GapMind for catabolism of small carbon sources

 

Alignments for a candidate for snatA in Escherichia coli BW25113

Align The SnatA carrier. Transports glycine, L-alanine, L-serine, L-threonine and a variety of neutral L-amino acids (characterized)
to candidate 15362 b1242 predicted inner membrane protein (NCBI)

Query= TCDB::Q8J305
         (216 letters)



>FitnessBrowser__Keio:15362
          Length = 215

 Score =  130 bits (328), Expect = 1e-35
 Identities = 71/198 (35%), Positives = 113/198 (57%), Gaps = 4/198 (2%)

Query: 17  GLFAITNPVGAVPVFLSVTHDLSWRERREIASKTAISVVATLVVFALLGQWIFKFFGSST 76
           GLFA+ NPVG +PVF+S+T   +   R +      +SV   L +   LG  I + FG S 
Sbjct: 17  GLFALVNPVGIIPVFISMTSYQTAAARNKTNLTANLSVAIILWISLFLGDTILQLFGISI 76

Query: 77  DAFAIAGGILLFRMALDMLSGKLSSVKISNEETEEFSEEVVTLEEVAIIPLAIPLISGPG 136
           D+F IAGGIL+  +A+ M+SGKL   K + +E      E    E + ++PLA+PL++GPG
Sbjct: 77  DSFRIAGGILVVTIAMSMISGKLGEDKQNKQE----KSETAVRESIGVVPLALPLMAGPG 132

Query: 137 AITTVMLYMAKSTTNLQRLAVILTIILIGITVWFVLCSANRIKARLGRVGIKVMTRMMGL 196
           AI++ +++  +  +        + I L  +  W +   A  +   L + GI V+TR+MGL
Sbjct: 133 AISSTIVWGTRYHSISYLFGFFVAIALFALCCWGLFRMAPWLVRVLRQTGINVITRIMGL 192

Query: 197 ILTSMAVQMIINGIKGAF 214
           +L ++ ++ I+ GIKG F
Sbjct: 193 LLMALGIEFIVTGIKGIF 210


Lambda     K      H
   0.327    0.141    0.396 

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: 137
Number of extensions: 5
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 216
Length of database: 215
Length adjustment: 22
Effective length of query: 194
Effective length of database: 193
Effective search space:    37442
Effective search space used:    37442
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: 45 (21.9 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