GapMind for catabolism of small carbon sources

 

Protein H281DRAFT_06484 in Paraburkholderia bryophila 376MFSha3.1

Annotation: H281DRAFT_06484 amino acid ABC transporter substrate-binding protein, PAAT family

Length: 266 amino acids

Source: Burk376 in FitnessBrowser

Candidate for 5 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, periplasmic substrate-binding component (characterized) 96% 100% 503.8
L-histidine catabolism hisJ med histidine ABC transporter, periplasmic histidine-binding protein HisJ (characterized) 50% 98% 269.2 ABC transporter for L-Arginine, periplasmic substrate-binding component 96% 503.8
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) 52% 98% 265 ABC transporter for L-Arginine, periplasmic substrate-binding component 96% 503.8
L-citrulline catabolism AO353_03055 med ABC transporter for L-Arginine and L-Citrulline, periplasmic substrate-binding component (characterized) 46% 95% 234.2 ABC transporter for L-Arginine, periplasmic substrate-binding component 96% 503.8
L-citrulline catabolism PS417_17590 med ABC transporter substrate-binding protein; SubName: Full=Histidine transport system substrate-binding protein (characterized, see rationale) 48% 97% 232.6 ABC transporter for L-Arginine, periplasmic substrate-binding component 96% 503.8

Sequence Analysis Tools

View H281DRAFT_06484 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MKMNWRNTAALALFATATATVTAGSAAAADIKEVRFGVEASYAPFESKSPSGELQGFDID
VGNAVCAKLKAKCVWVENSFDGLIPALQARKFNAINSDMTITDQRRQAVDFTDPIYTIPN
QMIAKKGSGLLPTPASLKGKHVGVLQGTIQETYAKARWAPAGVDVVPYQTQDQIYADLAS
GRLDASFQDAEAASKGFLKKPQGAGFEFAGPAVSDEKLLGAGVGFGIRKGDAALKDALNQ
ALKELKADGTIDRFAAKYFDVKVVLK

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

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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