NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2129476939|ref|XP_044836899|]
View 

ERI1 exoribonuclease 2-like isoform X1 [Mauremys mutica]

Protein Classification

ERI1 exoribonuclease 2( domain architecture ID 10150091)

ERI1 exoribonuclease 2 is a 3'-5' exonuclease family protein containing a GRF zinc finger; and may catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction

CATH:  3.30.420.10
EC:  3.1.-.-
Gene Ontology:  GO:0008408|GO:0003676|GO:0008270
PubMed:  11988770|11222749|17210253|12665246
SCOP:  4000547

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
ERI-1_3'hExo_like cd06133
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ...
 38-231 6.86e-82

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: 257.15  E-value: 6.86e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129476939  38 LIIIDFESTCWKDGKR-HYSQEIIEFPAVLLNTSTGEIESEFHMYVQPQEHPILSEFCTELTGIKQNQVDEGVPLNICLS 116
Cdd:cd06133     1 YLVIDFEATCWEGNSKpDYPNEIIEIGAVLVDVKTKEIIDTFSSYVKPVINPKLSDFCTELTGITQEDVDNAPSFPEVLK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129476939 117 QFSKWIQKIQKekkiifnsdvsshsvseaksSTFVTWSDWDLGVCLQYECKRKQLRKPDILNSWIDLRATYKLFY-TRKP 195
Cdd:cd06133    81 EFLEWLGKNGK--------------------YAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYgLKKR 140

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 2129476939 196 KGLNGALQDLGIEFAGREHSGLDDSRNTARLAWRMI 231
Cdd:cd06133   141 TGLSKALEYLGLEFEGRHHRGLDDARNIARILKRLL 176
zf-GRF pfam06839
GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding ...
 605-650 1.67e-14

GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to pfam01396.


:

Pssm-ID: 462017  Cd Length: 45  Bit Score: 67.81  E-value: 1.67e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 2129476939 605 PLCNCGRRAKRLNVSSAGPNHGKVFYSCPVgkheGKKRGCGYFKWE 650
Cdd:pfam06839   1 PLCPCGQRAVLLTVRKTGPNPGRQFYKCPV----GREKQCGFFQWA 42
 
Name Accession Description Interval E-value
ERI-1_3'hExo_like cd06133
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ...
 38-231 6.86e-82

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: 257.15  E-value: 6.86e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129476939  38 LIIIDFESTCWKDGKR-HYSQEIIEFPAVLLNTSTGEIESEFHMYVQPQEHPILSEFCTELTGIKQNQVDEGVPLNICLS 116
Cdd:cd06133     1 YLVIDFEATCWEGNSKpDYPNEIIEIGAVLVDVKTKEIIDTFSSYVKPVINPKLSDFCTELTGITQEDVDNAPSFPEVLK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129476939 117 QFSKWIQKIQKekkiifnsdvsshsvseaksSTFVTWSDWDLGVCLQYECKRKQLRKPDILNSWIDLRATYKLFY-TRKP 195
Cdd:cd06133    81 EFLEWLGKNGK--------------------YAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYgLKKR 140

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 2129476939 196 KGLNGALQDLGIEFAGREHSGLDDSRNTARLAWRMI 231
Cdd:cd06133   141 TGLSKALEYLGLEFEGRHHRGLDDARNIARILKRLL 176
KapD COG5018
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ...
 36-234 6.32e-52

3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction mechanisms];


Pssm-ID: 444042 [Multi-domain]  Cd Length: 181  Bit Score: 177.74  E-value: 6.32e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129476939  36 DYLIIIDFESTCW-KDGKRHYSQEIIEFPAVLLNtSTGEIESEFHMYVQPQEHPILSEFCTELTGIKQNQVDEGVPLNIC 114
Cdd:COG5018     2 MKYLVIDLEATCWdGKPPPGFPMEIIEIGAVKVD-ENGEIIDEFSSFVKPVRRPKLSPFCTELTGITQEDVDSAPSFAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129476939 115 LSQFSKWIqkiqkekkiifnsdvsshsvsEAKSSTFVTWSDWDLGVcLQYECKRKQLrKPDILNSWIDLRATYKLFY-TR 193
Cdd:COG5018    81 IEDFKKWI---------------------GSEDYILCSWGDYDRKQ-LERNCRFHGV-PYPFGDRHINLKKLFALYFgLK 137

