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Conserved domains on  [gi|1729154103|ref|XP_030434223|]
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ERI1 exoribonuclease 2 isoform X2 [Gopherus evgoodei]

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

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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 ...
 19-212 4.57e-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: 4.57e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729154103  19 LIIIDFESTCWKDGKR-HYSQEIIEFPAVLLNTSTGEIESEFHMYVQPQEHPILSEFCTELTGIKQNQVDEGVPLNICLS 97
Cdd:cd06133     1 YLVIDFEATCWEGNSKpDYPNEIIEIGAVLVDVKTKEIIDTFSSYVKPVINPKLSDFCTELTGITQEDVDNAPSFPEVLK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729154103  98 QFSKWIQKIQKekkitfnsdvsshsvseaksSTFVTWSDWDLGVCLQYECKRKQLRKPDILNSWIDLRATYKLFY-TRKP 176
Cdd:cd06133    81 EFLEWLGKNGK--------------------YAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYgLKKR 140

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1729154103 177 KGLNGALQDLGIEFAGREHSGLDDSRNTARLAWRMI 212
Cdd:cd06133   141 TGLSKALEYLGLEFEGRHHRGLDDARNIARILKRLL 176
zf-GRF pfam06839
GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding ...
 586-631 2.62e-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: 67.43  E-value: 2.62e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1729154103 586 PLCNCGRRAKRLNVSSAGPNHGKVFYSCPLgkheGKKRGCGYFKWE 631
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 ...
 19-212 4.57e-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: 4.57e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729154103  19 LIIIDFESTCWKDGKR-HYSQEIIEFPAVLLNTSTGEIESEFHMYVQPQEHPILSEFCTELTGIKQNQVDEGVPLNICLS 97
Cdd:cd06133     1 YLVIDFEATCWEGNSKpDYPNEIIEIGAVLVDVKTKEIIDTFSSYVKPVINPKLSDFCTELTGITQEDVDNAPSFPEVLK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729154103  98 QFSKWIQKIQKekkitfnsdvsshsvseaksSTFVTWSDWDLGVCLQYECKRKQLRKPDILNSWIDLRATYKLFY-TRKP 176
Cdd:cd06133    81 EFLEWLGKNGK--------------------YAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYgLKKR 140

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1729154103 177 KGLNGALQDLGIEFAGREHSGLDDSRNTARLAWRMI 212
Cdd:cd06133   141 TGLSKALEYLGLEFEGRHHRGLDDARNIARILKRLL 176
KapD COG5018
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ...
 17-215 5.04e-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: 5.04e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729154103  17 DYLIIIDFESTCW-KDGKRHYSQEIIEFPAVLLNtSTGEIESEFHMYVQPQEHPILSEFCTELTGIKQNQVDEGVPLNIC 95
Cdd:COG5018     2 MKYLVIDLEATCWdGKPPPGFPMEIIEIGAVKVD-ENGEIIDEFSSFVKPVRRPKLSPFCTELTGITQEDVDSAPSFAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729154103  96 LSQFSKWIqkiqkekkitfnsdvsshsvsEAKSSTFVTWSDWDLGVcLQYECKRKQLrKPDILNSWIDLRATYKLFY-TR 174
Cdd:COG5018    81 IEDFKKWI---------------------GSEDYILCSWGDYDRKQ-LERNCRFHGV-PYPFGDRHINLKKLFALYFgLK 137

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1729154103 175 KPKGLNGALQDLGIEFAGREHSGLDDSRNTARLAWRMICDG 215
Cdd:COG5018   138 KRIGLKKALELLGLEFEGTHHRALDDARNTAKLFKKILGDK 178
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 20-207 1.00e-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: 1.00e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729154103  20 IIIDFESTCWKDGKrhysQEIIEFPAVLLNTSTGEIESEFHMYVQPQEHPILSEFCTELTGIKQNQVDEGVPLNICLSQF 99
Cdd:pfam00929   1 VVIDLETTGLDPEK----DEIIEIAAVVIDGGENEIGETFHTYVKPTRLPKLTDECTKFTGITQAMLDNKPSFEEVLEEF 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729154103 100 SKWIQKIQKEKKitfnsdvssHSVseaksSTFVTWSDWDLGVCLQYECKrkqlRKPDILNSWIDLRATYKLFYTRkpkGL 179
Cdd:pfam00929  77 LEFLRKGNLLVA---------HNA-----SFDVGFLRYDDKRFLKKPMP----KLNPVIDTLILDKATYKELPGR---SL 135

