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Conserved domains on  [gi|157821045|ref|NP_001101050|]
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three prime repair exonuclease 2 [Rattus norvegicus]

Protein Classification

3'-5' exonuclease family protein; 3'-5' exonuclease( domain architecture ID 10150103)

3'-5' exonuclease family protein may cleave nucleotides one at a time from the end (exo) of a polynucleotide chain| 3'-5' exonuclease has a fundamental role in reducing polymerase errors and is involved in proofreading activity

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
TREX1_2 cd06136
DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar ...
 10-204 7.90e-82

DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins; Three prime repair exonuclease (TREX)1 and TREX2 are closely related DEDDh-type DnaQ-like 3'-5' exonucleases. They contain three conserved sequence motifs known as ExoI, II, and III, with a specific Hx(4)D conserved pattern at ExoIII. These motifs contain four conserved acidic residues that participate in coordination of divalent metal ions required for catalysis. Both proteins play a role in the metabolism and clearance of DNA. TREX1 is the major 3'-5' exonuclease activity detected in mammalian cells. Mutations in the human TREX1 gene can cause Aicardi-Goutieres syndrome (AGS), which is characterized by perturbed innate immunity and presents itself as a severe neurological disease. TREX1 degrades ssDNA generated by aberrant replication intermediates to prevent checkpoint activation and autoimmune disease. There are distinct structural differences between TREX1 and TREX2 that point to different biological roles for these proteins. The main difference is the presence of about 70 amino acids at the C-terminus of TREX1. In addition, TREX1 has a nonrepetitive proline-rich region that is not present in the TREX2 protein. Furthermore, TREX2 contains a conserved DNA binding loop positioned adjacent to the active site that has a sequence distinct from the corresponding loop in TREX1. Truncations in the C-terminus of human TREX1 cause autosomal dominant retinal vasculopathy with cerebral leukodystrophy (RVCL), a neurovascular syndrome featuring a progressive loss of visual acuity combined with a variable neurological picture.


:

Pssm-ID: 99839 [Multi-domain]  Cd Length: 177  Bit Score: 242.24  E-value: 7.90e-82
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821045  10 FVFLDLEATGLPNMD-PEIAEISLFAVHRSSLENPERDdsgSLVLPRVLDKLTLCMCPERPFTAKASEITGLSSEGLMnc 88
Cdd:cd06136    1 FVFLDLETTGLPKHNrPEITELCLVAVHRDHLLNTSRD---KPALPRVLDKLSLCFNPGRAISPGASEITGLSNDLLE-- 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821045  89 RKAAFNDAVVRTLQGFLSRQEGPICLVAHNGFDYDFPLLCTELQRLGAHLPRDTVCLDTLPALRGLDRvhshgtraqgrk 168
Cdd:cd06136   76 HKAPFDSDTANLIKLFLRRQPKPICLVAHNGNRFDFPILRSELERLGTKLPDDILCVDSLPAFRELDQ------------ 143

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 157821045 169 sySLASLFHRYFQAEPSAAHSAEGDVNTLLLIFLHR 204
Cdd:cd06136  144 --SLGSLYKRLFGQEPKNSHTAEGDVLALLKCALHK 177
 
Name Accession Description Interval E-value
TREX1_2 cd06136
DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar ...
 10-204 7.90e-82

DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins; Three prime repair exonuclease (TREX)1 and TREX2 are closely related DEDDh-type DnaQ-like 3'-5' exonucleases. They contain three conserved sequence motifs known as ExoI, II, and III, with a specific Hx(4)D conserved pattern at ExoIII. These motifs contain four conserved acidic residues that participate in coordination of divalent metal ions required for catalysis. Both proteins play a role in the metabolism and clearance of DNA. TREX1 is the major 3'-5' exonuclease activity detected in mammalian cells. Mutations in the human TREX1 gene can cause Aicardi-Goutieres syndrome (AGS), which is characterized by perturbed innate immunity and presents itself as a severe neurological disease. TREX1 degrades ssDNA generated by aberrant replication intermediates to prevent checkpoint activation and autoimmune disease. There are distinct structural differences between TREX1 and TREX2 that point to different biological roles for these proteins. The main difference is the presence of about 70 amino acids at the C-terminus of TREX1. In addition, TREX1 has a nonrepetitive proline-rich region that is not present in the TREX2 protein. Furthermore, TREX2 contains a conserved DNA binding loop positioned adjacent to the active site that has a sequence distinct from the corresponding loop in TREX1. Truncations in the C-terminus of human TREX1 cause autosomal dominant retinal vasculopathy with cerebral leukodystrophy (RVCL), a neurovascular syndrome featuring a progressive loss of visual acuity combined with a variable neurological picture.


