Finding step kgtP for 2-oxoglutarate (alpha-ketoglutarate) catabolism in Brucella microti CCM 4915
4 candidates for kgtP: 2-oxoglutarate:H+ symporter KgtP
| Score | Gene | Description | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| hi | BMI_RS06765 | MFS transporter | Alpha-ketoglutarate permease (characterized) | 66% | 95% | 545 | Citrate:H+ symporter | 34% | 228.8 |
| lo | BMI_RS14180 | MFS transporter | Alpha-ketoglutarate permease of the major facilitator superfamily protein (characterized, see rationale) | 35% | 77% | 217.6 | Acetate/haloacid transporter, Dehp2, with a possible atypical topology | 66% | 582.4 |
| lo | BMI_RS13345 | MHS family MFS transporter | Alpha-ketoglutarate permease, MFS superfamily (characterized) | 32% | 93% | 213.8 | Inner membrane metabolite transport protein YhjE | 58% | 474.9 |
| lo | BMI_RS07815 | MFS transporter | Alpha-ketoglutarate permease of the major facilitator superfamily protein (characterized, see rationale) | 31% | 95% | 184.9 | TphA aka ProP, component of The Icm/Dot or Dot/Icm multicomponent protein secretion system. IcmS and IcmW form a complex that interacts with and may translocate substrate proteins (Ninio et al., 2005; De Buck et al., 2007; Cambronne and Roy, 2007). The crystal structure of the IcmR-IcmQ complex has been solved (Raychaudhury et al., 2009). Legionella pneumophila survives and replicates inside host cells by secreting ~300 effectors through the defective in organelle trafficking (Dot)/intracellular multiplication (Icm) type IVB secretion system (T4BSS). Ghosal et al. 2019, using electron cryotomography mapped the location of the core and accessory components of the Legionella core transmembrane subcomplex, revealing a well-ordered central channel that opens into a large, windowed secretion chamber with an unusual 13-fold symmetry. Immunofluorescence microscopy deciphered an early-stage assembly process that begins with the targeting of Dot/Icm components to the bacterial poles. Polar targeting of this T4BSS is mediated by two Dot/Icm proteins, DotU and IcmF, that are homologues of the T6SS membrane complex components TssL and TssM, suggesting that the Dot/Icm T4BSS is a hybrid system. Thus, the Dot/Icm complex assembles in an 'axial-to-peripheral' pattern | 34% | 228.8 |
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 kgtP
- Curated sequence P0AEX3: Alpha-ketoglutarate permease. α-Ketoglutarate (oxoglutarate):H+ symporter. α-ketoglutarate:H+ symporter. α-ketoglutarate:H+ symporter
- Curated sequence AO353_03810: Alpha-ketoglutarate permease, MFS superfamily
- Curated sequence AO356_17790: alpha-ketoglutarate permease (MHS family)
- UniProt sequence D8J257: SubName: Full=Alpha-ketoglutarate permease of the major facilitator superfamily protein {ECO:0000313|EMBL:ADJ64840.1};
- Ignore hits to Q52000 when looking for 'other' hits (Dicarboxylate:H+ symporter)
- Comment: HSERO_RS16820 (D8J257) is similar and is important for 2-oxoglutarate utilization. Q52000 is a dicarboxylate transporter and could be active on 2-oxoglutarate as well, so is ignored.
Or cluster all characterized kgtP 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