GapMind for Amino acid biosynthesis

 

Protein BWI76_RS26375 in Klebsiella michiganensis M5al

Annotation: FitnessBrowser__Koxy:BWI76_RS26375

Length: 421 amino acids

Source: Koxy in FitnessBrowser

Candidate for 7 steps in Amino acid biosynthesis

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine biosynthesis argD med 4-aminobutyrate aminotransferase GabT; (S)-3-amino-2-methylpropionate transaminase; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT; EC 2.6.1.19; EC 2.6.1.22 (characterized) 58% 98% 475.3 4-aminobutyrate aminotransferase PuuE; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; EC 2.6.1.19 76% 651.4
L-proline biosynthesis argD med 4-aminobutyrate aminotransferase GabT; (S)-3-amino-2-methylpropionate transaminase; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT; EC 2.6.1.19; EC 2.6.1.22 (characterized) 58% 98% 475.3 4-aminobutyrate aminotransferase PuuE; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; EC 2.6.1.19 76% 651.4
L-lysine biosynthesis lysN med 2-aminoadipate transaminase (2.6.1.39) (characterized) 42% 99% 336.7 4-aminobutyrate aminotransferase PuuE; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; EC 2.6.1.19 76% 651.4
L-lysine biosynthesis dapC lo Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (uncharacterized) 37% 92% 253.4 4-aminobutyrate aminotransferase PuuE; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; EC 2.6.1.19 76% 651.4
L-arginine biosynthesis argD'B lo Succinylornithine transaminase; EC 2.6.1.81; Succinylornithine aminotransferase (uncharacterized) 38% 90% 238.4 4-aminobutyrate aminotransferase PuuE; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; EC 2.6.1.19 76% 651.4
glycine biosynthesis agx1 lo Alanine--glyoxylate aminotransferase 2 homolog 2, mitochondrial; Beta-alanine-pyruvate aminotransferase 2; EC 2.6.1.44 (characterized) 35% 86% 214.9 4-aminobutyrate aminotransferase PuuE; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; EC 2.6.1.19 76% 651.4
L-proline biosynthesis OAT lo ornithine aminotransferase (EC 2.6.1.13) (characterized) 34% 80% 214.5 4-aminobutyrate aminotransferase PuuE; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; EC 2.6.1.19 76% 651.4

Sequence Analysis Tools

View BWI76_RS26375 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

MKSSELNQRRQQATPRGVGVMCSYFVEKAENATLWDIEGNEVIDFAAGIAVLNTGHRHPK
IIAAVEQQLQAFTHTAYQIVPYESYVTLAERINALAPIDGPAKTAFFTTGAEAVENAVKI
ARAYTGRPGLITFGGGFHGRTFMTMALTGKVAPYKIGFGPFPGSVYHAVYPNAAHGITTA
DAMKSLDRIFKADIAADQVAAIVLEPIQGEGGFNVAPPEFMQALRALCDTHGILLIADEV
QTGFARTGKLFAMQHYDVKPDLMTMAKSLAGGFPLSGVVGRAEVMDAPAPGGLGGTYAGN
PLAVAAAHAVLDVIEEEQLCQRAERLGSHLKEVLNQARQSCPAIADVRGQGSMVAVEFND
PQTGEPSAEITRQIQQKAQENGLLLLSCGVYGNVIRFLYPLTIPDAQFTKALDILARVLK
P

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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