GapMind for catabolism of small carbon sources

 

L-histidine catabolism in Nostoc punctiforme PCC 73102 ATCC 29133; PCC 73102

Best path

bgtA, bgtB, 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 (28 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
bgtA L-histidine ABC transporter, ATPase component BgtA NPUN_RS14635 NPUN_RS32120
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) NPUN_RS14640 NPUN_RS32115
hutH histidine ammonia-lyase NPUN_RS10405
hutU urocanase
hutI imidazole-5-propionate hydrolase
hutG N-formiminoglutamate formiminohydrolase
Alternative steps:
aapJ L-histidine ABC transporter, substrate-binding component AapJ
aapM L-histidine ABC transporter, permease component 2 (AapM) NPUN_RS14640 NPUN_RS32115
aapP L-histidine ABC transporter, ATPase component AapP NPUN_RS32120 NPUN_RS14635
aapQ L-histidine ABC transporter, permease component 1 (AapQ) NPUN_RS14640
Ac3H11_2554 ABC transporter for L-Histidine, permease component 2 NPUN_RS14640 NPUN_RS32115
Ac3H11_2555 L-histidine ABC transporter, substrate-binding component 2 NPUN_RS14640
Ac3H11_2560 L-histidine ABC transporter, ATPase component NPUN_RS28780 NPUN_RS11810
Ac3H11_2561 L-histidine ABC transporter, permease component 1
Ac3H11_2562 L-histidine ABC transporter, substrate-binding component 1
BPHYT_RS24000 L-histidine ABC transporter, substrate-binding component
BPHYT_RS24005 L-histidine ABC transporter, permease component 1 NPUN_RS14640 NPUN_RS32115
BPHYT_RS24010 L-histidine ABC transporter, permease component 2 NPUN_RS14640 NPUN_RS32115
BPHYT_RS24015 L-histidine ABC transporter, ATPase component NPUN_RS14635 NPUN_RS32120
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) NPUN_RS25705
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) NPUN_RS25695
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) NPUN_RS25685 NPUN_RS19810
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) NPUN_RS25665 NPUN_RS05940
Ga0059261_1577 L-histidine transporter
hisJ L-histidine ABC transporter, substrate-binding component HisJ NPUN_RS32115 NPUN_RS03525
hisM L-histidine ABC transporter, permease component 1 (HisM) NPUN_RS14640 NPUN_RS32115
hisP L-histidine ABC transporter, ATPase component HisP NPUN_RS14635 NPUN_RS32120
hisQ L-histidine ABC transporter, permease component 2 (HisQ) NPUN_RS14640 NPUN_RS32115
hutF N-formiminoglutamate deiminase
hutG' N-formylglutamate amidohydrolase
hutV L-histidine ABC transporter, ATPase component HutV NPUN_RS13430 NPUN_RS28780
hutW L-histidine ABC transporter, permease component HutW NPUN_RS13435
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) NPUN_RS19810 NPUN_RS25685
natB L-histidine ABC transporter, substrate-binding component NatB NPUN_RS13990
natC L-histidine ABC transporter, permease component 1 (NatC) NPUN_RS19815
natD L-histidine ABC transporter, permease component 2 (NatD) NPUN_RS19325 NPUN_RS25705
natE L-histidine ABC transporter, ATPase component 2 (NatE) NPUN_RS05940 NPUN_RS25665
PA5503 L-histidine ABC transporter, ATPase component NPUN_RS27225 NPUN_RS31180
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.

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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