|
Name |
Accession |
Description |
Interval |
E-value |
| PolC |
COG2176 |
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ... |
20-197 |
2.86e-68 |
|
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair];
Pssm-ID: 441779 [Multi-domain] Cd Length: 181 Bit Score: 210.77 E-value: 2.86e-68
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 20 YIVLDLETTGLDPHYDDIIEVACLKFAGGKQVDSFRSYIQPRpfqdddgqlHFVDDFITDLTGITDDMLKDAPRFASIAP 99
Cdd:COG2176 10 YVVFDLETTGLSPKKDEIIEIGAVKVENGEIVDRFSTLVNPG---------RPIPPFITELTGITDEMVADAPPFEEVLP 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 100 ELFKYLGNSVLVGHNVNFDINFLYDNFmAALRKPLHNNFVDTMRIARIVMPDLPHHRLKDLCKAFSID-TDLHRADSDCM 178
Cdd:COG2176 81 EFLEFLGDAVLVAHNASFDLGFLNAAL-KRLGLPFDNPVLDTLELARRLLPELKSYKLDTLAERLGIPlEDRHRALGDAE 159
|
170
....*....|....*....
gi 2701625488 179 ATQKILVNLQKLAAESNID 197
Cdd:COG2176 160 ATAELFLKLLEKLEEKGIT 178
|
|
| DEDDh |
cd06127 |
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ... |
21-184 |
8.28e-54 |
|
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: 173.26 E-value: 8.28e-54
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 21 IVLDLETTGLDPHYDDIIEVACLKFAGGKQV-DSFRSYIQPRpfqdddgqlHFVDDFITDLTGITDDMLKDAPRFASIAP 99
Cdd:cd06127 1 VVFDTETTGLDPKKDRIIEIGAVKVDGGIEIvERFETLVNPG---------RPIPPEATAIHGITDEMLADAPPFEEVLP 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 100 ELFKYLGNSVLVGHNVNFDINFLYDNFMAALRKPLHNNFVDTMRIARIVMPDLPHHRLKDL-CKAFSIDT-DLHRADSDC 177
Cdd:cd06127 72 EFLEFLGGRVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGLRSHRLGLLlAERYGIPLeGAHRALADA 151
|
....*..
gi 2701625488 178 MATQKIL 184
Cdd:cd06127 152 LATAELL 158
|
|
| polC |
PRK00448 |
DNA polymerase III PolC; Validated |
18-196 |
1.46e-47 |
|
DNA polymerase III PolC; Validated
Pssm-ID: 234767 [Multi-domain] Cd Length: 1437 Bit Score: 171.17 E-value: 1.46e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 18 DSYIVLDLETTGLDPHYDDIIEVACLKFAGGKQVDSFRSYIQPRpfqdddgqlHFVDDFITDLTGITDDMLKDAPRFASI 97
Cdd:PRK00448 419 ATYVVFDVETTGLSAVYDEIIEIGAVKIKNGEIIDKFEFFIKPG---------HPLSAFTTELTGITDDMVKDAPSIEEV 489
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 98 APELFKYLGNSVLVGHNVNFDINFLYDNFMAALRKPLHNNFVDTMRIARIVMPDLPHHRLKDLCKAFSID-TDLHRADSD 176
Cdd:PRK00448 490 LPKFKEFCGDSILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSRFLYPELKSHRLNTLAKKFGVElEHHHRADYD 569
|
170 180
....*....|....*....|
gi 2701625488 177 CMATQKILVNLQKLAAESNI 196
Cdd:PRK00448 570 AEATAYLLIKFLKDLKEKGI 589
|
|
| EXOIII |
smart00479 |
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ... |
19-184 |
4.35e-41 |
|
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;
Pssm-ID: 214685 [Multi-domain] Cd Length: 169 Bit Score: 140.51 E-value: 4.35e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 19 SYIVLDLETTGLDPHYDDIIEVACLKFAGGKQVDSFRSYIQPRPfqdddgqlhFVDDFITDLTGITDDMLKDAPRFASIA 98
Cdd:smart00479 1 TLVVIDCETTGLDPGKDEIIEIAAVDVDGGEIIEVFDTYVKPDR---------PITDYATEIHGITPEMLDDAPTFEEVL 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 99 PELFKYLGNSVLV-GHNVNFDINFLYDNFMAALRKPLHNNFV-DTMRIARIVMPDLPHHRLKDLCKAFSIDTD--LHRAD 174
Cdd:smart00479 72 EELLEFLRGRILVaGNSAHFDLRFLKLEHPRLGIKQPPKLPViDTLKLARATNPGLPKYSLKKLAKRLLLEVIqrAHRAL 151
|
170
....*....|
gi 2701625488 175 SDCMATQKIL 184
Cdd:smart00479 152 DDARATAKLF 161
|
|
| RNase_T |
pfam00929 |
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ... |
21-184 |
9.60e-37 |
|
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: 129.39 E-value: 9.60e-37
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 21 IVLDLETTGLDPHYDDIIEVACLKFAGG--KQVDSFRSYIQPrpfqdddGQLHFVDDFITDLTGITDDMLKDAPRFASIA 98
Cdd:pfam00929 1 VVIDLETTGLDPEKDEIIEIAAVVIDGGenEIGETFHTYVKP-------TRLPKLTDECTKFTGITQAMLDNKPSFEEVL 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 99 PELFKYLG-NSVLVGHNVNFDINFLYDNFMAALRK--PLHNNFVDTMRIARIVMPDLPHHRLKDLCKAFSIDTD--LHRA 173
Cdd:pfam00929 74 EEFLEFLRkGNLLVAHNASFDVGFLRYDDKRFLKKpmPKLNPVIDTLILDKATYKELPGRSLDALAEKLGLEHIgrAHRA 153
|
170
....*....|.
gi 2701625488 174 DSDCMATQKIL 184
Cdd:pfam00929 154 LDDARATAKLF 164
|
|
| dnaq |
TIGR00573 |
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ... |
16-200 |
2.68e-29 |
|
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: 111.39 E-value: 2.68e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 16 VPDSYIVLDLETTGLDPHYDDIIEVACLKFAGGKQVDSFRSYIQP-RPFQDDdgqlhfvddfITDLTGITDDMLKDAPRF 94
Cdd:TIGR00573 5 VLDTETTGDNETTGLYAGHDIIEIGAVEIINRRITGNKFHTYIKPdRPIDPD----------AIKIHGITDDMLKDKPDF 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 95 ASIAPELFKYLGNSVLVGHNVNFDINFLYDNFMAALRK-PLHNNFVDTMRIARIVMPDLPHHRLKDLCKAFSIDTDLH-R 172
Cdd:TIGR00573 75 KEIAEDFADYIRGAELVIHNASFDVGFLNYEFSKLYKVePKTNDVIDTTDTLQYARPEFPGKRNTLDALCKRYEITNShR 154
|
170 180
....*....|....*....|....*...
gi 2701625488 173 ADSDCMATQKILVNLQKLAAESNIDLAA 200
Cdd:TIGR00573 155 ALHGALADAFILAKLYLVMTGKQTKYGE 182
|
|
| BRCT_DNA_ligase_like |
cd17748 |
BRCT domain of bacterial NAD-dependent DNA ligase (LigA) and similar proteins; LigA, also ... |
225-309 |
4.84e-23 |
|
BRCT domain of bacterial NAD-dependent DNA ligase (LigA) and similar proteins; LigA, also called NAD(+)-dependent polydeoxyribonucleotide synthase, catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA. The Trp-X-X-X-Cys/Ser signature motif of the BRCT family is not conserved in this family.
