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

NucPred

Fetching Q8BIK4 from www.uniprot.org...

The NucPred score for your sequence is 0.91 (see score help below)

   1  MGCTTSVILFKGIRTVFERNCAYMCKQPGESNALEYTAYNWSKEDSELSI    50
  51  AFCLAKPKLIEPLDYENVIVQKKTQILNDCLREMLLFPYDDFQTAILRRQ   100
 101  GRYLRSTVPANAEEEAQSLFVTECIKTYNSDWHLVTYKYEDYSGEFRQLP   150
 151  NKVPKLDKLPVHVYEVDEEADKDEDAASLGSQKGGITKHGWLYKGNMNSA   200
 201  ISVTMRSFKRRFFHLIQLGDGSYNLNFYKDEKISKEPKGSIFLDSCMGVI   250
 251  QNNRVRRFAFELKMQDKSSYLLAADSEAEMEEWVTVLNKILQLNFEAAMQ   300
 301  EKRNGDPHEDDEQSKLEGSGSGLDSYLPELAKSTREAEIKLKSESRVKLF   350
 351  YLDPDTQKLDFSSAEPEVKPFEEKFGKRILVKCNDLSFNLQCCVAENEEG   400
 401  PTTNVEPFFVTLSLFDIKYNRKISADFHVDLNHFSVRQMLAPTSPALMNG   450
 451  GQSPPAFQDALHTAMQYPKQGIFSVTCPHPDIFLVARIEKVLQGSITHCA   500
 501  EPYMRSSDSSKVAQKVLKNAKQACQRLGQYRMPFAWAARTLFKDTSGNLD   550
 551  KNARFSAIYRQDSNKLSNDDMLKLLADFRKPEKMAKLPVILGNLDITIDS   600
 601  VSCDFPNYLNSSYIPMRQFETCSKSPITFEVEEFVPCIPKHTQPYTVYSN   650
 651  HLYVYPKYLKYDSQKSFAKARNIAICIEFKDSDEEDSQPLKCIYGRPGGP   700
 701  VFTRSALAAVLHHQQNPEFYDEIKIELPAQLHERHHLLFTFFHVSCDNST   750
 751  KGSTKKKDAVETQVGFSWLPLLKDGRVLTSEQHIPVSANLPSGYLGYQEL   800
 801  GMGRHYGPEVKWVEGGKPLLKISTHLVSTVYTQDQHLHNFFQYCQKTESG   850
 851  AQASGSELVKYLKSLHAMEGHVMIAFLPTILNQLFRVLTRATQEEVAVNV   900
 901  TRVIIHVVAQCHEEGLESHLRSYVKFAYKAEPYVASEYKTVHEELTKSMT   950
 951  TILKPSADFLTSNKLLKYSWFFFDVLIKSMAQHLIENNKVKLLRNQRFPA  1000
1001  SYHHAVETVVNMLMPHITQKFRDNPEASKNANHSLAVFIKRCFTFMDRGF  1050
1051  VFKQINNYISCFAPGDPKTLFEYKFEFLRVVCNHEHYIPLNLPMPFGKGR  1100
1101  IQRYQDLQLDYSLTDEFCRNHFLVGLLLREVGTALQEFREVRVIAISMLK  1150
1151  NLLIKHSFDDRYNSRSHQARIATLYLPLFGLLIENVQRINVRDVSPFPVN  1200
1201  PGSIVKDEALAVPAGNPLMTPQKGNTLDHSLHKDLLGAISGIASPYTAST  1250
1251  PNINSVRNADSRGSLISTDSGNSLPDRNPEKSNSLDKQQQSGMLGNSVVR  1300
1301  CDKLDQSEIKSLLMCFLYVLKSMSDDALFTYWNKASTAELMDFFTISEVC  1350
1351  LHQFQYMGKRYIARTGMMHARLQQLGSLDNSVTFNHSYGHSEADVVHQSL  1400
1401  LEANIATEVCLTALDTLSLFTLAFKNQLLADHGHNPLMKKVFDVYLCFLQ  1450
1451  KHQSEMALKNVFTALRSLIYKFPSAFYEGRADMCASLCYEVLKCCNSKLS  1500
1501  SIRTEASQLLYFLMRNNFDYTGKKSFVRTHLQVIISVSQLIADVVGIGGT  1550
1551  RFQQSLSIINNCANSDRIIKHTSFSSDVKDLTKRIRTVLMATAQMKEHEN  1600
1601  DPEMLVDLQYSLAKSYASTPELRKTWLDSMARIHVKNGDLSEAAMCYVHV  1650
1651  TALVAEYLTRKGMFRQGCTAFRVITPNIDEEASMMEDVGMQDVHFNEDVL  1700
1701  MELLEQCADGLWKAERYELIADIYKLIIPIYEKRRDFERLAHLYDTLHRA  1750
1751  YSKVTEVMHSGRRLLGTYFRVAFFGQAAQYQFTDSETDVEGFFEDEDGKE  1800
1801  YIYKEPKLTPLSEISQRLLKLYSDKFGSENVKMIQDSGKVNPKDLDSKFA  1850
1851  YIQVTHVTPFFDEKELQERRTEFERCHNIRRFMFEMPFTQTGKRQGGVEE  1900
1901  QCKRRTILTAIHCFPYVKKRIPVMYQHHTDLNPIEVAIDEMSKKVAELRQ  1950
1951  LCSSAEVDMIKLQLKLQGSVSVQVNAGPLAYARAFLDDTNTKRYPDNKVK  2000
2001  LLKEVFRQFVEACGQALAVNERLIKEDQLEYQEEMKANYREMAKELSDIM  2050
2051  REQMG                                               2055

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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