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2129476939 194 KPKGLNGALQDLGIEFAGREHSGLDDSRNTARLAWRMICDG 234
Cdd:COG5018   138 KRIGLKKALELLGLEFEGTHHRALDDARNTAKLFKKILGDK 178
PTZ00315 PTZ00315
2'-phosphotransferase; Provisional
 33-310 6.19e-29

2'-phosphotransferase; Provisional


Pssm-ID: 240356 [Multi-domain]  Cd Length: 582  Bit Score: 122.31  E-value: 6.19e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129476939  33 QLFDYLIIIDFESTCWKDgKRHYSQEIIEFPAVLLNTSTGEIESEFHMYVQPQEHPILSEFCTELTGIKQNQVD--EGVP 110
Cdd:PTZ00315   53 QPFDAYVVLDFEATCEAD-RRIEDAEVIEFPMVLVDARTATPVAEFQRYVRPVKNPVLSRFCTELTGITQSMVSraDPFP 131

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129476939 111 LNICLS-QFskwiqkiqkekkiifnsdVSSHSVSEA---KSSTFVTWSDWDLGVCLQYECK-RKQLRKPDILNSWIDLRA 185
Cdd:PTZ00315  132 VVYCEAlQF------------------LAEAGLGDApplRSYCVVTCGDWDLKTMLPSQMRvSGQQGTPLSFQRWCNLKK 193

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129476939 186 TYKLFYTRK-------------PKGLNGALQDLGIEFAGREHSGLDDSRNTARLAWRMICDGCVMKITRSLDKVQPKKNS 252
Cdd:PTZ00315  194 YMSQLGFGNgsgcgggatpplgPSDMPDMLQMLGLPLQGRHHSGIDDCRNIAAVLCELLRRGLVIDPTFDTAPFRRWHAP 273

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2129476939 253 VSRSLNVnpTEENPLGSDDGAEtsdkdrICNSSCPAENEHNKLDKMDINSSVKGKDQQ 310
Cdd:PTZ00315  274 TEASLPA--LDALPSTLADGAA------QHSRDCREPGRRHARTEGDARASDTVNNQQ 323
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 39-226 1.05e-28

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: 112.44  E-value: 1.05e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129476939  39 IIIDFESTCWKDGKrhysQEIIEFPAVLLNTSTGEIESEFHMYVQPQEHPILSEFCTELTGIKQNQVDEGVPLNICLSQF 118
Cdd:pfam00929   1 VVIDLETTGLDPEK----DEIIEIAAVVIDGGENEIGETFHTYVKPTRLPKLTDECTKFTGITQAMLDNKPSFEEVLEEF 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129476939 119 SKWIQKIQKEKKiifnsdvssHSVseaksSTFVTWSDWDLGVCLQYECKrkqlRKPDILNSWIDLRATYKLFYTRkpkGL 198
Cdd:pfam00929  77 LEFLRKGNLLVA---------HNA-----SFDVGFLRYDDKRFLKKPMP----KLNPVIDTLILDKATYKELPGR---SL 135

                         170       180
                  ....*....|....*....|....*...
gi 2129476939 199 NGALQDLGIEFAGREHSGLDDSRNTARL 226
Cdd:pfam00929 136 DALAEKLGLEHIGRAHRALDDARATAKL 163
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 37-226 2.10e-24

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 100.45  E-value: 2.10e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129476939   37 YLIIIDFESTCWKDGKrhysQEIIEFPAVllNTSTGEIESEFHMYVQPQEHpiLSEFCTELTGIKQNQVDEGVPLNICLS 116
Cdd:smart00479   1 TLVVIDCETTGLDPGK----DEIIEIAAV--DVDGGEIIEVFDTYVKPDRP--ITDYATEIHGITPEMLDDAPTFEEVLE 72

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129476939  117 QFSKWIQKiqkEKKIIFNSdvsshsvseaksstfvtwSDWDLGVcLQYECKRKQLRKPdILNSWIDLRATYKLFYTRKPK 196
Cdd:smart00479  73 ELLEFLRG---RILVAGNS------------------AHFDLRF-LKLEHPRLGIKQP-PKLPVIDTLKLARATNPGLPK 129

                          170       180       190
                   ....*....|....*....|....*....|.
gi 2129476939  197 -GLNGALQDLGIEFAGREHSGLDDSRNTARL 226
Cdd:smart00479 130 ySLKKLAKRLLLEVIQRAHRALDDARATAKL 160
zf-GRF pfam06839
GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding ...
 605-650 1.67e-14

GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to pfam01396.


