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Conserved domains on  [gi|506585801|ref|WP_016052001|]
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terminase small subunit [Pseudomonas tolaasii]

Protein Classification

terminase small subunit( domain architecture ID 4118)

terminase small subunit binds to the packaging signal on phage DNA, allowing the terminase large subunit to cleave the DNA and thread it through the portal protein channel into the procapsid, powered by ATP hydrolysis

CATH:  1.10.10.1400
Gene Ontology:  GO:0051276|GO:0003677
SCOP:  4007498

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Terminase_2 super family cl01513
Terminase small subunit; Packaging of double-stranded viral DNA concatemers requires ...
 14-70 1.72e-04

Terminase small subunit; Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site.


The actual alignment was detected with superfamily member COG3728:

Pssm-ID: 470229  Cd Length: 131  Bit Score: 39.17  E-value: 1.72e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 506585801  14 PLTPKEKLdlYCEALCDGYNKTQAYIKAGFSA----AHAQRNVapyhrKNADyIKAYLSEQ 70
Cdd:COG3728    1 KLTDKQER--FCDEYLKDLNATQAAIRAGYSEktasVIGSRLL-----KKPK-IKAAIDEL 53
 
Name Accession Description Interval E-value
XtmA COG3728
Phage terminase, small subunit [Mobilome: prophages, transposons];
14-70 1.72e-04

Phage terminase, small subunit [Mobilome: prophages, transposons];


Pssm-ID: 442942  Cd Length: 131  Bit Score: 39.17  E-value: 1.72e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 506585801  14 PLTPKEKLdlYCEALCDGYNKTQAYIKAGFSA----AHAQRNVapyhrKNADyIKAYLSEQ 70
Cdd:COG3728    1 KLTDKQER--FCDEYLKDLNATQAAIRAGYSEktasVIGSRLL-----KKPK-IKAAIDEL 53
Terminase_2 pfam03592
Terminase small subunit; Packaging of double-stranded viral DNA concatemers requires ...
 15-70 6.27e-03

Terminase small subunit; Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site.


Pssm-ID: 427384  Cd Length: 143  Bit Score: 35.02  E-value: 6.27e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 506585801   15 LTPKEKLdlyceaLCDGY----NKTQAYIKAGFSAAHAqRNVAPYHRKNaDYIKAYLSEQ 70
Cdd:pfam03592   1 LTDKQKR------FCDEYikdfNATQAAIKAGYSKKTA-RSIGSRLLRN-PKIKKYIDEL 52
 
Name Accession Description Interval E-value
XtmA COG3728
Phage terminase, small subunit [Mobilome: prophages, transposons];
14-70 1.72e-04

Phage terminase, small subunit [Mobilome: prophages, transposons];


Pssm-ID: 442942  Cd Length: 131  Bit Score: 39.17  E-value: 1.72e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 506585801  14 PLTPKEKLdlYCEALCDGYNKTQAYIKAGFSA----AHAQRNVapyhrKNADyIKAYLSEQ 70
Cdd:COG3728    1 KLTDKQER--FCDEYLKDLNATQAAIRAGYSEktasVIGSRLL-----KKPK-IKAAIDEL 53
Terminase_2 pfam03592
Terminase small subunit; Packaging of double-stranded viral DNA concatemers requires ...
 15-70 6.27e-03

Terminase small subunit; Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site.


Pssm-ID: 427384  Cd Length: 143  Bit Score: 35.02  E-value: 6.27e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 506585801   15 LTPKEKLdlyceaLCDGY----NKTQAYIKAGFSAAHAqRNVAPYHRKNaDYIKAYLSEQ 70
Cdd:pfam03592   1 LTDKQKR------FCDEYikdfNATQAAIKAGYSKKTA-RSIGSRLLRN-PKIKKYIDEL 52
 
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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