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

NucPred

Fetching Q9UT43 from www.uniprot.org...

The NucPred score for your sequence is 0.95 (see score help below)

   1  MKSSGIAGDSNGFETNFLNETTNREEDGAFNWNAADDGTNERREDIHVRF    50
  51  QDSALPLGIDENELDEIDINGDSKKLDSVEVDESHDVNSPSDSRLKSSFK   100
 101  SVLELTANSMVSVLTPSTKTEQTSKGKGKKKKAHVSFLEGPVEEIPLDDI   150
 151  EPTSPREASPVFNGRPPIPPEFLKSRHKEFTIPNPLQFISNFLSNLFSRD   200
 201  TRYLKSSHGRIIIINPYDDSSQIDERTGKPYMQNSIVSSRYNKYNFVPLQ   250
 251  IIAQFSKTANCYFLLIAIMQMIPGWSTTGTYTTIIPLLIFISIAILREGF   300
 301  DNYRRYRQDRVENRIQTQVLRHVDVDPPIVEEHSSFFRRRRWRRSRSQES   350
 351  ASRSTIRSTDEREPERTSEDPPQLPPSPSSPSSPALSVKPNIDPQPPLYN   400
 401  STLTTTRSIPANKPTFFWASCDRKDVRVGDIIRLTSDQTLPADVIALSSP   450
 451  NPNGAIYIETAALDGETSLKTRLVNSTLRSLCKDINDLIRLSGTCTVEDP   500
 501  NGDLYNFNGSMKLDSIQGEIPLSNNDVLYRGSNLRNTSELFALVIFTGEE   550
 551  SKIRMNAVRNVSVKAPSMQKVTNRIVIFIFALVVSMAIYCTAAYFVWQKK   600
 601  VERKLWYLTNSKLSFVPILVSFIILYNTMVPISLYVSMEIIRVFQTFLVQ   650
 651  SDIDLYYPENDTRCEVRSSSILEELGQVTHVFSDKTGTLTDNIMLFRNLS   700
 701  VGGFAWQHVGAENPKLVSTSQKSDDLDGEAKPPQLENIQGTTIQLLQYVH   750
 751  DNPHTTFSKRVRIFLLNLAICHTCLPSFDEENQIYKYQSISPDELALVHA   800
 801  AQQLGYIVIDRDIDSLTIRLHYPLDPHSHPIAKTYRILNIIEFTSKRKCM   850
 851  SVIVRMPNGRICLFCKGADSAIIKRLRLSNLAKRKDKSVTKAEQARKSIE   900
 901  IDKAIIRNSQSTSRPSLTASRPSLSRRRNDYINNVTSWLDERREKMGVVR   950
 951  PRASTSILETRRRPAVGRHSLAGGERLMEDKKYLSKQEEAEGSIYESLNH  1000
1001  NDAKLFENTFEHVHAFATDGLRTLMYAHRFIDESEYQSWKLVNDAALNSL  1050
1051  SNRQQLLDEAADLIEKDLEFAGATAIEDKLQVGVPESINSLFRAGIKFWM  1100
1101  LTGDKKETAINIGHSCGVIKEYSTVVVMGSLDGVEGSDETVSGGQRLSLD  1150
1151  RPPTNDPASLMIHQLISCMNAIHSNSLAHLVIVIDGSTLADIENDPELFL  1200
1201  LFINTAVEADSVICCRSSPMQKALMVQKVRNTLEKAVTLAIGDGANDIAM  1250
1251  IQEAHVGIGIAGREGLQAARSSDFSIGRFKFLIKLLFCHGRWSYVRLSKY  1300
1301  ILGTFYKEQFFFLMQAIMQPFVGYTGQSLYESWGLTCFNTLFSSLCVIGL  1350
1351  GIFEKDLSASTVIAVPELYQKGINNEAFNWRVYFGWCSIAFIQAFLVFYV  1400
1401  TYSLFGMKELNDNNIFAYGQLIFTAAIFIMNFKLVFIEMQYINIISIIVL  1450
1451  VLTSLAWFLFNIFISEHYPDKNLYLARSQFLHHFGKNPSWWLTMLFVMVC  1500
1501  ALTIDIVAQMLRRTLRPTDTDIFVEMENDAFVRSRFEQESGEFLQANAPS  1550
1551  VDEIEQYLKSRD                                        1562

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.)

Go back to the NucPred Home Page.