GapMind for Amino acid biosynthesis

 

Protein WP_013707407.1 in Desulfobacca acetoxidans DSM 11109

Annotation: NCBI__GCF_000195295.1:WP_013707407.1

Length: 412 amino acids

Source: GCF_000195295.1 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-arginine biosynthesis argD hi acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized) 50% 93% 375.2
L-proline biosynthesis argD hi acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized) 50% 93% 375.2
L-arginine biosynthesis argD'B hi Succinylornithine transaminase (EC 2.6.1.81) (characterized) 46% 93% 356.3
L-lysine biosynthesis dapC med Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (uncharacterized) 42% 93% 333.6 acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) 50% 375.2
L-lysine biosynthesis lysJ lo [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized) 39% 96% 283.9 acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) 50% 375.2
L-proline biosynthesis OAT lo Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized) 39% 96% 282 acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) 50% 375.2
L-arginine biosynthesis lysJ lo Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized) 39% 99% 248.8 acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) 50% 375.2
L-proline biosynthesis lysJ lo Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized) 39% 99% 248.8 acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) 50% 375.2
L-lysine biosynthesis lysN lo 2-aminoadipate transaminase; 2-aminoadipate aminotransferase; L-2AA aminotransferase; EC 2.6.1.39 (characterized) 32% 96% 198.7 acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) 50% 375.2

Sequence Analysis Tools

View WP_013707407.1 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

MKTDIPIPDTRNSKLETHSASAAWMNRGKRTLMNTYARQPMVLMRGQGVRLWDLDGKEYL
DFLAGIAVCNLGHAHPAITEAVCRQVQDLVHVSNLYHTIPQIKLAERLVELSFADRVFFC
NSGAEANEGAIKLCRRYSWQKFGPDRYKIICAANSFHGRTLATLSATGQEKFWQGFAPLL
PGFVFVPFNDPAALEAAIDNQTCGVLLEPVQGEGGVKIPTADYFPEVRNLCDKHNLLLIL
DEIQVGLGRTGRLFAHEHFGITPDIMTLAKGLANGLPIGALLVTEEVAAGFVPGTHASTF
GGGPVVTAAALTVLEILAQPDFLAEVKAKGEYFLNGLRQLQPRHRFIQEVRGLGLILGIE
IDGDGVPLVDSCREKGALINCTQGNVLRFLPPLVVSREEIDRFLAILDDVLP

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