Pssm-ID: 349379 [Multi-domain] Cd Length: 76 Bit Score: 90.23 E-value: 4.84e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 225 LYGKNVVFTGKLQRFLRKDAAQIVCNIGGYCENNVTKKTNFLVIGSLEGnplveggksSKMKRARELILSGQDLQVLSET 304
Cdd:cd17748 1 LAGKTFVFTGTLSSMSRDEAEELIEALGGKVQSSVSKKTDYLVVGDNAG---------SKLKKGEELKAKGLGIKIISEE 71
|
....*
gi 2701625488 305 VFYDM 309
Cdd:cd17748 72 EFLDL 76
|
|
| Lig |
COG0272 |
NAD-dependent DNA ligase [Replication, recombination and repair]; |
222-311 |
4.93e-12 |
|
NAD-dependent DNA ligase [Replication, recombination and repair];
Pssm-ID: 440042 [Multi-domain] Cd Length: 668 Bit Score: 66.59 E-value: 4.93e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 222 SHPLYGKNVVFTGKLQRFLRKDAAQIVCNIGGYCENNVTKKTNFLVIGSlegNPlveggkSSKMKRARELilsgqDLQVL 301
Cdd:COG0272 593 DSPLAGKTFVLTGTLETMTRDEAKELIEALGGKVSGSVSKKTDYVVAGE---NA------GSKLDKAEEL-----GVPIL 658
|
90
....*....|
gi 2701625488 302 SETVFYDMIS 311
Cdd:COG0272 659 DEAEFLELLG 668
|
|
| ligA |
PRK07956 |
NAD-dependent DNA ligase LigA; Validated |
221-310 |
2.32e-07 |
|
NAD-dependent DNA ligase LigA; Validated
Pssm-ID: 236137 [Multi-domain] Cd Length: 665 Bit Score: 52.05 E-value: 2.32e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 221 PSHPLYGKNVVFTGKLQRFLRKDAAQIVCNIGGYCENNVTKKTNFLVIGSLEGnplveggksSKMKRARELilsgqDLQV 300
Cdd:PRK07956 587 EEVDLAGKTVVLTGTLEQLSRDEAKEKLEALGAKVSGSVSKKTDLVVAGEAAG---------SKLAKAQEL-----GIEV 652
|
90
....*....|
gi 2701625488 301 LSETVFYDMI 310
Cdd:PRK07956 653 LDEEEFLRLL 662
|
|
| BRCT |
smart00292 |
breast cancer carboxy-terminal domain; |
222-310 |
5.47e-03 |
|
breast cancer carboxy-terminal domain;
Pssm-ID: 214602 [Multi-domain] Cd Length: 78 Bit Score: 35.43 E-value: 5.47e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 222 SHPLYGKNVVFTGKLQRFLRKDAAQIVCNIGGYCENNVTKKTNFLVIGSlegnplVEGGKSSKMKRARELilsgqDLQVL 301
Cdd:smart00292 1 PKLFKGKTFYITGSFDKEERDELKELIEALGGKVTSSLSSKTTTHVIVG------SPEGGKLELLKAIAL-----GIPIV 69
|
....*....
gi 2701625488 302 SETVFYDMI 310
Cdd:smart00292 70 KEEWLLDCL 78
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| PolC |
COG2176 |
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ... |
20-197 |
2.86e-68 |
|
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair];
Pssm-ID: 441779 [Multi-domain] Cd Length: 181 Bit Score: 210.77 E-value: 2.86e-68
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 20 YIVLDLETTGLDPHYDDIIEVACLKFAGGKQVDSFRSYIQPRpfqdddgqlHFVDDFITDLTGITDDMLKDAPRFASIAP 99
Cdd:COG2176 10 YVVFDLETTGLSPKKDEIIEIGAVKVENGEIVDRFSTLVNPG---------RPIPPFITELTGITDEMVADAPPFEEVLP 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 100 ELFKYLGNSVLVGHNVNFDINFLYDNFmAALRKPLHNNFVDTMRIARIVMPDLPHHRLKDLCKAFSID-TDLHRADSDCM 178
Cdd:COG2176 81 EFLEFLGDAVLVAHNASFDLGFLNAAL-KRLGLPFDNPVLDTLELARRLLPELKSYKLDTLAERLGIPlEDRHRALGDAE 159
|
170
....*....|....*....
gi 2701625488 179 ATQKILVNLQKLAAESNID 197
Cdd:COG2176 160 ATAELFLKLLEKLEEKGIT 178
|
|
| DnaQ |
COG0847 |
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ... |
20-189 |
2.53e-55 |
|
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];
Pssm-ID: 440608 [Multi-domain] Cd Length: 163 Bit Score: 176.91 E-value: 2.53e-55
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 20 YIVLDLETTGLDPHYDDIIEVACLKFAGGKQVDSFRSYIQP-RPFqdddgqlhfvDDFITDLTGITDDMLKDAPRFASIA 98
Cdd:COG0847 2 FVVLDTETTGLDPAKDRIIEIGAVKVDDGRIVETFHTLVNPeRPI----------PPEATAIHGITDEDVADAPPFAEVL 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 99 PELFKYLGNSVLVGHNVNFDINFLYDNFMAALRKPLHNNFVDTMRIARIVMPDLPHHRLKDLCKAFSID-TDLHRADSDC 177
Cdd:COG0847 72 PELLEFLGGAVLVAHNAAFDLGFLNAELRRAGLPLPPFPVLDTLRLARRLLPGLPSYSLDALCERLGIPfDERHRALADA 151
|
170
....*....|..
gi 2701625488 178 MATQKILVNLQK 189
Cdd:COG0847 152 EATAELFLALLR 163
|
|
| DEDDh |
cd06127 |
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ... |
21-184 |
8.28e-54 |
|
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: 173.26 E-value: 8.28e-54
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 21 IVLDLETTGLDPHYDDIIEVACLKFAGGKQV-DSFRSYIQPRpfqdddgqlHFVDDFITDLTGITDDMLKDAPRFASIAP 99
Cdd:cd06127 1 VVFDTETTGLDPKKDRIIEIGAVKVDGGIEIvERFETLVNPG---------RPIPPEATAIHGITDEMLADAPPFEEVLP 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 100 ELFKYLGNSVLVGHNVNFDINFLYDNFMAALRKPLHNNFVDTMRIARIVMPDLPHHRLKDL-CKAFSIDT-DLHRADSDC 177
Cdd:cd06127 72 EFLEFLGGRVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGLRSHRLGLLlAERYGIPLeGAHRALADA 151
|
....*..
