GapMind for catabolism of small carbon sources

 

L-histidine catabolism in Sinorhizobium fredii NGR234

Best path

braC, braD, braE, braF, braG, hutH, hutU, hutI, hutF, 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 (38 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC NGR_RS23720 NGR_RS14075
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) NGR_RS23745 NGR_RS10925
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) NGR_RS23740 NGR_RS28285
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) NGR_RS23735 NGR_RS07020
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) NGR_RS23730 NGR_RS21555
hutH histidine ammonia-lyase NGR_RS06325 NGR_RS24860
hutU urocanase NGR_RS06315
hutI imidazole-5-propionate hydrolase NGR_RS06330
hutF N-formiminoglutamate deiminase NGR_RS24840
hutG' N-formylglutamate amidohydrolase NGR_RS06320 NGR_RS25520
Alternative steps:
aapJ L-histidine ABC transporter, substrate-binding component AapJ NGR_RS17855
aapM L-histidine ABC transporter, permease component 2 (AapM) NGR_RS17845 NGR_RS23815
aapP L-histidine ABC transporter, ATPase component AapP NGR_RS17840 NGR_RS10540
aapQ L-histidine ABC transporter, permease component 1 (AapQ) NGR_RS17850 NGR_RS02885
Ac3H11_2554 ABC transporter for L-Histidine, permease component 2 NGR_RS27540 NGR_RS11205
Ac3H11_2555 L-histidine ABC transporter, substrate-binding component 2 NGR_RS27535 NGR_RS01715
Ac3H11_2560 L-histidine ABC transporter, ATPase component NGR_RS23585 NGR_RS00910
Ac3H11_2561 L-histidine ABC transporter, permease component 1 NGR_RS08475
Ac3H11_2562 L-histidine ABC transporter, substrate-binding component 1
bgtA L-histidine ABC transporter, ATPase component BgtA NGR_RS10335 NGR_RS17840
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
BPHYT_RS24000 L-histidine ABC transporter, substrate-binding component NGR_RS19835 NGR_RS03320
BPHYT_RS24005 L-histidine ABC transporter, permease component 1 NGR_RS01710 NGR_RS19840
BPHYT_RS24010 L-histidine ABC transporter, permease component 2 NGR_RS03330 NGR_RS01705
BPHYT_RS24015 L-histidine ABC transporter, ATPase component NGR_RS12355 NGR_RS01720
Ga0059261_1577 L-histidine transporter
hisJ L-histidine ABC transporter, substrate-binding component HisJ NGR_RS19835 NGR_RS12350
hisM L-histidine ABC transporter, permease component 1 (HisM) NGR_RS19845 NGR_RS12340
hisP L-histidine ABC transporter, ATPase component HisP NGR_RS12355 NGR_RS01720
hisQ L-histidine ABC transporter, permease component 2 (HisQ) NGR_RS12345 NGR_RS01710
hutG N-formiminoglutamate formiminohydrolase
hutV L-histidine ABC transporter, ATPase component HutV NGR_RS24855 NGR_RS02380
hutW L-histidine ABC transporter, permease component HutW NGR_RS24850 NGR_RS15280
hutX L-histidine ABC transporter, substrate-binding component HutX NGR_RS24845 NGR_RS15275
LAT2 L-histidine transporter
LHT L-histidine transporter
natA L-histidine ABC transporter, ATPase component 1 (NatA) NGR_RS10935 NGR_RS28290
natB L-histidine ABC transporter, substrate-binding component NatB
natC L-histidine ABC transporter, permease component 1 (NatC) NGR_RS10930
natD L-histidine ABC transporter, permease component 2 (NatD) NGR_RS28280 NGR_RS10925
natE L-histidine ABC transporter, ATPase component 2 (NatE) NGR_RS10940 NGR_RS23730
PA5503 L-histidine ABC transporter, ATPase component NGR_RS25850 NGR_RS11220
PA5504 L-histidine ABC transporter, permease component NGR_RS25845
PA5505 L-histidine ABC transporter, substrate-binding component NGR_RS25840
permease L-histidine permease NGR_RS11085
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 Apr 09 2024. 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