Protein 5210215 in Shewanella loihica PV-4
Annotation: FitnessBrowser__PV4:5210215
Length: 227 amino acids
Source: PV4 in FitnessBrowser
Candidate for 23 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-asparagine catabolism | bgtA | med | ATPase (characterized, see rationale) | 42% | 77% | 155.6 | ABC transporter, component of Lantibiotic detoxification ABC transporter, VraD (252 aas)/VraE (626 aas; 10 TMSs)/VraH ( | 45% | 194.5 |
| L-aspartate catabolism | bgtA | med | ATPase (characterized, see rationale) | 42% | 77% | 155.6 | ABC transporter, component of Lantibiotic detoxification ABC transporter, VraD (252 aas)/VraE (626 aas; 10 TMSs)/VraH ( | 45% | 194.5 |
| L-glutamate catabolism | gltL | med | GluA aka CGL1950, component of Glutamate porter (characterized) | 41% | 88% | 152.5 | ABC transporter, component of Lantibiotic detoxification ABC transporter, VraD (252 aas)/VraE (626 aas; 10 TMSs)/VraH ( | 45% | 194.5 |
| L-histidine catabolism | hutV | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 39% | 74% | 149.4 | ABC transporter, component of Lantibiotic detoxification ABC transporter, VraD (252 aas)/VraE (626 aas; 10 TMSs)/VraH ( | 45% | 194.5 |
| L-lysine catabolism | hisP | lo | Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) | 37% | 84% | 147.1 | ABC transporter, component of Lantibiotic detoxification ABC transporter, VraD (252 aas)/VraE (626 aas; 10 TMSs)/VraH ( | 45% | 194.5 |
| L-asparagine catabolism | aatP | lo | PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized) | 40% | 84% | 146.7 | ABC transporter, component of Lantibiotic detoxification ABC transporter, VraD (252 aas)/VraE (626 aas; 10 TMSs)/VraH ( | 45% | 194.5 |
| L-aspartate catabolism | aatP | lo | PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized) | 40% | 84% | 146.7 | ABC transporter, component of Lantibiotic detoxification ABC transporter, VraD (252 aas)/VraE (626 aas; 10 TMSs)/VraH ( | 45% | 194.5 |
| D-cellobiose catabolism | msiK | lo | MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized) | 37% | 57% | 145.2 | ABC transporter, component of Lantibiotic detoxification ABC transporter, VraD (252 aas)/VraE (626 aas; 10 TMSs)/VraH ( | 45% | 194.5 |
| L-asparagine catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 35% | 90% | 144.8 | ABC transporter, component of Lantibiotic detoxification ABC transporter, VraD (252 aas)/VraE (626 aas; 10 TMSs)/VraH ( | 45% | 194.5 |
| L-aspartate catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 35% | 90% | 144.8 | ABC transporter, component of Lantibiotic detoxification ABC transporter, VraD (252 aas)/VraE (626 aas; 10 TMSs)/VraH ( | 45% | 194.5 |
| L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 36% | 55% | 144.4 | ABC transporter, component of Lantibiotic detoxification ABC transporter, VraD (252 aas)/VraE (626 aas; 10 TMSs)/VraH ( | 45% | 194.5 |
| L-histidine catabolism | Ac3H11_2560 | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 35% | 83% | 143.3 | ABC transporter, component of Lantibiotic detoxification ABC transporter, VraD (252 aas)/VraE (626 aas; 10 TMSs)/VraH ( | 45% | 194.5 |
| L-histidine catabolism | hisP | lo | Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) | 36% | 89% | 140.2 | ABC transporter, component of Lantibiotic detoxification ABC transporter, VraD (252 aas)/VraE (626 aas; 10 TMSs)/VraH ( | 45% | 194.5 |
| L-histidine catabolism | BPHYT_RS24015 | lo | ABC transporter related (characterized, see rationale) | 39% | 81% | 139.8 | ABC transporter, component of Lantibiotic detoxification ABC transporter, VraD (252 aas)/VraE (626 aas; 10 TMSs)/VraH ( | 45% | 194.5 |
| D-cellobiose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 35% | 54% | 137.9 | ABC transporter, component of Lantibiotic detoxification ABC transporter, VraD (252 aas)/VraE (626 aas; 10 TMSs)/VraH ( | 45% | 194.5 |
| D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 35% | 54% | 137.9 | ABC transporter, component of Lantibiotic detoxification ABC transporter, VraD (252 aas)/VraE (626 aas; 10 TMSs)/VraH ( | 45% | 194.5 |
| D-glucose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 35% | 54% | 137.9 | ABC transporter, component of Lantibiotic detoxification ABC transporter, VraD (252 aas)/VraE (626 aas; 10 TMSs)/VraH ( | 45% | 194.5 |
| lactose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 35% | 54% | 137.9 | ABC transporter, component of Lantibiotic detoxification ABC transporter, VraD (252 aas)/VraE (626 aas; 10 TMSs)/VraH ( | 45% | 194.5 |
| D-maltose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 35% | 54% | 137.9 | ABC transporter, component of Lantibiotic detoxification ABC transporter, VraD (252 aas)/VraE (626 aas; 10 TMSs)/VraH ( | 45% | 194.5 |
| sucrose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 35% | 54% | 137.9 | ABC transporter, component of Lantibiotic detoxification ABC transporter, VraD (252 aas)/VraE (626 aas; 10 TMSs)/VraH ( | 45% | 194.5 |
| trehalose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 35% | 54% | 137.9 | ABC transporter, component of Lantibiotic detoxification ABC transporter, VraD (252 aas)/VraE (626 aas; 10 TMSs)/VraH ( | 45% | 194.5 |
| L-citrulline catabolism | AO353_03040 | lo | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 34% | 89% | 132.9 | ABC transporter, component of Lantibiotic detoxification ABC transporter, VraD (252 aas)/VraE (626 aas; 10 TMSs)/VraH ( | 45% | 194.5 |
| glycerol catabolism | glpS | lo | GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) | 32% | 54% | 115.9 | ABC transporter, component of Lantibiotic detoxification ABC transporter, VraD (252 aas)/VraE (626 aas; 10 TMSs)/VraH ( | 45% | 194.5 |
Sequence Analysis Tools
View 5210215 at FitnessBrowser
Find papers: PaperBLAST
Find functional residues: SitesBLAST
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Predict transmenbrane helices: Phobius
Predict protein localization: PSORTb
Find homologs in fast.genomics
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Sequence
MTIAIQALTKIYNPESDFPVAAVKSLDLTIAQGEFVAIMGPSGSGKTTLLNMIGGIDSPS
SGAVFIDGEDITHLSEQALIAFRRDHVGFIFQDYSLLPVLTALENVEFVMQLQGHSEAEC
RDRAMALLAQVGLAAQQDKIPAKLSGGQQQRVAVARALAPRPRFVMADEPTANLDAKSTA
ELLDIMQSLNEQEGTTFIFSTHDPRVIARAKRVIVFEDGRLVEDRRQ
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