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

NucPred

Fetching Q8IUG5 from www.uniprot.org...

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

   1  MAISSRLALWEQKIREEDKSPPPSSPPPLFSVIPGGFIKQLVRGTEKEAK    50
  51  EARQRKQLAVASPEREIPEISISQPNSKSSSGTRSGSQQISQDDQSSSPG   100
 101  SSDILGKESEGSRSPDPEQMTSINGEKAQELGSSATPTKKTVPFKRGVRR   150
 151  GDVLLMVAKLDPDSAKPEKTHPHDAPPCKTSPPATDTGKEKKGETSRTPC   200
 201  GSQASTEILAPKAEKTRTGGLGDPGQGTVALKKGEEGQSIVGKGLGTPKT   250
 251  TELKEAEPQGKDRQGTRPQAQGPGEGVRPGKAEKEGAEPTNTVEKGNVSK   300
 301  DVGSEGKHVRPQIPGRKWGGFLGRRSKWDGPQNKKDKEGVLLSKAEKTGE   350
 351  PQTQMEKTSQVQGELGDDLRMGEKAGELRSTTGKAGESWDKKEKMGQPQG   400
 401  KSGNAGEARSQTEKGCEAPKEVSTMVESPAAPGKGGWPGSRGQEAEEPCS   450
 451  RAGDGAGALETELEGPSQPALEKDAERPRIRKENQDGPAPQEEGKGGQSR   500
 501  DSDQAPEDRWYEAEKVWLAQKDGFTLATVLKPDEGTADLPAGRVRLWIDA   550
 551  DKTITEVDEEHVHRANPPELDQVEDLASLISVNESSVLNTLLQRYKAQLL   600
 601  HTCTGPDLIVLQPRGPSVPSAGKVPKGRRDGLPAHIGSMAQRAYWALLNQ   650
 651  RRDQSIVALGWSGAGKTTCCEQVLEHLVGMAGSVDGRVSVEKIRATFTVL   700
 701  RAFGSVSMAHSRSATRFSMVMSLDFNATGRITAAQLQTMLLEKSRVARQP   750
 751  EGESNFLVFSQMLAGLDLDLRTELNLHQMADSSSFGMGVWSKPEDKQKAA   800
 801  AAFAQLQGAMEMLGISESEQRAVWRVLAAIYHLGAAGACKVGRKQFMRFE   850
 851  WANYAAEALGCEYEELNTATFKHHLRQIIQQMTFGPSRWGLEDEETSSGL   900
 901  KMTGVDCVEGMASGLYQELFAAVVSLINRSFSSHHLSMASIMVVDSPGFQ   950
 951  NPRHQGKDRAATFEELCHNYAHERLQLLFYQRTFVSTLQRYQEEGVPVQF  1000
1001  DLPDPSPGTTVAVVDQNPSQVRLPAGGGAQDARGLFWVLDEEVHVEGSSD  1050
1051  SVVLERLCAAFEKKGAGTEGSSALRTCEQPLQCEIFHQLGWDPVRYDLTG  1100
1101  WLHRAKPNLSALDAPQVLHQSKREELRSLFQARAKLPPVCRAVAGLEGTS  1150
1151  QQALQRSRMVRRTFASSLAAVRRKAPCSQIKLQMDALTSMIKRSRLHFIH  1200
1201  CLVPNPVVESRSGQESPPPPQPGRDKPGAGGPLALDIPALRVQLAGFHIL  1250
1251  EALRLHRTGYADHMGLTRFRRQFQVLDAPLLKKLMSTSEGIDERKAVEEL  1300
1301  LETLDLEKKAVAVGHSQVFLKAGVISRLEKQREKLVSQSIVLFQAACKGF  1350
1351  LSRQEFKKLKIRRLAAQCIQKNVAVFLAVKDWPWWQLLGSLQPLLSATIG  1400
1401  TEQLRAKEEELTTLRRKLEKSEKLRNELRQNTDLLESKIADLTSDLADER  1450
1451  FKGDVACQVLESERAERLQAFREVQELKSKHEQVQKKLGDVNKQLEEAQQ  1500
1501  KIQLNDLERNPTGGADEWQMRFDCAQMENEFLRKRLQQCEERLDSELTAR  1550
1551  KELEQKLGELQSAYDGAKKMAHQLKRKCHHLTCDLEDTCVLLENQQSRNH  1600
1601  ELEKKQKKFDLQLAQALGESVFEKGLREKVTQENTSVRWELGQLQQQLKQ  1650
1651  KEQEASQLKQQVEMLQDHKRELLGSPSLGENCVAGLKERLWKLESSALEQ  1700
1701  QKIQSQQENTIKQLEQLRQRFELEIERMKQMHQKDREDQEEELEDVRQSC  1750
1751  QKRLHQLEMQLEQEYEEKQMVLHEKQDLEGLIGTLCDQIGHRDFDVEKRL  1800
1801  RRDLRRTHALLSDVQLLLGTMEDGKTSVSKEELEKVHSQLEQSEAKCEEA  1850
1851  LKTQKVLTADLESMHSELENMTRNKSLVDEQLYRLQFEKADLLKRIDEDQ  1900
1901  DDLNELMQKHKDLIAQSAADIGQIQELQLQLEEAKKEKHKLQEQLQVAQM  1950
1951  RIEYLEQSTVDRAIVSRQEAVICDLENKTEFQKVQIKRFEVLVIRLRDSL  2000
2001  IKMGEELSQAATSESQQRESSQYYQRRLEELKADMEELVQREAEASRRCM  2050
2051  ELEKYVEELAAVRQTLQTDLETSIRRIADLQAALEEVASSDSDTESVQTA  2100
2101  VDCGSSGRKEMDNVSILSSQPEGSLQSWLSCTLSLATDTMRTPSRQSATS  2150
2151  SRILSPRINEEAGDTERTQSALALSRARSTNVHSKTSGDKPVSPHFVRRQ  2200
2201  KYCHFGDGEVLAVQRKSTERLEPASSPLASRSTNTSPLSREKLPSPSAAL  2250
2251  SEFVEGLRRKRAQRGQGSTLGLEDWPTLPIYQTTGASTLRRGRAGSDEGN  2300
2301  LSLRVGAKSPLEIEGAAGGLLRSTSLKCISSDGVGGTTLLPEKSKTQFSS  2350
2351  CESLLESRPSMGRKLSSPTTPRDMLLSPTLRPRRRCLESSVDDAGCPDLG  2400
2401  KEPLVFQNRQFAHLMEEPLGSDPFSWKLPSLDYERKTKVDFDDFLPAIRK  2450
2451  PQTPTSLAGSAKGGQDGSQRSSIHFETEEANRSFLSGIKTILKKSPEPKE  2500
2501  DPAHLSDSSSSSGSIVSFKSADSIKSRPGIPRLAGDGGERTSPERREPGT  2550
2551  GRKDDDVASIMKKYLQK                                   2567

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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