NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|225467138|ref|XP_002262993|]
View 

uncharacterized protein LOC100256584 [Vitis vinifera]

Protein Classification

beta clamp domain-containing protein( domain architecture ID 1903345)

beta clamp domain-containing protein such as bacterial beta sliding clamp and eukaryotic proliferating cell nuclear antigen (PCNA)

CATH:  3.70.10.10
Gene Ontology:  GO:0003677
PubMed:  10535734|11719243

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
beta_clamp super family cl42470
Beta clamp domain. The beta subunit (processivity factor) of DNA polymerase III holoenzyme, ...
 39-230 5.12e-18

Beta clamp domain. The beta subunit (processivity factor) of DNA polymerase III holoenzyme, refered to as the beta clamp, forms a ring shaped dimer that encircles dsDNA (sliding clamp) in bacteria. The beta-clamp is structurally similar to the trimeric ring formed by PCNA (found in eukaryotes and archaea) and the processivity factor (found in bacteriophages T4 and RB69). This structural correspondence further substantiates the mechanistic connection between eukaryotic and prokaryotic DNA replication that has been suggested on biochemical grounds.


The actual alignment was detected with superfamily member cd00577:

Pssm-ID: 478224 [Multi-domain]  Cd Length: 248  Bit Score: 80.37  E-value: 5.12e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225467138  39 PKYAFKHFlfSAQGQPRFGVSLCLFVDCLNTLlvPGHSNIIEIQYPELDMQLFLKSVDSmdaCIYGEIRTRIPDTISWDY 118
Cdd:cd00577   50 PKELFEEY--RCDEEISLGVNLKSLLKILKCA--GNEDCVTLRADDEDPLKILFESSKG---DVTSEFSLKLMDIDSEQL 122

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225467138 119 NFeHAGSTPLSFTLNSTALKEAINDLEWPGSSIQITLEPIPPSITFRGEGHGDLQIDFIYYVntDLLIAVHSDHRVSYRH 198
Cdd:cd00577  123 PI-PELEYDATVTLPSDELKDIVRDLESISDSVTISASKDGFKFSAEGELGGASVTLLPKDS--DLLVTIECSEPVSSTY 199

                        170       180       190
                 ....*....|....*....|....*....|..
gi 225467138 199 KYKFIRATTSNIPSSvtrdnrgSKLTIGESGD 230
Cdd:cd00577  200 SLKYLKDFTKAAPLS-------DKVTLSFGSD 224
Ribosomal_L5_C super family cl46659
ribosomal L5P family C-terminus; This region is found associated with pfam00281.
 214-256 2.03e-10

ribosomal L5P family C-terminus; This region is found associated with pfam00281.


The actual alignment was detected with superfamily member PTZ00156:

Pssm-ID: 480999  Cd Length: 172  Bit Score: 58.13  E-value: 2.03e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 225467138 214 VTRDNRGSKLTI----GESGDHLTRAAKVLKKLSGQIPVFFKVRNTV 256
Cdd:PTZ00156   7 PMRKIRIEKLVLnicvGESGDRLTRAAKVLEQLTGQKPVFSKARYTV 53
 
Name Accession Description Interval E-value
PCNA cd00577
Proliferating Cell Nuclear Antigen (PCNA) domain found in eukaryotes and archaea. These ...
 39-230 5.12e-18

Proliferating Cell Nuclear Antigen (PCNA) domain found in eukaryotes and archaea. These polymerase processivity factors play a role in DNA replication and repair. PCNA encircles duplex DNA in its central cavity, providing a DNA-bound platform for the attachment of the polymerase. The trimeric PCNA ring is structurally similar to the dimeric ring formed by the DNA polymerase processivity factors in bacteria (beta subunit DNA polymerase III holoenzyme) and in bacteriophages (catalytic subunits in T4 and RB69). This structural correspondence further substantiates the mechanistic connection between eukaryotic and prokaryotic DNA replication that has been suggested on biochemical grounds. PCNA is also involved with proteins involved in cell cycle processes such as DNA repair and apoptosis. Many of these proteins contain a highly conserved motif known as the PIP-box (PCNA interacting protein box) which contains the sequence Qxx[LIM]xxF[FY].


Pssm-ID: 238322 [Multi-domain]  Cd Length: 248  Bit Score: 80.37  E-value: 5.12e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225467138  39 PKYAFKHFlfSAQGQPRFGVSLCLFVDCLNTLlvPGHSNIIEIQYPELDMQLFLKSVDSmdaCIYGEIRTRIPDTISWDY 118
Cdd:cd00577   50 PKELFEEY--RCDEEISLGVNLKSLLKILKCA--GNEDCVTLRADDEDPLKILFESSKG---DVTSEFSLKLMDIDSEQL 122

