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

NucPred

Fetching Q9H583 from www.uniprot.org...

The NucPred score for your sequence is 0.71 (see score help below)

   1  MTSLAQQLQRLALPQSDASLLSRDEVASLLFDPKEAATIDRDTAFAIGCT    50
  51  GLEELLGIDPSFEQFEAPLFSQLAKTLERSVQTKAVNKQLDENISLFLIH   100
 101  LSPYFLLKPAQKCLEWLIHRFHIHLYNQDSLIACVLPYHETRIFVRVIQL   150
 151  LKINNSKHRWFWLLPVKQSGVPLAKGTLITHCYKDLGFMDFICSLVTKSV   200
 201  KVFAEYPGSSAQLRVLLAFYASTIVSALVAAEDVSDNIIAKLFPYIQKGL   250
 251  KSSLPDYRAATYMIICQISVKVTMENTFVNSLASQIIKTLTKIPSLIKDG   300
 301  LSCLIVLLQRQKPESLGKKPFPHLCNVPDLITILHGISETYDVSPLLHYM   350
 351  LPHLVVSIIHHVTGEETEGMDGQIYKRHLEAILTKISLKNNLDHLLASLL   400
 401  FEEYISYSSQEEMDSNKVSLLNEQFLPLIRLLESKYPRTLDVVLEEHLKE   450
 451  IADLKKQELFHQFVSLSTSGGKYQFLADSDTSLMLSLNHPLAPVRILAMN   500
 501  HLKKIMKTSKEGVDESFIKEAVLARLGDDNIDVVLSAISAFEIFKEHFSS   550
 551  EVTISNLLNLFQRAELSKNGEWYEVLKIAADILIKEEILSENDQLSNQVV   600
 601  VCLLPFMVINNDDTESAEMKIAIYLSKSGICSLHPLLRGWEEALENVIKS   650
 651  TKPGKLIGVANQKMIELLADNINLGDPSSMLKMVEDLISVGEEESFNLKQ   700
 701  KVTFHVILSVLVSCCSSLKETHFPFAIRVFSLLQKKIKKLESVITAVEIP   750
 751  SEWHIELMLDRGIPVELWAHYVEELNSTQRVAVEDSVFLVFSLKKFIYAL   800
 801  KAPKSFPKGDIWWNPEQLKEDSRDYLHLLIGLFEMMLNGADAVHFRVLMK   850
 851  LFIKVHLEDVFQLFKFCSVLWTYGSSLSNPLNCSVKTVLQTQALYVGCAM   900
 901  LSSQKTQCKHQLASISSPVVTSLLINLGSPVKEVRRAAIQCLQALSGVAS   950
 951  PFYLIIDHLISKAEEITSDAAYVIQDLATLFEELQREKKLKSHQKLSETL  1000
1001  KNLLSCVYSCPSYIAKDLMKVLQGVNGEMVLSQLLPMAEQLLEKIQKEPT  1050
1051  AVLKDEAMVLHLTLGKYNEFSVSLLNEDPKSLDIFIKAVHTTKELYAGMP  1100
1101  TIQITALEKITKPFFAAISDEKVQQKLLRMLFDLLVNCKNSHCAQTVSSV  1150
1151  FKGISVNAEQVRIELEPPDKAKPLGTVQQKRRQKMQQKKSQDLESVQEVG  1200
1201  GSYWQRVTLILELLQHKKKLRSPQILVPTLFNLLSRCLEPLPQEQGNMEY  1250
1251  TKQLILSCLLNICQKLSPDGGKIPKDILDEEKFNVELIVQCIRLSEMPQT  1300
1301  HHHALLLLGTVAGIFPDKVLHNIMSIFTFMGANVMRLDDTYSFQVINKTV  1350
1351  KMVIPALIQSDSGDSIEVSRNVEEIVVKIISVFVDALPHVPEHRRLPILV  1400
1401  QLVDTLGAEKFLWILLILLFEQYVTKTVLAAAYGEKDAILEADTEFWFSV  1450
1451  CCEFSVQHQIQSLMNILQYLLKLPEEKEETIPKAVSFNKSESQEEMLQVF  1500
1501  NVETHTSKQLRHFKFLSVSFMSQLLSSNNFLKKVVESGGPEILKGLEERL  1550
1551  LETVLGYISAVAQSMERNADKLTVKFWRALLSKAYDLLDKVNALLPTETF  1600
1601  IPVIRGLVGNPLPSVRRKALDLLNNKLQQNISWKKTIVTRFLKLVPDLLA  1650
1651  IVQRKKKEGEEEQAINRQTALYTLKLLCKNFGAENPDPFVPVLNTAVKLI  1700
1701  APERKEEKNVLGSALLCIAEVTSTLEALAIPQLPSLMPSLLTTMKNTSEL  1750
1751  VSSEVYLLSALAALQKVVETLPHFISPYLEGILSQVIHLEKITSEMGSAS  1800
1801  QANIRLTSLKKTLATTLAPRVLLPAIKKTYKQIEKNWKNHMGPFMSILQE  1850
1851  HIGVMKKEELTSHQSQLTAFFLEALDFRAQHSENDLEEVGKTENCIIDCL  1900
1901  VAMVVKLSEVTFRPLFFKLFDWAKTEDAPKDRLLTFYNLADCIAEKLKGL  1950
1951  FTLFAGHLVKPFADTLNQVNISKTDEAFFDSENDPEKCCLLLQFILNCLY  2000
2001  KIFLFDTQHFISKERAEALMMPLVDQLENRLGGEEKFQERVTKHLIPCIA  2050
2051  QFSVAMADDSLWKPLNYQILLKTRDSSPKVRFAALITVLALAEKLKENYI  2100
2101  VLLPESIPFLAELMEDECEEVEHQCQKTIQQLETVLGEPLQSYF        2144

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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