Protein PfGW456L13_2830 in Pseudomonas fluorescens GW456-L13
Annotation: FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2830
Length: 361 amino acids
Source: pseudo13_GW456_L13 in FitnessBrowser
Candidate for 22 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) | 44% | 94% | 291.2 | Uncharacterized ABC transporter ATP-binding protein YdcT | 47% | 292.0 |
D-cellobiose catabolism | gtsD | med | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 44% | 85% | 254.2 | Uncharacterized ABC transporter ATP-binding protein YdcT | 47% | 292.0 |
D-glucose catabolism | gtsD | med | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 44% | 85% | 254.2 | Uncharacterized ABC transporter ATP-binding protein YdcT | 47% | 292.0 |
lactose catabolism | gtsD | med | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 44% | 85% | 254.2 | Uncharacterized ABC transporter ATP-binding protein YdcT | 47% | 292.0 |
D-maltose catabolism | gtsD | med | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 44% | 85% | 254.2 | Uncharacterized ABC transporter ATP-binding protein YdcT | 47% | 292.0 |
sucrose catabolism | gtsD | med | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 44% | 85% | 254.2 | Uncharacterized ABC transporter ATP-binding protein YdcT | 47% | 292.0 |
trehalose catabolism | gtsD | med | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 44% | 85% | 254.2 | Uncharacterized ABC transporter ATP-binding protein YdcT | 47% | 292.0 |
D-galactose catabolism | PfGW456L13_1897 | med | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 42% | 93% | 251.9 | Uncharacterized ABC transporter ATP-binding protein YdcT | 47% | 292.0 |
D-xylose catabolism | gtsD | med | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 40% | 93% | 250.8 | Uncharacterized ABC transporter ATP-binding protein YdcT | 47% | 292.0 |
D-maltose catabolism | malK_Bb | med | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 51% | 70% | 248.4 | Uncharacterized ABC transporter ATP-binding protein YdcT | 47% | 292.0 |
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) | 41% | 89% | 247.7 | Uncharacterized ABC transporter ATP-binding protein YdcT | 47% | 292.0 |
D-sorbitol (glucitol) catabolism | mtlK | med | ABC transporter for D-Sorbitol, ATPase component (characterized) | 43% | 78% | 239.2 | Uncharacterized ABC transporter ATP-binding protein YdcT | 47% | 292.0 |
xylitol catabolism | HSERO_RS17020 | med | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 44% | 72% | 237.7 | Uncharacterized ABC transporter ATP-binding protein YdcT | 47% | 292.0 |
D-maltose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 41% | 86% | 234.6 | Uncharacterized ABC transporter ATP-binding protein YdcT | 47% | 292.0 |
sucrose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 41% | 86% | 234.6 | Uncharacterized ABC transporter ATP-binding protein YdcT | 47% | 292.0 |
trehalose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 41% | 86% | 234.6 | Uncharacterized ABC transporter ATP-binding protein YdcT | 47% | 292.0 |
D-glucosamine (chitosamine) catabolism | SM_b21216 | med | ABC transporter for D-Glucosamine, ATPase component (characterized) | 41% | 89% | 233 | Uncharacterized ABC transporter ATP-binding protein YdcT | 47% | 292.0 |
D-cellobiose catabolism | SMc04256 | med | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 43% | 87% | 227.3 | Uncharacterized ABC transporter ATP-binding protein YdcT | 47% | 292.0 |
lactose catabolism | lacK | lo | ABC transporter for Lactose, ATPase component (characterized) | 39% | 98% | 250.4 | Uncharacterized ABC transporter ATP-binding protein YdcT | 47% | 292.0 |
D-mannitol catabolism | mtlK | lo | ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) | 39% | 96% | 248.4 | Uncharacterized ABC transporter ATP-binding protein YdcT | 47% | 292.0 |
D-maltose catabolism | malK_Sm | lo | MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) | 40% | 91% | 238 | Uncharacterized ABC transporter ATP-binding protein YdcT | 47% | 292.0 |
trehalose catabolism | malK | lo | MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) | 40% | 91% | 238 | Uncharacterized ABC transporter ATP-binding protein YdcT | 47% | 292.0 |
Sequence Analysis Tools
View PfGW456L13_2830 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
Fitness BLAST: loading...
Sequence
MGHPTAIEVRNVSKRYSDDPGLAPALDNVSVDIADNEFFTLLGPSGCGKTTLLRTIAGFE
HVSDGEIRLAGEPVNDLPPFKRRVNTVFQSYALFPHMSVAQNIAFGLEMQGLDRKLIPQR
VDEMLALVQMQHLAKRKPAELSGGQQQRVALARALAPKPKVLLLDEPLSALDLKLRKEMQ
VELKRVQKEAGITFIFVTHDQEEALTLSDRIAVMSAGKILQIGSPNEIYERPQHQFVAQF
IGDINFLPGHIKRGQQNEKLFVPNGMPVEIPCPAQGFDGSKVQLAFRPERSQLVEPTQPH
HLRGVIEAVLYVGTATLYQCRLNNDIKVMLRENNEGLNHGRVVGDRVAVNLPPHACLLME
A
This GapMind analysis is from Sep 17 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