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

NucPred

Fetching Q61838 from www.uniprot.org...

The NucPred score for your sequence is 0.29 (see score help below)

   1  MRRNQLPTPAFLLLFLLLPRDATTATAKPQYVVLVPSEVYSGVPEKACVS    50
  51  LNHVNETVMLSLTLEYAMQQTKLLTDQAVDKDSFYCSPFTISGSPLPYTF   100
 101  ITVEIKGPTQRFIKKKSIQIIKAESPVFVQTDKPIYKPGQIVKFRVVSVD   150
 151  ISFRPLNETFPVVYIETPKRNRIFQWQNIHLAGGLHQLSFPLSVEPALGI   200
 201  YKVVVQKDSGKKIEHSFEVKEYVLPKFEVIIKMQKTMAFLEEELPITACG   250
 251  VYTYGKPVPGLVTLRVCRKYSRYRSTCHNQNSMSICEEFSQQADDKGCFR   300
 301  QVVKTKVFQLRQKGHDMKIEVEAKIKEEGTGIELTGIGSCEIANALSKLK   350
 351  FTKVNTNYRPGLPFSGQVLLVDEKGKPIPNKNITSVVSPLGYLSIFTTDE   400
 401  HGLANISIDTSNFTAPFLRVVVTYKQNHVCYDNWWLDEFHTQADHSATLV   450
 451  FSPSQSYIQLELVFGTLACGQTQEIRIHYLLNEDIMKNEKDLTFYYLIKA   500
 501  RGSIFNLGSHVLSLEQGNMKGVFSLPIQVEPGMAPEAQLLIYAILPNEEL   550
 551  VADAQNFEIEKCFANKVNLSFPSAQSLPASDTHLKVKAAPLSLCALTAVD   600
 601  QSVLLLKPEAKLSPQSIYNLLPGKTVQGAFFGVPVYKDHENCISGEDITH   650
 651  NGIVYTPKHSLGDNDAHSIFQSVGINIFTNSKIHKPRFCQEFQHYPAMGG   700
 701  VAPQALAVAASGPGSSFRAMGVPMMGLDYSDEINQVVEVRETVRKYFPET   750
 751  WIWDLVPLDVSGDGELAVKVPDTITEWKASAFCLSGTTGLGLSSTISLQA   800
 801  FQPFFLELTLPYSVVRGEAFTLKATVLNYMSHCIQIRVDLEISPDFLAVP   850
 851  VGGHENSHCICGNERKTVSWAVTPKSLGEVNFTATAEALQSPELCGNKLT   900
 901  EVPALVHKDTVVKSVIVEPEGIEKEQTYNTLLCPQDTELQDNWSLELPPN   950
 951  VVEGSARATHSVLGDILGSAMQNLQNLLQMPYGCGEQNMVLFVPNIYVLN  1000
1001  YLNETQQLTEAIKSKAINYLISGYQRQLNYQHSDGSYSTFGNHGGGNTPG  1050
1051  NTWLTAFVLKAFAQAQSHIFIEKTHITNAFNWLSMKQKENGCFQQSGYLL  1100
1101  NNAMKGGVDDEVTLSAYITIALLEMPLPVTHSAVRNALFCLETAWASISQ  1150
1151  SQESHVYTKALLAYAFALAGNKAKRSELLESLNKDAVKEEDSLHWQRPGD  1200
1201  VQKVKALSFYQPRAPSAEVEMTAYVLLAYLTSESSRPTRDLSSSDLSTAS  1250
1251  KIVKWISKQQNSHGGFSSTQDTVVALQALSKYGAATFTRSQKEVLVTIES  1300
1301  SGTFSKTFHVNSGNRLLLQEVRLPDLPGNYVTKGSGSGCVYLQTSLKYNI  1350
1351  LPVADGKAPFALQVNTLPLNFDKAGDHRTFQIRINVSYTGERPSSNMVIV  1400
1401  DVKMVSGFIPMKPSVKKLQDQPNIQRTEVNTNHVLIYIEKLTNQTLGFSF  1450
1451  AVEQDIPVKNLKPAPIKVYDYYETDEFTVEEYSAPFSDGSEQGNA       1495

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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