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Conserved domains on  [gi|50401206|sp|Q9Y2S7|]
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RecName: Full=Polymerase delta-interacting protein 2; AltName: Full=38 kDa DNA polymerase delta interaction protein; Short=p38; Flags: Precursor

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DUF525 super family cl01119
ApaG domain; The apaG domain is a ~125 amino acids domain present in bacterial apaG proteins ...
 234-355 2.16e-32

ApaG domain; The apaG domain is a ~125 amino acids domain present in bacterial apaG proteins and in eukaryotic F-box proteins. The domain is named after the bacterial apaG protein, of which it forms the core. The domain also occurs in the C-terminal part of eukaryotic proteins with an N-terminal F-box domain. The Salmonella typhimurium apaG domain protein corD is involved in Co(2+) resistance and Mg(2+) efflux. Tertiary structures from different apaG proteins show a fold of several beta-sheets. The apaG domain may be involved in protein-protein interactions which could be implicated in substrate-specificity.


The actual alignment was detected with superfamily member PRK05461:

Pssm-ID: 470082  Cd Length: 127  Bit Score: 117.94  E-value: 2.16e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50401206  234 HRETTENIRVTVIPFYMGMREAQNSHVYWWRYCIRLENLDSDVVQLRERHWRIFSLSGTLETVRGRGVVGREPVLskeQP 313
Cdd:PRK05461   2 YSAVTYGIEVSVQPRYLEEQSDPEEGRYVFAYTITIENLGRVPVQLLSRHWLITDANGRVQEVRGEGVVGEQPVL---AP 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 50401206  314 --AFQYSSHVSLQASSGHMWGTFRFERPDGSHFDVRIPPFSLES 355
Cdd:PRK05461  79 geSFEYTSGAVLETPSGTMQGHYQMVDEDGERFEVPIPPFRLAV 122
YccV-like super family cl01548
Hemimethylated DNA-binding protein YccV like; YccV is a hemimethylated DNA binding protein ...
 74-200 1.40e-12

Hemimethylated DNA-binding protein YccV like; YccV is a hemimethylated DNA binding protein which has been shown to regulate dnaA gene expression. The structure of one of the hypothetical proteins in this family has been solved and it forms a beta sheet structure with a terminating alpha helix.


The actual alignment was detected with superfamily member smart00992:

Pssm-ID: 445467  Cd Length: 98  Bit Score: 63.02  E-value: 1.40e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50401206     74 NGKYETGQLFLHSIFGYRGVVlFPWQA-RLYDRDVASAAPEKAENPaghgskevkgKTHTYYQVLIDARDCPHISqrsqt 152
Cdd:smart00992   1 HAKFRIGQVVRHKLFGYRGVV-FDWDPeFANTEEWYDEIPEDSRPP----------RDQPFYHVLVENDDSSYVA----- 64

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|..
gi 50401206    153 eavtflanhddsralyaipgldYVSHEDILPYTStdQVPIQH----ELFERF 200
Cdd:smart00992  65 ----------------------YVSEQNLEPDTS--GEPIDHplldELFDEF 92
 
Name Accession Description Interval E-value
apaG PRK05461
CO2+/MG2+ efflux protein ApaG; Reviewed
 234-355 2.16e-32

CO2+/MG2+ efflux protein ApaG; Reviewed


Pssm-ID: 180098  Cd Length: 127  Bit Score: 117.94  E-value: 2.16e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50401206  234 HRETTENIRVTVIPFYMGMREAQNSHVYWWRYCIRLENLDSDVVQLRERHWRIFSLSGTLETVRGRGVVGREPVLskeQP 313
Cdd:PRK05461   2 YSAVTYGIEVSVQPRYLEEQSDPEEGRYVFAYTITIENLGRVPVQLLSRHWLITDANGRVQEVRGEGVVGEQPVL---AP 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 50401206  314 --AFQYSSHVSLQASSGHMWGTFRFERPDGSHFDVRIPPFSLES 355
Cdd:PRK05461  79 geSFEYTSGAVLETPSGTMQGHYQMVDEDGERFEVPIPPFRLAV 122
ApaG COG2967
Uncharacterized conserved protein ApaG affecting Mg2+/Co2+ transport [Inorganic ion transport ...
 239-353 2.77e-32

