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

NucPred

Fetching Q925J9 from www.uniprot.org...

The NucPred score for your sequence is 0.95 (see score help below)

   1  MKAQGETEDSERLSKMSSLLERLHAKFNQNRPWSETIKLVRQVMEKRVVM    50
  51  SSGGHQHLVSCLETLQKALKVTSLPAMTDRLESIARQNGLGSHLSASGTE   100
 101  CYITSDMFYVEVQLDPAGQLCDVKVAHHGENPVSCPELVQQLREKNFEEF   150
 151  SKHLKGLVNLYNLPGDNKLKTKMYLALQSLEQDLSKMAIMYWKATNAAPL   200
 201  DKILHGSVGYLTPRSGGHLMNMKYYASPSDLLDDKTASPIILHEKNVPRS   250
 251  LGMNASVTIEGTSAMYKLPIAPLIMGSHPADNKWTPSFSAVTSANSVDLP   300
 301  ACFFLKFPQPIPVSKAFVQKLQNCTGIPLFETPPTYLPLYELITQFELSK   350
 351  DPDPLPLNHNMRFYAALPGQQHCYFLNKDAPLPDGQSLQGTLVSKITFQH   400
 401  PGRVPLILNMIRHQVAYNTLIGSCVKRTILKEDSPGLLQFEVCPLSESRF   450
 451  SVSFQHPVNDSLVCVVMDVQDSTHVSCKLYKGLSDALICTDDFIAKVVQR   500
 501  CMSIPVTMRAIRRKAETIQADTPALSLIAETVEDMVKKNLPPASSPGYGM   550
 551  TTGNNPMSGTTTPTNTFPGGPITTLFNMSMSIKDRHESVGHGEDFSKVSQ   600
 601  NPILTSLLQITGNGGSTIGSSPTPPHHTPPPVSSMAGNTKNHPMLMNLLK   650
 651  DNPAQDFSTLYGSSPLERQNSSSGSPRMEMCSGSNKAKKKKSSRVPPDKP   700
 701  KHQTEDDFQRELFSMDVDSQNPMFDVSMTADALDTPHITPAPSQCSTPPA   750
 751  TYPQPVSHPQPSIQRMVRLSSSDSIGPDVTDILSDIAEEASKLPSTSDDC   800
 801  PPIGTPVRDSSSSGHSQSALFDSDVFQTNNNENPYTDPADLIADAAGSPN   850
 851  SDSPTNHFFPDGVDFNPDLLNSQSQSGFGEEYFDESSQSGDNDDFKGFAS   900
 901  QALNTLGMPMLGGDNGEPKFKGSSQADTVDFSIISVAGKALGAADLMEHH   950
 951  SGSQSPLLTTGELGKEKTQKRVKEGNGTGASSGSGPGSDSKPGKRSRTPS  1000
1001  NDGKSKDKPPKRKKADTEGKSPSHSSSNRPFTPPTSTGGSKSPGSSGRSQ  1050
1051  TPPGVATPPIPKITIQIPKGTVMVGKPSSHSQYTSSGSVSSSGSKSHHSH  1100
1101  SSSSSSLASASTSGKVKSSKSEGSSSSKLSGSMYASQGSSGSSQSKNSSQ  1150
1151  TGGKPGSSPITKHGLSSGSSSTKMKPQGKPSSLMNPSISKPNISPSHSRP  1200
1201  PGGSDKLASPMKPVPGTPPSSKAKSPISSGSSGSHVSGTSSSSGMKSSSG  1250
1251  SASSGSVSQKTPPASNSCTPSSSSFSSSGSSMSSSQNQHGSSKGKSPSRN  1300
1301  KKPSLTAVIDKLKHGVVTSGPGGEDPIDSQMGASTNSSNHPMSSKHNTSG  1350
1351  GEFQSKREKSDKDKSKVSASGGSVDSSKKTSESKNVGSTGVAKIIISKHD  1400
1401  GGSPSIKAKVTLQKPGESGGDGLRPQIASSKNYGSPLISGSTPKHERGSP  1450
1451  SHSKSPAYTPQNVDSESESGSSIAERSYQNSPSSEDGIRPLPEYSTEKHK  1500
1501  KHKKEKKKVRDKDRDKKKSHSMKPENWSKSPISSDPTASVTNNPILSADR  1550
1551  PSRLSPDFMIGEEDDDLMDVALIGN                           1575

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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