Pssm-ID: 462017  Cd Length: 45  Bit Score: 67.81  E-value: 1.67e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 2129476939 605 PLCNCGRRAKRLNVSSAGPNHGKVFYSCPVgkheGKKRGCGYFKWE 650
Cdd:pfam06839   1 PLCPCGQRAVLLTVRKTGPNPGRQFYKCPV----GREKQCGFFQWA 42
 
Name Accession Description Interval E-value
ERI-1_3'hExo_like cd06133
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ...
 38-231 6.86e-82

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: 257.15  E-value: 6.86e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129476939  38 LIIIDFESTCWKDGKR-HYSQEIIEFPAVLLNTSTGEIESEFHMYVQPQEHPILSEFCTELTGIKQNQVDEGVPLNICLS 116
Cdd:cd06133     1 YLVIDFEATCWEGNSKpDYPNEIIEIGAVLVDVKTKEIIDTFSSYVKPVINPKLSDFCTELTGITQEDVDNAPSFPEVLK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129476939 117 QFSKWIQKIQKekkiifnsdvsshsvseaksSTFVTWSDWDLGVCLQYECKRKQLRKPDILNSWIDLRATYKLFY-TRKP 195
Cdd:cd06133    81 EFLEWLGKNGK--------------------YAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYgLKKR 140

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 2129476939 196 KGLNGALQDLGIEFAGREHSGLDDSRNTARLAWRMI 231
Cdd:cd06133   141 TGLSKALEYLGLEFEGRHHRGLDDARNIARILKRLL 176
KapD COG5018
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ...
 36-234 6.32e-52

3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction mechanisms];


Pssm-ID: 444042 [Multi-domain]  Cd Length: 181  Bit Score: 177.74  E-value: 6.32e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129476939  36 DYLIIIDFESTCW-KDGKRHYSQEIIEFPAVLLNtSTGEIESEFHMYVQPQEHPILSEFCTELTGIKQNQVDEGVPLNIC 114
Cdd:COG5018     2 MKYLVIDLEATCWdGKPPPGFPMEIIEIGAVKVD-ENGEIIDEFSSFVKPVRRPKLSPFCTELTGITQEDVDSAPSFAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129476939 115 LSQFSKWIqkiqkekkiifnsdvsshsvsEAKSSTFVTWSDWDLGVcLQYECKRKQLrKPDILNSWIDLRATYKLFY-TR 193
Cdd:COG5018    81 IEDFKKWI---------------------GSEDYILCSWGDYDRKQ-LERNCRFHGV-PYPFGDRHINLKKLFALYFgLK 137

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2129476939 194 KPKGLNGALQDLGIEFAGREHSGLDDSRNTARLAWRMICDG 234
Cdd:COG5018   138 KRIGLKKALELLGLEFEGTHHRALDDARNTAKLFKKILGDK 178
PTZ00315 PTZ00315
2'-phosphotransferase; Provisional
 33-310 6.19e-29

2'-phosphotransferase; Provisional


Pssm-ID: 240356 [Multi-domain]  Cd Length: 582  Bit Score: 122.31  E-value: 6.19e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129476939  33 QLFDYLIIIDFESTCWKDgKRHYSQEIIEFPAVLLNTSTGEIESEFHMYVQPQEHPILSEFCTELTGIKQNQVD--EGVP 110
Cdd:PTZ00315   53 QPFDAYVVLDFEATCEAD-RRIEDAEVIEFPMVLVDARTATPVAEFQRYVRPVKNPVLSRFCTELTGITQSMVSraDPFP 131

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129476939 111 LNICLS-QFskwiqkiqkekkiifnsdVSSHSVSEA---KSSTFVTWSDWDLGVCLQYECK-RKQLRKPDILNSWIDLRA 185
Cdd:PTZ00315  132 VVYCEAlQF------------------LAEAGLGDApplRSYCVVTCGDWDLKTMLPSQMRvSGQQGTPLSFQRWCNLKK 193

