GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mcm-small in Bacteroides thetaiotaomicron VPI-5482

Align methylmalonyl-CoA mutase (subunit 1/2) (EC 5.4.99.2) (characterized)
to candidate 349868 BT0340 trimethylamine corrinoid protein 2 (TCP 2) (NCBI ptt file)

Query= BRENDA::O58013
         (147 letters)



>FitnessBrowser__Btheta:349868
          Length = 602

 Score = 54.3 bits (129), Expect = 3e-12
 Identities = 33/82 (40%), Positives = 46/82 (56%), Gaps = 2/82 (2%)

Query: 20  DGHDRGAKVVARALRDAGYEVIYTGIRQTPEQIVEAVIEEDVDVLGISILSGAHMVLIPK 79
           D HD G  +VA  L   G+EVI  GI  T ++ VEAV E   D+L +S L    M  +  
Sbjct: 488 DLHDIGKNLVASMLEGCGFEVINIGIDVTCDKFVEAVKENKADILCMSALLTTTMTYMQD 547

Query: 80  ILKLLEEKGIKVNEDVLVVAGG 101
           +++ LEE GI+  + V V+ GG
Sbjct: 548 VIRALEEAGIR--DQVKVMIGG 567


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: 150
Number of extensions: 7
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: 147
Length of database: 602
Length adjustment: 26
Effective length of query: 121
Effective length of database: 576
Effective search space:    69696
Effective search space used:    69696
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