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

NucPred

Fetching Q92576 from www.uniprot.org...

The NucPred score for your sequence is 1.00 (see score help below)

   1  MDIVDTFNHLIPTEHLDDALFLGSNLENEVCEDFSASQNVLEDSLKNMLS    50
  51  DKDPMLGSASNQFCLPVLDSNDPNFQMPCSTVVGLDDIMDEGVVKESGND   100
 101  TIDEEELILPNRNLRDKVEENSVRSPRKSPRLMAQEQVRSLRQSTIAKRS   150
 151  NAAPLSNTKKASGKTVSTAKAGVKQPERSQVKEEVCMSLKPEYHKENRRC   200
 201  SRNSGQIEVVPEVSVSSSHSSVSSCLEMKDEDGLDSKHKCNNPGEIDVPS   250
 251  HELNCSLLSETCVTIGEKKNEALMECKAKPVGSPLFKFSDKEEHEQNDSI   300
 301  SGKTGETVVEEMIATRKVEQDSKETVKLSHEDDHILEDAGSSDISSDAAC   350
 351  TNPNKTENSLVGLPSCVDEVTECNLELKDTMGIADKTENTLERNKIEPLG   400
 401  YCEDAESNRQLESTEFNKSNLEVVDTSTFGPESNILENAICDVPDQNSKQ   450
 451  LNAIESTKIESHETANLQDDRNSQSSSVSYLESKSVKSKHTKPVIHSKQN   500
 501  MTTDAPKKIVAAKYEVIHSKTKVNVKSVKRNTDVPESQQNFHRPVKVRKK   550
 551  QIDKEPKIQSCNSGVKSVKNQAHSVLKKTLQDQTLVQIFKPLTHSLSDKS   600
 601  HAHPGCLKEPHHPAQTGHVSHSSQKQCHKPQQQAPAMKTNSHVKEELEHP   650
 651  GVEHFKEEDKLKLKKPEKNLQPRQRRSSKSFSLDEPPLFIPDNIATIRRE   700
 701  GSDHSSSFESKYMWTPSKQCGFCKKPHGNRFMVGCGRCDDWFHGDCVGLS   750
 751  LSQAQQMGEEDKEYVCVKCCAEEDKKTEILDPDTLENQATVEFHSGDKTM   800
 801  ECEKLGLSKHTTNDRTKYIDDTVKHKVKILKRESGEGRNSSDCRDNEIKK   850
 851  WQLAPLRKMGQPVLPRRSSEEKSEKIPKESTTVTCTGEKASKPGTHEKQE   900
 901  MKKKKVEKGVLNVHPAASASKPSADQIRQSVRHSLKDILMKRLTDSNLKV   950
 951  PEEKAAKVATKIEKELFSFFRDTDAKYKNKYRSLMFNLKDPKNNILFKKV  1000
1001  LKGEVTPDHLIRMSPEELASKELAAWRRRENRHTIEMIEKEQREVERRPI  1050
1051  TKITHKGEIEIESDAPMKEQEAAMEIQEPAANKSLEKPEGSEKQKEEVDS  1100
1101  MSKDTTSQHRQHLFDLNCKICIGRMAPPVDDLSPKKVKVVVGVARKHSDN  1150
1151  EAESIADALSSTSNILASEFFEEEKQESPKSTFSPAPRPEMPGTVEVEST  1200
1201  FLARLNFIWKGFINMPSVAKFVTKAYPVSGSPEYLTEDLPDSIQVGGRIS  1250
1251  PQTVWDYVEKIKASGTKEICVVRFTPVTEEDQISYTLLFAYFSSRKRYGV  1300
1301  AANNMKQVKDMYLIPLGATDKIPHPLVPFDGPGLELHRPNLLLGLIIRQK  1350
1351  LKRQHSACASTSHIAETPESAPPIALPPDKKSKIEVSTEEAPEEENDFFN  1400
1401  SFTTVLHKQRNKPQQNLQEDLPTAVEPLMEVTKQEPPKPLRFLPGVLIGW  1450
1451  ENQPTTLELANKPLPVDDILQSLLGTTGQVYDQAQSVMEQNTVKEIPFLN  1500
1501  EQTNSKIEKTDNVEVTDGENKEIKVKVDNISESTDKSAEIETSVVGSSSI  1550
1551  SAGSLTSLSLRGKPPDVSTEAFLTNLSIQSKQEETVESKEKTLKRQLQED  1600
1601  QENNLQDNQTSNSSPCRSNVGKGNIDGNVSCSENLVANTARSPQFINLKR  1650
1651  DPRQAAGRSQPVTTSESKDGDSCRNGEKHMLPGLSHNKEHLTEQINVEEK  1700
1701  LCSAEKNSCVQQSDNLKVAQNSPSVENIQTSQAEQAKPLQEDILMQNIET  1750
1751  VHPFRRGSAVATSHFEVGNTCPSEFPSKSITFTSRSTSPRTSTNFSPMRP  1800
1801  QQPNLQHLKSSPPGFPFPGPPNFPPQSMFGFPPHLPPPLLPPPGFGFAQN  1850
1851  PMVPWPPVVHLPGQPQRMMGPLSQASRYIGPQNFYQVKDIRRPERRHSDP  1900
1901  WGRQDQQQLDRPFNRGKGDRQRFYSDSHHLKRERHEKEWEQESERHRRRD  1950
1951  RSQDKDRDRKSREEGHKDKERARLSHGDRGTDGKASRDSRNVDKKPDKPK  2000
2001  SEDYEKDKEREKSKHREGEKDRDRYHKDRDHTDRTKSKR             2039

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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