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Conserved domains on  [gi|739719838|ref|WP_037573512|]
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MULTISPECIES: exonuclease subunit SbcD [Staphylococcus]

Protein Classification

exonuclease SbcCD subunit D( domain architecture ID 11417993)

exonuclease SbcCD subunit D is a component of SbcCD, which is involved in double-strand DNA break detection and repair by homologous recombination and non-homologous end joining of damaged DNA

CATH:  3.60.21.10|3.30.160.210
Gene Ontology:  GO:0003677|GO:0004529|GO:0006281|GO:0004519|GO:0006310
PubMed:  9653124|24531464

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SbcD COG0420
DNA repair exonuclease SbcCD nuclease subunit [Replication, recombination and repair];
1-264 1.64e-65

DNA repair exonuclease SbcCD nuclease subunit [Replication, recombination and repair];


:

Pssm-ID: 440189 [Multi-domain]  Cd Length: 250  Bit Score: 208.23  E-value: 1.64e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739719838   1 MKVIHTADWHLGKVLNGQSFLEDQSYILDEFIKKVEKECPDVVIIAGDIFDTSMPSKRAITLMEETIAQINiELGIPTVI 80
Cdd:COG0420    1 MRFLHTADWHLGKPLHGASRREDQLAALDRLVDLAIEEKVDAVLIAGDLFDSANPSPEAVRLLAEALRRLS-EAGIPVVL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739719838  81 INGNHDGKARLRYGSNWFQKNELFIRTEIEDFLNPIQFG-NVRIFTMPFFTLAEarqyldvtlttyEDAVAQLIAMIKPK 159
Cdd:COG0420   80 IAGNHDSPSRLSAGSPLLENLGVHVFGSVEPEPVELEDGlGVAVYGLPYLRPSD------------EEALRDLLERLPRA 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739719838 160 LDASFHNILVGHFTVYGAPKSdseREITVGTiesVAPSIL--EGFDAVMLGHIHHPFALNQS-NIYYSGSLLQYSFSEVN 236
Cdd:COG0420  148 LDPGGPNILLLHGFVAGASGS---RDIYVAP---VPLSALpaAGFDYVALGHIHRPQVLGGDpRIRYSGSPEPRSFSEAG 221

                        250       260
                 ....*....|....*....|....*....
gi 739719838 237 QpKGFRCFQILDDEMTQ-RFIQLMPKRKL 264
Cdd:COG0420  222 G-KGVLLVELDAGGLVSvEFVPLPATRRF 249
SbcD_C pfam12320
Type 5 capsule protein repressor C-terminal domain; This domain is found in bacteria and ...
 282-346 4.78e-04

Type 5 capsule protein repressor C-terminal domain; This domain is found in bacteria and archaea. This domain is about 90 amino acids in length. This domain is found associated with pfam00149. SbcD works in complex with SbdC (SbcDC) which is a transcription regulator. It down-regulates transcription of arl and mgr to inhibit type 5 capsule protein production. It acts as part of the SOS pathway of bacteria.


:

Pssm-ID: 463533  Cd Length: 100  Bit Score: 39.20  E-value: 4.78e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 739719838  282 DHQEDYFHFHLSELEFVKDPMQQLKQQFPNT------LALTQQVKEISSQERATKNIKKMKPMEIVNSFYK 346
Cdd:pfam12320  27 ADREDYLEVELTDEEPIPDLMERLREAYPNIpvellrIRRTREERQAEEEEEAAEDLEELSPLELFERFYE 97
 
Name Accession Description Interval E-value
SbcD COG0420
DNA repair exonuclease SbcCD nuclease subunit [Replication, recombination and repair];
1-264 1.64e-65

DNA repair exonuclease SbcCD nuclease subunit [Replication, recombination and repair];


Pssm-ID: 440189 [Multi-domain]  Cd Length: 250  Bit Score: 208.23  E-value: 1.64e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739719838   1 MKVIHTADWHLGKVLNGQSFLEDQSYILDEFIKKVEKECPDVVIIAGDIFDTSMPSKRAITLMEETIAQINiELGIPTVI 80
Cdd:COG0420    1 MRFLHTADWHLGKPLHGASRREDQLAALDRLVDLAIEEKVDAVLIAGDLFDSANPSPEAVRLLAEALRRLS-EAGIPVVL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739719838  81 INGNHDGKARLRYGSNWFQKNELFIRTEIEDFLNPIQFG-NVRIFTMPFFTLAEarqyldvtlttyEDAVAQLIAMIKPK 159
Cdd:COG0420   80 IAGNHDSPSRLSAGSPLLENLGVHVFGSVEPEPVELEDGlGVAVYGLPYLRPSD------------EEALRDLLERLPRA 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739719838 160 LDASFHNILVGHFTVYGAPKSdseREITVGTiesVAPSIL--EGFDAVMLGHIHHPFALNQS-NIYYSGSLLQYSFSEVN 236
Cdd:COG0420  148 LDPGGPNILLLHGFVAGASGS---RDIYVAP---VPLSALpaAGFDYVALGHIHRPQVLGGDpRIRYSGSPEPRSFSEAG 221

