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

NucPred

Fetching P27732 from www.uniprot.org...

The NucPred score for your sequence is 0.81 (see score help below)

   1  MMMMMMMKKMQHQRQQQEDHANEANYARGTRLPISGEGPTSQPNSSKQTV    50
  51  LSWQAAIDAARQAKAAQTMSTSAPPPVGSLSQRKRQQYAKSKKQGNSSNS   100
 101  RPARALFCLSLNNPIRRACISIVDWKPFDIFILLAIFANCVALAIYIPFP   150
 151  EDDSNSTNHNLEKVEYAFLIIFTVETFLKIIASGLLLHPNASVRNGWNLL   200
 201  DFVIVIVGLFSVILEQLTKETEGGNHSSGKSGGFDVKALRAFRVLRPLRL   250
 251  VSGVPSLQVVLNSIIKAMVPLLHIALLVLFVIIIYAIIGLELFIGKMHKT   300
 301  CFFADSDIVAEEDPAPCAFSGNGRQCAANGTECRSGWVGPNGGITNFDNF   350
 351  AFAMLTVFQCITMEGWTDVLYWVNDAIGWEWPWVYFVSLIILGSFFVLNL   400
 401  VLGVLSGEFSKEREKAKARGDFQKLREKQQLEEDLKGYLDWITQAEDIDP   450
 451  ENEEEGGEEGKRNTSMPTSETESVNTENVSGEGETQGCCGSLWCWWKRRG   500
 501  AAKTGPSGCRRWGQAISKSKLRSHGAREALCVCRCSLESLVKLWTSRFSA   550
 551  HLQAAYVRPYSRRWRRWNRFNRRRCRAAVKSVTFYWLVIVLVFLNTLTIS   600
 601  SEHYNQPDWLTQIQDIANKVLLALFTCEMLVKMYSLGLQAYFVSLFNRFD   650
 651  CFVVCGGITETILVELELMSPLGVSVFRCVRLLRIFKVTRHWTSLSNLVA   700
 701  SLLNSMKSIASLLLLLFLFIIIFSLLGMQLFGGKFNFDETQTKRSTFDNF   750
 751  PQALLTVFQILTGEDWNAVMYDGIMAYGGPSSSGMIVCIYFIILFICGNY   800
 801  ILLKLFLAIAVDNLADAESLNTAQKEEAEEKERKKIARKESLENKKNNKP   850
 851  EVNQIANSDNKVTIDDYQEEAEDKDPYPPCDVPVGEEEEEEEEDEPEVPA   900
 901  GPRPRRISELNMKEKIAPIPEGSAFFILSKTNPIRVGCHKLINHHIFTNL   950
 951  ILVFIMLSSAALAAEDPIRSHSFRNTILGYFDYAFTAIFTVEILLKMTTF  1000
1001  GAFLHKGAFCRNYFNLLDMLVVGVSLVSFGIQSSAISVVKILRVLRVLRP  1050
1051  LRAINRAKGLKHVVQCVFVAIRTIGNIMIVTTLLQFMFACIGVQLFKGKF  1100
1101  YRCTDEAKSNPEECRGLFILYKDGDVDSPVVRERIWQNSDFNFDNVLSAM  1150
1151  MALFTVSTFEGWPALLYKAIDSNGENVGPVYNYRVEISIFFIIYIIIVAF  1200
1201  FMMNIFVGFVIVTFQEQGEKEYKNCELDKNQRQCVEYALKARPLRRYIPK  1250
1251  NPYQYKFWYVVNSSPFEYMMFVLIMLNTLCLAMQHYEQSKMFNDAMDILN  1300
1301  MVFTGVFTVEMVLKVIAFKPKGYFSDAWNTFDSLIVIGSIIDVALSEADN  1350
1351  SEESNRISITFFRLFRVMRLVKLLSRGEGIRTLLWTFIKSFQALPYVALL  1400
1401  IAMLFFIYAVIGMQMFGKVAMRDNNQINRNNNFQTFPQAVLLLFRCATGE  1450
1451  AWQEIMLACLPGKLCDPDSDYNPGEEYTCGSNFAIVYFISFYMLCAFLII  1500
1501  NLFVAVIMDNFDYLTRDWSILGPHHLDEFKRIWSEYDPEAKGRIKHLDVV  1550
1551  TLLRRIQPPLGFGKLCPHRVACKRLVAMNMPLNSDGTVMFNATLFALVRT  1600
1601  ALKIKTEGNLEQANEELRAVIKKIWKKTSMKLLDQVVPPAGDDEVTVGKF  1650
1651  YATFLIQDYFRKFKKRKEQGLVGKYPAKNTTIALQAGLRTLHDIGPEIRR  1700
1701  AISCDLQDDEPEDSKPEEEDVFKRNGALLGNYVNHVNSDRRESLQQTNTT  1750
1751  HRPLHVQRPSIPPASDTEKPLFPPAGNSVCHNHHNHNSIGKQVPTSTNAN  1800
1801  LNNANMSKAAHGKRPSIGDLEHVSENGHYSYKHDRELQRRSSIKRTRYYE  1850
1851  TYIRSESGDEQLPTIFREDPEIHGYFRDPRCFGEQEYFSSEECCEDDSSP  1900
1901  TWSRQNYSYYNRYPGSSMDFERPRGYHHPQGFLEDDDSPIGYDSRRSPRR  1950
1951  RLLPPTPPSHRRSSFNFECLRRQNSQDDVLPSPALPHRAALPLHLMQQQI  2000
2001  MAVAGLDSSKAQKYSPSHSTRSWATPPATPPYRDWTPCYTPLIQVDRSES  2050
2051  MDQVNGSLPSLHRSSWYTDEPDISYRTFTPASLTVPSSFRNKNSDKQRSA  2100
2101  DSLVEAVLISEGLGRYARDPKFVSATKHEIADACDLTIDEMESAASTLLN  2150
2151  GSVCPRANGDMGPISHRQDYELQDFGPGYSDEEPDPGREEEDLADEMICI  2200
2201  TTL                                                 2203

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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