NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|446075700|ref|WP_000153555|]
View 

MULTISPECIES: terminase large subunit [Staphylococcus]

Protein Classification

terminase large subunit( domain architecture ID 11468530)

phage terminase large subunit may be involved in headful cutting of double-stranded concatemeric phage DNA and may be ATP-dependent

EC:  3.6.4.-
Gene Ontology:  GO:0004519|GO:0005524|GO:0140657

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

Name Accession Description Interval E-value
YmfN COG4626
Phage terminase-like protein, large subunit, contains N-terminal HTH domain [Mobilome: ...
15-538 0e+00

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


:

Pssm-ID: 443665 [Multi-domain]  Cd Length: 559  Bit Score: 608.40  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446075700  15 TTWYAEQVTQGKIKTSKYVRKECERHLRYLENGGkWVFDEELAHRPIRFIeKFCKPSKG--SKRQLVLQPWQHFIIGSLF 92
Cdd:COG4626    9 ATDYAEDVVDGEIIAGKLIKLACQRHLDDLKRPP-YYFDEEKAERAIRFI-KLLKHTKGplAGKPFELEPWQKFIVGAIF 86
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446075700  93 GWVHKETKLRRFKEALIFMGRKNGKTTTISGVANYAVSQDGENGAEIHLLANVMKQARILFDESKAMIKASPKLDKNFR- 171
Cdd:COG4626   87 GWVDKDTGLRRFREAYLLVPRKNGKSTLAAGIALYLLLADGEPGAEVYSAATTRDQAKIVFKEAKAMIKASPELAKRFKi 166
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446075700 172 -TLRDEIHYDATISKIMPQASDSDKLDGLNTHMGIFDEIHEFKDYKLISVIKNSRAARLQPLLIYITTAGYQLDGPLVDM 250
Cdd:COG4626  167 qDNAKTITHPKTGSKIKALSADADTLDGLNPSFAIVDELHAHKDRDLYDVIKSGMGARPQPLLIIITTAGDDPEGPCYEE 246
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446075700 251 VEAGRDTLDQIIEDERTFYYLASLDDDDDINDSSNWIKANPNLGVSINLDEMKEEWEKAKRTPAERGDFITKRFNIFANN 330
Cdd:COG4626  247 YEYARKVLDGEIEDDRFFPIIYELDEDDDWTDPENWIKANPNLGVSVSLEYLRDEARKAKESPSKRADFLTKHLNIWVGL 326
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446075700 331 DEMSFIDYPTLQKNNEIVSLEELEGRPCTIGYDLSETEDFTAACATFALDNGKVAVLSHSWIPKHKVEYS--NEKIPYRE 408
Cdd:COG4626  327 SADAWLDMDDWEACAEPVDLEDLRGRPCYGGLDLSSTDDLTALALVFRDDDGKWYVLSHFWIPEDTLEERekEDGVPYRD 406
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446075700 409 WEEDGLLTVQDKPYIDYQDVLNWIIKMNEHYVVEKITYDRANAFKLNQELKNYGFETEETRQGALTLSPALKDLKEMFLD 488
Cdd:COG4626  407 WAEQGLLTITPGNVIDYEEVAEWILELAERFDLKEIGYDPWGATYLVQALEEEGFPLVEVRQGFKTLSPPIKELERKLLD 486
                        490       500       510       520       530
                 ....*....|....*....|....*....|....*....|....*....|
gi 446075700 489 GKIIFNNNPLMKWYINNVQLKLDRNGNWLPSKQSRYRKIDGFAAFLNTYT 538
Cdd:COG4626  487 GKLVHGGNPLLRWCVSNVVVKEDANGNIKPTKKKSRGKIDGAVALIMAVG 536
 
Name Accession Description Interval E-value
YmfN COG4626
Phage terminase-like protein, large subunit, contains N-terminal HTH domain [Mobilome: ...
15-538 0e+00

