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

NucPred

Fetching O54754 from www.uniprot.org...

The NucPred score for your sequence is 0.19 (see score help below)

   1  MDPIQLLFYVNGQKVVEKNVDPEMMLLPYLRKNLRLTGTKYGCGGGGCGA    50
  51  CTVMISRYNPSTKAIRHHPVNACLTPICSLHGTAVTTVEGLGNTRTRLHP   100
 101  IQERIAKCHGTQCGFCTPGMVMSMYALLRNHPEPTLDQLTDALGGNLCRC   150
 151  TGYRPIIDACKTFCKASACCQSKENGVCCLDQEINGLAESQEEDKTSPEL   200
 201  FSEEEFLPLDPTQELIFPPELMRIAEKQPPKTRVFYGERVTWISPVTLKE   250
 251  LVEAKFKYPQAPIVMGYTSVGPEVKFKGVFHPIIISPDRIEELGVISQAR   300
 301  DGLTLGAGLSLDQVKDILADIVQKLPEEKTQTYRALLKHLRTLAGSQIRN   350
 351  MASLGGHIVSRHLDSDLNPLLAVGNCTLNLLSKDGERRIPLSEEFLRKCP   400
 401  EADLKPQEVLVSVNIPWSRKWEFVSAFRQAQRQQNALAIVNSGMRVLFRE   450
 451  GGGVIEELSILYGGVGSTIISAKNSCQRLIGRPWNEGMLDTRCRLVLDEV   500
 501  TLAASAPGGKVEFKRTLIISFLFKFYLEVSQGLKREDPGHSPSLAGNHES   550
 551  ALDDLHSKHPWRTLTHQNVDPAQLPQDPIGRPIMHLSGIKHATGEAIYCD   600
 601  DMPAVDRELFLTFVTSSRAHAKIVSIDLSEALSLPGVVDIITADHLQEAN   650
 651  TFGTETFLATDEVHCVGHLVCAVIADSETRAKQAAKQVKVVYQDLAPLIL   700
 701  TIEEAIQHKSFFKSERKLECGNVDEAFKIVDQILEGEIHIGGQEHFYMET   750
 751  QSMLVVPKGEDGEIDIYVSTQFPKYIQDIVAATLKLSANKVMCHVRRVGG   800
 801  AFGGKVGKTSILAAITAFAASKHGRAVRCILERGEDMLITGGRHPYLGKY   850
 851  KAGFMNEGRILALDVEHYCNGGCSLDESLWVIEMGLLKLDNAYKFPNLRC   900
 901  RGWACRTNLPSNTALRGFGFPQAGLVTEACITEVAIKCGLSPEQVRTINM   950
 951  YKHVDTTHYKQEFSAKALSECWRECMAKCSYFERKAAIGKFNAENSWKKR  1000
1001  GMAVIPLKFPVGIGSVAMGQAAALVHIYLDGSALVSHGGIEMGQGVHTKM  1050
1051  IQVVSRELRMPMSSVHLRGTSTETVPNTNASGGSVVADLNGLAVKDACQT  1100
1101  LLKRLEPIISKNPQGTWKDWAQTAFDQSISLSAVGYFRGYESNIDWEKGE  1150
1151  GHPFEYFVFGAACSEVEINCLTGDHKNIRTNIVMDVGHSINPALDIGQVE  1200
1201  GAFIQGMGLYTIEELSYSPQGTLYSRGPNQYKIPAICDIPTEMHISFLPP  1250
1251  SEHSNTLYSSKGLGESGVFLGCSVFFAIHDAVKAARQERGISGPWKLNSP  1300
1301  LTPEKIRMACEDKFTKMIPRDEPGSYVPCNIPV                   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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