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Conserved domains on  [gi|330858776|ref|YP_004415151|]
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MotA-like activator of middle period transcription [Shigella phage Shfl2]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
MotCF super family cl07687
Bacteriophage T4 MotA, C-terminal; Members of this family adopt a compact alpha/beta structure ...
 106-208 2.87e-65

Bacteriophage T4 MotA, C-terminal; Members of this family adopt a compact alpha/beta structure comprising three alpha-helices and six beta-strands in the order: alpha1-beta1-beta2-beta3-beta4-alpha2-beta5-beta6-alpha3. The beta-strands form a single anti-parallel beta-sheet and the three alpha-helices pack side-by-side onto one surface of the beta-sheet. In this architecture, the domain's hydrophobic core is at the sheet-helix interface, and the second surface of the beta-sheet is completely exposed. The domain is a DNA-binding motif, with a consensus sequence containing nine base pairs (5'-TTTGCTTTA-3'), that appears to bind to various mot boxes, allowing access to the minor groove towards the 5'-end of this sequence and the major groove towards the 3'-end.


The actual alignment was detected with superfamily member pfam09158:

Pssm-ID: 286268  Cd Length: 103  Bit Score: 196.78  E-value: 2.87e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330858776  106 ITSDMEEDKDFMLKLLDENGFVLKKVETYRSNYLAILEKRTHGIRNFEINNNGNMRIFGYKMMEHHIQKFTDIGMSCKIA 185
Cdd:pfam09158   1 ITSDMEEDKDLMLKLLDKNGFVLKKVEIYRSNYLAILEKRTNGIRNFEINNNGNMRIFGYKMMEHHIQKFTDIGMSCKIA 80

                          90       100
                  ....*....|....*....|...
gi 330858776  186 KNGNVYLDIKRSAENIEAVITVA 208
Cdd:pfam09158  81 KNGNVYLDIKRSAENIEAVITVA 103
MotA_activ super family cl07656
Transcription factor MotA, activation domain; Members of this family of viral protein domains ...
 2-96 1.10e-60

Transcription factor MotA, activation domain; Members of this family of viral protein domains are implicated in transcriptional activation. They are almost completely alpha-helical, with five alpha-helices and a short, two-stranded, beta-ribbon. Four alpha helices (alpha1, alpha3, alpha4 and alpha5) are amphipathic and pack their hydrophobic surfaces around the central helix alpha2.


The actual alignment was detected with superfamily member pfam09114:

Pssm-ID: 312591  Cd Length: 95  Bit Score: 184.54  E-value: 1.10e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330858776    2 SKVTYIIKASNDVLNEKTAAILITIAKKDFITAAEVREVHPDLGNAVVNSNIGVLIKKGLVEKSGDGLIITGEAQDIISN 81
Cdd:pfam09114   1 SKVTYIIKASNDVLNEKTATILITIAKKDFITAAEVREVHPDLGNAVVNSNIGVLIKKGLVEKSGDGLIITGEAQDIISN 80

                          90
                  ....*....|....*
gi 330858776   82 AATLYAQENAPELLK 96
Cdd:pfam09114  81 AATLYAQENAPELLK 95
 
Name Accession Description Interval E-value
MotCF pfam09158
Bacteriophage T4 MotA, C-terminal; Members of this family adopt a compact alpha/beta structure ...
 106-208 2.87e-65

Bacteriophage T4 MotA, C-terminal; Members of this family adopt a compact alpha/beta structure comprising three alpha-helices and six beta-strands in the order: alpha1-beta1-beta2-beta3-beta4-alpha2-beta5-beta6-alpha3. The beta-strands form a single anti-parallel beta-sheet and the three alpha-helices pack side-by-side onto one surface of the beta-sheet. In this architecture, the domain's hydrophobic core is at the sheet-helix interface, and the second surface of the beta-sheet is completely exposed. The domain is a DNA-binding motif, with a consensus sequence containing nine base pairs (5'-TTTGCTTTA-3'), that appears to bind to various mot boxes, allowing access to the minor groove towards the 5'-end of this sequence and the major groove towards the 3'-end.


