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Conserved domains on  [gi|755429639|gb|AJJ86212|]
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phage tail fiber repeat family protein (plasmid) [Yersinia pestis CO92]

Protein Classification

phage tail protein( domain architecture ID 13428948)

phage tail protein is part of a multi-protein structure that mediates the attachment, digestion and penetration of the cell wall and genome ejection

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Collar pfam07484
Phage Tail Collar Domain; This region is occasionally found in conjunction with pfam03335. ...
 724-771 6.20e-13

Phage Tail Collar Domain; This region is occasionally found in conjunction with pfam03335. Most of the family appear to be phage tail proteins; however some appear to be involved in other processes. For instance Swiss:Q03314 from Rhizobium leguminosarum may be involved in plant-microbe interactions. A related protein Swiss:Q9L3N1 is involved in the pathogenicity of Microcystis aeruginosa. The finding of this family in a structural component of the phage tail fibre baseplate suggests that its function is structural rather than enzymatic. Structural studies show this region consists of a helix and a loop and three beta-strands. This alignment does not catch the third strand as it is separated from the rest of the structure by around 100 residues. This strand is conserved in homologs but the intervening sequence is not. Much of the function of Swiss:P10930 appears to reside in this intervening region. In the tertiary structure of the phage baseplate this domain forms part of the 'collar'. The domain may bind SO4, however the residues accredited with this vary between the PDB file and the Swiss-Prot entry. The long unconserved region maybe due to domain swapping in and out of a loop or reflective of rapid evolution.


:

Pssm-ID: 429485 [Multi-domain]  Cd Length: 57  Bit Score: 64.12  E-value: 6.20e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 755429639  724 GAPIPWPNDVAPSGFAIMQGQTFDKSVYPKLAAA---------YPSGVLPDMRGWMI 771
Cdd:pfam07484   1 GEIRLFAGNFAPAGWLLCDGQTLSISQYPALFALlgttyggdgSTTFALPDLRGRFP 57
Phage_fiber_2 pfam03406
Phage tail fibre repeat; This repeat is found in the tail fibres of phage. For example protein ...
 405-438 3.05e-09

Phage tail fibre repeat; This repeat is found in the tail fibres of phage. For example protein K. The repeats are about 40 residues long.


:

Pssm-ID: 427282 [Multi-domain]  Cd Length: 38  Bit Score: 53.09  E-value: 3.05e-09
                          10        20        30
                  ....*....|....*....|....*....|....
gi 755429639  405 TTSQQGVVQLSSATDSESETLASTPKAVKTVMDA 438
Cdd:pfam03406   1 TLTQKGIVQLSSATNSTSETLAATPKAVKTAYDN 34
COG5301 super family cl34977
Phage-related tail fiber protein [Mobilome: prophages, transposons];
390-481 1.46e-07

Phage-related tail fiber protein [Mobilome: prophages, transposons];


The actual alignment was detected with superfamily member COG5301:

Pssm-ID: 444101 [Multi-domain]  Cd Length: 254  Bit Score: 53.91  E-value: 1.46e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755429639 390 DEAQEIAEGSKVNDATTSQQGVVQLSSATDSESETLASTPKAVKTVMDAVALKAPIDSPALSGAPTAPTPA----ITAAG 465
Cdd:COG5301  154 DKLAKHEKSRNHPDATLTEKGFVQLSSATDSNSETLAATPKAVKTAYDLADTAFVAASGNAAGTAATAAAAggltLNAAA 233

                         90
                 ....*....|....*.
gi 755429639 466 REIATAAFVASKVAQL 481
Cdd:COG5301  234 LSVSTYSATAGAVLGT 249
 
Name Accession Description Interval E-value
Collar pfam07484
Phage Tail Collar Domain; This region is occasionally found in conjunction with pfam03335. ...
 724-771 6.20e-13

Phage Tail Collar Domain; This region is occasionally found in conjunction with pfam03335. Most of the family appear to be phage tail proteins; however some appear to be involved in other processes. For instance Swiss:Q03314 from Rhizobium leguminosarum may be involved in plant-microbe interactions. A related protein Swiss:Q9L3N1 is involved in the pathogenicity of Microcystis aeruginosa. The finding of this family in a structural component of the phage tail fibre baseplate suggests that its function is structural rather than enzymatic. Structural studies show this region consists of a helix and a loop and three beta-strands. This alignment does not catch the third strand as it is separated from the rest of the structure by around 100 residues. This strand is conserved in homologs but the intervening sequence is not. Much of the function of Swiss:P10930 appears to reside in this intervening region. In the tertiary structure of the phage baseplate this domain forms part of the 'collar'. The domain may bind SO4, however the residues accredited with this vary between the PDB file and the Swiss-Prot entry. The long unconserved region maybe due to domain swapping in and out of a loop or reflective of rapid evolution.


