SBC logo Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred

Fetching P25304 from www.uniprot.org...

The NucPred score for your sequence is 0.33 (see score help below)

   1  MPPLPLEHRPRQEPGASMLVRYFMIPCNICLILLATSTLGFAVLLFLSNY    50
  51  KPGIHFTPAPPTPPDVCRGMLCGFGAVCEPSVEDPGRASCVCKKNACPAT   100
 101  VAPVCGSDASTYSNECELQRAQCNQQRRIRLLRQGPCGSRDPCANVTCSF   150
 151  GSTCVPSADGQTASCLCPTTCFGAPDGTVCGSDGVDYPSECQLLSHACAS   200
 201  QEHIFKKFNGPCDPCQGSMSDLNHICRVNPRTRHPEMLLRPENCPAQHTP   250
 251  ICGDDGVTYENDCVMSRIGATRGLLLQKVRSGQCQTRDQCPETCQFNSVC   300
 301  LSRRGRPHCSCDRVTCDGSYRPVCAQDGHTYNNDCWRQQAECRQQRAIPP   350
 351  KHQGPCDQTPSPCHGVQCAFGAVCTVKNGKAECECQRVCSGIYDPVCGSD   400
 401  GVTYGSVCELESMACTLGREIQVARRGPCDPCGQCRFGSLCEVETGRCVC   450
 451  PSECVESAQPVCGSDGHTYASECELHVHACTHQISLYVASAGHCQTCGEK   500
 501  VCTFGAVCSAGQCVCPRCEHPPPGPVCGSDGVTYLSACELREAACQQQVQ   550
 551  IEEAHAGPCEPAECGSGGSGSGEDDECEQELCRQRGGIWDEDSEDGPCVC   600
 601  DFSCQSVPRSPVCGSDGVTYGTECDLKKARCESQQELYVAAQGACRGPTL   650
 651  APLLPVAFPHCAQTPYGCCQDNFTAAQGVGLAGCPSTCHCNPHGSYSGTC   700
 701  DPATGQCSCRPGVGGLRCDRCEPGFWNFRGIVTDGHSGCTPCSCDPRGAV   750
 751  RDDCEQMTGLCSCRPGVAGPKCGQCPDGQVLGHLGCEADPMTPVTCVEIH   800
 801  CEFGASCVEKAGFAQCICPTLTCPEANSTKVCGSDGVTYGNECQLKAIAC   850
 851  RQRLDISTQSLGPCQESVTPGASPTSASMTTPRHILSKTLPFPHNSLPLS   900
 901  PGSTTHDWPTPLPISPHTTVSIPRSTAWPVLTVPPTAAASDVTSLATSIF   950
 951  SESGSANGSGDEELSGDEEASGGGSGGLEPPVGSIVVTHGPPIERASCYN  1000
1001  SPLGCCSDGKTPSLDSEGSNCPATKAFQGVLELEGVEGQELFYTPEMADP  1050
1051  KSELFGETARSIESTLDDLFRNSDVKKDFWSVRLRELGPGKLVRAIVDVH  1100
1101  FDPTTAFQASDVGQALLRQIQVSRPWALAVRRPLQEHVRFLDFDWFPTFF  1150
1151  TGAATGTTAAMATARATTVSRLPASSVTPRVYPSHTSRPVGRTTAPPTTR  1200
1201  RPPTTATNMDRPRTPGHQQPSKSCDSQPCLHGGTCQDQDSGKGFTCSCTA  1250
1251  GRGGSVCEKVQPPSMPAFKGHSFLAFPTLRAYHTLRLALEFRALETEGLL  1300
1301  LYNGNARGKDFLALALLDGRVQFRFDTGSGPAVLTSLVPVEPGRWHRLEL  1350
1351  SRHWRQGTLSVDGETPVVGESPSGTDGLNLDTNLYVGGIPEEQVAMVLDR  1400
1401  TSVGVGLKGCIRMLDINNQQLELSDWQRAAVQSSGVGECGDHPCLPNPCH  1450
1451  GGALCQALEAGMFLCQCPPGRFGPTCADEKSPCQPNPCHGAAPCRVLSSG  1500
1501  GAKCECPLGRSGTFCQTVLETAGSRPFLADFNGFSYLELKGLHTFERDLG  1550
1551  EKMALEMVFLARGPSGLLLYNGQKTDGKGDFVSLALHNRHLEFCYDLGKG  1600
1601  AAVIRSKEPIALGTWVRVFLERNGRKGALQVGDGPRVLGESPKSRKVPHT  1650
1651  MLNLKEPLYIGGAPDFSKLARGAAVSSGFSGVIQLVSLRGHQLLTQEHVL  1700
1701  RAVDVSPFADHPCTQALGNPCLNGGSCVPREATYECLCPGGFSGLHCEKG  1750
1751  LVEKSVGDLETLAFDGRTYIEYLNAVIESELTNEIPAPETLDSRALFSEK  1800
1801  ALQSNHFELSLRTEATQGLVLWIGKAAERADYMALAIVDGHLQLSYDLGS  1850
1851  QPVVLRSTVKVNTNRWLRIRAHREHREGSLQVGNEAPVTGSSPLGATQLD  1900
1901  TDGALWLGGLQKLPVGQALPKAYGTGFVGCLRDVVVGHRQLHLLEDAVTK  1950
1951  PELRPCPTP                                           1959

Positively and negatively influencing subsequences are coloured according to the following scale:

(non-nuclear) negative ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| positive (nuclear)

with NucPred



If you find NucPred useful, please cite this paper:
NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022
The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper.

NucPred score threshold Specificity Sensitivity
see above fraction of proteins predicted to be nuclear that actually are nuclear fraction of true nuclear proteins that are predicted (coverage)
0.10 0.45 0.88
0.20 0.52 0.83
0.30 0.57 0.77
0.40 0.63 0.69
0.50 0.70 0.62
0.60 0.71 0.53
0.70 0.81 0.44
0.80 0.84 0.32
0.90 0.88 0.21
1.00 1.00 0.02

Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.)

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