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

NucPred

Fetching P49025 from www.uniprot.org...

The NucPred score for your sequence is 0.97 (see score help below)

   1  MLKFKYGVRNPPEASASEPIASRASRLNLFFQGKPPLMTQQQMSALSREG    50
  51  MLDALFALFEECSQPALMKMKHVSSFVQKYSDTIAELRELQPSARDFEVR   100
 101  SLVGCGHFAEVQVVREKATGDVYAMKIMKKKALLAQEQVSFFEEERNILS   150
 151  RSTSPWIPQLQYAFQDKNNLYLVMEYQPGGDFLSLLNRYEDQLDESMIQF   200
 201  YLAELILAVHSVHQMGYVHRDIKPENILIDRTGEIKLVDFGSAAKMNSNK   250
 251  VDAKLPIGTPDYMAPEVLTVMNEDRRGTYGLDCDWWSVGVVAYEMVYGKT   300
 301  PFTEGTSARTFNNIMNFQRFLKFPDDPKVSSELLDLLQSLLCVQKERLKF   350
 351  EGLCCHPFFARTDWNNIRNSPPPFVPTLKSDDDTSNFDEPEKNSWVSSSV   400
 401  CQLSPSGFSGEELPFVGFSYSKALGYLGRSESVVSSLDSPAKVSSMEKKL   450
 451  LIKSKELQDSQDKCHKMEQEMTRLHRRVSEVEAVLSQKEVELKASETQRS   500
 501  LLEQDLATYITECSSLKRSLEQARMEVSQEDDKALQLLHDIREQSRKLQE   550
 551  IKEQEYQAQVEEMRLMMNQLEEDLVSARRRSDLYESELRESRLAAEEFKR   600
 601  KANECQHKLMKAKDQGKPEVGEYSKLEKINAEQQLKIQELQEKLEKAVKA   650
 651  STEATELLQNIRQAKERAERELEKLHNREDSSEGIKKKLVEAEERRHSLE   700
 701  NKVKRLETMERRENRLKDDIQTKSEQIQQMADKILELEEKHREAQVSAQH   750
 751  LEVHLKQKEQHYEEKIKVLDNQIKKDLADKESLENMMQRHEEEAHEKGKI   800
 801  LSEQKAMINAMDSKIRSLEQRIVELSEANKLAANSSLFTQRNMKAQEEMI   850
 851  SELRQQKFYLETQAGKLEAQNRKLEEQLEKISHQDHSDKSRLLELETRLR   900
 901  EVSLEHEEQKLELKRQLTELQLSLQERESQLTALQAARAALESQLRQAKT   950
 951  ELEETTAEAEEEIQALTAHRDEIQRKFDALRNSCTVITDLEEQLNQLTED  1000
1001  NAELNNQNFYLSKQLDEASGANDEIVQLRSEVDHLRREITEREMQLTSQK  1050
1051  QTMEALKTTCTMLEEQVLDLEALNDELLEKERQWEAWRSVLGDEKSQFEC  1100
1101  RVRELQRMLDTEKQSRARADQRITESRQVVELAVKEHKAEILALQQALKE  1150
1151  QKLKAESLSDKLNDLEKKHAMLEMNARSLQQKLETERELKQRLLEEQAKL  1200
1201  QQQMDLQKNHIFRLTQGLQEALDRADLLKTERSDLEYQLENIQVLYSHEK  1250
1251  VKMEGTISQQTKLIDFLQAKMDQPAKKKKVPLQYNELKLALEKEKARCAE  1300
1301  LEEALQKTRIELRSAREEAAHRKATDHPHPSTPATARQQIAMSAIVRSPE  1350
1351  HQPSAMSLLAPPSSRRKESSTPEEFSRRLKERMHHNIPHRFNVGLNMRAT  1400
1401  KCAVCLDTVHFGRQASKCLECQVMCHPKCSTCLPATCGLPAEYATHFTEA  1450
1451  FCRDKMNSPGLQSKEPGSSLHLEGWMKVPRNNKRGQQGWDRKYIVLEGSK  1500
1501  VLIYDNEAREAGQRPVEEFELCLPDGDVSIHGAVGASELANTAKADVPYI  1550
1551  LKMESHPHTTCWPGRTLYLLAPSFPDKQRWVTALESVVAGGRVSREKAEA  1600
1601  DAKLLGNSLLKLEGDDRLDMNCTLPFSDQVVLVGTEEGLYALNVLKNSLT  1650
1651  HIPGIGAVFQIYIIKDLEKLLMIAGEERALCLVDVKKVKQSLAQSHLPAQ  1700
1701  PDVSPNIFEAVKGCHLFAAGKIENSLCICAAMPSKVVILRYNDNLSKYCI  1750
1751  RKEIETSEPCSCIHFTNYSILIGTNKFYEIDMKQYTLDEFLDKNDHSLAP  1800
1801  AVFASSSNSFPVSIVQANSAGQREEYLLCFHEFGVFVDSYGRRSRTDDLK  1850
1851  WSRLPLAFAYREPYLFVTHFNSLEVIEIQARSSLGSPARAYLEIPNPRYL  1900
1901  GPAISSGAIYLASSYQDKLRVICCKGNLVKESGTEQHRVPSTSRSSPNKR  1950
1951  GPPTYNEHITKRVASSPAPPEGPSHPREPSTPHRYRDREGRTELRRDKSP  2000
2001  GRPLEREKSPGRMLSTRRERSPGRLFEDSSRGRLPAGAVRTPLSQVNKVW  2050
2051  DQSSV                                               2055

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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