Difference between revisions of "Reference Sequence BCKDHA"

From Bioinformatikpedia
(Sequence searches)
(Sequence searches)
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!colspan="3"| 99-90% Sequence Identity
 
!colspan="3"| 99-90% Sequence Identity
 
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|pdb 1X7Z||99%||PSI BLAST
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|gi|56967006|pdb|1X7Z||99%||PSI BLAST, 3 iterations, E-value cutoff 0.005
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|-
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|gi|7546384|pdb|1DTW||95%||BLAST
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|gi|34810149|pdb|1OLU||99%||PSI BLAST, 3 iterations, E-value cutoff 10E-6
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|gi|13277798|gb|AAH03787.1||95%||PSI BLAST, 3 iterations, E-value cutoff 10E-6
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Revision as of 12:29, 19 May 2011

Sequence

  • Uniprot:

>sp|P12694|ODBA_HUMAN 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial OS=Homo sapiens GN=BCKDHA PE=1 SV=2

MAVAIAAARVWRLNRGLSQAALLLLRQPGARGLARSHPPRQQQQFSSLDDKPQFPGASAE FIDKLEFIQPNVISGIPIYRVMDRQGQIINPSEDPHLPKEKVLKLYKSMTLLNTMDRILY ESQRQGRISFYMTNYGEEGTHVGSAAALDNTDLVFGQYREAGVLMYRDYPLELFMAQCYG NISDLGKGRQMPVHYGCKERHFVTISSPLATQIPQAVGAAYAAKRANANRVVICYFGEGA ASEGDAHAGFNFAATLECPIIFFCRNNGYAISTPTSEQYRGDGIAARGPGYGIMSIRVDG NDVFAVYNATKEARRRAVAENQPFLIEAMTYRIGHHSTSDDSSAYRSVDEVNYWDKQDHP ISRLRHYLLSQGWWDEEQEKAWRKQSRRKVMEAFEQAERKPKPNPNLLFSDVYQEMPAQL RKQQESLARHLQTYGEHYPLDHFDK

Sequence info: [1] The Uniprot sequence is 445 aa long, as is contains the transit peptide sequence from position 1-45.

  • PDB:

>1U5B:A|PDBID|CHAIN|SEQUENCE

SSLDDKPQFPGASAEFIDKLEFIQPNVISGIPIYRVMDRQGQIINPSEDPHLPKEKVLKLYKSMTLLNTMDRILYESQRQ GRISFYMTNYGEEGTHVGSAAALDNTDLVFGQYREAGVLMYRDYPLELFMAQCYGNISDLGKGRQMPVHYGCKERHFVTI SSPLATQIPQAVGAAYAAKRANANRVVICYFGEGAASEGDAHAGFNFAATLECPIIFFCRNNGYAISTPTSEQYRGDGIA ARGPGYGIMSIRVDGNDVFAVYNATKEARRRAVAENQPFLIEAMTYRIGHHSTSDDSSAYRSVDEVNYWDKQDHPISRLR HYLLSQGWWDEEQEKAWRKQSRRKVMEAFEQAERKPKPNPNLLFSDVYQEMPAQLRKQQESLARHLQTYGEHYPLDHFDK

Sequence info: [2]


Sequence Alignments

Sequence searches

  • FASTA

../bin/fasta36 sequence.fasta database > FastaOutput.txt

  • BLAST

blastall -p blastp -d database -i sequence.fasta > BlastOutput.txt

  • PSIBLAST

blastpgp -i sequence.fasta -j iterations -h evalueCutoff -d database > PsiblastOutput.txt

  • HHSearch

hhsearch -i query -d database -o output.txt


database = /data/blast/nr/nr

Sequences chosen for the multiple Alignment:

SeqIdentifier Seq Identity source
99-90% Sequence Identity
56967006|pdb|1X7Z 99% PSI BLAST, 3 iterations, E-value cutoff 0.005
7546384|pdb|1DTW 95% BLAST
34810149|pdb|1OLU 99% PSI BLAST, 3 iterations, E-value cutoff 10E-6
13277798|gb|AAH03787.1 95% PSI BLAST, 3 iterations, E-value cutoff 10E-6

Sequences for the Multiple Sequences Alignment were downloaded via NCBI, the sequence id can be changed in the link to retrieve the fasta format: http://www.ncbi.nlm.nih.gov/protein/76800932?report=fasta


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