GapMind for catabolism of small carbon sources

 

L-histidine catabolism

Analysis of pathway histidine in 35 genomes

Genome Best path
Acidovorax sp. GW101-3H11 Ac3H11_2562, Ac3H11_2561, Ac3H11_2560, Ac3H11_2555, Ac3H11_2554, hutH, hutU, hutI, hutF, hutG'
Azospirillum brasilense Sp245 Ac3H11_2562, Ac3H11_2561, Ac3H11_2560, Ac3H11_2555, Ac3H11_2554, hutH, hutU, hutI, hutF, hutG'
Bacteroides thetaiotaomicron VPI-5482 permease, hutH, hutU, hutI, hutG
Burkholderia phytofirmans PsJN BPHYT_RS24000, BPHYT_RS24005, BPHYT_RS24010, BPHYT_RS24015, hutH, hutU, hutI, hutF, hutG'
Caulobacter crescentus NA1000 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutF, hutG'
Cupriavidus basilensis 4G11 Ac3H11_2562, Ac3H11_2561, Ac3H11_2560, Ac3H11_2555, Ac3H11_2554, hutH, hutU, hutI, hutF, hutG'
Dechlorosoma suillum PS PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Desulfovibrio vulgaris Hildenborough permease, hutH, hutU, hutI, hutG
Desulfovibrio vulgaris Miyazaki F hutV, hutW, hutX, hutH, hutU, hutI, hutG
Dinoroseobacter shibae DFL-12 aapJ, aapQ, aapM, aapP, hutH, hutU, hutI, hutG
Dyella japonica UNC79MFTsu3.2 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutF, hutG'
Echinicola vietnamensis KMM 6221, DSM 17526 permease, hutH, hutU, hutI, hutG
Escherichia coli BW25113 hisP, hisM, hisQ, hisJ, hutH, hutU, hutI, hutG
Herbaspirillum seropedicae SmR1 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutF, hutG'
Klebsiella michiganensis M5al hisP, hisM, hisQ, hisJ, hutH, hutU, hutI, hutG
Magnetospirillum magneticum AMB-1 braC, braD, braE, braF, braG, hutH, hutU, hutI, hutG
Marinobacter adhaerens HP15 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Paraburkholderia bryophila 376MFSha3.1 BPHYT_RS24000, BPHYT_RS24005, BPHYT_RS24010, BPHYT_RS24015, hutH, hutU, hutI, hutF, hutG'
Pedobacter sp. GW460-11-11-14-LB5 LAT2, hutH, hutU, hutI, hutG
Phaeobacter inhibens BS107 hutV, hutW, hutX, hutH, hutU, hutI, hutF, hutG'
Pseudomonas fluorescens FW300-N1B4 hisP, hisM, hisQ, hisJ, hutH, hutU, hutI, hutF, hutG'
Pseudomonas fluorescens FW300-N2C3 hisP, hisM, hisQ, hisJ, hutH, hutU, hutI, hutF, hutG'
Pseudomonas fluorescens FW300-N2E2 hisP, hisM, hisQ, hisJ, hutH, hutU, hutI, hutF, hutG'
Pseudomonas fluorescens FW300-N2E3 hisP, hisM, hisQ, hisJ, hutH, hutU, hutI, hutF, hutG'
Pseudomonas fluorescens GW456-L13 hisP, hisM, hisQ, hisJ, hutH, hutU, hutI, hutF, hutG'
Pseudomonas putida KT2440 hisP, hisM, hisQ, hisJ, hutH, hutU, hutI, hutF, hutG'
Pseudomonas simiae WCS417 hisP, hisM, hisQ, hisJ, hutH, hutU, hutI, hutF, hutG'
Pseudomonas stutzeri RCH2 hisP, hisM, hisQ, hisJ, hutH, hutU, hutI, hutG
Shewanella amazonensis SB2B permease, hutH, hutU, hutI, hutG
Shewanella loihica PV-4 permease, hutH, hutU, hutI, hutG
Shewanella oneidensis MR-1 permease, hutH, hutU, hutI, hutG
Shewanella sp. ANA-3 permease, hutH, hutU, hutI, hutG
Sinorhizobium meliloti 1021 braC, braD, braE, braF, braG, hutH, hutU, hutI, hutF, hutG'
Sphingomonas koreensis DSMZ 15582 Ga0059261_1577, hutH, hutU, hutI, hutF, hutG'
Synechococcus elongatus PCC 7942 natA, natB, natC, natD, natE, hutH, hutU, hutI, hutG

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 May 21 2021. The underlying query database was built on May 21 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