Protein WP_089220514.1 in Sphingomonas laterariae LNB2
Annotation: NCBI__GCF_900188165.1:WP_089220514.1
Length: 233 amino acids
Source: GCF_900188165.1 in NCBI
Candidate for 26 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 | med | Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) | 40% | 84% | 153.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 214.5 |
| 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) | 40% | 81% | 142.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 214.5 |
| L-glutamate catabolism | gltL | lo | GluA aka CGL1950, component of Glutamate porter (characterized) | 40% | 92% | 153.3 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 214.5 |
| L-asparagine catabolism | aatP | lo | ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized) | 38% | 91% | 149.4 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 214.5 |
| L-aspartate catabolism | aatP | lo | ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized) | 38% | 91% | 149.4 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 214.5 |
| D-cellobiose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 38% | 61% | 147.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 214.5 |
| D-glucose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 38% | 61% | 147.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 214.5 |
| lactose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 38% | 61% | 147.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 214.5 |
| D-maltose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 38% | 61% | 147.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 214.5 |
| sucrose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 38% | 61% | 147.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 214.5 |
| trehalose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 38% | 61% | 147.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 214.5 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 39% | 64% | 147.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 214.5 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 39% | 64% | 147.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 214.5 |
| D-maltose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 37% | 59% | 144.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 214.5 |
| trehalose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 37% | 59% | 144.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 214.5 |
| D-glucosamine (chitosamine) catabolism | AO353_21725 | lo | ABC transporter for D-Glucosamine, putative ATPase component (characterized) | 37% | 85% | 139 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 214.5 |
| xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 36% | 62% | 132.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 214.5 |
| D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 61% | 131.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 214.5 |
| D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 61% | 131.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 214.5 |
| D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 61% | 131.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 214.5 |
| lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 61% | 131.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 214.5 |
| D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 61% | 131.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 214.5 |
| D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 61% | 131.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 214.5 |
| sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 61% | 131.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 214.5 |
| trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 61% | 131.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 214.5 |
| sucrose catabolism | thuK | lo | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 35% | 61% | 125.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 214.5 |
Sequence Analysis Tools
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
MRGGGTVLRLNHVQKAYGTPEQPIPVLHDISIDVADGEFCAILGPSGSGKSTLLNIIGVL
DHPDAGEIELGGVPIDFGSATEAARLRNQLLGFVFQSFQLLPRLTAWENVALPLLYRGTP
RPERKPRALAMLDRLGLGERVHHLPAELSGGQRQRVALARALIGDPKLVLADEPTGSLDS
VTAAEVLQLLRQLNRDFGVTLLMVTHDRGLAEACDRSIEILDGRVVSDVRRDG
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