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Conserved domains on  [gi|502911230|ref|WP_013146206|]
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MULTISPECIES: exonuclease SbcCD subunit D [unclassified Geobacillus]

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];
1-279 1.67e-85

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


:

Pssm-ID: 440189 [Multi-domain]  Cd Length: 250  Bit Score: 260.23  E-value: 1.67e-85
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502911230   1 MRILHTADWHLGRTLEGRSRMAEQEAFVDELVEIVKKEQIDIILVAGDVFDSVNPPAAAEQLFYESLARLSDKGrRPVAV 80
Cdd:COG0420    1 MRFLHTADWHLGKPLHGASRREDQLAALDRLVDLAIEEKVDAVLIAGDLFDSANPSPEAVRLLAEALRRLSEAG-IPVVL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502911230  81 ISGNHDHPDRISAARTLMCAHNIFLFGRPQAAVCRIDvpsCGETMMLAPLAYPSESRlaellssdckettmrdryDDRIR 160
Cdd:COG0420   80 IAGNHDSPSRLSAGSPLLENLGVHVFGSVEPEPVELE---DGLGVAVYGLPYLRPSD------------------EEALR 138

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502911230 161 ALLAAMAASFTAETVNIAMSHLYVAGGRTSdseRPIEVggaYTVAAESLPKA-AQYVALGHLHRPQDVkQAKTAARYSGS 239
Cdd:COG0420  139 DLLERLPRALDPGGPNILLLHGFVAGASGS---RDIYV---APVPLSALPAAgFDYVALGHIHRPQVL-GGDPRIRYSGS 211

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|
gi 502911230 240 PLAYSFSEAGQaKSVTVVDVHPGRKAKVAEIPLAAGKPLI 279
Cdd:COG0420  212 PEPRSFSEAGG-KGVLLVELDAGGLVSVEFVPLPATRRFL 250
SbcD_C pfam12320
Type 5 capsule protein repressor C-terminal domain; This domain is found in bacteria and ...
 276-365 7.24e-08

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: 49.99  E-value: 7.24e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502911230  276 KPLIRWKAT--EGLAQVYRWCEEGRDRSSWIDLEIHVTESLTmEEIDRLRKLHPG----FVHIRPVLPNRAEEMMEMSRE 349
Cdd:pfam12320   3 RDLRRIKGSleELLAALAYLEEEPADREDYLEVELTDEEPIP-DLMERLREAYPNipveLLRIRRTREERQAEEEEEAAE 81

                          90
                  ....*....|....*....
gi 502911230  350 ---PLSLEEMFHRFYERQT 365
Cdd:pfam12320  82 dleELSPLELFERFYEEQT 100
 
Name Accession Description Interval E-value
SbcD COG0420
DNA repair exonuclease SbcCD nuclease subunit [Replication, recombination and repair];
1-279 1.67e-85

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


Pssm-ID: 440189 [Multi-domain]  Cd Length: 250  Bit Score: 260.23  E-value: 1.67e-85
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502911230   1 MRILHTADWHLGRTLEGRSRMAEQEAFVDELVEIVKKEQIDIILVAGDVFDSVNPPAAAEQLFYESLARLSDKGrRPVAV 80
Cdd:COG0420    1 MRFLHTADWHLGKPLHGASRREDQLAALDRLVDLAIEEKVDAVLIAGDLFDSANPSPEAVRLLAEALRRLSEAG-IPVVL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502911230  81 ISGNHDHPDRISAARTLMCAHNIFLFGRPQAAVCRIDvpsCGETMMLAPLAYPSESRlaellssdckettmrdryDDRIR 160
Cdd:COG0420   80 IAGNHDSPSRLSAGSPLLENLGVHVFGSVEPEPVELE---DGLGVAVYGLPYLRPSD------------------EEALR 138

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502911230 161 ALLAAMAASFTAETVNIAMSHLYVAGGRTSdseRPIEVggaYTVAAESLPKA-AQYVALGHLHRPQDVkQAKTAARYSGS 239
Cdd:COG0420  139 DLLERLPRALDPGGPNILLLHGFVAGASGS---RDIYV---APVPLSALPAAgFDYVALGHIHRPQVL-GGDPRIRYSGS 211

