254780636

254780636

ribonuclease D

GeneID in NCBI database:8209637Locus tag:CLIBASIA_02615
Protein GI in NCBI database:254780636Protein Accession:YP_003065049.1
Gene range:+(633342, 633965)Protein Length:207aa
Gene description:ribonuclease D
COG prediction:[J] Ribonuclease D
KEGG prediction:ribonuclease D; K03684 ribonuclease D [EC:3.1.13.5]
SEED prediction:Ribonuclease D related protein
Pathway involved in KEGG:not defined
Subsystem involved in SEED:- none -
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-------
MTTIRVHEGDIPAECAARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKIFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDLATSCCNFLMDRAELDLLGWENVDIFSHS
ccEEEEEHHHHHHHHHcccccEEEEEEEcccccccccEEEEEEEEcccccEEEEEcccccccHHHHHHHHcccccEEEEEEHHHHHHHHHHHcccccccccHHHHHHHHHccccccccHHHHHHHHccccccccHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHccHHHHHHHHccccccccccc
ccEEEEccccccHHHHcccccEEEEEccHcccccccccEEEEEEEcccccEEEEEcccccccccHHHHHHHcccHHEEHHccHHHHHHHHHHcccccccccHHHHHHHHHHccccccHHHHHHHHHHcccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHccHHHHHHHcccccccHEccc
mttirvhegdipaECAARYVDAIAVdtetlglmprrdrlcivqlspgdgtVDIIRIAAgqknapnlVGMLVDEKREKIFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINiskaqqssdwsaddlsDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDLATSCCNFLMDRAeldllgwenvdifshs
mttirvhegdipaecAARYVDAIAVDTetlglmprrDRLCIVQLSPGDGTVDIIRIaagqknapnlVGMLVDEKREKIFHYGRFDIAVLFYTFGVRVRPVFCTKIASRltrtytnqhglKDNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDLATSCCNFLMDRAELDLLGWENVDIFSHS
MTTIRVHEGDIPAECAARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKIFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDLATSCCNFLMDRAELDLLGWENVDIFSHS
*TTIRVHEGDIPAECAARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKIFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDLATSCCNFLMDRAELDLLGWENVDIFS**
MTTIRVHEGDIPAECAARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKIFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKA**********LSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDLATSCCNFLMDRAELDLLGWENVDIFSHS
MTTIRVHEGDIPAECAARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKIFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDLATSCCNFLMDRAELDLLGWENVDIF***
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MTTIRVHEGDIPAECAARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKIFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDLATSCCNFLMDRAELDLLGWENVDIFSHS
MTTIRVHEGDIPAECAARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKIFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDLATSCCNFLMDRAELDLLGWENVDIFSHS
MTTIRVHEGDIPAECAARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKIFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDLATSCCNFLMDRAELDLLGWENVDIFSHS

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

Original result of BLAST against C. L. asiaticus genome

No hits with e-value below 0.05

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

Original result of PSI-BLAST first 2 iterations

IdentityAlignment graphLength Definition Round E-value
Target207 ribonuclease D [Candidatus Liberibacter asiaticus str.
315122172209 ribonuclease D [Candidatus Liberibacter solanacearum CL 1 6e-96
332716830208 Ribonuclease D [Agrobacterium sp. H13-3] Length = 208 1 1e-83
222147114208 ribonuclease D [Agrobacterium vitis S4] Length = 208 1 2e-83
209551599208 3'-5' exonuclease [Rhizobium leguminosarum bv. trifolii 1 4e-83
222084303208 RNAse D protein [Agrobacterium radiobacter K84] Length 1 1e-82
86355756208 RNAse D protein [Rhizobium etli CFN 42] Length = 208 1 2e-82
195970213208 hypothetical protein SMc00342 [Sinorhizobium meliloti 1 1 2e-82
218508865208 ribonuclease III protein [Rhizobium etli Brasil 5] Leng 1 2e-82
218661189208 ribonuclease III protein [Rhizobium etli IE4771] Length 1 2e-82
116249870208 ribonuclease [Rhizobium leguminosarum bv. viciae 3841] 1 3e-82
>gi|315122172|ref|YP_004062661.1| ribonuclease D [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 209 Back     alignment and organism information
 Score =  353 bits (907), Expect = 6e-96,   Method: Compositional matrix adjust.
 Identities = 166/206 (80%), Positives = 183/206 (88%)

Query: 1   MTTIRVHEGDIPAECAARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQ 60
           MTTIRVH GDIP EC ARY   IAVDTETLGL+PRRDRLC+VQLSPGDGT DIIRIAA Q
Sbjct: 1   MTTIRVHNGDIPTECIARYTGPIAVDTETLGLIPRRDRLCVVQLSPGDGTADIIRIAAEQ 60

Query: 61  KNAPNLVGMLVDEKREKIFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLK 120
           KNAPNLV ML +E +EKIFHY RFDIAVLFYTFGVRV+P+FCTKIASRLTRTY ++HGLK
Sbjct: 61  KNAPNLVTMLANETQEKIFHYARFDIAVLFYTFGVRVKPIFCTKIASRLTRTYIDRHGLK 120

Query: 121 DNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDLA 180
           DNL+ELLG++ISK QQ SDWS DDLS EQLQYAASDVVHLHALR +F  KLQ LGRSD+A
Sbjct: 121 DNLRELLGVDISKKQQLSDWSEDDLSHEQLQYAASDVVHLHALREKFIAKLQSLGRSDVA 180

Query: 181 TSCCNFLMDRAELDLLGWENVDIFSH 206
           ++C NFLM RAELDLLGW+N+DIFSH
Sbjct: 181 SACFNFLMSRAELDLLGWDNIDIFSH 206



Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|332716830|ref|YP_004444296.1| Ribonuclease D [Agrobacterium sp. H13-3] Length = 208 Back     alignment and organism information
>gi|222147114|ref|YP_002548071.1| ribonuclease D [Agrobacterium vitis S4] Length = 208 Back     alignment and organism information
>gi|209551599|ref|YP_002283516.1| 3'-5' exonuclease [Rhizobium leguminosarum bv. trifolii WSM2304] Length = 208 Back     alignment and organism information
>gi|222084303|ref|YP_002542832.1| RNAse D protein [Agrobacterium radiobacter K84] Length = 208 Back     alignment and organism information
>gi|86355756|ref|YP_467648.1| RNAse D protein [Rhizobium etli CFN 42] Length = 208 Back     alignment and organism information
>gi|195970213|ref|NP_384368.2| hypothetical protein SMc00342 [Sinorhizobium meliloti 1021] Length = 208 Back     alignment and organism information
>gi|218508865|ref|ZP_03506743.1| ribonuclease III protein [Rhizobium etli Brasil 5] Length = 208 Back     alignment and organism information
>gi|218661189|ref|ZP_03517119.1| ribonuclease III protein [Rhizobium etli IE4771] Length = 208 Back     alignment and organism information
>gi|116249870|ref|YP_765708.1| ribonuclease [Rhizobium leguminosarum bv. viciae 3841] Length = 208 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

Original result of RPS-BLAST against CDD database part I

Original result of RPS-BLASTagainst CDD database part II

IdentityAlignment graphLength Definition E-value
Target207 ribonuclease D [Candidatus Liberibacter asiaticus str.
cd06142178 cd06142, RNaseD_exo, DEDDy 3'-5' exonuclease domain of 2e-46
pfam01612172 pfam01612, 3_5_exonuc, 3'-5' exonuclease 1e-29
smart00474172 smart00474, 35EXOc, 3'-5' exonuclease 6e-26
cd00007155 cd00007, 35EXOc, 3'-5' exonuclease 1e-23
TIGR01388 367 TIGR01388, rnd, ribonuclease D 7e-20
PRK10829 373 PRK10829, PRK10829, ribonuclease D; Provisional 3e-09
cd09018150 cd09018, DEDDy_polA_RNaseD_like_exo, DEDDy 3'-5' exonuc 6e-09
cd06148197 cd06148, Egl_like_exo, DEDDy 3'-5' exonuclease domain o 2e-08
PRK05755 880 PRK05755, PRK05755, DNA polymerase I; Provisional 5e-08
COG0749 593 COG0749, PolA, DNA polymerase I - 3'-5' exonuclease and 2e-07
KOG2206 687 KOG2206, KOG2206, KOG2206, Exosome 3'-5' exoribonucleas 2e-05
cd06140178 cd06140, DNA_polA_I_Bacillus_like_exo, inactive DEDDy 3 4e-04
COG0349 361 COG0349, Rnd, Ribonuclease D [Translation, ribosomal st 7e-58
cd06129161 cd06129, RNaseD_like, DEDDy 3'-5' exonuclease domain of 2e-12
cd06141170 cd06141, WRN_exo, DEDDy 3'-5' exonuclease domain of WRN 9e-11
cd06139193 cd06139, DNA_polA_I_Ecoli_like_exo, DEDDy 3'-5' exonucl 9e-07
cd06147192 cd06147, Rrp6p_like_exo, DEDDy 3'-5' exonuclease domain 1e-05
PRK14975 553 PRK14975, PRK14975, bifunctional 3'-5' exonuclease/DNA 1e-07
cd06146193 cd06146, mut-7_like_exo, DEDDy 3'-5' exonuclease domain 2e-05
>gnl|CDD|176654 cd06142, RNaseD_exo, DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins Back     alignment and domain information
>gnl|CDD|144991 pfam01612, 3_5_exonuc, 3'-5' exonuclease Back     alignment and domain information
>gnl|CDD|128750 smart00474, 35EXOc, 3'-5' exonuclease Back     alignment and domain information
>gnl|CDD|28891 cd00007, 35EXOc, 3'-5' exonuclease Back     alignment and domain information
>gnl|CDD|130455 TIGR01388, rnd, ribonuclease D Back     alignment and domain information
>gnl|CDD|182762 PRK10829, PRK10829, ribonuclease D; Provisional Back     alignment and domain information
>gnl|CDD|176656 cd09018, DEDDy_polA_RNaseD_like_exo, DEDDy 3'-5' exonuclease domain of family-A DNA polymerases, RNase D, WRN, and similar proteins Back     alignment and domain information
>gnl|CDD|99851 cd06148, Egl_like_exo, DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins Back     alignment and domain information
>gnl|CDD|180237 PRK05755, PRK05755, DNA polymerase I; Provisional Back     alignment and domain information
>gnl|CDD|31092 COG0749, PolA, DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|37417 KOG2206, KOG2206, KOG2206, Exosome 3'-5' exoribonuclease complex, subunit PM/SCL-100 (Rrp6) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|176652 cd06140, DNA_polA_I_Bacillus_like_exo, inactive DEDDy 3'-5' exonuclease domain of Bacillus stearothermophilus DNA polymerase I and similar family-A DNA polymerases Back     alignment and domain information
>gnl|CDD|30697 COG0349, Rnd, Ribonuclease D [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|176650 cd06129, RNaseD_like, DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins Back     alignment and domain information
>gnl|CDD|176653 cd06141, WRN_exo, DEDDy 3'-5' exonuclease domain of WRN and similar proteins Back     alignment and domain information
>gnl|CDD|176651 cd06139, DNA_polA_I_Ecoli_like_exo, DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases Back     alignment and domain information
>gnl|CDD|99850 cd06147, Rrp6p_like_exo, DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen 100kDa, and similar proteins Back     alignment and domain information
>gnl|CDD|184938 PRK14975, PRK14975, bifunctional 3'-5' exonuclease/DNA polymerase; Provisional Back     alignment and domain information
>gnl|CDD|176655 cd06146, mut-7_like_exo, DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

