It can do the HMMER/RPS-BLAST searches and co-localization of specific set of COG/Pfam entries.
Updated: Mar-10-2016.       Recommended Browsers: Google Chrome.
Retrieve results

(i) Search Tool       
(ii) Query COG or Pfam ID set
Input the COG or Pfam IDs (<100 items), separated by "return" and with UPPER/lower case sensitivity.
[Example: 13 conserved components of Type VI secretion systems (T6SSs)
found in Vibrio cholerae O1 N16961 chromosome II and Pseudomonas aeruginosa PAO1 HSI-I]

More details about COG (COG list), and Pfam (Pfam list).

(iii) Subject bacterial genome sequence
Select a completely sequenced bacterial genome from NCBI genome database
        Example: Vibrio cholerae O1 biovar El Tor str. N16961 chromosome II [NC_002506]
How to prepare your complete or approximate complete sequence of a given bacterial genome as reference?
Easy to prepare the assembled contig/scaffold sequences from your partially sequenced bacterial genomes:
(1) Prepare a plain file containing the assembled contig/scaffold nucleotide sequences in the Multi-FASTA format, like mysequence.fas (3.9 Mb).
(2) Use CDSeasy to annotate your sequences.
  Upload your file, myseq.fas, into CDSeasy to generate a GenBank file, like, mysequence_.gbk;
  It takes ~10 minutes for CDSeasy to annotate the 5.3-Mb chromosomal sequence of K. pneumoniae strain HS11286.
(3) Upload your sequences as the subject sequence of COGviewer.
  Select the 'Upload sequence' and then click the radio " or Upload a GenBank file containing the nucleotide sequence and annotation";
  Upload the file CDSeasy-output file, mysequence_.gbk;

For partially sequenced bacterial genomes, CDSeasy firstly generates a 'virtual complete genome' ('pseudochromosome') by connecting contig sequence without considering contig order and provides both contig-specific gene coordinates and corresponding pseudochromosome data. CDSeasy outputs include the sequence and annotation files in commonly used formats, such as GenBank.
The CDSeasy-generated GenBank file can be used directly as the input for VRprofile, CGCfinder and COGviewer.
Run with Default options
(iv) Parameters (Optional)
     (1) E-value <  [What is the E-value for HMMer and that for RPS-BLAST ?]

     (2) Maximum distance between genes in locus < (0~100) Kb
(v) Results retrieval options
do not close the webpage while running

please do not close the webpage while data uploading
Note: Please retrieving the job result from the E-mail feedback when the number of the input COG or Pfam IDs > 50.
Retrieve results
Type in the Job_ID