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

NucPred

Fetching P34756 from www.uniprot.org...

The NucPred score for your sequence is 0.97 (see score help below)

   1  MSSEEPHASISFPDGSHVRSSSTGTSSVNTIDATLSRPNYIKKPSLHIMS    50
  51  TSTTSTTTDLVTNPILSNISVPKISPPTSSSIATATSTSHVTGTASHSNI   100
 101  KANANTSTSVNKKNLPPTTSGRIPSSTIKRYPSRYKPSHSLQLPIKNDSN   150
 151  FKRSSIYASKSTVTAIPIRNNRPISMQNSYARTPDSDHDDVGDEVSSIKS   200
 201  ASSSLTASLSKSFLFAFYNNRKKDKTSNNGVLSKEYWMKDESSKECFSCG   250
 251  KTFNTFRRKHHCRICGQIFCSSCTLLIDGDRFGCHAKMRVCYNCYEHADT   300
 301  YEDSSDEENDSTMQLNEPRSRSRSRSSNTNPYSHSHSHLHLISQDNHNGT   350
 351  DLHDPVAATDNPQQQNEVYLLNDDDVQSIMTSGEDSKLFISTPPPPPKMA   400
 401  IPATKQGGSLEISFDSENDRALHYQDDNPGRHHHLDSVPTRYTIRDMDNI   450
 451  SHYDTNSNSTLRPHYNTNNSTITINNLNNTTSNNSNYNNTNSNSNINNPA   500
 501  HSLRRSIFHYVSSNSVNKDSNNSSATPASSAQSSSILDPANRIIGNYAHR   550
 551  NYKFKFNYNSKGPSQQNDTANGNNDNNNNNNNNNNNNNNNSASGIADNNN   600
 601  IPSNDNGTTFTLDKKKRNPLTKSKSTSAYLEYPLNEEDSSEDEGSMSIYS   650
 651  VLNDDHKTDNPIRSMRNSTKSFQRAQASLQRMRFRRKSKSKHFPNNSKSS   700
 701  IYRDLNFLTNSTPNLLSVVSDDNLYDDSSPLQDKASSSAASRLTDRKFSN   750
 751  SSGSNNNSNSNSNINTDPWKRIASISGFKLKKEKKRELNEVSLLHMHALL   800
 801  KQLLNDQEISNLQEWITLLDGALRKVLRTILNARDLNTLDFRQTYVKIKR   850
 851  ISGGSPQNSEYIDGVVFSKALPSKTMPRHLKNPRILLIMFPLEYQKNNNH   900
 901  FLSIESVFRQEREYLDKLVSRLKSLHPDIIYVGANVSGYALELLNDSGIV   950
 951  VQFNMKPQVIERIAKLTEADIAISVDKLATNIKMGECETFEVKSYIYGNI  1000
1001  SKTYTFLRGCNPELGGTILLRGDSLENLRKIKQVSEFMVYAIFSLKLESS  1050
1051  FFNDNFIQLSTDVYLKRAESKKLQVFEGYFADFLIKFNNRILTVSPTVDF  1100
1101  PIPFLLEKARGLEKKLIERINQYESESDLDRQTQLNMLQGLESTITKKHL  1150
1151  GNLIKFLHEMEIENLELEFQKRSRQWEVSYSSSQNLLGTGSHQSITVLYS  1200
1201  MVSTKTATPCVGPQIVTIDYFWDSDISIGQFIENVVGTARYPCQQGCNGL  1250
1251  YLDHYRSYVHGSGKVDVLIEKFQTRLPKLKDIILTWSYCKKCGTSTPILQ  1300
1301  ISEKTWNHSFGKYLEVMFWSYKDSVTGIGKCPHDFTKDHVKYFGYNDLVV  1350
1351  RLEYSDLEVHELITPPRKIKWKPHIDIKLKVELYYKILEKINNFYGSVLS  1400
1401  RLERIKLDSMTKDKVLSGQAKIIELKSNATEEQKLMLQDLDTFYADSPCD  1450
1451  QHLPLNLVIKSLYDKAVNWNSTFAIFAKSYLPSETDISRITAKQLKKLFY  1500
1501  DSSRKDSEDKKSLHDEKAKTRKPEKNELPLEGLKDVEKPKIDSKNTTENR  1550
1551  DRTNEPQNAVTITTFKDDTPIIPTSGTSHLTVTPSASSVSSSLTPQTEER  1600
1601  PPISRSGTGISMTHDKSTRPNIRKMSSDSSLCGLASLANEYSKNNKVSKL  1650
1651  ATFFDQMHFDALSKEFELERERERLQLNKDKYQAIRLQTSTPIVEIYKNV  1700
1701  KDAVDEPLHSRSSGNNLSSANVKTLEAPVGEHSRANNCNPPNLDQNLETE  1750
1751  LENSISQWGENILNPSGKTTASTHLNSKPVVKETSENPKSIVRESDNSKS  1800
1801  EPLPPVITTTTVNKVESTPQPEKSLLMKTLSNFWADRSAYLWKPLVYPTC  1850
1851  PSEHIFTDSDVIIREDEPSSLIAFCLSTSDYRNKMMNLNVQQQQQQQTAE  1900
1901  AAPAKTGGNSGGTTQTGDPSVNISPSVSTTSHNKGRDSEISSLVTTKEGL  1950
1951  LNTPPIEGARDRTPQESQTHSQANLDTLQELEKIMTKKTATHLRYQFEEG  2000
2001  LTVMSCKIFFTEHFDVFRKICDCQENFIQSLSRCVKWDSNGGKSGSGFLK  2050
2051  TLDDRFIIKELSHAELEAFIKFAPSYFEYMAQAMFHDLPTTLAKVFGFYQ  2100
2101  IQVKSSISSSKSYKMDVIIMENLFYEKKTTRIFDLKGSMRNRHVEQTGKA  2150
2151  NEVLLDENMVEYIYESPIHVREYDKKLLRASVWNDTLFLAKMNVMDYSLV  2200
2201  IGIDNEGYTLTVGIIDFIRTFTWDKKLESWVKEKGLVGGASVIKQPTVVT  2250
2251  PRQYKKRFREAMERYILMVPDPWYREGN                        2278

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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