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

NucPred

Fetching Q3ZJ93 from www.uniprot.org...

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

   1  MQTTQNRLKTKRYASFFLNPKLNRPIQKKGWIKKADFNQLTDSLCKQSLK    50
  51  AYNEKLYSPLSQFKIPDFLNIQRSSFRQFLKSGLITEFKNCKSITNSNQT   100
 101  FEVFFYAEHYKLNRPKWTPKQAILKKKSYSSQLYLPIQLSNYQTEEVHLQ   150
 151  WVLLANLPLMTKNGHFILNGCPRVLMNQIVRSPGVYFRKVVKNQKTVYSA   200
 201  DFIAQRGSWLRLEVDTKKGDIWAKLKKTPKIPIFTFLRALGLTLPILNNS   250
 251  IDFAKLRYLLQFKEESKRSKKIKDFLGPGINNSLDIVEFRSLLKSLKKYM   300
 301  KPKPAKKSSKKQKTKKIKKWLTPFVCTTYFQSLLELCQKLYPQKKFLELD   350
 351  PKLAQKFLFRKFQNPRTYDLSILGREKINKKLGISIPLEKTILTSQDVLF   400
 401  ACLFLMDLLQGLVISDDIDDLKNRKIKPSGELIQTQLSTGLIRLEKIIRE   450
 451  KLKQPKQDSDSFSNLFSVKPLNQAFRDFFGTNPLSQLMDQTNALSEITHK   500
 501  RRLSSLGPGGINRETAGMAIRGIHPTHYGRICPIETPEGQNAGLVNSFTI   550
 551  FSHLNTKSFIETPFYKMYKGFILKNKNPFLFSSDQERNLVLAPGDIQTSL   600
 601  FHFLPPGVPIPSRQFKEFKRVSRNEINFIAVSPIQMISIATSLIPFLEHN   650
 651  DGNRALMGSNMQRQAVPTVRPSKPIVGTGLESRVISDVGHGLQVQKSGFV   700
 701  SYVDGNKIIIYSKKRIDQPFFFDTKKLHFPKKKVPFLNLDLQQQNTCRSS   750
 751  FKKKLVKSANIFTFKEKQLYQLSKIKNKKQRVCFEKSLKSQDFSSLLNFL   800
 801  TLFNIKTKVQAEKKASVQDASFILVPKKNLDLEVNKRIFLPVFLKKRNEY   850
 851  NFLNYYKLTERTLYSGFSILPFKLTNKGNYFNNKQISCLSNSLFLNDFLG   900
 901  QFHLLKFFSTKIFYSKLSRNFKPFISKRSLVLINKFSHQKLLFSYCKIIL   950
 951  IHFYTKFNKKTPKNFLLNTKLSSKLMKRKDFSHFFRKDEKTMPIQNLTNF  1000
1001  KSAHLHSQTAVKGVCQQIRSARKTQIANPFWYNSFPLFLIKSSPLTPLLF  1050
1051  RRSFVPKVFNPLGLHFAYQQSKGPKHVSRTFKTLDRNEQKFSYNQKFQKL  1100
1101  NFIFVKPYKFKRKNSPFAPFARSSKARGSAKAIFSQAQRLWGEKVFLVQN  1150
1151  KENLPQTLGSCKIMTNQFYLKFSLLLKQQKKNFSNKKTGMENQNCQNSLT  1200
1201  SQKNGFQCLKKMEPLHFPTKKSSISTLSFVKKILPYFQHPLLNLTTQNKI  1250
1251  KNKLMIFKKPFLFWSACFADKQSLRSILFSLKKSQKVTTLKKTKVKKKFE  1300
1301  IVYNENKKKYFQKINKNFFLPLLCRTRNLNFASNSLLFQISYPVAVNQSN  1350
1351  LIQRNLISQELKHNSKRFIKTLLKIKPFVGKFVFPFCPICLKRKASIETQ  1400
1401  SFVKKSDKNFQFCFCFSRKKQKTLKPLLRIKSSDKMNTLKPLQKFSLLEN  1450
1451  FKVPPQSSLTARDKILRSTIGTKGLNDSLSMKSTDGEYAINDKKRRVEII  1500
1501  NSSSLFYNNLIPQNYILNNYHRSNQDTYMIHRPLVQEGQWVEKGDILADS  1550
1551  SVSVQGELSIGQNILVGYIPWEGYNFEDAVLISERLIFDDLYTSLHIERY  1600
1601  EVEIRDTQFGLEQITNQIPNEKGEYDYIDSNGIAKIGTWVKEGDILVGKI  1650
1651  APIGQKKLTAYENLLYDILNKEIPKTRDTSLRVPRGVTGRVIHVEIVETT  1700
1701  KKKGNDSSIFAKSLKFPKKQKLKRVTSPEYWYPVNTKKDQKVQSFSFKNK  1750
1751  SEKLFLTPVQSYFNKEAKTKNPKLNSPFFYLNKRNPDFNLKRNKRIAKEM  1800
1801  YFFNKNEKIKLSTLQIKIKGLEKKEFSFPKILKARFSLLQKAQTANLKIE  1850
1851  KFLDDKFWNNVNYSNKNFSRNGSQKENSNADGLQFYNPLKKTKTKVLQPM  1900
1901  EKTSFSGPQKVHIYLAEKRKLQIGDKIAGRHGNKGIISNILPRQDMPYLS  1950
1951  DGTPLDIVLNPLGVPSRMNVGQILECLLGMAGYYLKQNFKIQPFDEIYGC  2000
2001  EASRSLVYSKLYEARIKTGQDWLFNANHPGKTRLFDGRTGDCFKQPVTVG  2050
2051  VAYILKLIHLVDDKIHARSTGPYSLVTQQPLRGRSKQGGQRVGEMEVWAL  2100
2101  EGFGAAYILQEILTIKSDDLKGRNQVMNSILNNKPVNFGLPESFKVLVRE  2150
2151  LQSLCLDIAIYRYRENGTPTKININNFW                        2178

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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