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

NucPred

Fetching Q9CUU3 from www.uniprot.org...

The NucPred score for your sequence is 1.00 (see score help below)

   1  MPVRPDLQQLEKCIDDALRKNDFKPLLALLQIDICEDVKIKCSKQFLRKL    50
  51  DDLICRELNKKDIQTVSSILISIGRCSKNIFILGQAGLQTMIKQGLVQKM   100
 101  VSWFENSKEIILNQQQSKDEAVMNMIEDLFDLLMVIYDISDEGKNQVLES   150
 151  FIPQICALVIDSRVNFCIQQEALKKMNLMLDRIPQDANKILSNQEMLTLM   200
 201  SNMGERILDVGDYELQVGIVEALCRMTTEKRRQELAYEWFSMDFIANAFK   250
 251  EIKDCEFETDCRIFLNLVNGILGDKRRVYTFPCLSAFLGKYELQIPSDEK   300
 301  LEEFWIDFNLGSHTLSFYIAGDEEDHQWEAVTVPEEKVQMYNIEVRESKK   350
 351  LLTLTLKNIVKISKKEGKELLFYFDESLEITNVTKKVFGGNKYKEFTRKQ   400
 401  GISVAKTSIHVLFDASGSQILVPESQPSPVKENLIHLKEKSDIQKKLVNP   450
 451  LELGNSSSQDEITTPSRKKMSEASMIVPDTDRYTVRSPILLINTSTPRRS   500
 501  REPLQAINSVEKAVSKTSESGMDYAASPKSRQSDGRKRWNNRANHNKTTA   550
 551  VIQNKQYEDNESPDQNFNEIEDTLSNVSSAVGKVDKPVLPGVLDISKNTT   600
 601  HSRWACWTPVTTIKLCNNQRSRALPGDTCTQDTGVNKKCTKQKSVSDDDS   650
 651  EETQKGKYSKDVIKCNKSDEAEFCERNIQEQNHPKYSQKKNTANAKKSDW   700
 701  HIESETTYKSVLLNKTTEESLIYKKTCVLSKDVNTTICDKSPSRKSKRNH   750
 751  TKSRKELMSELTSCELEEIPVRENSKGKRFTGASESLINQISRRYNPSDS   800
 801  MMSTRKLKEPQDGSGFSKKPDLQFNKVQRKSYRKLKATVVNVTSECPLDD   850
 851  VYNFSLNGADEPVIKLGIQEFQATTREASMDNSLKLVKNHDEHDPFLKTK   900
 901  DKRMLSYEKKTLLSDTETECGCDDSKTDISWLKEPKTKRLMDYSRNKNTT   950
 951  KYKSRKSRSSMEKGQPRPTMVLNKNSMKNDYEVVVDGRTRLPRRATKTKK  1000
1001  NYKDLSTSESESESEKECSYLFKDKLPTKEETIHSRAQTKKLPEKQQKVF  1050
1051  NSEALKGQPSEEQKNSSRLREGREDSLCLSSASVSRSSSSVEVMRCTEKI  1100
1101  TERDFTQDYDYITKSLSPYPKAPSPEFLNGNNSVVGRGQSPRISETSAMC  1150
1151  VRKSYSPASGPPFSPRHTPTKNNSVVNMKKANSVINNQRTQHCNSYSDVS  1200
1201  SNSSEKLYMEPESPESCDNHMQNKREGNHAASPLSLSSEKIEKMWFDMPS  1250
1251  ENTHVSGPSQRGSKRRMYLEDDELSNSNEAEVEEAEEREHLLSKKRCQWE  1300
1301  NSDQHTFKTSLSTPDFSVPKDWQQELQGAGMFYDNISSDYKRKTDSQHKI  1350
1351  MDDFTTKTLKLTQQHLMAMTSQAQGRRDENVEKFQVTLLDELEKVEKDSQ  1400
1401  TLRDLEKELVDIEEKLVQKMRAYHRCERERFRVLKTSLDKSFLVYNSVYE  1450
1451  ESVFTSEMCLMKANMKMLQDKLLKEMHEEEVLNIRRGLQSLFKAHEGNDA  1500

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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