Nama : Asep Badru Zaman (1111095000026)

UAS BIOINFORMATIKA

ANALISIS FUNGSI DAN LOKASI PROTEIN

1. TAHAP MEMILIH PROTEIN- MENGUNDUH SEKUEN PROTEIN BETACELLULIN

HASIL FASTA:

MNPTLGLAIFLAVLLTVKGLLKPSFSPRNYKALSEVQGWKQRMAAKELARQNMDLGFKLLKKLAFYNPGRNIFLSPLSISTAFSMLCLGAQDSTLDEIKQGFNFRKMPEKDLHEGFHYIIHELTQKTQDLKLSIGNTLFIDQRLQPQRKFLEDAKNFYSAETILTNFQNLEMAQKQINDFISQKTHGKINNLIENIDPGTVMLLANYIFFRARWKHEFDPNVTKEEDFFLEKNSSVKVPMMFRSGIYQVGYDDKLSCTILEIPYQKNITAIFILPDEGKLKHLEKGLQVDTFSRWKTLLSRRVVDVSVPRLHMTGTFDLKKTLSYIGVSKIFEEHGDLTKIAPHRSLKVGEAVHKAELKMDERGTEGAAGTGAQTLPMETPLVVKIDKPYLLLIYSEKIPSVLFLGKIVNPIGK

2. TAHAP MENGHITUNG Pi/Mw

Compute pI/Mw

Theoretical pI/Mw (average) for the user-entered sequence:

10 20 BETACELLUL INHOMOSAPI ENS

Theoretical pI/Mw: 4.24 / 2824.67

3. TAHAP ProtScale

ProtScale

User-provided sequence:

10 20 30 40 50 60 MDRAARCSGA SSLPLLLALA LGLVILHCVV ADGNSTRSPE TNGLLCGDPE ENCAATTTQS

70 80 90 100 110 120 KRKGHFSRCP KQYKHYCIKG RCRFVVAEQT PSCVCDEGYI GARCERVDLF YLRGDRGQIL

130 140 150 160 170 VICLIAVMVV FIILVIGVCT CCHPLRKRRK RKKKEEEMET LGKDITPINE DIEETNIA

SEQUENCE LENGTH: 178

Using the scale alpha-helix / Deleage & Roux, the individual values for the 20 amino acids are: Ala: 1.489 Arg: 1.224 Asn: 0.772 Asp: 0.924 Cys: 0.966 Gln: 1.164 Glu: 1.504 Gly: 0.510 His: 1.003 Ile: 1.003 Leu: 1.236 Lys: 1.172 Met: 1.363 Phe: 1.195 Pro: 0.492 Ser: 0.739 Thr: 0.785 Trp: 1.090 Tyr: 0.787 Val: 0.990 : 0.848 : 1.334 : 1.020

Weights for window positions 1,..,9, using linear weight variation model: 1 2 3 4 5 6 7 8 9 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 edge center edge

http://web.expasy.org/tmp/pscale7830.gif

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NMR Structure of Human Betacellulin-2 MMDB ID: 20079PDB ID: 1IP0PDB Deposition Date:2001/4/19

Updated in MMDB:07/2009  ▼Experimental

Method:Solution NMR 

Source Organism:Homo sapiensSimilar Structures:VAST+ 

Citation: Solution structure of betacellulin, a new member of egf-family ligands.Miura K, Doura H, Aizawa T, Tada H, Seno M, Yamada H, Kawano KBiochem.Biophys.Res.Commun. (2002) 294 p.1040

Cn3D

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Protein

Molecules and interactionsLabel Count Molecule Interactions

Protein and interactions (1 molecule)

1

Betacellulin

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no interaction recorded

* Click molecule labels to explore molecular sequence information.

