gcttttcattctgactgcaacgggcaatatgtctctgtgtggattaaaaaaagagtgtctgatagcagcttctgaactggttacctgccgtgagtaaattaaaattttattgactta

1
???????????????

• ?.?. ???????(24 ????? 2009 ?.)
• ????????? ???????????? ? ??????????????,
• 2 ????, ???????? ???????

2
gcttttcattctgactgcaacgggcaatatgtctctgtgtggattaaaaa
aagagtgtctgatagcagcttctgaactggttacctgccgtgagtaaatt
aaaattttattgactta ggtcactaaatactttaaccaatataggcata
gcgcacagacagataaaaattacagagtacacaacatccatgaaacgcat
tagcaccaccattaccaccaccatcaccattacca acggtgcgggctga
cgcgtacaggaaacacagaaaaaagcccgcacctgacagtgcgggctttt
tttttcgaccaaaggtaacgaggtaacaaccatgcgagtgttgaagttcg
gca catcagtggcaaatgcagaacgttttctgcgtgttgccgatattct
ggaaagcaatgccaggcaggggcaggtggccaccgtcctctctgcccccg
ccaaaatcaccaaccacctgg cgatgattgaaaaaaccattagcggcca
ggatgctttacccaatatcagcgatgccgaacgtatttttgccgaacttt
tgacgggactcgccgccgcccagccggggttcccgctgg aattgaaaac
tttcgtcgatcaggaatttgcccaaataaaacatgtcctgcatggcatta
gtttgttggggcagtgcccggatagcatcaacgctgcgctgatttgccgt
ggcgaga tgtcgatcgccattatggccggcgtattagaagcgcgcggtc
acaacgttactgttatcgatccggtcgaaaaactgctggcagtggggcat
tacctcgaatctaccgtcgatattg agtccacccgccgtattgcggcaa
gccgcattccggctgatcacatggtgctgatggcaggtttcaccgccggt
aatgaaaaaggcgaactggtggtgcttggacgcaacggttccg actctg
ctgcggtgctggctgcctgtttacgcgccgattgttgcgagatttggacg
gacgttgacggggtctatacctgcgacccgcgtcaggtgcccgatgcgag
gttgttgaagt tgtcctaccaggaagcgatggagctttcctacttcggc
gctaaagttcttcacccccgcaccattacccccatcgcccagttccagat
cccttgcctgattaaaaataccggaaatc aagcaccaggtacgctcatt
ggtgccagccgtgatgaagacgaattaccggtcaagggcatttccaatct
gaataacatggcaatgttcagcgtttctggtccggggatgaaaggga tc
ggcatggcggcgcgcgtctttgcagcgatgtcacgcgcccgtatttccgt
ggtgctgattacgcaatcatcttccgaatacagcatcagtttctgcgttc
cacaaagcgacttgc gagctgaacgggcaatgcaggaagagttctacct
ggaactgaaagaaggcttactggagccgctggcagtgacggaacggctgg
ccattatctcggtggtaggtgatggtagcacct tgcgtgggatctcggc
gaaattctttgccgcactggcccgcgccaatatcaacattgtcgccattg
ctcagggatcttctgaacgctcaatctctgtcgtggtaaataacgatgat
g ccactggcgtgcgcgttactcatcagatgctgttcaataccgatcagg
ttatcgaagtgtttgtgattggcgtcggtggcgttggcggtgcgctgctg
gagcaactgaagcgtcagc gctggctgaagaataaacatatcgacttac
gtgtctgcggtgttgccaactcgaaggctctgctcaccaatgtacatggc
cttaatctggaaaactggcaggaagaactggcgcaag aagagccgttta
atctcgggcgcttaattcgcctcgtgaaagaatatcatctgctgaacccg
gtcattgttgactgcacttccagccaggcagtggcggatcaatatgccga
cttgc gcgaaggtttccacgttgtcacgccgaacaaaaaggccaacacc
tcgtcgatggattactaccatcagttgcgttatgcggcggaaaaatcgcg
gcgtaaattcctctatgacacca ttggggctggattaccggttattgag
aacctgcaaaatctgctcaatgcaggtgatgaattgatgaagttctccgg
cattctttctggttcgctttcttatatcttcggcaagttag aaggcatg
agtttctccgaggcgaccacgctggcgcgggaaatgggttataccgaacc
ggacccgcgagatgatctttctggtatggatgtggcgcgtaaactattga
ttctcgct aaacgggacgtgaactggagctggcggatattgaaattgaa
cctgtgctgcccgcagagtttaacgccgagggtgatgttgccgcttttat
ggcgaatctgtcacaactcgacgatc ttgccgcgcgcgtggcgaaggcc
cgtgatgaaggaaaagttttgcgctatgttggcaatattgatgaagatgg