gi 2701625488 178 MATQKIL 184
Cdd:cd06127 152 LATAELL 158
|
|
| polC |
PRK00448 |
DNA polymerase III PolC; Validated |
18-196 |
1.46e-47 |
|
DNA polymerase III PolC; Validated
Pssm-ID: 234767 [Multi-domain] Cd Length: 1437 Bit Score: 171.17 E-value: 1.46e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 18 DSYIVLDLETTGLDPHYDDIIEVACLKFAGGKQVDSFRSYIQPRpfqdddgqlHFVDDFITDLTGITDDMLKDAPRFASI 97
Cdd:PRK00448 419 ATYVVFDVETTGLSAVYDEIIEIGAVKIKNGEIIDKFEFFIKPG---------HPLSAFTTELTGITDDMVKDAPSIEEV 489
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 98 APELFKYLGNSVLVGHNVNFDINFLYDNFMAALRKPLHNNFVDTMRIARIVMPDLPHHRLKDLCKAFSID-TDLHRADSD 176
Cdd:PRK00448 490 LPKFKEFCGDSILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSRFLYPELKSHRLNTLAKKFGVElEHHHRADYD 569
|
170 180
....*....|....*....|
gi 2701625488 177 CMATQKILVNLQKLAAESNI 196
Cdd:PRK00448 570 AEATAYLLIKFLKDLKEKGI 589
|
|
| EXOIII |
smart00479 |
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ... |
19-184 |
4.35e-41 |
|
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;
Pssm-ID: 214685 [Multi-domain] Cd Length: 169 Bit Score: 140.51 E-value: 4.35e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 19 SYIVLDLETTGLDPHYDDIIEVACLKFAGGKQVDSFRSYIQPRPfqdddgqlhFVDDFITDLTGITDDMLKDAPRFASIA 98
Cdd:smart00479 1 TLVVIDCETTGLDPGKDEIIEIAAVDVDGGEIIEVFDTYVKPDR---------PITDYATEIHGITPEMLDDAPTFEEVL 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 99 PELFKYLGNSVLV-GHNVNFDINFLYDNFMAALRKPLHNNFV-DTMRIARIVMPDLPHHRLKDLCKAFSIDTD--LHRAD 174
Cdd:smart00479 72 EELLEFLRGRILVaGNSAHFDLRFLKLEHPRLGIKQPPKLPViDTLKLARATNPGLPKYSLKKLAKRLLLEVIqrAHRAL 151
|
170
....*....|
gi 2701625488 175 SDCMATQKIL 184
Cdd:smart00479 152 DDARATAKLF 161
|
|
| PRK08074 |
PRK08074 |
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated |
18-190 |
1.16e-40 |
|
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236148 [Multi-domain] Cd Length: 928 Bit Score: 150.87 E-value: 1.16e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 18 DSYIVLDLETTGLDPHYDD-IIEVACLKFAGGKQVDSFRSYIQP-RPfqdddgqlhfVDDFITDLTGITDDMLKDAPRFA 95
Cdd:PRK08074 3 KRFVVVDLETTGNSPKKGDkIIQIAAVVVEDGEILERFSSFVNPeRP----------IPPFITELTGISEEMVKQAPLFE 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 96 SIAPELFKYLGNSVLVGHNVNFDINFLYDNFMAALRKPLHNNFVDTMRIARIVMPDLPHHRLKDLCKAFSIDTDL-HRAD 174
Cdd:PRK08074 73 DVAPEIVELLEGAYFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELARILLPTAESYKLRDLSEELGLEHDQpHRAD 152
|
170
....*....|....*..
gi 2701625488 175 SDCMATQKILVN-LQKL 190
Cdd:PRK08074 153 SDAEVTAELFLQlLNKL 169
|
|
| PRK06807 |
PRK06807 |
3'-5' exonuclease; |
16-183 |
1.83e-38 |
|
3'-5' exonuclease;
Pssm-ID: 235864 [Multi-domain] Cd Length: 313 Bit Score: 138.02 E-value: 1.83e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 16 VPDSYIVLDLETTGLDPHYDDIIEVACLKFAGGKQVDSFRSYIQPRpfqdddgqlHFVDDFITDLTGITDDMLKDAPRFA 95
Cdd:PRK06807 6 LPLDYVVIDFETTGFNPYNDKIIQVAAVKYRNHELVDQFVSYVNPE---------RPIPDRITSLTGITNYRVSDAPTIE 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 96 SIAPELFKYLGNSVLVGHNVNFDINFLYDNFMAALRKPLHNNFVDTMRIARIVMPDLPHHRLKDLCKAFSIDTDLHRADS 175
Cdd:PRK06807 77 EVLPLFLAFLHTNVIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAPNHKLETLKRMLGIRLSSHNAFD 156
|
....*...
gi 2701625488 176 DCMATQKI 183
Cdd:PRK06807 157 DCITCAAV 164
|
|
| RNase_T |
pfam00929 |
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ... |
21-184 |
9.60e-37 |
|
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: 129.39 E-value: 9.60e-37
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 21 IVLDLETTGLDPHYDDIIEVACLKFAGG--KQVDSFRSYIQPrpfqdddGQLHFVDDFITDLTGITDDMLKDAPRFASIA 98
Cdd:pfam00929 1 VVIDLETTGLDPEKDEIIEIAAVVIDGGenEIGETFHTYVKP-------TRLPKLTDECTKFTGITQAMLDNKPSFEEVL 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 99 PELFKYLG-NSVLVGHNVNFDINFLYDNFMAALRK--PLHNNFVDTMRIARIVMPDLPHHRLKDLCKAFSIDTD--LHRA 173
Cdd:pfam00929 74 EEFLEFLRkGNLLVAHNASFDVGFLRYDDKRFLKKpmPKLNPVIDTLILDKATYKELPGRSLDALAEKLGLEHIgrAHRA 153
|
170
....*....|.
gi 2701625488 174 DSDCMATQKIL 184
Cdd:pfam00929 154 LDDARATAKLF 164
|
|
| PRK06195 |
PRK06195 |
DNA polymerase III subunit epsilon; Validated |
47-310 |
7.98e-35 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 235735 [Multi-domain] Cd Length: 309 Bit Score: 128.36 E-value: 7.98e-35
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 47 GGKQVDSFRSYIQPRP--FQDDDGQLHfvddfitdltGITDDMLKDAPRFASIAPELFKYLGNSVLVGHNVNFDINFLyd 124
Cdd:PRK06195 28 DGEIVEKVHYLIKPKEmrFMPINIGIH----------GIRPHMVEDELEFDKIWEKIKHYFNNNLVIAHNASFDISVL-- 95
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 125 nfMAALRkpLHN------NFVDTMRIARIVMPDLPHHRLKDLCKAFSIDTDLHRADSDCMATQKILVNLQKLAAESNIDL 198
Cdd:PRK06195 96 --RKTLE--LYNipmpsfEYICTMKLAKNFYSNIDNARLNTVNNFLGYEFKHHDALADAMACSNILLNISKELNSKDINE 171
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 199 -----------------------AAYRRHHNINLSALAGDTTLNDPSHPLYGKNVVFTGKLQRFLRKDAAQIVCNIGGYC 255
Cdd:PRK06195 172 iskllgvtlgyvnengykpssrkGRILKRSNRQAPRKKKKIIESFGFTAFKEEVVVFTGGLASMTRDEAMILVRRLGGTV 251
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|....*
gi 2701625488 256 ENNVTKKTNFLVIGSLEGNPLVEGGKSSKMKRARELILSGQDLQVLSETVFYDMI 310
Cdd:PRK06195 252 GSSVTKKTTYLVTNTKDIEDLNREEMSNKLKKAIDLKKKGQNIKFLNEEEFLQKC 306
|
|
| PRK07883 |
PRK07883 |
DEDD exonuclease domain-containing protein; |
19-203 |
1.09e-32 |
|
DEDD exonuclease domain-containing protein;
Pssm-ID: 236123 [Multi-domain] Cd Length: 557 Bit Score: 126.96 E-value: 1.09e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 19 SYIVLDLETTGLDPHYDDIIEVACLKFAGGKQVDSFRSYIQP-RPfqdddgqlhfVDDFITDLTGITDDMLKDAPRFASI 97
Cdd:PRK07883 16 TFVVVDLETTGGSPAGDAITEIGAVKVRGGEVLGEFATLVNPgRP----------IPPFITVLTGITTAMVAGAPPIEEV 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 98 APELFKYLGNSVLVGHNVNFDINFLYDNFMAALRKPLHNNFVDTMRIARIVMP--DLPHHRLKDLCKAFSIDTD-LHRAD 174
Cdd:PRK07883 86 LPAFLEFARGAVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLARRVLPrdEAPNVRLSTLARLFGATTTpTHRAL 165
|
170 180 190
....*....|....*....|....*....|...
