GapMind for catabolism of small carbon sources

 

L-histidine catabolism in Clostridium kluyveri DSM 555

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 (33 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
PA5503 L-histidine ABC transporter, ATPase component CKL_RS04035 CKL_RS03265
PA5504 L-histidine ABC transporter, permease component CKL_RS03270 CKL_RS04040
PA5505 L-histidine ABC transporter, substrate-binding component CKL_RS14215 CKL_RS04045
hutH histidine ammonia-lyase
hutU urocanase
hutI imidazole-5-propionate hydrolase
hutG N-formiminoglutamate formiminohydrolase CKL_RS11780
Alternative steps:
aapJ L-histidine ABC transporter, substrate-binding component AapJ
aapM L-histidine ABC transporter, permease component 2 (AapM) CKL_RS04815
aapP L-histidine ABC transporter, ATPase component AapP CKL_RS04820 CKL_RS10155
aapQ L-histidine ABC transporter, permease component 1 (AapQ)
Ac3H11_2554 ABC transporter for L-Histidine, permease component 2 CKL_RS04815 CKL_RS03475
Ac3H11_2555 L-histidine ABC transporter, substrate-binding component 2 CKL_RS04810 CKL_RS11640
Ac3H11_2560 L-histidine ABC transporter, ATPase component CKL_RS05115 CKL_RS10650
Ac3H11_2561 L-histidine ABC transporter, permease component 1 CKL_RS13605
Ac3H11_2562 L-histidine ABC transporter, substrate-binding component 1
bgtA L-histidine ABC transporter, ATPase component BgtA CKL_RS04820 CKL_RS10155
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
BPHYT_RS24000 L-histidine ABC transporter, substrate-binding component CKL_RS11640
BPHYT_RS24005 L-histidine ABC transporter, permease component 1 CKL_RS04815 CKL_RS03475
BPHYT_RS24010 L-histidine ABC transporter, permease component 2 CKL_RS04815 CKL_RS03475
BPHYT_RS24015 L-histidine ABC transporter, ATPase component CKL_RS04820 CKL_RS10155
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) CKL_RS13425
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) CKL_RS13420
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) CKL_RS13415 CKL_RS13410
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) CKL_RS13410 CKL_RS03035
Ga0059261_1577 L-histidine transporter CKL_RS05310 CKL_RS03630
hisJ L-histidine ABC transporter, substrate-binding component HisJ CKL_RS11640 CKL_RS04810
hisM L-histidine ABC transporter, permease component 1 (HisM) CKL_RS04815 CKL_RS03475
hisP L-histidine ABC transporter, ATPase component HisP CKL_RS04820 CKL_RS10155
hisQ L-histidine ABC transporter, permease component 2 (HisQ) CKL_RS04815 CKL_RS03475
hutF N-formiminoglutamate deiminase
hutG' N-formylglutamate amidohydrolase CKL_RS18785
hutV L-histidine ABC transporter, ATPase component HutV CKL_RS03815 CKL_RS13695
hutW L-histidine ABC transporter, permease component HutW CKL_RS03820 CKL_RS13690
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) CKL_RS13415 CKL_RS13410
natB L-histidine ABC transporter, substrate-binding component NatB CKL_RS13405
natC L-histidine ABC transporter, permease component 1 (NatC) CKL_RS13420
natD L-histidine ABC transporter, permease component 2 (NatD) CKL_RS13425
natE L-histidine ABC transporter, ATPase component 2 (NatE) CKL_RS13410 CKL_RS13695
permease L-histidine permease CKL_RS07600 CKL_RS17165
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