Analysis of BlastN and BlastX

The best way to identify an unknown sequence is to see if that sequence already exists in a
public database. If the database sequence is a well-characterized sequence, then one will have
access to a wealth of biological information. Nucleotide Blast (BlastN) and BlastX can be used
to accomplish this goal. BlastN is specifically designed to alignment of unknown nucleotides
sequence to nucleotide sequence in database; BlastP is designed to alignments of unknown
protein sequence with protein sequence in database; while BlastX is designed to alignments of
translated 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 at
http://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 of
FASTA format sequence or accession number of unknown sequence, then press the
BLAST button at buttom left of page. By using accession number of AB453966.1 as
unknown 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 this
result, it is known unknown sequence with accession number AB453966.1 show maximal
alignment score at 1035 with nucleotide sequence of Methylococcaceae bacterium ET-SHO
mxaF gene for methanol dehydrogenase alpha subunit, partial cds at percent identity of
100%, followed by Uncultured bacterium clone LOM13.7 alpha subunit methanol
dehydrogenase (mxaF) gene, partial cds (max alignment score at 750 with percent identity
at 91%) and Hyphomicrobium sp. mxaF gene, partial, strain P 495 (max. alignment score at
749 with percent identity at 92%). Alignment of unknown sequence with nucleotide
sequence Methylococcaceae bacterium ET-SHO mxaF gene for methanol dehydrogenase
alpha subunit, partial cds by BlastN is shown as below:

Alignment of unknown sequence with nucleotide sequence Uncultured bacterium clone

LOM13.7 alpha subunit methanol dehydrogenase (mxaF) gene, partial cds by BlastN is
shown as below:

If it really an unknown sequence, BlastN likely that unknown sequence is belong to

Methylococcaceae bacterium ET-SHO mxaF gene for methanol dehydrogenase alpha
subunit. 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
http://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:

sites

at

3. Nucleotide sequence that subjected to local alignment can be input to BlastX in form of
FASTA format sequence or accession number of unknown sequence, then press the
BLAST button at buttom left of page. By using accession number of AB453966.1 as
unknown 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 this
result, it is nucleotide translated to protein of unknown unknown sequence with accession
number AB453966.1 show maximal alignment score at 389 with protein sequence of
methanol dehydrogenase alpha subunit [Methylococcaceae bacterium ET-SHO] at percent identity
of 100%, followed by alpha subunit methanol dehydrogenase [uncultured bacterium] (max
alignment 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 with
protein sequence Methylococcaceae bacterium ET-SHO mxaF gene for methanol
dehydrogenase 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 this
result, it is known unknown sequence with accession number AB453966.1 show maximal
alignment score at 1035 with nucleotide sequence of Methylococcaceae bacterium ET-SHO
mxaF gene for methanol dehydrogenase alpha subunit, partial cds at percent identity of
100%, followed by Uncultured bacterium clone LOM13.7 alpha subunit methanol
dehydrogenase (mxaF) gene, partial cds (max alignment score at 750 with percent identity
at 91%) and Hyphomicrobium sp. mxaF gene, partial, strain P 495 (max. alignment score at
749 with percent identity at 92%). Alignment of unknown sequence with nucleotide
sequence Methylococcaceae bacterium ET-SHO mxaF gene for methanol dehydrogenase
alpha subunit, partial cds by BlastN is shown as below:

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