Protein PP_5137 in Pseudomonas putida KT2440
Annotation: FitnessBrowser__Putida:PP_5137
Length: 352 amino acids
Source: Putida in FitnessBrowser
Candidate for 9 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| D-maltose catabolism | thuK | med | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 44% | 87% | 241.9 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 44% | 252.3 |
| trehalose catabolism | thuK | med | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 44% | 87% | 241.9 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 44% | 252.3 |
| xylitol catabolism | Dshi_0546 | med | ABC transporter for Xylitol, ATPase component (characterized) | 41% | 93% | 231.5 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 44% | 252.3 |
| L-arabinose catabolism | xacK | med | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 43% | 77% | 224.6 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 44% | 252.3 |
| L-proline catabolism | opuBA | med | BilEA aka OpuBA protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence) (characterized) | 42% | 74% | 183.7 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 44% | 252.3 |
| L-histidine catabolism | hutV | med | HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) | 42% | 87% | 174.1 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 44% | 252.3 |
| L-proline catabolism | hutV | med | HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) | 42% | 87% | 174.1 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 44% | 252.3 |
| L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 49% | 62% | 224.6 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 44% | 252.3 |
| D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 37% | 92% | 224.2 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 44% | 252.3 |
Sequence Analysis Tools
View PP_5137 at FitnessBrowser
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
MNHTTPGAQIKVRNIHKRFGAFTALNDVSLDIAAGELVCLLGPSGCGKTTLLRCIAGLER
QDRGTLYIGERDISDLSPQARDYGILFQSYALFPNLTVEANIAYGLTGSGREQARQRVAE
MLELVGLSGSEKKYPGQLSGGQQQRVALARALAPSPSLLLLDEPMSALDARVREHLCTEL
RQLQRQLGITTLMVTHNQDEAMLMADRIAVMNNGQVEQYATPQEIYDHPATPFVAEFVGQ
GNWLPFQRSSDSHALVGDMNMRLAPGSAQASSGRLFCRPEAITVNPVVHEENLFPAMVRE
ITFLGNRCRMSFELKALPGHALLAELAPEAMPRLGSQDIWVALPPQSLQVFA
This GapMind analysis is from Sep 17 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