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
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Find functional residues: SitesBLAST
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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:
- ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
- HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.
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:
- ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
- ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
- HMMer finds a hit (regardless of coverage or other bits).
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:
- our ignorance of proteins' functions,
- omissions in the gene models,
- frame-shift errors in the genome sequence, or
- the organism lacks the pathway.
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