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|
gi 502911230 240 PLAYSFSEAGQaKSVTVVDVHPGRKAKVAEIPLAAGKPLI 279
Cdd:COG0420  212 PEPRSFSEAGG-KGVLLVELDAGGLVSVEFVPLPATRRFL 250
sbcd TIGR00619
exonuclease SbcD; All proteins in this family for which functions are known are ...
 1-252 1.25e-81

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: 250.42  E-value: 1.25e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502911230    1 MRILHTADWHLGRTLEGRSRMAEQEAFVDELVEIVKKEQIDIILVAGDVFDSVNPPAAAEQLFYESLARLSDKGRRPVAV 80
Cdd:TIGR00619   1 MRILHTSDWHLGKTLEGVSRLAEQKAFLDDLLEFAKAEQVDALLVAGDVFDTANPPAEAQELFNAFFVNLSDTGIRPIVV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502911230   81 ISGNHDHPDRISAARTLMCAHNIFLFGRPQAAVCRIDVP--SCGETMMLAPLAYPSESRLAELLSSDCKETTMRDRYDDR 158
Cdd:TIGR00619  81 ISGNHDSAQRLSAAKKLLAELGVFVVGSPGHDPQILLLKdgTNGEGLCVGLFLLPREAILTRAGLDGFGLELLLAHTDVK 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502911230  159 IRALLAAMAASFTAETVNIAMSHLYVAGGRTSDSERPIEVGGAYTVAAESLPKAAQYVALGHLHRPQdvKQAKTAARYSG 238
Cdd:TIGR00619 161 LRQAAEALKLRLDQDLPKILLAHLFTAGATKSDAERRIYIGTLYAFPLQNFPEADYIALGHIHIHKI--SKGRERVRYSG 238

                         250
                  ....*....|....
gi 502911230  239 SPLAYSFSEAGQAK 252
Cdd:TIGR00619 239 SPFPLSFDEAGKDK 252
PRK10966 PRK10966
exonuclease subunit SbcD; Provisional
 1-315 4.07e-50

exonuclease subunit SbcD; Provisional


Pssm-ID: 182871 [Multi-domain]  Cd Length: 407  Bit Score: 173.59  E-value: 4.07e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502911230   1 MRILHTADWHLGRTLEGRSRMAEQEAFVDELVEIVKKEQIDIILVAGDVFDSVNPPAAAEQLFYESLARLSDKGRRPVaV 80
Cdd:PRK10966   1 MRILHTSDWHLGQNFYSKSRAAEHQAFLDWLLEQVQEHQVDAIIVAGDIFDTGSPPSYARELYNRFVVNLQQTGCQLV-V 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502911230  81 ISGNHDHPDRISAARTLMC--------------AHNIFLF----GRPQAAVCRIdvpscgetmmlaPLAYPsesrlAELL 142
Cdd:PRK10966  80 LAGNHDSVATLNESRDLLAflnttviasasddlGHQVIILprrdGTPGAVLCAI------------PFLRP-----RDVI 142

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502911230 143 SSDCKETTmrdryDDRIRALLAAMAASFTA---------ETVN-----IAMSHLYVAGGRTSDSERPIEVGGAYTVAAES 208
Cdd:PRK10966 143 TSQAGQSG-----IEKQQALQAAIADHYQQlyqlacelrDELGqplpiIATGHLTTVGASKSDSVRDIYIGTLDAFPAQA 217

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502911230 209 LPkAAQYVALGHLHRPQDVkqAKTA-ARYSGSPLAYSFSEAGQAKSVTVVDVHPGRKAKVAEIPLAAGKPL--IRWKATE 285
Cdd:PRK10966 218 FP-PADYIALGHIHRAQKV--GGTEhIRYSGSPIPLSFDELGKSKSVHLVEFDQGKLQSVTPLPVPVFQPMavLKGDLAS 294

                        330       340       350
                 ....*....|....*....|....*....|
gi 502911230 286 GLAQVYRWCEEGRDRSSWIDLEIHVTESLT 315
Cdd:PRK10966 295 ITAQLEQWRDVSQEPPVWLDIEVTTDDYLH 324
MPP_Mre11_N cd00840
Mre11 nuclease, N-terminal metallophosphatase domain; Mre11 (also known as SbcD in Escherichia ...
 2-246 1.75e-49

