=====Checking all inverse links==== [Checking inverses under class CCO] [Checking inverses under class Evidence] [Checking inverses under class People] [Checking inverses under class Proteins] [Checking inverses under class Reactions] [Checking inverses under class All-Genes] [Checking inverses under class Transcription-Units] [Checking inverses under class Compounds] [Checking inverses under class Enzymatic-Reactions] [Checking inverses under class Regulation] ===== Checking and removing any values from PATHWAY-LINKS that point to nonexistent frames ==== Removing link from pwy ASPARTATESYN-PWY to nonexistent pwys (TCA) Removing link from pwy ASPARTATESYN-PWY to nonexistent pwys (DENOVOPURINE2-PWY) Removing link from pwy CYSTSYN-PWY to nonexistent pwys (PWY-801) Removing link from pwy ARGASEDEG-PWY to nonexistent pwys (GLUTAMATE-DEG1-PWY) Removing link from pwy GLUTAMATE-SYN2-PWY to nonexistent pwys (ARGININE-SYN4-PWY GLUTORN-PWY) Removing link from pwy GLUTSYNIII-PWY to nonexistent pwys (DENOVOPURINE2-PWY) Removing link from pwy GLNSYN-PWY to nonexistent pwys (GLUTSYN-PWY) Removing link from pwy PWY-4361 to nonexistent pwys (PWY-5389) Removing link from pwy PWY-6151 to nonexistent pwys (PWY-6153 PWY-6154) Removing link from pwy HOMOSERSYN-PWY to nonexistent pwys (HOMOSER-METSYN-PWY HSERMETANA-PWY) Removing link from pwy CITRULBIO-PWY to nonexistent pwys (ARGININE-SYN4-PWY) Removing link from pwy PHESYN to nonexistent pwys ((TYRSYN . OUTGOING)) Removing link from pwy SERSYN-PWY to nonexistent pwys (PWY-6308) Removing link from pwy PWY-6120 to nonexistent pwys (PWY-5048) Removing link from pwy VALSYN-PWY to nonexistent pwys ((ALANINE-VALINESYN-PWY . OUTGOING)) Removing link from pwy PWY-5886 to nonexistent pwys (PWY-1581 PWY-5048) Removing link from pwy PWY-5886 to nonexistent pwys (TYRSYN PWY-3461) Removing link from pwy PWY-5901 to nonexistent pwys (PWY-5903 ENTBACSYN-PWY) Removing link from pwy PWY-6164 to nonexistent pwys (PWY-6163) Removing link from pwy PWY-6164 to nonexistent pwys (PWY-5770 PWY-5755 TYRSYN) Removing link from pwy PWY-5754 to nonexistent pwys (PWY3O-19) Removing link from pwy ARO-PWY to nonexistent pwys (PWY-5770 PWY-5755 TYRSYN) Removing link from pwy PWY-1061 to nonexistent pwys (PWY-4) Removing link from pwy PWY-1269 to nonexistent pwys (KDOSYN-PWY) Removing link from pwy PWY-5661 to nonexistent pwys (TREHALOSESYN-PWY) Removing link from pwy MANNOSYL-CHITO-DOLICHOL-BIOSYNTHESIS to nonexistent pwys (PWY-6129) Removing link from pwy PWY-5337 to nonexistent pwys (PWY-5342) Removing link from pwy PEPTIDOGLYCANSYN-PWY to nonexistent pwys (UDPNAGSYN-PWY) Removing link from pwy PWY-361 to nonexistent pwys (PWY-5710) Removing link from pwy PWY-361 to nonexistent pwys (PWY-5466) Removing link from pwy PWY-361 to nonexistent pwys (PWY-84) Removing link from pwy PWY-922 to nonexistent pwys (PWY-5666) Removing link from pwy PWY-922 to nonexistent pwys (PWY66-341 PWY-2921 ERGOSTEROL-SYN-PWY) Removing link from pwy SAM-PWY to nonexistent pwys (HOMOSER-METSYN-PWY HSERMETANA-PWY) Removing link from pwy PWY-5381 to nonexistent pwys (PWY-5388 PWY-5110) Removing link from pwy HEXPPSYN-PWY to nonexistent pwys (ERGOSTEROL-SYN-PWY) Removing link from pwy HEXPPSYN-PWY to nonexistent pwys (PWY-5853 PWY3O-19) Removing link from pwy NONMEVIPP-PWY to nonexistent pwys (PWY-6270) Removing link from pwy PWY-5122 to nonexistent pwys (PWY-5813 PWY-5290 PWY-5423 PWY-3061 PWY-3041) Removing link from pwy PWY-5123 to nonexistent pwys (PWY-5887 PWY66-4 PWY66-3 PWY-5875 PWY-5733 PWY-5725 PWY-5425 PWY-5195 2.5.1.58-RXN ERGOSTEROL-SYN-PWY PWY66-341 POLYISOPRENSYN-PWY PWY-2961 PWY-2921) Removing link from pwy PWY-5783 to nonexistent pwys (PWY-5852 UBISYN-PWY PWY-5870) Removing link from pwy PWY-5805 to nonexistent pwys (PWY-5856 PWY-5851 PWY-1581) Removing