GapMind for catabolism of small carbon sources

 

Protein WP_083848942.1 in Catellicoccus marimammalium M35/04/3

Annotation: NCBI__GCF_000313915.1:WP_083848942.1

Length: 553 amino acids

Source: GCF_000313915.1 in NCBI

Candidate for 23 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-maltose catabolism malEIICBA hi PTS system, IIABC components (characterized, see rationale) 65% 97%* 944.1 PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 43% 408.6
D-maltose catabolism malEIICB hi The Maltose group translocator, MalT of 470 aas and 10 TMSs. Takes up extracellular maltose, releasing maltose-phosphate into the cytoplasm (characterized) 65% 100% 723.8 PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 32% 277.3
N-acetyl-D-glucosamine catabolism nagEIIA lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 32% 73% 277.3 The maltose/maltotriose porter, MalT (31% identical to 4.A.1.1.9) 70% 776.2
D-cellobiose catabolism ptsG-crr lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 32% 73% 277.3 The maltose/maltotriose porter, MalT (31% identical to 4.A.1.1.9) 70% 776.2
D-glucosamine (chitosamine) catabolism nagEIIA lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 32% 73% 277.3 The maltose/maltotriose porter, MalT (31% identical to 4.A.1.1.9) 70% 776.2
D-glucose catabolism ptsG-crr lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 32% 73% 277.3 The maltose/maltotriose porter, MalT (31% identical to 4.A.1.1.9) 70% 776.2
lactose catabolism ptsG-crr lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 32% 73% 277.3 The maltose/maltotriose porter, MalT (31% identical to 4.A.1.1.9) 70% 776.2
D-maltose catabolism malEIIA lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 32% 73% 277.3 The maltose/maltotriose porter, MalT (31% identical to 4.A.1.1.9) 70% 776.2
D-maltose catabolism ptsG-crr lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 32% 73% 277.3 The maltose/maltotriose porter, MalT (31% identical to 4.A.1.1.9) 70% 776.2
sucrose catabolism ptsG-crr lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 32% 73% 277.3 The maltose/maltotriose porter, MalT (31% identical to 4.A.1.1.9) 70% 776.2
trehalose catabolism ptsG-crr lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 32% 73% 277.3 The maltose/maltotriose porter, MalT (31% identical to 4.A.1.1.9) 70% 776.2
trehalose catabolism treEIIA lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 32% 73% 277.3 The maltose/maltotriose porter, MalT (31% identical to 4.A.1.1.9) 70% 776.2
D-cellobiose catabolism ptsG lo protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) 31% 99% 244.2 The maltose/maltotriose porter, MalT (31% identical to 4.A.1.1.9) 70% 776.2
D-glucose catabolism ptsG lo protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) 31% 99% 244.2 The maltose/maltotriose porter, MalT (31% identical to 4.A.1.1.9) 70% 776.2
lactose catabolism ptsG lo protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) 31% 99% 244.2 The maltose/maltotriose porter, MalT (31% identical to 4.A.1.1.9) 70% 776.2
D-maltose catabolism ptsG lo protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) 31% 99% 244.2 The maltose/maltotriose porter, MalT (31% identical to 4.A.1.1.9) 70% 776.2
sucrose catabolism ptsG lo protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) 31% 99% 244.2 The maltose/maltotriose porter, MalT (31% identical to 4.A.1.1.9) 70% 776.2
trehalose catabolism ptsG lo protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) 31% 99% 244.2 The maltose/maltotriose porter, MalT (31% identical to 4.A.1.1.9) 70% 776.2
D-glucosamine (chitosamine) catabolism gamP lo Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized) 30% 74% 217.6 The maltose/maltotriose porter, MalT (31% identical to 4.A.1.1.9) 70% 776.2
N-acetyl-D-glucosamine catabolism nagEcb lo N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA (characterized) 31% 80% 208.4 The maltose/maltotriose porter, MalT (31% identical to 4.A.1.1.9) 70% 776.2
D-glucosamine (chitosamine) catabolism nagEcb lo N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA (characterized) 31% 80% 208.4 The maltose/maltotriose porter, MalT (31% identical to 4.A.1.1.9) 70% 776.2
N-acetyl-D-glucosamine catabolism nagPcb lo PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized) 31% 50% 109.4 The maltose/maltotriose porter, MalT (31% identical to 4.A.1.1.9) 70% 776.2
D-glucosamine (chitosamine) catabolism nagPcb lo PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized) 31% 50% 109.4 The maltose/maltotriose porter, MalT (31% identical to 4.A.1.1.9) 70% 776.2

Sequence Analysis Tools

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Find functional residues: SitesBLAST

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MKKIFSFEFWQKFGKALMVVIAVMPAAGLMISIGKLIAMAQVSLAVTIGGVTENIGWAII
GNLPILFALAIGGSWAKERAGGAFASGLAFILINRITGAVFGVTKEMLANPEATVHTIFG
QKILVNGYFTSVLEAPALNMGVFVGIIAGFAGAIIYNKYYNFRKLPNCLSFFNGKRFVPF
VVILWSVIIALLLSVFWPFAQTGINEFGKWIAQSGDSAPFWAPFIYGTLERLLLPFGLHH
MLTIPMNYTDLGGTYHILTGAQAGQAVLGQDPLWLAWVTDLINLKEKGDMTQYHQLLESI
RPARFKVGQMIGSSGILMGVTFAMYRNVEPKRKKVYKQIFLSAALAVFLTGVTEPLEFMF
MFAGIPLYVVYALLQGVAFGLADIIDLRLHAFGNIELLTRLPMSIKAGLGMDIINFIITC
IVFFFLAYFVANFMIKKFHIATPGRLGNYIEGNDDSSASDTTTATSSTKPSEANNQVMNI
IQLLGGKENIVDVDACMTRLRVTVKDTTKVADEEAWKKEGAMGLIHKNNGVQAVYGPKAD
VLKSDINDYLSQS

This GapMind analysis is from Sep 24 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