GapMind for catabolism of small carbon sources

 

L-histidine catabolism in Alicycliphilus denitrificans K601

Best path

Ac3H11_2562, Ac3H11_2561, Ac3H11_2560, Ac3H11_2555, Ac3H11_2554, 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
Ac3H11_2562 L-histidine ABC transporter, substrate-binding component 1 ALIDE2_RS08445
Ac3H11_2561 L-histidine ABC transporter, permease component 1 ALIDE2_RS08450
Ac3H11_2560 L-histidine ABC transporter, ATPase component ALIDE2_RS08455 ALIDE2_RS22605
Ac3H11_2555 L-histidine ABC transporter, substrate-binding component 2 ALIDE2_RS08490 ALIDE2_RS04040
Ac3H11_2554 ABC transporter for L-Histidine, permease component 2 ALIDE2_RS08495 ALIDE2_RS17655
hutH histidine ammonia-lyase ALIDE2_RS08465
hutU urocanase ALIDE2_RS08480
hutI imidazole-5-propionate hydrolase ALIDE2_RS08510
hutF N-formiminoglutamate deiminase ALIDE2_RS08515
hutG' N-formylglutamate amidohydrolase ALIDE2_RS08520
Alternative steps:
aapJ L-histidine ABC transporter, substrate-binding component AapJ
aapM L-histidine ABC transporter, permease component 2 (AapM)
aapP L-histidine ABC transporter, ATPase component AapP ALIDE2_RS03245 ALIDE2_RS17660
aapQ L-histidine ABC transporter, permease component 1 (AapQ) ALIDE2_RS17655 ALIDE2_RS03235
bgtA L-histidine ABC transporter, ATPase component BgtA ALIDE2_RS18825 ALIDE2_RS04050
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 ALIDE2_RS18835 ALIDE2_RS17655
BPHYT_RS24010 L-histidine ABC transporter, permease component 2 ALIDE2_RS18830 ALIDE2_RS08495
BPHYT_RS24015 L-histidine ABC transporter, ATPase component ALIDE2_RS18825 ALIDE2_RS04050
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC ALIDE2_RS06410 ALIDE2_RS18220
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) ALIDE2_RS18330 ALIDE2_RS06405
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) ALIDE2_RS18325 ALIDE2_RS06400
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) ALIDE2_RS06395 ALIDE2_RS20580
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) ALIDE2_RS06390 ALIDE2_RS20585
Ga0059261_1577 L-histidine transporter
hisJ L-histidine ABC transporter, substrate-binding component HisJ ALIDE2_RS18840 ALIDE2_RS04040
hisM L-histidine ABC transporter, permease component 1 (HisM) ALIDE2_RS18830 ALIDE2_RS08495
hisP L-histidine ABC transporter, ATPase component HisP ALIDE2_RS18825 ALIDE2_RS17660
hisQ L-histidine ABC transporter, permease component 2 (HisQ) ALIDE2_RS18835 ALIDE2_RS17655
hutG N-formiminoglutamate formiminohydrolase ALIDE2_RS01610
hutV L-histidine ABC transporter, ATPase component HutV ALIDE2_RS18590 ALIDE2_RS17025
hutW L-histidine ABC transporter, permease component HutW ALIDE2_RS18595
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) ALIDE2_RS20580 ALIDE2_RS07730
natB L-histidine ABC transporter, substrate-binding component NatB
natC L-histidine ABC transporter, permease component 1 (NatC) ALIDE2_RS13035
natD L-histidine ABC transporter, permease component 2 (NatD) ALIDE2_RS07720 ALIDE2_RS06405
natE L-histidine ABC transporter, ATPase component 2 (NatE) ALIDE2_RS18315 ALIDE2_RS06390
PA5503 L-histidine ABC transporter, ATPase component ALIDE2_RS13130 ALIDE2_RS04050
PA5504 L-histidine ABC transporter, permease component ALIDE2_RS13125 ALIDE2_RS18595
PA5505 L-histidine ABC transporter, substrate-binding component ALIDE2_RS06095 ALIDE2_RS13120
permease L-histidine permease ALIDE2_RS12155
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.

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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