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

NucPred

Fetching Q99KW3 from www.uniprot.org...

The NucPred score for your sequence is 0.88 (see score help below)

   1  MSMEQDTRALLPTQGTAWATASAPVARLQGPQGDSHQACSQEPHSPSSAE    50
  51  APYCDLPRCPPALQNPLRTTTCVGQSVHSLGLGLGQEPQRVWSPTTALPA   100
 101  EGPAAAPKNRHQDSEGIPYLEGLARSSCTDDNDNKDEDEDPNSNTSSSQD   150
 151  SNTPHDTSNSSSVDWDTTERPGVVPSRNRLTEMIPRRPQEGLRADSARKA   200
 201  TRSPARGDTAGQRKENSGSGGQSAGQHWAKLRSESGYFSLERQRSGQTQA   250
 251  SSGTPPSGPRGTTQASSAQRDVFQAAPAQEAPQTSSLPRNTQRDTQRSTP   300
 301  RTSSPSRVSQRDTPRVMSTQRKNTPLSSPLRATPETLKISAPEDGTHVTP   350
 351  SPCVQDSSLNRTSQRDSSRTPCIQWDNPRASSPNRTTQRDNPRTPCTQRD   400
 401  NPRASSPNRTTQRDNPRTPCTQRDNPRASSPNRTTQRDNPRTPCAQRDNP   450
 451  RAASPNRSTQRDSPRTPCAQRDNPRASSPNRTAQRDNPRTPCAQRDNPRT   500
 501  SCTSQNTPRTPSTQADKTTASCSKWEHLRSACTQRDNPRTFSQGCTQKDN   550
 551  PGPPSPRRATQGSNSRNPSPHRTNKDIPWASFPLRPTQSDSPRTSSPSRT   600
 601  KQNQVPWASISLRPTQGDKPQTSAPTRLAHNDPPQQYSPSLATTSSSSHN   650
 651  PGHSSASRTSSPLHAAPRGAPQTSLESSQPPCTVCIGHRDAPRASSPPRY   700
 701  FQYDPFPFFPDPRSSESESPHHEPPYMPPAVCIGHRDAPRATSPPRHTQF   750
 751  DPFPFLPDTSDADNESPQHDPPQFPPPVCIGYRDAPRASSPPRQFPEPSF   800
 801  FQDLPRASTESLVPSTDSMHEPPHIPTPVCIGHRDAPSFSSPPRQAPEPS   850
 851  LFFQDPPGTSMESLAPSIDSLHGCPLLPPQVCIGHRDAPRASSPPRHPPS   900
 901  DIGLLAPSPPPGSSGSRGSAPPGETRHNLEREEYTMLADLPPPRRLAQRG   950
 951  PEPQAQGSNEGRTRSPGRAEVERLFGQERRKSEAPGAFQTRDEGRSQRPS  1000
1001  QAQSQLRRQSSPAPSRQVTKPSAKQAEPTRQSRTGPPHPKSPDKRPEGDR  1050
1051  QLQRTSPPARTPARPPERKAQIERHLESGHTGPRQSLGGWQSQERLSGPQ  1100
1101  SPNRHPEKSWGSQKEGPSLGGWPELEGPSLEGIWRGPPQEHREQWGHSEA  1150
1151  WEEPPSNGIQGAPPRGQGRLQELSRPHQPTPSSENSWAGPAECSCALQPE  1200
1201  ASTAVGWRAEGTSPHQRSAERPPDLDWRDLLGLLRAPEDGAWTRLPRLDW  1250
1251  EGLLELLQARLPQKDPARHWHDPAKASGPEQGSSGTEDTLKTEPQTQPEG  1300
1301  RAKATLANGHRPGQQSESPAQLPSPACTSTQWPTTKVTSGPETSPLAALE  1350
1351  QIDHLESHSPPDLEFQPEEPEASEPSRGEDSRAVQKQADSADKRPAEGKA  1400
1401  GSPLKGRLVTSWRMPGDRPALFNPYLLSLGVLRWQRPDLLNFKKGWMSIL  1450
1451  DEPGEWKKHWFVLTDSSLKYYRDSTAEEADELDGEIDLRSCTDVTEYAVQ  1500
1501  RNYGFQIHTKDAVYTLSAMTSGIRRNWIEALRKTVRPTSAPDVTKLSDCN  1550
1551  KENTLHGYGTQKSSLKIGEQRTGSEVIGRGGPRKADGPRPSLDYVELSPL  1600
1601  APSSPQRMRTLSRSTPERPTKQEDLERDLAQRSEERRKWFESTDGRTPET  1650
1651  PSGDGSRRGLGAPLTDDQQSRLSEEIEKKWQELEKLPLRENKRVPLTALL  1700
1701  NQAHNDRRGPTSDSHEALEKEVQSLRAQLEAWRLRGEAPQNAPRLQEDSH  1750
1751  IPPGYISQEACERSLAEMESSHQQVMEQLQRHHERELQRLQQEKEWLLAE  1800
1801  ETAATASAIEAMKKAYQEELSRELSKTRSLQQGPESLRKQHQLDMEALKQ  1850
1851  ELQVLSERYSQKCLEIGALTRQAEEREHTLRRCQQEGQELLRHNQELHSH  1900
1901  LSEEIDRLRSFIASQGTGNSCGRSNERSSCELEVLLRVKENELQYLKKEV  1950
1951  QCLRDELQVIQKDKRFTGKYQDVYVELNHIKTRSEREIEQLKEHLRLAMA  2000
2001  ALQEKEAVRNSLAE                                      2014

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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