Protein WP_072910123.1 in Malonomonas rubra DSM 5091
Annotation: NCBI__GCF_900142125.1:WP_072910123.1
Length: 362 amino acids
Source: GCF_900142125.1 in NCBI
Candidate for 28 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| D-maltose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 42% | 63% | 176 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 190.3 |
| putrescine catabolism | potA | lo | PotG aka B0855, component of Putrescine porter (characterized) | 35% | 88% | 176 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 190.3 |
| trehalose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 42% | 63% | 176 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 190.3 |
| D-cellobiose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 39% | 68% | 171.4 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 190.3 |
| D-glucose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 39% | 68% | 171.4 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 190.3 |
| lactose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 39% | 68% | 171.4 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 190.3 |
| D-maltose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 39% | 68% | 171.4 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 190.3 |
| sucrose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 39% | 68% | 171.4 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 190.3 |
| trehalose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 39% | 68% | 171.4 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 190.3 |
| D-mannose catabolism | TT_C0211 | lo | Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) | 34% | 84% | 164.9 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 190.3 |
| sucrose catabolism | thuK | lo | Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) | 34% | 84% | 164.9 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 190.3 |
| D-maltose catabolism | malK_Aa | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 38% | 59% | 160.6 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 190.3 |
| D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 82% | 160.2 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 190.3 |
| D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 82% | 160.2 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 190.3 |
| D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 82% | 160.2 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 190.3 |
| lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 82% | 160.2 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 190.3 |
| D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 82% | 160.2 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 190.3 |
| D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 82% | 160.2 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 190.3 |
| sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 82% | 160.2 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 190.3 |
| trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 82% | 160.2 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 190.3 |
| D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 38% | 65% | 159.5 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 190.3 |
| L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 40% | 57% | 156.4 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 190.3 |
| xylitol catabolism | HSERO_RS17020 | lo | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 36% | 57% | 155.6 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 190.3 |
| trehalose catabolism | treV | lo | TreV, component of Trehalose porter (characterized) | 36% | 69% | 148.3 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 190.3 |
| 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) | 32% | 83% | 146.7 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 190.3 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 36% | 68% | 144.4 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 190.3 |
| glycerol catabolism | glpT | lo | GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) | 35% | 58% | 129.8 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 190.3 |
| glycerol catabolism | glpS | lo | ABC transporter for Glycerol, ATPase component 1 (characterized) | 32% | 70% | 122.9 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 190.3 |
Sequence Analysis Tools
View WP_072910123.1 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
MSILVCRLNYPLANYQLAAELTVAPGITVLLGPNGAGKTSLLRLLAGLNQPASGQIQLGE
RCLFDAEKRIDLPSEKRRIGMVFQDLALFPHLDVSGNIGFGLKMRRVSSSARQNRVQQLL
EKLAIEHLAKRNVTTLSGGERQKVALARTLATDPQLLLLDEPTAALDPAARGEIRRWLQT
VLTQLNIPTLLVTHDAEEVAYFRKRVAVMEQGKIVQQGSFHQLLREPASEFVARFVGVNY
ILGEVCEQAGKLIFCSRGGAKFLAPFKQVIPGAAFMTVLPWDIALYRELPDGSPRNHLYG
EIRDVVILGDRVRITLEKEDKLVAEISTRGYLALGEPQPGENFWAVFKAREARIENCEEL
PC
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
Links
Downloads
Related tools
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