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lozuponelab / AMON

Annotation of Metabolite Origin via Networks: A tool for predicting putative metabolite origins for microbes or between microbes and host with or without metabolomics data
MIT License
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Format of KEGG input files? #3

Closed deborah-chasman closed 4 years ago

deborah-chasman commented 5 years ago

Thank you very much for making your program available! It looks like the user would be able to input their own reaction and pathway files instead of KEGG's. Would you be able to share the expected file formats for those for use in AMON?

kthurimella commented 5 years ago

Hi @deborah-chasman that's a feature that we're working on. Not sure of an ETA but will ping here when it's deployed!

deborah-chasman commented 5 years ago

Great to hear it. Thanks for your response!

kthurimella commented 4 years ago

Hi @deborah-chasman I've copied below what each file should look like:

KO file: ENTRY K00001 KO NAME E1.1.1.1, adh DEFINITION alcohol dehydrogenase [EC:1.1.1.1] PATHWAY ko00010 Glycolysis / Gluconeogenesis ko00071 Fatty acid metabolism ko00350 Tyrosine metabolism ko00625 Chloroalkane and chloroalkene degradation ko00626 Naphthalene degradation ko00830 Retinol metabolism ko00980 Metabolism of xenobiotics by cytochrome P450 ko00982 Drug metabolism - cytochrome P450 CLASS Metabolism; Carbohydrate Metabolism; Glycolysis / Gluconeogenesis [PATH:ko00010] Metabolism; Lipid Metabolism; Fatty acid metabolism [PATH:ko00071] Metabolism; Amino Acid Metabolism; Tyrosine metabolism [PATH:ko00350] Metabolism; Metabolism of Cofactors and Vitamins; Retinol metabolism [PATH:ko00830] Metabolism; Xenobiotics Biodegradation and Metabolism; Chloroalkane and chloroalkene degradation [PATH:ko00625] Metabolism; Xenobiotics Biodegradation and Metabolism; Naphthalene degradation [PATH:ko00626] Metabolism; Xenobiotics Biodegradation and Metabolism; Metabolism of xenobiotics by cytochrome P450 [PATH:ko00980] Metabolism; Xenobiotics Biodegradation and Metabolism; Drug metabolism - cytochrome P450 [PATH:ko00982] DBLINKS RN: R00623 R00754 R02124 R04805 R04880 R05233 R05234 R06917 R06927 R07105 R08281 R08306 R08310 COG: COG0604 COG1062 COG1064 COG1454 GO: 0004022 0004023 0004024 0004025 GENES DME: Dmel_CG3481(Adh) DPO: Dpse_GA17214(Dpse_Adh) DAN: Dana_GF14888(Dana_Adh) DER: Dere_GG25120(Dere_Adh) DPE: Dper_GL25993(Dper_Adh) DSE: Dsec_GM15656(Dsec_Adh) DSI: Dsim_GD23968(Dsim_Adh) DWI: Dwil_GK18290(Dwil_Adh) DYA: Dyak_GE19037(Dyak_Adh) DGR: Dgri_GH13025(Dgri_Adh) DMO: Dmoj_GI17643(Dmoj_Adh2) DVI: Dvir_GJ18208(Dvir_Adh1) ATH: AT1G32780 AT1G64710 AT1G77120(ADH1) AT5G24760 POP: POPTR_1075155 POPTR_176894 POPTR_232962 POPTR_294427 POPTR_558388 POPTR_558390 POPTR_562436 POPTR_718546 POPTR_782655 POPTR_816232 POPTR_827290 POPTR_832230 RCU: RCOM_0138590 RCOM_0138830 RCOM_0236080 RCOM_1222910 RCOM_1313890 VVI: 100232853(ADH1) 100232854(ADH2) 100233102(ADH3) 100250633 100254635 100255814 100256495 100267821 OSA: 4330090 4348152 4350053 4350054 4350055 SBI: SORBI_01g025570 SORBI_01g025580 SORBI_04g027090 SORBI_05g009350 SORBI_05g009360 ZMA: 100272357 100272578(cl33662_1) 542363(adh1) 