e-15
TIGR01407 850 TIGR01407, dinG_rel, DnaQ family exonuclease/DinG famil 2e-15
PRK06807313 PRK06807, PRK06807, DNA polymerase III subunit epsilon; 5e-14
PRK06063313 PRK06063, PRK06063, DNA polymerase III subunit epsilon; 1e-12
cd06134189 cd06134, RNaseT, DEDDh 3'-5' exonuclease domain of RNas 6e-11
PRK07942232 PRK07942, PRK07942, DNA polymerase III subunit epsilon; 6e-11
TIGR01298200 TIGR01298, RNaseT, ribonuclease T 4e-10
PRK09145202 PRK09145, PRK09145, DNA polymerase III subunit epsilon; 3e-09
PRK07983219 PRK07983, PRK07983, exodeoxyribonuclease X; Provisional 1e-08
cd06133176 cd06133, ERI-1_3'hExo_like, DEDDh 3'-5' exonuclease dom 6e-08
PRK07246 820 PRK07246, PRK07246, bifunctional ATP-dependent DNA heli 1e-05
cd06136177 cd06136, TREX1_2, DEDDh 3'-5' exonuclease domain of thr 1e-04
cd06131167 cd06131, DNA_pol_III_epsilon_Ecoli_like, DEDDh 3'-5' ex 4e-62
cd06130156 cd06130, DNA_pol_III_epsilon_like, an uncharacterized b 1e-14
PRK06195309 PRK06195, PRK06195, DNA polymerase III subunit epsilon; 9e-07
PRK09182294 PRK09182, PRK09182, DNA polymerase III subunit epsilon; 4e-11
PRK09146239 PRK09146, PRK09146, DNA polymerase III subunit epsilon; 2e-07
PRK05168211 PRK05168, PRK05168, ribonuclease T; Provisional 3e-06
PRK05601377 PRK05601, PRK05601, DNA polymerase III subunit epsilon; 9e-05
cd0612596 cd06125, DnaQ_like_exo, DnaQ-like (or DEDD) 3'-5' exonu 4e-04
cd06138183 cd06138, ExoI_N, N-terminal DEDDh 3'-5' exonuclease dom 9e-04
PRK05359181 PRK05359, PRK05359, oligoribonuclease; Provisional 0.002
cd06135173 cd06135, Orn, DEDDh 3'-5' exonuclease domain of oligori 0.004
>gnl|CDD|180217 PRK05711, PRK05711, DNA polymerase III subunit epsilon; Provisional Back     alignment and domain information
>gnl|CDD|130473 TIGR01406, dnaQ_proteo, DNA polymerase III, epsilon subunit, Proteobacterial Back     alignment and domain information
>gnl|CDD|31188 COG0847, DnaQ, DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|129663 TIGR00573, dnaq, exonuclease, DNA polymerase III, epsilon subunit family Back     alignment and domain information
>gnl|CDD|176648 cd06127, DEDDh, DEDDh 3'-5' exonuclease domain family Back     alignment and domain information
>gnl|CDD|128755 smart00479, EXOIII, exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases Back     alignment and domain information
>gnl|CDD|179031 PRK00448, polC, DNA polymerase III PolC; Validated Back     alignment and domain information
>gnl|CDD|144506 pfam00929, Exonuc_X-T, Exonuclease Back     alignment and domain information
>gnl|CDD|162340 TIGR01405, polC_Gram_pos, DNA polymerase III, alpha chain, Gram-positive type Back     alignment and domain information
>gnl|CDD|32359 COG2176, PolC, DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|181157 PRK07883, PRK07883, hypothetical protein; Validated Back     alignment and domain information
>gnl|CDD|181223 PRK08074, PRK08074, bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>gnl|CDD|181100 PRK07740, PRK07740, hypothetical protein; Provisional Back     alignment and domain information
>gnl|CDD|180524 PRK06309, PRK06309, DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>gnl|CDD|181455 PRK08517, PRK08517, DNA polymerase III subunit epsilon; Provisional Back     alignment and domain information
>gnl|CDD|180525 PRK06310, PRK06310, DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>gnl|CDD|162341 TIGR01407, dinG_rel, DnaQ family exonuclease/DinG family helicase, putative Back     alignment and domain information
>gnl|CDD|180706 PRK06807, PRK06807, DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>gnl|CDD|180377 PRK06063, PRK06063, DNA polymerase III subunit epsilon; Provisional Back     alignment and domain information
>gnl|CDD|99837 cd06134, RNaseT, DEDDh 3'-5' exonuclease domain of RNase T Back     alignment and domain information
>gnl|CDD|181176 PRK07942, PRK07942, DNA polymerase III subunit epsilon; Provisional Back     alignment and domain information
>gnl|CDD|130365 TIGR01298, RNaseT, ribonuclease T Back     alignment and domain information
>gnl|CDD|181671 PRK09145, PRK09145, DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>gnl|CDD|181186 PRK07983, PRK07983, exodeoxyribonuclease X; Provisional Back     alignment and domain information
>gnl|CDD|99836 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
>gnl|CDD|180905 PRK07246, PRK07246, bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>gnl|CDD|99839 cd06136, TREX1_2, DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins Back     alignment and domain information
>gnl|CDD|99835 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
>gnl|CDD|99834 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
>gnl|CDD|180459 PRK06195, PRK06195, DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>gnl|CDD|181680 PRK09182, PRK09182, DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>gnl|CDD|181672 PRK09146, PRK09146, DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>gnl|CDD|179951 PRK05168, PRK05168, ribonuclease T; Provisional Back     alignment and domain information
>gnl|CDD|180158 PRK05601, PRK05601, DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>gnl|CDD|176647 cd06125, DnaQ_like_exo, DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily Back     alignment and domain information
>gnl|CDD|99841 cd06138, ExoI_N, N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins Back     alignment and domain information
>gnl|CDD|180037 PRK05359, PRK05359, oligoribonuclease; Provisional Back     alignment and domain information
>gnl|CDD|99838 cd06135, Orn, DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 245 DNA polymerase III subunit epsilon [Candidatus Liberiba
PRK06022234 consensus 100.0
TIGR01406246 dnaQ_proteo DNA polymerase III, epsilon subunit; InterP 100.0
PRK06859253 consensus 100.0
PRK05711240 DNA polymerase III subunit epsilon; Provisional 100.0
PRK07982243 consensus 100.0
PRK07009241 consensus 100.0
PRK08816244 consensus 100.0
PRK08858246 consensus 100.0
PRK06631229 consensus 100.0
TIGR01405 1264 polC_Gram_pos DNA polymerase III, alpha subunit, Gram-p 100.0
PRK06310250 DNA polymerase III subunit epsilon; Validated 100.0
COG0847243 DnaQ DNA polymerase III, epsilon subunit and related 3' 100.0
