Protein WP_013645098.1 in Methanobacterium lacus AL-21
Annotation: NCBI__GCF_000191585.1:WP_013645098.1
Length: 230 amino acids
Source: GCF_000191585.1 in NCBI
Candidate for 32 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-asparagine catabolism | glnQ | med | 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) | 43% | 89% | 166 | Bacitracin export ATP-binding protein BceA | 43% | 195.3 |
| L-glutamate catabolism | gltL | med | 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) | 43% | 89% | 166 | Bacitracin export ATP-binding protein BceA | 43% | 195.3 |
| L-asparagine catabolism | aatP | med | ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized) | 41% | 91% | 152.9 | Bacitracin export ATP-binding protein BceA | 43% | 195.3 |
| L-aspartate catabolism | aatP | med | ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized) | 41% | 91% | 152.9 | Bacitracin export ATP-binding protein BceA | 43% | 195.3 |
| L-lysine catabolism | hisP | med | Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) | 41% | 84% | 150.2 | Bacitracin export ATP-binding protein BceA | 43% | 195.3 |
| L-asparagine catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 40% | 92% | 152.9 | Bacitracin export ATP-binding protein BceA | 43% | 195.3 |
| L-aspartate catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 40% | 92% | 152.9 | Bacitracin export ATP-binding protein BceA | 43% | 195.3 |
| L-asparagine catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 37% | 86% | 148.3 | Bacitracin export ATP-binding protein BceA | 43% | 195.3 |
| L-aspartate catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 37% | 86% | 148.3 | Bacitracin export ATP-binding protein BceA | 43% | 195.3 |
| D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 63% | 148.3 | Bacitracin export ATP-binding protein BceA | 43% | 195.3 |
| D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 63% | 148.3 | Bacitracin export ATP-binding protein BceA | 43% | 195.3 |
| D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 63% | 148.3 | Bacitracin export ATP-binding protein BceA | 43% | 195.3 |
| lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 63% | 148.3 | Bacitracin export ATP-binding protein BceA | 43% | 195.3 |
| D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 63% | 148.3 | Bacitracin export ATP-binding protein BceA | 43% | 195.3 |
| D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 63% | 148.3 | Bacitracin export ATP-binding protein BceA | 43% | 195.3 |
| sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 63% | 148.3 | Bacitracin export ATP-binding protein BceA | 43% | 195.3 |
| trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 63% | 148.3 | Bacitracin export ATP-binding protein BceA | 43% | 195.3 |
| xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 40% | 62% | 146 | Bacitracin export ATP-binding protein BceA | 43% | 195.3 |
| L-asparagine catabolism | bgtA | lo | ATPase (characterized, see rationale) | 37% | 84% | 143.3 | Bacitracin export ATP-binding protein BceA | 43% | 195.3 |
| L-aspartate catabolism | bgtA | lo | ATPase (characterized, see rationale) | 37% | 84% | 143.3 | Bacitracin export ATP-binding protein BceA | 43% | 195.3 |
| D-maltose catabolism | malK1 | lo | MalK; aka Sugar ABC transporter, ATP-binding protein, component of The maltose, maltotriose, mannotetraose (MalE1)/maltose, maltotriose, trehalose (MalE2) porter (Nanavati et al., 2005). For MalG1 (823aas) and MalG2 (833aas), the C-terminal transmembrane domain with 6 putative TMSs is preceded by a single N-terminal TMS and a large (600 residue) hydrophilic region showing sequence similarity to MLP1 and 2 (9.A.14; e-12 & e-7) as well as other proteins (characterized) | 36% | 57% | 142.1 | Bacitracin export ATP-binding protein BceA | 43% | 195.3 |
| trehalose catabolism | thuK | lo | MalK; aka Sugar ABC transporter, ATP-binding protein, component of The maltose, maltotriose, mannotetraose (MalE1)/maltose, maltotriose, trehalose (MalE2) porter (Nanavati et al., 2005). For MalG1 (823aas) and MalG2 (833aas), the C-terminal transmembrane domain with 6 putative TMSs is preceded by a single N-terminal TMS and a large (600 residue) hydrophilic region showing sequence similarity to MLP1 and 2 (9.A.14; e-12 & e-7) as well as other proteins (characterized) | 36% | 57% | 142.1 | Bacitracin export ATP-binding protein BceA | 43% | 195.3 |
| L-arginine catabolism | artP | lo | Arginine transport ATP-binding protein ArtP; EC 7.4.2.- (characterized) | 38% | 92% | 137.9 | Bacitracin export ATP-binding protein BceA | 43% | 195.3 |
| L-histidine catabolism | bgtA | lo | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 39% | 83% | 137.9 | Bacitracin export ATP-binding protein BceA | 43% | 195.3 |
| D-glucosamine (chitosamine) catabolism | AO353_21725 | lo | ABC transporter for D-Glucosamine, putative ATPase component (characterized) | 35% | 86% | 135.6 | Bacitracin export ATP-binding protein BceA | 43% | 195.3 |
| D-maltose catabolism | musK | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 35% | 56% | 131.7 | Bacitracin export ATP-binding protein BceA | 43% | 195.3 |
| D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 35% | 60% | 123.2 | Bacitracin export ATP-binding protein BceA | 43% | 195.3 |
| L-arabinose catabolism | xylGsa | lo | Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) | 32% | 91% | 119.8 | Bacitracin export ATP-binding protein BceA | 43% | 195.3 |
| D-fructose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 31% | 85% | 101.3 | Bacitracin export ATP-binding protein BceA | 43% | 195.3 |
| D-mannose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 31% | 85% | 101.3 | Bacitracin export ATP-binding protein BceA | 43% | 195.3 |
| D-ribose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 31% | 85% | 101.3 | Bacitracin export ATP-binding protein BceA | 43% | 195.3 |
| sucrose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 31% | 85% | 101.3 | Bacitracin export ATP-binding protein BceA | 43% | 195.3 |
Sequence Analysis Tools
View WP_013645098.1 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
MNNENIIEIKDLKKGYDNGKIKALNGMNLNVKKGEFISIMGPSGSGKSSLLNMIGGLDVA
DEGTINVAGIDMMKTKNLNKFRSKEIGFVFQMHNLIPNLTVVENVEIPMYETNTSSKDMR
KKALALLKSVGLEDKVDQKPTKLSGGQRQRVAIARALVNNPSIILADEPTGSLDSKTGEV
ILNLLKDLHAKENVTLVMVTHEPYVGNMAERIVTVLDGKCLSDKKTSEST
This GapMind analysis is from Apr 09 2024. 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