Student ID: MC180402684

Student name: Amara Tahir

Course code: BIF401
Course Title: Bioinformatics I
Question 1:

1- Take a candidate human gene amino acid sequence, preferably whose

structure is not yet predicted.

keratin, partial [Homo sapiens]

>AAB59562.1 keratin [Homo sapiens]
MTTCSRQFTSSSSMKGSCGIGGGIGAGSSRISSVLAGGSCRAPNTYGGGLSVSSSRFSSGGAYGLGGGYG
GGFSSSSSSFGSGFGGGYGGGLGAGLGGGFGGGFAGGDGLLVGSEKVTMQNLNDRLASYLDKVRALEEAN
ADLEVKIRDWYQRQRPAEIKDYSPYFKTIEDLRNKILTATVDNANVLLQIDNARLAADDFRTKYETELNL
RMSVEADINGLRRVLDELTLARADLEMQIESLKEELAYLKKNHEEEMNALRGQVGGDVNVEMDAAPGVDL
SRILNEMRDQYEKMAEKNRKDAEEWFFTKTEELNREVATNSELVQSGKSEISELRRTMQNLEIELQSQLS
MKASLENSLEETKGRYCMQLAQIQEMIGSVEEQLAQLRCEMEQQNQEYKILLDVKTRLEQEIATYRRLLE
GEDAHLSSSQFSSGSQSSRDVTSSSRQIRTKVMDVHDGKVVSTHEQVLRTKN
1- Take the sequence of seven ortholog for same gene. (Like Mouse, rat,
Chimpanzee etc.)

energy transducer TonB, partial [Serratia marcescens]

>OZT19284.1 energy transducer TonB, partial [Serratia marcescens]
MYLLYRSRHLFSWLPALIVAGCLLFASQQAALKIQPRYDETAIELALVEPEPAPEPQPETPPEPQPEPPP
PEPEPLPEPVVSAPEPIVEAKPVP

Keratin, high-sulfur matrix protein, B2A, partial [Bos mutus]

>ELR53634.1 Keratin, high-sulfur matrix protein, B2A, partial [Bos mutus]
CCVVSCTSPSCCQLYYAQASCCRPSYCGQSCCRPACCCQPTCIEPICEPTCCQPTCCPSPDTMACCSTSF
CGFPTCSTGGTCGANFCQPTCCQTSCCQPISIQTSCCQPTCCQTSGCETSCGIGGSIGGSIGYGQVGSSG
AVSSRTRWCRPDCRVEGTSLPPCCVVSCTPPSCCQLYYAQASCCRPSYCGQSCCRPACCCQPTCIEPICE
PICCEPTC

protein sspF [Bacillus pumilus]

>ANT58860.1 protein sspF [Bacillus pumilus]
MGRRRGIMSDEFKYELAKDLGFYDTVKNGGWGEIRARDAGNMVKRAIELAQQHMAQEENQR
keratin, partial [Mus musculus]
>AAA39370.1 keratin, partial [Mus musculus]
EVVKKQCIGVQDSIADAEQHGEHAIKDARGKLTDLEEALQQCREDLARLLRDYQELMNTKLSLDVEIATY
RKLLEGEECRMSGDFSDNVSVSITSSTISSSMASKTGFGSGGQSSGGRGSYGGRGGGGGGGSSYGSGGRS
SGSRGSGSGSGGGGYSSGGGSRGGSGGGYGSGGGSRGGSGGGYGSGGGSGSGGGYSSGGGSRGGSGGGGA
SSGGGSRGGSSSGGGSRGGSSSGGGGYSSGGGSRGGSSSGGQDLALKREVLGQGKVVAQV

keratin [Ovis aries]

>AAA31554.1 keratin [Ovis aries]
MCGYYGNYYGGLGCGSYSYGGLGCGYGSCYGSGFRRLGCGYGCGYGYGSRSLCGSGYGYGSRSLCGSGYG
CGSGYGSGFGYYY

keratin, partial [Rattus norvegicus]

>AAA41474.1 keratin, partial [Rattus norvegicus]
LSVGGSGFSASSGQGGGFSSGGGSSSSVKFVSTTSSSRRSFKS

keratin, type II cuticular Hb4 [Cricetulus griseus]