                        250       260
                 ....*....|....*....|....*....
gi 739719838 237 QpKGFRCFQILDDEMTQ-RFIQLMPKRKL 264
Cdd:COG0420  222 G-KGVLLVELDAGGLVSvEFVPLPATRRF 249
sbcd TIGR00619
exonuclease SbcD; All proteins in this family for which functions are known are ...
 1-240 8.14e-49

exonuclease SbcD; All proteins in this family for which functions are known are double-stranded DNA exonuclease (as part of a complex with SbcC homologs). This complex functions in the initiation of recombination and recombinational repair and is particularly important in regulating the stability of DNA sections that can form secondary structures. This family is likely homologous to the MRE11 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273178 [Multi-domain]  Cd Length: 253  Bit Score: 165.29  E-value: 8.14e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739719838    1 MKVIHTADWHLGKVLNGQSFLEDQSYILDEFIKKVEKECPDVVIIAGDIFDTSMPSKRAITLMEETIAQINIELGIPTVI 80
Cdd:TIGR00619   1 MRILHTSDWHLGKTLEGVSRLAEQKAFLDDLLEFAKAEQVDALLVAGDVFDTANPPAEAQELFNAFFVNLSDTGIRPIVV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739719838   81 INGNHDGKARLRYGSNWFQKNELFIRTEIE---------DFLNPiQFGNVRIFTMPFFTLAeARQYLDVTLTT-----YE 146
Cdd:TIGR00619  81 ISGNHDSAQRLSAAKKLLAELGVFVVGSPGhdpqilllkDGTNG-EGLCVGLFLLPREAIL-TRAGLDGFGLElllahTD 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739719838  147 DAVAQLIAMIKPKLDASFHNILVGHFTVYGAPKSDSEREITVGTIESVAPS-ILEGFDAVMLGHIHHPFALNQSNIYYSG 225
Cdd:TIGR00619 159 VKLRQAAEALKLRLDQDLPKILLAHLFTAGATKSDAERRIYIGTLYAFPLQnFPEADYIALGHIHIHKISKGRERVRYSG 238

                         250
                  ....*....|....*
gi 739719838  226 SLLQYSFSEVNQPKG 240
Cdd:TIGR00619 239 SPFPLSFDEAGKDKY 253
MPP_Mre11_N cd00840
Mre11 nuclease, N-terminal metallophosphatase domain; Mre11 (also known as SbcD in Escherichia ...
 2-233 6.40e-40

Mre11 nuclease, N-terminal metallophosphatase domain; Mre11 (also known as SbcD in Escherichia coli) is a subunit of the MRX protein complex. This complex includes: Mre11, Rad50, and Xrs2/Nbs1, and plays a vital role in several nuclear processes including DNA double-strand break repair, telomere length maintenance, cell cycle checkpoint control, and meiotic recombination, in eukaryotes. During double-strand break repair, the MRX complex is required to hold the two ends of a broken chromosome together. In vitro studies show that Mre11 has 3'-5' exonuclease activity on dsDNA templates and endonuclease activity on dsDNA and ssDNA templates. In addition to the N-terminal phosphatase domain, the eukaryotic MRE11 members of this family have a C-terminal DNA binding domain (not included in this alignment model). MRE11-like proteins are found in prokaryotes and archaea was well as in eukaryotes. Mre11 belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination.


Pssm-ID: 277319 [Multi-domain]  Cd Length: 186  Bit Score: 139.71  E-value: 6.40e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739719838   2 KVIHTADWHLGKVLNGQSFL-EDQSYILDEFIKKVEKECPDVVIIAGDIFDTSMPSKRAITLMEETIAQINiELGIPTVI 80
Cdd:cd00840    1 RFLHTADWHLGYPLYGLSRReEDFFKAFEEIVDLAIEEKVDFVLIAGDLFDSNNPSPEALKLAIEGLRRLC-EAGIPVFV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739719838  81 INGNHDGKARlrygsnwfqknelfirteiedflnpiqfgnVRIFTMPFFTLAEARQYLDVTLttyedavaqliaMIKPKL 160
Cdd:cd00840   80 IAGNHDSPAR------------------------------VAIYGLPYLRDERLERLFEDLE------------LRPRLL 117

