GapMind for catabolism of small carbon sources

 

Protein Echvi_0577 in Echinicola vietnamensis KMM 6221, DSM 17526

Annotation: FitnessBrowser__Cola:Echvi_0577

Length: 413 amino acids

Source: Cola in FitnessBrowser

Candidate for 11 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism rocD hi Ornithine aminotransferase (EC 2.6.1.13) (characterized) 100% 100% 838.2 ornithine aminotransferase 56% 466.5
L-arginine catabolism rocD med rocD: ornithine--oxo-acid transaminase (EC 2.6.1.13) (TIGR01885) 100% 662.1 ornithine aminotransferase 56% 466.5
L-citrulline catabolism rocD hi Ornithine aminotransferase (EC 2.6.1.13) (characterized) 100% 100% 838.2 ornithine aminotransferase 56% 466.5
L-citrulline catabolism rocD med rocD: ornithine--oxo-acid transaminase (EC 2.6.1.13) (TIGR01885) 100% 662.1 ornithine aminotransferase 56% 466.5
L-arginine catabolism astC lo Succinylornithine transaminase (EC 2.6.1.81) (characterized) 34% 94% 232.6 Ornithine aminotransferase (EC 2.6.1.13) 100% 838.2
L-citrulline catabolism astC lo Succinylornithine transaminase (EC 2.6.1.81) (characterized) 34% 94% 232.6 Ornithine aminotransferase (EC 2.6.1.13) 100% 838.2
L-arginine catabolism patA lo putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized) 33% 81% 217.6 Ornithine aminotransferase (EC 2.6.1.13) 100% 838.2
L-citrulline catabolism patA lo putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized) 33% 81% 217.6 Ornithine aminotransferase (EC 2.6.1.13) 100% 838.2
L-lysine catabolism patA lo putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized) 33% 81% 217.6 Ornithine aminotransferase (EC 2.6.1.13) 100% 838.2
putrescine catabolism patA lo putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized) 33% 81% 217.6 Ornithine aminotransferase (EC 2.6.1.13) 100% 838.2
L-arginine catabolism gabT lo Probable 4-aminobutyrate aminotransferase; EC 2.6.1.19; (S)-3-amino-2-methylpropionate transaminase; EC 2.6.1.22; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT (uncharacterized) 31% 92% 209.5 Ornithine aminotransferase (EC 2.6.1.13) 100% 838.2
L-citrulline catabolism gabT lo Probable 4-aminobutyrate aminotransferase; EC 2.6.1.19; (S)-3-amino-2-methylpropionate transaminase; EC 2.6.1.22; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT (uncharacterized) 31% 92% 209.5 Ornithine aminotransferase (EC 2.6.1.13) 100% 838.2
putrescine catabolism gabT lo Probable 4-aminobutyrate aminotransferase; EC 2.6.1.19; (S)-3-amino-2-methylpropionate transaminase; EC 2.6.1.22; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT (uncharacterized) 31% 92% 209.5 Ornithine aminotransferase (EC 2.6.1.13) 100% 838.2

Sequence Analysis Tools

View Echvi_0577 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

MMQPITSSQQAIELENKHGAHNYHPLPVVLSRGEGVFMWDVEGEKYYDFLSSYSAVNQGH
CHPRILQTLIDQAGTLTLTSRAFHNDVLGPFEKFLTEYFGYDKVLPMNTGAEGVETAIKI
ARKWGYEKKGIPENEGTIIVAKNNFHGRTTTVISFSNDETARKNFGPYTPGFVTIPHDDI
DALKDVLSQSKNIIGYLVEPIQGEAGVYVPKEGYLKEVAAVCKDHGVLFMADEIQTGIAR
TGKLLACDHEGVKPDMLILGKAISGGFYPVSAVLADDHIMEVIQPGQHGSTFGGNPLGAK
VAMTALNVVKDEKLAENADKLGKLFRERIQQLVDKSDLVELVRGKGLLNAIVINDTEDSD
TAWRLCLALKENGLLAKPTHGNIIRFAPPLVITEEQLHDCCDIIEKTIQNFKK

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