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Conserved domains on  [gi|82793123|ref|YP_418246|]
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terminase small subunit [Vibrio phage VP4]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DNA_Packaging_2 super family cl23904
DNA packaging protein; This DNA packaging protein is also referred to as gene 18 product (gp18) ...
 1-77 1.89e-36

DNA packaging protein; This DNA packaging protein is also referred to as gene 18 product (gp18). This protein is required for DNA packaging and functions in a complex with gp19.


The actual alignment was detected with superfamily member PHA00425:

Pssm-ID: 420083  Cd Length: 88  Bit Score: 117.60  E-value: 1.89e-36
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 82793123   1 MNLEQLLQALDSESARLMLEDLKDPEKRTPQLYNAIGKLLDRHKFNISKVQPDESILGELASAL--------PDDVTESD 72
Cdd:PHA00425  4 KSLIKFLEMLDTEMAQRMLADLKDDEKRTPQLYNAIGKLLDRHKFQISKLQPDENILGGLAAALeeykekvgADGLTDDD 83


                ....*
gi 82793123  73 LYTLN 77
Cdd:PHA00425 84 VYTLQ 88
 
Name Accession Description Interval E-value
PHA00425 PHA00425
DNA packaging protein, small subunit
 1-77 1.89e-36

DNA packaging protein, small subunit


Pssm-ID: 164800  Cd Length: 88  Bit Score: 117.60  E-value: 1.89e-36
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 82793123   1 MNLEQLLQALDSESARLMLEDLKDPEKRTPQLYNAIGKLLDRHKFNISKVQPDESILGELASAL--------PDDVTESD 72
Cdd:PHA00425  4 KSLIKFLEMLDTEMAQRMLADLKDDEKRTPQLYNAIGKLLDRHKFQISKLQPDENILGGLAAALeeykekvgADGLTDDD 83


                ....*
gi 82793123  73 LYTLN 77
Cdd:PHA00425 84 VYTLQ 88
DNA_Packaging_2 pfam11123
DNA packaging protein; This DNA packaging protein is also referred to as gene 18 product (gp18) ...
 2-66 2.86e-19

DNA packaging protein; This DNA packaging protein is also referred to as gene 18 product (gp18). This protein is required for DNA packaging and functions in a complex with gp19.


Pssm-ID: 402615  Cd Length: 82  Bit Score: 73.94  E-value: 2.86e-19
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 82793123    2 NLEQLLQALDSESARLMLEDLKDPEKRTPQLYNAIGKLLDRHKFNISKVQPDESILGELASALPD 66
Cdd:pfam11123  3 SLITFLEMLDTAMAQRMLADLSDHERRSPQLYNAINKLLDRHKFQIGKLQPDVHILGGLAGALEE 67
 
Name Accession Description Interval E-value
PHA00425 PHA00425
DNA packaging protein, small subunit
 1-77 1.89e-36

DNA packaging protein, small subunit


Pssm-ID: 164800  Cd Length: 88  Bit Score: 117.60  E-value: 1.89e-36
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 82793123   1 MNLEQLLQALDSESARLMLEDLKDPEKRTPQLYNAIGKLLDRHKFNISKVQPDESILGELASAL--------PDDVTESD 72
Cdd:PHA00425  4 KSLIKFLEMLDTEMAQRMLADLKDDEKRTPQLYNAIGKLLDRHKFQISKLQPDENILGGLAAALeeykekvgADGLTDDD 83


                ....*
gi 82793123  73 LYTLN 77
Cdd:PHA00425 84 VYTLQ 88
DNA_Packaging_2 pfam11123
DNA packaging protein; This DNA packaging protein is also referred to as gene 18 product (gp18) ...
 2-66 2.86e-19

DNA packaging protein; This DNA packaging protein is also referred to as gene 18 product (gp18). This protein is required for DNA packaging and functions in a complex with gp19.


Pssm-ID: 402615  Cd Length: 82  Bit Score: 73.94  E-value: 2.86e-19
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 82793123    2 NLEQLLQALDSESARLMLEDLKDPEKRTPQLYNAIGKLLDRHKFNISKVQPDESILGELASALPD 66
Cdd:pfam11123  3 SLITFLEMLDTAMAQRMLADLSDHERRSPQLYNAINKLLDRHKFQIGKLQPDVHILGGLAGALEE 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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