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

NucPred

Fetching Q9HCK8 from www.uniprot.org...

The NucPred score for your sequence is 0.99 (see score help below)

   1  MADPIMDLFDDPNLFGLDSLTDDSFNQVTQDPIEEALGLPSSLDSLDQMN    50
  51  QDGGGGDVGNSSASELVPPPEETAPTELSKESTAPAPESITLHDYTTQPA   100
 101  SQEQPAQPVLQTSTPTSGLLQVSKSQEILSQGNPFMGVSATAVSSSSAGG   150
 151  QPPQSAPKIVILKAPPSSSVTGAHVAQIQAQGITSTAQPLVAGTANGGKV   200
 201  TFTKVLTGTPLRPGVSIVSGNTVLAAKVPGNQAAVQRIVQPSRPVKQLVL   250
 251  QPVKGSAPAGNPGATGPPLKPAVTLTSTPTQGESKRITLVLQQPQSGGPQ   300
 301  GHRHVVLGSLPGKIVLQGNQLAALTQAKNAQGQPAKVVTIQLQVQQPQQK   350
 351  IQIVPQPPSSQPQPQQPPSTQPVTLSSVQQAQIMGPGQSPGQRLSVPVKV   400
 401  VLQPQAGSSQGASSGLSVVKVLSASEVAALSSPASSAPHSGGKTGMEENR   450
 451  RLEHQKKQEKANRIVAEAIARARARGEQNIPRVLNEDELPSVRPEEEGEK   500
 501  KRRKKSAGERLKEEKPKKSKTSGASKTKGKSKLNTITPVVGKKRKRNTSS   550
 551  DNSDVEVMPAQSPREDEESSIQKRRSNRQVKRKKYTEDLDIKITDDEEEE   600
 601  EVDVTGPIKPEPILPEPVQEPDGETLPSMQFFVENPSEEDAAIVDKVLSM   650
 651  RIVKKELPSGQYTEAEEFFVKYKNYSYLHCEWATISQLEKDKRIHQKLKR   700
 701  FKTKMAQMRHFFHEDEEPFNPDYVEVDRILDESHSIDKDNGEPVIYYLVK   750
 751  WCSLPYEDSTWELKEDVDEGKIREFKRIQSRHPELKRVNRPQASAWKKLE   800
 801  LSHEYKNRNQLREYQLEGVNWLLFNWYNRQNCILADEMGLGKTIQSIAFL   850
 851  QEVYNVGIHGPFLVIAPLSTITNWEREFNTWTEMNTIVYHGSLASRQMIQ   900
 901  QYEMYCKDSRGRLIPGAYKFDALITTFEMILSDCPELREIEWRCVIIDEA   950
 951  HRLKNRNCKLLDSLKHMDLEHKVLLTGTPLQNTVEELFSLLHFLEPSQFP  1000
1001  SESEFLKDFGDLKTEEQVQKLQAILKPMMLRRLKEDVEKNLAPKQETIIE  1050
1051  VELTNIQKKYYRAILEKNFSFLSKGAGHTNMPNLLNTMMELRKCCNHPYL  1100
1101  INGAEEKILTEFREACHIIPHDFHLQAMVRSAGKLVLIDKLLPKLKAGGH  1150
1151  KVLIFSQMVRCLDILEDYLIQRRYLYERIDGRVRGNLRQAAIDRFSKPDS  1200
1201  DRFVFLLCTRAGGLGINLTAADTCIIFDSDWNPQNDLQAQARCHRIGQSK  1250
1251  AVKVYRLITRNSYEREMFDKASLKLGLDKAVLQSMSGRDGNITGIQQFSK  1300
1301  KEIEDLLRKGAYAAIMEEDDEGSKFCEEDIDQILLRRTTTITIESEGKGS  1350
1351  TFAKASFVASENRTDISLDDPNFWQKWAKKADLDMDLLNSKNNLVIDTPR  1400
1401  VRKQTRHFSTLKDDDLVEFSDLESEDDERPRSRRHDRHHAYGRTDCFRVE  1450
1451  KHLLVYGWGRWRDILSHGRFKRRMTERDVETICRAILVYCLLHYRGDENI  1500
1501  KGFIWDLISPAENGKTKELQNHSGLSIPVPRGRKGKKVKSQSTFDIHKAD  1550
1551  WIRKYNPDTLFQDESYKKHLKHQCNKVLLRVRMLYYLRQEVIGDQAEKVL  1600
1601  GGAIASEIDIWFPVVDQLEVPTTWWDSEADKSLLIGVFKHGYEKYNTMRA  1650
1651  DPALCFLEKAGRPDDKAIAAEHRVLDNFSDIVEGVDFDKDCEDPEYKPLQ  1700
1701  GPPKDQDDEGDPLMMMDEEISVIDGDEAQVTQQPGHLFWPPGSALTARLR  1750
1751  RLVTAYQRSYKREQMKIEAAERGDRRRRRCEAAFKLKEIARREKQQRWTR  1800
1801  REQTDFYRVVSTFGVEYDPDTMQFHWDRFRTFARLDKKTDESLTKYFHGF  1850
1851  VAMCRQVCRLPPAAGDEPPDPNLFIEPITEERASRTLYRIELLRRLREQV  1900
1901  LCHPLLEDRLALCQPPGPELPKWWEPVRHDGELLRGAARHGVSQTDCNIM  1950
1951  QDPDFSFLAARMNYMQNHQAGAPAPSLSRCSTPLLHQQYTSRTASPLPLR  2000
2001  PDAPVEKSPEETATQVPSLESLTLKLEHEVVARSRPTPQDYEMRVSPSDT  2050
2051  TPLVSRSVPPVKLEDEDDSDSELDLSKLSPSSSSSSSSSSSSSSTDESED  2100
2101  EKEEKLTDQSRSKLYDEESLLSLTMSQDGFPNEDGEQMTPELLLLQERQR  2150
2151  ASEWPKDRVLINRIDLVCQAVLSGKWPSSRRSQEMVTGGILGPGNHLLDS  2200
2201  PSLTPGEYGDSPVPTPRSSSAASMAEEEASAVSTAAAQFTKLRRGMDEKE  2250
2251  FTVQIKDEEGLKLTFQKHKLMANGVMGDGHPLFHKKKGNRKKLVELEVEC  2300
2301  MEEPNHLDVDLETRIPVINKVDGTLLVGEDAPRRAELEMWLQGHPEFAVD  2350
2351  PRFLAYMEDRRKQKWQRCKKNNKAELNCLGMEPVQTANSRNGKKGHHTET  2400
2401  VFNRVLPGPIAPESSKKRARRMRPDLSKMMALMQGGSTGSLSLHNTFQHS  2450
2451  SSGLQSVSSLGHSSATSASLPFMPFVMGGAPSSPHVDSSTMLHHHHHHPH  2500
2501  PHHHHHHHPGLRAPGYPSSPVTTASGTTLRLPPLQPEEDDDEDEEDDDDL  2550
2551  SQGYDSSERDFSLIDDPMMPANSDSSEDADD                     2581

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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