PRK07983219 exodeoxyribonuclease X; Provisional 100.0
PRK09182293 DNA polymerase III subunit epsilon; Validated 99.98
PRK06807313 DNA polymerase III subunit epsilon; Validated 100.0
PRK07740240 hypothetical protein; Provisional 100.0
PRK08517259 DNA polymerase III subunit epsilon; Provisional 100.0
PRK07883 575 hypothetical protein; Validated 100.0
cd06131167 DNA_pol_III_epsilon_Ecoli_like This subfamily is compos 100.0
PRK07246 820 bifunctional ATP-dependent DNA helicase/DNA polymerase 100.0
TIGR00573228 dnaq exonuclease, DNA polymerase III, epsilon subunit f 100.0
PRK05168213 ribonuclease T; Provisional 100.0
PRK08074 932 bifunctional ATP-dependent DNA helicase/DNA polymerase 100.0
PRK06309232 DNA polymerase III subunit epsilon; Validated 100.0
TIGR01407 944 dinG_rel DnaQ family exonuclease/DinG family helicase, 100.0
PRK00448 1436 polC DNA polymerase III PolC; Validated 100.0
PRK09145203 DNA polymerase III subunit epsilon; Validated 100.0
PRK06195309 DNA polymerase III subunit epsilon; Validated 100.0
cd06134189 RNaseT RNase T is a DEDDh-type DnaQ-like 3'-5' exoribon 100.0
PRK07942234 DNA polymerase III subunit epsilon; Provisional 100.0
PRK06063313 DNA polymerase III subunit epsilon; Provisional 100.0
COG2176 1444 PolC DNA polymerase III, alpha subunit (gram-positive t 100.0
cd06130156 DNA_pol_III_epsilon_like This subfamily is composed of 100.0
PRK09146239 DNA polymerase III subunit epsilon; Validated 100.0
PRK07247195 DNA polymerase III subunit epsilon; Validated 100.0
cd06136177 TREX1_2 Three prime repair exonuclease (TREX) 1 and 2 a 100.0
smart00479169 EXOIII exonuclease domain in DNA-polymerase alpha and e 100.0
pfam00929162 Exonuc_X-T Exonuclease. This family includes a variety 100.0
cd06133176 ERI-1_3'hExo_like This subfamily is composed of Caenorh 100.0
cd06127159 DEDDh DEDDh exonucleases, part of the DnaQ-like (or DED 100.0
cd06138183 ExoI_N This subfamily is composed of the N-terminal dom 100.0
PRK07748205 sporulation inhibitor KapD; Provisional 99.95
cd06144152 REX4_like This subfamily is composed of RNA exonuclease 99.94
TIGR01298201 RNaseT ribonuclease T; InterPro: IPR005987 Ribonuclease 99.91
PRK05601377 DNA polymerase III subunit epsilon; Validated 99.89
PRK11779 477 sbcB exonuclease I; Provisional 99.84
cd06137161 DEDDh_RNase This group is composed of eukaryotic exorib 99.79
cd06149157 ISG20 Interferon (IFN) Stimulated Gene product of 20 kD 99.72
cd06135173 Orn Oligoribonuclease (Orn) is a DEDDh-type DnaQ-like 3 99.7
KOG0542280 consensus 99.65
PTZ00315 570 2'-phosphotransferase; Provisional 99.47
KOG2249280 consensus 99.45
COG2925 475 SbcB Exonuclease I [DNA replication, recombination, and 99.44
cd06145150 REX1_like This subfamily is composed of RNA exonuclease 99.42
cd06139193 DNA_polA_I_Ecoli_like_exo The 3'-5' exonuclease domain 99.42
COG5018210 KapD Inhibitor of the KinA pathway to sporulation, pred 99.36
PRK05359181 oligoribonuclease; Provisional 99.3
cd06143174 PAN2_exo PAN2 is the catalytic subunit of poly(A) nucle 99.29
cd00007155 35EXOc 3'-5' exonuclease. The 35EXOc domain is responsi 99.06
cd06142178 RNaseD_exo Ribonuclease (RNase) D is a bacterial enzyme 98.99
pfam01612172 3_5_exonuc 3'-5' exonuclease. This domain is responsibl 98.97
KOG2248380 consensus 98.89
PRK07456 975 consensus 98.86
PRK06887 954 consensus 98.78
smart00474172 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofread 98.75
PRK07556 977 consensus 98.75
KOG4793318 consensus 98.73
PRK05755 889 DNA polymerase I; Provisional 98.71
PRK07625 922 consensus 98.68
COG3359278 Predicted exonuclease [DNA replication, recombination, 98.65
COG1949184 Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA proc 98.65
cd06140178 DNA_polA_I_Bacillus_like_exo Bacillus stearothermophilu 98.63
PRK08434 887 consensus 98.57
PRK05797 869 consensus 98.48
PRK07997 928 consensus 98.45
KOG3242208 consensus 98.43
PRK08835 931 consensus 98.4
COG0349 361 Rnd Ribonuclease D [Translation, ribosomal structure an 98.35
PRK08786 927 consensus 98.32
cd06147192 Rrp6p_like_exo Yeast Rrp6p and its human homolog, the P 98.32
cd06129159 RNaseD_like The RNase D-like group is composed of RNase 98.32
PTZ00166 1081 DNA polymerase delta catalytic subunit; Provisional 98.3
pfam04857235 CAF1 CAF1 family ribonuclease. The major pathways of mR 98.23
PRK05762 785 DNA polymerase II; Reviewed 97.91
PRK07898 902 consensus 97.91
COG0749 593 PolA DNA polymerase I - 3'-5' exonuclease and polymeras 97.82
smart00486 471 POLBc DNA polymerase type-B family. DNA polymerase alph 97.68
PRK08076 877 consensus 97.61
cd06148197 Egl_like_exo The Egalitarian (Egl) protein subfamily is 97.55
pfam10108211 Exon_PolB Predicted 3'-5' exonuclease related to the ex 97.48
COG0417 792 PolB DNA polymerase elongation subunit (family B) [DNA 97.39
KOG1798 2173 consensus 97.26
PRK10829 373 ribonuclease D; Provisional 96.5
KOG0304239 consensus 96.43
PRK07300 880 consensus 95.79
KOG0970 1429 consensus 91.96
cd06125130 DnaQ_like_exo The DnaQ-like exonuclease superfamily is 99.96
cd06128166 DNA_polA_exo The 3'-5' exonuclease domain of family-A D 99.19
cd06126181 DEDDy DEDDy exonucleases, part of the DnaQ-like (or DED 98.69
cd05779204 DNA_polB_epsilon_exo The 3'-5' exonuclease domain of eu 98.56
cd05781188 DNA_polB_B3_exo The 3'-5' exonuclease domain of archaea 98.51
cd05160200 DNA_polB_exo The 3'-5' exonuclease domain of family-B D 98.44
cd05785207 DNA_polB_like2_exo A subfamily of the 3'-5' exonuclease 98.35
cd05777230 DNA_polB_delta_exo The 3'-5' exonuclease domain of euka 98.33
pfam03104254 DNA_pol_B_exo DNA polymerase family B, exonuclease doma 98.22
cd05780195 DNA_polB_Kod1_like_exo The 3'-5' exonuclease domain of 98.14
cd05776234 DNA_polB_alpha_exo The 3'-5' exonuclease domain of euka 97.84
PRK05929 870 consensus 97.7
cd05778231 DNA_polB_zeta_exo The 3'-5' exonuclease domain of eukar 97.55
cd05784193 DNA_polB_II_exo The 3'-5' exonuclease domain of Escheri 97.29
cd05783204 DNA_polB_B1_exo The 3'-5' exonuclease domain of Sulfolo 96.43
PRK06722242 exonuclease; Provisional 99.94
KOG12751118 consensus 96.61
cd05782208 DNA_polB_like1_exo A subfamily of the 3'-5' exonuclease 98.62
cd06146191 mut-7_like_exo The mut-7 subfamily is composed of Caeno 97.78
