Protein WP_066601534.1 in Sphingobium czechense LL01
Annotation: NCBI__GCF_001046645.1:WP_066601534.1
Length: 225 amino acids
Source: GCF_001046645.1 in NCBI
Candidate for 25 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-asparagine catabolism | bgtA | med | ATPase (characterized, see rationale) | 40% | 78% | 132.9 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 207.2 |
| L-aspartate catabolism | bgtA | med | ATPase (characterized, see rationale) | 40% | 78% | 132.9 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 207.2 |
| D-cellobiose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 61% | 140.2 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 207.2 |
| D-glucose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 61% | 140.2 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 207.2 |
| lactose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 61% | 140.2 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 207.2 |
| D-maltose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 61% | 140.2 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 207.2 |
| sucrose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 61% | 140.2 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 207.2 |
| trehalose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 61% | 140.2 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 207.2 |
| L-glutamate catabolism | gltL | lo | GluA aka CGL1950, component of Glutamate porter (characterized) | 39% | 88% | 138.3 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 207.2 |
| D-glucosamine (chitosamine) catabolism | AO353_21725 | lo | ABC transporter for D-Glucosamine, putative ATPase component (characterized) | 37% | 86% | 136.7 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 207.2 |
| L-arginine catabolism | artP | lo | Arginine transport ATP-binding protein ArtM (characterized) | 38% | 89% | 136 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 207.2 |
| L-lysine catabolism | hisP | lo | Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) | 38% | 82% | 134 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 207.2 |
| L-citrulline catabolism | AO353_03040 | lo | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 36% | 83% | 128.6 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 207.2 |
| D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 33% | 61% | 127.5 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 207.2 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 36% | 62% | 127.5 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 207.2 |
| L-asparagine catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 38% | 76% | 118.6 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 207.2 |
| L-aspartate catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 38% | 76% | 118.6 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 207.2 |
| D-mannitol catabolism | mtlK | lo | MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) | 33% | 57% | 117.1 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 207.2 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 35% | 63% | 116.7 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 207.2 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 35% | 63% | 116.7 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 207.2 |
| L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 36% | 55% | 115.5 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 207.2 |
| D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 36% | 53% | 114.8 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 207.2 |
| D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 35% | 53% | 112.1 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 207.2 |
| trehalose catabolism | treV | lo | TreV, component of Trehalose porter (characterized) | 33% | 60% | 112.1 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 207.2 |
| L-histidine catabolism | Ac3H11_2560 | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 36% | 74% | 109 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 207.2 |
Sequence Analysis Tools
View WP_066601534.1 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
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Sequence
MNDILKVTGLARSFTQGGVTIDVLRGIDLTVGPGEIVALLGPSGSGKSTLLQAVGLLEGG
FDGSIRIDGEEAAKLDNDGRTRLRRDALGFVYQFHHLLPDFNATENVILPQVIRDVEMPA
AKARAESLLTALGLGHRLDHRPSQLSGGEQQRVAVARALANRPALVLADEPTGNLDERTA
DVVLSEFLRLVRGEGSAALVATHNERLAQKMDRVVRLHEGVLQGA
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