;;; --- Parse Results for Zea mays mays --- ;;; ;;; This report summarizes the findings of the PathoLogic parser for ;;; the annotation files for all new genetic elements. Through ;;; inspection of this report, the user can tell whether features of major ;;; importance were not recognized, possibly due to syntax errors or other ;;; problems in the annotation files. ;;; ;;; If you want to change annotation file(s) to improve their parsability, ;;; update the files, reinitialize the KB, and re-run the Build. If you want ;;; to avoid having to reinitialize in the future, use the Trial Parse ;;; command until you are satisfied with the parse results, and only then ;;; Build. ;;; ----------------------------------------------------------- ;;; Parsing results for annotation file: ;;; /usr/local/ptools-local/pgdbs/user/maizecyc/1.0-test-pankaj/input/chr_UNKNOWN.pf ;;; ;;; The annotation file used by the parser is: ;;; /local/ptools-local/pgdbs/user/maizecyc/1.0-test-pankaj/input/chr_UNKNOWN.pf gene-IDs : 52 gene-name : 52 gene-startbase : 52 gene-endbase : 52 gene-product-type : 52 gene-Proteins : 52 gene-tRNAs : 0 gene-rRNAs : 0 gene-snRNAs : 0 gene-miscRNAs : 0 product-IDs : 0 [cannot be supplied in Genbank files] product-names : 5 product-synonyms : 0 [cannot be supplied in Genbank files] total EC numbers : 2 genes with 1 EC number : 2 genes with >1 EC numbers : 0 total GO terms linked to reactions : 4 genes with 1 GO term linked to reactions : 3 genes with >1 GO terms linked to reactions : 1 gene-products: hypothetical : 0 predicted : 0 putative : 0 genes with synonyms : 0 ;;; ----------------------------------------------------------- ;;; Parsing results for annotation file: ;;; /usr/local/ptools-local/pgdbs/user/maizecyc/1.0-test-pankaj/input/chr_Pt.pf ;;; ;;; The annotation file used by the parser is: ;;; /local/ptools-local/pgdbs/user/maizecyc/1.0-test-pankaj/input/chr_Pt.pf gene-IDs : 57 gene-name : 57 gene-startbase : 57 gene-endbase : 57 gene-product-type : 57 gene-Proteins : 57 gene-tRNAs : 0 gene-rRNAs : 0 gene-snRNAs : 0 gene-miscRNAs : 0 product-IDs : 0 [cannot be supplied in Genbank files] product-names : 51 product-synonyms : 17 [cannot be supplied in Genbank files] total EC numbers : 42 genes with 1 EC number : 29 genes with >1 EC numbers : 10 total GO terms linked to reactions : 22 genes with 1 GO term linked to reactions : 18 genes with >1 GO terms linked to reactions : 2 gene-products: hypothetical : 0 predicted : 0 putative : 0 genes with synonyms : 28 The following 5 lines were ignored because they contain no separator character: (PEP)(Plastid-encoded RNA polymerase subunit beta)(RNA polymerase subunit beta) (PEP)(Plastid-encoded RNA polymerase subunit beta')(RNA polymerase subunit beta') (PEP)(Plastid-encoded RNA polymerase subunit beta'')(RNA polymerase subunit beta'') (F-ATPase subunit beta)(ATP synthase F1 sector subunit beta) (Plastid-encoded RNA polymerase subunit alpha)(RNA polymerase subunit alpha) ;;; ----------------------------------------------------------- ;;; Parsing results for annotation file: ;;; /usr/local/ptools-local/pgdbs/user/maizecyc/1.0-test-pankaj/input/chr_Mt.pf ;;; ;;; The annotation file used by the parser is: ;;; /local/ptools-local/pgdbs/user/maizecyc/1.0-test-pankaj/input/chr_Mt.pf gene-IDs : 124 gene-name : 124 gene-startbase : 123 gene-endbase : 124 gene-product-type : 124 gene-Proteins : 124 gene-tRNAs : 0 gene-rRNAs : 0 gene-snRNAs : 0 gene-miscRNAs : 0 product-IDs : 0 [cannot be supplied in Genbank files] product-names : 123 product-synonyms : 13 [cannot be supplied in Genbank files] total EC numbers : 28 genes with 1 EC number : 21 genes with >1 EC numbers : 7 total GO terms linked to reactions : 25 genes with 1 GO term linked to reactions : 18 genes with >1 GO terms linked to reactions : 7 gene-products: hypothetical : 1 predicted : 0 putative : 0 genes with synonyms : 9 The following 4 lines were ignored because they contain no separator character: (S-1 DNA ORF 3) (S-2 DNA ORF1) (Cytochrome c oxidase polypeptide III) (Cytochrome c oxidase polypeptide II) ;;; ----------------------------------------------------------- ;;; Parsing results for annotation file: ;;; /usr/local/ptools-local/pgdbs/user/maizecyc/1.0-test-pankaj/input/chr_10.pf ;;; ;;; The annotation file used by the parser is: ;;; /local/ptools-local/pgdbs/user/maizecyc/1.0-test-pankaj/input/chr_10.pf gene-IDs : 2727 gene-name : 2727 gene-startbase : 2727 gene-endbase : 2727 gene-product-type : 2727 gene-Proteins : 2727 gene-tRNAs : 0 gene-rRNAs : 0 gene-snRNAs : 0 gene-miscRNAs : 0 product-IDs : 0 [cannot be supplied in Genbank files] product-names : 775 product-synonyms : 36 [cannot be supplied in Genbank files] total EC numbers : 649 genes with 1 EC number : 469 genes with >1 EC numbers : 115 total GO terms linked to reactions : 730 genes with 1 GO term linked to reactions : 514 genes with >1 GO terms linked to reactions : 175 gene-products: hypothetical : 2 predicted : 0 putative : 2 genes with synonyms : 34 The following 8 lines were ignored because they contain no separator character: (Pectinase)(Galacturan 1,4-alpha-galacturonidase) (Gentiobiase)(Cellobiase)(Beta-D-glucoside glucohydrolase) (Orange pericarp 2) (GST-IV)(GST-27)(GST class-phi member 4) (Ubiquinol-cytochrome c reductase iron-sulfur subunit)(Rieske iron-sulfur protein)(RISP)(Complex III subunit 5) (Seed chitinase B) (Chromomethylase 1)(Zea methyltransferase2)(Zmet2)(DNA cytosine methyltransferase MET2a) (GS2)(Glutamate--ammonia ligase) ;;; ----------------------------------------------------------- ;;; Parsing results for annotation file: ;;; /usr/local/ptools-local/pgdbs/user/maizecyc/1.0-test-pankaj/input/chr_9.pf ;;; ;;; The annotation file used by the parser is: ;;; /local/ptools-local/pgdbs/user/maizecyc/1.0-test-pankaj/input/chr_9.pf gene-IDs : 3006 gene-name : 3006 gene-startbase : 3006 gene-endbase : 3006 gene-product-type : 3006 gene-Proteins : 3006 gene-tRNAs : 0 gene-rRNAs : 0 gene-snRNAs : 0 gene-miscRNAs : 0 product-IDs : 0 [cannot be supplied in Genbank files] product-names : 844 product-synonyms : 57 [cannot be supplied in Genbank files] total EC numbers : 680 genes with 1 EC number : 499 genes with >1 EC numbers : 110 total GO terms linked to reactions : 778 genes with 1 GO term linked to reactions : 524 genes with >1 GO terms linked to reactions : 199 gene-products: hypothetical : 3 predicted : 0 putative : 3 genes with synonyms : 50 The following 11 lines were ignored because they contain no separator character: (Sucrose-UDP glucosyltransferase 1)(Shrunken-1) (Flavonol 3-O-glucosyltransferase)(UDP-glucose flavonoid 3-O-glucosyltransferase)(Bronze-1)(Bz-W22 allele) (Trans-caffeoyl-CoA 3-O-methyltransferase 2)(CCoAOMT-2)(CCoAMT-2) (2-phosphoglycerate dehydratase 1)(2-phospho-D-glycerate hydro-lyase 1) (Granule-bound starch synthase