GapMind for catabolism of small carbon sources


Alignments for a candidate for mcm-small in Escherichia coli BW25113

Align methylmalonyl-CoA mutase (subunit 1/2) (EC (characterized)
to candidate 16996 b2917 methylmalonyl-CoA mutase (NCBI)

Query= BRENDA::O58013
         (147 letters)

          Length = 714

 Score =  117 bits (292), Expect = 5e-31
 Identities = 58/130 (44%), Positives = 87/130 (66%), Gaps = 7/130 (5%)

           R+L+AK G DGHDRGAKV+A A  D G++V  + +  TPE+I    +E DV V+G S L+

             H  LIP++++ L++ G    ED+ VVAGG+IPP D   L++ GVA ++GPGTP+    

Query: 127 REIIEFIDKN 136
           R+++  I ++
Sbjct: 703 RDVLNLISQH 712

Lambda     K      H
   0.318    0.140    0.383 

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: 176
Number of extensions: 11
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: 147
Length of database: 714
Length adjustment: 27
Effective length of query: 120
Effective length of database: 687
Effective search space:    82440
Effective search space used:    82440
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: 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