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Conserved domains on  [gi|550714326|ref|WP_022647215|]
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MULTISPECIES: exonuclease subunit SbcD [Enterobacter]

Protein Classification

exonuclease SbcCD subunit D( domain architecture ID 11485130)

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
PRK10966 PRK10966
exonuclease subunit SbcD; Provisional
 1-401 0e+00

exonuclease subunit SbcD; Provisional


:

Pssm-ID: 182871 [Multi-domain]  Cd Length: 407  Bit Score: 786.44  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 550714326   1 MRILHTSDWHLGQNFYSKSRAAEHEAFLNWLLETAQAHEVDAIIVAGDIFDTGSPPSYARELYNRFVVNLQQTGCHLVIV 80
Cdd:PRK10966   1 MRILHTSDWHLGQNFYSKSRAAEHQAFLDWLLEQVQEHQVDAIIVAGDIFDTGSPPSYARELYNRFVVNLQQTGCQLVVL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 550714326  81 AGNHDSVATLNESRDILAFLNTTVVASA----GHAPQILKKRDGTPGAVLCPIPFLRPRDIVQSQAGLSGSEKQQHLLQA 156
Cdd:PRK10966  81 AGNHDSVATLNESRDLLAFLNTTVIASAsddlGHQVIILPRRDGTPGAVLCAIPFLRPRDVITSQAGQSGIEKQQALQAA 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 550714326 157 ITRYYHQQHTEACALR--GEQAIPIVATGHLTTVGASKSDAVREIYIGTLDAFPAQNFPPADYIALGHIHRAQIVGGCEH 234
Cdd:PRK10966 161 IADHYQQLYQLACELRdeLGQPLPIIATGHLTTVGASKSDSVRDIYIGTLDAFPAQAFPPADYIALGHIHRAQKVGGTEH 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 550714326 235 IRYCGSPISLSFDETGKAKSVHLVSFTEGKLSAVETLEVPVTQPLAVLKGDLAAITAQLEQWRGAALNPPVWLDIEITTD 314
Cdd:PRK10966 241 IRYSGSPIPLSFDELGKSKSVHLVEFDQGKLQSVTPLPVPVFQPMAVLKGDLASITAQLEQWRDVSQEPPVWLDIEVTTD 320

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 550714326 315 DYLYDMQRKIQTLTEDLPVEVLLVRRSREQREKILLNAQRETLSELRVEEVFARRLAHEEVDEARRTRLNELFAHTLHSL 394
Cdd:PRK10966 321 DYLHDIQRRIQALTESLPVEVLLVRRSREQRERSLASEQRETLSELSVEEVFERRLALEELDEPQQQRLTQLFTQVLHEL 400


                 ....*..
gi 550714326 395 NDEDENA 401
Cdd:PRK10966 401 AEEHEAA 407
 
Name Accession Description Interval E-value
PRK10966 PRK10966
exonuclease subunit SbcD; Provisional
 1-401 0e+00

exonuclease subunit SbcD; Provisional


Pssm-ID: 182871 [Multi-domain]  Cd Length: 407  Bit Score: 786.44  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 550714326   1 MRILHTSDWHLGQNFYSKSRAAEHEAFLNWLLETAQAHEVDAIIVAGDIFDTGSPPSYARELYNRFVVNLQQTGCHLVIV 80
Cdd:PRK10966   1 MRILHTSDWHLGQNFYSKSRAAEHQAFLDWLLEQVQEHQVDAIIVAGDIFDTGSPPSYARELYNRFVVNLQQTGCQLVVL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 550714326  81 AGNHDSVATLNESRDILAFLNTTVVASA----GHAPQILKKRDGTPGAVLCPIPFLRPRDIVQSQAGLSGSEKQQHLLQA 156
Cdd:PRK10966  81 AGNHDSVATLNESRDLLAFLNTTVIASAsddlGHQVIILPRRDGTPGAVLCAIPFLRPRDVITSQAGQSGIEKQQALQAA 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 550714326 157 ITRYYHQQHTEACALR--GEQAIPIVATGHLTTVGASKSDAVREIYIGTLDAFPAQNFPPADYIALGHIHRAQIVGGCEH 234
Cdd:PRK10966 161 IADHYQQLYQLACELRdeLGQPLPIIATGHLTTVGASKSDSVRDIYIGTLDAFPAQAFPPADYIALGHIHRAQKVGGTEH 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 550714326 235 IRYCGSPISLSFDETGKAKSVHLVSFTEGKLSAVETLEVPVTQPLAVLKGDLAAITAQLEQWRGAALNPPVWLDIEITTD 314
Cdd:PRK10966 241 IRYSGSPIPLSFDELGKSKSVHLVEFDQGKLQSVTPLPVPVFQPMAVLKGDLASITAQLEQWRDVSQEPPVWLDIEVTTD 320

