Protein WP_012589810.1 in Methylocella silvestris BL2
Annotation: NCBI__GCF_000021745.1:WP_012589810.1
Length: 252 amino acids
Source: GCF_000021745.1 in NCBI
Candidate for 22 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-histidine catabolism | Ac3H11_2560 | hi | ABC transporter for L-Histidine, ATPase component (characterized) | 47% | 99% | 216.1 | Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- | 43% | 202.2 |
| putrescine catabolism | potA | lo | PotG aka B0855, component of Putrescine porter (characterized) | 42% | 61% | 165.6 | ABC transporter for L-Histidine, ATPase component | 47% | 216.1 |
| xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 41% | 68% | 156.8 | ABC transporter for L-Histidine, ATPase component | 47% | 216.1 |
| sucrose catabolism | thuK | lo | ABC transporter (characterized, see rationale) | 43% | 60% | 155.6 | ABC transporter for L-Histidine, ATPase component | 47% | 216.1 |
| D-mannitol catabolism | mtlK | lo | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) | 42% | 66% | 154.5 | ABC transporter for L-Histidine, ATPase component | 47% | 216.1 |
| L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 42% | 51% | 153.3 | ABC transporter for L-Histidine, ATPase component | 47% | 216.1 |
| D-glucosamine (chitosamine) catabolism | SM_b21216 | lo | ABC transporter for D-Glucosamine, ATPase component (characterized) | 43% | 58% | 151 | ABC transporter for L-Histidine, ATPase component | 47% | 216.1 |
| lactose catabolism | lacK | lo | ABC transporter for Lactose, ATPase component (characterized) | 42% | 59% | 149.4 | ABC transporter for L-Histidine, ATPase component | 47% | 216.1 |
| L-proline catabolism | opuBA | lo | 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) | 39% | 51% | 149.1 | ABC transporter for L-Histidine, ATPase component | 47% | 216.1 |
| D-maltose catabolism | malK | lo | Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 41% | 62% | 148.3 | ABC transporter for L-Histidine, ATPase component | 47% | 216.1 |
| xylitol catabolism | HSERO_RS17020 | lo | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 41% | 56% | 146.7 | ABC transporter for L-Histidine, ATPase component | 47% | 216.1 |
| D-cellobiose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 41% | 54% | 145.2 | ABC transporter for L-Histidine, ATPase component | 47% | 216.1 |
| D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 41% | 54% | 145.2 | ABC transporter for L-Histidine, ATPase component | 47% | 216.1 |
| D-glucose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 41% | 54% | 145.2 | ABC transporter for L-Histidine, ATPase component | 47% | 216.1 |
| lactose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 41% | 54% | 145.2 | ABC transporter for L-Histidine, ATPase component | 47% | 216.1 |
| D-maltose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 41% | 54% | 145.2 | ABC transporter for L-Histidine, ATPase component | 47% | 216.1 |
| sucrose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 41% | 54% | 145.2 | ABC transporter for L-Histidine, ATPase component | 47% | 216.1 |
| trehalose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 41% | 54% | 145.2 | ABC transporter for L-Histidine, ATPase component | 47% | 216.1 |
| D-maltose catabolism | thuK | lo | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 38% | 64% | 143.3 | ABC transporter for L-Histidine, ATPase component | 47% | 216.1 |
| trehalose catabolism | thuK | lo | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 38% | 64% | 143.3 | ABC transporter for L-Histidine, ATPase component | 47% | 216.1 |
| D-glucosamine (chitosamine) catabolism | AO353_21725 | lo | ABC transporter for D-Glucosamine, putative ATPase component (characterized) | 39% | 85% | 127.1 | ABC transporter for L-Histidine, ATPase component | 47% | 216.1 |
| glycerol catabolism | glpT | lo | ABC transporter for Glycerol, ATPase component 2 (characterized) | 33% | 54% | 104.8 | ABC transporter for L-Histidine, ATPase component | 47% | 216.1 |
Sequence Analysis Tools
View WP_012589810.1 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
MLTIQSVSKIYPGGAHALYSVSLDIDAAEIVAVIGGSGCGKSTLLRLVAGLDRPSSGRVL
IDNEPISAPHPAVGVVFQEPRLFPWLTVAQNVGFGLSDVSKPQQGARVAAALQRVGLADH
APRWPRQLSGGQAQRVALARALAPQPRALLLDEPFSALDAFTRADLQDHLLSLWDELRPT
LLLVTHDIEEALVLADRVVVMQPRPGRIAAVLPIALPRPRDRISPEFDELKREALRILGH
SWRAPPHAVAAE
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