Difference between revisions of "Reference Sequence BCKDHA"
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[[Sequence_Alignments]] |
[[Sequence_Alignments]] |
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| − | == Sequence Alignments == |
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| − | |||
| − | === Sequence searches === |
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| − | * FASTA |
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| − | ../bin/fasta36 sequence.fasta database > FastaOutput.txt |
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| − | |||
| − | * BLAST |
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| − | blastall -p blastp -d database -i sequence.fasta > BlastOutput.txt |
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| − | |||
| − | * PSIBLAST |
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| − | blastpgp -i sequence.fasta -j iterations -h evalueCutoff -d database > PsiblastOutput.txt |
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| − | |||
| − | * HHSearch |
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| − | hhsearch -i query -d database -o output.txt |
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| − | |||
| − | |||
| − | database = /data/blast/nr/nr |
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| − | |||
| − | Sequences chosen for the multiple Alignment: |
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| − | {| border="1" style="text-align:center; border-spacing:0;" |
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| − | !SeqIdentifier |
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| − | !Seq Identity |
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| − | !source |
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| − | |- |
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| − | !colspan="3"| 99-90% Sequence Identity |
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| − | |- |
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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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| − | |- |
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| − | |gi|34810149|pdb|1OLU||99%||PSI BLAST, 3 iterations, E-value cutoff 10E-6 |
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| − | |- |
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| − | |gi|13277798|gb|AAH03787.1||95%||PSI BLAST, 3 iterations, E-value cutoff 10E-6 |
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| − | |- |
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| − | |gi|148727347|ref|NP_001092034.1||95%||BLAST |
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| − | |- |
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| − | !colspan="3"| 89-60% Sequence Identity |
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| − | |- |
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| − | |gi|196011048|ref|XP_002115388.1||66%||PSI BLAST, 3 iterations, E-value cutoff 0.005 |
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| − | |- |
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| − | |gi|149543950|ref|XP_001517857.1||67%||BLAST |
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| − | |- |
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| − | |gi|47227873|emb|CAG09036.1||82,5%||FASTA |
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| − | |- |
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| − | |gi|47196273|emb|CAF88112.1||81%||PSI BLAST, 5 iterations, E-value cutoff 0.005 |
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| − | |- |
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| − | |gi|12964598|dbj|BAB32665.1||88%||PSI BLAST, 5 iterations, E-value cutoff 10E-6 |
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| − | |- |
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| − | !colspan="3"| 59-40% Sequence Identity |
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| − | |- |
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| − | |gi|193290664|gb|ACF17640.1||47%||BLAST |
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| − | |- |
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| − | |gi|215431443|ref|ZP_03429362.1||40%||FASTA |
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| − | |- |
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| − | |gi|225557347|gb|EEH05633.1||51%||PSI BLAST, 3 iterations, E-value cutoff 10E-6 |
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| − | |- |
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| − | |gi|58267618|ref|XP_570965.1||50%||PSI BLAST, 5 iterations, E-value cutoff 0.005 |
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| − | |- |
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| − | |gi|162449842|ref|YP_001612209.1||41%||PSI BLAST, 5 iterations, E-value cutoff 10E-6 |
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| − | |- |
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| − | !colspan="3"| 39-20% Sequence Identity |
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| − | |- |
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| − | |gi|56966700|pdb|1W85||31%||PSI BLAST, 3 iterations, E-value cutoff 0.005 |
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| − | |- |
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| − | |gi|5822330|pdb|1QS0||38.1%||FASTA |
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| − | |- |
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| − | |gi|13516864|dbj|BAB40585.1||33%||PSI BLAST, 3 iterations, E-value cutoff 10E-6 |
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| − | |- |
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| − | |gi|284166853|ref|YP_003405132.1||35%||PSI BLAST, 5 iterations, E-value cutoff 0.005 |
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| − | |- |
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| − | |gi|76800932|ref|YP_325940.1||34%||PSI BLAST, 5 iterations, E-value cutoff 10E-6 |
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| − | |||
| − | |} |
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| − | Sequences for the Multiple Sequences Alignment were downloaded via NCBI, the sequence id can be changed in the link to retrieve the fasta format: |
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| − | http://www.ncbi.nlm.nih.gov/protein/76800932?report=fasta |
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| − | |||
| − | === Multiple Alignments === |
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| − | * [[ClustalW]] |
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| − | clustalw sequences.fasta |
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| − | |||
| − | * [[T-Coffee]] |
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| − | t_coffee -seq sequences.fasta |
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| − | |||
| − | * [[T-Coffee(3D)]] |
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| − | t_coffee -seq sequences.fasta -mode expresso |
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| − | |||
| − | * [[Muscle]] |
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| − | muscle -in sequences.fasta -out output.aln |
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| − | |||
| − | * [[Cobalt]] |
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| − | |||
| − | download [ftp://ftp.ncbi.nlm.nih.gov/pub/cobalt cobalt] |
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| − | |||
| − | ./cobalt -i sequences.fasta -norps T > output.aln |
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| − | |||
| − | === Conservation and Gaps === |
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| − | |||
| − | {| border="1" style="text-align:center; border-spacing:0;" |
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| − | |'''Alignment methods''' |
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| − | |'''Gaps''' |
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| − | |'''Avg Gap Length''' |
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| − | |- |
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| − | |ClustalW |
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| − | |12 |
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| − | |3,75 |
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| − | |- |
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| − | |T-Coffee |
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| − | |25 |
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| − | |4,56 |
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| − | |- |
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| − | |T-Coffee (3D) |
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| − | |56 |
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| − | |4,75 |
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| − | |- |
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| − | |Cobalt |
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| − | |19 |
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| − | |3,26 |
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| − | |- |
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| − | |Muscle |
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| − | |17 |
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| − | |4,76 |
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| − | |} |
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| − | |||
| − | back to [[Maple syrup urine disease]] main page |
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Revision as of 00:02, 21 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]
