y‚qexssxq exh gyw€ „sxq wi„efyvsg €e„r‡e‰

he„e sx „i‚wƒ yp fsxe‚‰ ‚ive„syxƒ

— ˜

ƒF qy„yD rF fyxyD rF yqe„eD ‡F p tsf grsD „F xsƒrsyueD uF ƒe„yD

wF uexirsƒe

snstitute for ghemi™—l ‚ese—r™hD uyoto niversityD

jiD uyoto TIID t—p—n

e new d—t—˜—se system n—med uiqq is ˜ eing org—nized to ™omputerize fun™E

tion—l —sp e™ts of genes —nd genomes in terms of the ˜in—ry rel—tions of inter—™ting

mole™ules or genesF ‡e —re ™urrently working on the met—˜oli™ p—thw—y d—t—˜—se

th—t is ™omp osed of three inter™onne™ted se™tionsX genesD mole™ulesD —nd p—thw—ysD

whi™h —re —lso linked to — num˜ er of existing d—t—˜—ses through our hfqi„ reE

triev—l systemF rere we present the ˜—si™ ™on™ept of ˜in—ry rel—tions —nd hierE

—r™hi™—l ™l—ssi™—tions to represent the met—˜oli™ p—thw—y d—t—F „he d—t—˜—se

oper—tions —re then dened —s —n extension of the rel—tion—l oper—tionsD —nd the

p—th ™omput—tion pro˜lem is ™onsidered —s — dedu™tion from ˜in—ry rel—tionsF en

ex—mple of using uiqq for the fun™tion—l predi™tion of genomi™ sequen™es is preE

sentedF

I sntrodu™tion

I

„he rst ™omplete genome of —n org—nismD 0xIURD w—s determined in IWUUD

whi™hw—s followed ˜y the explosion of hxe sequen™e d—t— for sp e™i™ genesD

—s well —s for sm—ll genomes of viruses —nd org—nellesF „he rst ™omplete

genome of — freeEliving org—nismD r—emophilus inuenz—e Dw—s determined in

P

IWWSD whi™hwould ™ert—inly ˜ e followed ˜y the explosion of ™omplete genomi™

sequen™es —nd ™omplete gene ™—t—logs of — num˜ er of org—nisms from ˜—™teri—

to euk—ryotesF ‡here—s the exp eriment—l te™hnologies h—ve ˜ een rened to

system—ti™—lly —n—lyze — whole genomeD the ™omput—tion—l metho ds for de™iE

phering fun™tion—l impli™—tions —re still ˜—sed on the —n—lysis of e—™h gene or

gene pro du™t —t — timeF e system—ti™ ™omput—tion—l —n—lysis is required for

fun™tion—l predi™tion of — whole genomeF

et presen tD the fun™tion—l d—t— is ™omputerized —s —n —ttri˜ute of e—™h

sequen™eD for ex—mpleD in the fe—tures t—˜les of the sequen™e d—t—˜—ses —nd

Q

in the motif li˜r—ries su™h —s €‚yƒs„iF „husD the ˜—si™ ide— for fun™tion—l

predi™tion is to se—r™h simil—rities of e—™h sequen™e in the sequen™e d—t—˜—ses

or in the motif li˜r—ries —nd then to extend sequen™e simil—rities to fun™tion—l

—

€resent —ddressX qr—du—te s™hool of egri™ultureD uyoto niversityD ƒ—kyoEkuD uyoto

THTEHID t—p—n

˜

€erm—nent —ddressX gr—y ‚ese—r™h t—p—n v„hFD IPEPS riroshi˜—E™hoD ƒuit—EshiD ys—k— STRD t—p—n

simil—ritiesF „he pro˜lem here is the l—™k of — suit—˜le me—sure for the ™orE

re™tness of fun™tion—l —ssignmentD esp e™i—lly for the simil—rities in the soE™—lled

