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

NucPred

Fetching O88307 from www.uniprot.org...

The NucPred score for your sequence is 0.61 (see score help below)

   1  MATRSSRRESRLPFLFALVALLPRGALGGGWTQRLHGGPAPLPQDRGFFV    50
  51  VQGDPRDLRLGTHGDAPGASPAARKPLRTRRSAALQPQPIQVYGQVSLND   100
 101  SHNQMVVHWAGEKSNVIVALARDSLALARPKSSDVYVSYDYGKSFSKISE   150
 151  KLNFGVGNNSEAVISQFYHSPADNKRYIFVDAYAQYLWITFDFCSTIHGF   200
 201  SIPFRAADLLLHSKASNLLLGFDRSHPNKQLWKSDDFGQTWIMIQEHVKS   250
 251  FSWGIDPYDQPNAIYIERHEPFGFSTVLRSTDFFQSRENQEVILEEVRDF   300
 301  QLRDKYMFATKVVHLPGSQQQSSVQLWVSFGRKPMRAAQFVTKHPINEYY   350
 351  IADAAEDQVFVCVSHSNNSTNLYISEAEGLKFSLSLENVLYYSPGGAGSD   400
 401  TLVRYFANEPFADFHRVEGLQGVYIATLINGSMNEENMRSVITFDKGGTW   450
 451  EFLQAPAFTGYGEKINCELSQGCSLHLAQRLSQLLNLQLRRMPILSKESA   500
 501  PGLIIATGSVGKNLASKTNVYISSSAGARWREALPGPHYYTWGDHGGIIM   550
 551  AIAQGMETNELKYSTNEGETWKTFVFSEKPVFVYGLLTEPGEKSTVFTIF   600
 601  GSNKESVHSWLILQVNATDALGVPCTENDYKLWSPSDERGNECLLGHKTV   650
 651  FKRRTPHATCFNGEDFDRPVVVSNCSCTREDYECDFGFKMSEDLSLEVCV   700
 701  PDPEFSGKPYSPPVPCPVGSSYRRTRGYRKISGDTCSGGDVEARLEGELV   750
 751  PCPLAEENEFILYAMRKSIYRYDLASGATEQLPLSGLRAAVALDFDYERN   800
 801  CLYWSDLALDTIQRLCLNGSTGQEVIINSGLETVEALAFEPLSQLLYWVD   850
 851  AGFKKIEVANPDGDFRLTIVNSSVLDRPRALVLVPQEGVMFWTDWGDLKP   900
 901  GIYRSYMDGSAAYRLVSEDVKWPNGISVDSQWIYWTDAYLDCIERITFSG   950
 951  QQRSVILDSLPHPYAIAVFKNEIYWDDWSQLSIFRASKHSRSQVEILASQ  1000
1001  LTGLMDMKVFYKGKNAGSNACVPQPCSLLCLPKANNSKSCRCPEGVASSV  1050
1051  LPSGDLMCDCPQGYQRKNNTCVKEENTCLRNQYRCSNGNCINSIWWCDFD  1100
1101  NDCGDMSDERNCPTTVCDADTQFRCQESGTCIPLSYKCDLEDDCGDNSDE  1150
1151  SHCEMHQCRSDEFNCSSGMCIRSSWVCDGDNDCRDWSDEANCTAIYHTCE  1200
1201  ASNFQCHNGHCIPQRWACDGDADCQDGSDEDPVSCEKKCNGFHCPNGTCI  1250
1251  PSSKHCDGLRDCPDGSDEQHCEPFCTRFMDFVCKNRQQCLFHSMVCDGIV  1300
1301  QCRDGSDEDAAFAGCSQDPEFHKECDEFGFQCQNGVCISLIWKCDGMDDC  1350
1351  GDYSDEANCENPTEAPNCSRYFQFHCENGHCIPNRWKCDRENDCGDWSDE  1400
1401  KDCGDSHVLPSPTPGPSTCLPNYFHCSSGACVMGTWVCDGYRDCADGSDE  1450
1451  EACPSLANSTAASTPTQFGQCDRFEFECHQPKKCIPNWKRCDGHQDCQDG  1500
1501  QDEANCPTHSTLTCTSREFKCEDGEACIVLSERCDGFLDCSDESDEKACS  1550
1551  DELTVYKVQNLQWTADFSGDVTLTWMRPKKMPSASCVYNVYYRVVGESIW  1600
1601  KTLETHSNKTSTVLKVLKPDTTYQVKVQVHCLNKVHNTNDFVTLRTPEGL  1650
1651  PDAPRNLQLSLNSEEEGVILGHWAPPVHTHGLIREYIVEYSRSGSKMWAS  1700
1701  QRAASNSTEIKNLLLNALYTVRVAAVTSRGIGNWSDSKSITTIKGKVIQA  1750
1751  PNIHIDSYDENSLSFTLTMDGDIKVNGYVVNLFWSFDAHKQEKKTLSFRG  1800
1801  GSALSHRVSNLTAHTSYEISAWAKTDLGDSPLAFEHILTRGSSPPAPSLK  1850
1851  AKAINQTAVECIWTGPKNVVYGIFYATSFLDLYRNPKSVTTSLHNKTVIV  1900
1901  SKDEQYLFLVRVLIPYQGPSSDYVVVKMIPDSRLPPRHLHAVHIGKTSAL  1950
1951  IKWESPYDSPDQDLFYAIAVKDLIRKTDRSYKVRSRNSTVEYSLSKLEPG  2000
2001  GKYHIIVQLGNMSKDSSIKITTVSLSAPDALKIITENDHVLLFWKSLALK  2050
2051  EKQFNETRGYEIHMSDSAVNLTAYLGNTTDNFFKVSNLKMGHNYTFTVQA  2100
2101  RCLFGSQICGEPAVLLYDELSSGADAAVIQAARSTDVAAVVVPILFLILL  2150
2151  SLGVGFAILYTKHRRLQSSFSAFANSHYSSRLGSAIFSSGDDLGEDDEDA  2200
2201  PMITGFSDDVPMVIA                                     2215

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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