Supported by Dr. Osamu Ogasawara and  providing  . |
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Last data update: 2014.03.03 |
Retrieves given database entriesDescriptionRetrieves given database entries. Usage
keggGet(dbentries, option = c("aaseq", "ntseq", "mol", "kcf",
"image", "kgml"))
Arguments
DetailsRetrieves all entries from the KEGG database for a set of KEGG identifers.
ValueA list wrapping a KEGG flat file.
If Author(s)Dan Tenenbaum Referenceshttp://www.kegg.jp/kegg/docs/keggapi.html Examples
keggGet(c("cpd:C01290", "gl:G00092")) ## retrieves a compound entry
## and a glycan entry
keggGet(c("C01290", "G00092")) ## same as above, without prefixes
keggGet(c("hsa:10458", "ece:Z5100")) ## retrieves a human gene entry
## and an E.coli O157 gene entry
keggGet(c("hsa:10458", "ece:Z5100"), "aaseq") ## retrieves amino acid sequences
## of a human gene and an
## E.coli O157 gene
png <- keggGet("hsa05130", "image") ## retrieves the image file of a
## pathway map
t <- tempfile()
library(png)
writePNG(png, t)
keggGet("hsa05130", "kgml")
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(KEGGREST)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/KEGGREST/keggGet.Rd_%03d_medium.png", width=480, height=480)
> ### Name: keggGet
> ### Title: Retrieves given database entries
> ### Aliases: keggGet
> ### Keywords: get
>
> ### ** Examples
>
> keggGet(c("cpd:C01290", "gl:G00092")) ## retrieves a compound entry
[[1]]
[[1]]$ENTRY
Compound
"C01290"
[[1]]$NAME
[1] "beta-D-Galactosyl-(1->4)-beta-D-glucosyl-(1<->1)-ceramide;"
[2] "beta-D-Galactosyl-1,4-beta-D-glucosylceramide;"
[3] "Lactosylceramide;"
[4] "Gal-beta1->4Glc-beta1->1'Cer;"
[5] "LacCer;"
[6] "Lactosyl-N-acylsphingosine;"
[7] "D-Galactosyl-1,4-beta-D-glucosylceramide"
[[1]]$FORMULA
[1] "C31H56NO13R"
[[1]]$REMARK
[1] "Same as: G00092"
[[1]]$COMMENT
[1] "Generic compound in reaction hierarchy"
[[1]]$REACTION
[1] "R03354 R03355 R03486 R03488 R03489 R03490 R03491 R03492"
[2] "R03618 R04493"
[[1]]$PATHWAY
map00600 map01100
"Sphingolipid metabolism" "Metabolic pathways"
[[1]]$MODULE
M00066
"Lactosylceramide biosynthesis"
[[1]]$ENZYME
[1] "2.4.1.92" "2.4.1.206" "2.4.1.228" "2.4.1.274" "2.4.99.9" "2.4.99.11"
[7] "3.2.1.18" "3.2.1.22" "3.2.1.23" "3.2.1.47" "3.2.1.52"
[[1]]$BRITE
[1] "Compounds with biological roles [BR:br08001]"
[2] " Lipids"
[3] " Glycolipids"
[4] " Glycosphingolipids"
[5] " C01290 Lactosylceramide"
[[1]]$DBLINKS
[1] "PubChem: 4509" "ChEBI: 17950"
[3] "LIPIDMAPS: LMSP0501AB00" "LipidBank: GSG1147"
[[1]]$ATOM
