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Conserved domains on  [gi|569005655|ref|XP_006531746|]
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DNA polymerase alpha subunit B isoform X6 [Mus musculus]

Protein Classification

Pol_alpha_B_N and DNA_pol_E_B domain-containing protein( domain architecture ID 13566362)

Pol_alpha_B_N and DNA_pol_E_B domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DNA_pol_E_B pfam04042
DNA polymerase alpha/epsilon subunit B; This family contains a number of DNA polymerase ...
 302-552 2.09e-64

DNA polymerase alpha/epsilon subunit B; This family contains a number of DNA polymerase subunits. The B subunit of the DNA polymerase alpha plays an essential role at the initial stage of DNA replication in S. cerevisiae and is phosphorylated in a cell cycle-dependent manner. DNA polymerase epsilon is essential for cell viability and chromosomal DNA replication in budding yeast. In addition, DNA polymerase epsilon may be involved in DNA repair and cell-cycle checkpoint control. The enzyme consists of at least four subunits in mammalian cells as well as in yeast. The largest subunit of DNA polymerase epsilon is responsible for polymerase epsilon is responsible for polymerase activity. In mouse, the DNA polymerase epsilon subunit B is the second largest subunit of the DNA polymerase. A part of the N-terminal was found to be responsible for the interaction with SAP18. Experimental evidence suggests that this subunit may recruit histone deacetylase to the replication fork to modify the chromatin structure.


:

Pssm-ID: 461142  Cd Length: 210  Bit Score: 210.24  E-value: 2.09e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569005655  302 VVVACGPYTTSDSITYDPLLDLIAIIN-RDQPDVCILFGPFLDAKHEQVENCKL---TSPFEDVFKQCLRTVIEGTrrqq 377
Cdd:pfam04042   1 IVFASGLYLDSDNLSLEALRDLLDGYNeDSPPDRLILAGPFLDSKHNLIASGAVagdTLTYNFLFLKLLLSILEQL---- 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569005655  378 fssvkgatkikrrcvlsyvhqiqismfmcqevafpsrgpaSSGSHLVFVPSLRDVHHEPVYPQPPFTFSELSREDKK-RV 456
Cdd:pfam04042  77 ----------------------------------------LEKTPVILVPGPNDPANSTVLPQPPFPRCLLPRIKKNnSL 116

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569005655  457 QFVSEPCSLSINGVMFGLTSTDLLFHIGAEEIFSSSGTSDRFSRVLKHILTQRSYYPLYPPHeDMAIDYENFYTYAqLPV 536
Cdd:pfam04042 117 IFVTNPCRFSINGVEVVVTSGDNVSDLLRYELKFSSSDVDRFLRLVETILRQRHLAPLAPDT-LRPYPYDKDDAFV-LYP 194

                         250
                  ....*....|....*.
gi 569005655  537 TPDVFIVPSELRYFVK 552
Cdd:pfam04042 195 LPDVLILGSELPSFAK 210
Pol_alpha_B_N super family cl37775
DNA polymerase alpha subunit B N-terminal; This is the eukaryotic DNA polymerase alpha subunit ...
 71-198 7.33e-06

DNA polymerase alpha subunit B N-terminal; This is the eukaryotic DNA polymerase alpha subunit B N-terminal domain which is involved in complex formation. This domain adopts an OB fold.


The actual alignment was detected with superfamily member pfam08418:

Pssm-ID: 462470  Cd Length: 240  Bit Score: 47.71  E-value: 7.33e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569005655   71 SSYTTPSKGPLKRVS--------STPETPLTKRSVAARSPRQLLSPSSFSPSATPSQkYTSRTNRGEVVTTFGSAQGLSW 142
Cdd:pfam08418  95 LVPSTPALKKRKLGSgassakrkSAFETPLASRVSSPAPSSSPGANNTPATPSAGSS-FSSRQNAGEVVETLNPHLELAE 173

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 569005655  143 SGRGGSGSVSLKVVGDPEPLTGSYKAMFQQLMGVREVLTSKIEELGSELKEHHKIE 198
Cdd:pfam08418 174 PPIAPYSEPRVKLTANTDPKKYKYKTMAMKLSEASEVLDDRIDEFAELIQEHHKLD 229
 
Name Accession Description Interval E-value
DNA_pol_E_B pfam04042
DNA polymerase alpha/epsilon subunit B; This family contains a number of DNA polymerase ...
 302-552 2.09e-64

