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
Q8J1M8 UniProt NPD GO	YLO4_SCHPO	Hypothetical protein C1952.04c in chromosome II	0.57	-	nuc	0					158
Q09844 UniProt NPD GO	YAE3_SCHPO	Hypothetical protein C23D3.03c in chromosome I	0.57	-	nuc	0					472
P78890 UniProt NPD GO	YEPF_SCHPO	Hypothetical protein C23H3.15c in chromosome I	0.57	-	nuc	0					325
O01975 UniProt NPD GO	YJ05_CAEEL	Hypothetical protein C41D11.5	0.57	-	nuc	0					238
Q8SVP2 UniProt NPD GO	Y4G7_ENCCU	Hypothetical protein ECU04_1670	0.57	-	nuc	0					586
Q09550 UniProt NPD GO	YQU3_CAEEL	Hypothetical protein F26C11.3 precursor	0.57	-	exc	0	Secreted protein (Potential)				1317
P91301 UniProt NPD GO	YLPK_CAEEL	Hypothetical protein F46F11.3 in chromosome I	0.57	+	nuc	0					264
P34481 UniProt NPD GO	YMJ5_CAEEL	Hypothetical protein F59B2.5	0.57	-	nuc	1 *					468
Q10010 UniProt NPD GO	YSV4_CAEEL	Hypothetical protein T19C3.4 in chromosome III	0.57	-	nuc	2 *	Membrane; multi-pass membrane protein (Potential)				229
P34681 UniProt NPD GO	YO43_CAEEL	Hypothetical protein ZK757.3	0.57	+	mit	0					1040
Q9UTA1 UniProt NPD GO	YL8J_SCHPO	Hypothetical zinc finger protein C25B8.19c in chromosome I	0.57	-	nuc	0	Nucleus (Potential)				522
O04294 UniProt NPD GO	IMA2_ARATH	Importin alpha-2 subunit (Karyopherin alpha-2 subunit) (KAP alpha)	0.57	-	nuc	0	Cytoplasm (By similarity)				531
Q9XZU1 UniProt NPD GO	CSE1_DROME	Importin-alpha re-exporter (Cellular apoptosis susceptibility protein homolog)	0.57	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				975
P27092 UniProt NPD GO	INHBA_CHICK	Inhibin beta A chain precursor (Activin beta-A chain)	0.57	-	nuc	0	Secreted protein				424
O88959 UniProt NPD GO	INHBE_RAT	Inhibin beta E chain precursor (Activin beta-E chain)	0.57	-	exc	0	Secreted protein (By similarity)				350
Q59S85 UniProt NPD GO	LPE10_CANAL	Inner membrane magnesium transporter LPE10, mitochondrial precursor	0.57	-	nuc	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				453
Q5A970 UniProt NPD GO	MRS2_CANAL	Inner membrane magnesium transporter MRS2, mitochondrial precursor (RNA-splicing protein MRS2)	0.57	-	nuc	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				468
Q8LBP4 UniProt NPD GO	ALB3_ARATH	Inner membrane protein ALBINO3, chloroplast precursor	0.57	+	end	4	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				462
Q22549 UniProt NPD GO	INX10_CAEEL	Innexin-10	0.57	-	nuc	2 *	Membrane; multi-pass membrane protein				559
P52946 UniProt NPD GO	IPF1_MOUSE	Insulin promoter factor 1 (IPF-1) (Islet/duodenum homeobox 1) (IDX-1) (Somatostatin-transactivating ...	0.57	+	nuc	0	Nucleus	nucleus [IDA]			284
P17936 UniProt NPD GO	IBP3_HUMAN	Insulin-like growth factor-binding protein 3 precursor (IGFBP-3) (IBP-3) (IGF-binding protein 3)	0.57	-	exc	0	Secreted protein	extracellular region [NAS]	146732		291
P07351 UniProt NPD GO	IFNA4_MOUSE	Interferon alpha-4 precursor	0.57	-	cyt	0	Secreted protein				186
P97378 UniProt NPD GO	I12R2_MOUSE	Interleukin-12 receptor beta-2 chain precursor (IL-12 receptor beta-2) (IL-12R-beta2)	0.57	-	exc	0	Membrane; single-pass type I membrane protein				874
P01589 UniProt NPD GO	IL2RA_HUMAN	Interleukin-2 receptor alpha chain precursor (IL-2 receptor alpha subunit) (IL-2-RA) (IL2-RA) (p55) ...	0.57	-	cyt	1	Membrane; single-pass type I membrane protein	plasma membrane [TAS]	147730	2ERJ	272
P26896 UniProt NPD GO	IL2RB_RAT	Interleukin-2 receptor beta chain precursor (IL-2 receptor) (P70-75) (High affinity IL-2 receptor su ...	0.57	-	exc	2 *	Membrane; single-pass type I membrane protein				537
Q4IK03 UniProt NPD GO	MIA40_GIBZE	Intermembrane space import and assembly protein 40, mitochondrial precursor (Mitochondrial import in ...	0.57	-	mit	0	Mitochondrion; mitochondrial inner membrane; single-pass type II membrane protein; intermembrane sid ...				391
