GapMind for catabolism of small carbon sources

 

L-histidine catabolism

Analysis of pathway histidine in 201 genomes

Genome Best path
Acidimicrobium ferrooxidans DSM 10331 permease, hutH, hutU, hutI, hutG
Acidithiobacillus ferrooxidans ATCC 23270 permease, hutH, hutU, hutI, hutG
Acidovorax sp. GW101-3H11 Ac3H11_2562, Ac3H11_2561, Ac3H11_2560, Ac3H11_2555, Ac3H11_2554, hutH, hutU, hutI, hutF, hutG'
Algiphilus aromaticivorans DG1253 permease, hutH, hutU, hutI, hutG
Alicycliphilus denitrificans K601 Ac3H11_2562, Ac3H11_2561, Ac3H11_2560, Ac3H11_2555, Ac3H11_2554, hutH, hutU, hutI, hutF, hutG'
Alkalihalobacterium alkalinitrilicum DSM 22532 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Allochromatium vinosum DSM 180 permease, hutH, hutU, hutI, hutG
Ammonifex degensii KC4 natA, natB, natC, natD*, natE, hutH, hutU, hutI, hutG
Anaerobutyricum hallii DSM 3353 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Aquimarina longa SW024 permease, hutH, hutU, hutI, hutF, hutG'
Archaeoglobus veneficus SNP6 permease, hutH, hutU, hutI, hutG
Arcobacter nitrofigilis DSM 7299 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Azoarcus olearius BH72 aapJ, aapQ, aapM, aapP, hutH, hutU, hutI, hutF, hutG'
Azohydromonas australica DSM 1124 aapJ, aapQ, aapM, aapP, hutH, hutU, hutI, hutF, hutG'
Azorhizobium caulinodans ORS 571 braC, braD, braE, braF, braG, hutH, hutU, hutI, hutG
Azospirillum brasilense Sp245 Ac3H11_2562, Ac3H11_2561, Ac3H11_2560, Ac3H11_2555, Ac3H11_2554, hutH, hutU, hutI, hutF, hutG'
Azospirillum sp. B510 braC, braD, braE, braF, braG, hutH, hutU, hutI, hutF, hutG'
Bacteroides thetaiotaomicron VPI-5482 permease, hutH, hutU, hutI, hutG
Beijerinckia indica ATCC 9039 aapJ, aapQ, aapM, aapP, hutH, hutU, hutI, hutG
Beijerinckia mobilis UQM 1969 aapJ, aapQ, aapM, aapP, hutH, hutU, hutI, hutG
Billgrantia desiderata SP1 aapJ, aapQ, aapM, aapP, hutH, hutU, hutI, hutG
Bradyrhizobium sp. BTAi1 braC, braD, braE, braF, braG, hutH, hutU, hutI, hutF, hutG'
Brevundimonas sp. GW460-12-10-14-LB2 Ga0059261_1577, hutH, hutU, hutI, hutF, hutG'
Burkholderia phytofirmans PsJN BPHYT_RS24000, BPHYT_RS24005, BPHYT_RS24010, BPHYT_RS24015, hutH, hutU, hutI, hutF, hutG'
Burkholderia vietnamiensis G4 BPHYT_RS24000, BPHYT_RS24005, BPHYT_RS24010, BPHYT_RS24015, hutH, hutU, hutI, hutF, hutG'
Calditerrivibrio nitroreducens DSM 19672 permease, hutH, hutU, hutI, hutG
Caminibacter mediatlanticus TB-2 permease, hutH, hutU, hutI, hutG
Carboxydothermus pertinax Ug1 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Caulobacter crescentus NA1000 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutF, hutG'
Cereibacter sphaeroides ATCC 17029 aapJ, aapQ, aapM, aapP, hutH, hutU, hutI, hutF, hutG'
Chlorobaculum parvum NCIB 8327 permease, hutH, hutU, hutI, hutG
Chlorobaculum tepidum TLS Ga0059261_1577, hutH, hutU, hutI, hutG
Chlorobium limicola DSM 245 permease, hutH, hutU, hutI, hutG
Chlorobium phaeobacteroides BS1 permease, hutH, hutU, hutI, hutG