cd06141168 WRN_exo WRN is a unique RecQ DNA helicase exhibiting an 97.72
TIGR03491457 RecB family nuclease, putative, TM0106 family. Members 94.68
PRK08928 861 consensus 93.11
>PRK06022 consensus Back     alignment and domain information
>TIGR01406 dnaQ_proteo DNA polymerase III, epsilon subunit; InterPro: IPR006309 These represent DnaQ, the DNA polymerase III epsilon subunit, as found in most Proteobacteria Back     alignment and domain information
>PRK06859 consensus Back     alignment and domain information
>PRK05711 DNA polymerase III subunit epsilon; Provisional Back     alignment and domain information
>PRK07982 consensus Back     alignment and domain information
>PRK07009 consensus Back     alignment and domain information
>PRK08816 consensus Back     alignment and domain information
>PRK08858 consensus Back     alignment and domain information
>PRK06631 consensus Back     alignment and domain information
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha subunit, Gram-positive type; InterPro: IPR006308 These are the polypeptide chains of DNA polymerase III Back     alignment and domain information
>PRK06310 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
>PRK07983 exodeoxyribonuclease X; Provisional Back     alignment and domain information
>PRK09182 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK06807 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK07740 hypothetical protein; Provisional Back     alignment and domain information
>PRK08517 DNA polymerase III subunit epsilon; Provisional Back     alignment and domain information
>PRK07883 hypothetical protein; Validated Back     alignment and domain information
>cd06131 DNA_pol_III_epsilon_Ecoli_like This subfamily is composed of the epsilon subunit of Escherichia coli DNA polymerase III (polIII) and similar proteins Back     alignment and domain information
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>TIGR00573 dnaq exonuclease, DNA polymerase III, epsilon subunit family; InterPro: IPR006054 All proteins in this entry for which functions are known are components of the DNA polymerase III complex (epsilon subunit) Back     alignment and domain information
>PRK05168 ribonuclease T; Provisional Back     alignment and domain information
>PRK08074 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
>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative; InterPro: IPR006310 These are a family of proteins in Gram-positive bacteria Back     alignment and domain information
>PRK00448 polC DNA polymerase III PolC; Validated Back     alignment and domain information
>PRK09145 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK06195 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>cd06134 RNaseT RNase T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA Back     alignment and domain information
>PRK07942 DNA polymerase III subunit epsilon; Provisional Back     alignment and domain information
>PRK06063 DNA polymerase III subunit epsilon; Provisional 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
>cd06130 DNA_pol_III_epsilon_like This subfamily is composed of uncharacterized bacterial proteins with similarity to the epsilon subunit of DNA polymerase III (polIII), a multisubunit polymerase which is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase Back     alignment and domain information
>PRK09146 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK07247 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>cd06136 TREX1_2 Three prime repair exonuclease (TREX) 1 and 2 are closely related DEDDh-type DnaQ-like 3'-5' exonucleases 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
>pfam00929 Exonuc_X-T Exonuclease Back     alignment and domain information
>cd06133 ERI-1_3'hExo_like This subfamily is composed of Caenorhabditis elegans ERI-1, human 3' exonuclease (3'hExo), Drosophila exonuclease snipper (snp), and similar proteins from eukaryotes and bacteria Back     alignment and domain information
>cd06127 DEDDh DEDDh exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction Back     alignment and domain information
>cd06138 ExoI_N This subfamily is composed of the N-terminal domain of E Back     alignment and domain information
>PRK07748 sporulation inhibitor KapD; Provisional Back     alignment and domain information
>cd06144 REX4_like This subfamily is composed of RNA exonuclease 4 (REX4 or Rex4p), XPMC2, Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20), and similar proteins Back     alignment and domain information
>TIGR01298 RNaseT ribonuclease T; InterPro: IPR005987 Ribonuclease T (3 Back     alignment and domain information
>PRK05601 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK11779 sbcB exonuclease I; Provisional Back     alignment and domain information
>cd06137 DEDDh_RNase This group is composed of eukaryotic exoribonucleases that include PAN2, RNA exonuclease 1 (REX1 or Rex1p), REX3 (Rex3p), REX4 (or Rex4p), ISG20, and similar proteins Back     alignment and domain information
>cd06149 ISG20 Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20) is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA Back     alignment and domain information
>cd06135 Orn Oligoribonuclease (Orn) is a DEDDh-type DnaQ-like 3'-5' exoribonuclease that is responsible for degrading small oligoribonucleotides to mononucleotides Back     alignment and domain information
>KOG0542 consensus Back     alignment and domain information
>PTZ00315 2'-phosphotransferase; Provisional Back     alignment and domain information
>KOG2249 consensus Back     alignment and domain information
>COG2925 SbcB Exonuclease I [DNA replication, recombination, and repair] Back     alignment and domain information
>cd06145 REX1_like This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins Back     alignment and domain information
>cd06139 DNA_polA_I_Ecoli_like_exo The 3'-5' exonuclease domain of DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity 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
>PRK05359 oligoribonuclease; Provisional Back     alignment and domain information
>cd06143 PAN2_exo 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 Back     alignment and domain information