DNA polymerase alpha/epsilon subunit B; This family contains a number of DNA polymerase subunits. The B subunit of the DNA polymerase alpha plays an essential role at the initial stage of DNA replication in S. cerevisiae and is phosphorylated in a cell cycle-dependent manner. DNA polymerase epsilon is essential for cell viability and chromosomal DNA replication in budding yeast. In addition, DNA polymerase epsilon may be involved in DNA repair and cell-cycle checkpoint control. The enzyme consists of at least four subunits in mammalian cells as well as in yeast. The largest subunit of DNA polymerase epsilon is responsible for polymerase epsilon is responsible for polymerase activity. In mouse, the DNA polymerase epsilon subunit B is the second largest subunit of the DNA polymerase. A part of the N-terminal was found to be responsible for the interaction with SAP18. Experimental evidence suggests that this subunit may recruit histone deacetylase to the replication fork to modify the chromatin structure.


Pssm-ID: 461142  Cd Length: 210  Bit Score: 210.24  E-value: 2.09e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569005655  302 VVVACGPYTTSDSITYDPLLDLIAIIN-RDQPDVCILFGPFLDAKHEQVENCKL---TSPFEDVFKQCLRTVIEGTrrqq 377
Cdd:pfam04042   1 IVFASGLYLDSDNLSLEALRDLLDGYNeDSPPDRLILAGPFLDSKHNLIASGAVagdTLTYNFLFLKLLLSILEQL---- 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569005655  378 fssvkgatkikrrcvlsyvhqiqismfmcqevafpsrgpaSSGSHLVFVPSLRDVHHEPVYPQPPFTFSELSREDKK-RV 456
Cdd:pfam04042  77 ----------------------------------------LEKTPVILVPGPNDPANSTVLPQPPFPRCLLPRIKKNnSL 116

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569005655  457 QFVSEPCSLSINGVMFGLTSTDLLFHIGAEEIFSSSGTSDRFSRVLKHILTQRSYYPLYPPHeDMAIDYENFYTYAqLPV 536
Cdd:pfam04042 117 IFVTNPCRFSINGVEVVVTSGDNVSDLLRYELKFSSSDVDRFLRLVETILRQRHLAPLAPDT-LRPYPYDKDDAFV-LYP 194

                         250
                  ....*....|....*.
gi 569005655  537 TPDVFIVPSELRYFVK 552
Cdd:pfam04042 195 LPDVLILGSELPSFAK 210
POL12 COG5214
DNA polymerase alpha-primase complex, polymerase-associated subunit B [DNA replication, ...
 166-579 6.81e-61

DNA polymerase alpha-primase complex, polymerase-associated subunit B [DNA replication, recombination, and repair];


Pssm-ID: 227539 [Multi-domain]  Cd Length: 581  Bit Score: 212.15  E-value: 6.81e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569005655 166 YKAMFQQLMGVREVLTSKIEELGSELKEHHKI--EAFTPLLVPAQEPVILLGQIGCDS---NGKLNSKSVILEGDQEHSY 240
Cdd:COG5214  158 SRFMYQKLRKKSKVLDDRIELFSMKPYFLYLLsiEDFAPPNNVSQSSFYTVGRIVNPStnfGHKLNSESVFLESSRDGGN 237

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569005655 241 GAQIPVDLSELKEYSLFPGQVVIMEGFNTTGRRLTATKLYEGVPLP-FYQPTEEEGASEQ-------TMVVVACGPYTTS 312
Cdd:COG5214  238 GVRVRLNLAHLQRYSVFPGQIVAVKGKNTDGGKFTVEAILPIPVVPiNPASDGQEKKYFQantnnqpTSIVAFSGPYGPR 317

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569005655 313 DSITYDPLLDLIAIINRDQPDVCILFGPFLDAKHEQVENCKLTSP----FEDVFKQCLRTVIEgtrrqqfssvkgatkik 388
Cdd:COG5214  318 DDLSGSPLFDAIDRVNANDVDVLILIGPFIDINHILIQYGATQSTpdsmLKELFIPRITPILD----------------- 380

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569005655 389 rrcvlsyvhqiqismfmcqevafpsrgpASSGSHLVFVPSLRD-VHHEPVYPQPPFTFSELSREDKKRVqfVSEPCSLSI 467
Cdd:COG5214  381 ----------------------------RNAGPKAVLIPSTNDaTSCHNAFPQGPIGRNALRLPSNFKC--TGNPCEFFI 430

