GapMind for catabolism of small carbon sources

 

Protein 15742 in Escherichia coli BW25113

Annotation: b1621 fused maltose and glucose-specific PTS enzymes: IIB component -! IIC component (NCBI)

Length: 530 amino acids

Source: Keio in FitnessBrowser

Candidate for 27 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 ptsB med PTS system N-acetylglucosamine-specific EIIB component; PTS system GlcNAc-specific EIIB component; N-acetylglucosamine-specific phosphotransferase enzyme IIB component; GlcNAc-specific phosphotransferase enzyme IIB component; EC 2.7.1.193 (characterized) 41% 100% 57 PTS system maltose- and glucose-specific EIICB component; EC 2.7.1.69 100% 1048.1
D-glucosamine (chitosamine) catabolism ptsB med PTS system N-acetylglucosamine-specific EIIB component; PTS system GlcNAc-specific EIIB component; N-acetylglucosamine-specific phosphotransferase enzyme IIB component; GlcNAc-specific phosphotransferase enzyme IIB component; EC 2.7.1.193 (characterized) 41% 100% 57 PTS system maltose- and glucose-specific EIICB component; EC 2.7.1.69 100% 1048.1
N-acetyl-D-glucosamine catabolism nagEIIA lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 38% 73% 348.2 PTS system maltose- and glucose-specific EIICB component; EC 2.7.1.69 100% 1048.1
D-cellobiose catabolism ptsG-crr lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 38% 73% 348.2 PTS system maltose- and glucose-specific EIICB component; EC 2.7.1.69 100% 1048.1
D-glucosamine (chitosamine) catabolism nagEIIA lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 38% 73% 348.2 PTS system maltose- and glucose-specific EIICB component; EC 2.7.1.69 100% 1048.1
D-glucose catabolism ptsG-crr lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 38% 73% 348.2 PTS system maltose- and glucose-specific EIICB component; EC 2.7.1.69 100% 1048.1
lactose catabolism ptsG-crr lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 38% 73% 348.2 PTS system maltose- and glucose-specific EIICB component; EC 2.7.1.69 100% 1048.1
D-maltose catabolism malEIIA lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 38% 73% 348.2 PTS system maltose- and glucose-specific EIICB component; EC 2.7.1.69 100% 1048.1
D-maltose catabolism ptsG-crr lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 38% 73% 348.2 PTS system maltose- and glucose-specific EIICB component; EC 2.7.1.69 100% 1048.1
sucrose catabolism ptsG-crr lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 38% 73% 348.2 PTS system maltose- and glucose-specific EIICB component; EC 2.7.1.69 100% 1048.1
trehalose catabolism ptsG-crr lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 38% 73% 348.2 PTS system maltose- and glucose-specific EIICB component; EC 2.7.1.69 100% 1048.1
N-acetyl-D-glucosamine catabolism nagEcb lo N-acetylglucosamine-specific PTS system, IIBC components (nagE) (characterized) 38% 77% 303.5 PTS system maltose- and glucose-specific EIICB component; EC 2.7.1.69 100% 1048.1
D-glucosamine (chitosamine) catabolism nagEcb lo N-acetylglucosamine-specific PTS system, IIBC components (nagE) (characterized) 38% 77% 303.5 PTS system maltose- and glucose-specific EIICB component; EC 2.7.1.69 100% 1048.1
D-glucosamine (chitosamine) catabolism gamP lo Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized) 36% 74% 291.6 PTS system maltose- and glucose-specific EIICB component; EC 2.7.1.69 100% 1048.1
D-cellobiose catabolism ptsG lo PTS system glucose-specific EIICB component; EIICB-Glc; EII-Glc; EC 2.7.1.199 (characterized) 37% 97% 290 PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 38% 348.2
D-glucose catabolism ptsG lo PTS system glucose-specific EIICB component; EIICB-Glc; EII-Glc; EC 2.7.1.199 (characterized) 37% 97% 290 PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 38% 348.2
lactose catabolism ptsG lo PTS system glucose-specific EIICB component; EIICB-Glc; EII-Glc; EC 2.7.1.199 (characterized) 37% 97% 290 PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 38% 348.2
D-maltose catabolism ptsG lo PTS system glucose-specific EIICB component; EIICB-Glc; EII-Glc; EC 2.7.1.199 (characterized) 37% 97% 290 PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 38% 348.2
sucrose catabolism ptsG lo PTS system glucose-specific EIICB component; EIICB-Glc; EII-Glc; EC 2.7.1.199 (characterized) 37% 97% 290 PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 38% 348.2
trehalose catabolism ptsG lo PTS system glucose-specific EIICB component; EIICB-Glc; EII-Glc; EC 2.7.1.199 (characterized) 37% 97% 290 PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 38% 348.2
N-acetyl-D-glucosamine catabolism nagEcba lo protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized) 34% 70% 275 PTS system maltose- and glucose-specific EIICB component; EC 2.7.1.69 100% 1048.1
D-glucosamine (chitosamine) catabolism nagEcba lo protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized) 34% 70% 275 PTS system maltose- and glucose-specific EIICB component; EC 2.7.1.69 100% 1048.1
N-acetyl-D-glucosamine catabolism nagPcb lo PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized) 33% 99% 265.4 PTS system maltose- and glucose-specific EIICB component; EC 2.7.1.69 100% 1048.1
D-glucosamine (chitosamine) catabolism nagPcb lo PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized) 33% 99% 265.4 PTS system maltose- and glucose-specific EIICB component; EC 2.7.1.69 100% 1048.1
D-maltose catabolism malEIICBA lo The maltose/maltotriose porter, MalT (31% identical to 4.A.1.1.9) (characterized) 31% 76% 243.4 PTS system maltose- and glucose-specific EIICB component; EC 2.7.1.69 100% 1048.1
N-acetyl-D-glucosamine catabolism ptsC lo IIC' aka PtsC2, component of N-Acetylglucosamine (NAG) porter (PtsBC1C2)(also may facilitate xylose transport) (characterized) 35% 99% 241.9 PTS system maltose- and glucose-specific EIICB component; EC 2.7.1.69 100% 1048.1
D-glucosamine (chitosamine) catabolism ptsC lo IIC' aka PtsC2, component of N-Acetylglucosamine (NAG) porter (PtsBC1C2)(also may facilitate xylose transport) (characterized) 35% 99% 241.9 PTS system maltose- and glucose-specific EIICB component; EC 2.7.1.69 100% 1048.1

