Analisis Fungsi Dan Lokasi Protein

Nama

: Asep Badru Zaman (1111095000026) UAS BIOINFORMATIKA

ANALISIS FUNGSI DAN LOKASI PROTEIN

1. TAHAP MEMILIH PROTEIN -

MENGUNDUH SEKUEN PROTEIN BETACELLULIN HASIL FASTA:

MNPTLGLAIFLAVLLTVKGLLKPSFSPRNYKALSEVQGWKQRMAAKELARQNMDLGFKLLKKLAFYNPGR NIFLSPLSISTAFSMLCLGAQDSTLDEIKQGFNFRKMPEKDLHEGFHYIIHELTQKTQDLKLSIGNTLFI DQRLQPQRKFLEDAKNFYSAETILTNFQNLEMAQKQINDFISQKTHGKINNLIENIDPGTVMLLANYIFF RARWKHEFDPNVTKEEDFFLEKNSSVKVPMMFRSGIYQVGYDDKLSCTILEIPYQKNITAIFILPDEGKL KHLEKGLQVDTFSRWKTLLSRRVVDVSVPRLHMTGTFDLKKTLSYIGVSKIFEEHGDLTKIAPHRSLKVG EAVHKAELKMDERGTEGAAGTGAQTLPMETPLVVKIDKPYLLLIYSEKIPSVLFLGKIVNPIGK

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: Glu: Met: Tyr:

1.489 1.504 1.363 0.787

Arg: Gly: Phe: Val:

1.224 0.510 1.195 0.990

Asn: 0.772 His: 1.003 Pro: 0.492 : 0.848 :

Asp: 0.924 Cys: Ile: 1.003 Leu: Ser: 0.739 Thr: 1.334 : 1.020

0.966 1.236 0.785

Gln: Lys: Trp:

1.164 1.172 1.090

Weights for window positions 1,..,9, using linear weight variation model: model : 1 1.00 edge

2 1.00

3 1.00

4 1.00

5 6 1.00 1.00 center

7 1.00

8 1.00

9 1.00 edge

NMR Structure of Human Betacellulin-2

MMDB ID: 20079PDB ID: 1IP0

Citation:

PDB Deposition Date:2001/4/19 Updated in MMDB:07/2009 ▼ Experimental Method:Solution NMR Source Organism:Homo sapiens Similar Structures:VAST+

Solution structure of betacellulin, a new member of egf-family ligands.

Miura K, Doura H, Aizawa T, Tada H, Seno M, Yamada H, Kawano K Biochem.Biophys.Res.Commun. (2002) 294 p.1040

Interactions?

Molecular Graphic ?

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Protein

Molecules and interactions Label

Count

Molecule

Interactions

Protein and interactions (1 molecule)

Betacellulin 1

no interaction recorded Hide annotation ▲

* Click molecule labels to explore molecular sequence information.

ANALISIS SEKUENS HOMOLOGI

1. Jawaban : Putative ORF = Eukariotyc GeneMark.hmm version bp 3.9_2 Dec 2010-2012 Sequence name: Oryza sativa Sequence length: 864 bp G+C content: 44.91% Matrices file: /hom e/genmark/euk_ghm.matrices/rice_hmm3.0mod Tue Jan 7 22:14:10 2014

Predicted genes/exons Gene Exon Strand Exon # # Type

1 1 + Initial 1 2 + Internal

Exon Range Length

99 259

163 800

65 542

Exon Frame

Start/End

12-31--

# protein sequence of predicted genes >gene_1|GeneMark.hmm|202_aa MASVDPSRSFVRDVKRVIIKVKMLVLVRWLLPQEIVQGIYRGVNIYGGPIAHKALGFPKA VSFHHEYSSMACTVEFVDDVQSAIDHIHRYGSADGICHVYIDKSADMDMAKLIVMDAKTD YPAACNAMELDDVIDLVTPRGSNKLVSQIKASTKIPVLGHAEVADDLVLEKTSCPLGVLL IVFESRPDALVQVQIASLAIRS

# end protein sequence

2. Jawaban : Protein yang berkorelasi : delta-1-pyrroline-5-carboxylate s ynthase delta 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 716GenPeptGraphics Next MatchPrevious Match Alignmentstatistics

formatch#1

Score

Expec t

Method

Identities

Positives

Gaps

Fram e

1395 bits(3611)

0.0

Compositional matrix adjust.

