Protein WP_008485947.1 in Gallaecimonas xiamenensis 3-C-1
Annotation: NCBI__GCF_000299915.1:WP_008485947.1
Length: 229 amino acids
Source: GCF_000299915.1 in NCBI
Candidate for 27 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) | 41% | 83% | 163.3 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 209.1 |
| L-glutamate catabolism | gltL | med | GluA aka CGL1950, component of Glutamate porter (characterized) | 41% | 89% | 158.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 209.1 |
| L-arginine catabolism | artP | med | 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) | 41% | 79% | 149.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 209.1 |
| L-histidine catabolism | hisP | med | 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) | 41% | 79% | 149.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 209.1 |
| L-asparagine catabolism | aatP | lo | ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized) | 40% | 89% | 149.4 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 209.1 |
| L-aspartate catabolism | aatP | lo | ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized) | 40% | 89% | 149.4 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 209.1 |
| xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 38% | 56% | 127.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 209.1 |
| L-histidine catabolism | Ac3H11_2560 | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 38% | 76% | 125.6 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 209.1 |
| D-maltose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 37% | 53% | 124.4 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 209.1 |
| trehalose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 37% | 53% | 124.4 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 209.1 |
| trehalose catabolism | treV | lo | TreV, component of Trehalose porter (characterized) | 33% | 66% | 121.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 209.1 |
| D-cellobiose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 36% | 57% | 120.6 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 209.1 |
| D-glucose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 36% | 57% | 120.6 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 209.1 |
| lactose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 36% | 57% | 120.6 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 209.1 |
| D-maltose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 36% | 57% | 120.6 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 209.1 |
| sucrose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 36% | 57% | 120.6 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 209.1 |
| trehalose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 36% | 57% | 120.6 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 209.1 |
| D-maltose catabolism | malK1 | lo | MalK; aka Sugar ABC transporter, ATP-binding protein, component of The maltose, maltotriose, mannotetraose (MalE1)/maltose, maltotriose, trehalose (MalE2) porter (Nanavati et al., 2005). For MalG1 (823aas) and MalG2 (833aas), the C-terminal transmembrane domain with 6 putative TMSs is preceded by a single N-terminal TMS and a large (600 residue) hydrophilic region showing sequence similarity to MLP1 and 2 (9.A.14; e-12 & e-7) as well as other proteins (characterized) | 33% | 57% | 120.2 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 209.1 |
| D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 36% | 55% | 118.6 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 209.1 |
| xylitol catabolism | HSERO_RS17020 | lo | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 36% | 52% | 118.6 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 209.1 |
| D-maltose catabolism | malK | lo | Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 32% | 57% | 114.4 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 209.1 |
| 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) | 34% | 53% | 114 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 209.1 |
| 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) | 34% | 53% | 114 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 209.1 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 35% | 54% | 113.6 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 209.1 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 35% | 54% | 113.6 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 209.1 |
| trehalose catabolism | malK | lo | MsmK aka SMU.882, component of The raffinose/stachyose transporter, MsmEFGK (MalK (3.A.1.1.27) can probably substitute for MsmK; Webb et al., 2008). This system may also transport melibiose, isomaltotriose and sucrose as well as isomaltosaccharides (characterized) | 32% | 56% | 113.2 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 209.1 |
| lactose catabolism | lacK | lo | LacK, component of Lactose porter (characterized) | 32% | 59% | 112.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 209.1 |
Sequence Analysis Tools
View WP_008485947.1 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
MLKMDSIAKVYRTDTVATHALRDFSLHVKEGEFVAVTGPSGSGKTTFLNIAGLLETFEEG
QYQLDGVDVRDLKDSARSRLRNEKIGFIFQGFNLIPDLSLFDNVDVPLRYRGLGAKERKA
RIDEALEKVGLAARRHHLPSQLSGGQQQRVAIARALAGKPAFLLADEPTGNLDSLMARQV
MELLESINKDGTTIVMVTHDPDLARRAQRNIQIVDGQVSDFDFSQARRA
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