link from pwy PWY-5807 to nonexistent pwys (PWY-5855 PWY-5873 PWY-5839) Removing link from pwy PWY-5121 to nonexistent pwys (PWY-5660 PWY-5416 PWY-2981 CAROTENOID-PWY) Removing link from pwy PWY-5910 to nonexistent pwys (2.5.1.60-RXN RXN-3701 PWY-5660 PWY-5416 PWY-2981) Removing link from pwy PWY-5120 to nonexistent pwys (2.5.1.60-RXN RXN-3701 PWY-5660 PWY-5416 PWY-2981) Removing link from pwy PWY-5194 to nonexistent pwys (PWY-5297) Removing link from pwy PWY-5194 to nonexistent pwys (PWY-5189) Removing link from pwy CHLOROPHYLL-SYN to nonexistent pwys (PWY-5526) Removing link from pwy PWY-5918 to nonexistent pwys (RXN-8073) Removing link from pwy HEME-BIOSYNTHESIS-II to nonexistent pwys (PWY-5189) Removing link from pwy HEME-BIOSYNTHESIS-II to nonexistent pwys (RXN-8073) Removing link from pwy PWY-5791 to nonexistent pwys (PWY-5802 PWY-5801 PWY-5795 PWY-5027) Removing link from pwy PWY-5871 to nonexistent pwys (PWY-5755) Removing link from pwy PWY-5872 to nonexistent pwys (PWY-5806) Removing link from pwy PWY-5872 to nonexistent pwys (PWY-5755) Removing link from pwy PWY-5188 to nonexistent pwys (PWY-5507 PWY-5196 HEMESYN2-PWY P381-PWY) Removing link from pwy FOLSYN-PWY to nonexistent pwys (PWY-6125) Removing link from pwy PWY-6147 to nonexistent pwys (PWY-6148) Removing link from pwy PWY-6147 to nonexistent pwys (PWY-6125) Removing link from pwy PWY-695 to nonexistent pwys (PWY-5272) Removing link from pwy PWY-581 to nonexistent pwys (PWY-1782) Removing link from pwy PWY-2681 to nonexistent pwys (PWY-2901 PWY-2881) Removing link from pwy PWY-2781 to nonexistent pwys (PWY-2901 PWY-2881) Removing link from pwy PWY-2902 to nonexistent pwys (PWY-2901) Removing link from pwy PWY-5053 to nonexistent pwys (PWY-5052) Removing link from pwy PWY-5032 to nonexistent pwys (PWY-5047) Removing link from pwy PWY-5034 to nonexistent pwys (PWY-5070 PWY-5036) Removing link from pwy PWY-735 to nonexistent pwys (PWY-6235 PWY-6233 PWY-6220) Removing link from pwy PWY-401 to nonexistent pwys (PWY-782) Removing link from pwy PWY-401 to nonexistent pwys ((PWY-782 . OUTGOING)) Removing link from pwy PWY-3385 to nonexistent pwys (PWY-3542) Removing link from pwy PWY-4381 to nonexistent pwys (PWY-5971) Removing link from pwy PWY-5973 to nonexistent pwys (PHOSLIPSYN2-PWY) Removing link from pwy PWY-5973 to nonexistent pwys (PWY-6282) Removing link from pwy PWY-5995 to nonexistent pwys (PWY-5997 PWY-5998) Removing link from pwy PWY-6001 to nonexistent pwys (PWY-6000) Removing link from pwy PWY-6001 to nonexistent pwys (PWY-5997 PWY-5998) Removing link from pwy PWY-5147 to nonexistent pwys (PWY-5368 PWY-321) Removing link from pwy PWY-5996 to nonexistent pwys (PWY-5972) Removing link from pwy PWY-5366 to nonexistent pwys (PWY-5971) Removing link from pwy PWY-5989 to nonexistent pwys (PWY-5971) Removing link from pwy PWY-5989 to nonexistent pwys (PWY-5971) Removing link from pwy PWY-5367 to nonexistent pwys (PWY-5971) Removing link from pwy PWY-5667 to nonexistent pwys (PWY-5668) Removing link from pwy PWY-2541 to nonexistent pwys (PWY-5377 PWY-112 PWY-5203) Removing link from pwy PWY-6075 to nonexistent pwys (PWY-6074) Removing link from pwy PWY-6121 to nonexistent pwys (PWY0-661) Removing link from pwy PWY-6121 to nonexistent pwys (DENOVOPURINE2-PWY THISYN-PWY) Removing link from pwy PWY-6124 to nonexistent pwys (PWY-6125 PWY-6126) Removing link from pwy PWY-841 to nonexistent pwys (PWY0-661) Removing link from pwy PWY-841 to nonexistent pwys (THISYN-PWY) Removing link from pwy PWY-5043 to nonexistent pwys (PWY-5040 PWY-5039 PWY-5038 PWY-5037) Removing link from pwy SALVADEHYPOX-PWY to nonexistent pwys (DENOVOPURINE2-PWY) Removing link from pwy PWY0-181 to nonexistent pwys (PWY0-166) Removing link from pwy PWY0-181 to nonexistent pwys (PWY0-166) Removing