ANALISIS SEKUENS HOMOLOGI

1. Jawaban :Putative ORF =

Eukariotyc GeneMark.hmm version bp 3.9_2 Dec 2010-2012Sequence name: Oryza sativaSequence length: 864 bpG+C content: 44.91%Matrices file: /home/genmark/euk_ghm.matrices/rice_hmm3.0modTue Jan 7 22:14:10 2014

Predicted genes/exons

Gene Exon Strand Exon Exon Range Exon Start/End # # Type Length Frame

1 1 + Initial 99 163 65 1 2 - - 1 2 + Internal 259 800 542 3 1 - -

# protein sequence of predicted genes

>gene_1|GeneMark.hmm|202_aaMASVDPSRSFVRDVKRVIIKVKMLVLVRWLLPQEIVQGIYRGVNIYGGPIAHKALGFPKAVSFHHEYSSMACTVEFVDDVQSAIDHIHRYGSADGICHVYIDKSADMDMAKLIVMDAKTDYPAACNAMELDDVIDLVTPRGSNKLVSQIKASTKIPVLGHAEVADDLVLEKTSCPLGVLLIVFESRPDALVQVQIASLAIRS

# end protein sequence

2. Jawaban :Protein yang berkorelasi : delta-1-pyrroline-5-carboxylate synthasedelta l-pyrroline-5-carboxylate synthetase; This protein contains a glutamate 5-kinase.

3. Jawaban :

deltal-pyrroline-5-carboxylate synthetase [Oryza sativa (japonica cultivar-group)]Range 1: 1 to 716GenPept Graphics Next MatchPrevious Match

Alignment statistics for match #1

Score Expect Method Identities

Positives

Gaps Frame

1395 bits(3611)

0.0Compositional matrix adjust.

716/716(100%)

716/716(100%)

0/716(0%)