I)(GBSS-I) (Cytochrome c oxidase polypeptide III) (Cytochrome c oxidase polypeptide II) (Cytochrome c oxidase polypeptide III) (Sucrose-UDP glucosyltransferase 2) (Enhancer of zeste protein 2) (S-methylmethionine:homocysteine methyltransferase 1)(SMM:Hcy S-methyltransferase 1)(ZmHMT-1) ;;; ----------------------------------------------------------- ;;; Parsing results for annotation file: ;;; /usr/local/ptools-local/pgdbs/user/maizecyc/1.0-test-pankaj/input/chr_8.pf ;;; ;;; The annotation file used by the parser is: ;;; /local/ptools-local/pgdbs/user/maizecyc/1.0-test-pankaj/input/chr_8.pf gene-IDs : 3531 gene-name : 3531 gene-startbase : 3531 gene-endbase : 3531 gene-product-type : 3531 gene-Proteins : 3531 gene-tRNAs : 0 gene-rRNAs : 0 gene-snRNAs : 0 gene-miscRNAs : 0 product-IDs : 0 [cannot be supplied in Genbank files] product-names : 1041 product-synonyms : 41 [cannot be supplied in Genbank files] total EC numbers : 861 genes with 1 EC number : 616 genes with >1 EC numbers : 142 total GO terms linked to reactions : 1013 genes with 1 GO term linked to reactions : 683 genes with >1 GO terms linked to reactions : 269 gene-products: hypothetical : 2 predicted : 0 putative : 1 genes with synonyms : 41 The following 15 lines were ignored because they contain no separator character: (NAD(+) ADP-ribosyltransferase 2)(ADPRT-2)(Poly[ADP-ribose] synthase 2) FUNCTION (2E,6E)-farnesyl diphosphate synthase FUNCTION Farnesyl pyrophosphate synthase FUNCTION-SYNONYM FPP synthase FUNCTION-SYNONYM FPS FUNCTION-SYNONYM Farnesyl diphosphate synthase FUNCTION-SYNONYM Farnesyl pyrophosphate synthase (FPP synthase)(FPS)(Farnesyl diphosphate synthase) [Includes Dimethylallyltranstransferase(EC 2.5.1.1);Geranyltranstransferase(EC 2.5.1.10)] FUNCTION Dimethylallyltranstransferase FUNCTION Geranyltranstransferase (Pyruvate, orthophosphate dikinase 1) (rRNA N-glycosidase) [Contains Ribosome-inactivating protein alpha chain;Ribosome-inactivating protein beta chain] (AdoMet:Met S-methyltransferase) (UDP-glucose-fructose-phosphate glucosyltransferase) (PGAM-I) (GST-I)(GST-29)(GST class-phi member 1) ;;; ----------------------------------------------------------- ;;; Parsing results for annotation file: ;;; /usr/local/ptools-local/pgdbs/user/maizecyc/1.0-test-pankaj/input/chr_7.pf ;;; ;;; The annotation file used by the parser is: ;;; /local/ptools-local/pgdbs/user/maizecyc/1.0-test-pankaj/input/chr_7.pf gene-IDs : 3147 gene-name : 3147 gene-startbase : 3147 gene-endbase : 3147 gene-product-type : 3147 gene-Proteins : 3147 gene-tRNAs : 0 gene-rRNAs : 0 gene-snRNAs : 0 gene-miscRNAs : 0 product-IDs : 0 [cannot be supplied in Genbank files] product-names : 934 product-synonyms : 55 [cannot be supplied in Genbank files] total EC numbers : 748 genes with 1 EC number : 526 genes with >1 EC numbers : 128 total GO terms linked to reactions : 854 genes with 1 GO term linked to reactions : 567 genes with >1 GO terms linked to reactions : 223 gene-products: hypothetical : 1 predicted : 0 putative : 2 genes with synonyms : 43 The following 7 lines were ignored because they contain no separator character: (Carotene 7,8-desaturase) (Histone acetyltransferase HAT B)(Histone acetyltransferase HAT-B-p50) (1,4-alpha-D-glucan maltohydrolase) (Thioredoxin peroxidase)(Rehydrin homolog) (Fd-GOGAT) (Plasma membrane-bound peroxidase 2b)(pmPOX2b) (Plasma membrane-bound peroxidase 