gi 2701625488 175 SDCMATQKILVNLQKLAAESNI----DLAAYRR 203
Cdd:PRK07883 166 DDARATVDVLHGLIERLGNLGVhtleELLTYLP 198
|
|
| DNA_pol_III_epsilon_Ecoli_like |
cd06131 |
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ... |
20-177 |
1.02e-31 |
|
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: 116.09 E-value: 1.02e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 20 YIVLDLETTGLDP-HYDDIIEVACLKFAGGKQVD-SFRSYIQPrpfQDDdgqlhfVDDFITDLTGITDDMLKDAPRFASI 97
Cdd:cd06131 1 QIVLDTETTGLDPrEGHRIIEIGCVELINRRLTGnTFHVYINP---ERD------IPEEAFKVHGITDEFLADKPKFAEI 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 98 APELFKYLGNSVLVGHNVNFDINFL-YDNFMAALRKPL--HNNFVDTMRIARIVMPDLPHHrLKDLCKAFSIDT---DLH 171
Cdd:cd06131 72 ADEFLDFIRGAELVIHNASFDVGFLnAELSLLGLGKKIidFCRVIDTLALARKKFPGKPNS-LDALCKRFGIDNshrTLH 150
|
....*.
gi 2701625488 172 RADSDC 177
Cdd:cd06131 151 GALLDA 156
|
|
| DNA_pol_III_epsilon_like |
cd06130 |
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ... |
20-185 |
1.95e-30 |
|
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: 112.60 E-value: 1.95e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 20 YIVLDLETTglDPHYDDIIEVACLKFAGGKQVDSFRSYIQPRPfqdddgqlHFvDDFITDLTGITDDMLKDAPRFASIAP 99
Cdd:cd06130 1 FVAIDFETA--NADRASACSIGLVKVRDGQIVDTFYTLIRPPT--------RF-DPFNIAIHGITPEDVADAPTFPEVWP 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 100 ELFKYLGNSVLVGHNVNFDINFLydnfMAALRK----PLHNNFVDTMRIARIVMPDLPHHRLKDLCKAFSIDTDLHRADS 175
Cdd:cd06130 70 EIKPFLGGSLVVAHNASFDRSVL----RAALEAyglpPPPYQYLCTVRLARRVWPLLPNHKLNTVAEHLGIELNHHDALE 145
|
170
....*....|
gi 2701625488 176 DCMATQKILV 185
Cdd:cd06130 146 DARACAEILL 155
|
|
| dnaq |
TIGR00573 |
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ... |
16-200 |
2.68e-29 |
|
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: 111.39 E-value: 2.68e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 16 VPDSYIVLDLETTGLDPHYDDIIEVACLKFAGGKQVDSFRSYIQP-RPFQDDdgqlhfvddfITDLTGITDDMLKDAPRF 94
Cdd:TIGR00573 5 VLDTETTGDNETTGLYAGHDIIEIGAVEIINRRITGNKFHTYIKPdRPIDPD----------AIKIHGITDDMLKDKPDF 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 95 ASIAPELFKYLGNSVLVGHNVNFDINFLYDNFMAALRK-PLHNNFVDTMRIARIVMPDLPHHRLKDLCKAFSIDTDLH-R 172
Cdd:TIGR00573 75 KEIAEDFADYIRGAELVIHNASFDVGFLNYEFSKLYKVePKTNDVIDTTDTLQYARPEFPGKRNTLDALCKRYEITNShR 154
|
170 180
....*....|....*....|....*...
gi 2701625488 173 ADSDCMATQKILVNLQKLAAESNIDLAA 200
Cdd:TIGR00573 155 ALHGALADAFILAKLYLVMTGKQTKYGE 182
|
|
| PRK08517 |
PRK08517 |
3'-5' exonuclease; |
20-184 |
3.56e-27 |
|
3'-5' exonuclease;
Pssm-ID: 236281 [Multi-domain] Cd Length: 257 Bit Score: 106.64 E-value: 3.56e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 20 YIVLDLETTGLDPHYDDIIEVACLKFAGGKQVDSFRSYIQprpfqdddgqLHFVDDFITDLTGITDDMLKDAPRFASIAP 99
Cdd:PRK08517 70 FCFVDIETNGSKPKKHQIIEIGAVKVKNGEIIDRFESFVK----------AKEVPEYITELTGITYEDLENAPSLKEVLE 139
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 100 ELFKYLGNSVLVGHNVNFDINFLYDNFMAALRKPLHNNFVDTMRIARIVMPDlPHHRLKDLCKAFSIDTDL-HRADSDCM 178
Cdd:PRK08517 140 EFRLFLGDSVFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRTIES-PRYGLSFLKELLGIEIEVhHRAYADAL 218
|
....*.
gi 2701625488 179 ATQKIL 184
Cdd:PRK08517 219 AAYEIF 224
|
|
| PRK07740 |
PRK07740 |
hypothetical protein; Provisional |
19-205 |
1.51e-26 |
|
hypothetical protein; Provisional
Pssm-ID: 236085 [Multi-domain] Cd Length: 244 Bit Score: 104.75 E-value: 1.51e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 19 SYIVLDLETTGLDP-HYDDIIEVACLKFAGGK-QVDSFRSYIQP-RPfqdddgqlhfVDDFITDLTGITDDMLKDAPRFA 95
Cdd:PRK07740 60 PFVVFDLETTGFSPqQGDEILSIGAVKTKGGEvETDTFYSLVKPkRP----------IPEHILELTGITAEDVAFAPPLA 129
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 96 SIAPELFKYLGNSVLVGHNVNFDINFLYDNFMAALRKPLHNNFVDTMRIARIVMPDLPHHRLKDLCKAFSID-TDLHRAD 174
Cdd:PRK07740 130 EVLHRFYAFIGAGVLVAHHAGHDKAFLRHALWRTYRQPFTHRLIDTMFLTKLLAHERDFPTLDDALAYYGIPiPRRHHAL 209
|
170 180 190
....*....|....*....|....*....|....*
gi 2701625488 175 SDCMAT----QKILVNLQKLAAESNIDLAAYRRHH 205
Cdd:PRK07740 210 GDALMTaklwAILLVEAQQRGITTLHDLYAALSRC 244
|
|
| PRK06310 |
PRK06310 |
DNA polymerase III subunit epsilon; Validated |
20-189 |
1.84e-25 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180525 [Multi-domain] Cd Length: 250 Bit Score: 102.21 E-value: 1.84e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 20 YIVLDLETTGLDPHYDDIIEVACLKFAGGKQVDSFRSYIQP-RPFQDDDGQLHFvddfitdltgITDDMLKDAPRFASIA 98
Cdd:PRK06310 9 FVCLDCETTGLDVKKDRIIEFAAIRFTFDEVIDSVEFLINPeRVVSAESQRIHH----------ISDAMLRDKPKIAEVF 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 99 PELFKYLGNS-VLVGHNVNFDINFLYdnfMAALR-----KPLHNNFVDTMRIARIvMPDLPHHRLKDLCKAFSIDTDL-H 171
Cdd:PRK06310 79 PQIKGFFKEGdYIVGHSVGFDLQVLS---QESERigetfLSKHYYIIDTLRLAKE-YGDSPNNSLEALAVHFNVPYDGnH 154
|
170
....*....|....*...
gi 2701625488 172 RADSDCMATQKILVNLQK 189
Cdd:PRK06310 155 RAMKDVEINIKVFKHLCK 172
|
|
| BRCT_DNA_ligase_like |
cd17748 |
BRCT domain of bacterial NAD-dependent DNA ligase (LigA) and similar proteins; LigA, also ... |
225-309 |
4.84e-23 |
|
BRCT domain of bacterial NAD-dependent DNA ligase (LigA) and similar proteins; LigA, also called NAD(+)-dependent polydeoxyribonucleotide synthase, catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA. The Trp-X-X-X-Cys/Ser signature motif of the BRCT family is not conserved in this family.
