GapMind for catabolism of small carbon sources


Finding step braG for L-serine catabolism in Echinicola vietnamensis KMM 6221, DSM 17526

4 candidates for braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE)

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
lo Echvi_1333 ABC-type (unclassified) transport system, ATPase component NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 33% 94% 133.7 Probable ATP-binding component of ABC transporter, component of LPS export system, LptF (M), LptG (M) and LptB (C) 59% 283.5
lo Echvi_2909 ABC-type antimicrobial peptide transport system, ATPase component High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 32% 91% 111.7 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 45% 195.7
lo Echvi_4044 ABC-type transport system involved in resistance to organic solvents, ATPase component NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 30% 88% 104.4 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 168.3
lo Echvi_3653 ABC-type sulfate/molybdate transport systems, ATPase component NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 31% 81% 96.3 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 41% 170.2

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.

Also see fitness data for the candidates

Definition of step braG

Or cluster all characterized braG 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 (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:

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. 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:

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