Uncharacterized conserved protein ApaG affecting Mg2+/Co2+ transport [Inorganic ion transport and metabolism];


Pssm-ID: 442207  Cd Length: 119  Bit Score: 117.51  E-value: 2.77e-32
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50401206 239 ENIRVTVIPFYMGMREAQNSHVYWWRYCIRLENLDSDVVQLRERHWRIFSLSGTLETVRGRGVVGREPVLskeQP--AFQ 316
Cdd:COG2967   1 YGIKVSVETEYLPEQSDPEEGRYVFAYTITIENLGDVTVQLLSRHWIITDANGKVQEVEGEGVVGEQPVL---APgeSFE 77

                        90       100       110
                ....*....|....*....|....*....|....*..
gi 50401206 317 YSSHVSLQASSGHMWGTFRFERPDGSHFDVRIPPFSL 353
Cdd:COG2967  78 YTSGCVLETPVGTMQGSYQMVDEDGERFDVPIPPFSL 114
DUF525 pfam04379
ApaG domain; The apaG domain is a ~125 amino acids domain present in bacterial apaG proteins ...
 257-338 1.96e-30

ApaG domain; The apaG domain is a ~125 amino acids domain present in bacterial apaG proteins and in eukaryotic F-box proteins. The domain is named after the bacterial apaG protein, of which it forms the core. The domain also occurs in the C-terminal part of eukaryotic proteins with an N-terminal F-box domain. The Salmonella typhimurium apaG domain protein corD is involved in Co(2+) resistance and Mg(2+) efflux. Tertiary structures from different apaG proteins show a fold of several beta-sheets. The apaG domain may be involved in protein-protein interactions which could be implicated in substrate-specificity.


Pssm-ID: 461283  Cd Length: 87  Bit Score: 111.40  E-value: 1.96e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50401206   257 NSHVYWWRYCIRLENLDSDVVQLRERHWRIFSLSGTLETVRGRGVVGREPVLsKEQPAFQYSSHVSLQASSGHMWGTFRF 336
Cdd:pfam04379   7 EEGRYVFAYTIRIENLGDSSVQLLSRHWIITDANGKVEEVRGEGVVGEQPVL-APGESFEYTSGCPLETPSGSMEGSYTM 85


                  ..
gi 50401206   337 ER 338
Cdd:pfam04379  86 VR 87
YccV-like smart00992
Hemimethylated DNA-binding protein YccV like; YccV is a hemimethylated DNA binding protein ...
 74-200 1.40e-12

Hemimethylated DNA-binding protein YccV like; YccV is a hemimethylated DNA binding protein which has been shown to regulate dnaA gene expression. The structure of one of the hypothetical proteins in this family has been solved and it forms a beta sheet structure with a terminating alpha helix.


Pssm-ID: 214961  Cd Length: 98  Bit Score: 63.02  E-value: 1.40e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50401206     74 NGKYETGQLFLHSIFGYRGVVlFPWQA-RLYDRDVASAAPEKAENPaghgskevkgKTHTYYQVLIDARDCPHISqrsqt 152
Cdd:smart00992   1 HAKFRIGQVVRHKLFGYRGVV-FDWDPeFANTEEWYDEIPEDSRPP----------RDQPFYHVLVENDDSSYVA----- 64

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|..
gi 50401206    153 eavtflanhddsralyaipgldYVSHEDILPYTStdQVPIQH----ELFERF 200
Cdd:smart00992  65 ----------------------YVSEQNLEPDTS--GEPIDHplldELFDEF 92
YccV-like pfam08755
Hemimethylated DNA-binding protein YccV like; YccV is a hemimethylated DNA binding protein ...
 76-200 3.85e-10

Hemimethylated DNA-binding protein YccV like; YccV is a hemimethylated DNA binding protein which has been shown to regulate dnaA gene expression. The structure of one of the hypothetical proteins in this family has been solved and it forms a beta sheet structure with a terminating alpha helix.


