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

NucPred

Fetching P09208 from www.uniprot.org...

The NucPred score for your sequence is 0.99 (see score help below)

   1  MFNMPRGVTKSKSKRGKIKMENDMAAAATTTACTLGHICVLCRQEMLLDT    50
  51  CCCRQAVEAVDSPASSEEAYSSSNSSSCQASSEISAEEVWFLSHDDIVLC   100
 101  RRPKFDEVETTGKKRDVKCSGHQCSNECDDGSTKNNRQQRENFNIFSNCH   150
 151  NILRTLQSLLLLMFNCGIFNKRRRRQHQQQHHHHYQHHHQQHHQQHHQRQ   200
 201  QANVSYTKFLLLLQTLAAATTRLSLSPKNYKQQQQLQHNQQLPRATPQQK   250
 251  QQEKDRHKCFHYKHNYSYSPGISLLLFILLANTLAIQAVVLPAHQQHLLH   300
 301  NDIADGLDKTALSVSGTQSRWTRSESNPTMRLSQNVKPCKSMDIRNMVSH   350
 351  FNQLENCTVIEGFLLIDLINDASPLNRSFPKLTEVTDYIIIYRVTGLHSL   400
 401  SKIFPNLSVIRGNKLFDGYALVVYSNFDLMDLGLHKLRSITRGGVRIEKN   450
 451  HKLCYDRTIDWLEILAENETQLVVLTENGKEKECRLSKCPGEIRIEEGHD   500
 501  TTAIEGELNASCQLHNNRRLCWNSKLCQTKCPEKCRNNCIDEHTCCSQDC   550
 551  LGGCVIDKNGNESCISCRNVSFNNICMDSCPKGYYQFDSRCVTANECITL   600
 601  TKFETNSVYSGIPYNGQCITHCPTGYQKSENKRMCEPCPGGKCDKECSSG   650
 651  LIDSLERAREFHGCTIITGTEPLTISIKRESGAHVMDELKYGLAAVHKIQ   700
 701  SSLMVHLTYGLKSLKFFQSLTEISGDPPMDADKYALYVLDNRDLDELWGP   750
 751  NQTVFIRKGGVFFHFNPKLCVSTINQLLPMLASKPKFFEKSDVGADSNGN   800
 801  RGSCGTAVLNVTLQSVGANSAMLNVTTKVEIGEPQKPSNATIVFKDPRAF   850
 851  IGFVFYHMIDPYGNSTKSSDDPCDDRWKVSSPEKSGVMVLSNLIPYTNYS   900
 901  YYVRTMAISSELTNAESDVKNFRTNPGRPSKVTEVVATAISDSKINVTWS   950
 951  YLDKPYGVLTRYFIKAKLINRPTRNNNRDYCTEPLVKAMENDLPATTPTK  1000
1001  KISDPLAGDCKCVEGSKKTSSQEYDDRKVQAGMEFENALQNFIFVPNIRK  1050
1051  SKNGSSDKSDGAEGAALDSNAIPNGGATNPSRRRRDVALEPELDDVEGSV  1100
1101  LLRHVRSITDDTDAFFEKDDENTYKDEEDLSSNKQFYEVFAKELPPNQTH  1150
1151  FVFEKLRHFTRYAIFVVACREEIPSEKLRDTSFKKSLCSDYDTVFQTTKR  1200
1201  KKFADIVMDLKVDLEHANNTESPVRVRWTPPVDPNGEIVTYEVAYKLQKP  1250
1251  DQVEEKKCIPAADFNQTAGYLIKLNEGLYSFRVRANSIAGYGDFTEVEHI  1300
1301  KVEPPPSYAKVFFWLLGIGLAFLIVSLFGYVCYLHKRKVPSNDLHMNTEV  1350
1351  NPFYASMQYIPDDWEVLRENIIQLAPLGQGSFGMVYEGILKSFPPNGVDR  1400
1401  ECAIKTVNENATDRERTNFLSEASVMKEFDTYHVVRLLGVCSRGQPALVV  1450
1451  MELMKKGDLKSYLRAHRPEERDEAMMTYLNRIGVTGNVQPPTYGRIYQMA  1500
1501  IEIADGMAYLAAKKFVHRDLAARNCMVADDLTVKIGDFGMTRDIYETDYY  1550
1551  RKGTKGLLPVRWMPPESLRDGVYSSASDVFSFGVVLWEMATLAAQPYQGL  1600
1601  SNEQVLRYVIDGGVMERPENCPDFLHKLMQRCWHHRSSARPSFLDIIAYL  1650
1651  EPQCPNSQFKEVSFYHSEAGLQHREKERKERNQLDAFAAVPLDQDLQDRE  1700
1701  QQEDATTPLRMGDYQQNSSLDQPPESPIAMVDDQGSHLPFSLPSGFIASS  1750
1751  TPDGQTVMATAFQNIPAAQGDISATYVVPDADALDGDRGYEIYDPSPKCA  1800
1801  ELPTSRSGSTGGGKLSGEQHLLPRKGRQPTIMSSSMPDDVIGGSSLQPST  1850
1851  ASAGSSNASSHTGRPSLKKTVADSVRNKANFINRHLFNHKRTGSNASHKS  1900
1901  NASNAPSTSSNTNLTSHPVAMGNLGTIESGGSGSAGSYTGTPRFYTPSAT  1950
1951  PGGGSGMAISDNPNYRLLDESIASEQATILTTSSPNPNYEMMHPPTSLVS  2000
2001  TNPNYMPMNETPVQMAGVTISHNPNYQPMQAPLNARQSQSSSDEDNEQEE  2050
2051  DDEDEDDDVDDEHVEHIKMERMPLSRPRQRALPSKTQPPRSRSVSQTRKS  2100
2101  PTNPNSGIGATGAGNRSNLLKENWLRPASTPRPPPPNGFIGREA        2144

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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