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: 165.13  E-value: 1.75e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502911230   2 RILHTADWHLGRTLEGRSRMAE-QEAFVDELVEIVKKEQIDIILVAGDVFDSVNPPAAAEQLFYESLARLSDKGrRPVAV 80
Cdd:cd00840    1 RFLHTADWHLGYPLYGLSRREEdFFKAFEEIVDLAIEEKVDFVLIAGDLFDSNNPSPEALKLAIEGLRRLCEAG-IPVFV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502911230  81 ISGNHDHPDRisaartlmcahnIFLFGRPqaavcridvpscgetmmlaplaYPSESRLaellssdckettmrdrydDRIR 160
Cdd:cd00840   80 IAGNHDSPAR------------VAIYGLP----------------------YLRDERL------------------ERLF 107

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502911230 161 ALLAAMAASFTAETVNIAMSHLYVAGGRTSDSERPIEVGGAytvaaesLPKAAQYVALGHLHRPQDVKQAKTAARYSGSP 240
Cdd:cd00840  108 EDLELRPRLLKPDWFNILLLHQGVDGAGPSDSERPIVPEDL-------LPDGFDYVALGHIHKPQIIEGGGPPIVYPGSP 180


                 ....*.
gi 502911230 241 LAYSFS 246
Cdd:cd00840  181 EPTSFS 186
Metallophos pfam00149
Calcineurin-like phosphoesterase; This family includes a diverse range of phosphoesterases, ...
 1-86 1.15e-10

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: 58.38  E-value: 1.15e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502911230    1 MRILHTADWHLGRTLEGRSRMAEQeafvdelveIVKKEQIDIILVAGDVFDSvNPPAAAEQLFYESLARlsdkgRRPVAV 80
Cdd:pfam00149   1 MRILVIGDLHLPGQLDDLLELLKK---------LLEEGKPDLVLHAGDLVDR-GPPSEEVLELLERLIK-----YVPVYL 65


                  ....*.
gi 502911230   81 ISGNHD 86
Cdd:pfam00149  66 VRGNHD 71
SbcD_C pfam12320
Type 5 capsule protein repressor C-terminal domain; This domain is found in bacteria and ...
 276-365 7.24e-08

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: 49.99  E-value: 7.24e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502911230  276 KPLIRWKAT--EGLAQVYRWCEEGRDRSSWIDLEIHVTESLTmEEIDRLRKLHPG----FVHIRPVLPNRAEEMMEMSRE 349
Cdd:pfam12320   3 RDLRRIKGSleELLAALAYLEEEPADREDYLEVELTDEEPIP-DLMERLREAYPNipveLLRIRRTREERQAEEEEEAAE 81

                          90
                  ....*....|....*....
gi 502911230  350 ---PLSLEEMFHRFYERQT 365
Cdd:pfam12320  82 dleELSPLELFERFYEEQT 100
 
Name Accession Description Interval E-value
SbcD COG0420
DNA repair exonuclease SbcCD nuclease subunit [Replication, recombination and repair];
1-279 1.67e-85

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


Pssm-ID: 440189 [Multi-domain]  Cd Length: 250  Bit Score: 260.23  E-value: 1.67e-85
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502911230   1 MRILHTADWHLGRTLEGRSRMAEQEAFVDELVEIVKKEQIDIILVAGDVFDSVNPPAAAEQLFYESLARLSDKGrRPVAV 80
Cdd:COG0420    1 MRFLHTADWHLGKPLHGASRREDQLAALDRLVDLAIEEKVDAVLIAGDLFDSANPSPEAVRLLAEALRRLSEAG-IPVVL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502911230  81 ISGNHDHPDRISAARTLMCAHNIFLFGRPQAAVCRIDvpsCGETMMLAPLAYPSESRlaellssdckettmrdryDDRIR 160
Cdd:COG0420   80 IAGNHDSPSRLSAGSPLLENLGVHVFGSVEPEPVELE---DGLGVAVYGLPYLRPSD------------------EEALR 138

