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

NucPred

Fetching P82451 from www.uniprot.org...

The NucPred score for your sequence is 0.27 (see score help below)

   1  MSLSFCGNNISSYNIYDGVLQNPCFVDALNLVPHVFLLFITFPILFIGWG    50
  51  SQSSKVQIHHNTWLHFPGHNLRWILTFALLFVHVCEIAEGIVSDSRRESR   100
 101  HLHLFMPAVMGFVATTTSIVYYHNIETSNFPKLLLALFLYWVMAFITKTI   150
 151  KLVKYWQSGWGVSDLRFCITGIMVILNGLLMAVEINVIRIRRYVFFMNPQ   200
 201  KVKPPEDLQDLGVRFLQPFVNLLSKATYWWMNTLIISAHKKPIDLKAIGK   250
 251  LPIAMRAVTNYVCLKDAYEEQKKKAADHPNRTPSIWLAMYRAFGRPILLS   300
 301  STFRYLADLLGFAGPLCISGIVQRVNETQNGTNNTTGISEILSSKEFLEN   350
 351  AYVLAVLLFLALILQRTFLQASYYVTIETGINLRGALLAMIYNKILRLST   400
 401  SNLSMGEMTLGQINNLVAIETNQLMWFLFLCPNLWAMPVQIIMGVILLYN   450
 451  LLGSSALVGAAVIVLLAPMQYFIATKLAEAQKSTLDYSTERLKKTNEILK   500
 501  GIKLLKLYAWEHIFCKSVEETRVKELSSLKAFALYTSLSIFMNAAIPIAA   550
 551  VLATFVTHAYASGNNLQPAEAFASLSLFHILVTPLFLLSTVVRFAVKAII   600
 601  SVQKLNEFLLSDEIGDDSWRTGEASLPFESCKKHTGVQPKTINRKQPGRY   650
 651  HLDSYEQSTRRLRPMETEDIAIKVTNGCFSWGSGAATLSNIDIRIPTGQL   700
 701  TMIVGQVGCGKSSLLLAILGEMQTLDGKVHWSNVNESEPSFEATRSRNRY   750
 751  SVAYAAQKPWLLNATVEENITFGSPFNKQRYKAVTDACSLQPDIDLLPFG   800
 801  DQTEIGERGINLSGGQTERICVARALYQNTNIVFLDDPFSALDIHLSDHL   850
 851  MQEGILKFLQDDKRTLVLVTHKLQYLTHADWIIAMKDGSVLREGTLKDIQ   900
 901  TKDVELYEHWKTLMNRQDQELEKDMEADQTTLERKTLRRAMYSREAKAQM   950
 951  EDEDEEEEEEEDEDDNMSTVMRLRTKMPWKTCWRYLTSGGFFLLFLMIFS  1000
1001  KLLKHSVIVAIDYWLATWTSEYSINNTGKADQTYYVAGFSILCGAGIFLC  1050
1051  LVTSLTVEWMGLTAAKNLHHNLLNKIILGPIRFFDTTPLGLILNRFSADT  1100
1101  NIIDQHIPPTLESLTRSTLLCLSAIGMISYATPVFLVALVPLGVAFYFIQ  1150
1151  KYFRVASKDLQELDDSTQLPLLCHFSETAEGLTTIRAFRHEARFKQRMLE  1200
1201  LTDTNNIAYLFLSAANRWLEVRTDYLGACIVLTASIASISGSSNSGLVGL  1250
1251  GLLYALTITNYLNWVVRNLADLEVQMGAVKKVNSFLTMESENYEGTMDPS  1300
1301  QVPEHWPQEGEIKIHDLCVRYENNLKPVLKHVKAYIKPGQKVGICGRTGS  1350
1351  GKSSLSLAFFRMVDIFDGKIVIDGIDISKLPLHTLRSRLSIILQDPILFS  1400
1401  GSIRFNLDPECKCTDDRLWEALEIAQLKNMVKSLSGGLDAVVTEGGENFS  1450
1451  VGQRQLFCLARAFVRKSSILIMDEATASIDMATENILQKVVMTAFADRTV  1500
1501  VTIAHRVSSIVDADLVLVFSEGILVECDTGPNLLTHKNGLFSTLVMTNK   1549

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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