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

NucPred

Fetching Q03172 from www.uniprot.org...

The NucPred score for your sequence is 0.98 (see score help below)

   1  MPRTKQIHPRNLRDKIEEAQKELNGAEVSKKEVLEAGVKGTSESLKGVKR    50
  51  KKIVAENHLKKIPKSPLRNPLQTKHKQNTEEPPFSVLPSASESHKKHNCV   100
 101  PAKQGRQFTKQNGETPGMTAESSESGDLVSPKKTSSPHQRSELRRWRSEG   150
 151  SDPTRLSGLDGQRDSSSSSSKARTDNSECSSPCCSTTPPSYTSTAFDVLL   200
 201  KAMEPELSTLSQKGSSCAIKTEKLRPNKTVRSPSKLKNSSLDAPNATSPD   250
 251  LVVESPCPPCTSYPVHVASTQKSEQVAAQCVSHLYSSQDHLVPKLSQQNQ   300
 301  QLPGHLGFTGSLTNLHTLESTKLEPIYNTAVTSTVGLTSPSTRTQVTPPH   350
 351  QQMDSVSPLSVSPASSTQSPPGPIYSSAHVASVVSQSVEQMCSLLLRDQK   400
 401  PKKQGKYICEYCNRACAKPSVLLKHIRSHTGERPYPCVTCGFSFKTKSNL   450
 451  YKHKKSHAHTIKLGLVLQPEAGGLFLSQECPKALSVHSDIEDSGESDEEG   500
 501  LADGRQNNPCVKDLQPVQTMKTVSNPESLPKLIPSNSDHVVRGFSSQDRP   550
 551  SDSQAPTELPKVVVHPVSMPPLKTDCLQVANPNPELPSPQSPRDLHVASI   600
 601  LSHSASVSSLEMDESCHQKGDVIQSEGKPDSHSGTAHAQLQRQQATEDPQ   650
 651  EQQGKLLLSPRSLGSTDSGYFSRSESADQAVSPPTPFARTFPTMDPDPAK   700
 701  NGGAPGPRISAPAPSALATGEKSSVVTGQMRPPLATKTLEERISKLISDN   750
 751  EALVDDKQLDSVKPRRTSLSRRGSIDSPKSYIFKDSFQFDLKPMGRRTSS   800
 801  SSDIPKSPFTPTEKSKQVFLLSVPSLDCLPITRSNSMPTTGYSAIPANII   850
 851  PPPPSLRGSQSFDDKIGTLYDDVFVSGPNPSMPPSGHHRPLVRQAAVEDS   900
 901  TASESHVPGSGQSVDESCQGCPSSSEAGPVQSKAAQTPHLEKKKSHQGRG   950
 951  TMFECETCRNRYRKLENFENHKKFYCSELHGPKTKAAVREAEHGPAPGGA  1000
1001  QPQVLHYRVAAPTAVWEQTPQIRKRRKMKSVGDEEDLQPHESGRSPESAD  1050
1051  ALQLQPVPGAAPSPSKHTSATAADQAHRGVQLVARGPERALPLKQCPMVE  1100
1101  QQLNAAAQDKMEVKRQGGGISVIQHTNSLSRPNSFDKPEPLEGGITFSLQ  1150
1151  ELGRTGMPGALKVIGMAPEEGHPPQDAMHQTALSHNLRGEPRESARKIPS  1200
1201  ERYVLGQPLRLVRQHNIQVPEILVTEEPDRDLEAQSHDEEKSEKFTWPQR  1250
1251  SETLSKLPTEKLPPKKKRLRLAEIEHSSTESSFESTLSRSLSRESSLSHA  1300
1301  SSFSASLDLEDISKVELAPKIDFPSKAEFLLIPLGSNTLSVPGSHREMRR  1350
1351  AASEQISCVPTLMEVSDFRSKSFDCGSIAPSHVVPALVESQPSYSPSAVG  1400
1401  GTAHVPLLERRRGPLIRQISLNIASDSHLSPGSAAALQTIVLPSVNTVPF  1450
1451  QAPRLPDMASADCPAHTVHPQALAKDLQAEISSSSSTDTFPPQQLFGAHL  1500
1501  LNKTNTSLSHQNTPLPLPVSAQGGKPDAAPTACVSSTGEGSFAPKYQLQC  1550
1551  QAFTSDQGCSAPLRSSPNQVLPGQAGADPCPASEAPPAKAADPMAKPCPL  1600
1601  PPLELGLPRDEVLQKQLPSFVLPVPQKRNVTVDCFTPVTSLPQILVTQDL  1650
1651  PNMPICQTNQSLVPVSEEQNSMPKSQNYLQNASPTPEKELACKTVLPEVG  1700
1701  QSVPVSESSPTVQKVSVGRLSPQQESSASSKRMLSPANSLDIAMEKHQKR  1750
1751  AKDENGAVCSTNIRALELPSSRANESHKQKKPVLVRQLCTTEPLEGAALE  1800
1801  QGACSASGRSSNKAANLTQVLPTDSLSSRPSTFAVTDHVNELQEFKNTKV  1850
1851  STSLTPTVGSFPAPSESACVLPLKSIDNNQEKGSPGVRHEENKVIQGQRP  1900
1901  PLVSGLSLVSSSDTQQPSFPSLKTATSFTWCYLLRQKALPLAQNDQKTSA  1950
1951  YTGWTVSSSNPNPLGLPTKVALSLLNSKQKTGKSLYCQAITTHSKSDLVV  2000
2001  YSSKWKNNLSKRALGNQKATVVEFSNKDDSEINSEQDKENSLIKSEPRRI  2050
2051  KIFDGGYKSNEDYVYVRGRGRGKYICEECGIRCKKPSMLKKHIRTHTDVR  2100
2101  PYHCSYCNFSFKTKGNLTKHMKSKAHSKKCVDLGVSVGLIDEQDTEESDE  2150
2151  KQRFGCERSGYDLEESDGPDEDDNDNEEDDDDSQAESGLSAAPSVTASPQ  2200
2201  HLPSRSGLQDPGSVEEELRVSSCFSGVHTDPMDILPRALLTKMTVLSTVQ  2250
2251  SSPNRTDLPAKARQSTEKDEHEQAPPADTPRSPGHQLSVHSSESDVLRSP  2300
2301  AAGNPAAGSPGAAVQDSSVGLPPAVAQLNPQPAARISSSVSPHPDSQDQK  2350
2351  QQIILQPPPGLPSPQTHLFSHLPLHSQQQSRTPYNMVPVGGIHVVTAGLT  2400
2401  YSTFVPIQAGPMQLTIPAVSVIHRTVGTSGDTITEASGSPNRPTGVAELS  2450
2451  SVVPCIPIGQIHVPGLQNLSPPALQSLTSLGMETVNLVGLANATVGPQGH  2500
2501  PPGLALNAVGLQVLANAPAQSSPAPPAHIQGLQILNIALPTLIPSVGPVA  2550
2551  VGTTGTPETTAPNSKAMELQMPAGQGHSAEPPQGSPEGPQETPQTVSGPS  2600
2601  ADHARPEDSTKMDTKKGPSAGHVLPGRSPAQAQPAPTPEALQKVATSAPP  2650
2651  SLPTDRAAPRPPVPHRQPIVHFSDVSSDDDEDRLVIAT              2688

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.