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

NucPred

Fetching Q9Y493 from www.uniprot.org...

The NucPred score for your sequence is 0.76 (see score help below)

   1  MVPPVWTLLLLVGAALFRKEKPPDQKLVVRSSRDNYVLTQCDFEDDAKPL    50
  51  CDWSQVSADDEDWVRASGPSPTGSTGAPGGYPNGEGSYLHMESNSFHRGG   100
 101  VARLLSPDLWEQGPLCVHFAHHMFGLSWGAQLRLLLLSGEEGRRPDVLWK   150
 151  HWNTQRPSWMLTTVTVPAGFTLPTRLMFEGTRGSTAYLDIALDALSIRRG   200
 201  SCNRVCMMQTCSFDIPNDLCDWTWIPTASGAKWTQKKGSSGKPGVGPDGD   250
 251  FSSPGSGCYMLLDPKNARPGQKAVLLSPVSLSSGCLSFSFHYILRGQSPG   300
 301  AALHIYASVLGSIRKHTLFSGQPGPNWQAVSVNYTAVGRIQFAVVGVFGK   350
 351  TPEPAVAVDATSIAPCGEGFPQCDFEDNAHPFCDWVQTSGDGGHWALGHK   400
 401  NGPVHGMGPAGGFPNAGGHYIYLEADEFSQAGQSVRLVSRPFCAPGDICV   450
 451  EFAYHMYGLGEGTMLELLLGSPAGSPPIPLWKRVGSQRPYWQNTSVTVPS   500
 501  GHQQPMQLIFKGIQGSNTASVVAMGFILINPGTCPVKVLPELPPVSPVSS   550
 551  TGPSETTGLTENPTISTKKPTVSIEKPSVTTEKPTVPKEKPTIPTEKPTI   600
 601  STEKPTIPSEKPNMPSEKPTIPSEKPTILTEKPTIPSEKPTIPSEKPTIS   650
 651  TEKPTVPTEEPTTPTEETTTSMEEPVIPTEKPSIPTEKPSIPTEKPTISM   700
 701  EETIISTEKPTISPEKPTIPTEKPTIPTEKSTISPEKPTTPTEKPTIPTE   750
 751  KPTISPEKPTTPTEKPTISPEKLTIPTEKPTIPTEKPTIPTEKPTISTEE   800
 801  PTTPTEETTISTEKPSIPMEKPTLPTEETTTSVEETTISTEKLTIPMEKP   850
 851  TISTEKPTIPTEKPTISPEKLTIPTEKLTIPTEKPTIPIEETTISTEKLT   900
 901  IPTEKPTISPEKPTISTEKPTIPTEKPTIPTEETTISTEKLTIPTEKPTI   950
 951  SPEKLTIPTEKPTISTEKPTIPTEKLTIPTEKPTIPTEKPTIPTEKLTAL  1000
1001  RPPHPSPTATGLAALVMSPHAPSTPMTSVILGTTTTSRSSTERCPPNARY  1050
1051  ESCACPASCKSPRPSCGPLCREGCVCNPGFLFSDNHCIQASSCNCFYNND  1100
1101  YYEPGAEWFSPNCTEHCRCWPGSRVECQISQCGTHTVCQLKNGQYGCHPY  1150
1151  AGTATCLVYGDPHYVTFDGRHFGFMGKCTYILAQPCGNSTDPFFRVTAKN  1200
1201  EEQGQEGVSCLSKVYVTLPESTVTLLKGRRTLVGGQQVTLPAIPSKGVFL  1250
1251  GASGRFVELQTEFGLRVRWDGDQQLYVTVSSTYSGKLCGLCGNYDGNSDN  1300
1301  DHLKLDGSPAGDKEELGNSWQTDQDEDQECQKYQVVNSPSCDSSLQSSMS  1350
1351  GPGFCGRLVDTHGPFETCLLHVKAASFFDSCMLDMCGFQGLQHLLCTHMS  1400
