GapMind for catabolism of small carbon sources

 

Protein WP_048508309.1 in Chryseobacterium angstadtii KM

Annotation: NCBI__GCF_001045465.1:WP_048508309.1

Length: 415 amino acids

Source: GCF_001045465.1 in NCBI

Candidate for 17 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism rocD hi Ornithine aminotransferase (EC 2.6.1.13) (characterized) 70% 98% 595.5 ornithine aminotransferase 54% 473.0
L-arginine catabolism rocD med rocD: ornithine--oxo-acid transaminase (EC 2.6.1.13) (TIGR01885) 100% 674.3 ornithine aminotransferase 54% 473.0
L-citrulline catabolism rocD hi Ornithine aminotransferase (EC 2.6.1.13) (characterized) 70% 98% 595.5 ornithine aminotransferase 54% 473.0
L-citrulline catabolism rocD med rocD: ornithine--oxo-acid transaminase (EC 2.6.1.13) (TIGR01885) 100% 674.3 ornithine aminotransferase 54% 473.0
L-arginine catabolism astC lo succinylornithine transaminase (EC 2.6.1.81) (characterized) 34% 96% 246.9 Ornithine aminotransferase (EC 2.6.1.13) 70% 595.5
L-citrulline catabolism astC lo succinylornithine transaminase (EC 2.6.1.81) (characterized) 34% 96% 246.9 Ornithine aminotransferase (EC 2.6.1.13) 70% 595.5
L-arginine catabolism gabT lo Probable 4-aminobutyrate aminotransferase; EC 2.6.1.19; (S)-3-amino-2-methylpropionate transaminase; EC 2.6.1.22; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT (uncharacterized) 32% 91% 223.8 Ornithine aminotransferase (EC 2.6.1.13) 70% 595.5
L-arginine catabolism patA lo Putrescine aminotransferase; PAT; PATase; EC 2.6.1.82; Cadaverine transaminase; EC 2.6.1.-; Putrescine transaminase; Putrescine--2-oxoglutaric acid transaminase (uncharacterized) 34% 82% 223.8 Ornithine aminotransferase (EC 2.6.1.13) 70% 595.5
L-citrulline catabolism gabT lo Probable 4-aminobutyrate aminotransferase; EC 2.6.1.19; (S)-3-amino-2-methylpropionate transaminase; EC 2.6.1.22; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT (uncharacterized) 32% 91% 223.8 Ornithine aminotransferase (EC 2.6.1.13) 70% 595.5
L-citrulline catabolism patA lo Putrescine aminotransferase; PAT; PATase; EC 2.6.1.82; Cadaverine transaminase; EC 2.6.1.-; Putrescine transaminase; Putrescine--2-oxoglutaric acid transaminase (uncharacterized) 34% 82% 223.8 Ornithine aminotransferase (EC 2.6.1.13) 70% 595.5
putrescine catabolism gabT lo Probable 4-aminobutyrate aminotransferase; EC 2.6.1.19; (S)-3-amino-2-methylpropionate transaminase; EC 2.6.1.22; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT (uncharacterized) 32% 91% 223.8 Ornithine aminotransferase (EC 2.6.1.13) 70% 595.5
putrescine catabolism patA lo Putrescine aminotransferase; PAT; PATase; EC 2.6.1.82; Cadaverine transaminase; EC 2.6.1.-; Putrescine transaminase; Putrescine--2-oxoglutaric acid transaminase (uncharacterized) 34% 82% 223.8 Ornithine aminotransferase (EC 2.6.1.13) 70% 595.5
L-lysine catabolism patA lo putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized) 34% 82% 223.4 Ornithine aminotransferase (EC 2.6.1.13) 70% 595.5
L-arginine catabolism davT lo 5-aminovalerate transaminase (EC 2.6.1.48) (characterized) 35% 96% 219.5 Ornithine aminotransferase (EC 2.6.1.13) 70% 595.5
L-citrulline catabolism davT lo 5-aminovalerate transaminase (EC 2.6.1.48) (characterized) 35% 96% 219.5 Ornithine aminotransferase (EC 2.6.1.13) 70% 595.5
L-lysine catabolism davT lo 5-aminovalerate transaminase (EC 2.6.1.48) (characterized) 35% 96% 219.5 Ornithine aminotransferase (EC 2.6.1.13) 70% 595.5
L-proline catabolism davT lo 5-aminovalerate transaminase (EC 2.6.1.48) (characterized) 35% 96% 219.5 Ornithine aminotransferase (EC 2.6.1.13) 70% 595.5
L-lysine catabolism lat lo Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized) 32% 91% 211.5 Ornithine aminotransferase (EC 2.6.1.13) 70% 595.5
L-lysine catabolism lysN lo 2-aminoadipate transaminase (EC 2.6.1.39) (characterized) 33% 97% 193.7 Ornithine aminotransferase (EC 2.6.1.13) 70% 595.5

Sequence Analysis Tools

View WP_048508309.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

Fitness BLAST: loading...

Sequence

MSTAATAKNSQYFIDLEDKHGAHNYHPLPVVLDRGEGVFVWDVEGKKYYDFLSAYSAVNQ
GHSHPKIVAALVDQAQKLALTSRAFYNSKLGEYEQKITTLFGFDKVLPMNSGAEAVETAV
KIARKWSYEVKGISENAAKIIVCENNFHGRTTTIVSFSNDPDANQNYGPFTPGFIKIPYN
DTAALEEVLNREAGNIAAFLVEPIQGEAGVYVPDEGFLKNASELCKKHNVLFIADEVQTG
IARTGQLIACHHENVQPDILILGKALSGGMYPVSAVLANDEIMHVIKPGQHGSTFGGNPI
ACAVAVAALDVVADEKLSERAEQLGQLFRSEIEKIIEKNDLITKVRGKGLLNAILINDTP
DSSTAWNLCLQLKENGLLAKPTHGNIIRLAPPLVITEEQLLDCVRIIEKTITEFR

This GapMind analysis is from Sep 24 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:

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