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Conserved domains on  [gi|767950374|ref|XP_011542151|]
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3'-5' exoribonuclease 1 isoform X2 [Homo sapiens]

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 ...
 130-269 1.54e-61

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: 192.44  E-value: 1.54e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767950374 130 ICIIDFEATCEEGNPPE-FVHEIIEFPVVLLNTHTLEIEDTFQQYVRPEINTQLSDFCISLTGITQDQVDRADTFPQVLK 208
Cdd:cd06133    1 YLVIDFEATCWEGNSKPdYPNEIIEIGAVLVDVKTKEIIDTFSSYVKPVINPKLSDFCTELTGITQEDVDNAPSFPEVLK 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767950374 209 KVIDWmklkeLGTKYKYSLLTDGSWDMSKFLNIQCQLSRLKYPPFAKKWINIRKSYGNFYK 269
Cdd:cd06133   81 EFLEW-----LGKNGKYAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYG 136
SAP pfam02037
SAP domain; The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding ...
 76-110 3.20e-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: 43.16  E-value: 3.20e-06
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 767950374   76 INRMSKEELRAKLSEFKLETRGVKDVLKKRLKNYY 110
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 ...
 130-269 1.54e-61

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: 192.44  E-value: 1.54e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767950374 130 ICIIDFEATCEEGNPPE-FVHEIIEFPVVLLNTHTLEIEDTFQQYVRPEINTQLSDFCISLTGITQDQVDRADTFPQVLK 208
Cdd:cd06133    1 YLVIDFEATCWEGNSKPdYPNEIIEIGAVLVDVKTKEIIDTFSSYVKPVINPKLSDFCTELTGITQEDVDNAPSFPEVLK 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767950374 209 KVIDWmklkeLGTKYKYSLLTDGSWDMSKFLNIQCQLSRLKYPPFAKKWINIRKSYGNFYK 269
Cdd:cd06133   81 EFLEW-----LGKNGKYAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYG 136
KapD COG5018
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ...
 128-268 4.35e-40

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


Pssm-ID: 444042 [Multi-domain]  Cd Length: 181  Bit Score: 137.68  E-value: 4.35e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767950374 128 DYICIIDFEATCEEGNPPE-FVHEIIEFPVVLLNTHTlEIEDTFQQYVRPEINTQLSDFCISLTGITQDQVDRADTFPQV 206
Cdd:COG5018    2 MKYLVIDLEATCWDGKPPPgFPMEIIEIGAVKVDENG-EIIDEFSSFVKPVRRPKLSPFCTELTGITQEDVDSAPSFAEA 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767950374 207 LKKVIDWMKlkelgtKYKYSLLTDGSWDMSKFLNiQCQLSRLKYpPFAKKWINIRKSYGNFY 268
Cdd:COG5018   81 IEDFKKWIG------SEDYILCSWGDYDRKQLER-NCRFHGVPY-PFGDRHINLKKLFALYF 134
PTZ00315 PTZ00315
2'-phosphotransferase; Provisional
 123-262 3.23e-31

2'-phosphotransferase; Provisional


Pssm-ID: 240356 [Multi-domain]  Cd Length: 582  Bit Score: 121.92  E-value: 3.23e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767950374 123 ADSYYDYICIIDFEATCEEGNPPEfVHEIIEFPVVLLNTHTLEIEDTFQQYVRPEINTQLSDFCISLTGITQDQVDRADT 202
Cdd:PTZ00315  51 APQPFDAYVVLDFEATCEADRRIE-DAEVIEFPMVLVDARTATPVAEFQRYVRPVKNPVLSRFCTELTGITQSMVSRADP 129

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767950374 203 FPQVLKKVIDWMKLKELGTK---YKYSLLTDGSWDMSKFLNIQCQLS-RLKYPPFAKKWINIRK 262
Cdd:PTZ00315 130 FPVVYCEALQFLAEAGLGDApplRSYCVVTCGDWDLKTMLPSQMRVSgQQGTPLSFQRWCNLKK 193
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 132-269 1.31e-21

