GapMind for catabolism of small carbon sources

 

Protein Pf1N1B4_2538 in Pseudomonas fluorescens FW300-N1B4

Annotation: Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)

Length: 374 amino acids

Source: pseudo1_N1B4 in FitnessBrowser

Candidate for 15 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% 269.6 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 313.5
D-maltose catabolism malK med Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 43% 83% 253.4 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 313.5
D-maltose catabolism malK_Aa med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 47% 75% 248.8 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 313.5
D-maltose catabolism musK med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 46% 78% 245.7 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 313.5
L-arabinose catabolism xacK med Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 46% 79% 238.4 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 313.5
D-maltose catabolism malK_Bb med ABC-type maltose transport, ATP binding protein (characterized, see rationale) 41% 93% 238 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 313.5
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 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 313.5
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 89% 209.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 313.5
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 89% 209.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 313.5
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 89% 209.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 313.5
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 89% 209.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 313.5
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 89% 209.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 313.5
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 89% 209.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 313.5
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 89% 209.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 313.5
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 89% 209.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 47% 313.5

Sequence Analysis Tools

View Pf1N1B4_2538 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MSQVDSSAGASDILVSFRGVQKSYDGENLIVKDLNLDIRKGEFLTLLGPSGSGKTTSLMM
LAGFETPTAGEIQLAGRSINNVPPHKRDIGMVFQNYALFPHMTVAENLAFPLTVRGLNKN
DVSDRVKRVLSMVQLDTFAQRYPAQLSGGQQQRVALARALVFEPQLVLMDEPLGALDKQL
REHMQMEIKHLHQRLGVTVVYVTHDQGEALTMSDRVAVFHQGEIQQIAPPRSLYEEPKNT
FVANFIGENNRLNGRLHSHTGDRCVVELGRGEKVEALAVNVGKTGEPVTLSIRPERVSLN
GSSESCVNRFSGRVAEFIYLGDHVRVRLEVCGKTDFFVKQPIAELDPALAVGDVVPLGWQ
VEHVRALDPLLEAH

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, 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