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502911230 161 ALLAAMAASFTAETVNIAMSHLYVAGGRTSdseRPIEVggaYTVAAESLPKA-AQYVALGHLHRPQDVkQAKTAARYSGS 239
Cdd:COG0420  139 DLLERLPRALDPGGPNILLLHGFVAGASGS---RDIYV---APVPLSALPAAgFDYVALGHIHRPQVL-GGDPRIRYSGS 211

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|
gi 502911230 240 PLAYSFSEAGQaKSVTVVDVHPGRKAKVAEIPLAAGKPLI 279
Cdd:COG0420  212 PEPRSFSEAGG-KGVLLVELDAGGLVSVEFVPLPATRRFL 250
sbcd TIGR00619
exonuclease SbcD; All proteins in this family for which functions are known are ...
 1-252 1.25e-81

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: 250.42  E-value: 1.25e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502911230    1 MRILHTADWHLGRTLEGRSRMAEQEAFVDELVEIVKKEQIDIILVAGDVFDSVNPPAAAEQLFYESLARLSDKGRRPVAV 80
Cdd:TIGR00619   1 MRILHTSDWHLGKTLEGVSRLAEQKAFLDDLLEFAKAEQVDALLVAGDVFDTANPPAEAQELFNAFFVNLSDTGIRPIVV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502911230   81 ISGNHDHPDRISAARTLMCAHNIFLFGRPQAAVCRIDVP--SCGETMMLAPLAYPSESRLAELLSSDCKETTMRDRYDDR 158
Cdd:TIGR00619  81 ISGNHDSAQRLSAAKKLLAELGVFVVGSPGHDPQILLLKdgTNGEGLCVGLFLLPREAILTRAGLDGFGLELLLAHTDVK 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502911230  159 IRALLAAMAASFTAETVNIAMSHLYVAGGRTSDSERPIEVGGAYTVAAESLPKAAQYVALGHLHRPQdvKQAKTAARYSG 238
Cdd:TIGR00619 161 LRQAAEALKLRLDQDLPKILLAHLFTAGATKSDAERRIYIGTLYAFPLQNFPEADYIALGHIHIHKI--SKGRERVRYSG 238

                         250
                  ....*....|....
gi 502911230  239 SPLAYSFSEAGQAK 252
Cdd:TIGR00619 239 SPFPLSFDEAGKDK 252
PRK10966 PRK10966
exonuclease subunit SbcD; Provisional
 1-315 4.07e-50

exonuclease subunit SbcD; Provisional


Pssm-ID: 182871 [Multi-domain]  Cd Length: 407  Bit Score: 173.59  E-value: 4.07e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502911230   1 MRILHTADWHLGRTLEGRSRMAEQEAFVDELVEIVKKEQIDIILVAGDVFDSVNPPAAAEQLFYESLARLSDKGRRPVaV 80
Cdd:PRK10966   1 MRILHTSDWHLGQNFYSKSRAAEHQAFLDWLLEQVQEHQVDAIIVAGDIFDTGSPPSYARELYNRFVVNLQQTGCQLV-V 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502911230  81 ISGNHDHPDRISAARTLMC--------------AHNIFLF----GRPQAAVCRIdvpscgetmmlaPLAYPsesrlAELL 142
Cdd:PRK10966  80 LAGNHDSVATLNESRDLLAflnttviasasddlGHQVIILprrdGTPGAVLCAI------------PFLRP-----RDVI 142

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502911230 143 SSDCKETTmrdryDDRIRALLAAMAASFTA---------ETVN-----IAMSHLYVAGGRTSDSERPIEVGGAYTVAAES 208
Cdd:PRK10966 143 TSQAGQSG-----IEKQQALQAAIADHYQQlyqlacelrDELGqplpiIATGHLTTVGASKSDSVRDIYIGTLDAFPAQA 217

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502911230 209 LPkAAQYVALGHLHRPQDVkqAKTA-ARYSGSPLAYSFSEAGQAKSVTVVDVHPGRKAKVAEIPLAAGKPL--IRWKATE 285
Cdd:PRK10966 218 FP-PADYIALGHIHRAQKV--GGTEhIRYSGSPIPLSFDELGKSKSVHLVEFDQGKLQSVTPLPVPVFQPMavLKGDLAS 294