link from pwy PWY-5670 to nonexistent pwys (PWY-6095) Removing link from pwy PWY-5670 to nonexistent pwys (PWY-6132 PWY-6008 PWY-6007 PWY-6005 PWY-5992 PWY-5672 PWY-5377 PWY-112 PWY-5203) Removing link from pwy PWY0-662 to nonexistent pwys (PWY-6148) Removing link from pwy PWY0-662 to nonexistent pwys (RIBOKIN-PWY) Removing link from pwy BSUBPOLYAMSYN-PWY to nonexistent pwys (PWY-46 PWY-40) Removing link from pwy PWY0-823 to nonexistent pwys (PUTDEG-PWY) Removing link from pwy PWY-5410 to nonexistent pwys ((PWY-5997 . INCOMING)) Removing link from pwy PWY-6029 to nonexistent pwys (PWY-641) Removing link from pwy PWY1F-FLAVSYN to nonexistent pwys (PWY-5118 PWY-5116 PWY-5094 PWY-2083) Removing link from pwy PWY1F-FLAVSYN to nonexistent pwys (PWY-5161 PWY-2002) Removing link from pwy PWY1F-FLAVSYN to nonexistent pwys (PWY-5339 PWY-1901) Removing link from pwy PWY-5125 to nonexistent pwys (PWY-641) Removing link from pwy PWY-5125 to nonexistent pwys (PWY-5286 PWY-5284) Removing link from pwy PWY-5125 to nonexistent pwys (PWY-641 PWY-5160) Removing link from pwy PWY-5125 to nonexistent pwys (PWY-5286 PWY-5268) Removing link from pwy PWY-5125 to nonexistent pwys (PWY-641) Removing link from pwy PWY-5125 to nonexistent pwys (PWY-641) Removing link from pwy PWY-5139 to nonexistent pwys (PWY-5268) Removing link from pwy PWY-5153 to nonexistent pwys (PWY-641) Removing link from pwy PWY-5153 to nonexistent pwys (PWY-5307 PWY-5286) Removing link from pwy PWY-5153 to nonexistent pwys (PWY-641) Removing link from pwy PWY-5060 to nonexistent pwys (PWY-6239) Removing link from pwy PWY-5060 to nonexistent pwys (PWY-6015 PWY-6010 PWY-5119) Removing link from pwy PWY-5060 to nonexistent pwys (PWY-5105) Removing link from pwy PWY-3101 to nonexistent pwys (PWY-5321) Removing link from pwy PWY-3101 to nonexistent pwys (PWY-5348 PWY-5320) Removing link from pwy PWY-6199 to nonexistent pwys (PWY-5321) Removing link from pwy PWY1F-823 to nonexistent pwys (PWY-641) Removing link from pwy PWY1F-823 to nonexistent pwys (PWY-641) Removing link from pwy PWY1F-823 to nonexistent pwys (PWY-641) Removing link from pwy PWY-1187 to nonexistent pwys (PWY-1186) Removing link from pwy PWY-2181 to nonexistent pwys (PWY-3301) Removing link from pwy PWY-5049 to nonexistent pwys (PWY-5048 PWY-3461) Removing link from pwy PWY-5168 to nonexistent pwys (PWY-3301) Removing link from pwy PWY1F-467 to nonexistent pwys (PWY-4201) Removing link from pwy PWY1F-467 to nonexistent pwys (PWY-5710 PWY-5665) Removing link from pwy PWY-5176 to nonexistent pwys (PWY-5319) Removing link from pwy PWY-5063 to nonexistent pwys (PWY-5027) Removing link from pwy PWY-5829 to nonexistent pwys ((PWY-5835 . OUTGOING)) Removing link from pwy PWY-5942 to nonexistent pwys (PWY-6286) Removing link from pwy PWY-5942 to nonexistent pwys (PWY-6279 PWY-5946 PWY-5943 PWY-5305) Removing link from pwy PWY-5945 to nonexistent pwys (PWY-5174) Removing link from pwy PWY-5945 to nonexistent pwys ((PWY-5944 . INCOMING)) Removing link from pwy PWY-6287 to nonexistent pwys (PWY-6286) Removing link from pwy PWY-5912 to nonexistent pwys (PWY-5937 PWY-5925) Removing link from pwy PWY0-1391 to nonexistent pwys (PWY0-1303) Removing link from pwy PWY0-381 to nonexistent pwys ((TRANS-RXN-131 . INCOMING)) Removing link from pwy 2PHENDEG-PWY to nonexistent pwys (PWY0-321) Removing link from pwy ARGDEG-III-PWY to nonexistent pwys (PUTDEG-PWY) Removing link from pwy ARGDEG-V-PWY to nonexistent pwys (4AMINOBUTMETAB-PWY) Removing link from pwy ASPARAGINE-DEG1-PWY to nonexistent pwys (ASPARTATE-DEG1-PWY) Removing link from pwy PWY-5766 to nonexistent pwys ((TCA . OUTGOING)) Removing link from pwy GLUTAMINDEG-PWY to nonexistent pwys (GLUTDEG-PWY GLUTAMATE-DEG1-PWY) Removing link from pwy ILEUDEG-PWY to nonexistent pwys (PROPIONMET-PWY) Removing link from pwy LEU-DEG2-PWY to nonexistent pwys (ACETOACETATE-DEG-PWY) Removing link from pwy LYSINE-DEG1-PWY to nonexistent pwys (PWY-5177) Removing link from pwy METHIONINE-DEG1-PWY to nonexistent pwys (ADENOSYLHOMOCYSCAT-PWY HOMOCYSDEGR-PWY) Removing link from pwy METHIONINE-DEG1-PWY to nonexistent pwys (CYSTEINE-DEG-PWY) Removing link from pwy PWY-701 to nonexistent pwys (PWY-5130) Removing link from pwy CITRULLINE-DEG-PWY to nonexistent pwys (ARGDEGRAD-PWY) Removing link from pwy PROUT-PWY to nonexistent pwys (GLUTAMATE-DEG1-PWY) Removing link from pwy VALDEG-PWY to nonexistent pwys (PWY-5710) Removing link from pwy VALDEG-PWY to nonexistent pwys (PROPIONMET-PWY) Removing link from pwy PWY-283 to nonexistent pwys (CENTBENZCOA-PWY P321-PWY PWY-1361) Removing link from pwy PWY-1881 to nonexistent pwys (PWY-1722) Removing link from pwy PWY0-1300 to nonexistent pwys ((RXN0-2522 . INCOMING)) Removing link from pwy PWY0-1300 to nonexistent pwys (ANARESP1-PWY) Removing link from pwy PWY-5074 to nonexistent pwys (PWY-5451 ACETOACETATE-DEG-PWY) Removing link from pwy PWY-5749 to nonexistent pwys (TCA) Removing link from pwy PWY0-1313 to nonexistent pwys (PWY-5768) Removing link from pwy PYRUVDEHYD-PWY to nonexistent pwys (TCA) Removing link from pwy PWY-5098 to nonexistent pwys (PWY-5107) Removing link from pwy PWY0-1337 to nonexistent pwys ((FAO-PWY . INCOMING)) Removing link from pwy PWY0-1337 to nonexistent pwys (FAO-PWY) Removing link from pwy PWY-5340 to nonexistent pwys (PWY-2821 PWY-601) Removing link from pwy SO4ASSIM-PWY to nonexistent pwys (PWY-5344) Removing link from pwy PWY-5278 to nonexistent pwys (P223-PWY) Removing link from pwy P164-PWY to nonexistent pwys ((ADENINE-DEAMINASE-RXN . INCOMING)) Removing link from pwy PWY-4101 to nonexistent pwys (PWY-5054) Removing link from pwy PWY-5173 to nonexistent pwys (TCA) Removing link from pwy PWY-5172 to nonexistent pwys (TCA) Removing link from pwy ANAEROFRUCAT-PWY to nonexistent pwys ((TRANS-RXN-157 . INCOMING)) Removing link from pwy ANAEROFRUCAT-PWY to nonexistent pwys ((FRUCTOSEPHOSPHO-RXN . INCOMING)) Removing link from pwy PWY-5483 to nonexistent pwys (P341-PWY) Removing link from pwy ANAGLYCOLYSIS-PWY to nonexistent pwys (PWY-5100) Removing link from pwy GLYCOLYSIS to nonexistent pwys (SORBDEG-PWY P302-PWY PWY0-44) Removing link from pwy GLYCOLYSIS to nonexistent pwys (FERMENTATION-PWY) Removing link from pwy GLYCOLYSIS to nonexistent pwys (TCA-GLYOX-BYPASS) Removing link from pwy GLYCOLYSIS to nonexistent pwys ((TRANS-RXN-157 . INCOMING)) Removing link from pwy PWY-5484 to nonexistent pwys (SORBDEG-PWY P302-PWY PWY0-44) Removing link from pwy PWY-5484 to nonexistent pwys (FERMENTATION-PWY) Removing link from pwy PWY-5484 to nonexistent pwys (TCA-GLYOX-BYPASS) Removing link from pwy PWY-5484 to nonexistent pwys ((TRANS-RXN-157 . INCOMING)) Removing link from pwy METHFORM-PWY to nonexistent pwys (PWY-5261 PWY-5260 PWY-5259 PWY-5258 PWY-5250 PWY-5248 PWY-5247 METHANOGENESIS-PWY METH-ACETATE-PWY (CO2FORM-PWY . INCOMING)) Removing link from pwy METHFORM-PWY to nonexistent pwys (P241-PWY) Removing link from pwy METHFORM-PWY to nonexistent pwys (P261-PWY) Removing link from pwy OXIDATIVEPENT-PWY to nonexistent pwys (ENTNER-DOUDOROFF-PWY) Removing link from pwy PWY-181 to nonexistent pwys (GLYOXDEG-PWY) Removing link from pwy PWY-5913 to nonexistent pwys (HOMOSER-METSYN-PWY) ===== Checking modified protein links to eliminate nonexistent frames ==== ===== Cross-referencing compounds and reactions ==== ==== Calculating sub and super pathways ==== Adding PWY-5667 to SUB-PATHWAYS slot of PWY4FS-8 Adding PWY-1881 to SUB-PATHWAYS slot of P164-PWY Adding PWY-1881 to SUB-PATHWAYS slot of PWY-5497 Adding PWY-5535 to SUB-PATHWAYS slot of PWY-5483 ===== Finding missing sub pathway