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

NucPred

Fetching Q9BZ29 from www.uniprot.org...

The NucPred score for your sequence is 0.92 (see score help below)

   1  MSQPPLLPASAETRKFTRALSKPGTAAELRQSVSEVVRGSVLLAKPKLIE    50
  51  PLDYENVIVQKKTQILNDCLREMLLFPYDDFQTAILRRQGRYICSTVPAK   100
 101  AEEEAQSLFVTECIKTYNSDWHLVNYKYEDYSGEFRQLPNKVVKLDKLPV   150
 151  HVYEVDEEVDKDEDAASLGSQKGGITKHGWLYKGNMNSAISVTMRSFKRR   200
 201  FFHLIQLGDGSYNLNFYKDEKISKEPKGSIFLDSCMGVVQNNKVRRFAFE   250
 251  LKMQDKSSYLLAADSEVEMEEWITILNKILQLNFEAAMQEKRNGDSHEDD   300
 301  EQSKLEGSGSGLDSYLPELAKSAREAEIKLKSESRVKLFYLDPDAQKLDF   350
 351  SSAEPEVKSFEEKFGKRILVKCNDLSFNLQCCVAENEEGPTTNVEPFFVT   400
 401  LSLFDIKYNRKISADFHVDLNHFSVRQMLATTSPALMNGSGQSPSVLKGI   450
 451  LHEAAMQYPKQGIFSVTCPHPDIFLVARIEKVLQGSITHCAEPYMKSSDS   500
 501  SKVAQKVLKNAKQACQRLGQYRMPFAWAARTLFKDASGNLDKNARFSAIY   550
 551  RQDSNKLSNDDMLKLLADFRKPEKMAKLPVILGNLDITIDNVSSDFPNYV   600
 601  NSSYIPTKQFETCSKTPITFEVEEFVPCIPKHTQPYTIYTNHLYVYPKYL   650
 651  KYDSQKSFAKARNIAICIEFKDSDEEDSQPLKCIYGRPGGPVFTRSAFAA   700
 701  VLHHHQNPEFYDEIKIELPTQLHEKHHLLLTFFHVSCDNSSKGSTKKRDV   750
 751  VETQVGYSWLPLLKDGRVVTSEQHIPVSANLPSGYLGYQELGMGRHYGPE   800
 801  IKWVDGGKPLLKISTHLVSTVYTQDQHLHNFFQYCQKTESGAQALGNELV   850
 851  KYLKSLHAMEGHVMIAFLPTILNQLFRVLTRATQEEVAVNVTRVIIHVVA   900
 901  QCHEEGLESHLRSYVKYAYKAEPYVASEYKTVHEELTKSMTTILKPSADF   950
 951  LTSNKLLKYSWFFFDVLIKSMAQHLIENSKVKLLRNQRFPASYHHAVETV  1000
1001  VNMLMPHITQKFRDNPEASKNANHSLAVFIKRCFTFMDRGFVFKQINNYI  1050
1051  SCFAPGDPKTLFEYKFEFLRVVCNHEHYIPLNLPMPFGKGRIQRYQDLQL  1100
1101  DYSLTDEFCRNHFLVGLLLREVGTALQEFREVRLIAISVLKNLLIKHSFD  1150
1151  DRYASRSHQARIATLYLPLFGLLIENVQRINVRDVSPFPVNAGMTVKDES  1200
1201  LALPAVNPLVTPQKGSTLDNSLHKDLLGAISGIASPYTTSTPNINSVRNA  1250
1251  DSRGSLISTDSGNSLPERNSEKSNSLDKHQQSSTLGNSVVRCDKLDQSEI  1300
1301  KSLLMCFLYILKSMSDDALFTYWNKASTSELMDFFTISEVCLHQFQYMGK  1350
1351  RYIARTGMMHARLQQLGSLDNSLTFNHSYGHSDADVLHQSLLEANIATEV  1400
1401  CLTALDTLSLFTLAFKNQLLADHGHNPLMKKVFDVYLCFLQKHQSETALK  1450
1451  NVFTALRSLIYKFPSTFYEGRADMCAALCYEILKCCNSKLSSIRTEASQL  1500
1501  LYFLMRNNFDYTGKKSFVRTHLQVIISVSQLIADVVGIGGTRFQQSLSII  1550
1551  NNCANSDRLIKHTSFSSDVKDLTKRIRTVLMATAQMKEHENDPEMLVDLQ  1600
1601  YSLAKSYASTPELRKTWLDSMARIHVKNGDLSEAAMCYVHVTALVAEYLT  1650
1651  RKEAVQWEPPLLPHSHSACLRRSRGGVFRQGCTAFRVITPNIDEEASMME  1700
1701  DVGMQDVHFNEDVLMELLEQCADGLWKAERYELIADIYKLIIPIYEKRRD  1750
1751  FERLAHLYDTLHRAYSKVTEVMHSGRRLLGTYFRVAFFGQAAQYQFTDSE  1800
1801  TDVEGFFEDEDGKEYIYKEPKLTPLSEISQRLLKLYSDKFGSENVKMIQD  1850
1851  SGKVNPKDLDSKYAYIQVTHVIPFFDEKELQERKTEFERSHNIRRFMFEM  1900
1901  PFTQTGKRQGGVEEQCKRRTILTAIHCFPYVKKRIPVMYQHHTDLNPIEV  1950
1951  AIDEMSKKVAELRQLCSSAEVDMIKLQLKLQGSVSVQVNAGPLAYARAFL  2000
2001  DDTNTKRYPDNKVKLLKEVFRQFVEACGQALAVNERLIKEDQLEYQEEMK  2050
2051  ANYREMAKELSEIMHEQLG                                 2069

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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