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Conserved domains on  [gi|47086611|ref|NP_997879|]
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polymerase delta-interacting protein 2 [Danio rerio]

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 ...
 242-363 2.83e-35

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: 125.64  E-value: 2.83e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47086611  242 HRETTENIRVTVIPFYMGMREAQNSHVYWWRYCIRLENLGNEVVQLRERHWRIFSLSGTLETVRGRGVVGKEPVLsreQP 321
Cdd:PRK05461   2 YSAVTYGIEVSVQPRYLEEQSDPEEGRYVFAYTITIENLGRVPVQLLSRHWLITDANGRVQEVRGEGVVGEQPVL---AP 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 47086611  322 --AFQYSSHVSLQAPSGHMWGTFCFERTDGSHFDVRIPPFSLES 363
Cdd:PRK05461  79 geSFEYTSGAVLETPSGTMQGHYQMVDEDGERFEVPIPPFRLAV 122
YccV-like super family cl01548
Hemimethylated DNA-binding protein YccV like; YccV is a hemimethylated DNA binding protein ...
 82-208 1.76e-13

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: 65.72  E-value: 1.76e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47086611     82 HGKYETGQLFLHSVFGYRGIVlFPWHArlyDRDVSPATTDSKP-DSTGHgskevkgKMHTYYQVLIDTRDCPHISqrsqt 160
Cdd:smart00992   1 HAKFRIGQVVRHKLFGYRGVV-FDWDP---EFANTEEWYDEIPeDSRPP-------RDQPFYHVLVENDDSSYVA----- 64

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|..
gi 47086611    161 eavtflanhddsralyaipgldYVSHEDILPYNSTEqvPIQH----ELFERF 208
Cdd:smart00992  65 ----------------------YVSEQNLEPDTSGE--PIDHplldELFDEF 92
 
Name Accession Description Interval E-value
apaG PRK05461
CO2+/MG2+ efflux protein ApaG; Reviewed
 242-363 2.83e-35

CO2+/MG2+ efflux protein ApaG; Reviewed


Pssm-ID: 180098  Cd Length: 127  Bit Score: 125.64  E-value: 2.83e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47086611  242 HRETTENIRVTVIPFYMGMREAQNSHVYWWRYCIRLENLGNEVVQLRERHWRIFSLSGTLETVRGRGVVGKEPVLsreQP 321
Cdd:PRK05461   2 YSAVTYGIEVSVQPRYLEEQSDPEEGRYVFAYTITIENLGRVPVQLLSRHWLITDANGRVQEVRGEGVVGEQPVL---AP 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 47086611  322 --AFQYSSHVSLQAPSGHMWGTFCFERTDGSHFDVRIPPFSLES 363
Cdd:PRK05461  79 geSFEYTSGAVLETPSGTMQGHYQMVDEDGERFEVPIPPFRLAV 122
ApaG COG2967
Uncharacterized conserved protein ApaG affecting Mg2+/Co2+ transport [Inorganic ion transport ...
 247-361 2.87e-35

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


Pssm-ID: 442207  Cd Length: 119  Bit Score: 125.21  E-value: 2.87e-35
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47086611 247 ENIRVTVIPFYMGMREAQNSHVYWWRYCIRLENLGNEVVQLRERHWRIFSLSGTLETVRGRGVVGKEPVLsreQP--AFQ 324
Cdd:COG2967   1 YGIKVSVETEYLPEQSDPEEGRYVFAYTITIENLGDVTVQLLSRHWIITDANGKVQEVEGEGVVGEQPVL---APgeSFE 77

                        90       100       110
                ....*....|....*....|....*....|....*..
gi 47086611 325 YSSHVSLQAPSGHMWGTFCFERTDGSHFDVRIPPFSL 361
Cdd:COG2967  78 YTSGCVLETPVGTMQGSYQMVDEDGERFDVPIPPFSL 114
DUF525 pfam04379
ApaG domain; The apaG domain is a ~125 amino acids domain present in bacterial apaG proteins ...
 265-346 3.15e-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.