3-1)(pmPOX3-1) ;;; ----------------------------------------------------------- ;;; Parsing results for annotation file: ;;; /usr/local/ptools-local/pgdbs/user/maizecyc/1.0-test-pankaj/input/chr_6.pf ;;; ;;; The annotation file used by the parser is: ;;; /local/ptools-local/pgdbs/user/maizecyc/1.0-test-pankaj/input/chr_6.pf gene-IDs : 3293 gene-name : 3293 gene-startbase : 3293 gene-endbase : 3293 gene-product-type : 3293 gene-Proteins : 3293 gene-tRNAs : 0 gene-rRNAs : 0 gene-snRNAs : 0 gene-miscRNAs : 0 product-IDs : 0 [cannot be supplied in Genbank files] product-names : 927 product-synonyms : 46 [cannot be supplied in Genbank files] total EC numbers : 810 genes with 1 EC number : 543 genes with >1 EC numbers : 147 total GO terms linked to reactions : 878 genes with 1 GO term linked to reactions : 590 genes with >1 GO terms linked to reactions : 223 gene-products: hypothetical : 1 predicted : 0 putative : 0 genes with synonyms : 50 The following 9 lines were ignored because they contain no separator character: (ZmFRK2) (Trans-caffeoyl-CoA 3-O-methyltransferase 1)(CCoAOMT-1)(CCoAMT-1) (Enhancer of zeste protein 1) (ATP-dependent RNA helicase eIF4A) (Pectinase)(Galacturan 1,4-alpha-galacturonidase) (Pectinase)(Galacturan 1,4-alpha-galacturonidase) (Pectinase)(Galacturan 1,4-alpha-galacturonidase) (Pectinase)(Galacturan 1,4-alpha-galacturonidase) (Alpha-D-glucose-1-phosphate adenyl transferase)(ADP-glucose pyrophosphorylase)(AGPase S)(ADP-glucose synthase) ;;; ----------------------------------------------------------- ;;; Parsing results for annotation file: ;;; /usr/local/ptools-local/pgdbs/user/maizecyc/1.0-test-pankaj/input/chr_5.pf ;;; ;;; The annotation file used by the parser is: ;;; /local/ptools-local/pgdbs/user/maizecyc/1.0-test-pankaj/input/chr_5.pf gene-IDs : 4503 gene-name : 4503 gene-startbase : 4503 gene-endbase : 4503 gene-product-type : 4503 gene-Proteins : 4503 gene-tRNAs : 0 gene-rRNAs : 0 gene-snRNAs : 0 gene-miscRNAs : 0 product-IDs : 0 [cannot be supplied in Genbank files] product-names : 1317 product-synonyms : 65 [cannot be supplied in Genbank files] total EC numbers : 1143 genes with 1 EC number : 760 genes with >1 EC numbers : 194 total GO terms linked to reactions : 1173 genes with 1 GO term linked to reactions : 774 genes with >1 GO terms linked to reactions : 289 gene-products: hypothetical : 1 predicted : 0 putative : 5 genes with synonyms : 62 The following 12 lines were ignored because they contain no separator character: (Glucose phosphomutase 1) (Rotamase)(Cyclophilin) (Leucoanthocyanidin hydroxylase) (Brown-midrib 1 protein) (Acetohydroxy-acid synthase 1) (Rotamase)(Cyclophilin)(Cyclosporin A-binding protein) (Starch-branching enzyme IIB)(Q-enzyme) (Sucrose hydrolase)(Invertase) (GS112)(Glutamate--ammonia ligase) FUNCTION-SYNONYM Alcohol dehydrogenase class-3 FUNCTION-SYNONYM Alcohol dehydrogenase class-III FUNCTION L-lactate dehydrogenase ;;; ----------------------------------------------------------- ;;; Parsing results for annotation file: ;;; /usr/local/ptools-local/pgdbs/user/maizecyc/1.0-test-pankaj/input/chr_4.pf ;;; ;;; The annotation file used by the parser is: ;;; /local/ptools-local/pgdbs/user/maizecyc/1.0-test-pankaj/input/chr_4.pf gene-IDs : 4197 gene-name : 4197 gene-startbase : 4197 gene-endbase : 4197 gene-product-type : 4197 gene-Proteins : 4197 gene-tRNAs : 0 gene-rRNAs : 0 gene-snRNAs : 0 gene-miscRNAs : 0 product-IDs : 0 [cannot be supplied in