GapMind for catabolism of small carbon sources

 

L-histidine catabolism in Mesorhizobium ciceri biovar biserrulae 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_RS23340 MESCI_RS12995
aapQ L-histidine ABC transporter, permease component 1 (AapQ) MESCI_RS23335 MESCI_RS12990
aapM L-histidine ABC transporter, permease component 2 (AapM) MESCI_RS23330 MESCI_RS12985
aapP L-histidine ABC transporter, ATPase component AapP MESCI_RS23325 MESCI_RS28630
hutH histidine ammonia-lyase MESCI_RS22725 MESCI_RS15225
hutU urocanase MESCI_RS22715
hutI imidazole-5-propionate hydrolase MESCI_RS22730
hutF N-formiminoglutamate deiminase MESCI_RS22735
hutG' N-formylglutamate amidohydrolase MESCI_RS22720 MESCI_RS09410
Alternative steps:
Ac3H11_2554 ABC transporter for L-Histidine, permease component 2 MESCI_RS21675 MESCI_RS06580
Ac3H11_2555 L-histidine ABC transporter, substrate-binding component 2 MESCI_RS06575 MESCI_RS19705
Ac3H11_2560 L-histidine ABC transporter, ATPase component MESCI_RS16890 MESCI_RS13230
Ac3H11_2561 L-histidine ABC transporter, permease component 1 MESCI_RS16885 MESCI_RS13430
Ac3H11_2562 L-histidine ABC transporter, substrate-binding component 1 MESCI_RS16880 MESCI_RS13425
bgtA L-histidine ABC transporter, ATPase component BgtA MESCI_RS33060 MESCI_RS12595
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
BPHYT_RS24000 L-histidine ABC transporter, substrate-binding component MESCI_RS19705 MESCI_RS13060
BPHYT_RS24005 L-histidine ABC transporter, permease component 1 MESCI_RS13055 MESCI_RS01600
BPHYT_RS24010 L-histidine ABC transporter, permease component 2 MESCI_RS13050 MESCI_RS19715
BPHYT_RS24015 L-histidine ABC transporter, ATPase component MESCI_RS33060 MESCI_RS28120
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC MESCI_RS06170 MESCI_RS24305
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) MESCI_RS06145 MESCI_RS31055
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) MESCI_RS06150 MESCI_RS31060
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) MESCI_RS06155 MESCI_RS31065
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) MESCI_RS06160 MESCI_RS02790
Ga0059261_1577 L-histidine transporter
hisJ L-histidine ABC transporter, substrate-binding component HisJ MESCI_RS29850 MESCI_RS19705
hisM L-histidine ABC transporter, permease component 1 (HisM) MESCI_RS13050 MESCI_RS19715
hisP L-histidine ABC transporter, ATPase component HisP MESCI_RS33060 MESCI_RS01590
hisQ L-histidine ABC transporter, permease component 2 (HisQ) MESCI_RS13055 MESCI_RS28130
hutG N-formiminoglutamate formiminohydrolase
hutV L-histidine ABC transporter, ATPase component HutV MESCI_RS00400 MESCI_RS25750
hutW L-histidine ABC transporter, permease component HutW MESCI_RS00405 MESCI_RS10645
hutX L-histidine ABC transporter, substrate-binding component HutX MESCI_RS00410
LAT2 L-histidine transporter
LHT L-histidine transporter
natA L-histidine ABC transporter, ATPase component 1 (NatA) MESCI_RS26210 MESCI_RS31065
natB L-histidine ABC transporter, substrate-binding component NatB MESCI_RS26180
natC L-histidine ABC transporter, permease component 1 (NatC) MESCI_RS31060 MESCI_RS06150
natD L-histidine ABC transporter, permease component 2 (NatD) MESCI_RS26220 MESCI_RS20440
natE L-histidine ABC transporter, ATPase component 2 (NatE) MESCI_RS26215 MESCI_RS31070
PA5503 L-histidine ABC transporter, ATPase component MESCI_RS03445 MESCI_RS21685
PA5504 L-histidine ABC transporter, permease component MESCI_RS03450
PA5505 L-histidine ABC transporter, substrate-binding component MESCI_RS03440
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 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