GapMind for catabolism of small carbon sources

 

Protein 3609962 in Dinoroseobacter shibae DFL-12

Annotation: FitnessBrowser__Dino:3609962

Length: 413 amino acids

Source: Dino in FitnessBrowser

Candidate for 10 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism davT lo 5-aminovalerate transaminase (EC 2.6.1.48) (characterized) 31% 98% 192.6 Ethanolamine-phosphate phospho-lyase; Alanine--glyoxylate aminotransferase 2-like 1; EC 4.2.3.2 38% 280.8
L-citrulline catabolism davT lo 5-aminovalerate transaminase (EC 2.6.1.48) (characterized) 31% 98% 192.6 Ethanolamine-phosphate phospho-lyase; Alanine--glyoxylate aminotransferase 2-like 1; EC 4.2.3.2 38% 280.8
L-lysine catabolism davT lo 5-aminovalerate transaminase (EC 2.6.1.48) (characterized) 31% 98% 192.6 Ethanolamine-phosphate phospho-lyase; Alanine--glyoxylate aminotransferase 2-like 1; EC 4.2.3.2 38% 280.8
L-proline catabolism davT lo 5-aminovalerate transaminase (EC 2.6.1.48) (characterized) 31% 98% 192.6 Ethanolamine-phosphate phospho-lyase; Alanine--glyoxylate aminotransferase 2-like 1; EC 4.2.3.2 38% 280.8
L-arginine catabolism gabT lo 4-aminobutyrate transaminase subunit (EC 2.6.1.19) (characterized) 30% 98% 186.8 Ethanolamine-phosphate phospho-lyase; Alanine--glyoxylate aminotransferase 2-like 1; EC 4.2.3.2 38% 280.8
L-citrulline catabolism gabT lo 4-aminobutyrate transaminase subunit (EC 2.6.1.19) (characterized) 30% 98% 186.8 Ethanolamine-phosphate phospho-lyase; Alanine--glyoxylate aminotransferase 2-like 1; EC 4.2.3.2 38% 280.8
putrescine catabolism gabT lo 4-aminobutyrate transaminase subunit (EC 2.6.1.19) (characterized) 30% 98% 186.8 Ethanolamine-phosphate phospho-lyase; Alanine--glyoxylate aminotransferase 2-like 1; EC 4.2.3.2 38% 280.8
L-lysine catabolism lysN lo 2-aminoadipate transaminase (EC 2.6.1.39) (characterized) 35% 95% 184.9 Ethanolamine-phosphate phospho-lyase; Alanine--glyoxylate aminotransferase 2-like 1; EC 4.2.3.2 38% 280.8
L-arginine catabolism rocD lo Ornithine aminotransferase; OAT; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase (uncharacterized) 32% 95% 176.4 Ethanolamine-phosphate phospho-lyase; Alanine--glyoxylate aminotransferase 2-like 1; EC 4.2.3.2 38% 280.8
L-citrulline catabolism rocD lo Ornithine aminotransferase; OAT; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase (uncharacterized) 32% 95% 176.4 Ethanolamine-phosphate phospho-lyase; Alanine--glyoxylate aminotransferase 2-like 1; EC 4.2.3.2 38% 280.8

Sequence Analysis Tools

View 3609962 at FitnessBrowser

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

MSDLLKRRARLMGPNVPTFYDPPLHIVRGEGVWLWDAGGRRYLDCYNNVPHVGHCHPRVV
DAIARQARVLNTHTRYLHEGVLDYIERLTGTMDNGLDQALLVCTGSEAVDVALRMARAAT
GKTGLIATDNTYHGNTTAVAQLSTRRPPIGGYSDHVRLVPAPEPGTDGAAFGAHVARAAA
ELETAGHGVAALIVCPIFANEGLPCLPRGFLEPAVAALRTRGGLLISDEVQPGFGRLGDV
FWGYQALGIAPDVVTLGKSMGNGYPVAGVVARTEIMGAFREAFGYFNTFGGSPVAAAAAM
AVLDVLEDEGLVENAKRVGRYTLERLQALRHPAIDGVRGYGLAFALDLVDTDGAPNTALA
AAVTEEAKRRSVLINRIGRDMHILKIRPPLPFAPEHGDRLGDVLQAAFDACPR

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:

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