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

NucPred

Fetching Q9NZM3 from www.uniprot.org...

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

   1  MMAQFPTAMNGGPNMWAITSEERTKHDRQFDNLKPSGGYITGDQARNFFL    50
  51  QSGLPAPVLAEIWALSDLNKDGKMDQQEFSIAMKLIKLKLQGQQLPVVLP   100
 101  PIMKQPPMFSPLISARFGMGSMPNLSIPQPLPPAAPITSLSSATSGTNLP   150
 151  PLMMPTPLVPSVSTSSLPNGTASLIQPLPIPYSSSTLPHGSSYSLMMGGF   200
 201  GGASIQKAQSLIDLGSSSSTSSTASLSGNSPKTGTSEWAVPQPTRLKYRQ   250
 251  KFNTLDKSMSGYLSGFQARNALLQSNLSQTQLATIWTLADVDGDGQLKAE   300
 301  EFILAMHLTDMAKAGQPLPLTLPPELVPPSFRGGKQIDSINGTLPSYQKM   350
 351  QEEEPQKKLPVTFEDKRKANYERGNMELEKRRQALMEQQQREAERKAQKE   400
 401  KEEWERKQRELQEQEWKKQLELEKRLEKQRELERQREEERRKDIERREAA   450
 451  KQELERQRRLEWERIRRQELLNQKNREQEEIVRLNSKKKNLHLELEALNG   500
 501  KHQQISGRLQDVRLKKQTQKTELEVLDKQCDLEIMEIKQLQQELQEYQNK   550
 551  LIYLVPEKQLLNERIKNMQFSNTPDSGVSLLHKKSLEKEELCQRLKEQLD   600
 601  ALEKETASKLSEMDSFNNQLKCGNMDDSVLQCLLSLLSCLNNLFLLLKEL   650
 651  RETYNTQQLALEQLYKIKRDKLKEIERKRLELMQKKKLEDEAARKAKQGK   700
 701  ENLWKENLRKEEEEKQKRLQEEKTQEKIQEEERKAEEKQRKDKDTLKAEE   750
 751  KKRETASVLVNYRALYPFEARNHDEMSFNSGDIIQVDEKTVGEPGWLYGS   800
 801  FQGNFGWFPCNYVEKMPSSENEKAVSPKKALLPPTVSLSATSTSSEPLSS   850
 851  NQPASVTDYQNVSFSNLTVNTSWQKKSAFTRTVSPGSVSPIHGQGQVVEN   900
 901  LKAQALCSWTAKKDNHLNFSKHDIITVLEQQENWWFGEVHGGRGWFPKSY   950
 951  VKIIPGSEVKREEPEALYAAVNKKPTSAAYSVGEEYIALYPYSSVEPGDL  1000
1001  TFTEGEEILVTQKDGEWWTGSIGDRSGIFPSNYVKPKDQESFGSASKSGA  1050
1051  SNKKPEIAQVTSAYVASGSEQLSLAPGQLILILKKNTSGWWQGELQARGK  1100
1101  KRQKGWFPASHVKLLGPSSERATPAFHPVCQVIAMYDYAANNEDELSFSK  1150
1151  GQLINVMNKDDPDWWQGEINGVTGLFPSNYVKMTTDSDPSQQWCADLQTL  1200
1201  DTMQPIERKRQGYIHELIQTEERYMADLQLVVEVFQKRMAESGFLTEGEM  1250
1251  ALIFVNWKELIMSNTKLLKALRVRKKTGGEKMPVQMIGDILAAELSHMQA  1300
1301  YIRFCSCQLNGAALLQQKTDEDTDFKEFLKKLASDPRCKGMPLSSFLLKP  1350
1351  MQRITRYPLLIRSILENTPESHADHSSLKLALERAEELCSQVNEGVREKE  1400
1401  NSDRLEWIQAHVQCEGLAEQLIFNSLTNCLGPRKLLHSGKLYKTKSNKEL  1450
1451  HGFLFNDFLLLTYMVKQFAVSSGSEKLFSSKSNAQFKMYKTPIFLNEVLV  1500
1501  KLPTDPSSDEPVFHISHIDRVYTLRTDNINERTAWVQKIKAASEQYIDTE  1550
1551  KKKREKAYQARSQKTSGIGRLMVHVIEATELKACKPNGKSNPYCEISMGS  1600
1601  QSYTTRTIQDTLNPKWNFNCQFFIKDLYQDVLCLTLFDRDQFSPDDFLGR  1650
1651  TEIPVAKIRTEQESKGPMTRRLLLHEVPTGEVWVRFDLQLFEQKTLL     1697

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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