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

NucPred

Fetching P56699 from www.uniprot.org...

The NucPred score for your sequence is 0.90 (see score help below)

   1  MARFGEAVGSLSADASSEQGRSRHQVPVTGETAVAAAAAAVVAGAAQGSA    50
  51  GFKQTRAQRARTMALYNPIPVRHNCLTANRSLFLFGEDNIVRKSARRVIE   100
 101  WPPFEYMILATIIANCVVLALEQHLPNGDKTPMAKSLEQTEPYFIGIFCF   150
 151  EAGIKIVALGFVFHKGSYLRNGWNVMDFIVVLSGLLATAATHFNLRTLRA   200
 201  VRVLRPLKLVSGIPSLQIVLKSIMKAMVPLLQIGLLLFFAILMFAIIGLE   250
 251  FYYGKLHRTCYTDDAAAEELDLQFPCGTQEPTRLCPNGTVCSYWIGPNDG   300
 301  ITQFDNILFALLTVFQCITMEGWTTILYNTDDALGAMWNWLYFIPLIIIG   350
 351  SFFVLNLVLGVLSGEFAKERERVENRRSFLKLRRQQQIERELNGYRAWID   400
 401  KAEEVMLLEENKNAGEKSALHVLRRATIKKGRMEMIQTESSEDQYTEISS   450
 451  VGSPLARASIKSTKLLEGSSYFRRKERMLRISIRHMVKSHAFYWIVLGLV   500
 501  ALNTVCVAVVHYDQPLWLSNFLYYAEFTFLGLFSSEMFLKMYGCGPRLYF   550
 551  HSSFNCFDCGVIIGSIFDVVWTIIRPETSFGISVLRALRLLRIFKITKYW   600
 601  ASLRNLVVSLMSSMKSIISLLFLLFLFIVVFALLGMQLFGGQFNFEEGTP   650
 651  PTNFDTFPAAIITVFQILTGEDWNEVMYNGIKSQGGVNSGMWSSVYFIVL   700
 701  TLFGNYTLLNVFLAIAVDNLANAQELTKEEQEEEEAINQKHALQKAKEVS   750
 751  PMSAPGFPSTEREFRRHKHMSIWEARTSQLRRRMQMSSREALFTDALQGL   800
 801  EGSRYRRHRSRIFEAESLRRLAEQQAAESHQLGEVGRREAFKSRSLRNSW   850
 851  QPAGPDKRSSSIKVNGEQGRALGRSVEAGASFRMAEPIRARRRYRSLYKE   900
 901  AKMGLEESAETSLSRRPGKNKEGRLLQQLCEEQESGQLTQTPEVMDAQGQ   950
 951  MKAFSWQGEPHSSSMTRTPDVDTDPSGGNLEKESGRTPENGKEESANTSE  1000
1001  QVNEQSNWLNLQLNQQATPGDRELTTGTRDTKQDKTQEQTEIDVDCENTE  1050
1051  TPMDSLVTPGNAYSSSSSVKEDEKKSKAIIPYTSMFLFRKTNPIRRVCHF  1100
1101  IVNLRYFEMCILLVIAASSVALAAEDPIHKDSARNQVLRYFDYVFTGVFT  1150
1151  FEMVIKMIDIGLVFHEGSYFRDVWNILDFIVVSGALVAFAFTNLIGGSSG  1200
1201  KDINTIKSLRVLRVLRPLKTIKRLPKLKAVFDCVVTSLKNVFNILIVYKL  1250
1251  FMFIFAVIAVQLFKGKFFYCTDSSKMTKQDCRGQFVLYRQRTKLSIENGN  1300
1301  VTTFHYDNVVWALLTLFTVSTGEGWPQVLQHSVDVTEADQGPIPGNRMEM  1350
1351  SIFYIVYFVVFPFFFVNIFVALIIITFQEQGDKMLEESSLEKNERACIDF  1400
1401  AISAKPLTRYMPQNRQTFQYRVWQFVVSPSFEYTILTMIALNTVVLMMKH  1450
1451  HSPPPGFASVLKLMNIAFTITFTLECILKIIAFGFLNYFRDSWNVFDFVT  1500
1501  VVGSISEIIVTECNLKFVNLSFLKLFRAARLIKLLRQGITIRILLWTFVQ  1550
1551  SFKALPYVCLLIAMLFFIYAIIGMQLFGNIGLDDHTPINRHNNFHTFFNA  1600
1601  LMLLFRSATGESWQEIMLACLSGKECEGTREPSCGTDVAYFYFVSFIFLC  1650
1651  SFLMLNLFVAVIMDNFEYLTRDSSILGPHHLDEFVRVWAEYDRAACGRIH  1700
1701  YTDMYQMLTLMSPPLGLGKKCPSKVAYKRLVLMNMPVTEDKTVHFTSTLM  1750
1751  GLIRTALQIKLARGGADKQQLDAELRKEIMTIWPHLSQKTLDLLVPMHTY  1800
1801  SDLTVGKIYAAMMIMDYYKQSKNKKYQKLQEEQSRTPMFQRMEASSLPPQ  1850
1851  IISSTKGLPYLQTGTGPDVDSRSEFTPLVPLPPVMFQQGRTSSQGEEIHK  1900
1901  QRPKELKKIKLEYPHYGHYLPIENQGRAVSMPRLEIESAEDTSPLKRSLS  1950
1951  TFAANHSNSTWLNEYSLERAGPEDLYKRWSRRPLRPPSRSSNAGSRERGR  2000
2001  SRERKHLLSPERSVCSTGQCAHPSQHRGLDQRLSRSPSPGYSHRPREQVN  2050
2051  SSVSESPVPSSSGTSPPKQGQRQLPQTPSKPRPLVSYSPVAQRGDVSGHC  2100
2101  SPMCKETRYQSLRVQPSKALWSESPGRSRESESQHSTPLRYISEPSLTLH  2150
2151  DGPGSLDQALGEETLTFEAAVATSLGRSHTISSAPPLRQGWHLPNGSYRT  2200
2201  RMMQSGAPSTPDPYTHAEEDDRC                             2223

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.)

Go back to the NucPred Home Page.