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

NucPred

Fetching Q9P0X4 from www.uniprot.org...

The NucPred score for your sequence is 0.71 (see score help below)

   1  MAESASPPSSSAAAPAAEPGVTTEQPGPRSPPSSPPGLEEPLDGADPHVP    50
  51  HPDLAPIAFFCLRQTTSPRNWCIKMVCNPWFECVSMLVILLNCVTLGMYQ   100
 101  PCDDMDCLSDRCKILQVFDDFIFIFFAMEMVLKMVALGIFGKKCYLGDTW   150
 151  NRLDFFIVMAGMVEYSLDLQNINLSAIRTVRVLRPLKAINRVPSMRILVN   200
 201  LLLDTLPMLGNVLLLCFFVFFIFGIIGVQLWAGLLRNRCFLEENFTIQGD   250
 251  VALPPYYQPEEDDEMPFICSLSGDNGIMGCHEIPPLKEQGRECCLSKDDV   300
 301  YDFGAGRQDLNASGLCVNWNRYYNVCRTGSANPHKGAINFDNIGYAWIVI   350
 351  FQVITLEGWVEIMYYVMDAHSFYNFIYFILLIIVGSFFMINLCLVVIATQ   400
 401  FSETKQREHRLMLEQRQRYLSSSTVASYAEPGDCYEEIFQYVCHILRKAK   450
 451  RRALGLYQALQSRRQALGPEAPAPAKPGPHAKEPRHYHGKTKGQGDEGRH   500
 501  LGSRHCQTLHGPASPGNDHSGRELCPQHSPLDATPHTLVQPIPATLASDP   550
 551  ASCPCCQHEDGRRPSGLGSTDSGQEGSGSGSSAGGEDEADGDGARSSEDG   600
 601  ASSELGKEEEEEEQADGAVWLCGDVWRETRAKLRGIVDSKYFNRGIMMAI   650
 651  LVNTVSMGIEHHEQPEELTNILEICNVVFTSMFALEMILKLAAFGLFDYL   700
 701  RNPYNIFDSIIVIISIWEIVGQADGGLSVLRTFRLLRVLKLVRFMPALRR   750
 751  QLVVLMKTMDNVATFCMLLMLFIFIFSILGMHIFGCKFSLRTDTGDTVPD   800
 801  RKNFDSLLWAIVTVFQILTQEDWNVVLYNGMASTSPWASLYFVALMTFGN   850
 851  YVLFNLLVAILVEGFQAEGDANRSYSDEDQSSSNIEEFDKLQEGLDSSGD   900
 901  PKLCPIPMTPNGHLDPSLPLGGHLGPAGAAGPAPRLSLQPDPMLVALGSR   950
 951  KSSVMSLGRMSYDQRSLSSSRSSYYGPWGRSAAWASRRSSWNSLKHKPPS  1000
1001  AEHESLLSAERGGGARVCEVAADEGPPRAAPLHTPHAHHIHHGPHLAHRH  1050
1051  RHHRRTLSLDNRDSVDLAELVPAVGAHPRAAWRAAGPAPGHEDCNGRMPS  1100
1101  IAKDVFTKMGDRGDRGEDEEEIDYTLCFRVRKMIDVYKPDWCEVREDWSV  1150
1151  YLFSPENRFRVLCQTIIAHKLFDYVVLAFIFLNCITIALERPQIEAGSTE  1200
1201  RIFLTVSNYIFTAIFVGEMTLKVVSLGLYFGEQAYLRSSWNVLDGFLVFV  1250
1251  SIIDIVVSLASAGGAKILGVLRVLRLLRTLRPLRVISRAPGLKLVVETLI  1300
1301  SSLKPIGNIVLICCAFFIIFGILGVQLFKGKFYHCLGVDTRNITNRSDCM  1350
1351  AANYRWVHHKYNFDNLGQALMSLFVLASKDGWVNIMYNGLDAVAVDQQPV  1400
1401  TNHNPWMLLYFISFLLIVSFFVLNMFVGVVVENFHKCRQHQEAEEARRRE  1450
1451  EKRLRRLEKKRRKAQRLPYYATYCHTRLLIHSMCTSHYLDIFITFIICLN  1500
1501  VVTMSLEHYNQPTSLETALKYCNYMFTTVFVLEAVLKLVAFGLRRFFKDR  1550
1551  WNQLDLAIVLLSVMGITLEEIEINAALPINPTIIRIMRVLRIARVLKLLK  1600
1601  MATGMRALLDTVVQALPQVGNLGLLFMLLFFIYAALGVELFGKLVCNDEN  1650
1651  PCEGMSRHATFENFGMAFLTLFQVSTGDNWNGIMKDTLRDCTHDERSCLS  1700
1701  SLQFVSPLYFVSFVLTAQFVLINVVVAVLMKHLDDSNKEAQEDAEMDAEL  1750
1751  ELEMAHGLGPGPRLPTGSPGAPGRGPGGAGGGGDTEGGLCRRCYSPAQEN  1800
1801  LWLDSVSLIIKDSLEGELTIIDNLSGSIFHHYSSPAGCKKCHHDKQEVQL  1850
1851  AETEAFSLNSDRSSSILLGDDLSLEDPTACPPGRKDSKGELDPPEPMRVG  1900
1901  DLGECFFPLSSTAVSPDPENFLCEMEEIPFNPVRSWLKHDSSQAPPSPFS  1950
1951  PDASSPLLPMPAEFFHPAVSASQKGPEKGTGTGTLPKIALQGSWASLRSP  2000
2001  RVNCTLLRQATGSDTSLDASPSSSAGSLQTTLEDSLTLSDSPRRALGPPA  2050
2051  PAPGPRAGLSPAARRRLSLRGRGLFSLRGLRAHQRSHSSGGSTSPGCTHH  2100
2101  DSMDPSDEEGRGGAGGGGAGSEHSETLSSLSLTSLFCPPPPPPAPGLTPA  2150
2151  RKFSSTSSLAAPGRPHAAALAHGLARSPSWAADRSKDPPGRAPLPMGLGP  2200
2201  LAPPPQPLPGELEPGDAASKRKR                             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.)

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