GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapM in Escherichia coli BW25113

Align AapM, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized)
to candidate 16032 b1918 predicted transporter subunit: membrane component of ABC superfamily (NCBI)

Query= TCDB::Q52814
         (384 letters)



>FitnessBrowser__Keio:16032
          Length = 222

 Score =  115 bits (287), Expect = 2e-30
 Identities = 74/206 (35%), Positives = 108/206 (52%), Gaps = 8/206 (3%)

Query: 174 GLMVTLVLSFVGIAVSLPVGILLALGRRSRMPVIRMLCVTFIEVIRGVPLITVLFMASVM 233
           G   TL LS  G+   L +G +LAL R S +  +R L   +I + RG PLI  LFM    
Sbjct: 18  GAGYTLQLSIGGMFFGLLLGFILALMRLSPIWPVRWLARFYISIFRGTPLIAQLFMIYYG 77

Query: 234 LPLFLPTGWNVDKLLRALIGVSIFTSAYMAEVIRGGLQAIPKGQFEGADSLGLGYWQKTR 293
           LP F   G  +D +  A+IG+S+ T+AY AE +R  + +I KGQ+E A S+G+  WQ  R
Sbjct: 78  LPQF---GIELDPIPSAMIGLSLNTAAYAAETLRAAISSIDKGQWEAAASIGMTPWQTMR 134

Query: 294 LIIMPQAIKLVIPSIVNTFIGTFKDTSLVTIIGMFDLLGIVKLNFSDANWASAVTPITGL 353
             I+PQA ++ +P + N+FI   KDTSL   I + +L    +L  S       +   T  
Sbjct: 135 RAILPQAARVALPPLSNSFISLVKDTSLAATIQVPELFRQAQLITS-----RTLEVFTMY 189

Query: 354 IFAGFIFWLFCFGMSRYSGFMERHLD 379
           + A  I+W+    +S      E  L+
Sbjct: 190 LAASLIYWIMATVLSTLQNHFENQLN 215


Lambda     K      H
   0.330    0.145    0.469 

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: 210
Number of extensions: 6
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: 384
Length of database: 222
Length adjustment: 26
Effective length of query: 358
Effective length of database: 196
Effective search space:    70168
Effective search space used:    70168
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 (21.8 bits)
S2: 48 (23.1 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