Protein WP_012537671.1 in Acidithiobacillus ferrooxidans ATCC 23270
Annotation: NCBI__GCF_000021485.1:WP_012537671.1
Length: 309 amino acids
Source: GCF_000021485.1 in NCBI
Candidate for 45 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) | 38% | 85% | 134 | nodulation ATP-binding protein I | 48% | 285.0 |
| putrescine catabolism | potA | lo | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) | 36% | 59% | 133.7 | nodulation ATP-binding protein I | 48% | 285.0 |
| L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 33% | 89% | 133.3 | nodulation ATP-binding protein I | 48% | 285.0 |
| lactose catabolism | lacK | lo | ABC transporter for Lactose, ATPase component (characterized) | 36% | 61% | 133.3 | nodulation ATP-binding protein I | 48% | 285.0 |
| 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) | 35% | 90% | 131.7 | nodulation ATP-binding protein I | 48% | 285.0 |
| L-glutamate catabolism | gltL | 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) | 35% | 90% | 131.7 | nodulation ATP-binding protein I | 48% | 285.0 |
| L-proline catabolism | HSERO_RS00895 | lo | ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) | 33% | 93% | 130.2 | nodulation ATP-binding protein I | 48% | 285.0 |
| D-cellobiose catabolism | msiK | lo | 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) | 36% | 53% | 124.8 | nodulation ATP-binding protein I | 48% | 285.0 |
| L-isoleucine catabolism | livG | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 31% | 91% | 122.1 | nodulation ATP-binding protein I | 48% | 285.0 |
| L-leucine catabolism | livG | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 31% | 91% | 122.1 | nodulation ATP-binding protein I | 48% | 285.0 |
| L-phenylalanine catabolism | livG | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 31% | 91% | 122.1 | nodulation ATP-binding protein I | 48% | 285.0 |
| L-serine catabolism | Ac3H11_1693 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 31% | 91% | 122.1 | nodulation ATP-binding protein I | 48% | 285.0 |
| L-tyrosine catabolism | Ac3H11_1693 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 31% | 91% | 122.1 | nodulation ATP-binding protein I | 48% | 285.0 |
| L-alanine catabolism | braG | lo | High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 35% | 91% | 118.6 | nodulation ATP-binding protein I | 48% | 285.0 |
| L-isoleucine catabolism | livF | lo | High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 35% | 91% | 118.6 | nodulation ATP-binding protein I | 48% | 285.0 |
| L-leucine catabolism | livF | lo | High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 35% | 91% | 118.6 | nodulation ATP-binding protein I | 48% | 285.0 |
| L-serine catabolism | braG | lo | High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 35% | 91% | 118.6 | nodulation ATP-binding protein I | 48% | 285.0 |
| L-threonine catabolism | braG | lo | High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 35% | 91% | 118.6 | nodulation ATP-binding protein I | 48% | 285.0 |
| L-valine catabolism | livF | lo | High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 35% | 91% | 118.6 | nodulation ATP-binding protein I | 48% | 285.0 |
| D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 31% | 73% | 116.3 | nodulation ATP-binding protein I | 48% | 285.0 |
| L-histidine catabolism | Ac3H11_2560 | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 37% | 83% | 114.8 | nodulation ATP-binding protein I | 48% | 285.0 |
| L-phenylalanine catabolism | livF | lo | High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale) | 33% | 95% | 114.4 | nodulation ATP-binding protein I | 48% | 285.0 |
| L-proline catabolism | HSERO_RS00900 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 33% | 89% | 114 | nodulation ATP-binding protein I | 48% | 285.0 |
| L-serine catabolism | Ac3H11_1692 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 33% | 89% | 114 | nodulation ATP-binding protein I | 48% | 285.0 |
