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

NucPred

Fetching Q9FHA3 from www.uniprot.org...

The NucPred score for your sequence is 0.93 (see score help below)

   1  MSGDNSTETGRRRSRGAEASSRKDTLERLKAIRQGGIRSASGGGYDIRLQ    50
  51  KPIFDTVDDEEYDALVSRRREEARGFVVEDGEGGDLGYLDEGEEEDWSKP   100
 101  SGPESTDESDDGGRFSGRLKKKKKGKEQTQQPQVKKVNPALKAAATITGE   150
 151  GRLSSMFTSSSFKKVKETDKAQYEGILDEIIAQVTPDESDRKKHTRRKLP   200
 201  GTVPVTIFKNKKLFSVASSMGMKESEPTPSTYEGDSVSMDNELMKEEDMK   250
 251  ESEVIPSETMELLGSDIVKEDGSNKIRKTEVKSELGVKEVFTLNATIDMK   300
 301  EKDSALSATAGWKEAMGKVGTENGALLGSSSEGKTEFDLDADGSLRFFIL   350
 351  DAYEEAFGASMGTIYLFGKVKMGDTYKSCCVVVKNIQRCVYAIPNDSIFP   400
 401  SHELIMLEQEVKDSRLSPESFRGKLHEMASKLKNEIAQELLQLNVSNFSM   450
 451  APVKRNYAFERPDVPAGEQYVLKINYSFKDRPLPEDLKGESFSALLGSHT   500
 501  SALEHFILKRKIMGPCWLKISSFSTCSPSEGVSWCKFEVTVQSPKDITIL   550
 551  VSEEKVVHPPAVVTAINLKTIVNEKQNISEIVSASVLCFHNAKIDVPMPA   600
 601  PERKRSGILSHFTVVRNPEGTGYPIGWKKEVSDRNSKNGCNVLSIENSER   650
 651  ALLNRLFLELNKLDSDILVGHNISGFDLDVLLQRAQACKVQSSMWSKIGR   700
 701  LKRSFMPKLKGNSNYGSGATPGLMSCIAGRLLCDTDLCSRDLLKEVSYSL   750
 751  TDLSKTQLNRDRKEIAPNDIPKMFQSSKTLVELIECGETDAWLSMELMFH   800
 801  LSVLPLTLQLTNISGNLWGKTLQGARAQRIEYYLLHTFHSKKFILPDKIS   850
 851  QRMKEIKSSKRRMDYAPEDRNVDELDADLTLENDPSKGSKTKKGPAYAGG   900
 901  LVLEPKRGLYDKYVLLLDFNSLYPSIIQEYNICFTTIPRSEDGVPRLPSS   950
 951  QTPGILPKLMEHLVSIRKSVKLKMKKETGLKYWELDIRQQALKLTANSMY  1000
1001  GCLGFSNSRFYAKPLAELITLQGRDILQRTVDLVQNHLNLEVIYGDTDSI  1050
1051  MIHSGLDDIEEVKAIKSKVIQEVNKKYRCLKIDCDGIYKRMLLLRKKKYA  1100
1101  AVKLQFKDGKPCEDIERKGVDMVRRDWSLLSKEIGDLCLSKILYGGSCED  1150
1151  VVEAIHNELMKIKEEMRNGQVALEKYVITKTLTKPPAAYPDSKSQPHVQV  1200
1201  ALRMRQRGYKEGFNAKDTVPYIICYEQGNASSASSAGIAERARHPDEVKS  1250
1251  EGSRWLVDIDYYLAQQIHPVVSRLCAEIQGTSPERLAECLGLDPSKYRSK  1300
1301  SNDATSSDPSTSLLFATSDEERYKSCEPLALTCPSCSTAFNCPSIISSVC  1350
1351  ASISKKPATPETEESDSTFWLKLHCPKCQQEDSTGIISPAMIANQVKRQI  1400
1401  DGFVSMYYKGIMVCEDESCKHTTRSPNFRLLGERERGTVCPNYPNCNGTL  1450
1451  LRKYTEADLYKQLSYFCHILDTQCSLEKMDVGVRIQVEKAMTKIRPAVKS  1500
1501  AAAITRSSRDRCAYGWMQLTDIVI                            1524

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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