GapMind for catabolism of small carbon sources

 

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:

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:

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:

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