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Conserved domains on  [gi|1776695535|ref|XP_012672225|]
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3'-5' exoribonuclease 1 [Clupea harengus]

Protein Classification

SAP and ERI-1_3'hExo_like domain-containing protein( domain architecture ID 10488531)

SAP and ERI-1_3'hExo_like domain-containing protein

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 ...
 157-337 2.19e-86

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: 259.07  E-value: 2.19e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1776695535 157 ICVVDFEATCEENN-PQDFEHEIIEFPIVLIDTHTLEIVDSFQEYVKPEINPKLSDFCVQLTGITQKMVDEADTFPAVLR 235
Cdd:cd06133     1 YLVIDFEATCWEGNsKPDYPNEIIEIGAVLVDVKTKEIIDTFSSYVKPVINPKLSDFCTELTGITQEDVDNAPSFPEVLK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1776695535 236 RVVSWLQEKElgtkyRYTLLTDGSWDMSKFLNIQCRISGIRYPPFARKWINIRKSYGNFYKVPRtNTKLSSMLEKLGLKY 315
Cdd:cd06133    81 EFLEWLGKNG-----KYAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYGLKK-RTGLSKALEYLGLEF 154

                         170       180
                  ....*....|....*....|..
gi 1776695535 316 EGRPHCGLDDARNISRIALRML 337
Cdd:cd06133   155 EGRHHRGLDDARNIARILKRLL 176
SAP pfam02037
SAP domain; The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding ...
 101-135 4.53e-06

SAP domain; The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding domain found in diverse nuclear and cytoplasmic proteins.


:

Pssm-ID: 460424 [Multi-domain]  Cd Length: 35  Bit Score: 42.77  E-value: 4.53e-06
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1776695535 101 INRMNRDELRAKLSELKLDTRGVKDVLKKRLKSYY 135
Cdd:pfam02037   1 LSKLTVAELKEELRKRGLPTSGKKAELIERLQEYL 35
 
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 ...
 157-337 2.19e-86

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: 259.07  E-value: 2.19e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1776695535 157 ICVVDFEATCEENN-PQDFEHEIIEFPIVLIDTHTLEIVDSFQEYVKPEINPKLSDFCVQLTGITQKMVDEADTFPAVLR 235
Cdd:cd06133     1 YLVIDFEATCWEGNsKPDYPNEIIEIGAVLVDVKTKEIIDTFSSYVKPVINPKLSDFCTELTGITQEDVDNAPSFPEVLK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1776695535 236 RVVSWLQEKElgtkyRYTLLTDGSWDMSKFLNIQCRISGIRYPPFARKWINIRKSYGNFYKVPRtNTKLSSMLEKLGLKY 315
Cdd:cd06133    81 EFLEWLGKNG-----KYAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYGLKK-RTGLSKALEYLGLEF 154

                         170       180
                  ....*....|....*....|..
gi 1776695535 316 EGRPHCGLDDARNISRIALRML 337
Cdd:cd06133   155 EGRHHRGLDDARNIARILKRLL 176
KapD COG5018
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ...
 159-340 5.31e-58

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


Pssm-ID: 444042 [Multi-domain]  Cd Length: 181  Bit Score: 186.60  E-value: 5.31e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1776695535 159 VVDFEATC-EENNPQDFEHEIIEFPIVLIDTHTlEIVDSFQEYVKPEINPKLSDFCVQLTGITQKMVDEADTFPAVLRRV 237
Cdd:COG5018     6 VIDLEATCwDGKPPPGFPMEIIEIGAVKVDENG-EIIDEFSSFVKPVRRPKLSPFCTELTGITQEDVDSAPSFAEAIEDF 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1776695535 238 VSWLQEKElgtkyrYTLLTDGSWDMSKFLNiQCRISGIRYpPFARKWINIRKSYGNFYKVPRTnTKLSSMLEKLGLKYEG 317
Cdd:COG5018    85 KKWIGSED------YILCSWGDYDRKQLER-NCRFHGVPY-PFGDRHINLKKLFALYFGLKKR-IGLKKALELLGLEFEG 155

                         170       180
                  ....*....|....*....|...
gi 1776695535 318 RPHCGLDDARNISRIALRMLQDG 340
Cdd:COG5018   156 THHRALDDARNTAKLFKKILGDK 178
PTZ00315 PTZ00315
2'-phosphotransferase; Provisional
 133-340 2.11e-47