Pssm-ID: 286268  Cd Length: 103  Bit Score: 196.78  E-value: 2.87e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330858776  106 ITSDMEEDKDFMLKLLDENGFVLKKVETYRSNYLAILEKRTHGIRNFEINNNGNMRIFGYKMMEHHIQKFTDIGMSCKIA 185
Cdd:pfam09158   1 ITSDMEEDKDLMLKLLDKNGFVLKKVEIYRSNYLAILEKRTNGIRNFEINNNGNMRIFGYKMMEHHIQKFTDIGMSCKIA 80

                          90       100
                  ....*....|....*....|...
gi 330858776  186 KNGNVYLDIKRSAENIEAVITVA 208
Cdd:pfam09158  81 KNGNVYLDIKRSAENIEAVITVA 103
MotA_activ pfam09114
Transcription factor MotA, activation domain; Members of this family of viral protein domains ...
 2-96 1.10e-60

Transcription factor MotA, activation domain; Members of this family of viral protein domains are implicated in transcriptional activation. They are almost completely alpha-helical, with five alpha-helices and a short, two-stranded, beta-ribbon. Four alpha helices (alpha1, alpha3, alpha4 and alpha5) are amphipathic and pack their hydrophobic surfaces around the central helix alpha2.


Pssm-ID: 312591  Cd Length: 95  Bit Score: 184.54  E-value: 1.10e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330858776    2 SKVTYIIKASNDVLNEKTAAILITIAKKDFITAAEVREVHPDLGNAVVNSNIGVLIKKGLVEKSGDGLIITGEAQDIISN 81
Cdd:pfam09114   1 SKVTYIIKASNDVLNEKTATILITIAKKDFITAAEVREVHPDLGNAVVNSNIGVLIKKGLVEKSGDGLIITGEAQDIISN 80

                          90
                  ....*....|....*
gi 330858776   82 AATLYAQENAPELLK 96
Cdd:pfam09114  81 AATLYAQENAPELLK 95
 
Name Accession Description Interval E-value
MotCF pfam09158
Bacteriophage T4 MotA, C-terminal; Members of this family adopt a compact alpha/beta structure ...
 106-208 2.87e-65

Bacteriophage T4 MotA, C-terminal; Members of this family adopt a compact alpha/beta structure comprising three alpha-helices and six beta-strands in the order: alpha1-beta1-beta2-beta3-beta4-alpha2-beta5-beta6-alpha3. The beta-strands form a single anti-parallel beta-sheet and the three alpha-helices pack side-by-side onto one surface of the beta-sheet. In this architecture, the domain's hydrophobic core is at the sheet-helix interface, and the second surface of the beta-sheet is completely exposed. The domain is a DNA-binding motif, with a consensus sequence containing nine base pairs (5'-TTTGCTTTA-3'), that appears to bind to various mot boxes, allowing access to the minor groove towards the 5'-end of this sequence and the major groove towards the 3'-end.


Pssm-ID: 286268  Cd Length: 103  Bit Score: 196.78  E-value: 2.87e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330858776  106 ITSDMEEDKDFMLKLLDENGFVLKKVETYRSNYLAILEKRTHGIRNFEINNNGNMRIFGYKMMEHHIQKFTDIGMSCKIA 185
Cdd:pfam09158   1 ITSDMEEDKDLMLKLLDKNGFVLKKVEIYRSNYLAILEKRTNGIRNFEINNNGNMRIFGYKMMEHHIQKFTDIGMSCKIA 80

                          90       100
                  ....*....|....*....|...
gi 330858776  186 KNGNVYLDIKRSAENIEAVITVA 208
Cdd:pfam09158  81 KNGNVYLDIKRSAENIEAVITVA 103
MotA_activ pfam09114
Transcription factor MotA, activation domain; Members of this family of viral protein domains ...
 2-96 1.10e-60

Transcription factor MotA, activation domain; Members of this family of viral protein domains are implicated in transcriptional activation. They are almost completely alpha-helical, with five alpha-helices and a short, two-stranded, beta-ribbon. Four alpha helices (alpha1, alpha3, alpha4 and alpha5) are amphipathic and pack their hydrophobic surfaces around the central helix alpha2.


Pssm-ID: 312591  Cd Length: 95  Bit Score: 184.54  E-value: 1.10e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330858776    2 SKVTYIIKASNDVLNEKTAAILITIAKKDFITAAEVREVHPDLGNAVVNSNIGVLIKKGLVEKSGDGLIITGEAQDIISN 81
Cdd:pfam09114   1 SKVTYIIKASNDVLNEKTATILITIAKKDFITAAEVREVHPDLGNAVVNSNIGVLIKKGLVEKSGDGLIITGEAQDIISN 80

                          90
                  ....*....|....*
gi 330858776   82 AATLYAQENAPELLK 96
Cdd:pfam09114  81 AATLYAQENAPELLK 95
 
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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