                         170       180
                  ....*....|....*....|....*...
gi 1729154103 180 NGALQDLGIEFAGREHSGLDDSRNTARL 207
Cdd:pfam00929 136 DALAEKLGLEHIGRAHRALDDARATAKL 163
PTZ00315 PTZ00315
2'-phosphotransferase; Provisional
 14-254 1.01e-28

2'-phosphotransferase; Provisional


Pssm-ID: 240356 [Multi-domain]  Cd Length: 582  Bit Score: 121.54  E-value: 1.01e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729154103  14 QLFDYLIIIDFESTCWKDgKRHYSQEIIEFPAVLLNTSTGEIESEFHMYVQPQEHPILSEFCTELTGIKQNQVD--EGVP 91
Cdd:PTZ00315   53 QPFDAYVVLDFEATCEAD-RRIEDAEVIEFPMVLVDARTATPVAEFQRYVRPVKNPVLSRFCTELTGITQSMVSraDPFP 131

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729154103  92 LNICLS-QFskwiqkiqkekkitfnsdVSSHSVSEA---KSSTFVTWSDWDLGVCLQYECK-RKQLRKPDILNSWIDLRA 166
Cdd:PTZ00315  132 VVYCEAlQF------------------LAEAGLGDApplRSYCVVTCGDWDLKTMLPSQMRvSGQQGTPLSFQRWCNLKK 193

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729154103 167 TYKLFYTRK-------------PKGLNGALQDLGIEFAGREHSGLDDSRNTARLAWRMICDGCVMKITRSLDKVQPKKNS 233
Cdd:PTZ00315  194 YMSQLGFGNgsgcgggatpplgPSDMPDMLQMLGLPLQGRHHSGIDDCRNIAAVLCELLRRGLVIDPTFDTAPFRRWHAP 273

                         250       260
                  ....*....|....*....|.
gi 1729154103 234 VSRSLNVnpTEENPLGSDDGA 254
Cdd:PTZ00315  274 TEASLPA--LDALPSTLADGA 292
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 18-207 6.33e-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: 98.91  E-value: 6.33e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729154103   18 YLIIIDFESTCWKDGKrhysQEIIEFPAVllNTSTGEIESEFHMYVQPQEHpiLSEFCTELTGIKQNQVDEGVPLNICLS 97
Cdd:smart00479   1 TLVVIDCETTGLDPGK----DEIIEIAAV--DVDGGEIIEVFDTYVKPDRP--ITDYATEIHGITPEMLDDAPTFEEVLE 72

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729154103   98 QFSKWIqkiqkekkitfnsdvsshsvseAKSSTFV-TWSDWDLGVcLQYECKRKQLRKPdILNSWIDLRATYKLFYTRKP 176
Cdd:smart00479  73 ELLEFL----------------------RGRILVAgNSAHFDLRF-LKLEHPRLGIKQP-PKLPVIDTLKLARATNPGLP 128

                          170       180       190
                   ....*....|....*....|....*....|..
gi 1729154103  177 K-GLNGALQDLGIEFAGREHSGLDDSRNTARL 207
Cdd:smart00479 129 KySLKKLAKRLLLEVIQRAHRALDDARATAKL 160
zf-GRF pfam06839
GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding ...
 586-631 2.62e-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: 67.43  E-value: 2.62e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1729154103 586 PLCNCGRRAKRLNVSSAGPNHGKVFYSCPLgkheGKKRGCGYFKWE 631
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 ...
 19-212 4.57e-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: 4.57e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729154103  19 LIIIDFESTCWKDGKR-HYSQEIIEFPAVLLNTSTGEIESEFHMYVQPQEHPILSEFCTELTGIKQNQVDEGVPLNICLS 97
Cdd:cd06133     1 YLVIDFEATCWEGNSKpDYPNEIIEIGAVLVDVKTKEIIDTFSSYVKPVINPKLSDFCTELTGITQEDVDNAPSFPEVLK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729154103  98 QFSKWIQKIQKekkitfnsdvsshsvseaksSTFVTWSDWDLGVCLQYECKRKQLRKPDILNSWIDLRATYKLFY-TRKP 176
Cdd:cd06133    81 EFLEWLGKNGK--------------------YAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYgLKKR 140