twilight zoneF „he sequen™eEfun™tion rel—tionships of single mole™ules repreE

sent how individu—l ™omp onents of — ˜iologi™—l system workD —nd they do not

™ont—in higher level inform—tion of how ™omp onents —re ™onne™ted to form —

fun™tion—l unitD su™h —s — met—˜ oli™ p—thw—yD — sign—l tr—nsdu™tion —nd —n

op eronF es long —s the —ssignment is m—de for e—™h ™omp onent sep—r—telyDit

will ˜ e di™ult to ™he™k if su™h — fun™tion—l unit is prop erly formedF

™

‡eh—ve initi—ted — pro je™t n—med uiqqD uyoto in™y™lop edi— of qenes

—nd qenomesD to ™omputerize ™urren t knowledge of the inform—tion p—thw—ys

of genes —nd gene pro du™tsD whi™hm—y ˜ e ™onsidered —s wiring di—gr—ms of

˜iologi™—l systemsF uiqq ™onsists of three typ es of d—t—D p—thw—ysD genesD

—nd mole™ulesD th—t —re linked with e—™h other —nd with the existing d—t—˜—ses

d R

through our hfqi„ integr—ted d—t—˜—se systemF gurrentlyDwe fo™us our

—ttention to the met—˜ oli™ p—thw—ys —nd enzyme genesF „he d—t—˜—se pro je™t

S

vsqexh for enzyme re—™tionsD enzymesD —nd met—˜ oli™ ™omp ounds is —lso

tightly ™oupled with the uiqq pro je™tF sn this p—p erD we presen t the ˜—si™

™on™ept of the ˜in—ry rel—tion ˜ etween twointer—™ting mole™ules or genes —s

— fund—ment—l element to represen t the p—thw—yD the m—nipul—tion of ˜in—ry

rel—tions ˜—sed on rel—tion—l op er—tionsD —nd the p—th ™omput—tion —s — deE

du™tion from ˜in—ry rel—tionsF ‡e —lso ˜riey mention how the p—thw—y d—t—

™—n ˜ e utilized to m—ke — fun™tion—l —ssignment from — gene ™—t—logF

P h—t— ‚epresent—tion

PFI f—si™ h—t— stem

„he ˜—si™ d—t— item in uiqq is — geneD — gene pro du™tD — met—˜ oli™ ™omp oundD

or —ny other mole™ule in — ™ellD whi™hm—y ˜ e identied in the formX

d—t—˜—seXentry

or

org—nismXgene

where –d—t—˜—se9 is the d—t—˜—se n—me su™h —s gen˜—nk —nd swissprotD –entry9

is the entry n—me or the —™™ession num˜ erD –org—nism9 is the org—nism n—meD

—nd –gene9 is the gene n—meF „his is the uniform identier ˜ oth in uiqq —nd

hfqi„F por ex—mpleD

igXTFQFPFQ

—nd

™

httpXGGwwwFgenomeF—dFjpGkeggGkeggFhtml

d

httpXGGwwwFgenomeF—dFjpGd˜getGd˜getFlinksFhtml

„—˜le IX ix—mples of ˜in—ry rel—tions

h—t— item I h—t— item P „yp e of rel—tion

gen˜—nkXh‚yev€g medlineXWQPUQUWT f—™tu—l d—t— —nd referen™e

em˜lXhwev€g spXg„xe h‚ywi tr—nsl—tion from nu™leotides

to —mino —™ids

gen˜—nkXh‚yev€g em˜lXhwev€g s—me —™™ession

™p dXgHHIIV ™p dXgHHIII su˜str—te —nd pro du™t

igXRFPFIFI igXSFQFIFI two ™onse™utive enzymes in

the met—˜ oli™ p—thw—y

hFmel—nog—sterXdpp hFmel—nog—sterXs—x twointer—™ting genes

@lig—nd —nd re™eptorA

iF™oliXtpie spX„‚sƒ igyvs gene pro du™t —s stored in

pu˜li™ d—t—˜—se

iF™oliXtpie igXSFQFIFI gene —nd fun™tion

fFsu˜tilisXtpi igXSFQFIFI gene —nd fun™tion

iF™oliXtpie fFsu˜tilisXtpi orthologous genes

™p dXgHHHSI

represen t glut—thione synth—se —nd glut—thioneD resp e™tivelyD in the vsqexh

d—t—˜—seD —nd

iF™oliXtpie

represen ts triosephosph—te isomer—se gene in iF ™oli F

PFP fin—ry ‚el—tions

„o represen t the d—t— of inter—™ting mole™ules or genesD we use the simplest

form of represen t—tionX the ˜in—ry rel—tion th—t ™orresp onds to the p—irwise

inter—™tionF eny higher level inter—™tions involving more th—n two ™omp onents

—t — time will ˜ e —pproxim—ted ˜y the ™olle™tion of p—irwise inter—™tionsF „he

T

™on™ept of ˜in—ry rel—tions h—s —lre—dy ˜ een utilized in the vinkhf d—t—˜—se

of the hfqi„ systemF por ex—mpleD the link ˜ etween two d—t—˜—se entriesX

d—t—˜—seIXentryI A d—t—˜—sePXentryP

—nd the link ˜ etween — d—t—˜—se entry —nd — gene n—meX

d—t—˜—seXentry A org—nismXgene

—re usu—lly provided ˜y e—™h d—t—˜—se —nd implemented in vinkhfGhfqi„F

ix—mples of these —nd other typ es of ˜in—ry rel—tions —re shown in „—˜le IF

uiqq in™orp or—tes the links th—t exist in vinkhfGhfqi„ @pigF I@—AA

—ndD in —dditionD ™ont—ins more ˜iologi™—l links of twointer—™ting mole™ules Database:Entry Enzyme sp:TYRB_ECOLI 2.6.1.57 sp:PHHC_PSEAE 2.6.1.57 DBGET pir:XNECY 2.6.1.57 .. ..

genbank:BACGTPBP 4.2.1.51

@—A ‚el—tion ˜ etween — d—t—˜—se entry —nd —n enzymeF „his rel—tion is exE

T R

tr—™ted from vinkhf in the hfqi„ systemF

Enzyme Substrate Product 2.6.1.57 Prephenate Pretyrosine LIGAND 4.2.1.51 Prephenate Phenylpyruvate 4.2.1.51 Chorismate Prephenate .. .

.. .

@˜A fin—ry rel—tion ˜ etween ™hemi™—l ™omp ounds @su˜str—te —nd pro du™tA th—t

p—rti™ip—te in — ™hemi™—l re—™tionF „his rel—tion is extr—™ted from vsqexh

S ghemi™—l h—t—˜—se for inzyme ‚e—™tionF

(c-1) Map Enzyme Phe, try and trp biosynthesis 2.6.1.57 KEGG Phe, try and trp biosynthesis 4.2.1.51 .. Pathway .. Terpenoid biosynthesis 2.5.1.10

(c-2) Map Enzyme1 Enzyme2 Phe, try and trp biosynthesis 4.6.1.4 4.2.1.51 Phe, try and trp biosynthesis 4.2.1.51 2.6.1.57 ......

Terpenoid biosynthesis 2.5.1.1 2.5.1.10

@™A ‚el—tionship ˜ etween —n enzyme —nd its lo™—tion @m—pA in the met—˜ oli™

p—thw—ys @™EIAF fin—ry rel—tion ˜ etween two enzymes th—t —pp e—r ™onse™uE

tively in the p—thw—y @™EPAF „hese rel—tions —re extr—™ted from the p—thw—y di—gr—ms of uiqqF

Organism:Gene Enzyme KEGG H. influenzae:HI1145 4.2.1.51 Genes H. influenzae:HI0196 4.6.1.3 .. ..

H. sapiens:ADCY1 4.6.1.1

@dA ‚el—tion ˜ etween — gene —nd —n enzymeF st is extr—™ted from the uiqq

hier—r™hi™—l text d—t— in the genes se™tionF

pigure IX ‚el—tion—l t—˜les used in the ™omput—tion of p—thw—ys Enzyme Group (superfamily) 2.6.1.1 aspartate aminotransferase 2.6.1.5 aspartate aminotransferase .. .. KEGG Molecules Enzyme Group (motif) 2.6.1.1 Aminotransferase class-I 2.6.1.5 Aminotransferase class-I 2.6.1.57 Aminotransferase class-I ..

..

@eA ‚el—tion ˜ etween —n enzyme —nd the group to whi™h it ˜ elongsF „his

rel—tion is derived from the uiqq hier—r™hi™—l text d—t— in the mole™ules

U

se™tionF gurrentlyD there —re four ™l—ssi™—tions ˜—sed on ig num˜ ersD €s‚

V W Q

sup erf—miliesD ƒgy€ QhEfolds —nd €‚yƒs„i motifsF

pigure IX ‚el—tion—l t—˜les used in the ™omput—tion of p—thw—ys @™ontdFA

or genesF por the met—˜ oli™ p—thw—ysD the twotyp es of ˜in—ry rel—tions —re

identiedF yne is the su˜str—teEpro du™t rel—tion in the form of

™p dXgHHIIV A ™p dXgHHIII

whi™h is extr—™ted from the vsqexh d—t—˜—se @pigF I@˜AAF „he other is the

rel—tion of two ™onse™utive enzymes —pp e—ring in the known p—thw—ysD su™h —s

igXRFPFIFI A igXSFQFIFI

„his rel—tion is extr—™ted from the p—thw—y di—gr—ms of uiqq @pigF I@™AAF

PFQ rier—r™hi™—l gl—ssi™—tions

e hier—r™hy is often used to represen t fun™tion—l —nd stru™tur—l simil—rities of

genes —nd mole™ulesF „he hier—r™hi™—l ™l—ssi™—tion of ig num˜ ers is ˜—sed on

the n—ture of ™hemi™—l re—™tions ™—t—lyzed ˜y enzymesF „he degree of simil—rity

in sequen™es —nd Qh stru™tures of proteins is used for ™l—ssifying sup erf—milies

