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

NucPred

Fetching Q95Q95 from www.uniprot.org...

The NucPred score for your sequence is 0.79 (see score help below)

   1  MLQQHGISFQMNADRQNKAATTSNRIVSAPATNEFDERHRKQGIDAARAL    50
  51  ASQYRSRITENRDANQRQAARELSRYVRSELKDEPNTFSDAFLNAIDGRT   100
 101  DIASQSAIYNCMKSNSNIDQKRAGIYLIVCLAETHSGNVIRYANYLLKML   150
 151  NNGNGLDEDTVKMASKALAFLIATCKSYAAELVDRCLDHCHEWLGQNVPH   200
 201  SQQPKNQQEIDQIRRLAASHLSRELALATPTAFFLRVNLFFKYIFNAVRD   250
 251  KNPAVRIAGIDALHVVLTIVSQREAKNKTEWFKKCFDEALEGQPNPSQKD   300
 301  DLDRWHAVALILNELLRISDQRFELIRCESSQFIKQKFLKEDEEEGVEWL   350
 351  VLTKQQTIVESVTARKLVLERFPKILDCVRQIIPLANKTSSTKQQSSIYL   400
 401  NTVLMQLLPRICAFPQCDRTFQTISFDTSFTILQRNAVAAPAIGMMMLSN   450
 451  PDVHATHIEKTISFISAAIKKTTNSDVLDNYFTFLFLFVDAYHEQVTTQI   500
 501  KAIIPQLMDITLSRSLANVLKMIMMRIPKLRLNVQDGVMASVYQTLTGSL   550
 551  IPPKSEPIGRPASPKAILQKAETDPKELQRIVLAVDVLGEFYFSRGALQR   600
 601  IMQYVADYYLTADNVEIRLAAVSSCCEMVVPFVGVYKKVTSDKRNSLLQT   650
 651  IYGVLRAVCSVIVNDQDVRVRMQVISCFGQMPRPFLAHLAQPEMLEVQFM   700
 701  ALHDEKLEMQQACVTLLGRLAELNPALVLPRLRLMLLETLSQMQQSGQAR   750
 751  LEQHSAKMIAQLAKQSPKFMRPYVGSLMIAMIPKLRNDQKYAEVTAQVLN   800
 801  AVSEIAVIGGAEIVKNLKPLFEKLTHMINDSSSLHKREAALRAIGGICRS   850
 851  TAYVVDPYRDYPSLLDDLLRILKTVMSNTMRREAIKTLGILGAIDPYTHK   900
 901  VFTGSVQSSTAISTALSLPISETDSKDPRQDIIHWFNYEKCTLEEFYPAI   950
 951  TIANLMLMMQDEDSQSYAEIAQAIVTIFRSLGDMAPLYTEQVIPRLIEVC  1000
1001  RRATESSNRANLREFFLQQLANFVAIIRKHAAPYMPAIFTIIADAWKEDI  1050
1051  SVKMVVIEVLTDMGTAIGNDFSKYTGELIPYLLTVLQTDKTKERVLTVKV  1100
1101  MESIQKLTHCIVQHLHLVLPPLLIILDDFSLKLSIRNTALSTVLHMTQQV  1150
1151  DVSAYAPRMMQSWHHNISTAEMRDKLLLLLIEIIKQLGKFFDIFKRGVDQ  1200
1201  KLRDYNLDKSVHYEQYRKLAQRAQMSRDVLTSSVFAGSNGNIQYSSTQAG  1250
1251  MRGQANNVYANNDLHERLMNGSIDSGASRQDNRDDYYRYGVEEKKEVPKV  1300
1301  APTTARPTSELVTVQITKQRLNKDALMPQWKNENLTSKDEWLQWLMKIRI  1350
1351  GFLTYGSSPSLRAASSLGDQHPHLARDLFPAAFMSVWTELDSDVQNDLTS  1400
1401  CLLRAISTGIPELIQTILNLAEFMDHSEKGPLPISHDVLGRWAEQTKAFA  1450
1451  KACRYKEMSVLKKSGSMQTTFTRKVKLEPNDCQSLITYANKLNVQEEAAG  1500
1501  VVRYAERNEMNFQMRGRWYEKLNEWEKALGAYELEEKKKSSCPNLQVYDE  1550
1551  KDHLMTPEEAATAEEARMHEMRCLEALGRWDELNSKSVVWADQRGNRNDS  1600
1601  VRDEINKKQLDHKMAVIAARGAWAVDNWERMADYVSVISENTQDGAMLRA  1650
1651  VVAVHNDENTKAMGLIEKVREMIDSELTAMANESYERAYIPMVSVQQMAE  1700
1701  LEEAIEYKTRPERRPRIALLWSRRLQGCRRNVEQWQRLIMLRGLVLSPQE  1750
1751  MHPLRVKFSSMCRKQGKNSMSRAVLRELLSLPANSDLVRAKAPFDKPLLV  1800
1801  LALAKQLYQDDHKDEAIRALEDLANHWNKRINPIPKATGRELIPPSTKEP  1850
1851  ARICAKVLLKLGEWTELKSKTSNNMQVGELSFVRQQVSPQYRTKESRTPE  1900
1901  TIAFENTINYYQQATQYDPGWHKVWHKLASTHFYAVCRERPHPTTVISPP  1950
1951  QQPQQPKKMHIPPVTRATSPPPPAQKSPQPAPFHSITEPLSVIIDYPVPP  2000
2001  PLGSLVGLPPMPAYLSSNSSLPPQHHHVSPLSNDSPSNSAENKLYLKHAA  2050
2051  HAVRCFAKALMCSPGSRLEDTLRLMQLWFDHGDDKDQDVYFALTETIFDL  2100
2101  PVTTWLEAIPQLMARLDCPDDQKSVQLVLRVLCEIARHRPQAVIYALTVA  2150
2151  SRSKDVHRSKNAGTVLEKMMEYHSKLVREASLVTEELVRCAILWHEQWHD  2200
2201  ALDDASRVYFHRRLQDNNVQAMFDALRNMNDLMQKGAPTTMKEHSFQQTY  2250
2251  SSDLKEAGRYVQAFESSGNVKDLNQAWEIYCSVFKKLRDQLATLNSLDLV  2300
2301  YVSPNLVSAKDLELVVPGTYDPSAPIVSIQSFSSKMNVITSKQRPRKMVI  2350
2351  RGSNGLDYQFLLKGHEDPRQDERVMQLFGLVNTLLANNSETCRRNLTIQR  2400
2401  YSIVALSKDSGLIGWVPNCDTLHTLVKEYREKKAKIPLSIEHKTLQKLSL  2450
2451  ETEHLTLMQKLQLFESALSVTQGEDLRHVLWLKSPSSEVWFDRRTNYTRS  2500
2501  VACMSMVGYILGLGDRHPSNLMLDRLTGKVVHIDFGDCFEVAMLREKFPE  2550
2551  RVPFRLTRMLINAMEVTGLDGVYNYTAERVLKMLRTNQESLLAVLEAFVY  2600
2601  DPVINWRLVEGMKKDPKTRKDTGGRQNMAGAVLPSSSTTDSIMETIKRKL  2650
2651  DGTEFVHTDGSTPPEPLQVTEQLAMLTEQATSPLNLCQSYIGWCPFW     2697

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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