GapMind for catabolism of small carbon sources

 

Protein 3608039 in Dinoroseobacter shibae DFL-12

Annotation: FitnessBrowser__Dino:3608039

Length: 444 amino acids

Source: Dino in FitnessBrowser

Candidate for 15 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism gabT lo Gamma aminobutyrate transaminase 3, chloroplastic; Gamma-aminobutyrate transaminase isozyme 3; LeGABA-TP3; SlGABA-T3; EC 2.6.1.96 (characterized) 34% 79% 246.1 Uncharacterized aminotransferase C1771.03c; EC 2.6.-.- 44% 368.2
L-citrulline catabolism gabT lo Gamma aminobutyrate transaminase 3, chloroplastic; Gamma-aminobutyrate transaminase isozyme 3; LeGABA-TP3; SlGABA-T3; EC 2.6.1.96 (characterized) 34% 79% 246.1 Uncharacterized aminotransferase C1771.03c; EC 2.6.-.- 44% 368.2
putrescine catabolism gabT lo Gamma aminobutyrate transaminase 3, chloroplastic; Gamma-aminobutyrate transaminase isozyme 3; LeGABA-TP3; SlGABA-T3; EC 2.6.1.96 (characterized) 34% 79% 246.1 Uncharacterized aminotransferase C1771.03c; EC 2.6.-.- 44% 368.2
L-arginine catabolism davT lo 4-aminobutyrate aminotransferase GabT; 5-aminovalerate transaminase; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT; EC 2.6.1.19; EC 2.6.1.48 (characterized) 34% 92% 208 Uncharacterized aminotransferase C1771.03c; EC 2.6.-.- 44% 368.2
L-citrulline catabolism davT lo 4-aminobutyrate aminotransferase GabT; 5-aminovalerate transaminase; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT; EC 2.6.1.19; EC 2.6.1.48 (characterized) 34% 92% 208 Uncharacterized aminotransferase C1771.03c; EC 2.6.-.- 44% 368.2
L-lysine catabolism davT lo 4-aminobutyrate aminotransferase GabT; 5-aminovalerate transaminase; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT; EC 2.6.1.19; EC 2.6.1.48 (characterized) 34% 92% 208 Uncharacterized aminotransferase C1771.03c; EC 2.6.-.- 44% 368.2
L-proline catabolism davT lo 4-aminobutyrate aminotransferase GabT; 5-aminovalerate transaminase; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT; EC 2.6.1.19; EC 2.6.1.48 (characterized) 34% 92% 208 Uncharacterized aminotransferase C1771.03c; EC 2.6.-.- 44% 368.2
L-arginine catabolism astC lo Succinylornithine transaminase; SOAT; Succinylornithine aminotransferase; EC 2.6.1.81 (characterized) 34% 88% 200.7 Uncharacterized aminotransferase C1771.03c; EC 2.6.-.- 44% 368.2
L-citrulline catabolism astC lo Succinylornithine transaminase; SOAT; Succinylornithine aminotransferase; EC 2.6.1.81 (characterized) 34% 88% 200.7 Uncharacterized aminotransferase C1771.03c; EC 2.6.-.- 44% 368.2
L-arginine catabolism patA lo putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized) 34% 72% 192.2 Uncharacterized aminotransferase C1771.03c; EC 2.6.-.- 44% 368.2
L-citrulline catabolism patA lo putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized) 34% 72% 192.2 Uncharacterized aminotransferase C1771.03c; EC 2.6.-.- 44% 368.2
L-lysine catabolism patA lo putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized) 34% 72% 192.2 Uncharacterized aminotransferase C1771.03c; EC 2.6.-.- 44% 368.2
putrescine catabolism patA lo putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized) 34% 72% 192.2 Uncharacterized aminotransferase C1771.03c; EC 2.6.-.- 44% 368.2
L-arginine catabolism rocD lo Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized) 31% 56% 128.3 Uncharacterized aminotransferase C1771.03c; EC 2.6.-.- 44% 368.2
L-citrulline catabolism rocD lo Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized) 31% 56% 128.3 Uncharacterized aminotransferase C1771.03c; EC 2.6.-.- 44% 368.2

Sequence Analysis Tools

View 3608039 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

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Sequence

MAGHVFGRSAAQMPTAVAGAGCYIIDADGKRYLDGSGGAAVSCLGHDHPAVRAALHAQID
KIAFAHTGFFTSEPAEVLCDALIAAAPKGIEKVYLLSGGSESVEAALKLARQFFLETGEP
RRHRVIARRQSYHGNTLGALAAGGNAWRREKYAPLLVETYHIDPCYAYRHQAVGESDAAY
GRRAADALRTEIERLGPETVMAFIAEPVVGATAGAVPPAPGYFERIREICDEYGVLLILD
EVMCGMGRTGTLFACEQDGISPDIVTIAKGLGAGYAPIGAMLASGRIYDAIAQGSGSFQH
GHTYHGHPLAAAAAGAVVETLRAPGTMAQVRAKGATLQSRLEAALGQHSHVGDIRGRGLF
RGIELVEDRDTKRPLDPARKVSARIKAAAMARGLICYPGSGTIDGKHGDHILLAPPFIIE
DKQIDALVHMLAEAIDDAMAATQA

This GapMind analysis is from Sep 17 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