542364(adh2) KLA: KLLA0B00451g DDI: DDB_G0274085 PTI: PHATRDRAFT_12757(ADH_2) TPS: THAPSDRAFT_1394(ADH1) STY: STY3830 STT: t3575 STM: STM4044 SPT: SPA3887 SEK: SSPA3615 SEI: SPC_4148 SEC: SC3934(adh2) SET: SEN3835 SES: SARI_03603 ENT: Ent638_4074 KPN: KPN_04206 KPE: KPK_5475 KPU: KP1_0065 CKO: CKO_03104 PAM: PANA_3008(yphC) XCV: XCV2333 XAC: XAC2826 XOO: XOO1535 XOM: XOO_1325 XOO_1423 XOO_4231 XOP: PXO_04785 VVY: VV2175 PFS: PFLU4115 PMY: Pmen_0381 Pmen_2529 PSA: PST_0312 PST_2239 PBA: PSEBR_a3675 PAR: Psyc_0011 Psyc_1042 PCR: Pcryo_0018 Pcryo_1428 ACI: ACIAD1950 ACIAD2929 ACB: A1S_2053 A1S_2702 ABM: ABSDF0756 ABSDF2205 ABY: ABAYE0763 ABAYE1522 p2ABAYE0004 ABC: ACICU_02973 ABN: AB57_3141 ABB: ABBFA_000747 SON: SO_A0164 SSE: Ssed_2530 CPS: CPS_1431 PHA: PSHAa1488(yhdH) PAT: Patl_0425 MAQ: Maqu_1048 Maqu_1713 PIN: Ping_1955 TCX: Tcr_0211 HHA: Hhal_0140 HCH: HCH_05054 CSA: Csal_1091 ABO: ABO_0061 ABO_0817 ABO_1231(adhA) ABO_1352(adhB) ABO_2483 MMW: Mmwyl1_0234 Mmwyl1_2290 AHA: AHA_1331 ASA: ASA_2860 GPB: HDN1F_20690 NME: NMB1395 NGO: NGO0711 CVI: CV_0808 RSO: RS00889(RSp0430) REU: Reut_C6089 Reut_C6321 REH: H16_A3330 H16_B0517 H16_B1699 H16_B1745 RME: Rmet_4943 Rmet_5102 BVI: Bcep1808_1701 Bcep1808_4603 Bcep1808_6708 BUR: Bcep18194_B2077 Bcep18194_B2551 Bcep18194_C6773 BCN: Bcen_4360 Bcen_4742 BCH: Bcen2424_3424 Bcen2424_4006 BCM: Bcenmc03_3517 Bcenmc03_4093 BCJ: BCAM1109 BAM: Bamb_3412 BAC: BamMC406_1680 BamMC406_3919 BamMC406_6148 BMU: Bmul_1502 Bmul_4573 BMJ: BMULJ_01740(adh) BMULJ_03937(adh) BXE: Bxe_A1730 Bxe_B1066 Bxe_B2357 Bxe_B2518 Bxe_C1266 BPY: Bphyt_4061 BGL: bglu_2g14520 bglu_2g14850 BRH: RBRH_00012 BGD: bgla_2g10430 BPE: BP0777 BP2601 BPA: BPP2723 BBR: BB0342 BB2775 BPT: Bpet3517(attL) PUT: PT7_1590 PNA: Pnap_1291 AJS: Ajs_1375 VEI: Veis_3295 DAC: Daci_0183 HAR: HEAR0089 HSE: Hsero_2795(adhC2) NEU: NE0620 EBA: p2A334 AZO: azo1971 azo2700 azo3181 azo3317(yhdH) DAR: Daro_1348 TBD: Tbd_1767 GUR: Gura_3574 PCA: Pcar_1246 Pcar_2506 PPD: Ppro_1924 DVU: DVU2396 DVU2885 DVU2905 DVL: Dvul_0460 Dvul_0480 Dvul_0834 DVM: DvMF_1315 DDE: Dde_1164 Dde_3062 Dde_3126 Dde_3534 DSA: Desal_1318 DPS: DP0955 DOL: Dole_2290 DAL: Dalk_4478 DAT: HRM2_02030(adh3) AFW: Anae109_2555 PUB: SAR11_0529 SAR11_1244(yhdH) SAR11_1287 MLO: mlr1136 mlr1178 MCI: Mesci_3451 MES: Meso_1317 Meso_1868 PLA: Plav_3345 SME: SMc00105 SMc03929 SMc04270 SMD: Smed_0584 Smed_2128 Smed_2747 RHI: NGR_b16300 NGR_c07250 NGR_c18040 NGR_c25690 ATU: Atu1595 Atu2151(adh) Atu4289(adhC) Atu5240(adhP) ARA: Arad_1406 Arad_2774 AVI: Avi_2036 RET: RHE_CH00460(ypch00170) RHE_CH01189(ypch00392) RHE_CH02474(ypch00832) RHE_CH02884(ypch00995) RHE_PB00029(ypb00013) RHE_PD00107(adhE) RHE_PF00203(ypf00099) RHE_PF00365(ypf00190) REC: RHECIAT_CH0001280 RHECIAT_CH0002313 RHECIAT_CH0002576 RHECIAT_PB0000128(adhE) RLE: RL1325 RL2813 RL3344 pRL100135 pRL120042 pRL120182 pRL120602 pRL90098 RLT: Rleg2_0831 Rleg2_2113 RLG: Rleg_0950 BME: BMEI1114 BMEII0553 BMEII0867 BMI: BMEA_A0890 BMEA_B0380 BMF: BAB1_0871 BAB2_0506 BAB2_0821 BMB: BruAb1_0864 BruAb2_0498 BruAb2_0800 BMC: BAbS19_I08120 BAbS19_II07600 BMS: BR0852 BRA0401 BRA0734 BMT: BSUIS_A0890 BSUIS_B0404 BOV: BOV_0844 BOV_A0344 BCS: BCAN_A0865 BCAN_B0404 BMR: BMI_II398 OAN: Oant_3883 BJA: bll4101 blr2780 blr4874 BRA: BRADO0250 BRADO2457 BRADO3321 BRADO4151 BRADO6611 BBT: BBta_2803 BBta_3825 BBta_4528 RPA: RPA2018 RPA3067 RPA3655 RPB: RPB_0946 RPB_1148 RPB_2474 RPC: RPC_0105 RPC_2107 RPC_2307 RPC_2974 RPD: RPD_1250 RPD_2086 RPD_2972 RPD_3495 RPE: RPE_0587 RPE_1228 RPE_2019 RPE_3298 RPT: Rpal_3477 NHA: Nham_2346 BQU: BQ05280(adh) BBK: BARBAKC583_0618 BTR: Btr_1329(adh) XAU: Xaut_2610 BSB: Bresu_3195 SIL: SPO1889 SPO3399 SIT: TM1040_0040 RSP: RSP_1824(adh) RSP_3537 RSH: Rsph17029_0472 RSQ: Rsph17025_3061 RSK: RSKD131_0130 JAN: Jann_3964 DSH: Dshi_1078 MMR: Mmar10_2836 SWI: Swit_3018 SJP: SJA_C2-05100(adh) ACR: Acry_0843 GDJ: Gdia_2808 AZL: AZL_c00300(adh) BAN: BA_2222 BA_2588 BA_3566 BAR: GBAA_2222 GBAA_2588 GBAA_3566 BAT: BAS2066 BAS2412 BAS3306 BAH: BAMEG_1066 BAMEG_2009 BAI: BAA_2648 BAA_3595 BCE: BC0802 BC2529 BCA: BCE_0198 BCE_0742 BCE_0877 BCE_1099 BCE_2252 BCE_2604 BCE_3521 BCZ: BCZK0168 BCZK0681 BCZK2005(gbsB) BCZK2331(adhB) BCZK3221 BCR: BCAH187_A2642 BCAH187_A3528 BCB: BCB4264_A2561 BCB4264_A3507 BCU: BCAH820_2606 BCAH820_3522 BCG: BCG9842_B1741 BCG9842_B2765 BCQ: BCQ_2464(adhB) BCQ_3303 BCX: BCA_3586 BTK: BT9727_0165 BT9727_2006(gbsB) BT9727_2367(adhB) BT9727_3273 BTL: BALH_0175 BALH_0616 BALH_0714 BALH_1985 BALH_3158 BLD: BLi03502 OIH: OB2738 OB2801 GTN: GTNG_1754 SAC: SACOL0237 SACOL0241 SACOL2177 SACOL2178 SACOL2367 SAX: USA300HOU_0059(adhC) SAA: SAUSA300_0055 SAUSA300_0250 SAUSA300_2147 SAB: SAB1296c SEP: SE2098 SER: SERP0197 SERP1785 SERP1786 SERP1962 SERP2112 SERP2469 SHA: SH0373(adhC) SH0522 SSP: SSP0237 SCA: Sca_2269 Sca_2372(adhC) ESI: Exig_1536 AAC: Aaci_0920 LLA: L190278(ypjA) LLC: LACR_1641 LLM: llmg_0955 SPY: SPy_1111 SPZ: M5005_Spy_0834 SPM: spyM18_1073 SPG: SpyM3_0772 SPS: SPs0972 SPH: MGAS10270_Spy0950 SPI: MGAS10750_Spy0985 SPJ: MGAS2096_Spy0043 MGAS2096_Spy0044 MGAS2096_Spy0909 SPK: MGAS9429_Spy0953 SPF: SpyM50954 SPA: M6_Spy0832 M6_Spy0833 SPB: M28_Spy0811 SOZ: Spy49_0865c SPN: SP_1855 SP_2055 SPD: SPD_1636 SPD_1865 SPR: spr1670(adhB) spr1866(adh) SPW: SPCG_1829(adhB) SPCG_2022(adh) SPX: SPG_1970 SNE: SPN23F_18700 SPN23F_20780 SPV: SPH_2210 SNM: SP70585_2143 SJJ: SPJ_1760 SPJ_2061 SPP: SPP_2093 SNT: SPT_2050 SNC: HMPREF0837_10051(adh) SNB: SP670_2194 SNP: SPAP_2081 SAG: SAG0428 SAN: gbs1684 SMU: SMU.1867c SMC: SmuNN2025_0275 STC: str0882 str0936(adhB) STL: stu0882 stu0936(adhB) STE: STER_0949 SSA: SSA_0921(adhB) SSU: SSU05_1388 SSV: SSU98_1402 SGO: SGO_1774 SEQ: SZO_00450 SEZ: Sez_0045(adh) SEU: SEQ_0045 SUB: SUB0101 SUB1076 LPL: lp_1665(adh1) lp_2873(adh2) LJO: LJ1120 LAC: LBA1114 LSA: LSA0258 LSA0925(adh) LSA1364 LBR: LVIS_0869 LCA: LSEI_2787 LCB: LCABL_24040(adh2) LRE: Lreu_1589 LRF: LAR_1489 LFE: LAF_0169 CDF: CD2843 CKL: CKL_2967 CKL_3000 STH: STH2049 AFN: Acfer_0053 DSY: DSY0623 DSY2755 DHD: Dhaf_3921 SGY: Sgly_1635 EEL: EUBELI_01490 TMR: Tmar_1804 TTE: TTE0696(eutG) MTA: Moth_1911 CSC: Csac_0711 ATE: Athe_2244 TOC: Toce_0214 TTM: Tthe_0472 Tthe_0864 HAS: Halsa_1810 MAA: MAG_2740 MAG_4280(adhT) MTU: Rv0162c(adhE1) Rv1530(adh) MTC: MT0171 MT1581 MRA: MRA_0170(adhE1) MRA_1542(adh) MTF: TBFG_10163 TBFG_11563 MTB: TBMG_00163(TBMG_00163.1) TBMG_02447(TBMG_02447.1) MBO: Mb0167c(adhE1) Mb1557(adh) MBB: BCG_0198c(adhE1) BCG_1582(adh) MBT: JTY_0168(adhE1) JTY_1557(adh) MPA: MAP1613c(adhA_2) MAP3596c(adhE) MAV: MAV_1614 MAV_2812 MAV_5022 MSM: MSMEG_0127 MSMEG_0590(rhaD) MSMEG_1138 MSMEG_2048 MSMEG_3464 MSMEG_4167 MSMEG_6242 MSMEG_6833 MSMEG_6834 MUL: MUL_2965(adhC) MVA: Mvan_0669 MGI: Mflv_0236 Mflv_4626 MAB: MAB_0983c MAB_2041c MMC: Mmcs_0111 Mmcs_0137 Mmcs_1713 Mmcs_3225 MKM: Mkms_0120 Mkms_0513 Mkms_1759 Mkms_3287 MJL: Mjls_0101 Mjls_0499 Mjls_1690 Mjls_3236 MSP: Mspyr1_05400 MMI: MMAR_0405(adhE) MMAR_2782(adhC) MMAR_3163 CGL: NCgl0219(cgl0222) NCgl2449(cgl2537) CGB: cg0273 CAR: cauri_0635(adhC) NFA: nfa35620 nfa38820 RHA: RHA1_ro00325(adh1) RHA1_ro00525 RHA1_ro01205 RHA1_ro02497 RHA1_ro04547 RHA1_ro05321 RHA1_ro06735 RHA1_ro08443 RHA1_ro08965(adh2) RHA1_ro11170(adhB) RER: RER_26460 ROP: ROP_33600(adh) ROP_67230 TPR: Tpau_3448 SRT: Srot_0472 SMA: SAV_1357(adhA2) SAV_5335 SAV_7169 SCB: SCAB_58841 TWH: TWT326(adh) TWS: TW445(adh) CMI: CMM_2126 CMS: CMS_1091 MTS: MTES_1651 ART: Arth_1320 AAU: AAur_1148 AAur_1866 AAur_3716(rhaD) AAur_pTC20218 AAI: AARI_27050 KRH: KRH_02680 KRH_12360(adh) BCV: Bcav_3663 BFA: Bfae_07850 KSE: Ksed_07750 Ksed_22500 CFL: Cfla_2836 ICA: Intca_0899 KFL: Kfla_1230 Kfla_7026 SRO: Sros_0372 Sros_4357 Sros_6280 FRI: FraEuI1c_4356 FAL: FRAAL0199 FRAAL3122 FRAAL5274(adhC1) NML: Namu_4805 GOB: Gobs_4903 KRA: Krad_2496 Krad_4297 SEN: SACE_1535 SACE_2944 SACE_2945 SACE_3519(adh) SACE_4085(adh) SACE_4163(adh1) SACE_4852(adh1) AMD: AMED_7375(adh) AMED_8391(adh) PDX: Psed_5866 AMI: Amir_5014 STP: Strop_1166 Strop_2723 MAU: Micau_2032 SNA: Snas_0210 BLO: BL1090 BLJ: BLD_0844(tdh1) BLN: Blon_1915 BLF: BLIF_0541 BLL: BLJ_0603 BLB: BBMN68_838(tdh1) BLM: BLLJ_0522 BLA: BLA_0116(adh) BLC: Balac_0125 BLT: Balat_0125 BDE: BDP_1109(adh) BBI: BBIF_0901 BBP: BBPR_0945(adh) RXY: Rxyl_3153 ELE: Elen_2478 SSM: Spirs_1442 LIL: LA_0325(adhP) LA_1616 LA_2361(tdh) LA_2629 LIC: LIC10282 LIC11357 LIC11586 LIC12166 BHY: BHWA1_01827 BRM: Bmur_1381 BPO: BP951000_0786 ABA: Acid345_3044 Acid345_4584 ACM: AciX9_3151 SUS: Acid_1558 BFR: BF1290 BVU: BVU_0760 SRU: SRU_0710 SRU_2306 SRM: SRM_00890(adh) HHY: Halhy_5589 CHU: CHU_1246(adhP) GFO: GFO_1574 FSU: Fisuc_1458 AMU: Amuc_1911 GAU: GAU_2900 RBA: RB10805 RB13260(yhdH) RB4131(yjjN) RB5320 RB5856(adh) TAI: Taci_1643 SYG: sync_2669 CYA: CYA_0992 CYB: CYB_0338 GVI: gll2836 gll4111 CCH: Cag_0888 Cag_1128 Cag_1710 PVI: Cvib_0926 Cvib_0955 PAA: Paes_1246 RRS: RoseRS_3921 RCA: Rcas_3224 CAU: Caur_1113 CAG: Cagg_1718 CHL: Chy400_1218 HAU: Haur_4348 DDR: Deide_03550(adh) TRA: Trad_0212 TTH: TTC1572 AAE: aq_1240(adh2) HTH: HTH_0308 TAL: Thal_0399 TMA: TM0111 TM0920 TPT: Tpet_0007 Tpet_0813 TLE: Tlet_0180 TRQ: TRQ2_0836 TNA: CTN_0580 TNP: Tnap_0741 KOL: Kole_1524 DTH: DICTH_0069 DTU: Dtur_0334 DDF: DEFDS_0763 MMP: MMP0802 MBA: Mbar_A0784 HAL: VNG2617G(adh2) HMA: pNG7022(adh1) pNG7101(adh8) pNG7103(adh7) pNG7278(adh12) pNG7289(adh6) pNG7314(adhC) pNG7351(adh13) rrnAC0012(adh11) rrnAC0191(adh3) rrnAC1300(adh9) rrnAC1975(adh5) rrnAC2172(adh14) rrnAC3506(adh2) HWA: HQ1124A(adh) HQ1729A(adh) HQ2366A(adh) NPH: NP1260A(adh) HLA: Hlac_1808 HTU: Htur_2363 Htur_2867 NMG: Nmag_0345 Nmag_3786 HVO: HVO_2428(adh1) HJE: HacjB3_09660 