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

NucPred

Fetching Q5THR3 from www.uniprot.org...

The NucPred score for your sequence is 0.85 (see score help below)

   1  MCKMAIIPDWLRSHPHTRKFTHSRPHSSPCRVYSRNGSPNKFRSSSTTAV    50
  51  ANPTLSSLDVKRILFQKITDRGDELQKAFQLLDTGQNLTVSKSELRRIIT   100
 101  DFLMPLTREQFQDVLAQIPLSTSGTVPYLAFLSRFGGIDLYINGIKRGGG   150
 151  NEMNCCRTLRELEIQVGEKVFKNIKTVMKAFELIDVNKTGLVRPQELRRV   200
 201  LETFCMKLRDEEYEKFSKHYNIHKDTAVDYNVFLKNLSINNDLNLRYCMG   250
 251  NQEVSLENQQAKNSKKERLLGSASSEDIWRNYSLDEIERNFCLQLSKSYE   300
 301  KVEKALSAGDPCKGGYVSFNYLKIVLDTFVYQIPRRIFIQLMKRFGLKAT   350
 351  TKINWKQFLTSFHEPQGLQVSSKGPLTKRNSINSRNESHKENIITKLFRH   400
 401  TEDHSASLKKALLIINTKPDGPITREEFRYILNCMAVKLSDSEFKELMQM   450
 451  LDPGDTGVVNTSMFIDLIEENCRMRKTSPCTDAKTPFLLAWDSVEEIVHD   500
 501  TITRNLQAFYNMLRSYDLGDTGRIGRNNFKKIMHVFCPFLTNAHFIKLCS   550
 551  KIQDIGSGRILYKKLLACIGIDGPPTVSPVLVPKDQLLSEHLQKDEQQQP   600
 601  DLSERTKLTEDKTTLTKKMTTEEVIEKFKKCIQQQDPAFKKRFLDFSKEP   650
 651  NGKINVHDFKKVLEDTGMPMDDDQYALLTTKIGFEKEGMSYLDFAAGFED   700
 701  PPMRGPETTPPQPPTPSKSYVNSHFITAEECLKLFPRRLKESFRDPYSAF   750
 751  FKTDADRDGIINMHDLHRLLLHLLLNLKDDEFERFLGLLGLRLSVTLNFR   800
 801  EFQNLCEKRPWRTDEAPQRLIRPKQKVADSELACEQAHQYLVTKAKNRWS   850
 851  DLSKNFLETDNEGNGILRRRDIKNALYGFDIPLTPREFEKLWARYDTEGK   900
 901  GHITYQEFLQKLGINYSPAVHRPCAEDYFNFMGHFTKPQQLQEEMKELQQ   950
 951  STEKAVAARDKLMDRHQDISKAFTKTDQSKTNYISICKMQEVLEECGCSL  1000
1001  TEGELTHLLNSWGVSRHDNAINYLDFLRAVENSKSTGAQPKEKEESMPIN  1050
1051  FATLNPQEAVRKIQEVVESSQLALSTAFSALDKEDTGFVKATEFGQVLKD  1100
1101  FCYKLTDNQYHYFLRKLRIHLTPYINWKYFLQNFSCFLEETADEWAEKMP  1150
1151  KGPPPTSPKATADRDILARLHKAVTSHYHAITQEFENFDTMKTNTISREE  1200
1201  FRAICNRRVQILTDEQFDRLWNEMPVNAKGRLKYPDFLSRFSSETAATPM  1250
1251  ATGDSAVAQRGSSVPDVSEGTRSALSLPTQELRPGSKSQSHPCTPASTTV  1300
1301  IPGTPPLQNCDPIESRLRKRIQGCWRQLLKECKEKDVARQGDINASDFLA  1350
1351  LVEKFNLDISKEECQQLIIKYDLKSNGKFAYCDFIQSCVLLLKAKESSLM  1400
1401  HRMKIQNAHKMKEAGAETPSFYSALLRIQPKIVHCWRPMRRTFKSYDEAG  1450
1451  TGLLSVADFRTVLRQYSINLSEEEFFHILEYYDKTLSSKISYNDFLRAFL  1500
1501  Q                                                   1501

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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