NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|971763580|ref|YP_009216575|]
View 

tail fiber protein [Ralstonia phage RSJ2]

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
Collar pfam07484
Phage Tail Collar Domain; This region is occasionally found in conjunction with pfam03335. ...
 292-365 3.46e-11

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: 58.34  E-value: 3.46e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 971763580  292 GQIVFEARTSARAGYLKLNGALLNRADYPALWAYAnasgavvsegvwsagsqGCFSSGDGTTTFRVPDLRGEFV 365
Cdd:pfam07484   1 GEIRLFAGNFAPAGWLLCDGQTLSISQYPALFALL-----------------GTTYGGDGSTTFALPDLRGRFP 57
Phage_T7_tail super family cl44509
Phage T7 tail fibre protein; The bacteriophage T7 tail complex consists of a conical tail-tube ...
 20-168 2.07e-10

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.


The actual alignment was detected with superfamily member pfam03906:

Pssm-ID: 427579 [Multi-domain]  Cd Length: 157  Bit Score: 59.21  E-value: 2.07e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971763580   20 YSMNRFQCNGTANVFSINFAgaapgYLDRAHLKYYVingaDGTYVTPITPVpsgAFQSSTLIKLEQTPgvpyPLGLWVVI 99
Cdd:pfam03906   6 KTYLTYQLDGSNRDFNIPFE-----YLARAHVVVTV----DRKVLTINTDY---RWADRYTISLTKAP----ADGTVVEL 69

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 971763580  100 FRDTPKSVPLVDFTDGAVINEENLDLMAEQSIYVAAEMTDRFEEVIGSNQE-VID---RAAEALATANEALDA 168
Cdd:pfam03906  70 RRVTPTTDRLVDFTDGSTLRAYDLNVAQIQTMHVAQEARDLTTASIGVTNDgHLDargRRITNLANPVDAQDA 142
 
Name Accession Description Interval E-value
Collar pfam07484
Phage Tail Collar Domain; This region is occasionally found in conjunction with pfam03335. ...
 292-365 3.46e-11

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: 58.34  E-value: 3.46e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 971763580  292 GQIVFEARTSARAGYLKLNGALLNRADYPALWAYAnasgavvsegvwsagsqGCFSSGDGTTTFRVPDLRGEFV 365
Cdd:pfam07484   1 GEIRLFAGNFAPAGWLLCDGQTLSISQYPALFALL-----------------GTTYGGDGSTTFALPDLRGRFP 57
Phage_T7_tail pfam03906
Phage T7 tail fibre protein; The bacteriophage T7 tail complex consists of a conical tail-tube ...
 20-168 2.07e-10

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: 59.21  E-value: 2.07e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971763580   20 YSMNRFQCNGTANVFSINFAgaapgYLDRAHLKYYVingaDGTYVTPITPVpsgAFQSSTLIKLEQTPgvpyPLGLWVVI 99
Cdd:pfam03906   6 KTYLTYQLDGSNRDFNIPFE-----YLARAHVVVTV----DRKVLTINTDY---RWADRYTISLTKAP----ADGTVVEL 69

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 971763580  100 FRDTPKSVPLVDFTDGAVINEENLDLMAEQSIYVAAEMTDRFEEVIGSNQE-VID---RAAEALATANEALDA 168
Cdd:pfam03906  70 RRVTPTTDRLVDFTDGSTLRAYDLNVAQIQTMHVAQEARDLTTASIGVTNDgHLDargRRITNLANPVDAQDA 142
MdpB COG4675
Phage tail collar domain [Mobilome: prophages, transposons];
287-396 9.49e-04

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


Pssm-ID: 443711 [Multi-domain]  Cd Length: 173  Bit Score: 40.13  E-value: 9.49e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971763580 287 STALVGQIVFEARTSARAGYLKLNGALLNRADYPALwayanasgavvsegvwsagsqgcFS------SGDGTTTFRVPDL 360
Cdd:COG4675    1 MDPFIGEIRLFAGNFAPRGWALCDGQLLPISQNQAL-----------------------FSllgttyGGDGRTTFALPDL 57

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 971763580 361 RGEFVRGWDDARGVDgSRGIGTWQ-------ASANL-SHNHTAS 396
Cdd:COG4675   58 RGRVPVGQGQGPGLS-PRVLGQTGgtetvtlTTAQLpAHTHTLN 100
 
Name Accession Description Interval E-value
Collar pfam07484
Phage Tail Collar Domain; This region is occasionally found in conjunction with pfam03335. ...
 292-365 3.46e-11

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: 58.34  E-value: 3.46e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 971763580  292 GQIVFEARTSARAGYLKLNGALLNRADYPALWAYAnasgavvsegvwsagsqGCFSSGDGTTTFRVPDLRGEFV 365
Cdd:pfam07484   1 GEIRLFAGNFAPAGWLLCDGQTLSISQYPALFALL-----------------GTTYGGDGSTTFALPDLRGRFP 57
Phage_T7_tail pfam03906
Phage T7 tail fibre protein; The bacteriophage T7 tail complex consists of a conical tail-tube ...
 20-168 2.07e-10

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: 59.21  E-value: 2.07e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971763580   20 YSMNRFQCNGTANVFSINFAgaapgYLDRAHLKYYVingaDGTYVTPITPVpsgAFQSSTLIKLEQTPgvpyPLGLWVVI 99
Cdd:pfam03906   6 KTYLTYQLDGSNRDFNIPFE-----YLARAHVVVTV----DRKVLTINTDY---RWADRYTISLTKAP----ADGTVVEL 69

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 971763580  100 FRDTPKSVPLVDFTDGAVINEENLDLMAEQSIYVAAEMTDRFEEVIGSNQE-VID---RAAEALATANEALDA 168
Cdd:pfam03906  70 RRVTPTTDRLVDFTDGSTLRAYDLNVAQIQTMHVAQEARDLTTASIGVTNDgHLDargRRITNLANPVDAQDA 142
MdpB COG4675
Phage tail collar domain [Mobilome: prophages, transposons];
287-396 9.49e-04

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


Pssm-ID: 443711 [Multi-domain]  Cd Length: 173  Bit Score: 40.13  E-value: 9.49e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971763580 287 STALVGQIVFEARTSARAGYLKLNGALLNRADYPALwayanasgavvsegvwsagsqgcFS------SGDGTTTFRVPDL 360
Cdd:COG4675    1 MDPFIGEIRLFAGNFAPRGWALCDGQLLPISQNQAL-----------------------FSllgttyGGDGRTTFALPDL 57

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 971763580 361 RGEFVRGWDDARGVDgSRGIGTWQ-------ASANL-SHNHTAS 396
Cdd:COG4675   58 RGRVPVGQGQGPGLS-PRVLGQTGgtetvtlTTAQLpAHTHTLN 100
 
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