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1729154103 177 KGLNGALQDLGIEFAGREHSGLDDSRNTARLAWRMI 212
Cdd:cd06133   141 TGLSKALEYLGLEFEGRHHRGLDDARNIARILKRLL 176
KapD COG5018
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ...
 17-215 5.04e-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: 5.04e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729154103  17 DYLIIIDFESTCW-KDGKRHYSQEIIEFPAVLLNtSTGEIESEFHMYVQPQEHPILSEFCTELTGIKQNQVDEGVPLNIC 95
Cdd:COG5018     2 MKYLVIDLEATCWdGKPPPGFPMEIIEIGAVKVD-ENGEIIDEFSSFVKPVRRPKLSPFCTELTGITQEDVDSAPSFAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729154103  96 LSQFSKWIqkiqkekkitfnsdvsshsvsEAKSSTFVTWSDWDLGVcLQYECKRKQLrKPDILNSWIDLRATYKLFY-TR 174
Cdd:COG5018    81 IEDFKKWI---------------------GSEDYILCSWGDYDRKQ-LERNCRFHGV-PYPFGDRHINLKKLFALYFgLK 137

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1729154103 175 KPKGLNGALQDLGIEFAGREHSGLDDSRNTARLAWRMICDG 215
Cdd:COG5018   138 KRIGLKKALELLGLEFEGTHHRALDDARNTAKLFKKILGDK 178
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 20-207 1.00e-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: 1.00e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729154103  20 IIIDFESTCWKDGKrhysQEIIEFPAVLLNTSTGEIESEFHMYVQPQEHPILSEFCTELTGIKQNQVDEGVPLNICLSQF 99
Cdd:pfam00929   1 VVIDLETTGLDPEK----DEIIEIAAVVIDGGENEIGETFHTYVKPTRLPKLTDECTKFTGITQAMLDNKPSFEEVLEEF 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729154103 100 SKWIQKIQKEKKitfnsdvssHSVseaksSTFVTWSDWDLGVCLQYECKrkqlRKPDILNSWIDLRATYKLFYTRkpkGL 179
Cdd:pfam00929  77 LEFLRKGNLLVA---------HNA-----SFDVGFLRYDDKRFLKKPMP----KLNPVIDTLILDKATYKELPGR---SL 135

                         170       180
                  ....*....|....*....|....*...
gi 1729154103 180 NGALQDLGIEFAGREHSGLDDSRNTARL 207
Cdd:pfam00929 136 DALAEKLGLEHIGRAHRALDDARATAKL 163
PTZ00315 PTZ00315
2'-phosphotransferase; Provisional
 14-254 1.01e-28

2'-phosphotransferase; Provisional


Pssm-ID: 240356 [Multi-domain]  Cd Length: 582  Bit Score: 121.54  E-value: 1.01e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729154103  14 QLFDYLIIIDFESTCWKDgKRHYSQEIIEFPAVLLNTSTGEIESEFHMYVQPQEHPILSEFCTELTGIKQNQVD--EGVP 91
Cdd:PTZ00315   53 QPFDAYVVLDFEATCEAD-RRIEDAEVIEFPMVLVDARTATPVAEFQRYVRPVKNPVLSRFCTELTGITQSMVSraDPFP 131

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729154103  92 LNICLS-QFskwiqkiqkekkitfnsdVSSHSVSEA---KSSTFVTWSDWDLGVCLQYECK-RKQLRKPDILNSWIDLRA 166
Cdd:PTZ00315  132 VVYCEAlQF------------------LAEAGLGDApplRSYCVVTCGDWDLKTMLPSQMRvSGQQGTPLSFQRWCNLKK 193

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729154103 167 TYKLFYTRK-------------PKGLNGALQDLGIEFAGREHSGLDDSRNTARLAWRMICDGCVMKITRSLDKVQPKKNS 233
Cdd:PTZ00315  194 YMSQLGFGNgsgcgggatpplgPSDMPDMLQMLGLPLQGRHHSGIDDCRNIAAVLCELLRRGLVIDPTFDTAPFRRWHAP 273

                         250       260
                  ....*....|....*....|.
gi 1729154103 234 VSRSLNVnpTEENPLGSDDGA 254
Cdd:PTZ00315  274 TEASLPA--LDALPSTLADGA 292
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 18-207 6.33e-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: 98.91  E-value: 6.33e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729154103   18 YLIIIDFESTCWKDGKrhysQEIIEFPAVllNTSTGEIESEFHMYVQPQEHpiLSEFCTELTGIKQNQVDEGVPLNICLS 97
Cdd:smart00479   1 TLVVIDCETTGLDPGK----DEIIEIAAV--DVDGGEIIEVFDTYVKPDRP--ITDYATEIHGITPEMLDDAPTFEEVLE 72