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


Pssm-ID: 443665 [Multi-domain]  Cd Length: 559  Bit Score: 608.40  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446075700  15 TTWYAEQVTQGKIKTSKYVRKECERHLRYLENGGkWVFDEELAHRPIRFIeKFCKPSKG--SKRQLVLQPWQHFIIGSLF 92
Cdd:COG4626    9 ATDYAEDVVDGEIIAGKLIKLACQRHLDDLKRPP-YYFDEEKAERAIRFI-KLLKHTKGplAGKPFELEPWQKFIVGAIF 86
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446075700  93 GWVHKETKLRRFKEALIFMGRKNGKTTTISGVANYAVSQDGENGAEIHLLANVMKQARILFDESKAMIKASPKLDKNFR- 171
Cdd:COG4626   87 GWVDKDTGLRRFREAYLLVPRKNGKSTLAAGIALYLLLADGEPGAEVYSAATTRDQAKIVFKEAKAMIKASPELAKRFKi 166
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446075700 172 -TLRDEIHYDATISKIMPQASDSDKLDGLNTHMGIFDEIHEFKDYKLISVIKNSRAARLQPLLIYITTAGYQLDGPLVDM 250
Cdd:COG4626  167 qDNAKTITHPKTGSKIKALSADADTLDGLNPSFAIVDELHAHKDRDLYDVIKSGMGARPQPLLIIITTAGDDPEGPCYEE 246
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446075700 251 VEAGRDTLDQIIEDERTFYYLASLDDDDDINDSSNWIKANPNLGVSINLDEMKEEWEKAKRTPAERGDFITKRFNIFANN 330
Cdd:COG4626  247 YEYARKVLDGEIEDDRFFPIIYELDEDDDWTDPENWIKANPNLGVSVSLEYLRDEARKAKESPSKRADFLTKHLNIWVGL 326
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446075700 331 DEMSFIDYPTLQKNNEIVSLEELEGRPCTIGYDLSETEDFTAACATFALDNGKVAVLSHSWIPKHKVEYS--NEKIPYRE 408
Cdd:COG4626  327 SADAWLDMDDWEACAEPVDLEDLRGRPCYGGLDLSSTDDLTALALVFRDDDGKWYVLSHFWIPEDTLEERekEDGVPYRD 406
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446075700 409 WEEDGLLTVQDKPYIDYQDVLNWIIKMNEHYVVEKITYDRANAFKLNQELKNYGFETEETRQGALTLSPALKDLKEMFLD 488
Cdd:COG4626  407 WAEQGLLTITPGNVIDYEEVAEWILELAERFDLKEIGYDPWGATYLVQALEEEGFPLVEVRQGFKTLSPPIKELERKLLD 486
                        490       500       510       520       530
                 ....*....|....*....|....*....|....*....|....*....|
gi 446075700 489 GKIIFNNNPLMKWYINNVQLKLDRNGNWLPSKQSRYRKIDGFAAFLNTYT 538
Cdd:COG4626  487 GKLVHGGNPLLRWCVSNVVVKEDANGNIKPTKKKSRGKIDGAVALIMAVG 536
TerL_nuclease pfam20441
Terminase large subunit, endonuclease domain; This is the endonuclease domain of Terminase ...
262-538 2.43e-32

Terminase large subunit, endonuclease domain; This is the endonuclease domain of Terminase large subunit TerL, a key component of the DNA packing machinery in tailed bacteriophages and related viruses. TerL comprises a N-terminal ATPase domain (pfam03354) which powers the DNA translocation and this C-terminal endonuclease domain that cuts concatemeric DNA first in the initiation phase in a sequence specific site and later in the completion stage of the DNA packaging process when the capsid is full. Cryo-EM studies indicate that TerL forms a pentamer that binds to a dodecameric assembly called portal and attaches to the capsid. It has been proposed that nuclease domains form a radially arranged ring that is proximal to portal, playing a key role in pentamer assembly. This nuclease domain has a RNAse H-like fold and it has been proposed to utilize a two-metal catalysis mechanism like in other RNAse H-like endonucleases such as RNase H, transposases, retroviral integrases and RuvC Holliday junction resolvases.


