GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapM in Rhizorhabdus wittichii RW1

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 WP_012048835.1 SWIT_RS13330 ABC transporter permease subunit

Query= TCDB::Q52814
         (384 letters)



>NCBI__GCF_000016765.1:WP_012048835.1
          Length = 374

 Score = 75.1 bits (183), Expect = 3e-18
 Identities = 33/85 (38%), Positives = 58/85 (68%)

Query: 246 KLLRALIGVSIFTSAYMAEVIRGGLQAIPKGQFEGADSLGLGYWQKTRLIIMPQAIKLVI 305
           + +  L G  I+ SA+ AE++RGGL  +P+GQ+E + +LGL   Q  RL+I+PQA+++++
Sbjct: 242 EFVAVLWGSVIYASAFAAEIVRGGLDGVPRGQWEASRALGLSKRQSLRLVIVPQALRMIV 301

Query: 306 PSIVNTFIGTFKDTSLVTIIGMFDL 330
           P + + FI   K+++L  ++G  DL
Sbjct: 302 PPMNSQFITILKNSTLALVVGYPDL 326



 Score = 38.1 bits (87), Expect = 4e-07
 Identities = 23/67 (34%), Positives = 38/67 (56%), Gaps = 1/67 (1%)

Query: 174 GLMVTLVLSFVGIAVSLPVGILLALGRRSRMPVIRMLCVTFIEVIRGVPLIT-VLFMASV 232
           GL  ++ L+ + I +S   G+ +AL R S   + R L   F++++R VPL+  +LF   V
Sbjct: 78  GLGNSIALTLLIIVLSTMAGVPIALARHSGHMLARTLAGGFVDLVRNVPLVVQLLFWYGV 137

Query: 233 MLPLFLP 239
           +L  F P
Sbjct: 138 ILMAFPP 144


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: 388
Number of extensions: 17
Number of successful extensions: 2
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: 384
Length of database: 374
Length adjustment: 30
Effective length of query: 354
Effective length of database: 344
Effective search space:   121776
Effective search space used:   121776
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: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. 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