GapMind for catabolism of small carbon sources

 

Protein WP_054254773.1 in Acidovorax caeni R-24608

Annotation: NCBI__GCF_001298675.1:WP_054254773.1

Length: 253 amino acids

Source: GCF_001298675.1 in NCBI

Candidate for 10 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 ABC transporter for L-Arginine, substrate-binding component (characterized) 51% 98% 257.3
L-citrulline catabolism AO353_03055 hi ABC transporter for L-Arginine and L-Citrulline, periplasmic substrate-binding component (characterized) 51% 100% 253.4 histidine ABC transporter, periplasmic histidine-binding protein HisJ 45% 229.9
L-histidine catabolism hisJ med histidine ABC transporter, periplasmic histidine-binding protein HisJ (characterized) 45% 100% 229.9 ABC transporter for L-Arginine, substrate-binding component 51% 257.3
L-lysine catabolism argT med ArgT aka B2310, component of Histidine/Arginine/Lysine (basic amino acid) uptake porter, HisJ/ArgT/HisP/HisM/HisQ [R, R, C, M, M, respectively] (Gilson et al. 1982). HisJ binds L-His (preferred), but 1-methyl-L-His and 3-methyl-L-His also bind, while the dipeptide carnosine binds weakly; D-histidine and the histidine degradation products, histamine, urocanic acid and imidazole do not bind. L-Arg, homo-L-Arg, and post-translationally modified methylated Arg-analogs also bind with the exception of symmetric dimethylated-L-Arg. L-Lys and L-Orn show weaker interactions with HisJ and methylated and acetylated Lys variants show poor binding.The carboxylate groups of these amino acids and their variants are essential (characterized) 43% 100% 223.8 ABC transporter for L-Arginine, substrate-binding component 51% 257.3
L-citrulline catabolism PS417_17590 med ABC transporter substrate-binding protein; SubName: Full=Histidine transport system substrate-binding protein (characterized, see rationale) 42% 98% 209.5 ABC transporter for L-Arginine, substrate-binding component 51% 257.3
L-histidine catabolism BPHYT_RS24000 lo Extracellular solute-binding protein family 3; Flags: Precursor (characterized, see rationale) 31% 96% 115.5 ABC transporter for L-Arginine, substrate-binding component 51% 257.3
L-histidine catabolism Ac3H11_2555 lo ABC transporter for L-Histidine, periplasmic substrate-binding component 1 (characterized) 32% 96% 114 ABC transporter for L-Arginine, substrate-binding component 51% 257.3
L-asparagine catabolism peb1A lo major cell-binding factor (characterized) 31% 93% 83.6 ABC transporter for L-Arginine, substrate-binding component 51% 257.3
L-aspartate catabolism peb1A lo major cell-binding factor (characterized) 31% 93% 83.6 ABC transporter for L-Arginine, substrate-binding component 51% 257.3
L-glutamate catabolism peb1A lo major cell-binding factor (characterized) 31% 93% 83.6 ABC transporter for L-Arginine, substrate-binding component 51% 257.3

Sequence Analysis Tools

View WP_054254773.1 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

MRKTLFALAITTLAGAAFAADLRVGLNPAYEPFESKTATGEIVGFDVDIANALCAQIQRK
CVFVESEWDSIIPGLQAKKYDVIISSMSITPERARVVDFTNRYYKTPSAIVVKKGTKYDG
PASLKGMKIGVLKGSTQEKWALGELKPAGVNVVPYQSQNQVYLDIKAGRLDGTVADKVEV
HGGFLRKPEGQDFGYVGADQYDPKYYGEGIGIALRKGQGDLKKQLNDAIATIRANGTYAN
IAKKYFDFDPYGQ

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