GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mcm-small in Acidovorax sp. GW101-3H11

Align methylmalonyl-CoA mutase (subunit 1/2) (EC 5.4.99.2) (characterized)
to candidate Ac3H11_2278 Methylmalonyl-CoA mutase (EC 5.4.99.2)

Query= BRENDA::O58013
         (147 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2278
          Length = 722

 Score =  110 bits (274), Expect = 6e-29
 Identities = 57/131 (43%), Positives = 83/131 (63%), Gaps = 7/131 (5%)

Query: 11  RVLVAKPGLDGHDRGAKVVARALRDAGYEVIYTGIRQTPEQIVEAVIEEDVDVLGISILS 70
           RV++AK G DGHDRGAKVVA A  D G++V    + QTPE+     IE DV  +G+S L+
Sbjct: 594 RVMIAKLGQDGHDRGAKVVATAFADLGFDVDMGPLFQTPEECARQAIENDVHAVGVSTLA 653

Query: 71  GAHMVLIPKILKLLEEKGIKVNEDVLVVAGGIIPPDDAEELKKMGVAEVFGPGTPL---- 126
             H  L+P I++ L ++G    +D++V  GG+IP  D + L + GV  V+GPGTP+    
Sbjct: 654 AGHKTLVPAIIQSLRDQGA---DDIIVFVGGVIPAQDYDFLYESGVKGVYGPGTPIPASA 710

Query: 127 REIIEFIDKNV 137
           ++++E I K V
Sbjct: 711 KDVLEQIRKAV 721


Lambda     K      H
   0.318    0.140    0.383 

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: 186
Number of extensions: 7
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: 722
Length adjustment: 27
Effective length of query: 120
Effective length of database: 695
Effective search space:    83400
Effective search space used:    83400
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.

Links

Downloads

Related tools

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