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
Q64010 UniProt NPD GO	CRK_MOUSE	Proto-oncogene C-crk (P38) (Adapter molecule crk)	0.28	-	nuc	0	Cytoplasm (By similarity). Cell membrane (By similarity). Translocated to the plasma membrane upon c ...			1M3C	304
Q5DRF3 UniProt NPD GO	PCDAB_PANTR	Protocadherin alpha 11 precursor (PCDH-alpha11)	0.28	+	nuc	1	Membrane; single-pass type I membrane protein (By similarity)				949
Q767I8 UniProt NPD GO	PCDA4_RAT	Protocadherin alpha 4 precursor (PCDH-alpha4) (Cadherin-related neuronal receptor 4)	0.28	+	nuc	0	Membrane; single-pass membrane protein (By similarity)				947
Q9UN73 UniProt NPD GO	PCDA6_HUMAN	Protocadherin alpha 6 precursor (PCDH-alpha6)	0.28	+	end	0	Isoform 1: Cell membrane; single-pass type I membrane protein (By similarity). Isoform 2: Secreted p ...	integral to plasma membrane [TAS]	606312		950
Q9Y5H2 UniProt NPD GO	PCDGB_HUMAN	Protocadherin gamma A11 precursor (PCDH-gamma-A11)	0.28	-	nuc	2 *	Membrane; single-pass type I membrane protein (By similarity)		606298		935
Q5DRA9 UniProt NPD GO	PCDGE_PANTR	Protocadherin gamma B2 precursor (PCDH-gamma-B2)	0.28	-	nuc	1 *	Membrane; single-pass type I membrane protein (By similarity)				931
Q9Y5G1 UniProt NPD GO	PCDGF_HUMAN	Protocadherin gamma B3 precursor (PCDH-gamma-B3)	0.28	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)		606301		929
O14917 UniProt NPD GO	PCD17_HUMAN	Protocadherin-17 precursor (Protocadherin-68)	0.28	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				889
Q6BKW6 UniProt NPD GO	COX10_DEBHA	Protoheme IX farnesyltransferase, mitochondrial precursor (EC 2.5.1.-) (Heme O synthase)	0.28	-	mit	5	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (By similarity)				462
P17129 UniProt NPD GO	PSPB_CANFA	Pulmonary surfactant-associated protein B precursor (SP-B) (6 kDa protein) (Pulmonary surfactant-ass ...	0.28	-	end	0	Secreted protein; extracellular space				363
P53752 UniProt NPD GO	YN95_YEAST	Putative 49.7 kDa membrane glycoprotein in BIO3-HXT17 intergenic region	0.28	-	exc	0		membrane fraction [IDA]			436
Q84L31 UniProt NPD GO	RD23C_ARATH	Putative DNA repair protein RAD23-3 (RAD23-like protein 3) (AtRAD23-3)	0.28	-	nuc	0	Nucleus (Probable)				419
P23799 UniProt NPD GO	ESAG8_TRYBB	Putative adenylate cyclase regulatory protein (Leucine repeat protein) (VSG expression site-associat ...	0.28	+	nuc	0					630
Q09901 UniProt NPD GO	YAJ1_SCHPO	Putative family 31 glucosidase C30D11.01c precursor (EC 3.2.1.-)	0.28	-	mit	0					993
Q9LF80 UniProt NPD GO	GT3_ARATH	Putative glycosyltransferase 3 (EC 2.4.-.-) (AtGT3)	0.28	-	cyt	0	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				457
P58950 UniProt NPD GO	GR10A_DROME	Putative gustatory receptor 10a	0.28	-	end	7 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			408
Q8IPU5 UniProt NPD GO	GR77A_DROME	Putative gustatory receptor 77a	0.28	-	end	7 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			449
Q9LTX4 UniProt NPD GO	DMI1_ARATH	Putative ion channel DMI1	0.28	+	end	3	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein (Potential)				824
P25641 UniProt NPD GO	ATG15_YEAST	Putative lipase ATG15 (EC 3.1.1.3) (Autophagy-related protein 15) (Cytoplasm to vacuole targeting pr ...	0.28	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein. From ER ...	integral to membrane [IDA] vacuolar lumen [IDA]			520
O14162 UniProt NPD GO	YE7A_SCHPO	Putative lipase spac4a8.10 (EC 3.1.-.-)	0.28	-	nuc	0					723
P83100 UniProt NPD GO	MK14C_DROME	Putative mitogen-activated protein kinase 14C (EC 2.7.11.24) (MAP kinase p38c)	0.28	-	cyt	0					356
Q8IVU1 UniProt NPD GO	PUNC_HUMAN	Putative neuronal cell adhesion molecule precursor	0.28	-	nuc	1	Membrane; single-pass type I membrane protein		604184		814
P98205 UniProt NPD GO	ALA2_ARATH	Putative phospholipid-transporting ATPase 2 (EC 3.6.3.1) (Aminophospholipid flippase 2)	0.28	-	end	8	Membrane; multi-pass membrane protein				1107
P43122 UniProt NPD GO	QRI7_YEAST	Putative protease QRI7 (EC 3.4.24.-)	0.28	-	mit	0		mitochondrion [IDA]			407
Q12397 UniProt NPD GO	STCA_EMENI	Putative sterigmatocystin biosynthesis polyketide synthase (PKS)	0.28	-	vac	0					2181
Q09692 UniProt NPD GO	SYW_SCHPO	Putative tryptophanyl-tRNA synthetase (EC 6.1.1.2) (Tryptophan--tRNA ligase) (TrpRS)	0.28	-	cyt	0					395
Q5SY85 UniProt NPD GO	CI122_HUMAN	Putative uncharacterized protein C9orf122	0.28	-	mit	0					155
O36031 UniProt NPD GO	YEKJ_SCHPO	Putative zinc-finger protein C4F10.19c	0.28	-	nuc	0					154
Q9UUE1 UniProt NPD GO	PYC_SCHPO	Pyruvate carboxylase (EC 6.4.1.1) (Pyruvic carboxylase) (PCB)	0.28	-	cyt	0	Cytoplasm (By similarity)				1185
Q9YH18 UniProt NPD GO	QKI_CHICK	Quaking protein	0.28	+	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity)				340
P31179 UniProt NPD GO	NADA_CYAPA	Quinolinate synthetase A	0.28	-	nuc	0	Plastid; cyanelle				329
Q8LC69 UniProt NPD GO	ATL1R_ARATH	RING-H2 finger protein ATL1R (RING-H2 finger protein ATL8)	0.28	-	nuc	1 *					185
Q8RX29 UniProt NPD GO	ATL2I_ARATH	RING-H2 finger protein ATL2I	0.28	-	nuc	1					217
Q9BDY9 UniProt NPD GO	RBM4_RABIT	RNA-binding protein 4 (RNA-binding motif protein 4) (Lark homolog)	0.28	-	nuc	0	Nucleus (By similarity). Nucleus; nucleolus (By similarity). Cytoplasm (By similarity). May undergo ...				359
Q9BQ04 UniProt NPD GO	RBM4B_HUMAN	RNA-binding protein 4B (RNA-binding motif protein 4B) (RNA-binding protein 30) (RNA-binding motif pr ...	0.28	-	nuc	0	Nucleus; nucleolus				359
O97555 UniProt NPD GO	GDIA_CANFA	Rab GDP dissociation inhibitor alpha (Rab GDI alpha) (Guanosine diphosphate dissociation inhibitor 1 ...	0.28	-	nuc	0	Cytoplasm (By similarity)				447
Q38912 UniProt NPD GO	RAC3_ARATH	Rac-like GTP-binding protein ARAC3 (GTPase protein ROP6)	0.28	+	cyt	0	Cytoplasm. Membrane; peripheral membrane protein. Associated with the membrane when activated				198
P48148 UniProt NPD GO	RHO1_DROME	Ras-like GTP-binding protein Rho1	0.28	+	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				192
Q9NQL2 UniProt NPD GO	RRAGD_HUMAN	Ras-related GTP-binding protein D (Rag D)	0.28	-	nuc	0	Cytoplasm. Nucleus. Predominantly cytoplasmic. May shuttle between the cytoplasm and nucleus, depend ...	cytoplasm [IDA] nucleus [IDA]	608268		400
P62071 UniProt NPD GO	RRAS2_MOUSE	Ras-related protein R-Ras2	0.28	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (By similarity). Inner surface of plasma membrane poss ...	intracellular [IDA]			204
P62070 UniProt NPD GO	RRAS2_HUMAN	Ras-related protein R-Ras2 (Ras-like protein TC21) (Teratocarcinoma oncogene)	0.28	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (By similarity). Inner surface of plasma membrane poss ...		600098	2ERY	204
P56371 UniProt NPD GO	RAB4A_MOUSE	Ras-related protein Rab-4A	0.28	-	cyt	0	Membrane; peripheral membrane protein (By similarity). Generally associated with membranes. Cytoplas ...	endosome [IDA]			213
P61028 UniProt NPD GO	RAB8B_MOUSE	Ras-related protein Rab-8B	0.28	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				207
P70550 UniProt NPD GO	RAB8B_RAT	Ras-related protein Rab-8B	0.28	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				207
Q64612 UniProt NPD GO	PTPRV_RAT	Receptor-type tyrosine-protein phosphatase V precursor (EC 3.1.3.48) (Embryonic stem cell protein-ty ...	0.28	-	end	0	Membrane; single-pass type I membrane protein				1711
Q29RM9 UniProt NPD GO	RGS4_BOVIN	Regulator of G-protein signaling 4 (RGS4)	0.28	-	nuc	0					205
P49798 UniProt NPD GO	RGS4_HUMAN	Regulator of G-protein signaling 4 (RGS4) (RGP4)	0.28	-	nuc	0			602516		205
Q9CYB0 UniProt NPD GO	RFP2_MOUSE	Ret finger protein 2 (Putative tumor suppressor RFP2) (Tripartite motif-containing protein 13)	0.28	-	mit	1		cytoplasm [IDA]			407
Q8SQ04 UniProt NPD GO	RNAS1_LEMCA	Ribonuclease pancreatic precursor (EC 3.1.27.5) (RNase 1) (RNase A)	0.28	-	nuc	1 *	Secreted protein (By similarity)				156
Q8SQ12 UniProt NPD GO	RNAS1_PONPY	Ribonuclease pancreatic precursor (EC 3.1.27.5) (RNase 1) (RNase A)	0.28	-	nuc	1 *	Secreted protein				156

You are viewing entries 42651 to 42700 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.