GapMind for catabolism of small carbon sources

 

Protein 8501869 in Desulfovibrio vulgaris Miyazaki F

Annotation: DvMF_2584 phosphoenolpyruvate-protein phosphotransferase (RefSeq)

Length: 846 amino acids

Source: Miya in FitnessBrowser

Candidate for 6 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-fructose catabolism fruI med Phosphotransferase system transporter enzyme I, FruI, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA (characterized) 40% 83% 463 D-trehalose PTS system, I, HPr, and IIA components 38% 453.0
sucrose catabolism fruI med Phosphotransferase system transporter enzyme I, FruI, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA (characterized) 40% 83% 463 D-trehalose PTS system, I, HPr, and IIA components 38% 453.0
glycerol catabolism dhaM med PEP-dependent dihydroxyacetone kinase, phosphoryl donor subunit DhaM; Dihydroxyacetone kinase subunit M; EC 2.7.1.121 (characterized) 41% 95% 297.4 Phosphotransferase system transporter enzyme I, FruI, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA 40% 463.0
trehalose catabolism treEIIA lo D-trehalose PTS system, I, HPr, and IIA components (characterized) 38% 95% 450.7 Phosphotransferase system transporter enzyme I, FruI, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA 40% 463.0
N-acetyl-D-glucosamine catabolism nagF lo N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized) 36% 93% 412.9 Phosphotransferase system transporter enzyme I, FruI, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA 40% 463.0
D-glucosamine (chitosamine) catabolism nagF lo N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized) 36% 93% 412.9 Phosphotransferase system transporter enzyme I, FruI, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA 40% 463.0

Sequence Analysis Tools

View 8501869 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

MVGIVVVTHSAVLGQGVKELVEQMTQGRVPLAVAGGIDDPEHPIGTDPMRVMAAIEEVQQ
GDGVLVLMDLGSALMSAETALDLLPPEVAAQVRLRPAPLVEGVMAAAVQASIGADLDTVL
REAQSALAAKAELLGMALPQDGGGVDEAAPPAAGATPAASHELTLMVPNRLGLHARPAAR
IVTALGPFVADVQLARGERVVSARSVNRIATLAVRGGETITFRAAGTDAEQALKALADLA
AENFGDLPDATKSSGRTGVEGPEGPGEQGRAGVAGVPAAKGGVPASPGIAVGPAVWHRPA
FDAPPPDLAAGDPDSEAARLDGALDAARKELAALERRTAAMAGKQEAEIFVMHRLLLDDA
TIAGDARQRIAERREPAEAAWYAVIDQAAESFRQLPEGYMRERAADLVDVGARVLRLLTG
APPSGPRLERPSVLLAADLGPSDMAHLDPALVLGIVTAQGGATSHAAILARSMGIPAVAG
AGALAASVADGVTVALDGSTGEVWIAPAPDVLSTIESRRASWLAVRQAALAGAARPAVTV
DGRHMHVHANIGSPMDAAPALQNGAEGVGLFRTEFLFLDRVAAPDEEEQRAAYVAAAAAM
PGLPVVVRTLDIGGDKPVPYLGDFAAGEENPFLGLRGIRFCLARRELFLTQLRALLRAAA
EHPLRVMFPMVAHPGELAAAKALLEEARAALAAQGLPHGPVEVGIMVEVPAAVALADQLA
RESAFFSIGTNDLAQYVMAADRGNAAVADLSDALHPAVLRMVRDTVAAGKAAGIPVAMCG
ELAGNADAIPLLVGLGLDELSMNGPAIPRAKDVVRGCDMTACVRLAGRALELPDAAAVRR
LLRDGG

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 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