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
Q5CZK6 UniProt NPD GO	INSL4_PANTR	Early placenta insulin-like peptide precursor (EPIL) (Placentin) (Insulin-like peptide 4) [Contains: ...	0.65	-	exc	0	Secreted protein (By similarity)				139
P50402 UniProt NPD GO	EMD_HUMAN	Emerin	0.65	-	nuc	1	Nucleus; nuclear inner membrane; single-pass membrane protein; nucleoplasmic side. Colocalized with ...	nuclear envelope [TAS]	300384	1JEI	254
Q9Z1Z3 UniProt NPD GO	EPN2_RAT	Epsin-2 (EPS-15-interacting protein 2)	0.65	-	nuc	0	Cytoplasm (By similarity). In punctate structures throughout the cell and particularly concentrated ...	clathrin coat of endocytic vesicle [IDA]			583
O80339 UniProt NPD GO	ERF3_ARATH	Ethylene-responsive transcription factor 3 (Ethylene-responsive element-binding factor 3) (EREBP-3) ...	0.65	-	mit	0	Nucleus (Probable)				225
Q03387 UniProt NPD GO	IF41_WHEAT	Eukaryotic initiation factor iso-4F subunit p82-34 (eIF-(iso)4F p82-34)	0.65	-	nuc	0					788
P41375 UniProt NPD GO	IF2B_DROME	Eukaryotic translation initiation factor 2 subunit beta (eIF-2-beta)	0.65	+	nuc	0					312
Q80T14 UniProt NPD GO	FRAS1_MOUSE	Extracellular matrix protein FRAS1 precursor	0.65	-	end	1	Membrane; single-pass type I membrane protein (Potential)	basement membrane [IDA]			4010
P97480 UniProt NPD GO	EYA3_MOUSE	Eyes absent homolog 3 (EC 3.1.3.48)	0.65	-	nuc	0	Cytoplasm. Nucleus	nucleus [IDA]			510
Q8K2I9 UniProt NPD GO	FBX18_MOUSE	F-box only protein 18 (EC 3.6.1.-) (F-box DNA helicase 1)	0.65	-	nuc	0	Nucleus (Probable)				1042
Q8BG80 UniProt NPD GO	FBX46_MOUSE	F-box only protein 46 (F-box only protein 34-like)	0.65	-	nuc	0					603
Q920B9 UniProt NPD GO	SPT16_MOUSE	FACT complex subunit SPT16 (Facilitates chromatin transcription complex subunit SPT16) (FACT 140 kDa ...	0.65	+	mit	0	Nucleus. Colocalizes with RNA polymerase II on chromatin. Recruited to actively transcribed loci				1047
Q9Y5B9 UniProt NPD GO	SPT16_HUMAN	FACT complex subunit SPT16 (Facilitates chromatin transcription complex subunit SPT16) (hSPT16) (FAC ...	0.65	+	mit	0	Nucleus. Colocalizes with RNA polymerase II on chromatin. Recruited to actively transcribed loci		605012		1047
Q9LGR0 UniProt NPD GO	SSP1A_ORYSA	FACT complex subunit SSRP1-A (Facilitates chromatin transcription complex subunit SSRP1-A) (Recombin ...	0.65	+	cyt	0	Nucleus (By similarity)				641
Q9UNN5 UniProt NPD GO	FAF1_HUMAN	FAS-associated factor 1 (Protein FAF1) (hFAF1)	0.65	-	nuc	0	Nucleus (Potential)	CD95 death-inducing signaling complex [NAS] cytosol [IDA] nucleus [IDA] perinuclear region [IDA]	604460	1H8C	650
Q5BD53 UniProt NPD GO	YFAS1_EMENI	FAS1 domain-containing protein AN1527 precursor	0.65	-	mit	1 *	Vacuole (By similarity)				223
Q00342 UniProt NPD GO	FLT3_MOUSE	FL cytokine receptor precursor (EC 2.7.10.1) (Tyrosine-protein kinase receptor flk-2) (Fetal liver k ...	0.65	-	end	2 *	Membrane; single-pass type I membrane protein				992
