Protein PP_5137 in Pseudomonas putida KT2440
Annotation: PP_5137 ferric iron ABC transporter, ATP-binding protein
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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