Protein RR42_RS07815 in Cupriavidus basilensis 4G11
Annotation: FitnessBrowser__Cup4G11:RR42_RS07815
Length: 243 amino acids
Source: Cup4G11 in FitnessBrowser
Candidate for 17 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-arginine catabolism | artP | med | Arginine transport ATP-binding protein ArtM (characterized) | 59% | 100% | 281.2 | glutamine ABC transporter, ATP-binding protein GlnQ | 59% | 274.6 |
| 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) | 55% | 98% | 263.8 | Arginine transport ATP-binding protein ArtM | 59% | 281.2 |
| L-glutamate catabolism | gltL | 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) | 55% | 98% | 263.8 | Arginine transport ATP-binding protein ArtM | 59% | 281.2 |
| L-histidine catabolism | bgtA | med | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 54% | 96% | 255.4 | Arginine transport ATP-binding protein ArtM | 59% | 281.2 |
| L-lysine catabolism | hisP | med | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 54% | 96% | 255.4 | Arginine transport ATP-binding protein ArtM | 59% | 281.2 |
| L-asparagine catabolism | aatP | med | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 52% | 100% | 252.3 | Arginine transport ATP-binding protein ArtM | 59% | 281.2 |
| L-aspartate catabolism | aatP | med | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 52% | 100% | 252.3 | Arginine transport ATP-binding protein ArtM | 59% | 281.2 |
| L-citrulline catabolism | AO353_03040 | med | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 53% | 97% | 251.9 | Arginine transport ATP-binding protein ArtM | 59% | 281.2 |
| L-histidine catabolism | BPHYT_RS24015 | med | ABC transporter related (characterized, see rationale) | 52% | 94% | 251.1 | Arginine transport ATP-binding protein ArtM | 59% | 281.2 |
| L-histidine catabolism | hisP | med | Histidine transport ATP-binding protein HisP (characterized) | 54% | 95% | 250 | Arginine transport ATP-binding protein ArtM | 59% | 281.2 |
| 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) | 56% | 89% | 249.6 | Arginine transport ATP-binding protein ArtM | 59% | 281.2 |
| D-glucosamine (chitosamine) catabolism | AO353_21725 | med | ABC transporter for D-glucosamine, ATPase component (characterized) | 53% | 94% | 248.4 | Arginine transport ATP-binding protein ArtM | 59% | 281.2 |
| L-histidine catabolism | aapP | med | ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) | 52% | 93% | 243 | Arginine transport ATP-binding protein ArtM | 59% | 281.2 |
| D-alanine catabolism | Pf6N2E2_5405 | med | ABC transporter for D-Alanine, ATPase component (characterized) | 52% | 95% | 237.7 | Arginine transport ATP-binding protein ArtM | 59% | 281.2 |
| L-asparagine catabolism | peb1C | med | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 47% | 99% | 223.8 | Arginine transport ATP-binding protein ArtM | 59% | 281.2 |
| L-aspartate catabolism | peb1C | med | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 47% | 99% | 223.8 | Arginine transport ATP-binding protein ArtM | 59% | 281.2 |
| L-histidine catabolism | PA5503 | med | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) | 44% | 72% | 180.6 | Arginine transport ATP-binding protein ArtM | 59% | 281.2 |
Sequence Analysis Tools
View RR42_RS07815 at FitnessBrowser
Find papers: PaperBLAST
Find functional residues: SitesBLAST
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Predict transmenbrane helices: Phobius
Predict protein localization: PSORTb
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Sequence
MIKMEQLSKSYGAHRVLSNIDAEIRQGEVVCLIGPSGSGKSTMLRCINGLEQYQGGSITI
DGERVNAASPGIRQIRQRVSMVFQRFNLFPHRTALENVMEGPVHVKKESVAEAKERAAEI
LASVGLAEKMAHYPTQLSGGQQQRVAIARALAMRPDAILFDEPTSALDPELVGEVLGVMR
KLAEKGMTMVIVTHEMKFAREVSNRVLFLDGGRIAEQGPSAQVLTQPSNERMQDFLRRVT
HAG
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:
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