GapMind for catabolism of small carbon sources

 

L-histidine catabolism in Cupriavidus basilensis 4G11

Best path

Ac3H11_2562, Ac3H11_2561, Ac3H11_2560, Ac3H11_2555, Ac3H11_2554, hutH, hutU, hutI, hutF, hutG'

Also see fitness data for the top candidates

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 (37 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
Ac3H11_2562 L-histidine ABC transporter, substrate-binding component 1 RR42_RS16940
Ac3H11_2561 L-histidine ABC transporter, permease component 1 RR42_RS16935 RR42_RS33670
Ac3H11_2560 L-histidine ABC transporter, ATPase component RR42_RS16930 RR42_RS28620
Ac3H11_2555 L-histidine ABC transporter, substrate-binding component 2 RR42_RS31745 RR42_RS07805
Ac3H11_2554 ABC transporter for L-Histidine, permease component 2 RR42_RS31740 RR42_RS34310
hutH histidine ammonia-lyase RR42_RS14640 RR42_RS16920
hutU urocanase RR42_RS14645 RR42_RS16915
hutI imidazole-5-propionate hydrolase RR42_RS16905
hutF N-formiminoglutamate deiminase RR42_RS16900
hutG' N-formylglutamate amidohydrolase RR42_RS16895
Alternative steps:
aapJ L-histidine ABC transporter, substrate-binding component AapJ
aapM L-histidine ABC transporter, permease component 2 (AapM) RR42_RS27120 RR42_RS09485
aapP L-histidine ABC transporter, ATPase component AapP RR42_RS16370 RR42_RS02590
aapQ L-histidine ABC transporter, permease component 1 (AapQ) RR42_RS34310 RR42_RS31740
bgtA L-histidine ABC transporter, ATPase component BgtA RR42_RS07815 RR42_RS29660
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
BPHYT_RS24000 L-histidine ABC transporter, substrate-binding component
BPHYT_RS24005 L-histidine ABC transporter, permease component 1 RR42_RS29650 RR42_RS34310
BPHYT_RS24010 L-histidine ABC transporter, permease component 2 RR42_RS04400 RR42_RS29655
BPHYT_RS24015 L-histidine ABC transporter, ATPase component RR42_RS29660 RR42_RS34305
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC RR42_RS16980 RR42_RS14425
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) RR42_RS14420 RR42_RS16975
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) RR42_RS14415 RR42_RS16970
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) RR42_RS14410 RR42_RS29450
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) RR42_RS14405 RR42_RS16960
Ga0059261_1577 L-histidine transporter RR42_RS01585
hisJ L-histidine ABC transporter, substrate-binding component HisJ RR42_RS29645 RR42_RS31745
hisM L-histidine ABC transporter, permease component 1 (HisM) RR42_RS29655 RR42_RS16450
hisP L-histidine ABC transporter, ATPase component HisP RR42_RS29660 RR42_RS34305
hisQ L-histidine ABC transporter, permease component 2 (HisQ) RR42_RS29650 RR42_RS04400
hutG N-formiminoglutamate formiminohydrolase RR42_RS14625 RR42_RS31730
hutV L-histidine ABC transporter, ATPase component HutV RR42_RS04555 RR42_RS37305
hutW L-histidine ABC transporter, permease component HutW RR42_RS10790 RR42_RS04820
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) RR42_RS14410 RR42_RS34795
natB L-histidine ABC transporter, substrate-binding component NatB
natC L-histidine ABC transporter, permease component 1 (NatC)
natD L-histidine ABC transporter, permease component 2 (NatD) RR42_RS34785 RR42_RS14420
natE L-histidine ABC transporter, ATPase component 2 (NatE) RR42_RS20235 RR42_RS14405
PA5503 L-histidine ABC transporter, ATPase component RR42_RS04555 RR42_RS07815
PA5504 L-histidine ABC transporter, permease component RR42_RS04560 RR42_RS10790
PA5505 L-histidine ABC transporter, substrate-binding component RR42_RS03045 RR42_RS04565
permease L-histidine permease RR42_RS14635 RR42_RS11100
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 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