[1] "46" "1 C1y C 15.9666 -18.9599"
[3] "2 C1y C 15.9337 -17.5704" "3 O2a O 14.6552 -19.6363"
[5] "4 C1y C 17.0731 -19.6917" "5 O2x O 17.1379 -16.9034"
[7] "6 C1b C 14.7200 -16.8477" "7 C1y C 13.4603 -20.3126"
[9] "8 C1y C 18.3146 -19.0155" "9 O1a O 17.0361 -21.0907"
[11] "10 C1y C 18.3516 -17.6260" "11 O1a O 13.5250 -17.5795"
[13] "12 O2x O 12.2464 -19.5899" "13 C1y C 13.4138 -21.7206"
[15] "14 O1a O 19.5096 -19.7567" "15 O2a O 19.5838 -16.9684"
[17] "16 C1y C 11.0238 -20.2570" "17 C1y C 12.1817 -22.3786"
[19] "18 O1a O 14.4327 -22.2303" "19 C1b C 20.8066 -17.6631"
[21] "20 C1y C 10.9958 -21.6650" "21 C1b C 9.8285 -19.5342"
[23] "22 O1a O 12.1446 -23.7866" "23 C1c C 22.0202 -16.9404"
[25] "24 O1a O 9.7361 -22.3415" "25 O1a O 8.6335 -20.2570"
[27] "26 C1c C 23.2614 -17.6351" "27 N1b N 22.0108 -15.5323"
[29] "28 C2b C 24.4844 -16.9128" "29 O1a O 23.2708 -19.0435"
[31] "30 C5a C 23.2152 -14.8191" "31 C2b C 25.7073 -17.6074"
[33] "32 O5a O 23.2666 -13.4107" "33 R R 24.4473 -15.5044"
[35] "34 C1b C 26.9207 -16.8942" "35 C1b C 28.1529 -17.5889"
[37] "36 C1b C 29.3758 -16.8663" "37 C1b C 30.5987 -17.5610"
[39] "38 C1b C 31.8216 -16.8386" "39 C1b C 33.0537 -17.5242"
[41] "40 C1b C 34.2672 -16.8107" "41 C1b C 35.4993 -17.5056"
[43] "42 C1b C 36.7128 -16.7921" "43 C1b C 37.9543 -17.4777"
[45] "44 C1b C 39.1678 -16.7736" "45 C1b C 40.4001 -17.4591"
[47] "46 C1a C 41.6137 -16.7459"
[[1]]$BOND
[1] "47" "1 1 2 1" "2 1 3 1 #Down"
[4] "3 1 4 1" "4 2 5 1" "5 2 6 1 #Up"
[7] "6 7 3 1 #Up" "7 4 8 1" "8 4 9 1 #Up"
[10] "9 5 10 1" "10 6 11 1" "11 7 12 1"
[13] "12 7 13 1" "13 8 14 1 #Down" "14 10 15 1 #Up"
[16] "15 12 16 1" "16 13 17 1" "17 13 18 1 #Down"
[19] "18 15 19 1" "19 16 20 1" "20 16 21 1 #Up"
[22] "21 17 22 1 #Up" "22 19 23 1" "23 20 24 1 #Up"
[25] "24 21 25 1" "25 23 26 1" "26 23 27 1 #Down"
[28] "27 26 28 1" "28 26 29 1 #Up" "29 27 30 1"
[31] "30 28 31 2" "31 30 32 2" "32 30 33 1"
[34] "33 31 34 1" "34 34 35 1" "35 35 36 1"
[37] "36 36 37 1" "37 37 38 1" "38 38 39 1"
[40] "39 39 40 1" "40 40 41 1" "41 41 42 1"
[43] "42 42 43 1" "43 43 44 1" "44 44 45 1"
[46] "45 45 46 1" "46 8 10 1" "47 17 20 1"
[[2]]
[[2]]$ENTRY
Glycan
"G00092"
[[2]]$NAME
[1] "Lactosylceramide;" "CDw17;" "LacCer"
[[2]]$COMPOSITION
[1] "(Gal)1 (Glc)1 (Cer)1"
[[2]]$MASS
[1] "324.3 (Cer)"
[[2]]$CLASS
[1] "Glycolipid; Sphingolipid"
[[2]]$REMARK
[1] "Same as: C01290"
[[2]]$REACTION
[1] "R05937 R05938 R05960 R05961 R05971 R05999 R06001 R06099"
[2] "R06121 R06136 R06276"
[[2]]$PATHWAY
map00601
"Glycosphingolipid biosynthesis - lacto and neolacto series"
map00603
