 | Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden. |
NucPred
Fetching P54696 from www.uniprot.org...
The NucPred score for your sequence is 0.86 (see score help below)
1 MMIDNNCGKEKVWVPNPEKGWINGDLIKEIPGEGWLVRDENGKEIKIEKD 50
51 ELRMQNPVIQEGIDDMTSLSHLHEAAVIHNLIKRYEINSIYTYTGSILIA 100
101 INPYTKLPIYSKEMIESFCDQPVSKLAPHVYSIAESAYREMLNFQKNQSI 150
151 LVSGESGAGKTETTKFLLQYFAAMGEKGNGVNTSLISEEDIVEGNNIETQ 200
201 VIKSTPILEAFGNSKTLRNDNSSRFGKFIEIHFDKIKGTIVGAKLETYLL 250
251 EKSRIVKPPENERGYHIFYQLIKGFNNSCCLKNSSNNNKDEDSSSSSNNN 300
301 IDDLKSLLKCKASDFNYLISSGCDSIDGVDDSQVFIKTENALKVMGLSND 350
351 ELIGIYKILLSILHIGNIEFEKGKEEDSSIIKYGNSSFGESFSDDDAGGY 400
401 NPLEISCKLLGCSVDSLKSTFCSRKMKAGNESYTINHTVEQASQARDSLS 450
451 MFLYSRLFDWLVVRINQSIDKIGTEKKDNSFLFIGILDIYGFESFESNSY 500
501 EQFTINYANEKLQNQFNHQIFKLEQLEYEKEKIDWSYIEFSDNQECIDLI 550
551 EKKPLGILSILDEESQFPKSTPSTLCTKLYNNHSKSKNFEKPRFSQTHFI 600
601 IDHYAGKVEYDTNLFLEKNKDFIISEQVSALESSNWKFLTNLFQILSKKM 650
651 NGGGGTSGGGGAGGNKASSSAAGKSTFKFTSVSSQFKESLNSLMTTINST 700
701 NPHYIRCIKPNTEKRANLFDNVMVLHQLRCSGVIEQLRISRSGYPSRLVY 750
751 DNFIKRYKLIVAKDFKNDDDSNESKEWNSILKETDLNSSNGGTNNQIELK 800
801 RKGAELMINKLSIDISSVQFGLTKLFFKSGIIANLELLRSQTMINSATFI 850
851 QKIWRGYTDRKAYTSTKHSSIYFQSLIRSYLQQLEYNSMVEENSAIHLQS 900
901 LIRTNELEKQFNQLLSTTIHFQSLLRRLEDSKEFNTLMDRIKKIVKIQSL 950
951 WRSNLAKKQLKLLKAEAKSLTNVVAEKNKLASKLGDIQSKLDMESQLAQK 1000
1001 IKNENEQLSSQFSNIQIEKEKLQKDFGNINLEKEELLLKYSALESEYHQY 1050
1051 KQQNELIISKLKQHINDLEEKQHQHSYKNNEVVGNTSFEGSTTTNNGVTS 1100
1101 PPKSSPASPIRNSINSNSDTTISGSSDDSIDNTDSLILSPKQHKGEDRKR 1150
1151 NHEISSISPPRSRETIGHDDDDNNVDVIPRRQFNELEKEYKELKQMDETH 1200
1201 KQYIESLKLQITQLEEKVKKSSSHPRSLLPGIPSNINDSPKVVYTKSSIT 1250
1251 NDNSSSHHQQQQQQHNISPSNSITSTTSPINMMDSNIKSLSYKDFTNSQE 1300
1301 IDAQQQLHQYHLNNGTNPATSTTNGSGNPLSQSSPTGSDKHIQQSTISDL 1350
1351 VSALNFNNCQLESGKYLVDLIIKNHDSIVSKYVPSEMGGIPEPAFILSRC 1400
1401 FLKNIYDVDATVIGTPNSTNSGGGSGTGVLDPIETNVNILIYFCDKVEEV 1450
1451 IYRDPKSNCSALCYWFSNFYTLFNIMETYNQDTKDQLSLNDQDKALIEKL 1500
1501 KITLQTMIVKAHKNVVKNITDYIQPILHKSLNDTTSEIDFMDPITNYLNQ 1550
1551 IQISLSLENCYINNNLCKLLFEQLFSFINAMIFNEILLRKDLCCLRSSIP 1600
1601 IKMNISELEHWVKLHHGKEWSSSVCDKLRLLKEVVYILMIDKTQLQNDEL 1650
1651 RDEICPTLSIAQLKQLLTMYSPDVDSFEDPIPLEILTSLMDSPKYNPDEN 1700
1701 ILLDLSKIFTLKFINSNQTLSSSTSSENDLMATINLNALESVQYACDDLV 1750
1751 SNIVKKNIEIVSLNNQKSIKK 1771
Positively and negatively influencing subsequences are coloured according to the following scale:
(non-nuclear) negative ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| positive (nuclear)
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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