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 739719838 161 DASFHNILVGHFTVYGAPKSDSEREITVGTIesvapsILEGFDAVMLGHIHHPFAL--NQSNIYYSGSLLQYSFS 233
Cdd:cd00840  118 KPDWFNILLLHQGVDGAGPSDSERPIVPEDL------LPDGFDYVALGHIHKPQIIegGGPPIVYPGSPEPTSFS 186
PRK10966 PRK10966
exonuclease subunit SbcD; Provisional
 1-239 3.11e-24

exonuclease subunit SbcD; Provisional


Pssm-ID: 182871 [Multi-domain]  Cd Length: 407  Bit Score: 102.71  E-value: 3.11e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739719838   1 MKVIHTADWHLGKVLNGQSFLEDQSYILDEFIKKVEKECPDVVIIAGDIFDTSMPSKRAITLMEETIAQINiELGIPTVI 80
Cdd:PRK10966   1 MRILHTSDWHLGQNFYSKSRAAEHQAFLDWLLEQVQEHQVDAIIVAGDIFDTGSPPSYARELYNRFVVNLQ-QTGCQLVV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739719838  81 INGNHDGKARLrygsnwfqkNElfiRTEIEDFLNPIQFGNV------RIFTM--------------PFF----------- 129
Cdd:PRK10966  80 LAGNHDSVATL---------NE---SRDLLAFLNTTVIASAsddlghQVIILprrdgtpgavlcaiPFLrprdvitsqag 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739719838 130 -TLAEARQYLDVTLTTYEDAVAQLIAMIKPKLDASFHNILVGHFTVYGAPKSDSEREITVGTIESVAPSILEGFDAVMLG 208
Cdd:PRK10966 148 qSGIEKQQALQAAIADHYQQLYQLACELRDELGQPLPIIATGHLTTVGASKSDSVRDIYIGTLDAFPAQAFPPADYIALG 227

                        250       260       270
                 ....*....|....*....|....*....|..
gi 739719838 209 HIHHPFALNQS-NIYYSGSLLQYSFSEVNQPK 239
Cdd:PRK10966 228 HIHRAQKVGGTeHIRYSGSPIPLSFDELGKSK 259
Metallophos pfam00149
Calcineurin-like phosphoesterase; This family includes a diverse range of phosphoesterases, ...
 1-86 7.89e-09

Calcineurin-like phosphoesterase; This family includes a diverse range of phosphoesterases, including protein phosphoserine phosphatases, nucleotidases, sphingomyelin phosphodiesterases and 2'-3' cAMP phosphodiesterases as well as nucleases such as bacterial SbcD or yeast MRE11. The most conserved regions in this superfamily centre around the metal chelating residues.


Pssm-ID: 459691 [Multi-domain]  Cd Length: 114  Bit Score: 52.99  E-value: 7.89e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739719838    1 MKVIHTADWHLgkvlngqsflEDQSYILDEFIKKVEKEC-PDVVIIAGDIFDTSMPSKRAITLMEETIAQinielgIPTV 79
Cdd:pfam00149   1 MRILVIGDLHL----------PGQLDDLLELLKKLLEEGkPDLVLHAGDLVDRGPPSEEVLELLERLIKY------VPVY 64


                  ....*..
gi 739719838   80 IINGNHD 86
Cdd:pfam00149  65 LVRGNHD 71
SbcD_C pfam12320
Type 5 capsule protein repressor C-terminal domain; This domain is found in bacteria and ...
 282-346 4.78e-04

Type 5 capsule protein repressor C-terminal domain; This domain is found in bacteria and archaea. This domain is about 90 amino acids in length. This domain is found associated with pfam00149. SbcD works in complex with SbdC (SbcDC) which is a transcription regulator. It down-regulates transcription of arl and mgr to inhibit type 5 capsule protein production. It acts as part of the SOS pathway of bacteria.


