GapMind for catabolism of small carbon sources

 

Protein HSERO_RS11450 in Herbaspirillum seropedicae SmR1

Annotation: HSERO_RS11450 ABC transporter ATP-binding protein

Length: 257 amino acids

Source: HerbieS in FitnessBrowser

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 artP med Arginine transport ATP-binding protein ArtM (characterized) 57% 100% 265.4 GluA aka CGL1950, component of Glutamate porter 56% 264.2
L-glutamate catabolism gltL med GluA aka CGL1950, component of Glutamate porter (characterized) 56% 100% 265 Arginine transport ATP-binding protein ArtM 57% 265.4
L-asparagine catabolism glnQ med Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized) 56% 97% 255.4 Arginine transport ATP-binding protein ArtM 57% 265.4
L-histidine catabolism bgtA med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 54% 97% 247.7 Arginine transport ATP-binding protein ArtM 57% 265.4
L-citrulline catabolism AO353_03040 med ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 50% 98% 239.6 Arginine transport ATP-binding protein ArtM 57% 265.4
L-histidine catabolism hisP med histidine transport ATP-binding protein hisP (characterized) 50% 100% 234.2 Arginine transport ATP-binding protein ArtM 57% 265.4
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 39% 80% 136.7 Arginine transport ATP-binding protein ArtM 57% 265.4

Sequence Analysis Tools

View HSERO_RS11450 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

MTEPIVEVSGLRKSFGAHVVLKDLDLSVAPSQVVVVIGPSGSGKSTFLRCLNGLEKAEGG
TVKVCGRPVVEGGRMMPEAMLDLLRAEVGMVFQSFNLFPHLTVLDNITLAPTCLRGMSRK
AAQQQALQLLEKVGLAHKAKAYPGTLSGGQKQRVAIARALAMEPQVMLFDEPTSALDPEL
VGEVLQVIRALAAEGMTMIIVTHEMGFAREVADVVVVMDHGSIVEAGPPGAIFTAPQQAR
TRSFLQTMLARQVADGN

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