GapMind for catabolism of small carbon sources


Alignments for a candidate for tpi in Magnetospirillum magneticum AMB-1

Align Triosephosphate isomerase; TIM; TPI; EC; Triose-phosphate isomerase (uncharacterized)
to candidate WP_011385082.1 AMB_RS13590 thiazole synthase

Query= curated2:Q9YBR1
         (223 letters)

          Length = 324

 Score = 44.7 bits (104), Expect = 2e-09
 Identities = 42/128 (32%), Positives = 62/128 (48%), Gaps = 18/128 (14%)

           Y ++   +  A +L   G EV+  C+D P +A    L     VA+ P   LIG+G+ +  

             P  I      + +    V VL  AG+    DA  A+ELG  GVL+ +A+  AKDP   

Query: 213 MLELAEAM 220
            + +A AM
Sbjct: 286 -IRMARAM 292

Lambda     K      H
   0.316    0.130    0.359 

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: 135
Number of extensions: 10
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: 223
Length of database: 324
Length adjustment: 25
Effective length of query: 198
Effective length of database: 299
Effective search space:    59202
Effective search space used:    59202
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 47 (22.7 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