Protein BPHYT_RS02745 in Burkholderia phytofirmans PsJN
Annotation: FitnessBrowser__BFirm:BPHYT_RS02745
Length: 591 amino acids
Source: BFirm in FitnessBrowser
Candidate for 27 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% | 1162.1 | protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) | 57% | 549.3 |
| D-glucosamine (chitosamine) catabolism | nagEcb | hi | N-acetylglucosamine-specific PTS system, IIBC components (nagE) (characterized) | 100% | 100% | 1162.1 | protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) | 57% | 549.3 |
| N-acetyl-D-glucosamine catabolism | nagEcba | med | protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized) | 57% | 75% | 549.3 | N-acetylglucosamine-specific PTS system, IIBC components (nagE) | 100% | 1162.1 |
| D-glucosamine (chitosamine) catabolism | nagEcba | med | protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized) | 57% | 75% | 549.3 | N-acetylglucosamine-specific PTS system, IIBC components (nagE) | 100% | 1162.1 |
| D-glucosamine (chitosamine) catabolism | gamP | med | protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized) | 53% | 79% | 545.8 | N-acetylglucosamine-specific PTS system, IIBC components (nagE) | 100% | 1162.1 |
| N-acetyl-D-glucosamine catabolism | nagPcb | med | PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized) | 51% | 99% | 481.9 | N-acetylglucosamine-specific PTS system, IIBC components (nagE) | 100% | 1162.1 |
| D-glucosamine (chitosamine) catabolism | nagPcb | med | PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized) | 51% | 99% | 481.9 | N-acetylglucosamine-specific PTS system, IIBC components (nagE) | 100% | 1162.1 |
| N-acetyl-D-glucosamine catabolism | nagEIIA | med | Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized) | 48% | 77% | 441.4 | N-acetylglucosamine-specific PTS system, IIBC components (nagE) | 100% | 1162.1 |
| D-glucosamine (chitosamine) catabolism | nagEIIA | med | Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized) | 48% | 77% | 441.4 | N-acetylglucosamine-specific PTS system, IIBC components (nagE) | 100% | 1162.1 |
| D-maltose catabolism | malEIIA | med | Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized) | 48% | 77% | 441.4 | N-acetylglucosamine-specific PTS system, IIBC components (nagE) | 100% | 1162.1 |
| trehalose catabolism | treEIIA | med | Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized) | 48% | 77% | 441.4 | N-acetylglucosamine-specific PTS system, IIBC components (nagE) | 100% | 1162.1 |
| 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) | 51% | 95% | 392.1 | N-acetylglucosamine-specific PTS system, IIBC components (nagE) | 100% | 1162.1 |
| 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) | 51% | 95% | 392.1 | N-acetylglucosamine-specific PTS system, IIBC components (nagE) | 100% | 1162.1 |
| D-cellobiose catabolism | ptsG | med | protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) | 43% | 99% | 384.4 | N-acetylglucosamine-specific PTS system, IIBC components (nagE) | 100% | 1162.1 |
| D-glucose catabolism | ptsG | med | protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) | 43% | 99% | 384.4 | N-acetylglucosamine-specific PTS system, IIBC components (nagE) | 100% | 1162.1 |
| lactose catabolism | ptsG | med | protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) | 43% | 99% | 384.4 | N-acetylglucosamine-specific PTS system, IIBC components (nagE) | 100% | 1162.1 |
| D-maltose catabolism | ptsG | med | protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) | 43% | 99% | 384.4 | N-acetylglucosamine-specific PTS system, IIBC components (nagE) | 100% | 1162.1 |
| sucrose catabolism | ptsG | med | protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) | 43% | 99% | 384.4 | N-acetylglucosamine-specific PTS system, IIBC components (nagE) | 100% | 1162.1 |
| trehalose catabolism | ptsG | med | protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) | 43% | 99% | 384.4 | N-acetylglucosamine-specific PTS system, IIBC components (nagE) | 100% | 1162.1 |
| 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) | 42% | 80% | 374 | N-acetylglucosamine-specific PTS system, IIBC components (nagE) | 100% | 1162.1 |
| 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) | 42% | 80% | 374 | N-acetylglucosamine-specific PTS system, IIBC components (nagE) | 100% | 1162.1 |
| lactose catabolism | ptsG-crr | med | PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 (characterized) | 42% | 80% | 374 | N-acetylglucosamine-specific PTS system, IIBC components (nagE) | 100% | 1162.1 |
| 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) | 42% | 80% | 374 | N-acetylglucosamine-specific PTS system, IIBC components (nagE) | 100% | 1162.1 |
| sucrose catabolism | ptsG-crr | med | PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 (characterized) | 42% | 80% | 374 | N-acetylglucosamine-specific PTS system, IIBC components (nagE) | 100% | 1162.1 |
| trehalose catabolism | ptsG-crr | med | PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 (characterized) | 42% | 80% | 374 | N-acetylglucosamine-specific PTS system, IIBC components (nagE) | 100% | 1162.1 |
| 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) | 36% | 74% | 214.5 | N-acetylglucosamine-specific PTS system, IIBC components (nagE) | 100% | 1162.1 |
| D-maltose catabolism | malEIICBA | lo | PTS system, IIABC components (characterized, see rationale) | 34% | 58% | 199.9 | N-acetylglucosamine-specific PTS system, IIBC components (nagE) | 100% | 1162.1 |
Sequence Analysis Tools
View BPHYT_RS02745 at FitnessBrowser
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
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Sequence
MDGNPFLKIQRLGRALMLPIAVLPVAGLLLRLGQPDVFNIKMIADAGGAIFDNLPLLFAI
GVAVGFAKDNNGVAGLAGAIGYLIEVAVMKDINDKLNMGVLSGIVAGIVAGLLYNRYKDI
KLPDYLAFFGGKRFVPIVTGVVCLVLGIAFGYVWQPVQAVIDTAGHWLTTAGALGAFVFG
VLNRLLLVTGLHHILNSLTWFVFGTFTPPGGAAVTGDLHRFFAGDPTAGTFMTGFFPVMM
FGLPAACLAMFHEAPKERRAVVGGLLFSMALTSFLTGVTEPIEFSFMFLAPVLYVIHALL
TGISLAICSALGIHLGFTFSAGAIDYVLNYGLSTRGWWAIPIGLVYMVVYYGLFRFFIRK
FNMATPGREPAAADEQVDSFAAGGFVSPVAGTAVPRAQRYIAALGGASNLSVVDACTTRL
RLSVVDSNKVSENELKTIGARGVLKRGSTNVQVIIGPEADIIADEIRTVIAQGGGDAVKP
AAAAPAQVVAAAPVAASVAQGSGPLDPDPLRWLAVFGGAGNVLSLDAIAATRLRIVVRDP
SAVDRQRLATLDTAWISADTFHIVVGDAAQRYAEKLATRTTQSGGATPLPA
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:
- ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
- HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.
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:
- ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
- ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
- HMMer finds a hit (regardless of coverage or other bits).
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:
- our ignorance of proteins' functions,
- omissions in the gene models,
- frame-shift errors in the genome sequence, or
- the organism lacks the pathway.
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