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
O57524 UniProt NPD GO	APA12_ONCMY	Apolipoprotein A-I-2 precursor (Apo-AI-2) (ApoA-I-2)	0.42	-	exc	0	Secreted protein (By similarity)				262
Q96LR9 UniProt NPD GO	APLD1_HUMAN	Apolipoprotein-L domain-containing protein 1 (Vascular early response gene protein)	0.42	-	mit	3	Cell membrane; multi-pass membrane protein (Probable)				279
P24721 UniProt NPD GO	ASGR2_MOUSE	Asialoglycoprotein receptor 2 (ASGP-R 2) (ASGPR 2) (Hepatic lectin 2) (MHL-2)	0.42	-	mit	1	Membrane; single-pass type II membrane protein				301
Q99J86 UniProt NPD GO	ATRN_RAT	Attractin precursor (Zitter protein)	0.42	-	nuc	1	Isoform 1: Cell membrane; single-pass type I membrane protein (By similarity). Isoform 2: Secreted p ...				1432
Q75EB4 UniProt NPD GO	ATG12_ASHGO	Autophagy-related protein 12 (Autophagy-related ubiquitin-like modifier ATG12)	0.42	-	nuc	0	Cytoplasm (Probable)				189
Q75F47 UniProt NPD GO	ATG18_ASHGO	Autophagy-related protein 18	0.42	-	nuc	0	Membrane-associated. Peripheral membrane protein of pre-autophagosomal structure (PAS) and vacuole ( ...				537
Q96U88 UniProt NPD GO	ATG18_NEUCR	Autophagy-related protein 18	0.42	-	nuc	0	Membrane-associated. Peripheral membrane protein of pre-autophagosomal structure (PAS) and vacuole ( ...				461
Q871L5 UniProt NPD GO	ATG2_NEUCR	Autophagy-related protein 2	0.42	-	mit	0	Perivacuolar compartment (By similarity)				2011
Q7TSA3 UniProt NPD GO	BTLA_MOUSE	B- and T-lymphocyte attenuator precursor (B- and T-lymphocyte-associated protein) (CD272 antigen)	0.42	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)	integral to plasma membrane [IDA]		1XAU	306
Q3BCU0 UniProt NPD GO	BKRB1_MACFA	B1 bradykinin receptor (BK-1 receptor) (B1R)	0.42	+	end	7 *	Membrane; multi-pass membrane protein				352
Q8HZP1 UniProt NPD GO	BKRB1_TUPMI	B1 bradykinin receptor (BK-1 receptor) (B1R)	0.42	+	end	7 *	Membrane; multi-pass membrane protein				352
P06471 UniProt NPD GO	HOR3_HORVU	B3-hordein (Fragment)	0.42	-	nuc	0					264
P10163 UniProt NPD GO	PRB4S_HUMAN	Basic salivary proline-rich protein 4 allele S precursor (Salivary proline-rich protein Po) (Parotid ...	0.42	-	exc	0			180990		247
Q99N32 UniProt NPD GO	KLOTB_MOUSE	Beta klotho (BetaKlotho) (Klotho beta-like protein)	0.42	-	end	1	Membrane; single-pass type III membrane protein (Potential)				1043
Q05030 UniProt NPD GO	PGFRB_RAT	Beta platelet-derived growth factor receptor precursor (EC 2.7.10.1) (PDGF-R-beta)	0.42	-	end	1	Membrane; single-pass type I membrane protein				1097
Q10470 UniProt NPD GO	MGAT3_MOUSE	Beta-1,4-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase (EC 2.4.1.144) (N-glycosyl-oli ...	0.42	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein				538
Q30KL7 UniProt NPD GO	DB109_PANTR	Beta-defensin 109 precursor (Defensin, beta 109)	0.42	-	end	0	Secreted protein (By similarity)				87
Q30KJ7 UniProt NPD GO	DB132_PANTR	Beta-defensin 132 precursor (Defensin, beta 132)	0.42	-	nuc	0	Secreted protein (Potential)				95
P20060 UniProt NPD GO	HEXB_MOUSE	Beta-hexosaminidase beta chain precursor (EC 3.2.1.52) (N-acetyl-beta-glucosaminidase) (Beta-N-acety ...	0.42	-	vac	1 *	Lysosome	acrosome [IDA] membrane [IDA]			536
P13600 UniProt NPD GO	NGF_BOVIN	Beta-nerve growth factor precursor (Beta-NGF) (Fragment)	0.42	-	cyt	0	Secreted protein				231
Q8NE79 UniProt NPD GO	POPD1_HUMAN	Blood vessel epicardial substance (hBVES) (Popeye domain-containing protein 1) (Popeye protein 1)	0.42	-	nuc	3 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]	604577		360
Q9Z0L4 UniProt NPD GO	BMP15_MOUSE	Bone morphogenetic protein 15 precursor (BMP-15) (Growth/differentiation factor 9B) (GDF-9B)	0.42	-	nuc	0	Secreted protein				392
P36894 UniProt NPD GO	BMR1A_HUMAN	Bone morphogenetic protein receptor type IA precursor (EC 2.7.11.30) (Serine/threonine-protein kinas ...	0.42	-	mit	1	Membrane; single-pass type I membrane protein	integral to membrane [TAS]	158350	1REW	532
P01064 UniProt NPD GO	IBBD2_SOYBN	Bowman-Birk type proteinase inhibitor D-II precursor (IV)	0.42	-	nuc	0				1PI2	83
P12940 UniProt NPD GO	IBB_HORVU	Bowman-Birk type trypsin inhibitor	0.42	-	nuc	0				2FJ8	124