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129476939 186 TYKLFYTRK-------------PKGLNGALQDLGIEFAGREHSGLDDSRNTARLAWRMICDGCVMKITRSLDKVQPKKNS 252
Cdd:PTZ00315  194 YMSQLGFGNgsgcgggatpplgPSDMPDMLQMLGLPLQGRHHSGIDDCRNIAAVLCELLRRGLVIDPTFDTAPFRRWHAP 273

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2129476939 253 VSRSLNVnpTEENPLGSDDGAEtsdkdrICNSSCPAENEHNKLDKMDINSSVKGKDQQ 310
Cdd:PTZ00315  274 TEASLPA--LDALPSTLADGAA------QHSRDCREPGRRHARTEGDARASDTVNNQQ 323
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 39-226 1.05e-28

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: 112.44  E-value: 1.05e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129476939  39 IIIDFESTCWKDGKrhysQEIIEFPAVLLNTSTGEIESEFHMYVQPQEHPILSEFCTELTGIKQNQVDEGVPLNICLSQF 118
Cdd:pfam00929   1 VVIDLETTGLDPEK----DEIIEIAAVVIDGGENEIGETFHTYVKPTRLPKLTDECTKFTGITQAMLDNKPSFEEVLEEF 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129476939 119 SKWIQKIQKEKKiifnsdvssHSVseaksSTFVTWSDWDLGVCLQYECKrkqlRKPDILNSWIDLRATYKLFYTRkpkGL 198
Cdd:pfam00929  77 LEFLRKGNLLVA---------HNA-----SFDVGFLRYDDKRFLKKPMP----KLNPVIDTLILDKATYKELPGR---SL 135

                         170       180
                  ....*....|....*....|....*...
gi 2129476939 199 NGALQDLGIEFAGREHSGLDDSRNTARL 226
Cdd:pfam00929 136 DALAEKLGLEHIGRAHRALDDARATAKL 163
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 37-226 2.10e-24

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 100.45  E-value: 2.10e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129476939   37 YLIIIDFESTCWKDGKrhysQEIIEFPAVllNTSTGEIESEFHMYVQPQEHpiLSEFCTELTGIKQNQVDEGVPLNICLS 116
Cdd:smart00479   1 TLVVIDCETTGLDPGK----DEIIEIAAV--DVDGGEIIEVFDTYVKPDRP--ITDYATEIHGITPEMLDDAPTFEEVLE 72

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129476939  117 QFSKWIQKiqkEKKIIFNSdvsshsvseaksstfvtwSDWDLGVcLQYECKRKQLRKPdILNSWIDLRATYKLFYTRKPK 196
Cdd:smart00479  73 ELLEFLRG---RILVAGNS------------------AHFDLRF-LKLEHPRLGIKQP-PKLPVIDTLKLARATNPGLPK 129

                          170       180       190
                   ....*....|....*....|....*....|.
gi 2129476939  197 -GLNGALQDLGIEFAGREHSGLDDSRNTARL 226
Cdd:smart00479 130 ySLKKLAKRLLLEVIQRAHRALDDARATAKL 160
PRK07748 PRK07748
3'-5' exonuclease KapD;
38-234 5.99e-22

3'-5' exonuclease KapD;


Pssm-ID: 236087  Cd Length: 207  Bit Score: 94.37  E-value: 5.99e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129476939  38 LIIIDFESTCwKDGKRH---YSQEIIEFPAVllNTSTGEIESEFHMYVQPQEHPILSEFCTELTGIKQNQVDEGVplnic 114
Cdd:PRK07748    6 FLFLDFEFTM-PQHKKKpkgFFPEIIEVGLV--SVVGCEVEDTFSSYVKPKTFPSLTERCKSFLGITQEDVDKGI----- 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129476939 115 lsQFSKWIQKIQKekkiifnsdvsshsVSEAKSSTFVTWSDWDLGVcLQYECKRKQLRKPdILNSWIDLRATYKLFYT-R 193
Cdd:PRK07748   78 --SFEELVEKLAE--------------YDKRCKPTIVTWGNMDMKV-LKHNCEKAGVPFP-FKGQCRDLSLEYKKFFGeR 139