Original result of HHsearch against CDD database

IdentityAlignment graphLength Definition Probability
Target 207 ribonuclease D [Candidatus Liberibacter asiaticus str.
COG0349 361 Rnd Ribonuclease D [Translation, ribosomal structure an 100.0
TIGR01388 374 rnd ribonuclease D; InterPro: IPR006292 These proteins 100.0
PRK10829 373 ribonuclease D; Provisional 100.0
cd06142178 RNaseD_exo Ribonuclease (RNase) D is a bacterial enzyme 100.0
cd06147192 Rrp6p_like_exo Yeast Rrp6p and its human homolog, the P 100.0
cd06148197 Egl_like_exo The Egalitarian (Egl) protein subfamily is 100.0
cd06139193 DNA_polA_I_Ecoli_like_exo The 3'-5' exonuclease domain 100.0
PRK07556 977 consensus 100.0
PRK06887 954 consensus 100.0
PRK05755 889 DNA polymerase I; Provisional 100.0
PRK07997 928 consensus 100.0
PRK07456 975 consensus 100.0
PRK07625 922 consensus 100.0
PRK08786 927 consensus 100.0
PRK08835 931 consensus 99.98
cd06140178 DNA_polA_I_Bacillus_like_exo Bacillus stearothermophilu 99.97
PRK07898 902 consensus 99.97
PRK05797 869 consensus 99.97
PRK08434 887 consensus 99.96
PRK08076 877 consensus 99.96
PRK05929 870 consensus 99.95
PRK08928 861 consensus 99.93
COG0749 593 PolA DNA polymerase I - 3'-5' exonuclease and polymeras 99.92
PRK07300 880 consensus 99.86
PRK06309232 DNA polymerase III subunit epsilon; Validated 99.41
TIGR01405 1264 polC_Gram_pos DNA polymerase III, alpha subunit, Gram-p 99.19
COG2176 1444 PolC DNA polymerase III, alpha subunit (gram-positive t 98.97
cd06129159 RNaseD_like The RNase D-like group is composed of RNase 100.0
pfam01612172 3_5_exonuc 3'-5' exonuclease. This domain is responsibl 100.0
smart00474172 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofread 100.0
cd06146191 mut-7_like_exo The mut-7 subfamily is composed of Caeno 100.0
cd06141168 WRN_exo WRN is a unique RecQ DNA helicase exhibiting an 100.0
cd00007155 35EXOc 3'-5' exonuclease. The 35EXOc domain is responsi 100.0
cd06128166 DNA_polA_exo The 3'-5' exonuclease domain of family-A D 99.98
KOG2206 687 consensus 99.94
cd06126181 DEDDy DEDDy exonucleases, part of the DnaQ-like (or DED 99.78
KOG2207617 consensus 99.77
KOG4373319 consensus 99.38
PRK07740240 hypothetical protein; Provisional 99.31
PRK06310250 DNA polymerase III subunit epsilon; Validated 99.28
PRK06631229 consensus 99.28
PRK07942234 DNA polymerase III subunit epsilon; Provisional 99.22
PRK08074 932 bifunctional ATP-dependent DNA helicase/DNA polymerase 99.16
PRK06022234 consensus 99.14
PRK08517259 DNA polymerase III subunit epsilon; Provisional 99.14
PRK08858246 consensus 99.13
PRK07246 820 bifunctional ATP-dependent DNA helicase/DNA polymerase 99.13
PRK07009241 consensus 99.12
PRK05711240 DNA polymerase III subunit epsilon; Provisional 99.09
PRK08816244 consensus 99.08
cd06131167 DNA_pol_III_epsilon_Ecoli_like This subfamily is compos 99.07
PRK06807 313 DNA polymerase III subunit epsilon; Validated 99.07
PRK07982243 consensus 99.02
TIGR01406246 dnaQ_proteo DNA polymerase III, epsilon subunit; InterP 99.01
cd06134189 RNaseT RNase T is a DEDDh-type DnaQ-like 3'-5' exoribon 99.01
PRK00448 1436 polC DNA polymerase III PolC; Validated 99.01
PRK07883 575 hypothetical protein; Validated 98.99
PRK06859253 consensus 98.99
PRK05168213 ribonuclease T; Provisional 98.98
PRK09145203 DNA polymerase III subunit epsilon; Validated 98.97
cd06127159 DEDDh DEDDh exonucleases, part of the DnaQ-like (or DED 98.9
TIGR01407 944 dinG_rel DnaQ family exonuclease/DinG family helicase, 98.85
cd06144152 REX4_like This subfamily is composed of RNA exonuclease 98.84
PRK09146239 DNA polymerase III subunit epsilon; Validated 98.83
PRK06063313 DNA polymerase III subunit epsilon; Provisional 98.8
pfam00929162 Exonuc_X-T Exonuclease. This family includes a variety 98.79
smart00479169 EXOIII exonuclease domain in DNA-polymerase alpha and e 98.77
PRK07247195 DNA polymerase III subunit epsilon; Validated 98.67
PRK06195 309 DNA polymerase III subunit epsilon; Validated 98.6
cd06137161 DEDDh_RNase This group is composed of eukaryotic exorib 98.58
KOG2249280 consensus 98.5
cd06130156 DNA_pol_III_epsilon_like This subfamily is composed of 98.4
cd06138183 ExoI_N This subfamily is composed of the N-terminal dom 98.35
cd06149157 ISG20 Interferon (IFN) Stimulated Gene product of 20 kD 98.34
cd06145150 REX1_like This subfamily is composed of RNA exonuclease 98.29
KOG2405458 consensus 98.24
PRK07983219 exodeoxyribonuclease X; Provisional 98.21
cd06133176 ERI-1_3'hExo_like This subfamily is composed of Caenorh 98.19
cd05781188 DNA_polB_B3_exo The 3'-5' exonuclease domain of archaea 98.15
COG0847243 DnaQ DNA polymerase III, epsilon subunit and related 3' 98.1
COG3359278 Predicted exonuclease [DNA replication, recombination, 97.88
TIGR00573228 dnaq exonuclease, DNA polymerase III, epsilon subunit f 97.8
cd05780195 DNA_polB_Kod1_like_exo The 3'-5' exonuclease domain of 97.76
cd05160200 DNA_polB_exo The 3'-5' exonuclease domain of family-B D 97.74
cd05785207 DNA_polB_like2_exo A subfamily of the 3'-5' exonuclease 97.42
PRK05762 785 DNA polymerase II; Reviewed 97.37
cd05784193 DNA_polB_II_exo The 3'-5' exonuclease domain of Escheri 97.08
PRK11779 477 sbcB exonuclease I; Provisional 96.51
PTZ00166 1081 DNA polymerase delta catalytic subunit; Provisional 96.46
TIGR01298201 RNaseT ribonuclease T; InterPro: IPR005987 Ribonuclease 94.58
cd05783204 DNA_polB_B1_exo The 3'-5' exonuclease domain of Sulfolo 92.7
TIGR00593 1005 pola DNA polymerase I; InterPro: IPR002298 DNA carries 99.52
KOG12751118 consensus 97.24
cd06125130 DnaQ_like_exo The DnaQ-like exonuclease superfamily is 99.05
PRK09182293 DNA polymerase III subunit epsilon; Validated 97.57
pfam04857235 CAF1 CAF1 family ribonuclease. The major pathways of mR 97.48
KOG2405 458 consensus 96.66
cd06136177 TREX1_2 Three prime repair exonuclease (TREX) 1 and 2 a 98.55
cd06143174 PAN2_exo PAN2 is the catalytic subunit of poly(A) nucle 98.28
KOG3657 1075 consensus 97.69
cd05779204 DNA_polB_epsilon_exo The 3'-5' exonuclease domain of eu 97.55
cd05782208 DNA_polB_like1_exo A subfamily of the 3'-5' exonuclease 97.01
KOG2248380 consensus 96.74
cd05777230 DNA_polB_delta_exo The 3'-5' exonuclease domain of euka 96.7
cd05776234 DNA_polB_alpha_exo The 3'-5' exonuclease domain of euka 95.21
smart00486 471 POLBc DNA polymerase type-B family. DNA polymerase alph 94.25
PRK06722242 exonuclease; Provisional 94.77
cd06135173 Orn Oligoribonuclease (Orn) is a DEDDh-type DnaQ-like 3 92.78