Pssm-ID: 430193  Cd Length: 96  Bit Score: 56.06  E-value: 3.85e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50401206    76 KYETGQLFLHSIFGYRGVVlfpwqarlYDRDVASAAPEKAENPAGhgsKEVKGKTHTYYQVLIDARDCPHISQRsqteav 155
Cdd:pfam08755   2 KFRIGQVVRHRRYGYRGVI--------VGWDPECAASEEWIEQMG---VDSLGRDQPFYHVLVDNEDGSYVSVR------ 64

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 50401206   156 tflanhddsralyaipgldYVSHEDILPYTSTDQV--PIQHELFERF 200
Cdd:pfam08755  65 -------------------YVAEENLEPDESGEPIdhPEIGKYFKRF 92
yccV TIGR02097
hemimethylated DNA binding domain; This model describes the small protein from E. coli YccV ...
 76-146 8.21e-04

hemimethylated DNA binding domain; This model describes the small protein from E. coli YccV and its homologs in other Proteobacteria. YccV is now described as a hemimethylated DNA binding protein. The model also describes a domain in longer eukaryotic proteins.


Pssm-ID: 131152  Cd Length: 101  Bit Score: 38.51  E-value: 8.21e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 50401206    76 KYETGQLFLHSIFGYRGVVlfpwqarlYDRDVASAAPEKAENPAGHGSKEVkgKTHTYYQVLIDARDCPHI 146
Cdd:TIGR02097   3 KFRIGQVVRHKLFGYRGVV--------IDVDPEYSNTEEWLDAIPVEIRPL--RDQPFYHVLAEDDEGLPY 63
 
Name Accession Description Interval E-value
apaG PRK05461
CO2+/MG2+ efflux protein ApaG; Reviewed
 234-355 2.16e-32

CO2+/MG2+ efflux protein ApaG; Reviewed


Pssm-ID: 180098  Cd Length: 127  Bit Score: 117.94  E-value: 2.16e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50401206  234 HRETTENIRVTVIPFYMGMREAQNSHVYWWRYCIRLENLDSDVVQLRERHWRIFSLSGTLETVRGRGVVGREPVLskeQP 313
Cdd:PRK05461   2 YSAVTYGIEVSVQPRYLEEQSDPEEGRYVFAYTITIENLGRVPVQLLSRHWLITDANGRVQEVRGEGVVGEQPVL---AP 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 50401206  314 --AFQYSSHVSLQASSGHMWGTFRFERPDGSHFDVRIPPFSLES 355
Cdd:PRK05461  79 geSFEYTSGAVLETPSGTMQGHYQMVDEDGERFEVPIPPFRLAV 122
ApaG COG2967
Uncharacterized conserved protein ApaG affecting Mg2+/Co2+ transport [Inorganic ion transport ...
 239-353 2.77e-32

Uncharacterized conserved protein ApaG affecting Mg2+/Co2+ transport [Inorganic ion transport and metabolism];


Pssm-ID: 442207  Cd Length: 119  Bit Score: 117.51  E-value: 2.77e-32
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50401206 239 ENIRVTVIPFYMGMREAQNSHVYWWRYCIRLENLDSDVVQLRERHWRIFSLSGTLETVRGRGVVGREPVLskeQP--AFQ 316
Cdd:COG2967   1 YGIKVSVETEYLPEQSDPEEGRYVFAYTITIENLGDVTVQLLSRHWIITDANGKVQEVEGEGVVGEQPVL---APgeSFE 77

                        90       100       110
                ....*....|....*....|....*....|....*..
gi 50401206 317 YSSHVSLQASSGHMWGTFRFERPDGSHFDVRIPPFSL 353
Cdd:COG2967  78 YTSGCVLETPVGTMQGSYQMVDEDGERFDVPIPPFSL 114
DUF525 pfam04379
ApaG domain; The apaG domain is a ~125 amino acids domain present in bacterial apaG proteins ...
 257-338 1.96e-30

ApaG domain; The apaG domain is a ~125 amino acids domain present in bacterial apaG proteins and in eukaryotic F-box proteins. The domain is named after the bacterial apaG protein, of which it forms the core. The domain also occurs in the C-terminal part of eukaryotic proteins with an N-terminal F-box domain. The Salmonella typhimurium apaG domain protein corD is involved in Co(2+) resistance and Mg(2+) efflux. Tertiary structures from different apaG proteins show a fold of several beta-sheets. The apaG domain may be involved in protein-protein interactions which could be implicated in substrate-specificity.


