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Conserved domains on  [gi|1174928096|ref|WP_081601316|]
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exonuclease domain-containing protein [Thioalkalivibrio sp. HL-Eb18]

Protein Classification

3'-5' exonuclease family protein( domain architecture ID 1085)

3'-5' exonuclease family protein may cleave nucleotides one at a time from the end (exo) of a polynucleotide chain

CATH:  3.30.420.10
Gene Ontology:  GO:0003676
PubMed:  11988770|11222749
SCOP:  4000547

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DnaQ_like_exo super family cl10012
DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease ...
 13-222 2.02e-51

DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; 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. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer.


The actual alignment was detected with superfamily member PRK09146:

Pssm-ID: 447876 [Multi-domain]  Cd Length: 239  Bit Score: 167.41  E-value: 2.02e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096  13 HPIGHW--RFCHRRQRAAQhaptGALRACLGSPLPSARQAVADCRFLAVDLETTGLDPEHDAILSIGWVAMDGVRIDLST 90
Cdd:PRK09146    8 QPALDWpaKFAQKAEQAKD----PRLKRFYAAGLVSPDTPLSEVPFVALDFETTGLDAEQDAIVSIGLVPFTLQRIRCRQ 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096  91 ADQRLVRADCPVPEQSAVIHRITDREAAGGTTVDSALDALFEALQGRVLVAHHAALELGFLEEACHRLYGVRPPLPVVDT 170
Cdd:PRK09146   84 ARHWVVKPRRPLEEESVVIHGITHSELQDAPDLERILDELLEALAGKVVVVHYRRIERDFLDQALRNRIGEGIEFPVIDT 163

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1174928096 171 LRLAERQLRR---------AGRPIPAdgMRLHTLRGRYNLPQYRAHDALFDALAAGELFAA 222
Cdd:PRK09146  164 MEIEARIQRKqagglwnrlKGKKPES--IRLADSRLRYGLPAYSPHHALTDAIATAELLQA 222
 
Name Accession Description Interval E-value
PRK09146 PRK09146
DNA polymerase III subunit epsilon; Validated
 13-222 2.02e-51

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 236392 [Multi-domain]  Cd Length: 239  Bit Score: 167.41  E-value: 2.02e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096  13 HPIGHW--RFCHRRQRAAQhaptGALRACLGSPLPSARQAVADCRFLAVDLETTGLDPEHDAILSIGWVAMDGVRIDLST 90
Cdd:PRK09146    8 QPALDWpaKFAQKAEQAKD----PRLKRFYAAGLVSPDTPLSEVPFVALDFETTGLDAEQDAIVSIGLVPFTLQRIRCRQ 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096  91 ADQRLVRADCPVPEQSAVIHRITDREAAGGTTVDSALDALFEALQGRVLVAHHAALELGFLEEACHRLYGVRPPLPVVDT 170
Cdd:PRK09146   84 ARHWVVKPRRPLEEESVVIHGITHSELQDAPDLERILDELLEALAGKVVVVHYRRIERDFLDQALRNRIGEGIEFPVIDT 163

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1174928096 171 LRLAERQLRR---------AGRPIPAdgMRLHTLRGRYNLPQYRAHDALFDALAAGELFAA 222
Cdd:PRK09146  164 MEIEARIQRKqagglwnrlKGKKPES--IRLADSRLRYGLPAYSPHHALTDAIATAELLQA 222
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 55-224 6.58e-48

DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 155.72  E-value: 6.58e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096  55 RFLAVDLETTGLDPEHDAILSIGWVAMDGVRIdlSTADQRLVRADCPVPEQSAVIHRITDREAAGGTTVDSALDALFEAL 134
Cdd:COG0847     1 RFVVLDTETTGLDPAKDRIIEIGAVKVDDGRI--VETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096 135 QGRVLVAHHAALELGFLEEACHRLYGVRPPLPVVDTLRLAERQLRRAGRpipadgMRLHTLRGRYNLPQYRAHDALFDAL 214
Cdd:COG0847    79 GGAVLVAHNAAFDLGFLNAELRRAGLPLPPFPVLDTLRLARRLLPGLPS------YSLDALCERLGIPFDERHRALADAE 152

                         170
                  ....*....|
gi 1174928096 215 AAGELFAALV 224
Cdd:COG0847   153 ATAELFLALL 162
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 57-221 2.86e-46

DEDDh 3'-5' exonuclease domain family; 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. These proteins contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases are classified as such because of the presence of specific Hx(4)D conserved pattern at the ExoIII motif. The four conserved acidic residues are clustered around the active site and serve as ligands for the two metal ions required for catalysis. Most DEDDh exonucleases are the proofreading subunits (epsilon) or domains of bacterial DNA polymerase III, the main replicating enzyme in bacteria, which functions as the chromosomal replicase. Other members include other DNA and RNA exonucleases such as RNase T, Oligoribonuclease, and RNA exonuclease (REX), among others.


