GapMind for catabolism of small carbon sources

 

Protein BWI76_RS16295 in Klebsiella michiganensis M5al

Annotation: FitnessBrowser__Koxy:BWI76_RS16295

Length: 530 amino acids

Source: Koxy 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 IIB aka PtsB, component of N-Acetylglucosamine (NAG) porter (PtsBC1C2)(also may facilitate xylose transport) (characterized) 51% 74% 62.8 PTS system maltose- and glucose-specific EIICB component; EC 2.7.1.69 89% 951.0
D-glucosamine (chitosamine) catabolism ptsB med IIB aka PtsB, component of N-Acetylglucosamine (NAG) porter (PtsBC1C2)(also may facilitate xylose transport) (characterized) 51% 74% 62.8 PTS system maltose- and glucose-specific EIICB component; EC 2.7.1.69 89% 951.0
N-acetyl-D-glucosamine catabolism nagEIIA lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 40% 73% 359.8 PTS system maltose- and glucose-specific EIICB component; EC 2.7.1.69 89% 951.0
D-cellobiose catabolism ptsG-crr lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 40% 73% 359.8 PTS system maltose- and glucose-specific EIICB component; EC 2.7.1.69 89% 951.0
D-glucosamine (chitosamine) catabolism nagEIIA lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 40% 73% 359.8 PTS system maltose- and glucose-specific EIICB component; EC 2.7.1.69 89% 951.0
D-glucose catabolism ptsG-crr lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 40% 73% 359.8 PTS system maltose- and glucose-specific EIICB component; EC 2.7.1.69 89% 951.0
lactose catabolism ptsG-crr lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 40% 73% 359.8 PTS system maltose- and glucose-specific EIICB component; EC 2.7.1.69 89% 951.0
D-maltose catabolism malEIIA lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 40% 73% 359.8 PTS system maltose- and glucose-specific EIICB component; EC 2.7.1.69 89% 951.0
D-maltose catabolism ptsG-crr lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 40% 73% 359.8 PTS system maltose- and glucose-specific EIICB component; EC 2.7.1.69 89% 951.0
sucrose catabolism ptsG-crr lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 40% 73% 359.8 PTS system maltose- and glucose-specific EIICB component; EC 2.7.1.69 89% 951.0
trehalose catabolism ptsG-crr lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 40% 73% 359.8 PTS system maltose- and glucose-specific EIICB component; EC 2.7.1.69 89% 951.0
N-acetyl-D-glucosamine catabolism nagEcb lo N-acetylglucosamine-specific PTS system, IIBC components (nagE) (characterized) 38% 78% 306.6 PTS system maltose- and glucose-specific EIICB component; EC 2.7.1.69 89% 951.0
D-glucosamine (chitosamine) catabolism nagEcb lo N-acetylglucosamine-specific PTS system, IIBC components (nagE) (characterized) 38% 78% 306.6 PTS system maltose- and glucose-specific EIICB component; EC 2.7.1.69 89% 951.0
D-cellobiose catabolism ptsG lo PTS system glucose-specific EIICB component; EIICB-Glc; EII-Glc; EC 2.7.1.199 (characterized) 38% 97% 300.1 PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 40% 359.8
D-glucose catabolism ptsG lo PTS system glucose-specific EIICB component; EIICB-Glc; EII-Glc; EC 2.7.1.199 (characterized) 38% 97% 300.1 PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 40% 359.8
lactose catabolism ptsG lo PTS system glucose-specific EIICB component; EIICB-Glc; EII-Glc; EC 2.7.1.199 (characterized) 38% 97% 300.1 PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 40% 359.8
D-maltose catabolism ptsG lo PTS system glucose-specific EIICB component; EIICB-Glc; EII-Glc; EC 2.7.1.199 (characterized) 38% 97% 300.1 PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 40% 359.8
sucrose catabolism ptsG lo PTS system glucose-specific EIICB component; EIICB-Glc; EII-Glc; EC 2.7.1.199 (characterized) 38% 97% 300.1 PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 40% 359.8
trehalose catabolism ptsG lo PTS system glucose-specific EIICB component; EIICB-Glc; EII-Glc; EC 2.7.1.199 (characterized) 38% 97% 300.1 PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 40% 359.8
D-glucosamine (chitosamine) catabolism gamP lo Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized) 36% 74% 295 PTS system maltose- and glucose-specific EIICB component; EC 2.7.1.69 89% 951.0
N-acetyl-D-glucosamine catabolism nagEcba lo protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized) 35% 70% 278.9 PTS system maltose- and glucose-specific EIICB component; EC 2.7.1.69 89% 951.0
D-glucosamine (chitosamine) catabolism nagEcba lo protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized) 35% 70% 278.9 PTS system maltose- and glucose-specific EIICB component; EC 2.7.1.69 89% 951.0
N-acetyl-D-glucosamine catabolism nagPcb lo PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized) 34% 99% 269.2 PTS system maltose- and glucose-specific EIICB component; EC 2.7.1.69 89% 951.0
D-glucosamine (chitosamine) catabolism nagPcb lo PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized) 34% 99% 269.2 PTS system maltose- and glucose-specific EIICB component; EC 2.7.1.69 89% 951.0
D-maltose catabolism malEIICBA lo PTS system, IIABC components (characterized, see rationale) 31% 75% 235.3 PTS system maltose- and glucose-specific EIICB component; EC 2.7.1.69 89% 951.0
N-acetyl-D-glucosamine catabolism ptsC lo PTS system N-acetylglucosamine-specific EIIC component; PTS system GlcNAc-specific EIIC component; GlcNAc-specific transporter; N-acetylglucosamine permease IIC component; GlcNAc permease IIC component (characterized) 35% 96% 233 PTS system maltose- and glucose-specific EIICB component; EC 2.7.1.69 89% 951.0
D-glucosamine (chitosamine) catabolism ptsC lo PTS system N-acetylglucosamine-specific EIIC component; PTS system GlcNAc-specific EIIC component; GlcNAc-specific transporter; N-acetylglucosamine permease IIC component; GlcNAc permease IIC component (characterized) 35% 96% 233 PTS system maltose- and glucose-specific EIICB component; EC 2.7.1.69 89% 951.0

Sequence Analysis Tools

View BWI76_RS16295 at FitnessBrowser

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MTAKTASKITLWEFFQQLGKTFMLPVALLSFCGIMLGIGSSLSSHDVLTLLPWLDVPLLQ
AVFIWMGKVGSFAFSFLPVMFCIAIPLGLARENKGVAAFAGFVGYAVMNLAVNFWLTAKG
ILPTTDAAVLKANNIQNIIGIQSIDTGILGAVIAGIIVWMLHERFHNIRLPDALAFFGGT
RFVPIITTVVLGLVGLVIPLIWPVFAMGINALGQVINSAGDFGPMIFGTGERLLLPFGLH
HILVALIRFTEAGGTMDVCGHSVSGALTIFQAQLSCPTTHGFSESATRFLSQGKMPAFLG
GLPGAALAMYHCARPENRHKIKGLLISGVIACVVGGTTEPLEFLFLFVAPVLYVIHALLT
GLGFTMMAILGVTIGNTDGNVIDFVVFGILHGLSTKWYLVPVVAAIWFAVYYGIFRFAIT
RFNLKTPGRDIETNSAFEKAVTGVTGKSGYNVPAILAALGGAENIVSLDNCITRLRLSVN
DMSKVDSAALKANRAIGVVQLNQHNLQVVIGPQVQSVKDEMAVLMNTVEA

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:

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