=====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 ==== ===== 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:ASPARTATESYN-PWY is completely contained within ASPARAGINE-BIOSYNTHESIS but is not listed in the SUB-PATHWAYS slot Warning:HOMOCYSDEGR-PWY is completely contained within PWY-801 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:PANTO-PWY is completely contained within PWY-4221 but is not listed in the SUB-PATHWAYS slot Warning:PWY-5123 is completely contained within POLYISOPRENSYN-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-5123 is completely contained within PWY-5121 but is not listed in the SUB-PATHWAYS slot Warning:GLYSYN-PWY is completely contained within 1CMET2-PWY 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:PWY0-662 is completely contained within P1-PWY but is not listed in the SUB-PATHWAYS slot Warning:ARGDEG-III-PWY is completely contained within POLYAMINSYN3-PWY but is not listed in the SUB-PATHWAYS slot Warning:PWY0-823 is completely contained within POLYAMSYN-PWY but is not listed in the SUB-PATHWAYS slot Warning:PWY-1141 is completely contained within CAROTENOID-PWY but is not listed in the SUB-PATHWAYS slot Warning:PWY-4001 is completely contained within ASPARAGINE-DEG1-PWY but is not listed in the SUB-PATHWAYS slot Warning:ASPARTATESYN-PWY is completely contained within GLUTAMINEFUM-PWY but is not listed in the SUB-PATHWAYS slot Warning:GLUTSYN-PWY is completely contained within GLUTAMINEFUM-PWY 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-5340 is completely contained within SO4ASSIM-PWY but is not listed in the SUB-PATHWAYS slot Warning:P21-PWY is completely contained within NONOXIPENT-PWY but is not listed in the SUB-PATHWAYS slot Warning:PWY-1881 is completely contained within ANARESPDON-PWY 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 ==== [Sorting replicon GRAMENE-CHROM-1] [Sorting replicon GRAMENE-CHROM-2] [Sorting replicon GRAMENE-CHROM-3] [Sorting replicon GRAMENE-CHROM-4] [Sorting replicon GRAMENE-CHROM-5] [Sorting replicon GRAMENE-CHROM-6] [Sorting replicon GRAMENE-CHROM-7] [Sorting replicon GRAMENE-CHROM-8] [Sorting replicon GRAMENE-CHROM-9] [Sorting replicon GRAMENE-CHROM-10] [Sorting replicon GRAMENE-CHROM-11] [Sorting replicon GRAMENE-CHROM-12] [Sorting replicon GRAMENE-CHLOROPLAST] == Done verifying replicon components == ===== Validating Gene Ontology (GO) Terms ===== Deleting term GO:0016621 - cinnamoyl-CoA reductase activity because it has no subs, instances, term-members, or parts. Deleting term GO:0009039 - urease activity because it has no subs, instances, term-members, or parts. Deleting term GO:0009378 - four-way junction helicase activity because it has no subs, instances, term-members, or parts. Deleting term GO:0009379 - Holliday junction helicase complex because it has no subs, instances, term-members, or parts. Deleting term GO:0033202 - DNA helicase complex because it has no subs, instances, term-members, or parts. Deleting term GO:0048476 - Holliday junction resolvase complex because it has no subs, instances, term-members, or parts. == Done validating GO terms == ===== Changing compound name strings to frame IDs in a variety of slots ===== [Checking class Enzymatic-Reactions] [Checking class Reactions] --- Importing compounds [Copied 1 frames; overwrote 0 of them] "PEPTIDE DIPHTHAMIDE" --> CPD-10454 peptide diphthamide in 2.4.2.36-RXN --- Importing compounds [Copied 1 frames; overwrote 0 of them] "PEPTIDE N-(ADP-D-RIBOSYL)DIPHTHAMIDE" --> CPD-10461 peptide N-(ADP-D-ribosyl)diphthamide in 2.4.2.36-RXN "(ADP-D-RIBOSYL)(N)-ACCEPTOR" --> ADP-D-Ribosyl-Acceptors