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

NucPred

Fetching Q9V726 from www.uniprot.org...

The NucPred score for your sequence is 0.33 (see score help below)

   1  MFSMCKQTHSATAVEFSIACRFFNNLDENLVVAGANVLKVYRIAPNVEAS    50
  51  QRQKLNPSEMRLAPKMRLECLATYTLYGNVMSLQCVSLAGAMRDALLISF   100
 101  KDAKLSVLQHDPDTFALKTLSLHYFEEDDIRGGWTGRYFVPTVRVDPDSR   150
 151  CAVMLVYGKRLVVLPFRKDNSLDEIELADVKPIKKAPTAMVSRTPIMASY   200
 201  LIALRDLDEKIDNVLDIQFLHGYYEPTLLILYEPVRTCPGRIKVRSDTCV   250
 251  LVAISLNIQQRVHPIIWTVNSLPFDCLQVYPIQKPIGGCLVMTVNAVIYL   300
 301  NQSVPPYGVSLNSSADNSTAFPLKPQDGVRISLDCANFAFIDVDKLVISL   350
 351  RTGDLYVLTLCVDSMRTVRNFHFHKAAASVLTSCICVLHSEYIFLGSRLG   400
 401  NSLLLHFTEEDQSTVITLDEVEQQSEQQQRNLQDEDQNLEEIFDVDQLEM   450
 451  APTQAKSRRIEDEELEVYGSGAKASVLQLRKFIFEVCDSLMNVAPINYMC   500
 501  AGERVEFEEDGVTLRPHAESLQDLKIELVAATGHSKNGALSVFVNCINPQ   550
 551  IITSFELDGCLDVWTVFDDATKKSSRNDQHDFMLLSQRNSTLVLQTGQEI   600
 601  NEIENTGFTVNQPTIFVGNLGQQRFIVQVTTRHVRLLQGTRLIQNVPIDV   650
 651  GSPVVQVSIADPYVCLRVLNGQVITLALRETRGTPRLAINKHTISSSPAV   700
 701  VAISAYKDLSGLFTVKGDDINLTGSSNSAFGHSFGGYMKAEPNMKVEDEE   750
 751  DLLYGDAGSAFKMNSMADLAKQSKQKNSDWWRRLLVQAKPSYWLVVARQS   800
 801  GTLEIYSMPDMKLVYLVNDVGNGSMVLTDAMEFVPISLTTQENSKAGIVQ   850
 851  ACMPQHANSPLPLELSVIGLGLNGERPLLLVRTRVELLIYQVFRYPKGHL   900
 901  KIRFRKMDQLNLLDQQPTHIDLDENDEQEEIESYQMQPKYVQKLRPFANV   950
 951  GGLSGVMVCGVNPCFVFLTFRGELRIHRLLGNGDVRSFAAFNNVNIPNGF  1000
1001  LYFDTTYELKISVLPSYLSYDSVWPVRKVPLRCTPRQLVYHRENRVYCLI  1050
1051  TQTEEPMTKYYRFNGEDKELSEESRGERFIYPIGSQFEMVLISPETWEIV  1100
1101  PDASITFEPWEHVTAFKIVKLSYEGTRSGLKEYLCIGTNFNYSEDITSRG  1150
1151  NIHIYDIIEVVPEPGKPMTKFKIKEIFKKEQKGPVSAISDVLGFLVTGLG  1200
1201  QKIYIWQLRDGDLIGVAFIDTNIYVHQIITVKSLIFIADVYKSISLLRFQ  1250
1251  EEYRTLSLASRDFNPLEVYGIEFMVDNSNLGFLVTDAERNIIVYMYQPEA  1300
1301  RESLGGQKLLRKADYHLGQVVNTMFRVQCHQKGLHQRQPFLYENKHFVVY  1350
1351  GTLDGALGYCLPLPEKVYRRFLMLQNVLLSYQEHLCGLNPKEYRTLKSSK  1400
1401  KQGINPSRCIIDGDLIWSYRLMANSERNEVAKKIGTRTEEILGDLLEIER  1450
1451  LASVF                                               1455

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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