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

NucPred

Fetching Q9JKF1 from www.uniprot.org...

The NucPred score for your sequence is 0.81 (see score help below)

   1  MSAAEEVDGLGVVRPHYGSVLDNERLTAEEMDERRRQNVAYEYLCHLEEA    50
  51  KRWMEACLGEDLPPTTELEEGLRNGVYLAKLGNFFSPKVVSLKKIYDREQ   100
 101  TRYKATGLHFRHTDNVIQWLNAMDEIGLPKIFYPETTDIYDRKNMPRCIY   150
 151  CIHALSLYLFKLGLAPQIQDLYGKVDFTEEEINNMKIELEKYGIQMPAFS   200
 201  KIGGILANELSVDEAALHAAVIAINEAIDRRVAADTFTALKNPNAMLVNL   250
 251  EEGLAPTYQDVLYQAKQDKMTNAKNRTENSDRERDVYEELLTQAEIQGNV   300
 301  NKVNTSSALANISLALEQGCAVTLLKALQSLALGLRGLQTQNSDWYMKQL   350
 351  QSDLQQKRQSGQTDPLQKEEVQAGVDAANSAAQQYQRRLAAVAAINAAIQ   400
 401  KGIAEKTVLELMNPEAQLPQVYPFAADLYQKELATLQQQSPEHSLTHPEL   450
 451  TVAVEMLSSVALINRALESGDMTTVWKQLSSSVTGLTNIEEENCQRYLDE   500
 501  LMKLKAQAHAENNAFITWNDIQACVDHVNLVVHEEHERILAIGLINEALD   550
 551  EGDAQKTLQALQIPAAKLEGVLAEVAQHYQDTLIRAKREKAQETQDESAV   600
 601  LWLDEIQGGIWQSNKDTQEAQRFALGISAINEAVDSGDVGRTLSALRSPD   650
 651  VGLYGVIPECGETYQSDLAEAKKKRLAAGDNNSKWVKHWVKGGYHYYHNL   700
 701  ETQAGGWAEPPDFVQNSVQLSREEIQSSISGVTAAYNREQLWLANEGLIT   750
 751  KLQACCRGYLVRQEFRSRMNFLKKQIPAITCIQSQWRGYKQKKAYQDRLA   800
 801  YLHSHKDEVVKIQSLARMHQARKRYRDRLQYFRDHINDIIKIQAFIRANK   850
 851  ARDDYKTLINAEDPPMIVVRKFVHLLDQSDQDFQEELDLMKMREEVITLI   900
 901  RSNQQLENDLNLMDIKIGLLVKNKITLQDVVSHSKKLTKKNKEQLSDMMM   950
 951  INKQKGGLKALSKEKREKLEAYQHLFYLLQTNPTYLAKLIFQMPQNKSTK  1000
1001  FMDSVIFTLYNYASNQREEYLLLRLFQTALQEEIKSKVDQIQEIVTGNPT  1050
1051  VIKMVVSFNRGARGQNALRQILAPVVKEIMDDKSLNIKTDPVDIYKSWVN  1100
1101  QMESQTGEASKLPYDVTPEQALSHEEVKTRLDNSIRNMRAVTDKFLSAIV  1150
1151  SSVDKIPYGMRFIAKVLKDSLHEKFPDAGEDELLKIIGNLLYYRYMNPAI  1200
1201  VAPDAFDIIDLSAGGQLTTDQRRNLGSIAKMLQHAASNKMFLGDNAHLSI  1250
1251  INEYLSQSYQKFRRFFQVACDVPELQDKFNVDEYSDLVTLTKPVIYISIG  1300
1301  EIINTHTLLLDHQDAIAPEHNDPIHELLDDLGEVPTIESLIGESCGNSND  1350
1351  PNKEALAKTEVSLTLTNKFDVPGDENAEMDARTILLNTKRLIVDVIRFQP  1400
1401  GETLTEILETPATNEQEAEHQRAMQRRAIRDAKTPDKMKKSKPMKEDNNL  1450
1451  SLQEKKEKIQTGLKKLTELGTVDPKNRYQELINDIAKDIRNQRRYRQRRK  1500
1501  AELVKLQQTYSALNSKATFYGEQVDYYKSYIKTCLDNLASKGKVSKKPRE  1550
1551  MKGKKSKKISLKYTAARLHEKGVLLEIEDLQANQFKNVIFEIGPTEEVGD  1600
1601  FEVKAKFMGVQMETFMLHYQDLLQLQYEGVAVMKLFDRAKVNVNLLIFLL  1650
1651  NKKFYGK                                             1657

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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