GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapM in Paraburkholderia phymatum STM815

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_012404721.1 BPHY_RS27410 amino acid ABC transporter permease

Query= TCDB::Q52814
         (384 letters)



>NCBI__GCF_000020045.1:WP_012404721.1
          Length = 219

 Score =  110 bits (276), Expect = 3e-29
 Identities = 67/211 (31%), Positives = 110/211 (52%), Gaps = 8/211 (3%)

Query: 174 GLMVTLVLSFVGIAVSLPVGILLALGRRSRMPVIRMLCVTFIEVIRGVPLITVLFMASVM 233
           G MVTL  +     + L VG ++A+   S  P+I  +   ++ ++RG PL+  +F+    
Sbjct: 17  GAMVTLKFALASAVLGLLVGFIVAIMGISGQPIIAGIARAYVSLMRGTPLLVQIFVVYYG 76

Query: 234 LPLFLPTGWNVDKLLRALIGVSIFTSAYMAEVIRGGLQAIPKGQFEGADSLGLGYWQKTR 293
           LP     G ++D     ++ ++    AY++E +RG +  I +GQ+  A SLGL + Q  R
Sbjct: 77  LP---DLGISLDPTSAGILALTANAGAYLSESMRGAILGISQGQWGAAHSLGLTHMQTLR 133

Query: 294 LIIMPQAIKLVIPSIVNTFIGTFKDTSLVTIIGMFDLLGIVKLNFSDANWASAVTPITGL 353
            +I PQA+++ +PS+ NT I   KDTSLV++I + ++     L  +    AS   P+   
Sbjct: 134 YVICPQALRMAVPSLGNTLISLIKDTSLVSVITVTEM-----LRAAQEVIASTFQPLPLY 188

Query: 354 IFAGFIFWLFCFGMSRYSGFMERHLDTGHKR 384
           + A  I+WL   GMS     +E  L   H R
Sbjct: 189 LAAAAIYWLLSTGMSWVQRHVEVRLARAHVR 219


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: 226
Number of extensions: 13
Number of successful extensions: 3
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 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