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

NucPred

Fetching Q95209 from www.uniprot.org...

The NucPred score for your sequence is 0.63 (see score help below)

   1  MATRSSRRESRLPFLFTLVALLPPGALCEVWTRTLHGGRAPLPQERGFRV    50
  51  VQGDPRELRLWERGDARGASRADEKPLRRRRSAALQPEPIKVYGQVSLND   100
 101  SHNQMVVHWAGEKSNVIVALARDSLALARPRSSDVYVSYDYGKSFNKISE   150
 151  KLNFGAGNNTEAVVAQFYHSPADNKRYIFADAYAQYLWITFDFCNTIHGF   200
 201  SIPFRAADLLLHSKASNLLLGFDRSHPNKQLWKSDDFGQTWIMIQEHVKS   250
 251  FSWGIDPYDKPNTIYIERHEPSGYSTVFRSTDFFQSRENQEVILEEVRDF   300
 301  QLRDKYMFATKVVHLLGSPLQSSVQLWVSFGRKPMRAAQFVTRHPINEYY   350
 351  IADASEDQVFVCVSHSNNRTNLYISEAEGLKFSLSLENVLYYTPGGAGSD   400
 401  TLVRYFANEPFADFHRVEGLQGVYIATLINGSMNEENMRSVITFDKGGTW   450
 451  EFLQAPAFTGYGEKINCELSEGCSLHLAQRLSQLLNLQLRRMPILSKESA   500
 501  PGLIIATGSVGKNLASKTNVYISSSAGARWREALPGPHYYTWGDHGGIIM   550
 551  AIAQGMETNELKYSTNEGETWKAFTFSEKPVFVYGLLTEPGEKSTVFTIF   600
 601  GSNKENVHSWLILQVNATDALGVPCTENDYKLWSPSDERGNECLLGHKTV   650
 651  FKRRTPHATCFNGEDFDRPVVVSNCSCTREDYECDFGFRMSEDLALEVCV   700
 701  PDPGFSGKSSPPVPCPVGSTYRRSRGYRKISGDTCSGGDVEARLEGELVP   750
 751  CPLAEENEFILYATRKSIHRYDLASGTTEQLPLTGLRAAVALDFDYEHNC   800
 801  LYWSDLALDVIQRLCLNGSTGQEVIINSDLETVEALAFEPLSQLLYWVDA   850
 851  GFKKIEVANPDGDFRLTVVNSSVLDRPRALVLVPQEGIMFWTDWGDLKPG   900
 901  IYRSNMDGSAAYRLVSEDVKWPNGISVDDQWIYWTDAYLDCIERITFSGQ   950
 951  QRSVILDRLPHPYAIAVFKNEIYWDDWSQLSIFRASKYSGSQMEILASQL  1000
1001  TGLMDMKIFYKGKNTGSNACVPRPCSLLCLPRANNSKSCRCPDGVASSVL  1050
1051  PSGDLMCDCPKGYELKNNTCVKEEDTCLRNQYRCSNGNCINSIWWCDFDN  1100
1101  DCGDMSDEKNCPTTICDLDTQFRCQESGTCIPLSYKCDLEDDCGDNSDER  1150
1151  HCEMHQCRSDEYNCSSGMCIRSSWVCDGDNDCRDWSDEANCTAIYHTCEA  1200
1201  SNFQCRNGHCIPQRWACDGDADCQDGSDEDPANCEKKCNGFRCPNGTCIP  1250
1251  STKHCDGLHDCSDGSDEQHCEPLCTRFMDFVCKNRQQCLFHSMVCDGIIQ  1300
1301  CRDGSDEDPAFAGCSRDPEFHKVCDEFGFQCQNGVCISLIWKCDGMDDCG  1350
1351  DYSDEANCENPTEAPNCSRYFQFRCDNGHCIPNRWKCDRENDCGDWSDEK  1400
1401  DCGDSHVLPSTTPAPSTCLPNYYRCGGGACVIDTWVCDGYRDCADGSDEE  1450
1451  ACPSLPNVTATSSPSQPGRCDRFEFECHQPKKCIPNWRRCDGHQDCQDGQ  1500
1501  DEANCPTHSTLTCMSWEFKCEDGEACIVLSERCDGFLDCSDESDEKACSD  1550
1551  ELTVYKVQNLQWTADFSGNVTLTWMRPKKMPSAACVYNVYYRVVGESIWK  1600
1601  TLETHSNKTNTVLKVLKPDTTYQVKVQVQCLSKVHNTNDFVTLRTPEGLP  1650
1651  DAPQNLQLSLHGEEEGVIVGHWSPPTHTHGLIREYIVEYSRSGSKVWTSE  1700
1701  RAASNFTEIKNLLVNTLYTVRVAAVTSRGIGNWSDSKSITTVKGKAIPPP  1750
1751  NIHIDNYDENSLSFTLTVDGNIKVNGYVVNLFWAFDTHKQEKKTMNFQGS  1800
1801  SVSHKVGNLTAQTAYEISAWAKTDLGDSPLSFEHVTTRGVRPPAPSLKAR  1850
1851  AINQTAVECTWTGPRNVVYGIFYATSFLDLYRNPSSLTTPLHNATVLVGK  1900
1901  DEQYLFLVRVVMPYQGPSSDYVVVKMIPDSRLPPRHLHAVHTGKTSAVIK  1950
1951  WESPYDSPDQDLFYAIAVKDLIRKTDRSYKVKSRNSTVEYTLSKLEPGGK  2000
2001  YHVIVQLGNMSKDASVKITTVSLSAPDALKIITENDHVLLFWKSLALKEK  2050
2051  YFNESRGYEIHMFDSAMNITAYLGNTTDNFFKISNLKMGHNYTFTVQARC  2100
2101  LLGSQICGEPAVLLYDELGSGGDASAMQAARSTDVAAVVVPILFLILLSL  2150
2151  GVGFAILYTKHRRLQSSFTAFANSHYSSRLGSAIFSSGDDLGEDDEDAPM  2200
2201  ITGFSDDVPMVIA                                       2213

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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