Pssm-ID: 429485 [Multi-domain]  Cd Length: 57  Bit Score: 64.12  E-value: 6.20e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 755429639  724 GAPIPWPNDVAPSGFAIMQGQTFDKSVYPKLAAA---------YPSGVLPDMRGWMI 771
Cdd:pfam07484   1 GEIRLFAGNFAPAGWLLCDGQTLSISQYPALFALlgttyggdgSTTFALPDLRGRFP 57
Phage_fiber_2 pfam03406
Phage tail fibre repeat; This repeat is found in the tail fibres of phage. For example protein ...
 405-438 3.05e-09

Phage tail fibre repeat; This repeat is found in the tail fibres of phage. For example protein K. The repeats are about 40 residues long.


Pssm-ID: 427282 [Multi-domain]  Cd Length: 38  Bit Score: 53.09  E-value: 3.05e-09
                          10        20        30
                  ....*....|....*....|....*....|....
gi 755429639  405 TTSQQGVVQLSSATDSESETLASTPKAVKTVMDA 438
Cdd:pfam03406   1 TLTQKGIVQLSSATNSTSETLAATPKAVKTAYDN 34
COG5301 COG5301
Phage-related tail fiber protein [Mobilome: prophages, transposons];
390-481 1.46e-07

Phage-related tail fiber protein [Mobilome: prophages, transposons];


Pssm-ID: 444101 [Multi-domain]  Cd Length: 254  Bit Score: 53.91  E-value: 1.46e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755429639 390 DEAQEIAEGSKVNDATTSQQGVVQLSSATDSESETLASTPKAVKTVMDAVALKAPIDSPALSGAPTAPTPA----ITAAG 465
Cdd:COG5301  154 DKLAKHEKSRNHPDATLTEKGFVQLSSATDSNSETLAATPKAVKTAYDLADTAFVAASGNAAGTAATAAAAggltLNAAA 233

                         90
                 ....*....|....*.
gi 755429639 466 REIATAAFVASKVAQL 481
Cdd:COG5301  234 LSVSTYSATAGAVLGT 249
 
Name Accession Description Interval E-value
Collar pfam07484
Phage Tail Collar Domain; This region is occasionally found in conjunction with pfam03335. ...
 724-771 6.20e-13

Phage Tail Collar Domain; This region is occasionally found in conjunction with pfam03335. Most of the family appear to be phage tail proteins; however some appear to be involved in other processes. For instance Swiss:Q03314 from Rhizobium leguminosarum may be involved in plant-microbe interactions. A related protein Swiss:Q9L3N1 is involved in the pathogenicity of Microcystis aeruginosa. The finding of this family in a structural component of the phage tail fibre baseplate suggests that its function is structural rather than enzymatic. Structural studies show this region consists of a helix and a loop and three beta-strands. This alignment does not catch the third strand as it is separated from the rest of the structure by around 100 residues. This strand is conserved in homologs but the intervening sequence is not. Much of the function of Swiss:P10930 appears to reside in this intervening region. In the tertiary structure of the phage baseplate this domain forms part of the 'collar'. The domain may bind SO4, however the residues accredited with this vary between the PDB file and the Swiss-Prot entry. The long unconserved region maybe due to domain swapping in and out of a loop or reflective of rapid evolution.


Pssm-ID: 429485 [Multi-domain]  Cd Length: 57  Bit Score: 64.12  E-value: 6.20e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 755429639  724 GAPIPWPNDVAPSGFAIMQGQTFDKSVYPKLAAA---------YPSGVLPDMRGWMI 771
Cdd:pfam07484   1 GEIRLFAGNFAPAGWLLCDGQTLSISQYPALFALlgttyggdgSTTFALPDLRGRFP 57
Phage_fiber_2 pfam03406
Phage tail fibre repeat; This repeat is found in the tail fibres of phage. For example protein ...
 405-438 3.05e-09

Phage tail fibre repeat; This repeat is found in the tail fibres of phage. For example protein K. The repeats are about 40 residues long.


Pssm-ID: 427282 [Multi-domain]  Cd Length: 38  Bit Score: 53.09  E-value: 3.05e-09
                          10        20        30
                  ....*....|....*....|....*....|....
gi 755429639  405 TTSQQGVVQLSSATDSESETLASTPKAVKTVMDA 438
Cdd:pfam03406   1 TLTQKGIVQLSSATNSTSETLAATPKAVKTAYDN 34
COG5301 COG5301
Phage-related tail fiber protein [Mobilome: prophages, transposons];
390-481 1.46e-07

Phage-related tail fiber protein [Mobilome: prophages, transposons];


Pssm-ID: 444101 [Multi-domain]  Cd Length: 254  Bit Score: 53.91  E-value: 1.46e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755429639 390 DEAQEIAEGSKVNDATTSQQGVVQLSSATDSESETLASTPKAVKTVMDAVALKAPIDSPALSGAPTAPTPA----ITAAG 465
Cdd:COG5301  154 DKLAKHEKSRNHPDATLTEKGFVQLSSATDSNSETLAATPKAVKTAYDLADTAFVAASGNAAGTAATAAAAggltLNAAA 233

                         90
                 ....*....|....*.
gi 755429639 466 REIATAAFVASKVAQL 481
Cdd:COG5301  234 LSVSTYSATAGAVLGT 249
 
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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