NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|68299747|ref|YP_249596|]
View 

tail fiber protein [Vibrio phage VP4]

Protein Classification

PHA00430 and Collar domain-containing protein( domain architecture ID 11936053)

PHA00430 and Collar domain-containing protein

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
PHA00430 super family cl28018
tail fiber protein
 7-221 2.17e-79

tail fiber protein


The actual alignment was detected with superfamily member PHA00430:

Pssm-ID: 222790 [Multi-domain]  Cd Length: 568  Bit Score: 265.22  E-value: 2.17e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68299747    7 PKTIVVYDITG-QTDYTIPFEYLARKFVVVTLIGQDRKVLTLNTDYRFTTKTTIGLSDP-SPV-GYDKIEIRRFTSATDR 83
Cdd:PHA00430   5 IKTVRTYPLDGsNVDFNIPFEYLARKFVVVTLIGVDRKELILNQDYRFATKTTISTTKAwGPAdGYTLIEIRRFTSATDR 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68299747   84 LVDFHDGSILRAYDLNLSQIQTLHVAEEARDLAGDSIAVDDNGDLDARGRKIVNLADAENDTDAVNYGMLKKFDNSTFNN 163
Cdd:PHA00430  85 LVDFTDGSILRAYDLNISQIQTLHVAEEARDLTADTIGVNNDGHLDARGRRIVNLADAVDDGDAVPLGQIKTWNQSAWNA 164

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 68299747  164 AKRAEDSANAAKVSENKAKNSElrsieaeakclSSAGTAMTAAADANRSKEAAEDAEQ 221
Cdd:PHA00430 165 RNEANRSRNEADRARNQAERFN-----------NESGASATNTKQWRSEADGSNSEAN 211
Collar pfam07484
Phage Tail Collar Domain; This region is occasionally found in conjunction with pfam03335. ...
 267-311 8.85e-14

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: 66.43  E-value: 8.85e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 68299747   267 GSIFPFVK-TPPAGYLTCDGSTFSKDEYPDLYAYLGST---------TLPDMRGR 311
Cdd:pfam07484   1 GEIRLFAGnFAPAGWLLCDGQTLSISQYPALFALLGTTyggdgsttfALPDLRGR 55
 
Name Accession Description Interval E-value
PHA00430 PHA00430
tail fiber protein
 7-221 2.17e-79

tail fiber protein


Pssm-ID: 222790 [Multi-domain]  Cd Length: 568  Bit Score: 265.22  E-value: 2.17e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68299747    7 PKTIVVYDITG-QTDYTIPFEYLARKFVVVTLIGQDRKVLTLNTDYRFTTKTTIGLSDP-SPV-GYDKIEIRRFTSATDR 83
Cdd:PHA00430   5 IKTVRTYPLDGsNVDFNIPFEYLARKFVVVTLIGVDRKELILNQDYRFATKTTISTTKAwGPAdGYTLIEIRRFTSATDR 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68299747   84 LVDFHDGSILRAYDLNLSQIQTLHVAEEARDLAGDSIAVDDNGDLDARGRKIVNLADAENDTDAVNYGMLKKFDNSTFNN 163
Cdd:PHA00430  85 LVDFTDGSILRAYDLNISQIQTLHVAEEARDLTADTIGVNNDGHLDARGRRIVNLADAVDDGDAVPLGQIKTWNQSAWNA 164

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 68299747  164 AKRAEDSANAAKVSENKAKNSElrsieaeakclSSAGTAMTAAADANRSKEAAEDAEQ 221
Cdd:PHA00430 165 RNEANRSRNEADRARNQAERFN-----------NESGASATNTKQWRSEADGSNSEAN 211
Phage_T7_tail pfam03906
Phage T7 tail fibre protein; The bacteriophage T7 tail complex consists of a conical tail-tube ...
 7-160 1.45e-46

Phage T7 tail fibre protein; The bacteriophage T7 tail complex consists of a conical tail-tube surrounded by six kinked tail-fibres, which are oligomers of the viral protein gp17.


Pssm-ID: 427579 [Multi-domain]  Cd Length: 157  Bit Score: 162.83  E-value: 1.45e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68299747     7 PKTIVVYDITGQT-DYTIPFEYLARKFVVVTLigqDRKVLTLNTDYRFTTKTTIGLSDpSPVGYDKIEIRRFTSATDRLV 85
Cdd:pfam03906   5 IKTYLTYQLDGSNrDFNIPFEYLARAHVVVTV---DRKVLTINTDYRWADRYTISLTK-APADGTVVELRRVTPTTDRLV 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 68299747    86 DFHDGSILRAYDLNLSQIQTLHVAEEARDLAGDSIAVDDNGDLDARGRKIVNLADAENDTDAVNYGMLKKFDNST 160
Cdd:pfam03906  81 DFTDGSTLRAYDLNVAQIQTMHVAQEARDLTTASIGVTNDGHLDARGRRITNLANPVDAQDAVTFGQLKVTMNQN 155
Collar pfam07484
Phage Tail Collar Domain; This region is occasionally found in conjunction with pfam03335. ...
 267-311 8.85e-14

