Difference between revisions of "Reference Sequence BCKDHA"
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* [[Cobalt]] |
* [[Cobalt]] |
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| − | + | * [ftp://ftp.ncbi.nlm.nih.gov/pub/cobalt cobalt] (download) |
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./cobalt -i sequences.fasta -norps T > output.aln |
./cobalt -i sequences.fasta -norps T > output.aln |
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Revision as of 13:36, 20 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 |
| 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 sequences.fasta
t_coffee -seq sequences.fasta
t_coffee -seq sequences.fasta -mode expresso
muscle -in sequences.fasta -out output.aln
- cobalt (download)
./cobalt -i sequences.fasta -norps T > output.aln
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