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Conserved domains on  [gi|612671440|gb|EZS87536|]
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nuclease sbcCD subunit D [Staphylococcus aureus VET0159R]

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

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];
1-265 1.18e-76

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


:

Pssm-ID: 440189 [Multi-domain]  Cd Length: 250  Bit Score: 236.73  E-value: 1.18e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612671440   1 MKIIHTADWHLGKILNGKQLLEDQAYILDTFVEKMKEEEPDIIVIAGDLYDTTYPSKDAIMLLEQAIGKLNlELRIPIIM 80
Cdd:COG0420    1 MRFLHTADWHLGKPLHGASRREDQLAALDRLVDLAIEEKVDAVLIAGDLFDSANPSPEAVRLLAEALRRLS-EAGIPVVL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612671440  81 ISGNHDGKERLNYGASWFENNQLFIRTDFtsINSPIEIN---GVNFYTLPYATvsemkhyfeddtiETHQQGITRCIETI 157
Cdd:COG0420   80 IAGNHDSPSRLSAGSPLLENLGVHVFGSV--EPEPVELEdglGVAVYGLPYLR-------------PSDEEALRDLLERL 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612671440 158 APEIDEGAVNILISHLTVQGGKTSdseRPLTIGTVES---VQKGvfdiFDYVMLGHLHHPFSI-EDDKIKYSGSLLQYSF 233
Cdd:COG0420  145 PRALDPGGPNILLLHGFVAGASGS---RDIYVAPVPLsalPAAG----FDYVALGHIHRPQVLgGDPRIRYSGSPEPRSF 217

                        250       260       270
                 ....*....|....*....|....*....|...
gi 612671440 234 SEAGQaKGYRRVTINDGIINDV-FIPLKPLRQL 265
Cdd:COG0420  218 SEAGG-KGVLLVELDAGGLVSVeFVPLPATRRF 249
SbcD_C pfam12320
Type 5 capsule protein repressor C-terminal domain; This domain is found in bacteria and ...
 261-344 3.91e-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: 3.91e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612671440  261 PLRQLEIISGEYNDVINEKVHVK----NKDNYLHFKLKNMSHITDPMMSLKQIYPNT----LALTNETFSYNEENNAIEI 332
Cdd:pfam12320   1 PLRDLRRIKGSLEELLAALAYLEeepaDREDYLEVELTDEEPIPDLMERLREAYPNIpvelLRIRRTREERQAEEEEEAA 80

                          90
                  ....*....|..
gi 612671440  333 GEKDDMSIIEMF 344
Cdd:pfam12320  81 EDLEELSPLELF 92
 
Name Accession Description Interval E-value
SbcD COG0420
DNA repair exonuclease SbcCD nuclease subunit [Replication, recombination and repair];
1-265 1.18e-76

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


Pssm-ID: 440189 [Multi-domain]  Cd Length: 250  Bit Score: 236.73  E-value: 1.18e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612671440   1 MKIIHTADWHLGKILNGKQLLEDQAYILDTFVEKMKEEEPDIIVIAGDLYDTTYPSKDAIMLLEQAIGKLNlELRIPIIM 80
Cdd:COG0420    1 MRFLHTADWHLGKPLHGASRREDQLAALDRLVDLAIEEKVDAVLIAGDLFDSANPSPEAVRLLAEALRRLS-EAGIPVVL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612671440  81 ISGNHDGKERLNYGASWFENNQLFIRTDFtsINSPIEIN---GVNFYTLPYATvsemkhyfeddtiETHQQGITRCIETI 157
Cdd:COG0420   80 IAGNHDSPSRLSAGSPLLENLGVHVFGSV--EPEPVELEdglGVAVYGLPYLR-------------PSDEEALRDLLERL 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612671440 158 APEIDEGAVNILISHLTVQGGKTSdseRPLTIGTVES---VQKGvfdiFDYVMLGHLHHPFSI-EDDKIKYSGSLLQYSF 233
Cdd:COG0420  145 PRALDPGGPNILLLHGFVAGASGS---RDIYVAPVPLsalPAAG----FDYVALGHIHRPQVLgGDPRIRYSGSPEPRSF 217