Genbank files] product-names : 1159 product-synonyms : 64 [cannot be supplied in Genbank files] total EC numbers : 948 genes with 1 EC number : 664 genes with >1 EC numbers : 161 total GO terms linked to reactions : 1099 genes with 1 GO term linked to reactions : 730 genes with >1 GO terms linked to reactions : 282 gene-products: hypothetical : 1 predicted : 0 putative : 4 genes with synonyms : 58 The following 12 lines were ignored because they contain no separator character: (Benzoxazineless 1) (2,3-diketo-5-methylthio-1-phosphopentane phosphatase)] (S-adenosysl-L-methionine:caffeic acid 3-O-methyltransferase)(CAOMT)(COMT) (Orange pericarp 1) (Non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase)(Glyceraldehyde-3-phosphate dehydrogenase [NADP+])(Triosephosphate dehydrogenase) (Acetohydroxy-acid synthase 2) (GS107)(Glutamate--ammonia ligase) (ZmFer1) (Naringenin-chalcone synthase C2) (RPD3 homolog) (Vacuolar proton pump subunit alpha)(V-ATPase 69 kDa subunit) (tRNA(m7G46)-methyltransferase) ;;; ----------------------------------------------------------- ;;; Parsing results for annotation file: ;;; /usr/local/ptools-local/pgdbs/user/maizecyc/1.0-test-pankaj/input/chr_3.pf ;;; ;;; The annotation file used by the parser is: ;;; /local/ptools-local/pgdbs/user/maizecyc/1.0-test-pankaj/input/chr_3.pf gene-IDs : 4197 gene-name : 4197 gene-startbase : 4197 gene-endbase : 4197 gene-product-type : 4197 gene-Proteins : 4197 gene-tRNAs : 0 gene-rRNAs : 0 gene-snRNAs : 0 gene-miscRNAs : 0 product-IDs : 0 [cannot be supplied in Genbank files] product-names : 1174 product-synonyms : 55 [cannot be supplied in Genbank files] total EC numbers : 902 genes with 1 EC number : 660 genes with >1 EC numbers : 148 total GO terms linked to reactions : 1110 genes with 1 GO term linked to reactions : 768 genes with >1 GO terms linked to reactions : 276 gene-products: hypothetical : 0 predicted : 0 putative : 1 genes with synonyms : 51 The following 9 lines were ignored because they contain no separator character: (Choline phosphatase 1)(Phosphatidylcholine-hydrolyzing phospholipase D 1) (Plasma membrane-bound peroxidase 1)(pmPOX1) (S-methylmethionine:homocysteine methyltransferase 3)(SMM:Hcy S-methyltransferase 3)(ZmHMT-3) ((1->3)-beta-glucan endohydrolase)((1->3)-beta-glucanase)(Beta-1,3-endoglucanase) (GST-III)(GST class-phi member 3) (ZmFRK1) (S-methylmethionine:homocysteine methyltransferase 4)(SMM:Hcy S-methyltransferase 4)(ZmHMT-4) (Dihydrokaempferol 4-reductase) (Alpha-D-glucose-1-phosphate adenyl transferase)(ADP-glucose pyrophosphorylase)(AGPase S)(ADP-glucose synthase)(Shrunken-2) ;;; ----------------------------------------------------------- ;;; Parsing results for annotation file: ;;; /usr/local/ptools-local/pgdbs/user/maizecyc/1.0-test-pankaj/input/chr_2.pf ;;; ;;; The annotation file used by the parser is: ;;; /local/ptools-local/pgdbs/user/maizecyc/1.0-test-pankaj/input/chr_2.pf gene-IDs : 4766 gene-name : 4766 gene-startbase : 4766 gene-endbase : 4766 gene-product-type : 4766 gene-Proteins : 4766 gene-tRNAs : 0 gene-rRNAs : 0 gene-snRNAs : 0 gene-miscRNAs : 0 product-IDs : 0 [cannot be supplied in Genbank files] product-names : 1344 product-synonyms : 73 [cannot be supplied in Genbank files] total EC numbers : 1129 genes with 1 EC number : 770 genes with >1 EC numbers : 199 total GO terms linked to reactions : 1289 genes with 1 GO term linked to reactions : 869 genes