GapMind for catabolism of small carbon sources

 

L-histidine catabolism in Burkholderia phytofirmans PsJN

Best path

BPHYT_RS24000, BPHYT_RS24005, BPHYT_RS24010, BPHYT_RS24015, 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 (38 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
BPHYT_RS24000 L-histidine ABC transporter, substrate-binding component BPHYT_RS24000 BPHYT_RS29525
BPHYT_RS24005 L-histidine ABC transporter, permease component 1 BPHYT_RS24005 BPHYT_RS07675
BPHYT_RS24010 L-histidine ABC transporter, permease component 2 BPHYT_RS24010 BPHYT_RS24045
BPHYT_RS24015 L-histidine ABC transporter, ATPase component BPHYT_RS24015 BPHYT_RS05495
hutH histidine ammonia-lyase BPHYT_RS07555 BPHYT_RS24020
hutU urocanase BPHYT_RS07565
hutI imidazole-5-propionate hydrolase BPHYT_RS07575
hutF N-formiminoglutamate deiminase BPHYT_RS07580
hutG' N-formylglutamate amidohydrolase BPHYT_RS07585
Alternative steps:
aapJ L-histidine ABC transporter, substrate-binding component AapJ
aapM L-histidine ABC transporter, permease component 2 (AapM) BPHYT_RS24645 BPHYT_RS13585
aapP L-histidine ABC transporter, ATPase component AapP BPHYT_RS16685 BPHYT_RS34455
aapQ L-histidine ABC transporter, permease component 1 (AapQ) BPHYT_RS21915 BPHYT_RS16695
Ac3H11_2554 ABC transporter for L-Histidine, permease component 2 BPHYT_RS21915 BPHYT_RS13585
Ac3H11_2555 L-histidine ABC transporter, substrate-binding component 2 BPHYT_RS21910 BPHYT_RS08560
Ac3H11_2560 L-histidine ABC transporter, ATPase component BPHYT_RS25960 BPHYT_RS21720
Ac3H11_2561 L-histidine ABC transporter, permease component 1 BPHYT_RS25965 BPHYT_RS02465
Ac3H11_2562 L-histidine ABC transporter, substrate-binding component 1
bgtA L-histidine ABC transporter, ATPase component BgtA BPHYT_RS05495 BPHYT_RS21920
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC BPHYT_RS31715 BPHYT_RS19350
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) BPHYT_RS15605 BPHYT_RS31740
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) BPHYT_RS31745 BPHYT_RS15600
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) BPHYT_RS15595 BPHYT_RS31750
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) BPHYT_RS15590 BPHYT_RS31755
Ga0059261_1577 L-histidine transporter BPHYT_RS01785 BPHYT_RS33230
hisJ L-histidine ABC transporter, substrate-binding component HisJ BPHYT_RS10140 BPHYT_RS29525
hisM L-histidine ABC transporter, permease component 1 (HisM) BPHYT_RS05500 BPHYT_RS07680
hisP L-histidine ABC transporter, ATPase component HisP BPHYT_RS24015 BPHYT_RS07685
hisQ L-histidine ABC transporter, permease component 2 (HisQ) BPHYT_RS07675 BPHYT_RS05505
hutG N-formiminoglutamate formiminohydrolase BPHYT_RS21925
hutV L-histidine ABC transporter, ATPase component HutV BPHYT_RS25065 BPHYT_RS30485
hutW L-histidine ABC transporter, permease component HutW BPHYT_RS25070
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) BPHYT_RS15595 BPHYT_RS04435
natB L-histidine ABC transporter, substrate-binding component NatB
natC L-histidine ABC transporter, permease component 1 (NatC) BPHYT_RS31745
natD L-histidine ABC transporter, permease component 2 (NatD) BPHYT_RS31740 BPHYT_RS32510
natE L-histidine ABC transporter, ATPase component 2 (NatE) BPHYT_RS19445 BPHYT_RS15590
PA5503 L-histidine ABC transporter, ATPase component BPHYT_RS14820 BPHYT_RS22535
PA5504 L-histidine ABC transporter, permease component BPHYT_RS22540 BPHYT_RS14815
PA5505 L-histidine ABC transporter, substrate-binding component BPHYT_RS14810 BPHYT_RS02715
permease L-histidine permease BPHYT_RS15500 BPHYT_RS21680
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