GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aapM in Pseudomonas stutzeri RCH2

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 GFF18 Psest_0018 ectoine/hydroxyectoine ABC transporter, permease protein EhuC

Query= TCDB::Q52814
         (384 letters)



>lcl|FitnessBrowser__psRCH2:GFF18 Psest_0018 ectoine/hydroxyectoine
           ABC transporter, permease protein EhuC
          Length = 219

 Score = 94.4 bits (233), Expect = 3e-24
 Identities = 54/157 (34%), Positives = 89/157 (56%), Gaps = 1/157 (0%)

Query: 174 GLMVTLVLSFVGIAVSLPVGILLALGRRSRMPVIRMLCVTFIEVIRGVPLITVLFMASVM 233
           G  VT+ ++F G  +++   ++ AL R S +  +R L +T+IEV RG  L+  LF    +
Sbjct: 11  GAWVTVKVTFFGSLLAIACALIAALARLSPVAPLRWLAITYIEVFRGSSLLVQLFWLYFV 70

Query: 234 LPLFLPTGWNVDKLLRALIGVSIFTSAYMAEVIRGGLQAIPKGQFEGADSLGLGYWQKTR 293
           LP+  P    +     A++G+ +   AY AEV+RG ++++ +GQ E   +L +    + R
Sbjct: 71  LPM-PPFNIEMSAFAVAVVGLGLNIGAYGAEVLRGAIRSVHRGQHEACQALNMTPLTRMR 129

Query: 294 LIIMPQAIKLVIPSIVNTFIGTFKDTSLVTIIGMFDL 330
            II+PQA+   IP   N  I   K+TSLV++I + DL
Sbjct: 130 RIILPQALLAAIPPGTNLLIELLKNTSLVSLITLSDL 166


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: 203
Number of extensions: 9
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: 219
Length adjustment: 26
Effective length of query: 358
Effective length of database: 193
Effective search space:    69094
Effective search space used:    69094
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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