Pssm-ID: 176648 [Multi-domain]  Cd Length: 159  Bit Score: 151.30  E-value: 2.86e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096  57 LAVDLETTGLDPEHDAILSIGWVAMDGvRIDLSTADQRLVRADCPVPEQSAVIHRITDREAAGGTTVDSALDALFEALQG 136
Cdd:cd06127     1 VVFDTETTGLDPKKDRIIEIGAVKVDG-GIEIVERFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096 137 RVLVAHHAALELGFLEEACHRLYGVRPPLPVVDTLRLAERQLRRAGRPIPADgmrlhTLRGRYNLPQYRAHDALFDALAA 216
Cdd:cd06127    80 RVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGLRSHRLGL-----LLAERYGIPLEGAHRALADALAT 154


                  ....*
gi 1174928096 217 GELFA 221
Cdd:cd06127   155 AELLL 159
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 55-227 4.37e-33

exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 117.79  E-value: 4.37e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096   55 RFLAVDLETTGLDPEHDAILSIGWVAMDGVRIDLSTadQRLVRADCPVPEQSAVIHRITDREAAGGTTVDSALDALFEAL 134
Cdd:smart00479   1 TLVVIDCETTGLDPGKDEIIEIAAVDVDGGEIIEVF--DTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFL 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096  135 QGRVLVAHH-AALELGFLEEACHRLYGVRPP-LPVVDTLRLAERQLRRAGRpipadgMRLHTLRGRYNLPQY-RAHDALF 211
Cdd:smart00479  79 RGRILVAGNsAHFDLRFLKLEHPRLGIKQPPkLPVIDTLKLARATNPGLPK------YSLKKLAKRLLLEVIqRAHRALD 152

                          170
                   ....*....|....*.
gi 1174928096  212 DALAAGELFAALVSQL 227
Cdd:smart00479 153 DARATAKLFKKLLERL 168
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 57-220 1.89e-19

Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.;


Pssm-ID: 395743 [Multi-domain]  Cd Length: 164  Bit Score: 82.01  E-value: 1.89e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096  57 LAVDLETTGLDPEHDAILSIGWVAMDG-VRIDLSTADQrLVRADCP--VPEQSAVIHRITDREAAGGTTVDSALDALFEA 133
Cdd:pfam00929   1 VVIDLETTGLDPEKDEIIEIAAVVIDGgENEIGETFHT-YVKPTRLpkLTDECTKFTGITQAMLDNKPSFEEVLEEFLEF 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096 134 LQ-GRVLVAHHAALELGFLEEACHRLYGVRPPL--PVVDTLRLAerQLRRAGRPipadGMRLHTLRGRYNLP-QYRAHDA 209
Cdd:pfam00929  80 LRkGNLLVAHNASFDVGFLRYDDKRFLKKPMPKlnPVIDTLILD--KATYKELP----GRSLDALAEKLGLEhIGRAHRA 153

                         170
                  ....*....|.
gi 1174928096 210 LFDALAAGELF 220
Cdd:pfam00929 154 LDDARATAKLF 164
dnaq TIGR00573
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ...
 56-225 1.95e-14

exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which functions are known are components of the DNA polymerase III complex (epsilon subunit). There is, however, an outgroup that includes paralogs in some gamma-proteobacteria and the n-terminal region of DinG from some low GC gram positive bacteria. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, Degradation of DNA]


Pssm-ID: 129663 [Multi-domain]  Cd Length: 217  Bit Score: 69.79  E-value: 1.95e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096  56 FLAVDLETTGLDPEHDaILSIGWVAMDGVRIdlsTADQRLVRA--DCPVPEQSAVIHRITDREAAGGTTVDSALDALFEA 133
Cdd:TIGR00573   9 ETTGDNETTGLYAGHD-IIEIGAVEIINRRI---TGNKFHTYIkpDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFADY 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096 134 LQGRVLVAHHAALELGFLEEACHRLYGVRPPL-PVVDTLRLAE--RQLRRAGRpipadgMRLHTLRGRYNLPQYR--AHD 208
Cdd:TIGR00573  85 IRGAELVIHNASFDVGFLNYEFSKLYKVEPKTnDVIDTTDTLQyaRPEFPGKR------NTLDALCKRYEITNSHraLHG 158

                         170
                  ....*....|....*..
gi 1174928096 209 ALFDALAAGELFAALVS 225
Cdd:TIGR00573 159 ALADAFILAKLYLVMTG 175
 
Name Accession Description Interval E-value
PRK09146 PRK09146
DNA polymerase III subunit epsilon; Validated
 13-222 2.02e-51

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 236392 [Multi-domain]  Cd Length: 239  Bit Score: 167.41  E-value: 2.02e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096  13 HPIGHW--RFCHRRQRAAQhaptGALRACLGSPLPSARQAVADCRFLAVDLETTGLDPEHDAILSIGWVAMDGVRIDLST 90
Cdd:PRK09146    8 QPALDWpaKFAQKAEQAKD----PRLKRFYAAGLVSPDTPLSEVPFVALDFETTGLDAEQDAIVSIGLVPFTLQRIRCRQ 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096  91 ADQRLVRADCPVPEQSAVIHRITDREAAGGTTVDSALDALFEALQGRVLVAHHAALELGFLEEACHRLYGVRPPLPVVDT 170
Cdd:PRK09146   84 ARHWVVKPRRPLEEESVVIHGITHSELQDAPDLERILDELLEALAGKVVVVHYRRIERDFLDQALRNRIGEGIEFPVIDT 163

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1174928096 171 LRLAERQLRR---------AGRPIPAdgMRLHTLRGRYNLPQYRAHDALFDALAAGELFAA 222
Cdd:PRK09146  164 MEIEARIQRKqagglwnrlKGKKPES--IRLADSRLRYGLPAYSPHHALTDAIATAELLQA 222
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 55-224 6.58e-48

DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 155.72  E-value: 6.58e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096  55 RFLAVDLETTGLDPEHDAILSIGWVAMDGVRIdlSTADQRLVRADCPVPEQSAVIHRITDREAAGGTTVDSALDALFEAL 134
Cdd:COG0847     1 RFVVLDTETTGLDPAKDRIIEIGAVKVDDGRI--VETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096 135 QGRVLVAHHAALELGFLEEACHRLYGVRPPLPVVDTLRLAERQLRRAGRpipadgMRLHTLRGRYNLPQYRAHDALFDAL 214
Cdd:COG0847    79 GGAVLVAHNAAFDLGFLNAELRRAGLPLPPFPVLDTLRLARRLLPGLPS------YSLDALCERLGIPFDERHRALADAE 152

                         170
                  ....*....|
gi 1174928096 215 AAGELFAALV 224
Cdd:COG0847   153 ATAELFLALL 162
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 57-221 2.86e-46

DEDDh 3'-5' exonuclease domain family; 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. These proteins contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases are classified as such because of the presence of specific Hx(4)D conserved pattern at the ExoIII motif. The four conserved acidic residues are clustered around the active site and serve as ligands for the two metal ions required for catalysis. Most DEDDh exonucleases are the proofreading subunits (epsilon) or domains of bacterial DNA polymerase III, the main replicating enzyme in bacteria, which functions as the chromosomal replicase. Other members include other DNA and RNA exonucleases such as RNase T, Oligoribonuclease, and RNA exonuclease (REX), among others.


Pssm-ID: 176648 [Multi-domain]  Cd Length: 159  Bit Score: 151.30  E-value: 2.86e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096  57 LAVDLETTGLDPEHDAILSIGWVAMDGvRIDLSTADQRLVRADCPVPEQSAVIHRITDREAAGGTTVDSALDALFEALQG 136
Cdd:cd06127     1 VVFDTETTGLDPKKDRIIEIGAVKVDG-GIEIVERFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096 137 RVLVAHHAALELGFLEEACHRLYGVRPPLPVVDTLRLAERQLRRAGRPIPADgmrlhTLRGRYNLPQYRAHDALFDALAA 216
Cdd:cd06127    80 RVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGLRSHRLGL-----LLAERYGIPLEGAHRALADALAT 154


                  ....*
gi 1174928096 217 GELFA 221
Cdd:cd06127   155 AELLL 159
PolC COG2176
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ...
 53-227 1.86e-45

DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair];


Pssm-ID: 441779 [Multi-domain]  Cd Length: 181  Bit Score: 149.91  E-value: 1.86e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096  53 DCRFLAVDLETTGLDPEHDAILSIGWVAMDGVRIdlstAD--QRLVRADCPVPEQSAVIHRITDREAAGGTTVDSALDAL 130
Cdd:COG2176     7 DLTYVVFDLETTGLSPKKDEIIEIGAVKVENGEI----VDrfSTLVNPGRPIPPFITELTGITDEMVADAPPFEEVLPEF 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096 131 FEALQGRVLVAHHAALELGFLEEACHRLyGVRPPLPVVDTLRLAERQLRRAGRPipadgmRLHTLRGRYNLPQYRAHDAL 210
Cdd:COG2176    83 LEFLGDAVLVAHNASFDLGFLNAALKRL-GLPFDNPVLDTLELARRLLPELKSY------KLDTLAERLGIPLEDRHRAL 155

                         170
                  ....*....|....*..
gi 1174928096 211 FDALAAGELFAALVSQL 227
Cdd:COG2176   156 GDAEATAELFLKLLEKL 172
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 55-227 4.37e-33

exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 117.79  E-value: 4.37e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096   55 RFLAVDLETTGLDPEHDAILSIGWVAMDGVRIDLSTadQRLVRADCPVPEQSAVIHRITDREAAGGTTVDSALDALFEAL 134
Cdd:smart00479   1 TLVVIDCETTGLDPGKDEIIEIAAVDVDGGEIIEVF--DTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFL 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096  135 QGRVLVAHH-AALELGFLEEACHRLYGVRPP-LPVVDTLRLAERQLRRAGRpipadgMRLHTLRGRYNLPQY-RAHDALF 211
Cdd:smart00479  79 RGRILVAGNsAHFDLRFLKLEHPRLGIKQPPkLPVIDTLKLARATNPGLPK------YSLKKLAKRLLLEVIqRAHRALD 152

