GapMind for catabolism of small carbon sources

 

L-histidine catabolism in Methylobacterium nodulans ORS 2060

Best path

braC, braD, braE, braF, braG, 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 (36 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC MNOD_RS08385 MNOD_RS14755
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) MNOD_RS08415 MNOD_RS31080
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) MNOD_RS08410 MNOD_RS05615
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) MNOD_RS08405 MNOD_RS01650
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) MNOD_RS08395 MNOD_RS05610
hutH histidine ammonia-lyase MNOD_RS05000
hutU urocanase MNOD_RS04990
hutI imidazole-5-propionate hydrolase MNOD_RS05005
hutF N-formiminoglutamate deiminase
hutG' N-formylglutamate amidohydrolase MNOD_RS04995 MNOD_RS28130
Alternative steps:
aapJ L-histidine ABC transporter, substrate-binding component AapJ MNOD_RS30120 MNOD_RS38875
aapM L-histidine ABC transporter, permease component 2 (AapM) MNOD_RS38865 MNOD_RS04320
aapP L-histidine ABC transporter, ATPase component AapP MNOD_RS30125 MNOD_RS38860
aapQ L-histidine ABC transporter, permease component 1 (AapQ) MNOD_RS38870 MNOD_RS21090
Ac3H11_2554 ABC transporter for L-Histidine, permease component 2 MNOD_RS11495 MNOD_RS18770
Ac3H11_2555 L-histidine ABC transporter, substrate-binding component 2
Ac3H11_2560 L-histidine ABC transporter, ATPase component MNOD_RS01615 MNOD_RS39165
Ac3H11_2561 L-histidine ABC transporter, permease component 1 MNOD_RS01610 MNOD_RS23050
Ac3H11_2562 L-histidine ABC transporter, substrate-binding component 1 MNOD_RS01605
bgtA L-histidine ABC transporter, ATPase component BgtA MNOD_RS38860 MNOD_RS30125
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
BPHYT_RS24000 L-histidine ABC transporter, substrate-binding component MNOD_RS24395
BPHYT_RS24005 L-histidine ABC transporter, permease component 1 MNOD_RS24390 MNOD_RS24385
BPHYT_RS24010 L-histidine ABC transporter, permease component 2 MNOD_RS24385 MNOD_RS11495
BPHYT_RS24015 L-histidine ABC transporter, ATPase component MNOD_RS24380 MNOD_RS18765
Ga0059261_1577 L-histidine transporter
hisJ L-histidine ABC transporter, substrate-binding component HisJ MNOD_RS24395 MNOD_RS31675
hisM L-histidine ABC transporter, permease component 1 (HisM) MNOD_RS24385 MNOD_RS04315
hisP L-histidine ABC transporter, ATPase component HisP MNOD_RS24380 MNOD_RS38860
hisQ L-histidine ABC transporter, permease component 2 (HisQ) MNOD_RS24390 MNOD_RS11495
hutG N-formiminoglutamate formiminohydrolase
hutV L-histidine ABC transporter, ATPase component HutV MNOD_RS16110 MNOD_RS36940
hutW L-histidine ABC transporter, permease component HutW MNOD_RS16105 MNOD_RS36945
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) MNOD_RS07445 MNOD_RS18705
natB L-histidine ABC transporter, substrate-binding component NatB MNOD_RS07460
natC L-histidine ABC transporter, permease component 1 (NatC)
natD L-histidine ABC transporter, permease component 2 (NatD) MNOD_RS18715 MNOD_RS07455
natE L-histidine ABC transporter, ATPase component 2 (NatE) MNOD_RS07440 MNOD_RS18700
PA5503 L-histidine ABC transporter, ATPase component MNOD_RS24365 MNOD_RS11490
PA5504 L-histidine ABC transporter, permease component MNOD_RS24370
PA5505 L-histidine ABC transporter, substrate-binding component MNOD_RS24375 MNOD_RS12730
permease L-histidine permease MNOD_RS23565 MNOD_RS04385
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.

Links

Downloads

Related tools

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