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2129476939 194 KPKGLNGALQDLGIEFAGREHSGLDDSRNTARLAWRMICDG 234
Cdd:PRK07748  140 NQTGLWKAIEEYGKEGTGKHHCALDDAMTTYNIFKLVEKDK 180
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 38-231 1.70e-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: 74.44  E-value: 1.70e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129476939  38 LIIIDFESTcwkdGKRHYSQEIIEFPAVLLNTstGEIESEFHMYVQPQEHpiLSEFCTELTGIKQNQVDEGVPLNICLSQ 117
Cdd:COG0847     2 FVVLDTETT----GLDPAKDRIIEIGAVKVDD--GRIVETFHTLVNPERP--IPPEATAIHGITDEDVADAPPFAEVLPE 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129476939 118 FSKWIQkiqkekkiifNSDVSSHSVSeaksstFvtwsdwDLGVcLQYECKRKQLRKPDilNSWIDLRATYKLFYTRKPK- 196
Cdd:COG0847    74 LLEFLG----------GAVLVAHNAA------F------DLGF-LNAELRRAGLPLPP--FPVLDTLRLARRLLPGLPSy 128

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 2129476939 197 GLNGALQDLGIEFAGReHSGLDDSRNTARLAWRMI 231
Cdd:COG0847   129 SLDALCERLGIPFDER-HRALADAEATAELFLALL 162
zf-GRF pfam06839
GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding ...
 605-650 1.67e-14

GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to pfam01396.


Pssm-ID: 462017  Cd Length: 45  Bit Score: 67.81  E-value: 1.67e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 2129476939 605 PLCNCGRRAKRLNVSSAGPNHGKVFYSCPVgkheGKKRGCGYFKWE 650
Cdd:pfam06839   1 PLCPCGQRAVLLTVRKTGPNPGRQFYKCPV----GREKQCGFFQWA 42
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 39-226 1.39e-13

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: 68.87  E-value: 1.39e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129476939  39 IIIDFESTcwkdGKRHYSQEIIEFPAVLLNTStGEIESEFHMYVQPQEhPIlSEFCTELTGIKQNQVDEGVPLNICLSQF 118
Cdd:cd06127     1 VVFDTETT----GLDPKKDRIIEIGAVKVDGG-IEIVERFETLVNPGR-PI-PPEATAIHGITDEMLADAPPFEEVLPEF 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129476939 119 SKWIqkiqkekkiifnsdvsshsvseaKSSTFVTW-SDWDLGVcLQYECKRKQLRKPDilNSWIDLRATYKLFYTRKPKG 197
Cdd:cd06127    74 LEFL-----------------------GGRVLVAHnASFDLRF-LNRELRRLGGPPLP--NPWIDTLRLARRLLPGLRSH 127

                         170       180       190
                  ....*....|....*....|....*....|.
gi 2129476939 198 LNGAL--QDLGIEFAGReHSGLDDSRNTARL 226
Cdd:cd06127   128 RLGLLlaERYGIPLEGA-HRALADALATAEL 157
polC PRK00448
DNA polymerase III PolC; Validated
 58-231 1.21e-11

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 68.33  E-value: 1.21e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129476939   58 EIIEFPAVLLNTstGEIESEFHMYVQPQEHpiLSEFCTELTGIKQNQVDEGVPLNICLSQFSKWIQKiqkekkiifnsdv 137
Cdd:PRK00448   437 EIIEIGAVKIKN--GEIIDKFEFFIKPGHP--LSAFTTELTGITDDMVKDAPSIEEVLPKFKEFCGD------------- 499

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129476939  138 sshSVSEAKSSTFvtwsdwDLGvCLQYECKRKQLRKPDilNSWID-LRATYKLFYTRKPKGLNGALQDLGIEFAgREHSG 216
Cdd:PRK00448   500 ---SILVAHNASF------DVG-FINTNYEKLGLEKIK--NPVIDtLELSRFLYPELKSHRLNTLAKKFGVELE-HHHRA 566

                          170
                   ....*....|....*
gi 2129476939  217 LDDSRNTARLAWRMI 231
Cdd:PRK00448   567 DYDAEATAYLLIKFL 581
PRK06722 PRK06722
exonuclease; Provisional
 37-226 1.78e-07

exonuclease; Provisional


Pssm-ID: 180670 [Multi-domain]  Cd Length: 281  Bit Score: 53.13  E-value: 1.78e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129476939  37 YLIIIDFESTcWKDGKRHYSQEIIEFPAVLLNTSTGEIESEFHMYVQPQEHpiLSEFCTELTGIKQNQvdegvplnicLS 116
Cdd:PRK06722    6 HFIVFDIERN-FRPYKSEDPSEIVDIGAVKIEASTMKVIGEFSELVKPGAR--LTRHTTKLTGITKKD----------LI 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129476939 117 QFSKWIQKIQKEKKIIfnsdvsshsvseAKSSTFVTWSDWDLGVcLQYECKRKQLRKPDI-LNSWIDLRA----TYKLFY 191
Cdd:PRK06722   73 GVEKFPQIIEKFIQFI------------GEDSIFVTWGKEDYRF-LSHDCTLHSVECPCMeKERRIDLQKfvfqAYEELF 139

