GapMind for catabolism of small carbon sources

 

Protein WP_068009036.1 in Pseudovibrio axinellae Ad2

Annotation: NCBI__GCF_001623255.1:WP_068009036.1

Length: 569 amino acids

Source: GCF_001623255.1 in NCBI

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) 62% 100% 610.9 PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 49% 479.6
D-glucose catabolism ptsG hi protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) 62% 100% 610.9 PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 49% 479.6
lactose catabolism ptsG hi protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) 62% 100% 610.9 PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 49% 479.6
D-maltose catabolism ptsG hi protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) 62% 100% 610.9 PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 49% 479.6
sucrose catabolism ptsG hi protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) 62% 100% 610.9 PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 49% 479.6
trehalose catabolism ptsG hi protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) 62% 100% 610.9 PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 49% 479.6
N-acetyl-D-glucosamine catabolism nagEIIA med PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 49% 78% 479.6 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 62% 610.9
D-cellobiose catabolism ptsG-crr med PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 49% 78% 479.6 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 62% 610.9
D-glucosamine (chitosamine) catabolism nagEIIA med PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 49% 78% 479.6 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 62% 610.9
D-glucose catabolism ptsG-crr med PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 49% 78% 479.6 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 62% 610.9
lactose catabolism ptsG-crr med PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 49% 78% 479.6 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 62% 610.9
D-maltose catabolism malEIIA med PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 49% 78% 479.6 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 62% 610.9
D-maltose catabolism ptsG-crr med PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 49% 78% 479.6 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 62% 610.9
sucrose catabolism ptsG-crr med PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 49% 78% 479.6 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 62% 610.9
trehalose catabolism ptsG-crr med PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 49% 78% 479.6 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 62% 610.9
trehalose catabolism treEIIA med PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 49% 78% 479.6 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 62% 610.9
D-glucosamine (chitosamine) catabolism gamP med Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized) 50% 77% 458.8 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 62% 610.9
N-acetyl-D-glucosamine catabolism nagEcb med N-acetylglucosamine-specific PTS system, IIBC components (nagE) (characterized) 43% 98% 451.4 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 62% 610.9
D-glucosamine (chitosamine) catabolism nagEcb med N-acetylglucosamine-specific PTS system, IIBC components (nagE) (characterized) 43% 98% 451.4 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 62% 610.9
N-acetyl-D-glucosamine catabolism nagEcba med protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized) 41% 81% 373.2 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 62% 610.9
D-glucosamine (chitosamine) catabolism nagEcba med protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized) 41% 81% 373.2 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 62% 610.9
N-acetyl-D-glucosamine catabolism nagPcb med PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized) 43% 99% 365.2 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 62% 610.9
D-glucosamine (chitosamine) catabolism nagPcb med PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized) 43% 99% 365.2 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 62% 610.9
N-acetyl-D-glucosamine catabolism ptsC med IIC' aka PtsC2, component of N-Acetylglucosamine (NAG) porter (PtsBC1C2)(also may facilitate xylose transport) (characterized) 45% 99% 346.3 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 62% 610.9
D-glucosamine (chitosamine) catabolism ptsC med IIC' aka PtsC2, component of N-Acetylglucosamine (NAG) porter (PtsBC1C2)(also may facilitate xylose transport) (characterized) 45% 99% 346.3 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 62% 610.9
N-acetyl-D-glucosamine catabolism ptsB med IIB aka PtsB, component of N-Acetylglucosamine (NAG) porter (PtsBC1C2)(also may facilitate xylose transport) (characterized) 44% 89% 73.9 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 62% 610.9
D-glucosamine (chitosamine) catabolism ptsB med IIB aka PtsB, component of N-Acetylglucosamine (NAG) porter (PtsBC1C2)(also may facilitate xylose transport) (characterized) 44% 89% 73.9 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 62% 610.9
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% 99% 260.4 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 62% 610.9
D-maltose catabolism malEIICBA lo The maltose/maltotriose porter, MalT (31% identical to 4.A.1.1.9) (characterized) 31% 82% 251.1 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 62% 610.9

Sequence Analysis Tools

View WP_068009036.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

Fitness BLAST: loading...

Sequence

MSIFSNAFGALQKVGKSLMLPVSVLPAAGILLGVGAADLPFIPEFINHLMAQAGGSIFGN
LPIIFAVAVALGFAKNDGVAGLAAVVGYGVLLATMGVVAETIEMETKPILGITSIDTGVF
GGILVGALAAFLFNHFYRIKLPDYLGFFAGKRFVPIITAFACIGLGVILAFVWPPIGGAI
NAFSRWAAEENPELAFFIYGVIERGLIPFGLHHIWNVPFFFEAGSYIDPATGEAVTGEIQ
RYLAGDPTAGNMAGGYLFKMWGLPAAALAIWHCAKPENRTMVGGIMVSAALTSFLTGITE
PIEFAFLFVAPILYVAHALLAGVGYSLMIMLGIKHGMTFSHGFIDYVLLYPLSTNGWMLI
VFGLGYAALYYAVFRILIVTLNLKTPGREAKTETSAVLASGDEDAMSAALVKAFGGADNI
TNLDACITRLRVSTVDVSKVDDAALKALGARGVIRVGNGAQAIFGTASENLKTDMEIHLQ
GGGAAAKPAAEQGFNAEAIFTQLGGKANVVAAEAVANTRVRVEVRDIASVSMSDLSQAGI
QVMKAGDKALHLIVGDKYTKLAKDLSGQI

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