$re = '/\\\\VariantSimple=((?:\([^\)]+\))*) \\\\Processed=((?:\([^\)]+\))*) ([\s\S]*?)(?:>|$)/m';
$str = '>nxp:NX_A0A0A6YYD4-1 \\PName=T cell receptor beta variable 13 isoform Iso 1 \\GName=TRBV13 \\NcbiTaxId=9606 \\TaxName=Homo Sapiens \\Length=124 \\SV=5 \\EV=31 \\PE=3 \\ModResPsi=(52|MOD:00798|half cystine)(120|MOD:00798|half cystine) \\ModRes=(106||N-linked (GlcNAc...) asparagine) \\VariantSimple=(18|H)(27|V) \\Processed=(1|31|PEFF:0001021|signal peptide)(32|124|PEFF:0001020|mature protein) MLSPDLPDSAWNTRLLCRVMLCLLGAGSVAAGVIQSPRHLIKEKRETATLKCYPIPRHDT VYWYQQGPGQDPQFLISFYEKMQSDKGSIPDRFSAQQFSDYHSELNMSSLELGDSALYFC ASSL
>nxp:NX_A0A1B0GV90-1 \\PName=Cortexin domain containing 2 isoform Iso 1 \\GName=CTXND2 \\NcbiTaxId=9606 \\TaxName=Homo Sapiens \\Length=55 \\SV=1 \\EV=11 \\PE=3 \\VariantSimple=(13|N)(22|F)(29|T)(34|Q)(45|T) \\Processed=(1|55|PEFF:0001020|mature protein) MEDSSLSSGVDVDKGFAIAFVVLLFLFLIVMIFRCAKLVKNPYKASSTTTEPSLS';
preg_match_all($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