links ==== ==== Checking for missing sub pathway links ==== Warning:P401-PWY is completely contained within ASPSYNII-PWY but is not listed in the SUB-PATHWAYS slot Warning:THRESYN-PWY is completely contained within PWY-3001 but is not listed in the SUB-PATHWAYS slot Warning:PWY0-1391 is completely contained within PWY-4361 but is not listed in the SUB-PATHWAYS slot Warning:SAM-PWY is completely contained within PWY-5041 but is not listed in the SUB-PATHWAYS slot Warning:GLUTAMINDEG-PWY is completely contained within CITRULBIO-PWY but is not listed in the SUB-PATHWAYS slot Warning:PWY-6164 is completely contained within ARO-PWY but is not listed in the SUB-PATHWAYS slot Warning:PWY-5111 is completely contained within PWY-1269 but is not listed in the SUB-PATHWAYS slot Warning:PWY1F-467 is completely contained within PWY-1121 but is not listed in the SUB-PATHWAYS slot Warning:PWY-6040 is completely contained within PWY-361 but is not listed in the SUB-PATHWAYS slot Warning:PWY-5120 is completely contained within HEXPPSYN-PWY but is not listed in the SUB-PATHWAYS slot Warning:PWY-5122 is completely contained within PWY-5123 but is not listed in the SUB-PATHWAYS slot Warning:PWY-5807 is completely contained within PWY-5783 but is not listed in the SUB-PATHWAYS slot Warning:PWY-5783 is completely contained within PWY-5805 but is not listed in the SUB-PATHWAYS slot Warning:HEXPPSYN-PWY is completely contained within PWY-5807 but is not listed in the SUB-PATHWAYS slot Warning:PWY-6147 is completely contained within FOLSYN-PWY but is not listed in the SUB-PATHWAYS slot Warning:GLYSYN-PWY is completely contained within PWY-2161 but is not listed in the SUB-PATHWAYS slot Warning:GLYSYN-PWY is completely contained within PWY-2201 but is not listed in the SUB-PATHWAYS slot Warning:GLYSYN-PWY is completely contained within PWY-3841 but is not listed in the SUB-PATHWAYS slot Warning:SAM-PWY is completely contained within ETHYL-PWY but is not listed in the SUB-PATHWAYS slot Warning:PWY0-1299 is completely contained within PWY0-823 but is not listed in the SUB-PATHWAYS slot Warning:PWY0-1299 is completely contained within PWY-43 but is not listed in the SUB-PATHWAYS slot Warning:PWY0-823 is completely contained within PWY-6305 but is not listed in the SUB-PATHWAYS slot Warning:PWY-283 is completely contained within PWY-1187 but is not listed in the SUB-PATHWAYS slot Warning:PWY-6040 is completely contained within PWY-6039 but is not listed in the SUB-PATHWAYS slot Warning:PWY-5957 is completely contained within PWY-5912 but is not listed in the SUB-PATHWAYS slot Warning:SAM-PWY is completely contained within PWY-5912 but is not listed in the SUB-PATHWAYS slot Warning:PWY0-1313 is completely contained within PWY66-21 but is not listed in the SUB-PATHWAYS slot Warning:PWY0-1299 is completely contained within ARGDEG-III-PWY but is not listed in the SUB-PATHWAYS slot Warning:SAM-PWY is completely contained within METHIONINE-DEG1-PWY but is not listed in the SUB-PATHWAYS slot Warning:MANNCAT-PWY is completely contained within PWY-3861 but is not listed in the SUB-PATHWAYS slot Warning:GLUGLNSYN-PWY is completely contained within PWY-3282 but is not listed in the SUB-PATHWAYS slot Warning:PWY-4341 is completely contained within PWY-3282 but is not listed in the SUB-PATHWAYS slot Warning:GLNSYN-PWY is completely contained within PWY-3282 but is not listed in the SUB-PATHWAYS slot Warning:GLNSYN-PWY is completely contained within PWY-381 but is not listed in the SUB-PATHWAYS slot Warning:PWY-5481 is completely contained within ANAEROFRUCAT-PWY but is not listed in the SUB-PATHWAYS slot Warning:PWY-5484 is completely contained within GLYCOLYSIS but is not listed in the SUB-PATHWAYS slot Warning:PWYQT-4429 is completely contained within PWY-241 but is not listed