HBO: Hbor_35490 Hbor_37240 TAC: Ta0832m TVO: TVN0396 TVN1284 PTO: PTO0846 PHO: PH0743 PFU: PF0075 PF0608 TKO: TK1008 TK1569 APE: APE_1245.1 APE_1557.1 APE_1963.1 SMR: Smar_0045 Smar_0696 SSO: SSO1220(adh-3) SSO2494(adh-8) SSO2536(adh-10) SSO2878(adh-13) STO: ST0053 ST0075 ST2577 SAI: Saci_1115(adh) Saci_2205 Saci_2224(adh) SID: M164_0412 SIN: YN1551_2663 MSE: Msed_0398 Msed_0464 PAI: PAE2051 PAE2332 PAE2931 PIS: Pisl_0639 Pisl_1601 Pisl_1949 PCL: Pcal_1581 PAS: Pars_0547 Pars_1545 TPE: Tpen_1006 Tpen_1516 ///

Compound File: ENTRY C00004 Compound NAME NADH; DPNH; Reduced nicotinamide adenine dinucleotide FORMULA C21H29N7O14P2 EXACT_MASS 665.1248 MOL_WEIGHT 665.441 REACTION R00023 R00090 R00091 R00092 R00093 R00094 R00095 R00097 R00099 R00100 R00101 R00105 R00112 R00129 R00143 R00145 R00203 R00209 R00214 R00215 R00228 R00243 R00245 R00281 R00286 R00300 R00342 R00365 R00368 R00384 R00396 R00398 R00402 R00421 R00445 R00446 R00501 R00519 R00538 R00562 R00581 R00604 R00605 R00623 R00624 R00631 R00675 R00688 R00700 R00703 R00704 R00705 R00707 R00709 R00710 R00713 R00715 R00717 R00732 R00754 R00758 R00787 R00794 R00812 R00813 R00818 R00823 R00842 R00868 R00875 R00880 R00892 R00904 R00906 R00922 R00935 R00936 R00937 R00977 R00994 R01000 R01033 R01034 R01036 R01061 R01088 R01093 R01094 R01130 R01142 R01158 R01163 R01171 R01172 R01183 R01202 R01210 R01211 R01218 R01221 R01246 R01248 R01258 R01277 R01293 R01296 R01297 R01308 R01333 R01337 R01361 R01370 R01388 R01403 R01414 R01419 R01426 R01429 R01434 R01446 R01451 R01465 R01486 R01487 R01505 R01513 R01520 R01524 R01542 R01574 R01604 R01608 R01629 R01633 R01636 R01644 R01651 R01681 R01683 R01689 R01698 R01704 R01707 R01728 R01735 R01738 R01745 R01749 R01752 R01757 R01758 R01763 R01768 R01773 R01778 R01781 R01793 R01825 R01836 R01837 R01869 R01872 R01895 R01896 R01903 R01921 R01932 R01933 R01934 R01937 R01971 R01975 R01981 R01998 R02000 R02032 R02039 R02047 R02081 R02103 R02123 R02124 R02163 R02196 R02201 R02207 R02216 R02223 R02229 R02235 R02246 R02252 R02257 R02258 R02313 R02343 R02344 R02347 R02352 R02354 R02377 R02383 R02391 R02395 R02401 R02434 R02441 R02450 R02454 R02455 R02462 R02471 R02476 R02492 R02499 R02514 R02515 R02527 R02531 R02536 R02544 R02545 R02549 R02553 R02555 R02559 R02561 R02565 R02580 R02589 R02611 R02618 R02637 R02640 R02651 R02655 R02678 R02679 R02683 R02695 R02698 R02703 R02762 R02766 R02792 R02819 R02823 R02830 R02834 R02840 R02847 R02855 R02878 R02896 R02928 R02935 R02940 R02941 R02944 R02945 R02946 R02957 R02964 R02968 R02969 R02988 R02993 R02994 R03012 R03021 R03022 R03023 R03043 R03048 R03080 R03082 R03088 R03102 R03104 R03119 R03169 R03171 R03176 R03177 R03191 R03198 R03226 R03251 R03261 R03278 R03279 R03283 R03290 R03291 R03299 R03300 R03306 R03310 R03317 R03327 R03336 R03337 R03349 R03369 R03373 R03381 R03385 R03391 R03396 R03397 R03406 R03431 R03439 R03475 R03476 R03497 R03506 R03507 R03543 R03544 R03559 R03577 R03582 R03584 R03591 R03614 R03630 R03637 R03643 R03707 R03709 R03732 R03733 R03745 R03759 R03761 R03763 R03787 R03790 R03792 R03815 R03826 R03863 R03869 R03882 R03886 R03889 R03913 R03942 R03945 R03947 R03960 R03963 R03964 R03998 R04046 R04049 R04065 R04066 R04088 R04115 R04123 