GapMind for catabolism of small carbon sources

 

Protein GFF2607 in Pseudomonas stutzeri RCH2

Annotation: Psest_2657 acetate--CoA ligase

Length: 651 amino acids

Source: psRCH2 in FitnessBrowser

Candidate for 11 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
4-hydroxybenzoate catabolism acs hi Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized) 82% 100% 1132.1
4-hydroxybenzoate catabolism acs hi acs: acetate--CoA ligase (EC 6.2.1.1) (TIGR02188) 99% 1005.3
L-lactate catabolism acs hi Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized) 82% 100% 1132.1
L-lactate catabolism acs hi acs: acetate--CoA ligase (EC 6.2.1.1) (TIGR02188) 99% 1005.3
acetate catabolism acs hi Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized) 82% 100% 1132.1
acetate catabolism acs hi acs: acetate--CoA ligase (EC 6.2.1.1) (TIGR02188) 99% 1005.3
2'-deoxyinosine catabolism acs hi Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized) 82% 100% 1132.1
2'-deoxyinosine catabolism acs hi acs: acetate--CoA ligase (EC 6.2.1.1) (TIGR02188) 99% 1005.3
2-deoxy-D-ribose catabolism acs hi Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized) 82% 100% 1132.1
2-deoxy-D-ribose catabolism acs hi acs: acetate--CoA ligase (EC 6.2.1.1) (TIGR02188) 99% 1005.3
ethanol catabolism acs hi Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized) 82% 100% 1132.1
ethanol catabolism acs hi acs: acetate--CoA ligase (EC 6.2.1.1) (TIGR02188) 99% 1005.3
L-threonine catabolism acs hi Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized) 82% 100% 1132.1
L-threonine catabolism acs hi acs: acetate--CoA ligase (EC 6.2.1.1) (TIGR02188) 99% 1005.3
thymidine catabolism acs hi Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized) 82% 100% 1132.1
thymidine catabolism acs hi acs: acetate--CoA ligase (EC 6.2.1.1) (TIGR02188) 99% 1005.3
L-tryptophan catabolism acs hi Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized) 82% 100% 1132.1
L-tryptophan catabolism acs hi acs: acetate--CoA ligase (EC 6.2.1.1) (TIGR02188) 99% 1005.3
propionate catabolism prpE hi Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized) 66% 98% 912.5
4-hydroxybenzoate catabolism hcl lo Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized) 30% 66% 131.7 Acetyl-coenzyme A synthetase (EC 6.2.1.1) 82% 1132.1

Sequence Analysis Tools

View GFF2607 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: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MCAASVYPVSPEAAKHSLTDEAAYRAMYQQSVINPEGFWREQAARLNWIRPFTEVKRTSF
DDHHVDIKWFADGTLNVSANCLDRHLAERGDQVAIIWEGDEPSEHREITYRELYQEVCKF
ANALRGQDVHRGDVVTIYMPMIPEAAVAMLACARIGAIHSVVFGGFSPEALAGRIIDGQS
KVVITADEGIRGGKPIPLKENVDEALTHPQTRCVQKIIVVRRTGADIRWHPHRDVCYDDL
MRVAGEVCAPKEMGAEEPLFILYTSGSTGKPKGVLHTCGGYLLYAALTHERVFDYRPGDV
YWCTADIGWITGHSYLIYGPLANGATTLMYEGVPNYPDVTRIARIIDKHRVNILYTAPTA
IRAMMAEGAAAMEGADGSSLRLLGTVGEPINPEAWHWYYETVGRSRCPIVDTWWQTETGG
ILISPLPGATALKPGSATRPLFGVVPGLVDNLGNLLEGPAEGNLVILDSWPGQMRTIYRD
HDRFVDTYFKTFRGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHA
KVAEAAAVGVPHALKGQAIYVYVTLVAGVEPSDTLRQELQQWVRHEIGPIAVPDTIQWAP
GLPKTRSGKIMRRLLRKIATDDYDALGDTSTLADPGVVDQLIEAHEAVKQR

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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