| Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden. |
NucPred
Fetching Q4IAK7 from www.uniprot.org...
The NucPred score for your sequence is 0.99 (see score help below)
1 MPETASTANVLPKSDPDAIKTEQDALEGYENGGDALQGTMDGHVETNGDA 50
51 PATENHHEPNHIHDDERPAKRRRTRDSTPPQNTPKKMKPVSPPWKKISAD 100
101 GPTSYTENGRRKSGRINTLLPEPSPLSKSRTSKRSTGANSNTKTEIHLTN 150
151 GNSRKMPNGSHKASPATKAPSKQAPASTPKSASKKPTETRTSSRSTRRRS 200
201 PTPPPPPKNSTRSRRSARFSDAVIKDEAVQDSRTATSNSTNRSPRIKLRV 250
251 GRSGHIPLVHPGQVRKRPKIGTSFEDFWTRAGDIPVEEGGLQASEDGPQY 300
301 TDELAERDARVILRVEKEVEDGGMLSQGRCSIFLPEPAEEPPRQWARQDH 350
351 MVKAMTNFRKLMLAEQQRHRIAAKKVAEACRDEWLRRQPKSEEEIEAEQR 400
401 AVWISRYRIVAKTLFGTWENVRTEVNRRRLAEWEQEEQRRVKAALNEAVN 450
451 LSEQKLQARQAGLDSEQLSEEDGFDDLSDDMSMADDDELGLASGEDEDDE 500
501 DGDADSDIMSSDEEEGDEEDQKDIGDENLTQEQLRAKYAHIPELEKPSTE 550
551 TPVTEPTPKDTDAVDTAQATATENAETSDESVDMDDDMGSTDMDSDEEDE 600
601 EEESEEESDEDAGGLLGLLFGKSELKKMNSEAVAETPADSKEDSEMPDVE 650
651 AVSDGEGAEENEMSLIQMPDPEPHESGALEKSTKEAVEEKEQIPAAMQDV 700
701 AAGQDGLSNTDNNVQEPASQDNDVAMTGNDPEEPSALTFEKPHSPATEPA 750
751 TNPPSRVHSTSPPATSETKPSELDTASTEEMAVDKHDTSRSPSPQPSNHK 800
801 IEVPFLLRGTLREYQRDGLDWLAGLYANSTNGILADEMGLGKTIQTIALL 850
851 AHLACTHEVWGPHLVIVPTSVMLNWEMEFKKWCPGFKILAYYGSQEERKR 900
901 KRQGWNNDDIWNVCITSYQLVLQDQQVFKRRRWHYMILDEAHNIKNFKSQ 950
951 RWQTLLGFNTQARLLLTGTPLQNNLTELWSLLFFLMPAENGVGGFADLQE 1000
1001 FHDWFAKPESQILESGREQMDDEARAIISKLHKVLRPYLLRRLKADVEKQ 1050
1051 MPAKYEHVEFCRLSKRQRELYDGFLSRTDTKETLNSGNYLSIINCLMQLR 1100
1101 KVCNHPDLFVDRPIMTSFRMQKSVVSDFEVTEQRVQRLLHDPSPMKDVSL 1150
1151 GFLNLMPTQCESLSTTQAERISQLSSHRKLMELREAQKIRAQSAHANLDP 1200
1201 STVASNIGYLESGARWGRYEELQHCVYLNALRRQKKPIYGKNLIELLTIG 1250
1251 TDKRPYKPRPKIPRQVLAWFEEESTLVQSMIPTVNQRADSFKTIIEKFSC 1300
1301 VTPAVVTRDMEQFVLGRKGIEAFSDEDLKLSAPVRWAPFLPKEAPPDPWH 1350
1351 EGRMRLSIQFPDKRLLQYDCGKLQILDKLLRKLQAGGHRALIFTQMTKVL 1400
1401 DILEQFLNIHGHKYLRLDGATKVEQRQILTDRFNNDPRILCFILSTRSGG 1450
1451 LGINLTGADTVIFYDQDWNPAMDKQCQDRCHRIGQTRDVHIYRLVSEHTI 1500
1501 EANILRKASQKQMLDDVVIQEGEFTTDYFNKLSVRDVLSEKLDSKSEGLD 1550
1551 AADAALDRVLGGPDTNNDQRRVGRALEQAEDREDVAAARVAEKEIQADDA 1600
1601 DFTEKPSNNASGTSTARQGTPAGKSVLDGGLDDIDAPHVEEVLEYNAWGD 1650
1651 KMHTIDDYMLGIMAEQLKDTKLELPKDKKKGKKKGKDTRKR 1691
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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