GapMind for catabolism of small carbon sources

 

Protein H281DRAFT_01977 in Paraburkholderia bryophila 376MFSha3.1

Annotation: H281DRAFT_01977 Phosphocarrier protein HPr /phosphoenolpyruvate--protein phosphotransferase /PTS system IIA component, Glc family

Length: 854 amino acids

Source: Burk376 in FitnessBrowser

Candidate for 16 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
N-acetyl-D-glucosamine catabolism nagF hi N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized) 94% 100% 1550.4 D-trehalose PTS system, I, HPr, and IIA components 43% 611.3
D-glucosamine (chitosamine) catabolism nagF hi N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized) 94% 100% 1550.4 D-trehalose PTS system, I, HPr, and IIA components 43% 611.3
trehalose catabolism treEIIA med D-trehalose PTS system, I, HPr, and IIA components (characterized) 43% 98% 611.3 N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) 94% 1550.4
D-fructose catabolism fruI med Multiphosphoryl transfer protein; MTP; Triphosphoryl transfer protein; TTP; EC 2.7.3.9 (characterized) 41% 85% 479.6 N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) 94% 1550.4
sucrose catabolism fruI med Multiphosphoryl transfer protein; MTP; Triphosphoryl transfer protein; TTP; EC 2.7.3.9 (characterized) 41% 85% 479.6 N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) 94% 1550.4
N-acetyl-D-glucosamine catabolism nagEIIA med Putative phosphotransferase enzyme IIA component YpqE (characterized, see rationale) 43% 80% 115.2 N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) 94% 1550.4
D-glucosamine (chitosamine) catabolism nagEIIA med Putative phosphotransferase enzyme IIA component YpqE (characterized, see rationale) 43% 80% 115.2 N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) 94% 1550.4
D-maltose catabolism malEIIA med Putative phosphotransferase enzyme IIA component YpqE (characterized, see rationale) 43% 80% 115.2 N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) 94% 1550.4
D-cellobiose catabolism crr lo glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) 39% 89% 117.9 N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) 94% 1550.4
D-glucose catabolism crr lo glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) 39% 89% 117.9 N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) 94% 1550.4
lactose catabolism crr lo glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) 39% 89% 117.9 N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) 94% 1550.4
D-maltose catabolism crr lo glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) 39% 89% 117.9 N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) 94% 1550.4
sucrose catabolism crr lo glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) 39% 89% 117.9 N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) 94% 1550.4
trehalose catabolism crr lo glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) 39% 89% 117.9 N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) 94% 1550.4
N-acetyl-D-glucosamine catabolism crr lo Putative PTS system sugar phosphotransferase component IIA (characterized, see rationale) 35% 95% 90.9 N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) 94% 1550.4
D-glucosamine (chitosamine) catabolism crr lo Putative PTS system sugar phosphotransferase component IIA (characterized, see rationale) 35% 95% 90.9 N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) 94% 1550.4

Sequence Analysis Tools

View H281DRAFT_01977 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

MSHSEGHIVLLAPMTGPVVPLANVPDPVFSGGMFGDGIGVDPLEGRLVAPCEGTVTHLAR
TGHAVTLATAEGAEILLHIGIDTVELNGKGFAPMIEQGAHVHAGDVLIEFDQDQIALHAP
SLVSVIAIANSDAFEIVERAQGGMLKAGETPLLLLRPRDGAAADASRQLSATSVTEEARA
QVTLVHAGGLHARPAARAREAARGFDARVEVRYEGRKAAIESVVGLLGLGAGQGATVELL
GVGPQARAAVDAIADELTREAHGEVEEKPARQSSPAPQTVAPAAGETLAPNTLAGVCASP
GVAIGKLVCWDDADIDPPEQASGTSAAESRLLDKAIATVDTDLGTTVRDASQRGAVGEAG
IFAVHRVLLEDPTLLDAARDLISLGKSAGFAWREAIRAQIAILTNIEDALLAERAADLRD
IEKRVLRALGYTNAAARALPDEAVLAAEEFTPSDLSALDRSRVTALVMARGGATSHAAIL
ARQAGIPALVAMGDALYAIPEGTQVVVNATTGRLEFAPTELDVERARLERSRLAGVREAN
RRTSQEAAVTADGRAIEVAANIATLDDAKTAVENGADSVGLLRTELLFIHRAAAPTTDEH
RQSYQGIVDALSGRTAIIRTLDVGADKEVDYLTLPPEPNPALGLRGIRLAQVRPDLLDDQ
LRGLLSVKPFGAVRILLPMVTDVGELIRIRKRIDEFARELGRTEPIEVGVMIEVPSAALL
ADQLSQHADFLSIGTNDLTQYTLAMDRCQADLAAQSDGLHPAVLRLIAATVQGASKHGKW
VGVCGALAGDPLAMPLLVGLGVTELSVDPVSVPGIKARVRNLDYQLCRQRAQDALALESA
QAVRAVSRETWPLD

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