716/716(100% )

716/716(100% )

0/716(0% )

+3

Query

99

MASVDPSRSFVRDVKRVIIKVGTAVVSRQDGRLALGRVGALCEQVKELNSLGYEVILVTS

278

MASVDPSRSFVRDVKRVIIKVGTAVVSRQDGRLALGRVGALCEQVKELNSLGYEVILVTS Sbjct

1


60

Query

279

GAVGVGRQRLRYRKLVNSSFADLQKPQMELDGKACAAVGQSGLMALYDMLFNQLDVSSSQ

458

Sbjct

61

Query

459

GAVGVGRQRLRYRKLVNSSFADLQKPQMELDGKACAAVGQSGLMALYDMLFNQLDVSSSQ GAVGVGRQRLRYRKLVNSSFADLQKPQMELDGKACAAVGQSGLMALYDMLFNQLDVSSSQ

120

LLVTDSDFENPKFREQLTETVESLLDLKVIPIFNENDAISTRKAPYEDSSGIFWDNDSla 638 LLVTDSDFENPKFREQLTETVESLLDLKVIPIFNENDAISTRKAPYEDSSGIFWDNDSLA

Sbjct

121

LLVTDSDFENPKFREQLTETVESLLDLKVIPIFNENDAISTRKAPYEDSSGIFWDNDSLA

180

Query

639

gllalelkadllillSDVDGLYSGPPSEPSSKIIHTYIKEKHQQEITFGDKSRVGRGGMT

818

GLLALELKADLLILLSDVDGLYSGPPSEPSSKIIHTYIKEKHQQEITFGDKSRVGRGGMT

Sbjct

181


240

Query

819

AKVKAAVLASNSGTPVVITSGFENRSILKVLHGEKIGTLFHKNANLWESSKDVSTREMAV

998

Sbjct

241


300

Query

999

AARDCSRHLQNLSSEERKKILLDVADALEANEDLIRSENEADVAAAQVAGYEKPLVARLT

1178


AARDCSRHLQNLSSEERKKILLDVADALEANEDLIRSENEADVAAAQVAGYEKPLVARLT Sbjct

301


360

Query

1179

IKPGKIASLAKSIRTLANMEDPINQILKKTEVADDLVLEKTSCPLGVLLIVFESRPDALV

1358

IKPGKIASLAKSIRTLANMEDPINQILKKTEVADDLVLEKTSCPLGVLLIVFESRPDALV Sbjct

361


420

Query

1359

QIASLAIRSGNGLLLKGGKEAIRSNTILHKVITDAIPRNVGEKLIGLVTTRDEIAdllkl 1538 QIASLAIRSGNGLLLKGGKEAIRSNTILHKVITDAIPRNVGEKLIGLVTTRDEIADLLKL

Sbjct

421

QIASLAIRSGNGLLLKGGKEAIRSNTILHKVITDAIPRNVGEKLIGLVTTRDEIADLLKL

480

Query

1539

ddvidlvTPRGSNKLVSQIKASTKIPVLGHADGICHVYIDKSADMDMAKLIVMDAKTDYP

1718

DDVIDLVTPRGSNKLVSQIKASTKIPVLGHADGICHVYIDKSADMDMAKLIVMDAKTDYP Sbjct

481

DDVIDLVTPRGSNKLVSQIKASTKIPVLGHADGICHVYIDKSADMDMAKLIVMDAKTDYP

540

Query

1719

AACNAMETLLVHKDLMKSPGLDDILVALKTEGVNIYGGPIAHKALGFPKAVSFHHEYSSM

1898

Sbjct

541


600

Query

1899

ACTVEFVDDVQSAIDHIHRYGSAHTDCIVTTDDKVAETFLRRVDSAAVFHNASTRFSDGA

2078



Sbjct

601


Query

2079

RFGLGAEVGISTGRIHARGPVGVEGLLTTRWILRGRGQVVNGDKDVVYTHKSLPLQ

Sbjct

661

660

2246

RFGLGAEVGISTGRIHARGPVGVEGLLTTRWILRGRGQVVNGDKDVVYTHKSLPLQ RFGLGAEVGISTGRIHARGPVGVEGLLTTRWILRGRGQVVNGDKDVVYTHKSLPLQ

716

Os05g0455500 [Oryza sativa Japonica Group] Range 1: 1 to 716GenPeptGraphics Next MatchPrevious Match Alignmentstatistics

formatch#1

Score

Expec t

Method

Identities

Positives

Gaps

Fram e

1387 bits(3589)

0.0

Compositional matrix adjust.

