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
Q9Y5E8 UniProt NPD GO	PCDBF_HUMAN	Protocadherin beta 15 precursor (PCDH-beta15)	0.27	-	end	1	Membrane; single-pass type I membrane protein (By similarity)	integral to plasma membrane [TAS]	606341		787
Q9Y5H0 UniProt NPD GO	PCDG3_HUMAN	Protocadherin gamma A3 precursor (PCDH-gamma-A3)	0.27	-	end	1	Membrane; single-pass type I membrane protein (By similarity)		606290		932
Q5DRB7 UniProt NPD GO	PCDG3_PANTR	Protocadherin gamma A3 precursor (PCDH-gamma-A3)	0.27	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				932
Q96QE2 UniProt NPD GO	MYCT_HUMAN	Proton myo-inositol cotransporter (H(+)-myo-inositol cotransporter) (Hmit)	0.27	-	end	12	Membrane; multi-pass membrane protein				629
P22355 UniProt NPD GO	PSPB_RAT	Pulmonary surfactant-associated protein B precursor (SP-B) (Pulmonary surfactant-associated proteoli ...	0.27	-	end	0	Secreted protein; extracellular space				376
Q09966 UniProt NPD GO	YS97_CAEEL	Putative G-protein coupled receptor B0244.7	0.27	-	end	6 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			319
Q6QPM2 UniProt NPD GO	GAT21_ARATH	Putative GATA transcription factor 21	0.27	-	nuc	0	Nucleus (Probable)				211
P25612 UniProt NPD GO	AAD3_YEAST	Putative aryl-alcohol dehydrogenase AAD3 (EC 1.1.1.-)	0.27	-	mit	0					363
P34220 UniProt NPD GO	YBF5_YEAST	Putative deoxyribonuclease YBL055C (EC 3.1.21.-)	0.27	-	mit	0		cytoplasm [IDA]			418
O22727 UniProt NPD GO	DRL16_ARATH	Putative disease resistance protein At1g61190	0.27	-	nuc	0					967
O75642 UniProt NPD GO	IF1AH_HUMAN	Putative eukaryotic translation initiation factor 1A (eIF-1A) (eIF-4C)	0.27	-	nuc	0					143
O17438 UniProt NPD GO	DHX15_STRPU	Putative pre-mRNA-splicing factor ATP-dependent RNA helicase PRP1 (EC 3.6.1.-) (Fragment)	0.27	-	cyt	0	Nucleus (By similarity)				455
Q20939 UniProt NPD GO	PDXH_CAEEL	Putative pyridoxamine 5'-phosphate oxidase (EC 1.4.3.5) (PNP/PMP oxidase) (PNPOx)	0.27	-	mit	0					253
P36170 UniProt NPD GO	YK82_YEAST	Putative uncharacterized protein YKR102W precursor	0.27	-	exc	1 *	Cell wall (By similarity)				1169
P78992 UniProt NPD GO	PYC_PICPA	Pyruvate carboxylase (EC 6.4.1.1) (Pyruvic carboxylase) (PCB)	0.27	-	cyt	0	Cytoplasm				1189
Q91XU1 UniProt NPD GO	QKI_RAT	Quaking protein	0.27	+	nuc	0	Nucleus (By similarity). Cytoplasm				341
Q5W9D7 UniProt NPD GO	QKI_BOVIN	Quaking protein (BqkI)	0.27	+	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity)				341
Q9GMY1 UniProt NPD GO	QKI_CANFA	Quaking protein (CqkI)	0.27	+	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity)				341
Q5W9D6 UniProt NPD GO	QKI_HORSE	Quaking protein (EqkI)	0.27	+	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity)				341
Q7JJZ8 UniProt NPD GO	QKI_FELCA	Quaking protein (FqkI)	0.27	+	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity)				341
Q96PU8 UniProt NPD GO	QKI_HUMAN	Quaking protein (Hqk)	0.27	+	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity)		609590		341
Q5W9D5 UniProt NPD GO	QKI_PIG	Quaking protein (PqkI)	0.27	+	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity)				341
Q9QYS9 UniProt NPD GO	QKI_MOUSE	Quaking protein (qkI)	0.27	+	nuc	0	Cytoplasm. Nucleus. Isoform 1 localizes predominantly in the nucleus and at lower level in cytoplasm ...	cytoplasm [TAS] nucleus [TAS]			341
Q6P104 UniProt NPD GO	QKIB_BRARE	Quaking protein B (Quaking-related protein)	0.27	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity)				319
P34784 UniProt NPD GO	PHEG_AGLNE	R-phycoerythrin gamma chain, chloroplast precursor	0.27	-	nuc	0	Periphery of the rods of the phycobilisome (By similarity)				317
Q9QYK7 UniProt NPD GO	RNF11_MOUSE	RING finger protein 11 (NEDD4 WW domain-binding protein 2) (Sid 1669)	0.27	-	nuc	0		ubiquitin ligase complex [IPI]			154
Q9H6Y7 UniProt NPD GO	RN167_HUMAN	RING finger protein 167 precursor	0.27	-	end	1	Membrane; single-pass membrane protein (Potential)				350
Q9SLC4 UniProt NPD GO	ATL2K_ARATH	RING-H2 finger protein ATL2K	0.27	-	nuc	1 *					217