+3

Query 99 MASVDPSRSFVRDVKRVIIKVGTAVVSRQDGRLALGRVGALCEQVKELNSLGYEVILVTS 278

MASVDPSRSFVRDVKRVIIKVGTAVVSRQDGRLALGRVGALCEQVKELNSLGYEVILVTS

Sbjct 1 MASVDPSRSFVRDVKRVIIKVGTAVVSRQDGRLALGRVGALCEQVKELNSLGYEVILVTS 60

Query 279 GAVGVGRQRLRYRKLVNSSFADLQKPQMELDGKACAAVGQSGLMALYDMLFNQLDVSSSQ 458

GAVGVGRQRLRYRKLVNSSFADLQKPQMELDGKACAAVGQSGLMALYDMLFNQLDVSSSQ

Sbjct 61 GAVGVGRQRLRYRKLVNSSFADLQKPQMELDGKACAAVGQSGLMALYDMLFNQLDVSSSQ 120

Query 459 LLVTDSDFENPKFREQLTETVESLLDLKVIPIFNENDAISTRKAPYEDSSGIFWDNDSla 638

LLVTDSDFENPKFREQLTETVESLLDLKVIPIFNENDAISTRKAPYEDSSGIFWDNDSLA

Sbjct 121 LLVTDSDFENPKFREQLTETVESLLDLKVIPIFNENDAISTRKAPYEDSSGIFWDNDSLA 180

Query 639 gllalelkadllillSDVDGLYSGPPSEPSSKIIHTYIKEKHQQEITFGDKSRVGRGGMT 818

GLLALELKADLLILLSDVDGLYSGPPSEPSSKIIHTYIKEKHQQEITFGDKSRVGRGGMT

Sbjct 181 GLLALELKADLLILLSDVDGLYSGPPSEPSSKIIHTYIKEKHQQEITFGDKSRVGRGGMT 240

Query 819 AKVKAAVLASNSGTPVVITSGFENRSILKVLHGEKIGTLFHKNANLWESSKDVSTREMAV 998

AKVKAAVLASNSGTPVVITSGFENRSILKVLHGEKIGTLFHKNANLWESSKDVSTREMAV

Sbjct 241 AKVKAAVLASNSGTPVVITSGFENRSILKVLHGEKIGTLFHKNANLWESSKDVSTREMAV 300

Query 999 AARDCSRHLQNLSSEERKKILLDVADALEANEDLIRSENEADVAAAQVAGYEKPLVARLT 1178

AARDCSRHLQNLSSEERKKILLDVADALEANEDLIRSENEADVAAAQVAGYEKPLVARLT

Sbjct 301 AARDCSRHLQNLSSEERKKILLDVADALEANEDLIRSENEADVAAAQVAGYEKPLVARLT 360

Query 1179 IKPGKIASLAKSIRTLANMEDPINQILKKTEVADDLVLEKTSCPLGVLLIVFESRPDALV 1358

IKPGKIASLAKSIRTLANMEDPINQILKKTEVADDLVLEKTSCPLGVLLIVFESRPDALV

Sbjct 361 IKPGKIASLAKSIRTLANMEDPINQILKKTEVADDLVLEKTSCPLGVLLIVFESRPDALV 420

Query 1359 QIASLAIRSGNGLLLKGGKEAIRSNTILHKVITDAIPRNVGEKLIGLVTTRDEIAdllkl 1538

QIASLAIRSGNGLLLKGGKEAIRSNTILHKVITDAIPRNVGEKLIGLVTTRDEIADLLKL

Sbjct 421 QIASLAIRSGNGLLLKGGKEAIRSNTILHKVITDAIPRNVGEKLIGLVTTRDEIADLLKL 480

Query 1539 ddvidlvTPRGSNKLVSQIKASTKIPVLGHADGICHVYIDKSADMDMAKLIVMDAKTDYP 1718

DDVIDLVTPRGSNKLVSQIKASTKIPVLGHADGICHVYIDKSADMDMAKLIVMDAKTDYP

Sbjct 481 DDVIDLVTPRGSNKLVSQIKASTKIPVLGHADGICHVYIDKSADMDMAKLIVMDAKTDYP 540

Query 1719 AACNAMETLLVHKDLMKSPGLDDILVALKTEGVNIYGGPIAHKALGFPKAVSFHHEYSSM 1898

AACNAMETLLVHKDLMKSPGLDDILVALKTEGVNIYGGPIAHKALGFPKAVSFHHEYSSM

Sbjct 541 AACNAMETLLVHKDLMKSPGLDDILVALKTEGVNIYGGPIAHKALGFPKAVSFHHEYSSM 600

Query 1899 ACTVEFVDDVQSAIDHIHRYGSAHTDCIVTTDDKVAETFLRRVDSAAVFHNASTRFSDGA 2078

ACTVEFVDDVQSAIDHIHRYGSAHTDCIVTTDDKVAETFLRRVDSAAVFHNASTRFSDGA

Sbjct 601 ACTVEFVDDVQSAIDHIHRYGSAHTDCIVTTDDKVAETFLRRVDSAAVFHNASTRFSDGA 660

Query 2079 RFGLGAEVGISTGRIHARGPVGVEGLLTTRWILRGRGQVVNGDKDVVYTHKSLPLQ 2246

RFGLGAEVGISTGRIHARGPVGVEGLLTTRWILRGRGQVVNGDKDVVYTHKSLPLQ

Sbjct 661 RFGLGAEVGISTGRIHARGPVGVEGLLTTRWILRGRGQVVNGDKDVVYTHKSLPLQ 716

Os05g0455500 [Oryza sativa Japonica Group]Range 1: 1 to 716GenPept Graphics Next MatchPrevious Match

Alignment statistics for match #1

Score Expect

Method Identities Positives Gaps Frame

1387 bits(3589)

0.0Compositional matrix adjust.

713/716(99%)

713/716(99%)

0/716(0%)