Q7S3S2 UniProt NPD GO	MIA40_NEUCR	Intermembrane space import and assembly protein 40, mitochondrial precursor (Mitochondrial import in ...	0.57	-	mit	0	Mitochondrion; mitochondrial inner membrane; single-pass type II membrane protein; intermembrane sid ...				298
P25030 UniProt NPD GO	K1C20_RAT	Keratin, type I cytoskeletal 20 (Cytokeratin-20) (CK-20) (Keratin-20) (K20) (Cytokeratin-21) (CK-21) ...	0.57	-	mit	0					429
Q5R5B8 UniProt NPD GO	KCT2_PONPY	Keratinocytes-associated transmembrane protein 2 precursor	0.57	-	mit	1 *	Membrane; single-pass type I membrane protein (Potential)				265
Q8TD94 UniProt NPD GO	KLF14_HUMAN	Krueppel-like factor 14 (Transcription factor BTEB5) (Basic transcription element-binding protein 5) ...	0.57	-	nuc	0	Nucleus (By similarity)		609393		323
P36200 UniProt NPD GO	LHX3_XENLA	LIM/homeobox protein Lhx3 (Homeobox protein LIM-3) (xLIM-3)	0.57	+	nuc	0	Nucleus (Probable)				395
Q9R1R0 UniProt NPD GO	LHX61_MOUSE	LIM/homeobox protein Lhx6.1	0.57	-	nuc	0	Nucleus (Probable)				363
Q9UPM6 UniProt NPD GO	LHX61_HUMAN	LIM/homeobox protein Lhx6.1 (Lhx6)	0.57	-	nuc	0	Nucleus (Probable)		608215		363
P09849 UniProt NPD GO	LPH_RABIT	Lactase-phlorizin hydrolase precursor (Lactase-glycosylceramidase) [Includes: Lactase (EC 3.2.1.108) ...	0.57	-	nuc	1	Cell membrane; single-pass type I membrane protein. Brush border				1926
Q8HZI9 UniProt NPD GO	LAMC2_HORSE	Laminin gamma-2 chain precursor (Laminin 5 gamma 2 subunit)	0.57	-	exc	0	Secreted protein; extracellular space; extracellular matrix; basement membrane. Major component				1190
O64953 UniProt NPD GO	FL1_EUCGL	Leafy/floricaula homolog FL1 (ELF1)	0.57	-	cyt	0	Nucleus (Probable)				359
P09800 UniProt NPD GO	LEGB_GOSHI	Legumin B precursor (Beta-globulin B) (LEGB-C134) [Contains: Legumin B acidic chain; Legumin B basic ...	0.57	-	exc	0					516
P59178 UniProt NPD GO	LMBL2_MOUSE	Lethal(3)malignant brain tumor-like 2 protein (L(3)mbt-like 2 protein) (H-l(3)mbt-like protein)	0.57	+	mit	0	Nucleus (Probable)	nucleus [IDA]			703
Q8VDB8 UniProt NPD GO	LRRC2_MOUSE	Leucine-rich repeat-containing protein 2	0.57	-	cyt	0					371
Q8NHJ6 UniProt NPD GO	LIRB4_HUMAN	Leukocyte immunoglobulin-like receptor subfamily B member 4 precursor (Leukocyte immunoglobulin-like ...	0.57	-	nuc	1	Cell membrane; single-pass type I membrane protein. Ligand binding leads to internalization and tran ...	plasma membrane [NAS]	604821		448
Q8CGL2 UniProt NPD GO	NTAL_RAT	Linker for activation of T-cells family member 2 (Non-T-cell activation linker) (Linker for activati ...	0.57	-	nuc	1 *	Cell membrane; single-pass type III membrane protein. Present in lipid rafts (By similarity)				204
Q8BHB3 UniProt NPD GO	LAX1_MOUSE	Lymphocyte transmembrane adapter 1 (Membrane-associated adapter protein LAX) (Linker for activation ...	0.57	-	nuc	1 *	Cell membrane; single-pass type III membrane protein (By similarity)				407
O60341 UniProt NPD GO	LSD1_HUMAN	Lysine-specific histone demethylase 1 (EC 1.-.-.-) (Flavin-containing amine oxidase domain-containin ...	0.57	-	cyt	0	Nucleus		609132	2COM	852
O96935 UniProt NPD GO	AMP1_PLAFQ	M1-family aminopeptidase (EC 3.4.11.-) (Pfa-M1)	0.57	-	nuc	1 *	Cytoplasm	cytoplasm [IDA]			1085
O65874 UniProt NPD GO	MTF1_PEA	MADS-box transcription factor 1	0.57	-	nuc	0	Nucleus (Probable)	nucleus [IC]			247
Q40702 UniProt NPD GO	MADS2_ORYSA	MADS-box transcription factor 2 (OsMADS2) (RMADS219) (NMADS1)	0.57	-	nuc	0	Nucleus (Probable)				209
P08018 UniProt NPD GO	PBS2_YEAST	MAP kinase kinase PBS2 (EC 2.7.12.2) (Polymyxin B resistance protein 2) (Suppressor of fluoride sens ...	0.57	-	nuc	0	Cytoplasm	cytoplasm [IDA] NatB complex [IDA]			668
Q9WVS4 UniProt NPD GO	MOK_MOUSE	MAPK/MAK/MRK overlapping kinase (EC 2.7.11.22) (MOK protein kinase)	0.57	-	nuc	0	Cytoplasm				420
Q4R786 UniProt NPD GO	MAEL_MACFA	Maelstrom homolog	0.57	-	nuc	0	Nucleus (Potential)				434
Q9DFG8 UniProt NPD GO	MKRN2_BRARE	Makorin-2	0.57	-	nuc	0					414

You are viewing entries 20801 to 20850 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.