"Glycosphingolipid biosynthesis - globo series"
map00604
"Glycosphingolipid biosynthesis - ganglio series"
[[2]]$MODULE
M00068
"Glycosphingolipid biosynthesis, globo-series, LacCer => Gb4Cer"
M00069
"Glycosphingolipid biosynthesis, ganglio series, LacCer => GT3"
M00070
"Glycosphingolipid biosynthesis, lacto-series, LacCer => Lc4Cer"
M00071
"Glycosphingolipid biosynthesis, neolacto-series, LacCer => nLc4Cer"
[[2]]$ENZYME
[1] "2.4.1.92" "2.4.1.206" "2.4.1.228" "2.4.1.274" "2.4.99.9" "2.4.99.11"
[7] "3.2.1.18" "3.2.1.22" "3.2.1.23" "3.2.1.47" "3.2.1.52"
[[2]]$ORTHOLOGY
K00725
"(N-Acetylneuraminyl)-galactosylglucosylceramide N-acetylgalactosaminyltransferase [EC:2.4.1.92]"
K01189
"alpha-galactosidase [EC:3.2.1.22]"
K01988
"lactosylceramide 4-alpha-galactosyltransferase [EC:2.4.1.228]"
K03370
"lactosylceramide alpha-2,3-sialyltransferase (sialyltransferase 9) [EC:2.4.99.9]"
[[2]]$DBLINKS
[1] "CCSD: 83 84 2309 3311 3312 3314 4656 4728 5270 5511 5721 7517 9378 9972 10020 10305 11327 11408 11611 11640 11800 12377 14422 14495 14875 15723 15901 16352 16402 16459 16571 16867 17112 17685 17711 18546 18588 19340 20904 22110 23020 24110 24125 24437 24647 24765 24980 24987 25039 25254 25319 25327 25415 25635 25918 26178 26266 26397 26587 26596 26613 26735 27272 27460 27539 27631 27665 27667 27668 28496 28551 28993 29095 29267 29288 29400 29413 29704 29910 29959 29988 30832 30871 31629 31689 31974 32046 32547 32590 32592 32679 32729 32736 32739 32888 32927 33058 33106 33184 33203 33206 33244 33403 33465 33524 33586 33673 33711 33807 33894 34168 34751 35120 35270 35315 35363 35552 35591 35920 35948 35993 36113 36144 36163 36217 36282 36460 36581 36643 36655 36859 36981 36986 36990 36997 37006 37051 37061 37074 37089 37243 37260 37401 37603 37838 38058 38087 38089 38110 38140 38537 38674 39382 39519 39662 40781 40815 41776 41868 41900 42042 42730 42915 42981 43024 43460 43579 43795 44037 44063 44081 44242 44498 44962 44991 45299 45662 46197 46400 46801 46839 47203 47380 47423 47598 47631 47659 47700 47736 47855 48195 48203 48252 48376 48600 48901 49326 49446 49510 50270"
[2] "GlycomeDB: 118"
[3] "JCGGDB: JCGG-STR001961"
[4] "LipidBank: GSG1147"
[[2]]$NODE
[1] "3" "1 Cer 9 0"
[3] "2 Glc 0 0" "3 Gal -9 0"
[[2]]$EDGE
[1] "2" "1 2:b1 1:1" "2 3:b1 2:4"
[[2]]$REFERENCE
[[2]]$REFERENCE[[1]]
[[2]]$REFERENCE[[1]]$REFERENCE
[1] "1 [PMID:3392043]"
[2] "Larson G, Falk P, Hoskins LC."
[3] "Degradation of human intestinal glycosphingolipids by extracellular glycosidases from mucin-degrading bacteria of the human fecal flora."
