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

NucPred

Fetching Q80X90 from www.uniprot.org...

The NucPred score for your sequence is 0.17 (see score help below)

   1  MPVTEKDLAEDAPWKKIQQNTFTRWCNEHLKCVNKRIGNLQTDLSDGLRL    50
  51  IALLEVLSQKRMHHKYHQRPTFRQMKLENVSVALEFLDHESIKLVSIDSK   100
 101  AIVDGNLKLILGLVWTLILHYSISMPVWEDEGDDDAKKQTPKQRLLGWIQ   150
 151  NKIPYLPITNFNQNWQDGKALGALVDSCAPGLCPDWESWDPRKPVDNARE   200
 201  AMQQADDWLGVPQVITPEEIIHPDVDEHSVMTYLSQFPKAKLKPGAPLKP   250
 251  KLNPKKARAYGRGIEPTGNMVKQPAKFTVDTISAGQGDVMVFVEDPEGNK   300
 301  EEARVTPDSDKNKTYSVEYLPKVTGLHKVIVLFAGQHISKSPFEVNVDKA   350
 351  QGDASKVTAKGPGLETTGNIANKPTYFDIYTAGAGVGDIGIEVEDPQGKN   400
 401  SVELLVEDRGNQVYRCVYKPVQPGPHVVKVSFAGDAIPKSPFGVQIGEAC   450
 451  NPNACRASGRGLQPKGVRIRETADFKVDTKAAGSGELGVTVKGPKGLEEL   500
 501  VKQKGFLDGVYSFEYYPSTPGKYSVAVTWGGHHIPKSPFEVQVGPEAGMQ   550
 551  KVRAWGPGLHGGIVGRSADFVVESIGSEVGTLGFAIEGPSQAKIEYDDQN   600
 601  DGSCDVKYWPKEPGEYAVHIMCDDEDIKDSPYMAFIHPATGDYNPDLVQA   650
 651  YGPGLEKSGCTINNPAEFIVDPKDAGSAPLKILAQDGEGQPIDIQMKSRM   700
 701  DGTYACSYTPLKAIKHTIAVVWGGVNIPHSPYRVNIGQGSHPQKVKVFGP   750
 751  GVERSGLKANEPTHFTVDCTEAGEGDVSVGIKCDARVLSDDEEDVDFDII   800
 801  HNANDTFTVKYVPPAPGRYTIKVLFASQEIPASPFRVKVDPSHDASKVKA   850
 851  EGPGLSKAGVENGKPTHFTVHTKGAGKAPLNVQFSSPLPGEAVKDLDIID   900
 901  NYDYSHTVKYTPTQQGNMQVLVTYGGDPIPKSPFTVGVAAPLDLSKIKIN   950
 951  GLENRVEVGKDQEFAIDTNGAGGQGKLDVTILSPSRKVVPCLVAPVAGRE  1000
1001  CSTAKFIPREEGLFAVDVTYDGHPVPGSPYTVEASLPPDPTKVKAHGPGL  1050
1051  EGGLVGKPAEFTIDTKGAGTGGLGLTVEGPCEAKIECSDNGDGTCSVSYL  1100
1101  PTKPGEYFVNILFEEVHIPGSPFKADIEMPFDPSKVVASGPGLEHGKVGE  1150
1151  PGILCVDCSEAGPGTLGLEAVSDSGAKAEVSIQNNKDGTYAVTYVPLTAG  1200
1201  MYTLTMKYGGELVPHFPAWVKVEPAIDTSGIKAFGPGIEGKDVFREATTD  1250
1251  FTVDSRPLTQVGGDHIKAQITNPSGASTECFVKDNADGTYQVEYTPFEKG  1300
1301  FHVVEVTYDDVPIPNSPFKVAVTEGCQPSRVHAQGPGLKEAFTNKSNVFT  1350
1351  VVTRGAGIGGLGITVEGPSESKINCRDNKDGSCSAEYIPFAPGDYDVNIT  1400
1401  YGGVHIPGSPFRVPSKDVVDPSKVKIAGPGLSSCVRACIPQSFTVDSSKA  1450
1451  GLAPLEVRVLGPRGLVEPVNVVDNGDGTHTVTYTPSQEGPYIVSVKYADE  1500
1501  EIPRSPFKVKVLPTYDASKVTASGPGLSAYGVPASLPVEFAIDARDAGEG  1550
1551  LLAVQITDQEGKPQRATVHDNKDGTYAVTYIPDKTGRYMIGVTYGGDNIP  1600
1601  LSPYRIRATQTGDASKCLATGPGIAPTVKTGEEVGFVVDAKTAGKGKVTC  1650
1651  VILTPDGTEAEADVIENEDGTYDIFYTAAKPGTYVIYVRFGGVDIPNSPF  1700
1701  TVMATDGEVTAMEEAPVNACPPGFRPWVTEEAYVPVSDMNGLGFKPFDLV  1750
1751  IPFAVRKGEITGTVHMPSGKKATPEIVDNKDGTVTVRYAPTEVGLHEMHI  1800
1801  KYRGSHIPESPLQFYVNYPNSGSVSAYGPGLVYGVANKTATFTIVTEDAG  1850
1851  EGGLDLAIEGPSKAEISCIDNKDGTCTVTYLPTLPGDYSILVKYNDKHIP  1900
1901  GSPFTAKITDDNRRCSQVKLGSAADFLLDISETDLSTLTASIKAPSGRDE  1950
1951  PCLLKRLPNNHIGISFIPREVGEHLVSIKKNGNHVANSPVSIMVVQSEIG  2000
2001  DARRAKVYGQGLSEGRTFEMSDFIVDTRDAGYGGISLAVEGPSKVDIQTE  2050
2051  DLEDGTCKVSYFPTVPGVYIVSTKFADEHVPGSPFTVKISGEGRVRESIT  2100
2101  RTSRAPAVATVGSICDLNLKIPEINSSDMSAHVTSPSGHVTEAEIVPMGK  2150
2151  NSHCVRFVPQEMGVHTVSVKYRGQHVTGSPFQFTVGPLGEGGAHKVRAGG  2200
2201  PGLERGEAGIPAEFSIWTREAGAGGLSIAVEGPSKAEITFDDHKNGSCGV  2250
2251  SYIAQEPGNYEVSIKFNDEHIPDSPYLVPVIAPSDDARCLTVLSLQESGL  2300
2301  KVNQPASFAIRLNGAKGKIDAKVHSPSGAVEECHVSELEPDKYAVRFIPH  2350
2351  ENGIHTIDVKFNGSHVVGSPFKVRVGEPGQAGNPALVSAYGAGLETGTTG  2400
2401  IQSEFFINTTQAGPGTLSVTIEGPSKVKMDCQEIPEGYKVMYTPMAPGNY  2450
2451  LIGVKYGGPNHISRSPFKAKVTGQRLVSPGSANETSSILVESVTRSSTET  2500
2501  CYSAIPKSSSDASKVTSKGAGLSKAFVGQKSSFLVDCSKAGSNMLLIGVH  2550
2551  GPTTPCEEVSMKHVGKQQYNVTYVVKERGDYVLAVKWGEEHIPGSPFHVT  2600
2601  VP                                                  2602

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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