Question: blast against CDD database result interpretation
0
gravatar for huiyus97
3 months ago by
huiyus970
huiyus970 wrote:

Hi,

I wanted to find conserved domains in several proteins and I performed a blast against CDD database through my terminal. Here is what does it look like.

Mr727|g6813.t1  CDD:119357  58.974  351 137 5   509 858 1   345 3.95e-132   411
Mr727|g6813.t1  CDD:339407  51.852  108 40  4   1363    1464    1   102 3.88e-23    94.4
Mr727|g6813.t1  CDD:214753  27.604  384 194 15  509 858 1   334 2.16e-22    99.4
Mr727|g6813.t1  CDD:119351  25.568  352 212 10  531 861 22  344 4.17e-21    95.9
Mr727|g6813.t1  CDD:119365  28.873  284 144 10  511 755 2   266 9.43e-21    94.0
Mr727|g6813.t1  CDD:225862  27.517  298 166 10  508 764 38  326 1.08e-16    83.6
Mr727|g6813.t1  CDD:334217  29.183  257 146 10  509 755 1   231 2.40e-15    76.6
Mr727|g6813.t1  CDD:119349  32.308  195 106 9   511 697 2   178 1.52e-13    70.5

I have trouble interpret the result, is there any file contains cdd accession number with a description of the domain.

Thank you for your help!

blast protein cdd database • 163 views
ADD COMMENTlink modified 3 months ago by genomax92k • written 3 months ago by huiyus970

not really an answer to this specific question but I always prefer to do these kind of analyses using interproscan. That one combines all possible domain DBs (such as CDD) and it outputs domain descriptions by default.

did you do that blast remotely btw, or using a local DB? the remote one should also provide the descriptions (as it does when you do it on the NCBI website)

ADD REPLYlink written 3 months ago by lieven.sterck9.0k

CD search also combines most domain databases (COG+KOG+TIGRFAMs+SMART+PFAM etc) and outputs informative hits by default. In this case the output is not clear because the original poster most likely requested tabular output rather than pairwise alignments.

ADD REPLYlink written 3 months ago by Mensur Dlakic7.2k
1
gravatar for genomax
3 months ago by
genomax92k
United States
genomax92k wrote:

is there any file contains cdd accession number with a description of the domain.

If you download this file from NCBI it gives you the description of the CDD:ID's you have in the search. Number in column 1 is CDD ID (small example of file contents below).

214330  CHL00001        rpoB    RNA polymerase beta subunit     1070
214331  CHL00002        matK    maturase K      504
176948  CHL00003        psbA    photosystem II protein D1       338
176949  CHL00004        psbD    photosystem II protein D2       353
176950  CHL00005        rps16   ribosomal protein S16   82
176951  CHL00008        petG    cytochrome b6/f complex subunit V       37
176952  CHL00009        petN    cytochrome b6/f complex subunit VIII    29
ADD COMMENTlink modified 3 months ago • written 3 months ago by genomax92k
0
gravatar for Mensur Dlakic
3 months ago by
Mensur Dlakic7.2k
USA
Mensur Dlakic7.2k wrote:

You are presumably running rpsblast in this case, and choosing -outfmt 6. If you change that to -outfmt 0 or leave the -outfmt part completely out, you should get an output that is more informative.

ADD COMMENTlink written 3 months ago by Mensur Dlakic7.2k
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