Protein WP_052338455.1 in Luteimonas huabeiensis HB2
Annotation: NCBI__GCF_000559025.1:WP_052338455.1
Length: 246 amino acids
Source: GCF_000559025.1 in NCBI
Candidate for 40 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| D-glucosamine (chitosamine) catabolism | AO353_21725 | med | ABC transporter for D-Glucosamine, putative ATPase component (characterized) | 41% | 87% | 154.5 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 52% | 232.3 |
| L-arginine catabolism | artP | med | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 41% | 87% | 152.1 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 52% | 232.3 |
| L-histidine catabolism | bgtA | med | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 41% | 87% | 152.1 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 52% | 232.3 |
| L-lysine catabolism | hisP | med | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 41% | 87% | 152.1 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 52% | 232.3 |
| L-histidine catabolism | hutV | med | ABC transporter for L-Histidine, ATPase component (characterized) | 41% | 76% | 132.5 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 52% | 232.3 |
| L-asparagine catabolism | bgtA | lo | ATPase (characterized, see rationale) | 40% | 89% | 156.8 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 52% | 232.3 |
| L-aspartate catabolism | bgtA | lo | ATPase (characterized, see rationale) | 40% | 89% | 156.8 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 52% | 232.3 |
| putrescine catabolism | potA | lo | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) | 39% | 57% | 147.1 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 52% | 232.3 |
| L-histidine catabolism | aapP | lo | ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) | 37% | 90% | 146 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 52% | 232.3 |
| L-histidine catabolism | hisP | lo | Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) | 37% | 95% | 146 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 52% | 232.3 |
| D-cellobiose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 37% | 57% | 140.6 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 52% | 232.3 |
| D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 37% | 57% | 140.6 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 52% | 232.3 |
| D-glucose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 37% | 57% | 140.6 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 52% | 232.3 |
| lactose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 37% | 57% | 140.6 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 52% | 232.3 |
| D-maltose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 37% | 57% | 140.6 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 52% | 232.3 |
| sucrose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 37% | 57% | 140.6 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 52% | 232.3 |
| trehalose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 37% | 57% | 140.6 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 52% | 232.3 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 38% | 64% | 139.8 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 52% | 232.3 |
| L-asparagine catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 34% | 92% | 139 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 52% | 232.3 |
| L-aspartate catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 34% | 92% | 139 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 52% | 232.3 |
| L-glutamate catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 34% | 92% | 139 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 52% | 232.3 |
| L-leucine catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 34% | 92% | 139 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 52% | 232.3 |
| L-proline catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 34% | 92% | 139 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 52% | 232.3 |
| L-proline catabolism | proV | lo | glycine betaine/l-proline transport atp-binding protein prov (characterized) | 40% | 52% | 139 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 52% | 232.3 |
| L-asparagine catabolism | aatP | lo | ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) | 37% | 89% | 137.5 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 52% | 232.3 |
| L-aspartate catabolism | aatP | lo | ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) | 37% | 89% | 137.5 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 52% | 232.3 |
| L-glutamate catabolism | gltL | lo | ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) | 37% | 89% | 137.5 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 52% | 232.3 |
| D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 38% | 59% | 131 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 52% | 232.3 |
| D-glucosamine (chitosamine) catabolism | SM_b21216 | lo | ABC transporter for D-Glucosamine, ATPase component (characterized) | 36% | 63% | 130.6 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 52% | 232.3 |
| L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 37% | 54% | 128.6 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 52% | 232.3 |
| trehalose catabolism | treV | lo | TreV, component of Trehalose porter (characterized) | 32% | 65% | 127.5 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 52% | 232.3 |
| 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% | 55% | 120.6 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 52% | 232.3 |
| 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% | 55% | 120.6 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 52% | 232.3 |
| 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% | 55% | 120.6 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 52% | 232.3 |
| D-cellobiose catabolism | TM0027 | lo | TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) | 32% | 88% | 112.5 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 52% | 232.3 |
| L-isoleucine catabolism | livF | lo | high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized) | 32% | 84% | 93.6 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 52% | 232.3 |
| L-leucine catabolism | livF | lo | high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized) | 32% | 84% | 93.6 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 52% | 232.3 |
| L-phenylalanine catabolism | livF | lo | high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized) | 32% | 84% | 93.6 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 52% | 232.3 |
| L-valine catabolism | livF | lo | high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized) | 32% | 84% | 93.6 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 52% | 232.3 |
| D-cellobiose catabolism | TM0028 | lo | TM0028, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) | 31% | 69% | 89 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 52% | 232.3 |
Sequence Analysis Tools
View WP_052338455.1 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
MSAARAGVPVIETRGLGKVYSPGTEAEVVALRGVDLRIAHGDFVAIMGPSGSGKSTLMNL
IGCLDTPSSGAYFCDGVDVSTLDPEALAGLRRDKIGFVFQGFHLLPRMSALENVAMPLGY
ARVPPAERVERAQQALESVGLGARASHRPNELSGGQQQRVAIARALINRPPVLLADEPTG
ALDSRTGEEILALFKRLRDDGHTVVLITHDADVAAHADRTFVMRDGELHEEPGPGMGETG
PETARP
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