Protein WP_047094592.1 in Erythrobacter marinus HWDM-33
Annotation: NCBI__GCF_001013305.1:WP_047094592.1
Length: 224 amino acids
Source: GCF_001013305.1 in NCBI
Candidate for 21 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-lysine catabolism | hisP | med | Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) | 40% | 77% | 134.4 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 213.8 |
| L-asparagine catabolism | bgtA | med | ATPase (characterized, see rationale) | 40% | 78% | 134 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 213.8 |
| L-aspartate catabolism | bgtA | med | ATPase (characterized, see rationale) | 40% | 78% | 134 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 213.8 |
| L-arginine catabolism | artP | lo | AotP aka PA0892, component of Arginine/ornithine (but not lysine) porter (characterized) | 38% | 83% | 141 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 213.8 |
| 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) | 35% | 89% | 140.2 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 213.8 |
| xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 38% | 63% | 137.5 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 213.8 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 37% | 64% | 137.1 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 213.8 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 37% | 64% | 137.1 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 213.8 |
| L-citrulline catabolism | AO353_03040 | lo | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 39% | 83% | 136 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 213.8 |
| D-glucosamine (chitosamine) catabolism | AO353_21725 | lo | ABC transporter for D-glucosamine, ATPase component (characterized) | 38% | 85% | 136 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 213.8 |
| L-histidine catabolism | BPHYT_RS24015 | lo | ABC transporter related (characterized, see rationale) | 39% | 80% | 135.2 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 213.8 |
| L-citrulline catabolism | PS417_17605 | lo | ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale) | 36% | 87% | 131 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 213.8 |
| trehalose catabolism | thuK | lo | Trehalose import ATP-binding protein SugC; EC 7.5.2.- (characterized) | 36% | 53% | 131 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 213.8 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 36% | 63% | 129 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 213.8 |
| D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 34% | 61% | 126.7 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 213.8 |
| L-asparagine catabolism | aatP | lo | ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized) | 37% | 82% | 125.9 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 213.8 |
| L-aspartate catabolism | aatP | lo | ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized) | 37% | 82% | 125.9 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 213.8 |
| trehalose catabolism | treV | lo | TreV, component of Trehalose porter (characterized) | 32% | 65% | 124.8 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 213.8 |
| lactose catabolism | lacK | lo | LacK, component of Lactose porter (characterized) | 33% | 58% | 122.9 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 213.8 |
| D-mannitol catabolism | mtlK | lo | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) | 37% | 59% | 122.5 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 213.8 |
| 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) | 34% | 52% | 114 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 213.8 |
Sequence Analysis Tools
View WP_047094592.1 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
MSDPVVRLTELARSFEQGGVRIDVLNGVNLTIEPGEIVALVGPSGSGKSTMLQAVGLLEG
GFSGKIEIAGQDASTLDSAERTTLRRDHLGFVYQFHHLLPDFTARENIVLPQLLLGVSRA
DAVVRAEQLLGALGLEHRMDHRPSKLSGGEQQRVAVARALANKPQLVLADEPTGNLDEKT
SERVLGEFLELVRGQGSAALVATHNERLAARMDRVVRLHEGRIE
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