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
P36111 UniProt NPD GO	YKZ5_YEAST	Hypothetical 66.6 kDa protein in YPT52-DBP7 intergenic region	0.81	-	nuc	0					568
Q9HGP4 UniProt NPD GO	YK82_SCHPO	Hypothetical bromodomain protein C631.02	0.81	-	nuc	0					727
Q17865 UniProt NPD GO	YTE4_CAEEL	Hypothetical protein C09G1.4	0.81	-	nuc	0					546
P87132 UniProt NPD GO	YFK5_SCHPO	Hypothetical protein C167.05 in chromosome I	0.81	-	nuc	0					601
Q09249 UniProt NPD GO	YQ53_CAEEL	Hypothetical protein C16C10.3	0.81	-	nuc	0					1032
Q10070 UniProt NPD GO	YAN4_SCHPO	Hypothetical protein C3H1.04c in chromosome I	0.81	-	nuc	1					601
Q09303 UniProt NPD GO	YQP2_CAEEL	Hypothetical protein F07F6.2	0.81	+	mit	3 *	Membrane; multi-pass membrane protein (Potential)				261
Q09949 UniProt NPD GO	YSH8_CAEEL	Hypothetical protein F12A10.8	0.81	-	nuc	0					437
P41884 UniProt NPD GO	YPT6_CAEEL	Hypothetical protein F37A4.6	0.81	-	nuc	0					389
Q26768 UniProt NPD GO	AGI6_TRYBB	I/6 autoantigen	0.81	+	nuc	0					243
Q4I099 UniProt NPD GO	TIM50_GIBZE	Import inner membrane translocase subunit TIM50, mitochondrial precursor	0.81	-	mit	0	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				525
Q865X1 UniProt NPD GO	IFNG_LAMGL	Interferon gamma precursor (IFN-gamma)	0.81	+	exc	0	Secreted protein (By similarity)				166
Q8MKF5 UniProt NPD GO	IFNG_SAISC	Interferon gamma precursor (IFN-gamma)	0.81	-	exc	0	Secreted protein (By similarity)				166
Q7LBC6 UniProt NPD GO	JHD2B_HUMAN	JmjC domain-containing histone demethylation protein 2B (EC 1.14.11.-) (Jumonji domain-containing pr ...	0.81	+	nuc	0	Nucleus (By similarity)		609373		1761
P17119 UniProt NPD GO	KAR3_YEAST	Kinesin-like protein KAR3 (Nuclear fusion protein)	0.81	-	nuc	0		microtubule [TAS] spindle pole body [IDA]		3KAR	729
O08672 UniProt NPD GO	KIFC2_MOUSE	Kinesin-like protein KIFC2	0.81	-	nuc	0					792
Q9ERG0 UniProt NPD GO	LIMA1_MOUSE	LIM domain and actin-binding protein 1 (Epithelial protein lost in neoplasm) (mEPLIN)	0.81	-	nuc	0	Cytoplasm. Cytoskeleton. This cytoskeletal protein co-localizes with actin stress fibers	focal adhesion [ISS] stress fiber [ISS]			753
P53670 UniProt NPD GO	LIMK2_RAT	LIM domain kinase 2 (EC 2.7.11.1) (LIMK-2)	0.81	-	cyt	0	Cytoplasm (By similarity)	nucleus [IDA] soluble fraction [IDA]			638
Q9R0B6 UniProt NPD GO	LAMC3_MOUSE	Laminin gamma-3 chain precursor (Laminin 12 gamma 3 subunit)	0.81	-	nuc	0	Secreted protein; extracellular space				1581
Q9Z1R2 UniProt NPD GO	BAT3_MOUSE	Large proline-rich protein BAT3 (HLA-B-associated transcript 3)	0.81	-	nuc	0					1154
Q9Y250 UniProt NPD GO	LZTS1_HUMAN	Leucine zipper putative tumor suppressor 1 (F37/esophageal cancer-related gene-coding leucine-zipper ...	0.81	-	nuc	0	Cytoplasm (By similarity). Cell membrane (By similarity). Associated with the plasma membrane and wi ...	nucleus [NAS]	606551		595
Q91WK0 UniProt NPD GO	LRRF2_MOUSE	Leucine-rich repeat flightless-interacting protein 2 (LRR FLI-II-interacting protein 2)	0.81	-	nuc	0					415
Q38SD2 UniProt NPD GO	LRRK1_HUMAN	Leucine-rich repeat serine/threonine-protein kinase 1 (EC 2.7.11.1)	0.81	-	end	0	Cytoplasm				2038
Q3UHC2 UniProt NPD GO	LRRK1_MOUSE	Leucine-rich repeat serine/threonine-protein kinase 1 (EC 2.7.11.1)	0.81	-	end	0	Cytoplasm (By similarity)				2014
Q8K375 UniProt NPD GO	LRC56_MOUSE	Leucine-rich repeat-containing protein 56	0.81	-	nuc	0					552
Q96AG4 UniProt NPD GO	LRC59_HUMAN	Leucine-rich repeat-containing protein 59	0.81	+	nuc	1	Microsome; microsomal membrane; single-pass type II membrane protein (By similarity)				307
Q5RJR8 UniProt NPD GO	LRC59_RAT	Leucine-rich repeat-containing protein 59 (Protein p34)	0.81	+	nuc	1	Microsome; microsomal membrane; single-pass type II membrane protein				307
Q96NW7 UniProt NPD GO	LRRC7_HUMAN	Leucine-rich repeat-containing protein 7 (Protein LAP1) (Densin-180)	0.81	-	nuc	0	Cytoplasm				1537
P70587 UniProt NPD GO	LRRC7_RAT	Leucine-rich repeat-containing protein 7 (Protein LAP1) (Densin-180)	0.81	-	nuc	0	Cytoplasm (By similarity)				1495
O75427 UniProt NPD GO	LRCH4_HUMAN	Leucine-rich repeats and calponin homology domain-containing protein 4 (Leucine-rich neuronal protei ...	0.81	-	nuc	1					683
Q99088 UniProt NPD GO	LDLR2_XENLA	Low-density lipoprotein receptor 2 precursor (LDL receptor 2)	0.81	-	exc	1	Membrane; single-pass type I membrane protein				892
O74304 UniProt NPD GO	WIN1_SCHPO	MAP kinase kinase kinase win1 (EC 2.7.11.25)	0.81	-	nuc	0					1436
O14299 UniProt NPD GO	WIS4_SCHPO	MAP kinase kinase kinase wis4 (EC 2.7.11.25) (MAP kinase kinase kinase wak1) (MAP kinase kinase kina ...	0.81	-	nuc	0					1401
Q4G050 UniProt NPD GO	MKNK1_RAT	MAP kinase-interacting serine/threonine-protein kinase 1 (EC 2.7.11.1) (MAP kinase signal-integratin ...	0.81	+	cyt	0					413
Q9UQ07 UniProt NPD GO	MOK_HUMAN	MAPK/MAK/MRK overlapping kinase (EC 2.7.11.22) (MOK protein kinase) (Renal tumor antigen 1) (RAGE-1) ...	0.81	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [TAS]	605762		419
P22018 UniProt NPD GO	B4_USTMA	Mating-type locus allele B4 protein	0.81	-	nuc	0	Nucleus				410
P22019 UniProt NPD GO	B5_USTMA	Mating-type locus allele B5 protein	0.81	-	nuc	0	Nucleus				410
Q708A7 UniProt NPD GO	MATA1_CANGA	Mating-type-like protein A1 (MTL1a1 protein)	0.81	-	nuc	0	Nucleus (By similarity)				130
Q7HUK6 UniProt NPD GO	MATK_MENLI	Maturase K (Intron maturase)	0.81	-	cyt	0	Plastid; chloroplast				506
Q9UH92 UniProt NPD GO	MLX_HUMAN	Max-like protein X (Max-like bHLHZip protein) (BigMax protein) (Protein Mlx) (Transcription factor-l ...	0.81	-	nuc	0	Isoform Alpha, isoform Beta: Cytoplasm. Predominantly. Isoform Gamma: Nucleus. Predominantly	cytoplasm [IDA] nucleus [IDA]	602976		298
Q9BE18 UniProt NPD GO	MAGE1_MACFA	Melanoma-associated antigen E1 (MAGE-E1 antigen)	0.81	+	nuc	0		dendrite [ISS] nucleus [ISS] perinuclear region [ISS] plasma membrane [ISS] postsynaptic membrane [ISS]			957
Q07243 UniProt NPD GO	MTF1_MOUSE	Metal-regulatory transcription factor 1 (Transcription factor MTF-1) (MRE-binding transcription fact ...	0.81	-	nuc	0	Nucleus (Potential)	nucleus [IDA]			675
P46773 UniProt NPD GO	RT03_ORYSA	Mitochondrial ribosomal protein S3	0.81	-	nuc	0	Mitochondrion				538
P46745 UniProt NPD GO	RT07_PROWI	Mitochondrial ribosomal protein S7	0.81	-	nuc	0	Mitochondrion				222
Q99K90 UniProt NPD GO	TAB2_MOUSE	Mitogen-activated protein kinase kinase kinase 7-interacting protein 2 (TAK1-binding protein 2) (TAB ...	0.81	-	nuc	0	Nucleus. Cytoplasm; cytosol. Cytoplasmic when activated. Following IL1 stimulation, localized in the ...				693
P41279 UniProt NPD GO	M3K8_HUMAN	Mitogen-activated protein kinase kinase kinase 8 (EC 2.7.11.25) (COT proto-oncogene serine/threonine ...	0.81	-	cyt	0	Cytoplasm	cytosol [TAS]	191195		467
Q17103 UniProt NPD GO	MYC_ASTVU	Myc protein (c-myc) (Fragment)	0.81	+	nuc	0	Nucleus				407
Q60929 UniProt NPD GO	MEF2A_MOUSE	Myocyte-specific enhancer factor 2A	0.81	-	nuc	0	Nucleus	nucleus [IC]			498
Q06413 UniProt NPD GO	MEF2C_HUMAN	Myocyte-specific enhancer factor 2C	0.81	-	nuc	0	Nucleus		600662		473
P34061 UniProt NPD GO	MYF5_COTJA	Myogenic factor 5 (Myf-5) (Myogenic factor 3) (Fragment)	0.81	+	nuc	0	Nucleus (Potential)				246

You are viewing entries 8401 to 8450 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.