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Conserved domains on  [gi|2575928128|ref|WP_309402640|]
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phage tail protein [Aminobacter niigataensis]

Protein Classification

phage tail protein( domain architecture ID 11468723)

phage tail protein similar to the C-terminal region of a heat- and protease-stable fragment of the bacteriophage T4 short fiber

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
MdpB COG4675
Phage tail collar domain [Mobilome: prophages, transposons];
2-165 3.16e-88

Phage tail collar domain [Mobilome: prophages, transposons];


:

Pssm-ID: 443711 [Multi-domain]  Cd Length: 173  Bit Score: 255.07  E-value: 3.16e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2575928128   2 AQPYVGEVRMFAGNFAPAGWMFCEGQLLPISENETLFNLIGTTYGGDGESTFALPDLRGRVPLHQGNG-----FILAETG 76
Cdd:COG4675     1 MDPFIGEIRLFAGNFAPRGWALCDGQLLPISQNQALFSLLGTTYGGDGRTTFALPDLRGRVPVGQGQGpglspRVLGQTG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2575928128  77 GAEEITLTIGQIPAHSHPLLGSTVNGAQPAPEGNVLASSTV--ITPYAPEAVTVAMAQAAVGSVGGSQPHANFQPYLCIN 154
Cdd:COG4675    81 GTETVTLTTAQLPAHTHTLNASSAAGTTTTPAGNVLAAGTGggVNIYASGTPNVTLAPGTVGPTGGSQPHNNMQPYLALN 160

                         170
                  ....*....|.
gi 2575928128 155 FIISLFGIFPS 165
Cdd:COG4675   161 FIIALQGIFPS 171
 
Name Accession Description Interval E-value
MdpB COG4675
Phage tail collar domain [Mobilome: prophages, transposons];
2-165 3.16e-88

Phage tail collar domain [Mobilome: prophages, transposons];


Pssm-ID: 443711 [Multi-domain]  Cd Length: 173  Bit Score: 255.07  E-value: 3.16e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2575928128   2 AQPYVGEVRMFAGNFAPAGWMFCEGQLLPISENETLFNLIGTTYGGDGESTFALPDLRGRVPLHQGNG-----FILAETG 76
Cdd:COG4675     1 MDPFIGEIRLFAGNFAPRGWALCDGQLLPISQNQALFSLLGTTYGGDGRTTFALPDLRGRVPVGQGQGpglspRVLGQTG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2575928128  77 GAEEITLTIGQIPAHSHPLLGSTVNGAQPAPEGNVLASSTV--ITPYAPEAVTVAMAQAAVGSVGGSQPHANFQPYLCIN 154
Cdd:COG4675    81 GTETVTLTTAQLPAHTHTLNASSAAGTTTTPAGNVLAAGTGggVNIYASGTPNVTLAPGTVGPTGGSQPHNNMQPYLALN 160

                         170
                  ....*....|.
gi 2575928128 155 FIISLFGIFPS 165
Cdd:COG4675   161 FIIALQGIFPS 171
Collar pfam07484
Phage Tail Collar Domain; This region is occasionally found in conjunction with pfam03335. ...
 7-63 4.78e-30

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: 103.79  E-value: 4.78e-30
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2575928128   7 GEVRMFAGNFAPAGWMFCEGQLLPISENETLFNLIGTTYGGDGESTFALPDLRGRVP 63
Cdd:pfam07484   1 GEIRLFAGNFAPAGWLLCDGQTLSISQYPALFALLGTTYGGDGSTTFALPDLRGRFP 57
C24-like cd22641
Bizionia argentinensis C24 protein and similar proteins; C24 is a putative receptor-binding ...
 6-157 1.55e-10

Bizionia argentinensis C24 protein and similar proteins; C24 is a putative receptor-binding tip-like protein from Bizionia argentinensis JUB59. It may interact with lipopolysaccharide and membrane receptors. The C24 trimer binds a unique Mg2+ ion and shares structural similarity with the bacteriophage T4 long tail fiber receptor-binding tip, which adopts an overall rocket shape. However, there are marked differences in its domain organization, size and sequence identity. The C24 polypeptide chain contains four distinct domains: a globular proximal shoulder domain, a globular collar domain, an elongated, intertwined metal-binding needle domain and a globular receptor-binding-like unique distal head domain. This is a multi-domain model which includes all these four domains of C24 protein.


