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

NucPred

Fetching P23116 from www.uniprot.org...

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

   1  MPAYFQRPENALKRANEFLEVGKKQPALDVLYDVMKSKKHRTWQKIHEPI    50
  51  MLKYLELCVDLRKSHLAKEGLYQYKNICQQVNIKSLEDVVRAYLKLAEEK   100
 101  TEAAKEESQQMVLDIEDLDNIQTPESVLLSAVSGEDTQDRTDRLLLTPWV   150
 151  KFLWESYRQCLDLLRNNSRVERLYHDIAQQAFKFCLQYTRKAEFRKLCDN   200
 201  LRMHLSQIQRHHNQSTAINLNNPESQSMHLETRLVQLDSAISMELWQEAF   250
 251  KAVEDIHGLFSLSKKPPKPQLMANYYNKVSTVFWKSGNALFHASTLHRLY   300
 301  HLSREMRKNLTQEEMQRMSTRVLLATLSIPITPERTDIARLLDMDGIIVE   350
 351  KQRRLATLLGLQAPPTRIGLINDMVRFSVLQYVVPEVKDLYNWLEVEFNP   400
 401  LKLCERVTKVLNWVREQPEKEPELQQYVPQLQNNTILRLLQQVAQIYQSI   450
 451  EFSRLTSLVPFVDAFQLERAIVDAARHCDLQVRIDHTSRTLSFGSDLNYA   500
 501  TREDAPVGPHLQSMPSEQIRNQLTAMSSVLAKALEVIRPAHILQEKEEQH   550
 551  QLAVNAYLKNSRKEHQRILARRQTIEERKERLESLNIQREKEELEQREAE   600
 601  LQKVRKAEEERLRQEAKEREKERILQEHEQIKKKTVRERLEQIKKTELGA   650
 651  KAFKDIDIEDLEELDPDFIMAKQVEQLEKEKKELQERLKNQEKKIDYFER   700
 701  AKRLEEIPLIKSAYEEQRVKDMDLWEQQEEERITTMQLEREKALEHKNRM   750
 751  SRMLEDRDLFVMRLKAARQSVYEEKLKQFEERLAEERHSRLEDRKRQRKE   800
 801  ERKITYYREKEEEEQRRAEEQMLKEREERERAERAKREEELREYQERVKK   850
 851  LEEVERKKRQRELEIEERERRREEERRLGDDPLSRKDSRWGDRDSEGTWR   900
 901  KGPEADSEWRRGPPEKEWRRETRDDERPHRRDEDRLRRLGGDDEERESSL   950
 951  RPDDDRIPRRGLDDDRGPRRGPDEDRFSRRGTDDDRPSWRNADDDRPPRR  1000
1001  IGDDDRGSWRHTDDDRPPRRGLDDERGSWRTADEDRGPRRGMDDDRGPRR  1050
1051  GGADDERSSWRNADDDRGPRRGMDDDRGPRRGLDDDRGPWRNAAEDRISR  1100
1101  RGADDDRGPWRNMDDDRVPRRGDDARPGPWRPFVKPGGWREKEKAREESW  1150
1151  GPPRESRPSEEREWDRDKEKDRDNQDREENDKDLERDRDRERDGDREDRF  1200
1201  RRPRDEGGWRRGPAEESSSWRDSSRRDDRDREDRRRDRDDRRDLRDLRDR  1250
1251  RDLRDDRDRRGPPLRSEREEASSWRRTDDRKDDRTEERDPPRRVPPPALS  1300
1301  RDREREREREGEKEKASWRAEKDRESLRRTKNETDEDGWTTVRR        1344

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.)

Go back to the NucPred Home Page.