Finding step hutV for L-histidine catabolism in Rhodobacter viridis JA737
4 candidates for hutV: L-histidine ABC transporter, ATPase component HutV
| Score | Gene | Description | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| med | C8J30_RS14465 | glycine betaine/L-proline ABC transporter ATP-binding protein | ABC transporter for L-Histidine, ATPase component (characterized) | 57% | 95% | 297.4 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 54% | 301.6 |
| med | C8J30_RS16975 | betaine/proline/choline family ABC transporter ATP-binding protein | ABC transporter for L-Histidine, ATPase component (characterized) | 57% | 95% | 276.9 | BusAA, component of Uptake system for glycine-betaine (high affinity) and proline (low affinity) (OpuAA-OpuABC) or BusAA-ABC of Lactococcus lactis). BusAA, the ATPase subunit, has a C-terminal tandem cystathionine β-synthase (CBS) domain which is the cytoplasmic K+ sensor for osmotic stress (osmotic strength)while the BusABC subunit has the membrane and receptor domains fused to each other (Biemans-Oldehinkel et al., 2006; Mahmood et al., 2006; Gul et al. 2012). An N-terminal amphipathic α-helix of OpuA is necessary for high activity but is not critical for biogenesis or the ionic regulation of transport | 46% | 295.8 |
| med | C8J30_RS08610 | choline ABC transporter ATP-binding protein | ABC transporter for L-Histidine, ATPase component (characterized) | 49% | 95% | 245.7 | ABC transporter, nucleotide binding/ATPase protein (Proline/glycine betaine), component of High affinity (2mμM) choline uptake porter. The choline binding receptor exhibits a venus fly trap mechanism of substrate binding. (ChoX binds acetyl choline and betaine with low affinity (80μM and 470μM, respectively) (Aktas et al., 2011) (most similar to 3.A.1.12.7) | 59% | 377.1 |
| med | C8J30_RS09440 | ABC transporter ATP-binding protein | ABC transporter for L-Histidine, ATPase component (characterized) | 42% | 80% | 181 | Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- | 49% | 262.3 |
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 hutV
- Curated sequence Q9KKE1: HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine
- Curated sequence AO356_09610: ABC transporter for L-Histidine, ATPase component
- Comment: hutVWX from Sinorhizobium meliloti and Pseudomonas fluorescens FW300-N2C3
Or cluster all characterized hutV proteins
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