Pssm-ID: 466590  Cd Length: 284  Bit Score: 125.85  E-value: 2.43e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446075700  262 IEDERTFYYLASLDDDDDINDSSNWIKANPNLGVSINLDEMKEEWEKAKRTPAERGDFITKRFNIFAnNDEMSFIDYPTL 341
Cdd:pfam20441   2 DDDDSHFVFYAELDDYDEVKDSSKWIKANPALGYTLSLEDIQKDFIGAIGNPVSMAKIITKRFNLWM-TDETTIFSKQLW 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446075700  342 QKnnEIVSLEELEGRPCTIGYDLSETEDFTAACATFALDnGKVAVLSHSWIPKHKVEYSN--EKIPYREWEEDGLLTVQD 419
Cdd:pfam20441  81 DQ--CLVPPLDFSGRDVAIGVDLSVRGDVTGTVIGYPED-GHYYLKAIPFMPESAEDKFKhlGKTIYHEGINNGTDEAWD 157
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446075700  420 KPYIDYQDVLNWIIKMNEHYVVEKITYDRANA--FKLNQELKNYGFETEETRQGALTLSPALKDLKEMFLDGKIIFNNNP 497
Cdd:pfam20441 158 AGMIDMNQSVPIIGWIAKTFAVQALNYDPWYAknFIDKFEQTYLDIPYNEVMQNFFKLSNTLKATQKLVAEGRIHHDGNK 237
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|.
gi 446075700  498 LMKWYINNVQLKLDRNGNWLPSKQSRYRKIDGFAAFLNTYT 538
Cdd:pfam20441 238 LLAVHVMNAETKIDDFGNMKINKKGYTDKIDLADALINAMW 278
 
Name Accession Description Interval E-value
YmfN COG4626
Phage terminase-like protein, large subunit, contains N-terminal HTH domain [Mobilome: ...
15-538 0e+00

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


Pssm-ID: 443665 [Multi-domain]  Cd Length: 559  Bit Score: 608.40  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446075700  15 TTWYAEQVTQGKIKTSKYVRKECERHLRYLENGGkWVFDEELAHRPIRFIeKFCKPSKG--SKRQLVLQPWQHFIIGSLF 92
Cdd:COG4626    9 ATDYAEDVVDGEIIAGKLIKLACQRHLDDLKRPP-YYFDEEKAERAIRFI-KLLKHTKGplAGKPFELEPWQKFIVGAIF 86
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446075700  93 GWVHKETKLRRFKEALIFMGRKNGKTTTISGVANYAVSQDGENGAEIHLLANVMKQARILFDESKAMIKASPKLDKNFR- 171
Cdd:COG4626   87 GWVDKDTGLRRFREAYLLVPRKNGKSTLAAGIALYLLLADGEPGAEVYSAATTRDQAKIVFKEAKAMIKASPELAKRFKi 166
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446075700 172 -TLRDEIHYDATISKIMPQASDSDKLDGLNTHMGIFDEIHEFKDYKLISVIKNSRAARLQPLLIYITTAGYQLDGPLVDM 250
Cdd:COG4626  167 qDNAKTITHPKTGSKIKALSADADTLDGLNPSFAIVDELHAHKDRDLYDVIKSGMGARPQPLLIIITTAGDDPEGPCYEE 246
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446075700 251 VEAGRDTLDQIIEDERTFYYLASLDDDDDINDSSNWIKANPNLGVSINLDEMKEEWEKAKRTPAERGDFITKRFNIFANN 330
Cdd:COG4626  247 YEYARKVLDGEIEDDRFFPIIYELDEDDDWTDPENWIKANPNLGVSVSLEYLRDEARKAKESPSKRADFLTKHLNIWVGL 326
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446075700 331 DEMSFIDYPTLQKNNEIVSLEELEGRPCTIGYDLSETEDFTAACATFALDNGKVAVLSHSWIPKHKVEYS--NEKIPYRE 408
Cdd:COG4626  327 SADAWLDMDDWEACAEPVDLEDLRGRPCYGGLDLSSTDDLTALALVFRDDDGKWYVLSHFWIPEDTLEERekEDGVPYRD 406
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446075700 409 WEEDGLLTVQDKPYIDYQDVLNWIIKMNEHYVVEKITYDRANAFKLNQELKNYGFETEETRQGALTLSPALKDLKEMFLD 488
Cdd:COG4626  407 WAEQGLLTITPGNVIDYEEVAEWILELAERFDLKEIGYDPWGATYLVQALEEEGFPLVEVRQGFKTLSPPIKELERKLLD 486
                        490       500       510       520       530
                 ....*....|....*....|....*....|....*....|....*....|
gi 446075700 489 GKIIFNNNPLMKWYINNVQLKLDRNGNWLPSKQSRYRKIDGFAAFLNTYT 538
Cdd:COG4626  487 GKLVHGGNPLLRWCVSNVVVKEDANGNIKPTKKKSRGKIDGAVALIMAVG 536
TerL_nuclease pfam20441
Terminase large subunit, endonuclease domain; This is the endonuclease domain of Terminase ...
262-538 2.43e-32