R04130 R04139 R04142 R04151 R04163 R04185 R04198 R04200 R04203 R04210 R04228 R04236 R04263 R04278 R04304 R04307 R04309 R04330 R04339 R04375 R04412 R04418 R04426 R04429 R04444 R04483 R04501 R04506 R04517 R04556 R04598 R04600 R04678 R04681 R04687 R04724 R04737 R04739 R04741 R04743 R04745 R04748 R04805 R04810 R04812 R04818 R04824 R04829 R04831 R04832 R04834 R04835 R04837 R04842 R04844 R04845 R04847 R04849 R04862 R04876 R04880 R04882 R04888 R04891 R04903 R04916 R04955 R04958 R04961 R04966 R04969 R04996 R05049 R05050 R05051 R05066 R05119 R05147 R05148 R05154 R05156 R05157 R05158 R05190 R05217 R05232 R05233 R05234 R05235 R05236 R05239 R05240 R05241 R05243 R05247 R05261 R05263 R05266 R05271 R05272 R05273 R05274 R05275 R05281 R05282 R05283 R05286 R05288 R05290 R05292 R05294 R05305 R05307 R05309 R05310 R05311 R05312 R05313 R05314 R05315 R05321 R05322 R05347 R05348 R05349 R05351 R05353 R05354 R05355 R05395 R05397 R05399 R05414 R05417 R05418 R05422 R05423 R05425 R05426 R05428 R05429 R05430 R05431 R05434 R05435 R05437 R05439 R05440 R05442 R05443 R05444 R05446 R05447 R05448 R05449 R05450 R05487 R05515 R05537 R05571 R05575 R05581 R05582 R05604 R05607 R05621 R05623 R05632 R05643 R05649 R05653 R05654 R05655 R05665 R05668 R05678 R05679 R05681 R05683 R05685 R05689 R05690 R05693 R05699 R05700 R05705 R05715 R05724 R05729 R05730 R05733 R05734 R05746 R05831 R05837 R05843 R05875 R06117 R06180 R06289 R06357 R06366 R06376 R06377 R06378 R06379 R06382 R06383 R06384 R06385 R06398 R06399 R06406 R06407 R06408 R06413 R06594 R06621 R06782 R06783 R06784 R06785 R06786 R06787 R06831 R06832 R06847 R06848 R06856 R06857 R06883 R06884 R06888 R06891 R06894 R06909 R06910 R06914 R06915 R06916 R06917 R06918 R06919 R06926 R06927 R06928 R06930 R06931 R06935 R06936 R06937 R06939 R06941 R06945 R06946 R06947 R06954 R06980 R06983 R07058 R07104 R07105 R07133 R07134 R07135 R07136 R07141 R07145 R07146 R07148 R07156 R07164 R07168 R07171 R07188 R07194 R07326 R07327 R07345 R07349 R07351 R07354 R07358 R07410 R07417 R07428 R07441 R07477 R07478 R07618 R07658 R07665 R07667 R07675 R07703 R07704 R07705 R07709 R07765 R07781 R07799 R07890 R07894 R07898 R07936 R07952 R07954 R07955 R07957 R07959 R07961 R07963 R07965 R07967 R07969 R07971 R07973 R07975 R07985 R08017 R08018 R08042 R08043 R08044 R08045 R08046 R08047 R08086 R08087 R08094 R08096 R08100 R08101 R08103 R08104 R08105 R08108 R08109 R08110 R08111 R08112 R08113 R08140 R08141 R08198 R08209 R08210 R08214 R08215 R08240 R08281 R08282 R08306 R08307 R08310 R08382 R08385 R08536 R08544 R08549 R08550 R08557 R08569 R08590 R08709 R08721 R08723 R08724 R08728 R08764 R08767 R08846 R08892 R08914 R08916 R08918 R08919 R08926 R08945 R09069 R09078 R09097 R09129 R09130 R09132 R09137 R09141 R09148 R09159 R09160 R09162 R09165 R09183 R09201 R09204 R09209 R09213 R09219 R09223 R09224 R09227 R09228 R09230 R09231 R09232 R09233 R09235 R09236 R09288 R09312 R09375 R09385 R09388 PATHWAY ko00190 Oxidative phosphorylation ko01100 Metabolic pathways ko04020 Calcium signaling pathway ENZYME 1.1.1.1 1.1.1.3 1.1.1.4 1.1.1.6
1.1.1.7 1.1.1.8 1.1.1.9 1.1.1.11
1.1.1.12 1.1.1.13 1.1.1.14 1.1.1.15
1.1.1.16 1.1.1.17 1.1.1.18 1.1.1.21
1.1.1.22 1.1.1.23 1.1.1.24 1.1.1.26
1.1.1.27 1.1.1.28 1.1.1.29 1.1.1.30
