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

NucPred

Fetching Q12697 from www.uniprot.org...

The NucPred score for your sequence is 0.58 (see score help below)

   1  MDIPSSNQIQHGQRSERNRRMPRASFSSTATTSTAATLTSAMVLDQNNSE    50
  51  PYAGATFEAVPSSIVSFHHPHSFQSSNLPSPHSSGNLEQRGRRLTESEPL   100
 101  VLSSAEQSRSSSRNPSHFRFFTQEQISNAEGASTLENTDYDMAWDATPAY   150
 151  EQDRIYGTGLSSRRSSIRSFSRASSLSNAKSYGSFSKRGRSGSRAPQRLG   200
 201  ENSDTGFVYHSATHSSSSLSRYTTRERIPIELESQTDEILEDESSTHSLE   250
 251  SSDSRRSASENNRGSFSGHDDVHNQHSEYLKPDYHEKFYPQYAPNLHYQR   300
 301  FYIAEEDLVIGIAAYQTSKFWYIIYNLCCFLTFGLVYLLTRWLPHLKVKL   350
 351  YGVKVPLAKAEWVVIENEFGEFVIQPIDRQWYNRPLSTVLPFENYPNPSY   400
 401  EPNDINLSHHHANEINPNVPILITFEYRYIKFIYSPLDDLFKTNNNWIDP   450
 451  DWVDLSTVSNGLTKGVQEDRELAFGKNQINLRMKTTSEILFNEVLHPFYV   500
 501  FQVFSIILWGIDEYYYYAACIFLISVLSIFDSLNEQKKVSRNLAEMSHFH   550
 551  CDVRVLRDKFWTTISSSELVPGDIYEVSDPNITILPCDSILLSSDCIVNE   600
 601  SMLTGESVPVSKFPATEETMYQLCDDFQSTQISSFVSKSFLYNGTNIIRA   650
 651  RIAPGQTAALAMVVRTGFSTTKGSLVRSMVFPKPTGFKFYRDSFKYIGFM   700
 701  SLIAIFGFCVSCVQFIKLGLDKKTMILRALDIITIVVPPALPATLTIGTN   750
 751  FALSRLKEKGIFCISPTRLNISGKIDVMCFDKTGTLTEDGLDVLGVQISE   800
 801  PNGVRGQKFGELLSDIRQVFPKFSLNDCSSPLDFKSRNFFMSLLTCHSLR   850
 851  SVDGNLLGDPLDFKMFQFTGWSFEEDFQKRAFHSLYEGRHEDDVFPENSE   900
 901  IIPAVVHPDSNNRENTFTDNDPHNFLGVVRSFEFLSELRRMSVIVKTNND   950
 951  DVYWSFTKGAPEVISEICNKSTLPADFEEVLRCYTHNGYRVIACAGKTLP  1000
1001  KRTWLYSQKVSREEVESNLEFLGFIIFQNKLKKETSETLKSLQDANIRTI  1050
1051  MCTGDNILTAISVGREAGLIQCSRVYVPSINDTPLHGEPVIVWRDVNEPD  1100
1101  KILDTKTLKPVKLGNNSVESLRECNYTLAVSGDVFRLLFRDENEIPEEYL  1150
1151  NEILLNSSIYARMSPDEKHELMIQLQKLDYTVGFCGDGANDCGALKAADV  1200
1201  GISLSEAEASVAAPFTSKIFNISCVLDVIREGRAALVTSFACFQYMSLYS  1250
1251  AIQFITITILYSRGSNLGDFQFLYIDLLLIVPIAICMSWSKSYEKIDKKR  1300
1301  PSANLVSPKILVPLLISVFLVFLFQFIPWIIVQKMSWYIKPIVGGDDAVQ  1350
1351  SSDNTVLFFVSNFQYILTAIVLSVGPPYREPMSKNFEFIVDITVSIGASL  1400
1401  LLMTLDTESYLGKMLQLTPISNSFTMFIIVWVILNYYAQLYIPPSIKGWL  1450
1451  KKKKSSKKYKLLIQEEMKLKEV                              1472

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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