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
P03970 UniProt NPD GO	INHBA_PIG	Inhibin beta A chain precursor (Activin beta-A chain)	0.77	-	nuc	0	Secreted protein				424
P81122 UniProt NPD GO	IRS2_MOUSE	Insulin receptor substrate 2 (IRS-2) (4PS)	0.77	+	nuc	0					1321
Q28985 UniProt NPD GO	IBP5_PIG	Insulin-like growth factor-binding protein 5 precursor (IGFBP-5) (IBP-5) (IGF-binding protein 5)	0.77	-	exc	0	Secreted protein				271
P28341 UniProt NPD GO	IFNG_CALJA	Interferon gamma precursor (IFN-gamma)	0.77	+	exc	0	Secreted protein				166
O77763 UniProt NPD GO	IFNG_EQUAS	Interferon gamma precursor (IFN-gamma)	0.77	-	nuc	0	Secreted protein (By similarity)				166
P42160 UniProt NPD GO	IFNG_HORSE	Interferon gamma precursor (IFN-gamma)	0.77	-	nuc	0	Secreted protein				166
O57608 UniProt NPD GO	IFNG_PHACO	Interferon gamma precursor (IFN-gamma)	0.77	-	nuc	1 *	Secreted protein (By similarity)				164
Q64345 UniProt NPD GO	IFIT3_MOUSE	Interferon-induced protein with tetratricopeptide repeats 3 (IFIT-3) (Glucocorticoid-attenuated resp ...	0.77	-	nuc	0					403
Q8NFM7 UniProt NPD GO	I17RD_HUMAN	Interleukin-17 receptor D precursor (IL-17 receptor D) (IL-17RD) (Interleukin-17D receptor) (IL-17D ...	0.77	-	exc	0	Membrane; single-pass type I membrane protein. Isoform 4: Cytoplasm. Predominantly associated with t ...		606807		739
Q96LB3 UniProt NPD GO	IFT74_HUMAN	Intraflagellar transport 74 homolog (Coiled-coil domain-containing protein 2) (Capillary morphogenes ...	0.77	-	mit	0	Cytoplasmic vesicle. Intracellular vesicular compartment		608040		600
P48467 UniProt NPD GO	KINH_NEUCR	Kinesin heavy chain	0.77	-	nuc	0				1GOJ	928
P45962 UniProt NPD GO	KLP3_CAEEL	Kinesin-like protein klp-3	0.77	-	nuc	0					598
P32364 UniProt NPD GO	SMY1_YEAST	Kinesin-related protein SMY1 (Suppressor protein SMY1)	0.77	-	nuc	0		bud neck [TAS] bud tip [IDA]			656
O54785 UniProt NPD GO	LIMK2_MOUSE	LIM domain kinase 2 (EC 2.7.11.1) (LIMK-2)	0.77	-	cyt	0	Cytoplasm				638
Q9SRV3 UniProt NPD GO	LBD20_ARATH	LOB domain-containing protein 20	0.77	-	nuc	0					273
P42167 UniProt NPD GO	LAP2B_HUMAN	Lamina-associated polypeptide 2, isoforms beta/gamma (Thymopoietin, isoforms beta/gamma) (TP beta/ga ...	0.77	+	nuc	1	Nucleus; nuclear inner membrane; single-pass type II membrane protein. Tightly associated with the n ...	nuclear envelope [TAS] nucleus [TAS]	188380	1H9F	453
Q9UQ13 UniProt NPD GO	SHOC2_HUMAN	Leucine-rich repeat protein SHOC-2 (Ras-binding protein Sur-8)	0.77	-	nuc	0		cytoplasm [NAS]	602775		582
O88520 UniProt NPD GO	SHOC2_MOUSE	Leucine-rich repeat protein SHOC-2 (Ras-binding protein Sur-8)	0.77	-	nuc	0					582
Q6AYH9 UniProt NPD GO	LRC50_RAT	Leucine-rich repeat-containing protein 50	0.77	-	nuc	0					633
Q9NZR2 UniProt NPD GO	LRP1B_HUMAN	Low-density lipoprotein receptor-related protein 1B precursor (Low-density lipoprotein receptor-rela ...	0.77	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)		608766		4599
Q924X6 UniProt NPD GO	LRP8_MOUSE	Low-density lipoprotein receptor-related protein 8 precursor (Apolipoprotein E receptor 2)	0.77	-	exc	1	Cell membrane; single-pass type I membrane protein (Potential). Secreted protein. Isoforms that cont ...	plasma membrane [ISS]			996
Q04833 UniProt NPD GO	LRP_CAEEL	Low-density lipoprotein receptor-related protein precursor (LRP)	0.77	-	exc	1	Membrane; single-pass type I membrane protein				4753
Q95KG7 UniProt NPD GO	MANS1_MACFA	MANSC domain-containing protein 1 precursor	0.77	-	exc	1	Membrane; single-pass type I membrane protein (Potential)				431
