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

NucPred

Fetching P26361 from www.uniprot.org...

The NucPred score for your sequence is 0.62 (see score help below)

   1  MQKSPLEKASFISKLFFSWTTPILRKGYRHHLELSDIYQAPSADSADHLS    50
  51  EKLEREWDREQASKKNPQLIHALRRCFFWRFLFYGILLYLGEVTKAVQPV   100
 101  LLGRIIASYDPENKVERSIAIYLGIGLCLLFIVRTLLLHPAIFGLHRIGM   150
 151  QMRTAMFSLIYKKTLKLSSRVLDKISIGQLVSLLSNNLNKFDEGLALAHF   200
 201  IWIAPLQVTLLMGLLWDLLQFSAFCGLGLLIILVIFQAILGKMMVKYRDQ   250
 251  RAAKINERLVITSEIIDNIYSVKAYCWESAMEKMIENLREVELKMTRKAA   300
 301  YMRFFTSSAFFFSGFFVVFLSVLPYTVINGIVLRKIFTTISFCIVLRMSV   350
 351  TRQFPTAVQIWYDSFGMIRKIQDFLQKQEYKVLEYNLMTTGIIMENVTAF   400
 401  WEEGFGELLEKVQQSNGDRKHSSDENNVSFSHLCLVGNPVLKNINLNIEK   450
 451  GEMLAITGSTGSGKTSLLMLILGELEASEGIIKHSGRVSFCSQFSWIMPG   500
 501  TIKENIIFGVSYDEYRYKSVVKACQLQQDITKFAEQDNTVLGEGGVTLSG   550
 551  GQRARISLARAVYKDADLYLLDSPFGYLDVFTEEQVFESCVCKLMANKTR   600
 601  ILVTSKMEHLRKADKILILHQGSSYFYGTFSELQSLRPDFSSKLMGYDTF   650
 651  DQFTEERRSSILTETLRRFSVDDSSAPWSKPKQSFRQTGEVGEKRKNSIL   700
 701  NSFSSVRKISIVQKTPLCIDGESDDLQEKRLSLVPDSEQGEAALPRSNMI   750
 751  ATGPTFPGRRRQSVLDLMTFTPNSGSSNLQRTRTSIRKISLVPQISLNEV   800
 801  DVYSRRLSQDSTLNITEEINEEDLKECFLDDVIKIPPVTTWNTYLRYFTL   850
 851  HKGLLLVLIWCVLVFLVEVAASLFVLWLLKNNPVNSGNNGTKISNSSYVV   900
 901  IITSTSFYYIFYIYVGVADTLLALSLFRGLPLVHTLITASKILHRKMLHS   950
 951  ILHAPMSTISKLKAGGILNRFSKDIAILDDFLPLTIFDFIQLVFIVIGAI  1000
1001  IVVSALQPYIFLATVPGLVVFILLRAYFLHTAQQLKQLESEGRSPIFTHL  1050
1051  VTSLKGLWTLRAFRRQTYFETLFHKALNLHTANWFMYLATLRWFQMRIDM  1100
1101  IFVLFFIVVTFISILTTGEGEGTAGIILTLAMNIMSTLQWAVNSSIDTDS  1150
1151  LMRSVSRVFKFIDIQTEESMYTQIIKELPREGSSDVLVIKNEHVKKSDIW  1200
1201  PSGGEMVVKDLTVKYMDDGNAVLENISFSISPGQRVGLLGRTGSGKSTLL  1250
1251  SAFLRMLNIKGDIEIDGVSWNSVTLQEWRKAFGVITQKVFIFSGTFRQNL  1300
1301  DPNGKWKDEEIWKVADEVGLKSVIEQFPGQLNFTLVDGGYVLSHGHKQLM  1350
1351  CLARSVLSKAKIILLDEPSAHLDPITYQVIRRVLKQAFAGCTVILCEHRI  1400
1401  EAMLDCQRFLVIEESNVWQYDSLQALLSEKSIFQQAISSSEKMRFFQGRH  1450
1451  SSKHKPRTQITALKEETEEEVQETRL                          1476

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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