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

NucPred

Fetching Q24270 from www.uniprot.org...

The NucPred score for your sequence is 0.76 (see score help below)

   1  MNTGDRKEQASLTPQQQQSPQQPEQQQPITRHDALDSSSANNKLNHKHNN    50
  51  DKDKDTTSDKNWEAGRDLLPASVVIVDESCASKSQKQPIEPSIVSRSGAT   100
 101  SSSQRRRQLQFQRQKEAKLYDRGDGDRDREREREASTSTSTSTSASTTTT   150
 151  NTVMGGGELVNCIAYDDNTLVIERKPSPSSPSTSRRYLKAETPTRGSRKY   200
 201  NRKSSAKSDLEVVVVKPEHHHQHRSPTITLPVPANPLTTSASAGSSPTGA   250
 251  GLAAGLGTASGTVLQQSCSALDPPEDSNQPSGTRRRPTSTELALSNVTSQ   300
 301  IVNNATYKLDFKQRRHKSNNGGSESGSLTGIATGPATSPAGPTGPTSSSG   350
 351  KRRKSSCTSCGGGGISAPPPRLTPEEAWQLQPQNSVTSAGSTNSSFSSGG   400
 401  GRDDNSSYSAVGGDSSSSNSCNCDITGDNSTLHGFGVGDVCSFIADCDDN   450
 451  SEDDDGDPNNQDLSSQTLRTAAIVAAVAAAAKEQAQEQSLADCESFSDRR   500
 501  QDADEDVRIIQDCCGGNNDSLEDVGEVDDNADVVVRKNSRNRPSIRRTCR   550
 551  ITEEDDDEDENADYGDFDREDQELDDEEPEGTTIDIDEQEQQHDQGDSAE   600
 601  EEDDDEDVDEYFEEEEDDTQAFSPFYSSSAELIDNFGGGAGKFFNIMDFE   650
 651  RGASGEGGFSPNGNGGPGSGDVSRTARYDSGEGDLGGGNNIMGIDSMGIA   700
 701  NIPETMNGTTIGPSGAGGQKGGAAAGAAGQKRQQRRGKPQPDRPQRALFC   750
 751  LSVKNPLRALCIRIVEWKPFEFLILLTIFANCIALAVYTPYPGSDSNVTN   800
 801  QTLEKVEYVFLVIFTAECVMKILAYGFVLHNGAYLRNGWNLLDFTIVVIG   850
 851  AISTALSQLMKDAFDVKALRAFRVLRPLRLVSGVPSLQVVLNSILKAMVP   900
 901  LFHIALLVLFVIIIYAIIGLELFSGKLHKACRDEITGEYEENIRPCGVGY   950
 951  QCPPGYKCYGGWDGPNDGITNFDNFGLAMLTVFQCVTLEGWTDVLYSIQD  1000
1001  AMGSDWQWMYFISMVILGAFFVMNLILGVLSGEFSKERNKAKNRGDFQKL  1050
1051  REKQQIEEDLRGYLDWITQAEDIEPDAVGGLISDGKGKQPNEMDSTENLG  1100
1101  EEMPEVQMTESRWRKMKKDFDRVNRRMRRACRKAVKSQAFYWLIIVLVFL  1150
1151  NTGVLATEHYGQLDWLDNFQEYTNVFFIGLFTCEMLLKMYSLGFQGYFVS  1200
1201  LFNRFDCFVVIGSITETLLTNTGMMPPLGVSVLRCVRLLRVFKVTKYWRS  1250
1251  LSNLVASLLNSIQSIASLLLLLFLFIVIFALLGMQVFGGKFNFDGKEEKY  1300
1301  RMNFDCFWQALLTVFQIMTGEDWNAVMYVGINAYGGVSSYGALACIYFII  1350
1351  LFICGNYILLNVFLAIAVDNLADADSLSEVEKEEEPHDESAQKKSHSPTP  1400
1401  TIDGMDDHLSIDIDMEQQELDDEDKMDHETLSDEEVREMCEEEEEVDEEG  1450
1451  MITARPRRMSEVNTATKILPIPPGTSFFLFSQTNRFRVFCHWLCNHSNFG  1500
1501  NIILCCIMFSSAMLAAENPLRANDDLNKVLNKFDYFFTAVFTIELILKLI  1550
1551  SYGFVLHDGAFCRSAFNLLDLLVVCVSLISLVSSSNAISVVKILRVLRVL  1600
1601  RPLRAINRAKGLKHVVQCVIVAVKTIGNIVLVTCLLQFMFAVIGVQLFKG  1650
1651  KFFKCTDGSKMTQDECYGTYLVYDDGDVHKPRLREREWSNNRFHFDDVAK  1700
1701  GMLTLFTVSTFEGWPGLLYVSIDSNKENGGPIHNFRPIVAAYYIIYIIII  1750
1751  AFFMVNIFVGFVIVTFQNEGEQEYKNCDLDKNQRNCIEFALKAKPVRRYI  1800
1801  PKHGIQYKVWWFVTSSSFEYTIFILIMINTVTLAMKFYNQPLWYTELLDA  1850
1851  LNMIFTAVFALEFVFKLAAFRFKNYFGDAWNVFDFIIVLGSFIDIVYSEI  1900
1901  KSKDTSQIAECDIVEGCKSTKKSAGSNLISINFFRLFRVMRLVKLLSKGE  1950
1951  GIRTLLWTFIKSFQALPYVALLIVLLFFIYAVVGMQVFGKIALDGGNAIT  2000
2001  ANNNFQTFQQAVLVLFRSATGEAWQEIMMSCSAQPDVKCDMNSDTPGEPC  2050
2051  GSSIAYPYFISFYVLCSFLIINLFVAVIMDNFDYLTRDWSILGPHHLDEF  2100
2101  IRLWSEYDPDAKGRIKHLDVVTLLRKISPPLGFGKLCPHRMACKRLVSMN  2150
2151  MPLNSDGTVLFNATLFAVVRTSLSIKTDGNIDDANSELRATIKQIWKRTN  2200
2201  PKLLDQVVPPPGNDDEVTVGKFYATYLIQDYFRRFKKRKEQEGKEGHPDS  2250
2251  NTVTLQAGLRTLHEVSPALKRAISGNLDELDQEPEPMHRRHHTLFGSVWS  2300
2301  SIRRHGNGTFRRSAKATASQSNGALAIGGSASAALGVGGSSLVLGSSDPA  2350
2351  GGDYLYDTLNRSVADGVNNITRNIMQARLAAAGKLQDELQGAGSGGELRT  2400
2401  FGESISMRPLAKNGGGAATVAGTLPPEANAINYDNRNRGILLHPYNNVYA  2450
2451  PNGALPGHERMIQSTPASPYDQRRLPTSSDMNGLAESLIGGVLAAEGLGK  2500
2501  YCDSEFVGTAAREMREALDMTPEEMNLAAHQILSNEHSLSLIGSSNGSIF  2550
2551  GGSAGGLGGAGSGGVGGLGGSSSIRNAFGGSGSGPSSLSPQHQPYSGTLN  2600
2601  SPPIPDNRLRRVATVTTTNNNNKSQVSQNNSNSLNVRANANSQMNMSPTG  2650
2651  QPVQQQSPLRGQGNQTYSS                                 2669

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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