                        250       260       270
                 ....*....|....*....|....*....|...
gi 612671440 234 SEAGQaKGYRRVTINDGIINDV-FIPLKPLRQL 265
Cdd:COG0420  218 SEAGG-KGVLLVELDAGGLVSVeFVPLPATRRF 249
sbcd TIGR00619
exonuclease SbcD; All proteins in this family for which functions are known are ...
 1-241 1.77e-51

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: 172.22  E-value: 1.77e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612671440    1 MKIIHTADWHLGKILNGKQLLEDQAYILDTFVEKMKEEEPDIIVIAGDLYDTTYPSKDAIMLLEQAIGKLNLELRIPIIM 80
Cdd:TIGR00619   1 MRILHTSDWHLGKTLEGVSRLAEQKAFLDDLLEFAKAEQVDALLVAGDVFDTANPPAEAQELFNAFFVNLSDTGIRPIVV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612671440   81 ISGNHDGKERLNYGASWFENNQLFIRTDFTSINSPIEI----NG-VNFYTLPYATVSEMKHYFEDDTIETH--------- 146
Cdd:TIGR00619  81 ISGNHDSAQRLSAAKKLLAELGVFVVGSPGHDPQILLLkdgtNGeGLCVGLFLLPREAILTRAGLDGFGLElllahtdvk 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612671440  147 -QQGITRCIETIAPeideGAVNILISHLTVQGGKTSDSERPLTIGTVESVQKGVFDIFDYVMLGHLH-HPFSIEDDKIKY 224
Cdd:TIGR00619 161 lRQAAEALKLRLDQ----DLPKILLAHLFTAGATKSDAERRIYIGTLYAFPLQNFPEADYIALGHIHiHKISKGRERVRY 236

                         250
                  ....*....|....*..
gi 612671440  225 SGSLLQYSFSEAGQAKG 241
Cdd:TIGR00619 237 SGSPFPLSFDEAGKDKY 253
MPP_Mre11_N cd00840
Mre11 nuclease, N-terminal metallophosphatase domain; Mre11 (also known as SbcD in Escherichia ...
 2-234 2.26e-37

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: 133.16  E-value: 2.26e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612671440   2 KIIHTADWHLGKILNGK-QLLEDQAYILDTFVEKMKEEEPDIIVIAGDLYDTTYPSKDAIMLLEQAIGKLNlELRIPIIM 80
Cdd:cd00840    1 RFLHTADWHLGYPLYGLsRREEDFFKAFEEIVDLAIEEKVDFVLIAGDLFDSNNPSPEALKLAIEGLRRLC-EAGIPVFV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612671440  81 ISGNHDGKERlnygaswfennqlfirtdftsinspieingVNFYTLPYATVSEMKHYFEDdtiethqqgitrcIETIAPE 160
Cdd:cd00840   80 IAGNHDSPAR------------------------------VAIYGLPYLRDERLERLFED-------------LELRPRL 116

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 612671440 161 IDEGAVNILISHLTVQGGKTSDSERPLTIGTVesvqkgVFDIFDYVMLGHLHHPFSIEDDK--IKYSGSLLQYSFS 234
Cdd:cd00840  117 LKPDWFNILLLHQGVDGAGPSDSERPIVPEDL------LPDGFDYVALGHIHKPQIIEGGGppIVYPGSPEPTSFS 186
PRK10966 PRK10966
exonuclease subunit SbcD; Provisional
 1-290 3.51e-25

exonuclease subunit SbcD; Provisional


Pssm-ID: 182871 [Multi-domain]  Cd Length: 407  Bit Score: 105.41  E-value: 3.51e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612671440   1 MKIIHTADWHLGKILNGK-QLLEDQAYiLDTFVEKMKEEEPDIIVIAGDLYDTTYPSKDAIMLLEQAIGKLNlELRIPII 79
Cdd:PRK10966   1 MRILHTSDWHLGQNFYSKsRAAEHQAF-LDWLLEQVQEHQVDAIIVAGDIFDTGSPPSYARELYNRFVVNLQ-QTGCQLV 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612671440  80 MISGNHDGKERLNygaswfENNQLFIRTDFTSINS--------PIEINGVN------FYTLPY-----ATVSEMKHYFED 140
Cdd:PRK10966  79 VLAGNHDSVATLN------ESRDLLAFLNTTVIASasddlghqVIILPRRDgtpgavLCAIPFlrprdVITSQAGQSGIE 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612671440 141 ------DTIETHQQGITRCIETIAPEIDEGAVNILISHLTVQGGKTSDSERPLTIGTVESVQKGVFDIFDYVMLGHLHHP 214
Cdd:PRK10966 153 kqqalqAAIADHYQQLYQLACELRDELGQPLPIIATGHLTTVGASKSDSVRDIYIGTLDAFPAQAFPPADYIALGHIHRA 232