in the SUB-PATHWAYS slot Warning:ASPARTATESYN-PWY is completely contained within PWY-5913 but is not listed in the SUB-PATHWAYS slot Warning:GLUTSYNIII-PWY is completely contained within PWY-5913 but is not listed in the SUB-PATHWAYS slot Warning:PWYQT-4429 is completely contained within PWY-5913 but is not listed in the SUB-PATHWAYS slot ==Done checking all the links== ==== Checking pathways for duplicate reactions in REACTION-LIST slot ==== == Done checking pathways for duplicate reactions == ==== Verifying replicon components and positions ==== == Done verifying replicon components == ===== Validating Gene Ontology (GO) Terms ===== == Done validating GO terms == ===== Changing compound name strings to frame IDs in a variety of slots ===== [Checking class Enzymatic-Reactions] [Checking class Reactions] [Checking class Pathways] --- Importing compounds [Copied 1 frames; overwrote 0 of them] (DEOXYHYPUSINE-MONOOXYGENASE-RXN (CPD-9973) (CPD-9974)) --> (DEOXYHYPUSINE-MONOOXYGENASE-RXN (CPD-9973) (CPD-9974)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] (GLUTAMATESYN-RXN (GLN) (GLT)) --> (GLUTAMATESYN-RXN (GLN) (GLT)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] (RXN-5682 (CPD-659) (TYR)) --> (RXN-5682 (CPD-659) (TYR)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] (CHORPYRLY-RXN (CHORISMATE) (|4-hydroxybenzoate|)) --> (CHORPYRLY-RXN (CHORISMATE) (|4-hydroxybenzoate|)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] --- Importing compounds [Copied 1 frames; overwrote 0 of them] --- Importing compounds [Copied 1 frames; overwrote 0 of them] (KDOTRANS2-RXN (KDO-LIPID-IVA) (KDO2-LIPID-IVA)) --> (KDOTRANS2-RXN (KDO-LIPID-IVA) (KDO2-LIPID-IVA)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] (RXN-5482 (UDP-GLUCOSE) (UDP-L-RHAMNOSE)) --> (RXN-5482 (UDP-GLUCOSE) (UDP-L-RHAMNOSE)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] (DOLICHOL-KINASE-RXN (DOLICHOL) (DOLICHOLP)) --> (DOLICHOL-KINASE-RXN (#) (DOLICHOLP)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 3 frames; overwrote 0 of them] (RXN-5741 (CPD-195) (OCTANOYL-ACP)) --> (RXN-5741 (CPD-195) (OCTANOYL-ACP)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] --- Importing compounds [Copied 1 frames; overwrote 0 of them] (RXN-7772 (CPD-7078) (GDP-L-GALACTOSE)) --> (RXN-7772 (CPD-7078) (GDP-L-GALACTOSE)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] (RXN-7771 (GDP-MANNOSE) (CPD-7078)) --> (RXN-7771 (GDP-MANNOSE) (CPD-7078)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] Importing Note frame peifenz-3295879570 referenced by frame RXN-1883 [Copied 2 frames; overwrote 0 of them] (RXN-1883 (GDP-L-GALACTOSE) (L-GALACTOSE)) --> (RXN-1883 (GDP-L-GALACTOSE) (L-GALACTOSE)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] --- Importing compounds [Copied 1 frames; overwrote 0 of them] --- Importing compounds [Copied 1 frames; overwrote 0 of them] (RXN-6547 (CPD-6225) (CPD-6226)) --> (RXN-6547 (CPD-6225) (CPD-6226)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] (RXN-6546 (CPD1F-86) (CPD-6225)) --> (RXN-6546 (CPD1F-86) (CPD-6225)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] --- Importing compounds [Copied 1 frames; overwrote 0 of them] (RXN-1224 NIL (SULFOQUINOVOSYLDIACYLGLYCEROL)) --> (RXN-1224 NIL (SULFOQUINOVOSYLDIACYLGLYCEROL)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] (RXN-1223 (UDP-GLUCOSE) NIL) --> (RXN-1223 (UDP-GLUCOSE) NIL) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] (DHS-PHOSPHATASE-RXN (DIHYDRO-SPHINGOSINE) (CPD-649)) --> (DHS-PHOSPHATASE-RXN (DIHYDRO-SPHINGOSINE) (CPD-649)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] (ACP-S-ACETYLTRANSFER-RXN (ACETYL-COA) (ACETYL-ACP)) --> (ACP-S-ACETYLTRANSFER-RXN (ACETYL-COA) (ACETYL-ACP)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] (LINOLEOYL-RXN