                          170
                   ....*....|....*.
gi 1174928096  212 DALAAGELFAALVSQL 227
Cdd:smart00479 153 DARATAKLFKKLLERL 168
PRK09145 PRK09145
3'-5' exonuclease;
56-223 2.99e-25

3'-5' exonuclease;


Pssm-ID: 236391 [Multi-domain]  Cd Length: 202  Bit Score: 98.44  E-value: 2.99e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096  56 FLAVDLETTGLDPEHDAILSIGWVAMDGVRIDLSTADQRLVRADCPVPEQSAVIHRITDREAAGGTTVDSALDALFEALQ 135
Cdd:PRK09145   31 WVALDCETTGLDPRRAEIVSIAAVKIRGNRILTSERLELLVRPPQSLSAESIKIHRLRHQDLEDGLSEEEALRQLLAFIG 110

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096 136 GRVLVAHHAALELGFLEEACHRLYGVRPPLPVVDTLRLAERQLRRaGRPIPADGMRLHTLRGRYNLPQYRAHDALFDALA 215
Cdd:PRK09145  111 NRPLVGYYLEFDVAMLNRYVRPLLGIPLPNPLIEVSALYYDKKER-HLPDAYIDLRFDAILKHLDLPVLGRHDALNDAIM 189


                  ....*...
gi 1174928096 216 AGELFAAL 223
Cdd:PRK09145  190 AALIFLRL 197
PRK07883 PRK07883
DEDD exonuclease domain-containing protein;
40-229 1.22e-20

DEDD exonuclease domain-containing protein;


Pssm-ID: 236123 [Multi-domain]  Cd Length: 557  Bit Score: 90.36  E-value: 1.22e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096  40 LGSPLpsarqavADCRFLAVDLETTGLDPEHDAILSIGWVAMDGVRI--DLSTadqrLVRADCPVPEQSAVIHRITDREA 117
Cdd:PRK07883    8 LGTPL-------RDVTFVVVDLETTGGSPAGDAITEIGAVKVRGGEVlgEFAT----LVNPGRPIPPFITVLTGITTAMV 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096 118 AGGTTVDSALDALFEALQGRVLVAHHAALELGFLEEACHRLYGVRPPLPVVDTLRLAERQLRRAGRPipadGMRLHTLRG 197
Cdd:PRK07883   77 AGAPPIEEVLPAFLEFARGAVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLARRVLPRDEAP----NVRLSTLAR 152

                         170       180       190
                  ....*....|....*....|....*....|..
gi 1174928096 198 RYNLPQYRAHDALFDALAAGELFAALVSQLSP 229
Cdd:PRK07883  153 LFGATTTPTHRALDDARATVDVLHGLIERLGN 184
PRK07740 PRK07740
hypothetical protein; Provisional
 17-224 3.38e-20

hypothetical protein; Provisional


Pssm-ID: 236085 [Multi-domain]  Cd Length: 244  Bit Score: 86.26  E-value: 3.38e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096  17 HWRFCHRRQRAAQHAPTgalracLGSPLpsarqavADCRFLAVDLETTGLDPEH-DAILSIGWVAMDGVRIDLSTAdQRL 95
Cdd:PRK07740   35 QEAWIRSIQKEAKRDDV------LDIPL-------TDLPFVVFDLETTGFSPQQgDEILSIGAVKTKGGEVETDTF-YSL 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096  96 VRADCPVPEQSAVIHRITDREAAGGTTVDSALDALFEALQGRVLVAHHAALELGFLEEACHRLYGVRPPLPVVDTLRLAE 175
Cdd:PRK07740  101 VKPKRPIPEHILELTGITAEDVAFAPPLAEVLHRFYAFIGAGVLVAHHAGHDKAFLRHALWRTYRQPFTHRLIDTMFLTK 180

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 1174928096 176 RQlrragrPIPADGMRLHTLRGRYNLPQYRAHDALFDALAAGELFAALV 224
Cdd:PRK07740  181 LL------AHERDFPTLDDALAYYGIPIPRRHHALGDALMTAKLWAILL 223
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 57-220 1.89e-19

Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.;


Pssm-ID: 395743 [Multi-domain]  Cd Length: 164  Bit Score: 82.01  E-value: 1.89e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096  57 LAVDLETTGLDPEHDAILSIGWVAMDG-VRIDLSTADQrLVRADCP--VPEQSAVIHRITDREAAGGTTVDSALDALFEA 133
Cdd:pfam00929   1 VVIDLETTGLDPEKDEIIEIAAVVIDGgENEIGETFHT-YVKPTRLpkLTDECTKFTGITQAMLDNKPSFEEVLEEFLEF 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096 134 LQ-GRVLVAHHAALELGFLEEACHRLYGVRPPL--PVVDTLRLAerQLRRAGRPipadGMRLHTLRGRYNLP-QYRAHDA 209
Cdd:pfam00929  80 LRkGNLLVAHNASFDVGFLRYDDKRFLKKPMPKlnPVIDTLILD--KATYKELP----GRSLDALAEKLGLEhIGRAHRA 153