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612671440 215 FSI-EDDKIKYSGSLLQYSFSEAGQAKGYRRVTINDGIINDV-------FIPLKPLR-QLEIISG---EYNDVINEK--- 279
Cdd:PRK10966 233 QKVgGTEHIRYSGSPIPLSFDELGKSKSVHLVEFDQGKLQSVtplpvpvFQPMAVLKgDLASITAqleQWRDVSQEPpvw 312

                        330
                 ....*....|...
gi 612671440 280 --VHVKNKDnYLH 290
Cdd:PRK10966 313 ldIEVTTDD-YLH 324
Metallophos pfam00149
Calcineurin-like phosphoesterase; This family includes a diverse range of phosphoesterases, ...
 1-121 1.20e-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: 55.30  E-value: 1.20e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612671440    1 MKIIHTADWHLgkilngkqllEDQAYILDTFVEKMKEEE-PDIIVIAGDLYDTTYPSkDAIMLLEQAIGKlnlelRIPII 79
Cdd:pfam00149   1 MRILVIGDLHL----------PGQLDDLLELLKKLLEEGkPDLVLHAGDLVDRGPPS-EEVLELLERLIK-----YVPVY 64

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 612671440   80 MISGNHDGKERLNYGASWFENNQLFIRTDFTSINSPIEINGV 121
Cdd:pfam00149  65 LVRGNHDFDYGECLRLYPYLGLLARPWKRFLEVFNFLPLAGI 106
SbcD_C pfam12320
Type 5 capsule protein repressor C-terminal domain; This domain is found in bacteria and ...
 261-344 3.91e-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: 3.91e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612671440  261 PLRQLEIISGEYNDVINEKVHVK----NKDNYLHFKLKNMSHITDPMMSLKQIYPNT----LALTNETFSYNEENNAIEI 332
Cdd:pfam12320   1 PLRDLRRIKGSLEELLAALAYLEeepaDREDYLEVELTDEEPIPDLMERLREAYPNIpvelLRIRRTREERQAEEEEEAA 80

                          90
                  ....*....|..
gi 612671440  333 GEKDDMSIIEMF 344
Cdd:pfam12320  81 EDLEELSPLELF 92
 
Name Accession Description Interval E-value
SbcD COG0420
DNA repair exonuclease SbcCD nuclease subunit [Replication, recombination and repair];
1-265 1.18e-76

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


Pssm-ID: 440189 [Multi-domain]  Cd Length: 250  Bit Score: 236.73  E-value: 1.18e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612671440   1 MKIIHTADWHLGKILNGKQLLEDQAYILDTFVEKMKEEEPDIIVIAGDLYDTTYPSKDAIMLLEQAIGKLNlELRIPIIM 80
Cdd:COG0420    1 MRFLHTADWHLGKPLHGASRREDQLAALDRLVDLAIEEKVDAVLIAGDLFDSANPSPEAVRLLAEALRRLS-EAGIPVVL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612671440  81 ISGNHDGKERLNYGASWFENNQLFIRTDFtsINSPIEIN---GVNFYTLPYATvsemkhyfeddtiETHQQGITRCIETI 157
Cdd:COG0420   80 IAGNHDSPSRLSAGSPLLENLGVHVFGSV--EPEPVELEdglGVAVYGLPYLR-------------PSDEEALRDLLERL 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612671440 158 APEIDEGAVNILISHLTVQGGKTSdseRPLTIGTVES---VQKGvfdiFDYVMLGHLHHPFSI-EDDKIKYSGSLLQYSF 233
Cdd:COG0420  145 PRALDPGGPNILLLHGFVAGASGS---RDIYVAPVPLsalPAAG----FDYVALGHIHRPQVLgGDPRIRYSGSPEPRSF 217