Pssm-ID: 349379 [Multi-domain] Cd Length: 76 Bit Score: 90.23 E-value: 4.84e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 225 LYGKNVVFTGKLQRFLRKDAAQIVCNIGGYCENNVTKKTNFLVIGSLEGnplveggksSKMKRARELILSGQDLQVLSET 304
Cdd:cd17748 1 LAGKTFVFTGTLSSMSRDEAEELIEALGGKVQSSVSKKTDYLVVGDNAG---------SKLKKGEELKAKGLGIKIISEE 71
|
....*
gi 2701625488 305 VFYDM 309
Cdd:cd17748 72 EFLDL 76
|
|
| PRK07246 |
PRK07246 |
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated |
20-189 |
6.80e-22 |
|
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180905 [Multi-domain] Cd Length: 820 Bit Score: 96.29 E-value: 6.80e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 20 YIVLDLETTGLDPHYDdIIEVACLKFAGGKQVDSFRSYIQP-RPfqdddgqlhfVDDFITDLTGITDDMLKDAPRFASIA 98
Cdd:PRK07246 9 YAVVDLEATGAGPNAS-IIQVGIVIIEGGEIIDSYTTDVNPhEP----------LDEHIKHLTGITDQQLAQAPDFSQVA 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 99 PELFKYLGNSVLVGHNVNFDINFLYDN-FMAA--LRKPLhnnfVDTMRIARIVMPDLPHHRLKDLCKAFSID-TDLHRAD 174
Cdd:PRK07246 78 RHIYDLIEDCIFVAHNVKFDANLLAEAlFLEGyeLRTPR----VDTVELAQVFFPTLEKYSLSHLSRELNIDlADAHTAI 153
|
170
....*....|....*
gi 2701625488 175 SDCMATQKILVNLQK 189
Cdd:PRK07246 154 ADARATAELFLKLLQ 168
|
|
| PRK05711 |
PRK05711 |
DNA polymerase III subunit epsilon; Provisional |
21-179 |
1.60e-19 |
|
DNA polymerase III subunit epsilon; Provisional
Pssm-ID: 235574 [Multi-domain] Cd Length: 240 Bit Score: 85.68 E-value: 1.60e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 21 IVLDLETTGLDPHYDD-IIEVACL----KFAGGKqvdSFRSYIQP-RPFQDDDGQLHfvddfitdltGITDDMLKDAPRF 94
Cdd:PRK05711 7 IVLDTETTGLNQREGHrIIEIGAVelinRRLTGR---NFHVYIKPdRLVDPEALAVH----------GITDEFLADKPTF 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 95 ASIAPELFKYLGNSVLVGHNVNFDINFLyDNFMAALRKPL-----HNNFVDTMRIARIVMPDLPHHrLKDLCKAFSIDT- 168
Cdd:PRK05711 74 AEVADEFLDFIRGAELIIHNAPFDIGFM-DYEFALLGRDIpktntFCKVTDTLAMARRMFPGKRNS-LDALCKRYGIDNs 151
|
170
....*....|....*
gi 2701625488 169 --DLHRA--DSDCMA 179
Cdd:PRK05711 152 hrTLHGAllDAEILA 166
|
|
| PRK06309 |
PRK06309 |
DNA polymerase III subunit epsilon; Validated |
17-207 |
2.01e-18 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180524 [Multi-domain] Cd Length: 232 Bit Score: 82.55 E-value: 2.01e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 17 PDSYIVLDLETTGLDPHYDDIIEVACLKfagGKQVDSFRSYIQPR-PFQDDDGQLHfvddfitdltGITDDMLKDAPRFA 95
Cdd:PRK06309 1 MPALIFYDTETTGTQIDKDRIIEIAAYN---GVTSESFQTLVNPEiPIPAEASKIH----------GITTDEVADAPKFP 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 96 SIAPELFKYLGN-SVLVGHNV-NFDINFLYDNFMAALRKPLHNNFVDTMRIARIVMPDLPHHRLKDLCKAFSI-DTDLHR 172
Cdd:PRK06309 68 EAYQKFIEFCGTdNILVAHNNdAFDFPLLRKECRRHGLEPPTLRTIDSLKWAQKYRPDLPKHNLQYLRQVYGFeENQAHR 147
|
170 180 190
....*....|....*....|....*....|....*.
gi 2701625488 173 ADSDCMATQKILVNL-QKLAAESNIDLAAYRRHHNI 207
Cdd:PRK06309 148 ALDDVITLHRVFSALvGDLSPQQVYDLLNESCHPRI 183
|
|
| PRK06063 |
PRK06063 |
DEDDh family exonuclease; |
17-198 |
2.50e-18 |
|
DEDDh family exonuclease;
Pssm-ID: 180377 [Multi-domain] Cd Length: 313 Bit Score: 83.60 E-value: 2.50e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 17 PDSYIVLDLETTGLDPHYDDIIEVACLKF-AGGKQVDSFRSYIQPrpfQDDDGQLHfvddfitdLTGITDDMLKDAPRFA 95
Cdd:PRK06063 14 PRGWAVVDVETSGFRPGQARIISLAVLGLdADGNVEQSVVTLLNP---GVDPGPTH--------VHGLTAEMLEGQPQFA 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 96 SIAPELFKYLGNSVLVGHNVNFDINFLYDNFM-AALRKPlhnnfVD----TMRIARIVMPDLPHHRLKDLCKAFSI-DTD 169
Cdd:PRK06063 83 DIAGEVAELLRGRTLVAHNVAFDYSFLAAEAErAGAELP-----VDqvmcTVELARRLGLGLPNLRLETLAAHWGVpQQR 157
|
170 180
....*....|....*....|....*....
gi 2701625488 170 LHRADSDCMATQKILVNLQKLAAESNIDL 198
Cdd:PRK06063 158 PHDALDDARVLAGILRPSLERARERDVWL 186
|
|
| KapD |
COG5018 |
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ... |
18-189 |
1.23e-15 |
|
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction mechanisms];
Pssm-ID: 444042 [Multi-domain] Cd Length: 181 Bit Score: 73.35 E-value: 1.23e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 18 DSYIVLDLETTGLDP-----HYDDIIEV-ACLKFAGGKQVDSFRSYIQPRPFQDddgqlhfVDDFITDLTGITDDMLKDA 91
Cdd:COG5018 2 MKYLVIDLEATCWDGkpppgFPMEIIEIgAVKVDENGEIIDEFSSFVKPVRRPK-------LSPFCTELTGITQEDVDSA 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 92 PRFASIAPELFKYLG--NSVLV--GhnvNFDINFLYDNFMAA-LRKPLHNNFVDTMRIARIVMpDLPHHR-LKDLCKAFS 165
Cdd:COG5018 75 PSFAEAIEDFKKWIGseDYILCswG---DYDRKQLERNCRFHgVPYPFGDRHINLKKLFALYF-GLKKRIgLKKALELLG 150
|
170 180
....*....|....*....|....*.