>ERE83599.1 keratin, type II cuticular Hb4 [Cricetulus griseus]
MSRQSTITFHSGSRRGFSTASATTPTAGRSRFSSVSVARSSGNSGGLGRISGAGAGAGFGSRSLYNLGGT
KRVSIGGCAGSGFRSSFGGRASSGFGVSSGFGYGGGIGGAFGGPGFPVCPSGGIQEVTVNQSLLTPLNLQ
IDPTIQRVRKEEREQIKTLNNKFASFIDKVRFLEQQNKVLETKWNLLQEQGSRTVRQNLEPFFDAYLNDL
RRQLDGVTAERGRLDAELRSMQEVVEDFKVRYEDEINKRAAAENEFVGLKKDVDGAYMSKVELEAKVDSL
TDQINFYRMIYEAELSQMQNQVSDTSVVLSMDNNRSLDLDSIIAEVKAQYEDIANRSRAEAESWYQTKYE
ELQVTAGRHGDDLRNTKQEISEVNRMIQRLRSEIDAVKKQCSSLQTAISDAEQRGELALKDARAKLVDLE
DALQKAKQDMARLLREYQELMNVKLSLDVEIATYRKLLEGEECRLSGEGVSPVNISSTMTQRSSVTIKSG
GTRNFSASSASLLPGCRPGFSSVSVSQSGKSFGGGFGGGFGTRSLHSFGGNKRISIGGGYRSSRASFGGA
ACGLGVSGIGYRVGGAYGGYGFGGGMAPGAGGIHEVTVNQSLLTPLHLEIDPSLQRVRKEEKEQIKSLNN
KFASFIDKVRFLEQQNKVLETKWSLLQEHKTTRTNLEPMFEAYITNLRRQLECLGGERGRLETELKSMQD
VVEDFKNKYEEEIHRRTTAENEFVVLKKDVDAAYMNKVELEAKVDALMDEINFLRAFYEAELAQLQAQIS
ETSVVLSMDNNRSLDLNSIIAEVKAQYEDIANRSRAEAESWYQTKYEELQRSAGQHGDDLRSTKMEISEL
NRAMQRLRSEIDNLKKQCATLQASIADAEQRGELALKDAKHKLAELEEALQKAKQDMARQLREYQELMNV
KLALDIEIATYRKLLEGEECRLTGEGVGAVNISVVSSSGGTGYSGGGGLCMSGSSYSGGGYSGSGLCYGG
GGSGSFSSTSGRSMSGSSSSMRIVSKTSSSKKTMSCRNFQLSSRCGSRSFSSCSAVVPRMVTHYEVSKGP
CRPGGAGGLRALGCLGSRSLCNVGFGRPRVASRCGMPGFGYRAGAACGPPACITPVTINESLLVPLELEI
DPTVQRVKRDEKEQIKCLNNRFASFINKVRFLEQKNKLLETKWNFMQQQRSCQSNMEPLFEGYICALRRQ
LDCVSGDHGRLEAELCSLQDALEGYKKKYEEELSLRPCAENEFVTLKKDVDTAFLVKADLETNLEALEHE
IEFLKALFEEEISLLQSQISETSVIVKMDNSRELNVDGIIAEIKAQYDDIASRSKAEAEAWYQSRYEEMR
LTAGNHCDNLRNRKNEILEMNKLIQRLQQDIETVKGQRCKLEGAIAQAEQQGEAALSDAKCKLAGLEEAL
QKAKQDMACLLKEYQEVMNSKLGLDIEIATYRRLLEGEEHRLCEGIGPVNISVSSSKGAVLYEPCVVGTP
MLRTEYCMGTTGVLRNSGGCSVVGTGELYIPCEPQGLMGCGSGRSSSMKMGAGSNSCSPVTHKATMSCRS
YRVSSGHRVGSFSSCSAMTPQNLNRFQASSVSCRSGSGFRGLGCFGSRSVNFGSSSPRIAVGCSRPIRYG
VGFGAGNGMAFGSGDGCGVGLGFRASSGVGLGFGAGSSLGYGFGGPAFGGPGFGYRIGGIGGPSAPSITT
VTVNQSLLTPLNLEIDPNAQRVKKDEKEQIKTLNNKFASFIDKVRFLEQQNKLLETKWSFLQDQKCARSN
LDPLFDNYITSLRRQLEVLVSDQARLQAERNHMQDILEGFKKKYEEEVGCRANAENEFVALKKDVDTAFL
NKSDLEANVDALAQEVEFLKALYLEEIQLLQSHISETSVIVKMDNSRDLNLDGIIAEVKAQYEEVARRSR
ADVEAWYQTKYEEMRVTAGQHCDNLRNTRDEINELTRLIQRLKTEIEHSKAQCAKLEAAVAEAEQQGEAA
LNDAKCKLADLEGALQQAKQDMARQLREYQELMNAKLGLDIEIATYRQLLEGEEIRICEGVGPVNISVSS
SRGGVLCGPESLVSGSSLSRNCGVTFSSSSGIRTTGGVLTSSCLRAGGDLLSSGARGGSVLVSDTCAPSI
PCPLPTEGGFSSCSGGRGNRSSSVRFSSTTTSRRTSQPQLSPPIKGLQRIRETQRIPSLILCSLHQTPQP
LRRRHPAHTMSCRSYRISPGCGVTRNFSSCSAVAPKTGNRCCISAAPFRGVSCYRGLTGFSSRSLCNPSP
CGPRMAVGGFRSGSCGRSFGYRSGGVCGPSPPCITTVSVNESLLTPLNLEIDPNAQCVKHEEKEQIKCLN
SKFAAFIDKVRFLEQQNKLLETKWQFYQNQRCCESNLEPLFGGYIETLRREAECVEADSGRLAAELNHVQ
EAMEGYKKKYEEEVALRATAENEFVVLKKDVDCAYLRKSDLEANVEALVEESSFLKRLYEEEIRVLQAHI
SDTSVIVKMDNSRDLNMDCVVAEIKAQYDDVASRSRAEAESWYRTKCEEMKATVIRHGETLRRTREEMNE
LNRIIQRLTAEIENAKCQRAKLETAVAEAEQQGEAALTDARCKLAELEAALQKAKQDMACLLKEYQEVMN
SKLGLDIEIATYRRLLEGEEHRGSLVQHEEKEQIKCLNSKFAAFIDKWQFYQNRKCCESNVEPLFEGYIE
TLRREAECVEADSGRLAAELNHAQEAMEGYKKRYEEEVALRATAENEFVALKKDVDCAYLRKSDLEANAE
ALTQEIDFLRRLYEEEIRILHAHISDTSVIVKMDNSRDLNMDCIVAEIKAQYDDIATRSRAEAESWYRTK
EYQEVMNSKLGLDIEIATYRRLLEGEEQRLCEGVGSVNVCKYNGL

2- Make a phylogenetic tree after doing MSA (Multiple Sequence Alignment).

3- Predict the Secondary structure of the candidate gene a.a. sequence. (alpha
helix, beta sheets, strands)
1- Predict the tertiary structure of the sequence.