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Conserved domains on  [gi|488487499|ref|WP_002531068|]
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MULTISPECIES: terminase large subunit domain-containing protein [Cutibacterium]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YmfN super family cl44093
Phage terminase-like protein, large subunit, contains N-terminal HTH domain [Mobilome: ...
 18-199 6.05e-62

Phage terminase-like protein, large subunit, contains N-terminal HTH domain [Mobilome: prophages, transposons];


The actual alignment was detected with superfamily member COG4626:

Pssm-ID: 443665 [Multi-domain]  Cd Length: 559  Bit Score: 201.25  E-value: 6.05e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488487499  18 TYDKRKADFAVAFIQALKHTKGRWSGQPFQLIDWQEQIIRDLFGTV-KADGYRQFTTAYVEIPKKQGKSELAAAVALLLT 96
Cdd:COG4626   44 YFDEEKAERAIRFIKLLKHTKGPLAGKPFELEPWQKFIVGAIFGWVdKDTGLRRFREAYLLVPRKNGKSTLAAGIALYLL 123

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488487499  97 CGDGEERAEVYGCAADRRQASIVFEVAADMVRQSPALSKRVKILSSQKRIIYKPTNSFYQVLSAEAYFKHGFDISGVVFD 176
Cdd:COG4626  124 LADGEPGAEVYSAATTRDQAKIVFKEAKAMIKASPELAKRFKIQDNAKTITHPKTGSKIKALSADADTLDGLNPSFAIVD 203

                        170       180
                 ....*....|....*....|...
gi 488487499 177 ELHTQPNRALFDVMTKGSGdART 199
Cdd:COG4626  204 ELHAHKDRDLYDVIKSGMG-ARP 225
 
Name Accession Description Interval E-value
YmfN COG4626
Phage terminase-like protein, large subunit, contains N-terminal HTH domain [Mobilome: ...
 18-199 6.05e-62

Phage terminase-like protein, large subunit, contains N-terminal HTH domain [Mobilome: prophages, transposons];


Pssm-ID: 443665 [Multi-domain]  Cd Length: 559  Bit Score: 201.25  E-value: 6.05e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488487499  18 TYDKRKADFAVAFIQALKHTKGRWSGQPFQLIDWQEQIIRDLFGTV-KADGYRQFTTAYVEIPKKQGKSELAAAVALLLT 96
Cdd:COG4626   44 YFDEEKAERAIRFIKLLKHTKGPLAGKPFELEPWQKFIVGAIFGWVdKDTGLRRFREAYLLVPRKNGKSTLAAGIALYLL 123

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488487499  97 CGDGEERAEVYGCAADRRQASIVFEVAADMVRQSPALSKRVKILSSQKRIIYKPTNSFYQVLSAEAYFKHGFDISGVVFD 176
Cdd:COG4626  124 LADGEPGAEVYSAATTRDQAKIVFKEAKAMIKASPELAKRFKIQDNAKTITHPKTGSKIKALSADADTLDGLNPSFAIVD 203

                        170       180
                 ....*....|....*....|...
gi 488487499 177 ELHTQPNRALFDVMTKGSGdART 199
Cdd:COG4626  204 ELHAHKDRDLYDVIKSGMG-ARP 225
TerL_ATPase pfam03354
Terminase large subunit, ATPase domain; Terminase large subunit (TerL) from bacteriophages and ...
 51-193 5.48e-10

Terminase large subunit, ATPase domain; Terminase large subunit (TerL) from bacteriophages and evolutionarily related viruses, is an important component of the DNA packing machinery and comprises an ATPase domain, which powers DNA translocation and a nuclease domain that cuts concatemeric DNA. TerL forms pentamers in which the ATPase domains form a ring distal to the capsid. This is the ATPase domain which contains a C-terminal subdomain that sits above the ATPase active site, called the "Lid subdomain" with reference to analogous lid subdomains found in other ATPases. It contains a hydrophobic patch (Trp and Tyr residues) that mediates critical interactions in the interface between adjacent ATPase subunits and assists the positioning of the arginine finger residue that catalyzes ATP hydrolysis. This entry also includes bacterial proteins of unknown function.