gi 2701625488 166 IDTD--LHRADSDCMATQKILVNLQK 189
Cdd:COG5018 151 LEFEgtHHRALDDARNTAKLFKKILG 176
|
|
| ERI-1_3'hExo_like |
cd06133 |
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ... |
20-184 |
2.64e-13 |
|
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins; 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. These are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ERI-1 has been implicated in the degradation of small interfering RNAs (RNAi). 3'hExo participates in the degradation of histone mRNAs. Snp is a non-essential exonuclease that efficiently degrades structured RNA and DNA substrates as long as there is a minimum of 2 nucleotides in the 3' overhang to initiate degradation. Snp is not a functional homolog of either ERI-1 or 3'hExo.
Pssm-ID: 99836 [Multi-domain] Cd Length: 176 Bit Score: 66.86 E-value: 2.64e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 20 YIVLDLETTGLD----PHYD-DIIEVACLKF--AGGKQVDSFRSYIQPRpfqdDDGQLHfvdDFITDLTGITDDMLKDAP 92
Cdd:cd06133 1 YLVIDFEATCWEgnskPDYPnEIIEIGAVLVdvKTKEIIDTFSSYVKPV----INPKLS---DFCTELTGITQEDVDNAP 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 93 RFASIAPELFKYLG---NSVLVGhNVNFDINFLYDNFMAALRKPLHNNFVDTMRIARIVMPDLPHHR---LKDLCKAFSI 166
Cdd:cd06133 74 SFPEVLKEFLEWLGkngKYAFVT-WGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYGLKKrtgLSKALEYLGL 152
|
170 180
....*....|....*....|
gi 2701625488 167 DTD--LHRADSDCMATQKIL 184
Cdd:cd06133 153 EFEgrHHRGLDDARNIARIL 172
|
|
| Lig |
COG0272 |
NAD-dependent DNA ligase [Replication, recombination and repair]; |
222-311 |
4.93e-12 |
|
NAD-dependent DNA ligase [Replication, recombination and repair];
Pssm-ID: 440042 [Multi-domain] Cd Length: 668 Bit Score: 66.59 E-value: 4.93e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 222 SHPLYGKNVVFTGKLQRFLRKDAAQIVCNIGGYCENNVTKKTNFLVIGSlegNPlveggkSSKMKRARELilsgqDLQVL 301
Cdd:COG0272 593 DSPLAGKTFVLTGTLETMTRDEAKELIEALGGKVSGSVSKKTDYVVAGE---NA------GSKLDKAEEL-----GVPIL 658
|
90
....*....|
gi 2701625488 302 SETVFYDMIS 311
Cdd:COG0272 659 DEAEFLELLG 668
|
|
| PRK09182 |
PRK09182 |
DNA polymerase III subunit epsilon; Validated |
21-184 |
4.93e-12 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236397 [Multi-domain] Cd Length: 294 Bit Score: 65.38 E-value: 4.93e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 21 IVLDLETTGLDPHYDDIIEVACLKFAGGKQ------VDSFRSYIQP-RPFQDDdgqlhfvddfITDLTGITDDMLKDapr 93
Cdd:PRK09182 40 VILDTETTGLDPRKDEIIEIGMVAFEYDDDgrigdvLDTFGGLQQPsRPIPPE----------ITRLTGITDEMVAG--- 106
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 94 fASIAP-ELFKYLGNSVLV-GHNVNFDINFLYDNFMAALRKPLHNNFVDTmriarivmpDLPHH-----RLKDLCKAFSI 166
Cdd:PRK09182 107 -QTIDPaAVDALIAPADLIiAHNAGFDRPFLERFSPVFATKPWACSVSEI---------DWSARgfegtKLGYLAGQAGF 176
|
170
....*....|....*...
gi 2701625488 167 DTDLHRADSDCMATQKIL 184
Cdd:PRK09182 177 FHEGHRAVDDCQALLELL 194
|
|
| PRK07247 |
PRK07247 |
3'-5' exonuclease; |
18-114 |
2.80e-10 |
|
3'-5' exonuclease;
Pssm-ID: 180906 [Multi-domain] Cd Length: 195 Bit Score: 58.64 E-value: 2.80e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 18 DSYIVLDLETTGLDPHyDDIIEVACLKFAGGKQVDSFRSYIQPR-PFQDddgqlhfvddFITDLTGITDDMLKDAPRFAS 96
Cdd:PRK07247 5 ETYIAFDLEFNTVNGV-SHIIQVSAVKYDDHKEVDSFDSYVYTDvPLQS----------FINGLTGITADKIADAPKVEE 73
|
90
....*....|....*...
gi 2701625488 97 IAPELFKYLGNSVLVGHN 114
Cdd:PRK07247 74 VLAAFKEFVGELPLIGYN 91
|
|
| PRK07983 |
PRK07983 |
exodeoxyribonuclease X; Provisional |
22-191 |
4.51e-10 |
|
exodeoxyribonuclease X; Provisional
Pssm-ID: 181186 [Multi-domain] Cd Length: 219 Bit Score: 58.58 E-value: 4.51e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 22 VLDLETTGLDphyDDIIEVACLKFAGGKQVDSFRSYIQP-RPFQDDDGQLHfvddfitdltGITDDMLKDAPRFASIAPe 100
Cdd:PRK07983 4 VIDTETCGLQ---GGIVEIASVDVIDGKIVNPMSHLVRPdRPISPQAMAIH----------RITEAMVADKPWIEDVIP- 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 101 lfKYLGNSVLVGHNVNFDINFLYDnfmaalrkpLHNNFVDTMRIARIVMPDLPHHRLKdLCKAFSIDTDL------HRAD 174
Cdd:PRK07983 70 --HYYGSEWYVAHNASFDRRVLPE---------MPGEWICTMKLARRLWPGIKYSNMA-LYKSRKLNVQTppglhhHRAL 137
|
170
....*....|....*..
