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

NucPred

Fetching Q9NSI6 from www.uniprot.org...

The NucPred score for your sequence is 0.99 (see score help below)

   1  MAEPSSARRPVPLIESELYFLIARYLSAGPCRRAAQVLVQELEQYQLLPK    50
  51  RLDWEGNEHNRSYEELVLSNKHVAPDHLLQICQRIGPMLDKEIPPSISRV   100
 101  TSLLGAGRQSLLRTAKDCRHTVWKGSAFAALHRGRPPEMPVNYGSPPNLV   150
 151  EIHRGKQLTGCSTFSTAFPGTMYQHIKMHRRILGHLSAVYCVAFDRTGHR   200
 201  IFTGSDDCLVKIWSTHNGRLLSTLRGHSAEISDMAVNYENTMIAAGSCDK   250
 251  IIRVWCLRTCAPVAVLQGHTGSITSLQFSPMAKGSQRYMVSTGADGTVCF   300
 301  WQWDLESLKFSPRPLKFTEKPRPGVQMLCSSFSVGGMFLATGSTDHVIRM   350
 351  YFLGFEAPEKIAELESHTDKVDSIQFCNNGDRFLSGSRDGTARIWRFEQL   400
 401  EWRSILLDMATRISGDLSSEEERFMKPKVTMIAWNQNDSIVVTAVNDHVL   450
 451  KVWNSYTGQLLHNLMGHADEVFVLETHPFDSRIMLSAGHDGSIFIWDITK   500
 501  GTKMKHYFNMIEGQGHGAVFDCKFSQDGQHFACTDSHGHLLIFGFGCSKP   550
 551  YEKIPDQMFFHTDYRPLIRDSNNYVLDEQTQQAPHLMPPPFLVDVDGNPH   600
 601  PTKYQRLVPGRENSADEHLIPQLGYVATSDGEVIEQIISLQTNDNDERSP   650
 651  ESSILDGMIRQLQQQQDQRMGADQDTIPRGLSNGEETPRRGFRRLSLDIQ   700
 701  SPPNIGLRRSGQVEGVRQMHQNAPRSQIATERDLQAWKRRVVVPEVPLGI   750
 751  FRKLEDFRLEKGEEERNLYIIGRKRKTLQLSHKSDSVVLVSQSRQRTCRR   800
 801  KYPNYGRRNRSWRELSSGNESSSSVRHETSCDQSEGSGSSEEDEWRSDRK   850
 851  SESYSESSSDSSSRYSDWTADAGINLQPPLRTSCRRRITRFCSSSEDEIS   900
 901  TENLSPPKRRRKRKKENKPKKENLRRMTPAELANMEHLYEFHPPVWITDT   950
 951  TLRKSPFVPQMGDEVIYFRQGHEAYIEAVRRNNIYELNPNKEPWRKMDLR  1000
1001  DQELVKIVGIRYEVGPPTLCCLKLAFIDPATGKLMDKSFSIRYHDMPDVI  1050
1051  DFLVLRQFYDEARQRNWQSCDRFRSIIDDAWWFGTVLSQEPYQPQYPDSH  1100
1101  FQCYIVRWDNTEIEKLSPWDMEPIPDNVDPPEELGASISVTTDELEKLLY  1150
1151  KPQAGEWGQKSRDEECDRIISGIDQLLNLDIAAAFAGPVDLCTYPKYCTV  1200
1201  VAYPTDLYTIRMRLVNRFYRRLSALVWEVRYIEHNARTFNEPESVIARSA  1250
1251  KKITDQLLKFIKNQHCTNISELSNTSENDEQNAEDLDDSDLPKTSSGRRR  1300
1301  VHDGKKSIRATNYVESNWKKQCKELVNLIFQCEDSEPFRQPVDLVEYPDY  1350
1351  RDIIDTPMDFGTVRETLDAGNYDSPLEFCKDIRLIFSNAKAYTPNKRSKI  1400
1401  YSMTLRLSALFEEKMKKISSDFKIGQKFNEKLRRSQRFKQRQNCKGDSQP  1450
1451  NKSIRNLKPKRLKSQTKIIPELVGSPTQSTSSRTAYLGTHKTSAGISSGV  1500
1501  TSGDSSDSAESSERRKRNRPITNGSTLSESEVEDSLATSLSSSASSSSEE  1550
1551  SKESSRARESSSRSGLSRSSNLRVTRTRAAQRKTGPVSLANGCGRKATRK  1600
1601  RVYLSDSDNNSLETGEILKARAGNNRKVLRKCAAVAANKIKLMSDVEENS  1650
1651  SSESVCSGRKLPHRNASAVARKKLLHNSEDEQSLKSEIEEEELKDENQLL  1700
1701  PVSSSHTAQSNVDESENRDSESESDLRVARKNWHANGYKSHTPAPSKTKF  1750
1751  LKIESSEEDSKSHDSDHACNRTAGPSTSVQKLKAESISEEADSEPGRSGG  1800
1801  RKYNTFHKNASFFKKTKILSDSEDSESEEQDREDGKCHKMEMNPISGNLN  1850
1851  CDPIAMSQCSSDHGCETDLDSDDDKIEKPNNFMKDSASQDNGLSRKISRK  1900
1901  RVCSSDSDSSLQVVKKSSKARTGLLRITRRCAATAANKIKLMSDVEDVSL  1950
1951  ENVHTRSKNGRKKPLHLACTTAKKKLSDCEGSVHCEVPSEQYACEGKPPD  2000
2001  PDSEGSTKVLSQALNGDSDSEDMLNSEHKHRHTNIHKIDAPSKRKSSSVT  2050
2051  SSGEDSKSHIPGSETDRTFSSESTLAQKATAENNFEVELNYGLRRWNGRR  2100
2101  LRTYGKAPFSKTKVIHDSQETAEKEVKRKRSHPELENVKISETTGNSKFR  2150
2151  PDTSSKSSDLGSVTESDIDCTDNTKTKRRKTKGKAKVVRKEFVPRDREPN  2200
2201  TKVRTCMHNQKDAVQMPSETLKAKMVPEKVPRRCATVAANKIKIMSNLKE  2250
2251  TISGPENVWIRKSSRKLPHRNASAAAKKKLLNVYKEDDTTINSESEKELE  2300
2301  DINRKMLFLRGFRSWKENAQ                                2320

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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