GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglC in Escherichia coli BW25113

Align glucose transporter, permease component (characterized)
to candidate 16645 b2546 predicted sugar transporter subunit: membrane component of ABC superfamily (NCBI)

Query= reanno::Phaeo:GFF3640
         (433 letters)



>FitnessBrowser__Keio:16645
          Length = 332

 Score =  130 bits (326), Expect = 8e-35
 Identities = 93/310 (30%), Positives = 154/310 (49%), Gaps = 31/310 (10%)

Query: 140 VGFLTIPA-----FIVTLGGFLVWRNVAWYLTDGQTIGPLDSTFLVFGGTSGTLGTTLSW 194
           +G L + A     F +   GF+   N    L D  TIG + +  +     SG +  ++  
Sbjct: 27  IGLLVVIAILYLVFSLNAPGFISLNNQMNVLRDAATIG-IAAWAMTLIIISGEIDVSVGP 85

Query: 195 VVGIVATLLALAALWNSRRAKQGHGFPVKPAWAEAVIAGSIAASILG----------FVA 244
           +V  V+  LA    +           P+  A    ++ G++  ++ G          FVA
Sbjct: 86  MVAFVSVCLAFLLQFE---------VPLAVACLLVLLLGALMGTLAGVLRGVFNVPSFVA 136

Query: 245 ILNAYQIPARRLKRMMEAQGETMPEGLVVGY------GLPISVLILIATAVVMTIIARRT 298
            L  +         M  A    + E  V+ +      G+P+S LI+I    +   I+R+T
Sbjct: 137 TLGLWSALRGMGLFMTNALPVPIDENEVLDWLGGQFLGVPVSALIMIVLFALFVFISRKT 196

Query: 299 RLGRYIFATGGNPDAAELSGINTRLLTVKIFALMGFLCALSAVVASARLANHSNDIGTLD 358
             GR +FA GGN  AA+L GIN R + + IF L G L A++ ++ +ARL + +       
Sbjct: 197 AFGRSVFAVGGNATAAQLCGINVRRVRILIFTLSGLLAAVTGILLAARLGSGNAGAANGL 256

Query: 359 ELRVIAAAVIGGTALSGGFGTIYGAILGALIMQSLQSGMAMVGVDAPFQNIVVGTVLVAA 418
           E  VIAA V+GGTALSGG G+++G +LG L++  + +G+ ++G+++ FQ +V G ++V A
Sbjct: 257 EFDVIAAVVVGGTALSGGRGSLFGTLLGVLVITLIGNGLVLLGINSFFQQVVRGVIIVVA 316

Query: 419 VWIDILYRKR 428
           V  +IL  +R
Sbjct: 317 VLANILLTQR 326


Lambda     K      H
   0.327    0.141    0.419 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 400
Number of extensions: 22
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 433
Length of database: 332
Length adjustment: 30
Effective length of query: 403
Effective length of database: 302
Effective search space:   121706
Effective search space used:   121706
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory