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

NucPred

Fetching Q10105 from www.uniprot.org...

The NucPred score for your sequence is 0.75 (see score help below)

   1  MSVEEPGIEAHGHKDRMLYAMLLSKDTSLAFLGSKKIMIDILQHICRTQD    50
  51  IDEESAIAALEDIFETLPRNLSRDARKQIEITINHLVSRLPSIVLPFLVR   100
 101  RLTTIAGRLDRFRSTVSVSFDCLNWVNSMIPNLPEKELQYWILELLPLQS   150
 151  SFLSYALRDGKPSVADSAIKSTRRCYRSLFCKKMDSLKKLVSFLLTETEN   200
 201  AILPPKSLPLYGVIISTCYYFHQSPNPRNEISQQAELFSKIMAQNVLMAK   250
 251  PALEKYLYHEFCYSLGLLLSVDQLKLYLLPSIEKALLRSPEIIFSGILSS   300
 301  LAHGFADSKVDASSLILSSVLTSFVNGLKSSNAEVRRNCFQTFKDLSANA   350
 351  SDNESLSRVASELITSLRTGKVTASDQRVLFVDALSSLSLKHIDASMLLN   400
 401  ELLPLFTKAKESDFNSLASLIVKTLKFLLMNGRNPGDKIYDFLSKSLQRP   450
 451  VAHESMFWLTSLATMAWDLPASDDVQIEFINFFLNNLSILTEKALMSVSG   500
 501  ATQNGTYLAPIIYLSFGVNKLSVWNSERISHTLELQDILVKLSTPKNNDV   550
 551  FIFSSKITNKLNDDQSKLWYFQGLCDFAKVSDNLLFSNFVERWFQSVIGV   600
 601  FSFASRENSNRALKILKSAILYRPHLRMSICSQLWNYHADFEKSKSVGKF   650
 651  DSAKYDEISSLFQSLILSSMSADTSNFSNQELVDFDKYLVELLFLSFAFK   700
 701  DKFDWIRFCQVSKRDPATLVSERIHSIIEEIELLLSSAIKDSKETAAIAS   750
 751  ISMIVFVAPEESIPLFVNVFRNQLLHLNISSVSSTDLEIWKTPEGVLWDN   800
 801  VLEKKSSKKLDKNTKDYETKRWEAEVRAKQSAKKPAKLSKDQQALVDAQL   850
 851  DAEAKIRSRVNLIALSLERGLGIIRSLGEAVQLAPALWVEDAIDVLLFHN   900
 901  VLKYSEPFLKNLAYDTFLLTLKASGFSERLGDRSYSSSLASILAHTFSVN   950
 951  SSENIKELTKSILYKLRFAIEQNYFEPQMFACIFPLLYDLTFNITNSDEE  1000
1001  DEAELQLLVTEILEFQALYSASLRRMRSKLIKSLLHLLEIAPTQYQENKN  1050
1051  SLLSLCEGLHSTYTDEELNLLLSNLFHPESSIRSAVLQALQAFDLSRFEF  1100
1101  IKEIFLELYDDNETNASIAHQISTQNGLDATETSFFELQIFFTQDSDYLQ  1150
1151  QIIGKSLIDLLDEFEELGQFIPKELMRTYRENALPSAPEYDEYGIIKKET  1200
1201  IGRDLGRIARESVAVSFFHISKYLSSNLLLPFLEFLLTASEAEAQIPVTD  1250
1251  ASQKVSSKMLEAGKLAIFQSGAHQVEALMELFEQKLNVDSLPTDANDRLR  1300
1301  EATVVLFGTVAQHLPSNDPRLAVVMDSLLSVLSTPSESVQLAVAVCLPPL  1350
1351  VKKSLGKSKEYYELLSNKLMNSTSLADQKGAAYGLAGLVKGYGIKAFQDF  1400
1401  NILDSLSELISNRQNATHRQVALFAVEAFSRILGIYFEPYLPDLLPLLLT  1450
1451  SFGDNANEVREATMDAVKQIMSQLSAFGVKLLLPTLLDGLNEYNWRSKKA  1500
1501  SVEILGLMSYMAPKQLSVFLPTIIPKLSEVLTDSHSQVRNTANKSLLRFG  1550
1551  DVISNPEIQTLVPTLLKALSDCTRYTDDALEALLKTSFVHYLDPPSLALV  1600
1601  IPILKYGLRERNAGTKRQSAKIFGLMASLTEPENLAVYLESLMPRLREVL  1650
1651  IDPVPDTRATAAKALGSLIEKLGEKKFPTLIPELFNVLRSECSEVDRQGA  1700
1701  AQGLSEILAGLGLARLEDVLPEILKNTSSPVPHIRESFISLLIYLPATFG  1750
1751  SRFQPYLARAIPPILSGLADDSELVQTASLRAAKMIVNNYATKSVDLLLP  1800
1801  ELEKGLFDNAWRIRLSSVQLVGDLVFKLAGINRKALQEDEEEEGTHSDVS  1850
1851  RKALLDIIGQERHDRILSTLYIVRQDIAAVVRTPAIQIWKAIVVNTPRTV  1900
1901  REILPTLTSIIVSNLNSSSNDRRTMCVKSLGDLLKKAGFDVLPQLLPVLK  1950
1951  QGLESANSGDRIGVCIALEELINSATPEQLEIYSDDFVYAVRRALMDGDL  2000
2001  EVRETAAEAFDSLQSILGDRAVDDVLPQLLKLLESENQSEQALSALREII  2050
2051  SRRSSTIFPVLIPTLIKKPVSAFNARALSSLAQVAGVTLNKRLPSILNAL  2100
2101  MESSLASTGDDLVALNGAIDKVNLSVKDQEGLQILMAHFYSFSESEDFRK  2150
2151  RLFAAEHMLVFFQNCKLDYYRYVGDWVRHFITLFEDKSQDVVVAAVAAQN  2200
2201  TLVSALRKDQLDSLVSIAYHSLRDVGSQGVNLPAFEVAQGVNSILPIFLY  2250
2251  GLMHGTMDQREQSALGIADIVLKTEPSKLRPFVTQITGPLIRIIGERFPV  2300
2301  EVKCAILYTLNIILSKISTFLRPFLPQLQRTFAKCLGDPSSEVIRSRAAT  2350
2351  ALGTLITLQTRLAPIITELVSGARTPDAGVRKAMLNALFAVVSKSGQNMN  2400
2401  EASAEAIEQLLDEISAESSEHMVICAKLYGALFSHLPDAQAKQLLESKVL  2450
2451  SLEIQSEFSVLILNAAVKFGSQKIIELKLSDIVCSIISTASLQKEVTIAE  2500
2501  NGILALGKALLADIPQSFGNAKNLVEALKVNIEAPPSTSQDSRRLALLII  2550
2551  RVVSKENYSLIKPHISILAPAIFGCVRAIVIPVKLAAEAAFLALFQLVED  2600
2601  DSVLNKYIETLEGPRARSFVDYSRRVAVKLAAAERDRINSGSERVKLEEV  2650
2651  EDLAEINAVGRDNEVSTNDP                                2670

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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