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

NucPred

Fetching Q09429 from www.uniprot.org...

The NucPred score for your sequence is 0.42 (see score help below)

   1  MPLAFCGTENHSAAYRVDQGVLNNGCFVDALNVVPHVFLLFITFPILFIG    50
  51  WGSQSSKVHIHHSTWLHFPGHNLRWILTFILLFVLVCEIAEGILSDGVTE   100
 101  SRHLHLYMPAGMAFMAAITSVVYYHNIETSNFPKLLIALLIYWTLAFITK   150
 151  TIKFVKFYDHAIGFSQLRFCLTGLLVILYGMLLLVEVNVIRVRRYVFFKT   200
 201  PREVKPPEDLQDLGVRFLQPFVNLLSKGTYWWMNAFIKTAHKKPIDLRAI   250
 251  GKLPIAMRALTNYQRLCLAFDAQARKDTQSQQGARAIWRALCHAFGRRLV   300
 301  LSSTFRILADLLGFAGPLCIFGIVDHLGKENHVFQPKTQFLGVYFVSSQE   350
 351  FLGNAYVLAVLLFLALLLQRTFLQASYYVAIETGINLRGAIQTKIYNKIM   400
 401  HLSTSNLSMGEMTAGQICNLVAIDTNQLMWFFFLCPNLWAMPVQIIVGVI   450
 451  LLYYILGVSALIGAAVIILLAPVQYFVATKLSQAQRSTLEYSNERLKQTN   500
 501  EMLRGIKLLKLYAWENIFCSRVEKTRRKEMTSLRAFAVYTSISIFMNTAI   550
 551  PIAAVLITFVGHVSFFKESDFSPSVAFASLSLFHILVTPLFLLSSVVRST   600
 601  VKALVSVQKLSEFLSSAEIREEQCAPREPAPQGQAGKYQAVPLKVVNRKR   650
 651  PAREEVRDLLGPLQRLTPSTDGDADNFCVQIIGGFFTWTPDGIPTLSNIT   700
 701  IRIPRGQLTMIVGQVGCGKSSLLLATLGEMQKVSGAVFWNSSLPDSEGED   750
 751  PSNPERETAADSDARSRGPVAYASQKPWLLNATVEENITFESPFNKQRYK   800
 801  MVIEACSLQPDIDILPHGDQTQIGERGINLSGGQRQRISVARALYQHTNV   850
 851  VFLDDPFSALDVHLSDHLMQAGILELLRDDKRTVVLVTHKLQYLPHADWI   900
 901  IAMKDGTIQREGTLKDFQRSECQLFEHWKTLMNRQDQELEKETVMERKAP   950
 951  EPSQGLPRAMSSRDGLLLDEDEEEEEAAESEEDDNLSSVLHQRAKIPWRA  1000
1001  CTKYLSSAGILLLSLLVFSQLLKHMVLVAIDYWLAKWTDSALVLSPAARN  1050
1051  CSLSQECALDQSVYAMVFTVLCSLGIALCLVTSVTVEWTGLKVAKRLHRS  1100
1101  LLNRIILAPMRFFETTPLGSILNRFSSDCNTIDQHIPSTLECLSRSTLLC  1150
1151  VSALAVISYVTPVFLVALLPLAVVCYFIQKYFRVASRDLQQLDDTTQLPL  1200
1201  LSHFAETVEGLTTIRAFRYEARFQQKLLEYTDSNNIASLFLTAANRWLEV  1250
1251  RMEYIGACVVLIAAATSISNSLHRELSAGLVGLGLTYALMVSNYLNWMVR  1300
1301  NLADMEIQLGAVKRIHTLLKTEAESYEGLLAPSLIPKNWPDQGKIQIQNL  1350
1351  SVRYDSSLKPVLKHVNALISPGQKIGICGRTGSGKSSFSLAFFRMVDMFE  1400
1401  GRIIIDGIDIAKLPLHTLRSRLSIILQDPVLFSGTIRFNLDPEKKCSDST  1450
1451  LWEALEIAQLKLVVKALPGGLDAIITEGGENFSQGQRQLFCLARAFVRKT  1500
1501  SIFIMDEATASIDMATENILQKVVMTAFADRTVVTIAHRVHTILSADLVM  1550
1551  VLKRGAILEFDKPEKLLSQKDSVFASFVRADK                    1582

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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