                        330       340       350
                 ....*....|....*....|....*....|
gi 502911230 286 GLAQVYRWCEEGRDRSSWIDLEIHVTESLT 315
Cdd:PRK10966 295 ITAQLEQWRDVSQEPPVWLDIEVTTDDYLH 324
MPP_Mre11_N cd00840
Mre11 nuclease, N-terminal metallophosphatase domain; Mre11 (also known as SbcD in Escherichia ...
 2-246 1.75e-49

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: 165.13  E-value: 1.75e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502911230   2 RILHTADWHLGRTLEGRSRMAE-QEAFVDELVEIVKKEQIDIILVAGDVFDSVNPPAAAEQLFYESLARLSDKGrRPVAV 80
Cdd:cd00840    1 RFLHTADWHLGYPLYGLSRREEdFFKAFEEIVDLAIEEKVDFVLIAGDLFDSNNPSPEALKLAIEGLRRLCEAG-IPVFV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502911230  81 ISGNHDHPDRisaartlmcahnIFLFGRPqaavcridvpscgetmmlaplaYPSESRLaellssdckettmrdrydDRIR 160
Cdd:cd00840   80 IAGNHDSPAR------------VAIYGLP----------------------YLRDERL------------------ERLF 107

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502911230 161 ALLAAMAASFTAETVNIAMSHLYVAGGRTSDSERPIEVGGAytvaaesLPKAAQYVALGHLHRPQDVKQAKTAARYSGSP 240
Cdd:cd00840  108 EDLELRPRLLKPDWFNILLLHQGVDGAGPSDSERPIVPEDL-------LPDGFDYVALGHIHKPQIIEGGGPPIVYPGSP 180


                 ....*.
gi 502911230 241 LAYSFS 246
Cdd:cd00840  181 EPTSFS 186
YaeI COG1408
Predicted phosphohydrolase, MPP superfamily [General function prediction only];
1-103 3.76e-11

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


Pssm-ID: 441018 [Multi-domain]  Cd Length: 268  Bit Score: 62.89  E-value: 3.76e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502911230   1 MRILHTADWHLGRTLEGRsrmaeqeaFVDELVEIVKKEQIDIILVAGDVFDSVNPPAAAeqlFYESLARLsdKGRRPVAV 80
Cdd:COG1408   43 LRIVQLSDLHLGPFIGGE--------RLERLVEKINALKPDLVVLTGDLVDGSVAELEA---LLELLKKL--KAPLGVYA 109

                         90       100
                 ....*....|....*....|...
gi 502911230  81 ISGNHDHPDRISAARTLMCAHNI 103
Cdd:COG1408  110 VLGNHDYYAGLEELRAALEEAGV 132
Metallophos pfam00149
Calcineurin-like phosphoesterase; This family includes a diverse range of phosphoesterases, ...
 1-86 1.15e-10

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: 58.38  E-value: 1.15e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502911230    1 MRILHTADWHLGRTLEGRSRMAEQeafvdelveIVKKEQIDIILVAGDVFDSvNPPAAAEQLFYESLARlsdkgRRPVAV 80
Cdd:pfam00149   1 MRILVIGDLHLPGQLDDLLELLKK---------LLEEGKPDLVLHAGDLVDR-GPPSEEVLELLERLIK-----YVPVYL 65


                  ....*.
gi 502911230   81 ISGNHD 86
Cdd:pfam00149  66 VRGNHD 71
COG2129 COG2129
Predicted phosphoesterase, related to the Icc protein [General function prediction only];
2-95 1.24e-08

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


Pssm-ID: 441732 [Multi-domain]  Cd Length: 211  Bit Score: 54.64  E-value: 1.24e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502911230   2 RILHTADWHLGRTLegrsrmaeqeafVDELVEIVKKEQIDIILVAGDVFDSVNPPAAAEqlFYESLARLSdkgrRPVAVI 81
Cdd:COG2129    1 KILAVSDLHGNFDL------------LEKLLELARAEDADLVILAGDLTDFGTAEEARE--VLEELAALG----VPVLAV 62

                         90
                 ....*....|....
gi 502911230  82 SGNHDHPDRISAAR 95
Cdd:COG2129   63 PGNHDDPEVLDALE 76
SbcD_C pfam12320
Type 5 capsule protein repressor C-terminal domain; This domain is found in bacteria and ...
 276-365 7.24e-08

