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

NucPred

Fetching O95071 from www.uniprot.org...

The NucPred score for your sequence is 0.95 (see score help below)

   1  MTSIHFVVHPLPGTEDQLNDRLREVSEKLNKYNLNSHPPLNVLEQATIKQ    50
  51  CVVGPNHAAFLLEDGRVCRIGFSVQPDRLELGKPDNNDGSKLNSNSGAGR   100
 101  TSRPGRTSDSPWFLSGSETLGRLAGNTLGSRWSSGVGGSGGGSSGRSSAG   150
 151  ARDSRRQTRVIRTGRDRGSGLLGSQPQPVIPASVIPEELISQAQVVLQGK   200
 201  SRSVIIRELQRTNLDVNLAVNNLLSRDDEDGDDGDDTASESYLPGEDLMS   250
 251  LLDADIHSAHPSVIIDADAMFSEDISYFGYPSFRRSSLSRLGSSRVLLLP   300
 301  LERDSELLRERESVLRLRERRWLDGASFDNERGSTSKEGEPNLDKKNTPV   350
 351  QSPVSLGEDLQWWPDKDGTKFICIGALYSELLAVSSKGELYQWKWSESEP   400
 401  YRNAQNPSLHHPRATFLGLTNEKIVLLSANSIRATVATENNKVATWVDET   450
 451  LSSVASKLEHTAQTYSELQGERIVSLHCCALYTCAQLENSLYWWGVVPFS   500
 501  QRKKMLEKARAKNKKPKSSAGISSMPNITVGTQVCLRNNPLYHAGAVAFS   550
 551  ISAGIPKVGVLMESVWNMNDSCRFQLRSPESLKNMEKASKTTEAKPESKQ   600
 601  EPVKTEMGPPPSPASTCSDASSIASSASMPYKRRRSTPAPKEEEKVNEEQ   650
 651  WSLREVVFVEDVKNVPVGKVLKVDGAYVAVKFPGTSSNTNCQNSSGPDAD   700
 701  PSSLLQDCRLLRIDELQVVKTGGTPKVPDCFQRTPKKLCIPEKTEILAVN   750
 751  VDSKGVHAVLKTGNWVRYCIFDLATGKAEQENNFPTSSIAFLGQNERNVA   800
 801  IFTAGQESPIILRDGNGTIYPMAKDCMGGIRDPDWLDLPPISSLGMGVHS   850
 851  LINLPANSTIKKKAAVIIMAVEKQTLMQHILRCDYEACRQYLMNLEQAVV   900
 901  LEQNLQMLQTFISHRCDGNRNILHACVSVCFPTSNKETKEEEEAERSERN   950
 951  TFAERLSAVEAIANAISVVSSNGPGNRAGSSSSRSLRLREMMRRSLRAAG  1000
1001  LGRHEAGASSSDHQDPVSPPIAPPSWVPDPPAMDPDGDIDFILAPAVGSL  1050
1051  TTAATGTGQGPSTSTIPGPSTEPSVVESKDRKANAHFILKLLCDSVVLQP  1100
1101  YLRELLSAKDARGMTPFMSAVSGRAYPAAITILETAQKIAKAEISSSEKE  1150
1151  EDVFMGMVCPSGTNPDDSPLYVLCCNDTCSFTWTGAEHINQDIFECRTCG  1200
1201  LLESLCCCTECARVCHKGHDCKLKRTSPTAYCDCWEKCKCKTLIAGQKSA  1250
1251  RLDLLYRLLTATNLVTLPNSRGEHLLLFLVQTVARQTVEHCQYRPPRIRE  1300
1301  DRNRKTASPEDSDMPDHDLEPPRFAQLALERVLQDWNALKSMIMFGSQEN  1350
1351  KDPLSASSRIGHLLPEEQVYLNQQSGTIRLDCFTHCLIVKCTADILLLDT  1400
1401  LLGTLVKELQNKYTPGRREEAIAVTMRFLRSVARVFVILSVEMASSKKKN  1450
1451  NFIPQPIGKCKRVFQALLPYAVEELCNVAESLIVPVRMGIARPTAPFTLA  1500
1501  STSIDAMQGSEELFSVEPLPPRPSSDQSSSSSQSQSSYIIRNPQQRRISQ  1550
1551  SQPVRGRDEEQDDIVSADVEEVEVVEGVAGEEDHHDEQEEHGEENAEAEG  1600
1601  QHDEHDEDGSDMELDLLAAAETESDSESNHSNQDNASGRRSVVTAATAGS  1650
1651  EAGASSVPAFFSEDDSQSNDSSDSDSSSSQSDDIEQETFMLDEPLERTTN  1700
1701  SSHANGAAQAPRSMQWAVRNTQHQRAASTAPSSTSTPAASSAGLIYIDPS  1750
1751  NLRRSGTISTSAAAAAAALEASNASSYLTSASSLARAYSIVIRQISDLMG  1800
1801  LIPKYNHLVYSQIPAAVKLTYQDAVNLQNYVEEKLIPTWNWMVSIMDSTE  1850
1851  AQLRYGSALASAGDPGHPNHPLHASQNSARRERMTAREEASLRTLEGRRR  1900
1901  ATLLSARQGMMSARGDFLNYALSLMRSHNDEHSDVLPVLDVCSLKHVAYV  1950
1951  FQALIYWIKAMNQQTTLDTPQLERKRTRELLELGIDNEDSEHENDDDTNQ  2000
2001  SATLNDKDDDSLPAETGQNHPFFRRSDSMTFLGCIPPNPFEVPLAEAIPL  2050
2051  ADQPHLLQPNARKEDLFGRPSQGLYSSSASSGKCLMEVTVDRNCLEVLPT  2100
2101  KMSYAANLKNVMNMQNRQKKEGEEQPVLPEETESSKPGPSAHDLAAQLKS  2150
2151  SLLAEIGLTESEGPPLTSFRPQCSFMGMVISHDMLLGRWRLSLELFGRVF  2200
2201  MEDVGAEPGSILTELGGFEVKESKFRREMEKLRNQQSRDLSLEVDRDRDL  2250
2251  LIQQTMRQLNNHFGRRCATTPMAVHRVKVTFKDEPGEGSGVARSFYTAIA  2300
2301  QAFLSNEKLPNLECIQNANKGTHTSLMQRLRNRGERDREREREREMRRSS  2350
2351  GLRAGSRRDRDRDFRRQLSIDTRPFRPASEGNPSDDPEPLPAHRQALGER  2400
2401  LYPRVQAMQPAFASKITGMLLELSPAQLLLLLASEDSLRARVDEAMELII  2450
2451  AHGRENGADSILDLGLVDSSEKVQQENRKRHGSSRSVVDMDLDDTDDGDD  2500
2501  NAPLFYQPGKRGFYTPRPGKNTEARLNCFRNIGRILGLCLLQNELCPITL  2550
2551  NRHVIKVLLGRKVNWHDFAFFDPVMYESLRQLILASQSSDADAVFSAMDL  2600
2601  AFAIDLCKEEGGGQVELIPNGVNIPVTPQNVYEYVRKYAEHRMLVVAEQP  2650
2651  LHAMRKGLLDVLPKNSLEDLTAEDFRLLVNGCGEVNVQMLISFTSFNDES  2700
2701  GENAEKLLQFKRWFWSIVEKMSMTERQDLVYFWTSSPSLPASEEGFQPMP  2750
2751  SITIRPPDDQHLPTANTCISRLYVPLYSSKQILKQKLLLAIKTKNFGFV   2799

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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