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

NucPred

Fetching Q535K8 from www.uniprot.org...

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

   1  MLPCKKRSGVTESAQQQDDQEGEDLHLEAAVKPDTDQLPDCTSESLSWGQ    50
  51  SHDSAGCPEVHSMQDVGSQLSVEGTPLSSKMLTQRVNLAVSEAVDVPVSQ   100
 101  EIPVPSLESSHSLPVHMGKGRLQSTASRKGKKIAFMPGQVTREDGGDHTV   150
 151  PEEPPSGEHAEEVKAEGGELEMHSEGDLPSLSSGSQSAKPRAQPRKSFQP   200
 201  DGSAFPQEKSLGPLVRQAEEDMEDGGLFIPTEEQDGEESDKRKKTKKGTK   250
 251  RKRDGRGQEQGTMTYDPKVDDMLDRTLEDGAKQHNLTAVNVRNILHEVIT   300
 301  NEHVVAMMKAAISETEDMPLFEPKMTRSKLKEVVEKGVVIPTWNISPIKK   350
 351  ASETKQPPQFVDIHLEDDDSSDEEYQPDEEEEDETAEESLLESDVESAAS   400
 401  SPRGVKRSRLRLSSEAAEADEESGVLSEVEKVATPALRHISAEVVPMGPP   450
 451  PPPKPKQTRDSTFMEKLNAVDEELAASPVCMDSFQPMEDSLIAFRTRSKM   500
 501  PLKDVPLGQLEAELQAPDITPDMYDPNTADDEDWKLWLGGLLNDDVENED   550
 551  EADDDDDPEYNFLEDLDEPDTEDFRTDRAVRITKKEVNGLMEELFETVQS   600
 601  VVPSKFQDEMGFSNMEDDGPEEEERVTESRPSFNTPQALRFEEPLANLLN   650
 651  ERHRTVKELLEQLKMKKSSVRQQPEVEKLKPQTEKVHQTLVLDPAQRSRL   700
 701  QQQMQQHVQLLTQIYLLTTSNPNLSSEASTTRVFLKELGTFAENSTALHQ   750
 751  QFNPRFQTLFQPCNWVGAMQLIEDFTHISIDCSPHKTVKKTASEFPCLPK   800
 801  QVAWILATNKVFMYPELLPICSLKANNPRDKTIFTKAEDNLLALGLKHFE   850
 851  GTEFPKPLISKYLVTCKTAHQLTVRIKNLNLNRAPNNVIKFYKKTKQLPV   900
 901  LVRCCEEIQPHQWKPPIEKEEHRLPFWLKASLQSIQEELRNLAGGATAGG   950
 951  SVTAATETSTDQHLQKTSPVVGGDTQYPLLLPKGVVLKLKPGSKRFSRKA  1000
1001  WRQKRPLVQKPLLIQPSPSVQPVFNPGKMATWPTQSEVPPSNTVVQIPHL  1050
1051  IQPAAVLQTLPGFPSVGVCGEDSFESPAALPAMPSGSEARTSFPWSESQS  1100
1101  APPSSSAPKLMLPSLGPSKFRKPYVRRKPTRRKGAKASPCVKPAPIIHPT  1150
1151  PVIFTVPATTVKVVSLGGGCNMIQPVTAAVAPSPQTIPITTLLVNPTSFP  1200
1201  CSLNQPLVASSISPLLVSSNPLALPVTSLPEEKAHVSLDIAEGKNAPQNP  1250
1251  EPKIKPQEPTPQCATVFSKEEPRSWHPSADTGNQEAVSESSACSWAAVKT  1300
1301  EGQEGSSEKSVCGWTVVKTEDGGHAVQPLPQDPQDSLNSPSKDLLNMVKL  1350
1351  EAEDCMEEISSDFPKQDIGEEVKEECCMELDRDSPQEKASSVSEMSKQTA  1400
1401  TPREETQAAKSPTVSQDAPDAIRDASKGLPQSTLSSMDQGTVLNSPPGKP  1450
1451  EDSANADGQSVGTPAGTDTGAEKDGAEEEEEEDFDDLTQDEEDELSSASE  1500
1501  ESVLSVPELQETMEKLTWLASERRMSQEGESEEENSQEENSEPEEEEEEE  1550
1551  AEGMETLQKEDEATDEAGGGAAEKPPSTLASPHTAPEVETSITPAGESIK  1600
1601  AAGKGRSSHRARSRRGSRARASKDASKLLLLYDEDILDRDPLREQKDLAF  1650
1651  AQAYLTRVREALQHIPGKYEDFLQIIYEFESNAQMHSAVDLFKSLQTLLH  1700
1701  DWPQLLKDFAAFLLPEQALSCGLFEEQQAFEKSRKFLRQLEICFAENPSH  1750
1751  HQKIIKVLQGCADCLPQDITELKTQMWQLLRGHDHLQDEFSIFFDHLRPA  1800
1801  ANRMGDFEEINWTEEKEYEFDGFEEVILPEVEEEEEPAKVSTASKSKRRK  1850
1851  EIGVQHQDKESEWPEAAKDGSCPCHEGGPESKLKKSKRRNCHCSSKVCDS  1900
1901  KSYKSKEPLELVGSGPLQEASTVPGTKEAGQGKDMSEEETMEGQENVEVS  1950
1951  QNKTGRTTRKGEAPIPGSTVRTALLCSAEVTPIELSLEGPTCCSPETPRL  2000
2001  PPQTGAVVCSVRRNQAGPEVVSCLGTSSIPPKEGEDQKAVANSETIAPLP  2050
2051  ETSETERLPGTVELPAPLPSPVSLSTRDTGRRHIYGKAGTQSWLLDNRAE  2100
2101  AKAAHMVAPIRGTSSGASASEAAPTASREGLAEDSETQGKGPEAVLPKAS  2150
2151  EATVCANNSKVSSTGEKVVLWTREADRVILTMCQEQGAQPHTFSVISQQL  2200
2201  GNKTPVEVSHRFRELMQLFHTACEASSEDEDDATSTSNADQLSDHGDLLS  2250
2251  EEELDE                                              2256

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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