GapMind for catabolism of small carbon sources

 

Protein WP_013089091.1 in Paraburkholderia sp. CCGE1002

Annotation: NCBI__GCF_000092885.1:WP_013089091.1

Length: 411 amino acids

Source: GCF_000092885.1 in NCBI

Candidate for 14 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism astC hi Succinylornithine transaminase (EC 2.6.1.81) (characterized) 60% 99% 502.3 Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 57% 485.0
L-arginine catabolism astC med astC: succinylornithine transaminase family (EC 2.6.1.81) (TIGR03246) 100% 698 Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 57% 485.0
L-citrulline catabolism astC hi Succinylornithine transaminase (EC 2.6.1.81) (characterized) 60% 99% 502.3 Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 57% 485.0
L-citrulline catabolism astC med astC: succinylornithine transaminase family (EC 2.6.1.81) (TIGR03246) 100% 698 Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 57% 485.0
L-arginine catabolism rocD lo Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized) 33% 93% 234.2 Succinylornithine transaminase (EC 2.6.1.81) 60% 502.3
L-citrulline catabolism rocD lo Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized) 33% 93% 234.2 Succinylornithine transaminase (EC 2.6.1.81) 60% 502.3
L-arginine catabolism davT lo 5-aminovalerate transaminase (EC 2.6.1.48) (characterized) 36% 94% 230.7 Succinylornithine transaminase (EC 2.6.1.81) 60% 502.3
L-citrulline catabolism davT lo 5-aminovalerate transaminase (EC 2.6.1.48) (characterized) 36% 94% 230.7 Succinylornithine transaminase (EC 2.6.1.81) 60% 502.3
L-lysine catabolism davT lo 5-aminovalerate transaminase (EC 2.6.1.48) (characterized) 36% 94% 230.7 Succinylornithine transaminase (EC 2.6.1.81) 60% 502.3
L-proline catabolism davT lo 5-aminovalerate transaminase (EC 2.6.1.48) (characterized) 36% 94% 230.7 Succinylornithine transaminase (EC 2.6.1.81) 60% 502.3
L-lysine catabolism lysN lo 2-aminoadipate transaminase (EC 2.6.1.39) (characterized) 33% 95% 204.5 Succinylornithine transaminase (EC 2.6.1.81) 60% 502.3
L-arginine catabolism patA lo putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized) 35% 78% 191.8 Succinylornithine transaminase (EC 2.6.1.81) 60% 502.3
L-citrulline catabolism patA lo putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized) 35% 78% 191.8 Succinylornithine transaminase (EC 2.6.1.81) 60% 502.3
L-lysine catabolism patA lo putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized) 35% 78% 191.8 Succinylornithine transaminase (EC 2.6.1.81) 60% 502.3
putrescine catabolism patA lo putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized) 35% 78% 191.8 Succinylornithine transaminase (EC 2.6.1.81) 60% 502.3
L-lysine catabolism lat lo L-lysine-epsilon aminotransferase; L-lysine aminotransferase; EC 2.6.1.36; Lysine 6-aminotransferase (uncharacterized) 31% 71% 126.7 Succinylornithine transaminase (EC 2.6.1.81) 60% 502.3

Sequence Analysis Tools

View WP_013089091.1 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

MNDLTVTRQTFDEVMVPVFAPAAFVPDRGLGSRVWDTQGRDYIDFAGGIAVTALGHAHPE
LLKVLHEQGSKLWHIGNGYTNEPVLRLAKRLESLTFADRAFFANSGAEANEAALKLARRV
AVDRHGAQKDEIISFTQSFHGRTLFTVSVGGQPKYSEGFGPVPAGITHLPYNDIAAAKKA
IGAQTCAVIVEPIQGEGGVIPADPAFLKALREACDQHDAVLIFDEVQTGVGRSGYFYAYQ
DTGVTPDILTTAKALGNGFPIGAMLTTKELAAHFKVGVHGTTYGGNPLGSAIAEKVVELV
SDPKLLEGVRSRSEVLKGHLAKLNERLGLFSEVRGKGLLIGAELNDAYRGRAKDFVTAAG
QHGVIMLMAGPDVLRFVPSLIMPLDDMAEGFARLDKAFGELVGANAQAASR

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 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