                         170
                  ....*....|.
gi 1174928096 210 LFDALAAGELF 220
Cdd:pfam00929 154 LDDARATAKLF 164
polC PRK00448
DNA polymerase III PolC; Validated
 53-227 1.11e-17

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 81.81  E-value: 1.11e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096   53 DCRFLAVDLETTGLDPEHDAILSIGWVAM-DGVRIDlstADQRLVRADCPVPEQSAVIHRITDREAAGGTTVDSALDALF 131
Cdd:PRK00448   418 DATYVVFDVETTGLSAVYDEIIEIGAVKIkNGEIID---KFEFFIKPGHPLSAFTTELTGITDDMVKDAPSIEEVLPKFK 494

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096  132 EALQGRVLVAHHAALELGFLEEACHRLYGVRPPLPVVDTLRLAerqlrRAGRPIpADGMRLHTLRGRYNLPQYRAHDALF 211
Cdd:PRK00448   495 EFCGDSILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELS-----RFLYPE-LKSHRLNTLAKKFGVELEHHHRADY 568

                          170
                   ....*....|....*.
gi 1174928096  212 DALAAGELFAALVSQL 227
Cdd:PRK00448   569 DAEATAYLLIKFLKDL 584
PRK06310 PRK06310
DNA polymerase III subunit epsilon; Validated
 53-242 1.35e-16

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 180525 [Multi-domain]  Cd Length: 250  Bit Score: 76.41  E-value: 1.35e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096  53 DCRFLAVDLETTGLDPEHDAILSIGWVAMDGVRIDLSTadQRLVRADCPVPEQSAVIHRITDREAAGGTTVDSALDALFE 132
Cdd:PRK06310    6 DTEFVCLDCETTGLDVKKDRIIEFAAIRFTFDEVIDSV--EFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFPQIKG 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096 133 AL-QGRVLVAHHAALELGFLEEACHRLyGVRPPL---PVVDTLRLAerqlRRAG-RPIPAdgmrLHTLRGRYNLPQYRAH 207
Cdd:PRK06310   84 FFkEGDYIVGHSVGFDLQVLSQESERI-GETFLSkhyYIIDTLRLA----KEYGdSPNNS----LEALAVHFNVPYDGNH 154

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1174928096 208 DALFDALAAGELFAALVSQLSPEAQvpLERVLFRP 242
Cdd:PRK06310  155 RAMKDVEINIKVFKHLCKRFRTLEQ--LKQILSKP 187
PRK08074 PRK08074
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 55-236 6.18e-15

bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated


Pssm-ID: 236148 [Multi-domain]  Cd Length: 928  Bit Score: 73.83  E-value: 6.18e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096  55 RFLAVDLETTGLDPEH-DAILSIGWVAM-DGVRID-LSTadqrLVRADCPVPeqsAVIHR---ITDREAAGGTTVDSALD 128
Cdd:PRK08074    4 RFVVVDLETTGNSPKKgDKIIQIAAVVVeDGEILErFSS----FVNPERPIP---PFITEltgISEEMVKQAPLFEDVAP 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096 129 ALFEALQGRVLVAHHAALELGFLEEACHRLyGVRPPL-PVVDTLRLAeRQLrragrpIP-ADGMRLHTLRGRYNLPQYRA 206
Cdd:PRK08074   77 EIVELLEGAYFVAHNVHFDLNFLNEELERA-GYTEIHcPKLDTVELA-RIL------LPtAESYKLRDLSEELGLEHDQP 148

                         170       180       190
                  ....*....|....*....|....*....|
gi 1174928096 207 HDALFDALAAGELFAALVSQLSpeaQVPLE 236
Cdd:PRK08074  149 HRADSDAEVTAELFLQLLNKLE---RLPLV 175
dnaq TIGR00573
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ...
 56-225 1.95e-14

exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which functions are known are components of the DNA polymerase III complex (epsilon subunit). There is, however, an outgroup that includes paralogs in some gamma-proteobacteria and the n-terminal region of DinG from some low GC gram positive bacteria. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, Degradation of DNA]


Pssm-ID: 129663 [Multi-domain]  Cd Length: 217  Bit Score: 69.79  E-value: 1.95e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096  56 FLAVDLETTGLDPEHDaILSIGWVAMDGVRIdlsTADQRLVRA--DCPVPEQSAVIHRITDREAAGGTTVDSALDALFEA 133
Cdd:TIGR00573   9 ETTGDNETTGLYAGHD-IIEIGAVEIINRRI---TGNKFHTYIkpDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFADY 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096 134 LQGRVLVAHHAALELGFLEEACHRLYGVRPPL-PVVDTLRLAE--RQLRRAGRpipadgMRLHTLRGRYNLPQYR--AHD 208
Cdd:TIGR00573  85 IRGAELVIHNASFDVGFLNYEFSKLYKVEPKTnDVIDTTDTLQyaRPEFPGKR------NTLDALCKRYEITNSHraLHG 158

