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

NucPred

Fetching Q91YM2 from www.uniprot.org...

The NucPred score for your sequence is 0.97 (see score help below)

   1  MMMARKQDVRIPTYNISVVGLSGTEKEKGQCGIGKSCLCNRFVRPSADEF    50
  51  HLDHTSVLSTSDFGGRVVNNDHFLYWGEVSRSLEDCVECKMHIVEQTEFI   100
 101  DDQTFQPHRSTALQPYIKRAAATKLASAEKLMYFCTDQLGLEQDFEQKQM   150
 151  PDGKLLVDGFLLGIDVSRGMNRNFDDQLKFVSNLYNQLAKTKKPIVVVLT   200
 201  KCDEGVERYIRDAHTFALSKKNLQVVETSARSNVNVDLAFSTLVQLIDKS   250
 251  RGKTKIIPYFEALKQQSQQIATAKDKYEWLVSRIVKNHNENWPSVSRKMQ   300
 301  ASPEYQDYVYLEGTQKAKKLFLQHIHRLKHEHIERRRKLYLAALPLAFEA   350
 351  LIPNLDEVDHLSCIKAKKLLETKPEFLKWFVVLEETPWDATSHIDNMENE   400
 401  RIPFDLMDTVPAEQLYETHLEKLRNERKRAEMRRAFKENLETSPFITPGK   450
 451  PWEEARSFIMNEDFYQWLEESVYMDIYGKHQKQIIDRAKEEFQELLLEYS   500
 501  ELFYELELDAKPSKEKMGVIQDVLGEEQRFKALQKLQAERDALILKHIHF   550
 551  VYHPTKETCPSCPACVDAKIEHLISSRFIRPSDRNQKNSLSDLNIDRINL   600
 601  VILGKDGLARELANEIRALCTNDDKYVIDGKMYELSLRPIEGNVRLPVNS   650
 651  FQTPTFQPHGCLCLYNSKESLSYVVESIEKSRESTLGRRDNHLVHLPLTL   700
 701  ILVNKRGDTSGETLHSLIQQGQQIASKLQCVFLDPASAGIGYGRNINEKQ   750
 751  ISQVLKGLLDSKRNLNLVSSTASIKDLADVDLRIVMCLMCGDPFSADDVL   800
 801  SPVLQSQTCKSSHCGSSNSVLLELPIGLHKKRIELSVLSYHSSFSIRKSR   850
 851  LVHGYIVFYSAKRKASLAMLRAFLCEVQDIIPIQLVALTDGAIDVLDNDL   900
 901  SREQLTEGEEIAQEIDGRFTSIPCSQPQHKLELFHPFFKDVVEKKNIIEA   950
 951  THMYDNVAEACSTTEEVFNSPRAGSPLCNSNLQDSEEDVEPPSYHLFRED  1000
1001  ATLPSLSKDHSKFSMELEGNDGLSFIMSNFESKLNNKVPPPVKPKPPVHF  1050
1051  DITKDLSYLDQGHREGQRKSMSSSPWMPQDGFDPSDYAEPMDAVVKPRNE  1100
1101  EENIYSVPHDSTQGKIITIRNINKAQSNGSGNGSDSEMDTSSLERGRKVS  1150
1151  AVSKPVLYRTRCTRLGRFASYRTSFSVGSDDELGPIRKKEEDQASQGYKG  1200
1201  DNAVIPYETDEDPRRRNILRSLRRNTKKPKPKPRPSITKATWESNYFGVP  1250
1251  LTTVVTPEKPIPIFIERCIEYIEATGLSTEGIYRVSGNKSEMESLQRQFD  1300
1301  QDHNLDLAEKDFTVNTVAGAMKSFFSELPDPLVPYSMQIDLVEAHKINDR  1350
1351  EQKLHALKEVLKKFPKENHEVFKYVISHLNKVSHNNKVNLMTSENLSICF  1400
1401  WPTLMRPDFSSMDALTATRSYQTIIELFIQQCPFFFYNRPISEPPGAAPG  1450
1451  SPSAMAPTVPFLTSTPATSQPSPPQSPPPTPQSPMQPLLSSQLQAEHTL   1499

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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