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
Q05640 UniProt NPD GO	HMEN_ARTSF	Homeobox protein engrailed	0.83	-	nuc	0	Nucleus				349
O77215 UniProt NPD GO	UNC4_DROME	Homeobox protein unc-4 (Paired-like homeodomain protein unc-4) (DPHD-1)	0.83	+	nuc	0	Nucleus (By similarity)				428
Q03703 UniProt NPD GO	YMD7_YEAST	Hypothetical 38.0 kDa protein in CAT2-AMD1 intergenic region	0.83	-	nuc	0					340
P47166 UniProt NPD GO	YJ9C_YEAST	Hypothetical 81.2 kDa protein in NMD5-HOM6 intergenic region	0.83	+	nuc	0		Golgi apparatus [IDA]			707
O13826 UniProt NPD GO	YEEA_SCHPO	Hypothetical RING finger protein C19A8.10 in chromosome I	0.83	-	nuc	0					254
Q09231 UniProt NPD GO	YQ21_CAEEL	Hypothetical protein C09F5.1	0.83	-	nuc	1					571
O13683 UniProt NPD GO	YDY2_SCHPO	Hypothetical protein C11E3.02c in chromosome I	0.83	-	mit	0					1237
Q09819 UniProt NPD GO	YAC5_SCHPO	Hypothetical protein C16C9.05 in chromosome I	0.83	+	nuc	0					404
P87319 UniProt NPD GO	YOS1_SCHPO	Hypothetical protein C21C3.01c in chromosome II	0.83	+	nuc	0					3011
O13965 UniProt NPD GO	YE45_SCHPO	Hypothetical protein C24C9.05c in chromosome I	0.83	-	cyt	1	Membrane; multi-pass membrane protein (Potential)	cytoplasm [IDA] nucleus [IDA]			730
Q10172 UniProt NPD GO	YDC9_SCHPO	Hypothetical protein C25G10.09c in chromosome I	0.83	-	nuc	0		cell cortex [IDA] nucleus [IDA]			1794
Q10326 UniProt NPD GO	YD71_SCHPO	Hypothetical protein C32A11.01 in chromosome I	0.83	-	exc	0					720
Q10338 UniProt NPD GO	YBM4_SCHPO	Hypothetical protein C582.04c in chromosome II	0.83	-	nuc	0					601
Q9V719 UniProt NPD GO	Y105_DROME	Hypothetical protein CG10105	0.83	-	nuc	0					569
Q19753 UniProt NPD GO	YU0O_CAEEL	Hypothetical protein F23B12.7 in chromosome V	0.83	-	nuc	0					953
P53015 UniProt NPD GO	YPO4_CAEEL	Hypothetical protein F31E3.4	0.83	+	cyt	0					1131
P34431 UniProt NPD GO	YL52_CAEEL	Hypothetical protein F44E2.2 in chromosome III	0.83	-	end	0					2186
P34459 UniProt NPD GO	YMD5_CAEEL	Hypothetical protein F54H12.5	0.83	-	nuc	1					880
P11260 UniProt NPD GO	YO11_MOUSE	Hypothetical protein ORF-1137	0.83	-	nuc	0					379
Q9UPP2 UniProt NPD GO	IQEC3_HUMAN	IQ motif and Sec7 domain-containing protein 3	0.83	-	nuc	0	Cytoplasm (Potential)				1182
Q8CBR1 UniProt NPD GO	ILDR1_MOUSE	Immunoglobulin-like domain-containing receptor 1 precursor	0.83	-	exc	2 *	Cell membrane; single-pass type I membrane protein (By similarity)	extracellular space [RCA] integral to membrane [RCA]			537
Q32NM7 UniProt NPD GO	ILDR1_XENLA	Immunoglobulin-like domain-containing receptor 1 precursor	0.83	-	exc	1 *	Cell membrane; single-pass type I membrane protein (By similarity)				545
P18963 UniProt NPD GO	IRA1_YEAST	Inhibitory regulator protein IRA1	0.83	-	end	0		membrane [IMP] mitochondrion [IDA]			3092
Q9Y2U8 UniProt NPD GO	MAN1_HUMAN	Inner nuclear membrane protein Man1 (LEM domain-containing protein 3)	0.83	-	nuc	2	Nucleus; nuclear inner membrane; multi-pass membrane protein	integral to membrane [IDA] integral to nuclear inner membrane [TAS] membrane fraction [TAS]	607844	2CH0	911
P79154 UniProt NPD GO	IFNG_CAPHI	Interferon gamma precursor (IFN-gamma)	0.83	-	exc	1 *	Secreted protein				166
O57571 UniProt NPD GO	IFNG_COTJA	Interferon gamma precursor (IFN-gamma)	0.83	-	nuc	1 *	Secreted protein (By similarity)				164
Q647G2 UniProt NPD GO	IFNG_MOSBE	Interferon gamma precursor (IFN-gamma)	0.83	-	exc	0	Secreted protein (By similarity)				166