2'-phosphotransferase; Provisional


Pssm-ID: 240356 [Multi-domain]  Cd Length: 582  Bit Score: 169.69  E-value: 2.11e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1776695535 133 SYYKKQKLTLSAAEAAKTGMF-------YDLICVVDFEATCEENNPQDfEHEIIEFPIVLIDTHTLEIVDSFQEYVKPEI 205
Cdd:PTZ00315   27 SGQRPQRNTVAAAQSAASSQFpeiapqpFDAYVVLDFEATCEADRRIE-DAEVIEFPMVLVDARTATPVAEFQRYVRPVK 105

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1776695535 206 NPKLSDFCVQLTGITQKMVDEADTFPAVLRRVVSWLQEKELGTK---YRYTLLTDGSWDMSKFLNIQCRISGIR-YPPFA 281
Cdd:PTZ00315  106 NPVLSRFCTELTGITQSMVSRADPFPVVYCEALQFLAEAGLGDApplRSYCVVTCGDWDLKTMLPSQMRVSGQQgTPLSF 185

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1776695535 282 RKWINIRK-----------SYGNFYKVPRTNTKLSSMLEKLGLKYEGRPHCGLDDARNISRIALRMLQDG 340
Cdd:PTZ00315  186 QRWCNLKKymsqlgfgngsGCGGGATPPLGPSDMPDMLQMLGLPLQGRHHSGIDDCRNIAAVLCELLRRG 255
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 159-332 5.37e-34

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: 123.62  E-value: 5.37e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1776695535 159 VVDFEATCeeNNPQDfeHEIIEFPIVLIDTHTLEIVDSFQEYVKPEINPKLSDFCVQLTGITQKMVDEADTFPAVLRRVV 238
Cdd:pfam00929   2 VIDLETTG--LDPEK--DEIIEIAAVVIDGGENEIGETFHTYVKPTRLPKLTDECTKFTGITQAMLDNKPSFEEVLEEFL 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1776695535 239 SWLQE-KELGTKYRYTLLTDGSWDMSKFLNIQCrisgIRYPPFARKWINIRKSYGNFYkvprtNTKLSSMLEKLGLKYEG 317
Cdd:pfam00929  78 EFLRKgNLLVAHNASFDVGFLRYDDKRFLKKPM----PKLNPVIDTLILDKATYKELP-----GRSLDALAEKLGLEHIG 148

                         170
                  ....*....|....*
gi 1776695535 318 RPHCGLDDARNISRI 332
Cdd:pfam00929 149 RAHRALDDARATAKL 163
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 159-340 1.53e-33

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 122.41  E-value: 1.53e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1776695535  159 VVDFEATCeeNNPQdfEHEIIEFPIVLIDThtLEIVDSFQEYVKPEinPKLSDFCVQLTGITQKMVDEADTFPAVLRRVV 238
Cdd:smart00479   4 VIDCETTG--LDPG--KDEIIEIAAVDVDG--GEIIEVFDTYVKPD--RPITDYATEIHGITPEMLDDAPTFEEVLEELL 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1776695535  239 SWLQEKELgtkyrytLLTDGSWDMSKFLNIQCRISGIRYPPFaRKWINIRKsYGNFYKVPRTNTKLSSMLEKLGLKYEGR 318
Cdd:smart00479  76 EFLRGRIL-------VAGNSAHFDLRFLKLEHPRLGIKQPPK-LPVIDTLK-LARATNPGLPKYSLKKLAKRLLLEVIQR 146

                          170       180
                   ....*....|....*....|..
gi 1776695535  319 PHCGLDDARNISRIALRMLQDG 340
Cdd:smart00479 147 AHRALDDARATAKLFKKLLERL 168
SAP pfam02037
SAP domain; The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding ...
 101-135 4.53e-06

SAP domain; The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding domain found in diverse nuclear and cytoplasmic proteins.


