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

NucPred

Fetching P16086 from www.uniprot.org...

The NucPred score for your sequence is 0.91 (see score help below)

   1  MDPSGVKVLETAEDIQERRQQVLDRYHRFKELSTLRRQKLEDSYRFQFFQ    50
  51  RDAEELEKWIQEKLQVASDENYKDPTNLQGKLQKHQAFEAEVQANSGAIV   100
 101  KLDETGNLMISEGHFASETIRTRLMELHRQWELLLEKMREKGIKLLQAQK   150
 151  LVQYLRECEDVMDWINDKEAIVTSEELGQDLEHVEVLQKKFEEFQTDLAA   200
 201  HEERVNEVNQFAAKLIQEQHPEEELIKTKQEEVNAAWQRLKGLALQRQGK   250
 251  LFGAAEVQRFNRDVDETIGWIKEKEQLMASDDFGRDLASVQALLRKHEGL   300
 301  ERDLAALEDKVKALCAEADRLQQSHPLSANQIQVKREELITNWEQIRTLA   350
 351  AERHARLDDSYRLQRFLADFRDLTSWVTEMKALINADELANDVAGAEALL   400
 401  DRHQEHKGEIDAHEDSFKSADESGQALLAAGHYASDEVREKLSILSEERA   450
 451  ALLELWELRRQQYEQCMDLQLFYRDTEQVDNWMSKQEAFLLNEDLGDSLD   500
 501  SVEALLKKHEDFEKSLSAQEEKITALDEFATKLIQNNHYAMEDVATRRDA   550
 551  LLSRRNALHERAMHRRAQLADSFHLQQFFRDSDELKSWVNEKMKTATDEA   600
 601  YKDPSNLQGKVQKHQAFEAELSANQSRIDALEKAGQKLIDVNHYAKEEVA   650
 651  ARMNEVISLWKKLLEATELKGVKLREANQQQQFNRNVEDIELWLYEVEGH   700
 701  LASDDYGKDLTNVQNLQKKHALLEADVAAHQDRIDGITIQARQFQDAGHF   750
 751  DAENIKKKQEALVARYEALKEPMVARKQKLADSLRLQQLFRDVEDEETWI   800
 801  REKEPIAASTNRGKDLIGVQNLLKKHQALQAEIAGHEPRIKAVTQKGNAM   850
 851  VEEGHFAAEDVKAKLSELNQKWEALKAKASQRRQDLEDSLQAQQYFADAN   900
 901  EAESWMREKEPIVGSTDYGKDEDSAEALLKKHEALMSDLSAYGSSIQALR   950
 951  EQAQSCRQQVAPMDDETGKELVLALYDYQEKSPREVTMKKGDILTLLNST  1000
1001  NKDWWKVEVNDRQGFVPAAYVKKLDPAQSASRENLLEEQGSIALRQGQID  1050
1051  NQTRITKEAGSVSLRMKQVEELYQSLLELGEKRKGMLEKSCKKFMLFREA  1100
1101  NELQQWINEKEAALTSEEVGADLEQVEVLQKKFDDFQKDLKANESRLKDI  1150
1151  NKVAEDLESEGLMAEEVQAVQQQEVYGMMPRDEADSKTASPWKSARLMVH  1200
1201  TVATFNSIKELNERWRSLQQLAEERSQLLGSAHEVQRFHRDADETKEWIE  1250
1251  EKNQALNTDNYGHDLASVQALQRKHEGFERDLAALGDKVNSLGETAQRLI  1300
1301  QSHPESAEDLKEKCTELNQAWTSLGKRADQRKAKLGDSHDLQRFLSDFRD  1350
1351  LMSWINGIRGLVSSDELAKDVTGAEALLERHQEHRTEIDARAGTFQAFEQ  1400
1401  FGQQLLAHGHYASPEIKEKLDILDQERTDLEKAWVQRRMMLDHCLELQLF  1450
1451  HRDCEQAENWMAAREAFLNTEDKGDSLDSVEALIKKHEDFDKAINVQEEK  1500
1501  IAALQAFADQLIAVDHYAKGDIANRRNEVLDRWRRLKAQMIEKRSKLGES  1550
1551  QTLQQFSRDVDEIEAWISEKLQTASDESYKDPTNIQSKHQKHQAFEAELH  1600
1601  ANADRIRGVIDMGNSLIERGACAGSEDAVKARLAALADQWQFLVQKSAEK  1650
1651  SQKLKEANKQQNFNTGIKDFDFWLSEVEALLASEDYGKDLASVNNLLKKH  1700
1701  QLLEADISAHEDRLKDLNSQADSLMTSSAFDTSQVKEKRDTINGRFQKIK  1750
1751  SMATSRRAKLSESHRLHQFFRDMDDEESWIKEKKLLVSSEDYGRDLTGVQ  1800
1801  NLRKKHKRLEAELAAHEPAIQGVLDTGKKLSDDNTIGQEEIQQRLAQFVE  1850
1851  HWKELKQLAAARGQRLEESLEYQQFVANVEEEEAWINEKMTLVASEDYGD  1900
1901  TLAAIQGLLKKHEAFETDFTVHKDRVNDVCTNGQDLIKKNNHHEENISSK  1950
1951  MKGLNGKVSDLEKAAAQRKAKLDENSAFLQFNWKADVVESWIGEKENSLK  2000
2001  TDDYGRDLSSVQTLLTKQETFDAGLQAFQQEGIANITALKDQLLAAKHIQ  2050
2051  SKAIEARHASLMKRWTQLLANSATRKKKLLEAQSHFRKVEDLFLTFAKKA  2100
2101  SAFNSWFENAEEDLTDPVRCNSLEEIKALREAHDAFRSSLSSAQADFNQL  2150
2151  AELDRQIKSFRVASNPYTWFTMEALEETWRNLQKIIKERELELQKEQRRQ  2200
2201  EENDKLRQEFAQHANAFHQWIQETRTYLLDGSCMVEESGTLESQLEATKR  2250
2251  KHQEIRAMRSQLKKIEDLGAAMEEALILDNKYTEHSTVGLAQQWDQLDQL  2300
2301  GMRMQHNLEQQIQARNTTGVTEEALKEFSMMFKHFDKDKSGRLNHQEFKS  2350
2351  CLRSLGYDLPMVEEGEPDPEFEAILDTVDPNRDGHVSLQEYMAFMISRET  2400
2401  ENVKSSEEIESAFRALSSEGKPYVTKEELYQNLTREQADYCVSHMKPYVD  2450
2451  GKGRELPTAFDYVEFTRSLFVN                              2472

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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