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: 49.99  E-value: 7.24e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502911230  276 KPLIRWKAT--EGLAQVYRWCEEGRDRSSWIDLEIHVTESLTmEEIDRLRKLHPG----FVHIRPVLPNRAEEMMEMSRE 349
Cdd:pfam12320   3 RDLRRIKGSleELLAALAYLEEEPADREDYLEVELTDEEPIP-DLMERLREAYPNipveLLRIRRTREERQAEEEEEAAE 81

                          90
                  ....*....|....*....
gi 502911230  350 ---PLSLEEMFHRFYERQT 365
Cdd:pfam12320  82 dleELSPLELFERFYEEQT 100
MPP_YkuE_C cd07385
Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; YkuE is an ...
 2-87 9.97e-08

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: 52.28  E-value: 9.97e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502911230   2 RILHTADWHLGRTLegrsrmaeQEAFVDELVEIVKKEQIDIILVAGDVFDSvnpPAAAEQLFYESLARLsdKGRRPVAVI 81
Cdd:cd07385    3 RIVQLSDIHLGPFV--------GRTRLQKVVRKVNELNPDLIVITGDLVDG---DVSVLRLLASPLSKL--KAPLGVYFV 69


                 ....*.
gi 502911230  82 SGNHDH 87
Cdd:cd07385   70 LGNHDY 75
CpdA COG1409
3',5'-cyclic AMP phosphodiesterase CpdA [Signal transduction mechanisms];
1-94 2.34e-07

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


Pssm-ID: 441019 [Multi-domain]  Cd Length: 234  Bit Score: 51.23  E-value: 2.34e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502911230   1 MRILHTADWHLGRTlegrsRMAEQEAFVDELVEIVKKEQIDIILVAGDVfdsVNPPAAAE-QLFYESLARLsdkgRRPVA 79
Cdd:COG1409    1 FRFAHISDLHLGAP-----DGSDTAEVLAAALADINAPRPDFVVVTGDL---TDDGEPEEyAAAREILARL----GVPVY 68

                         90
                 ....*....|....*
gi 502911230  80 VISGNHDHPDRISAA 94
Cdd:COG1409   69 VVPGNHDIRAAMAEA 83
MPP_PF1019 cd07391
Pyrococcus furiosus PF1019 and related proteins, metallophosphatase domain; This family ...
 7-86 1.69e-06

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: 47.69  E-value: 1.69e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502911230   7 ADWHLGRTLEGRSR-----MAEQEAFVDELVEIVKKEQIDIILVAGDVFDSVnpPAAAEQLFYESLARLSDKGRRPVAVI 81
Cdd:cd07391    4 ADLHLGYEEELRRQginlpRRQKERLLERLDRLLEELGPDRLVILGDLKHSF--GRVSRQERREVPFFRLLAKDVDVILI 81


                 ....*
gi 502911230  82 SGNHD 86
Cdd:cd07391   82 RGNHD 86
MPP_superfamily cd00838
metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also ...
 4-86 7.44e-06

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: 44.95  E-value: 7.44e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502911230   4 LHTADWHLGRTLEGRSRMAEQeafvdelveiVKKEQIDIILVAGDVFDSVNPPAAAEQLFYESLARlsdkgRRPVAVISG 83
Cdd:cd00838    1 LVISDIHGNLEALEAVLEAAL----------AKAEKPDLVICLGDLVDYGPDPEEVELKALRLLLA-----GIPVYVVPG 65


                 ...
gi 502911230  84 NHD 86
Cdd:cd00838   66 NHD 68
MPP_GpdQ cd07402
Enterobacter aerogenes GpdQ and related proteins, metallophosphatase domain; GpdQ ...
 3-89 3.35e-05

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: 44.96  E-value: 3.35e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502911230   3 ILHTADWHLGRTLEGRSRMAEQEAFVDELVEIVKKEQ--IDIILVAGDVFDSVNPPAaaeqlfYESLARLSDKGRRPVAV 80
Cdd:cd07402    1 IAQISDTHLFAPGEGALLGVDTAARLAAAVAQVNALHprPDLVVVTGDLSDDGSPES------YERLRELLAPLPAPVYW 74