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 550714326 315 DYLYDMQRKIQTLTEDLPVEVLLVRRSREQREKILLNAQRETLSELRVEEVFARRLAHEEVDEARRTRLNELFAHTLHSL 394
Cdd:PRK10966 321 DYLHDIQRRIQALTESLPVEVLLVRRSREQRERSLASEQRETLSELSVEEVFERRLALEELDEPQQQRLTQLFTQVLHEL 400


                 ....*..
gi 550714326 395 NDEDENA 401
Cdd:PRK10966 401 AEEHEAA 407
sbcd TIGR00619
exonuclease SbcD; All proteins in this family for which functions are known are ...
 1-253 5.41e-110

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: 322.83  E-value: 5.41e-110
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 550714326    1 MRILHTSDWHLGQNFYSKSRAAEHEAFLNWLLETAQAHEVDAIIVAGDIFDTGSPPSYARELYNRFVVNLQQTGC-HLVI 79
Cdd:TIGR00619   1 MRILHTSDWHLGKTLEGVSRLAEQKAFLDDLLEFAKAEQVDALLVAGDVFDTANPPAEAQELFNAFFVNLSDTGIrPIVV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 550714326   80 VAGNHDSVATLNESRDILAFLNTTVVASAGHAPQILKKRDGTPGAVLCPIPFLRPRDIVQSQAGLSGSEKQqhLLQAITR 159
Cdd:TIGR00619  81 ISGNHDSAQRLSAAKKLLAELGVFVVGSPGHDPQILLLKDGTNGEGLCVGLFLLPREAILTRAGLDGFGLE--LLLAHTD 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 550714326  160 YYHQQHTEACALRGEQAIPIVATGHLTTVGASKSDAVREIYIGTLDAFPAQNFPPADYIALGHIHRAQIVGGCEHIRYCG 239
Cdd:TIGR00619 159 VKLRQAAEALKLRLDQDLPKILLAHLFTAGATKSDAERRIYIGTLYAFPLQNFPEADYIALGHIHIHKISKGRERVRYSG 238

                         250
                  ....*....|....
gi 550714326  240 SPISLSFDETGKAK 253
Cdd:TIGR00619 239 SPFPLSFDEAGKDK 252
SbcD COG0420
DNA repair exonuclease SbcCD nuclease subunit [Replication, recombination and repair];
1-279 1.22e-85

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


Pssm-ID: 440189 [Multi-domain]  Cd Length: 250  Bit Score: 260.62  E-value: 1.22e-85
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 550714326   1 MRILHTSDWHLGQNFYSKSRAAEHEAFLNWLLETAQAHEVDAIIVAGDIFDTGSPPSYARELYNRFVVNLQQTGCHLVIV 80
Cdd:COG0420    1 MRFLHTADWHLGKPLHGASRREDQLAALDRLVDLAIEEKVDAVLIAGDLFDSANPSPEAVRLLAEALRRLSEAGIPVVLI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 550714326  81 AGNHDSVATLNESRDILAFLNTTVVASAGHAPQILKKrdgTPGAVLCPIPFLRPRDIvqsqaglsgsEKQQHLLQAITRy 160
Cdd:COG0420   81 AGNHDSPSRLSAGSPLLENLGVHVFGSVEPEPVELED---GLGVAVYGLPYLRPSDE----------EALRDLLERLPR- 146

