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

NucPred

Fetching Q99323 from www.uniprot.org...

The NucPred score for your sequence is 0.94 (see score help below)

   1  MKSAWLALKSKSALHPKSEYPVSNIHYPKAANYRQTRNYLEIAAKMSEEV    50
  51  DRNDPELKYLSVERNQFNPIRPRRPSGHRSVLVWVPHENQGFVAASIKRE   100
 101  HGDEVEVELAETGKRVMILRDDIQKMNPPKFDKVEDMAELTCLNEASVLH   150
 151  NIKDRYYSGLIYTYSGLFCVVVNPYKKLPIYTEKIMERYKGIKRHEVPPH   200
 201  VFAITDSAYRNMLGDREDQSILCTGESGAGKTENTKKVIQFLAYVAASKP   250
 251  KGSGAVPHPAVLINFSVNTNKYIKVKIMAQNQNQTIEVVNGLKMVEVNSN   300
 301  CQEGELEQQLLQANPILEAFGNAKTVKNDNSSRFGKFIRINFDASGFISG   350
 351  ANIETYLLEKSRAIRQAKDERTFHIFYQLLAGATPEQREKFILDDVKSYA   400
 401  FLSNGSLPVPGVDDYAEFQATVKSMNIMGMTSEDFNSIFRIVSAVLLFGS   450
 451  MKFRQERNNDQATLPDNTVAQKIAHLLGLSVTDMTRAFLTPRIKVGRDFV   500
 501  TKAQTKEQVEFAVEAIAKACYERMFKWLVNRINRSLDRTKRQGASFIGIL   550
 551  DMAGFEIFELNSFEQLCINYTNEKLQQLFNHTMFILEQEEYQREGIEWKF   600
 601  IDFGLDLQPTIDLIDKPGGIMALLDEECWFPKATDKTFVDKLVSAHSMHP   650
 651  KFMKTDFRGVADFAIVHYAGRVDYSAAKWLMKNMDPLNENIVSLLQGSQD   700
 701  PFVVNIWKDAEIVGMAQQALTDTQFGARTRKGMFRTVSHLYKEQLAKLMD   750
 751  TLRNTNPNFVRCIIPNHEKRAGKIDAPLVLDQLRCNGVLEGIRICRQGFP   800
 801  NRIPFQEFRQRYELLTPNVIPKGFMDGKKACEKMIQALELDSNLYRVGQS   850
 851  KIFFRAGVLAHLEEERDFKISDLIVNFQAFCRGFLARRNYQKRLQQLNAI   900
 901  RIIQRNCAAYLKLRNWQWWRLYTKVKPLLEVTKQEEKLVQKEDELKQVRE   950
 951  KLDTLAKNTQEYERKYQQALVEKTTLAEQLQAEIELCAEAEESRSRLMAR  1000
1001  KQELEDMMQELETRIEEEEERVLALGGEKKKLELNIQDLEEQLEEEEAAR  1050
1051  QKLQLEKVQLDAKIKKYEEDLALTDDQNQKLLKEKKLLEERANDLSQTLA  1100
1101  EEEEKAKHLAKLKAKHEATITELEERLHKDQQQRQESDRSKRKIETEVAD  1150
1151  LKEQLNERRVQVDEMQAQLAKREEELTQTLLRIDEESATKATAQKAQREL  1200
1201  ESQLAEIQEDLEAEKAARAKAEKVRRDLSEELEALKNELLDSLDTTAAQQ  1250
1251  ELRSKREQELATLKKSLEEETVNHEGVLADMRHKHSQELNSINDQLENLR  1300
1301  KAKTVLEKAKGTLEAENADLATELRSVNSSRQENDRRRKQAESQIAELQV  1350
1351  KLAEIERARSELQEKCTKLQQEAENITNQLEEAELKASAAVKSASNMESQ  1400
1401  LTEAQQLLEEETRQKLGLSSKLRQIESEKEALQEQLEEDDEAKRNYERKL  1450
1451  AEVTTQMQEIKKKAEEDADLAKELEEGKKRLNKDIEALERQVKELIAQND  1500
1501  RLDKSKKKIQSELEDATIELEAQRTKVLELEKKQKNFDKILAEEKAISEQ  1550
1551  IAQERDTAEREAREKETKVLSVSRELDEAFDKIEDLENKRKTLQNELDDL  1600
1601  ANTQGTADKNVHELEKAKRALESQLAELKAQNEELEDDLQLTEDAKLRLE  1650
1651  VNMQALRSQFERDLLAKEEGAEEKRRGLVKQLRDLETELDEERKQRTAAV  1700
1701  ASKKKLEGDLKEIETTMEMHNKVKEDALKHAKKLQAQVKDALRDAEEAKA  1750
1751  AKEELQALSKEADGKVKALEAEVLQLTEDLASSERARRAAETERDELAEE  1800
1801  IANNANKGSLMIDEKRRLEARIATLEEELEEEQSNSEVLLDRSRKAQLQI  1850
1851  EQLTTELANEKSNSQKNENGRALLERQNKELKAKLAEIETAQRTKVKATI  1900
1901  ATLEAKIANLEEQLENEGKERLLQQKANRKMDKKIKELTMNIEDERRHVD  1950
1951  QHKEQMDKLNSRIKLLKRNLDETEEELQKEKTQKRKYQRECEDMIESQEA  2000
2001  MNREINSLKTKLRRTGGIGLSSSRLTGTPSSKRAGGGGGSDDSSVQDESL  2050
2051  DGEDSAN                                             2057

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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