Q9H9L3 UniProt NPD GO	I20L2_HUMAN	Interferon-stimulated 20 kDa exonuclease-like 2 (EC 3.1.-.-)	0.83	+	nuc	0	Nucleus; nucleolus				353
P25386 UniProt NPD GO	USO1_YEAST	Intracellular protein transport protein USO1 (Int-1)	0.83	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Probably present on vesicles operational between t ...	soluble fraction [IDA]			1790
Q9VHH9 UniProt NPD GO	JHD1_DROME	JmjC domain-containing histone demethylation protein 1 (EC 1.14.11.-)	0.83	-	nuc	0	Nucleus (By similarity)				1345
Q5HZN1 UniProt NPD GO	JD2AB_XENLA	JmjC domain-containing histone demethylation protein 2A-B (EC 1.14.11.-) (Jumonji domain-containing ...	0.83	-	nuc	0	Nucleus (By similarity)				1334
Q9H3R0 UniProt NPD GO	JHD3C_HUMAN	JmjC domain-containing histone demethylation protein 3C (EC 1.14.11.-) (Jumonji domain-containing pr ...	0.83	+	nuc	0	Nucleus (By similarity)		605469		1056
Q02241 UniProt NPD GO	KIF23_HUMAN	Kinesin-like protein KIF23 (Mitotic kinesin-like protein 1) (Kinesin-like protein 5)	0.83	+	nuc	0	Nucleus	kinesin complex [TAS] spindle [TAS]	605064		856
Q9W1U4 UniProt NPD GO	KI59C_DROME	Kinesin-like protein Klp59C (Kinesin-like protein at cytological position 59C)	0.83	+	nuc	0	Primarily restricted to centromeric regions of chromosomes during both metaphase and anaphase. Not l ...	kinetochore microtubule [IDA]			626
Q60980 UniProt NPD GO	KLF3_MOUSE	Krueppel-like factor 3 (Basic krueppel-like factor) (CACCC-box-binding protein BKLF) (TEF-2)	0.83	-	nuc	0	Nucleus (Probable)			1U86	344
P53666 UniProt NPD GO	LIMK2_CHICK	LIM domain kinase 2 (EC 2.7.11.1) (LIMK-2)	0.83	+	nuc	0					642
Q6MG49 UniProt NPD GO	BAT3_RAT	Large proline-rich protein BAT3 (HLA-B-associated transcript 3)	0.83	+	nuc	0					1096
Q6GNW0 UniProt NPD GO	LRRF2_XENLA	Leucine-rich repeat flightless-interacting protein 2 (LRR FLI-II-interacting protein 2)	0.83	+	nuc	0					405
Q8N1G4 UniProt NPD GO	LRC47_HUMAN	Leucine-rich repeat-containing protein 47	0.83	-	nuc	0					583
Q921G6 UniProt NPD GO	LRCH4_MOUSE	Leucine-rich repeats and calponin homology domain-containing protein 4	0.83	-	nuc	1		cytoplasm [IDA] PML body [IDA]			680
Q58CT8 UniProt NPD GO	LAX1_BOVIN	Lymphocyte transmembrane adapter 1 (Membrane-associated adapter protein LAX)	0.83	-	nuc	1 *	Cell membrane; single-pass type III membrane protein (By similarity)				387
Q6P431 UniProt NPD GO	MKNK2_XENLA	MAP kinase-interacting serine/threonine-protein kinase 2 (EC 2.7.11.1) (MAP kinase signal-integratin ...	0.83	-	nuc	0					467
Q7SYS2 UniProt NPD GO	MK67I_XENLA	MKI67 FHA domain-interacting nucleolar phosphoprotein-like	0.83	-	nuc	0	Nucleus; nucleolus (By similarity)				278
Q24741 UniProt NPD GO	OSKA_DROVI	Maternal effect protein oskar	0.83	-	mit	0					594
Q874N1 UniProt NPD GO	MTAL2_KLUDE	Mating-type protein ALPHA2	0.83	-	nuc	0	Nucleus (By similarity)				174
Q9MUY3 UniProt NPD GO	MATK_ARUDO	Maturase K (Intron maturase)	0.83	+	cyt	0	Plastid; chloroplast				513
Q9TIA9 UniProt NPD GO	MATK_ASTLA	Maturase K (Intron maturase)	0.83	-	nuc	0	Plastid; chloroplast				513
Q76LL9 UniProt NPD GO	MATK_HORSP	Maturase K (Intron maturase)	0.83	-	cyt	0	Plastid; chloroplast				511
Q76LM0 UniProt NPD GO	MATK_HORVD	Maturase K (Intron maturase)	0.83	-	cyt	0	Plastid; chloroplast				511
P17158 UniProt NPD GO	MATK_HORVU	Maturase K (Intron maturase)	0.83	-	cyt	0	Plastid; chloroplast				511

You are viewing entries 7401 to 7450 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.