                        250       260       270
                 ....*....|....*....|....*....|...
gi 612671440 234 SEAGQaKGYRRVTINDGIINDV-FIPLKPLRQL 265
Cdd:COG0420  218 SEAGG-KGVLLVELDAGGLVSVeFVPLPATRRF 249
sbcd TIGR00619
exonuclease SbcD; All proteins in this family for which functions are known are ...
 1-241 1.77e-51

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: 172.22  E-value: 1.77e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612671440    1 MKIIHTADWHLGKILNGKQLLEDQAYILDTFVEKMKEEEPDIIVIAGDLYDTTYPSKDAIMLLEQAIGKLNLELRIPIIM 80
Cdd:TIGR00619   1 MRILHTSDWHLGKTLEGVSRLAEQKAFLDDLLEFAKAEQVDALLVAGDVFDTANPPAEAQELFNAFFVNLSDTGIRPIVV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612671440   81 ISGNHDGKERLNYGASWFENNQLFIRTDFTSINSPIEI----NG-VNFYTLPYATVSEMKHYFEDDTIETH--------- 146
Cdd:TIGR00619  81 ISGNHDSAQRLSAAKKLLAELGVFVVGSPGHDPQILLLkdgtNGeGLCVGLFLLPREAILTRAGLDGFGLElllahtdvk 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612671440  147 -QQGITRCIETIAPeideGAVNILISHLTVQGGKTSDSERPLTIGTVESVQKGVFDIFDYVMLGHLH-HPFSIEDDKIKY 224
Cdd:TIGR00619 161 lRQAAEALKLRLDQ----DLPKILLAHLFTAGATKSDAERRIYIGTLYAFPLQNFPEADYIALGHIHiHKISKGRERVRY 236

                         250
                  ....*....|....*..
gi 612671440  225 SGSLLQYSFSEAGQAKG 241
Cdd:TIGR00619 237 SGSPFPLSFDEAGKDKY 253
MPP_Mre11_N cd00840
Mre11 nuclease, N-terminal metallophosphatase domain; Mre11 (also known as SbcD in Escherichia ...
 2-234 2.26e-37

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: 133.16  E-value: 2.26e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612671440   2 KIIHTADWHLGKILNGK-QLLEDQAYILDTFVEKMKEEEPDIIVIAGDLYDTTYPSKDAIMLLEQAIGKLNlELRIPIIM 80
Cdd:cd00840    1 RFLHTADWHLGYPLYGLsRREEDFFKAFEEIVDLAIEEKVDFVLIAGDLFDSNNPSPEALKLAIEGLRRLC-EAGIPVFV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612671440  81 ISGNHDGKERlnygaswfennqlfirtdftsinspieingVNFYTLPYATVSEMKHYFEDdtiethqqgitrcIETIAPE 160
Cdd:cd00840   80 IAGNHDSPAR------------------------------VAIYGLPYLRDERLERLFED-------------LELRPRL 116

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 612671440 161 IDEGAVNILISHLTVQGGKTSDSERPLTIGTVesvqkgVFDIFDYVMLGHLHHPFSIEDDK--IKYSGSLLQYSFS 234
Cdd:cd00840  117 LKPDWFNILLLHQGVDGAGPSDSERPIVPEDL------LPDGFDYVALGHIHKPQIIEGGGppIVYPGSPEPTSFS 186
PRK10966 PRK10966
exonuclease subunit SbcD; Provisional
 1-290 3.51e-25