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225467138 119 NFeHAGSTPLSFTLNSTALKEAINDLEWPGSSIQITLEPIPPSITFRGEGHGDLQIDFIYYVntDLLIAVHSDHRVSYRH 198
Cdd:cd00577  123 PI-PELEYDATVTLPSDELKDIVRDLESISDSVTISASKDGFKFSAEGELGGASVTLLPKDS--DLLVTIECSEPVSSTY 199

                        170       180       190
                 ....*....|....*....|....*....|..
gi 225467138 199 KYKFIRATTSNIPSSvtrdnrgSKLTIGESGD 230
Cdd:cd00577  200 SLKYLKDFTKAAPLS-------DKVTLSFGSD 224
PTZ00156 PTZ00156
60S ribosomal protein L11; Provisional
 214-256 2.03e-10

60S ribosomal protein L11; Provisional


Pssm-ID: 185485  Cd Length: 172  Bit Score: 58.13  E-value: 2.03e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 225467138 214 VTRDNRGSKLTI----GESGDHLTRAAKVLKKLSGQIPVFFKVRNTV 256
Cdd:PTZ00156   7 PMRKIRIEKLVLnicvGESGDRLTRAAKVLEQLTGQKPVFSKARYTV 53
Ribosomal_L5 pfam00281
Ribosomal protein L5;
222-256 4.87e-04

Ribosomal protein L5;


Pssm-ID: 425579 [Multi-domain]  Cd Length: 57  Bit Score: 37.37  E-value: 4.87e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 225467138  222 KLTI----GESGD---HLTRAAKVLKKLSGQIPVFFKVRNTV 256
Cdd:pfam00281  10 KVVVnmgvGEAGEdkkLLEKAAKVLEQITGQKPVVTKAKKSI 51
 
Name Accession Description Interval E-value
PCNA cd00577
Proliferating Cell Nuclear Antigen (PCNA) domain found in eukaryotes and archaea. These ...
 39-230 5.12e-18

Proliferating Cell Nuclear Antigen (PCNA) domain found in eukaryotes and archaea. These polymerase processivity factors play a role in DNA replication and repair. PCNA encircles duplex DNA in its central cavity, providing a DNA-bound platform for the attachment of the polymerase. The trimeric PCNA ring is structurally similar to the dimeric ring formed by the DNA polymerase processivity factors in bacteria (beta subunit DNA polymerase III holoenzyme) and in bacteriophages (catalytic subunits in T4 and RB69). This structural correspondence further substantiates the mechanistic connection between eukaryotic and prokaryotic DNA replication that has been suggested on biochemical grounds. PCNA is also involved with proteins involved in cell cycle processes such as DNA repair and apoptosis. Many of these proteins contain a highly conserved motif known as the PIP-box (PCNA interacting protein box) which contains the sequence Qxx[LIM]xxF[FY].


Pssm-ID: 238322 [Multi-domain]  Cd Length: 248  Bit Score: 80.37  E-value: 5.12e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225467138  39 PKYAFKHFlfSAQGQPRFGVSLCLFVDCLNTLlvPGHSNIIEIQYPELDMQLFLKSVDSmdaCIYGEIRTRIPDTISWDY 118
Cdd:cd00577   50 PKELFEEY--RCDEEISLGVNLKSLLKILKCA--GNEDCVTLRADDEDPLKILFESSKG---DVTSEFSLKLMDIDSEQL 122

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225467138 119 NFeHAGSTPLSFTLNSTALKEAINDLEWPGSSIQITLEPIPPSITFRGEGHGDLQIDFIYYVntDLLIAVHSDHRVSYRH 198
Cdd:cd00577  123 PI-PELEYDATVTLPSDELKDIVRDLESISDSVTISASKDGFKFSAEGELGGASVTLLPKDS--DLLVTIECSEPVSSTY 199

                        170       180       190
                 ....*....|....*....|....*....|..
gi 225467138 199 KYKFIRATTSNIPSSvtrdnrgSKLTIGESGD 230
Cdd:cd00577  200 SLKYLKDFTKAAPLS-------DKVTLSFGSD 224
PTZ00156 PTZ00156
60S ribosomal protein L11; Provisional
 214-256 2.03e-10

60S ribosomal protein L11; Provisional


Pssm-ID: 185485  Cd Length: 172  Bit Score: 58.13  E-value: 2.03e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 225467138 214 VTRDNRGSKLTI----GESGDHLTRAAKVLKKLSGQIPVFFKVRNTV 256
Cdd:PTZ00156   7 PMRKIRIEKLVLnicvGESGDRLTRAAKVLEQLTGQKPVFSKARYTV 53
Ribosomal_L5 pfam00281
Ribosomal protein L5;
222-256 4.87e-04

Ribosomal protein L5;


Pssm-ID: 425579 [Multi-domain]  Cd Length: 57  Bit Score: 37.37  E-value: 4.87e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 225467138  222 KLTI----GESGD---HLTRAAKVLKKLSGQIPVFFKVRNTV 256
Cdd:pfam00281  10 KVVVnmgvGEAGEdkkLLEKAAKVLEQITGQKPVVTKAKKSI 51
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH