Protein WP_084276573.1 in Nitratiruptor tergarcus DSM 16512
Annotation: NCBI__GCF_900176045.1:WP_084276573.1
Length: 224 amino acids
Source: GCF_900176045.1 in NCBI
Candidate for 18 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-asparagine catabolism | bgtA | lo | ATPase (characterized, see rationale) | 39% | 82% | 146.4 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 42% | 165.6 |
| L-aspartate catabolism | bgtA | lo | ATPase (characterized, see rationale) | 39% | 82% | 146.4 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 42% | 165.6 |
| L-arginine catabolism | artP | lo | AotP aka PA0892, component of Arginine/ornithine (but not lysine) porter (characterized) | 36% | 89% | 134.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 42% | 165.6 |
| L-arabinose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 35% | 62% | 132.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 42% | 165.6 |
| D-fructose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 35% | 62% | 132.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 42% | 165.6 |
| sucrose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 35% | 62% | 132.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 42% | 165.6 |
| D-xylose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 35% | 62% | 132.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 42% | 165.6 |
| L-citrulline catabolism | AO353_03040 | lo | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 34% | 89% | 124.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 42% | 165.6 |
| 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) | 32% | 57% | 123.6 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 42% | 165.6 |
| 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) | 32% | 57% | 123.6 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 42% | 165.6 |
| L-histidine catabolism | Ac3H11_2560 | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 34% | 74% | 111.3 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 42% | 165.6 |
| L-isoleucine catabolism | livF | lo | high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized) | 32% | 90% | 105.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 42% | 165.6 |
| L-leucine catabolism | livF | lo | high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized) | 32% | 90% | 105.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 42% | 165.6 |
| L-phenylalanine catabolism | livF | lo | high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized) | 32% | 90% | 105.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 42% | 165.6 |
| L-valine catabolism | livF | lo | high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized) | 32% | 90% | 105.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 42% | 165.6 |
| glycerol catabolism | glpS | lo | ABC transporter for Glycerol, ATPase component 1 (characterized) | 32% | 52% | 102.4 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 42% | 165.6 |
| D-cellobiose catabolism | cbtF | lo | CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) | 34% | 65% | 101.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 42% | 165.6 |
| citrate catabolism | fecE | lo | iron(III) dicitrate transport ATP-binding protein FecE (characterized) | 31% | 85% | 94.4 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 42% | 165.6 |
Sequence Analysis Tools
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
MISLEKVSKIYNLGTAKEVVALKDVSLQIKRSSLVLLMGPSGSGKSTLLSLIAALTRPTS
GKVVVDGQTISKLPDRFAAVYRREKIGFIFQKFNLLEDLTVFENVIVPLIPTPTPLKELE
LMASAVMERFAIAHKKDMVVRKLSGGEQQRCAIARALIDNPPIILADEPTANLDSALTEQ
FLQILGQLKQEGKTIVIATHDPRFADLEIVDEIYEVREGNVFLS
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