Clostridium acetobutylicum ATCC 824 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Clostridium kluyveri DSM 555 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Clostridium tyrobutyricum FAM22553 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Crocosphaera subtropica ATCC 51142 natA, natB, natC, natD, natE, hutH, hutU, hutI, hutG
Cupriavidus basilensis FW507-4G11 Ac3H11_2562, Ac3H11_2561, Ac3H11_2560, Ac3H11_2555, Ac3H11_2554, hutH, hutU, hutI, hutF, hutG'
Dechloromonas agitata is5 permease, hutH, hutU, hutI, hutG
Dechlorosoma suillum PS PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Dehalococcoides mccartyi 195 permease, hutH, hutU, hutI, hutG
Denitrovibrio acetiphilus DSM 12809 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Derxia gummosa DSM 723 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutF, hutG'
Desulfacinum hydrothermale DSM 13146 aapJ, aapQ, aapM, aapP, hutH, hutU, hutI, hutG
Desulfacinum infernum DSM 9756 aapJ, aapQ, aapM, aapP, hutH, hutU, hutI, hutG
Desulfarculus baarsii DSM 2075 permease, hutH, hutU, hutI, hutG
Desulfatibacillum aliphaticivorans DSM 15576 permease, hutH, hutU, hutI, hutG
Desulfatiglans anilini DSM 4660 LAT2, hutH, hutU, hutI, hutG
Desulfitobacterium hafniense DCB-2 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Desulfobacca acetoxidans DSM 11109 permease, hutH, hutU, hutI, hutG
Desulfobacter vibrioformis DSM 8776 permease, hutH, hutU, hutI, hutG
Desulfogranum mediterraneum DSM 13871 braC, braD, braE, braF, braG, hutH, hutU, hutI, hutG
Desulforamulus ruminis DSM 2154 LAT2, hutH, hutU, hutI, hutG
Desulfoscipio geothermicus DSM 3669 hutV, hutW, hutX, hutH, hutU, hutI, hutG
Desulfotalea psychrophila LSv54 aapJ, aapQ, aapM, aapP, hutH, hutU, hutI, hutG
Desulfovibrio oxyclinae DSM 11498 Ac3H11_2562, Ac3H11_2561, Ac3H11_2560, Ac3H11_2555, Ac3H11_2554, hutH, hutU, hutI, hutG
Desulfovibrio vulgaris Hildenborough JW710 permease, hutH, hutU, hutI, hutG
Desulfovibrio vulgaris Miyazaki F hutV, hutW, hutX, hutH, hutU, hutI, hutG
Desulfurobacterium atlanticum DSM 15668 permease, hutH, hutU, hutI, hutG
Desulfuromonas acetexigens permease, hutH, hutU, hutI, hutG
Desulfuromusa kysingii DSM 7343 aapJ, aapQ, aapM, aapP, 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
Ferroglobus placidus DSM 10642 permease, hutH, hutU, hutI, hutG
Frankia alni ACN14a Ga0059261_1577, hutH, hutU, hutI, hutG
Geobacter metallireducens GS-15 permease, hutH, hutU, hutI, hutG
Geotalea uraniireducens Rf4 permease, hutH, hutU, hutI, hutG
Halococcus hamelinensis 100A6 permease, hutH, hutU, hutI, hutG
Haloechinothrix alba DSM 45207 natA, natB, natC, natD, natE, hutH, hutU, hutI, hutF, hutG'
Haloferax volcanii DS2 permease, hutH, hutU, hutI, hutG
Haloglycomyces albus DSM 45210 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutF, hutG'
Halorhodospira halophila SL1 permease, hutH, hutU, hutI, hutG
Heliomicrobium modesticaldum Ice1; ATCC 51547 LAT2, hutH, hutU, hutI, hutG
