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Conserved domains on  [gi|1722886|sp|P39785|]
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RecName: Full=PBSX phage terminase small subunit

Protein Classification

Phage_terminase and Terminase_2 domain-containing protein( domain architecture ID 10306226)

Phage_terminase and Terminase_2 domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Terminase_2 pfam03592
Terminase small subunit; Packaging of double-stranded viral DNA concatemers requires ...
 67-230 7.58e-44

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: 145.19  E-value: 7.58e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722886     67 LNERQRLFCLYYVKSFNATQSAIKAGYSPDSAHVTGSRLLKNEKVAAEIRRIKKEMVNEMFIEAMDVLQVYIKIAFADIT 146
Cdd:pfam03592   1 LTDKQKRFCDEYIKDFNATQAAIKAGYSKKTARSIGSRLLRNPKIKKYIDELKAEREERTIIDADDVLEELTKIAFGDIT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722886    147 DYVTFGKkevqavgksgplfdeddnpimkeiSFVDVKDSGLVDGTIVTEAKLGK--EGIAIKLADKMKALEKLSLYFDLF 224
Cdd:pfam03592  81 DYVDFGE------------------------NYVKFKDSDEVDGTIISEVKQGKdkDGVKIKLKDKLKALELLGKRYGLF 136


                  ....*.
gi 1722886    225 PDQFKQ 230
Cdd:pfam03592 137 KEKLEA 142
Phage_terminase super family cl11724
Phage terminase small subunit; This family of small highly conserved proteins come from a ...
 2-64 2.69e-04

Phage terminase small subunit; This family of small highly conserved proteins come from a subset of Firmicute species. Its putative function is as a phage terminase small subunit.


The actual alignment was detected with superfamily member pfam10668:

Pssm-ID: 402346 [Multi-domain]  Cd Length: 67  Bit Score: 38.29  E-value: 2.69e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1722886      2 KTQQREQALAIYQQHQGKITNRAIADTIGVSAKTIGIWKKQDKWKEALFSASKNEQKQRPINN 64
Cdd:pfam10668   5 RDPNRDEAFQLWKESGGTKKCKDIADELGVSESQVRKWKAIDKWDDKNKVAQSKGKGCAPKRK 67
 
Name Accession Description Interval E-value
Terminase_2 pfam03592
Terminase small subunit; Packaging of double-stranded viral DNA concatemers requires ...
 67-230 7.58e-44

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: 145.19  E-value: 7.58e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722886     67 LNERQRLFCLYYVKSFNATQSAIKAGYSPDSAHVTGSRLLKNEKVAAEIRRIKKEMVNEMFIEAMDVLQVYIKIAFADIT 146
Cdd:pfam03592   1 LTDKQKRFCDEYIKDFNATQAAIKAGYSKKTARSIGSRLLRNPKIKKYIDELKAEREERTIIDADDVLEELTKIAFGDIT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722886    147 DYVTFGKkevqavgksgplfdeddnpimkeiSFVDVKDSGLVDGTIVTEAKLGK--EGIAIKLADKMKALEKLSLYFDLF 224
Cdd:pfam03592  81 DYVDFGE------------------------NYVKFKDSDEVDGTIISEVKQGKdkDGVKIKLKDKLKALELLGKRYGLF 136


                  ....*.
gi 1722886    225 PDQFKQ 230
Cdd:pfam03592 137 KEKLEA 142
XtmA COG3728
Phage terminase, small subunit [Mobilome: prophages, transposons];
66-238 1.71e-37

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


Pssm-ID: 442942  Cd Length: 131  Bit Score: 128.53  E-value: 1.71e-37
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722886   66 ELNERQRLFCLYYVKSFNATQSAIKAGYSPDSAHVTGSRLLKNEKVAAEIRRIKKEMVNEMFIEAMDVLQVYIKIAFADI 145
Cdd:COG3728   1 KLTDKQERFCDEYLKDLNATQAAIRAGYSEKTASVIGSRLLKKPKIKAAIDELKKERAERTEITADEVLQRLTDIAFADI 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722886  146 TDYVTFGKkevqavgksgplfdeDDNPIMKEisfvdvkdsglvdgtivteaklgkegiaIKLADKMKALEKLSLYFDLFP 225
Cdd:COG3728  81 TDYVEFGD---------------DTLEVKKK----------------------------IKLKDRLKALELLGKYYGLFT 117

                       170
                ....*....|...
gi 1722886  226 DQFKQKIENEKLK 238
Cdd:COG3728 118 DKVEHKGEEDELE 130
Phage_terminase pfam10668
Phage terminase small subunit; This family of small highly conserved proteins come from a ...
 2-64 2.69e-04

Phage terminase small subunit; This family of small highly conserved proteins come from a subset of Firmicute species. Its putative function is as a phage terminase small subunit.