Q02360 UniProt NPD GO	FD2_DROME	Fork head domain-containing protein FD2	0.65	-	nuc	0	Nucleus				365
Q61572 UniProt NPD GO	FOXC1_MOUSE	Forkhead box protein C1 (Forkhead-related protein FKHL7) (Forkhead-related transcription factor 3) ( ...	0.65	+	nuc	0	Nucleus				553
Q9UJU5 UniProt NPD GO	FOXD3_HUMAN	Forkhead box protein D3 (HNF3/FH transcription factor genesis)	0.65	-	nuc	0	Nucleus (Probable)	nucleus [ISS]			478
Q63245 UniProt NPD GO	FOXD3_RAT	Forkhead box protein D3 (HNF3/FH transcription factor genesis) (Hepatocyte nuclear factor 3 forkhead ...	0.65	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]		2HFH	101
O70220 UniProt NPD GO	FOXQ1_MOUSE	Forkhead box protein Q1 (Hepatocyte nuclear factor 3 forkhead homolog 1) (HNF-3/forkhead-like protei ...	0.65	-	nuc	0	Nucleus (By similarity)				400
P32604 UniProt NPD GO	F26_YEAST	Fructose-2,6-bisphosphatase (EC 3.1.3.46)	0.65	-	cyt	0					452
Q62833 UniProt NPD GO	GRK5_RAT	G protein-coupled receptor kinase 5 (EC 2.7.11.16) (G protein-coupled receptor kinase GRK5)	0.65	+	nuc	0					590
Q8CJ11 UniProt NPD GO	GPR64_RAT	G-protein coupled receptor 64 precursor (Epididymis-specific protein 6) (Re6 receptor)	0.65	-	end	7 *	Membrane; multi-pass membrane protein				1013
Q95QJ7 UniProt NPD GO	GPR1_CAEEL	G-protein regulator 1	0.65	-	nuc	0	Cytoplasm; cell cortex. Spindle. Located to the spindle and cell cortex when in complex with lin-5 a ...				525
P34638 UniProt NPD GO	CCNA1_CAEEL	G2/mitotic-specific cyclin-A1	0.65	-	nuc	0					485
Q8WR51 UniProt NPD GO	OFUT2_CAEEL	GDP-fucose protein O-fucosyltransferase 2 precursor (EC 2.4.1.221) (Peptide-O-fucosyltransferase) (O ...	0.65	-	end	0	Endoplasmic reticulum (By similarity)				424
Q96HH9 UniProt NPD GO	GRAM3_HUMAN	GRAM domain-containing protein 3 (HCV NS3-transactivated protein 2)	0.65	-	nuc	1					432
Q8CHG3 UniProt NPD GO	GCC2_MOUSE	GRIP and coiled-coil domain-containing protein 2 (Golgi coiled coil protein GCC185)	0.65	-	nuc	0	Cytoplasm. Golgi apparatus; Golgi membrane; peripheral membrane protein (By similarity)				1679
Q95KD9 UniProt NPD GO	DIRA2_MACFA	GTP-binding protein Di-Ras2 (Distinct subgroup of the Ras family member 2)	0.65	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				199
P33277 UniProt NPD GO	GAP1_SCHPO	GTPase-activating protein (Ras GTPase-activating protein)	0.65	-	nuc	0					766
P32873 UniProt NPD GO	BEM3_YEAST	GTPase-activating protein BEM3 (Bud emergence protein 3)	0.65	-	nuc	0	Cytoplasm	intracellular [TAS]			1128
Q6FWI1 UniProt NPD GO	GYP7_CANGA	GTPase-activating protein GYP7 (GAP for YPT7)	0.65	-	nuc	0					745
P15518 UniProt NPD GO	GIAB_GIALA	Giardin subunit beta (Protein 14B, cytoskeletal)	0.65	-	nuc	0	Microribbons of ventral disc				273
Q9R1M7 UniProt NPD GO	NMD3A_RAT	Glutamate [NMDA] receptor subunit 3A precursor (N-methyl-D-aspartate receptor subtype 3A) (NR3A) (NM ...	0.65	-	end	4	Cell membrane; multi-pass membrane protein. Enriched in post-synaptic plasma membrane and post-synap ...				1135
