Is there a modern alignment tool tailored for transmembrane regions?
Answer from @matteo-ferla converted from comment:
I assume you mean sequence (MSA), not structure alignment. Despite being a structural bioinformatician, I would slap a big caveat against structure based aligners. TCoffee:Espresso is probably the best structure-based aligner (browser and download and API), but the results are not as solid as some non-structural approaches such as training Psi-blast and aligning with that matrix. I am not familiar with MSA of TM regions, however, so this group may be an exception.
Given that helices are a repeat of 2 hydrophobic residues and 1.5 either polar (core-wards) or also hydrophobic (depending on how the helices pack), a pattern based aligner ought to do well from an evolutionary perspective. If you really want from a structure perspective and don't want to know about the cases where a loss of a turn at the top is compensated by the bottom, say, then TCoffee is definitely worth a try
Answer from @m converted from comment:
PSI-blast is a useful tool for deep alignment patterns, albeit it has its critics. I agree the vast majority of in vivo structures lack TM proteins, for different reasons