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: 88.95  E-value: 1.31e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767950374  132 IIDFEATCEEGNPpefvHEIIEFPVVLLNTHTLEIEDTFQQYVRPEINTQLSDFCISLTGITQDQVDRADTFPQVLKKVI 211
Cdd:pfam00929   2 VIDLETTGLDPEK----DEIIEIAAVVIDGGENEIGETFHTYVKPTRLPKLTDECTKFTGITQAMLDNKPSFEEVLEEFL 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 767950374  212 DWM-KLKELGTKYKYSLLTDGSWDMSKFLNIQCQlsrlKYPPFAKKWINIRKSYGNFYK 269
Cdd:pfam00929  78 EFLrKGNLLVAHNASFDVGFLRYDDKRFLKKPMP----KLNPVIDTLILDKATYKELPG 132
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 129-253 7.81e-19

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 81.58  E-value: 7.81e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767950374   129 YICIIDFEATceeGNPPEfVHEIIEFPVVllNTHTLEIEDTFQQYVRPEIntQLSDFCISLTGITQDQVDRADTFPQVLK 208
Cdd:smart00479   1 TLVVIDCETT---GLDPG-KDEIIEIAAV--DVDGGEIIEVFDTYVKPDR--PITDYATEIHGITPEMLDDAPTFEEVLE 72

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 767950374   209 KVIDWMKLKELgtkykysLLTDGSWDMSKFLNIQCQLSRLKYPPF 253
Cdd:smart00479  73 ELLEFLRGRIL-------VAGNSAHFDLRFLKLEHPRLGIKQPPK 110
SAP pfam02037
SAP domain; The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding ...
 76-110 3.20e-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: 43.16  E-value: 3.20e-06
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 767950374   76 INRMSKEELRAKLSEFKLETRGVKDVLKKRLKNYY 110
Cdd:pfam02037   1 LSKLTVAELKEELRKRGLPTSGKKAELIERLQEYL 35
SAP smart00513
Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation;
76-110 3.85e-05

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


Pssm-ID: 128789 [Multi-domain]  Cd Length: 35  Bit Score: 40.16  E-value: 3.85e-05
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 767950374    76 INRMSKEELRAKLSEFKLETRGVKDVLKKRLKNYY 110
Cdd:smart00513   1 LAKLKVSELKDELKKRGLSTSGTKAELVDRLLEAL 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 ...
 130-269 1.54e-61

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: 192.44  E-value: 1.54e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767950374 130 ICIIDFEATCEEGNPPE-FVHEIIEFPVVLLNTHTLEIEDTFQQYVRPEINTQLSDFCISLTGITQDQVDRADTFPQVLK 208
Cdd:cd06133    1 YLVIDFEATCWEGNSKPdYPNEIIEIGAVLVDVKTKEIIDTFSSYVKPVINPKLSDFCTELTGITQEDVDNAPSFPEVLK 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767950374 209 KVIDWmklkeLGTKYKYSLLTDGSWDMSKFLNIQCQLSRLKYPPFAKKWINIRKSYGNFYK 269
Cdd:cd06133   81 EFLEW-----LGKNGKYAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYG 136
KapD COG5018
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ...
 128-268 4.35e-40

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


Pssm-ID: 444042 [Multi-domain]  Cd Length: 181  Bit Score: 137.68  E-value: 4.35e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767950374 128 DYICIIDFEATCEEGNPPE-FVHEIIEFPVVLLNTHTlEIEDTFQQYVRPEINTQLSDFCISLTGITQDQVDRADTFPQV 206
Cdd:COG5018    2 MKYLVIDLEATCWDGKPPPgFPMEIIEIGAVKVDENG-EIIDEFSSFVKPVRRPKLSPFCTELTGITQEDVDSAPSFAEA 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767950374 207 LKKVIDWMKlkelgtKYKYSLLTDGSWDMSKFLNiQCQLSRLKYpPFAKKWINIRKSYGNFY 268
Cdd:COG5018   81 IEDFKKWIG------SEDYILCSWGDYDRKQLER-NCRFHGVPY-PFGDRHINLKKLFALYF 134
PTZ00315 PTZ00315
2'-phosphotransferase; Provisional
 123-262 3.23e-31

