GapMind for catabolism of small carbon sources

 

L-histidine catabolism in Paraburkholderia phymatum STM815

Best path

BPHYT_RS24000, BPHYT_RS24005, BPHYT_RS24010, BPHYT_RS24015, 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 (37 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
BPHYT_RS24000 L-histidine ABC transporter, substrate-binding component BPHY_RS25570 BPHY_RS19095
BPHYT_RS24005 L-histidine ABC transporter, permease component 1 BPHY_RS25575 BPHY_RS09110
BPHYT_RS24010 L-histidine ABC transporter, permease component 2 BPHY_RS25580 BPHY_RS25615
BPHYT_RS24015 L-histidine ABC transporter, ATPase component BPHY_RS25585 BPHY_RS11025
hutH histidine ammonia-lyase BPHY_RS09230 BPHY_RS25590
hutU urocanase BPHY_RS09220
hutI imidazole-5-propionate hydrolase BPHY_RS09210
hutF N-formiminoglutamate deiminase BPHY_RS09205
hutG' N-formylglutamate amidohydrolase BPHY_RS09200
Alternative steps:
aapJ L-histidine ABC transporter, substrate-binding component AapJ BPHY_RS29405
aapM L-histidine ABC transporter, permease component 2 (AapM) BPHY_RS13045 BPHY_RS27410
aapP L-histidine ABC transporter, ATPase component AapP BPHY_RS13040 BPHY_RS27405
aapQ L-histidine ABC transporter, permease component 1 (AapQ) BPHY_RS35860 BPHY_RS12035
Ac3H11_2554 ABC transporter for L-Histidine, permease component 2 BPHY_RS07800 BPHY_RS27410
Ac3H11_2555 L-histidine ABC transporter, substrate-binding component 2 BPHY_RS05860 BPHY_RS07805
Ac3H11_2560 L-histidine ABC transporter, ATPase component BPHY_RS30900 BPHY_RS16160
Ac3H11_2561 L-histidine ABC transporter, permease component 1 BPHY_RS30910 BPHY_RS30360
Ac3H11_2562 L-histidine ABC transporter, substrate-binding component 1
bgtA L-histidine ABC transporter, ATPase component BgtA BPHY_RS11025 BPHY_RS09100
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 BPHY_RS15375 BPHY_RS02950
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) BPHY_RS02955 BPHY_RS11455
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) BPHY_RS02960
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) BPHY_RS02965 BPHY_RS15490
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) BPHY_RS02970 BPHY_RS15485
Ga0059261_1577 L-histidine transporter BPHY_RS00475
hisJ L-histidine ABC transporter, substrate-binding component HisJ BPHY_RS19095 BPHY_RS11010
hisM L-histidine ABC transporter, permease component 1 (HisM) BPHY_RS11020 BPHY_RS09105
hisP L-histidine ABC transporter, ATPase component HisP BPHY_RS25585 BPHY_RS37105
hisQ L-histidine ABC transporter, permease component 2 (HisQ) BPHY_RS09110 BPHY_RS11015
hutG N-formiminoglutamate formiminohydrolase BPHY_RS30365
hutV L-histidine ABC transporter, ATPase component HutV BPHY_RS34180 BPHY_RS32770
hutW L-histidine ABC transporter, permease component HutW BPHY_RS17480 BPHY_RS34175
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) BPHY_RS15490 BPHY_RS02965
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)
natE L-histidine ABC transporter, ATPase component 2 (NatE) BPHY_RS15485 BPHY_RS02970
PA5503 L-histidine ABC transporter, ATPase component BPHY_RS03830 BPHY_RS19530
PA5504 L-histidine ABC transporter, permease component BPHY_RS03835
PA5505 L-histidine ABC transporter, substrate-binding component BPHY_RS03840 BPHY_RS01430
permease L-histidine permease BPHY_RS03010 BPHY_RS32965
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