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

NucPred

Fetching P38110 from www.uniprot.org...

The NucPred score for your sequence is 0.85 (see score help below)

   1  MEDHGIVETLNFLSSTKIKERNNALDELTTILKEDPERIPTKALSTTAEA    50
  51  LVELLASEHTKYCDLLRNLTVSTTNKLSLSENRLSTISYVLRLFVEKSCE   100
 101  RFKVKTLKLLLAVVPELMVKDGSKSLLDAVSVHLSFALDALIKSDPFKLK   150
 151  FMIHQWISLVDKICEYFQSQMKLSMVDKTLTNFISILLNLLALDTVGIFQ   200
 201  VTRTITWTVIDFLRLSKKENGNTRLIMSLINQLILKCHCFSVIDTLMLIK   250
 251  EAWSYNLTIGCTSNELVQDQLSLFDVMSSELMNHKLPYMIGQENYVEELR   300
 301  SESLVSLYREYILLRLSNYKPQLFTVNHVEFSYIRGSRDKNSWFALPDFR   350
 351  LRDRGGRSVWLKILGITKSLLTYFALNRKNENYSLLFKRRKCDSDIPSIL   400
 401  RISDDMDTFLIHLLEENSSHEFEVLGLQLCSFYGTLQDFTKSFAEQLKEL   450
 451  LFSKFEKIQCFNWVCFSFIPLLSQKECELSNGDMARLFKVCLPLVKSNES   500
 501  CQLSCLLLANSIKFSKQLLSDEKTINQIYDLYELSDILGPILVTNESFML   550
 551  WGYLQYVGKDFQSMNGISSADRIFEWLKSKWNQLRGTDAKQDQFCNFISW   600
 601  LGNKYDPENPFNDKKGEGANPVSLCWDESHKIWQHFQEQREFLLGVKPEE   650
 651  KSECFNTPFFNLPKVSLDLTRYNEILYRLLENIESDAFSSPLQKFTWVAK   700
 701  LIQIVDNLCGDSTFSEFIAAYKRTTLITIPQLSFDSQNSYQSFFEEVLSI   750
 751  RTINVDHLVLDKINMKEIVNDFIRMQKNKSQTGTSAINYFEASSEDTTQN   800
 801  NSPYTIGGRFQKPLHSTIDKAVRAYLWSSRNKSISERLVAILEFSDCVST   850
 851  DVFISYLGTVCQWLKQAIGEKSSYNKILEEFTEVLGEKLLCNHYSSSNQA   900
 901  MLLLTSYIEAIRPQWLSYPEQPLNSDCNDILDWIISRFEDNSFTGVAPTV   950
 951  NLSMLLLSLLQNHDLSHGSIRGGKQRVFATFIKCLQKLDSSNIINIMNSI  1000
1001  SSYMAQVSYKNQSIIFYEIKSLFGPPQQSIEKSAFYSLAMSMLSLVSYPS  1050
1051  LVFSLEDMMTYSGFNHTRAFIQQALNKITVAFRYQNLTELFEYCKFDLIM  1100
1101  YWFNRTKVPTSKLEKEWDISLFGFADIHEFLGRYFVEISAIYFSQGFNQK  1150
1151  WILDMLHAITGNGDAYLVDNSYYLCIPLAFISGGVNELIFDILPQISGKT  1200
1201  TVKYHKKYRLLMLKWIIRFTDLGSLTELRSTVEKLFPTSYLSPYLFENSS  1250
1251  VSMRYQYPLHIPLALGATLVQTQFAHEKNNTHEFKLLFLSVITDLEKTST  1300
1301  YIGKLRCARELKYLFVLYENVLVKSSTLNFIIIRLSKFLIDTQIHDEVIT  1350
1351  IFSSLLNLADKNTFEIEPSLPNLFCKIFIYLRENKQLSPSFQQAIKLLEH  1400
1401  RDLIKIKTWKYCLDAIFGNIVQDDIYENTELLDASDCGVDDVVLVSLLFS  1450
1451  YARRPVASKIGCSLSKAAAINILKHHVPKEYLSKNFKLWFAALSRRILQQ  1500
1501  EVQRERSTNFNNEVHLKNFEMVFRHPEQPHMIYQRISTFNKEAELYDSTE  1550
1551  VFFISECILTYLVGYSIGNSESEFCFRDNIMNENKDKVAPLDKDVLNAIY  1600
1601  PLANNFGMESFICDTYLSVNEPYNCWLSKFARSLIHQISFNIPPIVCLYP  1650
1651  LCKGSTAFCELVLTDLFFLSTTYDPKSCLNWSNRIFTQIAMLLHVKDSEI  1700
1701  KLKMLFNVIKMIRMGSRCKERNCLRIYSSLDLQEICQISLKIKEFKFGYL  1750
1751  LFEEMNMPNIREMNINTLQKIYECINDGDFLAGLPVPHSIEGVLNSINRI  1800
1801  DSDTWKRFLFNNADFDANYTTSLEEEKESLIKATEDSGFYGLTSLLESRL  1850
1851  SGSSDVYKWNLELGDWKLLTPKVVDSKAKGLYYAIKNLPQDVGFAEKSLE  1900
1901  KSLLTIFDSRQHFISQTEWMDTLNAIIEFIKIAAIPQDVTSFPQTLMSIM  1950
1951  KADKERLNTIDFYDHKTTLKSRHTLMNVLSRNSLDENVKCSKYLRLGSII  2000
2001  QLANYVQLAIANGAPQDALRNATLMSKTVKNIAKLYDDPSVVSQIEKLAS  2050
2051  FTSANALWESREYKAPVMIMRDLLAQNEKNISESILYDDFKLLINVPMDQ  2100
2101  IKARLVKWSSESRLEPAAAIYEKIIVNWDINVEDHESCSDVFYTLGSFLD  2150
2151  EQAQKLRSNGEIEDREHRSYTGKSTLKALELIYKNTKLPENERKDAKRHY  2200
2201  NRVLLQYNRDSEVLKALLLQKEKFLWHALHFYLNTLVFSNRYDNDIIDKF  2250
2251  CGLWFENDDNSKINQLLYKEIGTIPSWKFLPWVNQIASKISMEENEFQKP  2300
2301  LQLTMKRLLYKLPYDSLYSVMSILLYEKQSNKDTNISQKIQAVKKILLEL  2350
2351  QGYDRGAFAKKYLLPVQEFCEMSVELANLKFVQNTKTLRLANLKIGQYWL  2400
2401  KQLNMEKLPLPTSNFTVKSSADGRKARPYIVSVNETVGITTTGLSLPKIV  2450
2451  TFNISDGTTQKALMKGSNDDLRQDAIMEQVFQQVNKVLQNDKVLRNLDLG  2500
2501  IRTYKVVPLGPKAGIIEFVANSTSLHQILSKLHTNDKITFDQARKGMKAV  2550
2551  QTKSNEERLKAYLKITNEIKPQLRNFFFDSFPDPLDWFEAKKTYTKGVAA  2600
2601  SSIVGYILGLGDRHLNNILLDCSTGEPIHIDLGIAFDQGKLLPIPELVPF  2650
2651  RLTRDIVDGFGVTGVDGLFRRSCERVYAVLRKDYVKVMCVLNILKWDPLY  2700
2701  SWVMSPVKKYEHLFEEEHEITNFDNVSKFISNNDRNENQESYRALKGVEE  2750
2751  KLMGNGLSVESSVQDLIQQATDPSNLSVIYMGWSPFY               2787

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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