exonuclease subunit SbcD; Provisional


Pssm-ID: 182871 [Multi-domain]  Cd Length: 407  Bit Score: 105.41  E-value: 3.51e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612671440   1 MKIIHTADWHLGKILNGK-QLLEDQAYiLDTFVEKMKEEEPDIIVIAGDLYDTTYPSKDAIMLLEQAIGKLNlELRIPII 79
Cdd:PRK10966   1 MRILHTSDWHLGQNFYSKsRAAEHQAF-LDWLLEQVQEHQVDAIIVAGDIFDTGSPPSYARELYNRFVVNLQ-QTGCQLV 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612671440  80 MISGNHDGKERLNygaswfENNQLFIRTDFTSINS--------PIEINGVN------FYTLPY-----ATVSEMKHYFED 140
Cdd:PRK10966  79 VLAGNHDSVATLN------ESRDLLAFLNTTVIASasddlghqVIILPRRDgtpgavLCAIPFlrprdVITSQAGQSGIE 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612671440 141 ------DTIETHQQGITRCIETIAPEIDEGAVNILISHLTVQGGKTSDSERPLTIGTVESVQKGVFDIFDYVMLGHLHHP 214
Cdd:PRK10966 153 kqqalqAAIADHYQQLYQLACELRDELGQPLPIIATGHLTTVGASKSDSVRDIYIGTLDAFPAQAFPPADYIALGHIHRA 232

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612671440 215 FSI-EDDKIKYSGSLLQYSFSEAGQAKGYRRVTINDGIINDV-------FIPLKPLR-QLEIISG---EYNDVINEK--- 279
Cdd:PRK10966 233 QKVgGTEHIRYSGSPIPLSFDELGKSKSVHLVEFDQGKLQSVtplpvpvFQPMAVLKgDLASITAqleQWRDVSQEPpvw 312

                        330
                 ....*....|...
gi 612671440 280 --VHVKNKDnYLH 290
Cdd:PRK10966 313 ldIEVTTDD-YLH 324
YaeI COG1408
Predicted phosphohydrolase, MPP superfamily [General function prediction only];
1-172 3.31e-11

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


Pssm-ID: 441018 [Multi-domain]  Cd Length: 268  Bit Score: 62.89  E-value: 3.31e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612671440   1 MKIIHTADWHLGKILNGKQLledqayilDTFVEKMKEEEPDIIVIAGDLYDTTYPSKDAIMlleQAIGKLNleLRIPIIM 80
Cdd:COG1408   43 LRIVQLSDLHLGPFIGGERL--------ERLVEKINALKPDLVVLTGDLVDGSVAELEALL---ELLKKLK--APLGVYA 109

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612671440  81 ISGNHD---GKERL-----NYGASWFENNQLFIRTDftsiNSPIEINGVNFYTLpyatvsemkHYFEDdtiethqqgitr 152
Cdd:COG1408  110 VLGNHDyyaGLEELraaleEAGVRVLRNEAVTLERG----GDRLNLAGVDDPHA---------GRFPD------------ 164

                        170       180
                 ....*....|....*....|
gi 612671440 153 cIETIAPEIDEGAVNILISH 172
Cdd:COG1408  165 -LEKALAGVPPDAPRILLAH 183
MPP_YkuE_C cd07385
Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; YkuE is an ...
 2-172 7.71e-10

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: 58.45  E-value: 7.71e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612671440   2 KIIHTADWHLGKILNGKQLledqayilDTFVEKMKEEEPDIIVIAGDLYDTtypSKDAIMLLEQAIGKLNLELriPIIMI 81
Cdd:cd07385    3 RIVQLSDIHLGPFVGRTRL--------QKVVRKVNELNPDLIVITGDLVDG---DVSVLRLLASPLSKLKAPL--GVYFV 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612671440  82 SGNHDGKERLNYGASWFENNQLFIrtdfTSINSPIEINGVNFYTLPYatvsemkhYFEDDTIETHQQGITRcietIAPEI 161
Cdd:cd07385   70 LGNHDYYSGDVEVWIAALEKAGIT----VLRNESVELSRDGATIGLA--------GSGVDDIGGHGEDLEK----ALKGL 133

                        170
                 ....*....|.
gi 612671440 162 DEGAVNILISH 172
Cdd:cd07385  134 DENDPVILLAH 144
Metallophos pfam00149
Calcineurin-like phosphoesterase; This family includes a diverse range of phosphoesterases, ...
 1-121 1.20e-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: 55.30  E-value: 1.20e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612671440    1 MKIIHTADWHLgkilngkqllEDQAYILDTFVEKMKEEE-PDIIVIAGDLYDTTYPSkDAIMLLEQAIGKlnlelRIPII 79
Cdd:pfam00149   1 MRILVIGDLHL----------PGQLDDLLELLKKLLEEGkPDLVLHAGDLVDRGPPS-EEVLELLERLIK-----YVPVY 64

