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

NucPred

Fetching Q9NZN5 from www.uniprot.org...

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

   1  MSGTQSTITDRFPLKKPIRHGSILNRESPTDKKQKVERIASHDFDPTDSS    50
  51  SKKTKSSSEESRSEIYGLVQRCVIIQKDDNGFGLTVSGDNPVFVQSVKED   100
 101  GAAMRAGVQTGDRIIKVNGTLVTHSNHLEVVKLIKSGSYVALTVQGRPPG   150
 151  SPQIPLADSEVEPSVIGHMSPIMTSPHSPGASGNMERITSPVLMGEENNV   200
 201  VHNQKVEILRKMLQKEQERLQLLQEDYNRTPAQRLLKEIQEAKKHIPQLQ   250
 251  EQLSKATGSAQDGAVVTPSRPLGDTLTVSEAETDPGDVLGRTDCSSGDAS   300
 301  RPSSDNADSPKSGPKERIYLEENPEKSETIQDTDTQSLVGSPSTRIAPHI   350
 351  IGAEDDDFGTEHEQINGQCSCFQSIELLKSRPAHLAVFLHHVVSQFDPAT   400
 401  LLCYLYSDLYKHTNSKETRRIFLEFHQFFLDRSAHLKVSVPDEMSADLEK   450
 451  RRPELIPEDLHRHYIQTMQERVHPEVQRHLEDFRQKRSMGLTLAESELTK   500
 501  LDAERDKDRLTLEKERTCAEQIVAKIEEVLMTAQAVEEDKSSTMQYVILM   550
 551  YMKHLGVKVKEPRNLEHKRGRIGFLPKIKQSMKKDKEGEEKGKRRGFPSI   600
 601  LGPPRRPSRHDNSAIGRAMELQKARHPKHLSTPSSVSPEPQDSAKLRQSG   650
 651  LANEGTDAGYLPANSMSSVASGASFSQEGGKENDTGSKQVGETSAPGDTL   700
 701  DGTPRTLNTVFDFPPPPLDQVQEEECEVERVTEHGTPKPFRKFDSVAFGE   750
 751  SQSEDEQFENDLETDPPNWQQLVSREVLLGLKPCEIKRQEVINELFYTER   800
 801  AHVRTLKVLDQVFYQRVSREGILSPSELRKIFSNLEDILQLHIGLNEQMK   850
 851  AVRKRNETSVIDQIGEDLLTWFSGPGEEKLKHAAATFCSNQPFALEMIKS   900
 901  RQKKDSRFQTFVQDAESNPLCRRLQLKDIIPTQMQRLTKYPLLLDNIAKY   950
 951  TEWPTEREKVKKAADHCRQILNYVNQAVKEAENKQRLEDYQRRLDTSSLK  1000
1001  LSEYPNVEELRNLDLTKRKMIHEGPLVWKVNRDKTIDLYTLLLEDILVLL  1050
1051  QKQDDRLVLRCHSKILASTADSKHTFSPVIKLSTVLVRQVATDNKALFVI  1100
1101  SMSDNGAQIYELVAQTVSEKTVWQDLICRMAASVKEQSTKPIPLPQSTPG  1150
1151  EGDNDEEDPSKLKEEQHGISVTGLQSPDRDLGLESTLISSKPQSHSLSTS  1200
1201  GKSEVRDLFVAERQFAKEQHTDGTLKEVGEDYQIAIPDSHLPVSEERWAL  1250
1251  DALRNLGLLKQLLVQQLGLTEKSVQEDWQHFPRYRTASQGPQTDSVIQNS  1300
1301  ENIKAYHSGEGHMPFRTGTGDIATCYSPRTSTESFAPRDSVGLAPQDSQA  1350
1351  SNILVMDHMIMTPEMPTMEPEGGLDDSGEHFFDAREAHSDENPSEGDGAV  1400
1401  NKEEKDVNLRISGNYLILDGYDPVQESSTDEEVASSLTLQPMTGIPAVES  1450
1451  THQQQHSPQNTHSDGAISPFTPEFLVQQRWGAMEYSCFEIQSPSSCADSQ  1500
1501  SQIMEYIHKIEADLEHLKKVEESYTILCQRLAGSALTDKHSDKS        1544

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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