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569005655 468 NGVMFGLTSTDLLFHIGAEEIFSSSGTS--DRFSRVLKHILTQRSYYPLYPPHEDMAIDYENF-YTYAQLP-----VTPD 539
Cdd:COG5214  431 NEILFGISSLDTPLEISSEECFHDSLLSggDRLGRISYHLLFQRTFYPVFPGGSLEKCNPSSLdVVSLSLPefmsmTAPD 510

                        410       420       430       440
                 ....*....|....*....|....*....|....*....|
gi 569005655 540 VFIVPSELRYFVKDIFGCVCVNPGRLTKGQVGGTFGRLYL 579
Cdd:COG5214  511 IYIVPSKLKHFCRDVGNVVVVNPGLQAKETNEGIAAHITL 550
Pol_alpha_B_N pfam08418
DNA polymerase alpha subunit B N-terminal; This is the eukaryotic DNA polymerase alpha subunit ...
 71-198 7.33e-06

DNA polymerase alpha subunit B N-terminal; This is the eukaryotic DNA polymerase alpha subunit B N-terminal domain which is involved in complex formation. This domain adopts an OB fold.


Pssm-ID: 462470  Cd Length: 240  Bit Score: 47.71  E-value: 7.33e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569005655   71 SSYTTPSKGPLKRVS--------STPETPLTKRSVAARSPRQLLSPSSFSPSATPSQkYTSRTNRGEVVTTFGSAQGLSW 142
Cdd:pfam08418  95 LVPSTPALKKRKLGSgassakrkSAFETPLASRVSSPAPSSSPGANNTPATPSAGSS-FSSRQNAGEVVETLNPHLELAE 173

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 569005655  143 SGRGGSGSVSLKVVGDPEPLTGSYKAMFQQLMGVREVLTSKIEELGSELKEHHKIE 198
Cdd:pfam08418 174 PPIAPYSEPRVKLTANTDPKKYKYKTMAMKLSEASEVLDDRIDEFAELIQEHHKLD 229
MPP_DNA_pol_II_small_archeal_C cd07386
archeal DNA polymerase II, small subunit, C-terminal metallophosphatase domain; The small ...
 420-563 1.76e-03

archeal DNA polymerase II, small subunit, C-terminal metallophosphatase domain; The small subunit of the archeal DNA polymerase II contains a C-terminal metallophosphatase domain. This domain is thought to be functionally active because the active site residues required for phosphoesterase activity in other members of this superfamily are intact. The archeal replicative DNA polymerases are thought to possess intrinsic phosphatase activity that hydrolyzes the pyrophosphate released during nucleotide polymerization. This domain 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: 277332  Cd Length: 243  Bit Score: 40.36  E-value: 1.76e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569005655 420 GSHLVFVPSlrDVH-------HEPVY---PQPPFTFSELSREDKKRVQFVSEPCSLSINGVMFgltstdLLFH-IGAEEI 488
Cdd:cd07386   72 AEYLSDVPS--HIKiiiipgnHDAVRqaePQPALPEEIRKLFYPGNVEFLSNPALVKIHGVDV------LIYHgRSLDDV 143

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569005655 489 FSS-SGTS-DRFSRVLKHILTQRSYYPLY-------PPHED-MAIDyenfytyaqlPVtPDVFIVPSELRYFVKDIFGCV 558
Cdd:cd07386  144 VGLiPGLSyDKPGKAMEELLKRRHLAPIYggrtpiaPEAEDyLVID----------EV-PDILHTGHVHVYGVGVYRGVL 212


                 ....*
gi 569005655 559 CVNPG 563
Cdd:cd07386  213 LVNSG 217
Prefoldin_2 cd23163
prefoldin subunit 2; Prefoldin subunit 2 is one of the beta subunits of the eukaryotic ...
 167-203 3.87e-03

prefoldin subunit 2; Prefoldin subunit 2 is one of the beta subunits of the eukaryotic prefoldin complex. Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.


