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

NucPred

Fetching P01267 from www.uniprot.org...

The NucPred score for your sequence is 0.78 (see score help below)

   1  MALALWVFGLLDLICLASANIFEYQVDAQPLRPCELQRERAFLKREDYVP    50
  51  QCAEDGSFQTVQCGKDGASCWCVDADGREVPGSRQPGRPAACLSFCQLQK   100
 101  QQILLSSYINSTATSYLPQCQDSGDYSPVQCDLRRRQCWCVDAEGMEVYG   150
 151  TRQQGRPARCPRSCEIRNRRLLHGVGDRSPPQCSPDGAFRPVQCKLVNTT   200
 201  DMMIFDLVHSYSRFPDAFVTFSSFRSRFPEVSGYCYCADSQGRELAETGL   250
 251  ELLLDEIYDTIFAGLDLASTFAETTLYRILQRRFLAVQLVISGRFRCPTK   300
 301  CEVERFAATSFRHPYVPSCHPDGEYQAAQCQQGGPCWCVDSRGQEIPGTR   350
 351  QRGEPPSCAEDQSCPSERRRAFSRLRFGPSGYFSRRSLLLAPEEGPVSQR   400
 401  FARFTASCPPSIKELFLDSGIFQPMLQGRDTRFVAPESLKEAIRGLFPSR   450
 451  ELARLALQFTTNAKRLQQNLFGGRFLVKVGQFNLSGALGTRGTFNFSHFF   500
 501  QQLGLPGFQDGRALADLAKPLSVGLNSNPASEAPKASKIDVALRKPVVGS   550
 551  FGFEVNLQENQNALQFLSSFLELPEFLLFLQHAISVPEDIARDLGDVMEM   600
 601  VFSSQGCGQAPGSLFVPACTAEGSYEEVQCFAGDCWCVDAQGRELAGSRV   650
 651  RGGRPRCPTECEKQRARMQSLLGSQPAGSSLFVPACTSKGNFLPVQCFNS   700
 701  ECYCVDTEGQPIPGTRSALGEPKKCPSPCQLQAERAFLGTVRTLVSNPST   750
 751  LPALSSIYIPQCSASGQWSPVQCDGPPEQAFEWYERWEAQNSAGQALTPA   800
 801  ELLMKIMSYREAASRNFRLFIQNLYEAGQQGIFPGLARYSSFQDVPVSVL   850
 851  EGNQTQPGGNVFLEPYLFWQILNGQLDRYPGPYSDFSAPLAHFDLRSCWC   900
 901  VDEAGQKLEGTRNEPNKVPACPGSCEEVKLRVLQFIREAEEIVTYSNSSR   950
 951  FPLGESFLAAKGIRLTDEELAFPPLSPSRETFLEKFLSGSDYAIRLAAQS  1000
1001  TFDFYQRRLVTLAESPRAPSPVWSSAYLPQCDAFGGWEPVQCHAATGHCW  1050
1051  CVDGKGEYVPTSLTARSRQIPQCPTSCERLRASGLLSSWKQAGVQAEPSP  1100
1101  KDLFIPTCLETGEFARLQASEAGTWCVDPASGEGVPPGTNSSAQCPSLCE  1150
1151  VLQSGVPSRRTSPGYSPACRAEDGGFSPVQCDPAQGSCWCVLGSGEEVPG  1200
1201  TRVAGSQPACESPQCPLPFSVADVAGGAILCERASGLGAAAGQRCQLRCS  1250
1251  QGYRSAFPPEPLLCSVQRRRWESRPPQPRACQRPQFWQTLQTQAQFQLLL  1300
1301  PLGKVCSADYSGLLLAFQVFLLDELTARGFCQIQVKTAGTPVSIPVCDDS  1350
1351  SVKVECLSRERLGVNITWKLQLVDAPPASLPDLQDVEEALAGKYLAGRFA  1400
1401  DLIQSGTFQLHLDSKTFSADTSIRFLQGDRFGTSPRTQFGCLEGFGRVVA  1450
1451  ASDASQDALGCVKCPEGSYFQDEQCIPCPAGFYQEQAGSLACVPCPEGRT  1500
1501  TVYAGAFSQTHCVTDCQKNEVGLQCDQDSQYRASQRDRTSGKAFCVDGEG  1550
1551  RRLPWTEAEAPLVDAQCLVMRKFEKLPESKVIFSADVAVMVRSEVPGSES  1600
1601  SLMQCLADCALDEACGFLTVSTAGSEVSCDFYAWASDSIACTTSGRSEDA  1650
1651  LGTSQATSFGSLQCQVKVRSREGDPLAVYLKKGQEFTITGQKRFEQTGFQ  1700
1701  SALSGMYSPVTFSASGASLAEVHLFCLLACDHDSCCDGFILVQVQGGPLL  1750
1751  CGLLSSPDVLLCHVRDWRDPAEAQANASCPGVTYDQDSRQVTLRLGGQEI  1800
1801  RGLTPLEGTQDTLTSFQQVYLWKDSDMGSRSESMGCRRDTEPRPASPSET  1850
1851  DLTTGLFSPVDLIQVIVDGNVSLPSQQHWLFKHLFSLQQANLWCLSRCAG  1900
1901  EPSFCQLAEVTDSEPLYFTCTLYPEAQVCDDILESSPKGCRLILPRRPSA  1950
1951  LYRKKVVLQDRVKNFYNRLPFQKLTGISIRNKVPMSDKSISSGFFECERL  2000
2001  CDMDPCCTGFGFLNVSQLKGGEVTCLTLNSLGLQTCSEEYGGVWRILDCG  2050
2051  SPDTEVRTYPFGWYQKPVSPSDAPSFCPSVALPALTENVALDSWQSLALS  2100
2101  SVIVDPSIRNFDVAHISTAAVGNFSAARDRCLWECSRHQDCLVTTLQTQP  2150
2151  GAVRCMFYADTQSCTHSLQAQNCRLLLHEEATYIYRKPNIPLPGFGTSSP  2200
2201  SVPIATHGQLLGRSQAIQVGTSWKPVDQFLGVPYAAPPLGEKRFRAPEHL  2250
2251  NWTGSWEATKPRARCWQPGIRTPTPPGVSEDCLYLNVFVPQNMAPNASVL  2300
2301  VFFHNAAEGKGSGDRPAVDGSFLAAVGNLIVVTASYRTGIFGFLSSGSSE  2350
2351  LSGNWGLLDQVVALTWVQTHIQAFGGDPRRVTLAADRGGADIASIHLVTT  2400
2401  RAANSRLFRRAVLMGGSALSPAAVIRPERARQQAAALAKEVGCPSSSVQE  2450
2451  MVSCLRQEPARILNDAQTKLLAVSGPFHYWGPVVDGQYLRETPARVLQRA  2500
2501  PRVKVDLLIGSSQDDGLINRAKAVKQFEESQGRTSSKTAFYQALQNSLGG  2550
2551  EAADAGVQAAATWYYSLEHDSDDYASFSRALEQATRDYFIICPVIDMASH  2600
2601  WARTVRGNVFMYHAPESYSHSSLELLTDVLYAFGLPFYPAYEGQFTLEEK  2650
2651  SLSLKIMQYFSNFIRSGNPNYPHEFSRRAPEFAAPWPDFVPRDGAESYKE  2700
2701  LSVLLPNRQGLKKADCSFWSKYIQSLKASADETKDGPSADSEEEDQPAGS  2750
2751  GLTEDLLGLPELASKTYSK                                 2769

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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