GapMind for catabolism of small carbon sources

 

Protein Ac3H11_2058 in Acidovorax sp. GW101-3H11

Annotation: FitnessBrowser__acidovorax_3H11:Ac3H11_2058

Length: 360 amino acids

Source: acidovorax_3H11 in FitnessBrowser

Candidate for 16 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-maltose catabolism musK med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 41% 93% 248.4 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 53% 306.2
L-fucose catabolism SM_b21106 med ABC transporter for L-Fucose, ATPase component (characterized) 45% 82% 247.7 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 53% 306.2
lactose catabolism lacK med LacK, component of Lactose porter (characterized) 41% 96% 244.2 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 53% 306.2
D-cellobiose catabolism msiK med MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized) 45% 80% 242.7 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 53% 306.2
D-mannitol catabolism mtlK med SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 43% 84% 238.8 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 53% 306.2
D-sorbitol (glucitol) catabolism mtlK med ABC transporter for D-Sorbitol, ATPase component (characterized) 41% 92% 237.7 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 53% 306.2
D-maltose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 43% 86% 230.7 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 53% 306.2
sucrose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 43% 86% 230.7 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 53% 306.2
trehalose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 43% 86% 230.7 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 53% 306.2
putrescine catabolism potA lo Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized) 40% 89% 241.9 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 53% 306.2
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 40% 93% 240.7 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 53% 306.2
L-proline catabolism opuBA lo BusAA, component of Uptake system for glycine-betaine (high affinity) and proline (low affinity) (OpuAA-OpuABC) or BusAA-ABC of Lactococcus lactis). BusAA, the ATPase subunit, has a C-terminal tandem cystathionine β-synthase (CBS) domain which is the cytoplasmic K+ sensor for osmotic stress (osmotic strength)while the BusABC subunit has the membrane and receptor domains fused to each other (Biemans-Oldehinkel et al., 2006; Mahmood et al., 2006; Gul et al. 2012). An N-terminal amphipathic α-helix of OpuA is necessary for high activity but is not critical for biogenesis or the ionic regulation of transport (characterized) 35% 87% 191.4 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 53% 306.2
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 37% 61% 179.1 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 53% 306.2
L-histidine catabolism hutV lo HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 36% 96% 176.4 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 53% 306.2
L-proline catabolism hutV lo HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 36% 96% 176.4 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 53% 306.2
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 35% 97% 141 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 53% 306.2

Sequence Analysis Tools

View Ac3H11_2058 at FitnessBrowser

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

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Sequence

MNHSDAGIVFRNITKRYGTDSSAALAVKGISFEVPRGTLTTILGPSGCGKTTTLRMIAGL
ESPTSGEIFIGGKDVTTLGPAQRNVSMMFQSYALFPHMNVVENVMYGLRMSGQPKEQARA
KAVEALRGVGLVGFDDRLPSELSGGQQQRVALARALVLEPEVLLFDEPLSNLDARLRREM
REEIRALQQRLSLTVAYVTHDQAEAMAVSDQIIVMNQGLIAQKGSPRALYETPHSEFVAG
FMGEAMLFPAVADADGTVALGPLVLRPRVAVKSGPVKVAVRPEAWRITRQGEGLLPARLA
KSAYLGAVHEYTFETALGSIFVVSSDLDDVLAVGDDVQLGLGVHGVSVVGSTEGAAPDAE

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 paper from 2022 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