Pssm-ID: 463533  Cd Length: 100  Bit Score: 39.20  E-value: 4.78e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 739719838  282 DHQEDYFHFHLSELEFVKDPMQQLKQQFPNT------LALTQQVKEISSQERATKNIKKMKPMEIVNSFYK 346
Cdd:pfam12320  27 ADREDYLEVELTDEEPIPDLMERLREAYPNIpvellrIRRTREERQAEEEEEAAEDLEELSPLELFERFYE 97
 
Name Accession Description Interval E-value
SbcD COG0420
DNA repair exonuclease SbcCD nuclease subunit [Replication, recombination and repair];
1-264 1.64e-65

DNA repair exonuclease SbcCD nuclease subunit [Replication, recombination and repair];


Pssm-ID: 440189 [Multi-domain]  Cd Length: 250  Bit Score: 208.23  E-value: 1.64e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739719838   1 MKVIHTADWHLGKVLNGQSFLEDQSYILDEFIKKVEKECPDVVIIAGDIFDTSMPSKRAITLMEETIAQINiELGIPTVI 80
Cdd:COG0420    1 MRFLHTADWHLGKPLHGASRREDQLAALDRLVDLAIEEKVDAVLIAGDLFDSANPSPEAVRLLAEALRRLS-EAGIPVVL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739719838  81 INGNHDGKARLRYGSNWFQKNELFIRTEIEDFLNPIQFG-NVRIFTMPFFTLAEarqyldvtlttyEDAVAQLIAMIKPK 159
Cdd:COG0420   80 IAGNHDSPSRLSAGSPLLENLGVHVFGSVEPEPVELEDGlGVAVYGLPYLRPSD------------EEALRDLLERLPRA 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739719838 160 LDASFHNILVGHFTVYGAPKSdseREITVGTiesVAPSIL--EGFDAVMLGHIHHPFALNQS-NIYYSGSLLQYSFSEVN 236
Cdd:COG0420  148 LDPGGPNILLLHGFVAGASGS---RDIYVAP---VPLSALpaAGFDYVALGHIHRPQVLGGDpRIRYSGSPEPRSFSEAG 221

                        250       260
                 ....*....|....*....|....*....
gi 739719838 237 QpKGFRCFQILDDEMTQ-RFIQLMPKRKL 264
Cdd:COG0420  222 G-KGVLLVELDAGGLVSvEFVPLPATRRF 249
sbcd TIGR00619
exonuclease SbcD; All proteins in this family for which functions are known are ...
 1-240 8.14e-49

exonuclease SbcD; All proteins in this family for which functions are known are double-stranded DNA exonuclease (as part of a complex with SbcC homologs). This complex functions in the initiation of recombination and recombinational repair and is particularly important in regulating the stability of DNA sections that can form secondary structures. This family is likely homologous to the MRE11 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273178 [Multi-domain]  Cd Length: 253  Bit Score: 165.29  E-value: 8.14e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739719838    1 MKVIHTADWHLGKVLNGQSFLEDQSYILDEFIKKVEKECPDVVIIAGDIFDTSMPSKRAITLMEETIAQINIELGIPTVI 80
Cdd:TIGR00619   1 MRILHTSDWHLGKTLEGVSRLAEQKAFLDDLLEFAKAEQVDALLVAGDVFDTANPPAEAQELFNAFFVNLSDTGIRPIVV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739719838   81 INGNHDGKARLRYGSNWFQKNELFIRTEIE---------DFLNPiQFGNVRIFTMPFFTLAeARQYLDVTLTT-----YE 146
Cdd:TIGR00619  81 ISGNHDSAQRLSAAKKLLAELGVFVVGSPGhdpqilllkDGTNG-EGLCVGLFLLPREAIL-TRAGLDGFGLElllahTD 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739719838  147 DAVAQLIAMIKPKLDASFHNILVGHFTVYGAPKSDSEREITVGTIESVAPS-ILEGFDAVMLGHIHHPFALNQSNIYYSG 225
Cdd:TIGR00619 159 VKLRQAAEALKLRLDQDLPKILLAHLFTAGATKSDAERRIYIGTLYAFPLQnFPEADYIALGHIHIHKISKGRERVRYSG 238

                         250
                  ....*....|....*
gi 739719838  226 SLLQYSFSEVNQPKG 240
Cdd:TIGR00619 239 SPFPLSFDEAGKDKY 253
MPP_Mre11_N cd00840
Mre11 nuclease, N-terminal metallophosphatase domain; Mre11 (also known as SbcD in Escherichia ...
 2-233 6.40e-40

Mre11 nuclease, N-terminal metallophosphatase domain; Mre11 (also known as SbcD in Escherichia coli) is a subunit of the MRX protein complex. This complex includes: Mre11, Rad50, and Xrs2/Nbs1, and plays a vital role in several nuclear processes including DNA double-strand break repair, telomere length maintenance, cell cycle checkpoint control, and meiotic recombination, in eukaryotes. During double-strand break repair, the MRX complex is required to hold the two ends of a broken chromosome together. In vitro studies show that Mre11 has 3'-5' exonuclease activity on dsDNA templates and endonuclease activity on dsDNA and ssDNA templates. In addition to the N-terminal phosphatase domain, the eukaryotic MRE11 members of this family have a C-terminal DNA binding domain (not included in this alignment model). MRE11-like proteins are found in prokaryotes and archaea was well as in eukaryotes. Mre11 belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination.


