GapMind for catabolism of small carbon sources

 

L-histidine catabolism in Acidovorax caeni R-24608

Best path

PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG

Rules

Overview: Histidine utilization in GapMind is based on MetaCyc pathways L-histidine degradation I (link) or II (link). These pathways are very similar. Other pathways in MetaCyc (III-VI) are not complete or are not reported in prokaryotes, so they are not included.

48 steps (32 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
PA5503 L-histidine ABC transporter, ATPase component BN2503_RS17290 BN2503_RS07360
PA5504 L-histidine ABC transporter, permease component BN2503_RS07365 BN2503_RS17285
PA5505 L-histidine ABC transporter, substrate-binding component BN2503_RS16060 BN2503_RS07370
hutH histidine ammonia-lyase
hutU urocanase
hutI imidazole-5-propionate hydrolase
hutG N-formiminoglutamate formiminohydrolase BN2503_RS07760
Alternative steps:
aapJ L-histidine ABC transporter, substrate-binding component AapJ
aapM L-histidine ABC transporter, permease component 2 (AapM) BN2503_RS00885
aapP L-histidine ABC transporter, ATPase component AapP BN2503_RS14975 BN2503_RS00880
aapQ L-histidine ABC transporter, permease component 1 (AapQ) BN2503_RS14985 BN2503_RS00885
Ac3H11_2554 ABC transporter for L-Histidine, permease component 2 BN2503_RS00885 BN2503_RS00925
Ac3H11_2555 L-histidine ABC transporter, substrate-binding component 2 BN2503_RS00890 BN2503_RS00930
Ac3H11_2560 L-histidine ABC transporter, ATPase component BN2503_RS05895 BN2503_RS00225
Ac3H11_2561 L-histidine ABC transporter, permease component 1 BN2503_RS00220
Ac3H11_2562 L-histidine ABC transporter, substrate-binding component 1
bgtA L-histidine ABC transporter, ATPase component BgtA BN2503_RS00915 BN2503_RS00880
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
BPHYT_RS24000 L-histidine ABC transporter, substrate-binding component BN2503_RS00930
BPHYT_RS24005 L-histidine ABC transporter, permease component 1 BN2503_RS00925 BN2503_RS00885
BPHYT_RS24010 L-histidine ABC transporter, permease component 2 BN2503_RS00920 BN2503_RS00885
BPHYT_RS24015 L-histidine ABC transporter, ATPase component BN2503_RS00915 BN2503_RS00880
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC BN2503_RS02255 BN2503_RS06630
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) BN2503_RS06735 BN2503_RS02260
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) BN2503_RS02265 BN2503_RS06730
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) BN2503_RS02270 BN2503_RS09265
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) BN2503_RS02275 BN2503_RS06720
Ga0059261_1577 L-histidine transporter
hisJ L-histidine ABC transporter, substrate-binding component HisJ BN2503_RS00930 BN2503_RS00890
hisM L-histidine ABC transporter, permease component 1 (HisM) BN2503_RS00920 BN2503_RS00885
hisP L-histidine ABC transporter, ATPase component HisP BN2503_RS00915 BN2503_RS00880
hisQ L-histidine ABC transporter, permease component 2 (HisQ) BN2503_RS00925 BN2503_RS00885
hutF N-formiminoglutamate deiminase
hutG' N-formylglutamate amidohydrolase
hutV L-histidine ABC transporter, ATPase component HutV BN2503_RS13080 BN2503_RS17290
hutW L-histidine ABC transporter, permease component HutW BN2503_RS13085
hutX L-histidine ABC transporter, substrate-binding component HutX
LAT2 L-histidine transporter
LHT L-histidine transporter
natA L-histidine ABC transporter, ATPase component 1 (NatA) BN2503_RS08030 BN2503_RS06725
natB L-histidine ABC transporter, substrate-binding component NatB
natC L-histidine ABC transporter, permease component 1 (NatC) BN2503_RS02265
natD L-histidine ABC transporter, permease component 2 (NatD) BN2503_RS02260 BN2503_RS06735
natE L-histidine ABC transporter, ATPase component 2 (NatE) BN2503_RS06720 BN2503_RS02275
permease L-histidine permease BN2503_RS15280 BN2503_RS07220
PTR2 L-histidine:H+ symporter
S15A3 L-histidine transporter
SLC38A3 L-histidine:Na+ symporter

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

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:

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