>cd00007 35EXOc 3'-5' exonuclease Back     alignment and domain information
>cd06142 RNaseD_exo Ribonuclease (RNase) D is a bacterial enzyme involved in the maturation of small stable RNAs and the 3' maturation of tRNA Back     alignment and domain information
>pfam01612 3_5_exonuc 3'-5' exonuclease Back     alignment and domain information
>KOG2248 consensus Back     alignment and domain information
>PRK07456 consensus Back     alignment and domain information
>PRK06887 consensus Back     alignment and domain information
>smart00474 35EXOc 3'-5' exonuclease Back     alignment and domain information
>PRK07556 consensus Back     alignment and domain information
>KOG4793 consensus Back     alignment and domain information
>PRK05755 DNA polymerase I; Provisional Back     alignment and domain information
>PRK07625 consensus Back     alignment and domain information
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair] Back     alignment and domain information
>COG1949 Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification] Back     alignment and domain information
>cd06140 DNA_polA_I_Bacillus_like_exo Bacillus stearothermophilus-like Polymerase I (pol I), a subgroup of the family-A DNA polymerases, contains an inactive DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase region Back     alignment and domain information
>PRK08434 consensus Back     alignment and domain information
>PRK05797 consensus Back     alignment and domain information
>PRK07997 consensus Back     alignment and domain information
>KOG3242 consensus Back     alignment and domain information
>PRK08835 consensus Back     alignment and domain information
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK08786 consensus Back     alignment and domain information
>cd06147 Rrp6p_like_exo Yeast Rrp6p and its human homolog, the Polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100), are exosome-associated proteins involved in the degradation and processing of precursors to stable RNAs Back     alignment and domain information
>cd06129 RNaseD_like The RNase D-like group is composed of RNase D, WRN, and similar proteins Back     alignment and domain information
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional Back     alignment and domain information
>pfam04857 CAF1 CAF1 family ribonuclease Back     alignment and domain information
>PRK05762 DNA polymerase II; Reviewed Back     alignment and domain information
>PRK07898 consensus 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
>smart00486 POLBc DNA polymerase type-B family Back     alignment and domain information
>PRK08076 consensus Back     alignment and domain information
>cd06148 Egl_like_exo The Egalitarian (Egl) protein subfamily is composed of Drosophila Egl and similar proteins Back     alignment and domain information
>pfam10108 Exon_PolB Predicted 3'-5' exonuclease related to the exonuclease domain of PolB Back     alignment and domain information
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair] Back     alignment and domain information
>KOG1798 consensus Back     alignment and domain information
>PRK10829 ribonuclease D; Provisional Back     alignment and domain information
>KOG0304 consensus Back     alignment and domain information
>PRK07300 consensus Back     alignment and domain information
>KOG0970 consensus Back     alignment and domain information
>cd06125 DnaQ_like_exo The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction Back     alignment and domain information
>cd06128 DNA_polA_exo The 3'-5' exonuclease domain of family-A DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity Back     alignment and domain information
>cd06126 DEDDy DEDDy exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction Back     alignment and domain information
>cd05779 DNA_polB_epsilon_exo The 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon Back     alignment and domain information
>cd05781 DNA_polB_B3_exo The 3'-5' exonuclease domain of archaeal proteins with similarity to Sulfurisphaera ohwakuensis DNA polymerase B3 Back     alignment and domain information
>cd05160 DNA_polB_exo The 3'-5' exonuclease domain of family-B DNA polymerases Back     alignment and domain information
>cd05785 DNA_polB_like2_exo A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases Back     alignment and domain information
>cd05777 DNA_polB_delta_exo The 3'-5' exonuclease domain of eukaryotic DNA polymerase delta Back     alignment and domain information
>pfam03104 DNA_pol_B_exo DNA polymerase family B, exonuclease domain Back     alignment and domain information
>cd05780 DNA_polB_Kod1_like_exo The 3'-5' exonuclease domain of archaeal family-B DNA polymerases with similarity to Pyrococcus kodakaraensis Kod1, including polymerases from Desulfurococcus (D Back     alignment and domain information
>cd05776 DNA_polB_alpha_exo The 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha Back     alignment and domain information
>PRK05929 consensus Back     alignment and domain information
>cd05778 DNA_polB_zeta_exo The 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta Back     alignment and domain information
>cd05784 DNA_polB_II_exo The 3'-5' exonuclease domain of Escherichia coli DNA polymerase II (PolII) and similar bacterial proteins Back     alignment and domain information
>cd05783 DNA_polB_B1_exo The 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal proteins Back     alignment and domain information
>PRK06722 exonuclease; Provisional Back     alignment and domain information
>KOG1275 consensus Back     alignment and domain information
>cd05782 DNA_polB_like1_exo A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases Back     alignment and domain information
>cd06146 mut-7_like_exo The mut-7 subfamily is composed of Caenorhabditis elegans mut-7 and similar proteins found in plants and metazoans Back     alignment and domain information
>cd06141 WRN_exo WRN is a unique RecQ DNA helicase exhibiting an exonuclease activity Back     alignment and domain information
>TIGR03491 RecB family nuclease, putative, TM0106 family Back     alignment and domain information
>PRK08928 consensus Back     alignment and domain information

