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

NucPred

Fetching O70608 from www.uniprot.org...

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

   1  MPVRPDPQQLEKCIDDALRKNDFKPLVTLLQIDICEDVKIKCSKQFLRKL    50
  51  DDLICRELHKKDIQTISNILISIGRCSKNIFILGQTGLQTMIKQGLVQKM   100
 101  VSWFENSKEIILSQRQSKDEAVMNMIEDLFDLLMVVYDVNDEGKNQVLES   150
 151  FIPHICALVIDSRVNFCIQQEALKKMNLMLDRIPQDANKILCNQEILTLM   200
 201  SNMGERILDVGDYELQVGIVEALCRMTTEKRRQELAYEWFSMDFIANAFK   250
 251  KIKDCEFETDCRIFLNLVNGMLGDRRRVFTFPCLSAFLGKYELQIPSDEK   300
 301  LEEFWIDFNLGSHTLSFYIAGDDDDHQWEAVTVPEEKVDMYNIEVRESKK   350
 351  LLTLTLKNIVKISKKEGKELLLYFDAALEITNVTKKLFGGNKYKEFTRKQ   400
 401  DISVAKTSIHVLFDASGSQILVPESQPSPVKENLIHLKEKSNLQKKLTNP   450
 451  LEPDNSSSQRDRKNSQDEITTPSRKKMSEASMIVPDTDRYTVRSPILLIN   500
 501  TSTPRRSRAPLQAIHSAEKAVSKTSESGVDYAVSLKSRQSDGRNRGNNRA   550
 551  NHNKTATVQNKGHEHHESPDQTFNEIEETLSDAYAVEKVDKPVLPGVLDI   600
 601  SKNKAHSRWACWTPVTTIKLCNNQRSCALPGDTFTQDTGVNKKCTKQKSV   650
 651  SDDDSEETQRVKYSKDVIKCNKSEEAEVCERNIQEQNHPKYSQKKNTANA   700
 701  KKNDWHIESETTYKSVLLNKTTEESLIYKKTCVLSKDVNTTICDKSPSRK   750
 751  SMRSHTKSRKELMSEVTSCELDEIPVRENSKGKRFTGTAESLINLINKRY   800
 801  NSSDDMISTRKLKEPRDGSGFSKKPELQFNKVQRKSYRKLKTVVNVTSEC   850
 851  PLNDVYNFSLNGADEPVIKLGIQEFQATTREASMDNSIKLVDVRNRDERD   900
 901  LSLKTKDERILSHERKTLFSDTETECGWDDSKTDISWLRKPKSKRLMDYS   950
 951  RNKNTKKCKSIKSRSSTEKGQPRSTVVLSKNIAKNDYEVIVDGRTRLPRR  1000
1001  ATKTKKNYKDLSTSGSESESEKEISYLFKDKLPTKEETVHSSAQTKKLPK  1050
1051  KQQKVFNTEALKGQPSEEQKNSSTLRNGREDSLYLSSASVSGSSSSVEVM  1100
1101  RCTEKITERDFTQDYDYITKSLSPYPKAASPEFLNRSNRVVGHGKSPRIS  1150
1151  ETSAVCVRKSCSPASGLPFSPRHTTKNNSVMNIKNTNSVINNQRTQHCNS  1200
1201  YSDVSSNSSEKLYMEPESPDSCENHVQSKREENHAASPFSLSSEKIEKIW  1250
1251  FDMPNDNTHVSGPSQRGSKRRMYLEEDELSNPSEAEVQEAEEREHLVSKK  1300
1301  LCQREHFDQHTSETSLSTPEFSVPKDWQQELQGAGMFYDNINSDYKRKTD  1350
1351  TQHKIMDDFTTKTLKLTQQHLLAMACQARGHRDENIDKFQVTLLDELEKV  1400
1401  EKDSQTLRDLEKEFVDIEEKIVHKMRAFHQSERERFRALKTSLDKSLLVY  1450
1451  NSVYEENVLTSEMCLMKANMKMLQDKLLKEMHEEELLNIRRGLESLFKDH  1500
1501  EGNNA                                               1505

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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