Pssm-ID: 99839 [Multi-domain]  Cd Length: 177  Bit Score: 242.24  E-value: 7.90e-82
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821045  10 FVFLDLEATGLPNMD-PEIAEISLFAVHRSSLENPERDdsgSLVLPRVLDKLTLCMCPERPFTAKASEITGLSSEGLMnc 88
Cdd:cd06136    1 FVFLDLETTGLPKHNrPEITELCLVAVHRDHLLNTSRD---KPALPRVLDKLSLCFNPGRAISPGASEITGLSNDLLE-- 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821045  89 RKAAFNDAVVRTLQGFLSRQEGPICLVAHNGFDYDFPLLCTELQRLGAHLPRDTVCLDTLPALRGLDRvhshgtraqgrk 168
Cdd:cd06136   76 HKAPFDSDTANLIKLFLRRQPKPICLVAHNGNRFDFPILRSELERLGTKLPDDILCVDSLPAFRELDQ------------ 143

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 157821045 169 sySLASLFHRYFQAEPSAAHSAEGDVNTLLLIFLHR 204
Cdd:cd06136  144 --SLGSLYKRLFGQEPKNSHTAEGDVLALLKCALHK 177
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 9-209 4.79e-31

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 112.39  E-value: 4.79e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821045     9 TFVFLDLEATGLPNMDPEIAEISLFAVHRsslenperddsgslvlPRVLDKLTLCMCPERPFTAKASEITGLSSEGLMNc 88
Cdd:smart00479   1 TLVVIDCETTGLDPGKDEIIEIAAVDVDG----------------GEIIEVFDTYVKPDRPITDYATEIHGITPEMLDD- 63

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821045    89 rKAAFnDAVVRTLQGFLSRQegpiCLVAHNGFDYDFPLLCTELQRLGAHLPRDTVCLDTLPalrgLDRVHSHGtraqgRK 168
Cdd:smart00479  64 -APTF-EEVLEELLEFLRGR----ILVAGNSAHFDLRFLKLEHPRLGIKQPPKLPVIDTLK----LARATNPG-----LP 128

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|.
gi 157821045   169 SYSLASLFHRYFQAEPSAAHSAEGDVNTLLLIFLHRAPELL 209
Cdd:smart00479 129 KYSLKKLAKRLLLEVIQRAHRALDDARATAKLFKKLLERLE 169
PolC COG2176
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ...
 1-208 2.48e-22

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


Pssm-ID: 441779 [Multi-domain]  Cd Length: 181  Bit Score: 89.82  E-value: 2.48e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821045   1 MSEPLRAETFVFLDLEATGL-PNMDpEIAEISLFAVHRSslenperddsgslvlpRVLDKLTLCMCPERPFTAKASEITG 79
Cdd:COG2176    1 MSLDLEDLTYVVFDLETTGLsPKKD-EIIEIGAVKVENG----------------EIVDRFSTLVNPGRPIPPFITELTG 63

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821045  80 LSSEGLMNCRKAafnDAVVRTLQGFLsrqEGPIcLVAHN-GFDYDFplLCTELQRLGAHLPRDtvCLDTLPALRgldRVH 158
Cdd:COG2176   64 ITDEMVADAPPF---EEVLPEFLEFL---GDAV-LVAHNaSFDLGF--LNAALKRLGLPFDNP--VLDTLELAR---RLL 129

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 157821045 159 shgtraQGRKSYSLASLFhRYFQAEPSAAHSAEGDVNT---LLLIFLHRAPEL 208
Cdd:COG2176  130 ------PELKSYKLDTLA-ERLGIPLEDRHRALGDAEAtaeLFLKLLEKLEEK 175
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 11-201 2.11e-08