gi 2701625488 175 SDCMATQKILVNLQKLA 191
Cdd:PRK07983 138 YDCYITAALLIDIMNTS 154
|
|
| PRK09146 |
PRK09146 |
DNA polymerase III subunit epsilon; Validated |
23-147 |
1.77e-09 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236392 [Multi-domain] Cd Length: 239 Bit Score: 57.24 E-value: 1.77e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 23 LDLETTGLDPHYDDIIEVACLKFaggkqvDSFRSYIQ---------PRPFQDDDGQLHfvddfitdltGITDDMLKDAPR 93
Cdd:PRK09146 52 LDFETTGLDAEQDAIVSIGLVPF------TLQRIRCRqarhwvvkpRRPLEEESVVIH----------GITHSELQDAPD 115
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*
gi 2701625488 94 FASIAPELFKYLGNSVLVGHNVNFDINFLYDNFMAALRKPLHNNFVDTMRI-ARI 147
Cdd:PRK09146 116 LERILDELLEALAGKVVVVHYRRIERDFLDQALRNRIGEGIEFPVIDTMEIeARI 170
|
|
| PRK09145 |
PRK09145 |
3'-5' exonuclease; |
16-192 |
1.46e-08 |
|
3'-5' exonuclease;
Pssm-ID: 236391 [Multi-domain] Cd Length: 202 Bit Score: 53.75 E-value: 1.46e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 16 VPDSYIVLDLETTGLDPHYDDIIEVACLKFAGGKQVDS--FRSYIQP-RPFQDDDGQLHfvddfitdltGITDDMLKDAP 92
Cdd:PRK09145 27 PPDEWVALDCETTGLDPRRAEIVSIAAVKIRGNRILTSerLELLVRPpQSLSAESIKIH----------RLRHQDLEDGL 96
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 93 RFASIAPELFKYLGNSVLVGHNVNFDINFLYDNFMAALRKPLHNNFVD--------TMRIARIVMPDLphhRLKDLCKAF 164
Cdd:PRK09145 97 SEEEALRQLLAFIGNRPLVGYYLEFDVAMLNRYVRPLLGIPLPNPLIEvsalyydkKERHLPDAYIDL---RFDAILKHL 173
|
170 180
....*....|....*....|....*....
gi 2701625488 165 SI-DTDLHRADSDCMATQKILVNLQKLAA 192
Cdd:PRK09145 174 DLpVLGRHDALNDAIMAALIFLRLRKGDA 202
|
|
| BRCT_RFC1 |
cd17752 |
BRCT domain of replication factor C subunit 1 (RFC1) and similar proteins; RFC1, also termed ... |
225-311 |
3.09e-08 |
|
BRCT domain of replication factor C subunit 1 (RFC1) and similar proteins; RFC1, also termed activator 1 140 kDa subunit, or A1 140 kDa subunit, or activator 1 large subunit, or activator 1 subunit 1, or replication factor C 140 kDa subunit, or RF-C 140 kDa subunit, or RFC140, is the large subunit of replication factor C (RFC), which is a heteropentameric protein essential for DNA replication and repair. RFC1 can bind single- or double-stranded DNA. It could play a role in DNA transcription regulation as well as DNA replication and/or repair. The Trp-X-X-X-Cys/Ser signature motif of the BRCT family is not conserved in this family.
Pssm-ID: 349383 [Multi-domain] Cd Length: 79 Bit Score: 49.90 E-value: 3.09e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 225 LYGKNVVFTGKLQRFLRKDAAQIVCNIGGYCENNVTKKTNFLVIGslegnplvEGGKSSKMKRARELilsgqDLQVLSET 304
Cdd:cd17752 6 LEGLTFVITGVLESLEREEAEDLIKRYGGKVTGSVSKKTSYLVVG--------RDAGPSKLEKAKEL-----GTKIIDED 72
|
....*..
gi 2701625488 305 VFYDMIS 311
Cdd:cd17752 73 GLFDLIR 79
|
|
| Orn |
cd06135 |
DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Oligoribonuclease ... |
23-140 |
1.89e-07 |
|
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: 50.24 E-value: 1.89e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 23 LDLETTGLDPHYDDIIEVACLKFAG--GKQVDSFRSYIQPrpfqdDDGQLHFVDDFITDL---TGITDDMLKDAPRFASI 97
Cdd:cd06135 4 IDLEMTGLDPEKDRILEIACIITDGdlNIIAEGPELVIHQ-----PDEVLDGMDEWCTEMhtkSGLTERVRASTVTLAQA 78
|
90 100 110 120
....*....|....*....|....*....|....*....|....*....
gi 2701625488 98 APELFKYL------GNSVLVGHNVNFDINFLyDNFMAALRKPLHNNFVD 140
Cdd:cd06135 79 EAELLEFIkkyvpkGKSPLAGNSVHQDRRFL-DKYMPELEEYLHYRILD 126
|
|
| ligA |
PRK07956 |
NAD-dependent DNA ligase LigA; Validated |
221-310 |
2.32e-07 |
|
NAD-dependent DNA ligase LigA; Validated
Pssm-ID: 236137 [Multi-domain] Cd Length: 665 Bit Score: 52.05 E-value: 2.32e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 221 PSHPLYGKNVVFTGKLQRFLRKDAAQIVCNIGGYCENNVTKKTNFLVIGSLEGnplveggksSKMKRARELilsgqDLQV 300
Cdd:PRK07956 587 EEVDLAGKTVVLTGTLEQLSRDEAKEKLEALGAKVSGSVSKKTDLVVAGEAAG---------SKLAKAQEL-----GIEV 652
|
90
....*....|
gi 2701625488 301 LSETVFYDMI 310
Cdd:PRK07956 653 LDEEEFLRLL 662
|
|
| REX4_like |
cd06144 |
DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product ... |
73-180 |
4.42e-06 |
|
DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins; This subfamily is composed of RNA exonuclease 4 (REX4 or Rex4p), XPMC2, Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20), and similar proteins. REX4 is involved in pre-rRNA processing. It controls the ratio between the two forms of 5.8S rRNA in yeast. XPMC2 is a Xenopus gene which was identified through its ability to correct a mitotic defect in fission yeast. The human homolog of XPMC2 (hPMC2) may be involved in angiotensin II-induced adrenal cell cycle progression and cell proliferation. ISG20 is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. These proteins are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherchia coli RNase T.
Pssm-ID: 99847 Cd Length: 152 Bit Score: 45.97 E-value: 4.42e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 73 VDDFITDLTGITDDMLKDAPRFASIAPELFKYLGNSVLVGHNVNFDinflydnfMAALRkpLHNNFVDT---------MR 143
Cdd:cd06144 43 VTDYRTAVSGIRPEHLKDAPDFEEVQKKVAELLKGRILVGHALKND--------LKVLK--LDHPKKLIrdtskykplRK 112
|
90 100 110 120
....*....|....*....|....*....|....*....|
gi 2701625488 144 IARIVMPdlphhRLKDLCKAF---SIDTDLHRADSDCMAT 180
Cdd:cd06144 113 TAKGKSP-----SLKKLAKQLlglDIQEGEHSSVEDARAA 147
|
|
| DEDDh_RNase |
cd06137 |
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX) ... |
21-180 |
1.06e-05 |
|
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins; 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. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. 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. REX proteins are required for the processing and maturation of many RNA species, and ISG20 is an interferon-induced antiviral exonuclease with a strong preference for single-stranded RNA.
Pssm-ID: 99840 Cd Length: 161 Bit Score: 44.96 E-value: 1.06e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 21 IVLDLETTGLDPHYDDIIEVACLKFAGGKQVdsFRSYIQPrpfqddDGQlhfVDDFITDLTGITDDMLKDAPRfASIAP- 99
Cdd:cd06137 1 VALDCEMVGLADGDSEVVRISAVDVLTGEVL--IDSLVRP------SVR---VTDWRTRFSGVTPADLEEAAK-AGKTIf 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 100 -------ELFKYL-GNSVLVGHNVNFDINFLydnfmaalrKPLHNNFVDT---MRIARIVMPDLPHHRLKDLCKAF---S 165
Cdd:cd06137 69 gweaaraALWKFIdPDTILVGHSLQNDLDAL---------RMIHTRVVDTailTREAVKGPLAKRQWSLRTLCRDFlglK 139
|
170
....*....|....*..
gi 2701625488 166 I--DTDLHRADSDCMAT 180
Cdd:cd06137 140 IqgGGEGHDSLEDALAA 156
|
|
| DNA_polA_I_Ecoli_like_exo |
cd06139 |
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial ... |
17-162 |
1.45e-05 |
|
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases; Escherichia coli-like Polymerase I (Pol I), a subgroup of family-A DNA polymerases, contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase domain. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D 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 3'-5' exonuclease domain of DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. E. coli DNA Pol I is involved in genome replication but is not the main replicating enzyme. It is also implicated in DNA repair.
