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!
•
written
by
huiyus97 •
2 answers
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
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.
Log in to answer this question.
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)
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.