NucPred on Proteomes

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

NucPred - predictions for eukaryotic proteomes

Species:

Note: All filters/tests are combined with AND unless otherwise stated

Show only the proteins with links to database(s):
OMIM - human disease genes
PDB - protein 3D structure
( AND OR combination )

Annotation filters (can be slow! - Perl regexps allowed: e.g. nucleus|nucleolus)

UniProt ID (e.g. "PK3B_")
UniProt description (e.g. "kinase")
UniProt subcellular location
AND
UniProt GO component
AND
AND the
AND the

Only show proteins where the PredictNLS prediction is:

positive
negative

Only show proteins where the PSORT II predicted location

is is not

Click here: to filter by NucPred score

exclude all transmembrane proteins predicted by TMHMM
don't exclude lone N-terminal predicted transmembrane helices
(these could be signal peptides)

export all ACs and IDs as text file

Show proteins (ordered by NucPred score ) from to (currently 98716 matches)

You can bookmark/save your search criteria with this link. You can also start again with default settings.

UniProt accession	UniProt ID	UniProt description	NucPred score	Predict- NLS	PSORT II	TMHMM #helices	UniProt annotation for subcellular location	Uniprot GO cellular component	OMIM	PDB	sequence length
Q6B8N4 UniProt NPD GO	RR4_GRATL	Chloroplast 30S ribosomal protein S4	0.46	-	nuc	0	Plastid; chloroplast				201
P17072 UniProt NPD GO	RR4_GUITH	Chloroplast 30S ribosomal protein S4	0.46	-	nuc	0	Plastid; chloroplast				200
P59139 UniProt NPD GO	RR4_HOOLU	Chloroplast 30S ribosomal protein S4	0.46	-	mit	0	Plastid; chloroplast				202
P59148 UniProt NPD GO	RR4_LOPST	Chloroplast 30S ribosomal protein S4	0.46	-	mit	0	Plastid; chloroplast				203
Q6EW46 UniProt NPD GO	RR4_NYMAL	Chloroplast 30S ribosomal protein S4	0.46	-	mit	0	Plastid; chloroplast				201
Q9FSA4 UniProt NPD GO	RR4_SPHDO	Chloroplast 30S ribosomal protein S4	0.46	-	mit	0	Plastid; chloroplast				202
P69630 UniProt NPD GO	RR4_ALOPR	Chloroplast 30S ribosomal protein S4 (Fragment)	0.46	-	mit	0	Plastid; chloroplast				196
O47026 UniProt NPD GO	RR4_ASPSB	Chloroplast 30S ribosomal protein S4 (Fragment)	0.46	-	mit	0	Plastid; chloroplast				196
P36451 UniProt NPD GO	RR4_BROER	Chloroplast 30S ribosomal protein S4 (Fragment)	0.46	-	mit	0	Plastid; chloroplast				196
P69637 UniProt NPD GO	RR4_CALEP	Chloroplast 30S ribosomal protein S4 (Fragment)	0.46	-	mit	0	Plastid; chloroplast				196
P69638 UniProt NPD GO	RR4_CINLA	Chloroplast 30S ribosomal protein S4 (Fragment)	0.46	-	mit	0	Plastid; chloroplast				196
P69640 UniProt NPD GO	RR4_DESFL	Chloroplast 30S ribosomal protein S4 (Fragment)	0.46	-	mit	0	Plastid; chloroplast				196
P69641 UniProt NPD GO	RR4_ELYCA	Chloroplast 30S ribosomal protein S4 (Fragment)	0.46	-	mit	0	Plastid; chloroplast				196
P69644 UniProt NPD GO	RR4_HORMA	Chloroplast 30S ribosomal protein S4 (Fragment)	0.46	-	mit	0	Plastid; chloroplast				196
P69645 UniProt NPD GO	RR4_LAMAU	Chloroplast 30S ribosomal protein S4 (Fragment)	0.46	-	mit	0	Plastid; chloroplast				196
P69648 UniProt NPD GO	RR4_PHLPR	Chloroplast 30S ribosomal protein S4 (Fragment)	0.46	-	mit	0	Plastid; chloroplast				196
Q6EMB0 UniProt NPD GO	RR7_ARIMA	Chloroplast 30S ribosomal protein S7	0.46	-	nuc	0	Plastid; chloroplast				155
Q67IP2 UniProt NPD GO	RR7_BUTUM	Chloroplast 30S ribosomal protein S7	0.46	-	nuc	0	Plastid; chloroplast				155
P69663 UniProt NPD GO	RR7_CERJA	Chloroplast 30S ribosomal protein S7	0.46	-	nuc	0	Plastid; chloroplast				155
P69664 UniProt NPD GO	RR7_DRIWI	Chloroplast 30S ribosomal protein S7	0.46	-	nuc	0	Plastid; chloroplast				155
P19458 UniProt NPD GO	RR7_GUITH	Chloroplast 30S ribosomal protein S7	0.46	-	mit	0	Plastid; chloroplast				156