Pssm-ID: 467479  Cd Length: 100  Bit Score: 37.11  E-value: 3.87e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 569005655 167 KAMFQQLMGVREVLTSKIEELGSELKEHHK-IEAFTPL 203
Cdd:cd23163    3 VAQYNQLRQEQQQLASKIAELEQELNEHKLvIDTLKPL 40
 
Name Accession Description Interval E-value
DNA_pol_E_B pfam04042
DNA polymerase alpha/epsilon subunit B; This family contains a number of DNA polymerase ...
 302-552 2.09e-64

DNA polymerase alpha/epsilon subunit B; This family contains a number of DNA polymerase subunits. The B subunit of the DNA polymerase alpha plays an essential role at the initial stage of DNA replication in S. cerevisiae and is phosphorylated in a cell cycle-dependent manner. DNA polymerase epsilon is essential for cell viability and chromosomal DNA replication in budding yeast. In addition, DNA polymerase epsilon may be involved in DNA repair and cell-cycle checkpoint control. The enzyme consists of at least four subunits in mammalian cells as well as in yeast. The largest subunit of DNA polymerase epsilon is responsible for polymerase epsilon is responsible for polymerase activity. In mouse, the DNA polymerase epsilon subunit B is the second largest subunit of the DNA polymerase. A part of the N-terminal was found to be responsible for the interaction with SAP18. Experimental evidence suggests that this subunit may recruit histone deacetylase to the replication fork to modify the chromatin structure.


Pssm-ID: 461142  Cd Length: 210  Bit Score: 210.24  E-value: 2.09e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569005655  302 VVVACGPYTTSDSITYDPLLDLIAIIN-RDQPDVCILFGPFLDAKHEQVENCKL---TSPFEDVFKQCLRTVIEGTrrqq 377
Cdd:pfam04042   1 IVFASGLYLDSDNLSLEALRDLLDGYNeDSPPDRLILAGPFLDSKHNLIASGAVagdTLTYNFLFLKLLLSILEQL---- 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569005655  378 fssvkgatkikrrcvlsyvhqiqismfmcqevafpsrgpaSSGSHLVFVPSLRDVHHEPVYPQPPFTFSELSREDKK-RV 456
Cdd:pfam04042  77 ----------------------------------------LEKTPVILVPGPNDPANSTVLPQPPFPRCLLPRIKKNnSL 116

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569005655  457 QFVSEPCSLSINGVMFGLTSTDLLFHIGAEEIFSSSGTSDRFSRVLKHILTQRSYYPLYPPHeDMAIDYENFYTYAqLPV 536
Cdd:pfam04042 117 IFVTNPCRFSINGVEVVVTSGDNVSDLLRYELKFSSSDVDRFLRLVETILRQRHLAPLAPDT-LRPYPYDKDDAFV-LYP 194

                         250
                  ....*....|....*.
gi 569005655  537 TPDVFIVPSELRYFVK 552
Cdd:pfam04042 195 LPDVLILGSELPSFAK 210
POL12 COG5214
DNA polymerase alpha-primase complex, polymerase-associated subunit B [DNA replication, ...
 166-579 6.81e-61

DNA polymerase alpha-primase complex, polymerase-associated subunit B [DNA replication, recombination, and repair];


Pssm-ID: 227539 [Multi-domain]  Cd Length: 581  Bit Score: 212.15  E-value: 6.81e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569005655 166 YKAMFQQLMGVREVLTSKIEELGSELKEHHKI--EAFTPLLVPAQEPVILLGQIGCDS---NGKLNSKSVILEGDQEHSY 240
Cdd:COG5214  158 SRFMYQKLRKKSKVLDDRIELFSMKPYFLYLLsiEDFAPPNNVSQSSFYTVGRIVNPStnfGHKLNSESVFLESSRDGGN 237

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569005655 241 GAQIPVDLSELKEYSLFPGQVVIMEGFNTTGRRLTATKLYEGVPLP-FYQPTEEEGASEQ-------TMVVVACGPYTTS 312
Cdd:COG5214  238 GVRVRLNLAHLQRYSVFPGQIVAVKGKNTDGGKFTVEAILPIPVVPiNPASDGQEKKYFQantnnqpTSIVAFSGPYGPR 317

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569005655 313 DSITYDPLLDLIAIINRDQPDVCILFGPFLDAKHEQVENCKLTSP----FEDVFKQCLRTVIEgtrrqqfssvkgatkik 388
Cdd:COG5214  318 DDLSGSPLFDAIDRVNANDVDVLILIGPFIDINHILIQYGATQSTpdsmLKELFIPRITPILD----------------- 380

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569005655 389 rrcvlsyvhqiqismfmcqevafpsrgpASSGSHLVFVPSLRD-VHHEPVYPQPPFTFSELSREDKKRVqfVSEPCSLSI 467
Cdd:COG5214  381 ----------------------------RNAGPKAVLIPSTNDaTSCHNAFPQGPIGRNALRLPSNFKC--TGNPCEFFI 430

