I don't think you can identify anything from PAGE. You could use MALDI though. At our institution they developed fingerprint identification of some plant pathogenic bacteria and in principle the same shall be applicable to gut microbes. But PAGE has very low resolution to be used.

In normal PAGE, each band contains more than 1 protein. So the band pattern does not give much information. I assume 2-D gel electrophoresis which separates proteins first by their isoelectric focusing and then by their size is good for getting a specific protein pattern on the gel for a particular bacteria type.  As suggested by Tomas, MALDI is also an option. 

However, there are many hurdles for this kind of identification. The important thing is the expression of certain proteins depends on culture conditions and presence or absence of certain molecules in the medium.

And regarding a software for such identification, I could not find, which made me bring these reasons for its non-existence. You may have an opportunity to develop such software.

I even think about doing a PCR analysis for all known bacteria is a better idea.

I hope this information is helpful to you. Goodluck

 @Tomáš Hluska @Ramachandramouli Budida : Thanks for your response. I'm using Denaturing gradient gel electrophoresis (DGGE) technique not SDS PAGE. DGGE is basically a molecular fingerprinting method that separates PCR products based on sequence differences that results in differential denaturing characteristics of the DNA.This technique is specific for bacterial profiling. since it gives so many bands  so its not possible to do sequencing for all the bands.We just select those bands that differ from control samples for sequencing cox they might be some pathogenic bacteria and may be responsible for etiology of disease.

Regards.

I am sorry for the confusion and thank you for the additional information.

Oh, you're working with DNA, not proteins.

In that case you have your question in wrong topics (PAGE, Western blot) ;)

In that case I'm afraid I cannot help. Good luck.

Ooops .I didn''t noticed that :p . Thanks anyway  :)