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

NucPred

Fetching Q8MJ04 from www.uniprot.org...

The NucPred score for your sequence is 0.99 (see score help below)

   1  MSETSSTSVSMIHRSFEGQGPPRHLSVMHPVVAKKISFYKSGDPQFGGVK    50
  51  VVVNPRSFKTFDALLDNLSRKVPLPFGVRNISTPRGRHSITRLEELEDGA   100
 101  SYLCSHRRKVQPVDLDKARRRPRPWLSSRAISAHAQRSPPTSIGAAGAPG   150
 151  MLRAPRRLLVFRNGDPKIRRVVIVNRRVTQSFQAFLQHLTEVMRFPVTKL   200
 201  YATDGRKVPSLQAVILSSGAVVAAGREPFKPGNYDIQKYLLSARLPGTSH   250
 251  HVYIKGNTRSESRKMSTHVPSSPRSQIYSVSSGKMHNNDCYSDHSFASEN   300
 301  YLALEKNDSRNLLIYPSEDDIEKSIIFNQDGTMTVEMKVRFKIKEEETIK   350
 351  WTTVSRASLSHNNEKCEVGCFPGRTDDQSSHLKIAACSLSADVSSLEKDN   400
 401  NQEVSLTEEINTRITDQETETCTSVSWENGAMDTNICTRVTQDQAKHHFY   450
 451  RPPTPGPKRVRQKSVRGSVTLVSETEVEEEMIRQFSYSEAREDGENKSEY   500
 501  HMFTHSCSKMSSVSNKPLLVQINNNEQMESSLERKKESRLLKSGAIRAGV   550
 551  EITNQKMLEMSHNNGSPQTISENSIVGEVIVDSLTSDNKTNIKILRPYSR   600
 601  TRDRFSPILADTTHSLSNDSGIDKTVSEIPALVESSTVTTRIDRLINEFA   650
 651  QCDLTNSANEKQTSLSVASKKKMKSQQQVINSRHQIRKIATKGILSKNKR   700
 701  INTGRRIAQEIILEGSDGSLKGGVVCEEDLHVSDTVIESNYCSQSDLNPV   750
 751  NSKNFHVNKLNTLQNPKKFQGLLAKRKSRPLTKVSLGGPTKREIGQGDKV   800
 801  FPHNDFRYCKNNFEDQNLFPMFNFLEQRPSDFCGPQGQAEIASWYLGGIT   850
 851  KKNLVSKVNNSHITLKTQKKQKGDKLKSSTTVSKQQVTTRANSLGSLKKA   900
 901  VFPEAISHHSVQNYIQRWLQNTNPHSALQSRKSAPIYKKDRSVVSCNNNG   950
 951  FAGTKSHTSSGEGNNFARESNKYITKNASLTENLGKKVGKFFDKVNSEEL  1000
1001  SKDLCENQVESLNDACLLPLHENCALSQSAIDDHNTKIQVCAEKLGPEIS  1050
1051  LVYQEINVATKRHSVEAAIQVDLTEEDTSKDPLPILLLRQLQALVPSIHK  1100
1101  TQNGITQMPGSLADIPFSSPICKSYTNVLLAWLLVLTLKGSINSFCQGDA  1150
1151  HKTTNRASEILGLLEVLRHTAITEEADDLKAAVANLVESTTNHFGLTEKE  1200
1201  QDMVPVGLSANCSTPNLHRVPKCVENEKTQKISSGGGHSASEHCGPEACV  1250
1251  SELTCSCQMCIVNKTCPPKETCNLSDIFCPSDGCTVDQTPMNKACFQGEV  1300
1301  CSLTDALSSHRACAHEENHSRKATCPIDEAYIPNKICNTSDFLIFKENTC  1350
1351  TDNLELTEELERINKVQKDLNVLADPGCKHSFNILVSDQNISNLSYSSFP  1400
1401  INETEPEFDKERSSVAELKNYSLKTFQGKNAYTSSDKEDSKTSEEPGSIT  1450
1451  NSMTSSERNISELESFEELENQDTDTFHMKVNAREQAAEELIQKELEASK  1500
1501  NLQLIDGSRRNITEEEERNGIICEAIRRRLATPPSLVFCYDSKQNTEKDL  1550
1551  NEGETKMRVKMMVKSVEIGSYSESSLDFKNDFIGPVTSDWSEFRPSSENE  1600
1601  QPYKTSSDGPNGSCEEIVQDKDYNKGFVKRTIEKLYSKGEIIKPSFFSGS  1650
1651  IHRSQVCPYNSVEFQCARKVDLYDCEGQSFGSSEQLSSNSSMLQKFLEEG  1700
1701  QDKCDFNDVRANYHGGDILGHGTKQNDHNRIIRDIEEGVLIDKGKWLLKE  1750
1751  NHLLRISSPENSGLYGNADTISVDTLLNNDNEVPYSHFGNLAPDPTMAEL  1800
1801  SSSELEELSQPLELKCSYFNMPHCSDSEPFCEDLLDVQNKTCARERIPVH  1850
1851  HAEEKANHKSERVCTSVTHGFTSAGNKVHPVSDDTIKNQPLPVNNAIHGA  1900
1901  LQEGDSLDKLYAICGQHCPILTVIIQPINEEDRGFAYCKNSDIENFLGLH  1950
1951  LWMKVHPYLLPSNKTIFRDANNKANGRKAFIDNAFDDTFDLMDKRKLRNL  2000
2001  KGISSLGLEEENNLKKFQLYLKKKFCVNFLHTSLLIVDNRNSDTRDSINQ  2050
2051  TNEIFEVVDENNNFLNSRFQNSRTNLNQVVRECSDFFFEMHGQTCLFYQV  2100
2101  ETSLNISNRNTVEIFYVFEDENLFIWEEESQFDLESNDEDL           2141

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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