Reference Sequence BCKDHA

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
148727347|ref|NP_001092034.1	95%	BLAST
89-60% Sequence Identity
196011048|ref|XP_002115388.1	66%	PSI BLAST, 3 iterations, E-value cutoff 0.005
149543950|ref|XP_001517857.1	67%	BLAST
47227873|emb|CAG09036.1	82,5%	FASTA
47196273|emb|CAF88112.1	81%	PSI BLAST, 5 iterations, E-value cutoff 0.005
12964598|dbj|BAB32665.1	88%	PSI BLAST, 5 iterations, E-value cutoff 10E-6
59-40% Sequence Identity
193290664|gb|ACF17640.1	47%	BLAST
215431443|ref|ZP_03429362.1	40%	FASTA
225557347|gb|EEH05633.1	51%	PSI BLAST, 3 iterations, E-value cutoff 10E-6
58267618|ref|XP_570965.1	50%	PSI BLAST, 5 iterations, E-value cutoff 0.005
162449842|ref|YP_001612209.1	41%	PSI BLAST, 5 iterations, E-value cutoff 10E-6
39-20% Sequence Identity
56966700|pdb|1W85	31%	PSI BLAST, 3 iterations, E-value cutoff 0.005
5822330|pdb|1QS0	38.1%	FASTA
13516864|dbj|BAB40585.1	33%	PSI BLAST, 3 iterations, E-value cutoff 10E-6
284166853|ref|YP_003405132.1	35%	PSI BLAST, 5 iterations, E-value cutoff 0.005
76800932|ref|YP_325940.1	34%	PSI BLAST, 5 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

Multiple Alignments

• ClustalW

clustalw sequences.fasta

• T-Coffee

t_coffee -seq sequences.fasta

• T-Coffee(3D)

t_coffee -seq sequences.fasta -mode expresso

• Muscle

muscle -in sequences.fasta -out output.aln

• Cobalt

./cobalt -i sequences.fasta -norps T > output.aln

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