Protein WP_013835023.1 in Thiomicrospira cyclica ALM1
Annotation: NCBI__GCF_000214825.1:WP_013835023.1
Length: 263 amino acids
Source: GCF_000214825.1 in NCBI
Candidate for 41 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| 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) | 36% | 54% | 139.8 | Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- | 60% | 297.4 |
| L-histidine catabolism | hutV | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 37% | 81% | 139.4 | Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- | 60% | 297.4 |
| L-proline catabolism | hutV | lo | HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) | 37% | 82% | 137.5 | Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- | 60% | 297.4 |
| L-asparagine catabolism | glnQ | lo | Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized) | 33% | 96% | 135.6 | Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- | 60% | 297.4 |
| D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 32% | 65% | 135.6 | Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- | 60% | 297.4 |
| D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 32% | 65% | 135.6 | Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- | 60% | 297.4 |
| D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 32% | 65% | 135.6 | Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- | 60% | 297.4 |
| L-glutamate catabolism | gltL | lo | Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized) | 33% | 96% | 135.6 | Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- | 60% | 297.4 |
| lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 32% | 65% | 135.6 | Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- | 60% | 297.4 |
| D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 32% | 65% | 135.6 | Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- | 60% | 297.4 |
| D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 32% | 65% | 135.6 | Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- | 60% | 297.4 |
| sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 32% | 65% | 135.6 | Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- | 60% | 297.4 |
| trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 32% | 65% | 135.6 | Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- | 60% | 297.4 |
| L-arabinose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 34% | 61% | 135.2 | Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- | 60% | 297.4 |
| D-fructose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 34% | 61% | 135.2 | Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- | 60% | 297.4 |
| sucrose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 34% | 61% | 135.2 | Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- | 60% | 297.4 |
| D-xylose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 34% | 61% | 135.2 | Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- | 60% | 297.4 |
| L-isoleucine catabolism | livG | lo | ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) | 30% | 99% | 124.4 | Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- | 60% | 297.4 |
| L-leucine catabolism | livG | lo | ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) | 30% | 99% | 124.4 | Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- | 60% | 297.4 |
| L-valine catabolism | livG | lo | ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) | 30% | 99% | 124.4 | Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- | 60% | 297.4 |
| putrescine catabolism | potA | lo | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) | 32% | 58% | 123.2 | Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- | 60% | 297.4 |
| L-alanine catabolism | braF | lo | NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 35% | 90% | 122.5 | Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- | 60% | 297.4 |
| L-histidine catabolism | natA | lo | NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 35% | 90% | 122.5 | Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- | 60% | 297.4 |
| L-leucine catabolism | natA | lo | NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 35% | 90% | 122.5 | Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- | 60% | 297.4 |
| L-proline catabolism | natA | lo | NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 35% | 90% | 122.5 | Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- | 60% | 297.4 |
| L-serine catabolism | braF | lo | NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 35% | 90% | 122.5 | Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- | 60% | 297.4 |
| L-threonine catabolism | braF | lo | NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 35% | 90% | 122.5 | Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- | 60% | 297.4 |
| D-cellobiose catabolism | cbtD | lo | CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) | 34% | 67% | 119.4 | Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- | 60% | 297.4 |
| L-arginine catabolism | artP | lo | Histidine transport ATP-binding protein HisP (characterized) | 30% | 99% | 118.2 | Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- | 60% | 297.4 |
| L-histidine catabolism | hisP | lo | Histidine transport ATP-binding protein HisP (characterized) | 30% | 99% | 118.2 | Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- | 60% | 297.4 |
| L-lysine catabolism | hisP | lo | Histidine transport ATP-binding protein HisP (characterized) | 30% | 99% | 118.2 | Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- | 60% | 297.4 |
| trehalose catabolism | treV | lo | TreV, component of Trehalose porter (characterized) | 31% | 73% | 115.9 | Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- | 60% | 297.4 |
| glycerol catabolism | glpT | lo | GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) | 32% | 58% | 113.2 | Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- | 60% | 297.4 |
| D-alanine catabolism | AZOBR_RS08245 | lo | Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) | 30% | 91% | 105.9 | Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- | 60% | 297.4 |
| L-proline catabolism | AZOBR_RS08245 | lo | Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) | 30% | 91% | 105.9 | Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- | 60% | 297.4 |
| L-alanine catabolism | braG | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 30% | 85% | 99.4 | Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- | 60% | 297.4 |
| L-histidine catabolism | natE | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 30% | 85% | 99.4 | Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- | 60% | 297.4 |
| L-leucine catabolism | natE | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 30% | 85% | 99.4 | Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- | 60% | 297.4 |
| L-proline catabolism | natE | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 30% | 85% | 99.4 | Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- | 60% | 297.4 |
| L-serine catabolism | braG | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 30% | 85% | 99.4 | Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- | 60% | 297.4 |
| L-threonine catabolism | braG | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 30% | 85% | 99.4 | Intermembrane phospholipid transport system ATP-binding protein MlaF; EC 7.6.2.- | 60% | 297.4 |
Sequence Analysis Tools
View WP_013835023.1 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
MARPIIEVVDLSFSRGQRKIFEHLSFKVYPGKITAIMGPSGTGKTTLLKLMVGQLKPDSG
QVFFYGQDIQSLSRSALYKLRQKMGMLFQSGALLTDLTVYENVAFSVTEHYQHLAPVLIE
KLVAMKLEAVGLRGAKDLMPAQLSGGMARRVALARAIILDPEVIFYDEPFVGQDPITMGV
LIKLIKSLNDQLHLTSVLVSHDVNEVLSIADHACVLSEGRIIEEGTPAELLASDSAYVQQ
FLQGTADGPVPFHFPVEPWGVSK
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