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

NucPred

Fetching O43157 from www.uniprot.org...

The NucPred score for your sequence is 0.43 (see score help below)

   1  MPALGPALLQALWAGWVLTLQPLPPTAFTPNGTYLQHLARDPTSGTLYLG    50
  51  ATNFLFQLSPGLQLEATVSTGPVLDSRDCLPPVMPDECPQAQPTNNPNQL   100
 101  LLVSPGALVVCGSVHQGVCEQRRLGQLEQLLLRPERPGDTQYVAANDPAV   150
 151  STVGLVAQGLAGEPLLFVGRGYTSRGVGGGIPPITTRALWPPDPQAAFSY   200
 201  EETAKLAVGRLSEYSHHFVSAFARGASAYFLFLRRDLQAQSRAFRAYVSR   250
 251  VCLRDQHYYSYVELPLACEGGRYGLIQAAAVATSREVAHGEVLFAAFSSA   300
 301  APPTVGRPPSAAAGASGASALCAFPLDEVDRLANRTRDACYTREGRAEDG   350
 351  TEVAYIEYDVNSDCAQLPVDTLDAYPCGSDHTPSPMASRVPLEATPILEW   400
 401  PGIQLTAVAVTMEDGHTIAFLGDSQGQLHRVYLGPGSDGHPYSTQSIQQG   450
 451  SAVSRDLTFDGTFEHLYVMTQSTLLKVPVASCAQHLDCASCLAHRDPYCG   500
 501  WCVLLGRCSRRSECSRGQGPEQWLWSFQPELGCLQVAAMSPANISREETR   550
 551  EVFLSVPDLPPLWPGESYSCHFGEHQSPALLTGSGVMCPSPDPSEAPVLP   600
 601  RGADYVSVSVELRFGAVVIAKTSLSFYDCVAVTELRPSAQCQACVSSRWG   650
 651  CNWCVWQHLCTHKASCDAGPMVASHQSPLVSPDPPARGGPSPSPPTAPKA   700
 701  LATPAPDTLPVEPGAPSTATASDISPGASPSLLSPWGPWAGSGSISSPGS   750
 751  TGSPLHEEPSPPSPQNGPGTAVPAPTDFRPSATPEDLLASPLSPSEVAAV   800
 801  PPADPGPEALHPTVPLDLPPATVPATTFPGAMGSVKPALDWLTREGGELP   850
 851  EADEWTGGDAPAFSTSTLLSGDGDSAELEGPPAPLILPSSLDYQYDTPGL   900
 901  WELEEATLGASSCPCVESVQGSTLMPVHVEREIRLLGRNLHLFQDGPGDN   950
 951  ECVMELEGLEVVVEARVECEPPPDTQCHVTCQQHQLSYEALQPELRVGLF  1000
1001  LRRAGRLRVDSAEGLHVVLYDCSVGHGDCSRCQTAMPQYGCVWCEGERPR  1050
1051  CVTREACGEAEAVATQCPAPLIHSVEPLTGPVDGGTRVTIRGSNLGQHVQ  1100
1101  DVLGMVTVAGVPCAVDAQEYEVSSSLVCITGASGEEVAGATAVEVPGRGR  1150
1151  GVSEHDFAYQDPKVHSIFPARGPRAGGTRLTLNGSKLLTGRLEDIRVVVG  1200
1201  DQPCHLLPEQQSEQLRCETSPRPTPATLPVAVWFGATERRLQRGQFKYTL  1250
1251  DPNITSAGPTKSFLSGGREICVRGQNLDVVQTPRIRVTVVSRMLQPSQGL  1300
1301  GRRRRVVPETACSLGPSCSSQQFEEPCHVNSSQLITCRTPALPGLPEDPW  1350
1351  VRVEFILDNLVFDFATLNPTPFSYEADPTLQPLNPEDPTMPFRHKPGSVF  1400
1401  SVEGENLDLAMSKEEVVAMIGDGPCVVKTLTRHHLYCEPPVEQPLPRHHA  1450
1451  LREAPDSLPEFTVQMGNLRFSLGHVQYDGESPGAFPVAAQVGLGVGTSLL  1500
1501  ALGVIIIVLMYRRKSKQALRDYKKVQIQLENLESSVRDRCKKEFTDLMTE  1550
1551  MTDLTSDLLGSGIPFLDYKVYAERIFFPGHRESPLHRDLGVPESRRPTVE  1600
1601  QGLGQLSNLLNSKLFLTKFIHTLESQRTFSARDRAYVASLLTVALHGKLE  1650
1651  YFTDILRTLLSDLVAQYVAKNPKLMLRRTETVVEKLLTNWMSICLYTFVR  1700
1701  DSVGEPLYMLFRGIKHQVDKGPVDSVTGKAKYTLNDNRLLREDVEYRPLT  1750
1751  LNALLAVGPGAGEAQGVPVKVLDCDTISQAKEKMLDQLYKGVPLTQRPDP  1800
1801  RTLDVEWRSGVAGHLILSDEDVTSEVQGLWRRLNTLQHYKVPDGATVALV  1850
1851  PCLTKHVLRENQDYVPGERTPMLEDVDEGGIRPWHLVKPSDEPEPPRPRR  1900
1901  GSLRGGERERAKAIPEIYLTRLLSMKGTLQKFVDDLFQVILSTSRPVPLA  1950
1951  VKYFFDLLDEQAQQHGISDQDTIHIWKTNSLPLRFWINIIKNPQFVFDVQ  2000
2001  TSDNMDAVLLVIAQTFMDACTLADHKLGRDSPINKLLYARDIPRYKRMVE  2050
2051  RYYADIRQTVPASDQEMNSVLAELSWNYSGDLGARVALHELYKYINKYYD  2100
2101  QIITALEEDGTAQKMQLGYRLQQIAAAVENKVTDL                 2135

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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