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Conserved domains on  [gi|1469304866|ref|WP_117646379|]
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MULTISPECIES: hypothetical protein [Collinsella]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
MreD super family cl01087
rod shape-determining protein MreD; MreD (murein formation D) is involved in the rod shape ...
 12-156 4.29e-04

rod shape-determining protein MreD; MreD (murein formation D) is involved in the rod shape determination in E. coli, and more generally in cell shape determination of bacteria whether or not they are rod-shaped.


The actual alignment was detected with superfamily member TIGR03426:

Pssm-ID: 445259  Cd Length: 152  Bit Score: 39.13  E-value: 4.29e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1469304866  12 TFVIAAIVCVLLQAGLAPQISIAGGRVNFMIILVCLSVFSGDPTRAVVCGFCSGLFYDLSAAVPVGVMSLLLTVGSFALV 91
Cdd:TIGR03426   5 LILLSLLLALLLQLIPLPGFFLDGFRPDWVLLVLLYWAIALPHRVGIGTAFVLGLLQDVLSGSPLGVHALALTLVAYLAA 84

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1469304866  92 HSAAGQTGGTPSARGITVGAFAFVINVIYSIILLFMGLETSFVVAIFGHALPSSILTGLVAIPFL 156
Cdd:TIGR03426  85 SLFQRFRQFDLWQQALIIFLLLILGELLVFLILTLLGNAFFSLEYFWLFRLLPTLLLNLLWPWVF 149
 
Name Accession Description Interval E-value
shape_MreD TIGR03426
rod shape-determining protein MreD; Members of this protein family are the MreD protein of ...
 12-156 4.29e-04

rod shape-determining protein MreD; Members of this protein family are the MreD protein of bacterial cell shape determination. Most rod-shaped bacteria depend on MreB and RodA to achieve either a rod shape or some other non-spherical morphology such as coil or stalk formation. MreD is encoded in an operon with MreB, and often with RodA and PBP-2 as well. It is highly hydrophobic (therefore somewhat low-complexity) and highly divergent, and therefore sometimes tricky to discover by homology, but this model finds most examples. [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan]


Pssm-ID: 274574  Cd Length: 152  Bit Score: 39.13  E-value: 4.29e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1469304866  12 TFVIAAIVCVLLQAGLAPQISIAGGRVNFMIILVCLSVFSGDPTRAVVCGFCSGLFYDLSAAVPVGVMSLLLTVGSFALV 91
Cdd:TIGR03426   5 LILLSLLLALLLQLIPLPGFFLDGFRPDWVLLVLLYWAIALPHRVGIGTAFVLGLLQDVLSGSPLGVHALALTLVAYLAA 84

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1469304866  92 HSAAGQTGGTPSARGITVGAFAFVINVIYSIILLFMGLETSFVVAIFGHALPSSILTGLVAIPFL 156
Cdd:TIGR03426  85 SLFQRFRQFDLWQQALIIFLLLILGELLVFLILTLLGNAFFSLEYFWLFRLLPTLLLNLLWPWVF 149
 
Name Accession Description Interval E-value
shape_MreD TIGR03426
rod shape-determining protein MreD; Members of this protein family are the MreD protein of ...
 12-156 4.29e-04

rod shape-determining protein MreD; Members of this protein family are the MreD protein of bacterial cell shape determination. Most rod-shaped bacteria depend on MreB and RodA to achieve either a rod shape or some other non-spherical morphology such as coil or stalk formation. MreD is encoded in an operon with MreB, and often with RodA and PBP-2 as well. It is highly hydrophobic (therefore somewhat low-complexity) and highly divergent, and therefore sometimes tricky to discover by homology, but this model finds most examples. [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan]


Pssm-ID: 274574  Cd Length: 152  Bit Score: 39.13  E-value: 4.29e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1469304866  12 TFVIAAIVCVLLQAGLAPQISIAGGRVNFMIILVCLSVFSGDPTRAVVCGFCSGLFYDLSAAVPVGVMSLLLTVGSFALV 91
Cdd:TIGR03426   5 LILLSLLLALLLQLIPLPGFFLDGFRPDWVLLVLLYWAIALPHRVGIGTAFVLGLLQDVLSGSPLGVHALALTLVAYLAA 84

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1469304866  92 HSAAGQTGGTPSARGITVGAFAFVINVIYSIILLFMGLETSFVVAIFGHALPSSILTGLVAIPFL 156
Cdd:TIGR03426  85 SLFQRFRQFDLWQQALIIFLLLILGELLVFLILTLLGNAFFSLEYFWLFRLLPTLLLNLLWPWVF 149
 
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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