MetaPath Web Service
Manual
STEP 1. Choose a reference genome
aae=Aquifex aeolicus
afu=Archaeoglobus fulgidus
ana=Anabaena sp.
ape=Aeropyrum pernix
atc=Agrobacterium tumefaciens C58 Cereon
ath=Arabidopsis thaliana
atu=Agrobacterium tumefaciens C58 UWash
bab=Buchnera aphidicola Bp
ban=Bacillus anthracis
bas=Buchnera aphidicola Sg
bba=Bdellovibrio bacteriovorus
bbr=Bordetella bronchiseptica
bbu=Borrelia burgdorferi
bca=Bacillus cereus ATCC 10987
bce=Bacillus cereus
bfl=Blochmannia floridanus
bha=Bacillus halodurans
bja=Bradyrhizobium japonicum
blo=Bifidobacterium longum
bme=Brucella melitensis
bms=Brucella suis
bpa=Bordetella parapertussis
bpe=Bordetella pertussis
bsu=Bacillus subtilis
bth=Bacteroides thetaiotaomicron
buc=Buchnera sp.
cac=Clostridium acetobutylicum
cbu=Coxiella burnetii
cca=Chlamydophila caviae
ccr=Caulobacter crescentus
cdi=Corynebacterium diphtheriae
cef=Corynebacterium efficiens
cel=Caenorhabditis elegans
cgl=Corynebacterium glutamicum
cje=Campylobacter jejuni
cmu=Chlamydia muridarum
cpa=Chlamydophila pneumoniae AR39
cpe=Clostridium perfringens
cpj=Chlamydophila pneumoniae J138
cpn=Chlamydophila pneumoniae CWL029
cpt=Chlamydophila pneumoniae TW183
ctc=Clostridium tetani E88
cte=Chlorobium tepidum
ctr=Chlamydia trachomatis
cvi=Chromobacterium violaceum
dme=Drosophila melanogaster
dra=Deinococcus radiodurans
ecc=Escherichia coli CFT073
ece=Escherichia coli O157 EDL933
ecj=Escherichia coli K-12 W3110
eco=Escherichia coli K-12 MG1655
ecs=Escherichia coli O157 Sakai
ecu=Encephalitozoon cuniculi
efa=Enterococcus faecalis
fnu=Fusobacterium nucleatum
gsu=Geobacter sulfurreducens
gvi=Gloeobacter violaceus
hal=Halobacterium sp.
hdu=Haemophilus ducreyi
hhe=Helicobacter hepaticus
hin=Haemophilus influenzae
hpj=Helicobacter pylori J99
hpy=Helicobacter pylori 26695
hsa=Homo sapiens
lic=Leptospira interrogans Copenhageni
lil=Leptospira interrogans
lin=Listeria innocua
ljo=Lactobacillus johnsonii
lla=Lactococcus lactis
lmo=Listeria monocytogenes
lpl=Lactobacillus plantarum
mac=Methanosarcina acetivorans
mbo=Mycobacterium bovis
mga=Mycoplasma gallisepticum
mge=Mycoplasma genitalium
mja=Methanococcus jannaschii
mka=Methanopyrus kandleri
mle=Mycobacterium leprae
mlo=Mesorhizobium loti
mma=Methanosarcina mazei
mmp=Methanococcus maripaludis
mmu=Mus musculus
mmy=Mycoplasma mycoides
mpa=Mycobacterium avium paratuberculosis
mpe=Mycoplasma penetrans
mpn=Mycoplasma pneumoniae
mpu=Mycoplasma pulmonis
mtc=Mycobacterium tuberculosis CDC1551
mth=Methanobacterium thermoautotrophicum
mtu=Mycobacterium tuberculosis H37Rv
neu=Nitrosomonas europaea
nma=Neisseria meningitidis serogroup A
nme=Neisseria meningitidis serogroup B
oih=Oceanobacillus iheyensis
pab=Pyrococcus abyssi
pae=Pseudomonas aeruginosa
pai=Pyrobaculum aerophilum
pfa=Plasmodium falciparum
pfu=Pyrococcus furiosus
pgi=Porphyromonas gingivalis
pho=Pyrococcus horikoshii
plu=Photorhabdus luminescens
pma=Prochlorococcus marinus SS120
pmm=Prochlorococcus marinus MED4
pmt=Prochlorococcus marinus MIT9313
pmu=Pasteurella multocida
poy=Phytoplasma sp. onion yellows
ppu=Pseudomonas putida
pst=Pseudomonas syringae
rba=Rhodopirellula baltica
rco=Rickettsia conorii
rno=Rattus norvegicus
rpa=Rhodopseudomonas palustris CGA009
rpr=Rickettsia prowazekii
rso=Ralstonia solanacearum
