GapMind for catabolism of small carbon sources

 

L-histidine catabolism in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

Best path

aapJ, aapQ, aapM, aapP, hutH, hutU, hutI, 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 (32 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aapJ L-histidine ABC transporter, substrate-binding component AapJ HTA01S_RS18560
aapQ L-histidine ABC transporter, permease component 1 (AapQ) HTA01S_RS18555 HTA01S_RS13175
aapM L-histidine ABC transporter, permease component 2 (AapM) HTA01S_RS18550 HTA01S_RS13395
aapP L-histidine ABC transporter, ATPase component AapP HTA01S_RS18545 HTA01S_RS09510
hutH histidine ammonia-lyase HTA01S_RS17915
hutU urocanase HTA01S_RS17920
hutI imidazole-5-propionate hydrolase HTA01S_RS17905
hutG N-formiminoglutamate formiminohydrolase HTA01S_RS17900
Alternative steps:
Ac3H11_2554 ABC transporter for L-Histidine, permease component 2 HTA01S_RS13395 HTA01S_RS07500
Ac3H11_2555 L-histidine ABC transporter, substrate-binding component 2 HTA01S_RS09500 HTA01S_RS07510
Ac3H11_2560 L-histidine ABC transporter, ATPase component HTA01S_RS22420 HTA01S_RS12935
Ac3H11_2561 L-histidine ABC transporter, permease component 1 HTA01S_RS22425 HTA01S_RS22340
Ac3H11_2562 L-histidine ABC transporter, substrate-binding component 1
bgtA L-histidine ABC transporter, ATPase component BgtA HTA01S_RS08115 HTA01S_RS11785
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
BPHYT_RS24000 L-histidine ABC transporter, substrate-binding component HTA01S_RS08135
BPHYT_RS24005 L-histidine ABC transporter, permease component 1 HTA01S_RS08130 HTA01S_RS07505
BPHYT_RS24010 L-histidine ABC transporter, permease component 2 HTA01S_RS07500 HTA01S_RS11790
BPHYT_RS24015 L-histidine ABC transporter, ATPase component HTA01S_RS08115 HTA01S_RS09510
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC HTA01S_RS07615
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) HTA01S_RS16520 HTA01S_RS04360
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) HTA01S_RS16515 HTA01S_RS04365
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) HTA01S_RS16510 HTA01S_RS05080
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) HTA01S_RS16505 HTA01S_RS04375
Ga0059261_1577 L-histidine transporter
hisJ L-histidine ABC transporter, substrate-binding component HisJ HTA01S_RS08135 HTA01S_RS07510
hisM L-histidine ABC transporter, permease component 1 (HisM) HTA01S_RS08125 HTA01S_RS07500
hisP L-histidine ABC transporter, ATPase component HisP HTA01S_RS08115 HTA01S_RS13385
hisQ L-histidine ABC transporter, permease component 2 (HisQ) HTA01S_RS07505 HTA01S_RS08130
hutF N-formiminoglutamate deiminase
hutG' N-formylglutamate amidohydrolase
hutV L-histidine ABC transporter, ATPase component HutV HTA01S_RS06435 HTA01S_RS10510
hutW L-histidine ABC transporter, permease component HutW HTA01S_RS06440
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) HTA01S_RS16510 HTA01S_RS14295
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) HTA01S_RS16520 HTA01S_RS05630
natE L-histidine ABC transporter, ATPase component 2 (NatE) HTA01S_RS14300 HTA01S_RS16505
PA5503 L-histidine ABC transporter, ATPase component HTA01S_RS11785 HTA01S_RS13385
PA5504 L-histidine ABC transporter, permease component
PA5505 L-histidine ABC transporter, substrate-binding component
permease L-histidine permease
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