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

NucPred

Fetching Q6P1E8 from www.uniprot.org...

The NucPred score for your sequence is 0.86 (see score help below)

   1  MKRNGTRLNFAKANSTKSGSTRARDLMNKMSIIPEWHSLYSNTRKLPCSR    50
  51  PHSSPCKMQRTIFQDLCRPSSSTTAIANPVLSYLDIERILAQKISSRRDD   100
 101  IKKVFQILDRNHNQMVTKGDLKRVITAFLIPLTKDQFQDLLAQIPISSLG   150
 151  NVPYLEFLSRFGGGIDININGIKRVNENEVDNRRTVKEVQLTEKIFRNMR   200
 201  SIRKVFQVMDVNNTGLVQPQELRRVLETFCLRMQDGDYEKFLEQYNIDKT   250
 251  TAVDYNAFLKNLSVKNDASFKYLLSNAAELSRETQQGKNGKRLLDTGSSE   300
 301  DVWKNYSLDDLEKTFCQEFSKSYEKIEKALSAGDPSKGGYISLNYLKVVL   350
 351  DTFIYRLPRRIFIQLIRRFGLKTSTKINWKQFLTAIYERQKLEVSKTLPL   400
 401  KKRSSTEARNRSRKENIIKKLFKYSEDRYTALKKTLLIISSTPSGHITWE   450
 451  ELRHILNCMVAKLNDSEFSELKQTFDPEGTGAVRVNSLLDVLDDSTKVRK   500
 501  MSPSTDTKTPLPVAWDSVEELVLDSITRNLQAFYSMLQSYDLRDTGTIGK   550
 551  NNFRKVMRVFCPYLSNEHLVRFSSKFQEAGSGRILYKKFLLSIGVGIPPP   600
 601  TPPLSSPKVQLSDQFQIEEPGQQDERTQPSGEKTSEINNMTKEEVIDGLK   650
 651  HRIQQKDPVFRKQFLSISKEPDVKINQEEFRKVLERSGMPMNDCQYAMLA   700
 701  SKLGFKNEEGMSYQDFTMGFEDCMLSGLETVPLQSRTASRTNMDEHFISA   750
 751  EECLRIFPKKLKESFRDVYSAFFRIDLDRDGIISMHDFHRLLQYLQLNMV   800
 801  DLEFERFLSLLGLRLSVTLNFREFQNLCEKRPWKSDEAPQRLIRCKQKVA   850
 851  DSELACEQAHQYLIMKAKTRWADLSKNFIETDNEGNGILRRRDIKNSLYG   900
 901  FDIPLTPREFEKLWQNYDTEGRGYITYQEFLHRLGIRYSPKVHRPYKEDY   950
 951  FNFLGHFTKPKQVQEEIQELQQISEREKLMNHYEEISKAFNAMEKSKPVA  1000
1001  LCRVQKVLQECGCPLKEEELISLLKSLDVSVHNNHIDPVEFLRALEISWA  1050
1051  SKARPKEKEESSPPPISFSKVTPDEVIKTMQEVVESSQPALVEAFSALDK  1100
1101  EDTGFVKAMEFGDVLRSVCQKLTDNQYHYFLRRLRLHLTPNIHWKYFLEN  1150
1151  FSTFQDETADDWAENMPKAPPPMSPKETAHRDIVARVQKAVASHYHTIVQ  1200
1201  EFENFDTLKSNTVSRDEFRSICTRHIQILTDEQFDRLWSELPVNAKGRLK  1250
1251  YQDFLSKLSIERVPSPPMAAGDSGESTMAQRGSSAPEFSQGTRSNLYSPP  1300
1301  RDSRVGLKSRSHPCTPVGTPPLQNCEPIESRLRKQIQGCWRELLRECKEK  1350
1351  DTDKQGTISAAEFLALVEKFKLDISREESQQLIVKYDLKNNGKFAYCDFI  1400
1401  QSCVLLLKAKETSLMRRMRIQNADKMKEAGMETPSFYSALLRIQPKIVHC  1450
1451  WRPMRRSFKTYDKNGTGLLSVADFRKVLRQYSINLSEEEFFHVLEYYDKS  1500
1501  LSSKISYNDFLRAFLQ                                    1516

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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