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729154103   98 QFSKWIqkiqkekkitfnsdvsshsvseAKSSTFV-TWSDWDLGVcLQYECKRKQLRKPdILNSWIDLRATYKLFYTRKP 176
Cdd:smart00479  73 ELLEFL----------------------RGRILVAgNSAHFDLRF-LKLEHPRLGIKQP-PKLPVIDTLKLARATNPGLP 128

                          170       180       190
                   ....*....|....*....|....*....|..
gi 1729154103  177 K-GLNGALQDLGIEFAGREHSGLDDSRNTARL 207
Cdd:smart00479 129 KySLKKLAKRLLLEVIQRAHRALDDARATAKL 160
PRK07748 PRK07748
3'-5' exonuclease KapD;
19-215 5.79e-22

3'-5' exonuclease KapD;


Pssm-ID: 236087  Cd Length: 207  Bit Score: 94.37  E-value: 5.79e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729154103  19 LIIIDFESTCwKDGKRH---YSQEIIEFPAVllNTSTGEIESEFHMYVQPQEHPILSEFCTELTGIKQNQVDEGVplnic 95
Cdd:PRK07748    6 FLFLDFEFTM-PQHKKKpkgFFPEIIEVGLV--SVVGCEVEDTFSSYVKPKTFPSLTERCKSFLGITQEDVDKGI----- 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729154103  96 lsQFSKWIQKIQKekkitfnsdvsshsVSEAKSSTFVTWSDWDLGVcLQYECKRKQLRKPdILNSWIDLRATYKLFYT-R 174
Cdd:PRK07748   78 --SFEELVEKLAE--------------YDKRCKPTIVTWGNMDMKV-LKHNCEKAGVPFP-FKGQCRDLSLEYKKFFGeR 139

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1729154103 175 KPKGLNGALQDLGIEFAGREHSGLDDSRNTARLAWRMICDG 215
Cdd:PRK07748  140 NQTGLWKAIEEYGKEGTGKHHCALDDAMTTYNIFKLVEKDK 180
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 19-212 1.65e-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: 1.65e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729154103  19 LIIIDFESTcwkdGKRHYSQEIIEFPAVLLNTstGEIESEFHMYVQPQEHpiLSEFCTELTGIKQNQVDEGVPLNICLSQ 98
Cdd:COG0847     2 FVVLDTETT----GLDPAKDRIIEIGAVKVDD--GRIVETFHTLVNPERP--IPPEATAIHGITDEDVADAPPFAEVLPE 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729154103  99 FSKWIQkiqkekkitfNSDVSSHSVSeaksstFvtwsdwDLGVcLQYECKRKQLRKPDilNSWIDLRATYKLFYTRKPK- 177
Cdd:COG0847    74 LLEFLG----------GAVLVAHNAA------F------DLGF-LNAELRRAGLPLPP--FPVLDTLRLARRLLPGLPSy 128

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1729154103 178 GLNGALQDLGIEFAGReHSGLDDSRNTARLAWRMI 212
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 ...
 586-631 2.62e-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: 67.43  E-value: 2.62e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1729154103 586 PLCNCGRRAKRLNVSSAGPNHGKVFYSCPLgkheGKKRGCGYFKWE 631
Cdd:pfam06839   1 PLCPCGQRAVLLTVRKTGPNPGRQFYKCPV----GREKQCGFFQWA 42
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 20-207 1.34e-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: 1.34e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729154103  20 IIIDFESTcwkdGKRHYSQEIIEFPAVLLNTStGEIESEFHMYVQPQEhPIlSEFCTELTGIKQNQVDEGVPLNICLSQF 99
Cdd:cd06127     1 VVFDTETT----GLDPKKDRIIEIGAVKVDGG-IEIVERFETLVNPGR-PI-PPEATAIHGITDEMLADAPPFEEVLPEF 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729154103 100 SKWIqkiqkekkitfnsdvsshsvseaKSSTFVTW-SDWDLGVcLQYECKRKQLRKPDilNSWIDLRATYKLFYTRKPKG 178
Cdd:cd06127    74 LEFL-----------------------GGRVLVAHnASFDLRF-LNRELRRLGGPPLP--NPWIDTLRLARRLLPGLRSH 127

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1729154103 179 LNGAL--QDLGIEFAGReHSGLDDSRNTARL 207
Cdd:cd06127   128 RLGLLlaERYGIPLEGA-HRALADALATAEL 157
polC PRK00448
DNA polymerase III PolC; Validated
 39-212 1.15e-11

