Protein WP_028310576.1 in Derxia gummosa DSM 723
Annotation: NCBI__GCF_000482785.1:WP_028310576.1
Length: 402 amino acids
Source: GCF_000482785.1 in NCBI
Candidate for 18 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-proline catabolism | proV | hi | Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) | 48% | 99% | 369.4 | BusAA, component of Uptake system for glycine-betaine (high affinity) and proline (low affinity) (OpuAA-OpuABC) or BusAA-ABC of Lactococcus lactis). BusAA, the ATPase subunit, has a C-terminal tandem cystathionine β-synthase (CBS) domain which is the cytoplasmic K+ sensor for osmotic stress (osmotic strength)while the BusABC subunit has the membrane and receptor domains fused to each other (Biemans-Oldehinkel et al., 2006; Mahmood et al., 2006; Gul et al. 2012). An N-terminal amphipathic α-helix of OpuA is necessary for high activity but is not critical for biogenesis or the ionic regulation of transport | 45% | 332.0 |
| L-proline catabolism | opuBA | med | BusAA, component of Uptake system for glycine-betaine (high affinity) and proline (low affinity) (OpuAA-OpuABC) or BusAA-ABC of Lactococcus lactis). BusAA, the ATPase subunit, has a C-terminal tandem cystathionine β-synthase (CBS) domain which is the cytoplasmic K+ sensor for osmotic stress (osmotic strength)while the BusABC subunit has the membrane and receptor domains fused to each other (Biemans-Oldehinkel et al., 2006; Mahmood et al., 2006; Gul et al. 2012). An N-terminal amphipathic α-helix of OpuA is necessary for high activity but is not critical for biogenesis or the ionic regulation of transport (characterized) | 45% | 95% | 332 | Glycine betaine/choline transport system ATP-binding protein OusV | 51% | 377.1 |
| L-histidine catabolism | hutV | med | ABC transporter for L-Histidine, ATPase component (characterized) | 56% | 96% | 296.2 | Glycine betaine/choline transport system ATP-binding protein OusV | 51% | 377.1 |
| L-proline catabolism | hutV | med | HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) | 54% | 95% | 280 | Glycine betaine/choline transport system ATP-binding protein OusV | 51% | 377.1 |
| L-lysine catabolism | hisP | med | Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) | 40% | 89% | 160.6 | Glycine betaine/choline transport system ATP-binding protein OusV | 51% | 377.1 |
| L-histidine catabolism | PA5503 | lo | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) | 44% | 66% | 187.6 | Glycine betaine/choline transport system ATP-binding protein OusV | 51% | 377.1 |
| L-asparagine catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 38% | 85% | 159.1 | Glycine betaine/choline transport system ATP-binding protein OusV | 51% | 377.1 |
| L-aspartate catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 38% | 85% | 159.1 | Glycine betaine/choline transport system ATP-binding protein OusV | 51% | 377.1 |
| L-glutamate catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 38% | 85% | 159.1 | Glycine betaine/choline transport system ATP-binding protein OusV | 51% | 377.1 |
| L-histidine catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 38% | 85% | 159.1 | Glycine betaine/choline transport system ATP-binding protein OusV | 51% | 377.1 |
| L-leucine catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 38% | 85% | 159.1 | Glycine betaine/choline transport system ATP-binding protein OusV | 51% | 377.1 |
| L-proline catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 38% | 85% | 159.1 | Glycine betaine/choline transport system ATP-binding protein OusV | 51% | 377.1 |
| D-cellobiose catabolism | cbtD | lo | CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) | 35% | 68% | 142.1 | Glycine betaine/choline transport system ATP-binding protein OusV | 51% | 377.1 |
| D-mannose catabolism | TM1750 | lo | TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) | 34% | 70% | 141.4 | Glycine betaine/choline transport system ATP-binding protein OusV | 51% | 377.1 |
| D-cellobiose catabolism | TM0027 | lo | TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) | 34% | 94% | 135.2 | Glycine betaine/choline transport system ATP-binding protein OusV | 51% | 377.1 |
| D-maltose catabolism | malK_Ss | lo | MalK, component of Maltose and maltooligosaccharide porter (characterized) | 30% | 53% | 134.4 | Glycine betaine/choline transport system ATP-binding protein OusV | 51% | 377.1 |
| D-mannose catabolism | TM1749 | lo | TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) | 30% | 74% | 129 | Glycine betaine/choline transport system ATP-binding protein OusV | 51% | 377.1 |
| D-cellobiose catabolism | TM0028 | lo | TM0028, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) | 31% | 74% | 113.6 | Glycine betaine/choline transport system ATP-binding protein OusV | 51% | 377.1 |
Sequence Analysis Tools
View WP_028310576.1 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
MAKDKIVVENLTKIFGENSERWLSLMKAGWSKERLLAEHGVTVGVCDVSFTVREGEIFVL
MGLSGSGKSTLIRLINRLVEPTAGRVLIDGQDVVTLPADKLRDLRRRDMSMVFQSFALLP
NRTVLDNAAFGLEVAGVGRKERERAAMEVLEQVGLKPFARKHPHELSGGMRQRVGLARAL
AVNPSLMIMDEAFSALDPLKRREMQDVLLQLQAEHKRTIVFVSHDIEEAFRIGNRIAIME
GGRLIQLGEPRQIIENPANDYVRAFFDGFDTSRYLTAADLLRADAVPVLTRQDNSLDFDA
DALLGELFADERGWCFVLDRDRRVSGALDVPTLRNWRAGHGPRELIRVEPVRGACRLDQI
IPQLMRSAGPLPVVDDDGRYRGAINKRAVLGRLAAKGGALHG
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:
- 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