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

NucPred

Fetching Q13023 from www.uniprot.org...

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

   1  MLTMSVTLSPLRSQDLDPMATDASPMAINMTPTVEQGEGEEAMKDMDSDQ    50
  51  QYEKPPPLHTGADWKIVLHLPEIETWLRMTSERVRDLTYSVQQDSDSKHV   100
 101  DVHLVQLKDICEDISDHVEQIHALLETEFSLKLLSYSVNVIVDIHAVQLL   150
 151  WHQLRVSVLVLRERILQGLQDANGNYTRQTDILQAFSEETKEGRLDSLTE   200
 201  VDDSGQLTIKCSQNYLSLDCGITAFELSDYSPSEDLLSGLGDMTSSQVKT   250
 251  KPFDSWSYSEMEKEFPELIRSVGLLTVAADSISTNGSEAVTEEVSQVSLS   300
 301  VDDKGGCEEDNASAVEEQPGLTLGVSSSSGEALTNAAQPSSETVQQESSS   350
 351  SSHHDAKNQQPVPCENATPKRTIRDCFNYNEDSPTQPTLPKRGLFLKEET   400
 401  FKNDLKGNGGKRQMVDLKPEMSRSTPSLVDPPDRSKLCLVLQSSYPNSPS   450
 451  AASQSYECLHKVGNGNLENTVKFHIKEISSSLGRLNDCYKEKSRLKKPHK   500
 501  TSEEVPPCRTPKRGTGSGKQAKNTKSSAVPNGELSYTSKAIEGPQTNSAS   550
 551  TSSLEPCNQRSWNAKLQLQSETSSSPAFTQSSESSVGSDNIMSPVPLLSK   600
 601  HKSKKGQASSPSHVTRNGEVVEAWYGSDEYLALPSHLKQTEVLALKLENL   650
 651  TKLLPQKPRGETIQNIDDWELSEMNSDSEIYPTYHVKKKHTRLGRVSPSS   700
 701  SSDIASSLGESIESGPLSDILSDEESSMPLAGMKKYADEKSERASSSEKN   750
 751  ESHSATKSALIQKLMQDIQHQDNYEAIWEKIEGFVNKLDEFIQWLNEAME   800
 801  TTENWTPPKAEMDDLKLYLETHLSFKLNVDSHCALKEAVEEEGHQLLELI   850
 851  ASHKAGLKDMLRMIASQWKELQRQIKRQHSWILRALDTIKAEILATDVSV   900
 901  EDEEGTGSPKAEVQLCYLEAQRDAVEQMSLKLYSEQYTSSSKRKEEFADM   950
 951  SKVHSVGSNGLLDFDSEYQELWDWLIDMESLVMDSHDLMMSEEQQQHLYK  1000
1001  RYSVEMSIRHLKKTELLSKVEALKKGGVLLPNDLLEKVDSINEKWELLGK  1050
1051  TLGEKIQDTMAGHSGSSPRDLLSPESGSLVRQLEVRIKELKGWLRDTELF  1100
1101  IFNSCLRQEKEGTMNTEKQLQYFKSLCREIKQRRRGVASILRLCQHLLDD  1150
1151  RETCNLNADHQPMQLIIVNLERRWEAIVMQAVQWQTRLQKKMGKESETLN  1200
1201  VIDPGLMDLNGMSEDALEWDEMDISNKLISLNEESNDLDQELQPVIPSLK  1250
1251  LGETSNEDPGYDEEADNHGGSQYASNITAPSSPHIYQVYSLHNVELYEDN  1300
1301  HMPFLKNNPKVTGMTQPNVLTKSLSKDSSFSSTKSLPDLLGGSNLVKPCA  1350
1351  CHGGDMSQNSGSESGIVSEGDTETTTNSEMCLLNAVDGSPSNLETEHLDP  1400
1401  QMGDAVNVLKQKFTDEGESIKLPNSSQSSISPVGCVNGKVGDLNSITKHT  1450
1451  PDCLGEELQGKHDVFTFYDYSYLQGSKLKLPMIMKQSQSEKAHVEDPLLR  1500
1501  GFYFDKKSCKSKHQTTELQPDVPPHERILASASHEMDRISYKSGNIEKTF  1550
1551  TGMQNAKQLSLLSHSSSIESLSPGGDLFGLGIFKNGSDSLQRSTSLESWL  1600
1601  TSYKSNEDLFSCHSSGDISVSSGSVGELSKRTLDLLNRLENIQSPSEQKI  1650
1651  KRSVSDITLQSSSQKMSFTGQMSLDIASSINEDSAASLTELSSSDELSLC  1700
1701  SEDIVLHKNKIPESNASFRKRLTRSVADESDVNVSMIVNVSCTSACTDDE  1750
1751  DDSDLLSSSTLTLTEEELCIKDEDDDSSIATDDEIYEDCTLMSGLDYIKN  1800
1801  ELQTWIRPKLSLTRDKKRCNVSDEMKGSKDISSSEMTNPSDTLNIETLLN  1850
1851  GSVKRVSENNGNGKNSSHTHELGTKRENKKTIFKVNKDPYVADMENGNIE  1900
1901  GIPERQKGKPNVTSKVSENLGSHGKEISESEHCKCKALMDSLDDSNTAGK  1950
1951  EFVSQDVRHLPKKCPNHHHFENQSTASTPTEKSFSELALETRFNNRQDSD  2000
2001  ALKSSDDAPSMAGKSAGCCLALEQNGTEENASISNISCCNCEPDVFHQKD  2050
2051  AEDCSVHNFVKEIIDMASTALKSKSQPENEVAAPTSLTQIKEKVLEHSHR  2100
2101  PIQLRKGDFYSYLSLSSHDSDCGEVTNYIEEKSSTPLPLDTTDSGLDDKE  2150
2151  DIECFFEACVEGDSDGEEPCFSSAPPNESAVPSEAAMPLQATACSSEFSD  2200
2201  SSLSADDADTVALSSPSSQERAEVGKEVNGLPQTSSGCAENLEFTPSKLD  2250
2251  SEKESSGKPGESGMPEEHNAASAKSKVQDLSLKANQPTDKAALHPSPKTL  2300
2301  TCEENLLNLHEKRHRNMHR                                 2319

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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