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

NucPred

Fetching Q4WXH8 from www.uniprot.org...

The NucPred score for your sequence is 0.81 (see score help below)

   1  MPTRQPSKYGNKFRSSSASFKPKRTKTVEFSSLRSTEATSQDEKFEAIRL    50
  51  ANSIDEALGFPRFESGEKRVGWLINMHSTSIEDPNVPGGRAGVDYYFLED   100
 101  GGGSFKATVEYDPYFLLAVKKGHEAEVEEWCRRMFEGLIKTIKRVEKEDL   150
 151  QLPNHLLGHRRTFLQLNFANVSHLLDVRKTLLPLAEKNKKNVNVMDTYAE   200
 201  ISSANAGFDLFDDELINESRPNSNMNASDYIIDIREYDVPYHVRVAIDKD   250
 251  IRIGKWYTVEAKHGVISLTCLEERLQRADPVILAFDIETTKLPLKFPDSV   300
 301  IDQIMMISYMIDGQGFLITNREIVSEDIRDFEYTPKPEYSGPFMIFNEPN   350
 351  ERSVIERFFEHIKEAKPTVIATYNGDFFDWPFVEARASVLGIDMYKEIGF   400
 401  RKNSEDIYQSDHCVHMDCFAWVNRDSYLPQGSRGLKAVTVAKLGYDPDEL   450
 451  DPELMTPYASERPQTLAEYSVSDAVATYYLYMKYVHPFIFSLCTIIPLNP   500
 501  DDTLRKGTGTLCEMLLMVQAYKGEIVLPNKHKDPPESFYEGHLLESETYV   550
 551  GGHVESIEAGVFRSDIPVTFNIDTTAIDELLRDLDAALKFSIEVEEKKSM   600
 601  DDVVNYEDVKAQIAERLVNLREKPHRDEVPSIYHLDVASMYPNIMITNRL   650
 651  QPDSMIQESDCAACDFNRPGKTCDRRLPWAWRGEFLPAKRDEYNMIRQAV   700
 701  ANELFPGRTKNSPMRSFGEMSAEEQAAIIKKRLQDYSKKIYHKIHDSKTI   750
 751  VREAIICQRENPFYVDTVRSFRDRRYDFKGKQKVWKGKTEALKAAGASAA   800
 801  EIEEAKKMIVLFDSLQLAHKVILNSFYGYVMRKGSRWYSMEMAGVTCLTG   850
 851  AHIIQMARELVERIGRPLELDTDGIWCMLPGSFPEDFSFTLKNGKKLGIS   900
 901  YPCVMLNHLVHGKYTNHQYQTLVDPKTFRYETHSDNSIFFEVDGPYKAMI   950
 951  LPTSKEEDKNLKKRYAVFNHDGSLAELKGFEVKRRGELKLIKIFQTQIFR  1000
1001  FFLEGSTLEETYAAVARVADRWLDVLYDHGATLADEELIELISENRSMTK  1050
1051  TLEEYGNQKSTSITTARRLAEFLGEQMVKDKGLNCKYIISAKPKNTPVTE  1100
1101  RAIPVTIFSAEEPVKRFFLRKWLKDDPGDMDPRSVIDWDYYLERLGSVVQ  1150
1151  KLITIPAALQKVRNPVPRVAHPDWLQRRINMKEDKFKQTKMTDMFGKTEK  1200
1201  NPLSNISTNILDHRVQHHGDIGEAVANSTQKLKSSPNGKISQKRKHPEGL  1250
1251  TKTLLDPFASLPAIMPSLNDDYVGFLKYQKQKWKIQKQARARRRQLFGER  1300
1301  VNVATDSLSNLFRNQAELLYINTWQILQLCETGRPGLVRAFVLIDRKIHA  1350
1351  LTIKVPRQIYVNLKRDSLPDVDVPDCEVEKVNHTLPNGHPSVHLFKLTLS  1400
1401  EDTYLRETDKIDALLQHPSIEGVYEKNIPLSVRAVLKLGSVCTFDEEQRG  1450
1451  VLGEGLDRGFNLSTLCHTTPDEPYLLNSPLVYHYLYHVLSGDRQIFALFS  1500
1501  TTKSEAHIVILNRTRDVQGLPNVDKIYAELRARTMENMGGDQSQNAFEYQ  1550
1551  EKIHFKTTQVTTRRKAYLEIGDLIKKLKGEETQPVIMVIQSHQRHRLCHD  1600
1601  IPILKEYPVLPVKPEVSDMDLPPLGWQSFIAKRLVTHYLYLASWIHHLTM  1650
1651  LARYGDVPLCNLENDDPRYLIDISYARRLQQNNVVLWWSNGPRPDHAGYE  1700
1701  KDDVTGSLERVSMPSVNVPSAYNTVCIELEVRNLSINTILTSSIINELEG  1750
1751  ADTLLASSEPSADANGSGVLYSEKAFASAGAVVLREMVKHWWSEACEGNN  1800
1801  MADIMVQHLIRWVESPVSCLYDRSLHDYVRMLSRKSFQRLMAEFRRVGSN  1850
1851  VIFASPTRLLLQTTKTEVGNAYAYSQYVLKSIRANASFHFIDLEIKEYWD  1900
1901  YLVWYDEYNYGGKGCRKVTGSEDQELETVMHWQLSRFLPAPMQTIFHDWV  1950
1951  VEYIELMHGLKRTDSDDSSTPRLTQLPVGNHNEDNDEITSILAEKFSKPL  2000
2001  KKQISGLIRRQRDELLHPELASDYVFPVLPGVLVDPNNDKRNPVLELVKL  2050
2051  LMQVLSLSKTTTLETRLLRRELLAMFEVREFSKEGRFENPGASLKLPELS  2100
2101  CNACCLIRDLDLCRDEDVLPEMGSDPNKAAPKPWRCPFCQTEYDRLAQEE  2150
2151  ALIGQVQGLIVGWQTQDLKCSKCGGLKISDFMEHCSCSGHWVETMDRNEV  2200
2201  EKKLLLLSSVSKFHGLKLLESVVQGVLEQM                      2230

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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