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

NucPred

Fetching Q80TR1 from www.uniprot.org...

The NucPred score for your sequence is 0.23 (see score help below)

   1  MARLAAALWSLCVTTVLVTSATQGLSRAGLPFGLMRRELACEGYPIELRC    50
  51  PGSDVIMVENANYGRTDDKICDADPFQMENVQCYLPDAFKIMSQRCNNRT   100
 101  QCVVVAGSDAFPDPCPGTYKYLEVQYDCVPYIFVCPGTLQKVLEPTSTHE   150
 151  SEHQSGAWCKDPLQAGDRIYVMPWIPYRTDTLTEYASWEDYVAARHTTTY   200
 201  RLPNRVDGTGFVVYDGAVFYNKERTRNIVKYDLRTRIKSGETVINTANYH   250
 251  DTSPYRWGGKTDIDLAVDENGLWVIYATEGNNGRLVVSQLNPYTLRFEGT   300
 301  WETGYDKRSASNAFMVCGVLYVLRSVYVDDDSEAAGNRVDYAFNTNANRE   350
 351  EPVSLAFPNPYQFVSSVDYNPRDNQLYVWNNYFVVRYSLEFGPPDPSAGP   400
 401  ATSPPLSTTTTARPTPLTSTASPAATTPLRRAPLTTHPVGAINQLGPDLP   450
 451  PATAPAPSTRRPPAPNLHVSPELFCEPREVRRVQWPATQQGMLVERPCPK   500
 501  GTRGIASFQCLPALGLWNPRGPDLSNCTSPWVNQVAQKIKSGENAANIAS   550
 551  ELARHTRGSIYAGDVSSSVKLMEQLLDILDAQLQALRPIERESAGKNYNK   600
 601  MHKRERTCKDYIKAVVETVDNLLRPEALESWKDMNATEQVHTATMLLDVL   650
 651  EEGAFLLADNVREPARFLAAKQNVVLEVTVLNTEGQVQELVFPQEYPSEN   700
 701  SIQLSANTIKQNSRNGVVKVVFILYNNLGLFLSTENATVKLAGEAGTGGP   750
 751  GGASLVVNSQVIAASINKESSRVFLMDPVIFTVAHLEAKNHFNANCSFWN   800
 801  YSERSMLGYWSTQGCRLVESNKTHTTCACSHLTNFAVLMAHREIYQGRIN   850
 851  ELLLSVITWVGIVISLVCLAICISTFCFLRGLQTDRNTIHKNLCINLFLA   900
 901  ELLFLVGIDKTQYEVACPIFAGLLHYFFLAAFSWLCLEGVHLYLLLVEVF   950
 951  ESEYSRTKYYYLGGYCFPALVVGIAAAIDYRSYGTEKACWLRVDNYFIWS  1000
1001  FIGPVSFVIVVNLVFLMVTLHKMIRSSSVLKPDSSRLDNIKSWALGAIAL  1050
1051  LFLLGLTWAFGLLFINKESVVMAYLFTTFNAFQGVFIFVFHCALQKKVHK  1100
1101  EYSKCLRHSYCCIRSPPGGTHGSLKTSAMRSNTRYYTGTQSRIRRMWNDT  1150
1151  VRKQTESSFMAGDINSTPTLNRGTMGNHLLTNPVLQPRGGTSPYNTLIAE  1200
1201  SVGFNPSSPPVFNSPGSYREPKHPLGGREACGMDTLPLNGNFNNSYSLRS  1250
1251  GDFPPGDGGPEPPRGRNLADAAAFEKMIISELVHNNLRGASGGAKGPPPE  1300
1301  PPVPPVPGVSEDEAGGPGSADRAEIELLYKALEEPLLLPRAQSVLYQSDL  1350
1351  DESESCTAEDGATSRPLSSPPGRDSLYASGANLRDSPSYPDSSPEGPNEA  1400
1401  LPPPPPAPPGPPEIYYTSRPPALVARNPLQGYYQVRRPSHEGYLAAPSLE  1450
1451  GPGPDGDGQMQLVTSL                                    1466

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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