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

NucPred

Fetching P56716 from www.uniprot.org...

The NucPred score for your sequence is 0.98 (see score help below)

   1  MSDTPSTSFSMIHLTSEGQVPSPRHSNITHPVVAKRISFYKSGDPQFGGV    50
  51  RVVVNPRSFKTFDALLDSLSRKVPLPFGVRNISTPRGRHSITRLEELEDG   100
 101  KSYVCSHNKKVLPVDLDKARRRPRPWLSSRSISTHVQLCPATANMSTMAP   150
 151  GMLRAPRRLVVFRNGDPKNKHVVLLSRRITQSFEAFLQYLTQVMQCPVAK   200
 201  LYATDGRKVPSLQAVILSSGAVVAAGREPFKPGNYDIQKYLLPAKLPGIS   250
 251  HRVHQKGKAKIEKRKMSTHMPSDLRPQTDSLISEKTYDCFSDFSVAPENY   300
 301  LALETHESQSLSTYPSEDDVEKSIVFNQDGTMTVVMKVRFKIKEEETVKW   350
 351  TTTVNRAGLSNNDEKNKKSSYPGKTDYGPSSLKLEACSLPEDIVDTTQQG   400
 401  SLTEEENTQMTEQQALSCSSASWENASMETDIQESQKQVKHFYRPPTPGP   450
 451  RRMRQKKSVIGTVTVVSETEVQEKQFSYSEERKGGEKSEYHMFTHSCSKM   500
 501  SSVSNKLVQIGSDNEMESALERTRESGSLKSQAINAGAIEITSQKVLKMC   550
 551  HNNALPSTAPENSVVEEGTDNSAVSGTATIKHFRTCGNANDSFSSITADS   600
 601  TPTSVNNYSNDRNISELPSVGSPVLTMRLVNEFAHCGLTEKPENRKKVLS   650
 651  SSASKKKKKKSQQRMITSNDKKKVIETKGPPNIAGKIPRAGTTAQERLLQ   700
 701  ESDCPDKGGRVCEQGLNISPMAIESNNFFPKSNPTFSKNFYKNKLNTFQN   750
 751  PKTQKLLAKRKSRPRKIVSTERLRKQEIGQEDKILLHSDSKLCESHLEKQ   800
 801  SLFHVFNILEEDQKVLHRPPFQVEKVARNLKGMAKKSLVPKVNDLHIMLR   850
 851  NQKKQMGVKLKSGAEVSEQHVTTRADPLASLKKPDFPEGIPHHSGKSYVK   900
 901  RWLQNINSYPDFEHRKSGPLCQNRSDVVNYNRNGFLGNNLHTTSSKGNGF   950
 951  LMESNKSKTKNDNWSGNTNQETGKSLVAKDNGEELNKHHCESQNGSLYDS  1000
1001  YLVSLHDNCTLSQTTINEPSTKSHLSIEKSRPEVKLVYQEMNFATKRQSI  1050
1051  EVAIQVDTMGENVLKDYLPALLLRHLEAFVPNNQKHQNGISQIPGSLAEV  1100
1101  VFPSVIDNSSTNLLLAWLLVLNLKRTMNSFCQSDAHKMTNRPSETAALLE  1150
1151  VLKHVAITEEADDLKAAVANLMESTKTCSGSSGREQDMLPVNCTASSLHS  1200
1201  VDECNENGSAQKTLLDEGYSVMGDCTSEMVSKSCNSSCEMHMVSKTNPPK  1250
1251  QVDDQSDGLLTSNSCTVSQRSTGACFLTDGVYSHEACAQKEGVYEGACLS  1300
1301  DETHIPIRDCHTIHSVHSKENKCTDDLESTEELKTVDKVPKGLSILADSM  1350
1351  YKNDSNVSTFQNVNKLSSQRTLLSKTYLDSDKDYSPLEEFQNCPRKKIVN  1400
1401  KKKSISSDKEESRTSEEPRSITNSMTSSERNAISELESFEELESQDTSIF  1450
1451  NMNVRAEKKSTKETMQKQSEARMSSELINVSGRKIIEQERRNTAILETTA  1500
1501  RGQVTPPSLAFCYDSNKNTEKEISEGETKMRVKKMVDSMENESYSESSLN  1550
1551  FKKHHRSPGTLDWSDYGSDSESGYPCKASSNSHNDDSGQEKEPTRGIVKR  1600
1601  AIEKLYGKAEIIKPPFFHGSIHKSQVCPYNSVEVQCAKKTNFYESECQSL  1650
1651  VSSEQVSRSSLIFQEFPQVDANGMGDSFGDSSIENVTKSSAHDRVFTEKE  1700
1701  NGKLIDNGKWLLRENHLWRVSSDNPGMYGNADTTSVDTLIDKNSIEVPYS  1750
1751  HFGELAPGPTMAELSSSEIEEMTQPLEVKCNYFNFPHGSDSEPFGEDFPD  1800
1801  AQNKTCPKEKIPNHHTEEKGNYPSERLCTSVTQAFVSAGNKVHPVCSDAI  1850
1851  KTQPLPGSNITHGALQEGDSLDKLYALCGQHCPILTVIIQPVNEESRGFA  1900
1901  YRKDSDIENSLDFQLWMKIYPFMPQSKKHVFRSDGRNVSVGEEFAGNVIG  1950
1951  DLCDQLYFKSMIDLVDQRANSLGKEINLKKFQLYLKKSFSDPLSTSLLVV  2000
2001  ENRNSVSLSPSSWTDNFKSIDENNNFLNRLPNSSKNPNQVVRENTNFQFH  2050
2051  LELFGQVYLLDICQVEKPLNIKTRSKLEMYYILEGEVLFIWEEEK       2095

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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