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569005655 468 NGVMFGLTSTDLLFHIGAEEIFSSSGTS--DRFSRVLKHILTQRSYYPLYPPHEDMAIDYENF-YTYAQLP-----VTPD 539
Cdd:COG5214  431 NEILFGISSLDTPLEISSEECFHDSLLSggDRLGRISYHLLFQRTFYPVFPGGSLEKCNPSSLdVVSLSLPefmsmTAPD 510

                        410       420       430       440
                 ....*....|....*....|....*....|....*....|
gi 569005655 540 VFIVPSELRYFVKDIFGCVCVNPGRLTKGQVGGTFGRLYL 579
Cdd:COG5214  511 IYIVPSKLKHFCRDVGNVVVVNPGLQAKETNEGIAAHITL 550
Pol_alpha_B_N pfam08418
DNA polymerase alpha subunit B N-terminal; This is the eukaryotic DNA polymerase alpha subunit ...
 71-198 7.33e-06

DNA polymerase alpha subunit B N-terminal; This is the eukaryotic DNA polymerase alpha subunit B N-terminal domain which is involved in complex formation. This domain adopts an OB fold.


Pssm-ID: 462470  Cd Length: 240  Bit Score: 47.71  E-value: 7.33e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569005655   71 SSYTTPSKGPLKRVS--------STPETPLTKRSVAARSPRQLLSPSSFSPSATPSQkYTSRTNRGEVVTTFGSAQGLSW 142
Cdd:pfam08418  95 LVPSTPALKKRKLGSgassakrkSAFETPLASRVSSPAPSSSPGANNTPATPSAGSS-FSSRQNAGEVVETLNPHLELAE 173

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 569005655  143 SGRGGSGSVSLKVVGDPEPLTGSYKAMFQQLMGVREVLTSKIEELGSELKEHHKIE 198
Cdd:pfam08418 174 PPIAPYSEPRVKLTANTDPKKYKYKTMAMKLSEASEVLDDRIDEFAELIQEHHKLD 229
MPP_DNA_pol_II_small_archeal_C cd07386
archeal DNA polymerase II, small subunit, C-terminal metallophosphatase domain; The small ...
 420-563 1.76e-03

archeal DNA polymerase II, small subunit, C-terminal metallophosphatase domain; The small subunit of the archeal DNA polymerase II contains a C-terminal metallophosphatase domain. This domain is thought to be functionally active because the active site residues required for phosphoesterase activity in other members of this superfamily are intact. The archeal replicative DNA polymerases are thought to possess intrinsic phosphatase activity that hydrolyzes the pyrophosphate released during nucleotide polymerization. This domain 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: 277332  Cd Length: 243  Bit Score: 40.36  E-value: 1.76e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569005655 420 GSHLVFVPSlrDVH-------HEPVY---PQPPFTFSELSREDKKRVQFVSEPCSLSINGVMFgltstdLLFH-IGAEEI 488
Cdd:cd07386   72 AEYLSDVPS--HIKiiiipgnHDAVRqaePQPALPEEIRKLFYPGNVEFLSNPALVKIHGVDV------LIYHgRSLDDV 143

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569005655 489 FSS-SGTS-DRFSRVLKHILTQRSYYPLY-------PPHED-MAIDyenfytyaqlPVtPDVFIVPSELRYFVKDIFGCV 558
Cdd:cd07386  144 VGLiPGLSyDKPGKAMEELLKRRHLAPIYggrtpiaPEAEDyLVID----------EV-PDILHTGHVHVYGVGVYRGVL 212


                 ....*
gi 569005655 559 CVNPG 563
Cdd:cd07386  213 LVNSG 217
Prefoldin_2 cd23163
prefoldin subunit 2; Prefoldin subunit 2 is one of the beta subunits of the eukaryotic ...
 167-203 3.87e-03

prefoldin subunit 2; Prefoldin subunit 2 is one of the beta subunits of the eukaryotic prefoldin complex. Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.


Pssm-ID: 467479  Cd Length: 100  Bit Score: 37.11  E-value: 3.87e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 569005655 167 KAMFQQLMGVREVLTSKIEELGSELKEHHK-IEAFTPL 203
Cdd:cd23163    3 VAQYNQLRQEQQQLASKIAELEQELNEHKLvIDTLKPL 40
 
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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