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

NucPred

Fetching Q27571 from www.uniprot.org...

The NucPred score for your sequence is 0.87 (see score help below)

   1  MSQHFTSIFENLRFVTIKRSTNAQQQQQQQQQQLQQQQQQLQQQKAQTQQ    50
  51  QNSRKIKTQATPTLNGNGLLSGNPNGGGGDSSPSHEVDHPGGAQGAQAAG   100
 101  GLPSSSGTPLRHHKRASISTASPPIRERRGTNTSIVVELDGSGSGSGSGG   150
 151  GGVGVGQGAGCPPSGSCTASGKSSRELSPSPKNQQQPRKMSQDYRSRAGS   200
 201  FMHLDDEGRSLLMRKPMRLKNIEGRPEVYDTLHCKGREILSCSKATCTSS   250
 251  IMNIGNAAVEARKSDLILEHAKDFLEQYFTSIKRTSSTAHETRWKQVRQS   300
 301  IETTGHYQLTETELIYGAKLAWRNSSRCIGRIQWSKLQVFDCRYVTTTSG   350
 351  MFEAICNHIKYATNKGNLRSAITIFPQRTDAKHDYRIWNNQLISYAGYKQ   400
 401  ADGKIIGDPMNVEFTEVCTKLGWKSKGSEWDILPLVVSANGHDPDYFDYP   450
 451  PELILEVPLTHPKFEWFSDLGLRWYALPAVSSMLFDVGGIQFTATTFSGW   500
 501  YMSTEIGSRNLCDTNRRNMLETVALKMQLDTRTPTSLWKDKAVVEMNIAV   550
 551  LHSYQSRNVTIVDHHTASESFMKHFENESKLRNGCPADWIWIVPPLSGSI   600
 601  TPVFHQEMALYYLKPSFEYQDPAWRTHVWKKGRGESKGKKPRRKFNFKQI   650
 651  ARAVKFTSKLFGRALSKRIKATVLYATETGKSEQYAKQLCELLGHAFNAQ   700
 701  IYCMSDYDISSIEHEALLIVVASTFGNGDPPENGELFSQELYAMRVQESS   750
 751  EHGLQDSSIGSSKSFMKASSRQEFMKLPLQQVKRIDRWDSLRGSTSDTFT   800
 801  EETFGPLSNVRFAVFALGSSAYPNFCAFGQYVDNILGELGGERLLRVAYG   850
 851  DEMCGQEQSFRKWAPEVFKLACETFCLDPEESLSDASLALQNDSLTVNTV   900
 901  RLVPSANKGSLDSSLSKYHNKKVHCCKAKAKPHNLTRLSEGAKTTMLLEI   950
 951  CAPGLEYEPGDHVGIFPANRTELVDGLLNRLVGVDNPDEVLQLQLLKEKQ  1000
1001  TSNGIFKCWEPHDKIPPDTLRNLLARFFDLTTPPSRQLLTLLAGFCEDTA  1050
1051  DKERLELLVNDSSAYEDWRHWRLPHLLDVLEEFPSCRPPAPLLLAQLTPL  1100
1101  QPRFYSISSSPRRVSDEIHLTVAIVKYRCEDGQGDERYGVCSNYLSGLRA  1150
1151  DDELFMFVRSALGFHLPSDRSRPIILIGPGTGIAPFRSFWQEFQVLSDLD  1200
1201  PTAKLPKMWLFFGCRNRDVDLYAEEKAELQKDQILDRVFLALSREQAIPK  1250
1251  TYVQDLIEQEFDSLYQLIVQERGHIYVCGDVTMAEHVYQTIRKCIAGKEQ  1300
1301  KSEAEVETFLLTLRDESRYHEDIFGITLRTAEIHTKSRATARIRMASQP   1349

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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