cgtctgccgcgtgaagattgccgaagtggatggtaatgatccgc tcaaa
gtgaaaaatggcgaaaacgccctggccttctatagccactattatcagcc
gctgccgttggtactgcgcggatatggtgcgggcaatgacgttacagctg
ccggtgtctttg atctgctacgtaccctctcatggaagttaggagtctg
acatggttaaagtttatgccccggcttccagtgccaatatgagcgtcggg
tttgatgtgctcggggcggcggtgacacct gatggtgcattgctcggag
atgtagtcacggttgaggcggcagagacattcagtctcaacaacctcgga
cgctttgccgataagctgccgtcagaaccacgggaaaatatcgtttat t
gctgggagcgtttttgccaggaactgggtaagcaaattccagtggcgatg
accctggaaaagaatatgccgatcggttcgggcttaggctccagtgcctg
ttcggtggtcgcggcg atggcgatgaatgaacactgcggcaagccgctt
aatgacactcgtttgctggctttgatgggcgagctggaaggccgtatctc
cggcagcattcattacgacaacgtggcaccgtgt ctcggtggtatgcag
ttgatgatcgaagaaaacgacatcatcagccagcaagtgccagggtttga
tgagtggctgtgggtgctggcgtatccggggattaaagtctcgacggcag
aa agggctattttaccggcgcagtatcgccgccaggattgcattgcgca
cgggcgacatctggcaggcttcattcacgcctgctattcccgtcagcctg
agcttgccgcgaagctgatg gatgttatcgctgaaccctaccgtgaacg
gttactgccaggcttccggcaggcgcggcaggcggtcgcggaaatcggcg
cggtagcgagcggtatctccggctccggcccgaccttg gctctgtgtga
caagccggaaaccgcccagcgcgttgccgactggttgggtaagaactacc
tgcaaaatcaggaaggttttgttcatatttgccggctggatacggcgggc
gcacga ctggaaaactaaatgaaactctacaatctgaaagatcacaacg
agcaggtcagctttgcgcaagccgtaacccaggggttgggcaaaaatcag
gggctgttttttccgcacgacctg gaattcagcctgactgaaattgatg
agatgctgaagctggattttgtcacccgcagtgcgaagatcctctcggcg
tttattggtgatgaaatcccacaggaaatcctggaagagcgc cgcgcgg
cgtttgccttcccggctccggtcgccaatgttgaaagcgatgtcggttgt
ctggaattgttccacgggccaacgctggcatttaaagatttcggcggtcg
ctttatggca atgctgacccatattgcgggtgataagccagtgaccatt
ctgaccgcgacctccggtgataccggagcggcagtggctcatgctttcta
cggtttaccgaatgtgaaagtggttatc tatccacgaggcaaaatcagt
ccactgcaagaaaaactgttctgtacattgggcggcaatatcgaaactgt
tgccatcgacggcgatttcgatgcctgtcaggcgctggtgaagcag ttt
gatgatgaagaactgaaagtggcgctagggttaaactcggctaactcgat
taacatcagccgtttgctggcgcagatttgctactactttgaagctgttg
cgcagctgccgca acgcgcaaccagctggttgtctcggtgccaagcgga
aacttcggcgatttgacggcgggtctgctggcgaagtcactcggtctgcc
ggtgaaacgttttattgctgcgaccaacgtg gataccgtgccacgtttc
ctgcacgacggtcagtggtcacccaaagcgactcaggcgacgttatccaa
cgcgatggacgtgagtcagccgaacaactggccgcgtgtggaagagttg
cgccgcaaaatctggcaactgaaagagctgggttatgcagccgtggatga
tgaaaccacgcaacagacaatgcgtgagttaaaagaactgggctacactt
cggagccgcacgctgta gcttatcgtgcgctgcgtgatcagttgaatcc
aggcgaatatggcttgttcctcggcaccgcgcatccggcgaaatttaaag
agagcgtggaagcgattctcggtgaaacgttggat ccaaaagagctggc
agaacgtgctgatttacccttgctttcacataatctgcccgccgattttg
ctgcgttgcgtaaattgatgatgaatcatcagtaaaatctattcattatc
tca aggccgggtttgcttttatgcagcccggcttttttatgaagaaatt
atggagaaaaatgacagggaaaaaggagaaattctcaataaatgcggtaa
cttagagattaggattgcgga taacaaccgccgttctcatcgagtaatc
tccggatatcgacccataacgggcaatgataaaaggagtaacctgtgaaa
aagatgcaatctatcgtactcgcactttccctggttctg gctcccatgg
cagcacaggctgcggaaattacgttagtcccgtcagtaaaattacagata
ggcgatcgtgataatcgtggctattactgggatggaggtcactggcgcga
ccacggc
??????? ??????? ????
3
???? 2009