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 550714326 161 yhqqhteacalRGEQAIPIVATGHLTTVGASKSdavREIYIGT--LDAFPAQNFppaDYIALGHIHRAQIVGGCEHIRYC 238
Cdd:COG0420  147 -----------ALDPGGPNILLLHGFVAGASGS---RDIYVAPvpLSALPAAGF---DYVALGHIHRPQVLGGDPRIRYS 209

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|.
gi 550714326 239 GSPISLSFDETGKaKSVHLVSFTEGKLSAVETLEVPVTQPL 279
Cdd:COG0420  210 GSPEPRSFSEAGG-KGVLLVELDAGGLVSVEFVPLPATRRF 249
MPP_Mre11_N cd00840
Mre11 nuclease, N-terminal metallophosphatase domain; Mre11 (also known as SbcD in Escherichia ...
 2-247 4.41e-43

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: 148.96  E-value: 4.41e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 550714326   2 RILHTSDWHLGQNFYSKS-RAAEHEAFLNWLLETAQAHEVDAIIVAGDIFDTGSPPSYARELYNRFVVNLQQTGCHLVIV 80
Cdd:cd00840    1 RFLHTADWHLGYPLYGLSrREEDFFKAFEEIVDLAIEEKVDFVLIAGDLFDSNNPSPEALKLAIEGLRRLCEAGIPVFVI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 550714326  81 AGNHDSVAtlnesrdilaflnttvvasaghapqilkkrdgtpGAVLCPIPFLRPRDIVQSQAGlsgsekqqhllqaitry 160
Cdd:cd00840   81 AGNHDSPA----------------------------------RVAIYGLPYLRDERLERLFED----------------- 109

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 550714326 161 yhqqhTEACALRGEQAIPIVATGHLTTVGASKSDAVREIyigtldAFPAQNFPPADYIALGHIHRAQI-VGGCEHIRYCG 239
Cdd:cd00840  110 -----LELRPRLLKPDWFNILLLHQGVDGAGPSDSERPI------VPEDLLPDGFDYVALGHIHKPQIiEGGGPPIVYPG 178


                 ....*...
gi 550714326 240 SPISLSFD 247
Cdd:cd00840  179 SPEPTSFS 186
SbcD_C pfam12320
Type 5 capsule protein repressor C-terminal domain; This domain is found in bacteria and ...
 275-374 2.66e-25

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: 98.52  E-value: 2.66e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 550714326  275 VTQPLAVLKGDLAAITAQLEQWRGAALNPPVWLDIEITTDDYLYDMQRKIQTLTEDLPVEVLLVRRSREQREKILLNAQR 354
Cdd:pfam12320   1 PLRDLRRIKGSLEELLAALAYLEEEPADREDYLEVELTDEEPIPDLMERLREAYPNIPVELLRIRRTREERQAEEEEEAA 80

                          90       100
                  ....*....|....*....|
gi 550714326  355 ETLSELRVEEVFARRLAHEE 374
Cdd:pfam12320  81 EDLEELSPLELFERFYEEQT 100
 
Name Accession Description Interval E-value
PRK10966 PRK10966
exonuclease subunit SbcD; Provisional
 1-401 0e+00

