GapMind for catabolism of small carbon sources

 

Protein HSERO_RS21250 in Herbaspirillum seropedicae SmR1

Annotation: HSERO_RS21250 amino acid ABC transporter ATP-binding protein

Length: 244 amino acids

Source: HerbieS in FitnessBrowser

Candidate for 8 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism artP med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 55% 98% 263.5 Amino acid ABC transporter ATP binding protein, component of Hydroxy L-proline uptake porter, HprABC 57% 264.2
L-histidine catabolism bgtA med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 55% 98% 263.5 Amino acid ABC transporter ATP binding protein, component of Hydroxy L-proline uptake porter, HprABC 57% 264.2
L-lysine catabolism hisP med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 55% 98% 263.5 Amino acid ABC transporter ATP binding protein, component of Hydroxy L-proline uptake porter, HprABC 57% 264.2
D-glucosamine (chitosamine) catabolism AO353_21725 med ABC transporter for D-Glucosamine, putative ATPase component (characterized) 50% 96% 249.2 Amino acid ABC transporter ATP binding protein, component of Hydroxy L-proline uptake porter, HprABC 57% 264.2
L-histidine catabolism hisP med Probable ATP-binding component of ABC transporter, 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) 52% 97% 248.1 Amino acid ABC transporter ATP binding protein, component of Hydroxy L-proline uptake porter, HprABC 57% 264.2
L-histidine catabolism BPHYT_RS24015 med ABC transporter related (characterized, see rationale) 52% 95% 246.1 Amino acid ABC transporter ATP binding protein, component of Hydroxy L-proline uptake porter, HprABC 57% 264.2
L-citrulline catabolism AO353_03040 med ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 51% 98% 243.8 Amino acid ABC transporter ATP binding protein, component of Hydroxy L-proline uptake porter, HprABC 57% 264.2
L-citrulline catabolism PS417_17605 med ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale) 51% 89% 232.6 Amino acid ABC transporter ATP binding protein, component of Hydroxy L-proline uptake porter, HprABC 57% 264.2

Sequence Analysis Tools

View HSERO_RS21250 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 and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MPLIAIDNVKKRFGDNEVLKGISLDVEPGEVIAIIGKSGSGKSTLLRCINGLESIDEGNI
SVAGAKLGASELELRNLRLKVGMIFQQFNLFPHLSVGRNVMIAPMIVKGVSEAEAMKTAK
ANLEKVGLGHKFDAYPDQLSGGQQQRVAIARALSMSPQALLCDEITSALDPELVNEVLTV
MRGLAKEGMTLLMVTHEMRFAREVCNRLVFMHQGKVHEIGPPEELFGNPKTPELQQFIGM
TQGA

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 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, the preprint on GapMind for carbon sources, 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