Terminase large subunit, endonuclease domain; This is the endonuclease domain of Terminase large subunit TerL, a key component of the DNA packing machinery in tailed bacteriophages and related viruses. TerL comprises a N-terminal ATPase domain (pfam03354) which powers the DNA translocation and this C-terminal endonuclease domain that cuts concatemeric DNA first in the initiation phase in a sequence specific site and later in the completion stage of the DNA packaging process when the capsid is full. Cryo-EM studies indicate that TerL forms a pentamer that binds to a dodecameric assembly called portal and attaches to the capsid. It has been proposed that nuclease domains form a radially arranged ring that is proximal to portal, playing a key role in pentamer assembly. This nuclease domain has a RNAse H-like fold and it has been proposed to utilize a two-metal catalysis mechanism like in other RNAse H-like endonucleases such as RNase H, transposases, retroviral integrases and RuvC Holliday junction resolvases.


Pssm-ID: 466590  Cd Length: 284  Bit Score: 125.85  E-value: 2.43e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446075700  262 IEDERTFYYLASLDDDDDINDSSNWIKANPNLGVSINLDEMKEEWEKAKRTPAERGDFITKRFNIFAnNDEMSFIDYPTL 341
Cdd:pfam20441   2 DDDDSHFVFYAELDDYDEVKDSSKWIKANPALGYTLSLEDIQKDFIGAIGNPVSMAKIITKRFNLWM-TDETTIFSKQLW 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446075700  342 QKnnEIVSLEELEGRPCTIGYDLSETEDFTAACATFALDnGKVAVLSHSWIPKHKVEYSN--EKIPYREWEEDGLLTVQD 419
Cdd:pfam20441  81 DQ--CLVPPLDFSGRDVAIGVDLSVRGDVTGTVIGYPED-GHYYLKAIPFMPESAEDKFKhlGKTIYHEGINNGTDEAWD 157
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446075700  420 KPYIDYQDVLNWIIKMNEHYVVEKITYDRANA--FKLNQELKNYGFETEETRQGALTLSPALKDLKEMFLDGKIIFNNNP 497
Cdd:pfam20441 158 AGMIDMNQSVPIIGWIAKTFAVQALNYDPWYAknFIDKFEQTYLDIPYNEVMQNFFKLSNTLKATQKLVAEGRIHHDGNK 237
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|.
gi 446075700  498 LMKWYINNVQLKLDRNGNWLPSKQSRYRKIDGFAAFLNTYT 538
Cdd:pfam20441 238 LLAVHVMNAETKIDDFGNMKINKKGYTDKIDLADALINAMW 278
TerL_ATPase pfam03354
Terminase large subunit, ATPase domain; Terminase large subunit (TerL) from bacteriophages and ...
82-252 5.46e-28

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: 110.48  E-value: 5.46e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446075700   82 PWQHFIIGSLFGWvhKETKLRRFKEALIFMGRKNGKTTTISGVANYAVSQDGENGAEIHLLANVMKQARILFDESKAMIK 161
Cdd:pfam03354   1 PYQKFVLGSMYGW--RGCTPRQFDEFYVIVGRKNGKSILDVMIALIELLLFPKPNSQIALAATTKDQAEKIFKKFKNQVK 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446075700  162 ASP-----KLDKNFRTLRDEIHYDATISKIMPQASDSDKLDGLNTHMGIFDEIHEFKDYKLISVIKNSRAARLQPLLIYI 236
Cdd:pfam03354  79 LNKeqilvKDNSILKSMRKGIEISIVDGVIKCLSSNEDTLDGGRPQLVIIDEFGAFKDNEPLITIRQGMRKRANPGTLFI 158
                         170
                  ....*....|....*.
gi 446075700  237 TTAGYQLDGPLVDMVE 252
Cdd:pfam03354 159 TTAGVIRGSAYDDELE 174
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH