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

NucPred

Fetching Q9H254 from www.uniprot.org...

The NucPred score for your sequence is 0.82 (see score help below)

   1  MAQVPGEVDNMEGLPAPNNNPAARWESPDRGWEREQPAASTAAASLFECS    50
  51  RIKALADEREAVQKKTFTKWVNSHLARVGCHIGDLYVDLRDGFVLTRLLE   100
 101  VLSGEQLPRPTRGRMRIHSLENVDKALQFLKEQRVHLENVGSHDIVDGNH   150
 151  RLTLGLVWTIILRFQIQVIKIETEDNRETRSAKDALLLWCQMKTAGYPEV   200
 201  NIQNFTTSWRDGLAFNALIHRHRPDLVDFSKLTKSNANYNLQRAFRTAEQ   250
 251  HLGLARLLDPEDVNMEAPDEKSIITYVVSFYHYFSKMKALAVEGKRIGKV   300
 301  LDQVLEVGKIIERYEELAAELLAWIHRTVGLISNQKFANSLSGVQQQLQA   350
 351  FTAYCTLEKPVKFQEKGNLEVLLFSIQSKLRACNRRLFVPREGCGIWDID   400
 401  KAWGELEKAEHEREAALRAELIRQEKLELLAQRFDHKVAMRESWLNENQR   450
 451  LVSQDNFGYELPAVEAAMKKHEAIEADIAAYEERVQGVAELAQALAAEGY   500
 501  YDIRRVAAQRDSVLRQWALLTGLVGARRTRLEQNLALQKVFQEMVYMVDW   550
 551  MEEMQAQLLSRECGQHLVEADDLLQKHGLLEGDIAAQSERVEALNAAALR   600
 601  FSQLQGYQPCDPQVICNRVNHVHGCLAELQEQAARRRAELEASRSLWALL   650
 651  QELEEAESWARDKERLLEAAGGGGAAGAAGAAGTAGGAHDLSSTARLLAQ   700
 701  HKILQGELGGRRALLQQALRCGEELVAAGGAVGPGADTVHLVGLAERAAS   750
 751  ARRRWQRLEEAAARRERRLQEARALHQFGADLDGLLDWLRDAYRLAAAGD   800
 801  FGHDEASSRRLARQHRALTGEVEAHRGPVSGLRRQLATLGGASGAGPLVV   850
 851  ALQVRVVEAEQLFAEVTEVAALRRQWLRDALAVYRMFGEVHACELWIGEK   900
 901  EQWLLSMRVPDSLDDVEVVQHRFESLDQEMNSLMGRVLDVNHTVQELVEG   950
 951  GHPSSDEVRSCQDHLNSRWNRIVELVEQRKEEMSAVLLVENHVLEVAEVR  1000
1001  AQVREKRRAVESAPRAGGALQWRLSGLEAALQALEPRQAALLEEAALLAE  1050
1051  RFPAQAARLHQGAEELGAEWGALASAAQACGEAVAAAGRLQRFLHDLDAF  1100
1101  LDWLVRAQEAAGGSEGPLPNSLEEADALLARHAALKEEVDQREEDYARIV  1150
1151  AASEALLAADGAELGPGLALDEWLPHLELGWHKLLGLWEARREALVQAHI  1200
1201  YQLFLRDLRQALVVLRNQEMALSGAELPGTVESVEEALKQHRDFLTTMEL  1250
1251  SQQKMQVAVQAAEGLLRQGNIYGEQAQEAVTRLLEKNQENQLRAQQWMQK  1300
1301  LHDQLELQHFLRDCHELDGWIHEKMLMARDGTREDNHKLHKRWLRHQAFM  1350
1351  AELAQNKEWLEKIEREGQQLMQEKPELAASVRKKLGEIRQCWAELESTTQ  1400
1401  AKARQLFEASKADQLVQSFAELDKKLLHMESQLQDVDPGGDLATVNSQLK  1450
1451  KLQSMESQVEEWYREVGELQAQTAALPLEPASKELVGERQNAVGERLVRL  1500
1501  LEPLQERRRLLLASKELHQVAHDLDDELAWVQERLPLAMQTERGNGLQAV  1550
1551  QQHIKKNQGLRREIQAHGPRLEEVLERAGALASLRSPEAEAVRRGLEQLQ  1600
1601  SAWAGLREAAERRQQVLDAAFQVEQYYFDVAEVEAWLGEQELLMMSEDKG  1650
1651  KDEQSTLQLLKKHLQLEQGVENYEESIAQLSRQCRALLEMGHPDSEQISR  1700
1701  RQSQVDRLYVALKELGEERRVALEQQYWLYQLSRQVSELEHWIAEKEVVA  1750
1751  GSPELGQDFEHVSVLQEKFSEFASETGMAGRERLAAVNQMVDELIECGHT  1800
1801  AAATMAEWKDGLNEAWAELLELMGTRAQLLAASRELHKFFSDARELQGQI  1850
1851  EEKRRRLPRLTTPPEPRPSASSMQRTLRAFEHDLQLLVSQVRQLQEGAAQ  1900
1901  LRTVYAGEHAEAIASREQEVLQGWKELLSACEDARLHVSSTADALRFHSQ  1950
1951  VRDLLSWMDGIASQIGAADKPRDVSSVEVLMNYHQGLKTELEARVPELTT  2000
2001  CQELGRSLLLNKSAMADEIQAQLDKLGTRKEEVSEKWDRHWEWLQQMLEV  2050
2051  HQFAQEAVVADAWLTAQEPLLQSRELGSSVDEVEQLIRRHEAFRKAAAAW  2100
2101  EERFSSLRRLTTIEKIKAEQSKQPPTPLLGRKFFGDPTELAAKAAPLLRP  2150
2151  GGYERGLEPLARRASDTLSAEVRTRVGYVRQELKPERLQPRIDRLPEIPG  2200
2201  RVEPAALPAAPEDAAETPATPAAAEQVRPRPERQESADRAEELPRRRRPE  2250
2251  RQESVDQSEEAARRRRPERQESAEHEAAHSLTLGRYEQMERRRERRERRL  2300
2301  ERQESSEQEMPIRGDLVKGKATLADIVEQLQEKEAGPGLPAGPSLPQPRE  2350
2351  LPPGRLPNGLELPERTPRPDRPRARDRPKPRRRPRPREGGEGGGSRRSRS  2400
2401  APAQGGSAPAPPPPPTHTVQHEGFLLRKRELDANRKSSNRSWVSLYCVLS  2450
2451  KGELGFYKDSKGPASGSTHGGEPLLSLHKATSEVASDYKKKKHVFKLQTQ  2500
2501  DGSEFLLQAKDEEEMNGWLEAVASSVAEHAEIARWGQTLPTTSSTDEGNP  2550
2551  KREGGDRRASGRRK                                      2564

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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