GapMind for catabolism of small carbon sources

 

Protein AO353_15980 in Pseudomonas fluorescens FW300-N2E3

Annotation: FitnessBrowser__pseudo3_N2E3:AO353_15980

Length: 480 amino acids

Source: pseudo3_N2E3 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
trehalose catabolism treB hi Trehalose permease IIC protein (characterized, see rationale) 100% 100% 937.2 protein-Npi-phosphohistidine-sucrose phosphotransferase (EC 2.7.1.211) 45% 442.2
sucrose catabolism sacP med protein-Npi-phosphohistidine-sucrose phosphotransferase (EC 2.7.1.211) (characterized) 45% 99% 442.2 PTS system trehalose-specific EIIBC component; EIIBC-Tre; EII-Tre; EC 2.7.1.201 52% 485.7
sucrose catabolism ptsS med protein-Npi-phosphohistidine-sucrose phosphotransferase (EC 2.7.1.211) (characterized) 41% 71% 367.1 PTS system trehalose-specific EIIBC component; EIIBC-Tre; EII-Tre; EC 2.7.1.201 52% 485.7
D-cellobiose catabolism bglF lo β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized) 31% 71% 221.1 PTS system trehalose-specific EIIBC component; EIIBC-Tre; EII-Tre; EC 2.7.1.201 52% 485.7
D-cellobiose catabolism bglG lo β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized) 31% 71% 221.1 PTS system trehalose-specific EIIBC component; EIIBC-Tre; EII-Tre; EC 2.7.1.201 52% 485.7
D-glucose catabolism bglF lo β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized) 31% 71% 221.1 PTS system trehalose-specific EIIBC component; EIIBC-Tre; EII-Tre; EC 2.7.1.201 52% 485.7
lactose catabolism bglF lo β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized) 31% 71% 221.1 PTS system trehalose-specific EIIBC component; EIIBC-Tre; EII-Tre; EC 2.7.1.201 52% 485.7
D-maltose catabolism bglF lo β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized) 31% 71% 221.1 PTS system trehalose-specific EIIBC component; EIIBC-Tre; EII-Tre; EC 2.7.1.201 52% 485.7
sucrose catabolism bglF lo β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized) 31% 71% 221.1 PTS system trehalose-specific EIIBC component; EIIBC-Tre; EII-Tre; EC 2.7.1.201 52% 485.7
trehalose catabolism bglF lo β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized) 31% 71% 221.1 PTS system trehalose-specific EIIBC component; EIIBC-Tre; EII-Tre; EC 2.7.1.201 52% 485.7

Sequence Analysis Tools

View AO353_15980 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

MSHDYPTIASELLHSLGGADNLEQAAHCVTRLRLALKDPQRVDSATLNQIDLVKGSFFTG
GLFQVVIGPGEVEKVYAALRQQTGLAASTIADVKQKGADKTNAMQRLVRVFSDVFMPILP
ALIIAGLLMGVNNLIGAKGMFIAGKTLLEAYPTLDGVWSLINLMANTSFVFLPALVGWSA
AKRFGGSEILGIVLGLMLVHPDLLNAWNYGKAVAGLDGQSLPYFDIFGWFKIEKVGYQGQ
ILPILMAAYVMSVIEKWLRARVPNAIQLLVVPITTIVVTGVLALAVIGPVTRHLGILITE
GVVTLFDLAPMVGGAIFGLLYAPLVITGMHHMFLAVDLQLISTQGGTFIWPMIVMSNLAQ
GSAALGVFYMTRSARDKSMASTSAISAYFGITEPAMFGVNLRYKFPFYAALSGSALGCMF
LSLNKVQASAIGVGGLPGFISIIPQFIPMFIVGMVIAMVVPFVLTCGMSMKIVRAGYRVA

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