with >1 GO terms linked to reactions : 333 gene-products: hypothetical : 2 predicted : 0 putative : 0 genes with synonyms : 53 The following 21 lines were ignored because they contain no separator character: (Chromomethylase 3)(DNA methyltransferase 105) (Sucrose 1)(Invertase 1) (Pyrophosphate phospho-hydrolase)(PPase) (Seed chitinase A) (NADP-dependent glyceraldehydephosphate dehydrogenase subunit A) (NAD(+) ADP-ribosyltransferase 1)(ADPRT-1)(Poly[ADP-ribose] synthase 1) FUNCTION-SYNONYM Bifunctional aspartokinase/homoserine dehydrogenase 2, chloroplastic Precursor FUNCTION-SYNONYM Bifunctional aspartokinase/homoserine dehydrogenase 2, chloroplastic Precursor (AK-HSDH 2)(AK-HD 2) [Includes Aspartokinase(EC 2.7.2.4);Homoserine dehydrogenase(EC 1.1.1.3)] (F-ATPase subunit beta)(ATP synthase F1 sector subunit beta) FUNCTION Pyruvate, phosphate dikinase regulatory protein, chloroplastic Precursor FUNCTION-SYNONYM Pyruvate, phosphate dikinase regulatory protein, chloroplastic Precursor (EC 2.7.11.n1)(EC 2.7.4.n1)(Pyruvate, Pi dikinase regulatory protein)(PPDK regulatory protein)(PPDK RP)(Bifunctional dikinase regulatory protein)(BFRP) FUNCTION Pyruvate, Pi dikinase regulatory protein FUNCTION Bifunctional dikinase regulatory protein FUNCTION-SYNONYM BFRP EC 2.7.11.n1 EC 2.7.4.n1 (Plasma membrane-bound peroxidase 3-2)(pmPOX3-2) (Naringenin-chalcone synthase WHP1)(White pollen) (Phospholipid synthesis protein 1) (Urea amidohydrolase) (CK2-alpha)(CK II) ;;; ----------------------------------------------------------- ;;; Parsing results for annotation file: ;;; /usr/local/ptools-local/pgdbs/user/maizecyc/1.0-test-pankaj/input/chr_1.pf ;;; ;;; The annotation file used by the parser is: ;;; /local/ptools-local/pgdbs/user/maizecyc/1.0-test-pankaj/input/chr_1.pf gene-IDs : 6056 gene-name : 6056 gene-startbase : 6056 gene-endbase : 6056 gene-product-type : 6056 gene-Proteins : 6056 gene-tRNAs : 0 gene-rRNAs : 0 gene-snRNAs : 0 gene-miscRNAs : 0 product-IDs : 0 [cannot be supplied in Genbank files] product-names : 1835 product-synonyms : 104 [cannot be supplied in Genbank files] total EC numbers : 1480 genes with 1 EC number : 1037 genes with >1 EC numbers : 249 total GO terms linked to reactions : 1663 genes with 1 GO term linked to reactions : 1137 genes with >1 GO terms linked to reactions : 408 gene-products: hypothetical : 2 predicted : 0 putative : 1 genes with synonyms : 86 The following 21 lines were ignored because they contain no separator character: (p34cdc2) (IMP--aspartate ligase) (Myo-inositol-1-phosphate synthase)(MI-1-P synthase)(IPS) (GS122)(Glutamate--ammonia ligase) (Phosphoenolpyruvate carboxylase) (Enhancer of zeste protein 3) (Plasma membrane-bound peroxidase 2)(pmPOX2) (ZmIpk)(Low phytic acid protein 2) (2-phosphoglycerate dehydratase 2)(2-phospho-D-glycerate hydro-lyase 2) (S-methylmethionine:homocysteine methyltransferase 2)(SMM:Hcy S-methyltransferase 2)(ZmHMT-2) (O-acetylserine sulfhydrylase)(O-acetylserine (thiol)-lyase)(OAS-TL) (NADP-MDH) (Alpha-D-glucose-1-phosphate adenyl transferase)(ADP-glucose pyrophosphorylase)(AGPase B)(ADP-glucose synthase) (Cytochrome c oxidase polypeptide I) (Protein bronze-2) (Protein VIVIPAROUS14)(VP-14) (IAA-Glu synthase)((Uridine 5'-diphosphate-glucose:indol-3-ylacetyl)-beta-D-glucosyl transferase) (Glucose phosphomutase 2) (Glutamate--ammonia ligase) (Phosphoglucose isomerase)(PGI)(Phosphohexose isomerase)(PHI) (ZmMTHFR1)