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

NucPred

Fetching P01266 from www.uniprot.org...

The NucPred score for your sequence is 0.81 (see score help below)

   1  MALVLEIFTLLASICWVSANIFEYQVDAQPLRPCELQRETAFLKQADYVP    50
  51  QCAEDGSFQTVQCQNDGRSCWCVGANGSEVLGSRQPGRPVACLSFCQLQK   100
 101  QQILLSGYINSTDTSYLPQCQDSGDYAPVQCDVQQVQCWCVDAEGMEVYG   150
 151  TRQLGRPKRCPRSCEIRNRRLLHGVGDKSPPQCSAEGEFMPVQCKFVNTT   200
 201  DMMIFDLVHSYNRFPDAFVTFSSFQRRFPEVSGYCHCADSQGRELAETGL   250
 251  ELLLDEIYDTIFAGLDLPSTFTETTLYRILQRRFLAVQSVISGRFRCPTK   300
 301  CEVERFTATSFGHPYVPSCRRNGDYQAVQCQTEGPCWCVDAQGKEMHGTR   350
 351  QQGEPPSCAEGQSCASERQQALSRLYFGTSGYFSQHDLFSSPEKRWASPR   400
 401  VARFATSCPPTIKELFVDSGLLRPMVEGQSQQFSVSENLLKEAIRAIFPS   450
 451  RGLARLALQFTTNPKRLQQNLFGGKFLVNVGQFNLSGALGTRGTFNFSQF   500
 501  FQQLGLASFLNGGRQEDLAKPLSVGLDSNSSTGTPEAAKKDGTMNKPTVG   550
 551  SFGFEINLQENQNALKFLASLLELPEFLLFLQHAISVPEDVARDLGDVME   600
 601  TVLSSQTCEQTPERLFVPSCTTEGSYEDVQCFSGECWCVNSWGKELPGSR   650
 651  VRGGQPRCPTDCEKQRARMQSLMGSQPAGSTLFVPACTSEGHFLPVQCFN   700
 701  SECYCVDAEGQAIPGTRSAIGKPKKCPTPCQLQSEQAFLRTVQALLSNSS   750
 751  MLPTLSDTYIPQCSTDGQWRQVQCNGPPEQVFELYQRWEAQNKGQDLTPA   800
 801  KLLVKIMSYREAASGNFSLFIQSLYEAGQQDVFPVLSQYPSLQDVPLAAL   850
 851  EGKRPQPRENILLEPYLFWQILNGQLSQYPGSYSDFSTPLAHFDLRNCWC   900
 901  VDEAGQELEGMRSEPSKLPTCPGSCEEAKLRVLQFIRETEEIVSASNSSR   950
 951  FPLGESFLVAKGIRLRNEDLGLPPLFPPREAFAEQFLRGSDYAIRLAAQS  1000
1001  TLSFYQRRRFSPDDSAGASALLRSGPYMPQCDAFGSWEPVQCHAGTGHCW  1050
1051  CVDEKGGFIPGSLTARSLQIPQCPTTCEKSRTSGLLSSWKQARSQENPSP  1100
1101  KDLFVPACLETGEYARLQASGAGTWCVDPASGEELRPGSSSSAQCPSLCN  1150
1151  VLKSGVLSRRVSPGYVPACRAEDGGFSPVQCDQAQGSCWCVMDSGEEVPG  1200
1201  TRVTGGQPACESPRCPLPFNASEVVGGTILCETISGPTGSAMQQCQLLCR  1250
1251  QGSWSVFPPGPLICSLESGRWESQLPQPRACQRPQLWQTIQTQGHFQLQL  1300
1301  PPGKMCSADYADLLQTFQVFILDELTARGFCQIQVKTFGTLVSIPVCNNS  1350
1351  SVQVGCLTRERLGVNVTWKSRLEDIPVASLPDLHDIERALVGKDLLGRFT  1400
1401  DLIQSGSFQLHLDSKTFPAETIRFLQGDHFGTSPRTWFGCSEGFYQVLTS  1450
1451  EASQDGLGCVKCPEGSYSQDEECIPCPVGFYQEQAGSLACVPCPVGRTTI  1500
1501  SAGAFSQTHCVTDCQRNEAGLQCDQNGQYRASQKDRGSGKAFCVDGEGRR  1550
1551  LPWWETEAPLEDSQCLMMQKFEKVPESKVIFDANAPVAVRSKVPDSEFPV  1600
1601  MQCLTDCTEDEACSFFTVSTTEPEISCDFYAWTSDNVACMTSDQKRDALG  1650
1651  NSKATSFGSLRCQVKVRSHGQDSPAVYLKKGQGSTTTLQKRFEPTGFQNM  1700
1701  LSGLYNPIVFSASGANLTDAHLFCLLACDRDLCCDGFVLTQVQGGAIICG  1750
1751  LLSSPSVLLCNVKDWMDPSEAWANATCPGVTYDQESHQVILRLGDQEFIK  1800
1801  SLTPLEGTQDTFTNFQQVYLWKDSDMGSRPESMGCRKDTVPRPASPTEAG  1850
1851  LTTELFSPVDLNQVIVNGNQSLSSQKHWLFKHLFSAQQANLWCLSRCVQE  1900
1901  HSFCQLAEITESASLYFTCTLYPEAQVCDDIMESNAQGCRLILPQMPKAL  1950
1951  FRKKVILEDKVKNFYTRLPFQKLMGISIRNKVPMSEKSISNGFFECERRC  2000
2001  DADPCCTGFGFLNVSQLKGGEVTCLTLNSLGIQMCSEENGGAWRILDCGS  2050
2051  PDIEVHTYPFGWYQKPIAQNNAPSFCPLVVLPSLTEKVSLDSWQSLALSS  2100
2101  VVVDPSIRHFDVAHVSTAATSNFSAVRDLCLSECSQHEACLITTLQTQPG  2150
2151  AVRCMFYADTQSCTHSLQGQNCRLLLREEATHIYRKPGISLLSYEASVPS  2200
2201  VPISTHGRLLGRSQAIQVGTSWKQVDQFLGVPYAAPPLAERRFQAPEPLN  2250
2251  WTGSWDASKPRASCWQPGTRTSTSPGVSEDCLYLNVFIPQNVAPNASVLV  2300
2301  FFHNTMDREESEGWPAIDGSFLAAVGNLIVVTASYRVGVFGFLSSGSGEV  2350
2351  SGNWGLLDQVAALTWVQTHIRGFGGDPRRVSLAADRGGADVASIHLLTAR  2400
2401  ATNSQLFRRAVLMGGSALSPAAVISHERAQQQAIALAKEVSCPMSSSQEV  2450
2451  VSCLRQKPANVLNDAQTKLLAVSGPFHYWGPVIDGHFLREPPARALKRSL  2500
2501  WVEVDLLIGSSQDDGLINRAKAVKQFEESRGRTSSKTAFYQALQNSLGGE  2550
2551  DSDARVEAAATWYYSLEHSTDDYASFSRALENATRDYFIICPIIDMASAW  2600
2601  AKRARGNVFMYHAPENYGHGSLELLADVQFALGLPFYPAYEGQFSLEEKS  2650
2651  LSLKIMQYFSHFIRSGNPNYPYEFSRKVPTFATPWPDFVPRAGGENYKEF  2700
2701  SELLPNRQGLKKADCSFWSKYISSLKTSADGAKGGQSAESEEEELTAGSG  2750
2751  LREDLLSLQEPGSKTYSK                                  2768

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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