Pssm-ID: 460424 [Multi-domain]  Cd Length: 35  Bit Score: 42.77  E-value: 4.53e-06
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1776695535 101 INRMNRDELRAKLSELKLDTRGVKDVLKKRLKSYY 135
Cdd:pfam02037   1 LSKLTVAELKEELRKRGLPTSGKKAELIERLQEYL 35
SAP smart00513
Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation;
108-135 6.22e-05

Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation;


Pssm-ID: 128789 [Multi-domain]  Cd Length: 35  Bit Score: 39.78  E-value: 6.22e-05
                           10        20
                   ....*....|....*....|....*...
gi 1776695535  108 ELRAKLSELKLDTRGVKDVLKKRLKSYY 135
Cdd:smart00513   8 ELKDELKKRGLSTSGTKAELVDRLLEAL 35
 
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 ...
 157-337 2.19e-86

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: 259.07  E-value: 2.19e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1776695535 157 ICVVDFEATCEENN-PQDFEHEIIEFPIVLIDTHTLEIVDSFQEYVKPEINPKLSDFCVQLTGITQKMVDEADTFPAVLR 235
Cdd:cd06133     1 YLVIDFEATCWEGNsKPDYPNEIIEIGAVLVDVKTKEIIDTFSSYVKPVINPKLSDFCTELTGITQEDVDNAPSFPEVLK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1776695535 236 RVVSWLQEKElgtkyRYTLLTDGSWDMSKFLNIQCRISGIRYPPFARKWINIRKSYGNFYKVPRtNTKLSSMLEKLGLKY 315
Cdd:cd06133    81 EFLEWLGKNG-----KYAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYGLKK-RTGLSKALEYLGLEF 154

                         170       180
                  ....*....|....*....|..
gi 1776695535 316 EGRPHCGLDDARNISRIALRML 337
Cdd:cd06133   155 EGRHHRGLDDARNIARILKRLL 176
KapD COG5018
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ...
 159-340 5.31e-58

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


Pssm-ID: 444042 [Multi-domain]  Cd Length: 181  Bit Score: 186.60  E-value: 5.31e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1776695535 159 VVDFEATC-EENNPQDFEHEIIEFPIVLIDTHTlEIVDSFQEYVKPEINPKLSDFCVQLTGITQKMVDEADTFPAVLRRV 237
Cdd:COG5018     6 VIDLEATCwDGKPPPGFPMEIIEIGAVKVDENG-EIIDEFSSFVKPVRRPKLSPFCTELTGITQEDVDSAPSFAEAIEDF 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1776695535 238 VSWLQEKElgtkyrYTLLTDGSWDMSKFLNiQCRISGIRYpPFARKWINIRKSYGNFYKVPRTnTKLSSMLEKLGLKYEG 317
Cdd:COG5018    85 KKWIGSED------YILCSWGDYDRKQLER-NCRFHGVPY-PFGDRHINLKKLFALYFGLKKR-IGLKKALELLGLEFEG 155

                         170       180
                  ....*....|....*....|...
gi 1776695535 318 RPHCGLDDARNISRIALRMLQDG 340
Cdd:COG5018   156 THHRALDDARNTAKLFKKILGDK 178
PTZ00315 PTZ00315
2'-phosphotransferase; Provisional
 133-340 2.11e-47

2'-phosphotransferase; Provisional


Pssm-ID: 240356 [Multi-domain]  Cd Length: 582  Bit Score: 169.69  E-value: 2.11e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1776695535 133 SYYKKQKLTLSAAEAAKTGMF-------YDLICVVDFEATCEENNPQDfEHEIIEFPIVLIDTHTLEIVDSFQEYVKPEI 205
Cdd:PTZ00315   27 SGQRPQRNTVAAAQSAASSQFpeiapqpFDAYVVLDFEATCEADRRIE-DAEVIEFPMVLVDARTATPVAEFQRYVRPVK 105

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1776695535 206 NPKLSDFCVQLTGITQKMVDEADTFPAVLRRVVSWLQEKELGTK---YRYTLLTDGSWDMSKFLNIQCRISGIR-YPPFA 281
Cdd:PTZ00315  106 NPVLSRFCTELTGITQSMVSRADPFPVVYCEALQFLAEAGLGDApplRSYCVVTCGDWDLKTMLPSQMRVSGQQgTPLSF 185

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1776695535 282 RKWINIRK-----------SYGNFYKVPRTNTKLSSMLEKLGLKYEGRPHCGLDDARNISRIALRMLQDG 340
Cdd:PTZ00315  186 QRWCNLKKymsqlgfgngsGCGGGATPPLGPSDMPDMLQMLGLPLQGRHHSGIDDCRNIAAVLCELLRRG 255
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 159-332 5.37e-34

