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

NucPred

Fetching P08678 from www.uniprot.org...

The NucPred score for your sequence is 0.96 (see score help below)

   1  MSSKPDTGSEISGPQRQEEQEQQIEQSSPTEANDRSIHDEVPKVKKRHEQ    50
  51  NSGHKSRRNSAYSYYSPRSLSMTKSRESITPNGMDDVSISNVEHPRPTEP   100
 101  KIKRGPYLLKKTLSSLSMTSANSTHDDNKDHGYALNSSKTHNYTSTHNHH   150
 151  DGHHDHHHVQFFPNRKPSLAETLFKRFSGSNSHDGNKSGKESKVANLSLS   200
 201  TVNPAPANRKPSKDSTLSNHLADNVPSTLRRKVSSLVRGSSVHDINNGIA   250
 251  DKQIRPKAVAQSENTLHSSDVPNSKRSHRKSFLLGSTSSSSSRRGSNVSS   300
 301  MTNSDSASMATSGSHVLQHNVSNVSPTTKSKDSVNSESADHTNNKSEKVT   350
 351  PEYNENIPENSNSDNKREATTPTIETPISCKPSLFRLDTNLEDVTDITKT   400
 401  VPPTAVNSTLNSTHGTETASPKTVIMPEGPRKSVSMADLSVAAAAPNGEF   450
 451  TSTSNDRSQWVAPQSWDVETKRKKTKPKGRSKSRRSSIDADELDPMSPGP   500
 501  PSKKDSRHHHDRKDNESMVTAGDSNSSFVDICKENVPNDSKTALDTKSVN   550
 551  RLKSNLAMSPPSIRYAPSNLDGDYDTSSTSSSLPSSSISSEDTSSCSDSS   600
 601  SYTNAYMEANREQDNKTPILNKTKSYTKKFTSSSVNMNSPDGAQSSGLLL   650
 651  QDEKDDEVECQLEHYYKDFSDLDPKRHYAIRIFNTDDTFTTLSCTPATTV   700
 701  EEIIPALKRKFNITAQGNFQISLKVGKLSKILRPTSKPILIERKLLLLNG   750
 751  YRKSDPLHIMGIEDLSFVFKFLFHPVTPSHFTPEQEQRIMRSEFVHVDLR   800
 801  NMDLTTPPIIFYQHTSEIESLDVSNNANIFLPLEFIESSIKLLSLRMVNI   850
 851  RASKFPSNITKAYKLVSLELQRNFIRKVPNSIMKLSNLTILNLQCNELES   900
 901  LPAGFVELKNLQLLDLSSNKFMHYPEVINYCTNLLQIDLSYNKIQSLPQS   950
 951  TKYLVKLAKMNLSHNKLNFIGDLSEMTDLRTLNLRYNRISSIKTNASNLQ  1000
1001  NLFLTDNRISNFEDTLPKLRALEIQENPITSISFKDFYPKNMTSLTLNKA  1050
1051  QLSSIPGELLTKLSFLEKLELNQNNLTRLPQEISKLTKLVFLSVARNKLE  1100
1101  YIPPELSQLKSLRTLDLHSNNIRDFVDGMENLELTSLNISSNAFGNSSLE  1150
1151  NSFYHNMSYGSKLSKSLMFFIAADNQFDDAMWPLFNCFVNLKVLNLSYNN  1200
1201  FSDVSHMKLESITELYLSGNKLTTLSGDTVLKWSSLKTLMLNSNQMLSLP  1250
1251  AELSNLSQLSVFDVGANQLKYNISNYHYDWNWRNNKELKYLNFSGNRRFE  1300
1301  IKSFISHDIDADLSDLTVLPQLKVLGLMDVTLNTTKVPDENVNFRLRTTA  1350
1351  SIINGMRYGVADTLGQRDYVSSRDVTFERFRGNDDECLLCLHDSKNQNAD  1400
1401  YGHNISRIVRDIYDKILIRQLERYGDETDDNIKTALRFSFLQLNKEINGM  1450
1451  LNSVDNGADVANLSYADLLSGACSTVIYIRGKKLFAANLGDCMAILSKNN  1500
1501  GDYQTLTKQHLPTKREEYERIRISGGYVNNGKLDGVVDVSRAVGFFDLLP  1550
1551  HIHASPDISVVTLTKADEMLIVATHKLWEYMDVDTVCDIARENSTDPLRA  1600
1601  AAELKDHAMAYGCTENITILCLALYENIQQQNRFTLNKNSLMTRRSTFED  1650
1651  TTLRRLQPEISPPTGNLAMVFTDIKSSTFLWELFPNAMRTAIKTHNDIMR  1700
1701  RQLRIYGGYEVKTEGDAFMVAFPTPTSGLTWCLSVQLKLLDAQWPEEITS  1750
1751  VQDGCQVTDRNGNIIYQGLSVRMGIHWGCPVPELDLVTQRMDYLGPMVNK  1800
1801  AARVQGVADGGQIAMSSDFYSEFNKIMKYHERVVKGKESLKEVYGEEIIG  1850
1851  EVLEREIAMLESIGWAFFDFGEHKLKGLETKELVTIAYPKILASRHEFAS  1900
1901  EDEQSKLINETMLFRLRVISNRLESIMSALSGGFIELDSRTEGSYIKFNP  1950
1951  KVENGIMQSISEKDALLFFDHVITRIESSVALLHLRQQRCSGLEICRNDK  2000
2001  TSARSNIFNVVDELLQMVKNAKDLST                          2026

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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