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Conserved domains on  [gi|1844803493|ref|WP_171524503|]
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terminase gpA endonuclease subunit, partial [Acinetobacter baumannii]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
gpA1 super family cl44252
Phage terminase, large subunit GpA [Mobilome: prophages, transposons];
16-102 2.93e-30

Phage terminase, large subunit GpA [Mobilome: prophages, transposons];


The actual alignment was detected with superfamily member COG5525:

Pssm-ID: 444276 [Multi-domain]  Cd Length: 635  Bit Score: 112.34  E-value: 2.93e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844803493  16 GFWINELYSPWGSMREIAKAWSDSEGNPEKEQTFYNTRLGLPY--RGDissFADPENLKSRREKYDPEIVPKRAALLTAA 93
Cdd:COG5525   299 GFHLNGLYSPFQTWEDLVREFLDAKGDPEKLKTFVNTDLGEPYeeKGE---APDWERLRARAEDYPLGTVPAGVLFLTAG 375


                  ....*....
gi 1844803493  94 VDVQDDRLE 102
Cdd:COG5525   376 VDVQGDRLE 384
 
Name Accession Description Interval E-value
gpA1 COG5525
Phage terminase, large subunit GpA [Mobilome: prophages, transposons];
16-102 2.93e-30

Phage terminase, large subunit GpA [Mobilome: prophages, transposons];


Pssm-ID: 444276 [Multi-domain]  Cd Length: 635  Bit Score: 112.34  E-value: 2.93e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844803493  16 GFWINELYSPWGSMREIAKAWSDSEGNPEKEQTFYNTRLGLPY--RGDissFADPENLKSRREKYDPEIVPKRAALLTAA 93
Cdd:COG5525   299 GFHLNGLYSPFQTWEDLVREFLDAKGDPEKLKTFVNTDLGEPYeeKGE---APDWERLRARAEDYPLGTVPAGVLFLTAG 375


                  ....*....
gi 1844803493  94 VDVQDDRLE 102
Cdd:COG5525   376 VDVQGDRLE 384
GpA_nuclease pfam20454
Terminase large subunit gpA, endonuclease domain; Terminase enzymes mediate the packaging ...
 16-102 5.50e-25

Terminase large subunit gpA, endonuclease domain; Terminase enzymes mediate the packaging viral DNA into an empty procapsid in a process called DNA packaging and are composed of a heterotrimeric complex of a large subunit (TerL, gpA) and the small subunit (TerS, gpNu1) (TerL-TerS2). TerL contains all the catalytic activities required for for DNA maturation and packaging. At the N-terminal reside the DNA translocase (packaging) and ATPase activities, while at the C-terminal resides the DNA maturation (nuclease/helicase) catalytic activity. This entry represents the endonuclease domain found at the C-terminal of Terminase large subunit (GpA) from Bacteriophage lambda, which excises an individual genome from the concatemer at the cos site.


Pssm-ID: 466603  Cd Length: 293  Bit Score: 94.70  E-value: 5.50e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844803493  16 GFWINELYSPWGSMREIAKAW----SDSEGNPEKEQTFYNTRLGLPYRgDISSFADPENLKSRREKYDPEIVPKRAALLT 91
Cdd:pfam20454   3 GFHLNGLYSPFVSWGDLAREFleakREAKGDPEALKTFVNTDLGEPWE-EEGEALDADELAARAEDYPLGTVPDGVLVLT 81

                          90
                  ....*....|.
gi 1844803493  92 AAVDVQDDRLE 102
Cdd:pfam20454  82 AGVDVQGDRLE 92
 
Name Accession Description Interval E-value
gpA1 COG5525
Phage terminase, large subunit GpA [Mobilome: prophages, transposons];
16-102 2.93e-30

Phage terminase, large subunit GpA [Mobilome: prophages, transposons];


Pssm-ID: 444276 [Multi-domain]  Cd Length: 635  Bit Score: 112.34  E-value: 2.93e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844803493  16 GFWINELYSPWGSMREIAKAWSDSEGNPEKEQTFYNTRLGLPY--RGDissFADPENLKSRREKYDPEIVPKRAALLTAA 93
Cdd:COG5525   299 GFHLNGLYSPFQTWEDLVREFLDAKGDPEKLKTFVNTDLGEPYeeKGE---APDWERLRARAEDYPLGTVPAGVLFLTAG 375


                  ....*....
gi 1844803493  94 VDVQDDRLE 102
Cdd:COG5525   376 VDVQGDRLE 384
GpA_nuclease pfam20454
Terminase large subunit gpA, endonuclease domain; Terminase enzymes mediate the packaging ...
 16-102 5.50e-25

Terminase large subunit gpA, endonuclease domain; Terminase enzymes mediate the packaging viral DNA into an empty procapsid in a process called DNA packaging and are composed of a heterotrimeric complex of a large subunit (TerL, gpA) and the small subunit (TerS, gpNu1) (TerL-TerS2). TerL contains all the catalytic activities required for for DNA maturation and packaging. At the N-terminal reside the DNA translocase (packaging) and ATPase activities, while at the C-terminal resides the DNA maturation (nuclease/helicase) catalytic activity. This entry represents the endonuclease domain found at the C-terminal of Terminase large subunit (GpA) from Bacteriophage lambda, which excises an individual genome from the concatemer at the cos site.


Pssm-ID: 466603  Cd Length: 293  Bit Score: 94.70  E-value: 5.50e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844803493  16 GFWINELYSPWGSMREIAKAW----SDSEGNPEKEQTFYNTRLGLPYRgDISSFADPENLKSRREKYDPEIVPKRAALLT 91
Cdd:pfam20454   3 GFHLNGLYSPFVSWGDLAREFleakREAKGDPEALKTFVNTDLGEPWE-EEGEALDADELAARAEDYPLGTVPDGVLVLT 81

                          90
                  ....*....|.
gi 1844803493  92 AAVDVQDDRLE 102
Cdd:pfam20454  82 AGVDVQGDRLE 92
 
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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