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

NucPred

Fetching O95405 from www.uniprot.org...

The NucPred score for your sequence is 0.54 (see score help below)

   1  MENYFQAEAYNLDKVLDEFEQNEDETVSSTLLDTKWNKILDPPSHRLSFN    50
  51  PTLASVNESAVSNESQPQLKVFSLAHSAPLTTEEEDHCANGQDCNLNPEI   100
 101  ATMWIDENAVAEDQLIKRNYSWDDQCSAVEVGEKKCGNLACLPDEKNVLV   150
 151  VAVMHNCDKRTLQNDLQDCNNYNSQSLMDAFSCSLDNENRQTDQFSFSIN   200
 201  ESTEKDMNSEKQMDPLNRPKTEGRSVNHLCPTSSDSLASVCSPSQLKDDG   250
 251  SIGRDPSMSAITSLTVDSVISSQGTDGCPAVKKQENYIPDEDLTGKISSP   300
 301  RTDLGSPNSFSHMSEGILMKKEPAEESTTEESLRSGLPLLLKPDMPNGSG   350
 351  RNNDCERCSDCLVPNEVRADENEGYEHEETLGTTEFLNMTEHFSESQDMT   400
 401  NWKLTKLNEMNDSQVNEEKEKFLQISQPEDTNGDSGGQCVGLADAGLDLK   450
 451  GTCISESEECDFSTVIDTPAANYLSNGCDSYGMQDPGVSFVPKTLPSKED   500
 501  SVTEEKEIEESKSECYSNIYEQRGNEATEGSGLLLNSTGDLMKKNYLHNF   550
 551  CSQVPSVLGQSSPKVVASLPSISVPFGGARPKQPSNLKLQIPKPLSDHLQ   600
 601  NDFPANSGNNTKNKNDILGKAKLGENSATNVCSPSLGNISNVDTNGEHLE   650
 651  SYEAEISTRPCLALAPDSPDNDLRAGQFGISARKPFTTLGEVAPVWVPDS   700
 701  QAPNCMKCEARFTFTKRRHHCRACGKVFCASCCSLKCKLLYMDRKEARVC   750
 751  VICHSVLMNAQAWENMMSASSQSPNPNNPAEYCSTIPPLQQAQASGALSS   800
 801  PPPTVMVPVGVLKHPGAEVAQPREQRRVWFADGILPNGEVADAAKLTMNG   850
 851  TSSAGTLAVSHDPVKPVTTSPLPAETDICLFSGSITQVGSPVGSAMNLIP   900
 901  EDGLPPILISTGVKGDYAVEEKPSQISVMQQLEDGGPDPLVFVLNANLLS   950
 951  MVKIVNYVNRKCWCFTTKGMHAVGQSEIVILLQCLPDEKCLPKDIFNHFV  1000
1001  QLYRDALAGNVVSNLGHSFFSQSFLGSKEHGGFLYVTSTYQSLQDLVLPT  1050
1051  PPYLFGILIQKWETPWAKVFPIRLMLRLGAEYRLYPCPLFSVRFRKPLFG  1100
1101  ETGHTIMNLLADFRNYQYTLPVVQGLVVDMEVRKTSIKIPSNRYNEMMKA  1150
1151  MNKSNEHVLAGGACFNEKADSHLVCVQNDDGNYQTQAISIHNQPRKVTGA  1200
1201  SFFVFSGALKSSSGYLAKSSIVEDGVMVQITAENMDSLRQALREMKDFTI  1250
1251  TCGKADAEEPQEHIHIQWVDDDKNVSKGVVSPIDGKSMETITNVKIFHGS  1300
1301  EYKANGKVIRWTEVFFLENDDQHNCLSDPADHSRLTEHVAKAFCLALCPH  1350
1351  LKLLKEDGMTKLGLRVTLDSDQVGYQAGSNGQPLPSQYMNDLDSALVPVI  1400
1401  HGGACQLSEGPVVMELIFYILENIV                           1425

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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