NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1943461|pdb|1UNA|A]
View 

Chain A, GA UNASSEMBLED COAT PROTEIN DIMER

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

Name Accession Description Interval E-value
Levi_coat super family cl28115
Levivirus coat protein; The Levivirus coat protein forms the bacteriophage coat that ...
1-128 1.89e-81

Levivirus coat protein; The Levivirus coat protein forms the bacteriophage coat that encapsidates the viral RNA. 180 copies of this protein form the virion shell. The MS2 bacteriophage coat protein controls two distinct processes: sequence-specific RNA encapsidation and repression of replicase translation-by binding to an RNA stem-loop structure of 19 nucleotides containing the initiation codon of the replicase gene. The binding of a coat protein dimer to this hairpin shuts off synthesis of the viral replicase, switching the viral replication cycle to virion assembly rather than continued replication.


The actual alignment was detected with superfamily member PHA00026:

Pssm-ID: 421570  Cd Length: 129  Bit Score: 234.94  E-value: 1.89e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1UNA_A         1 ATLHSFVLVDNGGTGNVTVVPVSNANGVAEWLSNNSRSQAYRVTASYRASGADKRKYTIKLEVPKIVTQVVNGVELPVSA 80
Cdd:PHA00026   2 ANFRQFVLVDNGGTGDVTVAPSNFANGVAEWISNNSRSQAYKVTASVRASGADKRKYAIKLEVPKIATQTVGGVELPGAA 81
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
1UNA_A        81 WKAYASIDLTIPIFAATDDVTVISKSLTGLFKVGNPIAEAISSQSGFY 128
Cdd:PHA00026  82 WKAYANIDLTIPIFAANDDCELISKALAGLFKDGNPIAEAIAANSGFY 129
 
Name Accession Description Interval E-value
cp PHA00026
coat protein
1-128 1.89e-81

coat protein


Pssm-ID: 133846  Cd Length: 129  Bit Score: 234.94  E-value: 1.89e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1UNA_A         1 ATLHSFVLVDNGGTGNVTVVPVSNANGVAEWLSNNSRSQAYRVTASYRASGADKRKYTIKLEVPKIVTQVVNGVELPVSA 80
Cdd:PHA00026   2 ANFRQFVLVDNGGTGDVTVAPSNFANGVAEWISNNSRSQAYKVTASVRASGADKRKYAIKLEVPKIATQTVGGVELPGAA 81
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
1UNA_A        81 WKAYASIDLTIPIFAATDDVTVISKSLTGLFKVGNPIAEAISSQSGFY 128
Cdd:PHA00026  82 WKAYANIDLTIPIFAANDDCELISKALAGLFKDGNPIAEAIAANSGFY 129
Levi_coat pfam01819
Levivirus coat protein; The Levivirus coat protein forms the bacteriophage coat that ...
1-127 1.92e-39

Levivirus coat protein; The Levivirus coat protein forms the bacteriophage coat that encapsidates the viral RNA. 180 copies of this protein form the virion shell. The MS2 bacteriophage coat protein controls two distinct processes: sequence-specific RNA encapsidation and repression of replicase translation-by binding to an RNA stem-loop structure of 19 nucleotides containing the initiation codon of the replicase gene. The binding of a coat protein dimer to this hairpin shuts off synthesis of the viral replicase, switching the viral replication cycle to virion assembly rather than continued replication.


Pssm-ID: 396403  Cd Length: 132  Bit Score: 128.69  E-value: 1.92e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1UNA_A          1 ATLHSFVLVDNGGTGNVTVVP----VSNANGVAEWLSNNSRSQAY-RVTASYRASGADKRKYTIKLEVPKIVTQVVNGVE 75
Cdd:pfam01819   1 AKFQAFTLSDIGGNGDVTLALnprgVNFANGVAALIEAGARPAAEkRVTCSVRQPSANNKKYKIKVEIPKPASCTAGGTC 80
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
1UNA_A         76 LPVSAWKAYASIDLTIPIFAATDDVTVISKSLTGLFKVGNPIAEAISSQSGF 127
Cdd:pfam01819  81 DPSAARRAYADMEFSFPIFATDEDCALIRKALKALLADGMLIDAADAANPAI 132
 
Name Accession Description Interval E-value
cp PHA00026
coat protein
1-128 1.89e-81

coat protein


Pssm-ID: 133846  Cd Length: 129  Bit Score: 234.94  E-value: 1.89e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1UNA_A         1 ATLHSFVLVDNGGTGNVTVVPVSNANGVAEWLSNNSRSQAYRVTASYRASGADKRKYTIKLEVPKIVTQVVNGVELPVSA 80
Cdd:PHA00026   2 ANFRQFVLVDNGGTGDVTVAPSNFANGVAEWISNNSRSQAYKVTASVRASGADKRKYAIKLEVPKIATQTVGGVELPGAA 81
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
1UNA_A        81 WKAYASIDLTIPIFAATDDVTVISKSLTGLFKVGNPIAEAISSQSGFY 128
Cdd:PHA00026  82 WKAYANIDLTIPIFAANDDCELISKALAGLFKDGNPIAEAIAANSGFY 129
Levi_coat pfam01819
Levivirus coat protein; The Levivirus coat protein forms the bacteriophage coat that ...
1-127 1.92e-39

Levivirus coat protein; The Levivirus coat protein forms the bacteriophage coat that encapsidates the viral RNA. 180 copies of this protein form the virion shell. The MS2 bacteriophage coat protein controls two distinct processes: sequence-specific RNA encapsidation and repression of replicase translation-by binding to an RNA stem-loop structure of 19 nucleotides containing the initiation codon of the replicase gene. The binding of a coat protein dimer to this hairpin shuts off synthesis of the viral replicase, switching the viral replication cycle to virion assembly rather than continued replication.


Pssm-ID: 396403  Cd Length: 132  Bit Score: 128.69  E-value: 1.92e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1UNA_A          1 ATLHSFVLVDNGGTGNVTVVP----VSNANGVAEWLSNNSRSQAY-RVTASYRASGADKRKYTIKLEVPKIVTQVVNGVE 75
Cdd:pfam01819   1 AKFQAFTLSDIGGNGDVTLALnprgVNFANGVAALIEAGARPAAEkRVTCSVRQPSANNKKYKIKVEIPKPASCTAGGTC 80
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
1UNA_A         76 LPVSAWKAYASIDLTIPIFAATDDVTVISKSLTGLFKVGNPIAEAISSQSGF 127
Cdd:pfam01819  81 DPSAARRAYADMEFSFPIFATDEDCALIRKALKALLADGMLIDAADAANPAI 132
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.20
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