GapMind for catabolism of small carbon sources

 

Protein Pf6N2E2_4408 in Pseudomonas fluorescens FW300-N2E2

Annotation: FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4408

Length: 474 amino acids

Source: pseudo6_N2E2 in FitnessBrowser

Candidate for 10 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
2-deoxy-D-ribose catabolism drdehyd-cytc lo cytochrome c component of deoxyribose dehydrogenase (characterized) 38% 91% 272.7 Fructose dehydrogenase cytochrome subunit; Fructose dehydrogenase subunit II 47% 378.3
D-cellobiose catabolism gadh2 lo Gluconate 2-dehydrogenase cytochrome c subunit; GA 2-DH cytochrome c subunit; GADH cytochrome c subunit; EC 1.1.99.3 (characterized) 39% 95% 272.3 Fructose dehydrogenase cytochrome subunit; Fructose dehydrogenase subunit II 47% 378.3
D-gluconate catabolism gadh2 lo Gluconate 2-dehydrogenase cytochrome c subunit; GA 2-DH cytochrome c subunit; GADH cytochrome c subunit; EC 1.1.99.3 (characterized) 39% 95% 272.3 Fructose dehydrogenase cytochrome subunit; Fructose dehydrogenase subunit II 47% 378.3
D-glucose catabolism gadh2 lo Gluconate 2-dehydrogenase cytochrome c subunit; GA 2-DH cytochrome c subunit; GADH cytochrome c subunit; EC 1.1.99.3 (characterized) 39% 95% 272.3 Fructose dehydrogenase cytochrome subunit; Fructose dehydrogenase subunit II 47% 378.3
lactose catabolism gadh2 lo Gluconate 2-dehydrogenase cytochrome c subunit; GA 2-DH cytochrome c subunit; GADH cytochrome c subunit; EC 1.1.99.3 (characterized) 39% 95% 272.3 Fructose dehydrogenase cytochrome subunit; Fructose dehydrogenase subunit II 47% 378.3
D-maltose catabolism gadh2 lo Gluconate 2-dehydrogenase cytochrome c subunit; GA 2-DH cytochrome c subunit; GADH cytochrome c subunit; EC 1.1.99.3 (characterized) 39% 95% 272.3 Fructose dehydrogenase cytochrome subunit; Fructose dehydrogenase subunit II 47% 378.3
sucrose catabolism gadh2 lo Gluconate 2-dehydrogenase cytochrome c subunit; GA 2-DH cytochrome c subunit; GADH cytochrome c subunit; EC 1.1.99.3 (characterized) 39% 95% 272.3 Fructose dehydrogenase cytochrome subunit; Fructose dehydrogenase subunit II 47% 378.3
trehalose catabolism gadh2 lo Gluconate 2-dehydrogenase cytochrome c subunit; GA 2-DH cytochrome c subunit; GADH cytochrome c subunit; EC 1.1.99.3 (characterized) 39% 95% 272.3 Fructose dehydrogenase cytochrome subunit; Fructose dehydrogenase subunit II 47% 378.3
ethanol catabolism adhBqn lo Alcohol dehydrogenase (quinone), cytochrome c subunit; ADH; Alcohol dehydrogenase (quinone), subunit II; Cytochrome c-553; Cytochrome c553; Ethanol:Q2 reductase; G3-ADH subunit II; Quinohemoprotein-cytochrome c complex; Ubiquinol oxidase; EC 1.1.5.5 (characterized) 37% 89% 268.9 Fructose dehydrogenase cytochrome subunit; Fructose dehydrogenase subunit II 47% 378.3
ethanol catabolism etoh-dh-c lo alcohol dehydrogenase (cytochrome c) (EC 1.1.2.8) (characterized) 37% 90% 264.2 Fructose dehydrogenase cytochrome subunit; Fructose dehydrogenase subunit II 47% 378.3

Sequence Analysis Tools

View Pf6N2E2_4408 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

MYPQRRDQPLPGVGKVKSMRNMLAGGLALMTISLATHGETLDTSASPGKRLAVAADCVAC
HSTVGGKPFAGGYPLNSPMGTIYSTNITPSRSAGIGQYTQADFARAVRDGVTPDGTHLYP
AMPYTSYAKMTDSDVAALYQYFMDEVEPVDTPSPKTELDFPFNIRASMLGWNALFHRQKR
FEADPGKSAQVNRGDYLVNALAHCDTCHTPRNVLMAADNAKALSGGSLGAWYAPNITSDK
TSGIGAWSSDELVAYLRSGHVEGKAQAAGPMAEAVEHSLQYLGEEDLKAIAAYLLQTQPI
ATGERQARHTFGQASNDELNLRGGKPQDNPGWHIFSGTCANCHQANGEGTREYPSLFHNT
ATSRRDNLIATIVYGVHREVDGVAIDMPAFGPGALFTDRLDDQQIADVSNYVLSRYGNAG
LNVTAADVAQVREGGPKAPIAVLARYSVPALVVLGLLIILGLYRLKARRRLQEA

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:

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