P69665 UniProt NPD GO	RR7_ILLPA	Chloroplast 30S ribosomal protein S7	0.46	-	nuc	0	Plastid; chloroplast				155
P69666 UniProt NPD GO	RR7_LIRTU	Chloroplast 30S ribosomal protein S7	0.46	-	nuc	0	Plastid; chloroplast				155
Q6KGX6 UniProt NPD GO	RR7_MAGST	Chloroplast 30S ribosomal protein S7	0.46	-	nuc	0	Plastid; chloroplast				155
Q67IB6 UniProt NPD GO	RR7_MAIRA	Chloroplast 30S ribosomal protein S7	0.46	-	nuc	0	Plastid; chloroplast				155
Q67IB0 UniProt NPD GO	RR7_MUSCM	Chloroplast 30S ribosomal protein S7	0.46	-	nuc	0	Plastid; chloroplast				155
Q6EM84 UniProt NPD GO	RR7_NELLU	Chloroplast 30S ribosomal protein S7	0.46	-	nuc	0	Plastid; chloroplast				155
Q9TKZ6 UniProt NPD GO	RR7_NEPOL	Chloroplast 30S ribosomal protein S7	0.46	-	mit	0	Plastid; chloroplast				156
Q67IE3 UniProt NPD GO	RR7_PHOTN	Chloroplast 30S ribosomal protein S7	0.46	-	nuc	0	Plastid; chloroplast				155
Q6EM68 UniProt NPD GO	RR7_PLAOC	Chloroplast 30S ribosomal protein S7	0.46	-	nuc	0	Plastid; chloroplast				155
Q6KGW4 UniProt NPD GO	RR7_SCHCH	Chloroplast 30S ribosomal protein S7	0.46	-	nuc	0	Plastid; chloroplast				155
Q67IE0 UniProt NPD GO	RR7_SISMO	Chloroplast 30S ribosomal protein S7	0.46	-	nuc	0	Plastid; chloroplast				155
Q67II8 UniProt NPD GO	RR7_TYPAN	Chloroplast 30S ribosomal protein S7	0.46	-	nuc	0	Plastid; chloroplast				155
Q67IA4 UniProt NPD GO	RR7_YUCGL	Chloroplast 30S ribosomal protein S7	0.46	-	nuc	0	Plastid; chloroplast				155
Q85FI7 UniProt NPD GO	RR8_ADICA	Chloroplast 30S ribosomal protein S8	0.46	-	mit	1	Plastid; chloroplast				132
P06589 UniProt NPD GO	RK22_MAIZE	Chloroplast 50S ribosomal protein L22	0.46	-	nuc	0	Plastid; chloroplast				148
Q33BZ2 UniProt NPD GO	RK22_NICTO	Chloroplast 50S ribosomal protein L22	0.46	-	nuc	0	Plastid; chloroplast				155
P52771 UniProt NPD GO	RK22_PINTH	Chloroplast 50S ribosomal protein L22	0.46	-	nuc	0	Plastid; chloroplast				142
Q6L3F9 UniProt NPD GO	RK22_SACHY	Chloroplast 50S ribosomal protein L22	0.46	-	nuc	0	Plastid; chloroplast				148
Q6ENS4 UniProt NPD GO	RK22_SACOF	Chloroplast 50S ribosomal protein L22	0.46	-	nuc	0	Plastid; chloroplast				148
Q8S8U9 UniProt NPD GO	RK32_ATRBE	Chloroplast 50S ribosomal protein L32	0.46	-	mit	0	Plastid; chloroplast				55
P36493 UniProt NPD GO	RK32_LYCES	Chloroplast 50S ribosomal protein L32	0.46	-	mit	0	Plastid; chloroplast				55
Q9MTI3 UniProt NPD GO	RK32_OENHO	Chloroplast 50S ribosomal protein L32	0.46	-	mit	0	Plastid; chloroplast				51
P07668 UniProt NPD GO	CLAT_DROME	Choline O-acetyltransferase (EC 2.3.1.6) (CHOACTase) (Choline acetylase) (Acetyl-CoA) (ChAT) [Contai ...	0.46	-	nuc	0		cytosol [NAS] nucleus [NAS]			721
P49587 UniProt NPD GO	PCY1_PLAFK	Choline-phosphate cytidylyltransferase (EC 2.7.7.15) (Phosphorylcholine transferase) (CTP:phosphocho ...	0.46	+	nuc	0					370
Q9Y5K3 UniProt NPD GO	PCY1B_HUMAN	Choline-phosphate cytidylyltransferase B (EC 2.7.7.15) (Phosphorylcholine transferase B) (CTP:phosph ...	0.46	-	nuc	0	Endoplasmic reticulum	cytoplasm [TAS]	604926		369
O02197 UniProt NPD GO	CCA_SCHMA	Circulating cathodic antigen (CCA)	0.46	-	nuc	0					347
Q01301 UniProt NPD GO	CCG4_NEUCR	Clock-controlled pheromone ccg-4 precursor [Contains: Pheromone ccg-4]	0.46	-	exc	0	Secreted protein	extracellular region [IDA]			299
Q9D6Y1 UniProt NPD GO	CCDC3_MOUSE	Coiled-coil domain-containing protein 3 precursor	0.46	-	exc	0					273
Q3SYW2 UniProt NPD GO	CO2_BOVIN	Complement C2 precursor (EC 3.4.21.43) (C3/C5 convertase) [Contains: Complement C2b fragment; Comple ...	0.46	-	nuc	0	Secreted protein (By similarity)				750

You are viewing entries 27501 to 27550 of 98716. You can see more proteins by changing the limits in the form at the top of this page, or click here for the next page of proteins .

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.)

Go back to the NucPred Home Page.