Pssm-ID: 402346 [Multi-domain]  Cd Length: 67  Bit Score: 38.29  E-value: 2.69e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1722886      2 KTQQREQALAIYQQHQGKITNRAIADTIGVSAKTIGIWKKQDKWKEALFSASKNEQKQRPINN 64
Cdd:pfam10668   5 RDPNRDEAFQLWKESGGTKKCKDIADELGVSESQVRKWKAIDKWDDKNKVAQSKGKGCAPKRK 67
 
Name Accession Description Interval E-value
Terminase_2 pfam03592
Terminase small subunit; Packaging of double-stranded viral DNA concatemers requires ...
 67-230 7.58e-44

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: 145.19  E-value: 7.58e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722886     67 LNERQRLFCLYYVKSFNATQSAIKAGYSPDSAHVTGSRLLKNEKVAAEIRRIKKEMVNEMFIEAMDVLQVYIKIAFADIT 146
Cdd:pfam03592   1 LTDKQKRFCDEYIKDFNATQAAIKAGYSKKTARSIGSRLLRNPKIKKYIDELKAEREERTIIDADDVLEELTKIAFGDIT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722886    147 DYVTFGKkevqavgksgplfdeddnpimkeiSFVDVKDSGLVDGTIVTEAKLGK--EGIAIKLADKMKALEKLSLYFDLF 224
Cdd:pfam03592  81 DYVDFGE------------------------NYVKFKDSDEVDGTIISEVKQGKdkDGVKIKLKDKLKALELLGKRYGLF 136


                  ....*.
gi 1722886    225 PDQFKQ 230
Cdd:pfam03592 137 KEKLEA 142
XtmA COG3728
Phage terminase, small subunit [Mobilome: prophages, transposons];
66-238 1.71e-37

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


Pssm-ID: 442942  Cd Length: 131  Bit Score: 128.53  E-value: 1.71e-37
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722886   66 ELNERQRLFCLYYVKSFNATQSAIKAGYSPDSAHVTGSRLLKNEKVAAEIRRIKKEMVNEMFIEAMDVLQVYIKIAFADI 145
Cdd:COG3728   1 KLTDKQERFCDEYLKDLNATQAAIRAGYSEKTASVIGSRLLKKPKIKAAIDELKKERAERTEITADEVLQRLTDIAFADI 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722886  146 TDYVTFGKkevqavgksgplfdeDDNPIMKEisfvdvkdsglvdgtivteaklgkegiaIKLADKMKALEKLSLYFDLFP 225
Cdd:COG3728  81 TDYVEFGD---------------DTLEVKKK----------------------------IKLKDRLKALELLGKYYGLFT 117

                       170
                ....*....|...
gi 1722886  226 DQFKQKIENEKLK 238
Cdd:COG3728 118 DKVEHKGEEDELE 130
Phage_terminase pfam10668
Phage terminase small subunit; This family of small highly conserved proteins come from a ...
 2-64 2.69e-04

Phage terminase small subunit; This family of small highly conserved proteins come from a subset of Firmicute species. Its putative function is as a phage terminase small subunit.


Pssm-ID: 402346 [Multi-domain]  Cd Length: 67  Bit Score: 38.29  E-value: 2.69e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1722886      2 KTQQREQALAIYQQHQGKITNRAIADTIGVSAKTIGIWKKQDKWKEALFSASKNEQKQRPINN 64
Cdd:pfam10668   5 RDPNRDEAFQLWKESGGTKKCKDIADELGVSESQVRKWKAIDKWDDKNKVAQSKGKGCAPKRK 67
 
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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