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BIO421ProblemSet2 Name
1. Pickoneofthethreeproteinsequencesonthelastpage.Whichonedidyou
pick?_____________Then,pleasedothefollowing:
a. CompleteaproteinBLASTsearch.Whatisthenameoftheproteinthatyouchoseand
whatorganismisitfrom?
Sequence1:FOLT-1fromC.elegans
Sequence2:Presenilin-1fromMusmusculus
Sequence3:thiaminetransporterfromDaniorerio
b. FromtheBLASTsearch,whatarethenext3closestmatches?Giveorganismsthese
matchescomefrom.Whatarethenamesoftheproteins?
Sequence1: CBN-FOLT-1protein[Caenorhabditisbrenneri]
CBR-FOLT-1[Caenorhabditisbriggsae]
CRE-FOLT-1protein[Caenorhabditisremanei]
Sequence2:
presenilin-1[Rattusnorvegicus]
presenilin-1 isoform X1 [Mesocricetus auratus]
PREDICTED:presenilin-1[Peromyscusmaniculatusbairdii]
Sequence3:
thiaminetransporter1-like[Lepisosteusoculatus]
thiaminetransporter1-like[Astyanaxmexicanus]
thiaminetransporter1[Cynoglossussemilaevis]
c. Again,fromtheBLASTsearch,arefunctionaldomainspresentintheprotein?What
domainsarepresent?Whatdotheydo,andwhatdoesthistellyouaboutthefunctionof
yourprotein?
Sequence1: Folatecarriersuperfamily.Functionstotransportfolateintocells.
Probablefunction–folatetransport.
Sequence2:
Presenilin,signalpeptidepeptidase,family.Functionsasa
protease/bindsbeta-catenin.
Sequence3:
Folatecarriersuperfamily.Functionstotransportfolateintocells.
Probablefunction–folatetransport.
d. Determineiftheproteinhastransmembranedomains,andifso,howmany?Arethere
alternativemodelsforthedomains?
Sequence1: Yes,therearetransmembranedomainspresent:9totalandone
alternativeonTMPred
Sequence2: Yes,therearetransmembranedomainspresent:9totalandone
alternativeonTMPred
Sequence3:
Yes,therearetransmembranedomainspresent:11totalandone
alternativeonTMPred
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e. Determineiftheproteinhassitesforphosphorylation.Howmanyarethereandwhat
kindsdoyoufind(Ser,Thr,&Tyr)?
Sequence1:
Yes,therearephosphorylationsites,24inall,andallthreetypes
Sequence2:
Yes,therearephosphorylationsites,27inall,andallthreetypes
Sequence3:
Yes,therearephosphorylationsites,18inall,andallthreetypes
f. PleasegivethenumberofphosphorylationsitesforS,T,andY.
Sequence1:
Sequence2:
Sequence3:
Ser:9 Thr:9 Tyr:5
Ser:15Thr:9 Tyr:3
Ser:12Thr:3 Tyr:3
g. UsingtheInterProsite,pleaseidentifyanyfunctionaldomains.Whataretheyandwhat
functiondotheyhave?
Sequence1:
Sequence2:
Sequence3:
Reducedfolatecarrier;Majorfacilitatorsuperfamilydomain
Presenilin/signalpeptidepeptidase,PeptidaseA22A,presenilin
Reducedfolatecarrier;Majorfacilitatorsuperfamilydomain
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Sequence1:
MSWRTTTAILCLYGAVKEFRPATPFLTPFLASPEKNITLDELYSQVYPYWTYSYMLALIPMFILTDILRYKPIVMIEAIG
LVATWALLVFGKGVWQMQIMQVSFGVASAAEIAYYSYIYSIVDRKHYKRATSYIRAAALMGKLVAFGLGQTLISTHTSDY
LVLNQISLGAVCLVTIIAIFLPRVKSEKAKVSMRAHEIVEQQTVESVESVQTPKAVKMSYTREYFKKISEELQICSKNQE
LLKWSLWWALASCGVYQVQNYTQSLWKELQNNPDDVANGVVEFVNTALGAFLSLFIHHLSIDWTRHGQMILFITSAIVAV
LLYLCSQTTTVLVAYSSYVVITSIYHMLITAASANVAKELSSNNHGLIFGCNTFVAVCLQSLLTLVVVDSRFLHLDIRTQ
FVIYSGYFALVASIFAFFFMISLFSKSSNAHTAQTTYEATNEIQEETVFLDQN
Sequence2:
MTEIPAPLTYFQNAQMSEDSHSSSAIRSQNDSQERQQQHERQRLDNPEPISNGRPQSNSRQVVEQDCMEE
DEELTLKYGAKHVIMLFVPVTLCMVVVVATIKSVSFYTRKDGQLIYTPFTEDTETVGQRALHSILNAAIM
ISVIVIMTILLVVLYKYRCYKVIHAWLIISSLLLLFFFSFIYLGEVFKTYNVAVDYLTVALLIWNFGVVG
MIAIHWKGPLRLQQAYLIMISALMALVFIKYLPEWTAWLILAVISVYDLVAVLCPKGPLRMLVETAQERN
ETLFPALIYSSTMVWLVNMAEGDPEAQRRVPKNPKYNTQRARRDETQDSGSGNDDGGFSEEWEAQRDSHL
GPHRSTPESRAAVQELSGSILTSEDPEERGVKLGLGDFIFYSVLVGKASATASGDWNTTIACFVAILIGL
CLTLLLLAIFKKALPALPISITFGLVFYFATDYLVQPFMDQLAFHQFYI
Sequence3:
MSEPWLYPTVLLCIYGFFSSHRPLEAFLMPFLMGPDKNLTETEVVSEIYPLWTYSYLALLFPVFLATDYL
RYKPVIILQAASYVVTYALLVKAQGLQAMQIVEVFFGLATATEIAYYSYIYSVVEPSHYQMVTGFCRSVT
LLGSAMGSLLGQILFSVADIALFYLCVITLVSFCIAFVAPWFLPMPSKSLFFHQSESSSQDEAVLETVNT
SPLIEKPEDPESNKQPNANEKTTLKSNTSSSGLLDVLKMLWTDFLQCYSSSTLLAWSVWWALSTCGYLQV
INYAQALWEDILTSKNYDIYNGYVETISTLLGAFAAFVVGYVKVSWAVWGELALCIFTVVIAVCVYLMYA
VRNIWVCYTSYIIFRAVYMLLITIATYQIAANLSMKRYALVFGVNTFIALSLQMLLTVIVVDSAGLHLEI
SIQFLIYASYFAAVAVIFFIAGLYKLFRSRTSGGQNELSSAEA
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