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 612671440   80 MISGNHDGKERLNYGASWFENNQLFIRTDFTSINSPIEINGV 121
Cdd:pfam00149  65 LVRGNHDFDYGECLRLYPYLGLLARPWKRFLEVFNFLPLAGI 106
COG2129 COG2129
Predicted phosphoesterase, related to the Icc protein [General function prediction only];
2-172 2.14e-08

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


Pssm-ID: 441732 [Multi-domain]  Cd Length: 211  Bit Score: 53.87  E-value: 2.14e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612671440   2 KIIHTADWHLGKilngkqlledqaYILDTFVEKMKEEEPDIIVIAGDLYDTTyPSKDAIMLLEqAIGKLNlelrIPIIMI 81
Cdd:COG2129    1 KILAVSDLHGNF------------DLLEKLLELARAEDADLVILAGDLTDFG-TAEEAREVLE-ELAALG----VPVLAV 62

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612671440  82 SGNHDGKERLNYgaswfennqlFIRTDFTSI-NSPIEINGVNFYTLPYATVSEMKHYFEDDTIEthqqgitrcIETIAPE 160
Cdd:COG2129   63 PGNHDDPEVLDA----------LEESGVHNLhGRVVEIGGLRIAGLGGSRPTPFGTPYEYTEEE---------IEERLAK 123

                        170
                 ....*....|..
gi 612671440 161 IDEGAVNILISH 172
Cdd:COG2129  124 LREKDVDILLTH 135
CpdA COG1409
3',5'-cyclic AMP phosphodiesterase CpdA [Signal transduction mechanisms];
1-252 4.69e-08

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


Pssm-ID: 441019 [Multi-domain]  Cd Length: 234  Bit Score: 53.16  E-value: 4.69e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612671440   1 MKIIHTADWHLGKILNGkqlleDQAYILDTFVEKMKEEEPDIIVIAGDLydTTYPSKDAIMLLEQAIGKLNlelrIPIIM 80
Cdd:COG1409    1 FRFAHISDLHLGAPDGS-----DTAEVLAAALADINAPRPDFVVVTGDL--TDDGEPEEYAAAREILARLG----VPVYV 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612671440  81 ISGNHDgkerlNYGASWFENNQLFIRTDFTSINSPIEINGVNFYTLpyatvsemkhyfeDDTIETHQQG------ITRCI 154
Cdd:COG1409   70 VPGNHD-----IRAAMAEAYREYFGDLPPGGLYYSFDYGGVRFIGL-------------DSNVPGRSSGelgpeqLAWLE 131

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612671440 155 ETIApEIDEGAVnILISHLTVQGGkTSDSERPLTIGTVEsvqkgVFDIF-----DYVMLGHLHHPFSIEDDKIKYSGSLl 229
Cdd:COG1409  132 EELA-AAPAKPV-IVFLHHPPYST-GSGSDRIGLRNAEE-----LLALLarygvDLVLSGHVHRYERTRRDGVPYIVAG- 202

                        250       260
                 ....*....|....*....|....*.
gi 612671440 230 qysfSEAGQ---AKGYRRVTINDGII 252
Cdd:COG1409  203 ----STGGQvrlPPGYRVIEVDGDGL 224
MPP_Dcr2 cd07383
Saccharomyces cerevisiae DCR2 phosphatase and related proteins, metallophosphatase domain; ...
 2-87 8.33e-06

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: 46.13  E-value: 8.33e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612671440   2 KIIHTADWHLGKILNGKQllEDQAYILDT--FVEKM-KEEEPDIIVIAGDL---YDTTYpsKDAIMLLEQAIGKLNlELR 75
Cdd:cd07383    4 KILQFADLHFGEGEWTCW--EGCEADLKTveFIESVlDEEKPDLVVLTGDLitgENTAD--DNATSYLDKAVSPLV-ERG 78

