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

NucPred

Fetching P33144 from www.uniprot.org...

The NucPred score for your sequence is 0.84 (see score help below)

   1  MAVTSFPADSLASMESVKQTVRSTSTCSAATVLSLQTLFRSAGEMETTLR    50
  51  RTARGTKATATNATASSRAKTTRTKSTSTSTTRTKTPAQDVSTFTSTSAS   100
 101  LADTRLSNQEKLVLATEVFNSTLKTLSDAVKTVMSISKEKKDASPTKRGT   150
 151  TTKGRVKTSQPDLTDNENGVSAVAECARLSLSCLRMLRTDAMVDGGLPNL   200
 201  QLEQGACVLAGRLLALGLNDAAYKELRGLKRRIQSYLEELPSGRKRTGRK   250
 251  DAEDGEETAKERMSDLLSFSDIANARSIHGLLVSFQSNALRLIAAEKRPA   300
 301  TVQKLVPSLQLTDESSPANVIMASIDSGALTKDKAAVQLQLLSSTVLSLS   350
 351  ASGASTGKERLRPSIVLSLQLLALEIRCMSWKLSGHACEDNKEMWDPLAR   400
 401  YIGAFAQATKSIEKAEFAVIYKNIVRLQSAFSKTQNCATRSTDNLSVARI   450
 451  ATILGQLAQDAGCFDEALQLFTESLNPLSSSQCLGMATVRCKIAALHFQA   500
 501  FKSSVKLPGDVSDAVSQATAALSISLKGSSHDLDELLVQAAKLKKLAMGW   550
 551  FGDLISKGQGSQCENVVFPRICEFLSSFVRFLRRYIGRRPENDELNDREI   600
 601  FQKRIDAAQNIVLAAVDSTIAIGKLSVMSQRPAWEETVSTLLDCQRLLAT   650
 651  IEPFDEVDVATADSIDQALVKLSNLFWSRYLKEKEAGKNARELLPLLKQS   700
 701  AYLLSGCSPSQRATGFAPLKYERLAHTYIEGNMVSEAEVAFRQSITDHIA   750
 751  AGALDKIASSTDGCFPHQMNQDPKRSGFTLGRVLSAYLKVKLRNKRSAVN   800
 801  EIFDDETLPSVQRGHVLEWQLGILTEIHGTSNNDNVFRSVFAEVATRLFK   850
 851  VYPAEQHPVRRLRVLLSGLRFALEQPGFLDSSLLQRFADEGRKGLDDDDY   900
 901  QDDDDIKSLAVYLKNSVRLTLGLQQGSLGPEELELIVSTWTSILRFCHDL   950
 951  KSLVACVGNVEYFLLQMKAVVDYTEIHGLWKFQLSTLELVLRVTELHGAG  1000
1001  TFSEAIIVLSRLVLQYCRMGFCIKAHSLLSRADGYIANHEVSCLARLSYE  1050
1051  LARVGFLLETGDNQKAATVLSTARMIYEKHQATEDLDACSVLTKISWERL  1100
1101  VADAAFMSSRLSFAQGSIKDALYFAKLSVRLNCRIWAKVEKLAQKKQEKA  1150
1151  VVGDSSELEIVVEGMAKLEVSQTSSTYSQGAPFWPHIGSHHSSLLHLANL  1200
1201  SAHHGLFQDAIYYGEQALKINKSLNANVRLIASQAHLGSHWILGGHISEG  1250
1251  QQLLASAKALSDKLGSSIELVSLRLSLAALHRVEGDYRNEYRTLREAEKL  1300
1301  LGGLFESQADSADIPDLEEKMDKLRVRPKSRSTRQPATTATRRTRSATTS  1350
1351  ARSTPKPPQSVEATNASNTLLQMKSEILLQQAASLRAQREFEAASTLLSD  1400
1401  ARKFAVTRNSRISVHLGESEHLLADAIRNFANHAVYCVLPESTISLPSLE  1450
1451  PKAASESSSKSATRKTRAPTRGTRTKAQAATEDFSVMLSKAGDCLNGIFD  1500
1501  TATQLGSTLDSHSASRLMSRISMLSHVTASPNHILWPHSPANMNEVGRIG  1550
1551  AFARERAAIRIDKRLADYCDPLLWPRSELESEGVSPDFTKEYVDILPDNW  1600
1601  NVLSLSLSADRAEFVVSRLHRGCSPFLLRLPLRRGNSEDEEEQFTFEDGR  1650
1651  DEMKELIRLANESAHAAKLQVDRQMKKEWWKNREALDRRMENLLQNIENV  1700
1701  WFGGFRGIFSPIPLCEKSLARFASAFENILENHLPSRRKGSRAQGPKLTL  1750
1751  HPNVLELFVGVKGLDDQEDPEDTLMDLLYFVVDILQFQGERNAYDEVDFD  1800
1801  MMVVETLDAVRAYHEAAKDQATQRPNNTVLVLDKSLHLFPWESLPCLQGL  1850
1851  PVCRVPSLECLRDRVLHLRSGKQSALSIDRRNGTYILNPTGDLKTTQETF  1900
1901  EKDLSSLKGWTGMVNRQPTEDEFKDSLQSKSLFLYFGHGSGAQYIRGRTV  1950
1951  KRLDRCAVAFLMGCSSGTLTEAGEYEPYGTPMNYLQAGSPALVATLWDVT  2000
2001  DKDIDRFAKATFEHWGLIGNGHRGNEGIGEAGVALDAAVSQSRGACVLKY  2050
2051  LNGAAPVVYGVPGVFLH                                   2067

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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