sag=Streptococcus agalactiae
sam=Staphylococcus aureus MW2
san=Streptococcus agalactiae NEM316
sau=Staphylococcus aureus N315
sav=Staphylococcus aureus Mu50
sce=Saccharomyces cerevisiae
sco=Streptomyces coelicolor
sep=Staphylococcus epidermidis ATCC 12228
sfl=Shigella flexneri
sfx=Shigella flexneri 2457T
sma=Streptomyces avermitilis
sme=Sinorhizobium meliloti
smu=Streptococcus mutans
son=Shewanella oneidensis
spg=Streptococcus pyogenes M3
spm=Streptococcus pyogenes M18
spn=Streptococcus pneumoniae TIGR4
spo=Schizosaccharomyces pombe
spr=Streptococcus pneumoniae R6
sps=Streptococcus pyogenes SSI1
spy=Streptococcus pyogenes
sso=Sulfolobus solfataricus
stm=Salmonella typhimurium
sto=Sulfolobus tokodaii
stt=Salmonella typhi Ty2
sty=Salmonella typhi
syc=Synechococcus sp. PCC6301
syn=Synechocystis sp.
syw=Synechococcus sp. WH8102
tac=Thermoplasma acidophilum
tde=Treponema denticola
tel=Thermosynechococcus elongatus
tma=Thermotoga maritima
tpa=Treponema pallidum
tte=Thermoanaerobacter tengcongensis
tth=Thermus thermophilus
tvo=Thermoplasma volcanium
twh=Tropheryma whipplei
tws=Tropheryma whipplei TW08/27
uur=Ureaplasma urealyticum
vch=Vibrio cholerae
vpa=Vibrio parahaemolyticus
vvu=Vibrio vulnificus
vvy=Vibrio vulnificus YJ016
wbr=Wigglesworthia brevipalpis
wol=Wolbachia wMel
wsu=Wolinella succinogenes
xac=Xanthomonas axonopodis
xcc=Xanthomonas campestris
xfa=Xylella fastidiosa
xft=Xylella fastidiosa Temecula1
ype=Yersinia pestis
ypk=Yersinia pestis KIM
ypm=Yersinia pestis Mediaevails
STEP 2. Choose interesting metabolic pathway(s)
Carbohydrate Metabolism
no=No Select
00010=Glycolysis / Gluconeogenesis
00020=Citrate cycle (TCA cycle)
00030=Pentose phosphate pathway
00040=Pentose and glucuronate interconversions
00051=Fructose and mannose metabolism
00052=Galactose metabolism
00053=Ascorbate and aldarate metabolism
00620=Pyruvate metabolism
00630=Glyoxylate and dicarboxylate metabolism
00640=Propanoate metabolism
00650=Butanoate metabolism
00660=C5-Branched dibasic acid metabolism
00031=Inositol metabolism
Energy Metabolism
no=No Select
00190=Oxidative phosphorylation
00193=ATP synthesis
00195=Photosynthesis
00710=Carbon fixation
00720=Reductive carboxylate cycle (CO2 fixation)
00680=Methane metabolism
00910=Nitrogen metabolism
00920=Sulfur metabolism
Lipid Metabolism
no=No Select
00061=Fatty acid biosynthesis (path 1)
00062=Fatty acid biosynthesis (path 2)
00071=Fatty acid metabolism
00072=Synthesis and degradation of ketone bodies
00120=Bile acid biosynthesis
00140=C21-Steroid hormone metabolism
00150=Androgen and estrogen metabolism
Nucleotide Metabolism
no=No Select
00230=Purine metabolism
00240=Pyrimidine metabolism
00250=Nucleotide sugars metabolism
Amino Acid Metabolism
no=No Select
00251=Glutamate metabolism
00252=Alanine and aspartate metabolism
00260=Glycine, serine and threonine metabolism
00271=Methionine metabolism
00272=Cysteine metabolism
00280=Valine, leucine and isoleucine degradation
00290=Valine, leucine and isoleucine biosynthesis
00300=Lysine biosynthesis
00310=ysine degradation
00330=Lysine degradation
00330=Arginine and proline metabolism
00340=Histidine metabolism
00350=Tyrosine metabolism
00360=Phenylalanine metabolism
00380=Tryptophan metabolism
