NHase numbers to May 2013, and now nitrilase numbers too

Looking at the bare search term "nitrile hydratase" amongst protein sequences (and remember, most aren’t but it’s a rough measure), today gives me 4782 hits (+ 14% since last November), of which 2440 (+ 50% since August) were RefSeq data. It appears that there has been a lot of RefSeq going on with this enzyme class.

There are 24848 sequences labelled as "nitrilase" (not sure how robust that is currently), of which 12037 are pegged as RefSeq data.

NCBI numbers for September

It has been a while since I had done the usual text search for "nitrile hydratase" under proteins on NCBI's website. Having done the proper filtering job on this numbers in August, I know there is a lot of duplication, error and bizarre search engine behaviour going on but I do think it shows how quickly the number of vaguely applicable sequences is growing. As of today there are 3066 hits for the target phrase (+63 since July), and 1125 RefSeq hits (+20 in the same period).

Disappointingly there was no change in the number of structures listed on the Protein Data Bank.

The length of the beta unit in a nitrile hydratase

I have also had a quick look at the length of the beta chain in NHases using much the same method as I did for the alpha chains. I have to say that this time, I did do a bit of manual pruning because there was loads of inappropriate sequences in the list I downloaded. Anywhere here is the answer- about 200 again.

The length of the alpha chain in a nitrile hydratase

If you look at number of amino acids in the alpha chain of a nitrile hydratase, I think it is safe to say that you get suspicious of its attribution as NHase if the number was much different from 200. I was wondering if this is actually a reasonable hunch to have so here is a graph.

I got this in the usual not terribly robust way of using a text search for "nitrile hydratase alpha", and then downloading only those which were RefSeq. Today that gives you 174 sequences of which some are definitely bobbins, but I feel bad at hand-pruning datasets if your initial search is a bit of a rough design to start with. The mean length I calculated to be 199, and as you can see the mode in the histogram above is for sequences between 200 and 210. Nice to see that for once, a hunch is backed by some data! Other things of note are that the Monsiga brevicollis NHase is found by this search and is the tiny block to the far right, and a quick scan through the sequences with n=60-140 indicates these are non-NHase waifs and strays picked up by my rough search terms.