[4] "J. Biol. Chem. 263 (1988) 10790-8."
[5] "2 [PMID:14631106]"
[6] "Wu AM."
[7] "Carbohydrate structural units in glycoproteins and polysaccharides as important ligands for Gal and GalNAc reactive lectins."
[8] "J. Biomed. Sci. 10 (2003) 676-88."
[9] "3 [PMID:2960671]"
[10] "Holmes EH, Hakomori S, Ostrander GK."
[11] "Synthesis of type 1 and 2 lacto series glycolipid antigens in human colonic adenocarcinoma and derived cell lines is due to activation of a normally unexpressed beta 1----3N-acetylglucosaminyltransferase."
[12] "J. Biol. Chem. 262 (1987) 15649-58."
[13] "4 [PMID:15546874]"
[14] "Ideo H, Seko A, Yamashita K."
[15] "Galectin-4 binds to sulfated glycosphingolipids and carcinoembryonic antigen in patches on the cell surface of human colon adenocarcinoma cells."
[16] "J. Biol. Chem. 280 (2005) 4730-7."
> ## and a glycan entry
> keggGet(c("C01290", "G00092")) ## same as above, without prefixes
[[1]]
[[1]]$ENTRY
Compound
"C01290"
[[1]]$NAME
[1] "beta-D-Galactosyl-(1->4)-beta-D-glucosyl-(1<->1)-ceramide;"
[2] "beta-D-Galactosyl-1,4-beta-D-glucosylceramide;"
[3] "Lactosylceramide;"
[4] "Gal-beta1->4Glc-beta1->1'Cer;"
[5] "LacCer;"
[6] "Lactosyl-N-acylsphingosine;"
[7] "D-Galactosyl-1,4-beta-D-glucosylceramide"
[[1]]$FORMULA
[1] "C31H56NO13R"
[[1]]$REMARK
[1] "Same as: G00092"
[[1]]$COMMENT
[1] "Generic compound in reaction hierarchy"
[[1]]$REACTION
[1] "R03354 R03355 R03486 R03488 R03489 R03490 R03491 R03492"
[2] "R03618 R04493"
[[1]]$PATHWAY
map00600 map01100
"Sphingolipid metabolism" "Metabolic pathways"
[[1]]$MODULE
M00066
"Lactosylceramide biosynthesis"
[[1]]$ENZYME
[1] "2.4.1.92" "2.4.1.206" "2.4.1.228" "2.4.1.274" "2.4.99.9" "2.4.99.11"
[7] "3.2.1.18" "3.2.1.22" "3.2.1.23" "3.2.1.47" "3.2.1.52"
[[1]]$BRITE
[1] "Compounds with biological roles [BR:br08001]"
[2] " Lipids"
[3] " Glycolipids"
[4] " Glycosphingolipids"
[5] " C01290 Lactosylceramide"
[[1]]$DBLINKS
[1] "PubChem: 4509" "ChEBI: 17950"
[3] "LIPIDMAPS: LMSP0501AB00" "LipidBank: GSG1147"
[[1]]$ATOM
[1] "46" "1 C1y C 15.9666 -18.9599"
[3] "2 C1y C 15.9337 -17.5704" "3 O2a O 14.6552 -19.6363"
[5] "4 C1y C 17.0731 -19.6917" "5 O2x O 17.1379 -16.9034"
[7] "6 C1b C 14.7200 -16.8477" "7 C1y C 13.4603 -20.3126"
[9] "8 C1y C 18.3146 -19.0155" "9 O1a O 17.0361 -21.0907"
[11] "10 C1y C 18.3516 -17.6260" "11 O1a O 13.5250 -17.5795"
[13] "12 O2x O 12.2464 -19.5899" "13 C1y C 13.4138 -21.7206"
[15] "14 O1a O 19.5096 -19.7567" "15 O2a O 19.5838 -16.9684"
[17] "16 C1y C 11.0238 -20.2570" "17 C1y C 12.1817 -22.3786"