P49138 UniProt NPD GO	MAPK2_MOUSE	MAP kinase-activated protein kinase 2 (EC 2.7.11.1) (MAPK-activated protein kinase 2) (MAPKAP kinase ...	0.77	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			386
Q9HBH9 UniProt NPD GO	MKNK2_HUMAN	MAP kinase-interacting serine/threonine-protein kinase 2 (EC 2.7.11.1) (MAP kinase signal-integratin ...	0.77	-	nuc	0			605069	2AC5	465
P33076 UniProt NPD GO	C2TA_HUMAN	MHC class II transactivator (CIITA)	0.77	-	nuc	0	Nucleus		600005		1130
Q03162 UniProt NPD GO	YMZ0_YEAST	MYND-type zinc finger protein YMR100W	0.77	-	mit	0	Nucleus (Potential)				620
Q96JK9 UniProt NPD GO	MAML3_HUMAN	Mastermind-like protein 3 (Mam-3)	0.77	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle. Nuclear, in a punctate manner	nucleus [IDA]	608991		1133
Q870I4 UniProt NPD GO	MTL32_CANGA	Mating-type-like protein ALPHA2, silenced copy at MTL3 (MTL3alpha2 protein)	0.77	-	nuc	1	Nucleus (By similarity)				210
Q9GF59 UniProt NPD GO	MATK_ARAGL	Maturase K (Intron maturase)	0.77	-	nuc	0	Plastid; chloroplast				504
Q9GF50 UniProt NPD GO	MATK_ARALY	Maturase K (Intron maturase)	0.77	-	nuc	0	Plastid; chloroplast				504
P56784 UniProt NPD GO	MATK_ARATH	Maturase K (Intron maturase)	0.77	-	nuc	0	Plastid; chloroplast				504
Q7YKY4 UniProt NPD GO	MATK_CHAGO	Maturase K (Intron maturase)	0.77	-	cyt	0	Plastid; chloroplast				516
Q5YK05 UniProt NPD GO	MATK_CICAR	Maturase K (Intron maturase)	0.77	-	nuc	0	Plastid; chloroplast				509
Q6PSC4 UniProt NPD GO	MATK_DOLLA	Maturase K (Intron maturase)	0.77	-	nuc	0	Plastid; chloroplast				504
Q7HTB8 UniProt NPD GO	MATK_EMPNI	Maturase K (Intron maturase)	0.77	-	nuc	0	Plastid; chloroplast				506
Q5J309 UniProt NPD GO	MATK_FROFL	Maturase K (Intron maturase)	0.77	+	nuc	0	Plastid; chloroplast				505
Q7YKQ2 UniProt NPD GO	MATK_IBILU	Maturase K (Intron maturase)	0.77	-	pox	0	Plastid; chloroplast				509
Q9GF34 UniProt NPD GO	MATK_MATIN	Maturase K (Intron maturase)	0.77	-	mit	0	Plastid; chloroplast				504
Q507P6 UniProt NPD GO	MATK_RANGL	Maturase K (Intron maturase)	0.77	-	cyt	0	Plastid; chloroplast				508
Q5J2W5 UniProt NPD GO	MATK_SALKA	Maturase K (Intron maturase)	0.77	-	nuc	0	Plastid; chloroplast				507
P09364 UniProt NPD GO	MATK_SINAL	Maturase K (Intron maturase)	0.77	-	mit	0	Plastid; chloroplast				502
Q9TK08 UniProt NPD GO	MATK_STYHA	Maturase K (Intron maturase)	0.77	-	nuc	0	Plastid; chloroplast				509
Q8WJ18 UniProt NPD GO	MATK_SYZAU	Maturase K (Intron maturase)	0.77	-	cyt	0	Plastid; chloroplast				503
Q6LA06 UniProt NPD GO	MATK_TYPLA	Maturase K (Intron maturase)	0.77	-	nuc	0	Plastid; chloroplast				513
Q7YKL5 UniProt NPD GO	MATK_VERRI	Maturase K (Intron maturase)	0.77	-	cyt	0	Plastid; chloroplast				508
Q60948 UniProt NPD GO	MAD4_MOUSE	Max-interacting transcriptional repressor MAD4 (Max-associated protein 4) (MAX dimerization protein ...	0.77	-	nuc	0	Nucleus				209
P32489 UniProt NPD GO	MEI5_YEAST	Meiosis protein 5	0.77	-	nuc	0		condensed nuclear chromosome [IDA]			222
Q3UHE1 UniProt NPD GO	PITM3_MOUSE	Membrane-associated phosphatidylinositol transfer protein 3 (Phosphatidylinositol transfer protein, ...	0.77	-	nuc	0	Intracytoplasmic membrane; peripheral membrane protein (Probable)				974
P50495 UniProt NPD GO	MSP1_PLAFP	Merozoite surface protein 1 precursor (Merozoite surface antigens) (PMMSA) (GP195)	0.77	-	exc	1	Cell membrane; lipid-anchor; GPI-anchor				1726

You are viewing entries 10401 to 10450 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.