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 0.93 (see score help below)

   1  MKSAWLALKSKSALHPKSEYPVSNIHYPKAANYRQTRNYLEIAAKMSEEV    50
  51  DRNDPELKYLSVERNQFNDPATQAEWTQKRLVWVPHENQGFVAASIKREH   100
 101  GDEVEVELAETGKRVMILRDDIQKMNPPKFDKVEDMAELTCLNEASVLHN   150
 151  IKDRYYSGLIYTYSGLFCVVVNPYKKLPIYTEKIMERYKGIKRHEVPPHV   200
 201  FAITDSAYRNMLGDREDQSILCTGESGAGKTENTKKVIQFLAYVAASKPK   250
 251  GSGAVPHPAVLINFSVNTNKYIKVKIMAQNQNQTIEVVNGLKMVEVNSNC   300
 301  QEGELEQQLLQANPILEAFGNAKTVKNDNSSRFGKFIRINFDASGFISGA   350
 351  NIETYLLEKSRAIRQAKDERTFHIFYQLLAGATPEQREKFILDDVKSYAF   400
 401  LSNGSLPVPGVDDYAEFQATVKSMNIMGMTSEDFNSIFRIVSAVLLFGSM   450
 451  KFRQERNNDQATLPDNTVAQKIAHLLGLSVTDMTRAFLTPRIKVGRDFVT   500
 501  KAQTKEQVEFAVEAIAKACYERMFKWLVNRINRSLDRTKRQGASFIGILD   550
 551  MAGFEIFELNSFEQLCINYTNEKLQQLFNHTMFILEQEEYQREGIEWKFI   600
 601  DFGLDLQPTIDLIDKPGGIMALLDEECWFPKATDKTFVDKLVSAHSMHPK   650
 651  FMKTDFRGVADFAIVHYAGRVDYSAAKWLMKNMDPLNENIVSLLQGSQDP   700
 701  FVVNIWKDAEIVGMAQQALTDTQFGARTRKGMFRTVSHLYKEQLAKLMDT   750
 751  LRNTNPNFVRCIIPNHEKRAGKIDAPLVLDQLRCNGVLEGIRICRQGFPN   800
 801  RIPFQEFRQRYELLTPNVIPKGFMDGKKACEKMIQALELDSNLYRVGQSK   850
 851  IFFRAGVLAHLEEERDFKISDLIVNFQAFCRGFLARRNYQKRLQQLNAIR   900
 901  IIQRNCAAYLKLRNWQWWRLYTKVKPLLEVTKQEEKLVQKEDELKQVREK   950
 951  LDTLAKNTQEYERKYQQALVEKTTLAEQLQAEIELCAEAEESRSRLMARK  1000
1001  QELEDMMQELETRIEEEEERVLALGGEKKKLELNIQDLEEQLEEEEAARQ  1050
1051  KLQLEKVQLDAKIKKYEEDLALTDDQNQKLLKEKKLLEERANDLSQTLAE  1100
1101  EEEKAKHLAKLKAKHEATISELEERLHKDQQQRQESDRSKRKIETEVADL  1150
1151  KEQLNERRVQVDEMQAQLAKREEELTQTLLRIDEESATKATAQKAQRELE  1200
1201  SQLAEIQEDLEAEKAARAKAEKVRRDLSEELEALKNELLDSLDTTAAQQE  1250
1251  LRSKREQELATLKKSLEEETVNHEGVLADMRHKHSQELNSINDQLENLRK  1300
1301  AKTVLEKAKGTLEAENADLATELRSVNSSRQENDRRRKQAESQIAELQVK  1350
1351  LAEIERARSELQEKCTKLQQEAENITNQLEEAELKASAAVKSASNMESQL  1400
1401  TEAQQLLEEETRQKLGLSSKLRQIESEKEALQEQLEEDDEAKRNYERKLA  1450
1451  EVTTQMQEIKKKAEEDADLAKELEEGKKRLNKDIEALERQVKELIAQNDR  1500
1501  LDKSKKKIQSELEDATIELEAQRTKVLELEKKQKNFDKILAEEKAISEQI  1550
1551  AQERDTAEREAREKETKVLSVSRELDEAFDKIEDLENKRKTLQNELDDLA  1600
1601  NTQGTADKNVHELEKAKRALESQLAELKAQNEELEDDLQLTEDAKLRLEV  1650
1651  NMQALRSQFERDLLAKEEGAEEKRRGLVKQLRDLETELDEERKQRTAAVA  1700
1701  SKKKLEGDLKEIETTMEMHNKVKEDALKHAKKLQAQVKDALRDAEEAKAA  1750
1751  KEELQALSKEAERKVKALEAEVLQLTEDLASSERARRAAETERDELAEEI  1800
1801  ANNANKGSLMIDEKRRLEARIATLEEELEEEQSNSEVLLDRSRKAQLQIE  1850
1851  QLTTELANEKSNSQKNENGRALLERQNKELKAKLAEIETAQRTKVKATIA  1900
1901  TLEAKIANLEEQLENEGKERLLQQKANRKMDKKIKELTMNIEDERRHVDQ  1950
1951  HKEQMDKLNSRIKLLKRNLDETEEELQKEKTQKRKYQRECEDMIESQEAM  2000
2001  NREINSLKTKLRRTGGIGLSSSRLTGTPSSKRAGGGGGGDDSSVQDESLD  2050
2051  GEDSAN                                              2056

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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