GapMind for catabolism of small carbon sources

 

Protein WP_011383782.1 in Magnetospirillum magneticum AMB-1

Annotation: AMB_RS06945 phosphate ABC transporter ATP-binding protein

Length: 259 amino acids

Source: GCF_000009985.1 in NCBI

Candidate for 15 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-lysine catabolism hisP lo Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 39% 91% 160.2 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 57% 296.6
L-glutamate catabolism gltL lo GluA aka CGL1950, component of Glutamate porter (characterized) 37% 97% 159.1 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 57% 296.6
L-arginine catabolism artP lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 38% 95% 157.5 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 57% 296.6
L-histidine catabolism bgtA lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 38% 95% 157.5 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 57% 296.6
L-histidine catabolism hisP lo histidine transport ATP-binding protein hisP (characterized) 38% 98% 155.2 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 57% 296.6
L-asparagine catabolism glnQ lo 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) 36% 97% 152.9 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 57% 296.6
L-asparagine catabolism aatP lo ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 39% 91% 148.7 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 57% 296.6
L-aspartate catabolism aatP lo ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 39% 91% 148.7 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 57% 296.6
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 35% 94% 145.2 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 57% 296.6
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-Glucosamine, putative ATPase component (characterized) 38% 94% 142.9 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 57% 296.6
L-histidine catabolism aapP lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 35% 91% 142.5 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 57% 296.6
L-citrulline catabolism PS417_17605 lo 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) 37% 91% 140.6 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 57% 296.6
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 35% 98% 137.9 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 57% 296.6
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 38% 58% 134.8 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 57% 296.6
citrate catabolism fecE lo iron(III) dicitrate transport ATP-binding protein FecE (characterized) 32% 88% 104.4 phosphate ABC transporter, ATP-binding protein; EC 3.6.3.27 57% 296.6

Sequence Analysis Tools

View WP_011383782.1 at NCBI

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

MNQFIPRGTSKISARGLNVHYGEKQALHDIDLDIPAGEVTALIGPSGCGKSTFLRCINRM
NDMVDGAKVTGSLTLDGSDVYDRSLDVVQLRARVGMVFQKPNPFPKSIYDNVAYGPRIHG
LARDQAELDEIVMNSLEKAGLLAEVESRLSESGTGLSGGQQQRLCIARAIAVAPEVILMD
EPCSALDPIATAKVEELIDELRDNYTIVIVTHSMQQAARVSQRTAFFHLGKLIEVGGTEE
IFTNPKEPLTQGYITGRFG

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