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: 123.62  E-value: 5.37e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1776695535 159 VVDFEATCeeNNPQDfeHEIIEFPIVLIDTHTLEIVDSFQEYVKPEINPKLSDFCVQLTGITQKMVDEADTFPAVLRRVV 238
Cdd:pfam00929   2 VIDLETTG--LDPEK--DEIIEIAAVVIDGGENEIGETFHTYVKPTRLPKLTDECTKFTGITQAMLDNKPSFEEVLEEFL 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1776695535 239 SWLQE-KELGTKYRYTLLTDGSWDMSKFLNIQCrisgIRYPPFARKWINIRKSYGNFYkvprtNTKLSSMLEKLGLKYEG 317
Cdd:pfam00929  78 EFLRKgNLLVAHNASFDVGFLRYDDKRFLKKPM----PKLNPVIDTLILDKATYKELP-----GRSLDALAEKLGLEHIG 148

                         170
                  ....*....|....*
gi 1776695535 318 RPHCGLDDARNISRI 332
Cdd:pfam00929 149 RAHRALDDARATAKL 163
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 159-340 1.53e-33

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 122.41  E-value: 1.53e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1776695535  159 VVDFEATCeeNNPQdfEHEIIEFPIVLIDThtLEIVDSFQEYVKPEinPKLSDFCVQLTGITQKMVDEADTFPAVLRRVV 238
Cdd:smart00479   4 VIDCETTG--LDPG--KDEIIEIAAVDVDG--GEIIEVFDTYVKPD--RPITDYATEIHGITPEMLDDAPTFEEVLEELL 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1776695535  239 SWLQEKELgtkyrytLLTDGSWDMSKFLNIQCRISGIRYPPFaRKWINIRKsYGNFYKVPRTNTKLSSMLEKLGLKYEGR 318
Cdd:smart00479  76 EFLRGRIL-------VAGNSAHFDLRFLKLEHPRLGIKQPPK-LPVIDTLK-LARATNPGLPKYSLKKLAKRLLLEVIQR 146

                          170       180
                   ....*....|....*....|..
gi 1776695535  319 PHCGLDDARNISRIALRMLQDG 340
Cdd:smart00479 147 AHRALDDARATAKLFKKLLERL 168
PRK07748 PRK07748
3'-5' exonuclease KapD;
159-354 5.58e-26

3'-5' exonuclease KapD;


Pssm-ID: 236087  Cd Length: 207  Bit Score: 103.61  E-value: 5.58e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1776695535 159 VVDFEATCEEN--NPQDFEHEIIEFPIVLIDTHtlEIVDSFQEYVKPEINPKLSDFCVQLTGITQKMVDEADTFPAVLRR 236
Cdd:PRK07748    8 FLDFEFTMPQHkkKPKGFFPEIIEVGLVSVVGC--EVEDTFSSYVKPKTFPSLTERCKSFLGITQEDVDKGISFEELVEK 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1776695535 237 VVSWLQEKELgtkyryTLLTDGSWDMsKFLNIQCRISGIRYpPFARKWINIRKSYGNFYKVpRTNTKLSSMLEKLGLKYE 316
Cdd:PRK07748   86 LAEYDKRCKP------TIVTWGNMDM-KVLKHNCEKAGVPF-PFKGQCRDLSLEYKKFFGE-RNQTGLWKAIEEYGKEGT 156

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1776695535 317 GRPHCGLDDARNISRIALRMLQDGCQLRDNEHLHEGQL 354
Cdd:PRK07748  157 GKHHCALDDAMTTYNIFKLVEKDKEYLVKPEPPTIGER 194
PolC COG2176
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ...
 152-339 1.82e-21

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


Pssm-ID: 441779 [Multi-domain]  Cd Length: 181  Bit Score: 90.59  E-value: 1.82e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1776695535 152 MFYDL----ICVVDFEATceENNPQdfEHEIIEFPIVLIDTHtlEIVDSFQEYVKPEInpKLSDFCVQLTGITQKMVDEA 227
Cdd:COG2176     1 MSLDLedltYVVFDLETT--GLSPK--KDEIIEIGAVKVENG--EIVDRFSTLVNPGR--PIPPFITELTGITDEMVADA 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1776695535 228 DTFPAVLRRVVSWLQEKEL---GTKYrytlltdgswDMsKFLNIQCRISGIRYPP-------FARKWINIRKSYgnfykv 297
Cdd:COG2176    73 PPFEEVLPEFLEFLGDAVLvahNASF----------DL-GFLNAALKRLGLPFDNpvldtleLARRLLPELKSY------ 135