Pssm-ID: 439347 [Multi-domain]  Cd Length: 227  Bit Score: 57.51  E-value: 1.55e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2575928128   6 VGEVRMFAGNFA--PAGWMFCEGqllpisenetlfnligttyggdgesTFALPDLRGRVPLHQGNGFI----LAETGGAE 79
Cdd:cd22641   138 IGMIVMWSGSAAtiPAGWALCDG-------------------------TNGTPDLRGRFIVGADPSDTdfntIGKTGGAK 192

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2575928128  80 EITLTIGQIPAHSHpllgstvngaqpapegnvlasstvitpyapeavtvamaqaavgsvGGSQPHANFQPYLCINFII 157
Cdd:cd22641   193 THTLTIAEMPSHSH---------------------------------------------GGGQPHNNRPPYYALAFIM 225
 
Name Accession Description Interval E-value
MdpB COG4675
Phage tail collar domain [Mobilome: prophages, transposons];
2-165 3.16e-88

Phage tail collar domain [Mobilome: prophages, transposons];


Pssm-ID: 443711 [Multi-domain]  Cd Length: 173  Bit Score: 255.07  E-value: 3.16e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2575928128   2 AQPYVGEVRMFAGNFAPAGWMFCEGQLLPISENETLFNLIGTTYGGDGESTFALPDLRGRVPLHQGNG-----FILAETG 76
Cdd:COG4675     1 MDPFIGEIRLFAGNFAPRGWALCDGQLLPISQNQALFSLLGTTYGGDGRTTFALPDLRGRVPVGQGQGpglspRVLGQTG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2575928128  77 GAEEITLTIGQIPAHSHPLLGSTVNGAQPAPEGNVLASSTV--ITPYAPEAVTVAMAQAAVGSVGGSQPHANFQPYLCIN 154
Cdd:COG4675    81 GTETVTLTTAQLPAHTHTLNASSAAGTTTTPAGNVLAAGTGggVNIYASGTPNVTLAPGTVGPTGGSQPHNNMQPYLALN 160

                         170
                  ....*....|.
gi 2575928128 155 FIISLFGIFPS 165
Cdd:COG4675   161 FIIALQGIFPS 171
Collar pfam07484
Phage Tail Collar Domain; This region is occasionally found in conjunction with pfam03335. ...
 7-63 4.78e-30

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: 103.79  E-value: 4.78e-30
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2575928128   7 GEVRMFAGNFAPAGWMFCEGQLLPISENETLFNLIGTTYGGDGESTFALPDLRGRVP 63
Cdd:pfam07484   1 GEIRLFAGNFAPAGWLLCDGQTLSISQYPALFALLGTTYGGDGSTTFALPDLRGRFP 57
C24-like cd22641
Bizionia argentinensis C24 protein and similar proteins; C24 is a putative receptor-binding ...
 6-157 1.55e-10

Bizionia argentinensis C24 protein and similar proteins; C24 is a putative receptor-binding tip-like protein from Bizionia argentinensis JUB59. It may interact with lipopolysaccharide and membrane receptors. The C24 trimer binds a unique Mg2+ ion and shares structural similarity with the bacteriophage T4 long tail fiber receptor-binding tip, which adopts an overall rocket shape. However, there are marked differences in its domain organization, size and sequence identity. The C24 polypeptide chain contains four distinct domains: a globular proximal shoulder domain, a globular collar domain, an elongated, intertwined metal-binding needle domain and a globular receptor-binding-like unique distal head domain. This is a multi-domain model which includes all these four domains of C24 protein.


Pssm-ID: 439347 [Multi-domain]  Cd Length: 227  Bit Score: 57.51  E-value: 1.55e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2575928128   6 VGEVRMFAGNFA--PAGWMFCEGqllpisenetlfnligttyggdgesTFALPDLRGRVPLHQGNGFI----LAETGGAE 79
Cdd:cd22641   138 IGMIVMWSGSAAtiPAGWALCDG-------------------------TNGTPDLRGRFIVGADPSDTdfntIGKTGGAK 192

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2575928128  80 EITLTIGQIPAHSHpllgstvngaqpapegnvlasstvitpyapeavtvamaqaavgsvGGSQPHANFQPYLCINFII 157
Cdd:cd22641   193 THTLTIAEMPSHSH---------------------------------------------GGGQPHNNRPPYYALAFIM 225
 
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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