GapMind for catabolism of small carbon sources

 

L-histidine catabolism in Pseudomonas fluorescens FW300-N1B4

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 Pf1N1B4_1640 Pf1N1B4_3435
hisM L-histidine ABC transporter, permease component 1 (HisM) Pf1N1B4_1643 Pf1N1B4_3177
hisQ L-histidine ABC transporter, permease component 2 (HisQ) Pf1N1B4_1642 Pf1N1B4_3178
hisJ L-histidine ABC transporter, substrate-binding component HisJ Pf1N1B4_1641 Pf1N1B4_5844
hutH histidine ammonia-lyase Pf1N1B4_1582 Pf1N1B4_1581
hutU urocanase Pf1N1B4_1587
hutI imidazole-5-propionate hydrolase Pf1N1B4_1579
hutF N-formiminoglutamate deiminase Pf1N1B4_1591
hutG' N-formylglutamate amidohydrolase Pf1N1B4_1578
Alternative steps:
aapJ L-histidine ABC transporter, substrate-binding component AapJ Pf1N1B4_917
aapM L-histidine ABC transporter, permease component 2 (AapM) Pf1N1B4_915 Pf1N1B4_773
aapP L-histidine ABC transporter, ATPase component AapP Pf1N1B4_914 Pf1N1B4_774
aapQ L-histidine ABC transporter, permease component 1 (AapQ) Pf1N1B4_916 Pf1N1B4_772
Ac3H11_2554 ABC transporter for L-Histidine, permease component 2 Pf1N1B4_1694 Pf1N1B4_5644
Ac3H11_2555 L-histidine ABC transporter, substrate-binding component 2 Pf1N1B4_1693 Pf1N1B4_4791
Ac3H11_2560 L-histidine ABC transporter, ATPase component Pf1N1B4_5098 Pf1N1B4_1792
Ac3H11_2561 L-histidine ABC transporter, permease component 1 Pf1N1B4_1766 Pf1N1B4_3305
Ac3H11_2562 L-histidine ABC transporter, substrate-binding component 1
bgtA L-histidine ABC transporter, ATPase component BgtA Pf1N1B4_3175 Pf1N1B4_3435
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) Pf1N1B4_4805
BPHYT_RS24000 L-histidine ABC transporter, substrate-binding component Pf1N1B4_4400 Pf1N1B4_5844
BPHYT_RS24005 L-histidine ABC transporter, permease component 1 Pf1N1B4_3178 Pf1N1B4_1642
BPHYT_RS24010 L-histidine ABC transporter, permease component 2 Pf1N1B4_3433 Pf1N1B4_4398
BPHYT_RS24015 L-histidine ABC transporter, ATPase component Pf1N1B4_1640 Pf1N1B4_3435
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC Pf1N1B4_1382 Pf1N1B4_3218
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) Pf1N1B4_1381 Pf1N1B4_3217
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) Pf1N1B4_3216 Pf1N1B4_1380
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) Pf1N1B4_1379 Pf1N1B4_3215
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) Pf1N1B4_1378 Pf1N1B4_3214
Ga0059261_1577 L-histidine transporter
hutG N-formiminoglutamate formiminohydrolase
hutV L-histidine ABC transporter, ATPase component HutV Pf1N1B4_1583 Pf1N1B4_2420
hutW L-histidine ABC transporter, permease component HutW Pf1N1B4_1584 Pf1N1B4_2421
hutX L-histidine ABC transporter, substrate-binding component HutX Pf1N1B4_1585 Pf1N1B4_562
LAT2 L-histidine transporter
LHT L-histidine transporter
natA L-histidine ABC transporter, ATPase component 1 (NatA) Pf1N1B4_3215 Pf1N1B4_1346
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) Pf1N1B4_3214 Pf1N1B4_1378
PA5503 L-histidine ABC transporter, ATPase component Pf1N1B4_1866 Pf1N1B4_1702
PA5504 L-histidine ABC transporter, permease component Pf1N1B4_1865 Pf1N1B4_1703
PA5505 L-histidine ABC transporter, substrate-binding component Pf1N1B4_1864 Pf1N1B4_1714
permease L-histidine permease Pf1N1B4_1580 Pf1N1B4_801
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 Aug 02 2021. The underlying query database was built on Aug 02 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