GapMind for catabolism of small carbon sources

 

L-histidine catabolism in Paraburkholderia bryophila 376MFSha3.1

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 (36 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
BPHYT_RS24000 L-histidine ABC transporter, substrate-binding component H281DRAFT_05290 H281DRAFT_01522
BPHYT_RS24005 L-histidine ABC transporter, permease component 1 H281DRAFT_05291 H281DRAFT_06474
BPHYT_RS24010 L-histidine ABC transporter, permease component 2 H281DRAFT_05292 H281DRAFT_05299
BPHYT_RS24015 L-histidine ABC transporter, ATPase component H281DRAFT_05293 H281DRAFT_00221
hutH histidine ammonia-lyase H281DRAFT_04873 H281DRAFT_05294
hutU urocanase H281DRAFT_04871
hutI imidazole-5-propionate hydrolase H281DRAFT_04869
hutF N-formiminoglutamate deiminase H281DRAFT_04868
hutG' N-formylglutamate amidohydrolase H281DRAFT_04867
Alternative steps:
aapJ L-histidine ABC transporter, substrate-binding component AapJ
aapM L-histidine ABC transporter, permease component 2 (AapM) H281DRAFT_05402 H281DRAFT_04268
aapP L-histidine ABC transporter, ATPase component AapP H281DRAFT_04267 H281DRAFT_02565
aapQ L-histidine ABC transporter, permease component 1 (AapQ) H281DRAFT_02572 H281DRAFT_03349
Ac3H11_2554 ABC transporter for L-Histidine, permease component 2 H281DRAFT_03349 H281DRAFT_00383
Ac3H11_2555 L-histidine ABC transporter, substrate-binding component 2 H281DRAFT_03350 H281DRAFT_02615
Ac3H11_2560 L-histidine ABC transporter, ATPase component H281DRAFT_00837 H281DRAFT_00233
Ac3H11_2561 L-histidine ABC transporter, permease component 1
Ac3H11_2562 L-histidine ABC transporter, substrate-binding component 1
bgtA L-histidine ABC transporter, ATPase component BgtA H281DRAFT_00221 H281DRAFT_03348
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 H281DRAFT_02405 H281DRAFT_01194
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) H281DRAFT_04062 H281DRAFT_02378
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) H281DRAFT_04061 H281DRAFT_05513
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) H281DRAFT_04060 H281DRAFT_02383
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) H281DRAFT_04059 H281DRAFT_02384
Ga0059261_1577 L-histidine transporter H281DRAFT_02180
hisJ L-histidine ABC transporter, substrate-binding component HisJ H281DRAFT_00224 H281DRAFT_01522
hisM L-histidine ABC transporter, permease component 1 (HisM) H281DRAFT_00222 H281DRAFT_06475
hisP L-histidine ABC transporter, ATPase component HisP H281DRAFT_05293 H281DRAFT_06476
hisQ L-histidine ABC transporter, permease component 2 (HisQ) H281DRAFT_06474 H281DRAFT_00223
hutG N-formiminoglutamate formiminohydrolase H281DRAFT_03347
hutV L-histidine ABC transporter, ATPase component HutV H281DRAFT_00987 H281DRAFT_02450
hutW L-histidine ABC transporter, permease component HutW H281DRAFT_02451 H281DRAFT_00988
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) H281DRAFT_04060 H281DRAFT_02383
natB L-histidine ABC transporter, substrate-binding component NatB
natC L-histidine ABC transporter, permease component 1 (NatC)
natD L-histidine ABC transporter, permease component 2 (NatD) H281DRAFT_04062 H281DRAFT_06397
natE L-histidine ABC transporter, ATPase component 2 (NatE) H281DRAFT_02384 H281DRAFT_04059
PA5503 L-histidine ABC transporter, ATPase component H281DRAFT_03906 H281DRAFT_03194
PA5504 L-histidine ABC transporter, permease component H281DRAFT_03195 H281DRAFT_03905
PA5505 L-histidine ABC transporter, substrate-binding component H281DRAFT_03904 H281DRAFT_01982
permease L-histidine permease H281DRAFT_04042 H281DRAFT_01668
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