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: 51.97  E-value: 2.11e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821045   11 VFLDLEATGLPNMDPEIAEISLFAVHRSslENPERDDSGSLVLPRVLDKLtlcmcperpfTAKASEITGLSseGLMNCRK 90
Cdd:pfam00929   1 VVIDLETTGLDPEKDEIIEIAAVVIDGG--ENEIGETFHTYVKPTRLPKL----------TDECTKFTGIT--QAMLDNK 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821045   91 AAFNDAVVRTLQGFLSRQegpiCLVAHN-GFDYDFplLCTELQRLG-AHLPRDTVCLDTLPALRgldRVHshgtraQGRK 168
Cdd:pfam00929  67 PSFEEVLEEFLEFLRKGN----LLVAHNaSFDVGF--LRYDDKRFLkKPMPKLNPVIDTLILDK---ATY------KELP 131

                         170       180       190
                  ....*....|....*....|....*....|...
gi 157821045  169 SYSLASLFHRYFQAEPSAAHSAEGDVNTLLLIF 201
Cdd:pfam00929 132 GRSLDALAEKLGLEHIGRAHRALDDARATAKLF 164
PRK07883 PRK07883
DEDD exonuclease domain-containing protein;
4-193 3.93e-07

DEDD exonuclease domain-containing protein;


Pssm-ID: 236123 [Multi-domain]  Cd Length: 557  Bit Score: 50.30  E-value: 3.93e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821045   4 PLRAETFVFLDLEATGLPNMDPEIAEISLFAVHRSslenperddsgslvlpRVLDKLTLCMCPERPFTAKASEITGLSSE 83
Cdd:PRK07883  11 PLRDVTFVVVDLETTGGSPAGDAITEIGAVKVRGG----------------EVLGEFATLVNPGRPIPPFITVLTGITTA 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821045  84 GLMNCRKAafnDAVvrtLQGFLSRQEGPIcLVAHN-GFDYDFplLCTELQRLGAHLPRDTVcLDTLP-ALRGLDRvhshg 161
Cdd:PRK07883  75 MVAGAPPI---EEV---LPAFLEFARGAV-LVAHNaPFDIGF--LRAAAARCGYPWPGPPV-LCTVRlARRVLPR----- 139

                        170       180       190
                 ....*....|....*....|....*....|..
gi 157821045 162 traQGRKSYSLASLfHRYFQAEPSAAHSAEGD 193
Cdd:PRK07883 140 ---DEAPNVRLSTL-ARLFGATTTPTHRALDD 167
dnaq TIGR00573
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ...
 66-202 6.95e-05

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: 42.44  E-value: 6.95e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821045   66 PERPFTAKASEITGLSSEGLMNcrKAAFNDaVVRTLQGFLSRQEgpicLVAHNG-FDYDFplLCTELQRLGAHLP-RDTV 143
Cdd:TIGR00573  49 PDRPIDPDAIKIHGITDDMLKD--KPDFKE-IAEDFADYIRGAE----LVIHNAsFDVGF--LNYEFSKLYKVEPkTNDV 119

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 157821045  144 C--LDTLPALRGLdrvhshgtraQGRKSYSLASLFHRY-FQAEPSAAHSAEGDVNTLLLIFL 202
Cdd:TIGR00573 120 IdtTDTLQYARPE----------FPGKRNTLDALCKRYeITNSHRALHGALADAFILAKLYL 171
 
Name Accession Description Interval E-value
TREX1_2 cd06136
DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar ...
 10-204 7.90e-82

DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins; Three prime repair exonuclease (TREX)1 and TREX2 are closely related DEDDh-type DnaQ-like 3'-5' exonucleases. They contain three conserved sequence motifs known as ExoI, II, and III, with a specific Hx(4)D conserved pattern at ExoIII. These motifs contain four conserved acidic residues that participate in coordination of divalent metal ions required for catalysis. Both proteins play a role in the metabolism and clearance of DNA. TREX1 is the major 3'-5' exonuclease activity detected in mammalian cells. Mutations in the human TREX1 gene can cause Aicardi-Goutieres syndrome (AGS), which is characterized by perturbed innate immunity and presents itself as a severe neurological disease. TREX1 degrades ssDNA generated by aberrant replication intermediates to prevent checkpoint activation and autoimmune disease. There are distinct structural differences between TREX1 and TREX2 that point to different biological roles for these proteins. The main difference is the presence of about 70 amino acids at the C-terminus of TREX1. In addition, TREX1 has a nonrepetitive proline-rich region that is not present in the TREX2 protein. Furthermore, TREX2 contains a conserved DNA binding loop positioned adjacent to the active site that has a sequence distinct from the corresponding loop in TREX1. Truncations in the C-terminus of human TREX1 cause autosomal dominant retinal vasculopathy with cerebral leukodystrophy (RVCL), a neurovascular syndrome featuring a progressive loss of visual acuity combined with a variable neurological picture.


