Finding step hisP for L-lysine catabolism in Hippea jasoniae Mar08-272r
4 candidates for hisP: L-lysine ABC transporter, ATPase component HisP
| Score | Gene | Description | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| med | EK17_RS07620 | amino acid ABC transporter ATP-binding protein | Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) | 51% | 92% | 250.4 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
| lo | EK17_RS04610 | phosphate ABC transporter ATP-binding protein | Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) | 36% | 92% | 145.6 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 62% | 310.5 |
| lo | EK17_RS02730 | ABC transporter ATP-binding protein | histidine transport ATP-binding protein hisP (characterized) | 33% | 97% | 135.6 | Probable bifunctional ABC transport system, component of The cholesterol uptake porter (Mohn et al., 2008). Takes up cholesterol, 5-α-cholestanol, 5-α-cholestanone, β-sitosterol, etc. (It is not established that all of these proteins comprise the system or that other gene products are not involved.) | 43% | 206.5 |
| lo | EK17_RS04425 | ATP-binding cassette domain-containing protein | ABC transporter for L-Lysine, ATPase component (characterized) | 31% | 98% | 129.8 | Putative ATPase component of ABC transporter system aka LinL, component of The γ-hexachlorocyclohexane (γHCH) uptake permease, LinKLMN (most similar to 3.A.1.12.4, the QAT family) | 47% | 225.3 |
Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.
GapMind searches the predicted proteins for candidates by using ublast (a fast alternative to protein BLAST) to find similarities to characterized proteins or by using HMMer to find similarities to enzyme models (usually from TIGRFams). For alignments to characterized proteins (from ublast), scores of 44 bits correspond to an expectation value (E) of about 0.001.
Definition of step hisP
- Curated sequence CH_003210: histidine transport ATP-binding protein hisP. Histidine transport ATP-binding protein HisP, component of Histidine/Arginine/Lysine (basic amino acid) uptake porter, HisJ/ArgT/HisP/HisM/HisQ [R, R, C, M, M, respectively] (Gilson et al. 1982). HisJ binds L-His (preferred), but 1-methyl-L-His and 3-methyl-L-His also bind, while the dipeptide carnosine binds weakly; D-histidine and the histidine degradation products, histamine, urocanic acid and imidazole do not bind. L-Arg, homo-L-Arg, and post-translationally modified methylated Arg-analogs also bind with the exception of symmetric dimethylated-L-Arg. L-Lys and L-Orn show weaker interactions with HisJ and methylated and acetylated Lys variants show poor binding.The carboxylate groups of these amino acids and their variants are essential. lysine/arginine/ornithine ABC transporter / histidine ABC transporter, ATP binding subunit (EC 7.4.2.1)
- Curated sequence P02915: Histidine transport ATP-binding protein HisP. histidine transport atp-binding protein hisp. HisP aka STM2351, component of Histidine/arginine/lysine/ornithine porter (Heuveling et al. 2014). In contrast to some homologous homodimeric systems, the heterodimeric histidine transporter of Salmonella enterica Typhimurium
- Curated sequence P73721: BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter
- Curated sequence Q9HU32: Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR
- Curated sequence AO356_05515: ABC transporter for L-Lysine, ATPase component
- Curated sequence AO356_09895: ABC transporter for L-Lysine, ATPase component
- Curated sequence Pf6N2E2_2962: ABC transporter for L-Lysine, ATPase component
- UniProt sequence Q88GX0: SubName: Full=Amino-acid ABC transporter, ATP-binding protein {ECO:0000313|EMBL:AAN69197.1};
Or cluster all characterized hisP proteins
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Links
Downloads
Related tools
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