$re = '/([A-Z0-9]*_ECOLI)\n([A-Z\n]*)/';
$str = '>YBGC_ECOLI
MNTTLFRWPVRVYYEDTDAGGVVYHASYVAFYERARTEMLRHHHFSQQALMAERVAFVVRKMTVEYYAPA
RLDDMLEIQTEITSMRGTSLVFTQRIVNAENTLLNEAEVLVVCVDPLKMKPRALPKSIVAEFKQ
>USHA_ECOLI
MKLLQRGVALALLTTFTLASETALAYEQDKTYKITVLHTNDHHGHFWRNEYGEYGLAAQKTLVDGIRKEV
AAEGGSVLLLSGGDINTGVPESDLQDAEPDFRGMNLVGYDAMAIGNHEFDNPLTVLRQQEKWAKFPLLSA
NIYQKSTGERLFKPWALFKRQDLKIAVIGLTTDDTAKIGNPEYFTDIEFRKPADEAKLVIQELQQTEKPD
IIIAATHMGHYDNGEHGSNAPGDVEMARALPAGSLAMIVGGHSQDPVCMAAENKKQVDYVPGTPCKPDQQ
NGIWIVQAHEWGKYVGRADFEFRNGEMKMVNYQLIPVNLKKKVTWEDGKSERVLYTPEIAENQQMISLLS
PFQNKGKAQLEVKIGETNGRLEGDRDKVRFVQTNMGRLILAAQMDRTGADFAVMSGGGIRDSIEAGDISY
KNVLKVQPFGNVVVYADMTGKEVIDYLTAVAQMKPDSGAYPQFANVSFVAKDGKLNDLKIKGEPVDPAKT
YRMATLNFNATGGDGYPRLDNKPGYVNTGFIDAEVLKAYIQKSSPLDVSVYEPKGEVSWQ
>CN16_ECOLI
MIKFSATLLATLIAASVNAATVDLRIMETTDLHSNMMDFDYYKDTATEKFGLVRTASLINDARNEVKNSV
LVDNGDLIQGSPLADYMSAKGLKAGDIHPVYKALNTLDYTVGTLGNHEFNYGLDYLKNALAGAKFPYVNA
NVIDARTKQPMFTPYLIKDTEVVDKDGKKQTLKIGYIGVVPPQIMGWDKANLSGKVTVNDITETVRKYVP
EMREKGADVVVVLAHSGLSADPYKVMAENSVYYLSEIPGVNAIMFGHAHAVFPGKDFADIEGADIAKGTL
NGVPAVMPGMWGDHLGVVDLQLSNDSGKWQVTQAKAEARPIYDIANKKSLAAEDSKLVETLKADHDATRQ
FVSKPIGKSADNMYSYLALVQDDPTVQVVNNAQKAYVEHYIQGDPDLAKLPVLSAAAPFKVGGRKNDPAS
YVEVEKGQLTFRNAADLYLYPNTLIVVKASGKEVKEWLECSAGQFNQIDPNSTKPQSLINWDGFRTYNFD
VIDGVNYQIDVTQPARYDGECQMINANAERIKNLTFNGKPIDPNAMFLVATNNYRAYGGKFAGTGDSHIA
FASPDENRSVLAAWIADESKRAGEIHPAADNNWRLAPIAGDKKLDIRFETSPSDKAAAFIKEKGQYPMNK
VATDDIGFAIYQVDLSK
>6PGD_ECOLI
MSKQQIGVVGMAVMGRNLALNIESRGYTVSIFNRSREKTEEVIAENPGKKLVPYYTVKEFVESLETPRRI
LLMVKAGAGTDAAIDSLKPYLDKGDIIIDGGNTFFQDTIRRNRELSAEGFNFIGTGVSGGEEGALKGPSI
MPGGQKEAYELVAPILTKIAAVAEDGEPCVTYIGADGAGHYVKMVHNGIEYGDMQLIAEAYSLLKGGLNL
TNEELAQTFTEWNNGELSSYLIDITKDIFTKKDEDGNYLVDVILDEAANKGTGKWTSQSALDLGEPLSLI
TESVFARYISSLKDQRVAASKVLSGPQAQPAGDKAEFIEKVRRALYLGKIVSYAQGFSQLRAASEEYNWD
LNYGEIAKIFRAGCIIRAQFLQKITDAYAENPQIANLLLAPYFKQIADDYQQALRDVVAYAVQNGIPVPT
FSAAVAYYDSYRAAVLPANLIQAQRDYFGAHTYKRIDKEGVFHTEWLD
';
preg_match_all($re, $str, $matches, PREG_SET_ORDER, 0);
// Print the entire match result
var_dump($matches);
Please keep in mind that these code samples are automatically generated and are not guaranteed to work. If you find any syntax errors, feel free to submit a bug report. For a full regex reference for PHP, please visit: http://php.net/manual/en/ref.pcre.php