Homologous Structures in PDB Database
Detected by PSI-BLAST, RPS-BLAST and HHsearch

Homologous Structures Detected by PSI-BLAST against Nonredundant Database

IdentityAlignment graphLength Definition E-value
Target245 DNA polymerase III subunit epsilon [Candidatus Liberiba
2gui_A194 Structure And Function Of Cyclized Versions Of The 6e-21
1j53_A186 Structure Of The N-Terminal Exonuclease Domain Of T 7e-21
2p1j_A186 Crystal Structure Of A Polc-Type Dna Polymerase Iii 4e-13
3nh0_A235 Crystal Structure Of Rnase T In Complex With A Non- 9e-05
3ngy_A235 Crystal Structure Of Rnase T (E92g Mutant) Length = 9e-05
2is3_A215 Crystal Structure Of Escherichia Coli Rnase T Lengt 2e-04
>gi|145579465|pdb|2GUI|A Chain A, Structure And Function Of Cyclized Versions Of The Proofread Exonuclease Subunit Of E. Coli Dna Polymerase Iii Length = 194 Back     alignment and structure
 Score =  105 bits (261), Expect = 6e-21,   Method: Composition-based stats.
 Identities = 74/182 (40%), Positives = 110/182 (60%), Gaps = 11/182 (6%)

Query: 8   RKIVFDIETTGLD-----SKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKL 62
           R+IV D ETTG++      +  +IIEIGAVE+++   T   F V+L P+ R   PEA  +
Sbjct: 10  RQIVLDTETTGMNQIGAHYEGHKIIEIGAVEVVNRRLTGNNFHVYLKPD-RLVDPEAFGV 68

Query: 63  HGITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAEL---QRINKDPLD 119
           HGI DEFL DKP+F+ +  EF D+        + HNA FD+GF++ E    +R       
Sbjct: 69  HGIADEFLLDKPTFAEVADEFMDYIRGAE--LVIHNAAFDIGFMDYEFSLLKRDIPKTNT 126

Query: 120 PSRIIDTLSIARRKHPSSRNDLNSLCKRYGITISHRSKHGALLDSHLLSDVYIKMMVGGS 179
             ++ D+L++AR+  P  RN L++LC RY I  S R+ HGALLD+ +L++VY+ M  G +
Sbjct: 127 FCKVTDSLAVARKMFPGKRNSLDALCARYEIDNSKRTLHGALLDAQILAEVYLAMTGGQT 186

