GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mcm-small in Burkholderia phytofirmans PsJN

Align methylmalonyl-CoA mutase (subunit 1/2) (EC 5.4.99.2) (characterized)
to candidate BPHYT_RS02305 BPHYT_RS02305 methionine synthase

Query= BRENDA::A4YIE3
         (155 letters)



>FitnessBrowser__BFirm:BPHYT_RS02305
          Length = 902

 Score = 40.8 bits (94), Expect = 6e-08
 Identities = 27/91 (29%), Positives = 47/91 (51%), Gaps = 3/91 (3%)

Query: 22  KVVVAKLGLDGHDRGAKVIARALKDAGMEVVYTGLRQTPEQIVRTAIQEDADVIGISILS 81
           K+V+A +  D HD G  +++  L+    EVV  G+  +   I+  A  E AD+IG+S L 
Sbjct: 419 KIVIATVKGDVHDIGKNIVSVVLQCNNFEVVNMGVMVSCNDILAKAKVEGADIIGLSGLI 478

Query: 82  GAHLELMPKIVEALKKAG---LDDVGLVLGG 109
              LE M  +   +++     +  + L++GG
Sbjct: 479 TPSLEEMAYVASEMQRDDYFRVKKIPLLIGG 509


Lambda     K      H
   0.319    0.140    0.382 

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: 268
Number of extensions: 15
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: 155
Length of database: 902
Length adjustment: 29
Effective length of query: 126
Effective length of database: 873
Effective search space:   109998
Effective search space used:   109998
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 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