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

NucPred

Fetching Q9Z0U5 from www.uniprot.org...

The NucPred score for your sequence is 0.21 (see score help below)

   1  MDPPQLLFYVNGQKVVENNVDPEMMLLPYLRKNLRLTGTKYGCGGGGCGA    50
  51  CTVMISRYNPSTKSIRHHPVNACLTPICSLYGTAVTTVEGIGNTRTRLHP   100
 101  VQERIAKCHSTQCGFCTPGMVMSMYALLRNHPEPSLDQLTDALGGNLCRC   150
 151  TGYRPIIDACKTFCRASGCCESKENGVCCLDQGINGSAEFQEGDETSPEL   200
 201  FSEKEFQPLDPTQELIFPPELMRIAEKQPPKTRVFYSNRMTWISPVTLEE   250
 251  LVEAKFKYPGAPIVMGYTSVGPEVKFKGVFHPIIISPDRIEELSIINQTG   300
 301  DGLTLGAGLSLDQVKDILTDVVQKLPEETTQTYRALLKHLRTLAGSQIRN   350
 351  MASLGGHIVSRHLDSDLNPLLAVGNCTLNLLSKDGKRQIPLSEQFLRKCP   400
 401  DSDLKPQEVLVSVNIPCSRKWEFVSAFRQAQRQQNALAIVNSGMRVLFRE   450
 451  GGGVIKELSILYGGVGPTTIGAKNSCQKLIGRPWNEEMLDTACRLVLDEV   500
 501  TLAGSAPGGKVEFKRTLIISFLFKFYLEVLQGLKREDPGHYPSLTNNYES   550
 551  ALEDLHSKHHWRTLTHQNVDSMQLPQDPIGRPIMHLSGIKHATGEAIYCD   600
 601  DMPAVDRELFLTFVTSSRAHAKIVSIDLSEALSLPGVVDIITADHLQDAT   650
 651  TFGTETLLATDKVHCVGQLVCAVIADSETRAKQAAKHVKVVYRDLEPLIL   700
 701  TIEEAIQHKSFFESERKLECGNVDEAFKIADQILEGEIHIGGQEHFYMET   750
 751  QSMLVVPKGEDGEIDIYVSTQFPKHIQDIVAATLKLSVNKVMCHVRRVGG   800
 801  AFGGKVGKTSIMAAITAFAASKHGRAVRCTLERGEDMLITGGRHPYLGKY   850
 851  KVGFMRDGRIVALDVEHYCNGGSSLDESLWVIEMGLLKMDNAYKFPNLRC   900
 901  RGWACRTNLPSHTALRGFGFPQAGLVTEACVTEVAIRCGLSPEQVRTINM   950
 951  YKQIDNTHYKQEFSAKTLFECWRECMAKCSYSERKTAVGKFNAENSWKKR  1000
1001  GMAVIPLKFPVGVGSVAMGQAAALVHIYLDGSALVSHGGIEMGQGVHTKM  1050
1051  IQVVSRELKMPMSSVHLRGTSTETVPNTNASGGSVVADLNGLAVKDACQT  1100
1101  LLKRLEPIISKNPQGTWKDWAQTAFDQSVSLSAVGYFRGYESNINWEKGE  1150
1151  GHPFEYFVYGAACSEVEIDCLTGDHKNIRTDIVMDVGHSINPALDIGQVE  1200
1201  GAFIQGMGLYTIEELSYSPQGILYSRGPNQYKIPAICDIPTEMHISFLPP  1250
1251  SEHSNTLYSSKGLGESGVFLGCSVFFAIHDAVRAARQERGISGPWKLTSP  1300
1301  LTPEKIRMACEDKFTKMIPRDEPGSYVPWNIPV                   1333

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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