+3

Query 99 MASVDPSRSFVRDVKRVIIKVGTAVVSRQDGRLALGRVGALCEQVKELNSLGYEVILVTS 278

MASVDPSRSFVRDVKRVIIKVGTAVVSRQDGRLALGRVGALCEQVKELNSLGYEVILVTS

Sbjct 1 MASVDPSRSFVRDVKRVIIKVGTAVVSRQDGRLALGRVGALCEQVKELNSLGYEVILVTS 60

Query 279 GAVGVGRQRLRYRKLVNSSFADLQKPQMELDGKACAAVGQSGLMALYDMLFNQLDVSSSQ 458

GAVGVGRQRLRYRKLVNSSFADLQKPQMELDGKACAAVGQSGLMALYDMLFNQLDVSSSQ

Sbjct 61 GAVGVGRQRLRYRKLVNSSFADLQKPQMELDGKACAAVGQSGLMALYDMLFNQLDVSSSQ 120

Query 459 LLVTDSDFENPKFREQLTETVESLLDLKVIPIFNENDAISTRKAPYEDSSGIFWDNDSla 638

LLVTDSDFENPKFREQLTETVESLLDLKVIPIFNENDAISTRKAPYEDSSGIFWDNDSLA

Sbjct 121 LLVTDSDFENPKFREQLTETVESLLDLKVIPIFNENDAISTRKAPYEDSSGIFWDNDSLA 180

Query 639 gllalelkadllillSDVDGLYSGPPSEPSSKIIHTYIKEKHQQEITFGDKSRVGRGGMT 818

GLLALELKADLLILLSDVDGLYSGPPSEPSSKIIHTYIKEKHQQEITFGDKSRVGRGGMT

Sbjct 181 GLLALELKADLLILLSDVDGLYSGPPSEPSSKIIHTYIKEKHQQEITFGDKSRVGRGGMT 240

Query 819 AKVKAAVLASNSGTPVVITSGFENRSILKVLHGEKIGTLFHKNANLWESSKDVSTREMAV 998

AKVKAAVLASNSGTPVVITSGFENRSILKVLHGEKIGTLFHKNANLWESSKDVSTREMAV

Sbjct 241 AKVKAAVLASNSGTPVVITSGFENRSILKVLHGEKIGTLFHKNANLWESSKDVSTREMAV 300

Query 999 AARDCSRHLQNLSSEERKKILLDVADALEANEDLIRSENEADVAAAQVAGYEKPLVARLT 1178

AARDCSRHLQNLSSEERKKILLDVADALEANEDLIRSENEADVAAAQVAGYEKPLVARLT

Sbjct 301 AARDCSRHLQNLSSEERKKILLDVADALEANEDLIRSENEADVAAAQVAGYEKPLVARLT 360

Query 1179 IKPGKIASLAKSIRTLANMEDPINQILKKTEVADDLVLEKTSCPLGVLLIVFESRPDALV 1358

IKPGKIASLAKSIRTLANMEDPINQILKKTEVADDLVLEKTSCPLGVLLIVFESRPDALV

Sbjct 361 IKPGKIASLAKSIRTLANMEDPINQILKKTEVADDLVLEKTSCPLGVLLIVFESRPDALV 420

Query 1359 QIASLAIRSGNGLLLKGGKEAIRSNTILHKVITDAIPRNVGEKLIGLVTTRDEIAdllkl 1538

QIASLAIRSGNGLLLKGGKEAIRSNTILHKVITDAIPRNVGEKLIGLVTTRDEIADLLKL

Sbjct 421 QIASLAIRSGNGLLLKGGKEAIRSNTILHKVITDAIPRNVGEKLIGLVTTRDEIADLLKL 480

Query 1539 ddvidlvTPRGSNKLVSQIKASTKIPVLGHADGICHVYIDKSADMDMAKLIVMDAKTDYP 1718

DDVIDLV PRGSNKLVSQIKASTKIPVLGHADGICHVYIDKSADMDMAK IVMDAK DYP

Sbjct 481 DDVIDLVIPRGSNKLVSQIKASTKIPVLGHADGICHVYIDKSADMDMAKHIVMDAKIDYP 540

Query 1719 AACNAMETLLVHKDLMKSPGLDDILVALKTEGVNIYGGPIAHKALGFPKAVSFHHEYSSM 1898

AACNAMETLLVHKDLMKSPGLDDILVALKTEGVNIYGGPIAHKALGFPKAVSFHHEYSSM

Sbjct 541 AACNAMETLLVHKDLMKSPGLDDILVALKTEGVNIYGGPIAHKALGFPKAVSFHHEYSSM 600

Query 1899 ACTVEFVDDVQSAIDHIHRYGSAHTDCIVTTDDKVAETFLRRVDSAAVFHNASTRFSDGA 2078

ACTVEFVDDVQSAIDHIHRYGSAHTDCIVTTDDKVAETFLRRVDSAAVFHNASTRFSDGA

Sbjct 601 ACTVEFVDDVQSAIDHIHRYGSAHTDCIVTTDDKVAETFLRRVDSAAVFHNASTRFSDGA 660

Query 2079 RFGLGAEVGISTGRIHARGPVGVEGLLTTRWILRGRGQVVNGDKDVVYTHKSLPLQ 2246

RFGLGAEVGISTGRIHARGPVGVEGLLTTRWILRGRGQVVNGDKDVVYTHKSLPLQ

Sbjct 661 RFGLGAEVGISTGRIHARGPVGVEGLLTTRWILRGRGQVVNGDKDVVYTHKSLPLQ 716

4. Jawaban :Link tidak bisa dibuka.

5. Jawaban :Protein : 2Fe-2S ferredoxin-type iron-sulfur dan C-terminal cystine

PS00197   2FE2S_FER_1   2Fe-2S ferredoxin-type iron-sulfur binding region signature :

14 - 22:    [level tag: (-1)]  CAAGGCGGC

120 - 128:

   [level tag: (-1)]  CGGAGCTTC

302 - 310:

   [level tag: (-1)]  CAAGGCATC

499 - 507:

   [level tag: (-1)]  CAAATCAGC

640 - 648:

   [level tag: (-1)]  CAAGGCGTC

PS01185   CTCK_1   C-terminal cystine knot signature :

113 - 149:

   [level tag: (-1)]  CCcgtcccggagcttCgtGagggacgtgaagCgCgt..C

6. Jawaban :

Tidak ada novel gene yang homolog karena warna yang dihasilkan warna hitam sehingga tingkat homologinya rendah.

