GapMind for catabolism of small carbon sources

 

L-histidine catabolism in Mesorhizobium ciceri WSM1271

Best path

aapJ, aapQ, aapM, aapP, 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 (39 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aapJ L-histidine ABC transporter, substrate-binding component AapJ Mesci_4657 Mesci_2581
aapQ L-histidine ABC transporter, permease component 1 (AapQ) Mesci_4656 Mesci_2580
aapM L-histidine ABC transporter, permease component 2 (AapM) Mesci_4655 Mesci_2579
aapP L-histidine ABC transporter, ATPase component AapP Mesci_4654 Mesci_5725
hutH histidine ammonia-lyase Mesci_4533 Mesci_3024
hutU urocanase Mesci_4531
hutI imidazole-5-propionate hydrolase Mesci_4534
hutF N-formiminoglutamate deiminase Mesci_4535
hutG' N-formylglutamate amidohydrolase Mesci_4532 Mesci_1872
Alternative steps:
Ac3H11_2554 ABC transporter for L-Histidine, permease component 2 Mesci_4322 Mesci_1319
Ac3H11_2555 L-histidine ABC transporter, substrate-binding component 2 Mesci_1318 Mesci_3923
Ac3H11_2560 L-histidine ABC transporter, ATPase component Mesci_3354 Mesci_2628
Ac3H11_2561 L-histidine ABC transporter, permease component 1 Mesci_3353 Mesci_2669
Ac3H11_2562 L-histidine ABC transporter, substrate-binding component 1 Mesci_3352 Mesci_2668
bgtA L-histidine ABC transporter, ATPase component BgtA Mesci_2595 Mesci_2500
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
BPHYT_RS24000 L-histidine ABC transporter, substrate-binding component Mesci_3923 Mesci_2594
BPHYT_RS24005 L-histidine ABC transporter, permease component 1 Mesci_2593 Mesci_0319
BPHYT_RS24010 L-histidine ABC transporter, permease component 2 Mesci_2592 Mesci_3925
BPHYT_RS24015 L-histidine ABC transporter, ATPase component Mesci_2595 Mesci_5616
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC Mesci_1239 Mesci_4851
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) Mesci_1234 Mesci_6236
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) Mesci_1235 Mesci_6237
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) Mesci_1236 Mesci_6238
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) Mesci_1237 Mesci_0560
Ga0059261_1577 L-histidine transporter
hisJ L-histidine ABC transporter, substrate-binding component HisJ Mesci_5980 Mesci_3923
hisM L-histidine ABC transporter, permease component 1 (HisM) Mesci_2592 Mesci_3925
hisP L-histidine ABC transporter, ATPase component HisP Mesci_2595 Mesci_0317
hisQ L-histidine ABC transporter, permease component 2 (HisQ) Mesci_2593 Mesci_5618
hutG N-formiminoglutamate formiminohydrolase
hutV L-histidine ABC transporter, ATPase component HutV Mesci_0079 Mesci_5138
hutW L-histidine ABC transporter, permease component HutW Mesci_0080 Mesci_2118
hutX L-histidine ABC transporter, substrate-binding component HutX Mesci_0081
LAT2 L-histidine transporter
LHT L-histidine transporter
natA L-histidine ABC transporter, ATPase component 1 (NatA) Mesci_5232 Mesci_6238
natB L-histidine ABC transporter, substrate-binding component NatB Mesci_5226
natC L-histidine ABC transporter, permease component 1 (NatC) Mesci_6237 Mesci_1235
natD L-histidine ABC transporter, permease component 2 (NatD) Mesci_5234 Mesci_4071
natE L-histidine ABC transporter, ATPase component 2 (NatE) Mesci_5233 Mesci_6239
PA5503 L-histidine ABC transporter, ATPase component Mesci_0692 Mesci_4324
PA5504 L-histidine ABC transporter, permease component Mesci_0693
PA5505 L-histidine ABC transporter, substrate-binding component Mesci_0691
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 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