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

NucPred

Fetching P55824 from www.uniprot.org...

The NucPred score for your sequence is 0.79 (see score help below)

   1  MTFDTRRHTTGQPGSTAPSSSSSTTSTTTTTTSPAQSAGSGSGIGTGTGT    50
  51  VANSSLPGGGSGSLDGNQDQQPATDSQSSDDVAASLSANSVDSTITIVPP   100
 101  EKLISSFPTTKLRSLTQKISNPRWVVPVLPEQELEVLLNAAIELTQAGVD   150
 151  HDCEPCVEFYRNGLSTSFAKILTDEAVNSWKNNIHHCILVSCGKLLHLIA   200
 201  IHMQRDNPYLLDLLAIVFDPENKFNTFNAGRQPECFAAPDYIWGQLDSNK   250
 251  MYARPPPEPKNARGWLVDLINRFGQLGGFDNLLERFNIGLELLKRNQNKC   300
 301  TGKNISVEGRVENGAQDNRLTLALIHSLLRPFGQCYELLMPATIAKYFMP   350
 351  TWNVVLDLLDSFTDEELKREVKPEGRNDYINGIVKSARLLASRLTGQEEL   400
 401  IRDLEMFRLKMILRLLQVSSFNGKMNALNEINKVLSSVAYFSHRSQPLPH   450
 451  CMPEDEMDWLTADRMAQWIKSSDVLGVVLKDSLHQPQYVEKLEKIIRFLI   500
 501  KEQALTLDDLDAVWRAQAGKHEAIVKNVHDLLAKLAWDFTPEQLDHLFEA   550
 551  FQASMTTANKRQRERLLELIRRLAEDDKNGVMAQKVLKLFWTLAHSQEVP   600
 601  PEVLDQALGAHVKILDYSCSQERDAQKTIWLDKCVDELKSGDGWVLPALR   650
 651  LIRDICCLYDTTTNHAQRTQTSTNRQQVIERLQNDYSLVILVTNSLTAYM   700
 701  EKVRQMVTDSPGLDATRILIDGRFPHHVQIAERLEFLKFLLKDGQLWLCA   750
 751  DQAKQIWHCLAVNAVFPADREECFRWFGKLMGEEPDLDPGINKDFFENNI   800
 801  LQLDPHLLTESGIKCFERFFKAVNSKEDKLKAIHRGYMLDNEDLIGKDYL   850
 851  WRVITTGGEEIASKAIDLLKEVSTALGPRLQENIAEFHEMFIGECCSRLR   900
 901  THYGNIVILGKTQLQEELDAPDQSDNTNDESKDSKMRFIEAEKMCRILKV   950
 951  LQEYVKECDRSFSGDRVHLPLSRVTRGKNTILYIRFQNPGRSIDDMEIVT  1000
1001  HSNETMAAFKRNLLKRIKGTSTANIKVDLFYANDEMIGVSDEINPLYQYT  1050
1051  IRDKMNLTAKLTPVGTGLASSPDSSSDSSTGSPPRPCPDMQRVESESTLP  1100
1101  GVIISQNYQYTEFFLKLYQLGSDLEHGRLRDSAKVLLHLLPCDRQTIRQL  1150
1151  KIMCKVPKAAVTVAVTGDKIAKDEEEKLYPTEQAGIEDEEEHCTPEQMFL  1200
1201  HPTPAQVLYNLSVLHGLLIPALDPLGESALLVQSAWMHSGCAHFVLELLT  1250
1251  KNNFLPSADMHTKRASFQCVLRLAKLFLYIVGSVLSRVGDEPMICDLDNG  1300
1301  SRSQVDILKQNFSTMPSSSQGTLRAISAKLAVILAREMLSASPEGDRCRT  1350
1351  LFSSTLQWSCPDISTIKAVVQLAWASSCGNLQALGNSSGDFEDEVIVPDG  1400
1401  QDFSMCKEALEVLTISFILNPSANEALTSDPNWPKFITSIVLKNPLRHVR  1450
1451  QVASEQLFLASTYCAGDRRPFVYMVNLLVGALKTLVPQYESTCAEFFSVL  1500
1501  CRTLSYGCIYNWPLQISEGLLGDEIKWLQRIRENVHATGDTQVHEELLEG  1550
1551  HLCLAKELMFFLGADSKAQLNELIHELIDDFLFTASREFLHLRRHGSLRQ  1600
1601  DTVPPPVCRSPHTIAAACDLLIALCQLCVPNMKLLTNTLIDFVCTDTDPL  1650
1651  REWDYLPPVGARPTKGFCGLKNAGATCYMNSVLQQLYMVPAVRVGILRAH  1700
1701  GAATTDGEDFSGDSDLTGGGLGSALFSGPASALVSLPSSSSTIEDGLHDV  1750
1751  RKNYHVVILKHVQAIFAHLGHSALQYYVPRGLWTHFKLLGEPVNLREQQD  1800
1801  AVEFFMSLLESLDEGLKALGQPQLMNATLGGSFSDQKICQECPHRYSKEE  1850
1851  PFSVFSVDIRNHSSLTESLEQYVKGELLEGADAYHCDKCDKKVVTVKRVC  1900
1901  VKKLPPVLAIQLKRFEYDYERVCAIKFNDYFEFPRILDMEPYTVSGLAKL  1950
1951  EGEVVEVGDNCQTNVETTKYELTGIVVHSGQASGGHYFSYILSKNPANGK  2000
2001  CQWYKFDDGEVTECKMHEDEEMKAECFGGEYMGETYDNNLKRMQYRRQKR  2050
2051  WWNAYMLFYTRCDQTPVQYEPSVEQLSLAESRNMVLPLPKPIERSVRHQN  2100
2101  IRFLHSRSIFSVEFFNFIKKLVSCNLLSARSNKITPAAEELSLLGVQLAS  2150
2151  QFLFHTGFRTKKSLRGPVMEWYDALSHHIRSSALVRKWFANHALLSPPSR  2200
2201  LGEYILMAPSPDVRTVFVKLVVFFCHFAINDEPLTGYDGANLCEQVLISV  2250
2251  LRLLKSEAADYGKHLPHYFSLFSMYVGLGTREKQQLLRLNVPLQFIQVAL  2300
2301  DDGPGPAIKYQYPEFSKLHQVVSHLIRCSDVSEKCQSSNQNARPLSNPFK  2350
2351  DPNVAHEELTPLSTECMDLLFNRTGYIKKVIEDTNVGDEGLKLLQYCSWE  2400
2401  NPHFSRAVLTELLWQCGFAYCHDMRHHTDLLLNILLIDDSWQHHRIHNAL  2450
2451  NGVAEEREGLLETIQRAKTHYQKRAYQIIKCLTQLFHKSPIALQMLHTNS  2500
2501  NITRHWSIAVEWLQGELDRQRGIGCQYNSYSWSPPAQSNDNTNGYMLERS  2550
2551  QSAKNTWSMAFELCPDEVSEKTDENNEPNLETNMDENKSEPVAQPGGVLE  2600
2601  GSTGGTEQLPENKTPTTSSPSTAAWPARGDSNAIPRLSRQLFGAYTSTGS  2650
2651  GSTSGGSAPTSALTTTAGSGANSETESSAQETTGETTINGLTNSLDQMEI  2700
2701  TAKKKCRRVIIKKLVESKDEEDATTATTAATTEVTTSPATAIATAATLEP  2750
2751  AGMSELTTMVEKNLIISQENPQAKSSLQ                        2778

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.)

Go back to the NucPred Home Page.