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 2129476939 192 TRKPKgLNGALQDLGIEFAGREHSGLDDSRNTARL 226
Cdd:PRK06722  140 EHTPS-LQSAVEQLGLIWEGKQHRALADAENTANI 173
PRK08074 PRK08074
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 39-111 3.15e-04

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


Pssm-ID: 236148 [Multi-domain]  Cd Length: 928  Bit Score: 44.17  E-value: 3.15e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2129476939  39 IIIDFEST--CWKDGKRhysqeIIEFPAVLLntSTGEIESEFHMYVQPqEHPIlSEFCTELTGIKQNQVdEGVPL 111
Cdd:PRK08074    6 VVVDLETTgnSPKKGDK-----IIQIAAVVV--EDGEILERFSSFVNP-ERPI-PPFITELTGISEEMV-KQAPL 70
DUF730 pfam05325
Protein of unknown function (DUF730); This family consists of several uncharacterized ...
 598-654 7.19e-04

Protein of unknown function (DUF730); This family consists of several uncharacterized Arabidopsis thaliana proteins of unknown function.


Pssm-ID: 114071  Cd Length: 122  Bit Score: 40.13  E-value: 7.19e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2129476939 598 KSDKLTPPLCNCGrrAKRLNVSSAGP-NHGKVFYSCPVGKHEGKKRGCGYFKWEHVLL 654
Cdd:pfam05325  14 RRDKGVPIECDCN--AKVVVATSRDPvTSGKLYFSCPYEISDGPGRGCGFKRWWTVAL 69
PRK07740 PRK07740
hypothetical protein; Provisional
 39-228 2.37e-03

hypothetical protein; Provisional


Pssm-ID: 236085 [Multi-domain]  Cd Length: 244  Bit Score: 40.42  E-value: 2.37e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129476939  39 IIIDFESTCWkdgkrhYSQ---EIIEFPAVllNTSTGEIESE-FHMYVQPqEHPIlSEFCTELTGIKQNQVDEGVPLNIC 114
Cdd:PRK07740   62 VVFDLETTGF------SPQqgdEILSIGAV--KTKGGEVETDtFYSLVKP-KRPI-PEHILELTGITAEDVAFAPPLAEV 131

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129476939 115 LSQFSKWIqkiqkEKKIIfnsdVSSHSVSEAKSSTFVTWsdwdlgvclqyeckrKQLRKPdILNSWIDLRATYKLFYtrk 194
Cdd:PRK07740  132 LHRFYAFI-----GAGVL----VAHHAGHDKAFLRHALW---------------RTYRQP-FTHRLIDTMFLTKLLA--- 183

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 2129476939 195 PKGLNGALQDL----GIEFAGReHSGLDDSRNTARLaW 228
Cdd:PRK07740  184 HERDFPTLDDAlayyGIPIPRR-HHALGDALMTAKL-W 219
PRK06807 PRK06807
3'-5' exonuclease;
30-122 6.82e-03

3'-5' exonuclease;


Pssm-ID: 235864 [Multi-domain]  Cd Length: 313  Bit Score: 39.03  E-value: 6.82e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2129476939  30 KSRQLFDYLIIIDFESTcwkdGKRHYSQEIIEFPAVllNTSTGEIESEFHMYVQPqEHPILSEFcTELTGIKQNQVDEGV 109
Cdd:PRK06807    2 GNISLPLDYVVIDFETT----GFNPYNDKIIQVAAV--KYRNHELVDQFVSYVNP-ERPIPDRI-TSLTGITNYRVSDAP 73

                          90
                  ....*....|...
gi 2129476939 110 PLNICLSQFSKWI 122
Cdd:PRK06807   74 TIEEVLPLFLAFL 86
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH