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Conserved domains on  [gi|499240859|ref|WP_010938399|]
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phage tail protein [Nitratidesulfovibrio vulgaris]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
COG5301 COG5301
Phage-related tail fiber protein [Mobilome: prophages, transposons];
1-255 1.03e-64

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


:

Pssm-ID: 444101 [Multi-domain]  Cd Length: 254  Bit Score: 210.30  E-value: 1.03e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240859   1 MANELQGMWTAKGLEKLARHAAGGTALMLRELALGDGGGSpAPAPAPSWTALTRQVWRGMVNGVQTSPDNASQVQVDAVI 80
Cdd:COG5301    1 MTQKYYTLLTDIGAAKLANATALGTKLNLTQMAVGDGGGS-LPTPDPSQTALVNEVRRAPLNSLSVDPKNPNQIIAEQVI 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240859  81 PLNIGGFFIREWGLYDAEGDMVAVGAHAEFYKPVISSGASAEIVERILLPIANAGAITLTI-ASQAVATQQFVQAQVKAH 159
Cdd:COG5301   80 PEEVGGFWIREIGLFDDDGTLIAVGNCPESYKPLLTEGSGRTQTVRMVLIVSNTEAVTLKIdPSVVLATRQYVDDKLAKH 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240859 160 DESptahgdmvrrleeHTHPHATEDAAGLVE--RATDAEAQAGTdgeryVTPKQLADALNRV-------SGMPVGMPFww 230
Cdd:COG5301  160 EKS-------------RNHPDATLTEKGFVQlsSATDSNSETLA-----ATPKAVKTAYDLAdtafvaaSGNAAGTAA-- 219

                        250       260
                 ....*....|....*....|....*
gi 499240859 231 pgTTPPAGSLAIhDGPLLQRAAYPQ 255
Cdd:COG5301  220 --TAAAAGGLTL-NAAALSVSTYSA 241
Collar super family cl44561
Phage Tail Collar Domain; This region is occasionally found in conjunction with pfam03335. ...
 225-300 1.28e-03

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.


The actual alignment was detected with superfamily member pfam07484:

Pssm-ID: 429485 [Multi-domain]  Cd Length: 57  Bit Score: 37.15  E-value: 1.28e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 499240859  225 GMPFWWPGTTPPAGsLAIHDGPLLQRAAYPQLWAMaqasgniitesewqaqaavqssVGAFSSGDGATTFRCPRMR 300
Cdd:pfam07484   1 GEIRLFAGNFAPAG-WLLCDGQTLSISQYPALFAL----------------------LGTTYGGDGSTTFALPDLR 53
 
Name Accession Description Interval E-value
COG5301 COG5301
Phage-related tail fiber protein [Mobilome: prophages, transposons];
1-255 1.03e-64

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


Pssm-ID: 444101 [Multi-domain]  Cd Length: 254  Bit Score: 210.30  E-value: 1.03e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240859   1 MANELQGMWTAKGLEKLARHAAGGTALMLRELALGDGGGSpAPAPAPSWTALTRQVWRGMVNGVQTSPDNASQVQVDAVI 80
Cdd:COG5301    1 MTQKYYTLLTDIGAAKLANATALGTKLNLTQMAVGDGGGS-LPTPDPSQTALVNEVRRAPLNSLSVDPKNPNQIIAEQVI 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240859  81 PLNIGGFFIREWGLYDAEGDMVAVGAHAEFYKPVISSGASAEIVERILLPIANAGAITLTI-ASQAVATQQFVQAQVKAH 159
Cdd:COG5301   80 PEEVGGFWIREIGLFDDDGTLIAVGNCPESYKPLLTEGSGRTQTVRMVLIVSNTEAVTLKIdPSVVLATRQYVDDKLAKH 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240859 160 DESptahgdmvrrleeHTHPHATEDAAGLVE--RATDAEAQAGTdgeryVTPKQLADALNRV-------SGMPVGMPFww 230
Cdd:COG5301  160 EKS-------------RNHPDATLTEKGFVQlsSATDSNSETLA-----ATPKAVKTAYDLAdtafvaaSGNAAGTAA-- 219

                        250       260
                 ....*....|....*....|....*
gi 499240859 231 pgTTPPAGSLAIhDGPLLQRAAYPQ 255
Cdd:COG5301  220 --TAAAAGGLTL-NAAALSVSTYSA 241
DUF3751 pfam12571
Phage tail-collar fibre protein; This domain family is found in bacteria and viruses, and is ...
 1-150 3.24e-56

Phage tail-collar fibre protein; This domain family is found in bacteria and viruses, and is approximately 160 amino acids in length. There are two completely conserved residues (K and W) that may be functionally important. The members are annotated as being putative phage tail or tail-collar proteins.


Pssm-ID: 463631  Cd Length: 149  Bit Score: 184.33  E-value: 3.24e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240859    1 MANElQGMWTAKGLEKLARHAAGGTALMLRELALGDGGGSPaPAPAPSWTALTRQVWRGMVNGVQTSPDNASQVQVDAVI 80
Cdd:pfam12571   1 MATK-YTLLTNAGEAKLANAQALGTPLVITKMAVGDGGGLL-PTPTESQTALVNEVWRGAINQLGVDPVNPNQVVAELVI 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 499240859   81 PLNIGGFFIREWGLYDAEGDMVAVGAHAEFYKPVISSGASAEIVERILLPIANAGAITLTI-ASQAVATQQ 150
Cdd:pfam12571  79 PTTVGGFWIREIGLFDADGTLVAVGNCPETYKPKLADGSGNDLTIRMILEVSNAAAVTLKIdPTVVLATRD 149
34 PHA02584
long tail fiber, proximal subunit; Provisional
 153-212 1.01e-04

long tail fiber, proximal subunit; Provisional


Pssm-ID: 222890 [Multi-domain]  Cd Length: 1229  Bit Score: 45.13  E-value: 1.01e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 499240859  153 QAQVKAHDESPTAHGDMV--RRLEEHThphATEDAAGLVERATDAEAQAGTDGERYVTPKQL 212
Cdd:PHA02584  493 TAEVNQNTTFTFLDDVIItpKKLNERT---ATETRRGVAEIATQAETNAGTDDTTIITPKKL 551
Collar pfam07484
Phage Tail Collar Domain; This region is occasionally found in conjunction with pfam03335. ...
 225-300 1.28e-03

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: 37.15  E-value: 1.28e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 499240859  225 GMPFWWPGTTPPAGsLAIHDGPLLQRAAYPQLWAMaqasgniitesewqaqaavqssVGAFSSGDGATTFRCPRMR 300
Cdd:pfam07484   1 GEIRLFAGNFAPAG-WLLCDGQTLSISQYPALFAL----------------------LGTTYGGDGSTTFALPDLR 53
 
Name Accession Description Interval E-value
COG5301 COG5301
Phage-related tail fiber protein [Mobilome: prophages, transposons];
1-255 1.03e-64

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


Pssm-ID: 444101 [Multi-domain]  Cd Length: 254  Bit Score: 210.30  E-value: 1.03e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240859   1 MANELQGMWTAKGLEKLARHAAGGTALMLRELALGDGGGSpAPAPAPSWTALTRQVWRGMVNGVQTSPDNASQVQVDAVI 80
Cdd:COG5301    1 MTQKYYTLLTDIGAAKLANATALGTKLNLTQMAVGDGGGS-LPTPDPSQTALVNEVRRAPLNSLSVDPKNPNQIIAEQVI 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240859  81 PLNIGGFFIREWGLYDAEGDMVAVGAHAEFYKPVISSGASAEIVERILLPIANAGAITLTI-ASQAVATQQFVQAQVKAH 159
Cdd:COG5301   80 PEEVGGFWIREIGLFDDDGTLIAVGNCPESYKPLLTEGSGRTQTVRMVLIVSNTEAVTLKIdPSVVLATRQYVDDKLAKH 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240859 160 DESptahgdmvrrleeHTHPHATEDAAGLVE--RATDAEAQAGTdgeryVTPKQLADALNRV-------SGMPVGMPFww 230
Cdd:COG5301  160 EKS-------------RNHPDATLTEKGFVQlsSATDSNSETLA-----ATPKAVKTAYDLAdtafvaaSGNAAGTAA-- 219

