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
Q8BHL5 UniProt NPD GO	ELMO2_MOUSE	Engulfment and cell motility protein 2 (CED-12 homolog A)	0.79	-	nuc	0	Cytoplasm (By similarity)				732
Q96JJ3 UniProt NPD GO	ELMO2_HUMAN	Engulfment and cell motility protein 2 (CED-12 homolog A) (hCED-12A)	0.79	-	nuc	0	Cytoplasm		606421		720
Q05785 UniProt NPD GO	ENT2_YEAST	Epsin-2	0.79	+	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Localizes in a punctate pattern. Found in the acti ...	actin cortical patch [IPI]			613
Q9QZJ5 UniProt NPD GO	ESR1_MESAU	Estrogen receptor (ER) (Estradiol receptor) (ER-alpha)	0.79	+	nuc	0	Nucleus	chromatin remodeling complex [ISS] membrane [ISS]			595
P57781 UniProt NPD GO	ESR2_MICUN	Estrogen receptor beta (ER-beta)	0.79	+	nuc	0	Nucleus				673
Q9LDE4 UniProt NPD GO	ERF7_ARATH	Ethylene-responsive transcription factor 7 (Ethylene-responsive element-binding factor 7) (EREBP-7) ...	0.79	-	nuc	0	Nucleus (Probable)	nucleus [IDA]			244
Q6KAR6 UniProt NPD GO	EXOC3_MOUSE	Exocyst complex component 3 (Exocyst complex component Sec6)	0.79	-	cyt	0					755
O35382 UniProt NPD GO	EXOC4_MOUSE	Exocyst complex component 4 (Exocyst complex component Sec8)	0.79	-	nuc	0					975
Q62824 UniProt NPD GO	EXOC4_RAT	Exocyst complex component 4 (Exocyst complex component Sec8) (rSec8)	0.79	-	nuc	0		cell soma [IDA] dendritic shaft [IDA] exocyst [TAS] growth cone [IDA] neuron projection [IDA] postsynaptic density [IDA] synapse [IDA]			975
O13705 UniProt NPD GO	SEC10_SCHPO	Exocyst complex component sec10	0.79	-	nuc	0		cell cortex of cell tip [IDA] exocyst [IDA]			811
Q9Y2L1 UniProt NPD GO	RRP44_HUMAN	Exosome complex exonuclease RRP44 (EC 3.1.13.-) (Ribosomal RNA-processing protein 44) (DIS3 protein ...	0.79	-	nuc	0	Cytoplasm. Nucleus; nucleolus	exosome (RNase complex) [TAS]	607533		958
P19802 UniProt NPD GO	FMRF_LYMST	FMRFamide neuropeptides precursor [Contains: FLRF-amide 1; QFYRI-amide; FLRF-amide 2; PN (SEEPLY); F ...	0.79	-	nuc	0	Secreted protein				306
O88387 UniProt NPD GO	FGD4_RAT	FYVE, RhoGEF and PH domain-containing protein 4 (Actin filament-binding protein frabin) (FGD1-relate ...	0.79	+	nuc	0	Cytoplasm. Concentrated in filopodia and poorly detected at lamellipodia. Binds along the sides of a ...				766
Q17339 UniProt NPD GO	GLD1_CAEEL	Female germline-specific tumor suppressor gld-1 (Defective in germ line development protein 1)	0.79	-	nuc	0		cytosol [IDA]			463
Q8BUR3 UniProt NPD GO	FOXJ3_MOUSE	Forkhead box protein J3	0.79	+	nuc	0	Nucleus (Potential)				623
Q4VYR7 UniProt NPD GO	FOXP4_XENLA	Forkhead box protein P4 (xlFoxp4)	0.79	-	nuc	0	Nucleus (Probable)				641
P15408 UniProt NPD GO	FOSL2_HUMAN	Fos-related antigen 2	0.79	+	nuc	0	Nucleus	nucleus [TAS]	601575		326
P51145 UniProt NPD GO	FOSL2_RAT	Fos-related antigen 2	0.79	+	nuc	0	Nucleus				327
P48549 UniProt NPD GO	IRK3_HUMAN	G protein-activated inward rectifier potassium channel 1 (GIRK1) (Potassium channel, inwardly rectif ...	0.79	+	end	3	Membrane; multi-pass membrane protein	voltage-gated potassium channel complex [TAS]	601534		501
P24868 UniProt NPD GO	CG21_YEAST	G2/mitotic-specific cyclin-1	0.79	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			471
Q8NHY3 UniProt NPD GO	GA2L2_HUMAN	GAS2-like protein 2 (Growth arrest-specific 2-like 2) (GAS2-related protein on chromosome 17) (GAR17 ...	0.79	+	nuc	0					880
P23767 UniProt NPD GO	GAT1A_XENLA	GATA-binding factor 1-A (Transcription factor xGATA-1A)	0.79	-	nuc	0	Nucleus				359
P23768 UniProt NPD GO	GAT1B_XENLA	GATA-binding factor 1-B (Transcription factor xGATA-1B)	0.79	-	nuc	0	Nucleus				364
P43696 UniProt NPD GO	GAT5B_XENLA	GATA-binding factor 5-B (Transcription factor xGATA-5B)	0.79	-	nuc	0	Nucleus				388