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: 66.43  E-value: 8.85e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 68299747   267 GSIFPFVK-TPPAGYLTCDGSTFSKDEYPDLYAYLGST---------TLPDMRGR 311
Cdd:pfam07484   1 GEIRLFAGnFAPAGWLLCDGQTLSISQYPALFALLGTTyggdgsttfALPDLRGR 55
MdpB COG4675
Phage tail collar domain [Mobilome: prophages, transposons];
266-311 9.40e-05

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


Pssm-ID: 443711 [Multi-domain]  Cd Length: 173  Bit Score: 43.60  E-value: 9.40e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 68299747 266 IGSIFPFVKT-PPAGYLTCDGSTFSKDEYPDLYAYLG-------STT--LPDMRGR 311
Cdd:COG4675   5 IGEIRLFAGNfAPRGWALCDGQLLPISQNQALFSLLGttyggdgRTTfaLPDLRGR 60
 
Name Accession Description Interval E-value
PHA00430 PHA00430
tail fiber protein
 7-221 2.17e-79

tail fiber protein


Pssm-ID: 222790 [Multi-domain]  Cd Length: 568  Bit Score: 265.22  E-value: 2.17e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68299747    7 PKTIVVYDITG-QTDYTIPFEYLARKFVVVTLIGQDRKVLTLNTDYRFTTKTTIGLSDP-SPV-GYDKIEIRRFTSATDR 83
Cdd:PHA00430   5 IKTVRTYPLDGsNVDFNIPFEYLARKFVVVTLIGVDRKELILNQDYRFATKTTISTTKAwGPAdGYTLIEIRRFTSATDR 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68299747   84 LVDFHDGSILRAYDLNLSQIQTLHVAEEARDLAGDSIAVDDNGDLDARGRKIVNLADAENDTDAVNYGMLKKFDNSTFNN 163
Cdd:PHA00430  85 LVDFTDGSILRAYDLNISQIQTLHVAEEARDLTADTIGVNNDGHLDARGRRIVNLADAVDDGDAVPLGQIKTWNQSAWNA 164

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 68299747  164 AKRAEDSANAAKVSENKAKNSElrsieaeakclSSAGTAMTAAADANRSKEAAEDAEQ 221
Cdd:PHA00430 165 RNEANRSRNEADRARNQAERFN-----------NESGASATNTKQWRSEADGSNSEAN 211
Phage_T7_tail pfam03906
Phage T7 tail fibre protein; The bacteriophage T7 tail complex consists of a conical tail-tube ...
 7-160 1.45e-46

Phage T7 tail fibre protein; The bacteriophage T7 tail complex consists of a conical tail-tube surrounded by six kinked tail-fibres, which are oligomers of the viral protein gp17.


Pssm-ID: 427579 [Multi-domain]  Cd Length: 157  Bit Score: 162.83  E-value: 1.45e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68299747     7 PKTIVVYDITGQT-DYTIPFEYLARKFVVVTLigqDRKVLTLNTDYRFTTKTTIGLSDpSPVGYDKIEIRRFTSATDRLV 85
Cdd:pfam03906   5 IKTYLTYQLDGSNrDFNIPFEYLARAHVVVTV---DRKVLTINTDYRWADRYTISLTK-APADGTVVELRRVTPTTDRLV 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 68299747    86 DFHDGSILRAYDLNLSQIQTLHVAEEARDLAGDSIAVDDNGDLDARGRKIVNLADAENDTDAVNYGMLKKFDNST 160
Cdd:pfam03906  81 DFTDGSTLRAYDLNVAQIQTMHVAQEARDLTTASIGVTNDGHLDARGRRITNLANPVDAQDAVTFGQLKVTMNQN 155
Collar pfam07484
Phage Tail Collar Domain; This region is occasionally found in conjunction with pfam03335. ...
 267-311 8.85e-14

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: 66.43  E-value: 8.85e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 68299747   267 GSIFPFVK-TPPAGYLTCDGSTFSKDEYPDLYAYLGST---------TLPDMRGR 311
Cdd:pfam07484   1 GEIRLFAGnFAPAGWLLCDGQTLSISQYPALFALLGTTyggdgsttfALPDLRGR 55
MdpB COG4675
Phage tail collar domain [Mobilome: prophages, transposons];
266-311 9.40e-05

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


Pssm-ID: 443711 [Multi-domain]  Cd Length: 173  Bit Score: 43.60  E-value: 9.40e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 68299747 266 IGSIFPFVKT-PPAGYLTCDGSTFSKDEYPDLYAYLG-------STT--LPDMRGR 311
Cdd:COG4675   5 IGEIRLFAGNfAPRGWALCDGQLLPISQNQALFSLLGttyggdgRTTfaLPDLRGR 60
YadA_stalk pfam05662
Coiled stalk of trimeric autotransporter adhesin; This short motif is found in invasins and ...
 134-173 3.11e-03

Coiled stalk of trimeric autotransporter adhesin; This short motif is found in invasins and haemagglutinins, normally associated with (pfam05658).


Pssm-ID: 428572 [Multi-domain]  Cd Length: 43  Bit Score: 36.01  E-value: 3.11e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 68299747   134 KIVNLADAENDTDAVNYGMLKKFDNST---FNNAKRAEDSANA 173
Cdd:pfam05662   1 KITNVAAGTVSTDAVNGSQLYAVNQSVsngANNVTSGNANANA 43
 
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