2'-phosphotransferase; Provisional


Pssm-ID: 240356 [Multi-domain]  Cd Length: 582  Bit Score: 121.92  E-value: 3.23e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767950374 123 ADSYYDYICIIDFEATCEEGNPPEfVHEIIEFPVVLLNTHTLEIEDTFQQYVRPEINTQLSDFCISLTGITQDQVDRADT 202
Cdd:PTZ00315  51 APQPFDAYVVLDFEATCEADRRIE-DAEVIEFPMVLVDARTATPVAEFQRYVRPVKNPVLSRFCTELTGITQSMVSRADP 129

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767950374 203 FPQVLKKVIDWMKLKELGTK---YKYSLLTDGSWDMSKFLNIQCQLS-RLKYPPFAKKWINIRK 262
Cdd:PTZ00315 130 FPVVYCEALQFLAEAGLGDApplRSYCVVTCGDWDLKTMLPSQMRVSgQQGTPLSFQRWCNLKK 193
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 132-269 1.31e-21

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: 88.95  E-value: 1.31e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767950374  132 IIDFEATCEEGNPpefvHEIIEFPVVLLNTHTLEIEDTFQQYVRPEINTQLSDFCISLTGITQDQVDRADTFPQVLKKVI 211
Cdd:pfam00929   2 VIDLETTGLDPEK----DEIIEIAAVVIDGGENEIGETFHTYVKPTRLPKLTDECTKFTGITQAMLDNKPSFEEVLEEFL 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 767950374  212 DWM-KLKELGTKYKYSLLTDGSWDMSKFLNIQCQlsrlKYPPFAKKWINIRKSYGNFYK 269
Cdd:pfam00929  78 EFLrKGNLLVAHNASFDVGFLRYDDKRFLKKPMP----KLNPVIDTLILDKATYKELPG 132
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 129-253 7.81e-19

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 81.58  E-value: 7.81e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767950374   129 YICIIDFEATceeGNPPEfVHEIIEFPVVllNTHTLEIEDTFQQYVRPEIntQLSDFCISLTGITQDQVDRADTFPQVLK 208
Cdd:smart00479   1 TLVVIDCETT---GLDPG-KDEIIEIAAV--DVDGGEIIEVFDTYVKPDR--PITDYATEIHGITPEMLDDAPTFEEVLE 72

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 767950374   209 KVIDWMKLKELgtkykysLLTDGSWDMSKFLNIQCQLSRLKYPPF 253
Cdd:smart00479  73 ELLEFLRGRIL-------VAGNSAHFDLRFLKLEHPRLGIKQPPK 110
PRK07748 PRK07748
3'-5' exonuclease KapD;
132-268 2.48e-17

3'-5' exonuclease KapD;


Pssm-ID: 236087  Cd Length: 207  Bit Score: 78.58  E-value: 2.48e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767950374 132 IIDFEATCEEG--NPPEFVHEIIEFPVVLLNTHtlEIEDTFQQYVRPEINTQLSDFCISLTGITQDQVDRADTFPQVLKk 209
Cdd:PRK07748   8 FLDFEFTMPQHkkKPKGFFPEIIEVGLVSVVGC--EVEDTFSSYVKPKTFPSLTERCKSFLGITQEDVDKGISFEELVE- 84

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 767950374 210 vidwmKLKELGTKYKYSLLTDGSWDMsKFLNIQCQLSRLKYpPFAKKWINIRKSYGNFY 268
Cdd:PRK07748  85 -----KLAEYDKRCKPTIVTWGNMDM-KVLKHNCEKAGVPF-PFKGQCRDLSLEYKKFF 136
DnaQ_like_exo cd06125
DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease ...
 131-263 7.50e-15

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: 68.62  E-value: 7.50e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767950374 131 CIIDFEATCEEGnppeFVHEIIEFPVVLLNthtleIEDTFQQYVRpeintqlsdfcisltgitqdqvdradtfpqvlkkv 210
Cdd:cd06125    1 IAIDTEATGLDG----AVHEIIEIALADVN-----PEDTAVIDLK----------------------------------- 36

