Protein 6936959 in Shewanella amazonensis SB2B
Annotation: FitnessBrowser__SB2B:6936959
Length: 485 amino acids
Source: SB2B 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) | 45% | 99% | 438.3 | PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 | 38% | 331.6 |
| D-glucose catabolism | ptsG | hi | protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) | 45% | 99% | 438.3 | PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 | 38% | 331.6 |
| lactose catabolism | ptsG | hi | protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) | 45% | 99% | 438.3 | PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 | 38% | 331.6 |
| D-maltose catabolism | ptsG | hi | protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) | 45% | 99% | 438.3 | PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 | 38% | 331.6 |
| sucrose catabolism | ptsG | hi | protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) | 45% | 99% | 438.3 | PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 | 38% | 331.6 |
| trehalose catabolism | ptsG | hi | protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized) | 45% | 99% | 438.3 | PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 | 38% | 331.6 |
| N-acetyl-D-glucosamine catabolism | ptsB | med | IIB aka PtsB, component of N-Acetylglucosamine (NAG) porter (PtsBC1C2)(also may facilitate xylose transport) (characterized) | 43% | 76% | 61.6 | protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) | 45% | 438.3 |
| D-glucosamine (chitosamine) catabolism | ptsB | med | IIB aka PtsB, component of N-Acetylglucosamine (NAG) porter (PtsBC1C2)(also may facilitate xylose transport) (characterized) | 43% | 76% | 61.6 | protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) | 45% | 438.3 |
| D-cellobiose catabolism | ptsG-crr | lo | PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 (characterized) | 38% | 74% | 331.6 | protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) | 45% | 438.3 |
| D-glucose catabolism | ptsG-crr | lo | PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 (characterized) | 38% | 74% | 331.6 | protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) | 45% | 438.3 |
| lactose catabolism | ptsG-crr | lo | PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 (characterized) | 38% | 74% | 331.6 | protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) | 45% | 438.3 |
| D-maltose catabolism | ptsG-crr | lo | PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 (characterized) | 38% | 74% | 331.6 | protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) | 45% | 438.3 |
| sucrose catabolism | ptsG-crr | lo | PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 (characterized) | 38% | 74% | 331.6 | protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) | 45% | 438.3 |
| trehalose catabolism | ptsG-crr | lo | PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 (characterized) | 38% | 74% | 331.6 | protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) | 45% | 438.3 |
| N-acetyl-D-glucosamine catabolism | nagEIIA | lo | Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized) | 38% | 73% | 324.7 | protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) | 45% | 438.3 |
| D-glucosamine (chitosamine) catabolism | gamP | lo | Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized) | 38% | 73% | 324.7 | protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) | 45% | 438.3 |
| D-glucosamine (chitosamine) catabolism | nagEIIA | lo | Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized) | 38% | 73% | 324.7 | protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) | 45% | 438.3 |
| D-maltose catabolism | malEIIA | lo | Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized) | 38% | 73% | 324.7 | protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) | 45% | 438.3 |
| trehalose catabolism | treEIIA | lo | Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized) | 38% | 73% | 324.7 | protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) | 45% | 438.3 |
| N-acetyl-D-glucosamine catabolism | nagEcb | lo | N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA (characterized) | 38% | 80% | 298.5 | protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) | 45% | 438.3 |
| D-glucosamine (chitosamine) catabolism | nagEcb | lo | N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA (characterized) | 38% | 80% | 298.5 | protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) | 45% | 438.3 |
| N-acetyl-D-glucosamine catabolism | nagEcba | lo | protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized) | 35% | 71% | 296.6 | protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) | 45% | 438.3 |
| D-glucosamine (chitosamine) catabolism | nagEcba | lo | protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized) | 35% | 71% | 296.6 | protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) | 45% | 438.3 |
| N-acetyl-D-glucosamine catabolism | nagPcb | lo | PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized) | 36% | 97% | 277.7 | protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) | 45% | 438.3 |
| D-glucosamine (chitosamine) catabolism | nagPcb | lo | PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized) | 36% | 97% | 277.7 | protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) | 45% | 438.3 |
| N-acetyl-D-glucosamine catabolism | ptsC | lo | IIC' aka PtsC2, component of N-Acetylglucosamine (NAG) porter (PtsBC1C2)(also may facilitate xylose transport) (characterized) | 35% | 96% | 243.4 | protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) | 45% | 438.3 |
| D-glucosamine (chitosamine) catabolism | ptsC | lo | IIC' aka PtsC2, component of N-Acetylglucosamine (NAG) porter (PtsBC1C2)(also may facilitate xylose transport) (characterized) | 35% | 96% | 243.4 | protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) | 45% | 438.3 |
| D-maltose catabolism | malEIICBA | lo | The maltose/maltotriose porter, MalT (31% identical to 4.A.1.1.9) (characterized) | 31% | 75% | 220.7 | protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) | 45% | 438.3 |
| 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% | 99% | 216.5 | protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) | 45% | 438.3 |
Sequence Analysis Tools
View 6936959 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
MAPASSARPERLTRLNRHWFRFAQRLSQTLLIPIAILPAAGVMIGIATNPLPFIPDVANV
LMLSVGKLIFDIMPMLFAIAVAIGFCRDQGIAAFSAAFGYGVLLSTLAAAAKVYHLPSHI
VWGTPTIDTGIAGGMLVGGITCVAVRLSEKLRLPAVFSFFEGRRSAPLIMIPLVMLLAVM
LAFIWPPLALSIERLSDWAVYQEPAIAFGFYGMVERLLLPLGLHHIWNAPFYLEVGQYAH
DGEIVRGEMARYFAGDPSAGNLAGGYLIKMWGLPAAALAIWRCADRNQRNRVAGVMLSAA
TASWLTGVTEPIEFAFLFVAPLLYLCHALLTGLAYSIAILLDMHHSVVFSHGLVDFVLLF
PQSSNTHWIWFLGPLTFVIYYILFRASILAFNLKTPGRFEADTGQKRNLIAIVSALGGGG
NIADLSACLTRLRISVADPSQVDRQRLMSLGAKGVIVVGSGVQLVFGTKAETLRKLLQRY
LDTRS
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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