Protein WP_036134518.1 in Lysobacter daejeonensis GH1-9
Annotation: NCBI__GCF_000768355.1:WP_036134518.1
Length: 244 amino acids
Source: GCF_000768355.1 in NCBI
Candidate for 23 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 ArtP; EC 7.4.2.- (characterized) | 41% | 86% | 130.2 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 45% | 189.1 |
| L-histidine catabolism | PA5503 | lo | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) | 42% | 64% | 157.5 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 45% | 189.1 |
| D-cellobiose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 61% | 144.8 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 45% | 189.1 |
| D-glucose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 61% | 144.8 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 45% | 189.1 |
| lactose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 61% | 144.8 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 45% | 189.1 |
| D-maltose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 61% | 144.8 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 45% | 189.1 |
| sucrose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 61% | 144.8 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 45% | 189.1 |
| trehalose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 61% | 144.8 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 45% | 189.1 |
| L-asparagine catabolism | bgtA | lo | ATPase (characterized, see rationale) | 39% | 92% | 144.4 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 45% | 189.1 |
| L-aspartate catabolism | bgtA | lo | ATPase (characterized, see rationale) | 39% | 92% | 144.4 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 45% | 189.1 |
| D-glucosamine (chitosamine) catabolism | AO353_21725 | lo | ABC transporter for D-Glucosamine, putative ATPase component (characterized) | 39% | 89% | 142.1 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 45% | 189.1 |
| xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 40% | 60% | 135.6 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 45% | 189.1 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 36% | 68% | 133.7 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 45% | 189.1 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 36% | 68% | 133.7 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 45% | 189.1 |
| L-asparagine catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 36% | 86% | 129.8 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 45% | 189.1 |
| L-aspartate catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 36% | 86% | 129.8 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 45% | 189.1 |
| D-mannitol catabolism | mtlK | lo | ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) | 37% | 57% | 129.8 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 45% | 189.1 |
| D-glucosamine (chitosamine) catabolism | SM_b21216 | lo | ABC transporter for D-Glucosamine, ATPase component (characterized) | 36% | 57% | 129 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 45% | 189.1 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 36% | 56% | 128.6 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 45% | 189.1 |
| D-cellobiose catabolism | cbtF | lo | CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) | 31% | 59% | 94.4 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 45% | 189.1 |
| D-alanine catabolism | AZOBR_RS08250 | lo | Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) | 31% | 84% | 87.4 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 45% | 189.1 |
| L-proline catabolism | AZOBR_RS08250 | lo | Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) | 31% | 84% | 87.4 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 45% | 189.1 |
| L-proline catabolism | HSERO_RS00900 | lo | ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) | 31% | 85% | 80.1 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 45% | 189.1 |
Sequence Analysis Tools
Find papers: PaperBLAST
Find functional residues: SitesBLAST
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Predict transmenbrane helices: Phobius
Predict protein localization: PSORTb
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Sequence
MATAPSPLDPPQPVFRARGLTKVYRMGDVDVHALRGIDLDLFAGEFVVLLGASGSGKSTL
LNILGGLDAPTSGEVECQGHPLTGADEAVLTRFRREHVGFVFQFYNLIPSLTARENVALV
TEIAEQPMLPEEALALVGLKERMDHFPAQLSGGEQQRVAIARAIAKRPAVLLCDEPTGAL
DSPTGILVLQALERINHETGALTVVITHNEVIAGMADRVIRLSDGRVISQERNPARQPAS
GLRW
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