Protein WP_012116519.1 in Xanthobacter autotrophicus Py2
Annotation: NCBI__GCF_000017645.1:WP_012116519.1
Length: 473 amino acids
Source: GCF_000017645.1 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-asparagine catabolism | bztC | hi | BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 40% | 99% | 302 | ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 | 55% | 290.4 |
| L-aspartate catabolism | bztC | hi | BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 40% | 99% | 302 | ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 | 55% | 290.4 |
| L-glutamate catabolism | bztC | hi | BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 40% | 99% | 302 | ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 | 55% | 290.4 |
| L-histidine catabolism | aapM | med | ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 (characterized) | 55% | 77% | 290.4 | BztC, component of Glutamate/glutamine/aspartate/asparagine porter | 40% | 302.0 |
| D-alanine catabolism | Pf6N2E2_5404 | med | ABC transporter for D-Alanine, permease component 1 (characterized) | 51% | 77% | 276.2 | BztC, component of Glutamate/glutamine/aspartate/asparagine porter | 40% | 302.0 |
| L-asparagine catabolism | natH | med | NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) | 43% | 74% | 207.6 | BztC, component of Glutamate/glutamine/aspartate/asparagine porter | 40% | 302.0 |
| L-aspartate catabolism | natH | med | NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) | 43% | 74% | 207.6 | BztC, component of Glutamate/glutamine/aspartate/asparagine porter | 40% | 302.0 |
| L-asparagine catabolism | aapM | lo | AapM, 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) | 55% | 69% | 283.1 | BztC, component of Glutamate/glutamine/aspartate/asparagine porter | 40% | 302.0 |
| L-aspartate catabolism | aapM | lo | AapM, 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) | 55% | 69% | 283.1 | BztC, component of Glutamate/glutamine/aspartate/asparagine porter | 40% | 302.0 |
| L-glutamate catabolism | aapM | lo | AapM, 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) | 55% | 69% | 283.1 | BztC, component of Glutamate/glutamine/aspartate/asparagine porter | 40% | 302.0 |
| L-leucine catabolism | aapM | lo | AapM, 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) | 55% | 69% | 283.1 | BztC, component of Glutamate/glutamine/aspartate/asparagine porter | 40% | 302.0 |
| L-proline catabolism | aapM | lo | AapM, 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) | 55% | 69% | 283.1 | BztC, component of Glutamate/glutamine/aspartate/asparagine porter | 40% | 302.0 |
| L-asparagine catabolism | aatM | lo | ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 1 (characterized) | 33% | 99% | 125.9 | BztC, component of Glutamate/glutamine/aspartate/asparagine porter | 40% | 302.0 |
| L-aspartate catabolism | aatM | lo | ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 1 (characterized) | 33% | 99% | 125.9 | BztC, component of Glutamate/glutamine/aspartate/asparagine porter | 40% | 302.0 |
| L-glutamate catabolism | gltK | lo | ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 1 (characterized) | 33% | 99% | 125.9 | BztC, component of Glutamate/glutamine/aspartate/asparagine porter | 40% | 302.0 |
| L-asparagine catabolism | aatQ | lo | PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) | 31% | 92% | 109 | BztC, component of Glutamate/glutamine/aspartate/asparagine porter | 40% | 302.0 |
| L-asparagine catabolism | natG | lo | NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) | 32% | 59% | 109 | BztC, component of Glutamate/glutamine/aspartate/asparagine porter | 40% | 302.0 |
| L-aspartate catabolism | aatQ | lo | PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) | 31% | 92% | 109 | BztC, component of Glutamate/glutamine/aspartate/asparagine porter | 40% | 302.0 |
| L-aspartate catabolism | natG | lo | NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) | 32% | 59% | 109 | BztC, component of Glutamate/glutamine/aspartate/asparagine porter | 40% | 302.0 |
| L-glutamate catabolism | gltJ | lo | PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) | 31% | 92% | 109 | BztC, component of Glutamate/glutamine/aspartate/asparagine porter | 40% | 302.0 |
| L-asparagine catabolism | peb1D | lo | Amino acid ABC transporter, permease protein PEB1 (characterized, see rationale) | 31% | 90% | 104.4 | BztC, component of Glutamate/glutamine/aspartate/asparagine porter | 40% | 302.0 |
| L-aspartate catabolism | peb1D | lo | Amino acid ABC transporter, permease protein PEB1 (characterized, see rationale) | 31% | 90% | 104.4 | BztC, component of Glutamate/glutamine/aspartate/asparagine porter | 40% | 302.0 |
Sequence Analysis Tools
View WP_012116519.1 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
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Sequence
MSDTTVPLSAPRVSPAQAYVSTTLREQEPAPVATRGPVLWVRKHLVGSVPQVLLTLFGIW
LVYVTVPPMIKFFLIDAVWTGANREACLPEKVGRAVGACWPFVWAKLDQLIYGFYPASER
WRVNVVYALGVILLLPLLIQKLPGKRLNAILFFGIYPVVAFVLLTGGNLEMQRFLIGYFG
PTDLFAGAGIVQGMRISFWIDFLLSTAIVTGIAYLVSRIVAGPEAAPGAAKTTLSVFVLL
GLVIFAMDIDVGLPQVETRLWGGLLVTLVIAVTGITVSLPFGILLALGRRSKLPLVKALS
IIFIEFWRGVPLITVLFFATYMLPLFLPGRLTIDGLLRALVGVALFASAYMAEVVRGGLQ
AIPKGQYEGAMAVGLPSSLMLRLVVLPQALKLVIPGIVNNFIGLFKDTTLVLIVSIFDLL
GSMRAAFTDPNWASPTTLFTGFGFAGIIYFVFCFGMSRYSMALEKRLDRAQRH
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