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

NucPred

Fetching P40468 from www.uniprot.org...

The NucPred score for your sequence is 0.83 (see score help below)

   1  MASRFTFPPQRDQGIGFTFPPTNKAEGSSNNNQISIDIDPSGQDVLEEIN    50
  51  EAPLNTFPLHQSVTDAPIIDIPSPTDMSEGTSLNNQLLLRQQQQQGTGEG   100
 101  QALPPTFVEEQSDQNKISMLLPEQKQQRMQESAPPDITAKSVAEDYVTTL   150
 151  RQQMATDWKSPSEYALHILFTKFIRYAENKLNMCLQQLDMAEPPIVEILG   200
 201  EGVDPSFDEIIKSLGHIAKKKPKPVIDAMMFWRKTKSEAANSASEEMEKL   250
 251  LKEYEFEKAHPSQAHFLMNRRLSRSSSNTTSKYKHNNNTNNLPGMKRHVS   300
 301  SSFNNKVPLIKASSSNNSATSSPSIANSQLKSLENTIEVAKEEAFLADRK   350
 351  SLISIYILCRVLNEIVKQASSNEEEDLSDKLEEIVFTQLKTTDPLSISTS   400
 401  LIKSSNWNSFAELLGSMSEKKFLSVSDRFIADLEKIPAYIPPELEPSTHL   450
 451  LILGMRYLKLRNYPLEKFEESADFMKSLSKFFAKTENFPVCLAYAEVTNQ   500
 501  LLLPLAGSLTAEVNHPTWVEAMSTLLNTAKRLQADSKYWVSGFKLTVSIL   550
 551  CASPPDLFSKQWLSLLEANASKVKSKSLNERIIFAVGLSRLVWVYLYRCP   600
 601  ETLNNTTRTLTKLLQLYLNTRKKENWITGDFGLLNPLTDALISIGFLHPN   650
 651  FLMEQALIPLIRQSFNGSNLENINYEKLILTINTYKGLLVTKERPRFPED   700
 701  DNRLYELNLNNITVNQVQEASSINHTEISDYFYKLFLLLDSSIGSEVWSP   750
 751  ENQHQKQSSNAFSPFGFSFSNDNDSSKNKSLYVILFGTIIEAIPCCLSIS   800
 801  RTIPYKSTIEILSRNAVHSEVIISSSSQNALRALASKKNPYTLITWFAKY   850
 851  SFDFDEKTQSSYNMSYLSSKEYNRLLILYVELLECWLEEFQSSNKEENKK   900
 901  ETGLDGIRLLPIDAEQEESNETEKLEWKNTVTVIEEVEGNGLFFLCSHDA   950
 951  KIRRLGIQILRIIFKFDEAMMEKTEKLSNGHSRSSSHFAADRGTRLIDLL  1000
1001  NECNTTTLINPHKATLSAVEKTRFSRLNSKYKRGLLIKLAESEYGVDAAL  1050
1051  WQRAFPKLLALVFKTCPMAMALCRSIVCIRLVQVHEIILRVANDVDFKLK  1100
1101  NVLPETIVNQWKLYLIAACTSLTSTFDQKLHIPSNIPQHGRKKSQQIFTV  1150
1151  QHQKIKSAKSIFKMVLPLLNAKYIMIRDAIITGLSSMNINIFKAYVEAID  1200
1201  VFLVAWKEGSSNNQIRVEMFHILTILSPYLKSDMIFNDEWILRKLSEFLQ  1250
1251  KTKQFLEKDSVQISYEYQSLRSYFAGLILSYYMAVREHPLIDELFPFQAR  1300
1301  ASCFNFLKEWCGYGEYEPISEERYAIMIKNTESGRDRTAITTGIEFQKNR  1350
1351  LQMIVLETMVVLCSDPITQTLDDDLELPIVISFDTEDLLAWIEALFDSDN  1400
1401  TTVKNLGVRALENLLDKNRENFKLFRDVAFQCVSHHSHPSVAVLYYTTLC  1450
1451  KSVLKLDNLVLDEDELVSLGLYGLVADKEDTRTFAVDLLSAVETKLHNSS  1500
1501  YTKVFKERLANSSKTVYKSTAKEISSIFAELLSQDLCLRIFSSLVRILDL  1550
1551  FPFEIKRDLLVLMVPWVNKFTLKSLEELDTFMVLNNLFYITIDLNDSLPN  1600
1601  EVEQLWISLGKGNSFQNIHVSLEYIINSSMNHCNPLFVQYARDIVLYLAN  1650
1651  IPGGIGLLDTLLNNLEPKYMVPLAKHTFNEPMNNNKYSFLGNIWERLNYN  1700
1701  GKRIIFSKAQLSIIFLVNLLTNLSESVKAKIPLLLHMSICLLDHYVPLIH  1750
1751  ESACKIASTLIFGLAPSHEKSEETVKLLRNKHALWSYDNLMKKGARSPKT  1800
1801  MDLLIRNIISIFSDLDEFQVTWQRIALKWATTCSVRHIACRSFQIFRSLL  1850
1851  TFLDQEMLRDMLHRLSNTISDGNVDIQGFAMQILMTLNAIMAELDPTNLI  1900
1901  SFPQLFWSITACLSSIHEQEFIEVLSCLSKFISKIDLDSPDTVQCLVAIF  1950
1951  PSNWEGRFDGLQQIVMTGLRSANSLEITWKFLDKLNLLKDSRIIANTESR  2000
2001  LLFALIANLPRFLNAMDRKDFTGIQVAADSLIELANAYKQPSLSRLIDSL  2050
2051  AKNKFRSKKDFMSQVVSFISRNYFPSYSAQTLVFLLGLLFNKIGWIRVQT  2100
2101  LEILKYVFPLIDLRRPEFIGVGADLISPLLRLLFTEYEAKALEVLDCVPN  2150
2151  VSGSKMDKDVLRITMGNKDVKDGDNATTTLFGLPEDSGWSVPMPTMTAAT  2200
2201  TRHNVHAVFMTCGTGKSDEVSAHGSDDMDAVIEFHADGDYELGRMDTIVE  2250
2251  FHADGDYDLGRMDTNDSISVAEEKDASLSHMWAELDNLDSFFTKDTNVPN  2300
2301  ISSKMGMGIPHGRSDSIETTRTDQTFSFESAPQLYDKKVSVILNRSLSRT  2350
2351  PSNVSFKTHLADSFAVKINRNGKPRI                          2376

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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