—nd foldsF „he t—xonomy is the ™l—ssi™—tion of org—nismsD whi™h is import—nt

for extending sequen™e —nd Qh stru™tur—l simil—rities to fun™tion—l simil—ritiesF

sn the ™urrent version of uiqqD we ™onstru™t enzyme ™l—ssi™—tion t—˜les

U V W

—™™ording to ig num˜ ersD €s‚ sup erf—miliesD ƒgy€ QhEfoldsD —nd €‚yƒs„i

Q

motifs @pigF I@eAAF

yn™e the entire genome is sequen™ed —nd the ™omplete ™—t—log of genes is

o˜t—inedD it is n—tur—l to —ttempt to ™l—ssify —ll genes —™™ording to their fun™E

IH

tionsF ‚iley9s hier—r™hi™—l ™l—ssi™—tion —nd ™—tegoriz—tion of iF ™oli genes

is —n ex—mple of su™h —n —ttemptF sn uiqqD the fun™tion—l ™l—ssi™—tion is

˜—sed on the —™tu—l p—thw—y d—t— whi™hwe ™onsider —s —n o˜ je™tive ™riterion

for ™—tegoriz—tion of fun™tion—l unitsF sn the ‡‡‡ implement—tion of uiqqD

the ™l—ssi™—tion t—˜les ™—n ˜ e viewed —nd m—nipul—ted —s wh—t we ™—ll hierE

—r™hi™—l text d—t—D where ˜r—n™hes of the tree m—y ˜ e exp—nded or ™oll—psed

˜y simply ™li™king on the he—dings —nd su˜he—dingsF

PFR €—thw—y hi—gr—ms

II

„he met—˜ oli™ p—thw—y di—gr—ms su™h—s˜y fo ehringer —nd ˜y the t—p—nese

IP

fio ™hemi™—l ƒo ™iety represen t — ™onsensus view of known met—˜ oli™ p—thE

w—ys for hum—ns to underst—ndF ƒt—rting from these two ™ompil—tionsD weh—ve

™omputerized the met—˜ oli™ p—thw—y d—t— in the form of —˜ out VH gr—phi™—l

di—gr—msF i—™h di—gr—m ™ont—ins enzyme o˜ je™ts th—t ™—n ˜ e m—nipul—ted toE

gether with the rel—tion—l op er—tionsF „he di—gr—m is intended —s — dr—wing of

—ll ™hemi™—lly fe—si˜le p—thw—ysD r—ther th—n — ™onsensus of known p—thw—ysF

„husD —lthough the referen™e di—gr—m h—s to ˜ e dr—wn —nd ™ontinuously upE

d—ted m—nu—llyD the org—nismEspe™i™ p—thw—ys —re —utom—ti™—lly gener—ted

˜y m—t™hing the enzymes in the gene t—˜le with the enzymes on the p—thw—y

di—gr—msF por ex—mpleD pigure P shows the phenyl—l—nineD tyrosine —nd trypE

toph—n ˜iosynthesis p—thw—y for rF inuenz—e D where e—™h˜ox represen ts —n

enzyme with the ig num˜ er inside —nd those enzymes found in rF inuenz—e

—re m—rked for e—sy re™ognitionF „husD the org—nismEspe™i™ p—thw—y ™—n ˜ e

seen ˜y following the ™onne™tion of m—rked enzymesF

sn the ‡‡‡ implement—tion of uiqqD the su˜sets of enzymes stored in

IQ V IR IS

the pu˜li™ d—t—˜—ses in™luding €hfD €s‚D ƒ‡sƒƒE€‚y„D qenf—nkD —nd

IT

ywswD ™—n —lso ˜ e viewed —s m—rked ˜ oxes on e—™h p—thw—y di—gr—mF „he

pro ™ess of m—rking these enzyme su˜sets —nd the org—nismEsp e™i™ p—thw—ys is

—utom—ti™ —nd d—ily up d—ted in uiqqF sn —ll the p—thw—y di—gr—msD m—rked

or unm—rkedD —n enzyme in the ˜ ox is — ™li™k—˜le o˜ je™t @see pigF PA to retrieve

the ™orresp onding entry in the vsqexh d—t—˜—seD —nd then rel—ted entries ™—n

˜ e o˜t—ined from — num˜ er of d—t—˜—ses through hfqi„F „he ˜ oxed enzyme

is —lso — se—r™h—˜le o˜ je™tY the enzymes —s they —pp e—r in the known p—thw—ys

™—n ˜ e se—r™hed —nd viewed gr—phi™—llyF

Q gomput—tion

QFI €—rti—l toin yper—tion

„he pro ™ess of m—rking org—nismEspe™i™ p—thw—ys is ˜—sed on the m—t™hing

of the gene ™—t—log @pigF I@dAA

org—nismXgene A igXnum˜er

—nd the list of enzymes on e—™h p—thw—y di—gr—m @pigF I@™AA

m—pX—™™ession A igXnum˜er

pigure PX €henyl—l—nineD tyrosine —nd tryptoph—n ˜iosynthesis p—thw—y for rF inuenz—e