                        250       260
                 ....*....|....*....|....*
gi 499240859 231 pgTTPPAGSLAIhDGPLLQRAAYPQ 255
Cdd:COG5301  220 --TAAAAGGLTL-NAAALSVSTYSA 241
DUF3751 pfam12571
Phage tail-collar fibre protein; This domain family is found in bacteria and viruses, and is ...
 1-150 3.24e-56

Phage tail-collar fibre protein; This domain family is found in bacteria and viruses, and is approximately 160 amino acids in length. There are two completely conserved residues (K and W) that may be functionally important. The members are annotated as being putative phage tail or tail-collar proteins.


Pssm-ID: 463631  Cd Length: 149  Bit Score: 184.33  E-value: 3.24e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499240859    1 MANElQGMWTAKGLEKLARHAAGGTALMLRELALGDGGGSPaPAPAPSWTALTRQVWRGMVNGVQTSPDNASQVQVDAVI 80
Cdd:pfam12571   1 MATK-YTLLTNAGEAKLANAQALGTPLVITKMAVGDGGGLL-PTPTESQTALVNEVWRGAINQLGVDPVNPNQVVAELVI 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 499240859   81 PLNIGGFFIREWGLYDAEGDMVAVGAHAEFYKPVISSGASAEIVERILLPIANAGAITLTI-ASQAVATQQ 150
Cdd:pfam12571  79 PTTVGGFWIREIGLFDADGTLVAVGNCPETYKPKLADGSGNDLTIRMILEVSNAAAVTLKIdPTVVLATRD 149
34 PHA02584
long tail fiber, proximal subunit; Provisional
 153-212 1.01e-04

long tail fiber, proximal subunit; Provisional


Pssm-ID: 222890 [Multi-domain]  Cd Length: 1229  Bit Score: 45.13  E-value: 1.01e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 499240859  153 QAQVKAHDESPTAHGDMV--RRLEEHThphATEDAAGLVERATDAEAQAGTDGERYVTPKQL 212
Cdd:PHA02584  493 TAEVNQNTTFTFLDDVIItpKKLNERT---ATETRRGVAEIATQAETNAGTDDTTIITPKKL 551
34 PHA02584
long tail fiber, proximal subunit; Provisional
 181-214 4.78e-04

long tail fiber, proximal subunit; Provisional


Pssm-ID: 222890 [Multi-domain]  Cd Length: 1229  Bit Score: 42.82  E-value: 4.78e-04
                          10        20        30
                  ....*....|....*....|....*....|....
gi 499240859  181 ATEDAAGLVERATDAEAQAGTDGERYVTPKQLAD 214
Cdd:PHA02584  645 ATDTRIGLIEIATQAETNAGTDDTRAVTPKTLND 678
Collar pfam07484
Phage Tail Collar Domain; This region is occasionally found in conjunction with pfam03335. ...
 225-300 1.28e-03

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: 37.15  E-value: 1.28e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 499240859  225 GMPFWWPGTTPPAGsLAIHDGPLLQRAAYPQLWAMaqasgniitesewqaqaavqssVGAFSSGDGATTFRCPRMR 300
Cdd:pfam07484   1 GEIRLFAGNFAPAG-WLLCDGQTLSISQYPALFAL----------------------LGTTYGGDGSTTFALPDLR 53
34 PHA02584
long tail fiber, proximal subunit; Provisional
 181-212 4.51e-03

long tail fiber, proximal subunit; Provisional


Pssm-ID: 222890 [Multi-domain]  Cd Length: 1229  Bit Score: 39.74  E-value: 4.51e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 499240859  181 ATEDAAGLVERATDAEAQAGTDGERYVTPKQL 212
Cdd:PHA02584  783 ATETLEGIIRVATQAETVTGTSANLAVSPKNL 814
 
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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