T6SS prediction

T6SS prediction detects T6SS gene clusters in an annotated or unannotated genome sequence by BLASTp 2.10.1+ or hmmsearch (HMMER v3.3.1) against experimentally validated T6SSs recorded in SecReT6.

Note:

(1) If your genome sequence is unannotated, you can paste genome nucleotide sequence or upload FASTA format nucleotide file and run the prediction. In this case, gene-finding tool Prodigal v2.6.3 is first utilized to annotate the sequence before detection of T6SS gene clusters using BLASTp 2.10.1+ or hmmsearch (HMMER v3.3.1).

(2) If your genome sequence is already annotated, you can upload GenBank file (GenBank file example) containing both annotations and genome sequence. In this case, DNA sequences of annotated genes would be extracted and translated as queries for BLASTp 2.10.1+ or hmmsearch (HMMER v3.3.1).


Input Your Genome Sequence

      1. For annotated genome sequence


GenBank file             Example: NC_002506.gbk

      2. For unannotated genome sequence


FASTA nucleotide file             Example: NC_002506.fas

        Example: example.fas


Set Parameters

Select a similarity search tool:   [BLAST] [HMMER]
E-value threshold <
Blast identity threshold for T6SS prediction > % (0~100)
Blast Ha-value threshold for T6SS-related protein prediction > (0~1)
Maximum interval (bp) between two co-localized T6SS components: (0~100000) bp
Minimum number of the significant protein hits for each T6SS region:
Select the types of T6SS-related proteins to perform search
    





Retrieve Results

Input your job ID