GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__psRCH2:GFF18
          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.

Links

Downloads

Related tools

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