GapMind for catabolism of small carbon sources

 

Finding step PA5503 for L-histidine catabolism in Sphingomonas koreensis DSMZ 15582

4 candidates for PA5503: L-histidine ABC transporter, ATPase component

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
lo Ga0059261_1870 ABC-type transport system involved in resistance to organic solvents, ATPase component Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 41% 66% 157.1 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) 78% 402.9
lo Ga0059261_2293 cell division ATP-binding protein FtsE Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 39% 63% 147.5 cell division ATP-binding protein ftsE 44% 185.3
lo Ga0059261_0562 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 41% 63% 147.1 Uncharacterized ABC transporter ATP-binding protein Rv0986 41% 170.6
lo Ga0059261_2137 ABC-type multidrug transport system, ATPase and permease components Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 33% 75% 129 ATM1-type heavy metal exporter; ATP-binding cassette transporter Atm1; NaAtm1 34% 285.4

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

Also see fitness data for the candidates

Definition of step PA5503

Or cluster all characterized PA5503 proteins

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

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:

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. Gaps may be due to:

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 preprint 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