O08842 UniProt NPD GO	GFRA2_MOUSE	GDNF family receptor alpha-2 precursor (GFR-alpha-2) (Neurturin receptor alpha) (NTNR-alpha) (NRTNR- ...	0.79	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				463
Q9Z1S8 UniProt NPD GO	GAB2_MOUSE	GRB2-associated-binding protein 2 (GRB2-associated binder 2) (PH domain-containing adaptor molecule ...	0.79	-	nuc	0					665
Q9UQC2 UniProt NPD GO	GAB2_HUMAN	GRB2-associated-binding protein 2 (GRB2-associated binder 2) (pp100)	0.79	-	nuc	0			606203		676
Q96CW5 UniProt NPD GO	GCP3_HUMAN	Gamma-tubulin complex component 3 (GCP-3) (Spindle pole body protein Spc98 homolog) (hSpc98) (hGCP3) ...	0.79	-	nuc	0	Centrosome	centriole [IDA] cytoplasm [IDA] polar microtubule [IDA]			907
O75496 UniProt NPD GO	GEMI_HUMAN	Geminin	0.79	+	nuc	0			602842	1UII	209
Q5R9P5 UniProt NPD GO	GCR_PONPY	Glucocorticoid receptor (GR)	0.79	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Cytoplasmic in the absence of ligand; nuclear af ...				777
Q03445 UniProt NPD GO	GLK1_DROME	Glutamate receptor 1 precursor (Glutamate receptor I) (dGLUR-I) (Kainate-selective glutamate recepto ...	0.79	-	end	3	Membrane; multi-pass membrane protein				991
Q9C0E4 UniProt NPD GO	GRIP2_HUMAN	Glutamate receptor-interacting protein 2 (GRIP2 protein)	0.79	+	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)			1X5R	1043
Q92538 UniProt NPD GO	GBF1_HUMAN	Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 (BFA-resistant GEF 1)	0.79	-	nuc	0		Golgi apparatus [ISS]	603698		1859
O77681 UniProt NPD GO	GDF9_SHEEP	Growth/differentiation factor 9 precursor (GDF-9)	0.79	-	exc	0	Secreted protein (By similarity)				453
Q63406 UniProt NPD GO	MCF2L_RAT	Guanine nucleotide exchange factor DBS (DBL's big sister) (MCF2-transforming sequence-like protein) ...	0.79	-	nuc	0	Cytoplasm			1RJ2	937
Q61666 UniProt NPD GO	HIRA_MOUSE	HIRA protein (TUP1-like enhancer of split protein 1)	0.79	+	nuc	0	Nucleus (By similarity). Primarily, though not exclusively, localized to the nucleus (By similarity) ...	nuclear chromatin [IDA]			1015
Q8R316 UniProt NPD GO	HBP1_MOUSE	HMG box-containing protein 1 (HMG box transcription factor 1) (High mobility group box transcription ...	0.79	-	nuc	0	Nucleus			1S5R	516
Q9SCW5 UniProt NPD GO	HSF2_ARATH	Heat shock factor protein 2 (HSF 2) (Heat shock transcription factor 2) (HSTF 2)	0.79	-	nuc	0	Nucleus (By similarity)				468
Q56A36 UniProt NPD GO	HSH2D_BRARE	Hematopoietic SH2 domain-containing protein homolog	0.79	-	nuc	0					365
P16887 UniProt NPD GO	H2BS2_STRPU	Histone H2B.2, sperm	0.79	+	mit	0	Nucleus				143
Q5AZR6 UniProt NPD GO	HAT1_EMENI	Histone acetyltransferase type B catalytic subunit (EC 2.3.1.48)	0.79	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				496
Q613L4 UniProt NPD GO	HDA4_CAEBR	Histone deacetylase 4	0.79	-	nuc	0	Nucleus (By similarity)				892
Q9PWL5 UniProt NPD GO	HXA4A_BRARE	Homeobox protein Hox-A4a (Zf-26) (Hoxx4)	0.79	+	nuc	0	Nucleus (By similarity)				245
Q90VZ9 UniProt NPD GO	HXA7_CHICK	Homeobox protein Hox-A7	0.79	+	nuc	0	Nucleus (By similarity)				219
P14840 UniProt NPD GO	HXB4_CHICK	Homeobox protein Hox-B4 (Chox-Z)	0.79	+	nuc	0	Nucleus				245
Q8AWY9 UniProt NPD GO	HXB7A_BRARE	Homeobox protein Hox-B7a (Hox-B7)	0.79	+	nuc	0	Nucleus (By similarity)				227
P17482 UniProt NPD GO	HXB9_HUMAN	Homeobox protein Hox-B9 (Hox-2E) (Hox-2.5)	0.79	+	nuc	0	Nucleus	nucleus [NAS]	142964		250
Q99MA9 UniProt NPD GO	NKX61_MOUSE	Homeobox protein Nkx-6.1	0.79	+	nuc	0	Nucleus (Probable)	nucleus [IDA]			365
O35762 UniProt NPD GO	NKX61_RAT	Homeobox protein Nkx-6.1	0.79	+	nuc	0	Nucleus (Probable)				365
O35137 UniProt NPD GO	ALX4_MOUSE	Homeobox protein aristaless-like 4 (ALX-4)	0.79	+	nuc	0	Nucleus	transcription factor complex [IPI]			399

You are viewing entries 9351 to 9400 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.