Protein WP_028988674.1 in Thermithiobacillus tepidarius DSM 3134
Annotation: NCBI__GCF_000423825.1:WP_028988674.1
Length: 222 amino acids
Source: GCF_000423825.1 in NCBI
Candidate for 29 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-lysine catabolism | hisP | lo | Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) | 39% | 82% | 154.8 | cell division ATP-binding protein ftsE | 54% | 226.5 |
| L-glutamate catabolism | gltL | lo | GluA aka CGL1950, component of Glutamate porter (characterized) | 38% | 81% | 152.9 | cell division ATP-binding protein ftsE | 54% | 226.5 |
| L-asparagine catabolism | aatP | lo | PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized) | 37% | 84% | 145.2 | cell division ATP-binding protein ftsE | 54% | 226.5 |
| L-aspartate catabolism | aatP | lo | PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized) | 37% | 84% | 145.2 | cell division ATP-binding protein ftsE | 54% | 226.5 |
| L-asparagine catabolism | bgtA | lo | ATPase (characterized, see rationale) | 36% | 85% | 139.8 | cell division ATP-binding protein ftsE | 54% | 226.5 |
| L-aspartate catabolism | bgtA | lo | ATPase (characterized, see rationale) | 36% | 85% | 139.8 | cell division ATP-binding protein ftsE | 54% | 226.5 |
| putrescine catabolism | potA | lo | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) | 35% | 57% | 137.9 | cell division ATP-binding protein ftsE | 54% | 226.5 |
| L-asparagine catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 35% | 86% | 136.3 | cell division ATP-binding protein ftsE | 54% | 226.5 |
| L-aspartate catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 35% | 86% | 136.3 | cell division ATP-binding protein ftsE | 54% | 226.5 |
| L-glutamate catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 35% | 86% | 136.3 | cell division ATP-binding protein ftsE | 54% | 226.5 |
| L-histidine catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 35% | 86% | 136.3 | cell division ATP-binding protein ftsE | 54% | 226.5 |
| L-leucine catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 35% | 86% | 136.3 | cell division ATP-binding protein ftsE | 54% | 226.5 |
| L-proline catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 35% | 86% | 136.3 | cell division ATP-binding protein ftsE | 54% | 226.5 |
| L-arginine catabolism | artP | lo | ABC transporter for L-Arginine, putative ATPase component (characterized) | 34% | 86% | 135.6 | cell division ATP-binding protein ftsE | 54% | 226.5 |
| xylitol catabolism | HSERO_RS17020 | lo | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 38% | 50% | 134.4 | cell division ATP-binding protein ftsE | 54% | 226.5 |
| L-citrulline catabolism | PS417_17605 | lo | ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale) | 36% | 84% | 134 | cell division ATP-binding protein ftsE | 54% | 226.5 |
| L-histidine catabolism | BPHYT_RS24015 | lo | ABC transporter related (characterized, see rationale) | 36% | 84% | 134 | cell division ATP-binding protein ftsE | 54% | 226.5 |
| L-histidine catabolism | hisP | lo | Histidine transport ATP-binding protein HisP (characterized) | 34% | 90% | 132.9 | cell division ATP-binding protein ftsE | 54% | 226.5 |
| D-mannitol catabolism | mtlK | lo | ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) | 36% | 57% | 130.2 | cell division ATP-binding protein ftsE | 54% | 226.5 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) | 36% | 57% | 129.4 | cell division ATP-binding protein ftsE | 54% | 226.5 |
| D-cellobiose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 36% | 53% | 117.1 | cell division ATP-binding protein ftsE | 54% | 226.5 |
| D-glucose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 36% | 53% | 117.1 | cell division ATP-binding protein ftsE | 54% | 226.5 |
| lactose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 36% | 53% | 117.1 | cell division ATP-binding protein ftsE | 54% | 226.5 |
| D-maltose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 36% | 53% | 117.1 | cell division ATP-binding protein ftsE | 54% | 226.5 |
| D-maltose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 36% | 53% | 117.1 | cell division ATP-binding protein ftsE | 54% | 226.5 |
| sucrose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 36% | 53% | 117.1 | cell division ATP-binding protein ftsE | 54% | 226.5 |
| sucrose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 36% | 53% | 117.1 | cell division ATP-binding protein ftsE | 54% | 226.5 |
| trehalose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 36% | 53% | 117.1 | cell division ATP-binding protein ftsE | 54% | 226.5 |
| trehalose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 36% | 53% | 117.1 | cell division ATP-binding protein ftsE | 54% | 226.5 |
Sequence Analysis Tools
View WP_028988674.1 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
MIRAINVSKHYPGGRNVLQEIDLHLPKGQMAFLTGPSGAGKSTLLKLIARIETVSRGTLL
LDGQDLAKLKRRHIPQLRRQLGIVFQDHKLLADRSVFANVALTLQVAGVRRAHIKSRVRA
ALDQVGLSGREQDSPLSLSGGEQQRVGIARAIVHSPKVLIADEPTGNLDPQLSSEIMDLF
RNLNRHGMTLLIATHDLGQVERLDCPVYALQHGRLQNQEARP
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