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

NucPred

Fetching Q9BXT5 from www.uniprot.org...

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

   1  MPSDAKDSVNGDLLLNWTSLKNILSGLNASFPLHNNTGSSTVTTSKSIKD    50
  51  PRLMRREESMGEQSSTAGLNEVLQFEKSSDNVNSEIKSTPSNSASSSEVV   100
 101  PGDCAVLTNGLDTPCFKTSVNDSQSWAHNMGSEDYDCIPPNKVTMAGQCK   150
 151  DQGNFSFPISVSNVVSEVENQNHSEEKAQRAQQESGNAYTKEYSSHIFQD   200
 201  SQSSDLKTIYQTGCQTSTVFPLKKKVSIDEYLQNTGKMKNFADLEDSSKH   250
 251  EEKQTSWKEIDNDFTNETKISPIDNYIVLHQEYKESESHNSFGKSCDKIL   300
 301  ITQELEITKSSTSTIKDKDELDHLALEWQITPSFESLSQKHPQHSVEYEG   350
 351  NIHTSLAIAQKLMELKLGKINQNYASIITEAFPKPKDIPQAKEMFIDTVI   400
 401  SSYNIETAHDSSNCSITREHICVHRKNENEPVSLENIQRDYKETAYVEDR   450
 451  GQDHNLFCNSQLSNDIWLNVNFKKQTDRENQNEAKENSASCVENNIENIY   500
 501  GDKKQDSHTNENFSNIDEKEDKNYHNIEILSSEEFSTKFNLICREDNAVS   550
 551  AATALLESEEDTISAVKQKDTENTGRSVEHLASTTFPKTASSSVCVASNA   600
 601  AIQIASATMPALSLNNDDHQIYQFKETCSSESPDFGLLVKHRVSDCEIDT   650
 651  DKNKSQESFHQSINENLVLQSIELESEIEIELEDCDDAFIFQQDTHSHEN   700
 701  MLCEEFVTSYKALKSRISWEGLLALDNGEMEVLESTTGRENSDQHYSKES   750
 751  NYFYSSTQNNETELTSPILLPDLQIKITNIFRPGFSPTADSLALKDSFCT   800
 801  HVTEATKPEINKEDGEILGFDIYSQPFGENADYPCEDKVDNIRQESGPVS   850
 851  NSEISLSFDLSRNTDVNHTSENQNSESLFTEPSNVTTIDDGSRCFFTKSK   900
 901  TDYNDTKNKKEVESRISKRKLHISSRDQNIPHKDLRRHKIYGRKRRLTSQ   950
 951  DSSECFSSLSQGRIKTFSQSEKHIKSVLNILSDEASLCKSKCLSRKLDKA  1000
1001  VVHLKKAHRRVHTSLQLITKVGEERKGPLPKSYAIICNNFWESCDLQGYS  1050
1051  SVSQRKYYSTKHFSSKRKYDKRRKKRAPKADISKSLTHVSKHKSYKTSGE  1100
1101  KKCLSRKSMASSVSKSHPTTSHMGEFCNQEHPESQLPVSSTSQSTSQSVY  1150
1151  YNSSVSNPSLSEEHQPFSGKTAYLFSPDHSDEKLIEKENQIDTAFLSSTS  1200
1201  KYEKLEKHSANHNVKDATKENSCDANEVINESNSVSLSCIKENINSSTGN  1250
1251  DCDATCIGHTKAKTDVLISVLDSNVKHFLNDLYQQGNLILSDCKRNLEVK  1300
1301  WTDPIERPKQNIITGNFLMGPLNLTLIASKKYSIPQLSAAAVTDSEGESS  1350
1351  KSYLDKQRILTVDSFAASSTVPHCEQSCREKELLKTEQCSSGNCLHTDGN  1400
1401  ETNVTENYELDVASGTEEDKSYGENIVELSSSDSSLLLKDNVKGSSSETC  1450
1451  IVKKDTEDRITWKVKQAEKAKDSVYKRSMTEGSTVNTEYKNQKNQISEES  1500
1501  CLNEKIITTNLIDSHLSTKNTTTESVPLKNTVSNPLNKREKKGEIKVSKD  1550
1551  SQSDLTLHSEIAYISKPGILGVNHTPILPAHSETCKVPTLLKKPASYVSD  1600
1601  FKEKHCSANHTALIANLSQILQRADEASSLQILQEETKVCLNILPLFVEA  1650
1651  FERKQECSVEQILISRELLVDQNLWNNCKHTLKPCAVDTLVELQMMMETI  1700
1701  QFIENKKRHLEGEPTLRSLLWYDETLYAELLGKPRGFQQQSNFYPGFQGR  1750
1751  LKYNAFCELQTYHDQLVELLEETKREKNSYYVFLKYKRQVNECEAIMEHC  1800
1801  SDCFDFSLSVPFTCGVNFGDSLEDLEILRKSTLKLINVCGDSPKVHSYPG  1850
1851  KQDHLWIIIEMISSKVNFIKNNEAVRVKISLYGLEHIFFDAAKNLVWKER  1900
1901  TQSFSKKYSQKKDEERLLRVNKCAFSKLQKIYDTLSKDLNNEPISPIGLE  1950
1951  EDTIIASRKSDHPINEATISIENSKFNSNLLAHPDICCISEILDQAEFAD  2000
2001  LKKLQDLTLRCTDHLEILKKYFQMLQDNNMDNIFITEENVLDVVINHSHE  2050
2051  AIILKPEAIEMYIEIVMVSETIHFLKNSIAKKLDKQRFRGMLWFDLSLLP  2100
2101  ELVQCQEKMASFSFLKDNSTDVCLWKVIETAVSELKKDLDIICKYNEAVN  2150
2151  CSYAIHLLSRELQELSEIKKLLKKSKYFISTYIDFVPYIASINYGSTVTE  2200
2201  LEYNYNQFSTLLKNVMSAPRKDLGKMAHIRKVMKTIEHMKMICTKNAELT  2250
2251  ISFFLCQMLYNRRKILQLKRKEKMNIHIVKPGENNNKFSISTMLPPVSEC  2300
2301  INKNISNSSKKRPSTVDKCEDSQEQQQDTTVSSCKKLKVDMKDVTKINRE  2350
2351  KATFKHPRTTGSHPKSENKIVPSSCDSLKRNHLTPKKVEMQRSLPGSLLP  2400
2401  LENPKDTCASKSESKIDLTVSSDHFSGQQENLNSMKKRNVNFSAAETKSD  2450
2451  KKDCAAFAICDQKSVHGTFSPDHGTLLQKFLKNSPDPTQKSCLSDINPET  2500
2501  DVSLVPDASVLSKPIFCFVKDVHPDLEMNDTVFELQDNDIVNSSIKNSSC  2550
2551  MTSPEPICIQNKIPTLQINKLQPTETESEDKYMKDTLNPNTVHTFGASGH  2600
2601  ITLNVNQGAEYSLSEQQNDKNSKVLMQNAATYWNELPQSACNPTYNSSEH  2650
2651  LFGTSYPYSAWCVYQYSNSNGNAITQTYQGITSYEVQPSPSGLLTTVAST  2700
2701  AQGTHSNLLYSQYFTYFAGEPQANGFVPVNGYFQSQIPASNFRQPIFSQY  2750
2751  ASHQPLPQATYPYLPNRFVPPEVPWVYAPWHQESFHPGH             2789

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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