                         170
                  ....*....|....*..
gi 1174928096 209 ALFDALAAGELFAALVS 225
Cdd:TIGR00573 159 ALADAFILAKLYLVMTG 175
PRK06063 PRK06063
DEDDh family exonuclease;
59-244 9.93e-14

DEDDh family exonuclease;


Pssm-ID: 180377 [Multi-domain]  Cd Length: 313  Bit Score: 69.34  E-value: 9.93e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096  59 VDLETTGLDPEHDAILSIGWVAMDgvriDLSTADQRLVRADCPVPEQSAV-IHRITDREAAGGTTVDSALDALFEALQGR 137
Cdd:PRK06063   20 VDVETSGFRPGQARIISLAVLGLD----ADGNVEQSVVTLLNPGVDPGPThVHGLTAEMLEGQPQFADIAGEVAELLRGR 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096 138 VLVAHHAALELGFLEEACHRLYGVRPPLPVVDTLRLAerqlRRAGRPIPadGMRLHTLRGRYNLPQYRAHDALFDALA-A 216
Cdd:PRK06063   96 TLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTVELA----RRLGLGLP--NLRLETLAAHWGVPQQRPHDALDDARVlA 169

                         170       180
                  ....*....|....*....|....*...
gi 1174928096 217 GELFAALVSQLSPEAQVPLERVlFRPGW 244
Cdd:PRK06063  170 GILRPSLERARERDVWLPLHPV-TRRRW 196
PRK06309 PRK06309
DNA polymerase III subunit epsilon; Validated
 60-242 1.15e-13

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 180524 [Multi-domain]  Cd Length: 232  Bit Score: 67.91  E-value: 1.15e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096  60 DLETTGLDPEHDAILSIGwvAMDGVRidlSTADQRLVRADCPVPEQSAVIHRITDREAAGGTTVDSALDALFEALQGR-V 138
Cdd:PRK06309    8 DTETTGTQIDKDRIIEIA--AYNGVT---SESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQKFIEFCGTDnI 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096 139 LVAHHA-ALELGFLEEACHRlYGVRPP-LPVVDTLRLAERQlrragRP-IPADGmrLHTLRGRYNLPQYRAHDALFDALA 215
Cdd:PRK06309   83 LVAHNNdAFDFPLLRKECRR-HGLEPPtLRTIDSLKWAQKY-----RPdLPKHN--LQYLRQVYGFEENQAHRALDDVIT 154

                         170       180
                  ....*....|....*....|....*..
gi 1174928096 216 AGELFAALVSQLSPEAQVPLERVLFRP 242
Cdd:PRK06309  155 LHRVFSALVGDLSPQQVYDLLNESCHP 181
DNA_pol_III_epsilon_like cd06130
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ...
 56-222 2.26e-13

an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III; This subfamily is composed of uncharacterized bacterial proteins with similarity to the epsilon subunit of DNA polymerase III (Pol III), a multisubunit polymerase which is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. The Pol III holoenzyme is a complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The epsilon subunit of Pol III also functions as a stabilizer of the holoenzyme complex.


Pssm-ID: 99834 [Multi-domain]  Cd Length: 156  Bit Score: 65.61  E-value: 2.26e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096  56 FLAVDLETTglDPEHDAILSIGWVAM-DGVRIDLSTadqRLVRadcPVPEQSAV---IHRITDREAAGGTTVDSALDALF 131
Cdd:cd06130     1 FVAIDFETA--NADRASACSIGLVKVrDGQIVDTFY---TLIR---PPTRFDPFniaIHGITPEDVADAPTFPEVWPEIK 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096 132 EALQGRVLVAHHAALELGFLeEACHRLYGV-RPPLPVVDTLRLAerqlRRAGRPIPadGMRLHTLRGRYNLPqYRAHDAL 210
Cdd:cd06130    73 PFLGGSLVVAHNASFDRSVL-RAALEAYGLpPPPYQYLCTVRLA----RRVWPLLP--NHKLNTVAEHLGIE-LNHHDAL 144

                         170
                  ....*....|..
gi 1174928096 211 FDALAAGELFAA 222
Cdd:cd06130   145 EDARACAEILLA 156
PRK07942 PRK07942
DNA polymerase III subunit epsilon; Provisional
 57-236 6.44e-11