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1776695535 298 prtntKLSSMLEKLGLKYEGRpHCGLDDARNISRIALRMLQD 339
Cdd:COG2176   136 -----KLDTLAERLGIPLEDR-HRALGDAEATAELFLKLLEK 171
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 158-327 1.80e-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: 78.88  E-value: 1.80e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1776695535 158 CVVDFEATCeeNNPQdfEHEIIEFPIVLIDTHtLEIVDSFQEYVKPEInpKLSDFCVQLTGITQKMVDEADTFPAVLRRV 237
Cdd:cd06127     1 VVFDTETTG--LDPK--KDRIIEIGAVKVDGG-IEIVERFETLVNPGR--PIPPEATAIHGITDEMLADAPPFEEVLPEF 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1776695535 238 VSWLQEKelgtkyryTLLT-DGSWDMsKFLNIQCRISGIryPPFARKWINIRKSYGNFYKVPRtNTKLSSMLEKLGLKYE 316
Cdd:cd06127    74 LEFLGGR--------VLVAhNASFDL-RFLNRELRRLGG--PPLPNPWIDTLRLARRLLPGLR-SHRLGLLLAERYGIPL 141

                         170
                  ....*....|.
gi 1776695535 317 GRPHCGLDDAR 327
Cdd:cd06127   142 EGAHRALADAL 152
PRK06722 PRK06722
exonuclease; Provisional
 177-366 1.33e-14

exonuclease; Provisional


Pssm-ID: 180670 [Multi-domain]  Cd Length: 281  Bit Score: 73.16  E-value: 1.33e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1776695535 177 EIIEFPIVLIDTHTLEIVDSFQEYVKPeiNPKLSDFCVQLTGITQKMVDEADTFPAVLRRVVSWLQEKELgtkyrytLLT 256
Cdd:PRK06722   26 EIVDIGAVKIEASTMKVIGEFSELVKP--GARLTRHTTKLTGITKKDLIGVEKFPQIIEKFIQFIGEDSI-------FVT 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1776695535 257 DGSWDMsKFLNIQCRISGIRYPPFAR-KWINIRKSYGNFYKVPRTNT-KLSSMLEKLGLKYEGRPHCGLDDARNISRIAL 334
Cdd:PRK06722   97 WGKEDY-RFLSHDCTLHSVECPCMEKeRRIDLQKFVFQAYEELFEHTpSLQSAVEQLGLIWEGKQHRALADAENTANILL 175

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1776695535 335 RMLQDgcqlRD--NEHLHEGQLQSVPSSDPPEGA 366
Cdd:PRK06722  176 KAYSE----RDitKRYKRHGELELVKNGKLTEKA 205
polC PRK00448
DNA polymerase III PolC; Validated
 176-339 1.96e-12

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 68.71  E-value: 1.96e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1776695535  176 HEIIEFPIVLIdtHTLEIVDSFQEYVKPEInpKLSDFCVQLTGITQKMVDEADTFPAVLRRVVSWLQEkelgtkyryTLL 255
Cdd:PRK00448   436 DEIIEIGAVKI--KNGEIIDKFEFFIKPGH--PLSAFTTELTGITDDMVKDAPSIEEVLPKFKEFCGD---------SIL 502

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1776695535  256 T--DGSWDMSkFLNIQCRISGIRYP--------PFARKWINIRKSYgnfykvprtntKLSSMLEKLGLKYEgRPHCGLDD 325
Cdd:PRK00448   503 VahNASFDVG-FINTNYEKLGLEKIknpvidtlELSRFLYPELKSH-----------RLNTLAKKFGVELE-HHHRADYD 569

                          170
                   ....*....|....
gi 1776695535  326 ARNISRIALRMLQD 339
Cdd:PRK00448   570 AEATAYLLIKFLKD 583
DnaQ_like_exo cd06125
DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease ...
 158-300 1.33e-10

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: 57.45  E-value: 1.33e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1776695535 158 CVVDFEATCEENnpqdFEHEIIEFPIVlidthTLEIVDSFQEYVKPeinpklsdfcvqltgitqkmvdeadtfpavlrrv 237
Cdd:cd06125     1 IAIDTEATGLDG----AVHEIIEIALA-----DVNPEDTAVIDLKD---------------------------------- 37