Pssm-ID: 176651 [Multi-domain] Cd Length: 193 Bit Score: 44.82 E-value: 1.45e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 17 PDSYIVLDLETTGLDPHYDDIIevaCLKFAGGKQvDSFrsYIqPRPFQDDDGQLhfvddfitdltgITDDMLKdaprfas 96
Cdd:cd06139 4 KAKVFAFDTETTSLDPMQAELV---GISFAVEPG-EAY--YI-PLGHDYGGEQL------------PREEVLA------- 57
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2701625488 97 iapELFKYLGNSVL--VGHNVNFDINFLYDNFMaALRKPLHnnfvDTMRIARIVMPDLPHHRLKDLCK 162
Cdd:cd06139 58 ---ALKPLLEDPSIkkVGQNLKFDLHVLANHGI-ELRGPAF----DTMLASYLLNPGRRRHGLDDLAE 117
|
|
| REX1_like |
cd06145 |
DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This ... |
75-164 |
1.56e-05 |
|
DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T.
Pssm-ID: 99848 Cd Length: 150 Bit Score: 44.01 E-value: 1.56e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 75 DFITDLTGITDDMLKDAP-RFASIAPELFKYLG-NSVLVGHNVNFDINflydnfmaALrKPLHNNFVDTMRIARIVMPDL 152
Cdd:cd06145 42 DYNTRFSGITEEMLENVTtTLEDVQKKLLSLISpDTILVGHSLENDLK--------AL-KLIHPRVIDTAILFPHPRGPP 112
|
90
....*....|..
gi 2701625488 153 PHHRLKDLCKAF 164
Cdd:cd06145 113 YKPSLKNLAKKY 124
|
|
| BRCT_PARP1 |
cd17747 |
BRCT domain of poly [ADP-ribose] polymerase 1 (PARP-1) and similar proteins; PARP-1 (EC 2.4.2. ... |
225-311 |
3.76e-05 |
|
BRCT domain of poly [ADP-ribose] polymerase 1 (PARP-1) and similar proteins; PARP-1 (EC 2.4.2.30), also termed ADP-ribosyltransferase diphtheria toxin-like 1 (ARTD1), or NAD(+) ADP-ribosyltransferase 1 (ADPRT 1), or poly[ADP-ribose] synthase 1, is involved in the base excision repair (BER) pathway, by catalyzing the poly(ADP-ribosyl)ation of a limited number of acceptor proteins involved in chromatin architecture and in DNA metabolism.
Pssm-ID: 349378 [Multi-domain] Cd Length: 76 Bit Score: 41.36 E-value: 3.76e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 225 LYGKNVVFTGKL---QRFLRKDaaqiVCNIGGYCENNVTKKTNFLVIGSLEgnplVEgGKSSKMKRARELilsgqDLQVL 301
Cdd:cd17747 1 LTGMKFALIGKLsksKDELKKL----IEKLGGKVASKVTKKVTLCISTKAE----VE-KMSKKMKEAKEA-----GVPVV 66
|
90
....*....|
gi 2701625488 302 SETVFYDMIS 311
Cdd:cd17747 67 SEDFLEDCIK 76
|
|
| UvrD_C |
pfam13361 |
UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety ... |
21-76 |
7.47e-05 |
|
UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety of helicase enzymes. This domain has a AAA-like structural fold.
Pssm-ID: 433145 [Multi-domain] Cd Length: 377 Bit Score: 43.93 E-value: 7.47e-05
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*...
gi 2701625488 21 IVLDLETTGLDPHYDDIIEVACLKFAGGKQV-DSFRSYIQP-RPFQDDDGQLHFVDDF 76
Cdd:pfam13361 189 VVFDVETTGLDTTEDEIIQIAAIKLNKKGVViESFERFLRLkKPVGDSLQVHGFSDEF 246
|
|
| PRK05359 |
PRK05359 |
oligoribonuclease; Provisional |
21-43 |
2.10e-04 |
|
oligoribonuclease; Provisional
Pssm-ID: 235429 Cd Length: 181 Bit Score: 41.29 E-value: 2.10e-04
|
| Orn |
COG1949 |
Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification]; |
23-43 |
8.42e-04 |
|
Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification];
Pssm-ID: 441552 Cd Length: 177 Bit Score: 39.71 E-value: 8.42e-04
|
| BRCT |
smart00292 |
breast cancer carboxy-terminal domain; |
222-310 |
5.47e-03 |
|
breast cancer carboxy-terminal domain;
Pssm-ID: 214602 [Multi-domain] Cd Length: 78 Bit Score: 35.43 E-value: 5.47e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 222 SHPLYGKNVVFTGKLQRFLRKDAAQIVCNIGGYCENNVTKKTNFLVIGSlegnplVEGGKSSKMKRARELilsgqDLQVL 301
Cdd:smart00292 1 PKLFKGKTFYITGSFDKEERDELKELIEALGGKVTSSLSSKTTTHVIVG------SPEGGKLELLKAIAL-----GIPIV 69
|
....*....
gi 2701625488 302 SETVFYDMI 310
Cdd:smart00292 70 KEEWLLDCL 78
|
|
| ExoI_N |
cd06138 |
N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar ... |
24-184 |
7.66e-03 |
|
N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins; This subfamily is composed of the N-terminal domain of Escherichia coli exonuclease I (ExoI) and similar proteins. ExoI is a monomeric enzyme that hydrolyzes single stranded DNA in the 3' to 5' direction. It plays a role in DNA recombination and repair. It primarily functions in repairing frameshift mutations. The N-terminal domain of ExoI is a DEDDh-type DnaQ-like 3'-5 exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The ExoI structure is unique among DnaQ family enzymes in that there is a large distance between the two metal ions required for catalysis and the catalytic histidine is oriented away from the active site.
Pssm-ID: 99841 [Multi-domain] Cd Length: 183 Bit Score: 36.86 E-value: 7.66e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 24 DLETTGLDPHYDDIIEVACL----KFaggKQVDSFRSYIQPRPfqdddgqlhfvdDFITD-----LTGIT-DDMLKDAP- 92
Cdd:cd06138 4 DYETFGLNPSFDQILQFAAIrtdeNF---NEIEPFNIFCRLPP------------DVLPSpealiVTGITpQQLLKEGLs 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2701625488 93 --RFASIAPELFKyLGNSVLVGHN-VNFDINFLYDNFMAALRKP-----LHNNF----VDTMRIARIVMPD--------- 151
Cdd:cd06138 69 eyEFIAKIHRLFN-TPGTCIVGYNnIRFDDEFLRFAFYRNLYDPytwewKNGNSrwdlLDVVRAYYALRPDgivwpkndd 147
|
170 180 190
....*....|....*....|....*....|....*
gi 2701625488 152 -LPHHRLKDLCKAFSID-TDLHRADSDCMATQKIL 184
Cdd:cd06138 148 gKPSFKLEDLAQANGIEhSNAHDALSDVEATIALA 182
|
|
| |
