Searching for functions using conserved domains

WARNING: The VM distribution is unable to run RPSBLAST against the full CDD due to memory limitations of a 32-bit machine (64-bit machines in VMs will only work if your computer has sufficient virtualization capabilities, which mine unfortunately does not). Therefore if you try to run main4.sh it will fail unless you modify it to only search a particular database of interest (e.g. Pfam.pn instead of Cdd.pn) and not the entire CDD.

Finding conserved domains in the CDD by keyword search

If you are interested in conserved domains that match a particular description, you can search through the descriptions by using the db_getExternalClustersByDescription.py function. This script takes any number of possible descriptions to match in a case-insensitive manner and returns any of the CDD domains that match that description. For example, if you are interested in biotin synthase you can search for domains related to it using the following (some descriptions have been truncated for readability):

$ db_getExternalClustersByDescription.py "biotin synthase"
30848   COG0502 BioB    Biotin synthase and related enzymes [Coenzyme metabolism]       335
32586   COG2516 COG2516 Biotin synthase-related enzyme [General function prediction only]       339
178013  PLN02389        PLN02389        biotin synthase 379
180492  PRK06256        PRK06256        biotin synthase; Validated      336
180835  PRK07094        PRK07094        biotin synthase; Provisional    323
181453  PRK08508        PRK08508        biotin synthase; Provisional    279
185063  PRK15108        PRK15108        biotin synthase; Provisional    345
129447  TIGR00347       bioD    dethiobiotin synthase. [description truncated]       166
200012  TIGR00433       bioB    biotin synthase. [description truncated]     296
100105  cd01335 Radical_SAM     Radical SAM superfamily. ... Examples are biotin synthase (BioB),...  204
198863  cl06149 BATS    Biotin and Thiamin Synthesis associated domain. Biotin synthase (BioB), ...    0
148534  pfam06968       BATS    Biotin and Thiamin Synthesis associated domain. Biotin synthase (BioB), EC:2.8.1.6, c...   93
205678  pfam13500       AAA_26  AAA domain. ... found in a number of proteins involved in cofactor biosynthesis such as dethiobiotin synthase ...       197
197846  smart00729      Elp3    Elongator protein 3, MiaB family, Radical SAM. This superfamily contains ... biotin synthase ...    216
197944  smart00876      BATS    Biotin and Thiamin Synthesis associated domain...    94

You can also specify that you only want results from a specific database, such as PFAM here:

$ db_getExternalClustersByDescription.py "biotin synthesase" -d pfam
148534  pfam06968       BATS    Biotin and Thiamin Synthesis associated domain. Biotin synthase (BioB), EC:2.8.1.6, c...   93
205678  pfam13500       AAA_26  AAA domain. ... found in a number of proteins involved in cofactor biosynthesis such as dethiobiotin synthase ...       197

Searching for conserved domains associated with a protein

[TODO]

Searching for proteins associated with a conserved domain

Visualizing conserved domains associated with a protein