Pssm-ID: 99839 [Multi-domain]  Cd Length: 177  Bit Score: 242.24  E-value: 7.90e-82
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821045  10 FVFLDLEATGLPNMD-PEIAEISLFAVHRSSLENPERDdsgSLVLPRVLDKLTLCMCPERPFTAKASEITGLSSEGLMnc 88
Cdd:cd06136    1 FVFLDLETTGLPKHNrPEITELCLVAVHRDHLLNTSRD---KPALPRVLDKLSLCFNPGRAISPGASEITGLSNDLLE-- 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821045  89 RKAAFNDAVVRTLQGFLSRQEGPICLVAHNGFDYDFPLLCTELQRLGAHLPRDTVCLDTLPALRGLDRvhshgtraqgrk 168
Cdd:cd06136   76 HKAPFDSDTANLIKLFLRRQPKPICLVAHNGNRFDFPILRSELERLGTKLPDDILCVDSLPAFRELDQ------------ 143

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 157821045 169 sySLASLFHRYFQAEPSAAHSAEGDVNTLLLIFLHR 204
Cdd:cd06136  144 --SLGSLYKRLFGQEPKNSHTAEGDVLALLKCALHK 177
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 9-209 4.79e-31

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 112.39  E-value: 4.79e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821045     9 TFVFLDLEATGLPNMDPEIAEISLFAVHRsslenperddsgslvlPRVLDKLTLCMCPERPFTAKASEITGLSSEGLMNc 88
Cdd:smart00479   1 TLVVIDCETTGLDPGKDEIIEIAAVDVDG----------------GEIIEVFDTYVKPDRPITDYATEIHGITPEMLDD- 63

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821045    89 rKAAFnDAVVRTLQGFLSRQegpiCLVAHNGFDYDFPLLCTELQRLGAHLPRDTVCLDTLPalrgLDRVHSHGtraqgRK 168
Cdd:smart00479  64 -APTF-EEVLEELLEFLRGR----ILVAGNSAHFDLRFLKLEHPRLGIKQPPKLPVIDTLK----LARATNPG-----LP 128

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|.
gi 157821045   169 SYSLASLFHRYFQAEPSAAHSAEGDVNTLLLIFLHRAPELL 209
Cdd:smart00479 129 KYSLKKLAKRLLLEVIQRAHRALDDARATAKLFKKLLERLE 169
PolC COG2176
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ...
 1-208 2.48e-22

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


Pssm-ID: 441779 [Multi-domain]  Cd Length: 181  Bit Score: 89.82  E-value: 2.48e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821045   1 MSEPLRAETFVFLDLEATGL-PNMDpEIAEISLFAVHRSslenperddsgslvlpRVLDKLTLCMCPERPFTAKASEITG 79
Cdd:COG2176    1 MSLDLEDLTYVVFDLETTGLsPKKD-EIIEIGAVKVENG----------------EIVDRFSTLVNPGRPIPPFITELTG 63

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821045  80 LSSEGLMNCRKAafnDAVVRTLQGFLsrqEGPIcLVAHN-GFDYDFplLCTELQRLGAHLPRDtvCLDTLPALRgldRVH 158
Cdd:COG2176   64 ITDEMVADAPPF---EEVLPEFLEFL---GDAV-LVAHNaSFDLGF--LNAALKRLGLPFDNP--VLDTLELAR---RLL 129

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 157821045 159 shgtraQGRKSYSLASLFhRYFQAEPSAAHSAEGDVNT---LLLIFLHRAPEL 208
Cdd:COG2176  130 ------PELKSYKLDTLA-ERLGIPLEDRHRALGDAEAtaeLFLKLLEKLEEK 175
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 11-202 7.95e-17

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: 74.64  E-value: 7.95e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821045  11 VFLDLEATGLPNMDPEIAEISLFAVHRSSlenperddsgslvlpRVLDKLTLCMCPERPFTAKASEITGLSSEGLMNcrK 90
Cdd:cd06127    1 VVFDTETTGLDPKKDRIIEIGAVKVDGGI---------------EIVERFETLVNPGRPIPPEATAIHGITDEMLAD--A 63