Pssm-ID: 277319 [Multi-domain]  Cd Length: 186  Bit Score: 139.71  E-value: 6.40e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739719838   2 KVIHTADWHLGKVLNGQSFL-EDQSYILDEFIKKVEKECPDVVIIAGDIFDTSMPSKRAITLMEETIAQINiELGIPTVI 80
Cdd:cd00840    1 RFLHTADWHLGYPLYGLSRReEDFFKAFEEIVDLAIEEKVDFVLIAGDLFDSNNPSPEALKLAIEGLRRLC-EAGIPVFV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739719838  81 INGNHDGKARlrygsnwfqknelfirteiedflnpiqfgnVRIFTMPFFTLAEARQYLDVTLttyedavaqliaMIKPKL 160
Cdd:cd00840   80 IAGNHDSPAR------------------------------VAIYGLPYLRDERLERLFEDLE------------LRPRLL 117

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 739719838 161 DASFHNILVGHFTVYGAPKSDSEREITVGTIesvapsILEGFDAVMLGHIHHPFAL--NQSNIYYSGSLLQYSFS 233
Cdd:cd00840  118 KPDWFNILLLHQGVDGAGPSDSERPIVPEDL------LPDGFDYVALGHIHKPQIIegGGPPIVYPGSPEPTSFS 186
PRK10966 PRK10966
exonuclease subunit SbcD; Provisional
 1-239 3.11e-24

exonuclease subunit SbcD; Provisional


Pssm-ID: 182871 [Multi-domain]  Cd Length: 407  Bit Score: 102.71  E-value: 3.11e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739719838   1 MKVIHTADWHLGKVLNGQSFLEDQSYILDEFIKKVEKECPDVVIIAGDIFDTSMPSKRAITLMEETIAQINiELGIPTVI 80
Cdd:PRK10966   1 MRILHTSDWHLGQNFYSKSRAAEHQAFLDWLLEQVQEHQVDAIIVAGDIFDTGSPPSYARELYNRFVVNLQ-QTGCQLVV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739719838  81 INGNHDGKARLrygsnwfqkNElfiRTEIEDFLNPIQFGNV------RIFTM--------------PFF----------- 129
Cdd:PRK10966  80 LAGNHDSVATL---------NE---SRDLLAFLNTTVIASAsddlghQVIILprrdgtpgavlcaiPFLrprdvitsqag 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739719838 130 -TLAEARQYLDVTLTTYEDAVAQLIAMIKPKLDASFHNILVGHFTVYGAPKSDSEREITVGTIESVAPSILEGFDAVMLG 208
Cdd:PRK10966 148 qSGIEKQQALQAAIADHYQQLYQLACELRDELGQPLPIIATGHLTTVGASKSDSVRDIYIGTLDAFPAQAFPPADYIALG 227

                        250       260       270
                 ....*....|....*....|....*....|..
gi 739719838 209 HIHHPFALNQS-NIYYSGSLLQYSFSEVNQPK 239
Cdd:PRK10966 228 HIHRAQKVGGTeHIRYSGSPIPLSFDELGKSK 259
CpdA COG1409
3',5'-cyclic AMP phosphodiesterase CpdA [Signal transduction mechanisms];
1-258 1.35e-10

3',5'-cyclic AMP phosphodiesterase CpdA [Signal transduction mechanisms];


Pssm-ID: 441019 [Multi-domain]  Cd Length: 234  Bit Score: 60.86  E-value: 1.35e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739719838   1 MKVIHTADWHLGKVLNGqsfleDQSYILDEFIKKVEKECPDVVIIAGDIFDTSMPS--KRAITLMEetiaqiniELGIPT 78
Cdd:COG1409    1 FRFAHISDLHLGAPDGS-----DTAEVLAAALADINAPRPDFVVVTGDLTDDGEPEeyAAAREILA--------RLGVPV 67

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739719838  79 VIINGNHDgkARLRYGSNWFQknelFIRTEIEDFLNP-IQFGNVRIFTMpfFTLAEARQYLDVTLTTYeDAVAQLIAMIK 157
Cdd:COG1409   68 YVVPGNHD--IRAAMAEAYRE----YFGDLPPGGLYYsFDYGGVRFIGL--DSNVPGRSSGELGPEQL-AWLEEELAAAP 138