NIL (LINOLEIC_ACID)) --> (LINOLEOYL-RXN NIL (LINOLEIC_ACID)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] (GUANPHOSPHOR-RXN NIL (GUANINE)) --> (GUANPHOSPHOR-RXN NIL (GUANINE)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] (RXN-1541 (NARINGENIN-CMPD) (ISOFLAVONE)) --> (RXN-1541 (NARINGENIN-CMPD) (#)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] --- Importing compounds [Copied 1 frames; overwrote 0 of them] (RXN-7843 (CPD-7137) (CPD-7151)) --> (RXN-7843 (CPD-7137) (CPD-7151)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] --- Importing compounds [Copied 1 frames; overwrote 0 of them] (RXN-7842 (CPD-7137) (CPD-7150)) --> (RXN-7842 (CPD-7137) (CPD-7150)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] --- Importing compounds [Copied 1 frames; overwrote 0 of them] --- Importing compounds [Copied 1 frames; overwrote 0 of them] (RXN1F-475 (CPD1F-461) (CPD1F-462)) --> (RXN1F-475 (CPD1F-461) (CPD1F-462)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] (RXN1F-474 (CPD1F-90) (CPD1F-461)) --> (RXN1F-474 (CPD1F-90) (CPD1F-461)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] --- Importing compounds [Copied 1 frames; overwrote 0 of them] --- Importing compounds [Copied 1 frames; overwrote 0 of them] (RXN1F-444 (CPD1F-420) (CPD1F-431)) --> (RXN1F-444 (CPD1F-420) (CPD1F-431)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] (RXN1F-443 (CPD1F-453) (CPD1F-420)) --> (RXN1F-443 (CPD1F-453) (CPD1F-420)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] (RXN-7783 (CPD-474) (CPD-7087)) --> (RXN-7783 (CPD-474) (CPD-7087)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] --- Importing compounds [Copied 1 frames; overwrote 0 of them] (RXN-8026 (CPD-7409) (CPD1F-130)) --> (RXN-8026 (CPD-7409) (CPD1F-130)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] (RXN-8025 (CPD1F-129) (CPD-7409)) --> (RXN-8025 (CPD1F-129) (CPD-7409)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] --- Importing compounds [Copied 1 frames; overwrote 0 of them] --- Importing compounds [Copied 1 frames; overwrote 0 of them] (RXN-5962 (CPD-5661) (CPD1F-119)) --> (RXN-5962 (CPD-5661) (CPD1F-119)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] --- Importing compounds [Copied 1 frames; overwrote 0 of them] (RXN-5961 (CPD1F-118) (CPD-5661)) --> (RXN-5961 (CPD1F-118) (CPD-5661)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] (ACETYL-COA-HYDROLASE-RXN (ACET) (ACETYL-COA)) --> (ACETYL-COA-HYDROLASE-RXN (ACET) (ACETYL-COA)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] (UREIDOGLYCOLATE-LYASE-RXN (CPD-1091) (GLYOX)) --> (UREIDOGLYCOLATE-LYASE-RXN (CPD-1091) (GLYOX)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] (ALLOPHANATE-HYDROLASE-RXN NIL (AMMONIA)) --> (ALLOPHANATE-HYDROLASE-RXN NIL (AMMONIA)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] (ALLANTOICASE-RXN NIL (UREA CPD-1091)) --> (ALLANTOICASE-RXN NIL (UREA CPD-1091)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] (D-ALANINE-AMINOTRANSFERASE-RXN (D-ALANINE) (PYRUVATE)) --> (D-ALANINE-AMINOTRANSFERASE-RXN (D-ALANINE) (PYRUVATE)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] (GLUTAMATE-DEHYDROGENASE-RXN (GLT) (2-KETOGLUTARATE)) --> (GLUTAMATE-DEHYDROGENASE-RXN (GLT) (2-KETOGLUTARATE)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] --- Importing compounds [Copied 1 frames; overwrote 0 of them] (GLUTARYL-COA-DEHYDROG-RXN (GLUTARYL-COA) (GLUTACONYL-COA)) --> (GLUTARYL-COA-DEHYDROG-RXN (GLUTARYL-COA) (GLUTACONYL-COA)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] (GLUTACONYL-COA-DECARBOXYLASE-RXN (GLUTACONYL-COA) (CROTONYL-COA)) --> (GLUTACONYL-COA-DECARBOXYLASE-RXN (GLUTACONYL-COA) (CROTONYL-COA)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] (CYSTAGLY-RXN (L-CYSTATHIONINE) (CYS 2-OXOBUTANOATE)) --> (CYSTAGLY-RXN (L-CYSTATHIONINE) (CYS 2-OXOBUTANOATE)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] (ALPHA-KETOBUTYRATE-DEHYDROG-RXN (2-OXOBUTANOATE) (PROPIONYL-COA)) --> (ALPHA-KETOBUTYRATE-DEHYDROG-RXN (2-OXOBUTANOATE) (PROPIONYL-COA)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] --- Importing compounds [Copied 1 frames; overwrote 0 of them] (PROPIONYL-COA-CARBOXY-RXN (PROPIONYL-COA) (D-METHYL-MALONYL-COA)) --> (PROPIONYL-COA-CARBOXY-RXN (PROPIONYL-COA) (D-METHYL-MALONYL-COA)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] (CYSTATHIONASE-RXN (L-CYSTATHIONINE) (HOMO-SER)) --> (CYSTATHIONASE-RXN (L-CYSTATHIONINE) (HOMO-SER)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] --- Importing compounds [Copied 1 frames; overwrote 0 of them] (RXN0-2522 (2-O-ALPHA-MANNOSYL-D-GLYCERATE) (CPD0-1063)) --> (RXN0-2522 (2-O-ALPHA-MANNOSYL-D-GLYCERATE) (CPD0-1063)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] (RXN1F-165 (CPD1F-134) (CPD1F-137)) --> (RXN1F-165 (CPD1F-134) (CPD1F-137)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] (SULFITE-DEHYDROGENASE-RXN (SO3) (SULFATE)) --> (SULFITE-DEHYDROGENASE-RXN (SO3) (SULFATE)) in #, PRIMARIES --- Importing compounds [Copied 1 frames; overwrote 0 of them] (RXN-7610 (URATE) (ALLANTOIN)) --> (RXN-7610 (URATE) (ALLANTOIN)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] (FORMATEDEHYDROG-RXN NIL (CARBON-DIOXIDE)) --> (FORMATEDEHYDROG-RXN NIL (CARBON-DIOXIDE)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] --- Importing compounds [Copied 1 frames; overwrote 0 of them] (ALDOSE-6-PHOSPHATE-REDUCTASE-NADPH-RXN (D-SORBITOL-6-P) (GLC-6-P)) --> (ALDOSE-6-PHOSPHATE-REDUCTASE-NADPH-RXN (D-SORBITOL-6-P) (GLC-6-P)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] (MALATE-DEHYDROGENASE-ACCEPTOR-RXN (MAL) (OXALACETIC_ACID)) --> (MALATE-DEHYDROGENASE-ACCEPTOR-RXN (MAL) (OXALACETIC_ACID)) in PWY-5464, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] --- Importing compounds [Copied 1 frames; overwrote 0 of them] (MTAMBARKMULTI-RXN (|CoM| METOH) NIL) --> (MTAMBARKMULTI-RXN (|CoM| METOH) NIL) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] (RXN-974 (SER) (OH-PYR)) --> (RXN-974 (SER) (OH-PYR)) in #, PRIMARIES [Checking class Enzymatic-Reactions] == Done changing compound name strings to compound frame IDs == ===== Checking pathway predecessors/reactions/subs ==== Adjusting predecessor list of super-pathway NAD-BIOSYNTHESIS-II ===== Removing newlines from names ==== ===== Clearing read-only computed slot values ==== == Done running all the Misc automatic checks == ===== Classifying modified proteins as such ==== ===== Updating molecular weights of polypeptides from amino acid sequences ==== Updated 0 protein molecular weights from sequence == Done with protein updates == ===== Checking compound structures for redundancy ===== Checking Compound structures for redundant bonds == Done checking compound structure redundancies == ====Recomputing statistics for database brachycyc==== Recomputed statistics are as follows: (PSEUDOGENE-NUMBER 0 ENZYMATIC-REACTION-NUMBER 2095 CITATION-COUNT 237 GENOME-LENGTH 271148425 MAPPED-GENE-NUMBER 26523 UN-MAPPED-GENE-NUMBER 0 PROTEIN-GENE-NUMBER 26523 RNA-GENE-NUMBER 0 ORF-GENE-NUMBER 10579 REACTION-NUMBER 2144 NO-EC-REACTION-NUMBER 430 ORGANISM-REACTION-NUMBER 2144 TRANSPORT-REACTION-NUMBER 16 POLYPEPTIDE-NUMBER 26531 COMPLEX-NUMBER 1 ENZYME-NUMBER 7085 TRANSPORTER-NUMBER 148 CPD-NUMBER 1700 TOTAL-GENE-NUMBER 26523 OPERON-NUMBER 26209 TRNA-NUMBER 0 LAST-TIME-STAMP 09-Nov-2010 11:25:41) == Done recomputing statistics for database brachycyc == The report from this consistency checker run can be found at C:\Documents and Settings\jaiswalp\Application Data\ptools-local\pgdbs\user\brachycyc\1.2 beta\reports\consistency-checker-report-2010-11-09_11-24-52.txt