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

NucPred

Fetching P05990 from www.uniprot.org...

The NucPred score for your sequence is 0.36 (see score help below)

   1  MASTDCYLALEDGTVLPGYSFGYVPSENESKVGFGGEVVFQTGMVGYTEA    50
  51  LTDRSYSGQILVLTYPLIGNYGVPAPDEDEHGLPLHFEWMKGVVQATALV   100
 101  VGEVAEEAFHWRKWKTLPDWLKQHKVPGIQDIDTRALTKKLREQGSMLGK   150
 151  IVYEKPPVEGLPKSSFVDPNVRNLAKECSVKERQVYGNPNGKGPRIAILD   200
 201  CGLKLNQLRCLLQRGASVTLLPWSARLEDEQFDALFLSNGPGNPESCDQI   250
 251  VQQVRKVIEEGQKPVFGICLGHQLLAKAIGCSTYKMKYGNRGHNLPCLHR   300
 301  ATGRCLMTSQNHGYAVDLEQLPDGWSELFVNANDGTNEGIVHASKPYFSV   350
 351  QFHPEHHAGPQDTEFLFDVFMESIQQKDLTIPQLIEQRLRPTTPAIDSAP   400
 401  VMPRKVLILGSGGLSIGQAGEFDYSGSQAIKAMRESNIQTVLINPNIATV   450
 451  QTSKGMADKCYFLPLTPHYVEQVIKSERPNGVLLTFGGQTALNCGVQLER   500
 501  AGVFSKYNVRILGTPIQSIIETEDRKLFAERVNEIGEQVAPSEAVYSVAQ   550
 551  ALDAASRLGYPVMARAAFSLGGLGSGFANNEEELQSLAQQALAHSSQLIV   600
 601  DKSLKGWKEVEYEVVRDAYNNCITVCNMENFDPLGIHTGESIVVAPSQTL   650
 651  SDREYQMLRSTALKVIRHFGVVGECNIQYALCPHSEQYYIIEVNARLSRS   700
 701  SALASKATGYPLAYVAAKLALGLPLPDIKNSVTGNTTACFEPSLDYCVVK   750
 751  IPRWDLAKFVRVSKHIGSSMKSVGEVMAIGRNFEEAFQKALRMVDSDVLG   800
 801  FDPDVVPLNKEQLAEQLSEPTDRRPFVIAAALQLGMSLRELHQLTNIDYW   850
 851  FLEKLERIILLQSLLTRNGSRTDAALLLKAKRFGFSDKQIAKYIKSTELA   900
 901  VRHQRQEFGIRPHVKQIDTVAGEWPASTNYLYHTYNGSEHDVDFPGGHTI   950
 951  VVGSGVYRIGSSVEFDWCAVGCLRELRKLQRPTIMINYNPETVSTDYDMC  1000
1001  DRLYFEEISFEVVMDIYEMENSEGIILSMGGQLPNNIAMDLHRQQAKVLG  1050
1051  TSPESIDCAENRFKFSRMLDRKGILQPRWKELTNLQSAIEFCEEVGYPCL  1100
1101  VRPSYVLSGAAMNVAYSNQDLETYLNAASEVSREHPVVISKFLTEAKEID  1150
1151  VDAVASDGRILCMAVSEHVENAGVHSGDATLVTPPQDLNAETLEAIKRIT  1200
1201  CDLASVLDVTGPFNMQLIAKNNELKVIECNVRVSRSFPFVSKTLDHDFVA  1250
1251  TATRAIVGLDVEPLDVLHGVGKVGVKVPQFSFSRLAGADVQLGVEMASTG  1300
1301  EVACFGDNRYEAYLKAMMSTGFQIPKNAVLLSIGSFKHKMELLPSIRDLA  1350
1351  KMGYKLYASMGTGDFYAEHGVNVESVQWTFDKTTPDDINGELRHLAEFLA  1400
1401  NKQFDLVINLPMSGGGARRVSSFMTHGYRTRRLAVDYSIPLVTDVKCTKL  1450
1451  LVESMRMNGGKPPMKTHTDCMTSRRIVKLPGFIDVHVHLREPGATHKEDF  1500
1501  ASGTAAALAGGVTLVCAMPNTNPSIVDRETFTQFQELAKAGARCDYALYV  1550
1551  GASDDNWAQVNELASHACGLKMYLNDTFGTLKLSDMTSWQRHLSHWPKRS  1600
1601  PIVCHAERQSTAAVIMLAHLLDRSVHICHVARKEEIQLIRSAKEKGVKVT  1650
1651  CEVCPHHLFLSTKDVERLGHGMSEVRPLLCSPEDQEALWENIDYIDVFAT  1700
1701  DHAPHTLAEKRSERPPPGFPGVETILPLLLQAVHEGRLTMEDIKRKFHRN  1750
1751  PKIIFNLPDQAQTYVEVDLDEEWTITGNEMKSKSGWTPFEGTKVKGRVHR  1800
1801  VVLRGEVAFVDGQVLVQPGFGQNVRPKQSPLASEASQDLLPSDNDANDTF  1850
1851  TRLLTSEGPGGGVHGISTKVHFVDGANFLRPNSPSPRIRLDSASNTTLRE  1900
1901  YLQRTTNSNPVAHSLMGKHILAVDMFNKDHLNDIFNLAQLLKLRGTKDRP  1950
1951  VDELLPGKIMASVFYEVSTRTQCSFAAAMLRLGGRVISMDNITSSVKKGE  2000
2001  SLEDSIKVVSSYADVVVLRHPSPGAVARAATFSRKPLINAGDGVGEHPTQ  2050
2051  ALLDIFTIREEFGTVNGLTITMVGDLKNGRTVHSLARLLTLYNVNLQYVA  2100
2101  PNSLQMPDEVVQFVHQRGVKQLFARDLKNVLPDTDVLYMTRIQRERFDNV  2150
2151  EDYEKCCGHLVLTPEHMMRAKKRSIVLHPLPRLNEISREIDSDPRAAYFR  2200
2201  QAEYGMYIRMALLAMVVGGRNTAL                            2224

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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