Pssm-ID: 460895 [Multi-domain]  Cd Length: 178  Bit Score: 56.17  E-value: 5.48e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488487499   51 WQEQIIRDLFGTvKADGYRQFTTAYVEIPKKQGKSELAAAVALLLTCGDGEERAEVYGCAADRRQASIVFEVAADMVRQS 130
Cdd:pfam03354   2 YQKFVLGSMYGW-RGCTPRQFDEFYVIVGRKNGKSILDVMIALIELLLFPKPNSQIALAATTKDQAEKIFKKFKNQVKLN 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 488487499  131 PALS--KRVKILSSQKRIIYKP-TNSFYQVLSAEAYFKHGFDISGVVFDELHTQPNRALFDVMTKG 193
Cdd:pfam03354  81 KEQIlvKDNSILKSMRKGIEISiVDGVIKCLSSNEDTLDGGRPQLVIIDEFGAFKDNEPLITIRQG 146
 
Name Accession Description Interval E-value
YmfN COG4626
Phage terminase-like protein, large subunit, contains N-terminal HTH domain [Mobilome: ...
 18-199 6.05e-62

Phage terminase-like protein, large subunit, contains N-terminal HTH domain [Mobilome: prophages, transposons];


Pssm-ID: 443665 [Multi-domain]  Cd Length: 559  Bit Score: 201.25  E-value: 6.05e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488487499  18 TYDKRKADFAVAFIQALKHTKGRWSGQPFQLIDWQEQIIRDLFGTV-KADGYRQFTTAYVEIPKKQGKSELAAAVALLLT 96
Cdd:COG4626   44 YFDEEKAERAIRFIKLLKHTKGPLAGKPFELEPWQKFIVGAIFGWVdKDTGLRRFREAYLLVPRKNGKSTLAAGIALYLL 123

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488487499  97 CGDGEERAEVYGCAADRRQASIVFEVAADMVRQSPALSKRVKILSSQKRIIYKPTNSFYQVLSAEAYFKHGFDISGVVFD 176
Cdd:COG4626  124 LADGEPGAEVYSAATTRDQAKIVFKEAKAMIKASPELAKRFKIQDNAKTITHPKTGSKIKALSADADTLDGLNPSFAIVD 203

                        170       180
                 ....*....|....*....|...
gi 488487499 177 ELHTQPNRALFDVMTKGSGdART 199
Cdd:COG4626  204 ELHAHKDRDLYDVIKSGMG-ARP 225
TerL_ATPase pfam03354
Terminase large subunit, ATPase domain; Terminase large subunit (TerL) from bacteriophages and ...
 51-193 5.48e-10

Terminase large subunit, ATPase domain; Terminase large subunit (TerL) from bacteriophages and evolutionarily related viruses, is an important component of the DNA packing machinery and comprises an ATPase domain, which powers DNA translocation and a nuclease domain that cuts concatemeric DNA. TerL forms pentamers in which the ATPase domains form a ring distal to the capsid. This is the ATPase domain which contains a C-terminal subdomain that sits above the ATPase active site, called the "Lid subdomain" with reference to analogous lid subdomains found in other ATPases. It contains a hydrophobic patch (Trp and Tyr residues) that mediates critical interactions in the interface between adjacent ATPase subunits and assists the positioning of the arginine finger residue that catalyzes ATP hydrolysis. This entry also includes bacterial proteins of unknown function.


Pssm-ID: 460895 [Multi-domain]  Cd Length: 178  Bit Score: 56.17  E-value: 5.48e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488487499   51 WQEQIIRDLFGTvKADGYRQFTTAYVEIPKKQGKSELAAAVALLLTCGDGEERAEVYGCAADRRQASIVFEVAADMVRQS 130
Cdd:pfam03354   2 YQKFVLGSMYGW-RGCTPRQFDEFYVIVGRKNGKSILDVMIALIELLLFPKPNSQIALAATTKDQAEKIFKKFKNQVKLN 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 488487499  131 PALS--KRVKILSSQKRIIYKP-TNSFYQVLSAEAYFKHGFDISGVVFDELHTQPNRALFDVMTKG 193
Cdd:pfam03354  81 KEQIlvKDNSILKSMRKGIEISiVDGVIKCLSSNEDTLDGGRPQLVIIDEFGAFKDNEPLITIRQG 146
 
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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