• EMBL
• Number of entries - 155 587 665
  http//www3.ebi.ac.uk/Services/DBStats/
• TrEMBL
• Number of entries- 7 341 751
• Swiss-Prot
• Number of entries - 412 525
• http//www.expasy.ch/sprot

4
??? ?????? ??????? ????? ??? ?????

• ??????????? ?????? ? ????????????
• ????? ?????????? ? ???????????
• ???????????? ?????????
• ?????? ?????? ?????????, ..
• ????? ?????? ?.?.?????????
• - - - - - - - - - - - ????? ?????????- - - - - -
  - - -
• ?????????
• ?????? ??????, ?????? ???

5
A Summary of the E. coli chromosome(Gene Type
Distribution), data from http//genprotec.mbl.edu
/overview.html
Unknown 598
Miscellaneous, 27
RNAs, 156
Experimental 2121
By similarity 1098
Updated August 29st, 2007
6

• ???????? ?????????????????? ???? ??????
• ???????? ?? ???????????????????
• EMBL, GeneBank, UniProt, SwissProt.
• ??????????? PFAM,PROSITE, INTERPRO, dbEST,
  dbSNP.
• ?? 3D-???????? PDB.
• ??????????? SCOP, CATH, RNABase..
• ?? ? ????????????, ? ??????? ???????? ???????
  ??????? ????? ? ?? ????????? KEGG, BIOCYC,
  ENZYME, TC-DB, REACTOME.
• ????????? GO, OBO, HUGO......

7
??????? ????? ?????????

8
??? ???????? ???? ? ?? ????????
9
??????? ??????? ? Swiss-Prot ?
1 ?????, 2 ????
1 ?????, 4 ????
2 ??????
1 ??????
10
??????????????????, EC 1.1.1.37 (S)-malate
NAD oxaloacetate NADH H
????? ??????? 3 ???????? ? ? 43-50
??????????????
11
??? ????? "???????"?( ??? ??????? ????? ?
??????? ???????????? ??????)

• ????
• ??????????? (????? ? ?????????, ??????,
  ?????????)
• ??????
• ??????????????, ???? ? ????????? (??????)
• ????
• ??? ????????????? ?????????
• ? ????
• ??? ???????? ???? (?????????????)

12
????????,

• LACY_ECOLI
• ????????? ????????
• ????????? ??????? ?
• ????????????? ??????
• ??????? H/?????
• ????????? ???????????

• LDH_ECOLI
• ??????????
• ?????????? ????????
• ???????????????, ????? ?????? CH-OH, ????????
  ???
• D-???????????????????

13
??????? ?? ?????????? ??????, ?? ??? ? ?? ?????

• ???? ????? ? ????? ???????
• 1.1
• 1.2. ???????? ? ?????????????
  ????????????????
• ????????
  ????????
• ???? ??????? ? ????? ??????
• 2.1. ???????????? ??? ????????????????????
  ?
• 2.2. ??????????? ????????.

TRPC_ECOLI
?? 4.1.1.48 ?? 5.3.1.24
14
??? ?????? ???????? ???????

• ??????? ???????? ??????? ?????? ????? ? ?????? ??
  ?????? ??????? ??.
• ??????? ???????? ??????? ???????? ?????? ?
  ???????
• ??. ? ?
• ????????? ???????? ??????? ????? ? ?? ?????????
  ?? ? ?????????????, ????? ???
  ???
• ????????? ???????? ????????? ??????? ??????? ?
  ??????????????? ?????? ??. ? ??????????????????
  ??, ????? ??? ENZYME , ,
  ...

