GapMind for catabolism of small carbon sources

 

Protein AO353_04465 in Pseudomonas fluorescens FW300-N2E3

Annotation: FitnessBrowser__pseudo3_N2E3:AO353_04465

Length: 571 amino acids

Source: pseudo3_N2E3 in FitnessBrowser

Candidate for 26 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 nagEcb hi N-acetylglucosamine-specific PTS system, IIBC components (nagE) (characterized) 100% 100% 1117.1 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 49% 490.7
D-glucosamine (chitosamine) catabolism nagEcb hi N-acetylglucosamine-specific PTS system, IIBC components (nagE) (characterized) 100% 100% 1117.1 protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) 49% 490.7
N-acetyl-D-glucosamine catabolism nagEcba med protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized) 49% 80% 490.7 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 100% 1117.1
D-glucosamine (chitosamine) catabolism nagEcba med protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized) 49% 80% 490.7 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 100% 1117.1
D-glucosamine (chitosamine) catabolism gamP med protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized) 50% 80% 490 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 100% 1117.1
N-acetyl-D-glucosamine catabolism nagPcb med PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized) 52% 99% 466.5 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 100% 1117.1
D-glucosamine (chitosamine) catabolism nagPcb med PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized) 52% 99% 466.5 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 100% 1117.1
N-acetyl-D-glucosamine catabolism nagEIIA med Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized) 47% 79% 443.7 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 100% 1117.1
D-glucosamine (chitosamine) catabolism nagEIIA med Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized) 47% 79% 443.7 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 100% 1117.1
D-maltose catabolism malEIIA med Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized) 47% 79% 443.7 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 100% 1117.1
trehalose catabolism treEIIA med Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized) 47% 79% 443.7 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 100% 1117.1
D-cellobiose catabolism ptsG-crr med PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 (characterized) 43% 78% 380.2 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 100% 1117.1
D-glucose catabolism ptsG-crr med PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 (characterized) 43% 78% 380.2 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 100% 1117.1
lactose catabolism ptsG-crr med PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 (characterized) 43% 78% 380.2 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 100% 1117.1
D-maltose catabolism ptsG-crr med PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 (characterized) 43% 78% 380.2 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 100% 1117.1
sucrose catabolism ptsG-crr med PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 (characterized) 43% 78% 380.2 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 100% 1117.1
trehalose catabolism ptsG-crr med PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 (characterized) 43% 78% 380.2 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 100% 1117.1
N-acetyl-D-glucosamine catabolism ptsC med IIC' aka PtsC2, component of N-Acetylglucosamine (NAG) porter (PtsBC1C2)(also may facilitate xylose transport) (characterized) 48% 96% 375.2 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 100% 1117.1
D-glucosamine (chitosamine) catabolism ptsC med IIC' aka PtsC2, component of N-Acetylglucosamine (NAG) porter (PtsBC1C2)(also may facilitate xylose transport) (characterized) 48% 96% 375.2 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 100% 1117.1
D-cellobiose catabolism ptsG med protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) 42% 99% 366.3 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 100% 1117.1
D-glucose catabolism ptsG med protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) 42% 99% 366.3 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 100% 1117.1
lactose catabolism ptsG med protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) 42% 99% 366.3 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 100% 1117.1
D-maltose catabolism ptsG med protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) 42% 99% 366.3 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 100% 1117.1
sucrose catabolism ptsG med protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) 42% 99% 366.3 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 100% 1117.1
trehalose catabolism ptsG med protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) 42% 99% 366.3 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 100% 1117.1
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) 32% 98% 228.8 N-acetylglucosamine-specific PTS system, IIBC components (nagE) 100% 1117.1

Sequence Analysis Tools

View AO353_04465 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

MYQLFIEGLQRLGRALMLPIAILPIAGLLLRLGDTDLLNIAIIHDAGQVIFANLALIFAI
GIAVGFARDNNGTAGLAGAIGYLVMVSTLKVLDASINMGMLAGIISGLMAGALYNRFKDI
KLPEYLAFFGGRRFVPIATGFSAVGLGVIFGLIWPPIQHGINSFGQLLLESGSIGAFVFG
VFNRLLIVTGLHHILNNMAWFIFGSFTDPTTGAIVTGDLARYFAGDPKGGQFMTGMFPMM
IFGLPAACLAMYRNALPERRKVMGGIFLSMALTSFLTGVTEPIEFAFMFLAPLLYLLHVL
LTGMAMAITNALNIHLGFTFSGGAIDMALGWGKSTNGWLVFPVGLAYAVIYYVVFDFCIR
RFNLKTPGREGVVVGEKVVLSENQRAGAYIQALGGAENLITVGACTTRLRLEMVDRNKAS
DSELKALGAMAVVRPGKGGSLQVVVGPLADSIADEIRQAMPTAGSALVAAVVVTEEAPKA
APVETPEAQKWLNAVGGSDNVLQLDCVAMTRIRLQLADGKALSECQLKDLGCQGVSALDG
GVWHLLIGDKALSLSEALEGLVNRSEVSAKV

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