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

NucPred

Fetching Q875X3 from www.uniprot.org...

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

   1  MSFEVGTRCWYPSKEQGWIGAEVTKNDLKDGTYFMELTLEDNEVVNVETK    50
  51  DLTNEKDPSLPLLRNPPILESTEDLTTLSYLNEPAVLHAIKQRYSQLNIY   100
 101  TYSGIVLIATNPFDRMDQLYSQDMIQAYSGKRRGEIEPHLFAIAEEAYRL   150
 151  MKNDKQNQTIVVSGESGAGKTVSAKYIMRYFASCDEENSSNMGNLQHTAE   200
 201  MSETEERILATNPIMEAFGNAKTTRNDNSSRFGKYLEILFDKETAIIGAK   250
 251  MRTYLLERSRLVYQPKTERNYHIFYQILAGLPEDVKQELHLTKADDYFYM   300
 301  NQGGEPEIAGIDDVSEYGITIKALTLVGVAPETQQHIFKILAALLHIGNI   350
 351  EIKKTRNDSSLSSDEPNLKIACELLGVDPSNFAKWITKKQIVTRSEKIVS   400
 401  NLNYSQALVARDSVAKFIYSALFDWLVTNINTVLCNPAVLDQIHSFIGVL   450
 451  DIYGFEHFEKNSFEQFCINYANEKLQQEFNQHVFKLEQEEYIKEEIEWSF   500
 501  IEFNDNQPCIDLIENKLGILSLLDEESRLPAGSDESWTQKLYQTLDKPPT   550
 551  NKVFSKPRFGQTKFVVSHYALDVAYDVEGFIEKNRDTVSDGHLEVLKATT   600
 601  NDTLSTILESVEESARKVEEAKKNAASQDQKQLKKPTPIRQVQRKPTLGS   650
 651  MFKLSLIELMQTINSTNVHYIRCIKPNGEKEAWKFDNLMVLSQLRACGVL   700
 701  ETIRISCAGFPSRWTFNEFILRYYILIPPVEWAPIFQKNDLTEQDVINLC   750
 751  KKILAATVQDKEKYQIGNTKIFFKAGMLAYFEKLRSTKMNSAIVLIQKHI   800
 801  RSKYYRKQYMLMKASLSLLGAYSKGTVIRQRVEYELEQHAATLIQTMYRG   850
 851  YSKRSYISGVISSIVKLQSRIREELEQREMQSKYESNAAISIQSRIRAFV   900
 901  PRKAYESKRRDTIVVQSLIRRRIAQRDFKKLKADAKSVHHLKEVSYKLEN   950
 951  KVIQLTQNLAAKVKENRQLSKRLEELQATMVTVSELQDQLEAQKMENQKA  1000
1001  LADQKDGFVLDSKSLKDQLIKANKDVESVKFELATLTAKYTEMEAESKNQ  1050
1051  LDELERTKTLLTESKTQNSDLYSEIKSLKEELAHLQTSIALGTVTTNTNI  1100
1101  VPHTPSRENRMPSGHMRAAEENISPNQLKSIPSDTAADHVSVNGYGMDDD  1150
1151  IINTNTLTQINEELYRLLEGTDVLNNEITEGLLKGFQVPDAGVAIQLSRR  1200
1201  DVVYPARILIIVLSEMWRFGLTKQSESFLAQVLTTIQKVVTTLKGIDLIP  1250
1251  SGAFWLANVRELYSFVVFAQHSILTEESFKKGMNDEEYNEYVSLVTELKE  1300
1301  DFESLSYNIYNIWLKKLQKDLQKKAINAVVVSESLPGFNASESNGFLNKI  1350
1351  FNSGEEYTMDDILTFFNNIFWCMKSFHIENEVFRTVIITLLNYVDTICFN  1400
1401  DLIMKRNFLSWKRGLQLNYNVTRLEEWCKTHGLPDGAQYLQHLIQTAKLL  1450
1451  QLRKYTIEDIDMVRGICSSLSPAQLQKLISQYHVADYESPIPQDILKYVA  1500
1501  DIVKKESTSAHNDIFLHPETGPFNDPFVAVKTRKFDQVEAYIPSWLVLPV  1550
1551  TKRIVDLVAQQVTVPDA                                   1567

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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