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

NucPred

Fetching Q9QWN8 from www.uniprot.org...

The NucPred score for your sequence is 0.91 (see score help below)

   1  MSSTLSPTDFDSLEIQGQYSDINNRWDLPDSDWDNDSSSARLFERSRIKA    50
  51  LADEREAVQKKTFTKWVNSHLARVTCRVGDLYSDLRDGRNLLRLLEVLSG   100
 101  ETLPKPTKGRMRIHCLENVDKALQFLKEQKVHLENMGSHDIVDGNHRLTL   150
 151  GLVWTIILRFQIQDISVETEDNKEKKSAKDALLLWCQMKTAGYPNVNVHN   200
 201  FTTSWRDGLAFNAIVHKHRPDLLDFESLKKCNAHYNLQNAFNLAEKELGL   250
 251  TKLLDPEDVNVDQPDEKSIITYVATYYHYFSKMKALAVEGKRIGKVLDHA   300
 301  MEAEHLVEKYESLASELLQWIEQTIVTLNDRQLANSLSGVQNQLQSFNSY   350
 351  RTVEKPPKFTEKGNLEVLLFTIQSKLRANNQKVYTPREGRLISDINKAWE   400
 401  RLEKAEHERELALRTELIRQEKLEQLAARFDRKAAMRETWLSENQRLVSQ   450
 451  DNFGLELAAVEAAVRKHEAIETDIVAYSGRVQAVDAVAAELAAEHYHDIK   500
 501  RIAARQNNVARLWDFLREMVAARRERLLLNLELQKVFQDLLYLMDWMAEM   550
 551  KGRLQSQDLGKHLAGVEDLLQLHELVEADIAVQAERVRAVSASALRFCDP   600
 601  GKEYRPCDPQLVSERVATLEQSYEALCELAATRRARLEESRRLWRFLWEV   650
 651  GEAEAWVREQQHLLASAETGRDLTGVLRLLNKHTALRGEMSGRLGPLKLT   700
 701  LEQGQQLVAEGHPGANQASTRAAELQAQWERLEALAEERAQRLAQAASLY   750
 751  QFQADANDMEAWLVDALRLVSSPEVGHDEFSTQALARQHRALEEEIRAHR   800
 801  PTLDALREQAAALPPALSHTPEVQGRVPTLEQHYEELQARAGERARALEA   850
 851  ALAFYTMLSEAGACGLWVEEKEQWLNGLALPERLEDLEVVQQRFETLEPE   900
 901  MNALAARVTAVSDIAEQLLKASPPGKDRIIGTQEQLNQRWQQFRSLADGK   950
 951  KAALTSALSIQNYHLECTETQAWMREKTKVIESTQDLGNDLAGVLALQRK  1000
1001  LAGTERDLEAISARVGELTQEANALAAGHPAQAPAINTRLGEVQTGWEDL  1050
1051  RATMRRREESLGEARRLQDFLRSLDDFQAWLGRTQTAVASEEGPATLPEA  1100
1101  EALLAQHAALRGEVERAQSEYSRLRTLGEEVTRDQADPQCLFLRQRLEAL  1150
1151  GTGWEELGRMWESRQGRLAQAHGFQGFLRDARQAEGVLSSQEYFLSHTEM  1200
1201  PGTLQAADAAIKKLEDFMSTMDANGERIRGLLEAGRQLVSKGNIHAEKIQ  1250
1251  EKADSIEKRHRKNQEAVQQLLGRLRDNREQQHFLQDCQELKLWIDEKMLT  1300
1301  AQDVSYDEARNLHTKWQKHQAFMAELAANKDWLDKVDKEGRELTLEKPEL  1350
1351  KVLVSEKLEDLHRRWDELETTTQAKARSLFDANRAELFAQSCSALESWLE  1400
1401  SLQAQLHSDDYGKDLTSVNILLKKQQMLEREMAVREKEVEAIQAQAKALA  1450
1451  QEDQSAGEVERTSRAVEEKFRALCQPMKDRCRRLQASREQHQFHRDVEDE  1500
1501  ILWVTERLPMASSLEHGKDLPSVQLLMKKNQTLQKEIQGHEPRIADLKER  1550
1551  QRTLGTAAAGPELAELQEMWKRLSHELELRGKRLEEALRAQQFYRDAAEA  1600
1601  EAWMGEQELHMMGQEKAKDELSAQAEVKKHQVLEQALADYAQTIKQLAAS  1650
1651  SQDMIDHEHPESTRLTIRQAQVDKLYAGLKELAGERRERLQEHLRLCQLR  1700
1701  RELDDLEQWIQEREVVAASHELGQDYEHVTMLRDKFREFSRDTSTIGQER  1750
1751  VDSANALANGLIAGGHAARATVAEWKDSLNEAWADLLELLDTRGQVLAAA  1800
1801  YELQRFLHGARQALARVQHKQQQLPDGTGRDLNAAEALQRRHCAYEHDIQ  1850
1851  ALSTQVQQVQDDGLRLQKAYAGDKAEEIGRHMQAVAEAWAQLQGSSAARR  1900
1901  QLLLDTTDKFRFFKAVRELMLWMDGINLQMDAQERPRDVSSADLVIKNQQ  1950
1951  GIKAEIEARADRFSACIDMGQELLARNHYAAEEISEKLSQLQSRRQETAE  2000
2001  KWQEKMDWLQLVLEVLVFGRDAGMAEAWLCSQEPLVRSAELGCTVDEVES  2050
2051  LIKRHEAFQKSAVAWEERFSALEKLTALEERENEQKRKREEEERRKQPPT  2100
2101  SEPMASQPEGSLVDGQRVLDTAWDGTQSKLPPSTQAPSINGVCTDTESSQ  2150
2151  PLLEQQRLEQSNVPEGPGSGTGDESSGPRGERQTLPRGPAPSPMPQSRSS  2200
2201  ESAHVATLPARGAELSAQEQMEGTLCRKQEMEAFNKKAANRSWQNVYCVL  2250
2251  RRGSLGFYKDARAASAGVPYHGEVPVSLARAQGSVAFDYRKRKHVFKLGL  2300
2301  QDGKEYLFQAKDEAEMSSWLRVVNAAIATASSASGEPEEPVVPSASRGLT  2350
2351  RAMTMPPVSQPEGSIVLRSKDGREREREKRFSFFKKNK              2388

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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