Herbaspirillum autotrophicum IAM 14942 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Herbaspirillum seropedicae SmR1 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutF, hutG'
Hippea alviniae EP5-r permease, hutH, hutU, hutI, hutG
Hydrogenophaga taeniospiralis NBRC 102512 aapJ, aapQ, aapM, aapP, hutH, hutU, hutI, hutG
Hydrogenovibrio halophilus DSM 15072 permease, hutH, hutU, hutI, hutG
Hydrogenovibrio kuenenii DSM 12350 permease, hutH, hutU, hutI, hutG
Hydrogenovibrio marinus DSM 11271 permease, hutH, hutU, hutI, hutG
Hyphomicrobium sulfonivorans WDL6 braC, braD, braE, braF, braG, hutH, hutU, hutI, hutG
Klebsiella michiganensis M5al hisP, hisM, hisQ, hisJ, hutH, hutU, hutI, hutG
Klebsiella variicola At-22 hisP, hisM, hisQ, hisJ, hutH, hutU, hutI, hutG
Kyrpidia tusciae DSM 2912 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Leptospirillum ferrooxidans C2-3 permease, hutH, hutU, hutI, hutG
Magnetospirillum magneticum AMB-1 braC, braD, braE, braF, braG, hutH, hutU, hutI, hutG
Malonomonas rubra DSM 5091 aapJ, aapQ, aapM, aapP, hutH, hutU, hutI, hutG
Maridesulfovibrio bastinii DSM 16055 aapJ, aapQ, aapM, aapP, hutH, hutU, hutI, hutG
Maridesulfovibrio zosterae DSM 11974 aapJ, aapQ, aapM, aapP, hutH, hutU, hutI, hutG
Marinobacter adhaerens HP15 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Mesorhizobium ciceri WSM1271 aapJ, aapQ, aapM, aapP, hutH, hutU, hutI, hutF, hutG'
Methanobacterium lacus AL-21 permease, hutH, hutU, hutI, hutG
Methanococcus aeolicus Nankai-3 permease, hutH, hutU, hutI, hutG
Methanococcus maripaludis C5 permease, hutH, hutU, hutI, hutG
Methanosarcina acetivorans C2A permease, hutH, hutU, hutI, hutG
Methanosarcina mazei Go1 permease, hutH, hutU, hutI, hutG
Methanospirillum lacunae Ki8-1 permease, hutH, hutU, hutI, hutG
Methanothermobacter thermautotrophicus Delta H LAT2, hutH, hutU, hutI, hutG
Methylobacterium nodulans ORS 2060 braC, braD, braE, braF, braG, hutH, hutU, hutI, hutF, hutG'
Methylobacterium sp. 4-46 Apr-46 braC, braD, braE, braF, braG, hutH, hutU, hutI, hutF, hutG'
Methylocapsa acidiphila B2 braC, braD, braE, braF, braG, hutH, hutU, hutI, hutG
Methylocapsa aurea KYG braC, braD, braE, braF, braG, hutH, hutU, hutI, hutG
Methylocella silvestris BL2 braC, braD, braE, braF, braG, hutH, hutU, hutI, hutG
Methylococcus capsulatus Bath Ga0059261_1577, hutH, hutU, hutI, hutG
Methylocystis bryophila S285 permease, hutH, hutU, hutI, hutG
Methyloferula stellata AR4T braC, braD, braE, braF, braG, hutH, hutU, hutI, hutG
Methylohalobius crimeensis 10Ki permease, hutH, hutU, hutI, hutG
Methylomonas methanica MC09 permease, hutH, hutU, hutI, hutG
Methylosarcina fibrata AML-C10 permease, hutH, hutU, hutI, hutG
Methylotuvimicrobium alcaliphilum 20Z permease, hutH, hutU, hutI, hutG
Methylovulum miyakonense HT12 Ga0059261_1577, hutH, hutU, hutI, hutG
Mycolicibacterium vanbaalenii PYR-1 bgtA, bgtB, hutH, hutU, hutI, hutG
Nitratifractor salsuginis DSM 16511 aapJ, aapQ, aapM, aapP, hutH, hutU, hutI, hutG
