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

NucPred

Fetching P53552 from www.uniprot.org...

The NucPred score for your sequence is 0.87 (see score help below)

   1  MAEQTLLSKLNALSQKVIPPASPSQASILTEEVIRNWPERSKTLCSDFTA    50
  51  LESNDEKEDWLRTLFIELFDFINKNDENSPLKLSDVASFTNELVNHERQV   100
 101  SQASIVGKMFIAVSSTVPNINDLTTISLCKLIPSLHEELFKFSWISSKLL   150
 151  NKEQTTLLRHLLKKSKYELKKYNLLVENSVGYGQLVALLILAYYDPDNFS   200
 201  KVSAYLKEIYHIMGKYSLDSIRTLDVILNVSSQFITEGYKFFIALLRKSD   250
 251  SWPSSHVANNSNYSSLNEGGNMIAANIISFNLSQYNEEVDKENYERYMDM   300
 301  CCILLKNGFVNFYSIWDNVKPEMEFLQEYIQNLETELEEESTKGVENPLA   350
 351  MAAALSTENETDEDNALVVNDDVNMKDKISEETNADIESKGKQKTQQDIL   400
 401  LFGKIKLLERLLIHGCVIPVIHVLKQYPKVLYVSESLSRYLGRVFEYLLN   450
 451  PLYTSMTSSGESKDMATALMITRIDNGILAHKPRLIHKYKTHEPFESLEL   500
 501  NSSYVFYYSEWNSNLTPFASVNDLFENSHIYLSIIGPYLGRIPTLLSKIS   550
 551  RIGVADIQKNHGSESLHVTIDKWIDYVRKFIFPATSLLQNNPIATSEVYE   600
 601  LMKFFPFEKRYFIYNEMMTKLSQDILPLKVSFNKAEREAKSILKALSIDT   650
 651  IAKESRRFAKLISTNPLASLVPAVKQIENYDKVSELVVYTTKYFNDFAYD   700
 701  VLQFVLLLRLTYNRPAVQFDGVNQAMWVQRLSIFIAGLAKNCPNMDISNI   750
 751  ITYILKTLHNGNIIAVSILKELIITVGGIRDLNEVNMKQLLMLNSGSPLK   800
 801  QYARHLIYDFRDDNSVISSRLTSFFTDQSAISEIILLLYTLNLKANTQNS   850
 851  HYKILSTRCDEMNTLLWSFIELIKHCLKGKAFEENVLPFVELNNRFHLST   900
 901  PWTFHIWRDYLDNQLNSNENFSIDELIEGAEFSDVDLTKISKDLFTTFWR   950
 951  LSLYDIHFDKSLYDERKNALSGENTGHMSNRKKHLIQNQIKDILVTGISH  1000
1001  QRAFKKTSEFISEKSNVWNKDCGEDQIKIFLQNCVVPRVLFSPSDALFSS  1050
1051  FFIFMAFRTENLMSILNTCITSNILKTLLFCCTSSEAGNLGLFFTDVLKK  1100
1101  LEKMRLNGDFNDQASRKLYEWHSVITEQVIDLLSEKNYMSIRNGIEFMKH  1150
1151  VTSVFPVVKAHIQLVYTTLEENLINEEREDIKLPSSALIGHLKARLKDAL  1200
1201  ELDEFCTLTEEEAEQKRIREMELEEIKNYETACQNEQKQVALRKQLELNK  1250
1251  SQRLQNDPPKSVASGSAGLNSKDRYTYSRNEPVIPTKPSSSQWSYSKVTR  1300
1301  HVDDINHYLATNHLQKAISLVENDDETRNLRKLSKQNMPIFDFRNSTLEI  1350
1351  FERYFRTLIQNPQNPDFAEKIDSLKRYIKNISREPYPDTTSSYSEAAAPE  1400
1401  YTKRSSRYSGNAGGKDGYGSSNYRGPSNDRSAPKNIKPISSYAHKRSELP  1450
1451  TRPSKSKTYNDRSRALRPTGPDRGDGFDQRDNRLREEYKKNSSQRSQLRF  1500
1501  PEKPFQEGKDSSKANPYQASSYKRDSPSENEEKPNKRFKKDETIRNKFQT  1550
1551  QDYRNTRDSGAAHRANENQRYNGNRKSNTQALPQGPKGGNYVSRYQR     1597

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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