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

NucPred

Fetching Q6CP76 from www.uniprot.org...

The NucPred score for your sequence is 0.75 (see score help below)

   1  MSFSFEVSVIVTGLSSLKLKTRNDSLDNLNLLLKTSPTEVPVKAFSPILD    50
  51  AIITIIESEKTRYEKTRLENGKDARIELYENRLGSAAYTLRLFVERNCER   100
 101  FKPKHIKLLSMTLFELMTRPRSRSLITSVADHLTYSLVALCGSPVFQCNF   150
 151  ELHQWISLSHDISDAVTYHLDVSYNDKIIANLLQTLLELFQIDTIGIEDI   200
 201  ATPVVRMTIKYLTLITKENTNTRTILTLVNSAILRLHLIRFQDVINLSYY   250
 251  TIKHLLRIKLTNENNIGEIARFNLMISEVLYNKTPIIVGEDKDQSYVNKE   300
 301  KLLPALQDYLIHSLKQYDHTKFTLDCVTFIDGPASSKFNWYSFSDICQNE   350
 351  KNCLEDIWLYALSLTMMLKANYQFLEYKESSLAGGSLLFKRRKVKDTFAH   400
 401  MLKDSLTYDDFLCNCIDSDSIKIKTTGLHIGLLYLSIFDCSNIELSHLKE   450
 451  ELFRCSQDVRFMLLCLSCFIPMCSQSKNSFSPEEEIRLFKMCVPLLKTSN   500
 501  GCKTACSLLYKLIEFQLEPIKDKSVLQQMSDLYLLSDVNGPALVCNESFK   550
 551  FWMHLHYYAKTFQTVKSPITYVFSWLYARWDQLFTLVVSETHFYVFASWL   600
 601  CGCTHTTFPTFEYSRPSLFHDTWMGLSEERASITGFSLTIRTIELRKQKF   650
 651  APVFCEEAERVRFMYKLFDLIDESAISATFIDRAIQVLRTIESLVGQRNY   700
 701  TDYLSRFKEIFLLSSSVIDFGQNAQIFSVMEGMISLKDSLLRHIIMDILP   750
 751  TEKVLSTFMQRLAEHTQQTSHQDEFLSHHAKPEAGSIPISEMIEIGFEFA   800
 801  LQVHSVSKAFDPLSSFILYSKKLSLPMLNRTLPNLITYLENNENEIPTAS   850
 851  LERLTQFLGSSLLAPSFDTSSTSMKLLTRYLEGISKYWVMEDRSQVLTAD   900
 901  CNDIFDWIVTQYDESSFSGVEALYELARFMTLLLEKYNLSNSSISGGKQR   950
 951  VFKILSGCITRLPKYLTNRVVSLLGTYVKRVGVTNQRILFKELLQRFNPP  1000
1001  QESVETAAFFSLTCTKLSLINEFYLLNSILHLLDNTNFSHLLLYVEKSLD  1050
1051  TISTFYGLCSKQDLFHQCRYFIIDQWFTKSAKSKIYEPSIWKVELFEFEF  1100
1101  DEFCIRYQMELTSFFFAKSSTYYYIIDHLKKLLNLKQEALLTKYIAPTIA  1150
1151  LSYVDSGVKDLIFDIAADLLGRKFPNVLTINLDDVIYYFIKLSDLSNLAT  1200
1201  SLTFWCKIFNSSRFTNMLHYNSSNCMQLNDNVAIAFPIVYKVLKKNVFTD  1250
1251  IDDGRSFEYVIQRLVMDLQNCVLIDQKIRVLRQIKLLVLFFEHKLTLFKD  1300
1301  IDFFLLELSKFLFNADIFSEVYGFILDLLEFSANNKMDVARSLTELMRFC  1350
1351  FTVTDSNVKKTLFPKVNPVLFNFCVSDGKQLYATCYALLTLETNSFGWND  1400
1401  IAQVFKFQEVDRTSVSLLSDLFDNFDYDGSFDANLISPTTIQNLISIPRD  1450
1451  NARVSDKFRRWLGNILGEIVYTRPYDHIIPHHCSTLDLESGISGLLQILW  1500
1501  VQYQKADDISLRFLLDHIQSIILQDESVLAEISSDSYSSLVNLKNLTDIS  1550
1551  WEKFENCHGMLNIKLGETFLTLTFTDRSCHYQKWISAFICNILLVIVEKF  1600
1601  PSFRILALLCDNTAFLHSAIISQLIKILLVSFPKQRSSFLSDILNRADEI  1650
1651  FKTEDRTLKMEVITKVFSIIRGMALNGVQNALYVYDKIKLQPVIPIMLSL  1700
1701  GSEIWSLMIYEEFYGEYCTGKMLDYELLYQIYSKIDEKDLFYGLPLSSSL  1750
1751  ASSLTLISKTKFNSYTNFALSNGRFEEGLRNKDSSCLHEFASVTSSNGFT  1800
1801  GLATMLDSNFENPLLSANQYSWALKLNKWDLPIPEARDSFAKSAFSILKD  1850
1851  VKEIPDFFSFDDHILKVMDGGSLLKNSQLNLETMESLGLLVSLKKLGSAD  1900
1901  MNTLTTLNNLRVHDTLNADYLPENVFDILHWSRHFFIESKINNTSVIEHA  1950
1951  PGSNFTLQLAKILNLVHASTFCRDQGRFQDLINIVMTLEAAVDDITNNPA  2000
2001  IGPSDTITLFCKRISTVESARMLWANKESAMAINMLEDLLQTNLTAVNVE  2050
2051  NVSLADVQDILMPDAVVDSQLVEWSSFSRHRSPDVIFNDHILYYERDVLN  2100
2101  INEPNLRSSICYTYAEFCYKQSQKVDEGELLYLKQKIAKASNQLQEISSI  2150
2151  YKNPKLRDAERKEAKRHHNRLSLQNHHDKDRYNKISSSRIAFVSQALHFF  2200
2201  LTTLVHSNSRDAEVVDKFCSLWFSYSTDDIINSKLQKEIGTVPSFKFLPW  2250
2251  VSQMASKLADSVSPFQDTLQLTLKRMLYKLPYETLYPLISMSLQDSESKV  2300
2301  IDPVTKSRVEVVNKIIAALDMYDSGRYGSQFTRPVQAFCSMSVALACHKI  2350
2351  PPKMKFLQLDTLNIGKYWLETLPKVHLPLPTLPVKITCSQDGRREGRSYI  2400
2401  SSIDPKVLISSSGLSLPKIATFTVSDGTRHRVLLKGSNDDLRQDAIMEQV  2450
2451  FKQVNKILKANKTTRKQNLSVRTYEVIPLGPRAGLIEFVANSMSLHDILL  2500
2501  NLHCNDEISFDKARKTMKAAQNHSVEERVLTFSRITEKIKPQLRRFFFQS  2550
2551  FVHAHDWYESRNRYTKSVVTSSIVGYLLGLGDRHLNNILIDIKTGEPIHI  2600
2601  DLGVAFDQGKLLPIPELVPFRLTRDIVDGFGVAGIEGLFRNNCERVFKVL  2650
2651  QDEKERLLCVLNVLKWDPLYSWKMTPLKKQRLQAKFTGDYDEEEISVSDA  2700
2701  DFSELLEEDNNNDESIRALKGVESKLYGDGLSVEAIVQELLSSATDKQNL  2750
2751  ATIYMGWSPFY                                         2761

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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