00400=Phenylalanine, tyrosine and tryptophan biosynthesis
00220=Urea cycle and metabolism of amino groups
Metabolism of Other Amino Acid
no=No Select
00410=beta-Alanine metabolism
00430=Taurine and hypotaurine metabolism
00440=Aminophosphonate metabolism
00450=Selenoamino acid metabolism
00460=Cyanoamino acid metabolism
00471=D-Glutamine and D-glutamate metabolism
00472=D-Arginine and D-ornithine metabolism
00473=D-Alanine metabolism
00480=Glutathione metabolism
Metabolism of Complex Carbohydrates
no=No Select
00500=Starch and sucrose metabolism
00510=N-Glycans biosynthesis
00512=O-Glycans biosynthesis
00511=N-Glycan degradation
00530=Aminosugars metabolism
00540=Lipopolysaccharide biosynthesis
00550=Peptidoglycan biosynthesis
00531=Glycosaminoglycan degradation
00532=Chondroitin / heparan sulfate biosynthesis
00533=Keratan sulfate biosynthesis
Metabolism of Complex Lipids
no=No Select
00561=Glycerolipid metabolism
00563=Glycosylphosphatidylinositol(GPI)-anchor biosynthesis
00562=Inositol phosphate metabolism
00570=Sphingophospholipid biosynthesis
00580=Phospholipid degradation
00600=Sphingoglycolipid metabolism
0060=Blood group glycolipid biosynthesis - lactoseries
00602=Blood group glycolipid biosynthesis - neo-lactoseries
00603=Globoside metabolism
00604=Ganglioside biosynthesis
00590=Prostaglandin and leukotriene metabolism
Metabolism of Cofactors and Vitamins
no=No Select
00730=Thiamine metabolism
00740=Riboflavin metabolism
00750=Vitamin B6 metabolism
00100=Sterol, vitamin K, vitamin E and cartenoids biosynthesis
00760=Nicotinate and nicotinamide metabolism
00770=Pantothenate and CoA biosynthesis
00780=Biotin metabolism
00790=Folate biosynthesis
00670=One carbon pool by folate
00830=Retinol metabolism
00860=Porphyrin and chlorophyll metabolism
00130=Ubiquinone biosynthesis
Biosynthesis of Secondary Metabolites
no=No Select
00900=Terpenoid biosynthesis
00904=Diterpenoid biosynthesis
00902=Monoterpenoid biosynthesis
00903=Limonene and pinene degradation
00901=Indole and ipecac alkaloid biosynthesis
00940=Flavonoids, stilbene and lignin biosynthesis
00950=Alkaloid biosynthesis I
00960=Alkaloid biosynthesis II
00311=Penicillins and cephalosporins biosynthesis
00312=beta-Lactam resistance
00521=Streptomycin biosynthesis
00522=Erythromycin biosynthesis
00253=Tetracycline biosynthesis
00331=Clavulanic acid biosynthesis
00231=Puromycin biosynthesis
Biodegradation of Xenobiotics
no=No Select
00930=Caprolactam degradation
00621=Biphenyl degradation
00622=Toluene and xylene degradation
00361=gamma-Hexachlorocyclohexane degradation
00641=3-Chloroacrylic acid degradation
00351=1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation
00623=2,4-Dichlorobenzoate degradation
00631=1,2-Dichloroethane degradation
00625=Tetrachloroethene degradation
00643=Styrene degradation
00627=1,4-Dichlorobenzene degradation
00626=Nitrobenzene degradation
00642=Ethylbenzene degradation
00628=Fluorene degradation
00629=Carbazole degradation
00632=Benzoate degradation via CoA ligation
00362=Benzoate degradation via hydroxylation
00791=Atrazine degradation
OR cut and paste your FASTA format protein sequences
Paste your FASTA format protein sequences
Sample Sequence
or upload protein sequence file
Step 3. Choose interested genomes from the following list.