O14010 UniProt NPD GO	MED22_SCHPO	RNA polymerase II mediator complex subunit 22 (Suppressor of RNA polymerase B 6 homolog)	0.27	-	nuc	0	Nucleus (Probable)	mediator complex [IDA]			136
P50396 UniProt NPD GO	GDIA_MOUSE	Rab GDP dissociation inhibitor alpha (Rab GDI alpha) (Guanosine diphosphate dissociation inhibitor 1 ...	0.27	-	nuc	0	Cytoplasm (By similarity)				447
Q7YQM0 UniProt NPD GO	GDIA_PONPY	Rab GDP dissociation inhibitor alpha (Rab GDI alpha) (Guanosine diphosphate dissociation inhibitor 1 ...	0.27	-	nuc	0	Cytoplasm (By similarity)				447
P05774 UniProt NPD GO	RAS_CARAU	Ras-like protein (Fragment)	0.27	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				183
P32254 UniProt NPD GO	RASS_DICDI	Ras-like protein rasS	0.27	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				194
P62998 UniProt NPD GO	RAC1_BOVIN	Ras-related C3 botulinum toxin substrate 1 precursor (p21-Rac1)	0.27	+	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (By similarity). Inner surface of plasma membrane poss ...				192
P63001 UniProt NPD GO	RAC1_MOUSE	Ras-related C3 botulinum toxin substrate 1 precursor (p21-Rac1)	0.27	+	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (By similarity). Inner surface of plasma membrane poss ...	cytoplasm [IDA] cytoplasmic membrane-bound vesicle [IDA] extrinsic to plasma membrane [IDA] lamellipodium [IDA] membrane fraction [IDA]			192
Q6RUV5 UniProt NPD GO	RAC1_RAT	Ras-related C3 botulinum toxin substrate 1 precursor (p21-Rac1)	0.27	+	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (By similarity). Inner surface of plasma membrane poss ...				192
P62999 UniProt NPD GO	RAC1_CANFA	Ras-related C3 botulinum toxin substrate 1 precursor (p21-Rac1) (Rac2)	0.27	+	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (By similarity). Inner surface of plasma membrane poss ...				192
P63000 UniProt NPD GO	RAC1_HUMAN	Ras-related C3 botulinum toxin substrate 1 precursor (p21-Rac1) (Ras-like protein TC25)	0.27	+	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (By similarity). Inner surface of plasma membrane poss ...		602048	1RYH	192
P28188 UniProt NPD GO	ARA5_ARATH	Ras-related protein ARA-5	0.27	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				258
P36412 UniProt NPD GO	RAB11_DICDI	Ras-related protein Rab11	0.27	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				214
P62833 UniProt NPD GO	RAP1A_BOVIN	Ras-related protein Rap-1A precursor (GTP-binding protein smg-p21A)	0.27	-	cyt	0	Cell membrane; lipid-anchor				184
P62834 UniProt NPD GO	RAP1A_HUMAN	Ras-related protein Rap-1A precursor (GTP-binding protein smg-p21A) (Ras-related protein Krev-1) (C2 ...	0.27	-	cyt	0	Cell membrane; lipid-anchor		179520	1GUA	184
P62835 UniProt NPD GO	RAP1A_MOUSE	Ras-related protein Rap-1A precursor (Ras-related protein Krev-1)	0.27	-	cyt	0	Cell membrane; lipid-anchor (By similarity)				184
P62836 UniProt NPD GO	RAP1A_RAT	Ras-related protein Rap-1A precursor (Ras-related protein Krev-1)	0.27	-	cyt	0	Cell membrane; lipid-anchor (By similarity)				184
O15539 UniProt NPD GO	RGS5_HUMAN	Regulator of G-protein signaling 5 (RGS5)	0.27	-	nuc	0			603276	2CRP	181
P23800 UniProt NPD GO	RCC1_MESAU	Regulator of chromosome condensation (Chromosome condensation protein 1)	0.27	-	mit	0	Nucleus. Cytoplasm. Becomes dispersed throughout the cytoplasm during mitosis				421
Q8VE37 UniProt NPD GO	RCC1_MOUSE	Regulator of chromosome condensation (Chromosome condensation protein 1)	0.27	-	cyt	0	Nucleus (By similarity). Cytoplasm (By similarity). Becomes dispersed throughout the cytoplasm durin ...				421
Q94547 UniProt NPD GO	RGA_DROME	Regulator of gene activity (Protein regena)	0.27	-	cyt	0		nucleus [NAS]			585
P00797 UniProt NPD GO	RENI_HUMAN	Renin precursor (EC 3.4.23.15) (Angiotensinogenase)	0.27	-	end	0	Secreted protein. Membrane. Associated to membranes via binding to ATP6AP2		179820	2REN	406
P60016 UniProt NPD GO	RENI_PANTR	Renin precursor (EC 3.4.23.15) (Angiotensinogenase)	0.27	-	end	0	Secreted protein (By similarity). Membrane (By similarity). Associated to membranes via binding to A ...				406

You are viewing entries 43601 to 43650 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.