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

NucPred

Fetching Q9UPU5 from www.uniprot.org...

The NucPred score for your sequence is 0.88 (see score help below)

   1  MESEEEQHMTTLLCMGFSDPATIRKALRLAKNDINEAVALLTNERPGLDY    50
  51  GGYEPMDSGGGPSPGPGGGPRGDGGGDGGGGGPSRGGSTGGGGGFDPPPA   100
 101  YHEVVDAEKNDENGNCSGEGIEFPTTNLYELESRVLTDHWSIPYKREESL   150
 151  GKCLLASTYLARLGLSESDENCRRFMDRCMPEAFKKLLTSSAVHKWGTEI   200
 201  HEGIYNMLMLLIELVAERIKQDPIPTGLLGVLTMAFNPDNEYHFKNRMKV   250
 251  SQRNWAEVFGEGNMFAVSPVSTFQKEPHGWVVDLVNKFGELGGFAAIQAK   300
 301  LHSEDIELGAVSALIQPLGVCAEYLNSSVVQPMLDPVILTTIQDVRSVEE   350
 351  KDLKDKRLVSIPELLSAVKLLCMRFQPDLVTIVDDLRLDILLRMLKSPHF   400
 401  SAKMNSLKEVTKLIEDSTLSKSVKNAIDTDRLLDWLVENSVLSIALEGNI   450
 451  DQAQYCDRIKGIIELLGSKLSLDELTKIWKIQSGQSSTVIENIHTIIAAA   500
 501  AVKFNSDQLNHLFVLIQKSWETESDRVRQKLLSLIGRIGREARFETTSGK   550
 551  VLDVLWELAHLPTLPSSLIQQALEEHLTILSDAYAVKEAIKRSYIIKCIE   600
 601  DIKRPGEWSGLEKNKKDGFKSSQLNNPQFVWVVPALRQLHEITRSFIKQT   650
 651  YQKQDKSIIQDLKKNFEIVKLVTGSLIACHRLAAAVAGPGGLSGSTLVDG   700
 701  RYTYREYLEAHLKFLAFFLQEATLYLGWNRAKEIWECLVTGQDVCELDRE   750
 751  MCFEWFTKGQHDLESDVQQQLFKEKILKLESYEITMNGFNLFKTFFENVN   800
 801  LCDHRLKRQGAQLYVEKLELIGMDFIWKIAMESPDEEIANEAIQLIINYS   850
 851  YINLNPRLKKDSVSLHKKFIADCYTRLEAASSALGGPTLTHAVTRATKML   900
 901  TATAMPTVATSVQSPYRSTKLVIIERLLLLAERYVITIEDFYSVPRTILP   950
 951  HGASFHGHLLTLNVTYESTKDTFTVEAHSNETIGSVRWKIAKQLCSPVDN  1000
1001  IQIFTNDSLLTVNKDQKLLHQLGFSDEQILTVKTSGSGTPSGSSADSSTS  1050
1051  SSSSSSGVFSSSYAMEQEKSLPGVVMALVCNVFDMLYQLANLEEPRITLR  1100
1101  VRKLLLLIPTDPAIQEALDQLDSLGRKKTLLSESSSQSSKSPSLSSKQQH  1150
1151  QPSASSILESLFRSFAPGMSTFRVLYNLEVLSSKLMPTADDDMARSCAKS  1200
1201  FCENFLKAGGLSLVVNVMQRDSIPSEVDYETRQGVYSICLQLARFLLVGQ  1250
1251  TMPTLLDEDLTKDGIEALSSRPFRNVSRQTSRQMSLCGTPEKSSYRQLSV  1300
1301  SDRSSIRVEEIIPAARVAIQTMEVSDFTSTVACFMRLSWAAAAGRLDLVG  1350
1351  SSQPIKESNSLCPAGIRNRLSSSGSNCSSGSEGEPVALHAGICVRQQSVS  1400
1401  TKDSLIAGEALSLLVTCLQLRSQQLASFYNLPCVADFIIDILLGSPSAEI  1450
1451  RRVACDQLYTLSQTDTSAHPDVQKPNQFLLGVILTAQLPLWSPTSIMRGV  1500
1501  NQRLLSQCMEYFDLRCQLLDDLTTSEMEQLRISPATMLEDEITWLDNFEP  1550
1551  NRTAECETSEADNILLAGHLRLIKTLLSLCGAEKEMLGSSLIKPLLDDFL  1600
1601  FRASRIILNSHSPAGSAAISQQDFHPKCSTANSRLAAYEVLVMLADSSPS  1650
1651  NLQIIIKELLSMHHQPDPALTKEFDYLPPVDSRSSSGFVGLRNGGATCYM  1700
1701  NAVFQQLYMQPGLPESLLSVDDDTDNPDDSVFYQVQSLFGHLMESKLQYY  1750
1751  VPENFWKIFKMWNKELYVREQQDAYEFFTSLIDQMDEYLKKMGRDQIFKN  1800
1801  TFQGIYSDQKICKDCPHRYEREEAFMALNLGVTSCQSLEISLDQFVRGEV  1850
1851  LEGSNAYYCEKCKEKRITVKRTCIKSLPSVLVIHLMRFGFDWESGRSIKY  1900
1901  DEQIRFPWMLNMEPYTVSGMARQDSSSEVGENGRSVDQGGGGSPRKKVAL  1950
1951  TENYELVGVIVHSGQAHAGHYYSFIKDRRGCGKGKWYKFNDTVIEEFDLN  2000
2001  DETLEYECFGGEYRPKVYDQTNPYTDVRRRYWNAYMLFYQRVSDQNSPVL  2050
2051  PKKSRVSVVRQEAEDLSLSAPSSPEISPQSSPRPHRPNNDRLSILTKLVK  2100
2101  KGEKKGLFVEKMPARIYQMVRDENLKFMKNRDVYSSDYFSFVLSLASLNA  2150
2151  TKLKHPYYPCMAKVSLQLAIQFLFQTYLRTKKKLRVDTEEWIATIEALLS  2200
2201  KSFDACQWLVEYFISSEGRELIKIFLLECNVREVRVAVATILEKTLDSAL  2250
2251  FYQDKLKSLHQLLEVLLALLDKDVPENCKNCAQYFFLFNTFVQKQGIRAG  2300
2301  DLLLRHSALRHMISFLLGASRQNNQIRRWSSAQAREFGNLHNTVALLVLH  2350
2351  SDVSSQRNVAPGIFKQRPPISIAPSSPLLPLHEEVEALLFMSEGKPYLLE  2400
2401  VMFALRELTGSLLALIEMVVYCCFCNEHFSFTMLHFIKNQLETAPPHELK  2450
2451  NTFQLLHEILVIEDPIQVERVKFVFETENGLLALMHHSNHVDSSRCYQCV  2500
2501  KFLVTLAQKCPAAKEYFKENSHHWSWAVQWLQKKMSEHYWTPQSNVSNET  2550
2551  STGKTFQRTISAQDTLAYATALLNEKEQSGSSNGSESSPANENGDRHLQQ  2600
2601  GSESPMMIGELRSDLDDVDP                                2620

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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