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>TIGR01388 rnd ribonuclease D; InterPro: IPR006292 These proteins represent ribonuclease D, a 3-exonuclease shown to act on tRNA both in vitro and when overexpressed in vivo Back     alignment and domain information
>PRK10829 ribonuclease D; Provisional 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
>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
>cd06148 Egl_like_exo The Egalitarian (Egl) protein subfamily is composed of Drosophila Egl and similar 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
>PRK07556 consensus Back     alignment and domain information
>PRK06887 consensus Back     alignment and domain information
>PRK05755 DNA polymerase I; Provisional Back     alignment and domain information
>PRK07997 consensus Back     alignment and domain information
>PRK07456 consensus Back     alignment and domain information
>PRK07625 consensus Back     alignment and domain information
>PRK08786 consensus Back     alignment and domain information
>PRK08835 consensus 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
>PRK07898 consensus Back     alignment and domain information
>PRK05797 consensus Back     alignment and domain information
>PRK08434 consensus Back     alignment and domain information
>PRK08076 consensus Back     alignment and domain information
>PRK05929 consensus Back     alignment and domain information
>PRK08928 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
>PRK07300 consensus Back     alignment and domain information
>PRK06309 DNA polymerase III subunit epsilon; Validated 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
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair] 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
>pfam01612 3_5_exonuc 3'-5' exonuclease Back     alignment and domain information
>smart00474 35EXOc 3'-5' exonuclease 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
>cd00007 35EXOc 3'-5' exonuclease 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
>KOG2206 consensus 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
>KOG2207 consensus Back     alignment and domain information
>KOG4373 consensus Back     alignment and domain information
>PRK07740 hypothetical protein; Provisional Back     alignment and domain information
>PRK06310 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK06631 consensus Back     alignment and domain information
>PRK07942 DNA polymerase III subunit epsilon; Provisional Back     alignment and domain information
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK06022 consensus Back     alignment and domain information
>PRK08517 DNA polymerase III subunit epsilon; Provisional Back     alignment and domain information
>PRK08858 consensus Back     alignment and domain information
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK07009 consensus Back     alignment and domain information
>PRK05711 DNA polymerase III subunit epsilon; Provisional Back     alignment and domain information
>PRK08816 consensus 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
>PRK06807 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK07982 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
>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
>PRK00448 polC DNA polymerase III PolC; Validated Back     alignment and domain information
>PRK07883 hypothetical protein; Validated Back     alignment and domain information
>PRK06859 consensus Back     alignment and domain information
>PRK05168 ribonuclease T; Provisional Back     alignment and domain information
>PRK09145 DNA polymerase III subunit epsilon; Validated 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
>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
>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
>PRK09146 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK06063 DNA polymerase III subunit epsilon; Provisional Back     alignment and domain information
>pfam00929 Exonuc_X-T Exonuclease 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
>PRK07247 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK06195 DNA polymerase III subunit epsilon; Validated 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
>KOG2249 consensus 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
>cd06138 ExoI_N This subfamily is composed of the N-terminal domain of E 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
>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
>KOG2405 consensus Back     alignment and domain information
>PRK07983 exodeoxyribonuclease X; Provisional 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
>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
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair] Back     alignment and domain information
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair] 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
>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
>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
>PRK05762 DNA polymerase II; Reviewed 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
>PRK11779 sbcB exonuclease I; Provisional Back     alignment and domain information
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional Back     alignment and domain information
>TIGR01298 RNaseT ribonuclease T; InterPro: IPR005987 Ribonuclease T (3 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
>TIGR00593 pola DNA polymerase I; InterPro: IPR002298 DNA carries the biological information that instructs cells how to exist in an ordered fashion Back     alignment and domain information
>KOG1275 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
>PRK09182 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>pfam04857 CAF1 CAF1 family ribonuclease Back     alignment and domain information
>KOG2405 consensus 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
>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
>KOG3657 consensus 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
>cd05782 DNA_polB_like1_exo A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases Back     alignment and domain information
>KOG2248 consensus 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
>cd05776 DNA_polB_alpha_exo The 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha Back     alignment and domain information
>smart00486 POLBc DNA polymerase type-B family Back     alignment and domain information
>PRK06722 exonuclease; Provisional 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

