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

NucPred

Fetching Q09811 from www.uniprot.org...

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

   1  MTVTKTNLNRHLDWFFRESPQKIENVTSPIKTLDFVKVKVSSSDIVVKDS    50
  51  IPHKSKNVFDDFDDGYAIDLTEEHQSSSLNNLKWKDVEGPNILKPIKKIA   100
 101  VPASESEEDFDDVDEEMLRAAEMEVFQSCQPLAVNTADTTVSHSTSSSNV   150
 151  PRSLNKIHDPSRFIKDNDVENRIHVSSASKVASISNTSKPNPIVSENPIS   200
 201  ATSVSIEIPIKPKELSNNLPFPRLNNNNTNNNNDNNAIEKRDSASPTPSS   250
 251  VSSQISIDFSTWPHQNLLQYLDILRDEKSEISDRIIEVMERYPFSSRFKE   300
 301  WIPKRDILSQKISSVLEVLSNNNNSNNNNGNNGTVPNAKTFFTPPSSITQ   350
 351  QVPFPSTIIPESTVKENSTRPYVNSHLVANDKITATPFHSEAVVSPLQSN   400
 401  IRNSDIAEFDEFDIDDADFTFNTTDPINDESGASSDVVVIDDEEDDIENR   450
 451  PLNQALKASKAAVSNASLLQSSSLDRPLLGEMKDKNHKVLMPSLDDPMLS   500
 501  YPWSKEVLGCLKHKFHLKGFRKNQLEAINGTLSGKDVFILMPTGGGKSLC   550
 551  YQLPAVIEGGASRGVTLVISPLLSLMQDQLDHLRKLNIPSLPLSGEQPAD   600
 601  ERRQVISFLMAKNVLVKLLYVTPEGLASNGAITRVLKSLYERKLLARIVI   650
 651  DEAHCVSHWGHDFRPDYKQLGLLRDRYQGIPFMALTATANEIVKKDIINT   700
 701  LRMENCLELKSSFNRPNLFYEIKPKKDLYTELYRFISNGHLHESGIIYCL   750
 751  SRTSCEQVAAKLRNDYGLKAWHYHAGLEKVERQRIQNEWQSGSYKIIVAT   800
 801  IAFGMGVDKGDVRFVIHHSFPKSLEGYYQETGRAGRDGKPAHCIMFYSYK   850
 851  DHVTFQKLIMSGDGDAETKERQRQMLRQVIQFCENKTDCRRKQVLAYFGE   900
 901  NFDKVHCRKGCDICCEEATYIKQDMTEFSLQAIKLLKSISGKATLLQLMD   950
 951  IFRGSKSAKIVENGWDRLEGAGVGKLLNRGDSERLFHHLVSEGVFVEKVE  1000
1001  ANRRGFVSAYVVPGRQTIINSVLAGKRRIILDVKESSSKPDTSSRSLSRS  1050
1051  KTLPALREYQLKSTTASVDCSIGTREVDEIYDSQMPPVKPSLIHSRNKID  1100
1101  LEELSGQKFMSEYEIDVMTRCLKDLKLLRSNLMAIDDSRVSSYFTDSVLL  1150
1151  SMAKKLPRNVKELKEIHGVSNEKAVNLGPKFLQVIQKFIDEKEQNLEGTE  1200
1201  LDPSLQSLDTDYPIDTNALSLDHEQGFSDDSDSVYEPSSPIEEGDEEVDG  1250
1251  QRKDILNFMNSQSLTQTGSVPKRKSTSYTRPSKSYRHKRGSTSYSRKRKY  1300
1301  STSQKDSRKTSKSANTSFIHPMVKQNYR                        1328

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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