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

NucPred

Fetching Q9VXG8 from www.uniprot.org...

The NucPred score for your sequence is 0.85 (see score help below)

   1  MSTQRKDMWKLLYNHVNRNVSNFSGVYSVIEDILCQEPSLISCSLVRELH    50
  51  NKFQDTFLLWLLNKLAKCLSESPDSSECINLQRKILSSCCSNHPKLFERL   100
 101  VLAYVEAIEETHLQLSSLDLGQLSNERKPAITVRIFRCDVECLQEFDPHC   150
 151  AIEDIKVPLEQADMYAKSLLEVLQHAHHIGYATHGDIFSGSLHQALLILK   200
 201  ECDMDTKLASLNYCHNVLRSQSASSWITNPDVGHYAQLTLEATAIMWSAV   250
 251  AKWLDMGCMTRQELKRLNITTKLLLEVLHMRARPAHHLGYLLLNEILSLP   300
 301  TAIELDDGLLETLSSYIQGQLEHSVVPLEQLVHLQQLMLSHWHCHPTHLV   350
 351  PILALMGLKQTEMRSGVVQVLTQSLVEILKKEEVLSKDWQKLIAILRGFK   400
 401  QLEKLILSQSQHKIAEHEGHIDSSVLAMLPLQCEIIKVADTNWNNLSMQL   450
 451  VELESKCSADRRHIHLEICSLLMQITFIRHFLKTQTQHQLLAILQRHLKL   500
 501  SYLCAIRLETPSSVHTQMQSFYAQQYMRLFQSEETQEIFCSNLPQLYISG   550
 551  FIKPEQLMKALPTINNRSGRAQVIRLLLCSQPGKLSVFKVKDRIELYCPK   600
 601  CRPLPKKLPGIYLGKCKQQLPCPDFSSTNLEMIANDLLFYPDFECIAQHL   650
 651  DLLCFEPNVILGLLRETEALQKVSVKVIGQLVSAMRVRSPEFLEQLANLV   700
 701  LAAIKAMLAKPLTEQNVLQQRSMLNVLTAIAHMEDNEIWLFHWFKMTFFF   750
 751  LVHTRSLVAQEAVLAATEMCASQGLQTIHLWNWYKRDALDLTVRLALNVY   800
 801  LLDGVRFTRSLRALTKMLGFTCVQEFTCKYHRLLTAMVLPHCIVNPLCKG   850
 851  VLVLIAKQMQKHIGTLFSISFLRIYTHVFLTEEPELANSCIELVVSCTQS   900
 901  SLQQLMNADVKQTVAELLIYFNRNPTFVMRSFQSLLQLSIGSLEELSSQT   950
 951  ANAEFANFIAERFLGVITYFESCLSEPSFEKPLKEETLYSLGQIMRFVGS  1000
1001  QHVTQFRFKIIAMLSFVHTLQEPRLQRICLKIWHIFLHVVNVQELGPSLG  1050
1051  RIVATLQPLLADNESVKQVNDLYEFIILRNASMLGTFITDLYFLDRMENV  1100
1101  SPSIQKCIRRHTAHLDLKGLAEEENQSPPLVDQLRFLQKHITDECLQVRV  1150
1151  YALQHLGDLFGRRRPKLNSTILSELPLEPMLEQIVNVLMAGCQHDDSQLQ  1200
1201  MASAKCLGELGAIDASYLPSNYNFASPQHLPLNILSDDFAVLALTSLCRG  1250
1251  YQFQQNTKHVDSFSLAIQETLAICGISPKEQKKVQLWQSLPARMRQLMEP  1300
1301  MLHSCYTCVHRPSTCLQQPLFGSHYSHNYYEEWAFLWASRLIDYLPSSGR  1350
1351  RHLLSSYKPCIKRDSNMLSTFYPYILLHALLECTTEQRNHIQEEFMAVLQ  1400
1401  ANEESSSSVRGRQELGAIKENAFKQFESRKYAAGIKPLASTLVSDRKEDS  1450
1451  SRVPRLAGKLCAELLDFLQRWLREWQRIHGRSTGGKPPETIDSNYRKIHE  1500
1501  FLNLIPKLLVSRASYNCGEYARALSYLESYLEEGEDKSQRLLEQFTFLVE  1550
1551  VYGSLRDPDSVEGAVQVRSYDMSVTQDILVNRLVERQQDMITSYEQLLSS  1600
1601  TDQMQPDHVRAMIDAYLRDTPKTAQLIADGLWQRLSDRYSDQCFAECKSE  1650
1651  LLWRLGSYDEMEELQSNWPAQCSQGCLKLRRPLTTRIEFDSLLDGMRESV  1700
1701  LEELRSCSAVQQHSYANAYDAVLKLHLVHELHCSQELVEKLEQDRDEDNQ  1750
1751  EKLMKNYFDDWQYRLQIVQPQVRIQESIYSFRRNILAELQRRLTDRNHLL  1800
1801  PHLKTELARIWLNSAQINRNAGQLQRAQLYILKAAEYQPSGLFIERAKLL  1850
1851  WQKGDQVMAMNYLEEQLSIMRSGCQGNVKQLAAEQRHLFFRGKYLQAVYS  1900
1901  AESMHLCADAVLKYFQEAIAVHRQSESCHVQMAQFLEKILEARQGGKSEP  1950
1951  TGEQDDMLINVMVNYAKSLRYGSEHVYQSMPRLISLWLDTTESSTNTEQV  2000
2001  KKMNDLLTNCCTALPTAVFYTVYSQMLSRLCHPVNDVFTVLRNVIIKLVE  2050
2051  AYPQQSLWMLLPHFKSAKAHRIKRCKLVLTDSRLQNSTFQKLLQDFNSLT  2100
2101  ERLMDLTNKEVTLDRTYKLSDLDTRLSKLCKQPEFSQILLPFEKYMQPTL  2150
2151  PLNSDSNSSEGSHLPANQSTVNWFPYQQIYISGFQESVLILRSAAKPKKL  2200
2201  TIRCSDGKDYDVLVKPKDDLRRDARLMEFNGLVKRYLHQDAPARQRRLHI  2250
2251  RTYAVLPFNEECGLVEWLPNLASYRSICMNLYAQRRLVMSTRQLQSLAVP  2300
2301  LHESIERKREVFTKQLVPAHPPVFQEWLRQRFATPHSWYEARNTYIRTVA  2350
2351  VMSMVGYILGLGDRHGENILFAEGNGDAVHVDFNCLFNQGELLPYPEVVP  2400
2401  FRLTHNMIVAMGPLGVEGSFRKCCEITLRLLKQESKTLMSILRPFVYDVG  2450
2451  AQTRKGAATAKITKDVQRIADRLQGHVKRQQANSIPLSTEGQVNFLINEA  2500
2501  TKVDNLASMYIGWGAFL                                   2517

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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