Sequence Analysis Tools

View 15742 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

MTAKTAPKVTLWEFFQQLGKTFMLPVALLSFCGIMLGIGSSLSSHDVITLIPVLGNPVLQ
AIFTWMSKIGSFAFSFLPVMFCIAIPLGLARENKGVAAFAGFIGYAVMNLAVNFWLTNKG
ILPTTDAAVLKANNIQSILGIQSIDTGILGAVIAGIIVWMLHERFHNIRLPDALAFFGGT
RFVPIISSLVMGLVGLVIPLVWPIFAMGISGLGHMINSAGDFGPMLFGTGERLLLPFGLH
HILVALIRFTDAGGTQEVCGQTVSGALTIFQAQLSCPTTHGFSESATRFLSQGKMPAFLG
GLPGAALAMYHCARPENRHKIKGLLISGLIACVVGGTTEPLEFLFLFVAPVLYVIHALLT
GLGFTVMSVLGVTIGNTDGNIIDFVVFGILHGLSTKWYMVPVVAAIWFVVYYVIFRFAIT
RFNLKTPGRDSEVASSIEKAVAGAPGKSGYNVPAILEALGGADNIVSLDNCITRLRLSVK
DMSLVNVQALKDNRAIGVVQLNQHNLQVVIGPQVQSVKDEMAGLMHTVQA

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