GapMind for catabolism of small carbon sources

 

Protein HSERO_RS19995 in Herbaspirillum seropedicae SmR1

Annotation: HSERO_RS19995 3-oxoadipate CoA-transferase subunit B

Length: 213 amino acids

Source: HerbieS in FitnessBrowser

Candidate for 8 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
4-hydroxybenzoate catabolism pcaJ hi 3-oxoadipate CoA-transferase (subunit 1/2) (EC 2.8.3.6) (characterized) 79% 97% 334.3 acetyl-CoA:acetoacetate CoA transferase, B subunit (EC 2.8.3.8) 56% 240.7
L-tryptophan catabolism pcaJ hi 3-oxoadipate CoA-transferase (subunit 1/2) (EC 2.8.3.6) (characterized) 79% 97% 334.3 acetyl-CoA:acetoacetate CoA transferase, B subunit (EC 2.8.3.8) 56% 240.7
2-deoxy-D-ribonate catabolism atoD med acetyl-CoA:acetoacetate CoA transferase, B subunit (EC 2.8.3.8) (characterized) 56% 99% 240.7 3-oxoadipate CoA-transferase (subunit 1/2) (EC 2.8.3.6) 79% 334.3
2-deoxy-D-ribose catabolism atoD med acetyl-CoA:acetoacetate CoA transferase, B subunit (EC 2.8.3.8) (characterized) 56% 99% 240.7 3-oxoadipate CoA-transferase (subunit 1/2) (EC 2.8.3.6) 79% 334.3
L-leucine catabolism atoD med acetyl-CoA:acetoacetate CoA transferase, B subunit (EC 2.8.3.8) (characterized) 56% 99% 240.7 3-oxoadipate CoA-transferase (subunit 1/2) (EC 2.8.3.6) 79% 334.3
L-phenylalanine catabolism atoD med acetyl-CoA:acetoacetate CoA transferase, B subunit (EC 2.8.3.8) (characterized) 56% 99% 240.7 3-oxoadipate CoA-transferase (subunit 1/2) (EC 2.8.3.6) 79% 334.3
L-tyrosine catabolism atoD med acetyl-CoA:acetoacetate CoA transferase, B subunit (EC 2.8.3.8) (characterized) 56% 99% 240.7 3-oxoadipate CoA-transferase (subunit 1/2) (EC 2.8.3.6) 79% 334.3
L-lysine catabolism ctfB med Butyrate--acetoacetate CoA-transferase subunit B; Short=Coat B; EC 2.8.3.9 (characterized, see rationale) 44% 98% 181 3-oxoadipate CoA-transferase (subunit 1/2) (EC 2.8.3.6) 79% 334.3

Sequence Analysis Tools

View HSERO_RS19995 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MKRFTREEIAARVAQDIPEGAYVNLGIGLPTKVANYLPADKEIFLHSENGVLGMGPAPAP
GEEDEDLINAGKQPVTLLTGGAYFHHADSFAMMRGGHLDICVLGAFQVSAKGDLANWHTG
APDAIPAVGGAMDLAIGAKQVFVMMDHQTKTGESKLVEACSYPLTGIGCVNRIYTDLAVI
DVTPHGLQVREIVEGLSFDELQKLTGAPLRPAA

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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