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

NucPred

Fetching Q7SIA2 from www.uniprot.org...

The NucPred score for your sequence is 0.38 (see score help below)

   1  MAALCLTVNAGDPPLDALLAVEHVKGDVSVSVEEGKENLLRVSEDVVFTD    50
  51  INSILRYLARVATTSGLYGTNLMEHTEIDHWLEFSATKLSSCAALTSALT   100
 101  ELNHCLSLRTYLVGNSLTLADLCVWATLKGNAAWQEQLEQNKTLVHVKRW   150
 151  FGFLEAQQAFRSVGTKWDVSENKARVVPDKKQDVGKFVELPGAEMGKVTV   200
 201  RFPPEASGYLHIGHAKAALLNQHYQVNFKGKLIMRFDDTNPEKEKEDFEK   250
 251  VILEDVAMLHIKPDQFTYTSDHFETIMKYAEKLIQEGKAYVDDTPAEQMK   300
 301  AEREQRAESKHRQNSVEKNLQMWEEMKKGSPFGQSCCLRAKIDMSSNNGC   350
 351  MRDPTLYRCKIQPHPRTGNKYNVYPTYDFACPIVDSIEGVTHALRTTEYH   400
 401  DRDEQFYWIIEALGIRKPYIWEYSRLNLNNTVLSKRKLTWFVNEGLVDGW   450
 451  DDPRFPTVRGVLRRGMTVEGLKQFIAAQGSSRSVVNMEWDKIWAFNKKVI   500
 501  DPVAPRYVALLKKEVVPVNVPEAQEEMKEVARHPKNPDVGLKPVWYSPKV   550
 551  FIEGADAETFSEGEMVTFINWGNINITKIHKNADGKITSLDAKLNLENKD   600
 601  YKKTTKITWLAETTHALPIPAICVTYEHLITKPVLGKDEDFKQYVNKDSK   650
 651  HEELMLGDPCLKDLKKGDIIQLQRRGFFICDQPYEPVSPYSCKEAPCILI   700
 701  YIPDGHTKEMPTSGSKEKTKAEPLKKETSSAPKEGPVPAVSPCAASEESS   750
 751  VLYNRVAAQGDVVRELKAKKAAKEDVDAAVKQLLALKAEYKQKTGQEYKP   800
 801  GNPPSAAAQSASTKSLPSAGEDRSLYDKIAAQGEVVRKLKAEKAPKAKVT   850
 851  EAVECLLSLKAEYKEKTGKEYVPGQPPASQKSQPSPASKAEPAGPETTEA   900
 901  KALFDRVACQGEVVRKLKAEKASKDQVDPAVQELLQLKAQYKSLTGIEYK   950
 951  PVSATGSEDKDKKKKEKENKSEKQNKPQKQNDGPGKDSSKSQGGGLSSSG  1000
1001  AGEGQGPKKQTRLGLEAKKEENLAEWYSQVITKSEMIEYYDVSGCYILRP  1050
1051  WSYSIWESIKDFFDTEIKKLGVENCYFPIFVSQAALEKEKSHIEDFAPEV  1100
1101  AWVTRSGKTELAEPIAIRPTSETVMYPAYAKWVQSHRDLPIRLNQWCNVV  1150
1151  RWEFKHPQPFLRTREFLWQEGHSAFATFEEAADEVMQILELYARVYEELL  1200
1201  AIPVVRGRKTEKEKFAGGDYTTTVEAFISASGRAIQGATSHHLGQNFSKM  1250
1251  CEIVFEDPKTPGEKQFAFQCSWGLTTRTIGVMIMVHGDNMGLVLPPRVAC  1300
1301  VQVVVIPCGITNALSEEDREALMAKCNEYRKRLLGVNIRVRVDLRDNYSP  1350
1351  GWKFNHWELKGVPVRLEVGPRDMKSCQFVAVRRDTGEKLTIAEKEAESKL  1400
1401  QEILEDIQLNLFTRASEDLKTHMVVSNTLEDFQKVLDSGKIAQIPFCGEI  1450
1451  DCEDWIKKTTARDQDVEPGAPSMGAKSLCIPFTPLCELQPGAMCVCGKNP  1500
1501  AKFYTLFGRSY                                         1511

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.)

Go back to the NucPred Home Page.