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

Homologous Structures Detected by PSI-BLAST against Nonredundant Database

Original result of PSI-BLAST

IdentityAlignment graphLength Definition E-value
Target207 ribonuclease D [Candidatus Liberibacter asiaticus str.
1yt3_A 375 Crystal Structure Of Escherichia Coli Rnase D, An E 2e-22
1dpi_A 605 Structure Of Large Fragment Of Escherichia Coli Dna 2e-18
1kfs_A 605 Dna Polymerase I Klenow Fragment (E.C.2.7.7.7) Muta 2e-18
2hbj_A 410 Structure Of The Yeast Nuclear Exosome Component, R 3e-18
1kln_A 605 Dna Polymerase I Klenow Fragment (E.C.2.7.7.7) Muta 1e-16
1d8y_A 605 Crystal Structure Of The Complex Of Dna Polymerase 9e-15
3cym_A 440 Crystal Structure Of Protein Bad_0989 From Bifidoba 2e-10
2e6l_A208 Structure Of Mouse Wrn Exonuclease Domain Length = 3e-08
2fbt_A205 Wrn Exonuclease Length = 205 7e-08
gi|75765643|pdb|1YT3|A Chain A, Crystal Structure Of Escherichia Coli Rnase D, An Exoribonuclease Involved In Structured Rna Processing Length = 375 Back     alignment and structure 
 Score =  109 bits (272), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 48/192 (25%), Positives = 83/192 (43%), Gaps = 6/192 (3%)

Query: 2   TTIRVHEGD--IPAECAA-RYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAA 58
              ++   D  + + C A R   AIA+DTE +       +L ++QL  G+    I  +  
Sbjct: 1   MNYQMITTDDALASLCEAVRAFPAIALDTEFVRTRTYYPQLGLIQLFDGEHLALIDPL-- 58

Query: 59  GQKNAPNLVGMLVDEKREKIFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHG 118
           G  +   L  +L D    K  H G  D+ V    FG   +P+  T+I +          G
Sbjct: 59  GITDWSPLKAILRDPSITKFLHAGSEDLEVFLNVFGELPQPLIDTQILAAFCGRPM-SWG 117

Query: 119 LKDNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSD 178
               ++E  G+ + K++  +DW A  L++ Q +YAA+DV +L  +  +   + +  G   
Sbjct: 118 FASMVEEYSGVTLDKSESRTDWLARPLTERQCEYAAADVWYLLPITAKLMVETEASGWLP 177

Query: 179 LATSCCNFLMDR 190
            A   C  +  R
Sbjct: 178 AALDECRLMQMR 189
>gi|157830862|pdb|1DPI|A Chain A, Structure Of Large Fragment Of Escherichia Coli Dna Polymerase I Complexed With DTMP Length = 605 Back     alignment and structure
gi|2982102|pdb|1KFS|A Chain A, Dna Polymerase I Klenow Fragment (E.C.2.7.7.7) MutantDNA Complex Length = 605 Back     alignment and structure
>gi|112491261|pdb|2HBJ|A Chain A, Structure Of The Yeast Nuclear Exosome Component, Rrp6p, Reveals An Interplay Between The Active Site And The Hrdc Domain Length = 410 Back     alignment and structure
>gi|809180|pdb|1KLN|A Chain A, Dna Polymerase I Klenow Fragment (E.C.2.7.7.7) MutantDNA Complex Length = 605 Back     alignment and structure
>gi|6730276|pdb|1D8Y|A Chain A, Crystal Structure Of The Complex Of Dna Polymerase I Klenow Fragment With Dna Length = 605 Back     alignment and structure
>gi|189096244|pdb|3CYM|A Chain A, Crystal Structure Of Protein Bad_0989 From Bifidobacterium Adolescentis Length = 440 Back     alignment and structure
>gi|126030364|pdb|2E6L|A Chain A, Structure Of Mouse Wrn Exonuclease Domain Length = 208 Back     alignment and structure
>gi|99032230|pdb|2FBT|A Chain A, Wrn Exonuclease Length = 205 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

IdentityAlignment graphLength Definition E-value
Target207 ribonuclease D [Candidatus Liberibacter asiaticus str.
3cym_A 440 Uncharacterized protein BAD_0989; structural genomics, 2e-32
2e6m_A208 Werner syndrome ATP-dependent helicase homolog; APO for 6e-20
1vk0_A206 Hypothetical protein; homohexamer, AT5G06450, structura 3e-19
1yt3_A 375 Ribonuclease D, RNAse D; exoribonuclease, exonuclease, 2e-18
2hbj_A 410 Exosome complex exonuclease RRP6; RNA metabolism, RNA s 5e-17
1x9m_A 698 DNA polymerase; DNA ploymerase, N-2-acetylaminofluorene 4e-07
3m8r_A 540 DNA polymerase I, thermostable; DNA polymerase, DNA rep 8e-06
2hhv_A 580 DNA polymerase I; DNA replication, klenow fragment, pro 2e-16
2kfn_A 605 Klenow fragment of DNA polymerase I; complex (polymeras 7e-12
>3cym_A Uncharacterized protein BAD_0989; structural genomics, unknown function, ribonuclease D, exonuclease; 2.10A {Bifidobacterium adolescentis ATCC15703} Length = 440 Back     alignment and structure
 Score =  134 bits (338), Expect = 2e-32
 Identities = 37/175 (21%), Positives = 66/175 (37%), Gaps = 4/175 (2%)

Query: 17  ARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGML-VDEKR 75
           A    ++A D E            +VQ       + ++   A      +           
Sbjct: 35  ASSHGSLAADAERASGFRYGHEDWLVQFKRDGAGIGLLDPQALAAAGADWNDFNRAVGDA 94

Query: 76  EKIFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQ 135
             I H    D+       G+  + +F T+IA+RL      + GL    +  LG+ ++K  
Sbjct: 95  VWILHDSLQDLPGF-DELGMEPQRLFDTEIAARLL--GLKRFGLAAVTEHFLGLTLAKEH 151