Archaea
Crenarchaeota
Thermoprotei
Cenarchaeales
Desulfurococcales
marine archaeal group 1
Sulfolobales
Thermoproteales
Euryarchaeota
Archaeoglobi
Archaeoglobales
Halobacteria
Halobacteriales
Methanobacteria
Methanobacteriales
Methanococci
Methanococcales
Methanomicrobia
Methanomicrobiales
Methanosarcinales
Methanopyri
Methanopyrales
Thermococci
Thermococcales
Thermoplasmata
Thermoplasmatales
Bacteria
Acidobacteria
Acidobacteriales
Acidobacteriaceae
Solibacteres
Solibacterales
Actinobacteria
Actinobacteridae
Actinomycetales
Bifidobacteriales
Rubrobacteridae
Rubrobacterales
Aquificae
Aquificales
Aquificaceae
Hydrogenothermaceae
Bacteroidetes
Bacteroidetes (class)
Bacteroidales
Flavobacteria
Flavobacteriales
Sphingobacteria
Sphingobacteriales
Chlamydiae
Chlamydiales
Chlamydiaceae
Parachlamydiaceae
Chlorobi
Chlorobia
Chlorobiales
Chloroflexi
Chloroflexales
Chloroflexaceae
Dehalococcoidetes
Dehalococcoides
Herpetosiphonales
Herpetosiphonaceae
Cyanobacteria
Chroococcales
Cyanothece
Microcystis
Synechococcus
Synechocystis
Gloeobacteria
Gloeobacterales
Nostocales
Nostocaceae
Oscillatoriales
Trichodesmium
Prochlorophytes
Prochlorococcaceae
Deinococcus-Thermus
Deinococci
Deinococcales
Thermales
Firmicutes
Bacillales
Bacillaceae
Bacillales Family XII. Incertae Sedis
Listeriaceae
Planococcaceae
Staphylococcus
Clostridia
Clostridiales
Natranaerobiales
Thermoanaerobacterales
Lactobacillales
Enterococcaceae
Lactobacillaceae
Leuconostoc
Oenococcus
Streptococcaceae
Fusobacteria
Fusobacterales
Fusobacteriaceae
Planctomycetes
Planctomycetacia
Planctomycetales
Proteobacteria
Alphaproteobacteria
Caulobacterales
Rhizobiales
Rhodobacterales
Rhodospirillales
Rickettsiales
Sphingomonadales
Betaproteobacteria
Burkholderiales
Hydrogenophilales
Methylophilales
Neisseriales
Nitrosomonadales
Rhodocyclales
Deltaproteobacteria
Bdellovibrionales
Desulfobacterales
Desulfovibrionales
Desulfuromonadales
Myxococcales
Syntrophobacterales
Epsilonproteobacteria
Campylobacterales
Nitratiruptor
Sulfurovum
Gammaproteobacteria
Aeromonadales
Alteromonadales
Candidatus Baumannia
Candidatus Carsonella
Cardiobacteriales
Chromatiales
Enterobacteriales
Legionellales
Methylococcales
Oceanospirillales
Pasteurellales
Pseudomonadales
sulfur-oxidizing symbionts
Thiotrichales
Vibrionales
Xanthomonadales
Spirochaetes
Spirochaetales
Leptospiraceae
Spirochaetaceae
Tenericutes
Mollicutes
Acholeplasmatales
Entomoplasmatales
Mycoplasmataceae
Thermotogae
Thermotogales
Thermotogaceae
Verrucomicrobia
Opitutae
Opitutales
unclassified Verrucomicrobia
Methylacidiphilum
Verrucomicrobiae
Verrucomicrobiales
Eukaryota
Alveolata
Apicomplexa
Aconoidasida
Coccidia
Ciliophora
Intramacronucleata
Choanoflagellida
Codonosigidae
Monosiga
Cryptophyta
Cryptomonadaceae
Guillardia
Euglenozoa
Kinetoplastida
Trypanosomatidae
Fungi
Dikarya
Ascomycota
Basidiomycota
Microsporidia
Unikaryonidae
Metazoa
Arthropoda
Hexapoda
Chordata
Craniata
Cnidaria
Anthozoa
Nematoda
Chromadorea
Mycetozoa
Dictyosteliida
Dictyostelium
Viridiplantae
Chlorophyta
Prasinophyceae
Streptophyta
Embryophyta
Kwangmin Choi @ School of Informatics, Indiana University, Bloomington, IN, USA