Pssm-ID: 461283  Cd Length: 87  Bit Score: 116.41  E-value: 3.15e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47086611   265 NSHVYWWRYCIRLENLGNEVVQLRERHWRIFSLSGTLETVRGRGVVGKEPVLsREQPAFQYSSHVSLQAPSGHMWGTFCF 344
Cdd:pfam04379   7 EEGRYVFAYTIRIENLGDSSVQLLSRHWIITDANGKVEEVRGEGVVGEQPVL-APGESFEYTSGCPLETPSGSMEGSYTM 85


                  ..
gi 47086611   345 ER 346
Cdd:pfam04379  86 VR 87
YccV-like smart00992
Hemimethylated DNA-binding protein YccV like; YccV is a hemimethylated DNA binding protein ...
 82-208 1.76e-13

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: 65.72  E-value: 1.76e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47086611     82 HGKYETGQLFLHSVFGYRGIVlFPWHArlyDRDVSPATTDSKP-DSTGHgskevkgKMHTYYQVLIDTRDCPHISqrsqt 160
Cdd:smart00992   1 HAKFRIGQVVRHKLFGYRGVV-FDWDP---EFANTEEWYDEIPeDSRPP-------RDQPFYHVLVENDDSSYVA----- 64

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|..
gi 47086611    161 eavtflanhddsralyaipgldYVSHEDILPYNSTEqvPIQH----ELFERF 208
Cdd:smart00992  65 ----------------------YVSEQNLEPDTSGE--PIDHplldELFDEF 92
YccV-like pfam08755
Hemimethylated DNA-binding protein YccV like; YccV is a hemimethylated DNA binding protein ...
 84-208 1.08e-08

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: 52.21  E-value: 1.08e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47086611    84 KYETGQLFLHSVFGYRGIVlfpwharlYDRDVSPATTDSKPDSTGhgsKEVKGKMHTYYQVLIDTRDCPHISQRsqteav 163
Cdd:pfam08755   2 KFRIGQVVRHRRYGYRGVI--------VGWDPECAASEEWIEQMG---VDSLGRDQPFYHVLVDNEDGSYVSVR------ 64

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 47086611   164 tflanhddsralyaipgldYVSHEDILPYNSTEQV--PIQHELFERF 208
Cdd:pfam08755  65 -------------------YVAEENLEPDESGEPIdhPEIGKYFKRF 92
yccV TIGR02097
hemimethylated DNA binding domain; This model describes the small protein from E. coli YccV ...
 82-154 3.77e-03

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: 36.58  E-value: 3.77e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 47086611    82 HGKYETGQLFLHSVFGYRGIVlfpwharlYDRDVSPATTDSKPDSTGHGSKEVKGKmhTYYQVLIDTRDCPHI 154
Cdd:TIGR02097   1 AAKFRIGQVVRHKLFGYRGVV--------IDVDPEYSNTEEWLDAIPVEIRPLRDQ--PFYHVLAEDDEGLPY 63
 
Name Accession Description Interval E-value
apaG PRK05461
CO2+/MG2+ efflux protein ApaG; Reviewed
 242-363 2.83e-35

CO2+/MG2+ efflux protein ApaG; Reviewed


Pssm-ID: 180098  Cd Length: 127  Bit Score: 125.64  E-value: 2.83e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47086611  242 HRETTENIRVTVIPFYMGMREAQNSHVYWWRYCIRLENLGNEVVQLRERHWRIFSLSGTLETVRGRGVVGKEPVLsreQP 321
Cdd:PRK05461   2 YSAVTYGIEVSVQPRYLEEQSDPEEGRYVFAYTITIENLGRVPVQLLSRHWLITDANGRVQEVRGEGVVGEQPVL---AP 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 47086611  322 --AFQYSSHVSLQAPSGHMWGTFCFERTDGSHFDVRIPPFSLES 363
Cdd:PRK05461  79 geSFEYTSGAVLETPSGTMQGHYQMVDEDGERFEVPIPPFRLAV 122
ApaG COG2967
Uncharacterized conserved protein ApaG affecting Mg2+/Co2+ transport [Inorganic ion transport ...
 247-361 2.87e-35

