GapMind for catabolism of small carbon sources

 

L-histidine catabolism in Chromobacterium vaccinii MWU205

Best path

PA5503, PA5504, PA5505, 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 (35 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
PA5503 L-histidine ABC transporter, ATPase component VL52_RS00410 VL52_RS19750
PA5504 L-histidine ABC transporter, permease component VL52_RS07405 VL52_RS00405
PA5505 L-histidine ABC transporter, substrate-binding component VL52_RS07410
hutH histidine ammonia-lyase VL52_RS20875 VL52_RS01890
hutU urocanase VL52_RS20865
hutI imidazole-5-propionate hydrolase VL52_RS20855
hutG N-formiminoglutamate formiminohydrolase VL52_RS20860
Alternative steps:
aapJ L-histidine ABC transporter, substrate-binding component AapJ
aapM L-histidine ABC transporter, permease component 2 (AapM) VL52_RS19745 VL52_RS08850
aapP L-histidine ABC transporter, ATPase component AapP VL52_RS19750 VL52_RS06130
aapQ L-histidine ABC transporter, permease component 1 (AapQ) VL52_RS19740 VL52_RS19745
Ac3H11_2554 ABC transporter for L-Histidine, permease component 2 VL52_RS08005 VL52_RS08850
Ac3H11_2555 L-histidine ABC transporter, substrate-binding component 2 VL52_RS08000
Ac3H11_2560 L-histidine ABC transporter, ATPase component VL52_RS14840 VL52_RS15745
Ac3H11_2561 L-histidine ABC transporter, permease component 1
Ac3H11_2562 L-histidine ABC transporter, substrate-binding component 1
bgtA L-histidine ABC transporter, ATPase component BgtA VL52_RS06130 VL52_RS19750
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
BPHYT_RS24000 L-histidine ABC transporter, substrate-binding component VL52_RS06115
BPHYT_RS24005 L-histidine ABC transporter, permease component 1 VL52_RS06120 VL52_RS17820
BPHYT_RS24010 L-histidine ABC transporter, permease component 2 VL52_RS17815 VL52_RS06125
BPHYT_RS24015 L-histidine ABC transporter, ATPase component VL52_RS06130 VL52_RS08010
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC VL52_RS18885 VL52_RS09675
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) VL52_RS15500
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) VL52_RS15495
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) VL52_RS15490 VL52_RS08010
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) VL52_RS15485 VL52_RS03360
Ga0059261_1577 L-histidine transporter VL52_RS03530
hisJ L-histidine ABC transporter, substrate-binding component HisJ VL52_RS06115 VL52_RS17825
hisM L-histidine ABC transporter, permease component 1 (HisM) VL52_RS06125 VL52_RS17815
hisP L-histidine ABC transporter, ATPase component HisP VL52_RS06130 VL52_RS19750
hisQ L-histidine ABC transporter, permease component 2 (HisQ) VL52_RS06120 VL52_RS17820
hutF N-formiminoglutamate deiminase
hutG' N-formylglutamate amidohydrolase
hutV L-histidine ABC transporter, ATPase component HutV VL52_RS12370 VL52_RS00410
hutW L-histidine ABC transporter, permease component HutW VL52_RS12375 VL52_RS00405
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) VL52_RS15490 VL52_RS03360
natB L-histidine ABC transporter, substrate-binding component NatB
natC L-histidine ABC transporter, permease component 1 (NatC) VL52_RS15495
natD L-histidine ABC transporter, permease component 2 (NatD) VL52_RS15500
natE L-histidine ABC transporter, ATPase component 2 (NatE) VL52_RS15485 VL52_RS03360
permease L-histidine permease VL52_RS10410 VL52_RS13800
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