NEW YORK ( TheStreet) -- Even as the bank-stock rally accelerated this month, some of the best-performing large-cap companies may still be undervalued.

After the KBW Bank Index ( I:BKX) dropped 25% in 2011, with global firms like Bank of America ( BAC) and Citigroup ( C) posting epic declines, the index rocketed 30% last year. Bank of America led the way, more than doubling, while Citigroup jumped 51%.

The KBW Bank Index rose 6% from the start of the year through Friday's close at 51.28, putting it on track to double last year's returns if it continues at that pace.

Even with outsized gains, some of the best bank performers are still trading for relatively low prices compared with their laggard peers.

U.S. Bancorp ( USB) of Minneapolis, for example, recorded a 2012 operating return on average assets (ROA) of 1.62%, according to Thomson Reuters Bank Insight, making it one of the best performers among large-cap banks. This performance was not an aberration, as the company was in the top five for return on average equity among actively traded U.S. bank stocks from the beginning of 2006 through the third quarter of 2012.

U.S. Bancorp's shares closed at $33.17 Friday, trading for a relatively low 10 times the consensus 2014 earnings estimate of $3.30 among analysts polled by Thomson Reuters. Shares of Comerica ( CMA) of Dallas closed at $33.71 on Friday, trading for 12.1 times the consensus 2014 EPS estimate of $2.78, while the company's 2012 ROA was only 0.83%.

Of course, investors will want to consider expected future performance when making decisions. Stifel Nicolaus analyst Christopher Mutascio said in a report Friday that his firm's projected 2014 ROA for U.S. Bancorp was 1.62%, while the projected 2014 ROA for Comerica was only 0.85%. The analyst's 2014 EPS estimate for U.S. Bancorp is $3.25, while his 2014 EPS estimate for Comerica is $2.85.

Comerica "is currently being awarded the highest P/E multiple (by a wide margin) of any large cap we cover," Mutascio said. Its price-to-earnings multiple of 11.8 represents a 22% premium to the average and median of the group, he said.

So why does Comerica trade at one of the highest forward price-to-earnings estimates among large regional banks, while its projected ROA is one of the lowest in the group at just 0.75% versus the group's average/median range of 1% to 1.07%? Mutascio said "the market believes CMA is currently under-earning in the low interest rate environment and that our current 2014 EPS estimate does not reflect the earnings power of the franchise in a 'normal' short-term interest rate environment."

Mutascio said "the market seems to be more optimistic than us as to when short-term interest rates will rise," adding that the increase in the yield on 10-year U.S. Treasury securities -- which climbed to 1.98% on Friday from about 1.60% in early December -- "is not a needle mover," because Comerica's earnings power isn't tied to long-term rates.

With the Federal Reserve in December indicating that it would keep the short-term federal funds target rate in a range of zero to 0.25% as long as the unemployment rate remains above 6.5% and inflation is kept in check, Mutascio said "we think the market may be pricing in an operating environment for Comerica that is a bit too optimistic."

For more on how banks are fighting to boost their earnings in a hostile rate environment, see TheStreet's Bank Stocks and the Secret of NIM.

Stifel Nicolaus estimates that U.S. Bancorp will earn $3.25 a share in 2014. Mutascio said the bank "is projected to generate the highest 2014 ROA (by a wide margin) of any large-cap bank in our coverage universe," but asked why "for such substantially greater profitability, the market is only willing to pay a half-multiple premium" -- 10.2 times versus 9.7 times?

Before answering that question with another question, Mutascio compared U.S. Bancorp with BB&T ( BBT), also of Dallas, which had an ROA of 1.11% in 2012, with shares closing at $30.97 Friday, trading for 9.8 times the consensus 2014 EPS estimate of $3.15, for a forward P/E only slightly lower than U.S. Bancorp's. Stifel Nicolaus estimates that BB&T's 2014 ROA will be 1.23%, with EPS of $3.10.

"Both companies are buyers, not sellers, have solid management teams and are considered high quality institutions by many investors," Mutascio said. "We agree. But why are their profitability levels valued the same -- especially when a greater portion of BB&T's profits are enhanced by accretable yield contribution?"

Investors need to answer that question for themselves. Meanwhile, U.S. Bancorp continues to outperform, as far as earnings are concerned.

JPMorgan Chase ( JPM) is another interesting example of a stock that investors are punishing, apparently for last year's hedging debacle. The company's 2012 ROA was 0.94%. The shares closed at $47.16 Friday, trading for just 8.2 times the consensus 2014 EPS estimate of $5.75.

Stifel Nicolaus estimates that JPMorgan's 2014 ROA will be 0.95%. Mutascio said JPMorgan "now trades at the lowest P/E multiple within our large-cap bank coverage universe" -- 8.2 times versus 9.7 times, and that the company's "size, exposure to re-regulation, and the 'London Whale' fiasco all probably combine to play a role in the discounted valuation."

Still, Mutascio mused, why "should it trade at a 31% discount to Comerica, a 20% discount to SunTrust ( STI), and a 19% discount to KeyCorp ( KEY), all of which have the same, if not lower, projected ROAs than JPMorgan? These types of discounts seem a bit large to us."

Mutascio has "hold" ratings on U.S. Bancorp, Comerica, KeyCorp and JPMorgan Chase.

-- Written by Philip van Doorn in Jupiter, Fla.

>Contact by Email.

Philip W. van Doorn is a member of TheStreet's banking and finance team, commenting on industry and regulatory trends. He previously served as the senior analyst for Ratings, responsible for assigning financial strength ratings to banks and savings and loan institutions. Mr. van Doorn previously served as a loan operations officer at Riverside National Bank in Fort Pierce, Fla., and as a credit analyst at the Federal Home Loan Bank of New York, where he monitored banks in New York, New Jersey and Puerto Rico. Mr. van Doorn has additional experience in the mutual fund and computer software industries. He holds a bachelor of science in business administration from Long Island University.

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