GapMind for catabolism of small carbon sources

 

L-histidine catabolism in Desulfovibrio vulgaris Miyazaki F

Best path

hutV, hutW, hutX, hutH, hutU, hutI, hutG

Also see fitness data for the top candidates

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 (28 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
hutV L-histidine ABC transporter, ATPase component HutV DvMF_1045 DvMF_1587
hutW L-histidine ABC transporter, permease component HutW DvMF_1044
hutX L-histidine ABC transporter, substrate-binding component HutX
hutH histidine ammonia-lyase
hutU urocanase
hutI imidazole-5-propionate hydrolase
hutG N-formiminoglutamate formiminohydrolase
Alternative steps:
aapJ L-histidine ABC transporter, substrate-binding component AapJ DvMF_3152
aapM L-histidine ABC transporter, permease component 2 (AapM) DvMF_2786 DvMF_3154
aapP L-histidine ABC transporter, ATPase component AapP DvMF_2788 DvMF_3151
aapQ L-histidine ABC transporter, permease component 1 (AapQ) DvMF_1343
Ac3H11_2554 ABC transporter for L-Histidine, permease component 2 DvMF_1919 DvMF_0861
Ac3H11_2555 L-histidine ABC transporter, substrate-binding component 2 DvMF_1918 DvMF_0860
Ac3H11_2560 L-histidine ABC transporter, ATPase component DvMF_0522 DvMF_0802
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 DvMF_1920 DvMF_2788
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
BPHYT_RS24000 L-histidine ABC transporter, substrate-binding component DvMF_1918
BPHYT_RS24005 L-histidine ABC transporter, permease component 1 DvMF_1570 DvMF_1919
BPHYT_RS24010 L-histidine ABC transporter, permease component 2 DvMF_1568 DvMF_2786
BPHYT_RS24015 L-histidine ABC transporter, ATPase component DvMF_1920 DvMF_1342
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC DvMF_2607 DvMF_2750
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) DvMF_2608 DvMF_2751
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) DvMF_2609 DvMF_2752
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) DvMF_2610 DvMF_1481
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) DvMF_2611 DvMF_2754
Ga0059261_1577 L-histidine transporter
hisJ L-histidine ABC transporter, substrate-binding component HisJ DvMF_1571 DvMF_1918
hisM L-histidine ABC transporter, permease component 1 (HisM) DvMF_1570 DvMF_1568
hisP L-histidine ABC transporter, ATPase component HisP DvMF_1920 DvMF_3151
hisQ L-histidine ABC transporter, permease component 2 (HisQ) DvMF_1570 DvMF_1343
hutF N-formiminoglutamate deiminase
hutG' N-formylglutamate amidohydrolase
LAT2 L-histidine transporter
LHT L-histidine transporter
natA L-histidine ABC transporter, ATPase component 1 (NatA) DvMF_2753 DvMF_1481
natB L-histidine ABC transporter, substrate-binding component NatB
natC L-histidine ABC transporter, permease component 1 (NatC) DvMF_2609
natD L-histidine ABC transporter, permease component 2 (NatD) DvMF_2751 DvMF_2608
natE L-histidine ABC transporter, ATPase component 2 (NatE) DvMF_2754 DvMF_1584
PA5503 L-histidine ABC transporter, ATPase component DvMF_3151 DvMF_2788
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 Sep 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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