GapMind for catabolism of small carbon sources

 

L-histidine catabolism in Paenisporosarcina indica PN2

Best path

permease, 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 (33 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
permease L-histidine permease GY23_RS06985
hutH histidine ammonia-lyase GY23_RS13695
hutU urocanase GY23_RS16185
hutI imidazole-5-propionate hydrolase GY23_RS16180
hutG N-formiminoglutamate formiminohydrolase GY23_RS16175 GY23_RS06500
Alternative steps:
aapJ L-histidine ABC transporter, substrate-binding component AapJ GY23_RS09755
aapM L-histidine ABC transporter, permease component 2 (AapM) GY23_RS09765 GY23_RS08645
aapP L-histidine ABC transporter, ATPase component AapP GY23_RS09770 GY23_RS06990
aapQ L-histidine ABC transporter, permease component 1 (AapQ) GY23_RS09760 GY23_RS07000
Ac3H11_2554 ABC transporter for L-Histidine, permease component 2 GY23_RS12675 GY23_RS08105
Ac3H11_2555 L-histidine ABC transporter, substrate-binding component 2 GY23_RS08650 GY23_RS08455
Ac3H11_2560 L-histidine ABC transporter, ATPase component GY23_RS07675 GY23_RS07755
Ac3H11_2561 L-histidine ABC transporter, permease component 1 GY23_RS07670
Ac3H11_2562 L-histidine ABC transporter, substrate-binding component 1
bgtA L-histidine ABC transporter, ATPase component BgtA GY23_RS06990 GY23_RS08640
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
BPHYT_RS24000 L-histidine ABC transporter, substrate-binding component
BPHYT_RS24005 L-histidine ABC transporter, permease component 1 GY23_RS12675 GY23_RS08460
BPHYT_RS24010 L-histidine ABC transporter, permease component 2 GY23_RS08105 GY23_RS08645
BPHYT_RS24015 L-histidine ABC transporter, ATPase component GY23_RS08100 GY23_RS12670
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) GY23_RS09730
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) GY23_RS09735
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) GY23_RS09740 GY23_RS03815
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) GY23_RS09745 GY23_RS03810
Ga0059261_1577 L-histidine transporter
hisJ L-histidine ABC transporter, substrate-binding component HisJ GY23_RS12680 GY23_RS08110
hisM L-histidine ABC transporter, permease component 1 (HisM) GY23_RS12675 GY23_RS08645
hisP L-histidine ABC transporter, ATPase component HisP GY23_RS12670 GY23_RS08100
hisQ L-histidine ABC transporter, permease component 2 (HisQ) GY23_RS12675 GY23_RS08105
hutF N-formiminoglutamate deiminase
hutG' N-formylglutamate amidohydrolase
hutV L-histidine ABC transporter, ATPase component HutV GY23_RS03490 GY23_RS11220
hutW L-histidine ABC transporter, permease component HutW GY23_RS03495 GY23_RS11215
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) GY23_RS09740 GY23_RS03815
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) GY23_RS09730
natE L-histidine ABC transporter, ATPase component 2 (NatE) GY23_RS09745 GY23_RS03810
PA5503 L-histidine ABC transporter, ATPase component GY23_RS00685 GY23_RS13595
PA5504 L-histidine ABC transporter, permease component GY23_RS13590 GY23_RS00680
PA5505 L-histidine ABC transporter, substrate-binding component GY23_RS13585 GY23_RS00675
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 24 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:

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