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

NucPred

Fetching Q6PR54 from www.uniprot.org...

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

   1  MTAPGRSPLEPLLETWEDPSVPPGEQTDAYLTLTSRMTGEEGKEVIAEIE    50
  51  KNLSRLYTVLKAHISSQNSELSSAALQALGFCLYNPRITSGLSEANIQEL   100
 101  LLTLNGIIKSSDKNVCTRALWVISKQTFPAELVSKMVSSIIDSLEVILSK   150
 151  GEIHSAVVDFEALNVIIRLIEQAPVQMGEESVRWAKLVIPLVVHSAQKVH   200
 201  LRGATALEMGMPLLLQKQQEIALITEHLMTTKLISELQKLFKNKNETYVL   250
 251  KLWPLFVKLLGKTLHRSGSFINSLLQLEELGFRSGTPMIKKIAFIAWKSL   300
 301  IDNFALNPDILCSAKRLKLLMQPLSSIHVRTETLALTKLEVWWYLLMRLG   350
 351  PQLPANFEQVCVPLIQSTISVDSIPSPQGNSSRGSASPGLSPLTPGHKGA   400
 401  SPYGSPRGNLSSNTGGMAAIPSIQLLGLEMMLHFLLGPEVLSFAKQHKIV   450
 451  LSLEPLEHPLISSPSFFSKYAHTLITAVHDSFVSVGKDASDAVVSAIWKE   500
 501  LISLVKSVTEAGNRKEKSGSEVLTLLLKSLENIVKSEVFPVSKTLVLMEI   550
 551  TVKGLPPKVLGSPAYQVANMDILNGTPALFLIQLIFNNNLLECGVEDEKF   600
 601  FLNLETLVGCVLSGPTSPLAFSDSVLTVINQNAKQLVNKEHLWRMWSMIV   650
 651  SPLTDVIHQTNEVNQGDALEHNFSAIYGALTLPINHIFSAQTFPTGTMKA   700
 701  LLKTWSELYRAFTRCASLVATAEENLCCEELSSKIMCSLEDEVLSDLLFL   750
 751  DRISHIIIVMVDCIDFSPYNKKYQPKIKSPQRSSDWSRKKKEPLGKLASL   800
 801  FKLIVKVIDTFHTLSLKETFSDTLLAIGNSIISMLSNVFGHISLPSMIRE   850
 851  IFATFTRPLALLYENSKLDEAPKVYTSLNNKLEKLLGEIVACLQFSYLGA   900
 901  YDSELLEHLSPLLCVIFLHKNKQIRKQSALLWNATFAKATALVYPEELKP   950
 951  ILRQAKQKILLLLPGLENVEMMDESSEPYSESTENSQLNVKISGMERKSS  1000
1001  GKRDSILAHTKDKKKKVKLSAKLKLESSSPKIKSGKLLEEEKSTDFVFIP  1050
1051  PEGKETKARVLTEHQKEVLKTKRCDIPALYNNLDASQDTLFSAQFSQEES  1100
1101  MESLTLTEKPKEDAKIIKEEQMESTIFIHQDAPENCGIDEHSENASLPNC  1150
1151  GGSVAETNPETLITGFDARKEVLISSKILSAESSSSTETSVVSSSSVSNA  1200
1201  TFSGTPPQPTSRRQTFITLEKFDGSETRPFSPSPLNNISSTVTVRNNQDN  1250
1251  TTNTDMPPKARKREVTNSKSDSENLANAGKKSSRRWSKAEQSVTKKSKPS  1300
1301  LTSEQEEHSSENNSPDLLSPTEHVSENDDHPSEATLEHKDGDPKPAVENA  1350
1351  SLEDLTTEEKNVGINMESKESTASVVARTEQIVNEDSQAAALAPNPKTLR  1400
1401  RSSRRRSEAVDSCSDSQERESGQQKKERRKEEEKIISKSPLRIKDDKLPT  1450
1451  QKLTDESPIQENLTEKGNTLPERTSGEPSVNAEIDQNRRKPDLENVSSEG  1500
1501  GGGTLDNLDKSSEKPLRGRTRYQTRRASQGLISAVENSESDSSEAKEEVS  1550
1551  RKKRSGKWKNRSSDSVDIEEQEEKKAEEEVMKTANQTLDGQAVPDVDVNA  1600
1601  AAQVCEKSTNNNRVILQDSAGPADSLQAPPKGEEKSKINKCVDSSFVSLP  1650
1651  VPESNLRTRNASKRLLYKQDNDSNVRVSDSSLSPEKFTQVECQHKRSRRV  1700
1701  RRSKSCDCCGEKSQSQEKSFIGLKNTESYAIKSVEKKKTDLQVPETAPET  1750
1751  REARDHAETKLAGEEPLVNFHVGLKEENCTTGDSVKSEAELQEASLPPEI  1800
1801  VTVKEKTYDTDASEAVSEIQGPCSENHSPAEDPGLSECKDISQKQLSENG  1850
1851  ELDISDVGKACKVIAGSSPEGVETMELNVRNDAFVAADSEKSTQMDVSVD  1900
1901  VATEEDNKKDECEAVTTEVNVEGVATEDFNSGMDLSDTPIPVSKDVETEH  1950
1951  AASGEIEGESNESDSGSCEEMNKEMGSHKAQMSTEIDSARVKETDILASA  2000
2001  SKSEEALIGRLDVNTQSFVSDIEMSSGERTVNCKTETSIELNKLDEAKLS  2050
2051  GNEATVGNDTLQEVCFTSEKVEKLPQCLLVQVASELGAESNTTSPEKLEL  2100
2101  DSFGSVNESPSGMQQARCVWSPLASPSTSILKRGLKRSQEDEISPVNKIR  2150
2151  RVSFADPIYQAGLADDIDRRCSVVRSHSSNSSPIIKSVKTSPTSHSKHNT  2200
2201  TSAKGFLSPGSQSSKFKSPKKCLITEMAQESMLSPTESVYPALVNCAASV  2250
2251  DIILPQITSNMWARGLGQLIRAKNIKTIGDLSTLTASEIKTLPIRSPKVF  2300
2301  NVKKALRVYHEQQMKSRGLEEIPIFDISEKAVNGVESRTVSTDEERFASD  2350
2351  LIEPVTLDTPLSKNLVAQISALALQLDSEDLYSYTGSQLFEMHEKLGTMA  2400
2401  NSIIRNLQSRWRSPAHENS                                 2419

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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