Protein AO353_07265 in Pseudomonas fluorescens FW300-N2E3
Annotation: FitnessBrowser__pseudo3_N2E3:AO353_07265
Length: 374 amino acids
Source: pseudo3_N2E3 in FitnessBrowser
Candidate for 23 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| putrescine catabolism | potA | med | PotG aka B0855, component of Putrescine porter (characterized) | 45% | 93% | 272.3 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 315.5 |
| D-maltose catabolism | malK | med | Maltose-transporting ATPase (EC 3.6.3.19) (characterized) | 43% | 83% | 254.2 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 315.5 |
| D-maltose catabolism | musK | med | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 46% | 78% | 249.6 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 315.5 |
| D-maltose catabolism | malK_Aa | med | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 47% | 75% | 248.1 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 315.5 |
| D-maltose catabolism | malK1 | med | 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) | 44% | 87% | 245.7 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 315.5 |
| trehalose catabolism | thuK | med | 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) | 44% | 87% | 245.7 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 315.5 |
| D-xylose catabolism | gtsD | med | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 44% | 84% | 240.4 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 315.5 |
| D-cellobiose catabolism | msiK | med | 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) | 44% | 80% | 239.6 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 315.5 |
| lactose catabolism | lacK | med | LacK, component of Lactose porter (characterized) | 43% | 81% | 239.6 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 315.5 |
| D-maltose catabolism | malK_Bb | med | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 41% | 93% | 239.2 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 315.5 |
| L-arabinose catabolism | xacK | med | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 46% | 79% | 237.3 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 315.5 |
| D-cellobiose catabolism | SMc04256 | med | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 43% | 81% | 219.9 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 315.5 |
| L-proline catabolism | opuBA | med | BilEA aka OpuBA protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence) (characterized) | 41% | 75% | 193.4 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 315.5 |
| sucrose catabolism | thuK | lo | ABC transporter (characterized, see rationale) | 39% | 92% | 250.4 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 315.5 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 40% | 95% | 247.7 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 315.5 |
| D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 89% | 210.3 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 315.5 |
| D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 89% | 210.3 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 315.5 |
| D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 89% | 210.3 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 315.5 |
| lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 89% | 210.3 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 315.5 |
| D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 89% | 210.3 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 315.5 |
| D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 89% | 210.3 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 315.5 |
| sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 89% | 210.3 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 315.5 |
| trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 89% | 210.3 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 315.5 |
Sequence Analysis Tools
View AO353_07265 at FitnessBrowser
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
MSEVDSSAGANDVLVSFRGVQKSYDGENLIVKDLNLEIRKGEFLTLLGPSGSGKTTSLMM
LAGFETPTAGEILLAGRAINNVPPHKRDIGMVFQNYALFPHMTVAENLAFPLTVRGLNKS
DVSDRVKRVLSMVQLDAFAQRYPAQLSGGQQQRVALARALVFEPQLVLMDEPLGALDKQL
REHMQMEIKHLHQRLGVTVVYVTHDQGEALTMSDRVAVFHQGEIQQIAPPRELYEKPKNT
FVANFIGENNRLNGRLHSHTGDRCVVELGRGEKVEALAVNVGKTGEPVTLSIRPERVSLN
GSSESCVNRFSGRVAEFIYLGDHVRVRLEVCGKTDFFVKQPIAELDPALAVGDVVPLGWQ
VEHVRALDPLLEAN
This GapMind analysis is from Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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