DNA polymerase III subunit epsilon; Provisional


Pssm-ID: 181176 [Multi-domain]  Cd Length: 232  Bit Score: 60.38  E-value: 6.44e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096  57 LAVDLETTGLDPEHDAILS--IGWVAMDGVRIDLSTAdqrLVRADCPVPEQSAVIHRI-TDREAAGGTTVDSALDALFEA 133
Cdd:PRK07942    9 AAFDLETTGVDPETARIVTaaLVVVDADGEVVESREW---LADPGVEIPEEASAVHGItTEYARAHGRPAAEVLAEIADA 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096 134 LQ-----GRVLVAHHAALELGFLEEACHRlYGVRP--PLPVVDTLRLaERQLRRAGRpipadGMR-LHTLRGRYNLPQYR 205
Cdd:PRK07942   86 LReawarGVPVVVFNAPYDLTVLDRELRR-HGLPSlvPGPVIDPYVI-DKAVDRYRK-----GKRtLTALCEHYGVRLDN 158

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1174928096 206 AHDALFDALAAGELFAALVSQLSPEAQVPLE 236
Cdd:PRK07942  159 AHEATADALAAARVAWALARRFPELAALSPA 189
DNA_pol_III_epsilon_Ecoli_like cd06131
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ...
 60-223 1.62e-10

DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins; This subfamily is composed of the epsilon subunit of Escherichia coli DNA polymerase III (Pol III) and similar proteins. Pol III is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. It is a holoenzyme complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The epsilon subunit of Pol III also functions as a stabilizer of the holoenzyme complex.


Pssm-ID: 99835 [Multi-domain]  Cd Length: 167  Bit Score: 57.93  E-value: 1.62e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096  60 DLETTGLDPEH-DAILSIGWVAMDGVRIDLSTAdQRLVRADCPVPEQSAVIHRITDREAAGGTTVDSALDALFEALQGRV 138
Cdd:cd06131     5 DTETTGLDPREgHRIIEIGCVELINRRLTGNTF-HVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEFLDFIRGAE 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096 139 LVAHHAALELGFLEEACHRLYGVRPPLP---VVDTLRLAERqlRRAGRPIPADGmrlhtLRGRYNLP--QYRAHDALFDA 213
Cdd:cd06131    84 LVIHNASFDVGFLNAELSLLGLGKKIIDfcrVIDTLALARK--KFPGKPNSLDA-----LCKRFGIDnsHRTLHGALLDA 156

                         170
                  ....*....|
gi 1174928096 214 LAAGELFAAL 223
Cdd:cd06131   157 ELLAEVYLEL 166
PRK06807 PRK06807
3'-5' exonuclease;
56-220 7.58e-10

3'-5' exonuclease;


Pssm-ID: 235864 [Multi-domain]  Cd Length: 313  Bit Score: 57.90  E-value: 7.58e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096  56 FLAVDLETTGLDPEHDAILSIGWVAMDGVRIdlstADQ--RLVRADCPVPEQSAVIHRITDREAAGGTTVDSALDALFEA 133
Cdd:PRK06807   10 YVVIDFETTGFNPYNDKIIQVAAVKYRNHEL----VDQfvSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAF 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096 134 LQGRVLVAHHAALELGFLEEACHRLYGVRPPLPVVDTLRLAERQLRRagrpipADGMRLHTLRgRYNLPQYRAHDALFDA 213
Cdd:PRK06807   86 LHTNVIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKH------APNHKLETLK-RMLGIRLSSHNAFDDC 158


                  ....*..
gi 1174928096 214 LAAGELF 220
Cdd:PRK06807  159 ITCAAVY 165
PRK08517 PRK08517
3'-5' exonuclease;
44-220 1.47e-08

3'-5' exonuclease;


Pssm-ID: 236281 [Multi-domain]  Cd Length: 257  Bit Score: 53.87  E-value: 1.47e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096  44 LPSARQAVADCRFLAVDLETTGLDPEHDAILSIGWVAM-DGVRIDlstADQRLVRADcPVPEQSAVIHRITDREAAGGTT 122
Cdd:PRK08517   58 LKTRFTPIKDQVFCFVDIETNGSKPKKHQIIEIGAVKVkNGEIID---RFESFVKAK-EVPEYITELTGITYEDLENAPS 133

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096 123 VDSALDALFEALQGRVLVAHHAALELGFLEEACHRlYGVRPPL-PVVDTLRLAERQlrragrpIPADGMRLHTLRGRYNL 201
Cdd:PRK08517  134 LKEVLEEFRLFLGDSVFVAHNVNFDYNFISRSLEE-IGLGPLLnRKLCTIDLAKRT-------IESPRYGLSFLKELLGI 205

                         170
                  ....*....|....*....
gi 1174928096 202 PQYRAHDALFDALAAGELF 220
Cdd:PRK08517  206 EIEVHHRAYADALAAYEIF 224
PRK09182 PRK09182
DNA polymerase III subunit epsilon; Validated
 59-152 9.60e-07

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 236397 [Multi-domain]  Cd Length: 294  Bit Score: 48.82  E-value: 9.60e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096  59 VDLETTGLDPEHDAILSIGWVAM----DGVRIDLSTADQRLVRADCPVPEQSAVIHRITDREAAGGTTVDSALDALFEAL 134
Cdd:PRK09182   42 LDTETTGLDPRKDEIIEIGMVAFeyddDGRIGDVLDTFGGLQQPSRPIPPEITRLTGITDEMVAGQTIDPAAVDALIAPA 121

