Analysis of BlastN and BlastX

The best way to identify an unknown sequence is to see if that sequence already exists in apublic database. If the database sequence is a well-characterized sequence, then one will haveaccess to a wealth of biological information. Nucleotide Blast (BlastN) and BlastX can be usedto accomplish this goal. BlastN is specifically designed to alignment of unknown nucleotidessequence to nucleotide sequence in database; BlastP is designed to alignments of unknownprotein sequence with protein sequence in database; while BlastX is designed to alignments oftranslated nucleotide sequences to protein sequence with protein sequence in database.

Local alignment using BlastN programs will simulate in procedure below:

1. Browse to Basic Local Alignment Search Tool (BLAST) of NCBI sites athttp://blast.ncbi.nlm.nih.gov/Blast.cgi, and screen page will seen as below:

2. Click nucleotide blast word for BlastN, and screen page will seen as below:

3. Nucleotide sequence that subjected to local alignment can be input to BlastN in form ofFASTA format sequence or accession number of unknown sequence, then press theBLAST button at buttom left of page. By using accession number of AB453966.1 asunknown sequence, screen page of BlastN program will seen as below:

Alignment result from BlastN is limited to top ten of maximal alignment score. Based in thisresult, it is known unknown sequence with accession number AB453966.1 show maximalalignment score at 1035 with nucleotide sequence of Methylococcaceae bacterium ET-SHOmxaF gene for methanol dehydrogenase alpha subunit, partial cds at percent identity of100%, followed by Uncultured bacterium clone LOM13.7 alpha subunit methanoldehydrogenase (mxaF) gene, partial cds (max alignment score at 750 with percent identityat 91%) and Hyphomicrobium sp. mxaF gene, partial, strain P 495 (max. alignment score at749 with percent identity at 92%). Alignment of unknown sequence with nucleotidesequence Methylococcaceae bacterium ET-SHO mxaF gene for methanol dehydrogenasealpha subunit, partial cds by BlastN is shown as below:

Alignment of unknown sequence with nucleotide sequence Uncultured bacterium cloneLOM13.7 alpha subunit methanol dehydrogenase (mxaF) gene, partial cds by BlastN isshown as below:

If it really an unknown sequence, BlastN likely that unknown sequence is belong toMethylococcaceae bacterium ET-SHO mxaF gene for methanol dehydrogenase alphasubunit. Distance three of the result is seen as below:

Local alignment using BlastN programs will simulate in procedure below:

1. Browse to Basic Local Alignment Search Tool (BLAST) of NCBI sites athttp://blast.ncbi.nlm.nih.gov/Blast.cgi, and screen page will seen as below:

2. Click nucleotide blast word for BlastX, and screen page will seen as below:

3. Nucleotide sequence that subjected to local alignment can be input to BlastX in form ofFASTA format sequence or accession number of unknown sequence, then press theBLAST button at buttom left of page. By using accession number of AB453966.1 asunknown sequence, screen page of BlastN program will seen as below:

Alignment result from BlastX is limited to top ten of maximal alignment score. Based in thisresult, it is nucleotide translated to protein of unknown unknown sequence with accessionnumber AB453966.1 show maximal alignment score at 389 with protein sequence ofmethanol dehydrogenase alpha subunit [Methylococcaceae bacterium ET-SHO] at percent identityof 100%, followed by alpha subunit methanol dehydrogenase [uncultured bacterium] (maxalignment score at 334 with percent identity at 89%) and MxaF [uncultured bacterium] (max.alignment score at 333 with percent identity at 86%). Alignment of unknown sequence withprotein sequence Methylococcaceae bacterium ET-SHO mxaF gene for methanoldehydrogenase alpha subunit, partial cds by Blastx is shown as below:

Alignment result from BlastN is limited to top ten of maximal alignment score. Based in thisresult, it is known unknown sequence with accession number AB453966.1 show maximalalignment score at 1035 with nucleotide sequence of Methylococcaceae bacterium ET-SHOmxaF gene for methanol dehydrogenase alpha subunit, partial cds at percent identity of100%, followed by Uncultured bacterium clone LOM13.7 alpha subunit methanoldehydrogenase (mxaF) gene, partial cds (max alignment score at 750 with percent identityat 91%) and Hyphomicrobium sp. mxaF gene, partial, strain P 495 (max. alignment score at749 with percent identity at 92%). Alignment of unknown sequence with nucleotidesequence Methylococcaceae bacterium ET-SHO mxaF gene for methanol dehydrogenasealpha subunit, partial cds by BlastN is shown as below:

If it realy an unknown sequence, BlastX result also likely that unknown sequence is belongto Methylococcaceae bacterium ET-SHO mxaF gene for methanol dehydrogenase alphasubunit.