[19] "18 O1a O 14.4327 -22.2303" "19 C1b C 20.8066 -17.6631"
[21] "20 C1y C 10.9958 -21.6650" "21 C1b C 9.8285 -19.5342"
[23] "22 O1a O 12.1446 -23.7866" "23 C1c C 22.0202 -16.9404"
[25] "24 O1a O 9.7361 -22.3415" "25 O1a O 8.6335 -20.2570"
[27] "26 C1c C 23.2614 -17.6351" "27 N1b N 22.0108 -15.5323"
[29] "28 C2b C 24.4844 -16.9128" "29 O1a O 23.2708 -19.0435"
[31] "30 C5a C 23.2152 -14.8191" "31 C2b C 25.7073 -17.6074"
[33] "32 O5a O 23.2666 -13.4107" "33 R R 24.4473 -15.5044"
[35] "34 C1b C 26.9207 -16.8942" "35 C1b C 28.1529 -17.5889"
[37] "36 C1b C 29.3758 -16.8663" "37 C1b C 30.5987 -17.5610"
[39] "38 C1b C 31.8216 -16.8386" "39 C1b C 33.0537 -17.5242"
[41] "40 C1b C 34.2672 -16.8107" "41 C1b C 35.4993 -17.5056"
[43] "42 C1b C 36.7128 -16.7921" "43 C1b C 37.9543 -17.4777"
[45] "44 C1b C 39.1678 -16.7736" "45 C1b C 40.4001 -17.4591"
[47] "46 C1a C 41.6137 -16.7459"
[[1]]$BOND
[1] "47" "1 1 2 1" "2 1 3 1 #Down"
[4] "3 1 4 1" "4 2 5 1" "5 2 6 1 #Up"
[7] "6 7 3 1 #Up" "7 4 8 1" "8 4 9 1 #Up"
[10] "9 5 10 1" "10 6 11 1" "11 7 12 1"
[13] "12 7 13 1" "13 8 14 1 #Down" "14 10 15 1 #Up"
[16] "15 12 16 1" "16 13 17 1" "17 13 18 1 #Down"
[19] "18 15 19 1" "19 16 20 1" "20 16 21 1 #Up"
[22] "21 17 22 1 #Up" "22 19 23 1" "23 20 24 1 #Up"
[25] "24 21 25 1" "25 23 26 1" "26 23 27 1 #Down"
[28] "27 26 28 1" "28 26 29 1 #Up" "29 27 30 1"
[31] "30 28 31 2" "31 30 32 2" "32 30 33 1"
[34] "33 31 34 1" "34 34 35 1" "35 35 36 1"
[37] "36 36 37 1" "37 37 38 1" "38 38 39 1"
[40] "39 39 40 1" "40 40 41 1" "41 41 42 1"
[43] "42 42 43 1" "43 43 44 1" "44 44 45 1"
[46] "45 45 46 1" "46 8 10 1" "47 17 20 1"
[[2]]
[[2]]$ENTRY
Glycan
"G00092"
[[2]]$NAME
[1] "Lactosylceramide;" "CDw17;" "LacCer"
[[2]]$COMPOSITION
[1] "(Gal)1 (Glc)1 (Cer)1"
[[2]]$MASS
[1] "324.3 (Cer)"
[[2]]$CLASS
[1] "Glycolipid; Sphingolipid"
[[2]]$REMARK
[1] "Same as: C01290"
[[2]]$REACTION
[1] "R05937 R05938 R05960 R05961 R05971 R05999 R06001 R06099"
[2] "R06121 R06136 R06276"
[[2]]$PATHWAY
map00601
"Glycosphingolipid biosynthesis - lacto and neolacto series"
map00603
"Glycosphingolipid biosynthesis - globo series"
map00604
"Glycosphingolipid biosynthesis - ganglio series"
[[2]]$MODULE
M00068
"Glycosphingolipid biosynthesis, globo-series, LacCer => Gb4Cer"
M00069
"Glycosphingolipid biosynthesis, ganglio series, LacCer => GT3"
M00070
"Glycosphingolipid biosynthesis, lacto-series, LacCer => Lc4Cer"
M00071
"Glycosphingolipid biosynthesis, neolacto-series, LacCer => nLc4Cer"
[[2]]$ENZYME