exonuclease subunit SbcD; Provisional


Pssm-ID: 182871 [Multi-domain]  Cd Length: 407  Bit Score: 786.44  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 550714326   1 MRILHTSDWHLGQNFYSKSRAAEHEAFLNWLLETAQAHEVDAIIVAGDIFDTGSPPSYARELYNRFVVNLQQTGCHLVIV 80
Cdd:PRK10966   1 MRILHTSDWHLGQNFYSKSRAAEHQAFLDWLLEQVQEHQVDAIIVAGDIFDTGSPPSYARELYNRFVVNLQQTGCQLVVL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 550714326  81 AGNHDSVATLNESRDILAFLNTTVVASA----GHAPQILKKRDGTPGAVLCPIPFLRPRDIVQSQAGLSGSEKQQHLLQA 156
Cdd:PRK10966  81 AGNHDSVATLNESRDLLAFLNTTVIASAsddlGHQVIILPRRDGTPGAVLCAIPFLRPRDVITSQAGQSGIEKQQALQAA 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 550714326 157 ITRYYHQQHTEACALR--GEQAIPIVATGHLTTVGASKSDAVREIYIGTLDAFPAQNFPPADYIALGHIHRAQIVGGCEH 234
Cdd:PRK10966 161 IADHYQQLYQLACELRdeLGQPLPIIATGHLTTVGASKSDSVRDIYIGTLDAFPAQAFPPADYIALGHIHRAQKVGGTEH 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 550714326 235 IRYCGSPISLSFDETGKAKSVHLVSFTEGKLSAVETLEVPVTQPLAVLKGDLAAITAQLEQWRGAALNPPVWLDIEITTD 314
Cdd:PRK10966 241 IRYSGSPIPLSFDELGKSKSVHLVEFDQGKLQSVTPLPVPVFQPMAVLKGDLASITAQLEQWRDVSQEPPVWLDIEVTTD 320

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 550714326 315 DYLYDMQRKIQTLTEDLPVEVLLVRRSREQREKILLNAQRETLSELRVEEVFARRLAHEEVDEARRTRLNELFAHTLHSL 394
Cdd:PRK10966 321 DYLHDIQRRIQALTESLPVEVLLVRRSREQRERSLASEQRETLSELSVEEVFERRLALEELDEPQQQRLTQLFTQVLHEL 400


                 ....*..
gi 550714326 395 NDEDENA 401
Cdd:PRK10966 401 AEEHEAA 407
sbcd TIGR00619
exonuclease SbcD; All proteins in this family for which functions are known are ...
 1-253 5.41e-110

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: 322.83  E-value: 5.41e-110
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 550714326    1 MRILHTSDWHLGQNFYSKSRAAEHEAFLNWLLETAQAHEVDAIIVAGDIFDTGSPPSYARELYNRFVVNLQQTGC-HLVI 79
Cdd:TIGR00619   1 MRILHTSDWHLGKTLEGVSRLAEQKAFLDDLLEFAKAEQVDALLVAGDVFDTANPPAEAQELFNAFFVNLSDTGIrPIVV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 550714326   80 VAGNHDSVATLNESRDILAFLNTTVVASAGHAPQILKKRDGTPGAVLCPIPFLRPRDIVQSQAGLSGSEKQqhLLQAITR 159
Cdd:TIGR00619  81 ISGNHDSAQRLSAAKKLLAELGVFVVGSPGHDPQILLLKDGTNGEGLCVGLFLLPREAILTRAGLDGFGLE--LLLAHTD 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 550714326  160 YYHQQHTEACALRGEQAIPIVATGHLTTVGASKSDAVREIYIGTLDAFPAQNFPPADYIALGHIHRAQIVGGCEHIRYCG 239
Cdd:TIGR00619 159 VKLRQAAEALKLRLDQDLPKILLAHLFTAGATKSDAERRIYIGTLYAFPLQNFPEADYIALGHIHIHKISKGRERVRYSG 238

                         250
                  ....*....|....
gi 550714326  240 SPISLSFDETGKAK 253
Cdd:TIGR00619 239 SPFPLSFDEAGKDK 252
SbcD COG0420
DNA repair exonuclease SbcCD nuclease subunit [Replication, recombination and repair];
1-279 1.22e-85

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


Pssm-ID: 440189 [Multi-domain]  Cd Length: 250  Bit Score: 260.62  E-value: 1.22e-85
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 550714326   1 MRILHTSDWHLGQNFYSKSRAAEHEAFLNWLLETAQAHEVDAIIVAGDIFDTGSPPSYARELYNRFVVNLQQTGCHLVIV 80
Cdd:COG0420    1 MRFLHTADWHLGKPLHGASRREDQLAALDRLVDLAIEEKVDAVLIAGDLFDSANPSPEAVRLLAEALRRLSEAGIPVVLI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 550714326  81 AGNHDSVATLNESRDILAFLNTTVVASAGHAPQILKKrdgTPGAVLCPIPFLRPRDIvqsqaglsgsEKQQHLLQAITRy 160
Cdd:COG0420   81 AGNHDSPSRLSAGSPLLENLGVHVFGSVEPEPVELED---GLGVAVYGLPYLRPSDE----------EALRDLLERLPR- 146

