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

NucPred

Fetching Q9Y3S1 from www.uniprot.org...

The NucPred score for your sequence is 0.88 (see score help below)

   1  MDGDGGRRDVPGTLMEPGRGAGPAGMAEPRAKAARPGPQRFLRRSVVESD    50
  51  QEEPPGLEAAEAPGPQPPQPLQRRVLLLCKTRRLIAERARGRPAAPAPAA   100
 101  LVAQPGAPGAPADAGPEPVGTQEPGPDPIAAAVETAPAPDGGPREEAAAT   150
 151  VRKEDEGAAEAKPEPGRTRRDEPEEEEDDEDDLKAVATSLDGRFLKFDIE   200
 201  LGRGSFKTVYKGLDTETWVEVAWCELQDRKLTKLERQRFKEEAEMLKGLQ   250
 251  HPNIVRFYDFWESSAKGKRCIVLVTELMTSGTLKTYLKRFKVMKPKVLRS   300
 301  WCRQILKGLLFLHTRTPPIIHRDLKCDNIFITGPTGSVKIGDLGLATLKR   350
 351  ASFAKSVIGTPEFMAPEMYEEHYDESVDVYAFGMCMLEMATSEYPYSECQ   400
 401  NAAQIYRKVTCGIKPASFEKVHDPEIKEIIGECICKNKEERYEIKDLLSH   450
 451  AFFAEDTGVRVELAEEDHGRKSTIALRLWVEDPKKLKGKPKDNGAIEFTF   500
 501  DLEKETPDEVAQEMIESGFFHESDVKIVAKSIRDRVALIQWRRERIWPAL   550
 551  QPKEQQDVGSPDKARGPPVPLQVQVTYHAQAGQPGPPEPEEPEADQHLLP   600
 601  PTLPTSATSLASDSTFDSGQGSTVYSDSQSSQQSVMLGSLADAAPSPAQC   650
 651  VCSPPVSEGPVLPQSLPSLGAYQQPTAAPGLPVGSVPAPACPPSLQQHFP   700
 701  DPAMSFAPVLPPPSTPMPTGPGQPAPPGQQPPPLAQPTPLPQVLAPQPVV   750
 751  PLQPVPPHLPPYLAPASQVGAPAQLKPLQMPQAPLQPLAQVPPQMPPIPV   800
 801  VPPITPLAGIDGLPPALPDLPTATVPPVPPPQYFSPAVILPSLAAPLPPA   850
 851  SPALPLQAVKLPHPPGAPLAMPCRTIVPNAPATIPLLAVAPPGVAALSIH   900
 901  SAVAQLPGQPVYPAAFPQMAPTDVPPSPHHTVQNMRATPPQPALPPQPTL   950
 951  PPQPVLPPQPTLPPQPVLPPQPTRPPQPVLPPQPMLPPQPVLPPQPALPV  1000
1001  RPEPLQPHLPEQAAPAATPGSQILLGHPAPYAVDVAAQVPTVPVPPAAVL  1050
1051  SPPLPEVLLPAAPELLPQFPSSLATVSASVQSVPTQTATLLPPANPPLPG  1100
1101  GPGIASPCPTVQLTVEPVQEEQASQDKPPGLPQSCESYGGSDVTSGKELS  1150
1151  DSCEGAFGGGRLEGRAARKHHRRSTRARSRQERASRPRLTILNVCNTGDK  1200
1201  MVECQLETHNHKMVTFKFDLDGDAPDEIATYMVEHDFILQAERETFIEQM  1250
1251  KDVMDKAEDMLSEDTDADRGSDPGTSPPHLSTCGLGTGEESRQSQANAPV  1300
1301  YQQNVLHTGKRWFIICPVAEHPAPEAPESSPPLPLSSLPPEASQGPCRGL  1350
1351  TLPCLPWRRAACGAVFLSLFSAESAQSKQPPDSAPYKDQLSSKEQPSFLA  1400
1401  SQQLLSQAGPSNPPGAPPAPLAPSSPPVTALPQDGAAPATSTMPEPASGT  1450
1451  ASQAGGPGTPQGLTSELETSQPLAETHEAPLAVQPLVVGLAPCTPAPEAA  1500
1501  STRDASAPREPLPPPAPEPSPHSGTPQPALGQPAPLLPAAVGAVSLATSQ  1550
1551  LPSPPLGPTVPPQPPSALESDGEGPPPRVGFVDSTIKSLDEKLRTLLYQE  1600
1601  HVPTSSASAGTPVEVGDRDFTLEPLRGDQPRSEVCGGDLALPPVPKEAVS  1650
1651  GRVQLPQPLVEKSELAPTRGAVMEQGTSSSMTAESSPRSMLGYDRDGRQV  1700
1701  ASDSHVVPSVPQDVPAFVRPARVEPTDRDGGEAGESSAEPPPSDMGTVGG  1750
1751  QASHPQTLGARALGSPRKRPEQQDVSSPAKTVGRFSVVSTQDEWTLASPH  1800
1801  SLRYSAPPDVYLDEAPSSPDVKLAVRRAQTASSIEVGVGEPVSSDSGDEG  1850
1851  PRARPPVQKQASLPVSGSVAGDFVKKATAFLQRPSRAGSLGPETPSRVGM  1900
1901  KVPTISVTSFHSQSSYISSDNDSELEDADIKKELQSLREKHLKEISELQS  1950
1951  QQKQEIEALYRRLGKPLPPNVGFFHTAPPTGRRRKTSKSKLKAGKLLNPL  2000
2001  VRQLKVVASSTGHLADSSRGPPAKDPAQASVGLTADSTGLSGKAVQTQQP  2050
2051  CSVRASLSSDICSGLASDGGGARGQGWTVYHPTSERVTYKSSSKPRARFL  2100
2101  SGPVSVSIWSALKRLCLGKEHSSRSSTSSLAPGPEPGPQPALHVQAQVNN  2150
2151  SNNKKGTFTDDLHKLVDEWTSKTVGAAQLKPTLNQLKQTQKLQDMEAQAG  2200
2201  WAAPGEARAMTAPRAGVGMPRLPPAPGPLSTTVIPGAAPTLSVPTPDGAL  2250
2251  GTARRNQVWFGLRVPPTACCGHSTQPRGGQRVGSKTASFAASDPVRS     2297

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.