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 767950374 211 iDWMKLKElgtkyKYSLLTD-GSWDmSKFLNIQCQLSRLKYPPFAKKWINIRKS 263
Cdd:cd06125   37 -DILRDKP-----LAILVGHnGSFD-LPFLNNRCAELGLKYPLLAGSWIDTIKL 83
polC PRK00448
DNA polymerase III PolC; Validated
 149-215 2.39e-07

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 51.76  E-value: 2.39e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767950374  149 HEIIEF-PVVLLNThtlEIEDTFQQYVRPEIntQLSDFCISLTGITQDQVDRADTFPQVLKKVIDWMK 215
Cdd:PRK00448  436 DEIIEIgAVKIKNG---EIIDKFEFFIKPGH--PLSAFTTELTGITDDMVKDAPSIEEVLPKFKEFCG 498
SAP pfam02037
SAP domain; The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding ...
 76-110 3.20e-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: 43.16  E-value: 3.20e-06
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 767950374   76 INRMSKEELRAKLSEFKLETRGVKDVLKKRLKNYY 110
Cdd:pfam02037   1 LSKLTVAELKEELRKRGLPTSGKKAELIERLQEYL 35
SAP smart00513
Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation;
76-110 3.85e-05

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


Pssm-ID: 128789 [Multi-domain]  Cd Length: 35  Bit Score: 40.16  E-value: 3.85e-05
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 767950374    76 INRMSKEELRAKLSEFKLETRGVKDVLKKRLKNYY 110
Cdd:smart00513   1 LAKLKVSELKDELKKRGLSTSGTKAELVDRLLEAL 35
DNA_pol_III_epsilon_like cd06130
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ...
 165-214 1.29e-04

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: 41.34  E-value: 1.29e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 767950374 165 EIEDTFQQYVRPEinTQLSDFCISLTGITQDQVDRADTFPQVLKKVIDWM 214
Cdd:cd06130   28 QIVDTFYTLIRPP--TRFDPFNIAIHGITPEDVADAPTFPEVWPEIKPFL 75
PRK06807 PRK06807
3'-5' exonuclease;
121-251 2.01e-04

3'-5' exonuclease;


Pssm-ID: 235864 [Multi-domain]  Cd Length: 313  Bit Score: 42.11  E-value: 2.01e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767950374 121 NFADSYYDYICIIDFEATceeGNPPeFVHEIIEFPVVLLNTHtlEIEDTFQQYVRPEINtqLSDFCISLTGITQDQVDRA 200
Cdd:PRK06807   1 MGNISLPLDYVVIDFETT---GFNP-YNDKIIQVAAVKYRNH--ELVDQFVSYVNPERP--IPDRITSLTGITNYRVSDA 72

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 767950374 201 DTFPQVLKKVIDWMKLKELgtkykysLLTDGSWDMsKFLNIQCQLSRLKYP 251
Cdd:PRK06807  73 PTIEEVLPLFLAFLHTNVI-------VAHNASFDM-RFLKSNVNMLGLPEP 115
PRK06722 PRK06722
exonuclease; Provisional
 150-256 3.23e-03

exonuclease; Provisional


Pssm-ID: 180670 [Multi-domain]  Cd Length: 281  Bit Score: 38.50  E-value: 3.23e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767950374 150 EIIEFPVVLLNTHTLEIEDTFQQYVRPeiNTQLSDFCISLTGITQDQVDRADTFPQVLKKVIDWMKLKELgtkykysLLT 229
Cdd:PRK06722  26 EIVDIGAVKIEASTMKVIGEFSELVKP--GARLTRHTTKLTGITKKDLIGVEKFPQIIEKFIQFIGEDSI-------FVT 96

                         90       100
                 ....*....|....*....|....*..
gi 767950374 230 DGSWDMsKFLNIQCQLSRLKYPPFAKK 256
Cdd:PRK06722  97 WGKEDY-RFLSHDCTLHSVECPCMEKE 122
 
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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