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739719838 158 PKldasfHNILVGHFTVYgaPKSDSEREITVGTIESVAPsILE--GFDAVMLGHIHHPFALNQSNIYY--SGSllqySFS 233
Cdd:COG1409  139 AK-----PVIVFLHHPPY--STGSGSDRIGLRNAEELLA-LLAryGVDLVLSGHVHRYERTRRDGVPYivAGS----TGG 206

                        250       260
                 ....*....|....*....|....*
gi 739719838 234 EVNQPKGFRCFQILDDEMTQRFIQL 258
Cdd:COG1409  207 QVRLPPGYRVIEVDGDGLTVEVRRV 231
COG2129 COG2129
Predicted phosphoesterase, related to the Icc protein [General function prediction only];
2-214 6.04e-10

Predicted phosphoesterase, related to the Icc protein [General function prediction only];


Pssm-ID: 441732 [Multi-domain]  Cd Length: 211  Bit Score: 58.49  E-value: 6.04e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739719838   2 KVIHTADWHLGKvlngqsfledqsYILDEFIKKVEKECPDVVIIAGDIFDTSmPSKRAITLMEETIAqinieLGIPTVII 81
Cdd:COG2129    1 KILAVSDLHGNF------------DLLEKLLELARAEDADLVILAGDLTDFG-TAEEAREVLEELAA-----LGVPVLAV 62

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739719838  82 NGNHDGKARLRYGSNWFQKNelfirteIEDflNPIQFGNVRIFtmpFFTLAEARQYLDVTLTTYEDAVAQLIAMIKPKLD 161
Cdd:COG2129   63 PGNHDDPEVLDALEESGVHN-------LHG--RVVEIGGLRIA---GLGGSRPTPFGTPYEYTEEEIEERLAKLREKDVD 130

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 739719838 162 asfhnILVGHFTVYGAPKSDSEREITVG------TIESVAPsilegfDAVMLGHIHHPF 214
Cdd:COG2129  131 -----ILLTHAPPYGTTLDRVEDGPHVGskalreLIEEFQP------KLVLHGHIHESR 178
Metallophos pfam00149
Calcineurin-like phosphoesterase; This family includes a diverse range of phosphoesterases, ...
 1-86 7.89e-09

Calcineurin-like phosphoesterase; This family includes a diverse range of phosphoesterases, including protein phosphoserine phosphatases, nucleotidases, sphingomyelin phosphodiesterases and 2'-3' cAMP phosphodiesterases as well as nucleases such as bacterial SbcD or yeast MRE11. The most conserved regions in this superfamily centre around the metal chelating residues.


Pssm-ID: 459691 [Multi-domain]  Cd Length: 114  Bit Score: 52.99  E-value: 7.89e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739719838    1 MKVIHTADWHLgkvlngqsflEDQSYILDEFIKKVEKEC-PDVVIIAGDIFDTSMPSKRAITLMEETIAQinielgIPTV 79
Cdd:pfam00149   1 MRILVIGDLHL----------PGQLDDLLELLKKLLEEGkPDLVLHAGDLVDRGPPSEEVLELLERLIKY------VPVY 64


                  ....*..
gi 739719838   80 IINGNHD 86
Cdd:pfam00149  65 LVRGNHD 71
YaeI COG1408
Predicted phosphohydrolase, MPP superfamily [General function prediction only];
1-97 4.25e-08

Predicted phosphohydrolase, MPP superfamily [General function prediction only];


Pssm-ID: 441018 [Multi-domain]  Cd Length: 268  Bit Score: 53.65  E-value: 4.25e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739719838   1 MKVIHTADWHLGKVLNGQSfledqsyiLDEFIKKVEKECPDVVIIAGDIFDTSMPSKRAitlMEETIAQINIELGIptVI 80
Cdd:COG1408   43 LRIVQLSDLHLGPFIGGER--------LERLVEKINALKPDLVVLTGDLVDGSVAELEA---LLELLKKLKAPLGV--YA 109

                         90
                 ....*....|....*..
gi 739719838  81 INGNHDgkarlrYGSNW 97
Cdd:COG1408  110 VLGNHD------YYAGL 120
47 PHA02546
endonuclease subunit; Provisional
 1-257 5.63e-08

endonuclease subunit; Provisional


Pssm-ID: 222867 [Multi-domain]  Cd Length: 340  Bit Score: 53.85  E-value: 5.63e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739719838   1 MKVIHTADWHLGKVLNGQSFledQSYILDeFIKKV----EKECPDVVIIAGDIFDTsmpsKRAITLM-----EETIAQIN 71
Cdd:PHA02546   1 MKILLIGDQHLGVRKDDPWF---QNYQLK-FIKQAieysKAHGITTWIQLGDTFDV----RKAITQNtmnfvREKIFDLL 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739719838  72 IELGIPTVIINGNHDgkarlrygsnWFQKNELFIRTeIEDFLNpiQFGNVRIFTMPfftlaearqyldvTLTTYEDAVAQ 151
Cdd:PHA02546  73 KEAGITLHVLVGNHD----------MYYKNTIRPNA-PTELLG--QYDNITVIDEP-------------TTVDFDGCSID 126

