GapMind for catabolism of small carbon sources


Alignments for a candidate for bgtB' in Burkholderia phytofirmans PsJN

Align ABC-type permease for basic amino acids and glutamine (characterized, see rationale)
to candidate BPHYT_RS13290 BPHYT_RS13290 cysteine ABC transporter permease

Query= uniprot:Q31RP0
         (377 letters)

          Length = 225

 Score = 95.9 bits (237), Expect = 9e-25
 Identities = 46/128 (35%), Positives = 80/128 (62%)

           TA ++G     GA+ +E+IRG I S+P GQWEAA ++G+TR Q L + ++PQA RV +P 

           L++ ++   K++SLA  +  P+++  AQ   + T  P+ ++    L YL  ++V+S+   

Query: 366 GLQQRLQR 373
            L+++  R
Sbjct: 210 RLERKFGR 217

Lambda     K      H
   0.326    0.140    0.445 

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: 208
Number of extensions: 6
Number of successful extensions: 1
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: 377
Length of database: 225
Length adjustment: 26
Effective length of query: 351
Effective length of database: 199
Effective search space:    69849
Effective search space used:    69849
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 (21.7 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