713/716(99% )

713/716(99% )

0/716(0% )

+3

Query

99

Sbjct

1

Query

279


278

MASVDPSRSFVRDVKRVIIKVGTAVVSRQDGRLALGRVGALCEQVKELNSLGYEVILVTS MASVDPSRSFVRDVKRVIIKVGTAVVSRQDGRLALGRVGALCEQVKELNSLGYEVILVTS

60


458

GAVGVGRQRLRYRKLVNSSFADLQKPQMELDGKACAAVGQSGLMALYDMLFNQLDVSSSQ Sbjct

61


120

Query

459

LLVTDSDFENPKFREQLTETVESLLDLKVIPIFNENDAISTRKAPYEDSSGIFWDNDSla 638

Sbjct

121


180

Query

639

gllalelkadllillSDVDGLYSGPPSEPSSKIIHTYIKEKHQQEITFGDKSRVGRGGMT

818



Sbjct

181


240

Query

819


998

Sbjct

241


300

Query

999


1178


AARDCSRHLQNLSSEERKKILLDVADALEANEDLIRSENEADVAAAQVAGYEKPLVARLT Sbjct

301


360

Query

1179


1358

IKPGKIASLAKSIRTLANMEDPINQILKKTEVADDLVLEKTSCPLGVLLIVFESRPDALV Sbjct

361


420

Query

1359

QIASLAIRSGNGLLLKGGKEAIRSNTILHKVITDAIPRNVGEKLIGLVTTRDEIAdllkl 1538 QIASLAIRSGNGLLLKGGKEAIRSNTILHKVITDAIPRNVGEKLIGLVTTRDEIADLLKL

Sbjct

421

QIASLAIRSGNGLLLKGGKEAIRSNTILHKVITDAIPRNVGEKLIGLVTTRDEIADLLKL

480

Query

1539

ddvidlvTPRGSNKLVSQIKASTKIPVLGHADGICHVYIDKSADMDMAKLIVMDAKTDYP

1718

DDVIDLV PRGSNKLVSQIKASTKIPVLGHADGICHVYIDKSADMDMAK IVMDAK DYP Sbjct

481

DDVIDLVIPRGSNKLVSQIKASTKIPVLGHADGICHVYIDKSADMDMAKHIVMDAKIDYP

540

Query

1719


1898

Sbjct

541


600

Query

1899


2078



Sbjct

601


Query

2079

RFGLGAEVGISTGRIHARGPVGVEGLLTTRWILRGRGQVVNGDKDVVYTHKSLPLQ

Sbjct

661

2246

RFGLGAEVGISTGRIHARGPVGVEGLLTTRWILRGRGQVVNGDKDVVYTHKSLPLQ RFGLGAEVGISTGRIHARGPVGVEGLLTTRWILRGRGQVVNGDKDVVYTHKSLPLQ

716

660

4. Jawaban : Link tidak bisa dibuka. 5. Jawaban : Protein : 2Fe-2S ferredox in-type iron-sulfu r dan C - te r m i n a l c y s t i n e

PS00197 2FE2S_FER_1 2Fe-2S ferredoxin -type iron -sulfur binding region signature : 14 - 22: 120 128: 302 310: 499 507: 640 648:

[level tag: (-1)] CAAGGCGGC [level tag: (-1)] CGGAGCTTC [level tag: (-1)] CAAGGCATC [level tag: (-1)] CAAATCAGC [level tag: (-1)] CAAGGCGTC

PS01185 CTCK_1 C -t e r m i n a l c y s t i n e 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.

Analisis Fungsi Dan Lokasi Protein

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