ANALISIS DESIGN PRIMER

1 LEFT PRIMER 62 20 60.85 60.00 8.00 2.00 CACCTGAGGTCAGGAGTTCG

5' CACCTGAGGTCAGGAGTTCG 3'

+ ||||| +++++ +

3' GCTTGAGGACTGGAGTCCAC 5'

STACK AT 3 IS 5 BP LONG.

RIGHT PRIMER 237 19 59.52 57.89 4.00 1.00 GATCTCGGCTCACTGCAAC

5' GATCTCGGCTCACTGCAAC 3'

||||

3' CAACGTCACTCGGCTCTAG 5'

STACK AT 14 IS 4 BP LONG.

PRODUCT SIZE: 176, PAIR ANY COMPL: 4.00, PAIR 3' COMPL: 2.00

2 LEFT PRIMER 69 20 59.83 60.00 6.00 1.00 GGTCAGGAGTTCGAGACCAG

5' GGTCAGGAGTTCGAGACCAG 3'

+ |||| +

3' GACCAGAGCTTGAGGACTGG 5'

STACK AT 11 IS 4 BP LONG.

RIGHT PRIMER 236 20 62.31 55.00 4.00 1.00 ATCTCGGCTCACTGCAACCT

5' ATCTCGGCTCACTGCAACCT 3'

||||

3' TCCAACGTCACTCGGCTCTA 5'

STACK AT 13 IS 4 BP LONG.

PRODUCT SIZE: 168, PAIR ANY COMPL: 6.00, PAIR 3' COMPL: 3.00

3 LEFT PRIMER 64 20 59.98 60.00 8.00 2.00 CCTGAGGTCAGGAGTTCGAG

5' CCTGAGGTCAGGAGTTCGAG 3'

||||| +++++

3' GAGCTTGAGGACTGGAGTCC 5'

STACK AT 1 IS 5 BP LONG.

RIGHT PRIMER 279 19 61.75 63.16 5.00 2.00 ACGGAGTCTCGCTCTGTCG

5' ACGGAGTCTCGCTCTGTCG 3'

++ ||| +++ ++

3' GCTGTCTCGCTCTGAGGCA 5'

STACK AT 4 IS 3 BP LONG.

PRODUCT SIZE: 216, PAIR ANY COMPL: 4.00, PAIR 3' COMPL: 2.00

4 LEFT PRIMER 100 20 59.97 55.00 3.00 3.00 TGGTGAAACCCCGTCTCTAC

5' TGGTGAAACCCCGTCTCTAC 3'

||| +++

3' CATCTCTGCCCCAAAGTGGT 5'

STACK AT 2 IS 3 BP LONG.

RIGHT PRIMER 279 19 61.75 63.16 5.00 2.00 ACGGAGTCTCGCTCTGTCG

5' ACGGAGTCTCGCTCTGTCG 3'

++ ||| +++ ++

3' GCTGTCTCGCTCTGAGGCA 5'

STACK AT 4 IS 3 BP LONG.

PRODUCT SIZE: 180, PAIR ANY COMPL: 6.00, PAIR 3' COMPL: 2.00

Keterangan :

Yang ditandai tinta merah adalah hasil analisis dari Gene Runner.

Kesimpulan :

Jadi syarat DNA primer yang baik adalah yang tidak mengandung dimer dan komposisi G-C sebesar 40 – 60%.berdasarkan hasil analisis primer untuk manusia (NCBI – Blast) diatas maka dapat disimpulkan DNA primer yang baik adalah dari

1. RIGHT PRIMER 237 19 59.52 57.89 4.00 1.00 GATCTCGGCTCACTGCAAC

5' GATCTCGGCTCACTGCAAC 3'

||||

3' CAACGTCACTCGGCTCTAG 5'

STACK AT 14 IS 4 BP LONG.