GapMind for catabolism of small carbon sources

 

Protein Pf6N2E2_1005 in Pseudomonas fluorescens FW300-N2E2

Annotation: Ribose ABC transport system, periplasmic ribose-binding protein RbsB (TC 3.A.1.2.1)

Length: 317 amino acids

Source: pseudo6_N2E2 in FitnessBrowser

Candidate for 4 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
myo-inositol catabolism ibpA hi Inositol ABC transporter, periplasmic inositol-binding protein IbpA, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved (characterized) 45% 96% 260.8 RbsB, component of The probable autoinducer-2 (AI-2;, a furanosyl borate diester: 3aS,6S,6aR)-2,2,6,6a-tetrahydroxy-3a-methyltetrahydrofuro[3,2-d][1,3,2]dioxaborolan-2-uide) uptake porter (Shao et al., 2007) (50-70% identical to RbsABC of E. coli; TC# 3.A.1.2.1) 31% 147.9
myo-inositol catabolism PS417_11885 lo Rhizopine-binding protein (characterized, see rationale) 31% 98% 138.3 Inositol ABC transporter, periplasmic inositol-binding protein IbpA, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved 45% 260.8
L-arabinose catabolism araUsh lo Periplasmic binding protein/LacI transcriptional regulator (characterized, see rationale) 33% 72% 124.4 Inositol ABC transporter, periplasmic inositol-binding protein IbpA, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved 45% 260.8
D-galactose catabolism ytfQ lo Galactofuranose-binding protein YtfQ (characterized) 31% 71% 112.1 Inositol ABC transporter, periplasmic inositol-binding protein IbpA, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved 45% 260.8

Sequence Analysis Tools

View Pf6N2E2_1005 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

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

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MKAQKGGLLCSAVLAAGLTFQLSPAFAAGEKILINFQTLSIPYFIYMHEQASQEAKVLNV
ELLVQDAQSSSTKQSSDVENALTQGVDAMVVAPNDVTALAPALNEVLSEKVPLVTVDRRV
EGTDTPVPYVTADSVAGGRLMAELVTSNMKNGARVAFIGGTPGSSTAIDRAKGVHEGLKA
GGGKFQLVAEQSGEWERAKAMSVAENILTSLSANPPDAIICASGDMALGAAEAVRATGLK
GKVKVIGFDAYPEVLRAIRDGDIAGIVEQSPSKQIRTALRMAVKKVRGEGELETVIVQPF
MITPENLSQAEQYSAIQ

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:

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 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