Protein WP_010936527.1 in Dehalococcoides mccartyi 195
Annotation: NCBI__GCF_000011905.1:WP_010936527.1
Length: 305 amino acids
Source: GCF_000011905.1 in NCBI
Candidate for 24 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-asparagine catabolism | aatP | lo | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 35% | 91% | 125.9 | Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- | 37% | 198.4 |
| L-aspartate catabolism | aatP | lo | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 35% | 91% | 125.9 | Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- | 37% | 198.4 |
| L-glutamate catabolism | gltL | lo | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 35% | 91% | 125.9 | Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- | 37% | 198.4 |
| 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) | 31% | 91% | 123.6 | Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- | 37% | 198.4 |
| L-isoleucine catabolism | livF | lo | ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) | 35% | 95% | 122.5 | Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- | 37% | 198.4 |
| L-leucine catabolism | livF | lo | ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) | 35% | 95% | 122.5 | Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- | 37% | 198.4 |
| L-valine catabolism | livF | lo | ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) | 35% | 95% | 122.5 | Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- | 37% | 198.4 |
| L-arginine catabolism | artP | lo | Arginine transport ATP-binding protein ArtM (characterized) | 31% | 98% | 121.3 | Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- | 37% | 198.4 |
| 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) | 34% | 91% | 119.8 | Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- | 37% | 198.4 |
| 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) | 34% | 91% | 119.8 | Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- | 37% | 198.4 |
| 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) | 34% | 91% | 119.8 | Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- | 37% | 198.4 |
| L-phenylalanine catabolism | livF | lo | High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale) | 31% | 96% | 115.5 | Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- | 37% | 198.4 |
| D-glucosamine (chitosamine) catabolism | AO353_21725 | lo | ABC transporter for D-glucosamine, ATPase component (characterized) | 31% | 92% | 114 | Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- | 37% | 198.4 |
| L-arabinose catabolism | xylGsa | lo | Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) | 31% | 98% | 112.5 | Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- | 37% | 198.4 |
| D-cellobiose catabolism | mglA | lo | glucose transporter, ATPase component (characterized) | 31% | 84% | 110.5 | Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- | 37% | 198.4 |
| D-glucose catabolism | mglA | lo | glucose transporter, ATPase component (characterized) | 31% | 84% | 110.5 | Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- | 37% | 198.4 |
| lactose catabolism | mglA | lo | glucose transporter, ATPase component (characterized) | 31% | 84% | 110.5 | Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- | 37% | 198.4 |
| D-maltose catabolism | mglA | lo | glucose transporter, ATPase component (characterized) | 31% | 84% | 110.5 | Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- | 37% | 198.4 |
| sucrose catabolism | mglA | lo | glucose transporter, ATPase component (characterized) | 31% | 84% | 110.5 | Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- | 37% | 198.4 |
| trehalose catabolism | mglA | lo | glucose transporter, ATPase component (characterized) | 31% | 84% | 110.5 | Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- | 37% | 198.4 |
| L-arginine catabolism | braG | lo | ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) | 33% | 91% | 108.6 | Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- | 37% | 198.4 |
| L-glutamate catabolism | braG | lo | ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) | 33% | 91% | 108.6 | Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- | 37% | 198.4 |
| L-histidine catabolism | braG | lo | ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) | 33% | 91% | 108.6 | Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- | 37% | 198.4 |
| L-proline catabolism | HSERO_RS00900 | lo | ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) | 31% | 95% | 104.4 | Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- | 37% | 198.4 |
Sequence Analysis Tools
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Predict protein localization: PSORTb
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Sequence
MVIQVQDLVKVYGPIRAVDGISFEVKKGEVFGMLGPNGAGKTTTTEIIEGLRDADSGSVT
VMGMDVRKQREQIKQLIGIQLQAPALLPLLNVEEILKLFTSFYRNSLPVDKLLEMVALTE
SRKVLSKNLSGGQQQRLSVAMAMVNNPEITFLDEPTTGLDPQARRGLWSVIEELRAQGKT
VFLTTHYMDEAERLCDRIAVVDHGKIIALDTPKKLISSNFKESAIEFEMEPVPSGELLGS
FPCVTSASVEGFEVILYSADVPKTMGAILDYADKNKGNTELRNLHVRQATLEDVFLKLTG
RKIRE
This GapMind analysis is from Sep 24 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