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

NucPred

Fetching Q4WVM7 from www.uniprot.org...

The NucPred score for your sequence is 0.77 (see score help below)

   1  MCVIQRLTYAYLIRTSLNDKACHKIFESLFRFISVERSLYNRASSKGACA    50
  51  SRLSACASVIRTAINVFLRNLRTKSIRAIVDHITEILQVPGEGLWEHLGA   100
 101  DYLKCLTTLLRYPPHLEHLAANEWDKVLNLCLRSIGAPEDGDSQSSDHNG   150
 151  HPSTLDDFLDASSRSTPSRRTSSLALREKQSGDKRIVAEAIVCIQLLTAT   200
 201  PTAPVQVAAEKVLRGLGTFLKLSPIAGSEHQAAFNSINTVVMRVIFDQSD   250
 251  LVRMFLLDLIPVIRHLWSTKLMGLKDELLVTILLCMIILTDATRRAPTDS   300
 301  LALSIENLLDTIYSEYTKRSEKDILQIDELIFDRTSFTQIIDLALQPRLE   350
 351  VPRSEHNLTVVWVMAKLMRLSEESTAQLSHPAGETPSKKQRLNSASDQVF   400
 401  RDCVMSSGNRRVCALQLIPILLQGRLTMESKASLLQRLIPYILDDNGVIA   450
 451  SWTMVAISSISDSSLELWAIITRLCAQTNPGSVSNASKQICSWLREAWVI   500
 501  GTVTDRIQTAQVAAFARPLDLLNLFLACTNRQFEMPTPQFRGPSGIVAKG   550
 551  WHFYQSNRELLHYLFHVDGMLVPSSLHGRDDCISLQLATRKDHNDDIVLD   600
 601  LLQAKSEMFLQAWRSVSDSKSHHVTVDVVQILASFCIVAVLYTECIPEQL   650
 651  HTQIKDLRGNIQQLWDSLCSFMASRELVFVQYCLELLCPFLPQGGRVGFE   700
 701  KSVVNSSLYRLVSPLGAILENHRQDQKRLLSSDEEEPMDLDDQLLQSNDL   750
 751  LAENMCIINSNRESVPLFHDSATFQRSMTIRLSIFNIAYGSVVQPDQPAR   800
 801  SALVEYLTDLDEADILSSKDFLPDVYRACAGYERTSLLDLLEDMGEKCLQ   850
 851  TYQLERCETSQVLCIHMLDSFIKSWTTGDGDHLSDSASDIYNWVTDVLLV   900
 901  NGRASSRVSIAFSRLLEEIFSTNPAYTSGESNPSPRTTLFMILQESDILT   950
 951  KYNVGNLVPKLFRHFPLKDHDAIFDDILESLPRDPDWTEGIALRLFILAR  1000
1001  LASQWHTLLRRSIYHMFETPAQLPHSRWHAEKCIRHVASVFGLEDARQLF  1050
1051  RLFSSQILYTWTENESVMTMPFSIFGYSTLEDMLSDVQDEIVGQIMMRAN  1100
1101  EHEASELSTRLKIPFIELLATSFYKAEAYSIARDISTPPGQSSQPKGVEN  1150
1151  RLKKILGADRFVSLVEKQFPQVIATFFGTLDQCEQIERAFSKRANFQEAF  1200
1201  SILKSITAKGASKEILPPNQQPSFRARYLLDELEFLCKRSGYELETIWTP  1250
1251  TLASYVCRTLLESIHPALGSLHACSVIRKIRILICITGPVMLRDYPFEML  1300
1301  LHALRPFLTDIHCSEDALGMFWYLLDAGRSYLTENPSFTAGIAVSTLLSF  1350
1351  RKFLASTSATMQESESVAVLTIVQTFLQWFEDYLKSYESPHLSPEAHAFF  1400
1401  QRLMESSRRISTPDKELDGTEECNLLLEVIQDRNSKTRLLSQSISDHILS  1450
1451  LLCASFKSAPNYHQGLVERGYDAIADSVALYQTLQDFSPTKEYRLWAARV  1500
1501  IGRNFAATGMISDDLLREQQSTLFEPRMAKLSLHMSCQSKARILQVLCSM  1550
1551  LQNSSPLEVGLVERTLQLIVSNLAGAPGFENYEEIISPSLLKALIWSPYQ  1600
1601  CPSIPLPASQTKNHDTIVRWNPGISFAHWARSIGLFLTKAAPQDPVIGPL  1650
1651  RNILHVIPSLAVRILPYILHDVLLTEPDGVANVRKTISDVFQQGLHEADA  1700
1701  HSIPHVRLIINCLLYLRNQPRPQEATIVERDEWLEIDFAVASRAANTCGL  1750
1751  PKTALLFLEIQASRAVSGSRRSSLVKYEPPPDLLHDIFRNVDDPDLFYGV  1800
1801  QQSSSLESVMETLEHESSGFKNLLFQSAQYDCEIQMSGDADAHGLLKALN  1850
1851  SSNLQGIANSLTSTLRGSKSSVSFDSMMQAAIDLRQWDLPVSPMNHSPSA  1900
1901  ALFRTFQSLNTSTSLVDVSNSVNESLLAILGSLGSTSRSAMSFRAAMRDL  1950
1951  GIVTEISDVLSATSLEELSEEWRKIAERNSWLKATSVDEVGEILKCHEAL  2000
2001  FSSIKTRDYLKSAVGLSDRDAQLLEVKVIRQSLSITRSHGIPQVSLKSAM  2050
2051  RLSKLADLCVVQGINVEGATKFDLANVLWDQGEMAASIRMLQQLDNQGDL  2100
2101  HKQAIPISRPELLVTLGHHVAEARLEKPEAIIQGYLGPAVKELKNRSEAE  2150
2151  EAGRVYHGFATFCDQQLQNPDGLEDFRRAEQLRNRKEKEVLGLEEMMKNA  2200
2201  EGKEREALRHYRTKTKQWFDLDDREYQRLRRSREAFLQQCLENYLLCLKE  2250
2251  SDMYNNDALRFCALWLGKSDSEIANKAVSKYLNQVPSRKFAPLMNQLTSR  2300
2301  LQDTSDEFQNMLFALIFRICVEHPFHGMYQIFASSKSKGGKDPSALSRNR  2350
2351  AASRLVDCLKNDKRIGPTWVAVHNANISYVRFAVDRLDEKVKSGAKVPLK  2400
2401  KLLTGQRLEQDASTQKLPPPTMKIAIRVDCDYSEIPKLVRYHPEFTVASG  2450
2451  VSAPKIVTAVATDGHKYKQLFKGGNDDLRQDAIMEQVFEQVSSLLKDHQA  2500
2501  TQQRKLGIRTYKVLPLTSNAGIIEFVPHTIPLHDYLMPAHQRYFPKDMKP  2550
2551  NMCRKHISDVQTRSFEQRVKTFRQITEHFHPVMRYFFMEKFNSPDDWFSK  2600
2601  RLSYTRSTAAISILGHVLGLGDRHGHNILLDERTGEVVHIDLGVAFEQGR  2650
2651  VLPVPEVVPFRLTRDLVDGMGITKTEGVFRRCCEFTLEALRQESYSIMTI  2700
2701  LDVLRYDPLYSWTLSPLRMKRMQDAQEAGDGPPMISGAAEDQRSANEPSE  2750
2751  ADRALTVVAKKLSKTLSVTATVNELIQQATDERNLAVLYCGWAAYA      2796

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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