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

NucPred

Fetching Q91293 from www.uniprot.org...

The NucPred score for your sequence is 0.04 (see score help below)

   1  MTRILSVFKTAKTGVLNAAAHRYRGFSKAGVRLMSVKAQTANLVLEDGTK    50
  51  IKGYSFGHPASVAGEVIFNTGLGGYVEAVTDPSYHGQILTLTNPIIGNGG   100
 101  APDTKARDAYGLMKYIESENIQASGLLVLDYSHEYSHWGAVKSLSEWLHE   150
 151  EKVPALCGIDTRMLAKKIRDNKGAVLGKIEFEGQPVEFIDPNKRNLIAEV   200
 201  STKETKVFGKGNPVRIVAVDCGVKHNIIRQLVKRGAEVHLVPWNHDFSQM   250
 251  EYDGLLITSGPGNPELAKPLIQNLKKVFQSDRPEPIFGICKGNEIAALAA   300
 301  GGKTYRLPMANRGQNQPVMITLNGQAFITAQNHAYAVDNNSLPAGWKPLF   350
 351  VNINDQSNEGIMHETKPIFTSQFHPEANPGPVDTEFLFDVYMSLIKKGKG   400
 401  TTLTSVMPKPALQSKRIDVAKVLILGSGGLSIGQAGEFDYSGSQAVKAMK   450
 451  EENVKTVLMNPNIASVQTNEVGLKQADTVYFLPITPQFVTEVIKAEKTDG   500
 501  IILGMGGQTALNCGVELFKRGVLKEYGVRVLGTSVESIMFTEDRQLFSDK   550
 551  LNEIKEPIAPSFAVESVKDALEAADKIGYPVMIRSAYALGGLGSGLCPDK   600
 601  ETLTDLATKALAMTNQILVERSVVGWKEIEYEVVRDAADNCVTVCNMENV   650
 651  DAMGVHTGDSIVVAPCQTLSNEECQMLRAVSIKVVRHLGIVGECNIQFAL   700
 701  HPTSLEYVIIEVNARLSRSSALASKATGYPLAFIAAKIALGIPLPEIKNV   750
 751  VSGKTTACFEPSLDYMVTKIPRWDLDRFHGASGLIGSSMKSVGEVMAIGR   800
 801  TFEESFQKALRMCHPSVDGFTSNLPMNKAWSSDVNLRKEMAEPTSTRMYS   850
 851  MAKAIQSGISLDEINKLTAIDKWFLYKMQGILNMEKTLKGSRSESVPEET   900
 901  LRRAKQIGFSDRYIGKCLGLSETQTRELRLNKNVKPWVKQIDTLAAEYPA   950
 951  ITNYLYLTYNGQEHDIKFDDHGMMVLGCGPYHIGSSVEFDWCAVSSIRTL  1000
1001  RHVGKKTVVVNCNPETVSTDFDECDKLYFEELSQERIMDVFQLEQCDGCI  1050
1051  ISVGGQIPNNLAVPLYKNGVKIMGTSPMQIDRAEDRSIFSAVLDELQIAQ  1100
1101  APWKAVNSLDDALQFTKTVGYPCLLRPSYVLSGSAMNVVYGEEELKTFLA  1150
1151  EATRVSQEHPVVITKFIEGAREVEMDAVGKEGRVISHAISEHVEDAGVHS  1200
1201  GDATLMIPTQSISQGAIEKVKIATKKIATAFAISGPFNVQFLVRGNDVLV  1250
1251  IECNLRASRSFPFVSKTLGVDFIDVATKVMIGEKIDESSLPTLERPVIPA  1300
1301  DYVGIKAPMFSWPRLRGADPVLKCEMASTGEVACFGQNVYSAFLKAMIST  1350
1351  GFKLPQKGILIGIQHSFRPHFLGTAQTLKDEGFKLYATEATADWLNANDI  1400
1401  TATPVAWPSQEGQSGPSSIYKLIKEGNIDMVINLPNNNTKYVRDNFAIRR  1450
1451  TAVDTGTALLTNFQVVKMFAEAIKYSGDLDAKSLFHYRQFGGAKPS      1496

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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