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

NucPred

Fetching P98163 from www.uniprot.org...

The NucPred score for your sequence is 0.67 (see score help below)

   1  MCQAEHQVHPSEQRIRVESPKMTASRRGFNLTSQTRAHPSSGGSTSSRYG    50
  51  NCQRTHLIINGRHVAISLLLLVGLCGGTAAGTPGSADTRCDAGQFQCRDG   100
 101  GCILQAKMCDGRGDCKDSSDELDCDYRLCRPPHWFPCAQPHGACLAAELM   150
 151  CNGIDNCPGGEDELNCPVRPGFRFGDTAHRMRSCSKYEFMCQQDRTCIPI   200
 201  DFMCDGRPDCTDKSDEVAGCKQAEITCPGEGHLCANGRCLRRKQWVCDGV   250
 251  DDCGDGSDERGCLNLCEPQKGKFLCRNRETCLTLSEVCDGHSDCSDGSDE   300
 301  TDLCHSKPDCDAKKCALGAKCHMMPASGAECFCPKGFRLAKFEDKCEDVD   350
 351  ECKEQDDLCSQGCENTSGGYRCVCDAGYLLDKDNRTCRAVVYGSKEQQPL   400
 401  LLYTTQMTIMGMHLREDNVRNHVYQVAGNLSKVIGVAYDGSHIYWTNIQN   450
 451  EAESIVKANGDGSNAEILLTSGLDAPEDLAVDWLTQNIYFSDNIMRHIAV   500
 501  CSNDGLNCAVLVTQDVHQPRSLAVWPQKGLMFWTDWGEKPMIGRASMDGS   550
 551  RSRPIVSDNIEWPNGIALDMHQQRIYWVDAKLGSVQTVRPDGTGRRTVLD   600
 601  GMLKHPYGLAIFEDQLYWSDWATKSVHACHKFSGKDHRILAKDRTIYAVH   650
 651  IYHPAKQPNSPHGCENATCSHLCLLAEPEIGGHSCACPDGMRLAPDHRRC   700
 701  MLMEKRQRLFIGLGQVLLEIEHTAFGRHQVSKSYTLPCLINEMVYNRING   750
 751  SLIIADNDQRLILEFQPESHESNVLVRSNLGNVSALAFDHLSRNLYWADT   800
 801  ERAVIEVLSLQTRHRALIRFFPGQEVPIGLTVMPAEGYLYVVLKAKRHSH   850
 851  IDKIPLSGKGEQVHVFEDDLGDDDIKLVTDYETQTIFWSDSDLGRISYSN   900
 901  YRVPHSQIFRGKLRRPYSLAMVHHDLFWNELGTPRIYWTHKSNMGPRKVI   950
 951  DIMEKDDPAAIMPYVPVATPNGIPLAASSPVGQESHPCQQQNGGCSHICV  1000
1001  GEGPYHSICLCPAGFVYRDAGNRTCVEALDCEFRCHSGECLTMNHRCNGR  1050
1051  RDCVDNSDEMNCDEEHRRKPKVLCSPNQFACHSGEQCVDKERRCDNRKDC  1100
1101  HDHSDEQHCEKFDKSKKCHVHQHGCDNGKCVDSSLVCDGTNDCGDNSDEL  1150
1151  LCEATSRCEPGMFQCGSGSCIAGSWECDGRIDCSDGSDEHDKCVHRSCPP  1200
1201  DMQRCLLGQCLDRSLVCDGHNDCGDKSDELNCGTDSSTMNISCAEDQYQC  1250
1251  TSNLKICLPSTVRCNGTTECPRGEDEADCGDVCSIYEFKCRSGRECIRRE  1300
1301  FRCDGQKDCGDGSDELSCELEKGHHNQSQIQPWSTSSRSCRPHLFDCQDG  1350
1351  ECVDLSRVCNNFPDCTNGHDEGPKCATACRSASGRQVCQHKCRATPAGAV  1400
1401  CSCFDGYRLDADQKSCLDIDECQEQQPCAQLCENTLGGYQCQCHADFMLR  1450
1451  QDRVSCKSLQSGATLLFSSFNEVRNLSEQPVMLNVAWSANDSRITGFDLA  1500
1501  MHRQMGYFSAEDEGIVYQIDLQTKVIVRALGLPAPTKLSVDWVTGNVYVL  1550
1551  SGAQEIQACSFVGRMCGRIVHVKSPRHVKHLAVDGYHARIFYIVIRTEGY  1600
1601  GQTSSEIHMARLDGSRRDMLLQRSESFMTALTTDPHQQLLYFVDQHMRTL  1650
1651  ERISYRLKTGPMRRPEIMLQKSNALMHPSGLSVYENNAFIVNLGSVEAVQ  1700
1701  CALYGSRICHKISINVLNAQDIVVAGRSRQPQKASHPCAHAHCHGLCLQA  1750
1751  DYGYECMCGNRLVAEGERCPHGSGNEVAVLGAVNSLELEHEHEQNGHFHW  1800
1801  LMALFVLAAGSLIAGLGYMYYQYRQRGHTDLNINMHFQNPLATLGGTKAF  1850
1851  LEHERAEAGVGFTTETGTVSSRGSNDTFTTTSATSSFAAQQFSVPNALQR  1900
1901  LLRPRQSASGDPMAQELLLESPSRESKLHALDGGGAGGDGDGGRGVGRQV  1950
1951  PDILVADMDDDAAKSAGQFGGNYAGNDANARFVS                  1984

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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