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Conserved domains on  [gi|490243157|ref|WP_004141379|]
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terminase small subunit [Klebsiella pneumoniae]

Protein Classification

terminase small subunit( domain architecture ID 10007919)

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

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
XtmA COG3728
Phage terminase, small subunit [Mobilome: prophages, transposons];
14-173 2.91e-35

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


:

Pssm-ID: 442942  Cd Length: 131  Bit Score: 120.44  E-value: 2.91e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490243157  14 PLTVQQEAYCQEYVKCpENQTQAAINAGYSPNTAGKFASQNMRDARIQKRIAELMEDRNKRLRVSADYVLLRLVEIDQMD 93
Cdd:COG3728    1 KLTDKQERFCDEYLKD-LNATQAAIRAGYSEKTASVIGSRLLKKPKIKAAIDELKKERAERTEITADEVLQRLTDIAFAD 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490243157  94 VLDIlnddgglkpirewpkiwrttlsgfdlsstiMNMDETTIEtILKKIKWPDKVKNLELIGKHVDvmAFKERMEVNVNV 173
Cdd:COG3728   80 ITDY------------------------------VEFGDDTLE-VKKKIKLKDRLKALELLGKYYG--LFTDKVEHKGEE 126
 
Name Accession Description Interval E-value
XtmA COG3728
Phage terminase, small subunit [Mobilome: prophages, transposons];
14-173 2.91e-35

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


Pssm-ID: 442942  Cd Length: 131  Bit Score: 120.44  E-value: 2.91e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490243157  14 PLTVQQEAYCQEYVKCpENQTQAAINAGYSPNTAGKFASQNMRDARIQKRIAELMEDRNKRLRVSADYVLLRLVEIDQMD 93
Cdd:COG3728    1 KLTDKQERFCDEYLKD-LNATQAAIRAGYSEKTASVIGSRLLKKPKIKAAIDELKKERAERTEITADEVLQRLTDIAFAD 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490243157  94 VLDIlnddgglkpirewpkiwrttlsgfdlsstiMNMDETTIEtILKKIKWPDKVKNLELIGKHVDvmAFKERMEVNVNV 173
Cdd:COG3728   80 ITDY------------------------------VEFGDDTLE-VKKKIKLKDRLKALELLGKYYG--LFTDKVEHKGEE 126
Terminase_2 pfam03592
Terminase small subunit; Packaging of double-stranded viral DNA concatemers requires ...
15-168 1.69e-29

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: 106.28  E-value: 1.69e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490243157   15 LTVQQEAYCQEYVKCpENQTQAAINAGYSPNTAGKFASQNMRDARIQKRIAELMEDRNKRLRVSADYVLLRLVEI---DQ 91
Cdd:pfam03592   1 LTDKQKRFCDEYIKD-FNATQAAIKAGYSKKTARSIGSRLLRNPKIKKYIDELKAEREERTIIDADDVLEELTKIafgDI 79
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 490243157   92 MDVLDILNDDGGLKPIREWPKIWRTTLSGFDLSSTImnmdettietilkKIKWPDKVKNLELIGKHVDVMAFKERME 168
Cdd:pfam03592  80 TDYVDFGENYVKFKDSDEVDGTIISEVKQGKDKDGV-------------KIKLKDKLKALELLGKRYGLFKEKLEAE 143
 
Name Accession Description Interval E-value
XtmA COG3728
Phage terminase, small subunit [Mobilome: prophages, transposons];
14-173 2.91e-35

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


Pssm-ID: 442942  Cd Length: 131  Bit Score: 120.44  E-value: 2.91e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490243157  14 PLTVQQEAYCQEYVKCpENQTQAAINAGYSPNTAGKFASQNMRDARIQKRIAELMEDRNKRLRVSADYVLLRLVEIDQMD 93
Cdd:COG3728    1 KLTDKQERFCDEYLKD-LNATQAAIRAGYSEKTASVIGSRLLKKPKIKAAIDELKKERAERTEITADEVLQRLTDIAFAD 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490243157  94 VLDIlnddgglkpirewpkiwrttlsgfdlsstiMNMDETTIEtILKKIKWPDKVKNLELIGKHVDvmAFKERMEVNVNV 173
Cdd:COG3728   80 ITDY------------------------------VEFGDDTLE-VKKKIKLKDRLKALELLGKYYG--LFTDKVEHKGEE 126
Terminase_2 pfam03592
Terminase small subunit; Packaging of double-stranded viral DNA concatemers requires ...
15-168 1.69e-29

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: 106.28  E-value: 1.69e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490243157   15 LTVQQEAYCQEYVKCpENQTQAAINAGYSPNTAGKFASQNMRDARIQKRIAELMEDRNKRLRVSADYVLLRLVEI---DQ 91
Cdd:pfam03592   1 LTDKQKRFCDEYIKD-FNATQAAIKAGYSKKTARSIGSRLLRNPKIKKYIDELKAEREERTIIDADDVLEELTKIafgDI 79
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 490243157   92 MDVLDILNDDGGLKPIREWPKIWRTTLSGFDLSSTImnmdettietilkKIKWPDKVKNLELIGKHVDVMAFKERME 168
Cdd:pfam03592  80 TDYVDFGENYVKFKDSDEVDGTIISEVKQGKDKDGV-------------KIKLKDKLKALELLGKRYGLFKEKLEAE 143
 
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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