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

NucPred

Fetching Q8R526 from www.uniprot.org...

The NucPred score for your sequence is 0.65 (see score help below)

   1  MDVDEDQHAVAVLHHKIQANPELCVSDEQDSCPSDAPKGTARDPESQKPS    50
  51  SPAPWDKNVLNTGSEERLSFINGEPQAPPNWDEGTNSFSNPPPGISHTCN   100
 101  LSASWYHPESSSPLTQHPPRATLVTQPENVEHFAICCFPETDAQALPALG   150
 151  IRVHVASGTALCLLLDFGDNCGAQMRLCTLAGATTVTGYHQYRKEGVYEL   200
 201  KAVVHDFHRAEELGPYYVDISHGNVSVFMNSSSIHDSEALSFADSLPQQR   250
 251  GTVVVHCFSSISSYNVSFISQTQVASGQAWCGVTVGYKMQSVSVYTNGTV   300
 301  FAANTNITFVAITEETIPLEFAWYFGENPPVMTTSRSIRRRLSVPQWYRV   350
 351  KVKATSRIGSVVSEPHLIRVQKRIMANRLVSTASALVNANVSFECRLNFG   400
 401  TDVAYLWNFGDDTIELGSSSSSHVYSREGEFTVEVLAFNNVSSTTLRKQL   450
 451  FIVREPCQPPPVKNMGPAKVQIWRSQPLRLGVTFEAAILCNISQGLSYTW   500
 501  SFVSAEMTTVTLPTAVNTRRQTIMLPSYTLECGNYTAIAKVQIKGSMVYS   550
 551  NYCVGVEVRARAPVSVISEGTHIFISTATSTFIILRGAQSYDPDNPGAAL   600
 601  RYHWTCTAASSPRWPCFDNSTSYQVDTQAPAISFPAKWLSECCDQFLVTL   650
 651  TVSSRGQNSSQALMFLSTRPDLAFRFVHISWVNFRDISVNWNEEVSLRAV   700
 701  CEDCGDVPDLTYSWDLFLVNATEKSAVEVPFCSTVGLLGALALGTSLKSS   750
 751  KSDLPSNLRAPLTPHSPEPSPTPLGWTALSNLGSISAESTAGGHHVPASG   800
 801  AVAGSGEPMEEYSSLSSLAEEALMTNSSEGSWPSPSSSTDFDDFEAYYSD   850
 851  IQEAVLSLGRQPGTSTNFQEAGPSLSAEESASYGDNLLGPFLHTGRAKPT   900
 901  LMIDWPKALVSQAAFHGYTTSGIMGPAVTIKPFSLSSGKTYVLQASVASK   950
 951  HVLLGKAQLYLTVNQAPQDMSCQVRPHHGMEAYTIFSVFCMSGKPDFHYE  1000
1001  FRYRIGNTSSHTLYRGQDTQHYFLLPAGDSSDNYKVIVSTEITDGHGSKV  1050
1051  QPCTVAVTVLPRYHGNDCCDKELYNSTLESLSTLRLAGSYMETRNYITMI  1100
1101  TGILSRLYVESRNTSSCGQWSQIQDVLISSACKVPYTDQEGMMDSIHILR  1150
1151  DLISFPNKLSLTSAMCIFKYTKMFLAQGQFSRRLLVDKKLRVEFVLLISG  1200
1201  VWEAAKEDARDGDYLQEEGMKIISDMLLACLSDEHQIHVSTGQMEFQTLL  1250
1251  HRSPQSSIQNLGFVQVHFPSDLASLHSTTQEATQSSCYISQLMFFMKSPY  1300
1301  LGGQVPGQVGGVMIPRLYSCESRRPILRGQLETPVTMEFGEEDYLHKRNP  1350
1351  AMFVLLRDEVNVHRFTGLSENSQESLQIHIKFSKPVTRPFPIILLVRFSE  1400
1401  KATPSDFLVKRVYFWDEQTVQMYVPAAPWKGANVGYLSLLDADYDRKPPN  1450
1451  KYLAGAVNYTVHFQWIQCVFWDKTEWRSEGPYPQPGSSPEKVNCSYHHLA  1500
1501  PVSVLRRKLNATLEVSSISEFQSHPHNLLPGIFSAFLLVLYGILVSKSRY  1550
1551  VDCHEKKNPGFIFLEEDTLPGYQLYAVVIDTGFRSPVRFTSKVFIVLCGE  1600
1601  NGCSETKELCCPEKPLFGRNSRHTFILSIPNQLGPLQKIRLWHDSSGSSP  1650
1651  CWFISHVMVKELCSGQAWFFSAQCWLAVSKLGGHVLREFFCLSHGLGFWK  1700
1701  LFYSKFTEYLEDFHIWLSLYSQPPSRSYLHTQRLAVSFCLLCVYSCLTAL  1750
1751  VTVRDHQQRPLDVGPTAITLEPFCMALLCTLLACPVAQLLSLLFRCSKEA  1800
1801  RGDMQASTQWPLRGVKTETPQGHDSSGRPDSRQPSPHPTSDLLPWNDQAW  1850
1851  RIAASSSAVVCSPFPMEACSHKHHDLREKSHYSPPSSQAPGSGFEELGSQ  1900
1901  KSRVCLLWSSSVAWAISGSASLACGLGTGFLGYWFVPAQCMWWLYLLLLS  1950
1951  LVCCAFITQPLMICLAALVFAWKRKHDSKFFTESLQDATKGLDLELEEHS  2000
2001  RTRVPLSPISYSPDTAEEAERVLATRQRERHLRWAQTPSKAKLRVTGERL  2050
2051  RRESIMQAALRDMTTHSIMLLLLLFIAYGRFCPGEISLNHAIRKAFTRKA  2100
2101  NHSLGDLSSTEDWWDWTLSTLLDELYPERTSARAWGAQPGALGGQCHLIG  2150
2151  PPVVKLLKISAGTACTPPRPFSELVEDVLPMHSNDLDLENQNVSPGGPET  2200
2201  CGVKKESYMHSLGKTRHEAHAALTALRASKWIDHSTRAMSVHFTLYNPPT  2250
2251  QLFTSVILGTECLPSGGLVPSFLVESFRIFYSDSALKYLLMLSELLFLVL  2300
2301  NVIHLCFQLWGMTTKGILSYWRKPRHWLELSMVGVAIAYYAASGHLTTLA  2350
2351  VNITDQFHKGLYQRLVDIGLMVSWHQRARCLQGILLFLWMLKYVHLLSSL  2400
2401  STMTPFSAVTCFPLFRVLLVGALLLAAHYHSRWFLLFTGTLSHGTSAEAF  2450
2451  PGLLLQFPGRSKKDSWHNCLKSDHGVMRCYYGTLFLLLATLGFRMLRATF  2500
2501  LTVFQNRKSSHRKPLVTLKDIAVYTWHKVLTLLGLETTLEETEVATDHIY  2550
2551  YLDEFSSLLDELLMKIDGLSDSLELSILENQWKRALESRAGDSPPVGSSE  2600
2601  YQATGVSGPLAAESE                                     2615

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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