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 550714326 161 yhqqhteacalRGEQAIPIVATGHLTTVGASKSdavREIYIGT--LDAFPAQNFppaDYIALGHIHRAQIVGGCEHIRYC 238
Cdd:COG0420  147 -----------ALDPGGPNILLLHGFVAGASGS---RDIYVAPvpLSALPAAGF---DYVALGHIHRPQVLGGDPRIRYS 209

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|.
gi 550714326 239 GSPISLSFDETGKaKSVHLVSFTEGKLSAVETLEVPVTQPL 279
Cdd:COG0420  210 GSPEPRSFSEAGG-KGVLLVELDAGGLVSVEFVPLPATRRF 249
MPP_Mre11_N cd00840
Mre11 nuclease, N-terminal metallophosphatase domain; Mre11 (also known as SbcD in Escherichia ...
 2-247 4.41e-43

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: 148.96  E-value: 4.41e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 550714326   2 RILHTSDWHLGQNFYSKS-RAAEHEAFLNWLLETAQAHEVDAIIVAGDIFDTGSPPSYARELYNRFVVNLQQTGCHLVIV 80
Cdd:cd00840    1 RFLHTADWHLGYPLYGLSrREEDFFKAFEEIVDLAIEEKVDFVLIAGDLFDSNNPSPEALKLAIEGLRRLCEAGIPVFVI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 550714326  81 AGNHDSVAtlnesrdilaflnttvvasaghapqilkkrdgtpGAVLCPIPFLRPRDIVQSQAGlsgsekqqhllqaitry 160
Cdd:cd00840   81 AGNHDSPA----------------------------------RVAIYGLPYLRDERLERLFED----------------- 109

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 550714326 161 yhqqhTEACALRGEQAIPIVATGHLTTVGASKSDAVREIyigtldAFPAQNFPPADYIALGHIHRAQI-VGGCEHIRYCG 239
Cdd:cd00840  110 -----LELRPRLLKPDWFNILLLHQGVDGAGPSDSERPI------VPEDLLPDGFDYVALGHIHKPQIiEGGGPPIVYPG 178


                 ....*...
gi 550714326 240 SPISLSFD 247
Cdd:cd00840  179 SPEPTSFS 186
SbcD_C pfam12320
Type 5 capsule protein repressor C-terminal domain; This domain is found in bacteria and ...
 275-374 2.66e-25

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: 98.52  E-value: 2.66e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 550714326  275 VTQPLAVLKGDLAAITAQLEQWRGAALNPPVWLDIEITTDDYLYDMQRKIQTLTEDLPVEVLLVRRSREQREKILLNAQR 354
Cdd:pfam12320   1 PLRDLRRIKGSLEELLAALAYLEEEPADREDYLEVELTDEEPIPDLMERLREAYPNIPVELLRIRRTREERQAEEEEEAA 80

                          90       100
                  ....*....|....*....|
gi 550714326  355 ETLSELRVEEVFARRLAHEE 374
Cdd:pfam12320  81 EDLEELSPLELFERFYEEQT 100
Metallophos pfam00149
Calcineurin-like phosphoesterase; This family includes a diverse range of phosphoesterases, ...
 1-86 3.29e-13

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: 65.70  E-value: 3.29e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 550714326    1 MRILHTSDWHLGQNFYsksraaeheAFLNWLLETAQAHEVDAIIVAGDIFDTGSPPSYARELYNRFVVNLqqtgcHLVIV 80
Cdd:pfam00149   1 MRILVIGDLHLPGQLD---------DLLELLKKLLEEGKPDLVLHAGDLVDRGPPSEEVLELLERLIKYV-----PVYLV 66


