Protein WP_010529868.1 in Lentibacillus jeotgali Grbi
Annotation: NCBI__GCF_000224785.1:WP_010529868.1
Length: 404 amino acids
Source: GCF_000224785.1 in NCBI
Candidate for 35 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-proline catabolism | opuBA | med | BusAA, component of Uptake system for glycine-betaine (high affinity) and proline (low affinity) (OpuAA-OpuABC) or BusAA-ABC of Lactococcus lactis). BusAA, the ATPase subunit, has a C-terminal tandem cystathionine β-synthase (CBS) domain which is the cytoplasmic K+ sensor for osmotic stress (osmotic strength)while the BusABC subunit has the membrane and receptor domains fused to each other (Biemans-Oldehinkel et al., 2006; Mahmood et al., 2006; Gul et al. 2012). An N-terminal amphipathic α-helix of OpuA is necessary for high activity but is not critical for biogenesis or the ionic regulation of transport (characterized) | 58% | 97% | 454.9 | ABC-type quaternary amine transporter (EC 7.6.2.9) | 66% | 530.8 |
| L-proline catabolism | proV | med | glycine betaine/l-proline transport atp-binding protein prov (characterized) | 50% | 99% | 383.6 | ABC-type quaternary amine transporter (EC 7.6.2.9) | 66% | 530.8 |
| L-histidine catabolism | hutV | med | ABC transporter for L-Histidine, ATPase component (characterized) | 58% | 96% | 317.8 | ABC-type quaternary amine transporter (EC 7.6.2.9) | 66% | 530.8 |
| L-proline catabolism | hutV | med | HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) | 55% | 96% | 298.9 | ABC-type quaternary amine transporter (EC 7.6.2.9) | 66% | 530.8 |
| L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 34% | 92% | 186 | ABC-type quaternary amine transporter (EC 7.6.2.9) | 66% | 530.8 |
| putrescine catabolism | potA | lo | Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized) | 37% | 69% | 182.6 | ABC-type quaternary amine transporter (EC 7.6.2.9) | 66% | 530.8 |
| L-arabinose catabolism | xacK | lo | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 35% | 64% | 175.6 | ABC-type quaternary amine transporter (EC 7.6.2.9) | 66% | 530.8 |
| D-maltose catabolism | musK | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 38% | 61% | 172.2 | ABC-type quaternary amine transporter (EC 7.6.2.9) | 66% | 530.8 |
| D-mannitol catabolism | mtlK | lo | ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) | 36% | 69% | 171.4 | ABC-type quaternary amine transporter (EC 7.6.2.9) | 66% | 530.8 |
| D-cellobiose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 30% | 78% | 171 | ABC-type quaternary amine transporter (EC 7.6.2.9) | 66% | 530.8 |
| D-glucose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 30% | 78% | 171 | ABC-type quaternary amine transporter (EC 7.6.2.9) | 66% | 530.8 |
| lactose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 30% | 78% | 171 | ABC-type quaternary amine transporter (EC 7.6.2.9) | 66% | 530.8 |
| D-maltose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 30% | 78% | 171 | ABC-type quaternary amine transporter (EC 7.6.2.9) | 66% | 530.8 |
| sucrose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 30% | 78% | 171 | ABC-type quaternary amine transporter (EC 7.6.2.9) | 66% | 530.8 |
| trehalose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 30% | 78% | 171 | ABC-type quaternary amine transporter (EC 7.6.2.9) | 66% | 530.8 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) | 31% | 96% | 169.1 | ABC-type quaternary amine transporter (EC 7.6.2.9) | 66% | 530.8 |
| D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 31% | 85% | 168.7 | ABC-type quaternary amine transporter (EC 7.6.2.9) | 66% | 530.8 |
| D-cellobiose catabolism | msiK | lo | MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized) | 34% | 77% | 167.9 | ABC-type quaternary amine transporter (EC 7.6.2.9) | 66% | 530.8 |
