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

NucPred

Fetching Q7Z333 from www.uniprot.org...

The NucPred score for your sequence is 0.99 (see score help below)

   1  MSTCCWCTPGGASTIDFLKRYASNTPSGEFQTADEDLCYCLECVAEYHKA    50
  51  RDELPFLHEVLWELETLRLINHFEKSMKAEIGDDDELYIVDNNGEMPLFD   100
 101  ITGQDFENKLRVPLLEILKYPYLLLHERVNELCVEALCRMEQANCSFQVF   150
 151  DKHPGIYLFLVHPNEMVRRWAILTARNLGKVDRDDYYDLQEVLLCLFKVI   200
 201  ELGLLESPDIYTSSVLEKGKLILLPSHMYDTTNYKSYWLGICMLLTILEE   250
 251  QAMDSLLLGSDKQNDFMQSILHTMEREADDDSVDPFWPALHCFMVILDRL   300
 301  GSKVWGQLMDPIVAFQTIINNASYNREIRHIRNSSVRTKLEPESYLDDMV   350
 351  TCSQIVYNYNPEKTKKDSGWRTAICPDYCPNMYEEMETLASVLQSDIGQD   400
 401  MRVHNSTFLWFIPFVQSLMDLKDLGVAYIAQVVNHLYSEVKEVLNQTDAV   450
 451  CDKVTEFFLLILVSVIELHRNKKCLHLLWVSSQQWVEAVVKCAKLPTTAF   500
 501  TRSSEKSSGNCSKGTAMISSLSLHSMPSNSVQLAYVQLIRSLLKEGYQLG   550
 551  QQSLCKRFWDKLNLFLRGNLSLGWQLTSQETHELQSCLKQIIRNIKFKAP   600
 601  PCNTFVDLTSACKISPASYNKEESEQMGKTSRKDMHCLEASSPTFSKEPM   650
 651  KVQDSVLIKADNTIEGDNNEQNYIKDVKLEDHLLAGSCLKQSSKNIFTER   700
 701  AEDQIKISTRKQKSVKEISSYTPKDCTSRNGPERGCDRGIIVSTRLLTDS   750
 751  STDALEKVSTSNEDFSLKDDALAKTSKRKTKVQKDEICAKLSHVIKKQHR   800
 801  KSTLVDNTINLDENLTVSNIESFYSRKDTGVQKGDGFIHNLSLDPSGVLD   850
 851  DKNGEQKSQNNVLPKEKQLKNEELVIFSFHENNCKIQEFHVDGKELIPFT   900
 901  EMTNASEKKSSPFKDLMTVPESRDEEMSNSTSVIYSNLTREQAPDISPKS   950
 951  DTLTDSQIDRDLHKLSLLAQASVITFPSDSPQNSSQLQRKVKEDKRCFTA  1000
1001  NQNNVGDTSRGQVIIISDSDDDDDERILSLEKLTKQDKICLEREHPEQHV  1050
1051  STVNSKEEKNPVKEEKTETLFQFEESDSQCFEFESSSEVFSVWQDHPDDN  1100
1101  NSVQDGEKKCLAPIANTTNGQGCTDYVSEVVKKGAEGIEEHTRPRSISVE  1150
1151  EFCEIEVKKPKRKRSEKPMAEDPVRPSSSVRNEGQSDTNKRDLVGNDFKS  1200
1201  IDRRTSTPNSRIQRATTVSQKKSSKLCTCTEPIRKVPVSKTPKKTHSDAK  1250
1251  KGQNRSSNYLSCRTTPAIVPPKKFRQCPEPTSTAEKLGLKKGPRKAYELS  1300
1301  QRSLDYVAQLRDHGKTVGVVDTRKKTKLISPQNLSVRNNKKLLTSQELQM  1350
1351  QRQIRPKSQKNRRRLSDCESTDVKRAGSHTAQNSDIFVPESDRSDYNCTG  1400
1401  GTEVLANSNRKQLIKCMPSEPETIKAKHGSPATDDACPLNQCDSVVLNGT  1450
1451  VPTNEVIVSTSEDPLGGGDPTARHIEMAALKEGEPDSSSDAEEDNLFLTQ  1500
1501  NDPEDMDLCSQMENDNYKLIELIHGKDTVEVEEDSVSRPQLESLSGTKCK  1550
1551  YKDCLETTKNQGEYCPKHSEVKAADEDVFRKPGLPPPASKPLRPTTKIFS  1600
1601  SKSTSRIAGLSKSLETSSALSPSLKNKSKGIQSILKVPQPVPLIAQKPVG  1650
1651  EMKNSCNVLHPQSPNNSNRQGCKVPFGESKYFPSSSPVNILLSSQSVSDT  1700
1701  FVKEVLKWKYEMFLNFGQCGPPASLCQSISRPVPVRFHNYGDYFNVFFPL  1750
1751  MVLNTFETVAQEWLNSPNRENFYQLQVRKFPADYIKYWEFAVYLEECELA  1800
1801  KQLYPKENDLVFLAPERINEEKKDTERNDIQDLHEYHSGYVHKFRRTSVM  1850
1851  RNGKTECYLSIQTQENFPANLNELVNCIVISSLVTTQRKLKAMSLLGSRN  1900
1901  QLARAVLNPNPMDFCTKDLLTTTSERIIAYLRDFNEDQKKAIETAYAMVK  1950
1951  HSPSVAKICLIHGPPGTGKSKTIVGLLYRLLTENQRKGHSDENSNAKIKQ  2000
2001  NRVLVCAPSNAAVDELMKKIILEFKEKCKDKKNPLGNCGDINLVRLGPEK  2050
2051  SINSEVLKFSLDSQVNHRMKKELPSHVQAMHKRKEFLDYQLDELSRQRAL  2100
2101  CRGGREIQRQELDENISKVSKERQELASKIKEVQGRPQKTQSIIILESHI  2150
2151  ICCTLSTSGGLLLESAFRGQGGVPFSCVIVDEAGQSCEIETLTPLIHRCN  2200
2201  KLILVGDPKQLPPTVISMKAQEYGYDQSMMARFCRLLEENVEHNMISRLP  2250
2251  ILQLTVQYRMHPDICLFPSNYVYNRNLKTNRQTEAIRCSSDWPFQPYLVF  2300
2301  DVGDGSERRDNDSYINVQEIKLVMEIIKLIKDKRKDVSFRNIGIITHYKA  2350
2351  QKTMIQKDLDKEFDRKGPAEVDTVDAFQGRQKDCVIVTCVRANSIQGSIG  2400
2401  FLASLQRLNVTITRAKYSLFILGHLRTLMENQHWNQLIQDAQKRGAIIKT  2450
2451  CDKNYRHDAVKILKLKPVLQRSLTHPPTIAPEGSRPQGGLPSSKLDSGFA  2500
2501  KTSVAASLYHTPSDSKEITLTVTSKDPERPPVHDQLQDPRLLKRMGIEVK  2550
2551  GGIFLWDPQPSSPQHPGATPPTGEPGFPVVHQDLSHIQQPAAVVAALSSH  2600
2601  KPPVRGEPPAASPEASTCQSKCDDPEEELCHRREARAFSEGEQEKCGSET  2650
2651  HHTRRNSRWDKRTLEQEDSSSKKRKLL                         2677

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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