GapMind for catabolism of small carbon sources

 

Protein Ga0059261_1647 in Sphingomonas koreensis DSMZ 15582

Annotation: Ga0059261_1647 PTS system, N-acetylglucosamine-specific IIBC component

Length: 560 amino acids

Source: Korea in FitnessBrowser

Candidate for 26 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 nagEcb hi N-acetylglucosamine-specific PTS system, IIBC components (nagE) (characterized) 51% 94% 536.6 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 45% 448.7
D-glucosamine (chitosamine) catabolism nagEcb hi N-acetylglucosamine-specific PTS system, IIBC components (nagE) (characterized) 51% 94% 536.6 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 45% 448.7
N-acetyl-D-glucosamine catabolism nagEcba med protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized) 45% 82% 448 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 51% 523.5
D-glucosamine (chitosamine) catabolism nagEcba med protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized) 45% 82% 448 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 51% 523.5
D-glucosamine (chitosamine) catabolism gamP med protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized) 44% 82% 443.4 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 51% 523.5
N-acetyl-D-glucosamine catabolism nagPcb med PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized) 46% 100% 442.2 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 51% 523.5
D-glucosamine (chitosamine) catabolism nagPcb med PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized) 46% 100% 442.2 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 51% 523.5
N-acetyl-D-glucosamine catabolism ptsC med IIC' aka PtsC2, component of N-Acetylglucosamine (NAG) porter (PtsBC1C2)(also may facilitate xylose transport) (characterized) 50% 98% 384.8 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 51% 523.5
D-glucosamine (chitosamine) catabolism ptsC med IIC' aka PtsC2, component of N-Acetylglucosamine (NAG) porter (PtsBC1C2)(also may facilitate xylose transport) (characterized) 50% 98% 384.8 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 51% 523.5
N-acetyl-D-glucosamine catabolism nagEIIA med Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized) 41% 79% 373.2 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 51% 523.5
D-glucosamine (chitosamine) catabolism nagEIIA med Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized) 41% 79% 373.2 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 51% 523.5
D-maltose catabolism malEIIA med Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized) 41% 79% 373.2 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 51% 523.5
trehalose catabolism treEIIA med Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized) 41% 79% 373.2 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 51% 523.5
D-cellobiose catabolism ptsG med PTS system glucose-specific EIICB component; EIICB-Glc; EII-Glc; EC 2.7.1.199 (characterized) 42% 98% 357.8 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 51% 523.5
D-glucose catabolism ptsG med PTS system glucose-specific EIICB component; EIICB-Glc; EII-Glc; EC 2.7.1.199 (characterized) 42% 98% 357.8 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 51% 523.5
lactose catabolism ptsG med PTS system glucose-specific EIICB component; EIICB-Glc; EII-Glc; EC 2.7.1.199 (characterized) 42% 98% 357.8 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 51% 523.5
D-maltose catabolism ptsG med PTS system glucose-specific EIICB component; EIICB-Glc; EII-Glc; EC 2.7.1.199 (characterized) 42% 98% 357.8 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 51% 523.5
sucrose catabolism ptsG med PTS system glucose-specific EIICB component; EIICB-Glc; EII-Glc; EC 2.7.1.199 (characterized) 42% 98% 357.8 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 51% 523.5
trehalose catabolism ptsG med PTS system glucose-specific EIICB component; EIICB-Glc; EII-Glc; EC 2.7.1.199 (characterized) 42% 98% 357.8 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 51% 523.5
D-cellobiose catabolism ptsG-crr lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 40% 74% 349.4 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 51% 523.5
D-glucose catabolism ptsG-crr lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 40% 74% 349.4 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 51% 523.5
lactose catabolism ptsG-crr lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 40% 74% 349.4 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 51% 523.5
D-maltose catabolism ptsG-crr lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 40% 74% 349.4 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 51% 523.5
sucrose catabolism ptsG-crr lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 40% 74% 349.4 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 51% 523.5
trehalose catabolism ptsG-crr lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 40% 74% 349.4 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 51% 523.5
D-maltose catabolism malEIICB lo The Maltose group translocator, MalT of 470 aas and 10 TMSs. Takes up extracellular maltose, releasing maltose-phosphate into the cytoplasm (characterized) 32% 98% 212.6 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 51% 523.5

Sequence Analysis Tools

View Ga0059261_1647 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

MRKILETLQPLGRALMLPIAVLPVAGLLLRIGQPDLLDIAFVSAAGTAIFGNLGILFAIG
VAVGFARDGNGAAALAGVTCYLVSTTGAQTFLIAPPEVVAGLPDAAAKVVAQAWATGQID
RLEVPIGIISGLIGGKFYNRFATIALPEYLAFFGGRRFVPIAAGIAGLLLAGVLGYGYAH
ISSALDAASHAVVESGGAGMFVYGVLNRLLLVTGLHHLLNNVAWFLVGDFGGATGDLGRF
FAGDPNAGAFMSGFFPVMMFGLPAACLAMYHEARPERRKAVGGMLFSLAFTSFLTGVTEP
IEFTFMFLAPVLYAIHAVLTGVAMTLMDMLGIKLGFGFSAGLFDYVLNFKLSTRPWMLLP
VGAAYAVIYYTLFRFFIRKLDLATPGREKGEAVAAAGETAAGNERGAAFVKALGGAANLT
SVDACTTRLRLIVADQSAVDDAALNALGARGIIRPSANATQVVLGPIADLVAEEIRGAIG
GGAAAVSAAPAQALADEAVTLPAAILAALGGEANIRALQALHGRFRVEVVDAARTDEASL
LAAANGAVSPQPGVYHILHD

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