Protein Ga0059261_0341 in Sphingomonas koreensis DSMZ 15582
Annotation: Ga0059261_0341 ABC-type antimicrobial peptide transport system, ATPase component
Length: 224 amino acids
Source: Korea in FitnessBrowser
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-histidine catabolism | BPHYT_RS24015 | lo | ABC transporter related (characterized, see rationale) | 40% | 87% | 147.1 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 203.0 |
| L-arginine catabolism | artP | 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) | 38% | 90% | 146.4 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 203.0 |
| 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) | 38% | 90% | 146.4 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 203.0 |
| L-lysine 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) | 38% | 90% | 146.4 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 203.0 |
| D-glucosamine (chitosamine) catabolism | AO353_21725 | lo | ABC transporter for D-Glucosamine, putative ATPase component (characterized) | 36% | 87% | 135.6 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 203.0 |
| L-asparagine catabolism | bgtA | lo | ATPase (characterized, see rationale) | 38% | 83% | 133.7 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 203.0 |
| L-aspartate catabolism | bgtA | lo | ATPase (characterized, see rationale) | 38% | 83% | 133.7 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 203.0 |
| D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 35% | 61% | 129 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 203.0 |
| 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) | 33% | 85% | 127.1 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 203.0 |
| D-cellobiose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 34% | 60% | 124.4 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 203.0 |
| D-glucose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 34% | 60% | 124.4 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 203.0 |
| lactose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 34% | 60% | 124.4 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 203.0 |
| D-maltose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 34% | 60% | 124.4 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 203.0 |
| sucrose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 34% | 60% | 124.4 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 203.0 |
| trehalose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 34% | 60% | 124.4 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 203.0 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 36% | 60% | 120.9 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 203.0 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 36% | 60% | 120.9 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 203.0 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 34% | 60% | 118.6 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 203.0 |
| L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 36% | 57% | 115.9 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 203.0 |
| xylitol catabolism | HSERO_RS17020 | lo | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 35% | 52% | 112.1 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 203.0 |
| trehalose catabolism | treV | lo | TreV, component of Trehalose porter (characterized) | 32% | 62% | 105.1 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 203.0 |
Sequence Analysis Tools
View Ga0059261_0341 at FitnessBrowser
PaperBLAST (search for papers about homologs of this protein)
Search CDD (the Conserved Domains Database, which includes COG and superfam)
Predict protein localization: PSORTb (Gram negative bacteria)
Predict transmembrane helices and signal peptides: Phobius
Check the SEED with FIGfam search
Fitness BLAST: loading...
Sequence
MSEPVLQTSGLKRTFSQGGADIHVLRGIDLTVGQGEIVALLGPSGSGKSTLLQAVGLLEG
GFEGSIRISGVEVGKLESHARTVTRRDKLGFVYQFHHLLPDFNALENVELPQLIQNATLA
DARARSEGLLTALGLGARLTHRPSQLSGGEQQRVAVARALANRPALVLADEPTGNLDEHT
ADIVLAEFLRLVRGEGAAALIATHNERLAAKMDRVVRLHEGVLE
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