GapMind for catabolism of small carbon sources

 

L-histidine catabolism in Azospirillum brasilense Sp245

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 (36 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
Ac3H11_2562 L-histidine ABC transporter, substrate-binding component 1 AZOBR_RS00420 AZOBR_RS07675
Ac3H11_2561 L-histidine ABC transporter, permease component 1 AZOBR_RS00425 AZOBR_RS25220
Ac3H11_2560 L-histidine ABC transporter, ATPase component AZOBR_RS00430 AZOBR_RS22770
Ac3H11_2555 L-histidine ABC transporter, substrate-binding component 2 AZOBR_RS18075 AZOBR_RS27130
Ac3H11_2554 ABC transporter for L-Histidine, permease component 2 AZOBR_RS23520 AZOBR_RS27070
hutH histidine ammonia-lyase
hutU urocanase AZOBR_RS21740
hutI imidazole-5-propionate hydrolase AZOBR_RS21725
hutF N-formiminoglutamate deiminase AZOBR_RS23505
hutG' N-formylglutamate amidohydrolase AZOBR_RS23510 AZOBR_RS08115
Alternative steps:
aapJ L-histidine ABC transporter, substrate-binding component AapJ AZOBR_RS08655 AZOBR_RS00530
aapM L-histidine ABC transporter, permease component 2 (AapM) AZOBR_RS08665 AZOBR_RS15680
aapP L-histidine ABC transporter, ATPase component AapP AZOBR_RS08670 AZOBR_RS15690
aapQ L-histidine ABC transporter, permease component 1 (AapQ) AZOBR_RS08660 AZOBR_RS15675
bgtA L-histidine ABC transporter, ATPase component BgtA AZOBR_RS00690 AZOBR_RS08670
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
BPHYT_RS24000 L-histidine ABC transporter, substrate-binding component AZOBR_RS00685 AZOBR_RS27130
BPHYT_RS24005 L-histidine ABC transporter, permease component 1 AZOBR_RS00680 AZOBR_RS00675
BPHYT_RS24010 L-histidine ABC transporter, permease component 2 AZOBR_RS00675 AZOBR_RS23520
BPHYT_RS24015 L-histidine ABC transporter, ATPase component AZOBR_RS00690 AZOBR_RS29615
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC AZOBR_RS08260
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) AZOBR_RS08235 AZOBR_RS03565
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) AZOBR_RS08240 AZOBR_RS32410
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) AZOBR_RS08245 AZOBR_RS32405
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) AZOBR_RS08250 AZOBR_RS19790
Ga0059261_1577 L-histidine transporter
hisJ L-histidine ABC transporter, substrate-binding component HisJ AZOBR_RS27130 AZOBR_RS00685
hisM L-histidine ABC transporter, permease component 1 (HisM) AZOBR_RS00675 AZOBR_RS23520
hisP L-histidine ABC transporter, ATPase component HisP AZOBR_RS00690 AZOBR_RS29615
hisQ L-histidine ABC transporter, permease component 2 (HisQ) AZOBR_RS00680 AZOBR_RS23520
hutG N-formiminoglutamate formiminohydrolase
hutV L-histidine ABC transporter, ATPase component HutV AZOBR_RS23480 AZOBR_RS15760
hutW L-histidine ABC transporter, permease component HutW AZOBR_RS23475 AZOBR_RS15765
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) AZOBR_RS32405 AZOBR_RS04130
natB L-histidine ABC transporter, substrate-binding component NatB
natC L-histidine ABC transporter, permease component 1 (NatC) AZOBR_RS29675
natD L-histidine ABC transporter, permease component 2 (NatD) AZOBR_RS29670 AZOBR_RS32275
natE L-histidine ABC transporter, ATPase component 2 (NatE) AZOBR_RS19790 AZOBR_RS28570
PA5503 L-histidine ABC transporter, ATPase component AZOBR_RS19475 AZOBR_RS26405
PA5504 L-histidine ABC transporter, permease component AZOBR_RS19470
PA5505 L-histidine ABC transporter, substrate-binding component AZOBR_RS19465 AZOBR_RS25425
permease L-histidine permease
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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