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

NucPred

Fetching O54888 from www.uniprot.org...

The NucPred score for your sequence is 0.18 (see score help below)

   1  MDVDSRWRNLPSGPSLKHLTDPSYAVPPEQQKAALQDLTRAHVDSFNYAV    50
  51  LEGLSHAVQAIPPFEFAFKDERISLTIVDAAISPPAVPKGTICKELNIYP   100
 101  AECRGRRSTYRGKLTADISWAVNGVPKGIIKQFLGXVPIMVKSKLCNLYN   150
 151  LPPQVLIEHHEEAEEMGGYFIINGIEKVIRMLIMPRRNFPIAMIRPKWKS   200
 201  RGLGYTQFGVSIHCVREEHSAVNMNLHYVENGTVMLNFIYRKELFFLPLG   250
 251  FALKALVSFSDYQIFQELIKGKEEDSFFKNSVSQMLRIVMEEGCHTQKQV   300
 301  LDYLGERFRVKLSLPDWYPNAEAAEFLFNQCICIHLKSNTDKFYLLCLMT   350
 351  RKLFALARGECMEDNPDSLVNQEVLTPGQLFLMFLKEKMENWLLSIKIAL   400
 401  DKRAQKTNVSINNENLMKIFSMGTELTRPFEYLLATGNLRSKTGLGFMQD   450
 451  SGLCVVADKLNFIRYLSHFRCVHRGADFAKMRTTTVRKLLPESWGFLCPV   500
 501  HTPDGAPCGLLNHLTAVCEVVTKFVYTASIPALLCGLGVTPVDAAPCRPY   550
 551  SDCYPVLLDGVMVGWVDKELAPEVADTLRRFKVLRERRCSSLDGGGPDSH   600
 601  DRKAKPVPRAVPLHHSLQAGEACAEPGAGQRRARWNYGAALHEHCHLRGR   650
 651  GFWWSFHTPGALPSQPAEVIANFIPFSDHNQSPRNMYQCQMGKQTMGFPL   700
 701  LTYQDRSDNKLYRLQTPQSPLVRPCMYDHYDMDNYPIGTNAIVAVISYTG   750
 751  YDMEDAMIVNKASWERGFAHGSVYKSEFIDLSEKFKQGDDSLVFGVKPGD   800
 801  PRVMQKLDNDGLPFIGAKLEFGDPYYGYLNLNTGEGFVVYYKSKENCVVD   850
 851  NIKVCSNDTGSGKFKCVCVTVRVPRNPTIGDKFASRHGQKGILSRLWPAE   900
 901  DMPFTESGMMPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPF   950
 951  IFSEENSALEYFGEMLKAAGYNFYGTERLYSGISGMELEADIFIGVVYYQ  1000
1001  RLRHMVSDKFQVRTTGARDKVTNQPIGGRNVQGGIRFGEMERDALLAHGT  1050
1051  SFLLHDRLFNCSDRSVAHVCVKCGSLLSPLLEKPPPSWSAMRNRKYNCTV  1100
1101  CGRSDSIDTVSVPYVFRYFVAELAAMNIKVKLDVI                 1135

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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