Finding step artM for L-arginine catabolism in Klebsiella michiganensis M5al
5 candidates for artM: L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM)
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 artM
- Curated sequence P0A2I7: Histidine transport system permease protein HisM. Histidine transport system permease protein HisM aka STM2352, 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 P0AEU3: Histidine transport system permease protein HisM. Histidine transport system permease protein HisM, 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, membrane subunit HisM (EC 7.4.2.1)
- Curated sequence O50183: AotP aka AotM aka PA0890, component of Arginine/ornithine (but not lysine) porter
- Curated sequence Q9HU29: Amino acid (Lysine/arginine/ornithine/histidine/octopine) ABC transporter membrane protein, 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 BPHYT_RS07680: ABC transporter for L-Arginine, permease component 1
- Curated sequence GFF4243: ABC transporter for L-Arginine, permease component 2
- Curated sequence Pf1N1B4_3433: ABC transporter for L-Arginine and L-Citrulline, permease component 2
- Curated sequence AO353_03045: ABC transporter for L-Arginine and L-Citrulline, permease component 1
- Curated sequence AO356_18710: L-Arginine ABC transporter, permease component 1
- Curated sequence Pf6N2E2_5662: L-Arginine ABC transporter, permease protein AotM
- Curated sequence P0AE30: Arginine ABC transporter permease protein ArtM. Arginine transport system permease protein ArtM aka B0861, component of Arginine porter. L-arginine ABC transporter membrane subunit ArtM (EC 7.4.2.1). L-arginine ABC transporter membrane subunit ArtM (EC 7.4.2.1)
- Ignore hits to AO356_09910 when looking for 'other' hits (ABC transporter for L-Lysine, permease component 2)
- Ignore hits to Pf6N2E2_2960 when looking for 'other' hits (ABC transporter for L-Lysine, permease component 2)
- Ignore hits to AO356_05505 when looking for 'other' hits (ABC transporter for L-Lysine, permease component 2)
- Comment: ArtM and HisM are distantly related and were combined. TC 1.B.6.2.7 / F9GZA7 is annotated as ArtM but seems more likely to be an outer membrane porin, so it is not included. Ignore closely related lysine transporters from P. fluorescens (which may well transport arginine; AO356_09910 has a subtle defect in arginine utilization).
Or cluster all characterized artM 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:
- 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