Query: 180 QI 181
            +
Sbjct: 187 SM 188


>gi|24987377|pdb|1J53|A Chain A, Structure Of The N-Terminal Exonuclease Domain Of The Epsilon Subunit Of E.Coli Dna Polymerase Iii At Ph 8.5 Length = 186 Back     alignment and structure
>gi|145580424|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
>gi|323462912|pdb|3NH0|A Chain A, Crystal Structure Of Rnase T In Complex With A Non-Preferred Ssdna (Aac) Length = 235 Back     alignment and structure
>gi|323462903|pdb|3NGY|A Chain A, Crystal Structure Of Rnase T (E92g Mutant) Length = 235 Back     alignment and structure
>gi|146386891|pdb|2IS3|A Chain A, Crystal Structure Of Escherichia Coli Rnase T Length = 215 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target245 DNA polymerase III subunit epsilon [Candidatus Liberiba
2gui_A194 DNA polymerase III epsilon subunit; DNA polymerase proo 6e-30
2xri_A224 ERI1 exoribonuclease 3; hydrolase, metal binding; 2.15A 1e-24
2is3_A215 Ribonuclease T; RNAse, exoribonuclease, exonuclease, hy 8e-24
1zbu_A349 ERI-1 homolog, 3'-5' exonuclease ERI1; hydrolase; HET: 3e-23
2f96_A224 Ribonuclease T; RNAse, RNT, RNAse T, tRNA hydrolase, SA 1e-22
1y97_A238 Three prime repair exonuclease 2; TREX2, hydrolase; 2.5 5e-22
3cg7_A308 CRN-4, cell death-related nuclease 4; hydrolase, apopto 7e-22
2ioc_B242 Three prime repair exonuclease 1; proline helix, nucleo 2e-21
1zbh_A299 3'-5' exonuclease ERI1; histone mRNA 3'-END-specific re 2e-20
1w0h_A204 3'-5' exonuclease ERI1; nuclease domain, hydrolase; HET 2e-17
2p1j_A186 POLIII, DNA polymerase III POLC-type; structural genomi 1e-16
1wlj_A189 Interferon stimulated gene 20KDA; exoribonuclease, hydr 5e-12
2igi_A180 Oligoribonuclease; RNAse, exoribonuclease, exonuclease, 4e-11
2gbz_A194 Oligoribonuclease; ORN, deddh, structural genomics, X-R 2e-09
2kfn_A 605 Klenow fragment of DNA polymerase I; complex (polymeras 8e-04
2qxf_A 482 Exodeoxyribonuclease I; alpha-beta domain, DNAQ superfa 1e-15
1x9m_A 698 DNA polymerase; DNA ploymerase, N-2-acetylaminofluorene 5e-04
>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* Length = 194 Back     alignment and structure
 Score =  126 bits (316), Expect = 6e-30
 Identities = 77/190 (40%), Positives = 115/190 (60%), Gaps = 13/190 (6%)

Query: 7   MRKIVFDIETTGLD-----SKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALK 61
            R+IV D ETTG++      +  +IIEIGAVE+++   T   F V+L P  R   PEA  
Sbjct: 9   TRQIVLDTETTGMNQIGAHYEGHKIIEIGAVEVVNRRLTGNNFHVYLKP-DRLVDPEAFG 67

Query: 62  LHGITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDP- 120
           +HGI DEFL DKP+F+ +  EF D+   + AE + HNA FD+GF++ E   + +D     
Sbjct: 68  VHGIADEFLLDKPTFAEVADEFMDYI--RGAELVIHNAAFDIGFMDYEFSLLKRDIPKTN 125

Query: 121 --SRIIDTLSIARRKHPSSRNDLNSLCKRYGITISHRSKHGALLDSHLLSDVYIKMMVGG 178
              ++ D+L++AR+  P  RN L++LC RY I  S R+ HGALLD+ +L++VY+ M   G
Sbjct: 126 TFCKVTDSLAVARKMFPGKRNSLDALCARYEIDNSKRTLHGALLDAQILAEVYLAMT--G 183

