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

NucPred

Fetching P70388 from www.uniprot.org...

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

   1  MSRIEKMSILGVRSFGIEDKDKQIISFFSPLTILVGPNGAGKTTIIECLK    50
  51  YICTGDFPPGTKGNTFVHDPKVAQETDVRAQIRLQFRDVNGEMVAVHRSM   100
 101  LCSQKNKKTEFKTLEGVITRMKHGEKVSLSSKCAEIDREMISCLGVSKSV   150
 151  LNNVIFCHQEDSNWPLSEGKALKQKFDEIFSATRYIKALDTLRQVRQTQG   200
 201  QKVKECQTELKYLKQNKEKACEIRDQITSKEAQLASSQEIVRSYEDELEP   250
 251  LKNRLKEIEHNLSKIMKLDNEIKALESRKKQMEKDNSELEQKMEKVFQGT   300
 301  DEQLNDLYHNHQRTVREKERRLVDCQRELEKLNKEARLLNQEKAELLVEQ   350
 351  GRLQLQADRHQEHIRARDSLIQSLATHLELDGFERGPFSERQIKNFHELV   400
 401  KERQEREAKTASQLLSDLTDKEALKQRQLDELRDRKSGLGRTIELKTEIL   450
 451  TKKQSELRHVRSELQQLEGSSDRILELDQELTKAERELSKAEKNSSIETL   500
 501  KAEVMSLQNEKADLDRSLRKLDQEMEQLNHHTTTRTQMEMLTKDKTDKDE   550
 551  QIRKIKSRHSDELTSLLGYFPNKKQLEDWLHSKSKEINQTRDRLAKLNKE   600
 601  LASAEQNKNHINNELKKKEEQLSSYEDKLFDVCGSQDLESDLGRLKEEIE   650
 651  KSSKQRAMLAGATAVYSQFITQLTDENQSCCPVCQRVFQTEAELQEVISD   700
 701  LQSKLRLAPDKLKSTESELKKKERRRDEMLGLVPVRQSIIDLKEKEIPEL   750
 751  RNRLQSVNRDIQRLKNDIEEQETLLGTIMPEEESAKVCLTDVTIMERFQM   800
 801  ELKDVERKIAQQAAKLQGVDLDRTVQQVNQEKQEKQHRLDTVTSKIELNR   850
 851  KLIQDQQEQIQHLKSKTNELKSEKLQIATNLQRRQQMEEQSVELSTEVQS   900
 901  LNREIKDAKEQISPLETALEKLQQEKEELIHRKHTSNKMAQDKINDIKEK   950
 951  VKNIHGYMKDIENYIQDGKDDYKKQKETELNGVAVQLNECEKHREKINKD  1000
1001  MGTMRQDIDTQKIQERWLQDNLTLRKRRDELKEVEEEPKQHLKEMGQMQV  1050
1051  LQMKNEHQKLEENIDTIKRNHSLALGRQKGYEDEILHFKKELREPQFRDA  1100
1101  EEKYREMMIVMRTTELVNKDLDIYYKTLDQAIMKFHSMKMEEINKIIRDL  1150
1151  WRSTYRGQDIEYIEIRSDADENVSASDKRRNYNYRVVMLKGDTALDMRGR  1200
1201  CSAGQKVLASLIIRLALAETFCLNCGILALDEPTTNLDRENIESLAHALV  1250
1251  EIIKSRSQQRNFQLLVITHDEDFVELLGRSEYVEKFYRVKKNMDQCSEIV  1300
1301  KCSISSLGSYVH                                        1312

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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