| D-maltose catabolism | malK_Aa | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 36% | 56% | 165.6 | ABC-type quaternary amine transporter (EC 7.6.2.9) | 66% | 530.8 |
| D-maltose catabolism | thuK | lo | Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) | 36% | 61% | 165.6 | ABC-type quaternary amine transporter (EC 7.6.2.9) | 66% | 530.8 |
| D-mannose catabolism | TT_C0211 | lo | Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) | 36% | 61% | 165.6 | ABC-type quaternary amine transporter (EC 7.6.2.9) | 66% | 530.8 |
| sucrose catabolism | thuK | lo | Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) | 36% | 61% | 165.6 | ABC-type quaternary amine transporter (EC 7.6.2.9) | 66% | 530.8 |
| trehalose catabolism | thuK | lo | Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) | 36% | 61% | 165.6 | ABC-type quaternary amine transporter (EC 7.6.2.9) | 66% | 530.8 |
| D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 31% | 85% | 165.2 | ABC-type quaternary amine transporter (EC 7.6.2.9) | 66% | 530.8 |
| L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 36% | 62% | 164.5 | ABC-type quaternary amine transporter (EC 7.6.2.9) | 66% | 530.8 |
| D-glucosamine (chitosamine) catabolism | SM_b21216 | lo | ABC transporter for D-Glucosamine, ATPase component (characterized) | 34% | 65% | 160.6 | ABC-type quaternary amine transporter (EC 7.6.2.9) | 66% | 530.8 |
| D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 37% | 63% | 159.5 | ABC-type quaternary amine transporter (EC 7.6.2.9) | 66% | 530.8 |
| trehalose catabolism | treV | lo | TreV, component of Trehalose porter (characterized) | 34% | 80% | 156.4 | ABC-type quaternary amine transporter (EC 7.6.2.9) | 66% | 530.8 |
| L-asparagine catabolism | aatP | lo | ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) | 39% | 92% | 151.8 | ABC-type quaternary amine transporter (EC 7.6.2.9) | 66% | 530.8 |
| L-aspartate catabolism | aatP | lo | ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) | 39% | 92% | 151.8 | ABC-type quaternary amine transporter (EC 7.6.2.9) | 66% | 530.8 |
| L-histidine catabolism | Ac3H11_2560 | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 37% | 92% | 151.8 | ABC-type quaternary amine transporter (EC 7.6.2.9) | 66% | 530.8 |
| xylitol catabolism | HSERO_RS17020 | lo | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 35% | 51% | 149.1 | ABC-type quaternary amine transporter (EC 7.6.2.9) | 66% | 530.8 |
| L-arginine catabolism | artP | lo | ABC transporter for L-Arginine, putative ATPase component (characterized) | 34% | 95% | 145.2 | ABC-type quaternary amine transporter (EC 7.6.2.9) | 66% | 530.8 |
| L-citrulline catabolism | AO353_03040 | lo | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 32% | 98% | 132.9 | ABC-type quaternary amine transporter (EC 7.6.2.9) | 66% | 530.8 |
| glycerol catabolism | glpS | lo | GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) | 30% | 61% | 120.6 | ABC-type quaternary amine transporter (EC 7.6.2.9) | 66% | 530.8 |
Sequence Analysis Tools
View WP_010529868.1 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
Fitness BLAST: loading...
Sequence
MSKIKVDRLTKIFGRRPKQAIKYLEENKSKDEILELTGMTVGVNQASFDVEDGEVFVIMG
LSGSGKSTLVRMLNRLIEPTSGSVWLDDDNITEMNKEQLRNVRRKKMSMVFQNFALLPHK
SILKNAEYGLEIQGIDSEEREKKASEALELVGLGGYLEKRPSELSGGMQQRVGLARALAN
DPEILLMDEAFSALDPLIRKDMQDELMDLQQRVHKTIIFITHDLDEALRIGDRIALMKDG
SIVQIGTAEEILMDPANDYVERFVEDVDLAKVLTAAHVMKRAETVAVDRGPKVALQLMKN
DGVSTIYVVDKKQKLLGYVTADQAATAAKEGKGLEEILTSDIPTAHPETLLSDLFEPMSD
DKAPLSVVDDSGKLVGIVVRGAIIGALAGNDEVMNGNGGDVTDG
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Links
Downloads
Related tools
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