                 ....*....
gi 502911230  81 ISGNHDHPD 89
Cdd:cd07402   75 IPGNHDDRA 83
YfcE COG0622
Predicted phosphodiesterase, calcineurin family [General function prediction only];
29-88 4.64e-03

Predicted phosphodiesterase, calcineurin family [General function prediction only];


Pssm-ID: 440387 [Multi-domain]  Cd Length: 183  Bit Score: 37.97  E-value: 4.64e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 502911230  29 DELVEIVKKEQIDIILVAGDVFDS-VNPPAAAEQLFyeslarlsdkgRRPVAVISGNHDHP 88
Cdd:COG0622   16 EAVLEDLEREGVDLIVHLGDLVGYgPDPPEVLDLLR-----------ELPIVAVRGNHDGA 65
MPP_Cdc1_like cd07384
Saccharomyces cerevisiae CDC1 and related proteins, metallophosphatase domain; Cdc1 (also ...
 41-86 5.30e-03

Saccharomyces cerevisiae CDC1 and related proteins, metallophosphatase domain; Cdc1 (also known as XlCdc1 in Xenopus laevis) is an endoplasmic reticulum-localized transmembrane lipid phosphatase with a metallophosphatase domain facing the ER lumen. In budding yeast, the gene encoding CDC1 is essential while nonlethal mutations cause defects in Golgi inheritance and actin polarization. Cdc1 mutant cells accumulate an unidentified phospholipid, suggesting that Cdc1 is a lipid phosphatase. Cdc1 mutant cells also have highly elevated intracellular calcium levels suggesting a possible role for Cdc1 in calcium regulation. The 5' flanking region of Cdc1 is a regulatory region with conserved binding site motifs for AP1, AP2, Sp1, NF-1 and CREB. DNA polymerase delta consists of at least four subunits - Pol3, Cdc1, Cdc27, and Cdm1. This group also contains Saccharomyces cerevisiae TED1 (Trafficking of Emp24p/Erv25p-dependent cargo disrupted 1), which acts together with Emp24p and Erv25p in cargo exit from the ER, and human MPPE1. The human MPPE1 gene is a candidate susceptibility gene for bipolar disorder. These proteins 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: 277330 [Multi-domain]  Cd Length: 172  Bit Score: 37.33  E-value: 5.30e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 502911230  41 DIILVAGDVFDSvnPPAAAEQLFYESLARLS---------DKGRRPVAVISGNHD 86
Cdd:cd07384   47 DVVLFLGDLFDG--GRILDSEEWKEYLHRFQkifflkspgSLGSIPVIFIPGNHD 99
MPP_1 cd07400
Uncharacterized subfamily, metallophosphatase domain; Uncharacterized subfamily of the MPP ...
 3-86 5.42e-03

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: 36.89  E-value: 5.42e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502911230   3 ILHTADWHLGRtlegrSRMAEQEAFvdELVEIVKKEQIDIILVAGDVFDSvnppaAAEQLFYESLARLSDKGRRPVAVIS 82
Cdd:cd07400    1 IAHISDLHFGE-----ERKPEVLEL--NLLDEINALKPDLVVVTGDLTQR-----ARPAEFEEAREFLDALEPEPVVVVP 68


                 ....
gi 502911230  83 GNHD 86
Cdd:cd07400   69 GNHD 72
47 PHA02546
endonuclease subunit; Provisional
 1-86 8.35e-03

endonuclease subunit; Provisional


Pssm-ID: 222867 [Multi-domain]  Cd Length: 340  Bit Score: 38.06  E-value: 8.35e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502911230   1 MRILHTADWHLGRTLEGRSRMAEQEAFVDELVEIVKKEQIDIILVAGDVFD---SVNPPA---AAEQLFyeslARLSDKG 74
Cdd:PHA02546   1 MKILLIGDQHLGVRKDDPWFQNYQLKFIKQAIEYSKAHGITTWIQLGDTFDvrkAITQNTmnfVREKIF----DLLKEAG 76

                         90
                 ....*....|..
gi 502911230  75 RRpVAVISGNHD 86
Cdd:PHA02546  77 IT-LHVLVGNHD 87
 
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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