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

NucPred

Fetching Q9ERB4 from www.uniprot.org...

The NucPred score for your sequence is 0.70 (see score help below)

   1  MLINMNGILWMCSTLLLTHALHKAKMEENPPVKGSLSGKVILPCHFSTLP    50
  51  TLPPDYNTSEFLRIKWSKIEVDKNGKDIKETTVLVAQDGNIKIGQDYKGR   100
 101  VSVPTHPDDVGDASLTMVKLRASDAGVYRCDVMYGIEDTQNTMSLAVDGV   150
 151  VFHYRAATSRYTLNFESAQQACLDIGAVIATPEQLFAAYEDGFEQCDAGW   200
 201  LSDQTVRYPIRAPREGCYGDMMGKEGVRTYGFRSPQETYDVYCYVDHLDG   250
 251  DVFHITAPSKFTFEEAEAECANRDARLATVGELHAAWRNGFDQCDYGWLS   300
 301  DASVRHPVTVARAQCGGGLLGVRTLYRFENQTCFPLPDSRFDAYCFKRSP   350
 351  LSIIPKTEWSVSETSVPLEDEVLGKSDQDTLEQTHLEATMSPEALSTIEV   400
 401  TQGETQEEPQTPGIPFPALSSTAVMTKETTAFEEEGEGSTYTLSEDRLMT   450
 451  DSEIVPSLETTPVGTSYPGGAMTQQEVEMDTMVTQMSSIRPTVVLSTEPE   500
 501  VSYEAEGSSPMEFASTLKPFGTQVTQLVEETTEEGKKTPLDYTDLGSGLF   550
 551  EQPRVTELPDFSMTPSDISVFTAIDSLHRTTPLRPPSPFTEEPHIFEKEP   600
 601  SEKTTGDIILPRESVTQHPLTTLMDIIAKKTESDIDHEYHMTSKPPVMQP   650
 651  TRPSVVERKTTSKPQELSTSPPPAGTKFHPDINVYIIEVRENKTGRMSDM   700
 701  VVNGHPIDSESKEEEPCSEETDPLHDLFAEILPELPDSFEIDIYHSEEDE   750
 751  DGEEDCVNATDVTTTPSVQYITGKPHVTTVPKNPEAAEARRGLYESVAPS   800
 801  QNFSNTSATDTHQFIPAETELSTTMQFTKSKEATELLEITWKPETYPETP   850
 851  EHFSSGEPDVFPTLPSHDGKTTKWSEFITESNPNTENPEHKQPKPIPLFP   900
 901  EEFSGEGAIDQASQQTIFSRATEVALGKETDQSPTISTSSIRSGSVSVHA   950
 951  LEEDPIALTGISQTDESMSTVESWVEMTPSQTVEFSGSSSAPTIEGSGEV  1000
1001  EEYTNKIFNTVTDLPQREPTDTLIPLDMSNIMITDHHIYTPATTAPLDSQ  1050
1051  LPSTDARPTQFGIQTTTSEWVSSTSFEGRKTEEDKERDTNAAHTGEVQPA  1100
1101  TERSDRLLLTSELESSNVAASSPLDTWEGFVPETTSTVSEKEMANTTPVF  1150
1151  TETSDVANLETQSFEHSSSSQPRVQEELTTLSGKPPLIFMDLGSGDASTD  1200
1201  MEFITASSFTLDLESDTKVKKELPSTLSPSVETSSSSEPIGLAPSTVLDI  1250
1251  EIVEVMNQTSKKTLISELSGKPTSQAEVRDLYPGLGEDFSGDSSEYPTVS  1300
1301  STTMKEETVGMGGSENERVKDTQTLSSIPPTSDNINPVPDSKGFGSTVAS  1350
1351  TTAFPWEEFMTSAEGSGEELSSVRSSVSLVLPLGVDILPTTESPYFDQEF  1400
1401  EEAAAVTEAGKQSALPIAVSGNTVDLTENRDIEVNSTMSVDLPQTMEPAK  1450
1451  LWSKPEVNPEKQEIGSETVTQDKAQGQKSFESLHSSLAPEQTTLESQSLI  1500
1501  ETEVQTSYYSMLTTMKTYNTNEEVEEEGTSIAHMSTPGPGIKGLESYPTH  1550
1551  PEATGKSYSFSASALVTESGPARSVVMDSSTQEEESIKLFQKDMILTHKE  1600
1601  SNSDLSFSGLGSGEALPPLPTTSVSLTDMGKINSTLYPETSHMESLGTSI  1650
1651  LGDNHERMKNVSNEVRTLISETGSISQDSTEAPNTTLSDTRTEESTTSPL  1700
1701  PFMKLMDTEHSPKQTLRWEEEIQTHRPQTMTGQMTNDNSSVSEAEAAATS  1750
1751  APAFLPETYSVEMTKAFATSPSQTSDLFDANSGEGSGEVDGLDLVYTSRT  1800
1801  TQASSQGDSMFASHGFIEKHPEVSRTETGATDGSPTASAMFLHQSEYNES  1850
1851  SLYPTSTLPSTVTYESPSEGIADGLQDHIRFEVSTLKPSRRKATESVIID  1900
1901  LDKEDSKDLGLAITESAIVEILPELTSDRNIIIDIDHTKPVYEYIPGIQT  1950
1951  DLDSDIPLGSHGSSEESLEVQEKYEATINLSPTEEAFDGSGDALPAGHTQ  2000
2001  AIYNESVTPSDGKQPEDISFSFATGIPVSSTETELNTFFPTVSTLHIPSK  2050
2051  LTTASPEIDKPNIEAISLDDIFESSTLSDGQAIADQSEVISTLGHLEKTQ  2100
2101  EEYEEKKYGGPSFQPEFFSGVGEVFTDAPAYVSIGRTYSVAQPLTEFPNV  2150
2151  VGQSDSTHYTEATSAVSSVTELSPQTPSSPSPVYIDSGVSEFTEVPHKSA  2200
2201  QPAPTAASSQKLIEGSFKKVRANIEATIKSLGENDHGTESPSMSPSPALD  2250
2251  ISEDDSKPKLLEDLETSPTKTETSQDSPNKANDQIPGKTAGILAGIKTTE  2300
2301  SGPVVTAADDMELGDATQRPHSASAPAAFRVETSMVPQPIPQEPERPTFP  2350
2351  SLEINHETHTSLFEESILATSEKQVSQRILDYSNQATVSTLDLNTEHSIP  2400
2401  PFSILDNSNETAFLIGISEETVEGTAVYLPGPDLCKTNPCLNGGTCYPTE  2450
2451  TSYVCTCAPGYSGDQCELDFDECHSNPCRNGATCVDGLNTFRCLCLPSYV  2500
2501  GALCEQDTETCDYGWHKFQGQCYKYFAHRRTWDAAERECRLQGAHLTSIL  2550
2551  SHEEQMFVNRVGHDYQWIGLNDKMFEHDFRWTDGSALQYENWRPNQPDSF  2600
2601  FSAGEDCVVIIWHENGQWNDVPCNYHLTYTCKKGTVACGQPPVVENAKTF  2650
2651  GKMKPRYEINSLIRYHCKDGFIQRHLPTIRCLGNGRWAMPKITCMNPSAY  2700
2701  QRTYSKKYLKNSSSVKDNSINTSKHEHRWSRRWQETRR              2738

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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