I have a list of accession numbers, how can I search for there function in Pfam db http://pfam.xfam.org/ as a bulk?
For example:
If I have this accession PF07714.12 and I searched manually I will get;
A tyrosine kinase is an enzyme that can transfer a phosphate group from ATP to a protein in a cell. It functions as an "on" or "off" switch in many cellular functions. Tyrosine kinases are a subclass of protein kinase.
The phosphate group is attached to the amino acid tyrosine on the protein. Tyrosine kinases are a subgroup of the larger class of protein kinases that attach phosphate groups to other amino acids (serine and threonine). Phosphorylation of proteins by kinases is an important mechanism in communicating signals within a cell (signal transduction) and regulating cellular activity, such as cell division.
Protein kinases can become mutated, stuck in the "on" position, and cause unregulated growth of the cell, which is a necessary step for the development of cancer. Therefore, kinase inhibitors, such asimatinib, are often effective cancer treatments.
How can I do it for a list of accessions?
1 answer
Unlike what you have shown here, if one sentence description is enough to describe about the family you can use hmmfetch which first extract profiles and from that file you can separate ACC & DESC lines easily, ACC - accession id, DESC - description about family. Here you can download all pfam family HMM profiles in one file, then use it as a source to extract families of your interest.
The command should be
hmmfetch [options] <hmmfile> <key> # retrieves HMM named <key>
hmmfetch -f [options] <hmmfile> <keyfile> # retrieves all HMMs listed in <keyfile>
I think I shall use the second command but I used the first as a test
./hmmfetch ~/Downloads/pfam-files/Pfam-A.hmm PF07714.12
and the result was
HMMER3/f [3.1b1 | May 2013]
NAME PC_rep
ACC PF01851.17
DESC Proteasome/cyclosome repeat
LENG 35
ALPH amino
RF no
MM no
CONS yes
CS yes
MAP yes
DATE Thu Oct 11 22:09:41 2012
NSEQ 157
EFFN 157.000000
CKSUM 3600983919
GA 20.70 20.70
TC 20.70 20.70
NC 20.60 20.60
STATS LOCAL MSV -7.3958 0.73121
STATS LOCAL VITERBI -7.8668 0.73121
STATS LOCAL FORWARD -3.4237 0.73121
HMM A C D E F G H I K L M N P Q R S T V W Y
m->m m->i m->d i->m i->i d->m d->d
COMPO 2.13250 4.16340 2.99229 3.02036 3.87184 2.21440 3.80529 2.76276 3.25697 2.05995 3.61528 3.06644 3.81269 3.47054 3.36166 2.55389 2.94438 2.79865 5.94288 3.49720
2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
0.00026 8.64427 9.36662 0.61958 0.77255 0.00000 *
1 1.46753 8.28537 9.08330 9.14614 9.29530 0.65366 9.44329 8.83078 8.94404 8.52503 4.71174 3.07625 7.98521 8.93162 8.80150 2.07125 2.99882 4.10149 10.63242 9.68686 1 G - - H
also how do I get all pfam family HMM profiles in one file?
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