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
Q9DCH6 UniProt NPD GO	Z20D3_MOUSE	Zinc finger A20 domain-containing protein 3 (Associated with PRK1 protein)	0.51	-	nuc	0					223
Q8SUH6 UniProt NPD GO	ZA15_ENCCU	Zinc finger C2H2 protein ECU10_0150	0.51	-	nuc	0					388
P21506 UniProt NPD GO	ZNF10_HUMAN	Zinc finger protein 10 (Zinc finger protein KOX1)	0.51	-	nuc	0	Nucleus (Probable)		194538		573
Q96HQ0 UniProt NPD GO	ZN419_HUMAN	Zinc finger protein 419	0.51	-	nuc	0	Nucleus (Potential)				510
Q8NB42 UniProt NPD GO	ZN527_HUMAN	Zinc finger protein 527	0.51	-	nuc	0	Nucleus (Potential)				577
Q3US17 UniProt NPD GO	ZN553_MOUSE	Zinc finger protein 553	0.51	-	nuc	0	Nucleus (Probable)				591
Q5RB33 UniProt NPD GO	ZN620_PONPY	Zinc finger protein 620	0.51	-	nuc	0	Nucleus (Probable)				422
O95780 UniProt NPD GO	ZN682_HUMAN	Zinc finger protein 682	0.51	-	nuc	0	Nucleus (Probable)				498
Q5T5D7 UniProt NPD GO	ZN684_HUMAN	Zinc finger protein 684	0.51	+	nuc	0	Nucleus (Probable)				378
Q9UC07 UniProt NPD GO	ZNF69_HUMAN	Zinc finger protein 69 (hZNF3) (Fragment)	0.51	-	nuc	0	Nucleus (Potential)	nucleus [NAS]	194543		128
Q32M78 UniProt NPD GO	ZN699_HUMAN	Zinc finger protein 699 (Hangover homolog)	0.51	-	nuc	0	Nucleus (Potential)		609571		642
P17097 UniProt NPD GO	ZNF7_HUMAN	Zinc finger protein 7 (Zinc finger protein KOX4) (Zinc finger protein HF.16)	0.51	-	nuc	0	Nucleus (Probable)		194531		686
Q16587 UniProt NPD GO	ZNF74_HUMAN	Zinc finger protein 74 (hZNF7)	0.51	-	nuc	0	Nucleus		194548		643
O57311 UniProt NPD GO	ZIC3_XENLA	Zinc finger protein ZIC 3 (Zinc finger protein of the cerebellum 3) (ZIC3 protein)	0.51	-	nuc	0	Nucleus				441
P62447 UniProt NPD GO	ZFPL1_BRARE	Zinc finger protein-like 1	0.51	-	nuc	1					317
Q9N5R0 UniProt NPD GO	NAS2_CAEEL	Zinc metalloproteinase nas-2 precursor (EC 3.4.24.21) (Nematode astacin 2)	0.51	-	exc	0	Secreted protein (Potential)				293
P00514 UniProt NPD GO	KAP0_BOVIN	cAMP-dependent protein kinase type I-alpha regulatory subunit	0.51	-	mit	0				2EZW	379
Q9QXQ1 UniProt NPD GO	PDE7B_MOUSE	cAMP-specific 3',5'-cyclic phosphodiesterase 7B (EC 3.1.4.17)	0.51	-	cyt	0					446
Q9P6P1 UniProt NPD GO	TLG2_SCHPO	t-SNARE affecting a late Golgi compartment protein 2 (Syntaxin tlg2)	0.51	-	gol	1	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; single-pass type IV membrane pro ...				301
Q75A17 UniProt NPD GO	TRM10_ASHGO	tRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.31) (tRNA methyltransferase 10)	0.51	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				296
Q9P377 UniProt NPD GO	BGS3_SCHPO	1,3-beta-glucan synthase component bgs3 (EC 2.4.1.34) (1,3-beta-D-glucan-UDP glucosyltransferase)	0.50	-	end	16	Integral membrane protein. Found at the growing tips during interphase and at the septum prior to cy ...	site of polarized growth [IDA]			1826
P23746 UniProt NPD GO	ABRA_PLAFF	101 kDa malaria antigen (p101) (Acidic basic repeat antigen) (Fragment)	0.50	-	nuc	0	Cell surface. Parasitophorous vacuole. At the merozoite surface and within the parasitophorous vacuo ...				321
P23226 UniProt NPD GO	MA205_DROME	205 kDa microtubule-associated protein	0.50	-	nuc	0	Cytoplasm. Associated with cytoplasmic microtubules and with the mitotic spindle	microtubule associated complex [IDA]			1185
Q04908 UniProt NPD GO	PSD3_CAEEL	26S proteasome non-ATPase regulatory subunit 3 (26S proteasome regulatory subunit rpn-3)	0.50	-	cyt	0					504
P49406 UniProt NPD GO	RM19_HUMAN	39S ribosomal protein L19, mitochondrial precursor (L19mt) (MRP-L19) (MRP-L15)	0.50	-	mit	0	Mitochondrion	nuclear membrane [IDA] nucleus [IDA]			292
Q9BGI0 UniProt NPD GO	GABT_BOVIN	4-aminobutyrate aminotransferase, mitochondrial precursor (EC 2.6.1.19) ((S)-3-amino-2-methylpropion ...	0.50	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				500