Pssm-ID: 461283  Cd Length: 87  Bit Score: 111.40  E-value: 1.96e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50401206   257 NSHVYWWRYCIRLENLDSDVVQLRERHWRIFSLSGTLETVRGRGVVGREPVLsKEQPAFQYSSHVSLQASSGHMWGTFRF 336
Cdd:pfam04379   7 EEGRYVFAYTIRIENLGDSSVQLLSRHWIITDANGKVEEVRGEGVVGEQPVL-APGESFEYTSGCPLETPSGSMEGSYTM 85


                  ..
gi 50401206   337 ER 338
Cdd:pfam04379  86 VR 87
YccV-like smart00992
Hemimethylated DNA-binding protein YccV like; YccV is a hemimethylated DNA binding protein ...
 74-200 1.40e-12

Hemimethylated DNA-binding protein YccV like; YccV is a hemimethylated DNA binding protein which has been shown to regulate dnaA gene expression. The structure of one of the hypothetical proteins in this family has been solved and it forms a beta sheet structure with a terminating alpha helix.


Pssm-ID: 214961  Cd Length: 98  Bit Score: 63.02  E-value: 1.40e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50401206     74 NGKYETGQLFLHSIFGYRGVVlFPWQA-RLYDRDVASAAPEKAENPaghgskevkgKTHTYYQVLIDARDCPHISqrsqt 152
Cdd:smart00992   1 HAKFRIGQVVRHKLFGYRGVV-FDWDPeFANTEEWYDEIPEDSRPP----------RDQPFYHVLVENDDSSYVA----- 64

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|..
gi 50401206    153 eavtflanhddsralyaipgldYVSHEDILPYTStdQVPIQH----ELFERF 200
Cdd:smart00992  65 ----------------------YVSEQNLEPDTS--GEPIDHplldELFDEF 92
YccV-like pfam08755
Hemimethylated DNA-binding protein YccV like; YccV is a hemimethylated DNA binding protein ...
 76-200 3.85e-10

Hemimethylated DNA-binding protein YccV like; YccV is a hemimethylated DNA binding protein which has been shown to regulate dnaA gene expression. The structure of one of the hypothetical proteins in this family has been solved and it forms a beta sheet structure with a terminating alpha helix.


Pssm-ID: 430193  Cd Length: 96  Bit Score: 56.06  E-value: 3.85e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50401206    76 KYETGQLFLHSIFGYRGVVlfpwqarlYDRDVASAAPEKAENPAGhgsKEVKGKTHTYYQVLIDARDCPHISQRsqteav 155
Cdd:pfam08755   2 KFRIGQVVRHRRYGYRGVI--------VGWDPECAASEEWIEQMG---VDSLGRDQPFYHVLVDNEDGSYVSVR------ 64

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 50401206   156 tflanhddsralyaipgldYVSHEDILPYTSTDQV--PIQHELFERF 200
Cdd:pfam08755  65 -------------------YVAEENLEPDESGEPIdhPEIGKYFKRF 92
yccV TIGR02097
hemimethylated DNA binding domain; This model describes the small protein from E. coli YccV ...
 76-146 8.21e-04

hemimethylated DNA binding domain; This model describes the small protein from E. coli YccV and its homologs in other Proteobacteria. YccV is now described as a hemimethylated DNA binding protein. The model also describes a domain in longer eukaryotic proteins.


Pssm-ID: 131152  Cd Length: 101  Bit Score: 38.51  E-value: 8.21e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 50401206    76 KYETGQLFLHSIFGYRGVVlfpwqarlYDRDVASAAPEKAENPAGHGSKEVkgKTHTYYQVLIDARDCPHI 146
Cdd:TIGR02097   3 KFRIGQVVRHKLFGYRGVV--------IDVDPEYSNTEEWLDAIPVEIRPL--RDQPFYHVLAEDDEGLPY 63
 
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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