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

NucPred

Fetching P54282 from www.uniprot.org...

The NucPred score for your sequence is 0.83 (see score help below)

   1  MARFGDEMPGRYGAGGGGSGPAAGVVVGAAGGRGAGGSRQGGQPGAQRMY    50
  51  KQSMAQRARTMALYNPIPVRQNCLTVNRSLFLFSEDNVVRKYAKKITEWP   100
 101  PFEYMILATIIANCIVLALEQHLPDDDKTPMSERLDDTEPYFIGIFCFEA   150
 151  GIKIVALGFAFHKGSYLRNGWNVMDFVVVLTGILATVGTEFDLRTLRAVR   200
 201  VLRPLKLVSGIPSLQVVLKSIMKAMIPLLQIGLLLFFAILIFAIIGLEFY   250
 251  MGKFHTTCFEEGTDDIQGESPAPCGTEEPARTCPNGTKCQPYWEGPNNGI   300
 301  TQFDNILFAVLTVFQCITMEGWTDLLYNSNDASGNTWNWLYFIPLIIIGS   350
 351  FFMLNLVLGVLSGEFAKERERVENRRAFLKLRRQQQIERELNGYMEWISK   400
 401  AEEVILAEDETDVEQRHPFDGALRRATLKKSKTDLLNPEEAEDQLADIAS   450
 451  VGSPFARASIKSAKLENSTFFHKKERRMRFYIRRMVKTQAFYWTVLSLVA   500
 501  LNTLWLAIVHYNQPEWLSDFLYYAEFIFLGLFMSEMFIKMYGLGTRPYFH   550
 551  SSFNCFDCGVIIGSIFEVIWAVIKPGTSFGISVLRALRLLRIFKVTKYWA   600
 601  SLRNLVVSLLNSMKSIISLLFLLFLFIVVFALLGMQLFGGQFNFDEGTPP   650
 651  TNFDTFPAAIMTVFQILTGEDWNEVMYDEIKSQGGVQGGMVFSIYFIVLT   700
 701  LFGNYTLLNVFLAIAVDNLANAQELTKDEQEEEEAANQKLALQKAKEVAE   750
 751  VSPLSAANMSIAVKEQQKNQKPAKSVWEQRTSEMRKQNLLASREALYGDA   800
 801  AERWPTTYARPLRPDVKTHLDRPLVVDPQENRNNNTNKSRAPEALRQTAR   850
 851  PRESARDPDARRAWPSSPERAPGREGPYGRESEPQQREHAPPREHVPWDA   900
 901  DPERAKAGDAPRRHTHRPVAEGEPRRHRARRRPGDEPDDRPERRPRPRDA   950
 951  TRPARAADGEGDDGERKRRHRHGPPAHDDRERRHRRRKESQGSGVPMSGP  1000
1001  NLSTTRPIQQDLGRQDLPLAEDLDNMKNNKLATGEPASPHDSLGHSGLPP  1050
1051  SPAKIGNSTNPGPALATNPQNAASRRTPNNPGNPSNPGPPKTPENSLIVT  1100
1101  NPSSTQPNSAKTARKPEHMAVEIPPACPPLNHTVVQVNKNANPDPLPKKE  1150
1151  EEKKEEEEADPGEDGPKPMPPYSSMFILSTTNPLRRLCHYILNLRYFEMC  1200
1201  ILMVIAMSSIALAAEDPVQPNAPRNNVLRYFDYVFTGVFTFEMVIKMIDL  1250
1251  GLVLHQGAYFRDLWNILDFIVVSGALVAFAFTGNSKGKDINTIKSLRVLR  1300
1301  VLRPLKTIKRLPKLKAVFDCVVNSLKNVFNILIVYMLFMFIFAVVAVQLF  1350
1351  KGKFFHCTDESKEFERDCRGKYLLYEKNEVKARDREWKKYDFHYDNVLWA  1400
1401  LLTLFTVSTGEGWPQVLKHSVDATFENQGPSPGYRMEMSIFYVVYFVVFP  1450
1451  FFFVNIFVALIIITFQEQGDKMMEEYSLEKNERACIDFAISAKPLTRHMP  1500
1501  QNKQSFQYRMWQFVVSPPFEYTIMAMIALNTIVLMMKFYGASVAYENALR  1550
1551  VFNIVFTSLFSLECVLKVMAFGILNYFRDAWNIFDFVTVLGSITDILVTE  1600
1601  FGNNFINLSFLRLFRAARLIKLLRQGYTIRILLWTFVQSFKALPYVCLLI  1650
1651  AMLFFIYAIIGMQVFGNIGIDGEDEDSDEDEFQITEHNNFRTFFQALMLL  1700
1701  FRSATGEAWHNIMLSCLSGKPCDKNSGIQKPECGNEFAYFYFVSFIFLCS  1750
1751  FLMLNLFVAVIMDNFEYLTRDSSILGPHHLDEYVRVWAEYDPAACGRIHY  1800
1801  KDMYSLLRVISPPLGLGKKCPHRVACKRLLRMDLPVADDNTVHFNSTLMA  1850
1851  LIRTALDIKIAKGGADKQQMDAELRKEMMAIWPNLSQKTLDLLVTPHKST  1900
1901  DLTVGKIYAAMMIMEYYRQSKAKKLQAMREEQNRTPLMFQRMEPPSPTQE  1950
1951  GGPSQNALPSTQLDPGGGLMAQESSMKESPSWVTQRAQEMFQKTGTWSPE  2000
2001  RGPPIDMPNSQPNSQSVEMREMGTDGYSDSEHYLPMEGQTRAASMPRLPA  2050
2051  ENQRRRGRPRGNNLSTISDTSPMKRSASVLGPKARRLDDYSLERVPPEEN  2100
2101  QRYHQRRRDRGHRTSERSLGRYTDVDTGLGTDLSMTTQSGDLPSKDRDQD  2150
2151  RGRPKDRKHRPHHHHHHHHHHPPAPDRERYAQERPDTGRARAREQRWSRS  2200
2201  PSEGREHATHRQ                                        2212

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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