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

NucPred

Fetching Q9ESF1 from www.uniprot.org...

The NucPred score for your sequence is 0.57 (see score help below)

   1  MALIVHLKTVSELRGKGDRIAKVTFRGQSFYSRVLENCEGVADFDETFRW    50
  51  PVASSIDRNEVLEIQIFNYSKVFSNKLIGTFCMVLQKVVEENRVEVTDTL   100
 101  MDDSNAIIKTSLSMEVRYQATDGTVGPWDDGDFLGDESLQEEKDSQETDG   150
 151  LLPGSRPSTRISGEKSFRRAGRSVFSAMKLGKTRSHKEEPQRQDEPAVLE   200
 201  MEDLDHLAIQLGDGLDPDSVSLASVTALTSNVSNKRSKPDIKMEPSAGRP   250
 251  MDYQVSITVIEARQLVGLNMDPVVCVEVGDDKKYTSMKESTNCPYYNEYF   300
 301  VFDFHVSPDVMFDKIIKISVIHSKNLLRSGTLVGSFKMDVGTVYSQPEHQ   350
 351  FHHKWAILSDPDDISAGLKGYVKCDVAVVGKGDNIKTPHKANETDEDDIE   400
 401  GNLLLPEGVPPERQWARFYVKIYRAEGLPRMNTSLMANVKKAFIGENKDL   450
 451  VDPYVQVFFAGQKGKTSVQKSSYEPLWNEQVVFTDLFPPLCKRMKVQIRD   500
 501  SDKVNDVAIGTHFIDLRKISNDGDKGFLPTLGPAWVNMYGSTRNYTLLDE   550
 551  HQDLNEGLGEGVSFRARLMLGLAVEILDTSNPELTSSTEVQVEQATPVSE   600
 601  SCTGRMEEFFLFGAFLEASMIDRKNGDKPITFEVTIGNYGNEVDGMSRPL   650
 651  RPRPRKEPGDEEEVDLIQNSSDDEGDEAGDLASVSSTPPMRPQITDRNYF   700
 701  HLPYLERKPCIYIKSWWPDQRRRLYNANIMDHIADKLEEGLNDVQEMIKT   750
 751  EKSYPERRLRGVLEELSCGCHRFLSLSDKDQGRSSRTRLDRERLKSCMRE   800
 801  LESMGQQAKSLRAQVKRHTVRDKLRLCQNFLQKLRFLADEPQHSIPDVFI   850
 851  WMMSNNKRIAYARVPSKDLLFSIVEEELGKDCAKVKTLFLKLPGKRGFGS   900
 901  AGWTVQAKLELYLWLGLSKQRKDFLCGLPCGFEEVKAAQGLGLHSFPPIS   950
 951  LVYTKKQAFQLRAHMYQARSLFAADSSGLSDPFARVFFINQSQCTEVLNE  1000
1001  TLCPTWDQMLVFDNLELYGEAHELRDDPPIIVIEIYDQDSMGKADFMGRT  1050
1051  FAKPLVKMADEAYCPPRFPPQLEYYQIYRGSATAGDLLAAFELLQIGPSG  1100
1101  KADLPPINGPVDMDRGPIMPVPVGIRPVLSKYRVEVLFWGLRDLKRVNLA  1150
1151  QVDRPRVDIECAGKGVQSSLIHNYKKNPNFNTLVKWFEVDLPENELLHPP  1200
1201  LNIRVVDCRAFGRYTLVGSHAVSSLRRFIYRPPDRSAPNWNTTVRLLRGC  1250
1251  HRLRNGGPSSRPTGEVVVSMEPEEPVKKLETMVKLDATSDAVVKVDVAED  1300
1301  EKERKKKKKKGPSEEPEEEEPDESMLDWWSKYFASIDTMKEQLRQHETSG  1350
1351  TDLEEKEEMESAEGLKGPMKSKEKSRAAKEEKKKKNQSPGPGQGSEAPEK  1400
1401  KKAKIDELKVYPKELESEFDSFEDWLHTFNLLRGKTGDDEDGSTEEERIV  1450
1451  GRFKGSLCVYKVPLPEDVSREAGYDPTYGMFQGIPSNDPINVLVRIYVVR  1500
1501  ATDLHPADINGKADPYIAIKLGKTDIRDKENYISKQLNPVFGKSFDIEAS  1550
1551  FPMESMLTVAVYDWDLVGTDDLIGETKIDLENRFYSKHRATCGIAQTYSI  1600
1601  HGYNIWRDPMKPSQILTRLCKEGKVDGPHFGPHGRVRVANRVFTGPSEIE  1650
1651  DENGQRKPTDEHVALSALRHWEDIPRVGCRLVPEHVETRPLLNPDKPGIE  1700
1701  QGRLELWVDMFPMDMPAPGTPLDISPRKPKKYELRVIVWNTDEVVLEDDD  1750
1751  FFTGEKSSDIFVRGWLKGQQEDKQDTDVHYHSLTGEGNFNWRYLFPFDYL  1800
1801  AAEEKIVMSKKESMFSWDETEYKIPARLTLQIWDADHFSADDFLGAIELD  1850
1851  LNRFPRGAKTAKQCTMEMATGEVDVPLVSIFKQKRVKGWWPLLARNENDE  1900
1901  FELTGKVEAELHLLTAEEAEKNPVGLARNEPDPLEKPNRPDTSFIWFLNP  1950
1951  LKSARYFLWHTYRWLLLKFLLLFLLLLLFALFLYSLPGYLAKKILGA     1997

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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