In article <D0wvon.99z at gpu.utcc.utoronto.ca>,
lamoran at gpu.utcc.utoronto.ca (L.A. Moran) says:
>>
stuff deleted
>Peter Gogarten continues,
>> "The front half of the HSP70 homologues is homologous to the MreB
> proteins of E.coli and Bacillus (i.e. a gram positive and a gram
> negative). We (Elena Hilario and I) did some so far unpublished
> analyses including these proteins in a phylogenetic analyses of
> the HSP70 homologues. Using parsimony, distance matrix or maximum
> likelihood analysis, the MreB proteins always group between Eukaryotes
> on one side and all the prokaryotes on the other."
>>I have a problem with this. According to the published alignments of MreB
>and HSP70's there is no homology. For example, Gupta and Golding (1993)
>show an alignment of about 340 aa's with about 40 identities and 9 gaps.
>(The number of identities depends on which MreB or HSP70 sequences are
>looked at.) This corresponds to about 12% similarity and a normalized
>alignment score (NAS) of about 50. According to Doolittle, NAS has to be well
>above 200 (!) in order to claim homology. It looks to me like there may
>be an ATPase binding motif that has arisen independently in many proteins
>by convergent evolution. (Most of the MreB and HSP70 similarities are in
>short stretches of sequence that are involved in ATP binding.)
>
I used the Needleman Wunsch algorithm in conjunction with the unitary
matrix to calculate % identity and alignment scores for the different aa
sequences. The results I got leave little doubt concerning the homology
between mreB protein and the ATPase domain of HSP70 homologues:
z-values:
ATPase domain of HSP70 homologues from
E.coli Halobacterium Drosophila
marismortui melanogaster
E.coli mreB 9.9 7.2 4.4
B.subtilis mreB 6.8 8.7 5.0
calculated using the unitary matrix and 50 randomizations each;
usually z-values above 3 are considered as suggestive of homology,
as far as I know values above 5 have only been obtained for homologous
sequences.
% identity :
ATPase domain of HSP70 homologues
E.coli Halobacterium Drosophila
marismortui melanogaster
E.coli mreB 28.2 28.2 21.8
B.subtilis mreB 27 26.3 24.6
> "The insertion that according to Gupta et al unites gram negative
> eubacteria and eukaryotes appears in our analysis as an insertion
> that unites gram positives and archaebacteria."
>>I assume that you meant to say a "deletion" that unites gram positives and
>archaebacteria? That's what our data shows.
Yes, I meant "deletion that unites gram positives and archaebacteria".
Peter Gogarten