                  ....*.
gi 550714326   81 AGNHDS 86
Cdd:pfam00149  67 RGNHDF 72
CpdA COG1409
3',5'-cyclic AMP phosphodiesterase CpdA [Signal transduction mechanisms];
1-85 1.37e-09

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


Pssm-ID: 441019 [Multi-domain]  Cd Length: 234  Bit Score: 58.16  E-value: 1.37e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 550714326   1 MRILHTSDWHLGQNFYSKSRAAeheafLNWLLETAQAHEVDAIIVAGDIFDTGSPPSYArelynRFVVNLQQTGCHLVIV 80
Cdd:COG1409    1 FRFAHISDLHLGAPDGSDTAEV-----LAAALADINAPRPDFVVVTGDLTDDGEPEEYA-----AAREILARLGVPVYVV 70


                 ....*
gi 550714326  81 AGNHD 85
Cdd:COG1409   71 PGNHD 75
COG2129 COG2129
Predicted phosphoesterase, related to the Icc protein [General function prediction only];
2-92 4.66e-09

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


Pssm-ID: 441732 [Multi-domain]  Cd Length: 211  Bit Score: 56.18  E-value: 4.66e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 550714326   2 RILHTSDWHLgqnfysksraaEHEAFlNWLLETAQAHEVDAIIVAGDIFDTGsPPSYARELYNrfvvNLQQTGCHLVIVA 81
Cdd:COG2129    1 KILAVSDLHG-----------NFDLL-EKLLELARAEDADLVILAGDLTDFG-TAEEAREVLE----ELAALGVPVLAVP 63

                         90
                 ....*....|.
gi 550714326  82 GNHDSVATLNE 92
Cdd:COG2129   64 GNHDDPEVLDA 74
MPP_GpdQ cd07402
Enterobacter aerogenes GpdQ and related proteins, metallophosphatase domain; GpdQ ...
 3-92 5.08e-07

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: 50.35  E-value: 5.08e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 550714326   3 ILHTSDWHL----GQNFYSKSRAAEHEAFLNWLLetAQAHEVDAIIVAGDIFDTGSPPSY--ARELYNRFVvnlqqtgCH 76
Cdd:cd07402    1 IAQISDTHLfapgEGALLGVDTAARLAAAVAQVN--ALHPRPDLVVVTGDLSDDGSPESYerLRELLAPLP-------AP 71

                         90
                 ....*....|....*.
gi 550714326  77 LVIVAGNHDSVATLNE 92
Cdd:cd07402   72 VYWIPGNHDDRAAMRE 87
MPP_YbbF-LpxH cd07398
Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; YbbF/LpxH is an ...
 7-87 6.11e-06

Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; YbbF/LpxH is an Escherichia coli UDP-2,3-diacylglucosamine hydrolase thought to catalyze the fourth step of lipid A biosynthesis, in which a precursor UDP-2,3-diacylglucosamine is hydrolyzed to yield 2,3-diacylglucosamine 1-phosphate and UMP. YbbF 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: 277343 [Multi-domain]  Cd Length: 217  Bit Score: 46.97  E-value: 6.11e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 550714326   7 SDWHLGqnfyskSRAAEHEAFLNWLLETaQAHEVDAIIVAGDIFDT--GSPPSYARELYNRFVV--NLQQTGCHLVIVAG 82
Cdd:cd07398    4 SDLHLG------LRGCRADRLLDFLLVE-ELDEADALYLLGDIFDLwiGDDSVVWPGAHRALARllRLADRGTEVIYVPG 76


                 ....*
gi 550714326  83 NHDSV 87
Cdd:cd07398   77 NHDFL 81
MPP_1 cd07400
Uncharacterized subfamily, metallophosphatase domain; Uncharacterized subfamily of the MPP ...
 3-90 9.65e-06

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: 44.98  E-value: 9.65e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 550714326   3 ILHTSDWHLGQNFYSKSRAAEheaflnwLLETAQAHEVDAIIVAGDIFDTGSPPSY--ARELynrfvvnLQQTGCH-LVI 79
Cdd:cd07400    1 IAHISDLHFGEERKPEVLELN-------LLDEINALKPDLVVVTGDLTQRARPAEFeeAREF-------LDALEPEpVVV 66