Nitratiruptor tergarcus DSM 16512 permease, hutH, hutU, hutI, hutG
Nitriliruptor alkaliphilus DSM 45188 natA, natB, natC, natD, natE, hutH, hutU, hutI, hutG
Nocardioides dokdonensis FR1436 natA, natB, natC, natD, natE, hutH, hutU, hutI, hutF, hutG'
Nocardiopsis lucentensis DSM 44048 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutF, hutG'
Nostoc punctiforme ATCC 29133; PCC 73102 bgtA, bgtB, hutH, hutU, hutI, hutG
Novosphingobium aromaticivorans DSM 12444 Ga0059261_1577, hutH, hutU, hutI, hutG
Oleispira antarctica permease, hutH, hutU, hutI, hutG
Paraburkholderia atlantica CCGE1002 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutF, hutG'
Paraburkholderia bryophila 376MFSha3.1 BPHYT_RS24000, BPHYT_RS24005, BPHYT_RS24010, BPHYT_RS24015, hutH, hutU, hutI, hutF, hutG'
Paraburkholderia phymatum STM815 BPHYT_RS24000, BPHYT_RS24005, BPHYT_RS24010, BPHYT_RS24015, hutH, hutU, hutI, hutF, hutG'
Paucidesulfovibrio gracilis DSM 16080 braC, braD, braE, braF, braG, hutH, hutU, hutI, hutG
Pedobacter sp. GW460-11-11-14-LB5 LAT2, hutH, hutU, hutI, hutG
Pelobacter propionicus DSM 2379 permease, hutH, hutU, hutI, hutG
Persephonella marina EX-H1 permease, hutH, hutU, hutI, hutG
Phaeacidiphilus oryzae TH49 permease, hutH, hutU, hutI, hutF, hutG'
Phaeobacter inhibens BS107 hutV, hutW, hutX, hutH, hutU, hutI, hutF, hutG'
Polaromonas naphthalenivorans CJ2 Ac3H11_2562, Ac3H11_2561, Ac3H11_2560, Ac3H11_2555, Ac3H11_2554, hutH, hutU, hutI, hutG
Prosthecochloris aestuarii DSM 271 permease, hutH, hutU, hutI, hutG
Pseudarthrobacter sulfonivorans Ar51 permease, hutH, hutU, hutI, hutG
Pseudomonas benzenivorans DSM 8628 hisP, hisM, hisQ, hisJ, 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
Pyrolobus fumarii 1A permease, hutH, hutU, hutI, hutG
Rhizobium etli CFN 42 braC, braD, braE, braF, braG, hutH, hutU, hutI, hutF, hutG'
Rhizobium johnstonii 3841 braC, braD, braE, braF, braG, hutH, hutU, hutI, hutF, hutG'
Rhizobium leguminosarum WSM1325 braC, braD, braE, braF, braG, hutH, hutU, hutI, hutF, hutG'
Rhizorhabdus wittichii RW1 Ga0059261_1577, hutH, hutU, hutI, hutF, hutG'
Rhodanobacter denitrificans FW104-10B01 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutF, hutG'
Rhodomicrobium vannielii ATCC 17100 braC, braD, braE, braF, braG, hutH, hutU, hutI, hutG
Rhodopseudomonas palustris CGA009 braC, braD, braE, braF, braG, hutH, hutU, hutI, hutG
Rhodospirillum centenum SW; ATCC 51521 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutF, hutG'
Rhodospirillum rubrum ATCC 11170 hisP, hisM, hisQ, hisJ, hutH, hutU, hutI, hutF, hutG'
Roseburia faecis M72 permease, hutH, hutU, hutI, hutG
Saccharomonospora cyanea NA-134 permease, hutH, hutU, hutI, hutF, hutG'
Sedimenticola selenatireducens DSM 17993 braC, braD, braE, braF, braG, 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 fredii NGR234 braC, braD, braE, braF, braG, hutH, hutU, hutI, hutF, hutG'
