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

NucPred

Fetching Q6CT34 from www.uniprot.org...

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

   1  MDNPRVKYLEELILALKSAGTVGNGIELDSTLQLDEKNGKLLQTLLKNTQ    50
  51  STNTDEVIFHKSFQALDLFLRCNQHLFSANVKEITMIEVILNNMVSCSLM   100
 101  HWSNMQYIWLINKYVSAWLKAYSFASTSNLQIWFTEQMVQYEKLLVTCLR   150
 151  GKLEKPTFHSLLKKIVIVNGWIMRDGLLRNYSYRRWQSQFQKLMRLLAFV   200
 201  LKSTNEPSVEVASILQLLVRYISLSKESLSIFRFSFDLIQTLIKDHHQHI   250
 251  SPTILAKTLLRTLYLCIHDESKLAEIKNTFELHEWINTNKNADPLFIRSI   300
 301  KYVSVKLGFLESMEEFTFSNKQLHWLHQAIENPKLRLVSGNVRNCIADSA   350
 351  DIRSFYDKVKESLLNTIKDGDTAKLTHSMHSIRQLAIKEKFVNNNLVRSP   400
 401  QVEFNASQNMRLSSLNLVPLHKSLAFQLLAKHVIKSIPITDMPEAMLTGV   450
 451  VLILIEVFSRFEPPKLEETSDLIQQSDGYGCLQVFQRASNSRSRFLRLLS   500
 501  VRLLPYFASLGSKYEDINLKFLIIFLQKPKAPYLTETLHMSWINLIINCN   550
 551  SEYFDDLLLKLIDLFNSSDFAEHTMMAAQLRYLSKIQGKSPYQLLSPILP   600
 601  VLFKKMGRSLVEKKLGLQRIVQLVDYPAKTLLENFQRYVVPSALGQYKSD   650
 651  VITEVARIMSGNDKSLVEEKKLKLLDRNSRQIFAVALVKHGFFSIETIQT   700
 701  LFLNTAPKFRKNYITLYLPDYKTLAEVLKMSKQILTLDGQITETERCVLS   750
 751  SLRFLLITNFSKDKRRGTRFKNIEDWNEEMEEQFQQKLEQNVLGIFQVFS   800
 801  NDMHDSDGKTSYYEKLRVLNGISFLMKYASKKSIISALAQLSICLQTGSE   850
 851  IPEIQHNTLECWHLLIKLLNEEQITAIINDLFCLILQKWSTFSSSCKLEC   900
 901  QAIFDTLLKDRQKLVLEGRPFILLAFLNNPEFQVLERHPTVARKVLKVIS   950
 951  TTNWLKVFTENLGSNNRYVILQTLLELEKYFSTTIHRKHVDVVTKHDDSS  1000
1001  HLSTLLGALLDSTYKFRNRDLKICQIAASCISLIGLLDVTKHALPRNTNL  1050
1051  SEEICDFNNHSQTVKFLISIVNNILVPAFWQSENPTKQLFVALVMQESLK  1100
1101  YCGLSSVNWDINRPDDYPVEAKLWSRFNDISKTTLFPLLSSLYLAQSWKE  1150
1151  YVPLSYPSFKVKDGYQVWIRNLTLDLLKIGTEEDHPLHVFSSLIREDDGT  1200
1201  LSNFLLPFITMDIILRANKHNEYSKIIENLSIEFEFIFNFDLQQLNHFQI  1250
1251  DSLKMAYNTIFRVYEYCKKWVSSFKQDYQAANGTYMIQEDKVLQVLDRTE  1300
1301  RFVNTIPSDTLAKKSLETDSFERSALYLEQSYREHGTSSLASTDLLQCIQ  1350
1351  NTYAEIGDVDAVGGVLKMFSTGNLTTKIEELQYSKNWKMAQDCFEALGDF  1400
1401  KLSANSTTSSELVKSSNMKMLKSMYSHQLYEELLMKVKVHLPETKGFLVD  1450
1451  NDGDLLNMGIEAVSQTGNIVELTRWIERVEHIQMFNDPSLLLHYNIAKVL  1500
1501  QAVSRNQQQNVERYINKCFTLIGAQFTIPSTSTTLLKNREVLQKLHALTD  1550
1551  IKLLCSAHTQSEFSNASKALDGRLSHVGSDFSPNHYLLSIRKTVEIISKN  1600
1601  QHLQNDISNVYFQLSQLDRKENRLDLAAEDLMNALKYNHHSAELEFAEIL  1650
1651  WKQGEKDMALKTVAEITKRFKDDPSTASSENQDFKEVLLKYTEWLDLSNS  1700
1701  SVSEQIIKQYNELIRFDKNWDAPFYSMGLYYSKLLEKKKAEGYVSDGSLE  1750
1751  YRSITNFLTSFEKGSPNIRQSLPKVVTLWLDTAKNDVNNSISDVSNYSSR  1800
1801  ICNKIDTAVKNCGIHIWYTVLTQLLSRLMHPHTATIHTIVNILFHMTLEY  1850
1851  PSVMLWYISILLNSESLERRNIGKQIVEAFQKKNPRTKLPGTAISLVQSL  1900
1901  TRVCIKDVKNTASRSGRSIDSDFKFNLELAPNDMCVPVNINLKKLLPSTA  1950
1951  TSMNSDLFKSVMVSIARFSSQYMVFNSLKKPKKLTVIGSDGNIYGIMCKK  2000
2001  EDVRQDNQYMQFANTMSFLLSKDVESRKRNLGITTYGVLSLREDCGLLEI  2050
2051  VPNVVTLRSLLSMKYESMKIKYSLKSLQEKWQSIPSDQKLAFHKDCLKKF  2100
2101  PPVLYQWFLDNFPDPITWYNARNGFVRSYSVMAMVGHILGLGDRHCENIL  2150
2151  LDVLTGRVLHVDFDCLFEKGKKLPVPEIVPFRLTQNITDAFGIIGTEGTF  2200
2201  KKSSEVTLRVMRNNEIGLVNIIETIMYDRKIDESIQNALKVLRDKIRGID  2250
2251  ARDGLALSVSGQVEALTQESCSVENLSKMYIGWLPFW               2287

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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