where –m—p9 is the d—t—˜—se n—me for the p—thw—y di—gr—ms —nd –—™™ession9 is

the —™™ession num˜ er of e—™h di—gr—mF „he m—t™hing pro ™ess is m—de ˜y — join

op er—tion on igXnum˜ erF sn the st—nd—rd rel—tion—l d—t—˜—se the join is m—de

˜y ex—™tly m—t™hing the v—lues in two ™olumnsD ˜ut the join here ™ont—ins —n

interpret—tion of the ig num˜ er ™l—ssi™—tion where — wild ™—rd is p ermitted

for the lowest levels of the num˜ ering s™hemeF

fy —pplying this p—rti—l join op er—tion in — more org—nized w—yD the proE

IU

™ess of query rel—x—tion in the dedu™tive d—t—˜—se ™—n ˜ e implementedF

ƒupp ose —n enzyme is found to ˜ e missing —fter ex—mining the ™onne™tivity of

the p—thw—yF fe™—use the ig num˜ er —ssignment is usu—lly m—de ˜y sequen™e

simil—rityD it is ne™ess—ry to ™he™k if other enzymes ˜ elong to the s—me sup erE

f—mily of simil—r sequen™esF „his ™—n ˜ e done ˜y going up the hier—r™hyofthe

sup erf—mily @pigF I@eAAX

igXnum˜er A ƒpXnum˜er

—nd then ex—mining —ll ig num˜ ers in the sup erf—mily @going down the hierE

—r™hyAF

QFP €—th gomput—tion

‡hen no —ppropri—te enzymes —re found even ˜y going up the hier—r™hyD the

next step is to ex—mine if —ltern—tive re—™tion p—ths ™—n ˜ e foundD given two

™omp ounds —s the initi—l su˜str—te —nd the n—l pro du™tF ƒupp ose enzyme

i ™—t—lyzes — ™hemi™—l re—™tion with su˜str—te ˆ —nd pro du™t ‰ F „hen the

re—™tion is represen ted ˜y the following form in the dedu™tive d—t—˜—seF

r e—™tion @iY ˆY ‰ AX

‡hen the ™onversion of ™omp ound ˆ to ™omp ound ‰ is—multistep pro ™ess

™onsisting of — num˜ er of enzymesD the enzym—ti™ p—thw—y is represen ted ˜yX

p—th@ˆY ‰ Y ‘i “A 2 r e—™tion @iY ˆY ‰ AX

p—th@ˆY ‰ Y ‘i j iv“A 2 r e—™tion @iY ˆY  AY p—th@Y ‰ Y i vAX

„his is — simple dedu™tion from — ™olle™tion of ˜in—ry rel—tions of su˜str—tes

—nd pro du™ts orD equiv—lentlyD — list of enzymesF ‡eh—ve ˜ een exp erimenting

IV

this p—th ™omput—tion ˜y the dedu™tive d—t—˜—se gy‚evF roweverD when

we —™tu—lly provide the p—th ™omput—tion ™—p—˜ility in uiqq we will use

the gCC li˜r—ry th—t we —re ™urrently developing for e™ient m—nipul—tion of

˜in—ry rel—tions —nd hier—r™hiesF

enother typ e of pro˜lem in p—th ™omput—tion is to ™ompute from — given

list of enzymes —ll p ossi˜le p—thw—ys st—rting —nd ending —t —ll p ossi˜le ™omE

p oundsF „his will ˜ e™ome ne™ess—ry for —n—lyzing — ™olle™tion of enzymes th—t

h—ve not m—t™hed on —ny of the known met—˜ oli™ p—thw—ysF epp—rentlyD there

—re still — num˜ er of unknown p—thw—ysD esp e™i—lly for se™ond—ry met—˜ olisms

—nd met—˜ olisms th—t —re turned on under stressful ™onditionsF „his typ e of

™omput—tion m—y help underst—nd su™h —ddition—l p—thw—ysF

R en ix—mple

RFI sdentifying wissing inzymes

es shown in pigF PD the ™onne™tivity of m—rked enzymes ™—n ˜ e used —s —

™riterion to —ssess the —™™ur—™y of gene nding —nd fun™tion—l predi™tion from

genomi™ sequen™esF isp e™i—llyD missing enzymes in e—™h org—nism ™—n ˜ e found

immedi—tely ˜y just lo oking —t the ™onne™tivityF sn the ™—se of the phenylE

—l—nine ˜iosynthesis for rF inuenz—e D the enzymes missing —reD —mong othersD

tyrosine tr—ns—min—se @ig PFTFIFSAD —rom—ti™ —mino —™id tr—ns—min—se @ig

PFTFIFSUAD phenyl—l—nine dehydrogen—se @ig IFRFIFPHAD —nd ™y™lohex—dienyl deE

hydrogen—se @ig IFQFIFRQAF

e™™ording to the ™urrent knowledge in the m—pD the l—™k of these enzymes

results in the in™ompletion of the ˜iosynthesisD whi™hm—y ˜ e f—t—l to the

org—nismF „here —re ˜—si™—lly two p ossi˜ilities th—t we need to ex—mine to

resolve this pro˜lemF „he rst ™—se is th—t the genes ™o ding for the missing

enzymes h—ve not ˜ een identied in the gene nding pro ™essD even though the

org—nism —™tu—lly h—s themF sf the ™omplete genome is —lre—dy sequen™edD the

gene nding —nd fun™tion—l —ssignmenth—ve to ˜ e rep e—ted more ™—refullyF

„he se™ond ™—se is th—t the org—nism do es not h—ve the genes ™o ding for

those enzymesD —nd it uses other ™hemi™—l re—™tions @enzymesA to pro du™e

phenyl—l—nineF sn this ™—seD we need to se—r™h for —ltern—tive p—thw—ys from

the sour™e ™hemi™—l ™omp ound to the t—rget ™hemi™—l ™omp oundD st—rting from

the list of —ll enzymes identied or predi™ted in the genomeF

RFP ƒe—r™hing eltern—tive essignments sing rier—r™hies

es — w—y to reEex—mine the fun™tion—l —ssignment of genesD the sup erf—milyD

motif —nd QhEfold ™l—ssi™—tions —nd p—rti—l join op er—tions ™—n ˜ e usedF sing

the gy‚ev system we se—r™hed —ltern—tive —ssignments of enzyme genes for

the three p ossi˜le p—thw—ys from prephen—te to phenyl—l—nine in pigF PF „he

ig num˜ ers of the missing @unm—rkedA enzymes were given to the systemD

—nd it returned the result shown in „—˜le PF sf the enzyme PFTFIFSU h—d ˜ een

—ssigned to PFTFIFID or the enzyme IFRFIFPH h—d ˜ een —ssigned to IFRFIFRD the

p—thw—y from prephen—te to phenyl—l—nine would h—ve ˜ een formedF sn f—™tD

two genes rsHPVT —nd rsITIU —re given the s—me ig num˜ ers PFTFIFI —™™ording

to the result of the sequen™e simil—rity se—r™hF „hey m—y require more ™—reful

—n—lysisF „he enzyme IFRFIFR w—sD howeverD ™orre™tly —ssigned —nd utilized in

the other se™tions of our p—thw—y d—t—˜—seF ‡e will pro˜—˜ly need to se—r™h

hyp otheti™—l proteins —nd un—ssigned genes in the rF inuenz—e genome for

this missing enzymeF

RFQ gomputing eltern—tive €—ths

„he p—th ™omput—tion ˜ e™omes ne™ess—ry when we ™—nnot nd —ppropri—te

enzymesF nfortun—telyD the ™urren t version of our d—t—˜—se is not —dequ—te

to system—ti™—lly p erform the ™omput—tionF por the ex—mple of pigF PD the

vsqexh d—t—˜—se des™ri˜ es the ™hemi™—l re—™tion of enzyme PFTFIFSU —s the

™onversion ˜ etween —n —rom—ti™ —mino —™id —nd —n —rom—ti™ oxo —™idF st do es

not sp e™ify pretyrosine —nd prephen—teD —nd we do not ™urrently h—ve — hier—rE

™hy of ™omp ound n—mesF „he re—™tion ˜ etween prephen—te —nd phenylpyruv—te

˜y enzyme SFRFWWFS is not in™luded —t —ll in the ™urrent version of vsqexhF

„—˜le PX ‚esult of the se—r™h of —ltern—tive enzymes for those p—rti™ip—te in the phenyl—l—nine

˜iosynthesis for rF inuenz—e

wissing eltern—tive gl—ssi™—tion used

PFTFIFSU PFTFIFI motif @eminotr—nsfer—ses ™l—ssEs pyridox—lE

phosph—te —tt—™hment siteA

PFTFIFS PFTFIFI motif @eminotr—nsfer—ses ™l—ssEs pyridox—lE

phosph—te —tt—™hment siteA

sup erf—mily @—sp—rt—te —minotr—nsfer—seA

IFRFIFPH IFRFIFR motif @qlu G veu G €he G †—l dehydrogen—ses

—™tive siteA

IFRFQFP IFRFQFS ig num˜ er ™l—ssi™—tion

sn —ny ™—seD we tried to ™ompute —ltern—tive p—ths from phenylpyruv—te

to phenyl—l—nineD ˜ut no p—ths were foundF ‡e ˜ elieveD howeverD —s we —dd

more re—™tions —nd more ™omp ounds to vsqexhD whi™h —re then ™onverted

to rel—tion—l t—˜les in uiqqD —nd work out — hier—r™hy of ™omp ound n—mesD

the p—th ™omput—tion will ˜ e™ome — pr—™ti™—l to ol for ˜iologistsF

S his™ussion

„he ™omplete genome sequen™es of —t le—st ve freeEliving org—nismsD rF inE

P IW PH PI

uenz—e D wF genit—lium D wF j—nn—shii D ƒyne™ho™ystis spF —nd ƒF ™erevisiE

—e D —re —lre—dy —v—il—˜le vi— ‡‡‡ or p„€ servers of the origin—l sequen™ing

groupsF „hey —lso provide the list of predi™ted ™o ding regions —nd predi™ted

gene fun™tionsF „he m— jor purp ose of the uiqq met—˜ oli™ p—thw—y d—t—˜—se

is twoEfoldF pirstD we wish to est—˜lish —n integr—ted view of higher fun™tion—l

—sp e™ts of gene pro du™tsD n—melyDhow they —re inter—™tingD for —n in™re—sing

num˜ er of org—nismsF ƒe™ondD we will provide — pr—™ti™—l to ol for m—king

—ssignments of enzyme genes from genomi™ sequen™esF

por the rst purp oseD there —re —lso other met—˜ oli™ p—thw—y d—t—˜—sesD

PP PQ PRYPS

su™h —s i™ogy™D ringy™D iw€D whi™h often ™ont—in more det—iled

inform—tion of sp e™i™ p—thw—ys —nd sp e™i™ org—nisms th—n uiqqF €erh—psD

the m— jor fe—ture of uiqq is its link ™—p—˜ilitiesD ˜ oth in terms of the linking

to the existing d—t—˜—ses —nd dierent org—nisms —nd in terms of the linking

to ™ompute — p—thw—y from ˜in—ry rel—tionsF fe™—use of these links we exp e™t

uiqq ™—n ˜ e used to extr—™t dierent inform—tion from the other met—˜ oli™

p—thw—y d—t—˜—sesF sn uiqq the ˜in—ry rel—tions in the rel—tion—l t—˜les —re ee™tively utiE

lized for p—th —nd other ™omput—tions using logi™F yf ™ourseD we —re well —w—re

of the ™ompli™—tions of ˜iologi™—l pro˜lemsD whi™hm—y sometimes ˜ e ˜ etter

tre—ted ˜y o˜ je™tEoriented te™hnologiesF roweverD — ™omplex d—t— represen t—E

tion m—y result in —n inee™tive ™omput—tionF st rem—ins to ˜ e seen whether

the simple represen t—tion —nd e™ient ™omput—tion in uiqq ™—n result in

˜iologi™—lly signi™—nt o˜serv—tionsF „ow—rd th—t endD we —re in the pro ™ess of

m—nu—lly extr—™ting m—in su˜str—tesD pro du™tsD —nd ™of—™tors for e—™h of the

enzym—ti™ re—™tions of —ll known met—˜ oli™ p—thw—ysF fy represen ting e—™h

re—™tion —s — ™olle™tion of ˜in—ry rel—tionsD we will try to repro du™e the known

p—thw—ysF et the s—me timeD we need to ™omputerize the synonyms —nd hierE

—r™hies of ™omp ound n—mesF ‡e —re working on this in ™onjun™tion with the

gyw€y xh se™tion of the vsqexh d—t—˜—seF

„he hfqi„Gvinkhf system is ˜—sed on the mo del of lo oselyE™oupled inE

tegr—tionD where dierent d—t—˜—ses with dierent s™hem—s —re integr—ted —t

the level of d—t— entriesF „husD entries in dierent d—t—˜—ses ™—n ˜ e retrieved

uniformly —nd links —re m—de ˜ etween rel—ted entries in dierent d—t—˜—sesF

„his —ppro—™h h—s ˜ een su™™essful in view of the prolifer—tion of ‡‡‡ —nd

the r—pid progress of genome pro je™tsF „he textE˜—sed hfqi„ system h—s

˜ een extended to the multimedi— environmentD —nd hfqi„ h—s ˜ een —nd will

™ontinue to ˜ e —˜le to ™op e with the ever in™re—sing num˜ er —nd volume of

d—ily up d—ted d—t—˜—sesF ƒin™e uiqq inherits —nd sh—res hfqi„Gvinkhf

™—p—˜ilitiesD it will —lso ˜ e —˜le to provide the most upEtoEd—te met—˜ oli™ p—thE

