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

NucPred

Fetching Q6CUS7 from www.uniprot.org...

The NucPred score for your sequence is 0.92 (see score help below)

   1  MSAFKGSTTAKFVGRGNEYPTQANSFAQVAQQLLNSKKVDEIDEMMGFPR    50
  51  FIPSPALSDSKVGWLSNMHPTIISQEMLEEEGNLHSATVSGISGVDFYFI   100
 101  DEEGGSFKTTVTYDPYFFVSCTDETRIHDIEEYLKKTLEQCIKKVELVLK   150
 151  DDLAMNNHLVGLKKHLIKLSFSNSNQLFEARRILRPILKINEDENGKKDI   200
 201  YNTGSDYSTRDVKTLIEDIREYDVPYHVRVSIDKNIRVGKWYAVSAQGLV   250
 251  ELEEKVTFADPVVLAFDIETTKAPLKFPDSAIDQIMMISYMIDGEGFLIT   300
 301  NREIISEDIEDFEYTPKDEYKGQFAIFNEPDEMALLQRFFEHIRDVRPTV   350
 351  ISTFNGDFFDWPFVENRAKFHGLNMFDEIGFAPDSEGEYKSSYCTHMDCF   400
 401  RWVKRDSYLPQGSQGLKAVTQAKLGYNPLELDPELMTPYAYEKPQILSEY   450
 451  SVSDAVATYYLYMKYVHPFIFSLCTIIPLNPDEVLRKGTGTLCEMLLMVQ   500
 501  AYQNSVLLPNKHTDPIERFYDGHLLESETYVGGHVESLEAGVFRSDLKND   550
 551  FKIDPTVIDILLEDLPYALKFCIEVENNGNMEDVTNFEEIKQQITAQLTD   600
 601  LKINNKRNELPLIYHVDVASMYPNIMTTNRLQPDSMKDEKDCASCDFNRP   650
 651  GKSCDRRLKWAWRGEFFPAKMDEYGMVKRALQNELFPNKNPKSKKQFLTF   700
 701  EELSYSDQVSHIKKRLTDYSRKVYHRVKVTETVEREAIVCQRENPFYVNT   750
 751  VRSFRDRRYEFKGLAKLWKGKLSKIKPDDVHSKDEAKKMIVLYDSLQLAH   800
 801  KVILNSFYGYVMRKGSRWYSMEMAGITCLTGANIIQMARSVVERIGRPLE   850
 851  LDTDGIWCILPKSFPENFEIKLRNGKKLFLSYPCSMLNYKVHQKYTNHQY   900
 901  QDLVDPMKFKYQTKSDNSIFFEVDGPYKAMILPTSKEEGKGIKKRYAVFN   950
 951  EDGSLAELKGFELKRRGELQLIKNFQSDIFKLFLEGTTLESCYAAVATVA  1000
1001  NRWLDVLDSKGAMLETEDLIELICENKSMSKTLKEYQGQKSTSITTARRL  1050
1051  GEFLGEAMVKDAGLQCKFIISSKPHNAPVTERAIPVAIFSSDLHVKRTFL  1100
1101  RRWLLDSSLNDFDPRAIIDWDYYRERLASVVQKIITIPAALQNIKNPVPR  1150
1151  VEHPDWLRKKIAVSEDKFKQTSLNRFFKSTKAPPEVKDIEDSFDEHSANK  1200
1201  SRIAKVTYKRKSKRRNGDTALEEESLLLPSEMPPMLDDYVGWLQYQKTKW  1250
1251  KIQHIDRKKREKLFGKTSRASDRSALGNLIRKHVESYADKSWEILQCKPS  1300
1301  IDLGVVEIYALIDRKIQLLKVNIPKTVLMNFKTENFPSGGIENCIVEKSN  1350
1351  AELPNVKGINNESSSQLFKLTMSEDTYFNEVNKASSVLNNENVLGIYESS  1400
1401  ISSNERVIMRLGTCIQFSSEKMGALGKGLQNGFHMKNLHPVEADRYLQRF  1450
1451  DLDIAYLLHFVTDIGYEFYFLYKAWEDVVEIFVLKPSTHAQEVSNKAIES  1500
1501  LYNEIYEKKFEKLDKYYDLIKINKNVSFNVNDYTELKRLLKDLSKMLQNI  1550
1551  KEEKGSHTMVILQSPYTHRVAKLLQPLNAFPVVEIATAETHLPALNWQGQ  1600
1601  LMRKAVNHILSLGSWISNLITLSKYSNIPICNLKVDNLGYIIDLMYARQL  1650
1651  KKNNIVLWWNDKSPLPDHGGVERDFDPRKAELMTDLVFPIMNNPDIYDDV  1700
1701  IFEISVYNSVVNTVLSSTMLNEAEGTDLAQNSTSKEESFGFVEDSFSSSA  1750
1751  LSVLRALLKELWDDALGDNITADSLVHAFIGWVYNPDAKLFDYALRYHIH  1800
1801  TLTQKAVLQLINEFKLAGSSLIFADRNKLLIKTQKRSVENSYAYGQYLMK  1850
1851  AIRSKPMFAYLDLKIDRYWDVLIWMDKYNYGGRACLQIEDKEVQSFQAYS  1900
1901  HWHIKDFLPAIYQQEFDDWLVVILDSMVKTKEAYHERNASTQRLTQLPKN  1950
1951  TLADSDVDSQTDSLGGFTHNFSKALIKRAEKLYKNQQEYILDPNFGKDYL  2000
2001  SPTIPGSHLVVKNPLLELVKYLSHILSLSSNHLLEGRALRKELLKTFEIR  2050
2051  EFDRLAEFKDPSTSFVIPSFICEHCSYISDIDICRESMERVFICQSCNRS  2100
2101  LNKNLIEEHVIERLQAQVASFITQDVKCNKCHKIKEDAMSPYCPCSGKWE  2150
2151  LAVSKESFMAQLQIFKNLAESFDFRTLKETLNDFL                 2185

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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