Query: 136 QSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDLATSCCNFLMDR 190
            ++DWS   L  +   YAA DV  L  L  +   +L+R G+ + A    ++ +  
Sbjct: 152 SAADWSYRPLPRDWRNYAALDVELLIELETKMRAELKRQGKMEWAQEEFDYALKE 206
>2e6m_A Werner syndrome ATP-dependent helicase homolog; APO form, hydrolase; 2.00A {Mus musculus} PDB: 2e6l_A 2fby_A 2fbv_A 2fbx_A 2fbt_A 2fc0_A* Length = 208 Back     alignment and structure
>1vk0_A Hypothetical protein; homohexamer, AT5G06450, structural genomics, protein structure initiative, center for eukaryotic structural genomics; 2.10A {Arabidopsis thaliana} SCOP: c.55.3.5 PDB: 2q3s_A Length = 206 Back     alignment and structure
>1yt3_A Ribonuclease D, RNAse D; exoribonuclease, exonuclease, hydrolase, tRNA processing, hydrolase,translation; 1.60A {Escherichia coli} SCOP: a.60.8.3 a.60.8.3 c.55.3.5 Length = 375 Back     alignment and structure
>2hbj_A Exosome complex exonuclease RRP6; RNA metabolism, RNA surveillance, RNA processing, hydrolase, gene regulation; 2.10A {Saccharomyces cerevisiae} SCOP: a.60.8.4 c.55.3.5 PDB: 2hbk_A 2hbl_A* 2hbm_A* Length = 410 Back     alignment and structure
>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
>3m8r_A DNA polymerase I, thermostable; DNA polymerase, DNA replication, nucleotides, modified nucleotide, artificial nucleotide; HET: DNA DOC HXZ 15P; 2.00A {Thermus aquaticus} PDB: 1jxe_A* 3ktq_A* 3lwl_A* 3lwm_A* 3m8s_A* 1ktq_A* 5ktq_A* 4ktq_A* 1qtm_A* 2ktq_A* 1qss_A* 1qsy_A* Length = 540 Back     alignment and structure
>2hhv_A DNA polymerase I; DNA replication, klenow fragment, protein- DNA complex, O6-methyl-guanine, transferase/DNA complex; HET: DNA 6OG SUC; 1.55A {Geobacillus stearothermophilus} SCOP: c.55.3.5 e.8.1.1 PDB: 2hhs_A* 2hht_A* 2hhu_A* 2hhq_A* 2hhx_A* 2hw3_A* 1nk4_A* 1l3t_A* 1l3u_A* 1l3v_A* 1l5u_A* 1njw_A* 1l3s_A* 1njy_A* 1njz_A* 1nk0_A* 1njx_A* 1nk5_A* 1nk6_A* 1nk7_A* ... Length = 580 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

Homologous Structures in PDB70 Database Detected by HHsearch

Original result of HHsearch against PDB70 database

IdentityAlignment graphLength Definition Probability
Target207 ribonuclease D [Candidatus Liberibacter asiaticus str.
1yt3_A 375 Ribonuclease D, RNAse D; exoribonuclease, exonuclease, 100.0
2hbj_A 410 Exosome complex exonuclease RRP6; RNA metabolism, RNA s 100.0
3cym_A 440 Uncharacterized protein BAD_0989; structural genomics, 100.0
2e6m_A208 Werner syndrome ATP-dependent helicase homolog; APO for 100.0
2hhv_A 580 DNA polymerase I; DNA replication, klenow fragment, pro 100.0
1vk0_A206 Hypothetical protein; homohexamer, AT5G06450, structura 100.0
2kfn_A 605 Klenow fragment of DNA polymerase I; complex (polymeras 99.97
1x9m_A 698 DNA polymerase; DNA ploymerase, N-2-acetylaminofluorene 99.93
3m8r_A 540 DNA polymerase I, thermostable; DNA polymerase, DNA rep 99.9
1bgx_T 832 TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhibitio 99.73
1wlj_A189 Interferon stimulated gene 20KDA; exoribonuclease, hydr 99.38
2p1j_A186 POLIII, DNA polymerase III POLC-type; structural genomi 99.05
2is3_A215 Ribonuclease T; RNAse, exoribonuclease, exonuclease, hy 99.01
2ioc_B242 Three prime repair exonuclease 1; proline helix, nucleo 98.73
2qxf_A 482 Exodeoxyribonuclease I; alpha-beta domain, DNAQ superfa 98.39
2gui_A194 DNA polymerase III epsilon subunit; DNA polymerase proo 97.89
2d5r_A252 CCR4-NOT transcription complex subunit 7; poly(A) deade 97.58
2xri_A224 ERI1 exoribonuclease 3; hydrolase, metal binding; 2.15A 97.57
1qht_A 775 Protein (DNA polymerase); archaea, hyperthermostable, f 97.56
1uoc_A289 POP2; hydrolase, DEDD nuclease, mRNA degradation, poly( 97.5
1s5j_A 847 DNA polymerase I; replication, disulfide bonds, transfe 97.45
2py5_A 575 DNA polymerase; protein-DNA complex, replication, trans 97.34
2p51_A333 SPCC18.06C protein; DEDD nuclease fold, hydrolase, gene 97.31
3k59_A 786 POL II, DNA polymerase II; protein-DNA complex, DNA dam 95.83
3cg7_A308 CRN-4, cell death-related nuclease 4; hydrolase, apopto 94.39
1y97_A238 Three prime repair exonuclease 2; TREX2, hydrolase; 2.5 98.58
2f96_A224 Ribonuclease T; RNAse, RNT, RNAse T, tRNA hydrolase, SA 98.58
3ikm_A 1172 DNA polymerase subunit gamma-1; human mitochondrial DNA 98.19
3nae_A 903 DNA polymerase, GP43; RB69 DNA polymerase; HET: DNA G35 96.79
2gv9_A 1193 DNA polymerase; polymerase alpha fold, transferase; HET 96.73
3iay_A 919 DNA polymerase delta catalytic subunit; protein-DNA com 96.52
1w0h_A204 3'-5' exonuclease ERI1; nuclease domain, hydrolase; HET 95.45
3d45_A507 Poly(A)-specific ribonuclease PARN; CAP analogue, cytop 95.39
1noy_A388 Protein (DNA polymerase (E.C.2.7.7.7)); exonuclease, DN 95.14
2a1r_A430 Poly(A)-specific ribonuclease PARN; DEDD, nuclease doma 92.85
2gbz_A194 Oligoribonuclease; ORN, deddh, structural genomics, X-R 96.14
2igi_A180 Oligoribonuclease; RNAse, exoribonuclease, exonuclease, 96.01
>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
Probab=100.00  E-value=0  Score=307.87  Aligned_cols=188  Identities=24%  Similarity=0.361  Sum_probs=167.5