15
(No Transcript)
16
????? ???????, ?? ??????? ????????

• ??????? ?????? ????????
• phosphopyruvate hydratase,
  2-phosphoglycerate dehydratase, enolase

• 2-?????-D-????????ltgt ???????????????? H2O

2. ??? ????? ??, ??? ?????????, ??? ?????????? ?
tricarboxylic acid cycleTCA cycleKrebs
cyclecitrate cyclecitric acid cycle
BioCyc ????? TCA cycle ? tricarboxylic acid
cycle KEGG ???????? Citrate cycle ? TCA
cycle ? Reductive carboxylate cycle .

-- ?????????? ???? ? BioCyc ? KEGG, ?? ??? ????
?? ???????? oxygen transport

17
(No Transcript)
18
???? GO (Gene Ontology )

• ???????? ????????? ????????????? ?????
  ????????????? ?????? ?
• ???????????? ???????? (Function) (???? ? ????)
  ????????, carbohydrate binding ??? ATPase
  activity
• ????????????? ????????? (Process) (??????)
  ????????, ????? ??? ?????????
  ???????
• ????????? ??????????? (Component) (????)
  ????????, ???? ??? ???????????
  ???-?????????? II
• ???????? ?????? ?????, ??????????? ??? ????
  ??????????.
• ???????? ?????????? ???????????? ??? ?????????
  ????? ? ????????? ?????????? ? ?????? ?????.

19
??? ????? GO ?

• 3 ??????????? ??????? ????????
• Molecular Function (???? ? ????)
• Biological Process (??????)
• Cellular Component (????)
• ??????? ????? ??????????? ? ???????? ?????????.
• ??????? ? ???????? ????? ????????? ???????
  ??????????? "_is_a", "_is_part_of" ??? "has
  part_of"
• ??????? ????? ??????????? ??????????????.

20

• tricarboxylic acid cycle
• Accession GO0006099
• Ontology biological_process
• Synonyms
• exact citric acid cycle
• exact Krebs cycle
• exact TCA cycle
• Definition A nearly universal metabolic pathway
  in which the acetyl group of acetyl coenzyme A is
  effectively oxidized to two C02 and four pairs of
  electrons are transferred to coenzymes. The
  acetyl group combines with oxaloacetate to form
  citrate, which undergoes successive
  transformations to isocitrate, 2-oxoglutarate,
  succinyl-CoA, succinate, fumarate, malate, and
  oxaloacetate again, thus completing the cycle. In
  eukaryotes the tricarboxylic acid is confined to
  the mitochondria. See also glyoxylate cycle.

21
????????? GO ??? HBB_HUMAN (UniProt)

1. ??? ??? ??????? ???????????? ?? ????? ???
   ??????????? ????????? ?? ???? ???? ?????????.
2. ??????? ????? ??? ??????????? ?????????

22
DAG ??????????????? ???????????? ????

• ????????? "_is_a"
• "A is B" ????????, ???
• ? ??????? ?????? ?

• ????????? "is_part_of"
• "A is part of B" ????????, ??? ? ????? ?,
  ??
• ? ?? ??????????? ???????? ?.

23
Evidence Codes

• EXP Inferred from Experiment
• IDA Inferred from Direct Assay
• TAS Traceable Author Statement
• IMP Inferred from Mutant Phenotype
• IGI Inferred from Genetic Interaction
• IPI Inferred from Physical Interaction
• RCA Inferred from Reviewed Computational
  Analysis
• ISS Inferred from Sequence Similarity
• IEP Inferred from Expression Pattern
• NAS Non-traceable Author Statement
• IEA Inferred from Electronic Annotation
• IC Inferred by Curator
• ND No biological Data available

24
???? ? ?????? ?????????, ????????,
exon, promoter, binding_site, non_canonical_splice
_site, stop_codon. pseudogene
25
http//obo.sourceforge.net/main.htm
26
??????

• ?????????????? ????????? ??????? ??????
  ??????????????
• ?????????? ????????????, ??? ????? ?????? ?
  ???????? ????? ? ?? ?????????, ????????, BioCyc.
• ?????? ???????? ??????? ??? ?????? ?? ???????
  "????", "??????", "????, "? ????.
• GO ????????????? ?????? ?
• ?????????? ?????? ????? (??????? ????????
  ?????????),
• ?????????? ???????????????? ???????? ???????,
  ?????? ??? ???? ??????????.