GapMind for catabolism of small carbon sources

 

Protein WP_011384701.1 in Magnetospirillum magneticum AMB-1

Annotation: AMB_RS11645 propionyl-CoA synthetase

Length: 638 amino acids

Source: GCF_000009985.1 in NCBI

Candidate for 10 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
propionate catabolism prpE hi Propionate--CoA ligase (EC 6.2.1.17) (characterized) 65% 100% 864.4 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) 41% 472.6
4-hydroxybenzoate catabolism acs med propionate-CoA ligase (EC 6.2.1.17) (characterized) 54% 92% 710.3 Propionate--CoA ligase (EC 6.2.1.17) 65% 864.4
L-lactate catabolism acs med propionate-CoA ligase (EC 6.2.1.17) (characterized) 54% 92% 710.3 Propionate--CoA ligase (EC 6.2.1.17) 65% 864.4
acetate catabolism acs med propionate-CoA ligase (EC 6.2.1.17) (characterized) 54% 92% 710.3 Propionate--CoA ligase (EC 6.2.1.17) 65% 864.4
2'-deoxyinosine catabolism acs med propionate-CoA ligase (EC 6.2.1.17) (characterized) 54% 92% 710.3 Propionate--CoA ligase (EC 6.2.1.17) 65% 864.4
2-deoxy-D-ribose catabolism acs med propionate-CoA ligase (EC 6.2.1.17) (characterized) 54% 92% 710.3 Propionate--CoA ligase (EC 6.2.1.17) 65% 864.4
ethanol catabolism acs med propionate-CoA ligase (EC 6.2.1.17) (characterized) 54% 92% 710.3 Propionate--CoA ligase (EC 6.2.1.17) 65% 864.4
L-threonine catabolism acs med propionate-CoA ligase (EC 6.2.1.17) (characterized) 54% 92% 710.3 Propionate--CoA ligase (EC 6.2.1.17) 65% 864.4
thymidine catabolism acs med propionate-CoA ligase (EC 6.2.1.17) (characterized) 54% 92% 710.3 Propionate--CoA ligase (EC 6.2.1.17) 65% 864.4
L-tryptophan catabolism acs med propionate-CoA ligase (EC 6.2.1.17) (characterized) 54% 92% 710.3 Propionate--CoA ligase (EC 6.2.1.17) 65% 864.4

Sequence Analysis Tools

View WP_011384701.1 at NCBI

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

MTNAYQQAYEKSLKDPEGFWGEAAKEIHWYKTWDKVLDDSKKPFYRWFVGAETNTCYNAV
DRHVEQGRGAQTAIIYDSPVTSTKRKISYDELKDQVSRLAGAMAALGVAKGDRVLLYMPM
VPEAVVGMLAVARLGAIHSVVFGGFAPAELATRINDAKPKVILSASCGIEGSRVIAYKPM
LDEAIALSEHKPGHTIMLQRPQSVAVMDKAGDLDWTEVCAKAKPADCVPVLATDPLYILY
TSGTTGQPKGVVRDNGGHMVALMWSMKYVYDIKPGEVFWAASDVGWVVGHSYICYAPLLN
GSTTVVYEGKPVGTPDAGAFWRMISEYKMASLFTAPTAFRAIKREDPNGELLKKYDLTGF
RALFLAGERSDPDTINWAREKLKVPVVDHWWQTETGWAIAANCLGLHEFPIKPGSPTKPV
PGWGLEVLDEGHQPCEAGKVGSLVVRLPLPPGALLTLWNADQRCIDSYYSEFPGCYKTAD
AGMIDEDGYAYIMSRTDDIINVAGHRLSTGGMEEVLASHPDVAECAVIGVADQLKGQLPL
GFICLKAGVTKPHDQVIAEVVKLVREKIGPVAAFKTCTVVNRLPKTRSGKILRGTMQKIA
DNQDFKMPATIDDPSILDEIGESLESVGYAKARKEAVE

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