Q05586 UniProt NPD GO	NMDZ1_HUMAN	Glutamate [NMDA] receptor subunit zeta 1 precursor (N-methyl-D-aspartate receptor subunit NR1)	0.65	+	end	3	Cell membrane; multi-pass membrane protein (By similarity). Enriched in post-synaptic plasma membran ...	dendrite [IDA] growth cone [ISS] N-methyl-D-aspartate selective glutamate re... [IDA]	138249	2NR1	938
Q9Y3R0 UniProt NPD GO	GRIP1_HUMAN	Glutamate receptor-interacting protein 1 (GRIP1 protein)	0.65	-	nuc	0	Cytoplasmic and membrane-associated with vesicles, peri-Golgi complexes and endoplasmic reticulum. E ...		604597		1128
P34114 UniProt NPD GO	PHS2_DICDI	Glycogen phosphorylase 2 (EC 2.4.1.1) (GP2)	0.65	-	mit	0					992
O22151 UniProt NPD GO	GOS12_ARATH	Golgi SNARE 12 protein (AtGOS12) (Golgi SNAP receptor complex member 1-2)	0.65	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein (By similarity)				239
Q92805 UniProt NPD GO	GOGA1_HUMAN	Golgin subfamily A member 1 (Golgin-97)	0.65	-	nuc	0	Golgi apparatus; Golgi stack; Golgi stack membrane; peripheral membrane protein	Golgi apparatus [TAS]	602502		767
Q03113 UniProt NPD GO	GNA12_HUMAN	Guanine nucleotide-binding protein alpha-12 subunit (G alpha-12)	0.65	-	cyt	0	Membrane; lipid-anchor		604394		380
P27600 UniProt NPD GO	GNA12_MOUSE	Guanine nucleotide-binding protein alpha-12 subunit (G alpha-12)	0.65	-	mit	0	Membrane; lipid-anchor	heterotrimeric G-protein complex [TAS]		1ZCA	378
P30678 UniProt NPD GO	GNA15_MOUSE	Guanine nucleotide-binding protein alpha-15 subunit (G alpha-15)	0.65	-	cyt	0		heterotrimeric G-protein complex [NAS]			374
Q20910 UniProt NPD GO	GPA9_CAEEL	Guanine nucleotide-binding protein alpha-9 subunit	0.65	-	mit	0					390
Q9VR91 UniProt NPD GO	HERC2_DROME	HECT domain and RCC1-like domain-containing protein 2	0.65	+	end	0					4912
P61578 UniProt NPD GO	REC16_HUMAN	HERV-K_10p14 provirus Rec protein	0.65	-	nuc	0	Cytoplasm (By similarity). Nucleus; nucleolus (By similarity). Shuttles between the nucleus and the ...				105
P62683 UniProt NPD GO	GAK1_HUMAN	HERV-K_12q14.1 provirus ancestral Gag polyprotein (Gag polyprotein) [Contains: Matrix protein; Capsi ...	0.65	-	nuc	0	Cell membrane. Cytoplasmic membrane (in a transfection system) (By similarity)				665
P38532 UniProt NPD GO	HSF1_MOUSE	Heat shock factor protein 1 (HSF 1) (Heat shock transcription factor 1) (HSTF 1)	0.65	-	nuc	0	Cytoplasm. Nucleus. Cytoplasmic during normal growth and moves to the nucleus upon activation	cytoplasm [IDA] pronucleus [IDA]			525
Q6FU50 UniProt NPD GO	LHS1_CANGA	Heat shock protein 70 homolog LHS1 precursor	0.65	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				889
P41887 UniProt NPD GO	HSP90_SCHPO	Heat shock protein 90 homolog	0.65	-	cyt	0					704

You are viewing entries 16301 to 16350 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.