Blast microbial genome webpage:
http://www.ncbi.nlm.nih.gov/sutils/genom_table.cgi?organism=microb

It's help document...
http://www.ncbi.nlm.nih.gov/sutils/static/prokblasthelp.html

Using the interface

For both the text or the graphic methods of choosing target genomes, the user must provide the type of BLAST search to be performed. The type of BLAST is specifically predicated upon the specific sequence type - nucleic acid or protein for either the query sequence or the target genome. The relationships are shown in the following table.

Query Genome BLAST
nucleic acid nucleic acid blastn or tblastx
protein nucleic acid tblastn
nucleic acid protein blastx
protein protein blastp

The pull-down menus for the query sequence or target genomes or BLAST type are not independent. The choice of sequence types, both for the query and target genomes, determines the type of BLAST performed. Likewise choosing the type of BLAST determines the types of sequences, both for the query and the target genomes. The user is offered the opportunity to select BLAST parameters which are not default.

  1. Graphic tree

    The query sequence must be provided to the application before choosing the target genomes. Clicking on an outlined Linnaean group (order or family) name elicits a menu displaying the available genomes. If the group is comprised of two or more organisms, one can chose all of the group or one of the group. To chose a subset greater than two of those genomes available, the text tree must be employed. Clicking the choice initiates the BLAST query. It is possible toinclude all underlying taxonomic groups as target sequences by clicking on the area labeled with the encompassing taxonomic name - i.e. clicking on "Bacteria" offers all bacteria genomes (complete and partial) as target sequences.

  2. Text tree/alphabetic table

    In that initiation of the BLAST query is explicitly performed by clicking on the "BLAST" button at the top of the list, the order in which target genomes and query sequence are provided is not pertinent. The number of chosen target genomes is provided as an aid during choosing a lengthy list from the available genomes.

The NCBI BLAST family of programs includes:

blastp
compares an amino acid query sequence against a protein sequence database
blastn
compares a nucleotide query sequence against a nucleotide sequence database
blastx
compares a nucleotide query sequence translated in all reading frames against a protein sequence database
tblastn
compares a protein query sequence against a nucleotide sequence database dynamically translated in all reading frames
tblastx
compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database. Please note that tblastx program cannot be used with the nr database on the BLAST Web page.

  BLAST Search main parameters

DESCRIPTIONS
Restricts the number of short descriptions of matching sequences reported to the number specified; default limit is 100 descriptions. See also EXPECT.
ALIGNMENTS
Restricts database sequences to the number specified for which high-scoring segment pairs (HSPs) are reported; the default limit is 100. If more database sequences than this happen to satisfy the statistical significance threshold for reporting (see EXPECT below), only the matches ascribed the greatest statistical significance are reported.
EXPECT
The statistical significance threshold for reporting matches against database sequences; the default value is 10, such that 10 matches are expected to be found merely by chance, according to the stochastic model of Karlin and Altschul (1990). If the statistical significance ascribed to a match is greater than the EXPECT threshold, the match will not be reported.Lower EXPECT thresholds are more stringent, leading to fewer chance matches being reported. Fractional values are acceptable.
INCLUSION THRESHOLD
The statistical significance threshold for including a sequence in the model used by PSI-BLAST on the next iteration.
ORGANISM NAME
Enter the organism name in the form "Genus species" (e.g., "Homo sapiens"). A number of popular organism names are listed on a pull-down menu.
TAXONOMIC CLASSIFICATION
Enter any taxonomic group from the NCBI taxonomy (e.g. "Mammalia"). 
Some popular groups are:

Archaea
Bacteria
Eukaryota
Embryophyta (higher plants)
Fungi
Metazoa	(multicellular animals)
Vertebrata
Mammalia
Rodentia
Primates

Explore the taxonomy database at NCBI

FILTER (Low-complexity)
Mask off segments of the query sequence that have low compositional complexity, as determined by the SEG program of Wootton & Federhen (Computers and Chemistry, 1993) or, for BLASTN, by the DUST program of Tatusov and Lipman (in preparation). Filtering can eliminate statistically significant but biologically uninteresting reports from the blast output (e.g., hits against common acidic-, basic- or proline-rich regions), leaving the more biologically interesting regions of the query sequence available for specific matching against database sequences.
Filtering is only applied to the query sequence (or its translation products), not to database sequences. Default filtering is DUST for BLASTN, SEG for other programs.
It is not unusual for nothing at all to be masked by SEG, when applied to sequences in SWISS-PROT, so filtering should not be expected to always yield an effect. Furthermore, in some cases, sequences are masked in their entirety, indicating that the statistical significance of any matches reported against the unfiltered query sequence should be suspect.
FILTER (Human repeats)
This option masks Human repeats (LINE's and SINE's) and is especially useful for human sequences that may contain these repeats. This option is still experimental and under development, so it may change in the near future.
FILTER (Mask for lookup table only)
This option masks only for purposes of constructing the lookup table used by BLAST. The BLAST extensions are performed without masking. This option is still experimental and may change in the near future.
NCBI-gi
Causes NCBI gi identifiers to be shown in the output, in addition to the accession and/or locus name.
Query Genetic Code
Genetic code to be used in blastx translation of the query.
Graphical Overview
An overview of the database sequences aligned to the query sequence is shown. The score of each alignment is indicated by one of five different colors, which divides the range of scores into five groups. Multiple alignments on the same database sequence are connected by a striped line. Mousing over a hit sequence causes the definition and score to be shown in the window at the top, clicking on a hit sequence takes the user to the associated alignments.