GapMind for catabolism of small carbon sources

 

Protein 7025672 in Shewanella sp. ANA-3

Annotation: FitnessBrowser__ANA3:7025672

Length: 452 amino acids

Source: ANA3 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) 44% 95% 419.1 PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 36% 303.1
D-glucose catabolism ptsG hi protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) 44% 95% 419.1 PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 36% 303.1
lactose catabolism ptsG hi protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) 44% 95% 419.1 PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 36% 303.1
D-maltose catabolism ptsG hi protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) 44% 95% 419.1 PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 36% 303.1
sucrose catabolism ptsG hi protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) 44% 95% 419.1 PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 36% 303.1
trehalose catabolism ptsG hi protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) 44% 95% 419.1 PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 36% 303.1
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) 46% 87% 65.5 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 44% 419.1
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) 46% 87% 65.5 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 44% 419.1
N-acetyl-D-glucosamine catabolism nagEIIA lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 36% 71% 303.1 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 44% 419.1
D-cellobiose catabolism ptsG-crr lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 36% 71% 303.1 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 44% 419.1
D-glucosamine (chitosamine) catabolism nagEIIA lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 36% 71% 303.1 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 44% 419.1
D-glucose catabolism ptsG-crr lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 36% 71% 303.1 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 44% 419.1
lactose catabolism ptsG-crr lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 36% 71% 303.1 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 44% 419.1
D-maltose catabolism malEIIA lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 36% 71% 303.1 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 44% 419.1
D-maltose catabolism ptsG-crr lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 36% 71% 303.1 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 44% 419.1
sucrose catabolism ptsG-crr lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 36% 71% 303.1 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 44% 419.1
trehalose catabolism ptsG-crr lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 36% 71% 303.1 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 44% 419.1
trehalose catabolism treEIIA lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 36% 71% 303.1 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 44% 419.1
D-glucosamine (chitosamine) catabolism gamP lo Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized) 38% 70% 302.8 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 44% 419.1
N-acetyl-D-glucosamine catabolism nagEcba lo protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized) 35% 70% 271.2 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 44% 419.1
D-glucosamine (chitosamine) catabolism nagEcba lo protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized) 35% 70% 271.2 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 44% 419.1
N-acetyl-D-glucosamine catabolism nagEcb lo N-acetylglucosamine-specific PTS system, IIBC components (nagE) (characterized) 38% 77% 270 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 44% 419.1
D-glucosamine (chitosamine) catabolism nagEcb lo N-acetylglucosamine-specific PTS system, IIBC components (nagE) (characterized) 38% 77% 270 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 44% 419.1
N-acetyl-D-glucosamine catabolism nagPcb lo PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized) 34% 96% 259.2 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 44% 419.1
D-glucosamine (chitosamine) catabolism nagPcb lo PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized) 34% 96% 259.2 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 44% 419.1
N-acetyl-D-glucosamine catabolism ptsC lo IIC' aka PtsC2, component of N-Acetylglucosamine (NAG) porter (PtsBC1C2)(also may facilitate xylose transport) (characterized) 36% 93% 226.5 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 44% 419.1
D-glucosamine (chitosamine) catabolism ptsC lo IIC' aka PtsC2, component of N-Acetylglucosamine (NAG) porter (PtsBC1C2)(also may facilitate xylose transport) (characterized) 36% 93% 226.5 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 44% 419.1
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) 31% 96% 201.4 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 44% 419.1
D-maltose catabolism malEIICBA lo Maltose/Maltotriose PTS transporter, MalT (Shelburne et al., 2008) 631aas (68% identical to 4.A.1.1.11 from S. mutans (characterized) 30% 72% 167.5 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 44% 419.1

Sequence Analysis Tools

View 7025672 at FitnessBrowser

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

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Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MPAAGVMLGLTVSPIPFMPEVLTVLMLAVGKLIFAIMPILFAVAVAIGFCRDQGIAAFTA
VFGYGVMTATLAALADLYQLPTQLLLGMETLDTGIAGGMLIGGVTCFAVRWSQYIRLPAI
FSFFEGRRSASLLIIPLAMGLGYILAHVWPPLSLLIERVSDWAVYQKPAIAFGVYGALER
LLIPLGLHHIWNAPFYLEVGQYQLQNSEVVRGEVARYLAGDPQAGNLAGGYLIKMWGLPA
AALAIWRCAEPSERNRVAGIMLSAAAASWLTGVTEPIEFAFMFVAPFLFLIHVLLSGLAY
FVCIMLDIHHSIVFSHGLVDFTLLFSLSRNTGWFVFLGPLTAVIYYLLFRGSILAFNLKT
PGRLEPDEPHGAKESLRAIIAALGGRENIVELNACLTRLRLSVHSPELVNKVRLSQLGAK
GVIVMGKGVQVVYGTKAETLRKVLQRYLDTRR

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