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

NucPred

Fetching P42356 from www.uniprot.org...

The NucPred score for your sequence is 0.78 (see score help below)

   1  MAAAPARGGGGGGGGGGGCSGSGSSASRGFYFNTVLSLARSLAVQRPASL    50
  51  EKVQKLLCMCPVDFHGIFQLDERRRDAVIALGIFLIESDLQHKDCVVPYL   100
 101  LRLLKGLPKVYWVEESTARKGRGALPVAESFSFCLVTLLSDVAYRDPSLR   150
 151  DEILEVLLQVLHVLLGMCQALEIQDKEYLCKYAIPCLIGISRAFGRYSNM   200
 201  EESLLSKLFPKIPPHSLRVLEELEGVRRRSFNDFRSILPSNLLTVCQEGT   250
 251  LKRKTSSVSSISQVSPERGMPPPSSPGGSAFHYFEASCLPDGTALEPEYY   300
 301  FSTISSSFSVSPLFNGVTYKEFNIPLEMLRELLNLVKKIVEEAVLKSLDA   350
 351  IVASVMEANPSADLYYTSFSDPLYLTMFKMLRDTLYYMKDLPTSFVKEIH   400
 401  DFVLEQFNTSQGELQKILHDADRIHNELSPLKLRCQANAACVDLMVWAVK   450
 451  DEQGAENLCIKLSEKLQSKTSSKVIIAHLPLLICCLQGLGRLCERFPVVV   500
 501  HSVTPSLRDFLVIPSPVLVKLYKYHSQYHTVAGNDIKISVTNEHSESTLN   550
 551  VMSGKKSQPSMYEQLRDIAIDNICRCLKAGLTVDPVIVEAFLASLSNRLY   600
 601  ISQESDKDAHLIPDHTIRALGHIAVALRDTPKVMEPILQILQQKFCQPPS   650
 651  PLDVLIIDQLGCLVITGNQYIYQEVWNLFQQISVKASSVVYSATKDYKDH   700
 701  GYRHCSLAVINALANIAANIQDEHLVDELLMNLLELFVQLGLEGKRASER   750
 751  ASEKGPALKASSSAGNLGVLIPVIAVLTRRLPPIKEAKPRLQKLFRDFWL   800
 801  YSVLMGFAVEGSGLWPEEWYEGVCEIATKSPLLTFPSKEPLRSVLQYNSA   850
 851  MKNDTVTPAELSELRSTIINLLDPPPEVSALINKLDFAMSTYLLSVYRLE   900
 901  YMRVLRSTDPDRFQVMFCYFEDKAIQKDKSGMMQCVIAVADKVFDAFLNM   950
 951  MADKAKTKENEEELERHAQFLLVNFNHIHKRIRRVADKYLSGLVDKFPHL  1000
1001  LWSGTVLKTMLDILQTLSLSLSADIHKDQPYYDIPDAPYRITVPDTYEAR  1050
1051  ESIVKDFAARCGMILQEAMKWAPTVTKSHLQEYLNKHQNWVSGLSQHTGL  1100
1101  AMATESILHFAGYNKQNTTLGATQLSERPACVKKDYSNFMASLNLRNRYA  1150
1151  GEVYGMIRFSGTTGQMSDLNKMMVQDLHSALDRSHPQHYTQAMFKLTAML  1200
1201  ISSKDCDPQLLHHLCWGPLRMFNEHGMETALACWEWLLAGKDGVEVPFMR  1250
1251  EMAGAWHMTVEQKFGLFSAEIKEADPLAASEASQPKPCPPEVTPHYIWID  1300
1301  FLVQRFEIAKYCSSDQVEIFSSLLQRSMSLNIGGAKGSMNRHVAAIGPRF  1350
1351  KLLTLGLSLLHADVVPNATIRNVLREKIYSTAFDYFSCPPKFPTQGEKRL  1400
1401  REDISIMIKFWTAMFSDKKYLTASQLVPPDNQDTRSNLDITVGSRQQATQ  1450
1451  GWINTYPLSSGMSTISKKSGMSKKTNRGSQLHKYYMKRRTLLLSLLATEI  1500
1501  ERLITWYNPLSAPELELDQAGENSVANWRSKYISLSEKQWKDNVNLAWSI  1550
1551  SPYLAVQLPARFKNTEAIGNEVTRLVRLDPGAVSDVPEAIKFLVTWHTID  1600
1601  ADAPELSHVLCWAPTDPPTGLSYFSSMYPPHPLTAQYGVKVLRSFPPDAI  1650
1651  LFYIPQIVQALRYDKMGYVREYILWAASKSQLLAHQFIWNMKTNIYLDEE  1700
1701  GHQKDPDIGDLLDQLVEEITGSLSGPAKDFYQREFDFFNKITNVSAIIKP  1750
1751  YPKGDERKKACLSALSEVKVQPGCYLPSNPEAIVLDIDYKSGTPMQSAAK  1800
1801  APYLAKFKVKRCGVSELEKEGLRCRSDSEDECSTQEADGQKISWQAAIFK  1850
1851  VGDDCRQDMLALQIIDLFKNIFQLVGLDLFVFPYRVVATAPGCGVIECIP  1900
1901  DCTSRDQLGRQTDFGMYDYFTRQYGDESTLAFQQARYNFIRSMAAYSLLL  1950
1951  FLLQIKDRHNGNIMLDKKGHIIHIDFGFMFESSPGGNLGWEPDIKLTDEM  2000
2001  VMIMGGKMEATPFKWFMEMCVRGYLAVRPYMDAVVSLVTLMLDTGLPCFR  2050
2051  GQTIKLLKHRFSPNMTEREAANFIMKVIQSCFLSNRSRTYDMIQYYQNDI  2100
2101  PY                                                  2102

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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