1401  TMTTTCQDAGHAVKPWREPHFCPMACPPNSKYSLCAKPCPDTCHSGFSGM  1450
1451  FCSDRCVEACECNPGFVLSGLECIPRSQCGCLHPAGSYFKVGERWYKPGC  1500
1501  KELCVCESNNRIRCQPWRCRAQEFCGQQDGIYGCHAQGAATCTASGDPHY  1550
1551  LTFDGALHHFMGTCTYVLTRPCWSRSQDSYFVVSATNENRGGILEVSYIK  1600
1601  AVHVTVFDLSISLLRGCKVMLNGHRVALPVWLAQGRVTIRLSSNLVLLYT  1650
1651  NFGLQVRYDGSHLVEVTVPSSYGGQLCGLCGNYNNNSLDDNLRPDRKLAG  1700
1701  DSMQLGAAWKLPESSEPGCFLVGGKPSSCQENSMADAWNKNCAILINPQG  1750
1751  PFSQCHQVVPPQSSFASCVHGQCGTKGDTTALCRSLQAYASLCAQAGQAP  1800
1801  AWRNRTFCPMRCPPGSSYSPCSSPCPDTCSSINNPRDCPKALPCAESCEC  1850
1851  QKGHILSGTSCVPLGQCGCTDPAGSYHPVGERWYTENTCTRLCTCSVHNN  1900
1901  ITCFQSTCKPNQICWALDGLLHCRASGVGVCQLPGESHYVSFDGSNHSIP  1950
1951  DACTLVLVKVCHPAMALPFFKISAKHEKEEGGTEAFRLHEVYIDIYDAQV  2000
2001  TLQKGHRVLINSKQVTLPAISQIPGVSVKSSSIYSIVNIKIGVQVKFDGN  2050
2051  HLLEIEIPTTYYGKVCGMCGNFNDEEEDELMMPSDEVANSDSEFVNSWKD  2100
2101  KDIDPSCQSLLVDEQQIPAEQQENPSGNCRAADLRRAREKCEAALRAPVW  2150
2151  AQCASRIDLTPFLVDCANTLCEFGGLYQALCQALQAFGATCQSQGLKPPL  2200
2201  WRNSSFCPLECPAYSSYTNCLPSCSPSCWDLDGRCEGAKVPSACAEGCIC  2250
2251  QPGYVLSEDKCVPRSQCGCKDAHGGSIPLGKSWVSSGCTEKCVCTGGAIQ  2300
2301  CGDFRCPSGSHCQLTSDNSNSNCVSDKSEQCSVYGDPRYLTFDGFSYRLQ  2350
2351  GRMTYVLIKTVDVLPEGVEPLLVEGRNKMDPPRSSIFLQEVITTVYGYKV  2400
2401  QLQAGLELVVNNQKMAVPYRPNEHLRVTLWGQRLYLVTDFELVVSFGGRK  2450
2451  NAVISLPSMYEGLVSGLCGNYDKNRKNDMMLPSGALTQNLNTFGNSWEVK  2500
2501  TEDALLRFPRAIPAEEEGQGAELGLRTGLQVSECSPEQLASNSTQACRVL  2550
2551  ADPQGPFAACHQTVAPEPFQEHCVLDLCSAQDPREQEELRCQVLSGHGVS  2600
2601  SRYHISELYDTLPSILCQPGRPRGLRGPLRGRLRQHPRLCLQWHPEPPLA  2650
2651  DCGCTSNGIYYQLGSSFLTEDCSQRCTCASSRILLCEPFSCRAGEVCTLG  2700
2701  NHTQGCFPESPCLQNPCQNDGQCREQGATFTCECEVGYGGGLCMEPRDAP  2750
2751  PPRKPASNLVGVLLGLLVPVVVVLLAVTRECIYRTRRKREKTQEGDRLAR  2800
2801  LVDTDTVLDCAC                                        2812

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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