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

NucPred

Fetching Q02173 from www.uniprot.org...

The NucPred score for your sequence is 0.31 (see score help below)

   1  MSSVAVPFYQRRHKHFDQSYRNIQTRYVLEEYAARKAASRQAAHYESTGL    50
  51  GKTTCRLCARRARSLAHEAMQESRKRTHEQKSHASDEKRIKFASELSSLE   100
 101  REIHMARHHAREQLDRLAIQRMVEENMALERHVVEEKISRAPEILVRLRS   150
 151  HTVWEKMSVRLCFTVQGFPSPVVQWYKNEELITPASDPAKYSVENKYGVH   200
 201  VLHINRADFDDSATYSAVATNIHGQASTNCAVVVRRFRESEEPHPAGIMP   250
 251  FHLPLSYDVCFTHFDVQFLEKFGVTFATEGETLTLKCSVLVTPELKRLRP   300
 301  RAEWYRDDVLIKDSKWTKLYFGEGQAALSFTHLNKDDEGLYTLRMVTKGG   350
 351  VNECSAFLFVRDADALIAGAPGAPMDVKCHDANRDYVIVTWKPPNTTSQN   400
 401  PVIGYFVDKCEVGLENWVQCNDAPVKICKYPVTGLYEGRSYIFRVRAVNS   450
 451  AGISRPSRVSEPVAALDPVDLERTQTVHVDEGRKIVISKDDLEGDIQIPG   500
 501  PPTNVHASEISKTYVVLSWDPPVPRGREPLTYFIEKSMVGSGSWQRVNAQ   550
 551  VAVKSPRYAVFDLAEGKPYVFRVLSANKHGISDPSEITEPIQPQDIVVVP   600
 601  SAPGRVVATRNTKTSVVVQWDKPKHEENLYGYYIDYSVVGSNQWEPANHK   650
 651  PINYNRFVVHGLETGEQYIFRVKAVNAVGFSENSQESEAIKVQAALTCPS   700
 701  YPHGITLLNCDGHSMTLGWKAPKYSGGSPILGYYIDKREANHKNWHEVNS   750
 751  SVISRTIYTVEDLTEDAFYEFKIAAANVVGIGHPSDPSEHFKCKAWTMPE   800
 801  PGPAYDLTVCEVRNTSLVLLWKAPVYEGKSPITGYLVDYKEVDTEDWITA   850
 851  NEKPTSHRYFKVTDLHQGHTYVFKVRAVNDAGVGKSSEISEPVFVEASPG   900
 901  TKEIFSGVDEEGNIYLGFECKEATDASHFLWGKSYEEIEDSDKFKIETKG   950
 951  DHSKLYFKHPDKSDLGTYCISVSDTDGVSSSFVLDEEELERLMTLSNEIK  1000
1001  NPTIPLKSELAYEVLDKGEVRFWIQAESLSPNSTYRFVINDKEVENGDRH  1050
1051  KISCDHSNGIIEMVMDKFTIDNEGTYTVQIQDGKAKNQSSLVLIGDAFKA  1100
1101  ILAESELQRKEFLRKQGPHFSEFLYWEVTEECEVLLACKIANTKKETVFK  1150
1151  WYRNGSGIDVDEAPDLQKGECHLTVPKLSRKDEGVYKATLSDDRGHDVST  1200
1201  LELSGKVYNDIILALSRVSGKTASPLKILCTEEGIRLQCFLKYYNEEMKV  1250
1251  TWSHRESKISSGEKMKIGGGEDVAWLQITEPTEKDKGNYTFEIFSDKESF  1300
1301  KRTLDLSGQAFDDALTEFQRLKAAAFAEKNRGKVIGGLPDVVTIMDGKTL  1350
1351  NLTCTVFGNPDPEVVWFKNDKALELNEHYLVSLEQGKYASLTIKGVTSED  1400
1401  SGKYSIYVKNKYGGETVDVTVSVYRHGEKIPEVNQGQLAKPRLIPPSSST  1450

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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