GapMind for catabolism of small carbon sources

 

L-histidine catabolism in Pseudomonas simiae WCS417

Best path

hisP, hisM, hisQ, hisJ, 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 (37 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
hisP L-histidine ABC transporter, ATPase component HisP PS417_01500 PS417_13545
hisM L-histidine ABC transporter, permease component 1 (HisM) PS417_01485 PS417_26110
hisQ L-histidine ABC transporter, permease component 2 (HisQ) PS417_01490 PS417_06410
hisJ L-histidine ABC transporter, substrate-binding component HisJ PS417_01495 PS417_26100
hutH histidine ammonia-lyase PS417_01750 PS417_01745
hutU urocanase PS417_01720
hutI imidazole-5-propionate hydrolase PS417_01760
hutF N-formiminoglutamate deiminase PS417_01705
hutG' N-formylglutamate amidohydrolase PS417_01765
Alternative steps:
aapJ L-histidine ABC transporter, substrate-binding component AapJ PS417_23345 PS417_04900
aapM L-histidine ABC transporter, permease component 2 (AapM) PS417_04910 PS417_01810
aapP L-histidine ABC transporter, ATPase component AapP PS417_04915 PS417_26115
aapQ L-histidine ABC transporter, permease component 1 (AapQ) PS417_04905 PS417_18125
Ac3H11_2554 ABC transporter for L-Histidine, permease component 2 PS417_15485 PS417_01810
Ac3H11_2555 L-histidine ABC transporter, substrate-binding component 2 PS417_01105 PS417_10900
Ac3H11_2560 L-histidine ABC transporter, ATPase component PS417_16140 PS417_14415
Ac3H11_2561 L-histidine ABC transporter, permease component 1 PS417_01140 PS417_12950
Ac3H11_2562 L-histidine ABC transporter, substrate-binding component 1
bgtA L-histidine ABC transporter, ATPase component BgtA PS417_06395 PS417_18120
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
BPHYT_RS24000 L-histidine ABC transporter, substrate-binding component PS417_13550 PS417_21745
BPHYT_RS24005 L-histidine ABC transporter, permease component 1 PS417_06410 PS417_13555
BPHYT_RS24010 L-histidine ABC transporter, permease component 2 PS417_21735 PS417_01485
BPHYT_RS24015 L-histidine ABC transporter, ATPase component PS417_13545 PS417_01500
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC PS417_02655 PS417_06615
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) PS417_02660 PS417_06610
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) PS417_06605 PS417_02665
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) PS417_02670 PS417_06600
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) PS417_02675 PS417_06595
Ga0059261_1577 L-histidine transporter
hutG N-formiminoglutamate formiminohydrolase
hutV L-histidine ABC transporter, ATPase component HutV PS417_26325 PS417_04010
hutW L-histidine ABC transporter, permease component HutW PS417_01735 PS417_26320
hutX L-histidine ABC transporter, substrate-binding component HutX PS417_01730 PS417_11935
LAT2 L-histidine transporter
LHT L-histidine transporter
natA L-histidine ABC transporter, ATPase component 1 (NatA) PS417_06600 PS417_16795
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) PS417_06610 PS417_02660
natE L-histidine ABC transporter, ATPase component 2 (NatE) PS417_06595 PS417_02675
PA5503 L-histidine ABC transporter, ATPase component PS417_00360 PS417_01065
PA5504 L-histidine ABC transporter, permease component PS417_00355 PS417_01060
PA5505 L-histidine ABC transporter, substrate-binding component PS417_00350 PS417_01005
permease L-histidine permease PS417_01755 PS417_05405
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 (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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, 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