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1776695535 238 vsWLQEKELgtkyrYTLLTD-GSWDmSKFLNIQCRISGIRYPPFARKWINIRKSygNFYKVPRT 300
Cdd:cd06125    38 --ILRDKPL-----AILVGHnGSFD-LPFLNNRCAELGLKYPLLAGSWIDTIKL--AADDVENT 91
DNA_pol_III_epsilon_like cd06130
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ...
 192-335 5.04e-10

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


Pssm-ID: 99834 [Multi-domain]  Cd Length: 156  Bit Score: 57.52  E-value: 5.04e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1776695535 192 EIVDSFQEYVKPEinPKLSDFCVQLTGITQKMVDEADTFPAVLRRVVSWLQEKelgtkyryTLLT-DGSWDMSKFLNIqC 270
Cdd:cd06130    28 QIVDTFYTLIRPP--TRFDPFNIAIHGITPEDVADAPTFPEVWPEIKPFLGGS--------LVVAhNASFDRSVLRAA-L 96

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1776695535 271 RISGIRYPPFArkWINIRKSYGNFYKvPRTNTKLSSMLEKLGLKYegRPHCGLDDARNISRIALR 335
Cdd:cd06130    97 EAYGLPPPPYQ--YLCTVRLARRVWP-LLPNHKLNTVAEHLGIEL--NHHDALEDARACAEILLA 156
PRK08074 PRK08074
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 159-345 2.57e-08

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


Pssm-ID: 236148 [Multi-domain]  Cd Length: 928  Bit Score: 55.73  E-value: 2.57e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1776695535 159 VVDFEATceENNPQDfEHEIIEFPIVLIDTHtlEIVDSFQEYVKPE--INPklsdFCVQLTGITQKMVDEADTFPAVLRR 236
Cdd:PRK08074    7 VVDLETT--GNSPKK-GDKIIQIAAVVVEDG--EILERFSSFVNPErpIPP----FITELTGISEEMVKQAPLFEDVAPE 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1776695535 237 VVSWLQEkelgtkyRYTLLTDGSWDMSkFLNIQCRISGirYPPF----------ARKWINIRKSYgnfykvprtntKLSS 306
Cdd:PRK08074   78 IVELLEG-------AYFVAHNVHFDLN-FLNEELERAG--YTEIhcpkldtvelARILLPTAESY-----------KLRD 136

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1776695535 307 MLEKLGLKYEgRPHCGLDDARNISRIALRMLQdgcQLRD 345
Cdd:PRK08074  137 LSEELGLEHD-QPHRADSDAEVTAELFLQLLN---KLER 171
SAP pfam02037
SAP domain; The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding ...
 101-135 4.53e-06

SAP domain; The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding domain found in diverse nuclear and cytoplasmic proteins.


Pssm-ID: 460424 [Multi-domain]  Cd Length: 35  Bit Score: 42.77  E-value: 4.53e-06
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1776695535 101 INRMNRDELRAKLSELKLDTRGVKDVLKKRLKSYY 135
Cdd:pfam02037   1 LSKLTVAELKEELRKRGLPTSGKKAELIERLQEYL 35
PRK06807 PRK06807
3'-5' exonuclease;
159-325 5.94e-06

3'-5' exonuclease;


Pssm-ID: 235864 [Multi-domain]  Cd Length: 313  Bit Score: 47.50  E-value: 5.94e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1776695535 159 VVDFEATceENNPqdFEHEIIEFPIVLIDTHtlEIVDSFQEYVKPEINpkLSDFCVQLTGITQKMVDEADTFPAVLRRVV 238
Cdd:PRK06807   12 VIDFETT--GFNP--YNDKIIQVAAVKYRNH--ELVDQFVSYVNPERP--IPDRITSLTGITNYRVSDAPTIEEVLPLFL 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1776695535 239 SWLQEKELgtkyrytLLTDGSWDMsKFLNIQCRISGIRYP--------PFARKwinirksygnfYKVPRTNTKLSSMLEK 310
Cdd:PRK06807   84 AFLHTNVI-------VAHNASFDM-RFLKSNVNMLGLPEPknkvidtvFLAKK-----------YMKHAPNHKLETLKRM 144

