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

NucPred

Fetching Q8NI27 from www.uniprot.org...

The NucPred score for your sequence is 0.98 (see score help below)

   1  MAAAAVVVPAEWIKNWEKSGRGEFLHLCRILSENKSHDSSTYRDFQQALY    50
  51  ELSYHVIKGNLKHEQASNVLSDISEFREDMPSILADVFCILDIETNCLEE   100
 101  KSKRDYFTQLVLACLYLVSDTVLKERLDPETLESLGLIKQSQQFNQKSVK   150
 151  IKTKLFYKQQKFNLLREENEGYAKLIAELGQDLSGSITSDLILENIKSLI   200
 201  GCFNLDPNRVLDVILEVFECRPEHDDFFISLLESYMSMCEPQTLCHILGF   250
 251  KFKFYQEPNGETPSSLYRVAAVLLQFNLIDLDDLYVHLLPADNCIMDEHK   300
 301  REIAEAKQIVRKLTMVVLSSEKMDEREKEKEKEEEKVEKPPDNQKLGLLE   350
 351  ALLKIGDWQHAQNIMDQMPPYYAASHKLIALAICKLIHITIEPLYRRVGV   400
 401  PKGAKGSPVNALQNKRAPKQAESFEDLRRDVFNMFCYLGPHLSHDPILFA   450
 451  KVVRIGKSFMKEFQSDGSKQEDKEKTEVILSCLLSITDQVLLPSLSLMDC   500
 501  NACMSEELWGMFKTFPYQHRYRLYGQWKNETYNSHPLLVKVKAQTIDRAK   550
 551  YIMKRLTKENVKPSGRQIGKLSHSNPTILFDYILSQIQKYDNLITPVVDS   600
 601  LKYLTSLNYDVLAYCIIEALANPEKERMKHDDTTISSWLQSLASFCGAVF   650
 651  RKYPIDLAGLLQYVANQLKAGKSFDLLILKEVVQKMAGIEITEEMTMEQL   700
 701  EAMTGGEQLKAEGGYFGQIRNTKKSSQRLKDALLDHDLALPLCLLMAQQR   750
 751  NGVIFQEGGEKHLKLVGKLYDQCHDTLVQFGGFLASNLSTEDYIKRVPSI   800
 801  DVLCNEFHTPHDAAFFLSRPMYAHHISSKYDELKKSEKGSKQQHKVHKYI   850
 851  TSCEMVMAPVHEAVVSLHVSKVWDDISPQFYATFWSLTMYDLAVPHTSYE   900
 901  REVNKLKVQMKAIDDNQEMPPNKKKKEKERCTALQDKLLEEEKKQMEHVQ   950
 951  RVLQRLKLEKDNWLLAKSTKNETITKFLQLCIFPRCIFSAIDAVYCARFV  1000
1001  ELVHQQKTPNFSTLLCYDRVFSDIIYTVASCTENEASRYGRFLCCMLETV  1050
1051  TRWHSDRATYEKECGNYPGFLTILRATGFDGGNKADQLDYENFRHVVHKW  1100
1101  HYKLTKASVHCLETGEYTHIRNILIVLTKILPWYPKVLNLGQALERRVHK  1150
1151  ICQEEKEKRPDLYALAMGYSGQLKSRKSYMIPENEFHHKDPPPRNAVASV  1200
1201  QNGPGGGPSSSSIGSASKSDESSTEETDKSRERSQCGVKAVNKASSTTPK  1250
1251  GNSSNGNSGSNSNKAVKENDKEKGKEKEKEKKEKTPATTPEARVLGKDGK  1300
1301  EKPKEERPNKDEKARETKERTPKSDKEKEKFKKEEKAKDEKFKTTVPNAE  1350
1351  SKSTQEREREKEPSRERDIAKEMKSKENVKGGEKTPVSGSLKSPVPRSDI  1400
1401  PEPEREQKRRKIDTHPSPSHSSTVKDSLIELKESSAKLYINHTPPPLSKS  1450
1451  KEREMDKKDLDKSRERSREREKKDEKDRKERKRDHSNNDREVPPDLTKRR  1500
1501  KEENGTMGVSKHKSESPCESPYPNEKDKEKNKSKSSGKEKGSDSFKSEKM  1550
1551  DKISSGGKKESRHDKEKIEKKEKRDSSGGKEEKKHHKSSDKHR         1593

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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