GapMind for catabolism of small carbon sources

 

Protein WP_023431721.1 in Lutibaculum baratangense AMV1

Annotation: NCBI__GCF_000496075.1:WP_023431721.1

Length: 257 amino acids

Source: GCF_000496075.1 in NCBI

Candidate for 7 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism artJ hi L-Arginine ABC transporter, periplasmic substrate-binding component (characterized) 45% 100% 202.2
L-lysine catabolism argT med Putative amino-acid binding periplasmic protein (characterized, see rationale) 42% 99% 204.1 L-Arginine ABC transporter, periplasmic substrate-binding component 45% 202.2
L-citrulline catabolism AO353_03055 med ABC transporter for L-Arginine and L-Citrulline, periplasmic substrate-binding component (characterized) 44% 100% 199.5 Amino acid (Lysine/arginine/ornithine/histidine/octopine) ABC transporter periplasmic binding protein, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR 41% 189.9
L-histidine catabolism hisJ med Amino acid (Lysine/arginine/ornithine/histidine/octopine) ABC transporter periplasmic binding protein, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) 41% 98% 189.9 L-Arginine ABC transporter, periplasmic substrate-binding component 45% 202.2
L-citrulline catabolism PS417_17590 med ABC transporter substrate-binding protein; SubName: Full=Histidine transport system substrate-binding protein (characterized, see rationale) 40% 96% 162.5 L-Arginine ABC transporter, periplasmic substrate-binding component 45% 202.2
L-histidine catabolism BPHYT_RS24000 lo Extracellular solute-binding protein family 3; Flags: Precursor (characterized, see rationale) 31% 96% 129 L-Arginine ABC transporter, periplasmic substrate-binding component 45% 202.2
L-histidine catabolism Ac3H11_2555 lo ABC transporter for L-Histidine, periplasmic substrate-binding component 1 (characterized) 32% 97% 124.8 L-Arginine ABC transporter, periplasmic substrate-binding component 45% 202.2

Sequence Analysis Tools

View WP_023431721.1 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

MKKTILAAAAALSLAMAPGAFAQEPLKVGVAAEPYPPFSSVDSAGNWSGFDIEIGQAICE
EMGRECVTTPVAWDGIIPALTSGKIDMIVGSMSITEERQKVIDFSDRYYYTPAAFVAPAP
VEVDTDSADLGGLVLGVQSGTTSAAYVRKAYPDAEIKLYNTQDEVNADLAAGRIDVMLAD
QAAMVEYVKTPEGSQFEVKAVAPEDEAFGEGIGVGLRKEDDDLQADVNDAIAALLESGRY
DEIAGQYFEFDIYGGRE

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