P80147 UniProt NPD GO	GABT_PIG	4-aminobutyrate aminotransferase, mitochondrial precursor (EC 2.6.1.19) ((S)-3-amino-2-methylpropion ...	0.50	-	mit	0	Mitochondrion; mitochondrial matrix			1OHY	500
P50554 UniProt NPD GO	GABT_RAT	4-aminobutyrate aminotransferase, mitochondrial precursor (EC 2.6.1.19) ((S)-3-amino-2-methylpropion ...	0.50	-	mit	0	Mitochondrion; mitochondrial matrix				500
Q945U1 UniProt NPD GO	RS15_ELAOL	40S ribosomal protein S15	0.50	-	cyt	0					153
O42984 UniProt NPD GO	RS17A_SCHPO	40S ribosomal protein S17-A	0.50	-	nuc	0					131
Q9SIK2 UniProt NPD GO	RS25A_ARATH	40S ribosomal protein S25-1	0.50	-	nuc	0					108
P39939 UniProt NPD GO	RS26B_YEAST	40S ribosomal protein S26-B	0.50	-	nuc	0		cytosolic small ribosomal subunit (sensu Eu... [TAS]			119
P47904 UniProt NPD GO	RS27_XENLA	40S ribosomal protein S27	0.50	+	nuc	0					83
P31165 UniProt NPD GO	RK15_PEA	50S ribosomal protein L15, chloroplast precursor (CL15) (Fragment)	0.50	-	nuc	0	Plastid; chloroplast				258
Q27389 UniProt NPD GO	RL13A_CAEEL	60S ribosomal protein L13a	0.50	-	nuc	0					202
P40429 UniProt NPD GO	RL13A_HUMAN	60S ribosomal protein L13a (23 kDa highly basic protein)	0.50	+	cyt	0		large ribosomal subunit [TAS]			202
P36525 UniProt NPD GO	RM24_YEAST	60S ribosomal protein L24, mitochondrial precursor (YmL14/YmL24)	0.50	-	mit	0	Mitochondrion	mitochondrial large ribosomal subunit [TAS]			258
P35684 UniProt NPD GO	RL3_ORYSA	60S ribosomal protein L3	0.50	-	nuc	0	Cytoplasm				388
P40372 UniProt NPD GO	RL3A_SCHPO	60S ribosomal protein L3-A	0.50	-	mit	0	Cytoplasm				387
P49405 UniProt NPD GO	RL5_CAEEL	60S ribosomal protein L5	0.50	-	mit	0					293
Q9R1V4 UniProt NPD GO	ADA11_MOUSE	ADAM 11 precursor (A disintegrin and metalloproteinase domain 11) (Metalloproteinase-like, disintegr ...	0.50	-	end	2 *	Membrane; single-pass type I membrane protein				773
Q9JLN6 UniProt NPD GO	ADA28_MOUSE	ADAM 28 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase domain 28) (Thymic epithelial c ...	0.50	+	exc	1	Membrane; single-pass type I membrane protein	plasma membrane [IDA]			793
Q8TC27 UniProt NPD GO	ADA32_HUMAN	ADAM 32 precursor (A disintegrin and metalloproteinase domain 32)	0.50	-	end	1	Membrane; single-pass type I membrane protein (Potential)				787
Q8TE58 UniProt NPD GO	ATS15_HUMAN	ADAMTS-15 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase with thrombospondin motifs 15 ...	0.50	-	nuc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)		607509		950
O88512 UniProt NPD GO	AP1G2_MOUSE	AP-1 complex subunit gamma-2 (Adapter-related protein complex 1 gamma-2 subunit) (Gamma2-adaptin) (A ...	0.50	-	nuc	0	Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi compl ...	AP-1 adaptor complex [ISS] Golgi trans face [TAS] Golgi-associated vesicle [ISS] membrane [ISS] transport vesicle [ISS]			791
Q85AL8 UniProt NPD GO	ATPF_ANTFO	ATP synthase B chain (EC 3.6.3.14) (ATPase subunit I)	0.50	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane				184
Q91YY4 UniProt NPD GO	ATPF2_MOUSE	ATP synthase mitochondrial F1 complex assembly factor 2, mitochondrial precursor	0.50	-	mit	0	Mitochondrion (By similarity)				289
P41233 UniProt NPD GO	ABCA1_MOUSE	ATP-binding cassette sub-family A member 1 (ATP-binding cassette transporter 1) (ATP-binding cassett ...	0.50	-	end	13 *		Golgi apparatus [IDA] integral to plasma membrane [IDA]			2261
O15523 UniProt NPD GO	DDX3Y_HUMAN	ATP-dependent RNA helicase DDX3Y (EC 3.6.1.-) (DEAD box protein 3, Y-chromosomal)	0.50	-	nuc	0	Cytoplasm. Nucleus. Shuttles between the nucleus and the cytoplasm in an XPO1-dependent manner		400042		660
Q6GVM6 UniProt NPD GO	DDX3Y_PANTR	ATP-dependent RNA helicase DDX3Y (EC 3.6.1.-) (DEAD box protein 3, Y-chromosomal)	0.50	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Shuttles between the nucleus and the cytoplasm i ...				660

You are viewing entries 24751 to 24800 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.