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739719838 152 LI--------AMIKPKLDASFHNILVGH-----FTVYGAPKSDSereitvgtieSVAPSILEGFDAVMLGHIHHpfALNQ 218
Cdd:PHA02546 127 LIpwickentEEILEFIKNSKSEYCVGHwelngFYFYKGMKSDH----------GLDPDFLKKYKQVWSGHFHT--ISEK 194

                        250       260       270
                 ....*....|....*....|....*....|....*....
gi 739719838 219 SNIYYSGSLLQYSFSEVNQPKGFRCFQILDDEMTqrFIQ 257
Cdd:PHA02546 195 GNVTYIGTPYTLTAGDENDPRGFWVFDTETHKLE--FIA 231
MPP_YkuE_C cd07385
Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; YkuE is an ...
 2-91 3.78e-07

Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; YkuE is an uncharacterized Bacillus subtilis protein with a C-terminal metallophosphatase domain and an N-terminal twin-arginine (RR) motif. An RR-signal peptide derived from the Bacillus subtilis YkuE protein can direct Tat-dependent secretion of agarase in Streptomyces lividans. This is an indication that YkuE is transported by the Bacillus subtilis Tat (Twin-arginine translocation) pathway machinery. YkuE belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination.


Pssm-ID: 277331 [Multi-domain]  Cd Length: 224  Bit Score: 50.36  E-value: 3.78e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739719838   2 KVIHTADWHLGKVLnGQSFLedqsyilDEFIKKVEKECPDVVIIAGDIFDTSMPSkraITLMEETIAQINIELGIPTVIi 81
Cdd:cd07385    3 RIVQLSDIHLGPFV-GRTRL-------QKVVRKVNELNPDLIVITGDLVDGDVSV---LRLLASPLSKLKAPLGVYFVL- 70

                         90
                 ....*....|
gi 739719838  82 nGNHDGKARL 91
Cdd:cd07385   71 -GNHDYYSGD 79
MPP_PF1019 cd07391
Pyrococcus furiosus PF1019 and related proteins, metallophosphatase domain; This family ...
 7-87 3.63e-05

Pyrococcus furiosus PF1019 and related proteins, metallophosphatase domain; This family includes bacterial and archeal proteins homologous to PF1019, an uncharacterized Pyrococcus furiosus protein. The domain present in members of this family belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination.


Pssm-ID: 277337  Cd Length: 175  Bit Score: 43.84  E-value: 3.63e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739719838   7 ADWHLGKV----LNGQSFLEDQSY-ILDEFIKKVEKECPDVVIIAGDIFDTSMPSKRAITlmEETIAQINIELGIPTVII 81
Cdd:cd07391    4 ADLHLGYEeelrRQGINLPRRQKErLLERLDRLLEELGPDRLVILGDLKHSFGRVSRQER--REVPFFRLLAKDVDVILI 81


                 ....*.
gi 739719838  82 NGNHDG 87
Cdd:cd07391   82 RGNHDG 87
SbcD_C pfam12320
Type 5 capsule protein repressor C-terminal domain; This domain is found in bacteria and ...
 282-346 4.78e-04

Type 5 capsule protein repressor C-terminal domain; This domain is found in bacteria and archaea. This domain is about 90 amino acids in length. This domain is found associated with pfam00149. SbcD works in complex with SbdC (SbcDC) which is a transcription regulator. It down-regulates transcription of arl and mgr to inhibit type 5 capsule protein production. It acts as part of the SOS pathway of bacteria.


Pssm-ID: 463533  Cd Length: 100  Bit Score: 39.20  E-value: 4.78e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 739719838  282 DHQEDYFHFHLSELEFVKDPMQQLKQQFPNT------LALTQQVKEISSQERATKNIKKMKPMEIVNSFYK 346
Cdd:pfam12320  27 ADREDYLEVELTDEEPIPDLMERLREAYPNIpvellrIRRTREERQAEEEEEAAEDLEELSPLELFERFYE 97
MPP_1 cd07400
Uncharacterized subfamily, metallophosphatase domain; Uncharacterized subfamily of the MPP ...
 31-86 7.38e-04

Uncharacterized subfamily, metallophosphatase domain; Uncharacterized subfamily of the MPP superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination.