Q ss_pred             CCEEECCC--CCCHHH-HCCCCCCEEEECCCCCCCCCCCEEEEEEEEECCCCEEEECCCCCCCCCHHHHHHHHCCCCCEE
Q ss_conf             72153257--888578-424898279971777898544507999984189428997465778570677677732364023
Q gi|254780636|r    2 TTIRVHEG--DIPAEC-AARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKI   78 (207)
Q Consensus         2 ~~~~~~~~--dl~~~~-~l~~~~~iaiDtEt~~l~~~~~~l~LiQl~~~~~~~~l~~~~~~~~~~~~L~~ll~d~~i~KV   78 (207)
                      |||+++..  +|.+.+ .++.+++|||||||+++++|++++||||||++++ +|++++.... ....|+++|+|++|+||
T Consensus         1 m~y~~I~t~~~L~~~~~~l~~~~~ia~DtE~~~~~ty~~~l~LiQi~~~~~-~~liD~l~~~-~~~~L~~ll~~~~i~kv   78 (375)
T 1yt3_A            1 MNYQMITTDDALASLCEAVRAFPAIALDTEFVRTRTYYPQLGLIQLFDGEH-LALIDPLGIT-DWSPLKAILRDPSITKF   78 (375)
T ss_dssp             CCCEEECSHHHHHHHHHHHTTSSEEEEEEEEECCSCSSCEEEEEEEECSSC-EEEECGGGCS-CCHHHHHHHHCTTSEEE
T ss_pred             CCEEEECCHHHHHHHHHHHHCCCEEEEECCCCCCCCCCCEEEEEEEEECCE-EEEEECCCCC-CHHHHHHHHHCCCCEEE
T ss_conf             927998989999999999847990899798489888888789999876892-7999658987-78999999819886199


Q ss_pred             ECCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCCHHHHHHHHHHHH
Q ss_conf             01000016888654200000004578988652110000008877765420024675200365654432368999986459
Q gi|254780636|r   79 FHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVV  158 (207)
Q Consensus        79 ~Hn~~~D~~~L~~~~gi~~~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs~~Qi~YAA~Dv~  158 (207)
                      |||+++|+.+|.+++|+.+.|+||||+|+.+++ ++.++||+.+++++||++++|+.|+|||+.||||++|+.|||.||+
T Consensus        79 ~h~~~~D~~~L~~~~~~~~~~~fDt~ia~~~~~-~~~~~~l~~l~~~~l~~~l~K~~~~sdW~~rPLs~~ql~YAa~Dv~  157 (375)
T 1yt3_A           79 LHAGSEDLEVFLNVFGELPQPLIDTQILAAFCG-RPMSWGFASMVEEYSGVTLDKSESRTDWLARPLTERQCEYAAADVW  157 (375)
T ss_dssp             ESSCHHHHHHHHHHHSSCCSSEEEHHHHHHHTT-CCTTCCHHHHHHHHHCCCCCCTTTTSCTTSSSCCHHHHHHHHHHHH
T ss_pred             EECHHHHHHHHHHHCCCCCCCEEECHHHHHHHC-CCCHHHHHHHHHHHHHHCCCHHHHHHHCCCCCCCHHHHHHHHCCCE
T ss_conf             725586799999964988887166388898838-7506788899999864503305545222566687899999840732


