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

NucPred

Fetching Q8CJH3 from www.uniprot.org...

The NucPred score for your sequence is 0.31 (see score help below)

   1  MSVLGPVLLQVFWAGCVVTLRSPLPAAFTANGTHLQHLARDPTTGTLYVG    50
  51  ATNFLFQLSPGLQLEAVVSTGPVNDSRDCLPPVIPDECPQAQPTNNPNQL   100
 101  LLVSPEALVVCGSVHQGICELRSLGQIRQLLLRPERPGDTQYVAANDPAV   150
 151  STVGLVAQGLVGEPLLFVGRGYTSRGVGGGIPPITTRALRPPDPQAAFSY   200
 201  EETAKLAVGRLSEYSHHFVSAFVRGASAYFLFLRRDLKAPSRAFRAYVSR   250
 251  VCLQDQHYYSYVELPLACQGGRYGLIQAAAVATSKEVARGDVLFAAFSSV   300
 301  APPTVDWPLSASTGASGTSVLCAFPLDEVDQLANYTRDACYTREGRAENG   350
 351  TKVADIAYDVLSDCAQLPVDTPDAFPCGSDHTPSPMVSCVPLEATPILEL   400
 401  PGVQLTAVAVTMEDGHTIAFLGDSQGQLHRVYLGPGRSAAPYSKQSIQPG   450
 451  SPVNRDLTFDGTFEHLYVATQTTLVKVPVAPCAQHLDCDSCLAHRDPYCG   500
 501  WCVLLGRCSRRSECSRDQGPEQWLWSFQPELGCLRVVAVSPANISREERR   550
 551  EVFLSVPGLPSLWPGESYFCYFGDQQSPALLTSSGVMCPSPDPSEAPVLQ   600
 601  RGADHISVNVELRFGAVVIASTSLSFYDCVAVTASSPSAPCRACVSSRWG   650
 651  CNWCVWQQLCTHKASCDAGPMVASQQSPLLPLIPPARDELTPFPPTVPQT   700
 701  TVTPTPNSFPIEPRAPSTASDVLPGAKPSRLSLWGPWAGPGPILSPTSTE   750
 751  SPLHEKPLPPDPPTIPGTTVPAPTGLGPSTTPEDLLASYPFPSDAAAVSP   800
 801  AEPGPEALPSMVALDQPPGTVPDTTFPGAPGSMKPVLDWLTKGGGELPEA   850
 851  DEWMGGDTPAFSTSTLLSGDGDSAEHEGPPAPLILLSSLDYQYDTPGLWE   900
 901  LGEVNQRVSSCPCVETVQGSLLIPVHVEREVQLRGRNLWLFQDGPRSSEC   950
 951  VLELGSREVAVEAQVECAPPPDVWCHIKCQQHQFSYEALKPELQVGLFLR  1000
1001  WAGGLRVDSADGLHVVLYDCSVGHGDCSRCQTAMPQYDCVWCEGERPRCV  1050
1051  AREACNEAETVATQCPAPLIHSVDPLTGPIDGGTRVTIRGSNLGQHVQDV  1100
1101  LDMVRVAGVPCAVDAGEYDVSSSLVCITGASGEEVTGTVAVEVPGRGHGV  1150
1151  SEFSFAYQDPKVHSIFPARGPRAGGTRLTLHGSKLLTGRLEDIRVVVGDQ  1200
1201  PCHLLLEQQSEQLHCETGPYPVPAELPVTVLFGATERRLQHGQFKYTSDP  1250
1251  NVTSVGPSKSFFSGGREIWVRGQDLDVVQRPRIRVTVVPRQHGQGLAQKQ  1300
1301  HVVPEKFEEPCLVNSSHLLMCRTPALPGPPWDSGVQVEFILDNMVFDFAA  1350
1351  LSPTPFSYEADPTLRSLNPEDPSTPFRHKPGSVFSVEGENLDLAMSKEEV  1400
1401  VAMIGDGPCVVKTLTRNHLYCEPPVEQPLPHPHALREAPDALPEFTVQMG  1450
1451  NLRFSLGHVQYDGESPVAFPVAAQVGLGVGTSLLALGVIIIVLIYRRKSK  1500
1501  QALRDYKKVQIQLENLESSVRDRCKKEFTDLMTEMTDLTSDLLGSGIPFL  1550
1551  DYKVYAERVFFPGYRESPLHRDLGVPDSRRPTVEQGLGQLSNLLNSKLFL  1600
1601  TKFIHTLESQRTFSARDRAYVASLLTVALHGKLEYFTDILRTLLSDLVAQ  1650
1651  YVAKNPKLMLRRTETVVEKLLTNWMSICLYTFVRDSVGEPLYMLFRGIKH  1700
1701  QVDKGPVDSVTGKAKYTLNDNRLLREDVEYRPLTLNALLAVGPGAGEAQC  1750
1751  VPVKVLDCDTISQAKEKMLDQLYKGVPLAQRPDSCTLDVEWRSGVAGHLI  1800
1801  LSDEDVTSELQGLWRRLNTLQHYKVPDGATVALVPCLTKHILRENQDYVP  1850
1851  GERTPMLEDVDEGGIRPWHLVKPSDEPEPPRPRRGSLRGGERERAKAIPE  1900
1901  IYLTRLLSMKGTLQKFVDDLFQVILSTSRPVPLAVKYFFDLLDEQAQQHG  1950
1951  ISDQDTIHIWKTNSLPLRFWINIIKNPQFVFDVQTSDNMDAVLLVIAQTF  2000
2001  MDACTLADHKLGRDSPINKLLYARDIPRYKQMVERYYADIRQTVPASDQE  2050
2051  MNSVLAELSRNCSADLGARVALHELYKYINKYYDQIITALEEDGTAQKMQ  2100
2101  LGYRLQQIAAAVENKVTDL                                 2119

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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