GapMind for Amino acid biosynthesis

 

Protein WP_011382998.1 in Magnetospirillum magneticum AMB-1

Annotation: NCBI__GCF_000009985.1:WP_011382998.1

Length: 400 amino acids

Source: GCF_000009985.1 in NCBI

Candidate for 9 steps in Amino acid biosynthesis

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-phenylalanine biosynthesis ilvE hi aspartate transaminase (EC 2.6.1.1); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized) 68% 100% 570.1 2-aminoadipate:2-oxoglutarate aminotransferase (EC 2.6.1.39) 58% 472.2
L-phenylalanine biosynthesis ptransferase hi aspartate transaminase (EC 2.6.1.1); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized) 68% 100% 570.1 2-aminoadipate:2-oxoglutarate aminotransferase (EC 2.6.1.39) 58% 472.2
L-tyrosine biosynthesis ptransferase hi aspartate transaminase (EC 2.6.1.1); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized) 68% 100% 570.1 2-aminoadipate:2-oxoglutarate aminotransferase (EC 2.6.1.39) 58% 472.2
L-tyrosine biosynthesis tyrB hi aspartate transaminase (EC 2.6.1.1); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized) 68% 100% 570.1 2-aminoadipate:2-oxoglutarate aminotransferase (EC 2.6.1.39) 58% 472.2
L-lysine biosynthesis lysN med 2-aminoadipate:2-oxoglutarate aminotransferase (EC 2.6.1.39) (characterized) 58% 97% 472.2 aspartate transaminase (EC 2.6.1.1); glutamate-prephenate aminotransferase (EC 2.6.1.79) 68% 570.1
L-phenylalanine biosynthesis PPYAT lo Aromatic-amino-acid aminotransferase 2; ARAT-II; AROAT; EC 2.6.1.57 (characterized) 37% 99% 258.1 aspartate transaminase (EC 2.6.1.1); glutamate-prephenate aminotransferase (EC 2.6.1.79) 68% 570.1
L-lysine biosynthesis dapX lo Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized) 38% 93% 235.3 aspartate transaminase (EC 2.6.1.1); glutamate-prephenate aminotransferase (EC 2.6.1.79) 68% 570.1
L-methionine biosynthesis metC lo kynurenine-oxoglutarate transaminase (EC 2.6.1.7) (characterized) 30% 98% 179.1 aspartate transaminase (EC 2.6.1.1); glutamate-prephenate aminotransferase (EC 2.6.1.79) 68% 570.1
L-lysine biosynthesis DAPtransferase lo LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized) 31% 98% 172.9 aspartate transaminase (EC 2.6.1.1); glutamate-prephenate aminotransferase (EC 2.6.1.79) 68% 570.1

Sequence Analysis Tools

View WP_011382998.1 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

MPFIADRLSAIKPSPTIAVTQKAAELKAAGRDVIGLGAGEPDFDTPDNIKAAAKAAIDKG
LTKYGPPAGTVDLRQAIAAKFKRENGLDYTADQVTVGVGGKGVIFNAFMATINPGDEVIV
PAPYWVSYPDIALMFGGKPVFVPCPETAGFKLQPADLEKAITPRTKWLVLNSPSNPTGAA
YSWDEMKALTDVLLRHPHVWIMSDDMYEHLVYDDFKFCTPAQVEPKLYDRTLTMNGVSKA
YAMTGWRVGYAAGPAAIIKAINMIQSQSVTHTSSISQAASVEALNGTQDFIPKNAAVFKR
RRDLIVGLLNQCPGITCRTPEGAFYVYPSCAGVIGKKTPDGKVIANDTDFVGALLEAEGV
AVVQGAAFGLEPYFRISYATSDAALTKAAERIKRFCESLK

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