[1] "2.4.1.92" "2.4.1.206" "2.4.1.228" "2.4.1.274" "2.4.99.9" "2.4.99.11"
[7] "3.2.1.18" "3.2.1.22" "3.2.1.23" "3.2.1.47" "3.2.1.52"
[[2]]$ORTHOLOGY
K00725
"(N-Acetylneuraminyl)-galactosylglucosylceramide N-acetylgalactosaminyltransferase [EC:2.4.1.92]"
K01189
"alpha-galactosidase [EC:3.2.1.22]"
K01988
"lactosylceramide 4-alpha-galactosyltransferase [EC:2.4.1.228]"
K03370
"lactosylceramide alpha-2,3-sialyltransferase (sialyltransferase 9) [EC:2.4.99.9]"
[[2]]$DBLINKS
[1] "CCSD: 83 84 2309 3311 3312 3314 4656 4728 5270 5511 5721 7517 9378 9972 10020 10305 11327 11408 11611 11640 11800 12377 14422 14495 14875 15723 15901 16352 16402 16459 16571 16867 17112 17685 17711 18546 18588 19340 20904 22110 23020 24110 24125 24437 24647 24765 24980 24987 25039 25254 25319 25327 25415 25635 25918 26178 26266 26397 26587 26596 26613 26735 27272 27460 27539 27631 27665 27667 27668 28496 28551 28993 29095 29267 29288 29400 29413 29704 29910 29959 29988 30832 30871 31629 31689 31974 32046 32547 32590 32592 32679 32729 32736 32739 32888 32927 33058 33106 33184 33203 33206 33244 33403 33465 33524 33586 33673 33711 33807 33894 34168 34751 35120 35270 35315 35363 35552 35591 35920 35948 35993 36113 36144 36163 36217 36282 36460 36581 36643 36655 36859 36981 36986 36990 36997 37006 37051 37061 37074 37089 37243 37260 37401 37603 37838 38058 38087 38089 38110 38140 38537 38674 39382 39519 39662 40781 40815 41776 41868 41900 42042 42730 42915 42981 43024 43460 43579 43795 44037 44063 44081 44242 44498 44962 44991 45299 45662 46197 46400 46801 46839 47203 47380 47423 47598 47631 47659 47700 47736 47855 48195 48203 48252 48376 48600 48901 49326 49446 49510 50270"
[2] "GlycomeDB: 118"
[3] "JCGGDB: JCGG-STR001961"
[4] "LipidBank: GSG1147"
[[2]]$NODE
[1] "3" "1 Cer 9 0"
[3] "2 Glc 0 0" "3 Gal -9 0"
[[2]]$EDGE
[1] "2" "1 2:b1 1:1" "2 3:b1 2:4"
[[2]]$REFERENCE
[[2]]$REFERENCE[[1]]
[[2]]$REFERENCE[[1]]$REFERENCE
[1] "1 [PMID:3392043]"
[2] "Larson G, Falk P, Hoskins LC."
[3] "Degradation of human intestinal glycosphingolipids by extracellular glycosidases from mucin-degrading bacteria of the human fecal flora."
[4] "J. Biol. Chem. 263 (1988) 10790-8."
[5] "2 [PMID:14631106]"
[6] "Wu AM."
[7] "Carbohydrate structural units in glycoproteins and polysaccharides as important ligands for Gal and GalNAc reactive lectins."
[8] "J. Biomed. Sci. 10 (2003) 676-88."
[9] "3 [PMID:2960671]"
[10] "Holmes EH, Hakomori S, Ostrander GK."
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Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and