GapMind for catabolism of small carbon sources

 

Protein WP_019613932.1 in Psychromonas ossibalaenae JAMM 0738

Annotation: NCBI__GCF_000381745.1:WP_019613932.1

Length: 468 amino acids

Source: GCF_000381745.1 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) 66% 99% 617.8 PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 47% 425.6
D-glucose catabolism ptsG hi protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) 66% 99% 617.8 PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 47% 425.6
lactose catabolism ptsG hi protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) 66% 99% 617.8 PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 47% 425.6
D-maltose catabolism ptsG hi protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) 66% 99% 617.8 PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 47% 425.6
sucrose catabolism ptsG hi protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) 66% 99% 617.8 PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 47% 425.6
trehalose catabolism ptsG hi protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) 66% 99% 617.8 PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 47% 425.6
N-acetyl-D-glucosamine catabolism nagEIIA med Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized) 46% 74% 382.9 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 66% 617.8
D-glucosamine (chitosamine) catabolism gamP med Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized) 46% 74% 382.9 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 66% 617.8
D-glucosamine (chitosamine) catabolism nagEIIA med Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized) 46% 74% 382.9 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 66% 617.8
D-maltose catabolism malEIIA med Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized) 46% 74% 382.9 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 66% 617.8
trehalose catabolism treEIIA med Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized) 46% 74% 382.9 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 66% 617.8
N-acetyl-D-glucosamine catabolism nagPcb med PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized) 43% 98% 373.2 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 66% 617.8
D-glucosamine (chitosamine) catabolism nagPcb med PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized) 43% 98% 373.2 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 66% 617.8
N-acetyl-D-glucosamine catabolism nagEcba med protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized) 41% 72% 365.2 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 66% 617.8
D-glucosamine (chitosamine) catabolism nagEcba med protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized) 41% 72% 365.2 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 66% 617.8
N-acetyl-D-glucosamine catabolism nagEcb med N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA (characterized) 42% 80% 360.5 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 66% 617.8
D-glucosamine (chitosamine) catabolism nagEcb med N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA (characterized) 42% 80% 360.5 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 66% 617.8
N-acetyl-D-glucosamine catabolism ptsC med 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) 42% 95% 303.1 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 66% 617.8
D-glucosamine (chitosamine) catabolism ptsC med 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) 42% 95% 303.1 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 66% 617.8
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) 48% 87% 66.6 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 66% 617.8
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) 48% 87% 66.6 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 66% 617.8
D-cellobiose catabolism ptsG-crr lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 47% 66% 374.8 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 66% 617.8
D-glucose catabolism ptsG-crr lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 47% 66% 374.8 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 66% 617.8
lactose catabolism ptsG-crr lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 47% 66% 374.8 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 66% 617.8
D-maltose catabolism ptsG-crr lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 47% 66% 374.8 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 66% 617.8
sucrose catabolism ptsG-crr lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 47% 66% 374.8 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 66% 617.8
trehalose catabolism ptsG-crr lo PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized) 47% 66% 374.8 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 66% 617.8
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) 34% 90% 248.8 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 66% 617.8
D-maltose catabolism malEIICBA lo The maltose/maltotriose porter, MalT (31% identical to 4.A.1.1.9) (characterized) 32% 72% 233 protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) 66% 617.8

Sequence Analysis Tools

View WP_019613932.1 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

MNIFGSLQKVGKSLMLPVSVLPIAGILLGVGAAKFAILPEVVSQLMEQAGGAVFGNMALL
FAIGVALGFTKNDGVAGLAAAVGYYIMMQTVETLAPGANTGVLGGIIAGGIAAAMFNRFY
NITLPEYLGFFAGKRAVPIMTGLSAIVMGAVLAVIWPPIGSAIAAFSDWAAHQNPTVAFG
IYGVVERSLIPFGLHHIWNVPFFFEAGSCTSASGEQLNGILTCYLSADDATRAAGNGFGQ
LAGGYMFKMFGLPAAAIAIAHSAKPENRAKVMGIMASAALTSFLTGITEPIEFAFLFVAP
VLYAIHALLAGSAFVVTNMLGMVHGTSFSHGLIDFLVLSANAEKMIYFVVIGLVYAAIYY
TLFRIVIKALDLKTPGREDEEAEEEVHVNSSEMAILLVAAFGGKANIENLDACITRLRIS
VNDIALVDKAELKKLGAAGVVVSGNGVQAIFGTKSDNLKTDMEAYLAK

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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