Query: 179 SQINFGFKTN 188
            Q +   + +
Sbjct: 184 GQTSMATRES 193


>2xri_A ERI1 exoribonuclease 3; hydrolase, metal binding; 2.15A {Homo sapiens} Length = 224 Back     alignment and structure
>2is3_A Ribonuclease T; RNAse, exoribonuclease, exonuclease, hydrolase, stable RNA maturation, tRNA END-turnover; 3.10A {Escherichia coli K12} Length = 215 Back     alignment and structure
>1zbu_A ERI-1 homolog, 3'-5' exonuclease ERI1; hydrolase; HET: AMP; 3.00A {Homo sapiens} Length = 349 Back     alignment and structure
>2f96_A Ribonuclease T; RNAse, RNT, RNAse T, tRNA hydrolase, SAD, PSI, MCSG, protein structure initiative; 2.09A {Pseudomonas aeruginosa PAO1} SCOP: c.55.3.5 Length = 224 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
>3cg7_A CRN-4, cell death-related nuclease 4; hydrolase, apoptosis, 3'-5' exonuclease, deddh; 2.50A {Caenorhabditis elegans} PDB: 3cm5_A 3cm6_A Length = 308 Back     alignment and structure
>2ioc_B Three prime repair exonuclease 1; proline helix, nucleotide complex, DNAQ family, hydrolase; HET: D5M; 2.10A {Mus musculus} SCOP: c.55.3.5 PDB: 3b6o_A* 2o4g_A* 3b6p_A* 2o4i_A 2oa8_A Length = 242 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} Length = 299 Back     alignment and structure
>1w0h_A 3'-5' exonuclease ERI1; nuclease domain, hydrolase; HET: AMP; 1.59A {Homo sapiens} SCOP: c.55.3.5 Length = 204 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} Length = 186 Back     alignment and structure
>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
>2igi_A Oligoribonuclease; RNAse, exoribonuclease, exonuclease, hydrolase, mRNA decay; 1.70A {Escherichia coli K12} SCOP: c.55.3.5 PDB: 1yta_A 1j9a_A Length = 180 Back     alignment and structure
>2gbz_A Oligoribonuclease; ORN, deddh, structural genomics, X-RAY diffraction, hydrolase; 2.30A {Xanthomonas campestris PV} Length = 194 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
>2qxf_A Exodeoxyribonuclease I; alpha-beta domain, DNAQ superfamily, SH3-like domain, product bound structure, DNA damage, DNA repair, exonuclease; HET: TMP; 1.50A {Escherichia coli K12} SCOP: c.55.3.5 PDB: 1fxx_A* 3c94_A 3c95_A Length = 482 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* Length = 698 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target245 DNA polymerase III subunit epsilon [Candidatus Liberiba
2gui_A194 DNA polymerase III epsilon subunit; DNA polymerase proo 100.0
2p1j_A186 POLIII, DNA polymerase III POLC-type; structural genomi 100.0
2is3_A215 Ribonuclease T; RNAse, exoribonuclease, exonuclease, hy 100.0
2ioc_B242 Three prime repair exonuclease 1; proline helix, nucleo 100.0
1y97_A238 Three prime repair exonuclease 2; TREX2, hydrolase; 2.5 100.0
2xri_A224 ERI1 exoribonuclease 3; hydrolase, metal binding; 2.15A 100.0
3cg7_A308 CRN-4, cell death-related nuclease 4; hydrolase, apopto 100.0
1zbh_A299 3'-5' exonuclease ERI1; histone mRNA 3'-END-specific re 100.0
1wlj_A189 Interferon stimulated gene 20KDA; exoribonuclease, hydr 100.0
1zbu_A349 ERI-1 homolog, 3'-5' exonuclease ERI1; hydrolase; HET: 99.98
2qxf_A 482 Exodeoxyribonuclease I; alpha-beta domain, DNAQ superfa 99.97
2f96_A224 Ribonuclease T; RNAse, RNT, RNAse T, tRNA hydrolase, SA 99.97
1w0h_A204 3'-5' exonuclease ERI1; nuclease domain, hydrolase; HET 99.96
2gbz_A194 Oligoribonuclease; ORN, deddh, structural genomics, X-R 99.84
2igi_A180 Oligoribonuclease; RNAse, exoribonuclease, exonuclease, 99.81
1x9m_A 698 DNA polymerase; DNA ploymerase, N-2-acetylaminofluorene 99.38
2hhv_A 580 DNA polymerase I; DNA replication, klenow fragment, pro 98.96
2d5r_A252 CCR4-NOT transcription complex subunit 7; poly(A) deade 98.75
1yt3_A 375 Ribonuclease D, RNAse D; exoribonuclease, exonuclease, 98.63
2gv9_A 1193 DNA polymerase; polymerase alpha fold, transferase; HET 98.52
1uoc_A289 POP2; hydrolase, DEDD nuclease, mRNA degradation, poly( 98.47
2p51_A333 SPCC18.06C protein; DEDD nuclease fold, hydrolase, gene 98.34
3iay_A 919 DNA polymerase delta catalytic subunit; protein-DNA com 98.33
2hbj_A410 Exosome complex exonuclease RRP6; RNA metabolism, RNA s 98.3
3cym_A 440 Uncharacterized protein BAD_0989; structural genomics, 98.07
1qht_A 775 Protein (DNA polymerase); archaea, hyperthermostable, f 97.98
2py5_A 575 DNA polymerase; protein-DNA complex, replication, trans 97.84
3k59_A 786 POL II, DNA polymerase II; protein-DNA complex, DNA dam 97.71
1s5j_A 847 DNA polymerase I; replication, disulfide bonds, transfe 97.53
3m8r_A 540 DNA polymerase I, thermostable; DNA polymerase, DNA rep 97.16
3nae_A 903 DNA polymerase, GP43; RB69 DNA polymerase; HET: DNA G35 96.54
1noy_A388 Protein (DNA polymerase (E.C.2.7.7.7)); exonuclease, DN 93.52
2kfn_A 605 Klenow fragment of DNA polymerase I; complex (polymeras 99.19
3d45_A507 Poly(A)-specific ribonuclease PARN; CAP analogue, cytop 98.62
2a1r_A430 Poly(A)-specific ribonuclease PARN; DEDD, nuclease doma 98.59
2e6m_A208 Werner syndrome ATP-dependent helicase homolog; APO for 97.61
1vk0_A206 Hypothetical protein; homohexamer, AT5G06450, structura 95.91
3ikm_A 1172 DNA polymerase subunit gamma-1; human mitochondrial DNA 93.96
1bgx_T 832 TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhibitio 92.29
>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* Back     alignment and structure
Probab=100.00  E-value=4.4e-40  Score=269.05  Aligned_cols=174  Identities=44%  Similarity=0.782  Sum_probs=156.4