Sinorhizobium medicae WSM419 braC, braD, braE, braF, braG, hutH, hutU, hutI, hutF, 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'
Stenotrophomonas chelatiphaga DSM 21508 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutF, hutG'
Steroidobacter denitrificans DSM 18526 permease, hutH, hutU, hutI, hutG
Stutzerimonas stutzeri A1501 hisP, hisM, hisQ, hisJ, hutH, hutU, hutI, hutG
Sulfuricurvum kujiense DSM 16994 permease, hutH, hutU, hutI, hutG
Sulfurihydrogenibium azorense Az-Fu1 permease, hutH, hutU, hutI, hutG
Sulfurihydrogenibium subterraneum DSM 15120 permease, hutH, hutU, hutI, hutG
Sulfurimonas denitrificans DSM 1251 permease, hutH, hutU, hutI, hutG
Sulfuritalea hydrogenivorans DSM 22779 permease, hutH, hutU, hutI, hutG
Sulfurivirga caldicuralii DSM 17737 permease, hutH, hutU, hutI, hutG
Synechococcus elongatus PCC 7942 natA, natB, natC, natD, natE, hutH, hutU, hutI, hutG
Teredinibacter turnerae T7901 permease, hutH, hutU, hutI, hutG
Thauera aminoaromatica S2 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Thermithiobacillus tepidarius DSM 3134 Ga0059261_1577, hutH, hutU, hutI, hutG
Thermocrinis albus DSM 14484 permease, hutH, hutU, hutI, hutG
Thermodesulforhabdus norvegica DSM 9990 aapJ, aapQ, aapM, aapP, hutH, hutU, hutI, hutG
Thermomonospora curvata DSM 43183 Ga0059261_1577, hutH, hutU, hutI, hutF, hutG'
Thermovibrio ammonificans HB-1 permease, hutH, hutU, hutI, hutG
Thermus aquaticus YT-1 permease, hutH, hutU, hutI, hutG
Thioalkalivibrio denitrificans ALJD permease, hutH, hutU, hutI, hutG
Thioalkalivibrio halophilus HL17 permease, hutH, hutU, hutI, hutG
Thioalkalivibrio paradoxus ARh 1 permease, hutH, hutU, hutI, hutG
Thioalkalivibrio thiocyanodenitrificans ARhD 1 permease, hutH, hutU, hutI, hutG
Thiohalomonas denitrificans HLD2 permease, hutH, hutU, hutI, hutG
Thiohalospira halophila HL 3 permease, hutH, hutU, hutI, hutG
Thiomicrorhabdus arctica DSM 13458 permease, hutH, hutU, hutI, hutG
Thiomicrorhabdus chilensis DSM 12352 permease, hutH, hutU, hutI, hutG
Thiomicrospira cyclica ALM1 permease, hutH, hutU, hutI, hutG
Thiomicrospira microaerophila ASL8-2 permease, hutH, hutU, hutI, hutG
Thiomicrospira pelophila DSM 1534 permease, hutH, hutU, hutI, hutG
Thiothrix lacustris DSM 21227 hisP, hisM, hisQ, hisJ, hutH, hutU, hutI, hutG
Tistlia consotensis USBA 355 aapJ, aapQ, aapM, aapP, hutH, hutU, hutI, hutF, hutG'
Trichlorobacter lovleyi SZ permease, hutH, hutU, hutI, hutG
Trichodesmium erythraeum IMS101 Annotated Metagenome-Assembled Genome permease, hutH, hutU, hutI, hutG
Trichormus variabilis ATCC 29413 natA, natB, natC, natD, natE, hutH, hutU, hutI, hutG
Xanthobacter autotrophicus Py2 braC, braD, braE, braF, braG, hutH, hutU, hutI, hutG
Xenophilus azovorans DSM 13620 aapJ, aapQ, aapM, aapP, hutH, hutU, hutI, hutF, 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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

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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