Pssm-ID: 277345 [Multi-domain]  Cd Length: 138  Bit Score: 39.20  E-value: 7.38e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 739719838  31 FIKKVEKECPDVVIIAGDIFDTSMPSKRAITlmEETIAQINIElgiPTVIINGNHD 86
Cdd:cd07400   22 LLDEINALKPDLVVVTGDLTQRARPAEFEEA--REFLDALEPE---PVVVVPGNHD 72
UshA COG0737
2',3'-cyclic-nucleotide 2'-phosphodiesterase/5'- or 3'-nucleotidase, 5'-nucleotidase family ...
 2-215 1.34e-03

2',3'-cyclic-nucleotide 2'-phosphodiesterase/5'- or 3'-nucleotidase, 5'-nucleotidase family [Nucleotide transport and metabolism, Defense mechanisms];


Pssm-ID: 440500 [Multi-domain]  Cd Length: 471  Bit Score: 40.61  E-value: 1.34e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739719838   2 KVIHTADWHlgkvlngqSFLEDQSYILDE------------FIKKVEKECPDVVII-AGDIFDTSMPSkrAITLMEETIA 68
Cdd:COG0737    6 TILHTNDLH--------GHLEPYDYFDDKygkagglarlatLIKQLRAENPNTLLLdAGDTIQGSPLS--TLTKGEPMIE 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739719838  69 QINiELGIPTVIInGNHD---GKARLR----------YGSNWFQKNELfirteiEDFLNP---IQFGNVRI----FTMPF 128
Cdd:COG0737   76 AMN-ALGYDAATL-GNHEfdyGLDVLLelldganfpvLSANVYDKDTG------EPLFKPytiKEVGGVKVgvigLTTPD 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739719838 129 F-TLAEARQYLDVTLTTYEDAVAQLIAMIK-PKLDAsfhNILVGHFtvyGAPKSDSEreitvgtiesVAPSiLEGFDAVM 206
Cdd:COG0737  148 TpTWSSPGNIGGLTFTDPVEAAQKYVDELRaEGADV---VVLLSHL---GLDGEDRE----------LAKE-VPGIDVIL 210


                 ....*....
gi 739719838 207 LGHIHHPFA 215
Cdd:COG0737  211 GGHTHTLLP 219
MPP_Dcr2 cd07383
Saccharomyces cerevisiae DCR2 phosphatase and related proteins, metallophosphatase domain; ...
 2-87 3.25e-03

Saccharomyces cerevisiae DCR2 phosphatase and related proteins, metallophosphatase domain; DCR2 phosphatase (Dosage-dependent Cell Cycle Regulator 2) functions together with DCR1 (Gid8) in a common pathway to accelerate initiation of DNA replication in Saccharomyces cerevisiae. Genetic analysis suggests that DCR1 functions upstream of DCR2. DCR2 interacts with and dephosphorylates Sic1, an inhibitor of mitotic cyclin/cyclin-dependent kinase complexes, which may serve to trigger the initiation of cell division. DCR2 belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination.


Pssm-ID: 277329 [Multi-domain]  Cd Length: 202  Bit Score: 38.43  E-value: 3.25e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739719838   2 KVIHTADWHLGKVLNGQSFLEDQSYILDEFIKKV-EKECPDVVIIAGDIF--DTSMPSKrAITLMEETIAQInIELGIPT 78
Cdd:cd07383    4 KILQFADLHFGEGEWTCWEGCEADLKTVEFIESVlDEEKPDLVVLTGDLItgENTADDN-ATSYLDKAVSPL-VERGIPW 81


                 ....*....
gi 739719838  79 VIINGNHDG 87
Cdd:cd07383   82 AATFGNHDG 90
MPP_superfamily cd00838
metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also ...
 4-86 7.14e-03

metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination.


Pssm-ID: 277317 [Multi-domain]  Cd Length: 130  Bit Score: 36.48  E-value: 7.14e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739719838   4 IHTADWHLGkvlngqsFLEDQSYILDEFIKKVEkecPDVVIIAGDIFDtsmpsKRAITLMEETIAQINIELGIPTVIING 83
Cdd:cd00838    1 LVISDIHGN-------LEALEAVLEAALAKAEK---PDLVICLGDLVD-----YGPDPEEVELKALRLLLAGIPVYVVPG 65


                 ...
gi 739719838  84 NHD 86
Cdd:cd00838   66 NHD 68
 
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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