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

NucPred

Fetching Q9NY15 from www.uniprot.org...

The NucPred score for your sequence is 0.51 (see score help below)

   1  MAGPRGLLPLCLLAFCLAGFSFVRGQVLFKGCDVKTTFVTHVPCTSCAAI    50
  51  KKQTCPSGWLRELPDQITQDCRYEVQLGGSMVSMSGCRRKCRKQVVQKAC   100
 101  CPGYWGSRCHECPGGAETPCNGHGTCLDGMDRNGTCVCQENFRGSACQEC   150
 151  QDPNRFGPDCQSVCSCVHGVCNHGPRGDGSCLCFAGYTGPHCDQELPVCQ   200
 201  ELRCPQNTQCSAEAPSCRCLPGYTQQGSECRAPNPCWPSPCSLLAQCSVS   250
 251  PKGQAQCHCPENYHGDGMVCLPKDPCTDNLGGCPSNSTLCVYQKPGQAFC   300
 301  TCRPGLVSINSNASAGCFAFCSPFSCDRSATCQVTADGKTSCVCRESEVG   350
 351  DGRACYGHLLHEVQKATQTGRVFLQLRVAVAMMDQGCREILTTAGPFTVL   400
 401  VPSVSSFSSRTMNASLAQQLCRQHIIAGQHILEDTRTQQTRRWWTLAGQE   450
 451  ITVTFNQFTKYSYKYKDQPQQTFNIYKANNIAANGVFHVVTGLRWQAPSG   500
 501  TPGDPKRTIGQILASTEAFSRFETILENCGLPSILDGPGPFTVFAPSNEA   550
 551  VDSLRDGRLIYLFTAGLSKLQELVRYHIYNHGQLTVEKLISKGRILTMAN   600
 601  QVLAVNISEEGRILLGPEGVPLQRVDVMAANGVIHMLDGILLPPTILPIL   650
 651  PKHCSEEQHKIVAGSCVDCQALNTSTCPPNSVKLDIFPKECVYIHDPTGL   700
 701  NVLKKGCASYCNQTIMEQGCCKGFFGPDCTQCPGGFSNPCYGKGNCSDGI   750
 751  QGNGACLCFPDYKGIACHICSNPNKHGEQCQEDCGCVHGLCDNRPGSGGV   800
 801  CQQGTCAPGFSGRFCNESMGDCGPTGLAQHCHLHARCVSQEGVARCRCLD   850
 851  GFEGDGFSCTPSNPCSHPDRGGCSENAECVPGSLGTHHCTCHKGWSGDGR   900
 901  VCVAIDECELDMRGGCHTDALCSYVGPGQSRCTCKLGFAGDGYQCSPIDP   950
 951  CRAGNGGCHGLATCRAVGGGQRVCTCPPGFGGDGFSCYGDIFRELEANAH  1000
1001  FSIFYQWLKSAGITLPADRRVTALVPSEAAVRQLSPEDRAFWLQPRTLPN  1050
1051  LVRAHFLQGALFEEELARLGGQEVATLNPTTRWEIRNISGRVWVQNASVD  1100
1101  VADLLATNGVLHILSQVLLPPRGDVPGGQGLLQQLDLVPAFSLFRELLQH  1150
1151  HGLVPQIEAATAYTIFVPTNRSLEAQGNSSHLDADTVRHHVVLGEALSME  1200
1201  TLRKGGHRNSLLGPAHWIVFYNHSGQPEVNHVPLEGPMLEAPGRSLIGLS  1250
1251  GVLTVGSSRCLHSHAEALREKCVNCTRRFRCTQGFQLQDTPRKSCVYRSG  1300
1301  FSFSRGCSYTCAKKIQVPDCCPGFFGTLCEPCPGGLGGVCSGHGQCQDRF  1350
1351  LGSGECHCHEGFHGTACEVCELGRYGPNCTGVCDCAHGLCQEGLQGDGSC  1400
1401  VCNVGWQGLRCDQKITSPQCPRKCDPNANCVQDSAGASTCACAAGYSGNG  1450
1451  IFCSEVDPCAHGHGGCSPHANCTKVAPGQRTCTCQDGYMGDGELCQEINS  1500
1501  CLIHHGGCHIHAECIPTGPQQVSCSCREGYSGDGIRTCELLDPCSKNNGG  1550
1551  CSPYATCKSTGDGQRTCTCDTAHTVGDGLTCRARVGLELLRDKHASFFSL  1600
1601  RLLEYKELKGDGPFTIFVPHADLMSNLSQDELARIRAHRQLVFRYHVVGC  1650
1651  RRLRSEDLLEQGYATALSGHPLRFSEREGSIYLNDFARVVSSDHEAVNGI  1700
1701  LHFIDRVLLPPEALHWEPDDAPIPRRNVTAAAQGFGYKIFSGLLKVAGLL  1750
1751  PLLREASHRPFTMLWPTDAAFRALPPDRQAWLYHEDHRDKLAAILRGHMI  1800
1801  RNVEALASDLPNLGPLRTMHGTPISFSCSRTRAGELMVGEDDARIVQRHL  1850
1851  PFEGGLAYGIDQLLEPPGLGARCDHFETRPLRLNTCSICGLEPPCPEGSQ  1900
1901  EQGSPEACWRFYPKFWTSPPLHSLGLRSVWVHPSLWGRPQGLGRGCHRNC  1950
1951  VTTTWKPSCCPGHYGSECQACPGGPSSPCSDRGVCMDGMSGSGQCLCRSG  2000
2001  FAGTACELCAPGAFGPHCQACRCTVHGRCDEGLGGSGSCFCDEGWTGPRC  2050
2051  EVQLELQPVCTPPCAPEAVCRAGNSCECSLGYEGDGRVCTVADLCQDGHG  2100
2101  GCSEHANCSQVGTMVTCTCLPDYEGDGWSCRARNPCTDGHRGGCSEHANC  2150
2151  LSTGLNTRRCECHAGYVGDGLQCLEESEPPVDRCLGQPPPCHSDAMCTDL  2200
2201  HFQEKRAGVFHLQATSGPYGLNFSEAEAACEAQGAVLASFPQLSAAQQLG  2250
2251  FHLCLMGWLANGSTAHPVVFPVADCGNGRVGIVSLGARKNLSERWDAYCF  2300
2301  RVQDVACRCRNGFVGDGISTCNGKLLDVLAATANFSTFYGMLLGYANATQ  2350
2351  RGLDFLDFLDDELTYKTLFVPVNEGFVDNMTLSGPDLELHASNATLLSAN  2400
2401  ASQGKLLPAHSGLSLIISDAGPDNSSWAPVAPGTVVVSRIIVWDIMAFNG  2450
2451  IIHALASPLLAPPQPQAVLAPEAPPVAAGVGAVLAAGALLGLVAGALYLR  2500
2501  ARGKPMGFGFSAFQAEDDADDDFSPWQEGTNPTLVSVPNPVFGSDTFCEP  2550
2551  FDDSLLEEDFPDTQRILTVK                                2570

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.)

Go back to the NucPred Home Page.