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821045  91 AAFNDAvvrtLQGFLSRQEGPIcLVAHNGfDYDFPLLCTELQRLGaHLPRDTVCLDTLPALRGLDRvhshgtraqGRKSY 170
Cdd:cd06127   64 PPFEEV----LPEFLEFLGGRV-LVAHNA-SFDLRFLNRELRRLG-GPPLPNPWIDTLRLARRLLP---------GLRSH 127

                        170       180       190
                 ....*....|....*....|....*....|..
gi 157821045 171 SLASLFHRYFQAEPSAAHSAEGDVNTLLLIFL 202
Cdd:cd06127  128 RLGLLLAERYGIPLEGAHRALADALATAELLL 159
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 10-203 4.38e-15

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 70.21  E-value: 4.38e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821045  10 FVFLDLEATGLPNMDPEIAEISLFAVhrsslenperdDSGslvlpRVLDKLTLCMCPERPFTAKASEITGLSSEGLMNCR 89
Cdd:COG0847    2 FVVLDTETTGLDPAKDRIIEIGAVKV-----------DDG-----RIVETFHTLVNPERPIPPEATAIHGITDEDVADAP 65

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821045  90 KAAfndAVVRTLQGFLSRQEgpicLVAHN-GFDYDFplLCTELQRLGAHLPRDTVcLDTLPALRGLDRvhshgtraqGRK 168
Cdd:COG0847   66 PFA---EVLPELLEFLGGAV----LVAHNaAFDLGF--LNAELRRAGLPLPPFPV-LDTLRLARRLLP---------GLP 126

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 157821045 169 SYSLASLfHRYFQAEPSAAHSAEGDVNTLLLIFLH 203
Cdd:COG0847  127 SYSLDAL-CERLGIPFDERHRALADAEATAELFLA 160
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 11-201 2.11e-08

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: 51.97  E-value: 2.11e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821045   11 VFLDLEATGLPNMDPEIAEISLFAVHRSslENPERDDSGSLVLPRVLDKLtlcmcperpfTAKASEITGLSseGLMNCRK 90
Cdd:pfam00929   1 VVIDLETTGLDPEKDEIIEIAAVVIDGG--ENEIGETFHTYVKPTRLPKL----------TDECTKFTGIT--QAMLDNK 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821045   91 AAFNDAVVRTLQGFLSRQegpiCLVAHN-GFDYDFplLCTELQRLG-AHLPRDTVCLDTLPALRgldRVHshgtraQGRK 168
Cdd:pfam00929  67 PSFEEVLEEFLEFLRKGN----LLVAHNaSFDVGF--LRYDDKRFLkKPMPKLNPVIDTLILDK---ATY------KELP 131

                         170       180       190
                  ....*....|....*....|....*....|...
gi 157821045  169 SYSLASLFHRYFQAEPSAAHSAEGDVNTLLLIF 201
Cdd:pfam00929 132 GRSLDALAEKLGLEHIGRAHRALDDARATAKLF 164
PRK07883 PRK07883
DEDD exonuclease domain-containing protein;
4-193 3.93e-07

DEDD exonuclease domain-containing protein;


Pssm-ID: 236123 [Multi-domain]  Cd Length: 557  Bit Score: 50.30  E-value: 3.93e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821045   4 PLRAETFVFLDLEATGLPNMDPEIAEISLFAVHRSslenperddsgslvlpRVLDKLTLCMCPERPFTAKASEITGLSSE 83
Cdd:PRK07883  11 PLRDVTFVVVDLETTGGSPAGDAITEIGAVKVRGG----------------EVLGEFATLVNPGRPIPPFITVLTGITTA 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821045  84 GLMNCRKAafnDAVvrtLQGFLSRQEGPIcLVAHN-GFDYDFplLCTELQRLGAHLPRDTVcLDTLP-ALRGLDRvhshg 161
Cdd:PRK07883  75 MVAGAPPI---EEV---LPAFLEFARGAV-LVAHNaPFDIGF--LRAAAARCGYPWPGPPV-LCTVRlARRVLPR----- 139

                        170       180       190
                 ....*....|....*....|....*....|..
gi 157821045 162 traQGRKSYSLASLfHRYFQAEPSAAHSAEGD 193
Cdd:PRK07883 140 ---DEAPNVRLSTL-ARLFGATTTPTHRALDD 167
dnaq TIGR00573
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ...
 66-202 6.95e-05