Q ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999974918999999964006899
Q gi|254780636|r  159 HLHALRLQFTEKLQRLGRSDLATSCCNFLMDRAE  192 (207)
Q Consensus       159 ~l~~L~~~l~~~L~~~~~~~~~~~e~~~l~~~~~  192 (207)
                      ||++||+.|.++|.+.|+.+|+.+||+.+.....
T Consensus       158 ~l~~l~~~l~~~L~~~~~~~~~~ee~~~l~~~~~  191 (375)
T 1yt3_A          158 YLLPITAKLMVETEASGWLPAALDECRLMQMRRQ  191 (375)
T ss_dssp             THHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH
T ss_pred             EHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             3799999999877630004678999999874431
>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
>3cym_A Uncharacterized protein BAD_0989; structural genomics, unknown function, ribonuclease D, exonuclease; 2.10A {Bifidobacterium adolescentis ATCC15703} 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
>2hhv_A DNA polymerase I; DNA replication, klenow fragment, protein- DNA complex, O6-methyl-guanine, transferase/DNA complex; HET: DNA 6OG SUC; 1.55A {Geobacillus stearothermophilus} SCOP: c.55.3.5 e.8.1.1 PDB: 2hhs_A* 2hht_A* 2hhu_A* 2hhq_A* 2hhx_A* 2hw3_A* 1nk4_A* 1l3t_A* 1l3u_A* 1l3v_A* 1l5u_A* 1njw_A* 1l3s_A* 1njy_A* 1njz_A* 1nk0_A* 1njx_A* 1nk5_A* 1nk6_A* 1nk7_A* ... Back     alignment and structure
>1vk0_A Hypothetical protein; homohexamer, AT5G06450, structural genomics, protein structure initiative, center for eukaryotic structural genomics; 2.10A {Arabidopsis thaliana} SCOP: c.55.3.5 PDB: 2q3s_A Back     alignment and structure
>2kfn_A Klenow fragment of DNA polymerase I; complex (polymerase/DNA), exonuclease, transferase, transferase/DNA complex; HET: US1; 2.03A {Escherichia coli} SCOP: c.55.3.5 e.8.1.1 PDB: 1d9f_A* 1d9d_A* 1krp_A* 1ksp_A* 1qsl_A* 1kfs_A* 2kfz_A* 2kzm_A* 2kzz_A* 1dpi_A* 1kfd_A* 1kln_A* 1d8y_A* Back     alignment and structure
>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
>3m8r_A DNA polymerase I, thermostable; DNA polymerase, DNA replication, nucleotides, modified nucleotide, artificial nucleotide; HET: DNA DOC HXZ 15P; 2.00A {Thermus aquaticus} PDB: 1jxe_A* 3ktq_A* 3lwl_A* 3lwm_A* 3m8s_A* 1ktq_A* 5ktq_A* 4ktq_A* 1qtm_A* 2ktq_A* 1qss_A* 1qsy_A* Back     alignment and structure
>1bgx_T TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhibition, helix-coil dynamics, inhibitor design, complex (polymerase/inhibitor); 2.30A {Thermus aquaticus} SCOP: a.60.7.1 c.120.1.2 c.55.3.5 e.8.1.1 PDB: 1cmw_A 1tau_A* 1taq_A* Back     alignment and structure
>1wlj_A Interferon stimulated gene 20KDA; exoribonuclease, hydrolase; HET: U5P; 1.90A {Homo sapiens} SCOP: c.55.3.5 Back     alignment and structure
>2p1j_A POLIII, DNA polymerase III POLC-type; structural genomics, exonuclease, PSI-2, protein structure initiative; HET: DNA; 2.50A {Thermotoga maritima MSB8} Back     alignment and structure
>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
>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
>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
>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
>2xri_A ERI1 exoribonuclease 3; hydrolase, metal binding; 2.15A {Homo sapiens} Back     alignment and structure
>1qht_A Protein (DNA polymerase); archaea, hyperthermostable, family B polymerase, POL alpha family polymerase, transferase; 2.10A {Thermococcus SP} SCOP: c.55.3.5 e.8.1.1 PDB: 1tgo_A 2vwj_A* 2vwk_A* 1wns_A* 1wn7_A 1qqc_A* 3a2f_A* 2jgu_A* 1d5a_A 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
>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
>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
>2p51_A SPCC18.06C protein; DEDD nuclease fold, hydrolase, gene regulation; 1.40A {Schizosaccharomyces pombe} PDB: 3g0z_A 3g10_A 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 k-12} PDB: 3k57_A* 3k58_A* 3k5l_A* 3k5m_A* 3k5n_A* 3k5o_A* 3maq_A* 1q8i_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
>1y97_A Three prime repair exonuclease 2; TREX2, hydrolase; 2.50A {Homo sapiens} SCOP: c.55.3.5 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
>3ikm_A DNA polymerase subunit gamma-1; human mitochondrial DNA polymerase, disease mutation, DNA replication, DNA-binding, DNA-directed DNA polymerase; HET: DNA; 3.24A {Homo sapiens} Back     alignment and structure
>3nae_A DNA polymerase, GP43; RB69 DNA polymerase; HET: DNA G35 DOC DTP; 2.00A {Enterobacteria phage RB69} PDB: 3lzi_A* 3lzj_A* 1ig9_A* 1q9x_A* 2atq_A* 2dy4_A* 2oyq_A* 2ozm_A* 2ozs_A* 2p5g_A* 2p5o_A* 1q9y_A* 3l8b_A* 3lds_A* 3cq8_A* 1ih7_A* 1clq_A* 1waf_A* 1waj_A* 3cfr_A* ... Back     alignment and structure
>2gv9_A DNA polymerase; polymerase alpha fold, transferase; HET: DNA; 2.68A {Human herpesvirus 1 strain kos} PDB: 1dml_B* Back     alignment and structure
>3iay_A DNA polymerase delta catalytic subunit; protein-DNA complex, DNA replication, DNA- binding, DNA-directed DNA polymerase, exonuclease; HET: DNA DOC DCP; 2.00A {Saccharomyces cerevisiae} 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
>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, cytoplasm, exonuclease, hydrolase, magnesium, metal-binding, nonsense- mediated mRNA decay; HET: 7MG GDP; 3.00A {Mus musculus} 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
>2a1r_A Poly(A)-specific ribonuclease PARN; DEDD, nuclease domain, hydrolase/RNA complex; 2.60A {Homo sapiens} PDB: 2a1s_A 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

Homologous Domains in SCOP and MMDB Database
Detected by RPS-BLAST and HHsearch

Homologous Domains in SCOP70 (Version1.75) Database Detected by RPS-BLAST

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

IdentityAlignment graphLength Definition E-value
Target 207 ribonuclease D [Candidatus Liberibacter asiaticus str.
d2hbka2292 c.55.3.5 (A:129-420) Exosome complex exonuclease RRP6 { 5e-21
d1vk0a_206 c.55.3.5 (A:) Hypothetical protein AT5G06450 {Thale-cre 3e-19
d1yt3a3193 c.55.3.5 (A:1-193) Ribonuclease D, catalytic domain {Es 9e-19
d2hhva1171 c.55.3.5 (A:298-468) Exonuclease domain of prokaryotic 3e-15
d1kfsa1195 c.55.3.5 (A:324-518) Exonuclease domain of prokaryotic 4e-12
>d2hbka2 c.55.3.5 (A:129-420) Exosome complex exonuclease RRP6 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 292 Back     information, alignment and structure

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: DnaQ-like 3'-5' exonuclease
domain: Exosome complex exonuclease RRP6
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 94.9 bits (235), Expect = 5e-21
 Identities = 39/170 (22%), Positives = 61/170 (35%), Gaps = 3/170 (1%)

Query: 21  DAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKIFH 80
             IAVD E          +C++Q+S  +    ++     ++N   L  +  +    K+FH
Sbjct: 105 KEIAVDLEHHDYRSYYGIVCLMQISTRERDY-LVDTLKLRENLHILNEVFTNPSIVKVFH 163

Query: 81  YGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDW 140
               DI  L    G+ V  +F T  AS+       +H L   L+       SK  Q +DW
Sbjct: 164 GAFMDIIWLQRDLGLYVVGLFDTYHASKAIGLP--RHSLAYLLENFANFKTSKKYQLADW 221

Query: 141 SADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDLATSCCNFLMDR 190
               LS      A +D   L  +  Q   KL    +          +  R
Sbjct: 222 RIRPLSKPMTAAARADTHFLLNIYDQLRNKLIESNKLAGVLYESRNVAKR 271
>d1vk0a_ c.55.3.5 (A:) Hypothetical protein AT5G06450 {Thale-cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 206 Back     information, alignment and structure
>d1yt3a3 c.55.3.5 (A:1-193) Ribonuclease D, catalytic domain {Escherichia coli [TaxId: 562]} Length = 193 Back     information, alignment and structure
>d2hhva1 c.55.3.5 (A:298-468) Exonuclease domain of prokaryotic DNA polymerase {Bacillus stearothermophilus, newly identified strain as yet unnamed [TaxId: 1422]} Length = 171 Back     information, alignment and structure