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 68.33  E-value: 1.15e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729154103   39 EIIEFPAVLLNTstGEIESEFHMYVQPQEHpiLSEFCTELTGIKQNQVDEGVPLNICLSQFSKWIQKiqkekkitfnsdv 118
Cdd:PRK00448   437 EIIEIGAVKIKN--GEIIDKFEFFIKPGHP--LSAFTTELTGITDDMVKDAPSIEEVLPKFKEFCGD------------- 499

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729154103  119 sshSVSEAKSSTFvtwsdwDLGvCLQYECKRKQLRKPDilNSWID-LRATYKLFYTRKPKGLNGALQDLGIEFAgREHSG 197
Cdd:PRK00448   500 ---SILVAHNASF------DVG-FINTNYEKLGLEKIK--NPVIDtLELSRFLYPELKSHRLNTLAKKFGVELE-HHHRA 566

                          170
                   ....*....|....*
gi 1729154103  198 LDDSRNTARLAWRMI 212
Cdd:PRK00448   567 DYDAEATAYLLIKFL 581
PRK06722 PRK06722
exonuclease; Provisional
 18-207 1.58e-07

exonuclease; Provisional


Pssm-ID: 180670 [Multi-domain]  Cd Length: 281  Bit Score: 53.52  E-value: 1.58e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729154103  18 YLIIIDFESTcWKDGKRHYSQEIIEFPAVLLNTSTGEIESEFHMYVQPQEHpiLSEFCTELTGIKQNQVdegvplnICLS 97
Cdd:PRK06722    6 HFIVFDIERN-FRPYKSEDPSEIVDIGAVKIEASTMKVIGEFSELVKPGAR--LTRHTTKLTGITKKDL-------IGVE 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729154103  98 QFSKWIqkiqkEKKITFNSDvsshsvseakSSTFVTWSDWDLGVcLQYECKRKQLRKPDI-LNSWIDLRA----TYKLFY 172
Cdd:PRK06722   76 KFPQII-----EKFIQFIGE----------DSIFVTWGKEDYRF-LSHDCTLHSVECPCMeKERRIDLQKfvfqAYEELF 139

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1729154103 173 TRKPKgLNGALQDLGIEFAGREHSGLDDSRNTARL 207
Cdd:PRK06722  140 EHTPS-LQSAVEQLGLIWEGKQHRALADAENTANI 173
PRK08074 PRK08074
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 20-92 3.03e-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: 3.03e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1729154103  20 IIIDFEST--CWKDGKRhysqeIIEFPAVLLntSTGEIESEFHMYVQPqEHPIlSEFCTELTGIKQNQVdEGVPL 92
Cdd:PRK08074    6 VVVDLETTgnSPKKGDK-----IIQIAAVVV--EDGEILERFSSFVNP-ERPI-PPFITELTGISEEMV-KQAPL 70
DUF730 pfam05325
Protein of unknown function (DUF730); This family consists of several uncharacterized ...
 579-635 6.46e-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: 6.46e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1729154103 579 KSDKLTPPLCNCGrrAKRLNVSSAGP-NHGKVFYSCPLGKHEGKKRGCGYFKWEHVLL 635
Cdd:pfam05325  14 RRDKGVPIECDCN--AKVVVATSRDPvTSGKLYFSCPYEISDGPGRGCGFKRWWTVAL 69
PRK07740 PRK07740
hypothetical protein; Provisional
 20-209 2.95e-03

hypothetical protein; Provisional


Pssm-ID: 236085 [Multi-domain]  Cd Length: 244  Bit Score: 40.04  E-value: 2.95e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729154103  20 IIIDFESTCWkdgkrhYSQ---EIIEFPAVllNTSTGEIESE-FHMYVQPqEHPIlSEFCTELTGIKQNQVDEGVPLNIC 95
Cdd:PRK07740   62 VVFDLETTGF------SPQqgdEILSIGAV--KTKGGEVETDtFYSLVKP-KRPI-PEHILELTGITAEDVAFAPPLAEV 131

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729154103  96 LSQFskwiqkiqkekkITFNSD---VSSHSVSEAKSSTFVTWsdwdlgvclqyeckrKQLRKPdILNSWIDLRATYKLFY 172
Cdd:PRK07740  132 LHRF------------YAFIGAgvlVAHHAGHDKAFLRHALW---------------RTYRQP-FTHRLIDTMFLTKLLA 183

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1729154103 173 trkPKGLNGALQDL----GIEFAGReHSGLDDSRNTARLaW 209
Cdd:PRK07740  184 ---HERDFPTLDDAlayyGIPIPRR-HHALGDALMTAKL-W 219
 
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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