GapMind for catabolism of small carbon sources

 

Protein 15223 in Escherichia coli BW25113

Annotation: b1101 fused glucose-specific PTS enzymes: IIB component/IIC component (NCBI)

Length: 477 amino acids

Source: Keio in FitnessBrowser

Candidate for 29 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-cellobiose catabolism ptsG hi protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) 100% 100% 941.4 PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 47% 447.6
D-glucose catabolism ptsG hi protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) 100% 100% 941.4 PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 47% 447.6
lactose catabolism ptsG hi protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) 100% 100% 941.4 PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 47% 447.6
D-maltose catabolism ptsG hi protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) 100% 100% 941.4 PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 47% 447.6
sucrose catabolism ptsG hi protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) 100% 100% 941.4 PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 47% 447.6
trehalose catabolism ptsG hi protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) 100% 100% 941.4 PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 47% 447.6
N-acetyl-D-glucosamine catabolism nagEIIA med PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 47% 74% 447.6 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 100% 941.4
D-cellobiose catabolism ptsG-crr med PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 47% 74% 447.6 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 100% 941.4
D-glucosamine (chitosamine) catabolism nagEIIA med PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 47% 74% 447.6 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 100% 941.4
D-glucose catabolism ptsG-crr med PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 47% 74% 447.6 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 100% 941.4
lactose catabolism ptsG-crr med PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 47% 74% 447.6 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 100% 941.4
D-maltose catabolism malEIIA med PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 47% 74% 447.6 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 100% 941.4
D-maltose catabolism ptsG-crr med PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 47% 74% 447.6 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 100% 941.4
sucrose catabolism ptsG-crr med PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 47% 74% 447.6 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 100% 941.4
trehalose catabolism ptsG-crr med PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 47% 74% 447.6 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 100% 941.4
trehalose catabolism treEIIA med PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 47% 74% 447.6 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 100% 941.4
D-glucosamine (chitosamine) catabolism gamP med Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized) 48% 74% 424.1 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 100% 941.4
N-acetyl-D-glucosamine catabolism nagEcba med protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized) 42% 71% 389.8 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 100% 941.4
D-glucosamine (chitosamine) catabolism nagEcba med protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized) 42% 71% 389.8 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 100% 941.4
N-acetyl-D-glucosamine catabolism nagEcb med N-acetylglucosamine-specific PTS system, IIBC components (nagE) (characterized) 43% 80% 384.4 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 100% 941.4
D-glucosamine (chitosamine) catabolism nagEcb med N-acetylglucosamine-specific PTS system, IIBC components (nagE) (characterized) 43% 80% 384.4 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 100% 941.4
N-acetyl-D-glucosamine catabolism nagPcb med PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized) 44% 99% 365.9 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 100% 941.4
D-glucosamine (chitosamine) catabolism nagPcb med PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized) 44% 99% 365.9 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 100% 941.4
N-acetyl-D-glucosamine catabolism ptsC med IIC' aka PtsC2, component of N-Acetylglucosamine (NAG) porter (PtsBC1C2)(also may facilitate xylose transport) (characterized) 44% 100% 337.4 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 100% 941.4
D-glucosamine (chitosamine) catabolism ptsC med IIC' aka PtsC2, component of N-Acetylglucosamine (NAG) porter (PtsBC1C2)(also may facilitate xylose transport) (characterized) 44% 100% 337.4 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 100% 941.4
N-acetyl-D-glucosamine catabolism ptsB med IIB aka PtsB, component of N-Acetylglucosamine (NAG) porter (PtsBC1C2)(also may facilitate xylose transport) (characterized) 46% 80% 73.2 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 100% 941.4
D-glucosamine (chitosamine) catabolism ptsB med IIB aka PtsB, component of N-Acetylglucosamine (NAG) porter (PtsBC1C2)(also may facilitate xylose transport) (characterized) 46% 80% 73.2 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 100% 941.4
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) 34% 99% 271.9 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 100% 941.4
D-maltose catabolism malEIICBA lo The maltose/maltotriose porter, MalT (31% identical to 4.A.1.1.9) (characterized) 33% 75% 263.5 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 100% 941.4

Sequence Analysis Tools

View 15223 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 and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MFKNAFANLQKVGKSLMLPVSVLPIAGILLGVGSANFSWLPAVVSHVMAEAGGSVFANMP
LIFAIGVALGFTNNDGVSALAAVVAYGIMVKTMAVVAPLVLHLPAEEIASKHLADTGVLG
GIISGAIAAYMFNRFYRIKLPEYLGFFAGKRFVPIISGLAAIFTGVVLSFIWPPIGSAIQ
TFSQWAAYQNPVVAFGIYGFIERCLVPFGLHHIWNVPFQMQIGEYTNAAGQVFHGDIPRY
MAGDPTAGKLSGGFLFKMYGLPAAAIAIWHSAKPENRAKVGGIMISAALTSFLTGITEPI
EFSFMFVAPILYIIHAILAGLAFPICILLGMRDGTSFSHGLIDFIVLSGNSSKLWLFPIV
GIGYAIVYYTIFRVLIKALDLKTPGREDATEDAKATGTSEMAPALVAAFGGKENITNLDA
CITRLRVSVADVSKVDQAGLKKLGAAGVVVAGSGVQAIFGTKSDNLKTEMDEYIRNH

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, 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