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

NucPred

Fetching Q9P7R0 from www.uniprot.org...

The NucPred score for your sequence is 0.29 (see score help below)

   1  MSNESNIITVPILGKDTVRVGFGIHQYICTEILENFKSSTYVVITDSNIA    50
  51  PLYLEKIESTFNKSIKDAKAEARLLTYVIPPGESSKCRAMKAEIEDWLLT   100
 101  QSCTRDTILIAMGGGVIGDLVGYVAASFMRGIRFIQMPTTLLAMVDSSIG   150
 151  GKTGIDTPLGKNLVGAFWQPLRVYVDMVFLHTLPPRQVINGLSEIIKTAA   200
 201  MWNENDFQLLENNSAVLLDALNKPSVPGEYKFDSIKPLLQKIILSSIRTK   250
 251  CEVVTLDEHEGGLRNLLNFGHSIGHAYEAILYPQILHGECVAIGMVKEAE   300
 301  LARYLGILKPNAVGRLTKCLVSYNLPISVNDPKVKKYASFKHCPVEKLIE   350
 351  YMAVDKKNQGSKKRIVILKAIGETYEKHATVVSDDDIRFILSRDVKVDEF   400
 401  TKSSWDVVVTPPGSKSISNRALVLAAMGNGTCRLTNMLHSDDTQFMMSAL   450
 451  ESLGAATFSWEDGGETLVVKGNGGKLAVPKEELYLGNAGTAARFLTGIAA   500
 501  LVSSKDGAKVVLTGNHRMKVRPIGPLVDALRANGCEINYLEKQGSLPLDL   550
 551  SSKNGLKGGIIELAATVSSQYVSSILMCAPYASQPVTLKLVGGKPISQLY   600
 601  IDMTIAMMASFGVNVTKSTTEENTYNIPCGKYQNPPHYEIESDASSATYP   650
 651  LAIAAITGTKCTVPNIGSASLQGDARFACDVLRPMGCTVEQTATSTTVQG   700
 701  PPKGTLKPLESIDMETMTDAFLTASVVAAVACNVSEGDPVTRITGIANQR   750
 751  VKECNRIAAMVHELAKFGVRTGELEDGIYIFGKNYKELKKPEEGIYTYDD   800
 801  HRIAMSFSVLSLICPSRTLIIDKACVEKTWPYWWDVLHQSFGVKLTGATS   850
 851  VASDPLKGSISKNASIILIGMRGAGKTTIGKIIAKQLNFKFLDLDELLED   900
 901  YLEMPIAEVIFRMGWDAFRLEEHKVLRKFITEHPEGYVAASGGGVIEMDE   950
 951  SRNLLSNFVKEGGIVLHVHRNLEHIKSYLSEDQTRPTYKDQESIDDVYKR  1000
1001  RHVWYRECRSHYFISPVLSNQVIDEKIQYSMSRFLDVVTGSSQVLQKFKT  1050
1051  KKRSTFLTLNYPRIEDALPTLRDVTVGCDAIEVRVDYLKDPKSSNGISSL  1100
1101  DFVAEQISLLRCSTTLPIIFTIRTISQGGLFPNDKEEEAKELMLSAMRYG  1150
1151  CDFVDVELGWSSETINILYQHKGYTKLIMSWHDLSGTWSWARPHEWMQKV  1200
1201  ELASSYADVIKLVGMANNLNDNLELEEFRTRITNSMDIPLILFNMGRFGQ  1250
1251  LSRILNKFMTPVTHPLLPSKAAPGQLTVKQLNEARVLIGEILPEKFFLFG  1300
1301  KPIKHSRSPILHSTAYELLGLPHTYEAFETDTVDEVQKVLNLPDFGGANV  1350
1351  TIPYKLSVMKFMDELSDEARFFGAVNTIIPIRIGDKLVLRGDNTDWRGIY  1400
1401  DTFANALDGVSLRDTNGLVIGAGGTSRAAIYSLHRLGVSRIYLLNRTLAN  1450
1451  SYRVQDVFPPDYNIHIIDSDNIPSEELSSVTLSAVVSTIPADIELPEKVA  1500
1501  SVIKALLANKADGGVFLDMAYKPLHTPLMAVASDLEWKCCNGLEALVRQG  1550
1551  LASFHLWTGMTAPFDAVYQKVIE                             1573

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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