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

NucPred

Fetching Q22258 from www.uniprot.org...

The NucPred score for your sequence is 0.93 (see score help below)

   1  MNIDKDVSALLCTAKKYVTQKEFNRQKMKFLLDDITKLLSKSFVSRIEQL    50
  51  DENEFMEKIMILQSITFTLHLITEKQELSSEEKIRLFQSVIASMCAFEDE   100
 101  ELAKCFDRILSVLMISVTKQDPRETIYFLQGLLEVVKYCDVEPSSSLPQL   150
 151  ITPEIASAISLGASGFFRYHLKWNIISTLFGENAGECVHFDELVLFWPHC   200
 201  RSQLEDKLKNDCSMTENCLRAGLTILKYKKLHNSILDQALFIDELFATFN   250
 251  SLTAKKSTNHMTFPKLLNEIQHFLQDHGKVLIMHKELRQKPVQWLIIYLE   300
 301  LIDDANDKFGLLENFSLLLLDLSTNHDIHEFPARLCMTASEICMRRIKHS   350
 351  IQSTHTDCLADYLDILASLLKLARIQKLDIFQCFATEIEAHHSLNNPLWP   400
 401  RILRSLLSVQNPHCQQFCKKFVPSIDKLWITLLNGESSRATLNSLVIVTA   450
 451  SCPFANNNDEGVKQIIPFLLIPCFQDFRDRVGSKWDNFRFIGLPKSEPSE   500
 501  LINLERFTTVLERSTSESTKLRAVNCALQLEKKTGKYINLVAEMSLAVFS   550
 551  KSQTDRIANSFEPLILFLTDNLQLINDFITILIAKLCEKQEFYSELTILK   600
 601  YFKTLQKLFCLAANGRNSCKKCGEECFVDPDSKENVKIDYESLSGLIKGI   650
 651  VARRNTFSQELIREFLQTSRVMLLHVDSKGIASSFTSIIKALDIGFSENA   700
 701  NAYFRVWELVCCRSEATVEKKLQMYIPLIGRSFALLGDDAALKVHGFLSN   750
 751  VLSARLSSTVKATLFASSFAHSVLKNCEIDWNVSYTWKTQFSQCLIKAPV   800
 801  GTCEEALQIMFKRYSTIFTRCFLNRLFFDASSAGAQKPSYDEHRIREITR   850
 851  CYLSHVLSDFNFPNQKITFNMIRPSLLYWSLLSSARGINSKLTLSVIDFI   900
 901  CQEMSAASVSMSSISPNPSDIRIVMIQRKSLITETFAQLVQFLAFENNRN   950
 951  TTSFWKFCSDHCDFKDEDIRTVISSYRKQVFMHLLLVSAREFLNPRNPSM  1000
1001  IVEQLRATYENIKKGEKFMISTAIETRNEGIEFLFIFRTYFTNDQYFLTR  1050
1051  EATAESFRILLQNMKQDFFDTNWYIILMTLRQIPLNLDSTQSSWISFIEQ  1100
1101  INYSILRSNIWRILTDISRIENNDILIEKVWNRLSYDMVIDKISTDAMIK  1150
1151  RVFWLIPLEVEKRIDLKFEISKSRQIEDVLEFIRMFPQYPSVQFADNLAS  1200
1201  KIERKTVYKEELPKLIGSLSRILPQCHSKREQNKIIKILQKLPIICSDLP  1250
1251  DHNFIRWDTRFKFFCEPRQLTQAVLEDCAGIVEVMTGTSKIEYVDRTMCE  1300
1301  IYKFFNPNEASPEMKSTLDGIKNMYAKMICSQKPEPSMIEQKTIDELSLG  1350
1351  GSRRESFSRWLTVIILKCAEMSEDAPLSSLASIAHVDDTRFLSKLAMRFI  1400
1401  LTVIHMERDSVTQWILSTFEEALTNTNHRRLTNSDRGPASFVFYVFDFIY  1450
1451  SYSSSEELRKKKKIWEKVISFWKSMMSWTFKDENGHGQPLIVKVAETFGM  1500
1501  EKRCILWLEMFMEQKRKTSTEIESETEAAYYFTLMNLYGRIHELNGVRGA  1550
1551  YARLSRIQIDHVYGKISMREAFGDFNSAACFARMTGKGKPFNSTEAIQKL  1600
1601  IDELNCLEYSQIERNEQEDYLNSLKTLSQWVNIDNDIGPSPHIFSRNIEY  1650
1651  WATESTILKMIRNDERDEIVNNAIENAKSKVIERLSECAIGGSCSYEIAT  1700
1701  PFLVELQKLNEIVELKNVSNDELSAFNSDFWKNIQKRTDDSEQKISILEP  1750
1751  ILRVRRSMLDIRMQSMTGRDKENIRSRIVEVHLQSARIARLTGCFERAQL  1800
1801  SLINAKKVLPFENKIVLEEAKLQLQTSDELNGMSLLDSIISKNFGDLHTI  1850
1851  YTDTQQSVNLDVQKSAKLKIEHYQEETKNLFSSVQMLRISHMIKAGNTIG  1900
1901  FDKVYHETTQLLQCFAHSGVMYEAAWLLDYLSNYKERSKHVLPLLKAYKE  1950
1951  VAKYEKNQVLQARAVERMTSLWLSNTRKISTHISSVPKLPEGQISDLRQN  2000
2001  IKSMNREIQTALEHIGWRAFYPAYAVLARHIDHQDEEVTRTIKQIMKQLI  2050
2051  LRMPHQCMWQSAYLLRQNIASVKEKYMEVLTEVKRKAPCYVTLIDQYDYA  2100
2101  SGVFNTVSGKVESDDCKLSEKVDGLKTMFRDKKYDPKELVMNRRVDCDCK  2150
2151  ILSGIMVPVRSVIDESVHDTEIRDDGFEESCHLPDRYLIHDFSDKVKVLH  2200
2201  SNTKPVIIKLTTKTGRIVRLICKKDDDLSKDYHFTKMVEMCNDLLMKDEQ  2250
2251  TRIQKMTATTYSVIPLGKQGGIIEFMEGVTSFYETLDKLMGMTSGEWLEK  2300
2301  LKFWNTHMKPMGKEERTKYFREVACKNTPVVMGKWFRIQYPEAGQWFASR  2350
2351  KLFAKSTAVMSVIGYIFGLGDRHTKNLMVHTTGKCIHVDFDMIFNKGETL  2400
2401  GTPELVPFRLTQNMINGMGEVALDGEFRTVCEQALRVFRENSYEIEKYIA  2450
2451  DLPNLVADFPSNKRAPKDFDMSEAKRLVSGRLRGQIMTAKLYRSNPISHP  2500
2501  MQVSQLASSLIELATSEEKLSEMYLGWMATL                     2531

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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