GapMind for Amino acid biosynthesis

 

Protein WP_057508832.1 in Stenotrophomonas chelatiphaga DSM 21508

Annotation: NCBI__GCF_001431535.1:WP_057508832.1

Length: 425 amino acids

Source: GCF_001431535.1 in NCBI

Candidate for 5 steps in Amino acid biosynthesis

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-phenylalanine biosynthesis ptransferase lo aspartate transaminase (EC 2.6.1.1); aspartate-prephenate aminotransferase (EC 2.6.1.78); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized) 31% 99% 186 valine-3-methyl-2-oxovalerate transaminase (EC 2.6.1.32) 45% 345.5
L-tyrosine biosynthesis ptransferase lo aspartate transaminase (EC 2.6.1.1); aspartate-prephenate aminotransferase (EC 2.6.1.78); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized) 31% 99% 186 valine-3-methyl-2-oxovalerate transaminase (EC 2.6.1.32) 45% 345.5
L-lysine biosynthesis lysN lo Aspartate aminotransferase; AAT; AspAT; Putative 2-aminoadipate transaminase; Transaminase A; EC 2.6.1.1; EC 2.6.1.39 (characterized) 31% 96% 175.6 valine-3-methyl-2-oxovalerate transaminase (EC 2.6.1.32) 45% 345.5
L-lysine biosynthesis dapX lo Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized) 31% 96% 163.7 valine-3-methyl-2-oxovalerate transaminase (EC 2.6.1.32) 45% 345.5
L-histidine biosynthesis hisC lo Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized) 31% 56% 79 valine-3-methyl-2-oxovalerate transaminase (EC 2.6.1.32) 45% 345.5

Sequence Analysis Tools

View WP_057508832.1 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

MSTPTPKPLAIRERLSEVRYEIRGELARRARELEAQGRTLIKLNIGNPGNFGFRAPEHLQ
RAIADDMGRTDPYTHQQGLPEAREAIAAAYARRGAPDAHPDRVFIGNGVSELIDLSLRAL
LNPGDEVLVPSPDYPLWSAATILNDGRPVYYRCAPENGFQPDPSEIEALVSSRTRAIVLI
NPNNPSGASYSRELLERIVAIARKHNLLLMVDEIYDQILYDDAVFQPVAPLAGDQPCITF
SGLSKVHRACGWRVGWAMLSGDAGRLGEFRAAMDLLSALRLCANVPGQYAIDAAVNGPDT
ITPLCTPGGRLYETRRAVIDACAASEHLSLVAPAGALYAFPAVVGDAAKGLDDHDFALDL
MTDEGVLVVPGSSFNVPYRHHFRVTLLPEATVMREVFSRIDRALARRAEANRKVVPLKPR
RSAVA

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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