A boutique bank just pushed Wall Street aside on biggest US e-commerce deal ever

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Allen & Co. represents Wal-Mart in the latest sign that smaller upstarts are challenging the big banks on merger deals.

Once again, a boutique bank is claiming a monster acquisition deal, as Allen & Co. was named as the lead adviser for Wal-Mart's $3.3 billion acquisition of e-commerce start-up Jet.com.

The Arkansas-based mega retailer's buyout of the New Jersey-based website is the biggest U.S. e-commerce M&A deal ever.

The arrival of Allen & Co. at Wal-Mart's side in the Jet.com deal is notable for several reasons. Not only is the rising tide of boutique banks, sometimes led by former Wall Street banks' ex-rainmakers, continuing to pose a threat to bigger institutions. Allen & Co.'s working for Wal-Mart is also a sign that little banks are making big in-roads toward institutional firms' cherished business relationships with large-cap clients.

It's going to mean big bucks at Allen & Co., said Jeffrey Nassof, director at mergers and acquisitions consulting firm Freeman & Co. Altogether, the banks that work both sides of the Wal-Mart acquisition of Jet stand to make up to $45 million combined, he said.

Jet's advisers on the deal were not publicized, and a CNBC request for comment was not returned.

So far this year, boutique banks have nudged bigger banks aside to claim advisory roles on deals like Microsoft's acquisition of LinkedIn and the ongoing dance between Bayer and Monsanto .

Wal-Mart, in prior tech acquisitions, did little by way of announcing which banks, if any, it worked with. Monday morning's announcement said that along with lead bank Allen & Co., JPMorgan Securities worked on the Jet deal. In contrast, Wal-Mart's 2015 acquisition of Chinese e-commerce firm Yihaodian made no mention of an adviser. It also made no such mention during its 2015 acquisition of Silicon Valley-based PunchTab for its WalmartLabs division. And when the mega retailer bought its way into the South African market in 2010 with the $4.6 billion deal for MassMart, another smaller bank (albeit one with a far longer track record), Rothschild, was on the deal.

Boutique investment banks saw their share of revenue from M&A rise year over year in the first half of 2016 — and if more deals like Wal-Mart's Jet buyout fly their way, it could make for an all-time high for small banks.

At a time when Wall Street banks are having a tough time meeting analysts' expectations for return on equity, the deals may mark one more challenge in a difficult year.

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