GapMind for Amino acid biosynthesis

 

Protein H281DRAFT_06478 in Paraburkholderia bryophila 376MFSha3.1

Annotation: FitnessBrowser__Burk376:H281DRAFT_06478

Length: 411 amino acids

Source: Burk376 in FitnessBrowser

Candidate for 8 steps in Amino acid biosynthesis

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine biosynthesis argD'B hi succinylornithine transaminase (EC 2.6.1.81) (characterized) 60% 98% 506.5 acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] 59% 490.7
L-arginine biosynthesis argD'B med astC: succinylornithine transaminase family (EC 2.6.1.81) (TIGR03246) 100% 701.3 acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] 59% 490.7
L-arginine biosynthesis argD hi succinylornithine transaminase (EC 2.6.1.81) (characterized) 60% 98% 506.5
L-proline biosynthesis argD hi succinylornithine transaminase (EC 2.6.1.81) (characterized) 60% 98% 506.5
L-lysine biosynthesis dapC med Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (characterized) 57% 100% 490.7 succinylornithine transaminase (EC 2.6.1.81) 60% 506.5
L-arginine biosynthesis lysJ lo [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (uncharacterized) 40% 92% 260.8 succinylornithine transaminase (EC 2.6.1.81) 60% 506.5
L-lysine biosynthesis lysJ lo [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (uncharacterized) 40% 92% 260.8 succinylornithine transaminase (EC 2.6.1.81) 60% 506.5
L-proline biosynthesis lysJ lo [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (uncharacterized) 40% 92% 260.8 succinylornithine transaminase (EC 2.6.1.81) 60% 506.5
L-proline biosynthesis OAT lo Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized) 37% 95% 245 succinylornithine transaminase (EC 2.6.1.81) 60% 506.5

Sequence Analysis Tools

View H281DRAFT_06478 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

MNDLTVTRKTFDEVMVPVFAPAAFVPDRGLGSRVWDTQGRDYIDFAGGIAVTALGHAHPE
LLKVLHEQGSKLWHIGNGYTNEPVLRLARRLEELTFADRAFFANSGAEANEAALKLARRV
AFERHGADKYEIISFTQSFHGRTFFTVSVGGQPKYSEGFGPVPQGIVHLPYNDIQAAQKA
IGAKTCAVIVEPIQGEGGVIPADPAFLKALREACDQHGALLIFDEVQTGVGRSGYFYAYQ
DTGVTPDILTTAKALGNGFPIGAMLTTNELAAHFKVGVHGTTYGGNPLGSAIAEKVVELI
SDPKLLEGVRTRSEVLKGHLAKLNERFGLFDEVRGKGLLIGAQLTDAYKGRAKDFVTAAG
QHGVIMLMAGPDVLRFVPSLIMPLDDMNEGFERLAKAIADVVGVKAEAASR

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