Q9H6U6 UniProt NPD GO	BCAS3_HUMAN	Breast carcinoma amplified sequence 3 (GAOB1) (Maab1 protein)	0.42	-	nuc	0	Nucleus (Potential)		607470		928
Q8CCN5 UniProt NPD GO	BCAS3_MOUSE	Breast carcinoma amplified sequence 3 homolog (K20D4)	0.42	-	nuc	0	Nucleus (Potential)				928
P23949 UniProt NPD GO	TISD_MOUSE	Butyrate response factor 2 (TIS11D protein)	0.42	-	nuc	0	Nucleus (Potential)	cytoplasm [IDA] nucleus [IDA]			367
P70194 UniProt NPD GO	CLC4F_MOUSE	C-type lectin domain family 4 member F (C-type lectin superfamily member 13) (C-type lectin 13) (Kup ...	0.42	-	nuc	1 *	Membrane; single-pass type II membrane protein				548
Q8HYC0 UniProt NPD GO	CLC4M_PANTR	C-type lectin domain family 4 member M (CD209 antigen-like protein 1) (CD299 antigen)	0.42	-	nuc	0	Membrane; single-pass type II membrane protein (By similarity)				445
P20944 UniProt NPD GO	CD44_CRIGR	CD44 antigen precursor (Phagocytic glycoprotein I) (PGP-1) (HUTCH-I) (Extracellular matrix receptor- ...	0.42	-	end	1	Membrane; single-pass type I membrane protein				362
Q60522 UniProt NPD GO	CD44_MESAU	CD44 antigen precursor (Phagocytic glycoprotein I) (PGP-1) (HUTCH-I) (Extracellular matrix receptor- ...	0.42	-	end	1	Membrane; single-pass type I membrane protein				431
Q923L3 UniProt NPD GO	CSMD1_MOUSE	CUB and sushi domain-containing protein 1 precursor (CUB and sushi multiple domains protein 1)	0.42	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)				3564
P55283 UniProt NPD GO	CADH4_HUMAN	Cadherin-4 precursor (Retinal-cadherin) (R-cadherin) (R-CAD)	0.42	-	end	1	Membrane; single-pass type I membrane protein		603006		916
Q9JKK0 UniProt NPD GO	CCP3_MOUSE	Calcipressin-3 (Down syndrome candidate region 1-like protein 2) (Myocyte-enriched calcineurin-inter ...	0.42	-	nuc	0					239
Q07009 UniProt NPD GO	CAN2_RAT	Calpain-2 catalytic subunit precursor (EC 3.4.22.53) (Calpain-2 large subunit) (Calcium-activated ne ...	0.42	-	cyt	0	Cytoplasm (By similarity). Cell membrane (By similarity). Translocates to the plasma membrane upon C ...	cytoplasm [TAS]		1U5I	699
O35920 UniProt NPD GO	CAN9_RAT	Calpain-9 (EC 3.4.22.-) (Digestive tract-specific calpain) (nCL-4) (Fragment)	0.42	-	cyt	0					674
Q63120 UniProt NPD GO	MRP2_RAT	Canalicular multispecific organic anion transporter 1 (ATP-binding cassette sub-family C member 2) ( ...	0.42	+	end	14 *	Membrane; multi-pass membrane protein	membrane [IDA]			1541
O13849 UniProt NPD GO	CBPY_SCHPO	Carboxypeptidase Y precursor (EC 3.4.16.5) (CPY)	0.42	-	exc	0	Vacuole. Lysosome-like vacuoles				1002
P21868 UniProt NPD GO	CSK21_CHICK	Casein kinase II subunit alpha (EC 2.7.11.1) (CK II)	0.42	-	mit	0					391
Q9P3A7 UniProt NPD GO	CDC48_SCHPO	Cell division cycle protein 48	0.42	+	nuc	0		cytoplasm [IDA] nuclear chromatin [IDA]			815
Q9Y719 UniProt NPD GO	MOK13_SCHPO	Cell wall alpha-1,3-glucan synthase mok13 (EC 2.4.1.183)	0.42	-	end	13					2358
P50488 UniProt NPD GO	DAF4_CAEEL	Cell-surface receptor daf-4 precursor (EC 2.7.11.30) (Abnormal dauer formation protein 4)	0.42	-	end	1 *	Membrane; single-pass type I membrane protein				744
O48626 UniProt NPD GO	ZW10_ARATH	Centromere/kinetochore protein zw10 homolog	0.42	-	cyt	0	Kinetochore. In prometaphase, associated with the kinetochore. Spindle. At metaphase, mostly associa ...				742
P69376 UniProt NPD GO	DNAK_PORPU	Chaperone protein dnaK (Heat shock protein 70) (Heat shock 70 kDa protein) (HSP70)	0.42	-	cyt	0	Plastid; chloroplast				620
P69377 UniProt NPD GO	DNAK_PORUM	Chaperone protein dnaK (Heat shock protein 70) (Heat shock 70 kDa protein) (HSP70)	0.42	-	cyt	0	Plastid; chloroplast				620
Q6NXD2 UniProt NPD GO	CHM2B_BRARE	Charged multivesicular body protein 2b (Chromatin-modifying protein 2b) (CHMP2b)	0.42	-	nuc	0	Cytoplasm; cytosol (By similarity)				214
O74161 UniProt NPD GO	CHS5_CANAL	Chitin biosynthesis protein CHS5	0.42	+	nuc	0	Golgi apparatus (By similarity)				562
Q8GX93 UniProt NPD GO	CLCE_ARATH	Chloride channel protein CLC-e (AtCLC-e)	0.42	+	end	8 *	Membrane; multi-pass membrane protein				710
P59381 UniProt NPD GO	RR11_ANTFO	Chloroplast 30S ribosomal protein S11	0.42	-	nuc	0	Plastid; chloroplast				130

You are viewing entries 30201 to 30250 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.