| L-tyrosine catabolism | Ac3H11_1692 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 33% | 89% | 114 | nodulation ATP-binding protein I | 48% | 285.0 |
| L-isoleucine catabolism | natE | lo | NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) | 33% | 85% | 113.2 | nodulation ATP-binding protein I | 48% | 285.0 |
| L-leucine catabolism | natE | lo | NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) | 33% | 85% | 113.2 | nodulation ATP-binding protein I | 48% | 285.0 |
| L-proline catabolism | natE | lo | NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) | 33% | 85% | 113.2 | nodulation ATP-binding protein I | 48% | 285.0 |
| L-valine catabolism | natE | lo | NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) | 33% | 85% | 113.2 | nodulation ATP-binding protein I | 48% | 285.0 |
| D-alanine catabolism | AZOBR_RS08250 | lo | Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) | 31% | 100% | 112.1 | nodulation ATP-binding protein I | 48% | 285.0 |
| L-proline catabolism | AZOBR_RS08250 | lo | Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) | 31% | 100% | 112.1 | nodulation ATP-binding protein I | 48% | 285.0 |
| L-arabinose catabolism | xylGsa | lo | Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) | 30% | 86% | 109.8 | nodulation ATP-binding protein I | 48% | 285.0 |
| L-histidine catabolism | natE | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 32% | 88% | 107.8 | nodulation ATP-binding protein I | 48% | 285.0 |
| D-fructose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 30% | 89% | 106.7 | nodulation ATP-binding protein I | 48% | 285.0 |
| D-mannose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 30% | 89% | 106.7 | nodulation ATP-binding protein I | 48% | 285.0 |
| D-ribose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 30% | 89% | 106.7 | nodulation ATP-binding protein I | 48% | 285.0 |
| sucrose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 30% | 89% | 106.7 | nodulation ATP-binding protein I | 48% | 285.0 |
| D-lactate catabolism | PGA1_c12640 | lo | D-lactate transporter, ATP-binding component (characterized) | 30% | 94% | 102.4 | nodulation ATP-binding protein I | 48% | 285.0 |
| L-arginine catabolism | braG | lo | ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) | 34% | 95% | 101.7 | nodulation ATP-binding protein I | 48% | 285.0 |
| L-glutamate catabolism | braG | lo | ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) | 34% | 95% | 101.7 | nodulation ATP-binding protein I | 48% | 285.0 |
| L-histidine catabolism | braG | lo | ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) | 34% | 95% | 101.7 | nodulation ATP-binding protein I | 48% | 285.0 |
| D-ribose catabolism | rbsA | lo | Ribose ABC transporter ATPase; SubName: Full=Sugar ABC transporter ATP-binding protein; SubName: Full=Sugar ABC transporter ATPase (characterized, see rationale) | 30% | 58% | 97.1 | nodulation ATP-binding protein I | 48% | 285.0 |
| D-alanine catabolism | AZOBR_RS08245 | lo | Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) | 30% | 83% | 90.5 | nodulation ATP-binding protein I | 48% | 285.0 |
| L-proline catabolism | AZOBR_RS08245 | lo | Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) | 30% | 83% | 90.5 | nodulation ATP-binding protein I | 48% | 285.0 |
| glycerol catabolism | glpS | lo | GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) | 31% | 59% | 87.4 | nodulation ATP-binding protein I | 48% | 285.0 |
Sequence Analysis Tools
View WP_012537671.1 at NCBI
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
Fitness BLAST: loading...
Sequence
MNPAFLELRALHKRYGGREVLRGVDLAVAAGECFALVGPNGAGKSTTVRAIQGLTPTDGG
EVRIDGRTLAEMGRTARTGMGVVPQTDNLDPDFTVQENLWTYGRYFGLPKALIRQRSAEL
LEFMALSGYATQPIHALSGGMQRRLTIARALINAPKLLLLDEPTTGLDPQARHLIWQRLR
ELRRQGTTLLLTTHYMDEAERLADRVGIIDHGRILAEDSPRGLIATHIPGGVVELRRVDG
DLPDPQDLHRQWVSFSERVGDTLICYGTNLTPLLTHFGDDPAYRWIQRPASLEDVFLRLT
GRDLREETE
This GapMind analysis is from Apr 09 2024. 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:
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