Q ss_pred             CCCCCCEEEEECCCCCCCCC-----CCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCC
Q ss_conf             66777589998467888888-----8889999999999998803137989858882288657242021012322485210
Q gi|254780818|r    3 RKNKMRKIVFDIETTGLDSK-----NDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFS   77 (245)
Q Consensus         3 ~~~~mr~iv~D~ETTGl~~~-----~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~   77 (245)
                      ...++|+||||||||||+|.     .|||||||||++.++..++++|+.+|+|. .++.+.+.++|||+++++.++|+|.
T Consensus         5 ~~~~~r~vv~D~ETTGl~~~~~~~~~drIieigav~~~~~~~~~~~~~~~v~P~-~~~~~~~~~i~gi~~e~~~~~~~~~   83 (194)
T 2gui_A            5 STAITRQIVLDTETTGMNQIGAHYEGHKIIEIGAVEVVNRRLTGNNFHVYLKPD-RLVDPEAFGVHGIADEFLLDKPTFA   83 (194)
T ss_dssp             ---CCEEEEEEEEESCCCSSSSTTTTCCEEEEEEEEEETTEECSCCEEEECCCS-SCCCHHHHHHHCCCHHHHTTSCCHH
T ss_pred             CCCCCCEEEEEEECCCCCCCCCCCCCCEEEEEEEEEEECCEEECEEEEEEECCC-CCCCHHHHHHHCCCHHHHHHHHHHH
T ss_conf             878883799997379998764567895499999999999999740789998999-8655778987075576643345589


Q ss_pred             HHHHHHHHHHHCCCCEEEEECCCCCCCEEEECHHCCCCCCCC---CCHHCCCHHCCCCCCCCCCCCHHHHHHHHCCCCCC
Q ss_conf             023447775300232023102322431121000001122221---00001100000001776422237899971875455
Q gi|254780818|r   78 SIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLD---PSRIIDTLSIARRKHPSSRNDLNSLCKRYGITISH  154 (245)
Q Consensus        78 ev~~~f~~fi~~~~~~lVaHNa~FD~~fL~~el~r~~~~~~~---~~~~iDTl~lar~~~p~~~~~L~~l~~~~~i~~~~  154 (245)
                      +++.+|.+|++  +.++|+||+.||..+++..+.+++.+...   .+.++|++.++|..+|+.+++|+.||.+|+++..+
T Consensus        84 ~v~~~~~~~l~--~~~~v~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~p~~~~~L~~l~~~~~i~~~~  161 (194)
T 2gui_A           84 EVADEFMDYIR--GAELVIHNAAFDIGFMDYEFSLLKRDIPKTNTFCKVTDSLAVARKMFPGKRNSLDALCARYEIDNSK  161 (194)
T ss_dssp             HHHHHHHHHHT--TSEEEETTHHHHHHHHHHHHHHTCSCCCCGGGTSEEEEHHHHHHHHSTTSCCSHHHHHHHTTCCCTT
T ss_pred             HHHHHHHHHHC--CCEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCEEHHHHHHHHCCCCCCCHHHHHHHCCCCCCC
T ss_conf             98899998708--9738997851319999999998099976555442000199999997489878899999985999899


Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHCCC
Q ss_conf             5666402699999999999973057
Q gi|254780818|r  155 RSKHGALLDSHLLSDVYIKMMVGGS  179 (245)
Q Consensus       155 r~~H~Al~Da~~~a~v~~~ll~g~~  179 (245)
                      +++|+||+||++|++||++|++|+.
T Consensus       162 ~~~H~Al~Da~~t~~l~~~m~~~~~  186 (194)
T 2gui_A          162 RTLHGALLDAQILAEVYLAMTGGQT  186 (194)
T ss_dssp             CSSCCHHHHHHHHHHHHHHHTC---
T ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCH
T ss_conf             9874889999999999999977855



>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
>2is3_A Ribonuclease T; RNAse, exoribonuclease, exonuclease, hydrolase, stable RNA maturation, tRNA END-turnover; 3.10A {Escherichia coli K12} Back     alignment and structure
>2ioc_B Three prime repair exonuclease 1; proline helix, nucleotide complex, DNAQ family, hydrolase; HET: D5M; 2.10A {Mus musculus} SCOP: c.55.3.5 PDB: 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
>2xri_A ERI1 exoribonuclease 3; hydrolase, metal binding; 2.15A {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
>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
>1wlj_A Interferon stimulated gene 20KDA; exoribonuclease, hydrolase; HET: U5P; 1.90A {Homo sapiens} SCOP: c.55.3.5 Back     alignment and structure
>1zbu_A ERI-1 homolog, 3'-5' exonuclease ERI1; hydrolase; HET: AMP; 3.00A {Homo sapiens} Back     alignment and structure
>2qxf_A Exodeoxyribonuclease I; alpha-beta domain, DNAQ superfamily, SH3-like domain, product bound structure, DNA damage, DNA repair, exonuclease; HET: TMP; 1.50A {Escherichia coli K12} SCOP: c.55.3.5 PDB: 1fxx_A* 3c94_A 3c95_A 3hl8_A* 3hp9_A* Back     alignment and structure
>2f96_A Ribonuclease T; RNAse, RNT, RNAse T, tRNA hydrolase, SAD, PSI, MCSG, protein structure initiative; 2.09A {Pseudomonas aeruginosa PAO1} SCOP: c.55.3.5 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
>2gbz_A Oligoribonuclease; ORN, deddh, structural genomics, X-RAY diffraction, hydrolase; 2.30A {Xanthomonas campestris PV} Back     alignment and structure
>2igi_A Oligoribonuclease; RNAse, exoribonuclease, exonuclease, hydrolase, mRNA decay; 1.70A {Escherichia coli K12} SCOP: c.55.3.5 PDB: 1yta_A 1j9a_A Back     alignment and structure