                          90
                  ....*....|....*...
gi 1174928096 135 QgrVLVAHHAALELGFLE 152
Cdd:PRK09182  122 D--LIIAHNAGFDRPFLE 137
PRK05711 PRK05711
DNA polymerase III subunit epsilon; Provisional
 60-176 2.09e-06

DNA polymerase III subunit epsilon; Provisional


Pssm-ID: 235574 [Multi-domain]  Cd Length: 240  Bit Score: 47.16  E-value: 2.09e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096  60 DLETTGLDPEH-DAILSIGWVAMdgvridlstADQRL--------VRADCPVPEQSAVIHRITDREAAGGTTVDSALDAL 130
Cdd:PRK05711   10 DTETTGLNQREgHRIIEIGAVEL---------INRRLtgrnfhvyIKPDRLVDPEALAVHGITDEFLADKPTFAEVADEF 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1174928096 131 FEALQGRVLVAHHAALELGFLEEACHRLYGVRPPLP----VVDTLRLAER 176
Cdd:PRK05711   81 LDFIRGAELIIHNAPFDIGFMDYEFALLGRDIPKTNtfckVTDTLAMARR 130
Orn COG1949
Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification];
59-98 3.22e-04

Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification];


Pssm-ID: 441552  Cd Length: 177  Bit Score: 40.09  E-value: 3.22e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1174928096  59 VDLETTGLDPEHDAILSIGWVAMDGvriDLSTADQRLVRA 98
Cdd:COG1949     7 IDLEMTGLDPETDRIIEIATIVTDS---DLNILAEGPVLV 43
Orn cd06135
DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Oligoribonuclease ...
 59-83 8.80e-04

DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Oligoribonuclease (Orn) is a DEDDh-type DnaQ-like 3'-5' exoribonuclease that is responsible for degrading small oligoribonucleotides to mononucleotides. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Orn is essential for Escherichia coli survival. The human homolog, also called Sfn (small fragment nuclease), is able to hydrolyze short single-stranded RNA and DNA oligomers. It plays a role in cellular nucleotide recycling.


Pssm-ID: 99838 [Multi-domain]  Cd Length: 173  Bit Score: 39.07  E-value: 8.80e-04
                          10        20
                  ....*....|....*....|....*
gi 1174928096  59 VDLETTGLDPEHDAILSIGWVAMDG 83
Cdd:cd06135     4 IDLEMTGLDPEKDRILEIACIITDG 28
PRK05359 PRK05359
oligoribonuclease; Provisional
 59-76 3.91e-03

oligoribonuclease; Provisional


Pssm-ID: 235429  Cd Length: 181  Bit Score: 37.06  E-value: 3.91e-03
                          10
                  ....*....|....*...
gi 1174928096  59 VDLETTGLDPEHDAILSI 76
Cdd:PRK05359    8 IDLEMTGLDPERDRIIEI 25
PRK05601 PRK05601
DNA polymerase III subunit epsilon; Validated
 49-151 6.10e-03

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 235529 [Multi-domain]  Cd Length: 377  Bit Score: 37.50  E-value: 6.10e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174928096  49 QAVADCRFLAVDLETTGLDPEHDAILSIGWVAMDGVRIDLSTADQRLVRADCPVPEQsavIHRITDREAAGGTTVDSALD 128
Cdd:PRK05601   41 EAIEAAPFVAVSIQTSGIHPSTSRLITIDAVTLTADGEEVEHFHAVLNPGEDPGPFH---LHGLSAEEFAQGKRFSQILK 117

                          90       100
                  ....*....|....*....|...
gi 1174928096 129 ALFEALQGRVLVAHHAALELGFL 151
Cdd:PRK05601  118 PLDRLIDGRTLILHNAPRTWGFI 140
CAF1 pfam04857
CAF1 family ribonuclease; The major pathways of mRNA turnover in eukaryotes initiate with ...
 44-74 7.05e-03

CAF1 family ribonuclease; The major pathways of mRNA turnover in eukaryotes initiate with shortening of the polyA tail. CAF1 encodes a critical component of the major cytoplasmic deadenylase in yeast. Both Caf1p is required for normal mRNA deadenylation in vivo and localizes to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent polyA-specific exonuclease activity. Some members of this family include and inserted RNA binding domain pfam01424. This family of proteins is related to other exonucleases pfam00929 (Bateman A pers. obs.). The crystal structure of Saccharomyces cerevisiae Pop2 has been resolved at 2.3 Angstrom resolution.


Pssm-ID: 461457  Cd Length: 375  Bit Score: 37.01  E-value: 7.05e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1174928096  44 LPSARQAVADCRFLAVDLETTGLDPEHDAIL 74
Cdd:pfam04857  10 LPEILKAIKEADFVAIDLEFTGLGSPWRKSS 40
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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