=====Checking all inverse links==== [Checking inverses under class Publications] [Checking inverses under class CCO] [Checking inverses under class Organizations] [Checking inverses under class Gene-Ontology-Terms] [Checking inverses under class People] [Checking inverses under class Protein-Features] [Checking inverses under class Paralogous-Gene-Groups] [Checking inverses under class Databases] [Checking inverses under class EC-BOOKKEEPING] [Checking inverses under class Polymer-Segments] [Checking inverses under class Chemicals] [Checking inverses under class Enzymatic-Reactions] [Checking inverses under class Organisms] [Checking inverses under class Generalized-Reactions] [Checking inverses under class Regulation] [Checking inverses under class Evidence] [Checking inverses under class KB-DESCRIPTOR] [Checking inverses under class Notes] [Checking inverses under class Compound-Mixtures] ===== Checking and removing any values from PATHWAY-LINKS that point to nonexistent frames ==== Removing link from pwy SO4ASSIM-PWY to nonexistent pwys (PWY-5344) Removing link from pwy PWY0-41 to nonexistent pwys ((PWY-5044 . INCOMING)) Removing link from pwy PWY-5456 to nonexistent pwys ((METHGLYSYN-RXN . INCOMING) PWY-5451 THRDLCTCAT-PWY) Removing link from pwy PWY-6510 to nonexistent pwys (PWY-1801 P185-PWY) Removing link from pwy PWY-5173 to nonexistent pwys (TCA) Removing link from pwy PWY-6629 to nonexistent pwys (GLNSYN-PWY) Removing link from pwy PWY-3001 to nonexistent pwys (TCA) 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-6277 to nonexistent pwys (PWY0-661) Removing link from pwy PWY-6277 to nonexistent pwys (DENOVOPURINE2-PWY THISYN-PWY) Removing link from pwy PWY-6555 to nonexistent pwys (PWY-6364) Removing link from pwy PWY-6555 to nonexistent pwys (PWY-6369) Removing link from pwy PWY-5053 to nonexistent pwys (PWY-5052) Removing link from pwy PWY-2541 to nonexistent pwys (PWY-699) Removing link from pwy PWY-5918 to nonexistent pwys (RXN-8073) Removing link from pwy PWY-6612 to nonexistent pwys (PWY-6125) Removing link from pwy PWY-5121 to nonexistent pwys (PWY-5660 PWY-5416 PWY-5063 PWY-2981 CAROTENOID-PWY) Removing link from pwy PWY-5910 to nonexistent pwys (RXN-3701 PWY-5660 PWY-5416 PWY-5063 PWY-2981) Removing link from pwy PWY-6151 to nonexistent pwys (PWY-6153 PWY-6154) Removing link from pwy PWY-5943 to nonexistent pwys (PWY-6280 PWY-5291 PWY-5288) Removing link from pwy PWY-5403 to nonexistent pwys (PWY-5439) Removing link from pwy PWY-5403 to nonexistent pwys (PWY-5394) Removing link from pwy PWY-5381 to nonexistent pwys (PWY-5388 PWY-5110) ===== Checking modified protein links to eliminate nonexistent frames ==== ===== Cross-referencing compounds and reactions ==== ==== Calculating sub and super pathways ==== ===== Finding missing sub pathway links ==== ==== Checking for missing sub pathway links ==== Warning:PWY-5173 is completely contained within PYRUVDEHYD-PWY but is not listed in the SUB-PATHWAYS slot Warning:PWY-6537 is completely contained within PWY3O-210 but is not listed in the SUB-PATHWAYS slot Warning:PWY-6535 is completely contained within GLUDEG-I-PWY but is not listed in the SUB-PATHWAYS slot Warning:PWY-6554 is completely contained within PWY-4562 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:PWY4FS-5 is completely contained within PHOSLIPSYN2-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-6040 is completely contained within PWY-361 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:METHIONINE-DEG1-PWY is completely contained within PWY-5041 but is not listed in the SUB-PATHWAYS slot Warning:GLUTATHIONESYN-PWY is completely contained within PWYQT-4470 but is not listed in the SUB-PATHWAYS slot Warning:PWY-5486 is completely contained within PWY-6333 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:PWY0-823 is completely contained within PWY-6305 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] [Copied 0 primary frames; overwrote 0 of them] -- Removing ENZRXN-223 from ENZYMATIC-REACTION of FEFDCP-RXN [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] (FEFDCP-RXN (|Reduced-ferredoxins| |Oxidized-nitrogenase-reductases|) (|Oxidized-ferredoxins| |Reduced-nitrogenase-reductases|)) --> (FEFDCP-RXN (|Reduced-ferredoxins| |Oxidized-nitrogenase-reductases|) (|Oxidized-ferredoxins| |Reduced-nitrogenase-reductases|)) in #, PRIMARIES [Copied 0 primary frames; overwrote 0 of them] -- Removing ENZRXN-222 from ENZYMATIC-REACTION of MOFECP-RXN [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] (MOFECP-RXN (|Reduced-nitrogen-reductases| NITROGEN-MOLECULE) (|Oxidized-nitrogen-reductases| AMMONIA)) --> (MOFECP-RXN (|Reduced-nitrogen-reductases| NITROGEN-MOLECULE) (|Oxidized-nitrogen-reductases| AMMONIA)) in #, PRIMARIES [Copied 0 primary frames; overwrote 0 of them] -- Removing ENZRXN-223 from ENZYMATIC-REACTION of FEMOFECP-RXN [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] (FEMOFECP-RXN (|Reduced-nitrogenase-reductases| |Oxidized-nitrogen-reductases|) (|Oxidized-nitrogenase-reductases| |Reduced-nitrogen-reductases|)) --> (FEMOFECP-RXN (|Reduced-nitrogenase-reductases| |Oxidized-nitrogen-reductases|) (|Oxidized-nitrogenase-reductases| |Reduced-nitrogen-reductases|)) in #, PRIMARIES [Copied 0 primary frames; overwrote 0 of them] -- Removing ENZRXN-12204 from ENZYMATIC-REACTION of GUANOSINE-DEAMINASE-RXN -- Removing # from IN-PATHWAY of GUANOSINE-DEAMINASE-RXN [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] (GUANOSINE-DEAMINASE-RXN (GUANOSINE) (XANTHOSINE)) --> (GUANOSINE-DEAMINASE-RXN (GUANOSINE) (XANTHOSINE)) in #, PRIMARIES [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] -- Removing ENZRXN-17817 from ENZYMATIC-REACTION of RXN-11451 -- Removing # from IN-PATHWAY of RXN-11451 [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] (RXN-11451 (METOH) (FORMALDEHYDE)) --> (RXN-11451 (METOH) (FORMALDEHYDE)) in #, PRIMARIES [Copied 0 primary frames; overwrote 0 of them] -- Removing ENZRXN-14008 from ENZYMATIC-REACTION of METHANOL-OXIDASE-RXN -- Removing # from IN-PATHWAY of METHANOL-OXIDASE-RXN [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] (METHANOL-OXIDASE-RXN NIL (HYDROGEN-PEROXIDE FORMALDEHYDE)) --> (METHANOL-OXIDASE-RXN NIL (HYDROGEN-PEROXIDE FORMALDEHYDE)) in #, PRIMARIES [Copied 0 primary frames; overwrote 0 of them] -- Removing ENZRXN-17509 from ENZYMATIC-REACTION of RXN-6724 -- Removing ENZRXN-10367 from ENZYMATIC-REACTION of RXN-6724 -- Removing # from IN-PATHWAY of RXN-6724 -- Removing # from IN-PATHWAY of RXN-6724 [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] --- Importing compounds [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] --- Importing compounds [Copied 0 primary frames; overwrote 0 of them] (RXN-6724 (BENZOYLCOA BENZYL-ALCOHOL) (CPD-6443)) --> (RXN-6724 (BENZOYLCOA BENZYL-ALCOHOL) (CPD-6443)) in #, PRIMARIES [Copied 0 primary frames; overwrote 0 of them] -- Removing # from IN-PATHWAY of RXN-2003 -- Removing # from IN-PATHWAY of RXN-2003 [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] --- Importing compounds [Copied 0 primary frames; overwrote 0 of them] (RXN-2003 (CPD-513) (CPD-514)) --> (RXN-2003 (CPD-513) (CPD-514)) in #, PRIMARIES [Copied 0 primary frames; overwrote 0 of them] -- Removing ENZRXN-17689 from ENZYMATIC-REACTION of RXN-2006 -- Removing ENZRXN-17513 from ENZYMATIC-REACTION of RXN-2006 -- Removing # from IN-PATHWAY of RXN-2006 -- Removing # from IN-PATHWAY of RXN-2006 -- Removing # from IN-PATHWAY of RXN-2006 [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] (RXN-2006 (CPD-514) (BENZOYLCOA)) --> (RXN-2006 (CPD-514) (BENZOYLCOA)) in #, PRIMARIES [Copied 0 primary frames; overwrote 0 of them] -- Removing ENZRXN-17353 from ENZYMATIC-REACTION of RXN-1981 -- Removing ENZRXN-17334 from ENZYMATIC-REACTION of RXN-1981 -- Removing # from IN-PATHWAY of RXN-1981 [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] (RXN-1981 (ISOCHORISMATE) (CPD-110)) --> (RXN-1981 (ISOCHORISMATE) (CPD-110)) in #, PRIMARIES [Copied 0 primary frames; overwrote 0 of them] -- Removing ENZRXN-17697 from ENZYMATIC-REACTION of RXN-8024 -- Removing ENZRXN-16676 from ENZYMATIC-REACTION of RXN-8024 -- Removing # from IN-PATHWAY of RXN-8024 [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] --- Importing compounds [Copied 0 primary frames; overwrote 0 of them] (RXN-8024 (CPD-7408) (CPD1F-98)) --> (RXN-8024 (CPD-7408) (CPD1F-98)) in #, PRIMARIES [Copied 0 primary frames; overwrote 0 of them] -- Removing ENZRXN-17698 from ENZYMATIC-REACTION of RXN-8023 -- Removing ENZRXN-16675 from ENZYMATIC-REACTION of RXN-8023 -- Removing # from IN-PATHWAY of RXN-8023 [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] (RXN-8023 (CPD-12321) (CPD-7408)) --> (RXN-8023 (CPD-12321) (CPD-7408)) in #, PRIMARIES [Copied 0 primary frames; overwrote 0 of them] -- Removing ADENPHOSPHOR-ENZRXN from ENZYMATIC-REACTION of ADENPHOSPHOR-RXN -- Removing ENZRXN-17992 from ENZYMATIC-REACTION of ADENPHOSPHOR-RXN -- Removing # from IN-PATHWAY of ADENPHOSPHOR-RXN -- Removing # from IN-PATHWAY of ADENPHOSPHOR-RXN -- Removing # from IN-PATHWAY of ADENPHOSPHOR-RXN -- Removing # from IN-PATHWAY of ADENPHOSPHOR-RXN -- Removing # from IN-PATHWAY of ADENPHOSPHOR-RXN [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] (ADENPHOSPHOR-RXN (ADENOSINE) (ADENINE)) --> (ADENPHOSPHOR-RXN (ADENOSINE) (ADENINE)) in #, PRIMARIES --- Importing compounds [Copied 0 primary frames; overwrote 0 of them] (DEOXYHYPUSINE-MONOOXYGENASE-RXN (CPD-9973) (CPD-9974)) --> (DEOXYHYPUSINE-MONOOXYGENASE-RXN (CPD-9973) (CPD-9974)) in #, PRIMARIES [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] (SPERMIDINE-DEHYDROGENASE-RXN (SPERMIDINE) (4-AMINO-BUTYRALDEHYDE CPD-313)) --> (SPERMIDINE-DEHYDROGENASE-RXN (SPERMIDINE) (4-AMINO-BUTYRALDEHYDE CPD-313)) in #, PRIMARIES [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] (RXN-4311 (CPD-4203) (CPD-4205)) --> (RXN-4311 (CPD-4203) (CPD-4205)) in #, PRIMARIES [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] (RXN-4309 (CPD-4201) (CPD-4203)) --> (RXN-4309 (CPD-4201) (CPD-4203)) in #, PRIMARIES [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] (RXN-4318 (CPD-4208) (CPD-4210)) --> (RXN-4318 (CPD-4208) (CPD-4210)) in #, PRIMARIES [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] (RXN-4315 (CPD-4207) (CPD-4209)) --> (RXN-4315 (CPD-4207) (CPD-4209)) in #, PRIMARIES [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] -- Removing ENZRXN-2821 from ENZYMATIC-REACTION of RXN-1402 -- Removing ENZRXN-1825 from ENZYMATIC-REACTION of RXN-1402 [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] (RXN-1402 (TRP) (INDOLE-3-ACETALDOXIME)) --> (RXN-1402 (TRP) (INDOLE-3-ACETALDOXIME)) in #, PRIMARIES [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] -- Removing ENZRXN-16773 from ENZYMATIC-REACTION of RXN-1401 -- Removing # from IN-PATHWAY of RXN-1401 -- Removing # from IN-PATHWAY of RXN-1401 [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] [Copied 0 primary frames; overwrote 0 of them] (RXN-1401 (TRYPTAMINE) (INDOLE_ACETALDEHYDE)) --> (RXN-1401 (TRYPTAMINE) (INDOLE_ACETALDEHYDE)) 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 PWY-5381 ===== Removing newlines from names ==== (|GO:0000155| "two-component system sensor activity ") ===== Clearing read-only computed slot values ==== == Done running all the Misc automatic checks == ===== Checking compound structures for redundancy ===== Checking Compound structures for redundant bonds == Done checking compound structure redundancies == ====Recomputing statistics for database maizecyc==== Recomputed statistics are as follows: (PSEUDOGENE-NUMBER 0 ENZYMATIC-REACTION-NUMBER 2109 CITATION-COUNT 515 GENOME-LENGTH 2066432718 MAPPED-GENE-NUMBER 39655 UN-MAPPED-GENE-NUMBER 1 PROTEIN-GENE-NUMBER 39656 RNA-GENE-NUMBER 0 ORF-GENE-NUMBER 28135 REACTION-NUMBER 2214 NO-EC-REACTION-NUMBER 526 ORGANISM-REACTION-NUMBER 2214 TRANSPORT-REACTION-NUMBER 68 POLYPEPTIDE-NUMBER 39656 COMPLEX-NUMBER 4 ENZYME-NUMBER 8894 TRANSPORTER-NUMBER 291 CPD-NUMBER 1467 TOTAL-GENE-NUMBER 39656 OPERON-NUMBER 0 TRNA-NUMBER 6 LAST-TIME-STAMP 12-Jul-2011 12:33:47) == Done recomputing statistics for database maizecyc == The report from this consistency checker run can be found at /usr/local/ptools-local/pgdbs/user/maizecyc/1.0-test-pankaj/reports/consistency-checker-report-2011-07-12_12-32-40.txt