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: 42.44  E-value: 6.95e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821045   66 PERPFTAKASEITGLSSEGLMNcrKAAFNDaVVRTLQGFLSRQEgpicLVAHNG-FDYDFplLCTELQRLGAHLP-RDTV 143
Cdd:TIGR00573  49 PDRPIDPDAIKIHGITDDMLKD--KPDFKE-IAEDFADYIRGAE----LVIHNAsFDVGF--LNYEFSKLYKVEPkTNDV 119

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 157821045  144 C--LDTLPALRGLdrvhshgtraQGRKSYSLASLFHRY-FQAEPSAAHSAEGDVNTLLLIFL 202
Cdd:TIGR00573 120 IdtTDTLQYARPE----------FPGKRNTLDALCKRYeITNSHRALHGALADAFILAKLYL 171
DnaQ_like_exo cd06125
DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease ...
 11-147 1.99e-04

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.


Pssm-ID: 176647 [Multi-domain]  Cd Length: 96  Bit Score: 39.34  E-value: 1.99e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821045  11 VFLDLEATGLPNMDPEIAEISLFAVHrsslenPErddsgslvlprvlDKLTLCmcperpftakaseitglsseglmncrk 90
Cdd:cd06125    1 IAIDTEATGLDGAVHEIIEIALADVN------PE-------------DTAVID--------------------------- 34

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 157821045  91 aafndavvrtLQGFLsRQEGPICLVAHNGfDYDFPLLCTELQRLGAHLPRD-TVCLDT 147
Cdd:cd06125   35 ----------LKDIL-RDKPLAILVGHNG-SFDLPFLNNRCAELGLKYPLLaGSWIDT 80
DNA_pol_III_epsilon_Ecoli_like cd06131
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ...
 11-152 4.46e-04

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: 39.82  E-value: 4.46e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821045  11 VFLDLEATGL-PNMDPEIAEISlfAVHrsslenperddsgslVLPRVLDKLTL-CMC-PERPFTAKASEITGLSSEGLMN 87
Cdd:cd06131    2 IVLDTETTGLdPREGHRIIEIG--CVE---------------LINRRLTGNTFhVYInPERDIPEEAFKVHGITDEFLAD 64

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 157821045  88 crKAAFNDaVVRTLQGFLSRQEgpicLVAHN-GFDYDFplLCTELQRLGAHLPRDTVC--LDTLPALR 152
Cdd:cd06131   65 --KPKFAE-IADEFLDFIRGAE----LVIHNaSFDVGF--LNAELSLLGLGKKIIDFCrvIDTLALAR 123
PRK06309 PRK06309
DNA polymerase III subunit epsilon; Validated
 66-201 1.51e-03

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 180524 [Multi-domain]  Cd Length: 232  Bit Score: 38.64  E-value: 1.51e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821045  66 PERPFTAKASEITGLSSEGLMNCRKaaFNDAvvrtLQGFLSRQEGPICLVAHNGFDYDFPLLCTELQRLGAHLPRdtvcL 145
Cdd:PRK06309  41 PEIPIPAEASKIHGITTDEVADAPK--FPEA----YQKFIEFCGTDNILVAHNNDAFDFPLLRKECRRHGLEPPT----L 110

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 157821045 146 DTLPALRGLDRVHSHGTRaqgrksYSLASLFHRYFQAEpSAAHSAEGDVNTLLLIF 201
Cdd:PRK06309 111 RTIDSLKWAQKYRPDLPK------HNLQYLRQVYGFEE-NQAHRALDDVITLHRVF 159
PRK06807 PRK06807
3'-5' exonuclease;
10-154 5.18e-03

3'-5' exonuclease;


Pssm-ID: 235864 [Multi-domain]  Cd Length: 313  Bit Score: 37.49  E-value: 5.18e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157821045  10 FVFLDLEATGLPNMDPEIAEISlfAVHRSSLEnperddsgslvlprVLDKLTLCMCPERPFTAKASEITGLSSEGLMNCr 89
Cdd:PRK06807  10 YVVIDFETTGFNPYNDKIIQVA--AVKYRNHE--------------LVDQFVSYVNPERPIPDRITSLTGITNYRVSDA- 72

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 157821045  90 kaafnDAVVRTLQGFLSRQeGPICLVAHNG-FDYDFplLCTELQRLGAHLPRDTVcLDTLPALRGL 154
Cdd:PRK06807  73 -----PTIEEVLPLFLAFL-HTNVIVAHNAsFDMRF--LKSNVNMLGLPEPKNKV-IDTVFLAKKY 129
 
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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