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

NucPred

Fetching Q8IWB6 from www.uniprot.org...

The NucPred score for your sequence is 0.95 (see score help below)

   1  MSRAVRLPVPCPVQLGTLRNDSLEAQLHEYVKQGNYVKVKKILKKGIYVD    50
  51  AVNSLGQTALFVAALLGLRKFVDVLVDYGSDPNHRCFDGSTPVHAAAFSG   100
 101  NQWILSKLLDAGGDLRLHDERGQNPKTWALTAGKERSTQIVEFMQRCASH   150
 151  MQAIIQGFSYDLLKKIDSPQRLVYSPSWCGGLVQGNPNGSPNRLLKAGVI   200
 201  SAQNIYSFGFGKAMPWFQFYLTGATQMAYLGSLPVIGEKEVIQADDEPTF   250
 251  SFFSGPYMVMTNLVWNGSRVTVKELNLPTHPHCSRLRLADLLIAEQEHSS   300
 301  KLRHPYLLQLMAVCLSQDLEKTRLVYERITIGTLFSVLHERRSQFPVLHM   350
 351  EVIVHLLLQISDALRYLHFQGFIHRSLSSYAVHIISPGEARLTNLEYMLE   400
 401  SEDRGVQRDLTRVPLPTQLYNWAAPEVILQKAATVKSDIYSFSMIMQEIL   450
 451  TDDIPWKGLDGSVVKKAVVSGNYLEADVRLPKPYYDIVKSGIHVKQKDRT   500
 501  MNLQDIRYILKNDLKDFTGAQRTQPTESPRVQRYGLHPDVNVYLGLTSEH   550
 551  PRETPDMEIIELKEMGSQPHSPRVHSLFTEGTLDPQAPDPCLMARETQNQ   600
 601  DAPCPAPFMAEEASSPSTGQPSLCSFEINEIYSGCLILEDDIEEPPGAAS   650
 651  SLEADGPNQVDELKSMEEELDKMEREACCFGSEDESSSKAETEYSFDDWD   700
 701  WQNGSLSSLSLPESTREAKSNLNNMSTTEEYLISKCVLDLKIMQTIMHEN   750
 751  DDRLRNIEQILDEVEMKQKEQEERMSLWATSREFTNAYKLPLAVGPPSLN   800
 801  YIPPVLQLSGGQKPDTSGNYPTLPRFPRMLPTLCDPGKQNTDEQFQCTQG   850
 851  AKDSLETSRIQNTSSQGRPRESTAQAKATQFNSALFTLSSHRQGPSASPS   900
 901  CHWDSTRMSVEPVSSEIYNAESRNKDDGKVHLKWKMEVKEMAKKAATGQL   950
 951  TVPPWHPQSSLTLESEAENEPDALLQPPIRSPENTDWQRVIEYHRENDEP  1000
1001  RGNGKFDKTGNNDCDSDQHGRQPRLGSFTSIRHPSPRQKEQPEHSEAFQA  1050
1051  SSDTLVAVEKSYSHQSMQSTCSPESSEDITDEFLTPDGEYFYSSTAQENL  1100
1101  ALETSSPIEEDFEGIQGAFAQPQVSGEEKFQMRKILGKNAEILPRSQFQP  1150
1151  VRSTEDEQEETSKESPKELKEKDISLTDIQDLSSISYEPDSSFKEASCKT  1200
1201  PKINHAPTSVSTPLSPGSVSSAASQYKDCLESITFQVKTEFASCWNSQEF  1250
1251  IQTLSDDFISVRERAKKLDSLLTSSETPPSRLTGLKRLSSFIGAGSPSLV  1300
1301  KACDSSPPHATQRRSLPKVEAFSQHHIDELPPPSQELLDDIELLKQQQGS  1350
1351  STVLHENTASDGGGTANDQRHLEEQETDSKKEDSSMLLSKETEDLGEDTE  1400
1401  RAHSTLDEDLERWLQPPEESVELQDLPKGSERETNIKDQKVGEEKRKRED  1450
1451  SITPERRKSEGVLGTSEEDELKSCFWKRLGWSESSRIIVLDQSDLSD     1497

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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