                         90
                 ....*....|..
gi 612671440  76 IPIIMISGNHDG 87
Cdd:cd07383   79 IPWAATFGNHDG 90
MPP_1 cd07400
Uncharacterized subfamily, metallophosphatase domain; Uncharacterized subfamily of the MPP ...
 3-86 1.01e-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: 41.90  E-value: 1.01e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612671440   3 IIHTADWHLGKILNGKQLLEDqayildtFVEKMKEEEPDIIVIAGDLYDTTYPS--KDAIMLLEqaigKLNLElriPIIM 80
Cdd:cd07400    1 IAHISDLHFGEERKPEVLELN-------LLDEINALKPDLVVVTGDLTQRARPAefEEAREFLD----ALEPE---PVVV 66


                 ....*.
gi 612671440  81 ISGNHD 86
Cdd:cd07400   67 VPGNHD 72
MPP_GpdQ cd07402
Enterobacter aerogenes GpdQ and related proteins, metallophosphatase domain; GpdQ ...
 3-86 1.62e-04

Enterobacter aerogenes GpdQ and related proteins, metallophosphatase domain; GpdQ (glycerophosphodiesterase Q, also known as Rv0805 in Mycobacterium tuberculosis) is a binuclear metallophosphoesterase from Enterobacter aerogenes that catalyzes the hydrolysis of mono-, di-, and triester substrates, including some organophosphate pesticides and products of the degradation of nerve agents. The GpdQ homolog, Rv0805, has 2',3'-cyclic nucleotide phosphodiesterase activity. GpdQ and Rv0805 belong 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: 277347 [Multi-domain]  Cd Length: 240  Bit Score: 42.65  E-value: 1.62e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612671440   3 IIHTADWHLGKILNGKQLLEDQAYILDTFVEKMKEE--EPDIIVIAGDLYDttYPSKDAIMLLEQAIGKLnlelRIPIIM 80
Cdd:cd07402    1 IAQISDTHLFAPGEGALLGVDTAARLAAAVAQVNALhpRPDLVVVTGDLSD--DGSPESYERLRELLAPL----PAPVYW 74


                 ....*.
gi 612671440  81 ISGNHD 86
Cdd:cd07402   75 IPGNHD 80
SbcD_C pfam12320
Type 5 capsule protein repressor C-terminal domain; This domain is found in bacteria and ...
 261-344 3.91e-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: 3.91e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612671440  261 PLRQLEIISGEYNDVINEKVHVK----NKDNYLHFKLKNMSHITDPMMSLKQIYPNT----LALTNETFSYNEENNAIEI 332
Cdd:pfam12320   1 PLRDLRRIKGSLEELLAALAYLEeepaDREDYLEVELTDEEPIPDLMERLREAYPNIpvelLRIRRTREERQAEEEEEAA 80

                          90
                  ....*....|..
gi 612671440  333 GEKDDMSIIEMF 344
Cdd:pfam12320  81 EDLEELSPLELF 92
MPP_superfamily cd00838
metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also ...
 4-86 6.58e-04

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: 39.56  E-value: 6.58e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612671440   4 IHTADWHLGKILNGKQLLEDQAyildtfvekmKEEEPDIIVIAGDL-YDTTYPSkdaimlLEQAIGKLNLELRIPIIMIS 82
Cdd:cd00838    1 LVISDIHGNLEALEAVLEAALA----------KAEKPDLVICLGDLvDYGPDPE------EVELKALRLLLAGIPVYVVP 64


                 ....
gi 612671440  83 GNHD 86
Cdd:cd00838   65 GNHD 68
RpfG COG3437
Response regulator c-di-GMP phosphodiesterase, RpfG family, contains REC and HD-GYP domains ...
 18-98 1.41e-03

Response regulator c-di-GMP phosphodiesterase, RpfG family, contains REC and HD-GYP domains [Signal transduction mechanisms];


Pssm-ID: 442663 [Multi-domain]  Cd Length: 224  Bit Score: 39.76  E-value: 1.41e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612671440  18 KQLLEDQAYILDTF------VEKMKEEEPDIIVIagdlyDTTYPSKDAIMLLEQaIGKLNLELRIPIIMISGNHDGKER- 90
Cdd:COG3437   23 RQLLRTLGYDVVTAesgeeaLELLLEAPPDLILL-----DVRMPGMDGFELLRL-LRADPSTRDIPVIFLTALADPEDRe 96

                         90
                 ....*....|
gi 612671440  91 --LNYGASWF 98
Cdd:COG3437   97 raLEAGADDY 106
 
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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