                         90
                 ....*....|.
gi 550714326  80 VAGNHDSVATL 90
Cdd:cd07400   67 VPGNHDAIVAL 77
47 PHA02546
endonuclease subunit; Provisional
 1-85 1.01e-05

endonuclease subunit; Provisional


Pssm-ID: 222867 [Multi-domain]  Cd Length: 340  Bit Score: 46.92  E-value: 1.01e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 550714326   1 MRILHTSDWHLG--------QNFYSKsraaeheaFLNWLLETAQAHEVDAIIVAGDIFD-----TGSPPSYARELYNRFv 67
Cdd:PHA02546   1 MKILLIGDQHLGvrkddpwfQNYQLK--------FIKQAIEYSKAHGITTWIQLGDTFDvrkaiTQNTMNFVREKIFDL- 71

                         90
                 ....*....|....*...
gi 550714326  68 vnLQQTGCHLVIVAGNHD 85
Cdd:PHA02546  72 --LKEAGITLHVLVGNHD 87
YaeI COG1408
Predicted phosphohydrolase, MPP superfamily [General function prediction only];
1-98 2.16e-05

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


Pssm-ID: 441018 [Multi-domain]  Cd Length: 268  Bit Score: 45.56  E-value: 2.16e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 550714326   1 MRILHTSDWHLGQNFysksraaeHEAFLNWLLETAQAHEVDAIIVAGDIFDTGSPPsyarelYNRFVVNLQQ-TGCHLVI 79
Cdd:COG1408   43 LRIVQLSDLHLGPFI--------GGERLERLVEKINALKPDLVVLTGDLVDGSVAE------LEALLELLKKlKAPLGVY 108

                         90       100
                 ....*....|....*....|
gi 550714326  80 -VAGNHDSVATLNESRDILA 98
Cdd:COG1408  109 aVLGNHDYYAGLEELRAALE 128
MPP_superfamily cd00838
metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also ...
 4-89 1.89e-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: 41.10  E-value: 1.89e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 550714326   4 LHTSDWHLGqnfysksraaeHEAFLNWL-LETAQAHEVDAIIVAGDIFDTGSPPsyarELYNRFVVNLQQTGCHLVIVAG 82
Cdd:cd00838    1 LVISDIHGN-----------LEALEAVLeAALAKAEKPDLVICLGDLVDYGPDP----EEVELKALRLLLAGIPVYVVPG 65


                 ....*..
gi 550714326  83 NHDSVAT 89
Cdd:cd00838   66 NHDILVT 72
MPP_YkuE_C cd07385
Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; YkuE is an ...
 2-104 6.04e-04

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: 41.11  E-value: 6.04e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 550714326   2 RILHTSDWHLGQNFysksraaeHEAFLNWLLETAQAHEVDAIIVAGDIFDtgSPPSYAReLYNRFVVNLQQT-GCHLVIv 80
Cdd:cd07385    3 RIVQLSDIHLGPFV--------GRTRLQKVVRKVNELNPDLIVITGDLVD--GDVSVLR-LLASPLSKLKAPlGVYFVL- 70

                         90       100
                 ....*....|....*....|....*
gi 550714326  81 aGNHD-SVATLNESRDILAFLNTTV 104
Cdd:cd07385   71 -GNHDyYSGDVEVWIAALEKAGITV 94
YfcE COG0622
Predicted phosphodiesterase, calcineurin family [General function prediction only];
28-86 1.60e-03

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


Pssm-ID: 440387 [Multi-domain]  Cd Length: 183  Bit Score: 39.13  E-value: 1.60e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 550714326  28 LNWLLETAQAHEVDAIIVAGDIFDTGSPPsyarelynRFVVNLQQTGChLVIVAGNHDS 86
Cdd:COG0622   15 LEAVLEDLEREGVDLIVHLGDLVGYGPDP--------PEVLDLLRELP-IVAVRGNHDG 64
 
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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