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


Pssm-ID: 442207  Cd Length: 119  Bit Score: 125.21  E-value: 2.87e-35
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47086611 247 ENIRVTVIPFYMGMREAQNSHVYWWRYCIRLENLGNEVVQLRERHWRIFSLSGTLETVRGRGVVGKEPVLsreQP--AFQ 324
Cdd:COG2967   1 YGIKVSVETEYLPEQSDPEEGRYVFAYTITIENLGDVTVQLLSRHWIITDANGKVQEVEGEGVVGEQPVL---APgeSFE 77

                        90       100       110
                ....*....|....*....|....*....|....*..
gi 47086611 325 YSSHVSLQAPSGHMWGTFCFERTDGSHFDVRIPPFSL 361
Cdd:COG2967  78 YTSGCVLETPVGTMQGSYQMVDEDGERFDVPIPPFSL 114
DUF525 pfam04379
ApaG domain; The apaG domain is a ~125 amino acids domain present in bacterial apaG proteins ...
 265-346 3.15e-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.


Pssm-ID: 461283  Cd Length: 87  Bit Score: 116.41  E-value: 3.15e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47086611   265 NSHVYWWRYCIRLENLGNEVVQLRERHWRIFSLSGTLETVRGRGVVGKEPVLsREQPAFQYSSHVSLQAPSGHMWGTFCF 344
Cdd:pfam04379   7 EEGRYVFAYTIRIENLGDSSVQLLSRHWIITDANGKVEEVRGEGVVGEQPVL-APGESFEYTSGCPLETPSGSMEGSYTM 85


                  ..
gi 47086611   345 ER 346
Cdd:pfam04379  86 VR 87
YccV-like smart00992
Hemimethylated DNA-binding protein YccV like; YccV is a hemimethylated DNA binding protein ...
 82-208 1.76e-13

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: 65.72  E-value: 1.76e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47086611     82 HGKYETGQLFLHSVFGYRGIVlFPWHArlyDRDVSPATTDSKP-DSTGHgskevkgKMHTYYQVLIDTRDCPHISqrsqt 160
Cdd:smart00992   1 HAKFRIGQVVRHKLFGYRGVV-FDWDP---EFANTEEWYDEIPeDSRPP-------RDQPFYHVLVENDDSSYVA----- 64

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|..
gi 47086611    161 eavtflanhddsralyaipgldYVSHEDILPYNSTEqvPIQH----ELFERF 208
Cdd:smart00992  65 ----------------------YVSEQNLEPDTSGE--PIDHplldELFDEF 92
YccV-like pfam08755
Hemimethylated DNA-binding protein YccV like; YccV is a hemimethylated DNA binding protein ...
 84-208 1.08e-08

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: 52.21  E-value: 1.08e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47086611    84 KYETGQLFLHSVFGYRGIVlfpwharlYDRDVSPATTDSKPDSTGhgsKEVKGKMHTYYQVLIDTRDCPHISQRsqteav 163
Cdd:pfam08755   2 KFRIGQVVRHRRYGYRGVI--------VGWDPECAASEEWIEQMG---VDSLGRDQPFYHVLVDNEDGSYVSVR------ 64

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 47086611   164 tflanhddsralyaipgldYVSHEDILPYNSTEQV--PIQHELFERF 208
Cdd:pfam08755  65 -------------------YVAEENLEPDESGEPIdhPEIGKYFKRF 92
yccV TIGR02097
hemimethylated DNA binding domain; This model describes the small protein from E. coli YccV ...
 82-154 3.77e-03

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: 36.58  E-value: 3.77e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 47086611    82 HGKYETGQLFLHSVFGYRGIVlfpwharlYDRDVSPATTDSKPDSTGHGSKEVKGKmhTYYQVLIDTRDCPHI 154
Cdd:TIGR02097   1 AAKFRIGQVVRHKLFGYRGVV--------IDVDPEYSNTEEWLDAIPVEIRPLRDQ--PFYHVLAEDDEGLPY 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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