1.1.1.31 1.1.1.32 1.1.1.35 1.1.1.37
1.1.1.38 1.1.1.39 1.1.1.41 1.1.1.43
1.1.1.45 1.1.1.46 1.1.1.47 1.1.1.48
1.1.1.50 1.1.1.51 1.1.1.52 1.1.1.53
1.1.1.56 1.1.1.57 1.1.1.58 1.1.1.59
1.1.1.60 1.1.1.61 1.1.1.62 1.1.1.63
1.1.1.66 1.1.1.67 1.1.1.69 1.1.1.71
1.1.1.72 1.1.1.73 1.1.1.75 1.1.1.76
1.1.1.77 1.1.1.78 1.1.1.79 1.1.1.81
1.1.1.83 1.1.1.84 1.1.1.85 1.1.1.87
1.1.1.88 1.1.1.90 1.1.1.92 1.1.1.93
1.1.1.94 1.1.1.95 1.1.1.96 1.1.1.98
1.1.1.99 1.1.1.103 1.1.1.104 1.1.1.105
1.1.1.106 1.1.1.107 1.1.1.108 1.1.1.110
1.1.1.111 1.1.1.112 1.1.1.114 1.1.1.116
1.1.1.117 1.1.1.118 1.1.1.121 1.1.1.122
1.1.1.125 1.1.1.127 1.1.1.129 1.1.1.130
1.1.1.131 1.1.1.132 1.1.1.135 1.1.1.136
1.1.1.137 1.1.1.140 1.1.1.141 1.1.1.143
1.1.1.144 1.1.1.145 1.1.1.146 1.1.1.147
1.1.1.148 1.1.1.149 1.1.1.150 1.1.1.152
1.1.1.154 1.1.1.158 1.1.1.159 1.1.1.161
1.1.1.163 1.1.1.164 1.1.1.165 1.1.1.166
1.1.1.167 1.1.1.170 1.1.1.172 1.1.1.173
1.1.1.174 1.1.1.175 1.1.1.178 1.1.1.181
1.1.1.185 1.1.1.186 1.1.1.187 1.1.1.190
1.1.1.192 1.1.1.196 1.1.1.198 1.1.1.199
1.1.1.202 1.1.1.203 1.1.1.205 1.1.1.209
1.1.1.211 1.1.1.212 1.1.1.213 1.1.1.218
1.1.1.221 1.1.1.222 1.1.1.223 1.1.1.226
1.1.1.227 1.1.1.228 1.1.1.232 1.1.1.233
1.1.1.237 1.1.1.239 1.1.1.240 1.1.1.241
1.1.1.244 1.1.1.245 1.1.1.250 1.1.1.251
1.1.1.254 1.1.1.255 1.1.1.256 1.1.1.257
1.1.1.258 1.1.1.259 1.1.1.260 1.1.1.261
1.1.1.262 1.1.1.264 1.1.1.265 1.1.1.268
1.1.1.269 1.1.1.272 1.1.1.275 1.1.1.281
1.1.1.282 1.1.1.284 1.1.1.285 1.1.1.286
1.1.1.288 1.1.1.290 1.1.1.291 1.1.1.294
1.1.1.295 1.1.1.296 1.1.1.297 1.1.1.302
1.1.1.303 1.1.1.304 1.1.1.305 1.1.1.306
1.1.1.312 1.1.1.- 1.1.-.- 1.2.1.2
1.2.1.3 1.2.1.5 1.2.1.8 1.2.1.10
1.2.1.12 1.2.1.15 1.2.1.16 1.2.1.18
1.2.1.19 1.2.1.20 1.2.1.21 1.2.1.22
1.2.1.23 1.2.1.24 1.2.1.25 1.2.1.27
1.2.1.28 1.2.1.29 1.2.1.31 1.2.1.32
1.2.1.33 1.2.1.36 1.2.1.39 1.2.1.40
1.2.1.42 1.2.1.46 1.2.1.47 1.2.1.48
1.2.1.53 1.2.1.54 1.2.1.57 1.2.1.58
1.2.1.59 1.2.1.60 1.2.1.61 1.2.1.62
1.2.1.64 1.2.1.65 1.2.1.67 1.2.1.68
1.2.1.69 1.2.1.71 1.2.1.72 1.2.1.73
1.2.1.74 1.2.1.- 1.2.3.9 1.2.4.1
1.2.4.2 1.2.4.- 1.3.1.1 1.3.1.5
1.3.1.6 1.3.1.7 1.3.1.9 1.3.1.11
1.3.1.12 1.3.1.14 1.3.1.18 1.3.1.19
1.3.1.21 1.3.1.24 1.3.1.25 1.3.1.26
1.3.1.28 1.3.1.29 1.3.1.31 1.3.1.32
1.3.1.35 1.3.1.41 1.3.1.43 1.3.1.44
1.3.1.47 1.3.1.48 1.3.1.49 1.3.1.52
1.3.1.53 1.3.1.56 1.3.1.58 1.3.1.60
1.3.1.62 1.3.1.64 1.3.1.65 1.3.1.66
1.3.1.67 1.3.1.68 1.3.1.74 1.3.1.76
1.3.1.77 1.3.1.79 1.3.1.- 1.3.8.1
1.4.1.1 1.4.1.2 1.4.1.3 1.4.1.4
1.4.1.5 1.4.1.7 1.4.1.8 1.4.1.9
1.4.1.10 1.4.1.11 1.4.1.12 1.4.1.14
1.4.1.15 1.4.1.18 1.4.1.19 1.4.1.20
1.4.1.21 1.4.1.- 1.4.4.2 1.5.1.1
1.5.1.2 1.5.1.3 1.5.1.7 1.5.1.9
1.5.1.11 1.5.1.12 1.5.1.15 1.5.1.17
1.5.1.18 1.5.1.20 1.5.1.21 1.5.1.22
1.5.1.23 1.5.1.25 1.5.1.26 1.5.1.28
1.5.1.29 1.5.1.34 1.5.1.- 1.5.99.8
1.6.1.1 1.6.1.2 1.6.2.2 1.6.2.6
1.6.3.1 1.6.5.2 1.6.5.3 1.6.5.4
1.6.5.7 1.6.5.- 1.6.6.9 1.6.99.3
1.6.99.5 1.7.1.1 1.7.1.2 1.7.1.4
1.7.1.5 1.7.1.9 1.7.1.10 1.7.1.12
1.7.1.14 1.7.1.- 1.7.99.1 1.8.1.3
1.8.1.4 1.8.1.6 1.8.1.7 1.8.1.8
1.8.1.11 1.8.1.14 1.8.1.15 1.11.1.1
1.12.1.2 1.13.11.20 (C) 1.13.11.29 1.13.11.30
1.13.11.- 1.13.12.- 1.14.12.1 1.14.12.3
1.14.12.4 1.14.12.7 1.14.12.8 1.14.12.9
1.14.12.10 1.14.12.11 1.14.12.12 1.14.12.13