a ADP-D-ribosyl acceptor in NAD+-ADP-RIBOSYLTRANSFERASE-RXN "(ADP-D-RIBOSYL)(N+1)-ACCEPTOR" --> ADP-D-Ribosyl-Acceptors a ADP-D-ribosyl acceptor in NAD+-ADP-RIBOSYLTRANSFERASE-RXN [Checking class Pathways] [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] (RXN-7381 (CPD-1825) (UDP-L-ARABINOSE)) --> (RXN-7381 (CPD-1825) (UDP-L-ARABINOSE)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] (RXN-6341 (CPD-5981) (CPD-5981)) --> (RXN-6341 (CPD-5981) (CPD-5981)) 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] (RXN1F-461 (CPD1F-90) (CPD1F-453)) --> (RXN1F-461 (CPD1F-90) (CPD1F-453)) 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] (RXN1F-462 (CPD-520) (CPD1F-437)) --> (RXN1F-462 (CPD-520) (CPD1F-437)) 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-3602 (CPD-3441) (CPD-3402)) --> (RXN-3602 (CPD-3441) (CPD-3402)) 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-8564 (GERANYL-PP) (CPD-8755)) --> (RXN-8564 (GERANYL-PP) (CPD-8755)) 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-8563 (GERANYL-PP) (CPD-8754)) --> (RXN-8563 (GERANYL-PP) (CPD-8754)) 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] (4.2.3.20-RXN (GERANYL-PP) (CPD-8785)) --> (4.2.3.20-RXN (GERANYL-PP) (CPD-8785)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] (ACETYL-COA-HYDROLASE-RXN NIL (ACETYL-COA)) --> (ACETYL-COA-HYDROLASE-RXN NIL (ACETYL-COA)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] (SARCOSINE-DEHYDROGENASE-RXN (SARCOSINE) (GLY)) --> (SARCOSINE-DEHYDROGENASE-RXN (SARCOSINE) (GLY)) 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] (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] (METHIONINE--GLYOXYLATE-TRANSAMINASE-RXN (MET) NIL) --> (METHIONINE--GLYOXYLATE-TRANSAMINASE-RXN (MET) NIL) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] (BENZOATE--COA-LIGASE-RXN (BENZOATE) (BENZOYLCOA)) --> (BENZOATE--COA-LIGASE-RXN (BENZOATE) (BENZOYLCOA)) 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] (R281-RXN (CPD-575) (CPD-577)) --> (R281-RXN (CPD-575) (CPD-577)) 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 [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] --- Importing compounds [Copied 1 frames; overwrote 0 of them] (ENZRXN-141-RXN (BUTYRYL-COA) (BUTANAL)) --> (ENZRXN-141-RXN (BUTYRYL-COA) (BUTANAL)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] (2.8.3.9-RXN (ACETOACETYL-COA) (3-KETOBUTYRATE)) --> (2.8.3.9-RXN (ACETOACETYL-COA) (3-KETOBUTYRATE)) in #, PRIMARIES [Copied 0 frames; overwrote 0 of them] [Copied 1 frames; overwrote 0 of them] (RXNI-2 (SUC) (SUC-COA)) --> (RXNI-2 (SUC) (SUC-COA)) in #, PRIMARIES [Checking class Enzymatic-Reactions] == Done changing compound name strings to compound frame IDs == ===== Checking pathway predecessors/reactions/subs ==== ===== 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 ricecyc==== Recomputed statistics are as follows: (PSEUDOGENE-NUMBER 1 ENZYMATIC-REACTION-NUMBER 2111 CITATION-COUNT 319 GENOME-LENGTH 372702846 MAPPED-GENE-NUMBER 47883 UN-MAPPED-GENE-NUMBER 3 PROTEIN-GENE-NUMBER 47883 RNA-GENE-NUMBER 0 ORF-GENE-NUMBER 27 REACTION-NUMBER 2141 NO-EC-REACTION-NUMBER 609 ORGANISM-REACTION-NUMBER 2141 TRANSPORT-REACTION-NUMBER 8 POLYPEPTIDE-NUMBER 47898 COMPLEX-NUMBER 2 ENZYME-NUMBER 8875 TRANSPORTER-NUMBER 136 CPD-NUMBER 1581 TOTAL-GENE-NUMBER 47886 OPERON-NUMBER 0 TRNA-NUMBER 0 LAST-TIME-STAMP 06-Apr-2010 08:07:49) == Done recomputing statistics for database ricecyc == The report from this consistency checker run can be found at /usr/local/pathway-tools/ptools-local/pgdbs/user/ricecyc/2.0.1.1.3/reports/consistency-checker-report-2010-04-06_08-06-22.txt