                         170
                  ....*....|....*
gi 1776695535 311 LGLKYEGrpHCGLDD 325
Cdd:PRK06807  145 LGIRLSS--HNAFDD 157
PRK07246 PRK07246
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 159-237 3.92e-05

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


Pssm-ID: 180905 [Multi-domain]  Cd Length: 820  Bit Score: 45.83  E-value: 3.92e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1776695535 159 VVDFEATCEENNPqdfehEIIEFPIVLIDTHtlEIVDSFQEYVKPeiNPKLSDFCVQLTGITQKMVDEADTFPAVLRRV 237
Cdd:PRK07246   11 VVDLEATGAGPNA-----SIIQVGIVIIEGG--EIIDSYTTDVNP--HEPLDEHIKHLTGITDQQLAQAPDFSQVARHI 80
SAP smart00513
Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation;
108-135 6.22e-05

Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation;


Pssm-ID: 128789 [Multi-domain]  Cd Length: 35  Bit Score: 39.78  E-value: 6.22e-05
                           10        20
                   ....*....|....*....|....*...
gi 1776695535  108 ELRAKLSELKLDTRGVKDVLKKRLKSYY 135
Cdd:smart00513   8 ELKDELKKRGLSTSGTKAELVDRLLEAL 35
PRK08517 PRK08517
3'-5' exonuclease;
158-236 7.70e-05

3'-5' exonuclease;


Pssm-ID: 236281 [Multi-domain]  Cd Length: 257  Bit Score: 43.86  E-value: 7.70e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1776695535 158 CVVDFEATCEENNpqdfEHEIIEFPIVLIDTHtlEIVDSFQEYVK-PEINPKLSdfcvQLTGITQKMVDEADTFPAVLRR 236
Cdd:PRK08517   71 CFVDIETNGSKPK----KHQIIEIGAVKVKNG--EIIDRFESFVKaKEVPEYIT----ELTGITYEDLENAPSLKEVLEE 140
PRK07883 PRK07883
DEDD exonuclease domain-containing protein;
158-327 8.81e-05

DEDD exonuclease domain-containing protein;


Pssm-ID: 236123 [Multi-domain]  Cd Length: 557  Bit Score: 44.52  E-value: 8.81e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1776695535 158 CVVDFEATCEENNpqdfEHEIIEFPIVLIdtHTLEIVDSFQEYVKPE--INPklsdFCVQLTGITQKMVDEADTFPAVLR 235
Cdd:PRK07883   18 VVVDLETTGGSPA----GDAITEIGAVKV--RGGEVLGEFATLVNPGrpIPP----FITVLTGITTAMVAGAPPIEEVLP 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1776695535 236 RVVSWLQEkelgtkyryTLLT--DGSWDMSkFLNIQCRISGIRYPPF--------ARKwinirksygnfyKVPRT---NT 302
Cdd:PRK07883   88 AFLEFARG---------AVLVahNAPFDIG-FLRAAAARCGYPWPGPpvlctvrlARR------------VLPRDeapNV 145

                         170       180
                  ....*....|....*....|....*
gi 1776695535 303 KLSSMLEKLGLKYEGRpHCGLDDAR 327
Cdd:PRK07883  146 RLSTLARLFGATTTPT-HRALDDAR 169
PRK06195 PRK06195
DNA polymerase III subunit epsilon; Validated
 192-339 7.56e-03

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 235735 [Multi-domain]  Cd Length: 309  Bit Score: 37.84  E-value: 7.56e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1776695535 192 EIVDSFQEYVKPEiNPKLSDFCVQLTGITQKMVDEADTFPAVLRRVVSWLQEkelgtkyryTLLT--DGSWDMSkFLNIQ 269
Cdd:PRK06195   30 EIVEKVHYLIKPK-EMRFMPINIGIHGIRPHMVEDELEFDKIWEKIKHYFNN---------NLVIahNASFDIS-VLRKT 98

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1776695535 270 CRISGIRYPPFarKWINIRKSYGNFYK-VPrtNTKLSSMLEKLGlkYEGRPHCGLDDARNISRIALRMLQD 339
Cdd:PRK06195   99 LELYNIPMPSF--EYICTMKLAKNFYSnID--NARLNTVNNFLG--YEFKHHDALADAMACSNILLNISKE 163
 
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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