w—ys for — num˜ er of org—nisms in™luding —ll org—nisms with ™omplete genomes

knownF

„he —lgorithm used in ™omputing p—thw—ys ˜ etween two ™omp ounds is

PT

˜—sed on w—vrovouniotis9s —lgorithmF rere it is implemented in — simpler

w—y˜y represen ting re—™tions —s ˜in—ry rel—tionsD whi™h en—˜les us to tre—t

the p—th ™omput—tion —s — logi™—l deriv—tionF sing v—rious hier—r™hies —nd

IU

the fr—mework of query rel—x—tionsD the ™omput—tion of —ltern—tive p—thw—ys

PS

™—n ˜ e —™™omplishedF por ex—mpleD q——sterl—nd —nd ƒelkov —dopted the

t—xonomyofwy™opl—sm— —s — me—sure of proximity˜etween org—nisms for use

in the query rel—x—tionF es — next step it will ˜ e ne™ess—ry to ™om˜ine dierent

typ es of hier—r™hiesD su™h —s t—xonomyD sequen™e simil—rityD —nd ™omp ound

simil—rityD to ™ompute —ltern—tive p—thw—ysF

e™knowledgement

„his work w—s supp orted in p—rt ˜y — qr—ntEinEeid for ƒ™ienti™ ‚ese—r™h

on €riority ere—s –qenome ƒ™ien™e9 from the winistry of idu™—tionD ƒ™ien™eD

ƒp orts —nd gulture in t—p—nF „he ™omput—tion time w—s provided ˜y the

ƒup er™omputer v—˜ or—toryD snstitute of ghemi™—l ‚ese—r™ hD uyoto niversityF

‚eferen™es

IF pF ƒ—nger et —l D x—ture PTSD TUV @IWUUAF

PF ‚FhF pleis™hm—nn et —l D ƒ™ien™e PTWD RWT @IWWSAF

QF eF f—iro ™h et —l D xu™lei™ e™ids ‚esF PRD IVW @IWWTAF

RF ‰F ekiy—m— et —l Din€ro™eedings of the IWWS weeting on the snE

ter™onne™tion of wele™ul—r fiology h—t—˜—ses @€F u—rp et —l edsA

hhttpXGGwwwF—iFsriF™omG~pk—rpGmim˜ dGWSG—˜str—™tsFhtmliF

SF wF ƒuy—m— et —l D gomputF epplF fios™i WD W @IWWQAF

TF ƒF qoto et —l D in €ro™eedings of the IWWS weeting on the snE

ter™onne™tion of wele™ul—r fiology h—t—˜—ses @€F u—rp et —l edsA

hhttpXGGwwwF—iFsriF™omG~pk—rpGmim˜ dGWSG—˜str—™tsFhtmliF

UF inzyme xomen™l—tureD e™—demi™ €ress sn™F @IWWPAF

VF hFqF qeorge et —l D xu™lei™ e™ids ‚esF PRD IU @IWWTAF

WF eFqF wurzin et —l D tF wolF fiolF PRUD SQT @IWWSAF

IHF wF ‚iley et —l D is™heri™hi— ™oli —nd ƒ—lmonel l—X gel lul—r —nd wole™ul—r

fiology Pnd idFD PIIV{PPHPD eƒw €ress @IWWTAF

IIF wF qerh—rd edFD fiologi™—l €—thw—ysD „hird iditionF foehringer

w—nnheim @IWWPAF

IPF „F xishizuk— edFD wet—˜ oli™ w—psF fio™hemi™—l ƒo™iety of t—p—n @IWVHA

@in t—p—neseAF

IQF pFgF fernstein et —l D tF wolF fiolF IIPD SQS @IWUUAF

IRF eF f—iro ™h —nd ‚F epweilerD xu™lei™ e™ids ‚esF PRD PI @IWWTAF

ISF hFeF fenson et —l D xu™lei™ e™ids ‚esF PRD I @IWWTAF

ITF €F€e—rson et —l D xu™lei™ e™ids ‚esF PPD QRUH @IWWRAF

IUF „F q——sterl—nd et —l D tF sntel ligent snform—tion ƒystems ID PWQ @IWWPAF

IVF ‚F ‚—m—krishn—n et —l D „he gy‚ev w—nu—lX e tutori—l intro du™tion

to gy‚ev @IWWQAF

IWF gFwF pr—ser et —l D ƒ™ien™e PUHD QWU @IWWSAF

PHF gFtF fult et —l D ƒ™ien™e PUQD IHSV @IWWTAF

PIF „F u—neko et —l D hxe ‚esF QD IHW @IWWTAF

PPF €FhF u—rp et —l D xu™lei™ e™ids ‚esF PRD QP @IWWTAF

PQF €FhF u—rp et —l D ssm˜ RD IIT @IWWTAF

PRF iF ƒelkov et —l D xu™lei™ e™ids ‚esF PRD PT @IWWTAF

PSF „F q——sterl—nd —nd iF ƒelkovD ssm˜ QD IPU @IWWSAF

PTF wFvF w—vrovouniotisD in erti™i—l sntel ligen™e —nd wole™ul—r fiology @vF

runter edFAD QPS @IWWQAF