1.14.12.14 1.14.12.15 1.14.12.16 1.14.12.17
1.14.12.18 1.14.12.19 1.14.12.- 1.14.13.1
1.14.13.3 1.14.13.4 1.14.13.5 1.14.13.6
1.14.13.8 1.14.13.10 1.14.13.18 1.14.13.19
1.14.13.24 1.14.13.25 1.14.13.26 1.14.13.27
1.14.13.29 1.14.13.33 1.14.13.40 1.14.13.44
1.14.13.61 1.14.13.62 1.14.13.63 1.14.13.64
1.14.13.69 1.14.13.72 1.14.13.82 1.14.13.83
1.14.13.90 1.14.13.107 1.14.13.114 1.14.13.-
1.14.14.1 1.14.15.- 1.14.18.1 1.14.21.6
1.14.99.2 1.14.99.3 (C) 1.14.99.9 (C) 1.14.99.31
1.14.99.32 1.14.-.- 1.16.1.2 1.16.1.3
1.16.1.4 1.16.1.7 1.17.1.1 1.17.1.2
1.17.1.4 1.18.1.1 1.18.1.3 1.18.1.4
1.20.1.1 1.-.-.- 2.1.2.10 2.3.1.12
2.3.1.61 2.3.1.86 2.3.1.119 2.5.1.46
2.7.1.86 3.1.2.18 (I) 3.1.2.19 (I) 4.2.1.93
4.3.1.22 5.2.1.6 (C) 5.3.3.1 DBLINKS CAS: 58-68-4 PubChem: 3306 ChEBI: 16908 KNApSAcK: C00019343 3DMET: B01127 NIKKAJI: J213.546I ATOM 44 1 N4y N 31.4354 -15.6994 2 C8y C 30.1607 -15.2991 3 C1y C 30.7466 -17.9407 4 C8x C 32.2050 -14.6094 5 C8y C 30.1484 -13.9630 6 N5x N 28.9907 -15.9827 7 O2x O 29.6384 -17.1404 8 C1y C 30.3403 -19.1970 9 N5x N 31.4170 -13.5442 10 C8y C 28.9783 -13.2855 11 C8x C 27.8146 -15.3300 12 C1y C 28.5546 -17.9161 13 C1y C 28.9794 -19.1970 14 O1a O 31.1346 -20.2808 15 N5x N 27.8085 -13.9691 16 N1a N 28.9723 -11.9494 17 C1b C 27.2922 -17.5222 18 O1a O 28.2098 -20.2808 19 O2b O 26.2145 -17.4729 20 P1b P 24.7675 -17.4666 21 O2c O 22.9571 -17.4729 22 O1c O 24.7675 -19.0308 23 O1c O 24.7675 -15.9703 24 P1b P 21.2821 -17.4666 25 O2b O 19.8412 -17.4789 26 O1c O 21.2884 -18.9631 27 O1c O 21.2821 -15.9641 28 C1b C 18.5135 -17.5306 29 C1y C 17.2635 -17.9677 30 O2x O 16.1488 -17.2288 31 C1y C 16.9124 -19.3347 32 C1y C 15.0713 -18.0663 33 C1y C 15.5270 -19.3656 34 O1a O 17.7069 -20.3899 35 N1y N 13.7473 -16.7730 36 O1a O 14.7695 -20.4185 37 C2x C 14.7757 -16.0157 38 C2x C 12.4666 -16.0711 39 C2y C 14.7818 -14.6671 40 C2x C 12.4480 -14.8087 41 C1x C 13.5811 -14.0698 42 C5a C 15.8965 -13.9282 43 N1a N 15.8965 -12.7397 44 O5a O 17.0972 -14.5317 BOND 48 1 1 2 1 2 3 1 1 #Up 3 1 4 1 4 2 5 2 5 2 6 1 6 3 7 1 7 3 8 1 8 4 9 2 9 5 10 1 10 6 11 2 11 7 12 1 12 8 13 1 13 8 14 1 #Down 14 10 15 2 15 10 16 1 16 12 17 1 #Up 17 13 18 1 #Down 18 17 19 1 19 19 20 1 20 20 21 1 21 20 22 1 22 20 23 2 23 21 24 1 24 24 25 1 25 24 26 1 26 24 27 2 27 25 28 1 28 29 28 1 #Down 29 29 30 1 30 29 31 1 31 30 32 1 32 31 33 1 33 31 34 1 #Up 34 32 35 1 #Down 35 33 36 1 #Up 36 35 37 1 37 35 38 1 38 37 39 2 39 38 40 2 40 39 41 1 41 39 42 1 42 42 43 1 43 42 44 2 44 5 9 1 45 11 15 1 46 12 13 1 47 32 33 1 48 40 41 1 ///

reaction file: /// ENTRY R00199 Reaction NAME ATP:pyruvate,water phosphotransferase DEFINITION ATP + Pyruvate + H2O <=> AMP + Phosphoenolpyruvate + Orthophosphate EQUATION C00002 + C00022 + C00001 <=> C00020 + C00074 + C00009 COMMENT multi-step reaction RPAIR RP00010 C00002_C00009 leave RP00036 C00022_C00074 main RP05676 C00001_C00009 leave RP12346 C00002_C00020 main RP12347 C00002_C00074 trans ENZYME 2.7.9.2 PATHWAY rn00620 Pyruvate metabolism rn00680 Methane metabolism rn00720 Carbon fixation pathways in prokaryotes rn01100 Metabolic pathways rn01120 Microbial metabolism in diverse environments ORTHOLOGY K01007 pyruvate, water dikinase [EC:2.7.9.2] ///

I hope this helps!