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

NucPred

Fetching Q9C0A1 from www.uniprot.org...

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

   1  MATLNSASTTGTTPSPGHNAPSLPSDTFSSSTPSDPVTKDPPAASSTSEN    50
  51  MRSSEPGGQLLESGCGLVPPKEIGEPQEGPDCGHFPPNDPGVEKDKEQEE   100
 101  EEEGLPPMDLSNHLFFTAGGEAYLVAKLSLPGGSELLLPKGFPWGEAGIK   150
 151  EEPSLPFLAYPPPSHLTALHIQHGFDPIQGFSSSDQILSHDTSAPSPAAC   200
 201  EERHGAFWSYQLAPNPPGDPKDGPMGNSGGNHVAVFWLCLLCRLGFSKPQ   250
 251  AFMDHTQSHGVKLTPAQYQGLSGSPAVLQEGDEGCKALISFLEPKLPARP   300
 301  SSDIPLDNSSTVNMEANVAQTEDGPPEAEVQALILLDEEVMALSPPSPPT   350
 351  ATWDPSPTQAKESPVAAGEAGPDWFPEGQEEDGGLCPPLNQSSPTSKEGG   400
 401  TLPAPVGSPEDPSDPPQPYRLADDYTPAPAAFQGLSLSSHMSLLHSRNSC   450
 451  KTLKCPKCNWHYKYQQTLDVHMREKHPESNSHCSYCSAGGAHPRLARGES   500
 501  YNCGYKPYRCDVCNYSTTTKGNLSIHMQSDKHLANLQGFQAGPGGQGSPP   550
 551  EASLPPSAGDKEPKTKSSWQCKVCSYETNISRNLRIHMTSEKHMQNVLML   600
 601  HQGLPLGLPPGLMGPGPPPPPGATPTSPPELFQYFGPQALGQPQTPLAGP   650
 651  GLRPDKPLEAQLLLNGFHHVGAPARKFPTSAPGSLSPDAHLPPSQLLGSS   700
 701  SDSLPTSPPPDDSLSLKVFRCLVCQAFSTDSLELLLYHCSIGRSLPEAEW   750
 751  KEVAGDTHRCKLCCYGTQLKANFQLHLKTDKHAQKYQLAAHLREGGGAMG   800
 801  TPSPASLGDGAPYGSVSPLHLRCNICDFESNSKEKMQLHARGAAHEENSQ   850
 851  IYKFLLDMEGAEAGAELGLYHCLLCAWETPSRLAVLQHLRTPAHRDAQAQ   900
 901  RRLQLLQNGPTTEEGLAALQSILSFSHGQLRTPGKAPVTPLAEPPTPEKD   950
 951  AQNKTEQLASEETENKTGPSRDSANQTTVYCCPYCSFLSPESSQVRAHTL  1000
1001  SQHAVQPKYRCPLCQEQLVGRPALHFHLSHLHNVVPECVEKLLLVATTVE  1050
1051  MTFTTKVLSAPTLSPLDNGQEPPTHGPEPTPSRDQAAEGPNLTPEASPDP  1100
1101  LPEPPLASVEVPDKPSGSPGQPPSPAPSPVPEPDAQAEDVAPPPTMAEEE  1150
1151  EGTTGELRSAEPAPADSRHPLTYRKTTNFALDKFLDPARPYKCTVCKESF  1200
1201  TQKNILLVHYNSVSHLHKMKKAAIDPSAPARGEAGAPPTTTAATDKPFKC  1250
1251  TVCRVSYNQSSTLEIHMRSVLHQTRSRGTKTDSKIEGPERSQEEPKEGET  1300
1301  EGEVGTEKKGPDTSGFISGLPFLSPPPPPLDLHRFPAPLFTPPVLPPFPL  1350
1351  VPESLLKLQQQQLLLPFYLHDLKVGPKLTLAGPAPVLSLPAATPPPPPQP  1400
1401  PKAELAEREWERPPMAKEGNEAGPSSPPDPLPNEAARTAAKALLENFGFE  1450
1451  LVIQYNEGKQAVPPPPTPPPPEALGGGDKLACGACGKLFSNMLILKTHEE  1500
1501  HVHRRFLPFEALSRYAAQFRKSYDSLYPPLAEPPKPPDGSLDSPVPHLGP  1550
1551  PFLVPEPEAGGTRAPEERSRAGGHWPIEEEESSRGNLPPLVPAGRRFSRT  1600
1601  KFTEFQTQALQSFFETSAYPKDGEVERLASLLGLASRVVVVWFQNARQKA  1650
1651  RKNACEGGSMPTGGGTGGASGCRRCHATFSCVFELVRHLKKCYDDQTLEE  1700
1701  EEEEAERGEEEEEVEEEEVEEEQGLEPPAGPEGPLPEPPDGEELSQAEAT  1750
1751  KAGGKEPEEKATPSPSPAHTCDQCAISFSSQDLLTSHRRLHFLPSLQPSA  1800
1801  PPQLLDLPLLVFGERNPLVAATSPMPGPPLKRKHEDGSLSPTGSEAGGGG  1850
1851  EGEPPRDKRLRTTILPEQLEILYRWYMQDSNPTRKMLDCISEEVGLKKRV  1900
1901  VQVWFQNTRARERKGQFRSTPGGVPSPAVKPPATATPASLPKFNLLLGKV  1950
1951  DDGTGREAPKREAPAFPYPTATLASGPQPFLPPGKEATTPTPEPPLPLLP  2000
2001  PPPPSEEEGPEEPPKASPESEACSLSAGDLSDSSASSLAEPESPGAGGTS  2050
2051  GGPGGGTGVPDGMGQRRYRTQMSSLQLKIMKACYEAYRTPTMQECEVLGE  2100
2101  EIGLPKRVIQVWFQNARAKEKKAKLQGTAAGSTGGSSEGLLAAQRTDCPY  2150
2151  CDVKYDFYVSCRGHLFSRQHLAKLKEAVRAQLKSESKCYDLAPAPEAPPA  2200
2201  LKAPPATTPASMPLGAAPTLPRLAPVLLSGPALAQPPLGNLAPFNSGPAA  2250
2251  SSGLLGLATSVLPTTTVVQTAGPGRPLPQRPMPDQTNTSTAGTTDPVPGP  2300
2301  PTEPLGDKVSSERKPVAGPTSSSNDALKNLKALKTTVPALLGGQFLPFPL  2350
2351  PPAGGTAPPAVFGPQLQGAYFQQLYGMKKGLFPMNPMIPQTLIGLLPNAL  2400
2401  LQPPPQPPEPTATAPPKPPELPAPGEGEAGEVDELLTGSTGISTVDVTHR  2450
2451  YLCRQCKMAFDGEAPATAHQRSFCFFGRGSGGSMPPPLRVPICTYHCLAC  2500
2501  EVLLSGREALASHLRSSAHRRKAAPPQGGPPISITNAATAASAAVAFAKE  2550
2551  EARLPHTDSNPKTTTTSTLLAL                              2572

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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