GapMind for catabolism of small carbon sources

 

Protein Ac3H11_3200 in Acidovorax sp. GW101-3H11

Annotation: Amino acid ABC transporter permease protein

Length: 604 amino acids

Source: acidovorax_3H11 in FitnessBrowser

Candidate for 33 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-glutamate catabolism gltL med GluA aka CGL1950, component of Glutamate porter (characterized) 54% 99% 260.4 uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ 54% 260.4
L-lysine catabolism hisP med Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 49% 98% 257.3 uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ 54% 260.4
L-histidine catabolism aapP med ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 53% 93% 254.2 uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ 54% 260.4
L-arginine catabolism artP med Arginine transport ATP-binding protein ArtM (characterized) 53% 100% 252.7 uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ 54% 260.4
L-asparagine catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 52% 93% 251.1 uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ 54% 260.4
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 51% 97% 251.1 uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ 54% 260.4
L-aspartate catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 52% 93% 251.1 uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ 54% 260.4
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 51% 97% 251.1 uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ 54% 260.4
D-glucosamine (chitosamine) catabolism AO353_21725 med ABC transporter for D-glucosamine, ATPase component (characterized) 54% 92% 251.1 uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ 54% 260.4
L-glutamate catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 52% 93% 251.1 uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ 54% 260.4
L-leucine catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 52% 93% 251.1 uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ 54% 260.4
L-proline catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 52% 93% 251.1 uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ 54% 260.4
D-alanine catabolism Pf6N2E2_5405 med ABC transporter for D-Alanine, ATPase component (characterized) 52% 95% 249.2 uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ 54% 260.4
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) 53% 96% 249.2 uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ 54% 260.4
L-histidine catabolism bgtA med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 53% 96% 243.8 uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ 54% 260.4
L-asparagine catabolism aatP med Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 51% 99% 243 uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ 54% 260.4
L-aspartate catabolism aatP med Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 51% 99% 243 uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ 54% 260.4
L-asparagine catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 51% 91% 242.7 uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ 54% 260.4
L-aspartate catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 51% 91% 242.7 uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ 54% 260.4
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) 51% 97% 241.1 uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ 54% 260.4
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% 94% 236.1 uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ 54% 260.4
L-histidine catabolism BPHYT_RS24015 med ABC transporter related (characterized, see rationale) 49% 97% 234.6 uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ 54% 260.4
L-asparagine catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 49% 99% 232.3 uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ 54% 260.4
L-aspartate catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 49% 99% 232.3 uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ 54% 260.4
L-citrulline catabolism AO353_03040 med ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 49% 99% 228.4 uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ 54% 260.4
L-histidine catabolism PA5503 med Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 45% 72% 188.3 uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ 54% 260.4
L-asparagine catabolism aatM med Glutamate/aspartate import permease protein GltK (characterized) 34% 94% 104.4
L-aspartate catabolism aatM med Glutamate/aspartate import permease protein GltK (characterized) 34% 94% 104.4
L-glutamate catabolism gltK med Glutamate/aspartate import permease protein GltK (characterized) 34% 94% 104.4
L-arginine catabolism artM med ABC transporter for L-Arginine and L-Citrulline, permease component 2 (characterized) 30% 86% 89.7
L-citrulline catabolism AO353_03045 med ABC transporter for L-Arginine and L-Citrulline, permease component 2 (characterized) 30% 86% 89.7
L-arginine catabolism artQ med Arginine ABC transporter permease protein ArtQ (characterized) 31% 95% 88.2
L-histidine catabolism aapM lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 (characterized) 31% 60% 104.4

Sequence Analysis Tools

View Ac3H11_3200 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

VHPAAPATPVGSHAPSAPPATPSPAPAKGDYSHYRVVPARHRARAVGTVFATVVIALVLY
SVLTNPRWGWGVFGEYFFSEPVLVGLGRTLLLTALGALFGFTLGTALALARVSRSPLLAG
LSWTFIWIFRSIPVIVLLLIINNLGYLYETVSVGLPFTDWTFFSYPTTQLISPFVAALIG
LTLNQAAFASEIVRGGILSVDQGQLEAAAALGLPRRRQAFRIVLPQAMRSILPAGFNDII
GLAKGTSNVYILALPELFYTIQIIYRRNLEVIPLLMVATVWYLVILTVLSLLQYYIERHF
SKGALRSPPPSIFSAVAARLWPARRAVVAPGPVVPAAPAPVAVPRWTGALNRGGEVTIHG
VSKRYGALEVLKDVTLTVLPGSVTVILGPSGSGKSTLLRSINHLERVDGGFIAIDGELIG
YRQDADALYELGENDILKRRVDVGMVFQNFNLFPHLTVLENIVEAPVTVRKLARAEAEAL
ALELLARVGLSDKAHSYPRQLSGGQQQRVAIARALALKPKVLLFDEPTSALDPELVGEVL
DVIKELARTGTTLVIVTHEIGFAREVADTVVFMEQGRVVETGTPAKVFSQPDHPRTAAFL
AKVL

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 (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 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